Dr. Jason Rosenhouse “Among the Creationists”

The Debate:

Jason Rosenhouse Dr. Jason Rosenhouse is an associate professor of mathematics at James Madison University in Virginia.  In his spare time, he enjoys engaging in the debate over Creation vs. Evolution and has even written an interesting book about his experiences visiting creation events around the United States entitled, “Among the Creationists.” I personally enjoyed reading this book very much, and found it to be very similar to my own experience discussing this topic with both creationists and evolutionists alike.  Most on both sides of this issue simply aren’t very well informed about arguments from the opposing side, or even from their own side of the debate.  I think reading about these experiences is helpful, for those on both sides of this issue, to at least start to understand how much we seem to be talking past each other, and to understand the mindset and motivations of those within opposing camps. Harry AllenI was asked to read Rosenhouse’s book by Harry Allen, a radio host for “Nonfiction“, the on-air magazine of the arts, ideas, and fact in New York (airs Fridays, 2-3pm, on WBAI-NY/99.5 FM (wbai.org), flagship of the non-commercial Pacifica radio network).  He wanted me to have an on-air debate with Dr. Rosenhouse regarding his book and the Evolution/Creation debate at large and why I’m involved with this debate and have written my own book, “Turtles All the Way Down.”  So, on Friday, January 17th, we did just that (see Link below).

Jason Rosenhouse vs. Sean Pitman

Jason Rosenhouse Book I personally enjoyed the discussion very much, and I think that Dr. Rosenhouse did as well (given his description of our debate on his own Blog).  As far as a summary of our discussion, Mr. Allen started us off with asking us something about ourselves, how we became interested in the Creation/Evolution debate, and why we wrote our books.  He then asked me what I thought of Dr. Rosenhouse’s book and commented that he also really enjoyed reading the book.  I explained that I really enjoyed reading “Among the Creationists”, that I read the whole book in one sitting, and agreed with most of what Dr. Rosenhouse had to say, at least 85% of it.  Of course, Mr. Allen then asked me what parts I didn’t agree with…   Turtles All The Way Down2When I first started reading, “Among the Creationists”, I thought the book was going to be more about the problems with standard Creationist arguments, and the rational scientific reasons why evolution had to be true in light of these arguments.  I was especially intrigued by the fact that Dr. Rosenhouse is a mathematician and the cover to the book explained that creationists get into real trouble whenever they start to get into a discussion with Dr. Rosenhouse within his own field of expertise – i.e., mathematics/probability arguments for intelligent design.  However, as I read through the book, I was disappointed to discover that Dr. Rosenhouse had not included a single mathematical/probability argument in favor of the creative potential of the evolutionary mechanism of random mutations and natural selection.  In fact, as is almost always the case for modern neo-Darwinists, he claimed, in his book and during our debate, that the modern Theory of Evolution is not dependent upon mathematical arguments or statistical analysis at all – at least with regard to the creative potential of the evolutionary mechanism of random mutations and natural selection.  In this, he seemed to argue that his own field of expertise is effective irrelevant to the discussion – that, “It is the wrong tool to use.”    Beyond this, he also explained that he wasn’t a biologist or a geneticist and that any discussion of biology would require bringing in someone with more expertise and knowledge of the field of biology than he had. At this point I began to wonder why we were having a debate at all if his own field of expertise was, according to him, effectively irrelevant to the conversation and that he was not prepared to present arguments from biology or genetics regarding the main topic at hand – i.e., the potential and/or limits of the evolutionary mechanism of random mutations combined with natural selection.

Sequence Space

Perhaps this is the main reason why Dr. Rosenhouse started to get rather irritated and flustered in the second half of our debate when I started asking him to explain how the evolutionary mechanism could reasonably and predictably do what he claims it did – i.e., actually come up with new functional systems beyond very low levels of functional complexity.  In order to do this, of course, the evolutionary mechanism would have to get across an extremely vast ocean of non-beneficial sequence options at these higher levels of functional complexity in order to somehow find the very very rare beneficial islands or “steppingstones” in an otherwise very empty and very large ocean (i.e., many times larger than the size of our entire universe).  How could these extremely rare beneficial steppingstones actually be discovered in a timely manner?  After all, as I explained during our discussion, the ratio of beneficial vs. non-beneficial sequences decreases, exponentially, with each increase in the level of functional complexity of the protein-based system in question – an observation that holds true for every language/information system that is known to us (to include the English language system, Russian, German, Italian, Morse Code, computer code, DNA codes, etc.).  Given this exponential decline in the ratio of beneficial vs. non-beneficial, how then can random mutations continue to find, via a truly random search algorithm, new qualitatively novel beneficial sequences at higher and higher levels of functional complexity within what anyone would consider to be a reasonable amount of time?

Closely-Spaced Steppingstones

In response to what I consider to be a fundamental challenge for evolutionary theory, Dr. Rosenhouse made a very interesting claim that I’ve heard only a couple of times before in my debates a few years ago on Talk.Origins.org.  Dr. Rosenhouse explained that while I was correct that the beneficial steppingstones in sequence space are very very rare indeed, and that the ratio of potentially beneficial sequences vs. non-beneficial sequences does in fact decrease in an exponential manner with each increase in the level of functional complexity (i.e, the minimum structural threshold requirements, which includes the minimum size and specificity requirements of more and more complex systems), that this concept is entirely irrelevant to the potential for evolutionary progress.  He argued that regardless of what the beneficial ratio might or might not be at a particular level of functional complexity evolution could still make real progress in a reasonable amount of time (i.e., this side of trillions upon trillions of years).  When I asked him to explain how this might be so, this is what he said in a nutshell: stepping-stones

“Because the very rare beneficial steppingstones are not randomly scattered around Lake Superior, but are lined up in a straight line one right after the other, it is easy to cross the lake from one shoreline to the other along a path of closely spaced steppingstones…”

It is in this way, Rosenhouse argued, that one can walk from one side of a massive lake or ocean, regardless of its size or the overall rarity of steppingstones, all the way to the other side without having to get into the water and blindly swim around randomly in an effort to try to find another steppingstone. Therefore, the most important concept to understand is not the rarity of the steppingstones, but “how they are arranged in sequence space”.  So, it’s the arrangement of the beneficial steppingstones, not their rarity, that is key to understanding the creative potential of the evolutionary mechanism.  That is why such statistical arguments having nothing to do with understanding the potential and/or limits of the evolutionary mechanism – according to Rosenhouse. This is a great argument!  Why didn’t I think of it before?  After all, this proposal does actually solve, quite nicely, the statistical problems for the evolutionary mechanism. In fact, it’s such a neat solution to the problem that it seems downright obvious - especially from the perspective of a mathematician who has apparently had little exposure to the real world of biology or genetics.  Given some understanding of the real world of proteins and how the rare beneficial or even stable sequences are actually distributed in sequence space, one starts to see the real problem for Rosenhouse’s hypothesis – i.e., it just doesn’t match the real world.  Unfortunately, science isn’t just based on hypotheses and theories that work well on paper.  It is based on theories that actually represent empirical reality in a testable potentially falsifiable manner.  Now, it isn’t that Rosenhouse’s hypothesis isn’t testable.  It is testable.  The problem is that it fails the test.  It simply doesn’t represent reality.  In the real world that exists outside of Rosenhouse’s very neat imagination, the distribution of potentially beneficial, or even stable, protein sequences with sequences space is known by experimental observations.  And, contrary to Dr. Rosenhouse’s wonderful solution to the problem, the distribution of real beneficial protein sequences is not a linear distribution, but a random, effectively uniform, distribution that becomes more and more so with each step up the ladder of functional complexity.  At higher and higher levels of sequence space, as the total number of protein sequences within the space grows exponentially, the ratio of potentially beneficial vs. non-beneficial sequences decreases exponentially – and the distribution of these more and more rare beneficial steppingstones becomes more and more uniformly random in appearance.  It’s much like stretching a sticky sheet until it starts to get holes in it.  As the sheet stretches, the holes get exponentially bigger relative to the remaining material of the sheet.  Pretty soon, the bridges between areas of fabric start to break down and fall apart, leaving truly isolated islands of fabric (or “steppingstones”) that are not connected to any other island  (for a more detailed discussion of this particular problem see:  Link).

Sequence Space

That, in a nutshell, is the fundamental problem for the theory of evolution – it’s mechanism simply isn’t capable of going beyond very very low levels of functional complexity this side of a practical eternity of time (trillions upon trillions of years).  And, the reason for this is the exponential decline in potentially beneficial options that random mutations are capable of evolving in a given span of time, combined with the non-linear or non-clustered distribution of these potentially beneficial sequences within sequence space. This is a fundamental problem for evolution that natural selection simply can’t solve.  The reason for this is that, as explained during the debate, natural selection cannot look into the future.  It can only select, in a positive manner, what is working to some beneficial advantage right now.  Intelligence, on the other hand, can look into the future to see potential advantages to various combinations of sequences that natural selection could never envision – as Dr. Stephen Meyer explains:

Stephen Meyer“[Intelligent] agents can arrange matter with distant goals in mind. In their use of language, they routinely ‘find’ highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities.”

Stephen C. Meyer, “The Cambrian Information Explosion,” Debating Design, pg. 388 (Dembski and Ruse eds., Cambridge University Press 2004). 
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Circumstantial Evidence

What’s left at this point is very frustrating for evolutionists because, without a viable mechanism, pretty much all there is to prop up neo-Darwinism are what Rosenhouse referred to in our discussion as “circumstantial evidence” (35:34 in the discussion), to include the very popular argument that complex biomachines (like the human eye or the bacterial flagellar motor) are poorly designed and are full of “flaws” – that no one, certainly no omnipotent God, would have designed these machines with so many obvious flaws.  However, as far as I see things, the main problem with the “design flaw” arguments is that these arguments don’t really have anything to do with explaining how the evolutionary mechanism could have done the job.  Beyond this, they don’t really rule out intelligent design either because, even if someone could make it better, that doesn’t mean that an inferior design was therefore not the result of deliberate intelligence.  Lots of “inferior” human designed systems are none-the-less intelligently designed. Also, since when has anyone made a better human eye than what already exists?  It’s like my four year old son trying to explain to the head engineer of the team designing the Space Shuttle that he and his team aren’t doing it right.  I dare say that until Dr. Rosenhouse or Richard Dawkins can produce something as good or better themselves, that it is the height of arrogance to claim that such marvelously and beautifully functional systems are actually based on “bad design”.

Downhill Evolution

Kenneth MillerBeyond this, consider the fairly well-known arguments of Dr. Kenneth Miller (cell and molecular biologist at Brown University) who once claimed that the Type III secretory system (TTSS: a toxin injector responsible for some pretty nasty bacteria – like the ones responsible for the Bubonic Plague) is evidence against intelligent design – specifically Michael Behe’s “irreducible complexity” argument for design (Link).  How so?  Miller argued that the TTSS demonstrates how more complex systems, like the flagellar motility system, can be formed from more simple systems, like the TTSS since its 10 protein parts are also contained within the 50 or so protein parts, according to Miller at the time, of the flagellar motility system (actually requires a minimum of about 23 structural parts).  The only problem with this argument, of course, is that it was later demonstrated that the TTSS toxin injector actually devolved from the fully formed flagellar system, not the other way around (Link).  So, as it turns out, Miller’s argument against intelligent design is actually an example of a degenerative change over time – i.e., a form of devolution, not evolution.  Of course, devolution is right in line with the predictions of intelligent design.  Consider, for example, that it is fairly easy to take parts away from a system, destroying the function of the more complex system (motility in the case of the bacterial flagellum) while maintaining subsystem functionality (like the T3SS toxin injector) – as originally explained by Behe (Link).  It is another thing entirely to add parts to system to achieve a qualitatively new higher level system of function that requires numerous additional parts to be in a specific arrangement relative to each other before the new function can be realized to any selectable advantage.  Such a scenario simply doesn’t happen beyond very low levels of functional complexity because the significant number of non-selectable non-beneficial modifications to pre-existing systems within a gene pool that would be required to achieve such a feat would take far far too long – i.e., trillions upon trillions of years. (See the following video of a lecture I gave on this topic – starting at 27:00):

SETI, Granite Cubes, and Useful Predictions

Granite cubesFinally, of course, there is the standard argument that intelligent design isn’t science because it produces nothing useful – i.e., no useful predictions.  Does this mean that SETI science isn’t a real scientific enterprise?  What about anthropology or forensic sciences, which are based on the scientific ability to detect deliberate design behind various artifacts found in nature?  How then is it any different to apply the very same arguments used to detect design in these various modern scientific disciplines in a universal manner?  And, if artificial features are also found within the DNA and/or protein-based systems of living things, so be it!  How long does one have to look for a mindless natural mechanism to explain something like a highly symmetrical polished granite cube, even if found on an alien planet like Mars, before it is recognized as a true artifact of intelligent design? – regardless of if this conclusion is deemed to be “useful” or not by this or that mathematician or scientist?

Junk DNA

Junk DNAIn this light, consider the fairly recent confirmation of a long-standing prediction of intelligent design regarding the likely key functionality of portions of non-coding or “junk-DNA”.  As it turns out, the more and more research that is done on non-coding DNA (DNA that does not code for proteins), the more and more functionality is being discovered.  Such discoveries simply weren’t predictable from the Darwinian perspective where many, such as Richard Dawkins in particular, had argued that non-coding DNA was evolutionary garbage or remnants of past trials and errors.  In contrast, those favoring the intelligent design or even the creationist position had long argued that at least some proportion of non-coding DNA probably had beneficial functionality to one degree or another.  And, it turns out that the predictions of intelligent design have proved true.  It seems like protein-coding genes are like the bricks and mortar for a house while the blueprint for what type of house to build resides within the non-coding DNA. Along these lines, many creationists have highlighted the fairly recent published claims from the ENCODE human genome project. In 2012, the science journal Nature  published a very interesting news item (ENCODE: The human encyclopaedia, Sept 5, 2012).  This article reported on the ongoing human genome project called the “Encyclopedia of DNA Elements” or ENCODE project.  The scientists at ENCODE made a very startling, and very controversial, claim – that at least 80% of our genome is functional to one degree or another! Of course, many scientists have responded rather strongly against this 80% functionality number (Link).  And, the truth of the matter is that, while non-coding DNA probably does represent the blue print for higher organisms, directing how protein-coding DNA functions to a significant degree, this does not necessarily or even likely mean that most non-coding DNA is actually required – or even useful.  After all, some ferns and salamander have genomes the same size or smaller than the human genome, and other ferns and salamander have genomes 50 times the size of the human genome (the human genome is comprise of ~3.5 billion bases). For additional comparisons, consider that a chicken’s genome contains about 1.3 billion bases, a clam about 3.2 billion, some frogs have 6.5 billion, and a lady bug genome has about 0.3 billion (~300 million) bases – similar to the genome of a Japanese pufferfish which is 8 times smaller than the human genome (just 385 million base pairs compared to 3 billion base pairs for humans), yet does just fine.  It is clearly impossible to guess the genome size of an organism just by looking at its apparent “complexity” or “simplicity” or the number of protein-coding “genes” in the genome – which doesn’t seem to correlate with the overall size of eukaryotic genomes.  This curious fact is currently known as the C-value enigma. C-valueGiven the reality of the C-value enigma, it seems likely that most non-coding DNA may not be vital for life or even beneficially functional.  For example, consider the argument of Dr. Ryan Gregory known as  “The Onion Test, with additional commentary from Dr. Larry Moran (Link):

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human? The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear. Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

However, there is the problem of the expense of maintaining stretches of DNA for long periods of time that don’t provide any useful advantage to the organism.  Such maintenance might seem to be fairly expensive if there is no return on the investment.

Nick_MatzkeThe counter argument, as presented by Dr. Nick Matzke, is that such maintenance really isn’t very expensive at all relative to the other costs that the organism must pay.  What’s a few pennies here and there when you’re spending thousands of dollars every day?  Well, over millions of years a few pennies here and there might seem to add up to quite a lot.  And, in a dog-eat-dog world, this could make all the difference. To add to the credibility of this observation, consider a paper by Holloway et al. (2007) where the authors observed a significant survivability cost disadvantage in various environments for bacteria that carried extra non-beneficial copies of DNA (Link).  However, the argument is that the cost is much higher for single-celled organisms compared to multi-celled organisms – like most eukaryotes. In this line, consider  In 1980, two papers published in 1980 by Orgel and Crick (Link) and by Doolittle and Sapienza (Link) which that “selfish DNA” elements, such as transposons, essentially act as molecular parasites, replicating and increasing their numbers at the relatively slight expense of a host genome – so slight that natural selection simply can’t keep up with the rate of expansion of these self-replicating elements within the genome.

However, a few scientists have suggested various functional options that might help to explain, to at least some degree, the C-value enigma.  For example, non-coding DNA seems to act as a sort of clock to regulate the timing of expression of various genes and genetic elements during development (Swinburne, 2010). There is also the interesting discovery that the initiation of DNA replication and the transition from G1 to S is dependent upon nuclear volume.  “Replication appears to initiate and terminate at the nuclear periphery and require a critical nuclear volume for onset (Nicolini et al., 1986); G1 nuclear volume growth must depend on concerted expansion of both chromatin and the nuclear envelope.” (Cavalier-Smith, 2004)  In short, “A genome’s sheer bulk can influence the rate of cell division and thereby that of development.” (Link)

Of course, the obvious counter is that such functionality for repetitive DNA is not dependent on the nature of the sequence itself, but only upon the absolute size of the sequence.  And, while this appears to be true, having the right size in just the right place can obviously be quite beneficial.  In other words, on occasion, size does matter…

This isn’t all, of course.  There are times when the actual specificity of the sequence matters as well – and this is what has also been discovered about non-coding DNA.  It appears to be the blueprint that controls how the building blocks (i.e., the protein-coding genes) are used.  In other words, non-coding DNA does seem to be more important than the protein-coding genes themselves. It seems, for instance, that it is the non-coding DNA that determines if a mouse or a pig or a monkey or a human is to be built given a set of very similar protein-coding genes for each of these types of creatures (for further discussion of this topic see: Link).

“I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules – may well go down as one of the biggest mistakes in the history of molecular biology.”

Wayt T. Gibbs, “The Unseen Genome: Gems Among the Junk,” Scientific American (Nov. 2003).

158 thoughts on “Dr. Jason Rosenhouse “Among the Creationists”

  1. Hi Sean. As I said during our discussion, it was a pleasure to meet you and to discuss this topic with you. I enjoyed our conversation very much, despite our obvious and many disagreements.

    Like Comment: Thumb up 8

  2. Hi Dr. Rosenhouse,

    I am a graduate student and frequent visitor to this site, and am pleased to see your comment to his article. I appreciate what I sense is a collegial approach on your part to a sensitive topic.

    I have independently arrived at similar conclusions as Dr. Pitman has, and am wondering if you have any experimental data with which to counter the argument he presents in this article. I am open-minded to arguments from both sides, and would give your thoughts fair consideration if you wish to share further. Thanks for considering this!

    Like Comment: Thumb up 4

    • @A Servant:

      Hi Dr. Rosenhouse! I have been watching for your reply, but have seen none. It makes it hard for me to favor your arguments if you don’t have a good response to the counterarguments Pitman has presentet. I would still enjoy hearing your reply to Pitman’s specific points in this article.

      Like Comment: Thumb up 1

      • Dr. Rosenhouse won’t respond because he has no idea how to respond. He believes in the truth of the Darwinian Theory of Evolution because of what he calls “circumstantial evidence”. He has no idea how to address the evident problems with his idea that the steppingstones in sequence space are lined up in nice neat little rows. He simply cannot give a reason for how this can possibly be the case aside from the fact that this simply has to be the case for his favorite theory to be true.

        Like Comment: Thumb up 2

      • @A Servant:

        Have you read both Sean turtles and Jason’s “among the creationists” that were cited in this blog and the repetitive exchanges between Sean and Nick/Jason?

        Unless you have and can articulate a question with specificity, Jason really has no obligation at all to spend time and effort to try to enlighten you personally.

        You should not imagine that an academic’s silence indicates lack of response when it can be interpreted as simply efficiency and prioritization of time and effort.

        Like Comment: Thumb up 1

  3. Jason Rosenhouse:
    Hi Sean.As I said during our discussion, it was a pleasure to meet you and to discuss this topic with you.I enjoyed our conversation very much, despite our obvious and many disagreements.

    Just came across this. Short-short version:

    1. Re: sequence space, Rosenhouse is right and Pitman is wrong. We can see this by the fact that virtually any protein can tolerate a lot of different point mutations, and retain function. Thus, every protein has a lot of stepping stones around it, and those stepping stones have stepping stones around them, etc. It is true that a lot of point mutations are “bad”, but all evolution needs is some narrow paths through sequence space, not big highways. Natural selection eliminates the bad mutations and keeps the population on the “ridges” (or paths, if you will). John Maynard Smith pointed this out back in the 1970s.

    Confirming evidence: (1) virtually any protein falls into a family with a large number of other proteins, variously diverged from less than 1%, to over 50%, which often all have about the same function, and in many cases can substitute for each other. (2) These sequences have strong phylogenetic tree structure, and their change is well-modeled by a Markov chain modeling a stepwise point-substitution process. The entirety of modern bioinformatics and genomics rests on these models (BLAST, gene identification, genome annotation, etc.), so a few half-baked analogies that assume the problem is “finding a sequence all-at-once by random generation from scratch” fail to deal with the data, and will not convince anyone who knows anything about the modern field.

    2. Junk DNA. Genome sizes vary a huge amount between very similar organisms. Most of this difference is in repetitive sequences. Finding bits and pieces of function here and there doesn’t change this big picture. Any discussion of whether or not most of the genome is functional that fails to deal with the huge variability in genome sizes is worthless. I.e., the ENCODE claims, and the creationist claims, and Pitman’s discussion here.

    3. Flagellum: google Panda’s Thumb Matzke flagellum. Pitman doesn’t even have his homology numbers right. And even if T3SS are derived from flagella, (a) this assertion rests entirely on phylogenetics and evolutionary assumptions, which Pitman et al. deny; (b) it still shows that the reduced system retains function; and (c) Type 3 secretion is just one of five or six known types of cross-membrane secretion, and at least one other one has evolved into a different sorts of motility (Type 4 secretion is related to archaeal flagella, and is apparently ancestral).

    In short, you guys have to try harder to even get started with having a real argument.

    Like Comment: Thumb up 2

    • Just came across this. Short-short version:

      1. Re: sequence space, Rosenhouse is right and Pitman is wrong. We can see this by the fact that virtually any protein can tolerate a lot of different point mutations, and retain function. Thus, every protein has a lot of stepping stones around it, and those stepping stones have stepping stones around them, etc. It is true that a lot of point mutations are “bad”, but all evolution needs is some narrow paths through sequence space, not big highways. Natural selection eliminates the bad mutations and keeps the population on the “ridges” (or paths, if you will). John Maynard Smith pointed this out back in the 1970s.

      Confirming evidence: (1) virtually any protein falls into a family with a large number of other proteins, variously diverged from less than 1%, to over 50%, which often all have about the same function, and in many cases can substitute for each other. (2) These sequences have strong phylogenetic tree structure, and their change is well-modeled by a Markov chain modeling a stepwise point-substitution process. The entirety of modern bioinformatics and genomics rests on these models (BLAST, gene identification, genome annotation, etc.), so a few half-baked analogies that assume the problem is “finding a sequence all-at-once by random generation from scratch” fail to deal with the data, and will not convince anyone who knows anything about the modern field.

      No one is asking for “evolution from scratch”. All that I’m asking for here are the odds of evolving something new at a various levels of functional complexity.

      As far as your claim that narrow paths exist within sequence space between various steppingstones, this simply isn’t true when it comes to steppingstones that have qualitatively novel functionality. You have long been confused on this point. While it is true that there are in fact “islands clusters” of function within sequence space, where all the proteins that make up a particular island carry the same type of functionality, it is simply not true that these island clusters are connected to other island clusters with qualitatively unique functionality along narrow “ridges” between islands in sequence space (i.e., different “steppingstones”) beyond very low levels of functional complexity.

      Now, is it in fact true that your argument that most proteins are flexible so that most positions can be mutated, one at a time, without a complete loss of function. However, it isn’t quite like you claim. After all, pretty much all of the letters in this paragraph could be mutated, one at a time, without a significant qualitatively loss in the intended meaning of the paragraph. However, the more and more mutations that occur at the same time, the exponentially less and less likely it is that the sequence will maintain beneficial functionality. The reason for this is because there is an “experimentally observed exponential decline in the fraction of functional proteins with increasing numbers of mutations (Bloom et al. 2005).”

      “Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. . . Our work unifies observations about the clustering of functional proteins in sequence space. . . ”

      Bloom goes on to point out that,

      “Experiments have demonstrated that proteins can be extremely tolerant to single substitutions; for example, 84% of single-residue mutants of T4 lysozyme and 65% of single-residue mutants of lac repressor were scored as functional. However, for multiple substitutions, the fraction of functional proteins decreases roughly exponentially with the number of substitutions, although the severity of this decline varies among proteins.”

      In short, most mutations that affect a region or island cluster of thermodynamically stable sequences in sequence space are destabilizing in such a way that each additional mutation has an exponentially destabilizing effect. Obviously, this means that the vast majority of sequences in sequence space would not produce viably stable proteins. It also suggests that as sequence space increases in size by 20^N, the ratio of viable vs. non-viable sequences, not just systems, decreases exponentially.

      “This is the reason why “simulations (Taverna and Goldstein 2002a) and experiments (Davidson et al. 1995; Keefe and Szostak 2001) clearly show that the vast majority of protein sequences do not stably fold into any structure (meaning the least stable folded protein is still far more stable than the typical random sequence).”

      Consider also the observations of Nelson and Onuchic regarding these islands within sequence space:

      Sequence space as being populated by families, each folding to a particular coarse grained structure and each surrounded by a shell of increasingly frustrated sequences. . . This produces a frustration barrier, e.g., a region of frustrated sequences between each pair of minimally frustrated families. Any stepwise mutational path between one minimally frustrated sequence family and another must then visit a region of slow or nonfolding sequences. . . In the case of real proteins, the sequences in these high frustration regions are much less likely to meet physiological requirements on foldability. . . If the requirement is sufficient, the region between two families will be completely excluded, which cuts sequence space into separate fast-folding, stable parts. This provides a mechanism for partitioning protein sequence information into evolutionarily stable, biochemically useful (foldable) subsets.”

      - Erik David Nelson and Jose Nelson Onuchic, Proposed mechanism for stability of proteins to evolutionary mutations, Evolution, Vol. 95, pp. 10682-10686, September 1998

      Consider also that even for much smaller proteins with sizes of only 18aa (very very low level of functional complexity) having average minimum Hamming gap distances of less than half a dozen or so between one novel island cluster and the next, consider that Cui et. al., suggest that such distances are essentially beyond the realm of crossability by point mutations.

      Evolutionary explorations by point mutations may be likened to diffusion. Their extent is limited on a fragmented mortality landscape, because sequences belonging to different networks (Table 1) are beyond reach.

      Yan Cui, Wing Hung Wong, Erich Bornberg-Bauer, Hue Sun Chan, Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes., PNAS, Vol. 99, Issue 2, 809-814, January 22, 2002.

      And, this effect only gets exponentially worse and worse with each step up the ladder of functional complexity.

      2. Junk DNA. Genome sizes vary a huge amount between very similar organisms. Most of this difference is in repetitive sequences. Finding bits and pieces of function here and there doesn’t change this big picture. Any discussion of whether or not most of the genome is functional that fails to deal with the huge variability in genome sizes is worthless. I.e., the ENCODE claims, and the creationist claims, and Pitman’s discussion here.

      It isn’t just bits and pieces of function, it is a significant proportion of non-coding sequences that appear to have functionality to one degree or another. Does this mean that all functional aspects are therefore vital to life? No, not at all. However, the notion that non-coding sequences are largely or almost entirely evolutionary garbage doesn’t make much sense. Even from an evolutionary perspective, it makes no sense to maintain junk that is expensive to reproduce and maintain, from one generation to the next.

      3. Flagellum: google Panda’s Thumb Matzke flagellum. Pitman doesn’t even have his homology numbers right.

      I’ve discussed this topic with you before, quite extensively. In my fairly lengthy discussion of your arguments (Link), where have I gone significantly off base with my homology numbers? – or any other key argument for that matter? The key problem with your argument is that you assume that the novel steppingstones that you list off are actually close enough in sequence space to be easily found from the perspective of the previous steppingstone. This simply isn’t true. The steppingstones that you yourself list off are far too far away from each other for random mutations to get from one to the other in what anyone would consider to be a reasonable amount of time. There simply are no known “narrow ridges” from one of your proposed steppingstones to the next to make evolutionary progress statistically feasible. Beyond this, you don’t have a single example of evolution in action between any one of your proposed steppingstones. If they are in fact so close together, as you imagine, why is there no demonstration of this?

      And even if T3SS are derived from flagella, (a) this assertion rests entirely on phylogenetics and evolutionary assumptions, which Pitman et al. deny; (b) it still shows that the reduced system retains function; and (c) Type 3 secretion is just one of five or six known types of cross-membrane secretion, and at least one other one has evolved into a different sorts of motility (Type 4 secretion is related to archaeal flagella, and is apparently ancestral).

      In short, you guys have to try harder to even get started with having a real argument.

      The devolution of TTSS secretory systems is generally accepted in the literature. I don’t think there’s any real argument on this point. Also, I personally have no problem with arguments that evolution can remove parts from a system while maintaining subsystem functionality – like removing the engine and tires from a car while having the radio still work. This sort of thing is statistically likely. The problem is when one assumes, as you do, that this situation can be reversed – that it is just as easy to go uphill as it is to go downhill. That’s a false assumption. It is much much harder to co-opt subsystems to work together to produce a more complex system that requires a larger number of parts before its function can be realized to any useful advantage. The reason for this is because independently functioning subsystems would require numerous modifications to work together in a qualitatively new way. And, as the minimum part requirement for the larger system increases, so do the minimum number of required modifications to the subsystems at hand. And, with each linear increase in the minimum number of required non-selectable modifications, the average number of random mutations required to achieve these modifications increases exponentially.

      And, that’s the problem with your argument in a nutshell. It simply isn’t statistically reasonable and it hasn’t been demonstrated or observed beyond very very low levels of functional complexity.

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  4. Stepping stones to get around Lake Superior without getting your feet wet? What a unique idea? Not only would these stepping stones need to be perfectly spaced, but they would also need to be the right size and shape, and height!! Imagine, if these stones were not the right height, one might have to climb impossible heights, and/or sink beneath the water if they did not reach water surface. Furthermore, they would have to be stable enough to allow one to walk on them!! Impossible? Do you really need to be a mathematician to calculate the odds of this occurring?

    Some of those featured are believers in Intelligent Design. There are really three groups: 1. Darwinian evolutionists 2. Intelligent Design 3. Creationists. Yes, unfortunately, there are some who mingle Creationism with Evolution. That doesn’t work and is an inconsistent belief system. Creationists believe the God of the Bible created the world as per the Genesis account. Intelligent Designers believe that ANY intelligent being created the world, not necessarily the God of the Bible. The Albigenses believed that Satan created the world. The Albigenses were NOT Christians, in spite of what some claim. If Intelligent Designers believe God created the world, they would call themselves Creationists. Many in the ID movement consistently deny that God created the world.

    Is SETI a legitimate scientific endeavor? Absolutely not. Does one really believe God will respond through SETI mechanisms? Absolutely not. He has already spoken via the Bible. Would Satan respond via SETI? That is a troubling thought.

    As far as computing probabilities, perhaps one could begin by computing the probability of all the Old Testament prophets, Isaiah, David, Daniel, etc. all predicting with amazing accuracy the minutest details of the life and death of Jesus. A sheer coincidence that they were all 100% correct in their predictions centuries in advance? In my book, this is 100% positive proof of a God who was Who He said He was, and also created just as He said He did.

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  5. Drs. Rosenhouse and Pitman

    I listened to and enjoyed your radio interview. Both of you are to be commended for your civility and decorum.

    The issue appears to be the application of mathematical probability to macro evolution. As a YLC, Dr. Pitman concedes to an old earth, just not old life. In light of all the evidence that life in some form has been around for billions of years as opposed to less than 10,000 years, YLC seems a theological premise as opposed to one supported by the weight of the evidence according to scientific consensus. Dr. Pitman needs a lot of ‘stepping stones’ to line up to convince the scientific community that life is young.

    Moreover Dr. Pitman admits to the RM/NS mechanism working at a certain level. Creationists fatuously argue that macro evolution can’t be proven in the lab so its not scientific. How does one run a lab experiment over hundreds of millions of years? The issue is whether the extrapolation of micro to macro evolution is rational in light of any other scientific explanation for the life appearing on earth. Of course it is, unless supplanted by theological creationism.

    But to Dr. Pitman’s great credit, because he is not a foaming at the mouth zealot, he posits that mathmatically, macro evolution could not occur without trillions of years of time. There are mathmatical models that macro evolution can work, but Dr. Pitman disputes those because he says they don’t consider the right biological factors. Fair enough. Dr. Rosenhouse, as you are a mathmetican, I would encourage you to enquire into this issue further for all of our erudition. Why, precisely is Dr Pitman wrong in his mathematical biometric assertions?

    I look forward to the ongoing civil, scientific debate.

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    • @george: “In light of all the evidence that life in some form has been around for billions of years as opposed to less than 10,000 years, YLC seems a theological premise as opposed to one supported by the weight of the evidence according to scientific consensus.”

      George, the problem with your assertion is two-fold: 1) You make a very general statement about the weight of evidence for very ancient life without stating what that evidence is. 2) When we actually examine that weighty evidence, it turns out to be largely in the eye of the beholder. You see overwhelming evidence for very ancient life because you are looking at the data through uniformitarian glasses. But if you take off your uniformitarian glasses and put on catastrophist glasses (which is difficult because it involves a paradigm shift), you are still looking at the same data, but from a different perspective, and much of what you thought was overwhelming evidence for the great age of the biosphere simply evaporates.

      Furthermore, a scientific consensus may be invalid or at least partly invalid. Such a consensus should never be defined as rigid dogma, and there is a place for challenges to scientific consensus.

      With all this said, I believe that Dr. Pitman and Dr. Rosenhouse have behaved like gentlemen, and I commend them for this. Furthermore, I also look forward to hearing more from Dr. Rosenhouse as to where he thinks DR. Pitman has gone wrong in his biometric assertions.

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    • George: Creationists fatuously argue that macro evolution can’t be proven in the lab so its not scientific.
      That is a straw man, Creationists argue that RM/NS has an edge, and that it is incapable of producing new organs / body types. So far the evidence is on the side of intelligence.

      George: How does one run a lab experiment over hundreds of millions of years?
      One doesn’t, one makes up a historical narrative.
      It is called a “Just So Story”, like “How the Camel Got His Hump”.
      They are common in evolutionary literature.

      George: there are mathematical models that macro evolution can work,

      There are also over 60 mathematical models that have been proven wrong by empirical data that are used to justify $billions to fight Climate Change . Another “consensus’ to avoid debate.

      George: weight of the evidence according to scientific consensus

      > I regard consensus science as an extremely pernicious development that ought to be stopped cold in its tracks. Historically, the claim of consensus has been the first refuge of scoundrels; it is a way to avoid debate by claiming that the matter is already settled. Whenever you hear the consensus of scientists agrees on something or other, reach for your wallet because you’re being had.
      >
      > Let’s be clear: the work of science has nothing whatever to do with consensus. Consensus is the business of politics. Science, on the contrary, requires only one investigator who happens to be right, which means that he or she has results that are verifiable by reference to the real world. In science consensus is irrelevant. What is relevant is reproducible results. The greatest scientists in history are great precisely because they broke with the consensus.
      >
      Michael Crichton
      @george:

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      • @Gene Fortner: Indeed the greatest scientists in history have been the ones (singular, individual) who broke from consensus, whereupon the greatest MASS (critical mass) of scientists agglutinated upon him to be the new consensus and peer review.

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  6. Dr. Jason Rosenhouse wrote (on his own Blog):

    The question of whether natural selection can craft complex adaptions, which Sean is so keen to discuss, is actually both trivial and unimportant. Of course it can craft complexity, what on earth is the reason for thinking it cannot? Proofs of concept are easy to come by. The important question is whether it did craft complex adaptations in natural history. There is rather a lot of evidence to suggest that it did, as I discuss briefly at the end of this post. Not the least of that evidence are the routine successes of adaptationist reasoning in biology.

    The reason for thinking that RM/NS cannot “craft complexity”, at least not beyond very low levels of functional complexity, is because sequence space simply is not set up like it would need to be before any “crafting” could take place. In other words, your argument that the beneficial steppingstones in Lake Superior are all closely spaced and lined up in a neat little row simply doesn’t reflect reality. They are not lined up in this manner and there is no rational reason to think that this might have been the case. Your entire theory is, therefore, dependent upon an assumption that doesn’t reflect known reality.

    As I noted during the debate, if massive amounts of physical evidence say something happened, but some abstract mathematical model says it cannot happen, then it is the model and not the evidence that should be discarded.

    The problem here is that you’re the one presenting a mathematical model that doesn’t represent known empirical reality. My position, on the other hand, is backed up by real observations as to the nature of sequence space. It is therefore your model that is based on an erroneous mathematical model, not mine.

    There are three obvious reasons why probability theory has no role to play in validating the creative abilities of natural selection. The first is that there are so many unquantifiable variables in natural history that a meaningful calculation would simply be impossible. Probability calculations take place in the context of a properly defined probability space. This means that you must have a grasp on all the things that might have happened in lieu of the event you are studying, and you must have some basis for assigning a probability distribution to that collection of events. (For example, if you want to know the probability of rolling a one with a six-sided die, you need to know not only that there are six possible outcomes, but also that the die is not loaded in a way that makes certain outcomes more likely than others). Good luck trying to define the appropriate probability space for studying the long-term development of natural history.

    The size of sequence space is definitely known for various levels of functional complexity. Also, there is very very good evidence as to the ratio of beneficial vs. non-beneficial sequences in that space. Finally, there is also very good evidence as to the distribution clusters of beneficial sequences within beneficial islands within sequence space – and their minimum likely distances relative to the other islands within that space.

    What you are basically saying here is that there is no way to estimate how long it will take for the evolutionary mechanism of RM/NS to produce anything at a given level of functional complexity. Everything you believe is based on “circumstantial evidence” which is largely irrelevant to the actual evolutionary mechanism. In other words, your evidence is largely interpreted as what you think an intelligent designer would or would not do – not upon what your mechanism could or could not do. In short, there really is no science or predictability, from your perspective, with regard to the creative limits or potential of your mechanism. You simply don’t know how to calculate or estimate such potential or limitations. Where then is your “science” when it comes to your assumed mechanism in particular?

    The second reason is that it is not clear what you should be finding the probability of. Should we determine the probability of evolving the modern vertebrate eye, or do we care instead about the probability of evolving some kind of organ for using light to glean information about the environment? Any specific adaptation might have a very small probability, but the probability of evolving some representative of a class to which that adaptation belongs could be rather large. So even if you could define an appropriate space, you would still have the problem of determining the relevant event within the space.

    Any and all discoveries of new beneficial island or steppingstones count as success. The problem is that all of the various potential solutions to the problem at hand are very far away in sequence space. There is no solution that is significantly closer or more evolvable this side of a practical eternity of time at higher levels of functional complexity – all potentially solutions are far far too far away. That is why your argument that “The probability of evolving some representative of a class to which that adaptation belongs could be rather large” is simply not true. The probability simply is not improved to any significant degree by including all possible solutions to a problem within sequence space. That’s the key point here – all possible solutions, all possible beneficial steppingstones of any kind whatsoever, are too far away from any given starting point within sequence space at higher levels of functional complexity.

    This leads naturally into the third problem. Let us suppose you could perform a relevant probability calculation and the result was a very small number. So what? What would that prove? Unlikely events occur all the time, after all. Any particular outcome of billions of years of evolution likely occurs with very small probability, but that is simply irrelevant to determining the credibility of evolution. The particular sequence of heads and tails you get when flipping a coin five hundred times is extremely unlikely, but something had to happen. The endpoints of eons of evolution are very much like that.

    I’m genuinely surprised to see a mathematician with an interest in biological evolution produce this common, but mistaken, argument. It’s like saying that one shouldn’t be surprised if Arnold Schwarzenegger happens to win the California Lottery 10 times in a row. After all, unlikely events happen all the time!

    You see, this argument, as presented by Dr. Rosenhouse, undermines science in general. It undermines the very concept of predictive value and estimating the likelihood that a particular hypothesis was actually responsible or the true explanation for a particular event.

    As another example, let’s say that there are 10 randomly distributed steppingstones, each measuring one meter square, within Lake Superior. Is it possible that a blind swimmer might swim directly from one to the other in a straight line without missing it? Yes, it is possible, but is it likely? Is it possible that this blind swimmer might swim directly to all 10 steppingstones in a row without a single error? Yes, this is also possible, but is it likely?

    You see, science isn’t based on what is possible (almost anything is possible). Science is based on what is most likely… which is why this particular point that Dr. Rosenhouse presents highlights a fundamental misunderstanding of the very basis of science itself.

    Now, this is the point where ID folks might point to William Dembski, and start going on about “complex specified information.” They might argue that while certain events are of the “something had to happen” sort, others are not. If five hundred heads came up, you would reject the hypothesis that a fair coin had been flipped in a fair manner. Indeed, but that is simply a bad analogy. Dembski’s attempts to define his notion of “specificity” in a useful, non-vague way that can be applied to biology (or much of anything for that matter) have been entirely unsuccessful. The relentless use of the term “complex specified information” by ID proponents, as though this term actually meant anything, is an example of what I meant in saying that evolution’s critics rely frequently on misapplied jargon.

    The concept of functional or meaningful complexity is defined by many others besides Dembski – to include a number of mainstream scientists. And, the concept is not too hard to understand. Basically, it is based on the minimum size requirement to achieve a particular type of function, combined with the limitations or minimum flexibility allowed for the characters in the sequence as far as their arrangement is concerned. This is where the concept of “specificity” comes into play. It simply isn’t enough to have all the right characters for a sequence. These characters must also be properly arranged, relative to each other in 3D space, before the function in question can be realized to any useful or selectable degree of functionality.

    I fail to see how the meaning for this concept is unclear? It is very clear. It is so clear in fact that small children can understand it. And, what is interesting and relevant here, is what a linear increase in the minimum size and/or specificity requirement of a meaningful/functional sequence does to the overall ratio of potentially meaningful/beneficial sequences in sequence space with the same minimum structural threshold requirements – i.e., the ratio of these sequences is reduced, exponentially, relative to the number of non-meaningful/non-functional sequences of any and all kinds.

    I don’t know why Sean makes such a fetish of probability. During the debate he said that my refusal to supply a probability calculation somehow rendered evolution unscientific, which is rather bizarre. Probability theory is wonderful stuff (my first book was mostly about probability theory) but it is hardly the last word on what is science and what is not.

    Again, as mentioned in our debate, science is and must be based on probability in all of its claims. Your notion that something only needs to be shown to be possible to be a scientific conclusion is simply not a scientific argument. One must also demonstrate the likelihood, not just the possibility, of a particular event to occur within a given span of time. If you can’t do this, then you just don’t have a scientific theory with regard to the creative potential of your Darwinian mechanism at various levels of functional complexity. You simply don’t know and cannot say how it will work or how long it will take for your mechanism to do anything at any level of functional complexity. All you have are bold claims, unsupported by either demonstration or relevant statistical calculations or extrapolations, regarding the creative potential of your mechanism.

    I certainly agree that natural selection has never been observed to produce something as complex as the vertebrate eye. Intelligent agents have never been observed to bring universes into being or to create life from scratch, but Sean has no trouble believing that occurred. The fact remains that there is voluminous circumstantial evidence supporting the claim that natural selection can in principle and has in natural history produced complex adaptations. When you contrast this with the perfect vacuum of evidence supporting the existence of intelligent designers who can do what ID folks say they can do, it becomes clear why scientists are all but unanimous in preferring evolution over intelligent design.

    What circumstantial evidence are you talking about that actually suggests that your mechanism of RM/NS did what you claim it did? Remember, arguing for common descent isn’t the same thing as arguing that your mechanism was responsible for the required changes over time. These arguments are often confused by evolutionists, but they simply aren’t the same thing.

    As far as your argument that ID has never been observed to do certain things, therefore extrapolations are necessary, I agree – hence the title of my book, “Turtles All the Way Down.”

    As the title of my book suggests, it’s either “turtles all the way up” or “turtles all the way down”. You claim that a mindless mechanism is the most likely explanation for all that exists while I claim that an intelligence source is the most likely explanation. In order to determine which claim is most likely true, one is required to extrapolate from very limited information. However, I believe that a reasonable extrapolation is possible based on what is currently known about which way the turtles are going.

    In other words, is RM/NS known to be more or less creative than what known intelligent agents (i.e., humans) are able to produce? The answer is quite clear. The mechanism of RM/NS is far far less creative, in a given amount of time (observable time) than is ID. Intelligence can create very complex machines in very short order. This simply isn’t true for RM/NS.

    The obvious question is, why not? Why is ID so much quicker than RM/NS beyond very low levels of functional complexity? Why does the mechanism of RM/NS show a truly exponential decline in creative ability with each linear step up the ladder of functional complexity? Well, the answer is quite clear for anyone who has carefully considered the nature of sequence space and noticed the exponential decline in potentially beneficial vs. non-beneficial and isolated nature of clusters or islands of sequences with the same type of function – and how this isolation becomes exponentially more and more dramatic with each step up the ladder of functional complexity.

    This observation can be extrapolated to get a very good idea as to the limitations of mindless mechanisms like RM/NS.
    The same is true of ID. There are various levels of intelligence and knowledge. The ancient peopled would have considered some of our technology “miraculous” from their perspective. And, there is therefore no reason to doubt that a few thousand years from now discoveries will be made that will seem truly miraculous from our current perspective.

    Therefore, it seems like there is no theoretical limit for the creative potential of intelligent design, while there is a very clear limitation, that is actually measurable, for RM/NS.

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  7. I’ve just listened to the full audio of the debate (as per click in the lead piece to this thread). As talk shows often are, this one was occasioned by the books the debaters had recently written (“Among the Creationists” and “Turtles All The Way Down” respectively).

    Although Sean’s antagonist and fellow author is a mathematician, his book’s focus isn’t the mathematics of evolution but the culture of creationists, about which he indulges delicate chuckles and delicate cordiality.

    To my delight, Sean, known for his no nonsense science mode, picked up, delicately, the whimsy, starting with the title, “Among The…” noting that it is reminiscent of all those “Among The Apes” books, and then, having opened with delicate humor, expressed serious puzzlement that a mathematician’s book, even if focused on culture, didn’t grapple much with the mathematics of evo, while announcing (surprise!) that the debate really isn’t subject to mathematics anyway, and dismissing ID’s mathematics as unworthy of notice. (I would have run away with that irony-clad semi-syllogism.)

    My critique of the broadcast isn’t from the scientific (certainly not mathematical) perspective but the cultural (I identify with Rosenhouse on that: ): 1. Both seemed of about the same age, at their primes. 2. Rosenhouse’s voice is more musical than Sean’s, at least as Sean’s came through on the transcontinental satellite phone connection to New York, while Rosenhouse’s seemed tinged with a hint of happy hubris, ironic from a mathematician if characteristic of an Evoean, and Sean’s sounded more the mathematician, ironic from a haranguing creationist. Role reversal, revealing.

    Having thus given him a sort of talent audition and pronounced him a worthy didactician, with which I would suppose Rosenhouse concurs, I’d like to see Sean segue on to a more public venue, like talk shows, like PBS and why not Bill O’Reilly?

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  8. @ Dr.Pitman

    “The ancient people would have considered some of our technology “miraculous” from their perspective.”

    In fact ancient people – some of whom wrote the bible – might well think modern people were gods with the extent of technology they possess. Thus if ancient people did not understand physics or biology it is reasonable that they would ascribe supernatural causes to natural phenomena. Science of course, has, and will continue to dispel superstitious notions.

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    • If some of the observations that were recorded in the Bible were observed today, such as the resurrection of Jesus from the dead, even modern scientists would recognized such events as true miracles of Divine power.

      You see, true science, properly applied, is indeed able to dispel superstitious notions – to include the modern Darwinian superstition and the superstition that mindless natural mechanisms are somehow ultimately able to explain everything that exists in this universe.

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  9. @ Dr. Pitman

    “If some of the observations that were recorded in the Bible were observed today, such as the resurrection of Jesus from the dead, even modern scientists would recognized such events as true miracles of Divine power.”

    Good point. So why do you think scientists today do not witness any miracles? Did miracles suddenly stop after the Bible was written or coincidentally after scienctific method was able to dispel same. Hmmmm…..

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  10. Sean Pitman

    42.07 “I agree with Jason as far as the moral issues are concerned. I dont think creationism is a moral issue I dont think there is a moral difference between creationist or evolution or even atheist.

    If God exists and I think he does I think He respects the honest atheistic position as well as the honest Christian position and if I am correct and God exists and there is a second coming I am sure Jason is going to be very surprised to find himself in heaven some day. For me for me ethics and the morality of things is based on how a person obeys the royal law and for me that is love. If you love your neighbour as yourself that is what it all boils down to. The rest of this is just gravy. To me the concept of creation and biblical value and all that stuff just helps to make your life better now. it doesnt have anything to do with salvation or making you are a god or bad person.”

    Sean
    Was this just a soothing rhetorical flourish meant to camouflage the hostility and graceless campaign that is being waged from this site or can we really expect to see the attacks on LSU disappear from this site?

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  11. Dear Sean and George,

    I have brought this up before in my posts without getting any response, but I’m going to say it again. I wish we could arrive at a working definition of the terms “miracle” and “supernatural.” I believe this is important because these are slippery terms, and I don’t think that we are using them in the same way. Unless we have an understanding of these terms, I fear that we are talking past one another.

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  12. Jason Rosenhouse wrote (on his own Blog):

    I am not a biochemist, but it seems pretty obvious that you cannot possibly make a good argument for your claims here [regarding the limits of RM/NS with regard to levels of functional complexity]. We can do no more than study minuscule portions of protein space, and that only in modern organisms. The precise nature of protein space is itself something that evolves with time, which complicates things considerably. The fitness of a gene that codes for a given protein is often dependent on the environment in which it finds itself. The reachability of a given gene likewise depends on what happened previously in natural history. Furthermore, the overall size of the space is imply irrelevant, as I explained during the radio show. Natural selection guarantees that most of the space will never be explored in natural history, while guiding organisms to the functional genes. The result is a vast space where we have no good way of assigning a probability distribution, precisely as I said in my post.

    You claim that natural selection guides organisms to functional genes. The problem with this notion is, of course, that natural selection cannot guide, in a positive manner, the random mutations of a mutating sequence at all, not even a little bit, until the mutations happen to hit upon a novel sequence that is actually functionally beneficial over what already exists within the gene pool. Until this happens, natural selection is completely helpless in the process of searching for the edges of novel beneficial islands in sequence space. It simply has not part to play aside from preserving what already exists. It is therefore more of a preserving force rather than a creative force of nature. RM/NS simply stalls out, in an exponential manner, with each step up the ladder of functional complexity. That is why there are no examples of evolution in action beyond a relatively low level of functional complexity. We aren’t talking about the evolution of highly complex machines here – like the human eye or the mammalian ear. We are talking about the lack of evolution of any qualitatively novel system that requires more than just 1000 specifically arranged residues. That’s not a very high level of functional complexity. That’s a very low level of complexity beyond which evolution simply stalls out – despite huge population sizes in bacteria and very rapid generation times and very high selection pressures. Despite all of these things favoring evolutionary progress at higher levels, the mechanism of RM/NS completely stalls out on a rather low-level rung of the ladder of functional complexity. Why do you think that might be? – if your vision of closely spaced steppingstones were actually correct at higher levels of functional complexity?

    Also, the overall nature of protein sequence space simply does not evolve with time in a manner which would actually favor evolutionary discoveries at higher levels of complexity. Most of the problem with protein sequence space is that the vast majority of sequence options within the space are simply not structurally stable and could not form useful proteins of any kind. Beyond this, say the environment changes so that new protein sequences are beneficial within sequence space (which does of course happen). How does this not provide an evolutionary advantage? Because, such changes to the potential targets in sequence space does nothing to the overall ratio of beneficial vs. non-beneficial since new islands appear while others disappear with such environmental changes. Also, it does nothing as far as setting up the steppingstones in a nice line of very closely spaced steppingstones as you originally claimed.

    In short, this key argument upon which your entire theory is dependent, is simply mistaken and does not solve the problem of the exponential decline in potentially beneficial islands within sequence space with each step up the ladder of minimum structural threshold requirements.

    That’s an in principle argument for being highly skeptical of big bold claims about the nature of sequence space. When you then factor in the myriad practical successes in the field of molecular evolution, and the fact that not many biochemists seem to share your view, it looks like you are once again just waving your hands.

    Where are these “practical successes” in the field of molecular evolution? – beyond very very low levels of functional complexity? Where is there a single example of evolution in action that produced any qualitatively novel system of function that requires a minimum of more than 1000 specifically arranged residues? As far as I’m aware, there are no such examples in literature – not a single one.

    As I pointed out during our debate, all the practical successes of the mechanism of RM/NS are based on low-levels of functional complexity – to include antibiotic resistance, novel single-protein enzymes, antifreeze proteins, and all of the other examples that you listed off in your book.

    The size of the space is irrelevant, as I have already explained. Your other claims are nonsense. At most we can make some judgments about small, local areas of sequence space as we see them in modern organisms and modern environments. That’s plainly insufficient for drawing grand conclusions about the viability of evolution.

    This size of sequence space is not irrelevant because it demonstrates the exponential nature of the increase in the overall size of sequence space with each increase in the minimum structural threshold requirements of systems at higher and higher levels of functional complexity. This observation would only be irrelevant if it could be shown that potentially beneficial sequences increase at the same rate. The problem, of course, is that the increase in potentially beneficial sequences is dwarfed by the increase in non-beneficial sequences – which in turn creates the exponentially declining ratio problem.

    As far as your claim that we can only make judgments about small local areas of sequence space, that’s true. As you point out, it is completely impossible to explore all of sequence space at higher levels of complexity – since the size of sequence space beyond the level of 1000 specifically arranged residues is beyond imagination – being larger than universes upon universes. However, science, but definition, is about extrapolating the information that is currently in hand to make predictions about things which cannot be definitively known. And, given the information that is in fact currently in hand, we can gain a very good idea as to the nature of all of sequence space. The same can be said of the universal Law of Gravity, for example. It is thought that this Law of nature is true everywhere in the universe even though we haven’t actually tested it in all parts of the universe. It’s a scientific prediction based on the relatively little evidence that we have in hand. The very same thing is true of protein sequence space – or any other form of sequence space that is based on information that is coded into character sequences (i.e., English, French, Russian, computer code, Morse Code, etc). All of these language/information systems have the same basic features of sequence space where meaningful/beneficial sequences are randomly distributed throughout sequence space at various levels of functional complexity.

    And, for all of these language/information systems we can actually know, with very high confidence and high predictive value, that the ratio of potentially beneficial vs. non-beneficial sequence does in fact decrease, in an exponential manner, with each increase in the minimum size and/or specificity requirement of a sequence.

    In this line, consider an argument from a paper published in 2000 by Thirumalai and Klimov:

    The minimum energy compact structures (MECSs), which have protein-like properties, require that the ground states have H residues surrounded by a large number of hydrophobic residues as is topologically allowed. . . There are implications of the spectacular finding that the number of MECSs, which have protein-like characteristics, is very small and does not grow significantly with the size of the polypeptide chain.

    The number of possible sequences for a protein with N amino acids is 20^N which, for N = 100, is approximately 10^130. The number of folds in natural proteins, which are low free energy compact structures, is clearly far less than the number of possible sequences. . .

    By imposing simple generic features of proteins (low energy and compaction) on all possible sequences we show that the structure space is sparse compared to the sequence space. Even though the sequence space grows exponentially with N (the number of amino acid residues [by 20^N]) we conjecture that the number of low energy compact structures only scales as lnN [The natural logarithm or the power to which e (2.718 . . . ) would have to be raised to reach N] . . . The number of sequences for which a given fold emerges as a native structure is further reduced by the dual requirements of stability and kinetic accessibility. . . We also suggest that the functional requirement may further reduce the number of sequences that are biologically competent.

    So if, as sequence space size grows by 20^N the number of even theoretically useful protein systems only scales by the natural log of N, this differential rapidly produces an unimaginably huge discrepancy between potential target and non-target systems (given that the structures themselves require a certain degree of specificity). For example, the sequence space size of 1000aa space is 20^1000 = ~1e1301. According to these authors, what is the number of potentially useful protein structures contained within this space? It is 20^ln1000 = ~1e9.

    All we really have left then is your argument that these exponentially rarer and rarer beneficial sequences are somehow all lined up in a nice neat little row. Is this a testable claim or not? If not, your claim simply isn’t scientific. If it is testable, what are the results of the tests? What is the best evidence that pertains to this hypothesis of yours? Is it likely to be truly representative of any aspect of sequence space? – or not?

    In answer to this question, consider the work of Babajidge et. al. (1997) where the observation is made, regarding stable protein and RNA sequences:

    “The sequences folding into a common structure are distributed randomly in sequence space. No clustering is visible.”

    While this paper was admittedly based on very very short low-level sequences, it provides a good idea as to what higher levels of sequence space look like. The extrapolation is a very reasonable one that can be tested in a potentially falsifiable manner – a testable position which has been continually verified and has yet to be falsified (increasing its predictive value). Upon what, then, do you base your hypothesis that the line-up of closely spaced steppingstones that you envision remotely represents reality anywhere in sequence space at any level of functional complexity? – past, present, or future? It seems to me like you’re hiding behind the unknown, hopeful that someday someone will find some evidence to support your vision of what reality needs to be in order for your hypothesis to be true. I’m sorry, but that’s just wishful thinking, not science. The evidence that is currently in hand strongly counters your imagined scenario.

    You absolutely insist on discussing this at a highly abstract level. But for actual biologists this is not an abstract question. They do not apply natural selection as some vague principle in their work. Instead they do the hard work of studying actual complex systems, and in every case their findings are the same. They find that once the systems are well understood, and once similar systems in other organisms are studied and understood, plausible gradualistic scenarios inevitably appear. Those scenarios are hardly the end of the story, however, as I explained to you during our radio debate. Once you think you have a good scenario for how something evolved, that scenario can be used to generate testable hypotheses. Subsequent testing of these hypotheses then leads to new knowledge. This type of reasoning has been applied so frequently and so successfully that, if it is fundamentally flawed, we must conclude scientists are getting mighty lucky.

    Do you have even one example of what you call a “plausible gradualistic scenario”? – beyond very low levels of functional complexity? Take, for example, a scenario proposed for flagellar evolution by Nicholas J. Matzke in this 2003 paper, “Evolution in (Brownian) space: a model for the origin of the bacterial flagellum.” In this paper Matzke lists off what appear to him to be fairly closely-spaced steppingstones, each of which would be beneficially selectable in most environments, along a pathway from simple to much more complex – i.e., the fully functional flagellar motility system. It looks great on paper! The steps certainly seem “plausible”. The only problem, of course, being that none of Matzke’s proposed steppingstones are actually close enough to each other, in sequence space, for random mutations to get across what initially seems like a fairly small gap (i.e., a series of non-selectable required mutational changes to get from one steppingstone to the next) this side of a practical eternity of time. And, in fact, there are no laboratory demonstrations of the crossing of any of Matzke’s proposed steppingstones – not a single one. You’d think that if Matzke’s proposed steppingstones were really as close together in sequence space as he suggests, that a real life demonstration of the crossing of at least one of his proposed gaps wouldn’t be much a problem. The problem, of course, is that there is no such demonstraiton because of the fact that his proposed steppingstones are far too far apart in sequence space to be reached from a lower-level steppingstone this side of a practical eternity of time. Yet, this is about as good as it gets in literature as far as any attempt to produce a truly plausible story of evolvability.

    http://www.detectingdesign.com/flagellum.html

    So, if you have anything better, I’d love to see it…

    The reason scientists routinely find plausible gradualistic scenarios is that these complex systems all carry clear evidence of their evolutionary past. We are not talking about “design flaws” in some abstract sense and we are not trying to psychoanalyze some hypothesized creative supermind. Instead we are talking about structures that are hard to understand from the standpoint of what a human engineer would do, but are easy to understand once the history of the structure is taken into consideration. Not one or two examples, but every complex structure studied to date. Apparently it amused the designer to create in a way that perfectly mimics what we would expect if these systems were actually produced gradually by natural selection.

    Again, one does not judge design or non-design based on supposed design flaws or a nested hierarchical pattern or any other such pattern or sequence that supposedly can only be produced by mindless mechanisms. All of these features can be and have been produced by human designers for various systems and for various reasons. I’m sorry, but appeals to design flaws and other such patterns simply doesn’t explain how your proposed mechanism could reasonable have done the job – especially in the light of very clear factors that strongly suggest that it simply cannot move around in sequence space like you imagine.

    In short, despite your claims to the contrary, your entire theory is based on what you think an intelligent designer would or would not do (which is very subjective since intelligent designers can do and often do all kinds of things for all kinds of reasons). Your position simply is not based upon evidence for what your mechanism can actually do. I’m sorry, but arguing what an intelligent designer wouldn’t do, in your estimation, is just not a scientific argument when it comes to determining the creative potential and/or limitations of your proposed mechanism.

    There’s so much more, of course. In some cases, like the mammalian inner ear, we have strong evidence from paleontology and embryology to show how a complex structure evolved gradually. Likewise for molecular evolution where, in cases like anti-freeze proteins in fish, we have strong evidence for how the proteins evolved from simpler precursors. I could point also to the success of game theoretic models in ethology. In every case scientists are approaching their work with theoretical models based on an assumption of natural selection, and they get results. This consistent success, again, is mighty coincidental if the theory is just fundamentally flawed.

    Again, antifreeze proteins are not very complex. They are very simple, requiring a minimum of no more than a few dozen specifically arranged residues – the same as the similar examples in your book.

    As far as your story of the evolution of the mammalian inner ear, it is indeed a lovely story, but it says nothing as far as how your proposed mechanism could have done the job. It just shows a serious of what appear to you to be gradual enough modifications, and you simply wave your hand and claim, without any other support, that your mechanism could easy produce such changes. Really? Where is your description of the mutations that would be required, on a genetic level, to get from one selectable steppingstone to the next in your proposed pathway?

    Again, what seems to you to be easily explained from an anatomic level is not so easily explained once you start to actually look at the number of non-selectable genetic changes that would be required. It’s much like computer programming where apparently simple changes to the function and/or appearance of a computer program require fairly significant changes to the underlying computer code for the program.

    Yes, the evidence is circumstantial, since this process plainly takes too long to be observed in toto. That’s not biologists’s fault. Nor is it their fault that the metaphor of sequence space, useful in many contexts, is not so useful for drawing grand conclusions about the viability of evolution.

    You yourself draw grand conclusions about the viability of evolution given a little bit of circumstantial evidence that is almost entirely based on what you think an intelligent designer would or would not do. Based on these assumptions, you make grand conclusions about the potential for evolutionary progress via a mechanism that you really don’t understand beyond what you know must be true if your theory is to remain viable. Therefore, you dream up a picture of sequence space which is completely contrary to what is currently known about sequence space. You’re willing to argue that sequence space must somehow have these very very closely spaced steppingstones all lined up in nice little rows and that these neat little rows are not at all effected by the exponential decline in the ratio of beneficial vs. non-beneficial. You make these claims, not based on some superior understanding of the nature of sequence space, but based on your claimed ignorance of the actual nature of sequence space.

    I’m sorry, but that isn’t a scientific position when it comes to a useful understanding of the evolutionary mechanism. Science isn’t about what is possible, but what is probable. If you don’t understand sequence space, you don’t understand your mechanism. And, if you don’t understand your mechanism, you really don’t have a scientific basis for the creative potential you ascribe to it.

    I’m genuinely surprised to see a mathematician with an interest in biological evolution produce this common, but mistaken, argument. It’s like saying that one shouldn’t be surprised if Arnold Schwarzenegger happens to win the California Lottery 10 times in a row. After all, unlikely events happen all the time! – Sean Pitman

    Oh please. Since I plainly discuss this point in my next paragraph, you have a lot of nerve cutting me off where you did. The whole question at issue is whether the endpoints of evolution are like getting 500 heads on 500 tosses of a coin, or whether they are more like firing an arrow into a wall and then painting a target wherever it lands. You claim it is the former; more sensible people claim it is the latter. And that is why the end result of any probability calculation you carried out would be irrelevant.

    I’m sorry, I must have misunderstood your argument. Even after reading your entire argument several times, it seemed to me like you were trying to argue that rare events happen all the time, so it doesn’t matter if the odds are not favorable to your position.

    In any case, your scenario is still very much misguided. You do realize that the sequences in sequence space are pre-defined as being beneficial or non-beneficial? Beneficial “targets” cannot be “pained later” after the randomly shot arrow hits the wall in just any location. If the arrow lands on a non-beneficial sequence, no one can claim that the sequence is in fact beneficial. The sequence is what it is. Therefore, it is perfectly reasonable to argue that the odds of actually hitting a novel beneficial target are extremely low and get exponentially worse and worse at higher and higher levels of functional complexity – worse than the odds than getting 500 heads in a row at relatively low levels of functional complexity (still at the level of small subcellular machines). Yet, you reject the implications of this statistical problem and argue that I’m painting targets after the arrow hits the wall? How can you possibly suggest such a thing when nature defines the targets ahead of time, not me?

    But the issue wasn’t merely coming up with a definition of functional complexity. It was doing so in a manner that is in any way relevant for determining what natural selection can do with eons in which to work. Show me in concrete terms how the definitions you’ve produced here permit a calculation that shows natural selection to be ineffective, and then I will be impressed. This is precisely what William Dembski attempted to do, but his work was so shot through with false assumptions and vague premises that it did not amount to much.

    It’s not just calculations, it is observations and statistical extrapolations based on those empirical observations of the real world. This isn’t just a mathematical world we’re talking about here. This is the real world observations and mathematical extrapolations based on those real world observations – i.e., a real scientific theory.

    In any case, as already noted, the definition of levels of functional complexity is easy. It’s been published as well. For example, Hazen et. al. (2007) define functional complexity as follows:

    1. n, the number of letters in the sequence.
    2. Ex, the degree of function x of that sequence. In the case of the fire example cited above, Ex might represent the probability that a local fire department will understand and respond to the message (a value that might, in principle, be measured through statistical studies of the responses of many fire departments). Therefore, Ex is a measure (in this case from 0 to 1) of the effectiveness of the message in invoking a response.
    3. M(Ex), the total number of different letter sequences that will achieve the desired function, in this case, the threshold degree of response, rEx. The functional information, I(Ex), for a system that achieves a degree of function, rEx, for sequences of exactly n letters is therefore

    I(Ex)= – log(sub2) [M(Ex) / C^n] (C = number of possible characters per position)

    What is also interesting is that Hazen et. al. go on to note that, “In every system, the fraction of configurations, F(Ex), capable of achieving a specified degree of function will generally decrease with increasing Ex.” And, according to their own formulas, this decrease is an exponential decrease with each linear increase in n – or the number of “letters” or characters (or in this case amino acid residues), at minimum, required by the system to achieve the beneficial function in question.

    So, yet again, the basic concept of levels of functional complexity is well defined in literature. It isn’t that science can’t define the concept or that the basic concept is difficult to understand, contrary to what you seemed to suggest in your book and during our debate. The only real question is if the potentially beneficial target islands are closely spaced and lined up in a nice little line across sequence space like you imagine – as must be the case if the claims of evolutionists for the creative power of RM/NS is actually “plausible”.

    Given all that is currently known, through empirical observations, about sequence space and how beneficial islands are actually arranged in sequence space, your imagined scenario simply isn’t tenable. And, there is no evidence for why it might ever have been tenable – outside of intelligent design. There simply is no empirical evidence that sequence/structure space remotely resembles your description of it.

    Beyond this, the hypothesis that all of sequence space at various levels of functional complexity has beneficial islands scattered around in a randomly uniform appearance, is a testable hypothesis with predictive value. This hypothesis can therefore be compared to your hypothesis to see which one produces the best results. The scenario I describe can be used to predict an exponential decline in evolution with each linear increase in the level of functional complexity under consideration. Your hypothesis, in comparison, predicts no such decline in evolutionary potential whatsoever. In fact, according to your hypothesis of sequence space, evolution should proceed at higher levels of functional complexity at pretty much the same rate as occurs at lower levels of functional complexity. Of course, this simply isn’t what happens. Lower-level functions that require no more than a few hundred specifically arranged characters (or amino acid residues for protein-based sequence space) evolve commonly and rapidly in fairly small populations with fairly slow reproductive rates. However, even given very large population with very rapid reproductive rates, short generation times, and high mutation rates, nothing evolves beyond the level of systems that require a minimum of at least 1000 specifically arranged amino acid residues. It just doesn’t happen – as predicted by my view of sequence space, not yours.

    Therefore, your view of sequence space has effectively no predictive power. You cannot predict how often your mechanism will succeed in finding something qualitatively new at a given level of functional complexity within a given span of time. My model, on the other hand, can predict how often success can be expected at a given level of functional complexity within a given span of time. That is why my view of sequence space carries far more scientific predictive value compared to your view.

    Your further remarks in this paragraph strike me as very confused. Science makes rather a lot of claims that do not depend on probability in any way, so I don’t know where you came up with this idea that probability is the most important thing there is. And since unlikely things occur all the time, I don’t see why I have to show that an event was likely to occur before I can conclude that it happened. Moreover, showing that something is likely or unlikely rarely involves performing an actual probability calculation. Usually you just follow the evidence where it leads, and if it points strongly to the conclusion that something happened then that’s good enough. Abstract probability calculations are irrelevant in most cases.

    Science is dependent upon predictive value among competing hypotheses. One must therefore be able to demonstrate that the favored hypothesis actually has greater predictive value than the competing or opposing hypothesis, and that the predictions of the hypothesis have not been effectively falsified by various potentially falsifying tests. In other words, it must be shown that a given hypothesis has greater probability of predicting the future, of predicting future observations, than the opposing hypothesis when put to the test. If you cannot do this, if you cannot quantify the degree to which your hypothesis has greater predictive value than the opposing hypothesis, if your hypothesis cannot be effectively falsified by another hypothesis, even in theory, then you simply don’t have a scientific position. What you have is a just-so story.

    Anyway, I do appreciate that you took the time to respond to my comments. Believe me, I know the time it takes, as I have very little time for such things myself. All the best to you and I hope to hear from you again in the future…

    Sean

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    • @Sean Pitman: Sean, I listened to the debate, and I commend you for your kindness. It also seems to me that you are making a strong argument from biochemistry for the limit of evolution. However, I certainly do not speak as molecular biologist and am therefore not qualified to make a formal judgment regarding this matter.

      As far as I can discern, you have presented this material in the debate and on the “Educate Truth” blog, but quite frankly, that is not enough. You need to publish this material in a journal – even a creationist journal – where it can be critiqued by bright minds who have expertise in molecular biology. I realize that I have mentioned this before, but if your argument is valid, it deserves to be widely known, and if it is scientifically flawed, the flaw deserves to be pointed out. Please don’t hide whatever scientific light you may have under a basket or bush! Your argument should not simply appear on this blog. It needs to see the light of day! Please think seriously about what I am saying!

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  13. “Having thus given him a sort of talent audition and pronounced him a worthy didactician, with which I would suppose Rosenhouse concurs, I’d like to see Sean segue on to a more public venue, like talk shows, like PBS and why not Bill O’Reilly?”

    Maybe Oprah :)

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  14. Hi Sean,

    No one is asking for “evolution from scratch”. All that I’m asking for here are the odds of evolving something new at a various levels of functional complexity.

    That is incorrect. Your arguments and probability calculations are based on the effects of many simultaneous mutations, with no opportunities for selection between them. Thus, under your model, large moves in sequence space have to happen all-at-once. Your criticisms of that model are valid, but they say nothing about the evolutionary model, which is stepwise.
    An example from your own comment:

    Now, is it in fact true that your argument that most proteins are flexible so that most positions can be mutated, one at a time, without a complete loss of function. However, it isn’t quite like you claim. After all, pretty much all of the letters in this paragraph could be mutated, one at a time, without a significant qualitatively loss in the intended meaning of the paragraph. However, the more and more mutations that occur at the same time, the exponentially less and less likely it is that the sequence will maintain beneficial functionality.

    This doesn’t matter, since in evolution, all the mutations don’t occur at the same time. Each is exposed to long periods of selection, drift, etc. The real process is that after a substitution happens in a population (either beneficial, beneficial but with some negative side effects, or neutral, or nearly neutral but slightly deleterious), a variety of new mutations accumulate over subsequent generations. Some of these mutations are neutral, some are slightly deleterious, and some compensate for some deleterious feature introduced by a previous substitution. Compensatory substitutions, in particular, are crucial to include in the model. Creationist arguments, including yours, universally ignore the role they play.

    Also, proteins are much more flexible than, say, English. It is commonplace to find protein families where 50% or even 80% of the amino acids have changed, yet the structure and function remain the same. Not so for English. Protein evolution is more like language evolution, where most / all of the words can be modified, the resulting languages are incomprehensible to each other, but the same message can be communicated via different sentence, each within the overall context of its language.

    Your arguments are rather like arguing that French and Romanian could not have evolved from a common ancestor, because if you take a French sentence and randomly mutate most of the letters in each of the words, you get something incomprehensible. This is nothing like the actual proposed historical process, and so is not a rebuttal of it.

    Language space is surely huge just like sequence space, and it is surely true that most random assemblages of sounds don’t mean anything in any modern or extinct language, yet languages have evolved nonetheless, through a long process of step-by-step changes, with the participating humans mostly or completely oblivious.

    Other examples of this mistake in your comment:

    The reason for this is because there is an “experimentally observed exponential decline in the fraction of functional proteins with increasing numbers of mutations (Bloom et al. 2005).”

    …and again:

    Bloom goes on to point out that,

    “Experiments have demonstrated that proteins can be extremely tolerant to single substitutions; for example, 84% of single-residue mutants of T4 lysozyme and 65% of single-residue mutants of lac repressor were scored as functional. However, for multiple substitutions, the fraction of functional proteins decreases roughly exponentially with the number of substitutions, although the severity of this decline varies among proteins.”

    …and again:

    In short, most mutations that affect a region or island cluster of thermodynamically stable sequences in sequence space are destabilizing in such a way that each additional mutation has an exponentially destabilizing effect. Obviously, this means that the vast majority of sequences in sequence space would not produce viably stable proteins.

    It is true that most mutations have this effect, but this doesn’t matter, since they happen for the most part one at a time, and (1) selection removes the severely deleterious mutations, and (2) the slightly deleterious ones can later be corrected by compensatory substitutions.

    The “vast majority of sequences” therefore don’t matter, since evolution doesn’t have to search through all possible sequences in order to explain the data. To explain the data, it just has to, *sometimes*, find *some* of the paths between proteins with different-but-related sequences but the same function, and, occasionally, find *some* of the paths between proteins with different-but-related sequences and different functions. It doesn’t have to do it *all* the time for *everything*, because the data indicates that failures are common (extinctions are observed, imperfect adaptations are observed), and the data indicate that biology doesn’t occupy all of functional space or sequence space, just little bits of it.

    It also suggests that as sequence space increases in size by 20^N, the ratio of viable vs. non-viable sequences, not just systems, decreases exponentially.

    This is just the all-at-once fallacy repeated again.

    You conclude with:

    And, this effect only gets exponentially worse and worse with each step up the ladder of functional complexity.

    This is raw assertion, not something your references say, and you haven’t defined the “ladder of functional complexity” anyway. Most of protein complexity involves fusing protein domains or evolving binding sites between them, these are pretty trivial processes.

    JUNK DNA

    It isn’t just bits and pieces of function, it is a significant proportion of non-coding sequences that appear to have functionality to one degree or another.

    This is false, based on the ENCODE project’s claim that any measurable binding to any bit of DNA, even at negligible/noise levels (say, <1 binding event per cell) constitutes "function." Most of this just shows that DNA binding is a sloppy process and our techniques have gotten good enough to detect the noise.

    Does this mean that all functional aspects are therefore vital to life? No, not at all. However, the notion that non-coding sequences are largely or almost entirely evolutionary garbage doesn’t make much sense. Even from an evolutionary perspective, it makes no sense to maintain junk that is expensive to reproduce and maintain, from one generation to the next.

    This isn’t really a modern evolutionary perspective, this is 1960s-style panadaptationism, most famously corrected by Stephen Jay Gould in his articles on “spandrels”, “exaptation”, etc. Most modern evolutionary biologists read these critiques of panadaptationism as part of routine coursework, but some molecular biologists/genome jockeys, and virtually all creationists, remain clueless.

    Also, it’s intuitively “obvious”, but mistaken, to think that having a large amount of junk DNA in the genome is “expensive”. The energetic & material cost of replicating/maintaining the genome in a typical large eukaryotic cell is trivial compared to the costs of protein synthesis, energy generation for muscle action, etc.

    This is junk DNA 101 stuff, and you are getting it wrong.

    While we’re at it, why do some ferns and salamander have genomes the same size or smaller than the human genome, and other ferns and salamander have genomes 50 times the size of the human genome? And all with approximately the same number of genes, and the difference being due mostly to parasitic repetitive elements? If your discussion of junk DNA doesn’t include these facts, it’s just uninformed, no more useful than a poorly researched undergraduate research paper.

    FLAGELLUM

    I’ve discussed this topic with you before, quite extensively. In my fairly lengthy discussion of your arguments (Link), where have I gone significantly off base with my homology numbers?

    See the table at Panda’s Thumb from Pallen & Matzke 2006. There is a lot more to the argument than just the 10 proteins homologous to nonflagellar T3SS.

    The key problem with your argument is that you assume that the novel steppingstones that you list off are actually close enough in sequence space to be easily found from the perspective of the previous steppingstone. This simply isn’t true. The steppingstones that you yourself list off are far too far away from each other for random mutations to get from one to the other in what anyone would consider to be a reasonable amount of time.

    There is no point in discussing this until we resolve your misconception about the ability of single proteins to evolve along narrow paths through huge sequence space, in some cases retaining the same function, in other cases changing function.

    Those paths exist. Phylogenies of proteins are one of the proofs. The branches of the phylogenies are actual statistical estimates of these paths. They exist both for cases where all the proteins at the tips have the same function, and for cases where some of the proteins at tips of the tree have different functions.

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    • Hi Nick, welcome back.

      You write:

      Your arguments and probability calculations are based on the effects of many simultaneous mutations, with no opportunities for selection between them. Thus, under your model, large moves in sequence space have to happen all-at-once. Your criticisms of that model are valid, but they say nothing about the evolutionary model, which is stepwise.

      You seem to have a mistaken view of sequence space, islands within sequence space, and how mutational changes can move around within this space.

      To illustrate the problem here, imagine that our population starts out on an island within a higher level of sequence space. This island is made up of many protein sequences that can all produce the same qualitative type of function to at least some selectable advantage. Along the edges of the island are sequences that are marginally beneficial while in the center of the island are sequences that are strongly beneficial for the particular type of function in question (creating a peak for the island with exponentially declining slopes toward the surrounding ocean). Surrounding this island, on all sides, are sequences that are not beneficial at all. They may be functionally detrimental to one degree or another, or they may be functionally neutral, but they aren’t selectably beneficial.

      Now, say our population happens to land on the edge of such an island. A selectable advantage is suddenly realized. So, this population will be preferentially maintained by natural selection. After this point, it is very easy to move the population rapidly up the slopes of the island to the very peak of the island in relatively short order (which has the effect of reducing the size of the island that will be considered “beneficial” for the population by natural selection). The reason for this is that the sequences with a stepwise increase in selectability are very closely spaced on this island. So, improving functionality of a given type on a particular island isn’t a problem for RM/NS – even by mutations that only produce single character changes (point mutations).

      The problems, of course, happen when one tries to leave the island and find other islands within sequence space. In order to do this, mutations, of various types, start to explore the sequences in the ocean around the island. Point mutations take very small steps off the island. If these point mutations land on neutral (or near neutral) areas of the ocean, they are not immediately deleted by natural selection. They can wander around a bit looking for other islands along a “random walk”. If these point mutations land on strongly detrimental regions of the surrounding ocean, natural selection quickly deletes them and the random walk starts over from the starting island. Of course, this “start over” process takes time.

      Now, imagine a scenario where the next closest beneficially selectable island in sequence space is a Hamming distance of 50 non-selectable mutations (character changes) away from the starting island within a sequence space that holds 1000 character sequences. How long would it take to get to that next island? Say that your population on the starting island is at a steady state of 1e31 (the size of the number of all the bacteria on Earth). Say that our mutation rate is one mutation per 1000 character sequence per generation, and our generation time is 10 minutes. The number of non-beneficial sequences within a Hamming distance of 50 within this sequence space is ~1e65. Given these parameters, our population could explore a maximum of 1e31 sequences within the surrounding ocean in each generation. Of course, this means, on average, that it would take our population about 1e34 generations, on average, to reach an island that is just 50 character differences away from the starting island (i.e., ~1e29 years).

      But, you argue, any mutations that are detrimental will be selected against my natural selection, which is true. However, this doesn’t improve the odds of success. All natural selection does in such a case is bring back to random walk sequence to the original starting point. The effect that this has is to increase the searches very close to the starting point island. However, it doesn’t really help to find something that is 50 mutational steps away any faster. If anything, it increases the average number of mutations required to achieve success.

      In this light, let’s consider the rest of your specific arguments:

      This doesn’t matter, since in evolution, all the mutations don’t occur at the same time. Each is exposed to long periods of selection, drift, etc. The real process is that after a substitution happens in a population (either beneficial, beneficial but with some negative side effects, or neutral, or nearly neutral but slightly deleterious), a variety of new mutations accumulate over subsequent generations. Some of these mutations are neutral, some are slightly deleterious, and some compensate for some deleterious feature introduced by a previous substitution. Compensatory substitutions, in particular, are crucial to include in the model. Creationist arguments, including yours, universally ignore the role they play.

      My model does not ignore compensatory mutations at all. The effect of compensatory mutations is simply to reverse the random walk of a sequence back onto the original island from which it started. That’s all. Compensatory mutations do not help to reduce the average time required to find a qualitatively novel island within sequence space.

      Beyond this, I’ll point out that I’m not arguing that mutations need to occur at the same time. They don’t. Mutations can and generally do occur one at a time and are generally comprised of single-character mutations. Multi-character mutations (indels) can also occasionally occur, and these types of mutations can make long leaps into the ocean of sequence space, far away from the original island. However, the odds of successfully landing on any part of any other island within sequence space is not statistically improved. The average time to success is still the same.

      Also, proteins are much more flexible than, say, English. It is commonplace to find protein families where 50% or even 80% of the amino acids have changed, yet the structure and function remain the same. Not so for English. Protein evolution is more like language evolution, where most / all of the words can be modified, the resulting languages are incomprehensible to each other, but the same message can be communicated via different sentence, each within the overall context of its language.

      What you’re talking about here are entirely different non-connected islands within sequence space that have the same type of functionality. In other words, it is possible to say the same thing in a very different way. The same is true with protein-based systems. It is possible to produce the same qualitative type of function with very different protein sequences. That, however, doesn’t solve the problem.

      Beyond this, it is not generally true that most of the amino acid residues of a protein can be modified without a loss of function. As already explained, most protein-based systems suffer an exponential loss of function for each individual amino acid residue change in the sequence. It is for this reason that most of sequence space is simply not functional nor are most sequences even capable of forming stable protein folds. It is also for this reason that the beneficial islands in sequence space have sharp peaks and steep slopes.

      Your arguments are rather like arguing that French and Romanian could not have evolved from a common ancestor, because if you take a French sentence and randomly mutate most of the letters in each of the words, you get something incomprehensible. This is nothing like the actual proposed historical process, and so is not a rebuttal of it. Language space is surely huge just like sequence space, and it is surely true that most random assemblages of sounds don’t mean anything in any modern or extinct language, yet languages have evolved nonetheless, through a long process of step-by-step changes, with the participating humans mostly or completely oblivious.

      This is a mistaken analogy for the very reason that humans are intelligent and can make leaps within sequence space that cannot be made by random mutations in a comparable amount of time. You mistakenly assume that human languages evolve via the same mechanism as Darwinian evolution. They do not.

      Beyond this, different human languages are effectively the same with the exception that different letters and words are used for the very same ideas. The same can be true of protein-based systems. Note, however, that the problems for evolutionary progress from lower to higher level systems is the same for human languages as it is for protein-based systems. As in the human-language system, there are many possible ways of saying the same thing. However, these many possible ways of saying the same thing get farther and farther apart in sequence space as the thing that is trying to be said increases in the required minimum number of characters that have to be used to get the idea across. The very same thing is true of protein-based systems. While there are many very different options of producing the very same type of system, these options become more and more widely spaced in sequence space with each step up the ladder of minimum structural threshold requirements. That is why it doesn’t matter what “language” once uses, one cannot get from a given higher level island within sequence space to any other, regardless of the “language” that would be recognized in a given environment, in a reasonable amount of time.

      Another problem here is that you seem to imagine that going from lower-level to higher-level systems is a smooth process where there are no significant gaps between lower-level and higher-level islands within different levels of sequence space. That’s just not a correct vision of sequence space (human language or otherwise). The lower level islands are also separated from higher level islands by gaps comprised of non-beneficial sequences. And, these minimum gap distances become linearly wider and wider with each step up the ladder of functional complexity.

      Other examples of this mistake in your comment:

      The reason for this is because there is an “experimentally observed exponential decline in the fraction of functional proteins with increasing numbers of mutations (Bloom et al. 2005).”

      …and again:

      Bloom goes on to point out that, “Experiments have demonstrated that proteins can be extremely tolerant to single substitutions; for example, 84% of single-residue mutants of T4 lysozyme and 65% of single-residue mutants of lac repressor were scored as functional. However, for multiple substitutions, the fraction of functional proteins decreases roughly exponentially with the number of substitutions, although the severity of this decline varies among proteins.”

      …and again:

      In short, most mutations that affect a region or island cluster of thermodynamically stable sequences in sequence space are destabilizing in such a way that each additional mutation has an exponentially destabilizing effect. Obviously, this means that the vast majority of sequences in sequence space would not produce viably stable proteins.

      It is true that most mutations have this effect, but this doesn’t matter, since they happen for the most part one at a time, and (1) selection removes the severely deleterious mutations, and (2) the slightly deleterious ones can later be corrected by compensatory substitutions.

      While both of your points here are true, they really don’t help to lessen the average time required to fine a novel beneficial island within sequence space (as already explained). My point in referencing the experiments of Bloom et. al. was to show you how the islands of beneficial sequences actually appear in sequence space. They are islands with steep slopes and sharply pointed peaks as I originally said.

      The “vast majority of sequences” therefore don’t matter, since evolution doesn’t have to search through all possible sequences in order to explain the data. To explain the data, it just has to, *sometimes*, find *some* of the paths between proteins with different-but-related sequences but the same function, and, occasionally, find *some* of the paths between proteins with different-but-related sequences and different functions. It doesn’t have to do it *all* the time for *everything*, because the data indicates that failures are common (extinctions are observed, imperfect adaptations are observed), and the data indicate that biology doesn’t occupy all of functional space or sequence space, just little bits of it.

      There are two misconceptions here. The first is, as already explained, that moving around between sequences that are located on the same island with the same type of function is very easy for RM/NS. This is not a problem whatsoever. However, this doesn’t get you a new type of function. Such mutations stay on the very same island and produce the very same type of function with “different-but-related sequences”. As you know, this isn’t the same thing as finding a different island with a qualitatively new type of function.

      Now, you also claim that “occasionally” some of the paths between “different-but-related protein sequences” can be found with “different functions”. This is the entire question at hand. What is the average expected time for such a feat to be realized? – at various levels of functional complexity? You simply don’t know since you believe that, regardless of the level of functional complexity, that closely-spaced steppingstone islands exist somewhere in sequence space whereby random mutations can actually get from one novel island to the next without having to make much of a random walk. This claim of yours (identical to the claim of Jason Rosenhouse), simply doesn’t reflect what is known about sequence space at various levels of functional complexity. There simply are no such closely-space islands at higher levels of functional complexity that are actually known, and no reason to think that such a situation will ever be discovered.

      But, you write, “The data indicate that biology doesn’t occupy all of functional space or sequence space, just little bits of it.”

      That’s just the point. Since a population can only occupy the tiniest fraction of sequence space at a higher level of functional complexity, the finding of novel islands at the same level or higher involves crossing vast gaps of non-beneficial sequences that do in fact exist between each one of these higher-level islands and the next closest island. And that, my friend, is the fundamental problem for the ToE.

      It also suggests that as sequence space increases in size by 20^N, the ratio of viable vs. non-viable sequences, not just systems, decreases exponentially. – Sean Pitman

      This is just the all-at-once fallacy repeated again.

      No, it isn’t. What it means is that your one-at-a-time mutations simply cannot cross the resulting gap distances in a reasonable amount of time beyond very low levels of functional complexity. It’s the very same problem regardless of if there are many random mutations at a time or just one random mutation at a time. The odds of success are the same.

      You conclude with:

      And, this effect only gets exponentially worse and worse with each step up the ladder of functional complexity. – Sean Pitman

      This is raw assertion, not something your references say, and you haven’t defined the “ladder of functional complexity” anyway. Most of protein complexity involves fusing protein domains or evolving binding sites between them, these are pretty trivial processes.

      I have defined the “ladder of functional complexity” (as have others in literature) as the minimum size and specificity of the parts required to produce a given type of function. In other words, some protein-based systems have a minimum amino acid residue requirement of only a dozen or so specifically arranged residues, while other protein-based systems have a minimum requirement of several thousand specifically arranged residues. These systems are on very different levels of functional complexity. And, the sequences spaces needed to hold these different systems are also very different when it comes to the ratio of beneficial vs. non-beneficial and the resulting distances between the beneficial islands of proteins within these sequence spaces.

      As far your comments on junk-DNA, that’s a separate topic. I’ll have to respond at a later time.

      FLAGELLUM

      See the table at Panda’s Thumb from Pallen & Matzke 2006. There is a lot more to the argument than just the 10 proteins homologous to nonflagellar T3SS.

      I’ve responded to your argument extensively at:

      http://www.detectingdesign.com/flagellum.html

      There is no point in discussing this until we resolve your misconception about the ability of single proteins to evolve along narrow paths through huge sequence space, in some cases retaining the same function, in other cases changing function.

      Those paths exist. Phylogenies of proteins are one of the proofs. The branches of the phylogenies are actual statistical estimates of these paths. They exist both for cases where all the proteins at the tips have the same function, and for cases where some of the proteins at tips of the tree have different functions.

      Phylogenies say nothing of the gap distances between the proposed steppingstones and how the distance between these steppingstones can be traversed along “narrow paths” via random mutations – which is the main problem with your flagellar evolution papers. You simply wave your hand and blindly assume that the gap distances are small enough because of the phylogenetic relationships or similarities between proteins within different systems. You see, the problem isn’t with the similarities. The problem for your mechanism is with the number of required non-selectable differences to get from one system, from one steppingstone, to the next. Phylogenetic similarities do suggest a common origin of some kind, but they do not tell you that the mechanism of RM/NS was in fact capable of producing the required differences – a key mistake on the part of evolutionists such as yourself.

      For example, the steppingstones you list off in your flagellar evolution pathway are each far too far apart in sequence space for random mutations to get from any one to any other in a reasonable amount of time. The required non-selectable changes are simply far far too numerous for your theory to be tenable. Beyond this, as confirmation of this problem, not one of your proposed steps from one steppingstone to the next has been demonstrated in the lab. If these steppingstones are truly as close together as you seem to imagine, such a demonstration should be no problem. Take the wild-type system for one steppingstone and show how, given the appropriate selective environment, the next steppingstone in your sequence is actually reachable.

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    • Junk DNA:

      Regarding your comments on “Junk DNA”, I actually agree with everything you said. I do think that the ENCODE team dramatically overstated their case for the functionality of non-coding DNA. So, I think you’re correct in this regard – especially given your examples of the extreme variability of the amount of non-coding DNA within organisms that have a similar number of protein-coding genes. However, what I think was not predictable from the evolutionary perspective was the idea that protein-coding genes are really the most basic of building blocks within the genome while the real information for what type of creature is to be built resides within the non-coding DNA. In other words, non-coding DNA is like the blueprint for the house that details where the basic “bricks and mortar” are to go for building a particular type of house. I don’t think that this was predictable from the evolutionary perspective where most believed that not much of real importance was going on within non-coding DNA – that the protein-coding genes were the primary source of functionality within the genome.

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    • @Nick (Matzke):

      Also, it’s intuitively “obvious”, but mistaken, to think that having a large amount of junk DNA in the genome is “expensive”. The energetic & material cost of replicating/maintaining the genome in a typical large eukaryotic cell is trivial compared to the costs of protein synthesis, energy generation for muscle action, etc.

      An interesting paper has been published that seems relevant to this claim. Holloway et al. (2007) argue that it is in fact rather expensive for a cell to maintain extra DNA that doesn’t provide a significant survival/reproductive advantage (Link).

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  15. @ Bob

    “George, the problem with your assertion is two-fold: 1) You make a very general statement about the weight of evidence for very ancient life without stating what that evidence is. 2) When we actually examine that weighty evidence, it turns out to be largely in the eye of the beholder.”

    Which means you think Dr. Ben Clausen, an Adventist nuclear physicist who works for the GRI is wrong. Or should I not be appealing to authority even if it is an esteemed Adventist scientist. Maybe you should check his work out?

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    • @george: I am aware of Ben Clausen’s work. Maybe you should check out the work of Ariel Roth, who has a very different opinion. Also, Robert Brown was a specialist in radiometric dating who used to work for GRI, and he also had a very different opinion. Of course, the radiometric dating of igneous rocks is a challenge to a short chronology for life. But then, the carbon dating of organic material in fossils is a challenge to a long chronology for life – because, so far, all Phanerozoic organics yield a C14 age of 40,000 years BP or less. C14 dating of Phanerozoic organic has only been carried out for about ten years, but the results are now so universal that it’s hard to imagine how they could be attributed to contamination. There’s nothing wrong with appealing to authorities, as long as you read authorities on both sides of an issue and think for yourself.

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  16. @ Dr. Kime

    “Indeed the greatest scientists in history have been the ones (singular, individual) who broke from consensus, whereupon the greatest MASS (critical mass) of scientists agglutinated upon him to be the new consensus and peer review.”

    Exactly right. Perhaps Dr. Pitman- with his blend of ID, YLC, statistical probability, educate truthy- will supplant the giant Darwin as the new consensus maker. To do so he will likely have to escape the Adventist paradigm and become a full fledged ID’er- seems like he is kind of moving in that direction.

    Problem with ID is that the biblical baker ain’t necessarily the cosmic maker. But Dr. Pitman solves that problem with bland dough of the
    weight of the evidence, while using the scapel to make surgical cuts to
    sequence spaces. Give me some of that ole time religion indeed, with a little scientific icing on top.

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  17. @ Bob

    ” You need to publish this material in a journal – even a creationist journal – where it can be critiqued by bright minds who have expertise in molecular biology. I realize that I have mentioned this before, but if your argument is valid, it deserves to be widely known, ”

    Yesiree!

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  18. My model does not ignore compensatory mutation at all. The effect of compensatory mutations is simply to reverse the random walk of a sequence back onto the original island from which it started. That’s all. Compensatory mutations do not help to reduce the average time required to find a qualitatively novel island within sequence space.

    You’re not getting the basics. After a slightly deleterious substitution, followed by a compensatory mutation, you are not returning to where you started, you have moved to a different place in sequence space. The compensatory mutation makes the sequence more different from the original sequence, not more similar to it. The “space” we are talking about is sequence space, unless you want to abandon all your previous arguments.

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    • You’re not getting the basics. After a slightly deleterious substitution, followed by a compensatory mutation, you are not returning to where you started, you have moved to a different place in sequence space. The compensatory mutation makes the sequence more different from the original sequence, not more similar to it. The “space” we are talking about is sequence space, unless you want to abandon all your previous arguments.

      This is certainly basic stuff here…

      Consider that compensatory mutations maintain the same function at the same or, more often than not, at an improved but still reduced level of original functionality by compensating, with a different mutation, for a detrimental mutation that came before. All such compensations therefore relocate the evolving sequence back onto the very same starting island – an island, as already explained to you, that is comprised of a cluster of all sequences that can produce the same basic structure with the same original function in question. So, even though a compensatory mutation produces a different sequence compared to the original, the new sequence is still on the very same starting island of sequences. It’s just on little different spot on the same island – not a different island. It’s like taking a step off the beach and into the water and then back onto the beach again a couple feet or so away from where you first stepped off the beach. Big deal! It’s lovely that you’ve figured out how to walk all around the beach of the very same island, but how does this ability reduce the time it takes to actually swim, blindly, to the next closest island that has a qualitatively different type of function?

      This is why compensatory mutations don’t help reduce the time required to find a new island. They just help sequences to stay on the same starting island is all. It is for this reason that natural selection is a preserving force, not a creative force beyond very low levels of functional complexity.

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  19. Pingback: Nick Matzke vs. Sean Pitman Debate | Educate Truth

  20. “Maybe Oprah.” Good shot, pard.

    Why thankee pard! Always good to have a glass of mirth with you on the ole’ dusty, ontological trail.

    Ya’all paint a purty picture in prose, which late at night warms my toes, and I suppose in a fictive setting, would be quite a rose…. who knows?

    Time for a glass of agnog….

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  21. Just wondering if we can replace the depicted brown stepping stones ostensibly lined up in Lake Superior by with highly polished symmetrical granite cubes? Better surface to walk on – albeit a tad slippery with the polish – but definitive proof of sequence space ID!

    That one is for my good pard Wes, with apologies to Dr. Pitman for the non linear humour :)

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  22. Jason Rosenhouse (from his Blog):

    The relevant comparison is not what human intelligence can create in the short run versus what natural selection can create in the short run. The question is what natural selection can create in the long run. Moreover, I have no idea what your metric of creativity is. When applied to problems in engineering and medicine, evolutionary algorithms routinely find solutions to problems that had eluded scientists applying other methods. The successes of breeders in modifying the form of organisms in short periods of time are likewise impressive. None of this supports the rather facile comparisons you are trying to make.

    First off, breeding isn’t primarily based on Darwinian evolution, but upon Mendelian genetics – i.e., the pre-programmed potential for variation that exists within sexually reproducing populations that doesn’t require the evolution of anything functionally new within the gene pool. It’s already there – pre-programmed. I know this concept can be confusing for many who haven’t taken or don’t remember basic biology. In fact, many of Darwin’s own observations weren’t really Darwinian in nature, but were simply observations of Mendelian variation over time.

    As far as evolutionary algorithms routinely solving problems that have eluded scientists, this only happens within very restricted regions of search space – i.e., at very low levels of functional complexity where evolutionary algorithms are very good at sifting through large numbers of variables in relatively short order. However, when it comes to solving problems that require the invention of complex machines or information systems, machines and systems that require multiple parts working together in specific arrangements, evolutionary algorithms aren’t helpful at all beyond very low levels of functional complexity because the non-beneficial search space is simply too large to be searched this side of a practical eternity of time. Now, it would be great if such an evolutionary algorithm could be creative at higher levels of functional/meaningful complexity. Such an algorithm would put human engineers, computer programmers, and authors out of business and make whomever came up with such an algorithm far far more wealthy than Bill Gates! Good luck with that…

    Of course, as previously explained, the reason for the clear limits to the creative potential for the evolutionary algorithm of RM/NS is due to the exponential decline in the ratio of potentially beneficial vs. non-beneficial in sequence space and the fact that a function-based selection mechanism cannot look into the future as intelligence can.

    Your suggested solution to this problem (a nice neat little line of closely spaced steppingstones in sequence space) just doesn’t represent known reality. No such a pattern has never been identified in sequence space beyond very low levels of functional complexity. And, given what we do known about sequence space, your vision of a nice line of sequentially selectable steppingstones is very very unlikely to be found.

    In short, what we do know and can observe is that intelligent design is superior to your evolutionary algorithm beyond very low levels of functional complexity within observable time. And, there is absolutely no reason to believe that your algorithm somehow gets better beyond what can be observed given the known exponential decline of the ratio of potentially beneficial vs. non-beneficial with each step up the ladder of functional complexity. All that is left is wishful thinking and your usual appeal to “circumstantial evidence” that is based on what you think an intelligent designer would or would not do – not demonstration or statistically tenable arguments regarding the nature of sequence space or the actual creative potential of the mindless Darwinian mechanism.

    I’ll address your claims about sequence space in the Probability and Evolution post. Your remarks about intelligence, though, are an utterly breathtaking extrapolation. I can’t even imagine how you go from, “We have technology today that would have seemed miraculous to the ancients,” to “There’s no limit on what intelligence can do.”

    Your claim is especially dubious in light of the fact that there seem to be clear limits on what intelligence can do. So far as we know, intelligence cannot bring universes into being or adjust fundamental constants. Nor have we been able to create life of any sort, much less life equipped with complex biochemical machines. And since every intelligence we know of is embodied, it is not clear at all that an unembodied intelligence is even a possibility.

    I am actually quite surprised that you appear to be arguing for a theoretical limit to what intelligence can achieve given enough knowledge and technological advancement. Are you actually suggesting that the creation of biological machines, equivalent to something like a flagellar motor, is clearly beyond what human intelligence could ever achieve? – regardless of future knowledge and technological achievements? Really? Also, given our limited intelligence and creative ability, and how we clearly learn and improve over time, how can you possible argue that no form of intelligence, regardless of level or technological know how or learning or advancement, is theoretically limited to what you know how to do or can possibly imagine with your very limited brainpower? Do you really think you can define the limits of where even human intelligence can go and where learning and creative potential ends?

    Not “greater creative potential” (whatever that means). Just different creative potential. For example, the physicists tell us that matter spontaneously creates itself all the time. I am not aware of any instance of intelligent agents creating matter from nothing. As for the relative merits of natural selection versus ID, you simply ignored all the evidence I cited, briefly, at the end of this post.

    Please do cite where matter has been created from absolutely nothing. This simply hasn’t been observed. Even theoretically an “empty” vacuum isn’t exactly “nothing.” It is thought to be a combination of matter and antimatter — particles and antiparticles.

    As far as your “evidences” for the creative power of natural selection, I’m sure I did miss such an argument in your post. Where was it again?

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  23. A Servant: I have been watching for your reply, but have seen none. It makes it hard for me to favor your arguments if you don’t have a good response to the counterarguments Pitman has presentet.

    I would have thought by now as a graduate student you would have the perspecuity and insight to know how this site actually works.

    An highly intelligent MD with little scientific training and absolutely no scientific credibility as measured by peer reviewed publications in this area but inculturated in the theological premises of an increasingly fundamentalist sect regularly goads credible scientists into responding to what they perceive as fundamentally flawed arguments and questions given in good faith.

    Because of the intransigence and perseveration evident in his prolix responses they eventually recognize that this is not a good faith exchange and graciously withdraw.

    The perception of this by the MD and his acolytes who imagine an MD the pinnacle of intellectual and academic achievement is that any counter argument has been silenced and that there is in fact no adequate response to his queries (see Seans response to you).

    Shouldnt a person like me follow this same pattern and completely withdraw in frustration. I indeed do but unlike Nick and Jason I have an investment in a common faith community and cannot remain completely silent while there is a campaign against centres of learning of this faith community. In particular I cannot let pass without comment Sean’s faithless modus operandi and meme

    “I, personally, would have to go with what I saw as the weight of empirical evidence. This is why if I ever honestly became convinced that the weight of empirical evidence was on the side of life existing on this planet for hundreds of millions of years, I would leave not only the SDA Church, but Christianity as well” (http://www.educatetruth.com/theological/the-credibility-of-faith/comment-page-1/#comment-18717).

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    • I simply can’t comprehend how an individual can hold to the ideas of scientism and also be a Christian. The basic philosophy of scientism contradicts explicitly the “mind of God” as described within the Bible. A Christian is supposed to believe that God created the universe. Paul states that it’s our observation of God’s creation that yields His invisible qualities. Every place in the Scriptures where the “mind of God” or God’s abilities are compared with the “mind” of His creations or His creations abilities, the “mind” of His creations and His creations abilities are substantially inferior. Consider for example Isaiah 55:8-9.
      “For my thoughts are not your thoughts, neither are your ways my ways saith the LORD. For as the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than you thoughts.” (KJ)
      Then consider Romans 11:33.
      “O the depth of the riches both of the wisdom and knowledge of God! how unsearchable are his judgments, and his ways past finding out!” (KJ)
      Consequently, it should be impossible for scientists to describe or comprehend all of the details of how our universe and the entities it contains were created or sustained from the beginning of creation. Later in this book when I discuss in more detail the D-model, you’ll see that this scientific model actually establishes as mathematical truth such statements as Isaiah 55:8-9, Romans 11:33 and many more.

      Dr. Robert A. Herrmann
      Professor of Mathematics (Ret.)
      U. S. Naval Academy**

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    • How is it that those who side with you on this topic are the ones of “good faith” while I am not responding in equally “good faith”? How can you possibly judge my motive on this issue? I do think that Jason and Nick honestly believe that neoDarwinism is true and that the evidence in its favor is essentially overwhelming. Why not extend the same courtesy to me and how I feel about my position?

      In any case, Jason Rosenhouse, who is actually replying to my comments on his own blog, clearly doesn’t understand how the evolutionary mechanism works at various level of functional complexity. He’s a mathematician, not a biologist. He knows, mathematically, how it must work if the theory is actually true (via a nice little closely-spaced line-up of steppingstones in sequence space). However, he doesn’t seem to yet realize that this imagined scenario doesn’t remotely represent known reality when it comes to applying this mathematical concept to real biological systems and protein sequence space. Sequence space simply isn’t set up like he imagines.

      Nick Matzke, on the other hand, has tried, valiantly to be sure, to invoke conversion mutations to explain how this problem can be overcome. Of course, the problem here is that conversion mutations simply reproduce the same structure/function – usually at a lower level of functionality compared to the original. They don’t produce any qualitatively new structure/function. And, they don’t tend to narrow the non-selectable gap distances at higher levels of functional complexity. Matzke’s own proposed steppingstones in his published papers on flagellar evolution present steppingstones that are themselves dozens and dozens of required mutational changes away from each other – a gap distance that is simply uncrossable by random mutations in what anyone would consider to be a reasonable amount of time.

      And, not even you understand how the mechanism of RM/NS is remotely tenable beyond very very low levels of functional complexity. You’ve even admitted as much in this forum. If you have no idea how evolution can work beyond the lowest levels of functional complexity that exist within all living things, why are Earth do you think it still works? I know, because of the “circumstantial evidence” cited by Rosenhouse in our debate – evidence which is almost entirely based on how you and Jason and other evolutionary scientists think that an intelligent designer would or would not behave (not upon some actual evidence for how your mechanism could tenably have done the job).

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  24. “Please do cite where matter has been created from absolutely nothing. This simply hasn’t been observed. ”

    Book of Genesis

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  25. @ Dr. Pitman

    “he is a mathematician, not a biologist.”

    This is the height of hypocrisy due to your professed expertise in math as applied to biology. Wnen I challenged you in the past as to your mathematical credentials you brushed off this criticiticism. What makes you such an interdisciplinary expert but not others?

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    • I don’t care what credentials a person holds, as long as the arguments make sense and are reasonably informed along at least a basic level of understanding of the disciplines required to be conversant on a topic. Beyond this, Rosenhouse himself pointed out, in our debate, that he wasn’t a biologist or a geneticist and that any discussion of biology would require bringing in someone with more expertise and knowledge of the field of biology than he had.

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  26. @ Gene

    ” I simply can’t comprehend how an individual can hold to the ideas of scientism and also be a Christian. The basic philosophy of scientism contradicts explicitly the “mind of God” as described within the Bible.”

    Agreed. Religion or atheism are different disciplines than Science. Science cannot difinitively prove or disprove God especially when it comes to First Cause. Hawkings has suggested that the universe(s) can spontaneously emanate from nothing, a quantum fluctuation resulting in the big bang. But, even if this was the case, why is there even the potential for this state of affairs? The mere fact of our concious appreciation of this universe raises the possibility of an originating force that approximates the notion of a God beyond time, space and matter. The biblical concept of God is one iteration of such a First Cause. There are many other such cultural iterations of same. What Science can do is casf doubt on these iterations as being accurate – what God is not.

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    • @george:

      On this I think most Christians would agree. Sean however seems to be exceptionsal with his endorsement of scientism in his statement

      “I, personally, would have to go with what I saw as the weight of empirical evidence. This is why if I ever honestly became convinced that the weight of empirical evidence was on the side of life existing on this planet for hundreds of millions of years, I would leave not only the SDA Church, but Christianity as well” (http://www.educatetruth.com/theological/the-credibility-of-faith/comment-page-1/#comment-18717).

      He believes in Christianity only because he thinks it is supported by science.

      “Scientism is a term used to refer to belief in the universal applicability of the scientific method and approach, and the view that empirical science constitutes the most authoritative worldview or most valuable part of human learning to the exclusion of other viewpoints.[1] It has been defined as “the view that the characteristic inductive methods of the natural sciences are the only source of genuine factual knowledge and, in particular, that they alone can yield true knowledge about man and society.”

      http://en.wikipedia.org/wiki/Scientism

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      • You fideists confuse a need for the personally perceived “weight of evidence” with “scientism”. Tell me, what separates your beliefs, on any topic, from wishful thinking?

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        • @Sean Pitman:

          There is no confusion. I can parse your clearly articulated message. You are saying in this statement that your religious beliefs are completely subservient to your personal scientific understandings of origins. On this your completely agree with Provine and Dawkins. unless it agrees with science religions is worthless.

          If you perceive at any time that science as you understand it contradicts your literal reading of the Bible then you privilege science and empiricism over any other mode of understanding and will reject Christianity.

          Christians who do not do so and believe that God speaks to us through revelation you label as fideist and wishful thinkers. If you do not understand faith so be it.

          In the interest of transparency you should make it very clear to your disciples where you are leading.

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          • So, God speaks directly to you and gives you privileged information via personal “revelations”? – information that isn’t generally accessible to anyone else beyond you and your own personal experience with God and what he reveals especially to you? – regardless of what the weight of empirical evidence in the world around you may or may not be saying? Again, how is this not the very definition of fideism? Upon what basis do you test your revelations? How do you know your revelations are superior to wishful thinking? – that they are actually reasonable vs. self-generated delusions or fables? And, how are such personal revelations helpful to anyone other than you?

            Don’t get me wrong. I believe that God does, on occasion, give certain individuals privileged revelations. These prophets of God, however, are not given these revelations only for their own edification, but to share with others. And, the message from God is also given additional evidences as confirmation of its Divine origin so that others might believe it actually came from God. Such was the case throughout the Bible whenever God sent a prophet to speak to the people. God never expects faith without a basis in the weight of evidence upon which to base a rational faith and trust in Him and His Word. Anything short of this is fideism – indistinguishable from wishful thinking and no more useful.

            In any case, I think people are well aware of my position on this topic and why I value empirical evidence as a basis for rational Biblical faith. I simply don’t see the need to rehash your fideistic views over and over again. This isn’t the forum for such things. If you have something to say about the actual topic at hand, by all means present your arguments. Otherwise, I’m not going to continue posting arguments about faith vs. evidence over and over and over again.

            1 Peter 3:15

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    • In Faith and Reason, pp. 162 ff, the late Ronald Nash summarises an argument to God by Gordon Clark that apparently traces to Augustine, that we may cite and slightly adapt following bloggist and commenter Ilion (HT):

      P1. Truth exists.
      P2. Truth is immutable (unchangeable).
      P3. Truth is eternal (–> without beginning or end; lasting for ever).
      P4. Truth is mental (pertaining to mind or minds).
      P5. Truth is superior to the human mind
      ________________________________
      So

      C6. Truth is God

      @george:

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  27. Sean Pitman: So, God speaks directly to you and gives you privileged information via personal “revelations”? – information that isn’t generally accessible to anyone else beyond you and your own personal experience with God and what he reveals especially to you? – regardless of what the weight of empirical evidence in the world around you may or may not be saying? Again, how is this not the very definition of fideism? Upon what basis do you test your revelations? How do you know your revelations are superior to wishful thinking? – that they are actually reasonable vs. self-generated delusions or fables? And, how are such personal revelations helpful to anyone other than you?

    It seems you have a less than nuanced view of many things. I do not imagine my faith as action can exist in isolation any more than I imagine I alone can understand all areas of science in their entirety. As you well know I wholeheartedly accept that I belong to both a community of faith and a scientific community. Unlike Vernon Howell I do not imagine I alone can individually apprehend the Will of God except from within that community of faith whence derives any understanding I may have of Gods revelation. Just as one can appreciate the search for natural scientific explanations within a framework created by people with expertise so I look to the Christian community for its experience, expertise and knowledge to guide my experience of God and the transcendent.

    I am happy for you to continue your pursuit of empirical evidence for faith and develop your peculiar synthesis of science and religion and even to garner a cadre of similar minded followers but I do fear the consequences of your attacks on LSU and that any chink in your wall of defence protected by Mortons demon* may well result in the scenario you have stated;

    “This is why if I ever honestly became convinced that the weight of empirical evidence was on the side of life existing on this planet for hundreds of millions of years, I would leave not only the SDA Church, but Christianity as well”

    I would certainly be much less fearful if you simply admit this was something of an overstatement and that you do indeed see some value in Christianity independent of any consideration of the age of life on earth.

    * http://www.australasianscience.com.au/article/issue-may-2011/confirmation-bias-denialism-and-morton%E2%80%99s-demon.html

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    • I’ll let you have the final word on this. I think my position has been made clear, as has yours. I see no point in going round and round on this topic.

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  28. @ Dr. Pitman

    “So, God speaks directly to you and gives you privileged information via personal “revelations”?”

    Excellent point. Never happened for me and presumably not for you Dr. Pitman? Thus we use reason, Science being the best empirical tool of same, to examine and make conclusions to the best of our abilities. All good so far. But tell me, why on earth from a scientific point of view would you think God directly to EGW? Are you saying your faith plays no part in your conclusion?

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  29. Sean Pitman: In any case, I think people are well aware of my position on this topic and why I value empirical evidence as a basis for rational Biblical faith.
    I simply don’t see the need to rehash your fideistic views over and over again. This isn’t the forum for such things. If you have something to say about the actual topic at hand, by all means present your arguments. Otherwise, I’m not going to continue posting arguments about faith vs. evidence over and over and over again.

    1 I do not think they are aware of your position since you use words in a different way to what people would expect. You claim you are not advancing scientism with you statements about empirical evidence and the bible. But you do not accept what most people would think of as empirical evidence.

    Wiki states it as:

    “Empirical evidence (also empirical data, sense experience, empirical knowledge, or the a posteriori) is a source of knowledge acquired by means of observation or experimentation.[1] Empirical evidence is information that justifies a belief in the truth or falsity of an empirical claim. In the empiricist view, one can only claim to have knowledge when one has a true belief based on empirical evidence. This stands in contrast to the rationalist view under which reason or reflection alone is considered to be evidence for the truth or falsity of some propositions.[2] The senses are the primary source of empirical evidence. Although other sources of evidence, such as memory, and the testimony of others ultimately trace back to some sensory experience, they are considered to be secondary, or indirect.[2]

    In another sense, empirical evidence may be synonymous with the outcome of an experiment. In this sense, an empirical result is a unified confirmation. In this context, the term semi-empirical is used for qualifying theoretical methods which use in part basic axioms or postulated scientific laws and experimental results. Such methods are opposed to theoretical ab initio methods which are purely deductive and based on first principles.”

    2. We cannot really have any argument about the topic at hand if we have no agreement on what we accept as valid evidence on which your empiricism can be based.

    I know you do not want to talk about these fundamental underlying assumptions and would rather have the unending woolly arguments about granite cubes, SETI, sequence space and probability without questioning the foundations and assumptions.

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    • How can you describe my arguments about the designed nature of something like a highly symmetrical polished granite cube as “woolly”? – especially considering your own argument that such a cube is in fact a “blindingly obvious” artifact of deliberate design? – even if found on an alien planet like Mars?

      Paul Cameron wrote:

      That this [granite cube] is an artefact and that it was made by a life form and not [by] magic is so blindingly obvious that to state it would be an insult to the review panel. (Link)

      The problems is that like monty python you confuse categories. You argue from an obvious artefact to suggest that anything that appears designed for a purpose must have a divine creator… You are arguing that a molecular “machine” is precisely the same as an artefact and therefore must accept the same implications of design. That is not at all established…

      You make no distinction between a molecular machine and a physical machine or an artefact. If we take [your] logic to its extreme it is completely reductionist. Biology is just mechanics. This is certainly consistent with your incredulity about emergent properties.
      (Link)

      So, we obviously agree about the origin of the granite cube. The granite cube, as you yourself argue, is a blindly obvious artefact of intelligent design (or “creative intelligence” if you prefer) – regardless of if God or some other intelligent designer did the job. It really doesn’t matter as far as the basic detection of design is concerned.

      As far as the rest of your basic argument is concerned, pleased do explain it to me a bit more. Are you really suggesting here that a molecular machine, built of amino acid parts as basic building blocks, is not really a “physical machine”? – that a rotary flagellar motility system is something more than “just mechanics”? Are you suggesting here that humans cannot possibly build such a biological machine? – because there’s something mystical or magical about such machines? something that makes them “emergent” when “physical machines” that humans build are somehow less than “emergent”? What is your definition of “emergence” such that human-designed machines (like jet engines for example) are not emergent? – while equivalent biological machines somehow are?

      As far as your argument for design based on “modest complexity, found out of context”, this is exactly what I’m proposing – a signal coming from an biological environment from which neither it nor anything like it is either expected or observed by any known mindless natural mechanism. That is why SETI scientists claim that anything from a very simple sinusoidal radio signal whistle to a radio signal carrying a complex mathematical sequence would be “blindingly obvious artefacts” – the products of intelligent design. Again, no one is proposing a “supernatural biochemist” at this point. What is being proposed, at minimum, is an intelligent biochemist with a level of intelligence no less than that needed to explain SETI radio signals.

      The SETI conclusion that certain types of radio signals are “artefacts” is rational because mindless natural processes are not currently known which can produce the types of signals that SETI scientists are looking for, while still being within the realm of what intelligent designers (i.e., humans) are capable of producing. Exactly the same thing is true for why you claim that a highly symmetrical granite cube is a “blindingly obvious artefact” of creative intelligence. And, given that no known mindless mechanism is capable of producing certain types of sequences in DNA or certain types of biological machines, the very same thing would be true for these features as well – since these machines are very much like machines that humans do in fact create.

      For example, you didn’t respond to my earlier illustration of you finding a DNA sequence in a virus that showed a Morse Code pattern that read, “Hi Dr. Cameron. Just checking to see if you’re paying attention. All the best. – God”

      Don’t tell me that you wouldn’t recognize such a coded sequence, even if coded within a sequence of DNA, as a true artefact of intelligent design (the same as if it came in a radio signal) – even though you’d most likely not consider God as the source of such a sequence. You’d probably think that one of your lab partners is trying to play a trick on you. However, you’d not think, not for a minute, that such a sequence might be the result of some “natural” mindless mechanism.

      Why then do you argue that something like a rotary bacterial flagellum is somehow less clearly an artefact of creative intelligence? – given that the Darwinian mechanism cannot explain it? Because, you’re not a “reductionist”? That’s your reason?

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  30. @ Dr. Pitman

    ” That, in a nutshell, is the fundamental problem for the theory of evolution – it’s mechanism simply isn’t capable of going beyond very very low levels of functional complexity this side of a practical eternity of time (trillions upon trillions of years).”

    So, given enough time, you think macro evolution is statistically possible?

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    • Everything is statistically possible (like you winning the California Lottery 10 times in a row). However, not everything is statistically likely…

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    • Actually, because it violates the laws of physics and chemistry. See Wilder-Smith “The Natural Sciences Know Nothing of Evolution”@george:

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  31. Good point.

    So would EGW seeing life on other planets as a vision from God be like winning the California Lottery 1000 times in a row? I presume as a scientist and an Adventist you believe this vision is a true picture of life on another planet? If so how is such truth empirically supported or statitstically probable? Those are genuine scientific questions, right?

    I trust dear Dr. Pitman, that when is scientifically advocating ‘educate truth’ in a public forum, everything such advocate believes is subject to examination on a scientific basis.

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    • As I think I’ve mentioned before (Link), for me, it’s all based on credibility.

      Consider, as a hypothetical example a situation where you personally saw Jesus raise someone that you knew was dead back to life again, or where you saw Him heal a paralyzed man right before your eyes, etc. Would such demonstrations rationally affect, for you personally, the credibility of His metaphysical claims regarding His ability to forgive sins or the future life in Heaven to come that He claims to offer to us all? (Mark 2:9) Why do you think that the New Testament authors cite, in particular, the bodily Resurrection of Jesus, which they personally saw and touched, as the lynchpin for their faith and their claims of credibility regarding their Divine commission? (1 Corinthians 15:14 and 2 Peter 1:16).

      You see, it’s all based on the empirical evidence that establishes the credibility of the witness. That is why the Bible itself explains that the status of a prophet of God can be tested – if the testable claims of the prophet do or do not come true (Deuteronomy 18:21-22). It’s perfectly rational that such evidence will have an effect upon credibility – and therefore believability.

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  32. This website features debates by those who seem convicted that only one side has all the right cards. The simple reality is that there is much we don’t understand. We can use genetics models and state-of-the-art science to buttress our arguments, but we err when we make sweeping, arrogant statements that dismiss the other side.

    Here are the latest eye-popping findings that should prompt us to question how well we understand the limits and constraints of genetic change and evolution:

    http://discovermagazine.com/2014/jan-feb/100-genomes-change-with-temperature

    Neither of our highly-trained genetics experts, Dr. Cameron or Dr. Pitman, could have predicted these findings. Humility is always a good thing.

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    • Interesting observations, but I fail to see the relevance to the question of how novel protein-based systems can be produced beyond very low levels of functional complexity by any kind of mindless mechanism? How does the observation of such programmed flexibility to rapidly react to environmental changes remotely challenge the ID hypothesis when it comes to explaining the origin of functional complexity beyond very low levels?

      Now, I do agree that humility is a fine quality, very fine indeed. However, don’t let it turn your brain off or cause you to be unable to take risks or take positions that might actually be wrong. Science is about proposing testable hypotheses that could in fact fail the test – that could in fact be wrong. The question is, what seems to be most likely true given what we currently know? Which hypothesis, among the competing options, carries the best predictive value? Anyone with any solid opinion at all on any topic must take on a just a little chutzpah as well as the risk of failure – of being wrong.

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    • Epigenetics does predict rapid changes, they have been noted in nature many times. What is interesting is that the rapid changes always result in the same kind, ala the Law of Biogenesis and Heredity. In the debate between Design and Evolution, the tide is turning to the Design side.@Harold A.:

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      • Except these particular changes in summer/winter phenotype do not appear to be based on epigenetics, but upon standard allelic variations within the gene pool depending upon variations in the environment.

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  33. @ Dr. Pitman

    ” Why do you think that the New Testament authors cite, in particular, the bodily Resurrection of Jesus, which they personally saw and touched, as the lynchpin for their faith and their claims of credibility regarding their Divine ”

    Why do you think the followers of David Koresh thought he was divine and died for it? Even now some of his followers think so. What if they wrote their own account and say that they had witnessed him rising? Do you think there would be at least some people who believed that?

    Is martyrdom, or accounts written and redacted after the fact , scientific bases for determining divinity?

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  34. “Consider, as a hypothetical example a situation where you personally saw Jesus raise someone that you knew was dead back to life again, or where you saw Him heal a paralyzed man right before your eyes, etc. Would such demonstrations rationally affect, for you personally, the credibility of His metaphysical claims regarding His ability to forgive sins or the future life in Heaven to come that He claims to offer to us all?”

    Excellent question which I’m happy to answer.

    Of course I would do so in my natural state as a skeptic and supporter of the scientific method. I’d apply the same amount of scrutiny that you apply to your theory about the threshold of RMNS not working beyond low levels of functional complexity. I’d get Jesus to repeat the miracle in a controlled setting while hundreds of observers, including medical doctors – even pathologists- were present and taking notes. If it worked I have him repeat it again and again. I’d try to rule out any other rational explanation or why the phenomenom occured – including mass hysteria or a magic trick.

    If only there was only one story about men claiming to be divine or rising from the dead. But of course there are many with great similarities. Which one(s) are true, if any? Why do they seems to borrow from each other. And most importantly, why are we not seeing such miracles, that could be scientifically tested in this modern age- happen today? Hmmm?

    Am I a doubting George? You betcha in spades. When looking for truth it’s a sine qua nom.

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    • I simply don’t believe you…

      You’re asking for far far more than the “weight of evidence” – the weight of evidence that would convince the vast majority of rational people, including scientists, if they were to personally witness the miracles of Jesus as they are described in the Bible. There simply would be no rational reason to doubt given such evidence. The only reason anyone would continue to doubt in the face of such evidence (like personally witnessing the resurrection of the body of someone who had already started decomposing or personally seeing someone born blind healed or personally witnessing the Transfiguration and hearing the voice of God and seeing Moses and Elijah show up at the same time, or seeing Jesus crucified, stabbed in the side, and then raised from the dead as an angel from Heaven showed up and flattened an entire legion of Roman guards, etc) would be due to a desire not to accept the obvious conclusion for personal or philosophical reasons (i.e., a desire for the truth not to be true) – as was the case for the Jewish leadership in Jesus’ day. They refused to see what should have been blindingly obvious (Mark 4:12).

      You seem to be of a very similar mentality to that of the Pharaoh who refused to recognize the Signature of God, arguing, like you, for “magic tricks” despite being shown miracle after miracle at higher and higher levels of Divine power far beyond what his magicians could imitate. You seem to be demanding a form of absolute proof that goes well beyond what is needed for a conclusion to be rational or scientific. Now, its fine and even wise to be skeptical to a point. However, a demand for such absolute proof removes the need for science. Science is only useful when there is the available information is limited. So, you’re not really asking for a scientific conclusion, based on the weight of evidence in hand, but an absolute demonstration. Well, you’re simply never going to get what you’re asking for – as least not in this life.

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    • @george:

      The way I understand the Bible, we will all be able witness a miracle when Christ comes. Be patient.

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      • One doesn’t have to wait till the Second Coming if one is open to the miracles of fantastic design that are all around and within us on a daily basis…

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  35. Dr. Pitman, I pointed readers to the recent and totally unexpected research demonstrating that genomes can change substantially with a mere change in temperature. No one predicted that. Here again is the story, but at another website which offers more detail:

    http://www.sciencenewsline.com/articles/2013060519430066.html

    You responded by stating that you fail to see the relevance to the question of how novel protein-based systems can be produced beyond very low levels of functional complexity by any kind of mindless mechanism. Genomes, of course, produce the proteins that interact with the environment. If new, beneficial protein systems can result within a few weeks or months time due to a mere temperature change, and within a single generation, who are YOU to proclaim that more substantial changes cannot occur in trillions upon trillions of years? You can only do so by claiming you have full understanding of the factors that influence genome changes. And neither you nor the published models you cite could possibly possess full understanding.

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    • It has long been known that mutational changes and other forms of genetic changes (especially changes in allelic frequency within a population) can and do occur very rapidly. This particular concept is nothing new. Low-level evolution and Mendelian variation of pre-existing alleles can happen and usually does happen very very quickly.

      Now, it is indeed interesting that such genetic changes can be triggered by temperature changes within a single season. That’s pretty cool! ;-) However, the problem is that such genetic changes simply do not produce anything qualitatively new beyond very low levels of functional complexity – regardless of if they were to happen minute by minute for every gene throughout an entire gene pool. That simply wouldn’t solve the problem – not even close.

      The non-beneficial gap distances are simply too great beyond very low levels of functional complexity. Your news article reference does nothing, nothing at all, to even suggest how any mindless mechanism could cross these gaps this side of trillions of years of time. Variations of allelic ratios or even novel inversion mutations, temperature dependent or otherwise, simply don’t address this problem at all. If anything, these particular types of temperature dependent frequency variations of summer/winter alleles are very similar to the pre-programmed mechanism of Mendelian variation of allelic expression within a gene pool depending upon environment – a wonderfully designed system that allows for very rapid adaptation to environmental changes.

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  36. Dr. Pitman, you also wrote, “The question is, what seems to be most likely true given what we currently know? Which hypothesis, among the competing options, carries the best predictive value? Anyone with any solid opinion at all on any topic must take on a just a little chutzpah as well as the risk of failure – of being wrong.”

    Most scientists I know personally are content to say they lean one or the other on an opinion without locking themselves into it, particularly when a hypothesis has very limited empirical support. Many creationists in the past locked onto promising hypotheses, displaying the very chutzpah you seem to admire, only to embarrass themselves later when their hypotheses proved so very wrong. Those who refuse to learn from history will repeat it.

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    • I dare say that most modern scientists don’t just “lean toward” believing in neo-Darwinism. They are adamant about it, arguing that the modern theory of evolution is supported by “overwhelming” evidence from multiple scientific disciplines. They are not at all humble about such claims. Did you actually listen to the recording of my radio debate with Dr. Rosenhouse? Was he at all hesitant about his belief in neo-Darwinism?

      Now, it’s fine to take on a solid position or make a solid claim one way or another. The only trouble is when one is so worried about being embarrassed by some potentially falsifying evidence that one refuses to accept what the evidence seems to be saying if it goes contrary to ones original position.

      You see, the problem isn’t with being wrong or opening ones self up for being proved wrong. The problem is with this fear of embarrassment of being proved wrong. That’s what science is all about. If you’re so afraid of being wrong for fear of embarrassment, well, you shouldn’t be a scientist. Science is all about trying to prove your own theories wrong. There is no absolute certainty in science. One could always be wrong. All real scientists must gracefully accept that potentiality and be willing to admit error when errors are demonstrated by the evidence.

      Bottom Line: Could I be wrong? Absolutely! And, if I am wrong, I’m most willing to face the “embarrassment” and admit the error of my ways once the evidence is shown to me. But, for now, as Charles Barkley once said, “I could be wrong, but I doubt it.”

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  37. @ Dr.Pitman

    “I simply don’t believe you…

    You’re asking for far far more than the “weight of evidence” – the weight of evidence that would convince the vast majority of rational people, including scientists, if they were to personally witness the miracles of Jesus as they are described in the Bible. There simply would be no rational reason to doubt given such evidence.”

    Are you saying that you actually understand more what is going on in my mind than I do? That is quite a feat from a cyber distance :)

    Your problem is that you have already concluded that the reported activities of Jesus are true – hence miracles- because accounts of same were written. You base this on the ‘empirical evidence’ of witnesses that may not have written the accounts themselves, that may have had a strong bias, and that were never cross examined to determine their credibility. Is this rational deduction or a leap of faith on your part. I respectfully suggest the latter.

    Your hypothetical reasoning is circular because essentially you are asking: if you witnessed a miracle then would you conclude it was a miracle? Let me give you a hypothetical back to demonstrate my point. Let us say there is a remote tribe in South America that has had no access to modern medicine and has no ability to revive someone after they have a heart attack – no pulse, no breathing, no signs of life. One day an old man dies. On the scene is Dr. Justin Time, an explorer/ doctor with a battery operated defibrillator. Pulls out the paddles and zap our oldster is miraculously brought back to life. The local witch doctor – isn’t there always one in these stories tells all witnessing the event that Mr. Time is a god having resurrected the living from the dead. Ole Justin, wanting to stay in the village, knowing a bit of the language, likes the notion and says: : ” Well actually I’m a son of god and I’ve some other nifty miracles for you as well. Would you like to talk to God in heaven?” The villagers nod yes. Justin pulls out his satellite phone and calls his buddy, an anthropology professor specializing in remote cultures and the language at hand. He puts buddy on speaker phone who solemnly intones : ” This is God and obey my son whom is before you”

    The villagers fall down on their knees including the local scribe who records the event for posterity. Eventually Justin Time, leaves just in time with miracles intact. The scribe passes the story down, which over generations gets embellished, redacted and contradicted by other competing versions of disciples and their respective scribes. Jungle Bible behold.

    Now, probably every one of those villagers were behaving rationally at the time thinking Justin Time was a son of god, but educated scientists would know better wouldn’ t they? Name me one doctor or scientist that witnessed the resurrection of Jesus? If you can’t why do you think I am being irrational in how I would approach a supposed miracle? If you apply such methodical scrutiny to the ability of RMNS to act as an agent of macro evolution, why to you scoff at the suggestion that the alleged miracles of Jesus would not be just as scrutinized by a modern rational mind?

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    • I just asked you what you would accept as valid empirical evidence, not absolute proof, for a Supernatural Signature?

      I asked if you saw a man born blind given the ability to see would that not qualify as valid empirical evidence of Supernatural power? You said no. I asked you if you personally saw a dead man who’d already started decomposing brought back to life, would you conceded that such a demonstration was pretty good evidence of Supernatural power? You said no. I asked you if you saw a shiny being come down from the sky, flatten 100 Roman guards, flick away a stone weighing several tons as if it were made out of Styrofoam, call out the the dead man inside that God called Him back to life, and then saw the man who claimed to be the Son of God, who’d been stabbed in the side by a spear and was quite clearly dead, step out of the grave alive and well, would that be good evidence? You said no.

      You’d really still have doubts, given your own eye-witness observations of such things, that perhaps these demonstrations were probably just some kind of trick being played on you? or that some kind of superior technology was being used to imitate angels and supernatural power? Really? That’s what you’d be thinking in the face of such evidence? I simply don’t believe that you still would not believe after having personally witnessed such demonstrations – based only on the potentiality that you might be wrong (as is true of any scientific hypothesis or theory). It just doesn’t get any better than this. What I have as the “weight of evidence” to offer you certainly doesn’t match what the disciples claim they saw with their own eyes. So, if you would not be convinced even if you saw what they saw, there’s certainly nothing that I can offer you that comes remotely close – except for biblical prophecy.

      That being the case, I really don’t see the point of further discussion along these lines since you seem unwilling to accept what most would consider truly overwhelming evidence that goes well beyond the mere “weight of evidence”. You see, you could always argue, “This is just a trick,” or “This is maybe due to superior technology”. Come on now. At some point the superior technology is so superior to what you or any other human can achieve or has ever achieved that it is indistinguishable from what you’d expect to see from a real God. Right? Your very same arguments could have been, and no doubt where, used by Pharaoh to justify is continued course against the supposed requests of “God” to “let my people go”. Was Pharaoh really being rational, do you think, given the reality of what the Bible says he saw with his own eyes? Would you really have done the same thing given the same set of demonstrations? That’s just hard for me to believe.

      Again, given your arguments, it seems like nothing could possibly be presented to you which you would accept as valid empirical evidence of Divine power, nothing, since there always exists the possibility of being wrong (as is always the case for any scientific hypothesis by the way – to include the hypothesis that winning the California lottery 10 times in a row, if it ever were to happen, would be the result of deliberate cheating). However, even given your argument of the possibility of modern technology being used in a third-world country, the evidence of intelligent design would still be quite overwhelming. You seem to be arguing that Divine power cannot be rationally detected by empirical means, yet even your own arguments invoke higher level intelligent design and technology as the most likely explanation for certain types of phenomena.

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  38. Bottom Line: Could I be wrong? Absolutely! And, if I am wrong, I’m most willing to face the “embarrassment” and admit the error of my ways once the evidence is shown to me. But, for now, as Charles Barkley once said, “I could be wrong, but I doubt it.”

    But you insist that if you’re a SDA professor you cannot teach uncertainty, you can only teach that overwhelming evidence favors the church’s position and that any other position cannot possibly be right, otherwise you must be fired.

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    • The professors at LSU weren’t teaching uncertainty much less that they weight of evidence seems to favor the biblical model. They were teaching that the weight of evidence overwhelmingly favors the Darwinian position on origins – directly contrary to the church’s position on origins.

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  39. @ Dr.Pitman

    “The only reason anyone would continue to doubt in the face of such evidence”

    In otherwards your statement is not scientific is it , because such evidence is not subject to being falsifiable is it? Yet you would believe such evidence as being blindly obvious without testing wouldn’t you? Double standard for your bilblical miracles v your standard to prove macro evolution my friend. Your relgious bias is so deep, that you have convinced yourself that you don’t have to apply the same degree of scrutiny to biblical claims (‘ weight of the evidence’) v absolute, demonstrable, scientific proof of macro evolution. This is an inflexible, creationist mind set, not an objective fair analysis of competing scientic theories. That is why Dr. Ben Clausen, a faithful Adventist, rather than deny the weight of the evidence says that he can’t recocile it with YEC/YLC models. Your fellow Adventist scientists see this double standard in you, which you are not prepared to concede. Then again you don’t believe me….. :)

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    • In otherwards your statement is not scientific is it , because such evidence is not subject to being falsifiable is it?

      Not true. It is empirically-based and it is subject to fallibility. If you could find any other rational way to explain it, the ID-only (or the God-only) hypothesis would be effectively falsified as the only rational solution to the cause of a given phenomenon… as I’ve already mentioned. It is the very same reason why the SETI hypothesis is also potentially falsifiable and why the ID hypothesis for a highly symmetrical polished granite cube is falsifiable. It’s the very same argument.

      You’ve tried to argue that superior technology could explain the miracles of Jesus – that Divine power wouldn’t be required to explain such miracles and that you’d still have your doubts even if you were to personally witness such demonstrations. You’re basically arguing that there’s always the possibility of being wrong, so you’ll always be skeptical regardless of the evidence presented. While it is true that it is always possible to be wrong, to be tricked or misinterpret the evidence, after a point it is no longer rational to be skeptical, to refuse to act based on the weight of evidence in hand – just because there remains the possibility of error. For example, if you did happen to win the lottery 10 times in a row, I would hypothesize that you cheated. Could my hypothsis be wrong? Yes, of course it could be wrong. However, the odds would be strongly against this possibility given the evidence in hand. The same thing is true of someone being raised from the dead after decomposing in the grave outside of Supernatural power.

      Yet, you will refuse to believe until absolute evidence in provided – until there is absolutely no possibility of error. I’m sorry, but this is not a rational or a scientific mindset.I think you must realize this, but are just trying to save face here. I just don’t believe that you’d be this resistant to such demonstrations. But, even if you would be resistant to this extreme degree, your own arguments would still invoke higher levels of intelligent design to explain such phenomena.

      In any case, I do see myself as applying the very same degree of scrutiny to the biblical claims that I apply to evolutionary claims. I see the biblical claims as being supported by the clear weight of empirical evidence just as I see the claims for certain features of living things being intelligently designed supported by the clear weight of empirical evidence. I’m not claiming absolute evidence here or perfection of demonstration. I’m only claiming what any real scientist claims – that the weight of evidence that is currently in hand clearly points in a particular direction. And, as far as the Bible is concerned, the very same thing is true. The biblical claims that are in fact open to testing and potential falsification have proven themselves, to me, to be very resilient in the face of continued attacks over the centuries. It’s the claims of the biblical critics that have been shown to be false, time and again, while the claims of the Bible have been vindicated over and over and over again.

      Of course, there are those who disagree with me on both counts. I’m certainly in the minority – obviously. Of course, that’s irrelevant if no one can present falsifying evidence against my falsifiable positions – positions which are in fact easily falsifiable if the evidence where actually available. You certainly have brought nothing to the table that remotely challenges anything I’ve presented regarding intelligent design or Biblical credibility. All you’ve done is demanded absolute proof, not the weight of evidence. You don’t seem willing to step out on your own and question the status quo; to do your own thinking for yourself regardless of what anyone else (like Ben Clausen or the vast majority of modern scientists) thinks or says. Where are these arguments you find so convincing for the evolutionary mechanism? – beyond appeals to the authoritative claims of others which you don’t personally understand beyond the fact that a bunch of apparently smart people disagree with me?

      What is your counter evidence for your opposing position? Prove me wrong… show me how a mindless naturalistic mechanism could actually do the job in a reasonable amount of time beyond very low levels of functional complexity.

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  40. Sean Pitman: I just asked you what you would accept as valid empirical evidence, not absolute proof, for a Supernatural Signature?

    This precisely illustrates what I was referring to in my last comment and the frustration in trying to discuss science and faith on this site. What do you mean by empirical evidence? It , not at all the accepted definition as explained in wiki. It is not what almost everyone else would understand as scientific evidence where such things a reproducibility sample size statistical significance and inference play a role.

    You say the words empirical evidence and imagine it is somehow “scientific” when in fact you are talking about anecdote and personal opinion. A sample size of 1 and a post hoc statistical probability of 1 may describe a miracle but that has no validity in science. Though I disagree with him Paul Giem at least allowed for reproducible miracles as the only way miracles could be studied as part of science. You don’t even seem to add that caveat but make your faith based positions absolutely part of your empirical evidence.

    Further while railing against appeals to expertise or consensus within the scientific disciplines you imagine that history is science and credibility of historical sources on any one testable event renders that source authoritative on all other events whether testable or not. Science recognizes that every event must be subject to hypothesis testing. There is absolutely no inherited verification in science.

    You are quite welcome to pursue your idiosyncratic version of science and empirical evidence but it is hardly truth in advertising to pretend that your private version is somehow legitimate science.

    As an aside your conclusions on genetic changes (actually redistribution of allelic/genomic variations within a population induced by weather) in drosophila is also highly suspect but I will leave you to issue a correction now you have had a chance to read the original paper and read up on populations genetics.

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    • History is not repeatable, but the study of history can still be done in a scientific manner.

      If you find a highly symmetrical polished granite cube on an alien planet, you can’t directly reproduce the history of how it was made or how it got there. You can only hypothesize about these things. Yet, despite the non-reproducibility of the original events that produced the cube, even you have declared that such a discovery would be a “blindingly obvious” artifact of creative intelligence – without needing to directly see how it was actually done. The same thing is true of the radio signals that SETI scientists are looking for. In other words, such a cube or such a radio signal would be “miraculous” from any other perspective outside of intelligent design. That is the reproducible/testable element of the argument for design – that no other known mechanism is capable of producing the phenomenon in question. This would be true for you regardless of if anyone else agreed with you or not. You don’t need a committee of scientists or peer review to tell you the truth of such a conclusion given your own personal experience and background (at least I hope not). Science can be done, very effectively, on the individual level.

      Exactly the same thing would be true if you were to personally see the Resurrection of Jesus or the healing of a man born blind. Such empirical demonstrations, like your own arguments for the intelligent origin of the granite cube, simply do not need to be repeated before then can be instantly recognized as requiring very very high level creative intelligence and power that is indistinguishable from what anyone would expect from a God. And, Jesus Himself appealed to such empirical demonstrations as evidence of His claims (Luke 7:20-23). Was Jesus being obtuse here? Of course not. The works of an author’s hands testify of their origin – like reading a book. The Book of Nature also says something about her Author.

      And, a demonstration that a historical source is credible in those aspects that can be tested in a falsifiable manner does in fact lend credibility to those claims of the source that cannot be directly tested. It’s a rational argument that is used all the time in many different disciplines. This is in fact the basis of much of what historical scientists believe about historical events which cannot be directly tested. It’s all about establishing degrees of credibility.

      If you will not call this sort of argument an empirical argument, a scientific argument, then you must be consistent and argue that various sciences that are based on the very same concept aren’t real sciences – to include all the historical sciences as well as anthropology, forensic science, and SETI science.

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  41. “You’ve tried to argue that superior technology could explain the miracles of Jesus – that Divine power wouldn’t be required to explain such miracles and that you’d still have your doubts even if you were to personally witness such demonstrations”

    You are ignoring my point of the circular reasoning of your hypothetical: you already presume it is a miracle!!!! It’s like asking if someone gave you ice cream to eat would you conclude itnis ice cream. This is not syllogistic reasoning but rather a tautology.

    Have you ever witnessed a miracle? Proof me wrong that miracles happened. Anecdotal, second hand, non cross examined, redacted tales of same don’t proof anything other than someone told them. Do you really think that meets the criteria for scientific proof? Come on now Dr. Pitman, we are not children here!

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    • It’s not circular reasoning to ask you what it would take for you to actually recognize a phenomenon as a miracle of supernatural power? That’s the question. You have basically claimed that nothing would convince you of such – not even if you personally witnessed the Resurrection of Jesus, or any other such claimed “miracle” as described in the Bible. Even such a personal demonstration, you claim, would not be sufficient to convince you that a true miracle had just taken place before your own eyes.

      I’m not just talking about children’s stories here. There’s no need to talk about any kind of evidence that I might present if you wouldn’t accept even the most direct and overwhelming evidence that could possibly be presented. You see, I’m trying to establish what qualifies as valid evidence from your own perspective? You appear to define a rational empirical basis for belief, or science, as something akin to absolute proof…

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  42. “It’s not circular reasoning to ask you what it would take for you to actually recognize a phenomenon as a miracle of supernatural power?”

    It is, because it presumes that such miracles exist. If they don’t exist then there cannot be evidence of same. That is why I asked you if you have witnessed a miracle? If not, how do you know they exist – like the tooth fairy, Santa Claus, or the Spaghetti Monster? :)

    I don’t fault you for believing in the Bible, but you were raised to do so. You refer to the credibility of witnesses you have never met, were never cross examined – and may not themselves have left any written account of the miracles of Jesus ( accounts left decades after his death) . If so such stories are hearsay. As far as I can tell, it is this unreliable evidence, that you, a man of science, are saying proves on the weight of evidence the miracles of Christ. You are certainly entitled to believe that as a matter of faith but it s most assuredly not science.

    It’s fine to ask hypothetical questions, but if they are not grounded in reality then you get hypothetical responses. This frustrates you because you think I’m being evasive or disingenuous. Ever watch late night religious shows where the hucksters come on and claim to heal people? Ever see people in rapture claiming they have heard the voice of God? Ever heard the doom and gloom soothsayers claiming the end of the world is nigh? Ever seen faith healers? I have.

    What’s the remedy against this type of charlantanism. A rational, sceptical mind. You certainly have that facility when it comes to examining the likelihood of macro evolution. Good for you! But when the tables are turned and you are asked questions about the proof of Christian miracles you resort to the old chestnut of credibility of non examined witnessess. Do you see the ironic juxtaposition of your bifurcated approach to examining reality as a scientist?

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    • “It’s not circular reasoning to ask you what it would take for you to actually recognize a phenomenon as a miracle of supernatural power?”

      It is, because it presumes that such miracles exist.

      No it doesn’t. It presumes that I’d be able to recognize a miracle if I were to actually witness one. That’s not a circular statement. It’s just as rational as arguing that I’d be able to recognize intelligent design behind certain types of shapes made out of granite if found on an alien planet – like my highly symmetrical granite cube for instance. That’s not a circular argument – even if I have yet to see such a cube on an alien planet like Mars.

      Your argument, on the other hand, presumes that you wouldn’t be able to recognize the signature of supernatural power even if you happened to see one of the best examples possible with your own eyes. This means, of course, that there’s simply no point talking about such signatures with you. Your position effectively ends the conversation because you’re arguing that, by definition, there’s nothing that I could possibly bring to the table that you would accept as evidence against your position of skepticism. Your position simply isn’t falsifiable given the arguments you’ve presented on this topic. Your mind appears to be made up on this topic and cannot be moved by evidence of any kind. That’s not a rational much less a scientific position.

      It’s fine to ask hypothetical questions, but if they are not grounded in reality then you get hypothetical responses. This frustrates you because you think I’m being evasive or disingenuous.

      I do believe that you are being evasive and disingenuous. I’ve been asking very straightforward hypotheticals to see where you are in your thinking, to determine the level of the bar that would need to be crossed, and I don’t think you’ve responded honestly to these questions since you’ve raised the bar beyond even theoretical crossability. And, if you did respond honestly to my questions, and I’m misreading you here regarding the true genuineness of your responses to my questions, there’s simply no point in my going into detail regarding evidence for God – given the truth of your claims that you would not recognize some of the most miraculous demonstrations that could possibly be offered as valid evidence of supernatural power even if you were to personally witness such demonstrations. Given the genuineness of this claim of yours, there’s simply no point in my continuing this discussion with you.

      What’s the remedy against this type of charlantanism. A rational, sceptical mind.

      But it’s not rational to be skeptical to the point of rejecting all possible evidence for identifying the real thing if it ever did happen to come along. There’d be no rational scientific basis for searching for anything given this mindset of yours. There’d be no rational basis for anthropology or forensic science or the search for extraterrestrial intelligence.

      You see, there’s always the possibility of being tricked or of being wrong in science – of misreading the evidence given one’s limited experience and the limited nature of the evidence in hand. If you’re not willing to take that risk, you’re not being scientific. Science, by definition, requires a leap of faith beyond that which can be absolutely demonstrated or proved. That’s why you could always be wrong in science. Science requires a risky leap of faith, but a rational leap as well…

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  43. @ Dr.Pitman

    You continue to refuse to answer whether you have ever witnessed a miracle. When was the last miracle? Other than hypothetical speculation who judges what is a miracle? You seem scared to answer that question even though I have answered yours. This a dialogue Sean, not just you trying to paint me in your hypothetical corner to establish a rational basis for recognizing miracles.

    Do you truly think you are rational and scientific if you believe in miracles you have never seen based on second hand accounts? Funny, when I took science and philosophy at university there was never any mention of miracles. How come miracles aren’t on the curriculum of the science courses? Could it be that miracles are the sole domain of religious belief?

    Your real complaint with me is not that I’m rational, it’s that I refuse to speculate on the nature of the unproven supernatural – like miracles, tooth fairies, Santa Claus and the Spaghetti Monster. That is the epitomime of Rationalism that has brought Mankind out of the dark ages of myth and superstition and into the Age of Reason. On the other hand you believe that all land animals came off a boat about 4000 years ago, contrary to the enormity of evidence from a variety of disciplines indicating this is utter nonsense. Be nice for us to step before a panel of judges and see who they thought was more rational :)

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    • You continue to refuse to answer whether you have ever witnessed a miracle. When was the last miracle? Other than hypothetical speculation who judges what is a miracle? You seem scared to answer that question even though I have answered yours. This a dialogue Sean, not just you trying to paint me in your hypothetical corner to establish a rational basis for recognizing miracles.

      There’s nothing I could present to you that you would accept as valid evidence for a Supernatural Signature if you would not accept personally witnessing something like the Resurrection or healing a man born blind a valid evidence. There’s just no point continuing this conversation given your mindset.

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  44. “But it’s not rational to be skeptical to the point of rejecting all possible evidence for identifying the real thing if it ever did happen to come along.

    I agree with you. So given the vast weight of evidence supporting evolution in many discipliines, why do you remain so skeptical? You simply reject all evidence that does not fit into your pre conceived YLC mould. There simply are not any other competing scientific theory for origins other than evolution. Miracles aren’t scientific my friend.

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    • I disagree, obviously. I see that the weight of evidence strongly counters the Darwinian story of origins, and, at the same time, strongly supports the Biblical story of origins. The Darwinian mechanism is very clearly untenable beyond very low levels of functional complexity and you’ve added nothing to support your claims to the contrary. My position is testable and has shown itself to have very high predictive value – which is what science is all about my friend.

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    • @george:
      George,

      The “Pillars of Evolution” are decaying rapidly,
      Human Origins(?) by Brian Thomas, M.S. – December 20, 2013 (Link)

      Excerpt: Three major pillars supporting a human-chimp link crashed in 2013.

      1. Genetic similarity (70% instead of 98%)
      2. beta-globin pseudogene (functional instead of leftover junk)
      3. Chromosome 2 fusion site (encodes a functional feature within an important gene instead of a being a fusion site) All three key genetic pillars of human evolution (for Darwinists) turned out to be specious—overstatements based on ignorance of genetic function.

      The Fossil record does not support it, long term experiments in genetics do not support it.

      So why is it still popular dogma;

      Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) – Casey Luskin April 12, 2011

      Excerpt: Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it–changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, “You know, we’ve tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I’ve told you about.” This just appalled me. So I said, “Richard Lewontin, you are a great lecturer to have the courage to say it’s gotten you nowhere. But then why do you continue to do this work?” And he looked around and said, “It’s the only thing I know how to do, and if I don’t do it I won’t get grant money.”

      - Lynn Margulis – biologist

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      • The Fusion of Human Chromosome 2

        The arguments against the fusion of human chromosome 2 (HC2), in particular, do not seem to me to be remotely convincing and I don’t think that it is wise to use this argument against evolutionists.

        First off, the fusion models for HC2 are not dependent upon the local configuration of bases at the proposed fusion site. The main evidence for HC2 fusion has always been the fact that the two pieces of HC2 are nearly identical to chimpanzee chromosome 13 (equivalent to human 2p), and chimpanzee chromosome 12 (equivalent to human 2q). The chromatin binding patterns line up, the sequence analysis confirms, and FISH studies show the correspondence between the genetic sequences. The genes are almost entirely in the same order, the inter-genic regions are very similar along the entire lengths of these segments – millions of bases.

        Given this evidence a prediction was made that there ought to be fragments of telomeres (the end caps of chromosomes) in the middle of chromosome 2, at the fusion site – which was then examined. And, surprise surprise, the prediction was been confirmed. Bergman and Tomkins (who published the original argument against the fusion of HC2) simply ignore all of this evidence. Instead, what they do is focus on just the region of the fusion, and complain that it is a tangled mess – which is only to be expected since the fusion event. It is simply unrealistic to expect a pristine fusion site and every paper published on the structure of the fusion region makes the point that it is degenerate. The fact that the fusion site has suffered some modifications since the fusion event does not effectively counter the evidence for fusion nor is it unexpected. The chances are so infinitesimally small that HC2 would so closely resemble those of other primates by random chance that it is pretty much an impossibility that this hypothesis is actually true.

        In short, don’t get sidetracked by this argument, promoted by Bergman and Tomkins (2011 and 2012), against the fusion of HC2.

        For further discussion of the relevance of the fusion of human chromosome 2 to the creation/evolution debate see: Link

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      • Human/Chimp Genetic Similarities

        It is also a mistake to argue that humans and chimps do not share significant genetic similarities. As far as the actual protein-coding gene sequences are concerned, they are remarkably similar. To then say that there is only a 70% similarity based on differences in crossover sites is quite misleading. Now, there are greater unique differences when it comes to functional non-coding regions of DNA, which presents more of an argument for possible key functional differences between the gene pools. However, even this argument remains rather weak given that so little is currently known about the functionality of these non-coding DNA regions.

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  45. “You see, there’s always the possibility of being tricked or of being wrong in science – of misreading the evidence given one’s limited experience and the limited nature of the evidence in hand. If you’re not willing to take that risk, you’re not being scientific. Science, by definition, requires a leap of faith beyond that which can be absolutely demonstrated or proved. That’s why you could always be wrong in science. Science requires a risky leap of faith, but a rational leap as well…”

    Agreed: no such thing as absolute proof of anything. Epistomology 101. Agreed: Scientists, even the most brilliant ones can be wrong ( Einstein reversing himslef on the cosmological constant, Hawkings recently reversing himself on black holes) Agreed: One can always be wrong in science. Not agreed: science requires a leap of faith. Science is based on hypothesis and theories that are tested by observation or experimentation. Faith is the domain of religion not science and that is what distinguishes them. What you are doing is trying to conflate them by semantically joining them at the hip with fused bone ‘Faith’ . By doing so you hobble both.

    And don”t get me wrong: nothing wrong with faith in God! It gives many people hope, purpose, delivery from despair, meaning in life. I have many family and friends that have a deep faith in God- from many religious stripes. Some are moved by scripture, some by church, some by spirit. Church often forms a useful social community of like minded indivduals trying to find meaning in their lives. Wonderful stuff. I don’t try to talk people out of faith in God. However, my lifelong enquiry has caused me to think at this stage that the many iterations of God(s) are the invention of Man that do not match the reality of nature. And Science is the objective barometer to help determine what God is not ( an intervening force in the cosmological life of the universe and the lives of man). That is rationalism and the beauty and elegance of the unbiased collective human mind to discern same. Is there a purposeful design to the universe or is a random quantum fluctuation ( cosmic role of the dice that resulted in a universe with anthropic principles and physical constants that gave rise to and supported the evolution of life). Don’t know but that is big question for Science to continually examine irrespective of faith, hope or despair.

    ID is a modern form of Deism. I do find it intriguing and don’t automatically rule out the concept of a design to the univesrse. But was it purposeful or accidental? That is the question?

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    • Agreed: no such thing as absolute proof of anything. Epistomology 101. Agreed: Scientists, even the most brilliant ones can be wrong ( Einstein reversing himslef on the cosmological constant, Hawkings recently reversing himself on black holes) Agreed: One can always be wrong in science. Not agreed: science requires a leap of faith. Science is based on hypothesis and theories that are tested by observation or experimentation. Faith is the domain of religion not science and that is what distinguishes them. What you are doing is trying to conflate them by semantically joining them at the hip with fused bone ‘Faith’ . By doing so you hobble both.

      Not true. A leap of faith is a step into that which cannot be absolutely known. One can take a blind leap or an educated or “reasonable” leap of faith based on what little knowledge is in hand. Science is about taking the most reasonable leap of faith into the unknown that one can take based on what is known. Blind faith, on the other hand, is the basis of fideism – a form of wishful thinking.

      Now, when it comes to belief in God and God’s character or that God speaks through the Bible, etc., such faith can be based on wishful thinking, to be sure. However, it is also possible that such faith could be based on the “weight of evidence” as one is able to evaluate the evidence in hand. In other words, biblical faith or any other kind of faith in a God is not required to be a blind leap of faith. It can be the same type of faith that is required for the acceptance of any scientific hypothesis or theory as “most likely true” (Link).

      In short, science requires faith but faith doesn’t require science. Faith can be irrational, independent of empirical evidence or logical argument. However, faith does not have to be blind or irrational. It can be empirically based and supported by empirically rational arguments just as much as any valid scientific hypothesis or theory. After all, if God exists He is the origin of our ability to think scientifically and to use science to detect Him and His handiwork through the things that He has made. If God doesn’t exist, then science wouldn’t be able to detect the tel-tail signs of such high level design in nature at all…

      And Science is the objective barometer to help determine what God is not ( an intervening force in the cosmological life of the universe and the lives of man). That is rationalism and the beauty and elegance of the unbiased collective human mind to discern same. Is there a purposeful design to the universe or is a random quantum fluctuation ( cosmic role of the dice that resulted in a universe with anthropic principles and physical constants that gave rise to and supported the evolution of life). Don’t know but that is big question for Science to continually examine irrespective of faith, hope or despair.

      Science contains a subjective element that no one can escape. Still, science is useful in that it enables one to evaluate one’s thoughts and beliefs in a potentially falsifiable manner (if one is open to such falsification), but science is nothing more than a testable way of thinking (a basic BS-detector if you will). If there is a intelligent designer behind this or that phenomenon, it would therefore be possible to use scientific methodologies to detect the signature of this designer – vs. the signature of non-intelligent mechanisms. This is in fact well within the realm of scientific investigation. Your claim, on the other hand, that you would not recognize a the Signature of God regardless of the evidence that might be presented to you (The Resurrection, healing a man born blind, etc) is not scientific or rational – nor is it believable. I simply do not believe that you’d refuse to accept the implications of such evidence if you saw it with your own eyes. I believe you’re being disingenuous.

      ID is a modern form of Deism. I do find it intriguing and don’t automatically rule out the concept of a design to the univesrse. But was it purposeful or accidental? That is the question?

      By definition something that is “accidental” cannot be deliberately designed. The anthropic qualities of the universe, for example, do not appear to be accidental by any stretch of the imagination. That is why some try to get around the otherwise obvious implications of this by appealing to “multi-universe” theories and “quantum fluxuations” to try to explain away the extreme odds against some accidental cause. Such efforts are not based in science or rational thought but in personal philosophy – a desire to maintain skepticism at all costs regardless of the evidence presented (as seems to be your situation). In fact, such objections are anti-science because these arguments could be used to explain anything and everything – to include a situation where you happened to win the California Lottery 10 times in a row (you must have been in the right universe). After a point, it just gets quite ridiculous…

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      • @Sean Pitman:

        Faith, Trust, and Evidence:
        by Tom Price

        I’ve been trying to avoid using the word ‘faith’ recently. It just doesn’t get the message across. ‘Faith’ is a word that’s now misused and twisted. ‘Faith’ today is what you try to use when the reasons are stacking up against what you think you ought to believe. Greg Koukl sums up the popular view of faith, “It’s religious wishful thinking, in which one squeezes out spiritual hope by intense acts of sheer will. People of ‘faith’ believe the impossible. People of ‘faith’ believe that which is contrary to fact. People of ‘faith’ believe that which is contrary to evidence. People of ‘faith’ ignore reality.” It shouldn’t therefore come as a great surprise to us, that people raise their eyebrows when ‘faith’ in Christ is mentioned. Is it strange that they seem to prefer what seems like reason over insanity?

        It’s interesting that the Bible doesn’t overemphasize the individual elements of the whole picture of faith, like we so often do. But what does the Bible say about faith? Is it what Simon Peter demonstrates when he climbs out of the boat and walks over the water towards Jesus? Or is it what Thomas has after he has put his hand in Jesus’s side? Interestingly, biblical faith isn’t believing against the evidence. Instead, faith is a kind of knowing that results in action. The clearest definition comes from Hebrews 11:1. This verse says, “Faith is the assurance of things hoped for, the conviction of things not seen.” In fact, when the New Testament talks about faith positively it only uses words derived from the Greek root [pistis], which means ‘to be persuaded.’ In those verses from Hebrews, we find the words, “hope,” “assurance,” “conviction” that is, confidence. Now, what gives us this confidence?

        Christian faith is not belief in the absence of evidence. It is the proper response to the evidence. Koukl explains that, “Christian faith cares about the evidence…the facts matter. You can’t have assurance for something you don’t know you’re going to get. You can only hope for it. This is why the resurrection of Jesus is so important. It gives assurance to the hope. Because of a Christian view of faith, Paul is able to say in 1 Corinthians 15 that when it comes to the resurrection, if we have only hope, but no assurance—if Jesus didn’t indeed rise from the dead in time/space history—then we are of most men to be pitied. This confidence Paul is talking about is not a confidence in a mere ‘faith’ resurrection, a mythical resurrection, a story-telling resurrection. Instead, it’s a belief in a real resurrection. If the real resurrection didn’t happen, then we’re in trouble. The Bible knows nothing of a bold leap-in-the-dark faith, a hope-against-hope faith, a faith with no evidence. Rather, if the evidence doesn’t correspond to the hope, then the faith is in vain, as even Paul has said.”

        So in conclusion, faith is not a kind of religious hoping that you do in spite of the facts. In fact, faith is a kind of knowing that results in doing. A knowing that is so passionately and intelligently faithful to Jesus Christ that it will not submit to fideism, scientism, nor any other secularist attempt to divert and cauterize the human soul by hijacking knowledge.

        Tom Price is an academic tutor at the Oxford Centre for Christian Apologetics and a member of the speaking team at Ravi Zacharias International Ministries in Oxford, England.

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  46. Sean Pitman: You see, there’s always the possibility of being tricked or of being wrong in science – of misreading the evidence given one’s limited experience and the limited nature of the evidence in hand. If you’re not willing to take that risk, you’re not being scientific. Science, by definition, requires a leap of faith beyond that which can be absolutely demonstrated or proved. That’s why you could always be wrong in science. Science requires a risky leap of faith, but a rational leap as well…

    Sean I never cease to be amazed at your flights of fancy.

    Have you actually used this approach to apply for research funding from NIH or any charitable trust? If so you would realize that science and its funding like venture capital is nothing if not conservative. You have to define the background and basis for your hypothesis. Why it is not a stupid idea but is feasible and significant. Then you have to state your hypothesis with specificity and describe the specific tests aimed at falsifying your hypothesis. then you do the experiments and then you publish the results in the peer reviewed literature. And then you repeat this iterative process with a hypothsis modified according to the observations. You can of course publish anywhere you want but only the literature of science qualifies as of any signficance for track record in terms of getting further funding.

    I dont see much role for the risky leap of faith you describe in all that. Much more a calculated stumble.

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    • How does this counter anything I’ve said? Of course science is a calculated step or leap or “stumble”, if you will, into the unknown. That doesn’t mean that this step is necessarily going to be successful. The beliefs of the scientist, no matter how reasonable and how apparently supported by evidence, are always subject to potential falsification (i.e., to being absolutely wrong). That is why a degree of faith is always involved whenever a scientists takes on a particular point of view or interpretation of the data. The leap of faith may be very reasonable indeed given the evidence currently in hand, but it is still a leap of faith none-the-less. Your fideistic arguments for realities that supposedly exist outside of your own mind, on the other hand, require no basis in empirical evidence or rational argument. Such a blind leap of faith is equivalent to wishful thinking. It doesn’t matter if you’re in a community that believes the same way. It’s still nothing more than collective wishful thinking if you have no empirical, testable, potentially falsifiable arguments…

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  47. Sean Pitman: You can only hypothesize about these things. Yet, despite the non-reproducibility of the original events that produced the cube, even you have declared that such a discovery would be a “blindingly obvious” artifact of creative intelligence – without needing to directly see how it was actually done.

    At the risk of perseveration I Indeed would recognize it as a blindingly obvious artefact but not at all because of any science or hypothesis testing or some disembodied mind but because of my physical brain which is wired to recognize pattern and artefact which I have done since at least the time I had preverbal cognition and acquired verbal or language skills. A brain which as I pointed out naturally thinks teleologically. A brain that would see this a reflecting intelligence like mine and because of the teleological bias would see it as reflecting intelligence and manipulation whether it was the product of mindful intelligence or mindless intelligence
    http://jordanpollack.com/ectomental/mindlessintelligence.pdf.

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    • At the risk of perseveration I Indeed would recognize it [the granite cube] as a blindingly obvious artefact but not at all because of any science or hypothesis testing or some disembodied mind but because of my physical brain which is wired to recognize pattern and artefact which I have done since at least the time I had preverbal cognition and acquired verbal or language skills. A brain which as I pointed out naturally thinks teleologically. A brain that would see this a reflecting intelligence like mine and because of the teleological bias would see it as reflecting intelligence and manipulation whether it was the product of mindful intelligence or mindless intelligence

      Why then wouldn’t you hypothesize that a pyrite cube or a salt crystal requires intelligence to explain? – that these cubes are in fact consistent with mindless non-intelligent natural mechanisms?

      You see, you’re not being consistent. The very same pattern in different materials is not necessarily evidence of intelligent design – regardless of your mind’s bias for detecting patterns. That is why the ID-only hypothesis is in fact testable in a potentially falsifiable manner. That’s what makes it a valid scientific hypothesis.

      Another common illustration of this is our human ability to see things in the clouds of the sky or in the patterns of toasted bread or in the pebbles on the beach or the stars in the sky – like elephants, the face of an angel, or the Virgin Mary, etc. Yet, no one thinks that these shapes in the clouds or on burnt toast were intelligently designed – only that our brains impose teleological patterns onto the various shapes in the clouds or toast, etc. However, this is only true to a point. It all depends upon the degree of specificity. For example, if you saw the clouds forming well-defined letters that said, “Hi Dr. Cameron! I hope you’re having a wonderful day.” That wouldn’t be very easily interpreted as your brain imposing unnatural patterns on the clouds. That would be interpreted, by most people, even scientists, as a clearly designed pattern (probably drawn by an airplane) – and for very good scientific/empirical reasons with very high predictive value based on our past experience with clouds.

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  48. @ Dr. Pitman

    ” A knowing that is so passionately and intelligently faithful to Jesus Christ that it will not submit to fideism, scientism, nor any other secularist attempt to divert and cauterize”

    But you do submit to scientism don’t you? If you don’t you have no right to use the scientific method to detect God.

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    • Scientism, in its pejorative sense, is generally defined as the view that only scientific claims are meaningful or “true”.

      There are, however, lots of truths that exist outside of the realm of scientific investigation, to include everything from moral truths to personal tastes like art and music or the fact that I like pralines and cream ice cream. All of these are internally derived truths that are not subject to scientific methodologies – methodologies that are limited to investigating the external world in which we live and how it predictably operates and how we might best function within it.

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  49. @ Dr.Pitman

    “You continue to refuse to answer whether you have ever witnessed a miracle. When was the last miracle?”

    You can call me disingenous if you like but your continued evasion of this direct, honest question speaks volumes as to your lack of candour and stacking the rhetorical deck. And when you don’t get your way you say there is no sense in discussing the issue further. You are in great danger of solipsism my friend because the only truth you are prepared to recognize is your own unique brand. That’s not science, that’s hubris of the most dangerous kind. That is why you find such strong reaction to your inflexible approach on this forum. You see, we that believe in rational, non biased, non religious, non atheist, scientific exploration of truth have a duty to confront your mindset. And I can assure this in this I am entirely genuine.

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    • How am I stacking the deck by asking you for what you would accept as a valid empirical evidence for a “miracle”? – or expecting some kind of honest reasonable response? Your answer was that essentially no evidence, no matter how fantastic, not even if you personally were to witness something like the Resurrection of Jesus or the healing of a man born blind, etc., would be enough to convince you that a miracle had occurred. How is it solipistic of me to refuse to continue a conversation with someone who claims that there is nothing I could possibly say, no evidence that I could possibly present, which would be convincing to you? If anything is solipistic, that’s it. Your position is effectively immune from even the possibility of challenge or falsification – definitively stacking the deck so that you can’t possibly be shown to be wrong by anything I could possibly present. In other words, it seems to me like you’re guilty of everything you’re accusing me of doing. It is pointless, therefore, to discuss this topic with you since your mind is, apparently, already made up and cannot be changed regardless of what anyone might be able to bring to the table. You’ve set the bar so high that it cannot be crossed, even in theory – which makes further conversation futile by definition.

      Why should I tell you about the miracles I’ve personally witnessed? – to include those I see on a daily basis and the many miracles of life, the universe, and those in the Scriptures that I’ve already discussed with you in this forum? for what purpose? I’ve already pointed these things out to you, but these evidences are obviously going to be meaningless for someone who wouldn’t be impressed even if the Resurrection itself could be directly shown to you – or any of the other fantastic miracles described in the Bible. What I have to offer will not put the smallest dent in such a mindset, so why bother?

      As far as upsetting people by what I’ve said in this forum and the positions I hold and promote, it seems to me that the only ones I’ve really upset in this forum are those evolutionists and fideists who view faith like you do – as religious wishful thinking devoid of the need for empirical evidence or rational argument. In any case, I’m not here to win any popularity contests.

      Beyond this, my position on miracles is no secret. It’s not something I’m trying to hide, obviously. I am, after all, arguing for the detectably designed nature of the origin and diversity of life on this planet and the miraculous credibility of the Bible that cannot be readily distinguished from what most would expect from a God or God-like intelligence and creative power. Consider, for example, the following video where I present my thoughts on miracles (from the 25:53 to the 43:21 minute marks):

      Or, see the following video (from the 15:20 to the 18:50 minute marks):

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  50. Sean Pitman: Which hypothesis, among the competing options, carries the best predictive value? Anyone with any solid opinion at all on any topic must take on a just a little chutzpah as well as the risk of failure – of being wrong.

    Indeed, but to qualify as a scientist one has to commit that hypothesis to experimental testing and publish the results both of which you have consistently refused to do over the last 3 years that I have been urging you to do so including yet again on this thread by Bob and George.

    You seem incapable or unwilling to commit your signature 1000FSAAR model to the scientific literature. Why is that? I know it is easier to boldly proclaim this on this site that you completely control but publication via the mediocrity of blogs takes very little chutzpah or risk. Do you really not think your ideas will stand up to scrutiny of experts or is it a defence against perhaps discovering weakness in your position and having to follow through on your promise to

    ““I, personally, would have to go with what I saw as the weight of empirical evidence. This is why if I ever honestly became convinced that the weight of empirical evidence was on the side of life existing on this planet for hundreds of millions of years, I would leave not only the SDA Church, but Christianity as well” (http://www.educatetruth.com/theological/the-credibility-of-faith/comment-page-1/#comment-18717).

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    • We’ve already talked about publishing against the basis of the ToE in mainstream journals before – not very likely. So, if you see a clear weakness in my position, by all means present it. I’d be most interested. Otherwise, is the very best that you can suggest is that someone else is bound to know what’s wrong with my position? – even if you, Jason Rosenhouse, Nick Matzke, and many many others I’ve debated over the years who should be very very well informed about evolutionary theory seem to have absolutely no idea?

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  51. Sean Pitman: There are, however, lots of truths that exist outside of the realm of scientific investigation, to include everything from moral truths to personal tastes like art and music or the fact that I like pralines and cream ice cream. All of these are internally derived truths that are not subject to scientific methodologies – methodologies that are limited to investigating the external world in which we live and how it predictably operates and how we might best function within it.

    Thank you Sean this is exactly what many of us have argued on this site over the last few years. Religion and faith in God is just such a thing. it is not subject to scientific methodologies or falsification by science or empirical evidence.
    As Jonathon Sacks argues science is a restricted human activity concerned with how the physical world works. Religion is about the meaning of things the why of our life and activities. I would disagree that scientific methodologies tell us “how we might best function within it”. That is the new atheists approach of Provine and Dawkins which I do understand you admire a great deal.

    To those who regularly or automatically upvote Seans comments I would ask that you remember history. Sadam Hussain comes to mind. It is probably better to hedge your bets and not feed those who may become your worse enemy. As I have said before I fear the logic and sentiment behind Sean’s statement that says

    “I, personally, would have to go with what I saw as the weight of empirical evidence. This is why if I ever honestly became convinced that the weight of empirical evidence was on the side of life existing on this planet for hundreds of millions of years, I would leave not only the SDA Church, but Christianity as well” (http://www.educatetruth.com/theological/the-credibility-of-faith/comment-page-1/#comment-18717).

    Such a person is likely to be an extremely smart articulate dogged critic who knows where the bodies are buried if they move from fundamentalist Adventist Christian to fundamentalist atheist. Viewed from the stated intellectual stance on favoured epistemology I worry but I do take some consolation in the understanding that Mortons Demon is very strong and the Adventist inculturation manifest is very deep and broad.

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    • Thank you Sean. This is exactly what many of us have argued on this site over the last few years. Religion and faith in God is just such a thing. it is not subject to scientific methodologies or falsification by science or empirical evidence.

      I’m sorry, but for most people God is not in the same category as my personal preference for pralines and cream or the works of Beethoven. You see, while I do believe that God has implanted a sense of morality, of right and wrong, within everyone, I do not believe that God has implanted inherent knowledge as to His personal existence and care for us. Such knowledge is learned knowledge that is, or at least should be, based on the weight of evidence that God has revealed in the works of His own hands that speak for His existence, identity, and character. Without these evidences, there would be no rational reason to believe in a personal loving God who came to this world and died to save you and me from the sin, death, and suffering that this place has to offer.

      As Jonathon Sacks argues science is a restricted human activity concerned with how the physical world works. Religion is about the meaning of things the why of our life and activities. I would disagree that scientific methodologies tell us “how we might best function within it”. That is the new atheists approach of Provine and Dawkins which I do understand you admire a great deal.

      Religion is more than assigning meaning to things. One can do that just fine without religion based on personal preferences and an internal sense of morality. However, when it comes to establishing a solid hope in an eternal future, such knowledge is not inherent – obviously, or there would be no atheists. Such knowledge is learned knowledge and a useful religion that proposes to offer this knowledge had better come up with something better than wishful thinking and lovely just-so stories. There had better be some solid empirical evidence to back up such fantastic stories that appear to counter so many realities of this world. And yes, in this regard, Dawkins and Provine are spot on.

      To those who regularly or automatically upvote Seans comments I would ask that you remember history. Sadam Hussain comes to mind. It is probably better to hedge your bets and not feed those who may become your worse enemy.

      So now I’m being compared to Sadam Hussain? – because I ask for an evidentiary basis for faith? – as opposed to religious wishful thinking? Methinks thou dost protest just a wee bit too much here…

      As I have said before I fear the logic and sentiment behind Sean’s statement that says

      “I, personally, would have to go with what I saw as the weight of empirical evidence. This is why if I ever honestly became convinced that the weight of empirical evidence was on the side of life existing on this planet for hundreds of millions of years, I would leave not only the SDA Church, but Christianity as well” (http://www.educatetruth.com/theological/the-credibility-of-faith/comment-page-1/#comment-18717).

      Why not just automatically insert this quote in all of your posts? – since you seem to insert it in most of them already? Are you really that worried that someone will miss the umpteen times you’ve already cited it in this very thread?

      Such a person is likely to be an extremely smart articulate dogged critic who knows where the bodies are buried if they move from fundamentalist Adventist Christian to fundamentalist atheist. Viewed from the stated intellectual stance on favoured epistemology I worry but I do take some consolation in the understanding that Mortons Demon is very strong and the Adventist inculturation manifest is very deep and broad.

      But obviously cannot be applied to you or your arguments? – which are completely free of all bias and the temptations of Mortons Demon?

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  52. Sean Pitman: We’ve already talked about publishing against the basis of the ToE in mainstream journals before – not very likely

    And where is your empirical evidence for this? It is a baseless claim as we have discussed before

    1] Creationist including Adventist YEC publish regularly in the peer reviewed literature as you very well know.
    2] Citing historical precedent including a normal response to clear lack of integrity hardly counts as evidence of bias against anything except dishonesty http://en.wikipedia.org/wiki/Sternberg_peer_review_controversy
    3] You have have not even tried to publish your ideas where it counts.
    4] You have had no expert opinion on your work because you have not published it in the proper scientific forum. Scientist like myself who respond here are not experts in this area and comments for various reasons outside a desire to point out technical or methodological errors of which I freely admit I may well be unaware. I comment because I am concerned about your role as rabble rouser against Adventist tertiary education. Scientist have enough to do in reviewing the scientific literature to spend time playing whack a mole by correting error in the blogospere.

    You protested about me suggesting you were not acting in good faith with your questions. Well here you can show that you are truly acting in good fiath by publishing your work in the forum where it will be dealt with by the experts. I somehow have this nagging feeling you will not. Surprise me.

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    • I’ve published several papers in prominent medical journals myself. That’s quite different from publishing against the mechanism of the ToE in a mainstream journal. No one publishes “regularly” against the very basis of the ToE. It just ain’t going to happen. I’m too well-known as a conservative creationist and I don’t know any Sternbergs who are willing to put their careers on the line for me…

      But, I do appreciate your admission that you personally have no idea why I’m wrong. It seems to be a very common admission among those who are otherwise very ardent believers and supporters of neo-Darwinism – without really knowing how the mechanism could actually do what you claim it did? Really? I got exactly the same thing from Rosenhouse and nothing but crickets chirping from Matzke – and from many many others like him and you. I also find it interesting that you don’t consider Matzke, in particular, an “expert” when it comes to understanding and explaining the evolutionary mechanism. He’s published some very popular papers on the topic… none of which address the problem of the exponential decay of beneficial sequences in sequence space with each step up the ladder of functional complexity. The only way that the mechanism of RM/NS could remotely do the job is if Rosenhouse’s vision of a nice line of closely-space steppingstones actually reflects reality – which it doesn’t.

      But why am I wasting my breath on you? There’s nothing I could say that would convince you – right? You have to have a consensus of “experts” tell you what to think and believe. Do you have no personal ideas all your own that are not dependent upon the approval of your experts? What if the experts told you that our granite cube wasn’t really the “blindingly obvious artifact” that you claim it to be? Would you just accept their word for it? – no need to understand the arguments used for yourself?

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  53. Sean Pitman: Otherwise, is the very best that you can suggest is that someone else is bound to know what’s wrong with my position? – even if you, Jason Rosenhouse, Nick Matzke, and many many others I’ve debated over the years who should be very very well informed about evolutionary theory seem to have absolutely no idea?

    Herein lies one of the problems. You see your role as debating. Goad what experts you can entice to respond into an exchange completely devoid of terms of agreement of the exchange or even definitions of terms. That may be the approach of a lawyer or an apologist but it is not that of a scientist. A scientist presents data and argument in the forum of science and does not take anything below that as having any evidentiarly value. If you want to act in good faith present your data where it will be considered seriously and appear as a contribution indexed in the literature of science. Anything short of that is to manifest a lack of good faith in trying to get answers to your questions or proposing an alternative model.

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    • The terms are quite clear and obvious. They’ve all been published and well defined in mainstream science journals. Beyond this, if you and the many many other well-educated evolutionists have no idea how to respond in any meaningful way to observations that should be very very obvious, I really have no need to convince you or anyone else of anything. These are my ideas and I don’t care who else does or doesn’t agree. I lose no sleep at night…

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  54. Sean Pitman: I’m too well known as a conservative creationist and I don’t know any Sternbergs who are willing to put their careers on the line for me…

    I think that is a little hyperbolic. I suspect that to editors of scientific journals you have absolutely no profile. Enough Chutzpah to claim celebrity status but not to actually publish in science?

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    • Any editor worth his/her salt is going to do an internet search these days to profile any new author… as I’m sure you know.

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      • @Sean Pitman:

        And you know his because? Dont be silly editors are looking for good scientific work that will be cited. Look up the paper in Science coming from a homeopathy group that purported to show the memory of IgE molecules in water. No editor worth his salt makes a decision based on his prejudices. Often external review will be blinded. No editor will look beyond scopus, ISI or pubmed where you will appear with the publications you have already pointed out to me as your credentials.

        Why the continual “yes but”. I’m sure you didn’t get through medical school with that attitude of justified inaction.

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        • You’re very naive about how papers are chosen and published if you really believe that no one looks beyond PubMed or Scopus or ISI… especially when someone is obviously trying to challenge the very basis of neo-Darwinism in a submitted paper. Observations about IgE molecules simply don’t elicit the same gut reaction – and you know it.

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  55. Sean Pitman: I’ve published several papers in medical prominent medical journals myself. That’s quite different from publishing against the mechanism of the ToE in a mainstream journal. No one publishes “regularly” against the very basis of the ToE.

    You clearly published cited work early in your career (2003-2007) but have not done so since then. You clearly could write a paper my only question is why not? Are you really so jaded as to think that no indexed journal will publish anything new iconoclastic and innovative? As I have said before that idea truly beggars belief.

    I think it rather an oversimplification to suggest that there are no critiques of Darwinian evolution and natural selection in the literature. Have you actually been to the literature to look at this? What is the denominator for your zero publications? There are actually very few publications on the grand scheme of evolution. What you find are many many research papers about specific experimental observations not grand handwaving ideas based on reviews of the existing literature. But each of these relate in some way to the grand theme of natural selection. If you do look at the literature on lmits natural selection genetic drift you will find that the vast majority is about what you would consider “microevolution” which you would not really consider evolution at all. This is because you have an arbitrary distinction between macro and micro evolution that most biologist would not make. I you truly want to publish you will have to generate a paper that fits within the scope of the journal just as you did with your pathology publications. You are not trying to pin your 95 theses on the Cathedral door. And dont even think about trying to game the system with a rubbish paper like Meyers did in a taxonomy journal.

    Have you talked to Leonard Brand or others who publish regularly on evolution? I am sure that they would be happy to provide critique and guidance. I certainly would be delighted to see you publish your work.

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    • Leonard Brand, as brilliant and as cleaver as he is, has never published anything in a mainstream journal that directly attacks the fundamentals of Darwinism. It just doesn’t happen without someone losing his/her job over it. I might talk to him about trying to get something more tangential published, but unless it is very tangential indeed, it simply won’t get published – as we all know.

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  56. Sean Pitman: These are my ideas and I don’t care who else does or doesn’t agree. I lose no sleep at night…

    But I do because your reactionary attitudes are destructive of Adventist institutions. I do not care whether you are right or wrong but when you start a witchhunt based on your personal views I worry as should every other Adventist and faithful follower of God.

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    • Do you honestly think if no one else shared my views about the importance of the literal creation week to Adventist theology that anyone would have paid me any attention within the church? Obviously, I’m not alone in my views regarding the importance of these concepts to the fundamental identity and belief system of the Seventh-day Adventist Church. Also, I’m not alone in my conviction that employed representatives of the church are being dishonest, are in fact stealing from the church, if they teach or preach contrary to the church’s fundamental positions on various topics.

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  57. Sean Pitman: Beyond this, if you and the many many other well-educated evolutionists have no idea how to respond in any meaningful way to observations that should be very very obvious

    This is where your fundamentalism comes up agaisnt the realities of knowledge. You want it to be black or white, obvious and certain. It is not and there is great amounts of ignorance which motivates the scientific endeavour. Scientists admit ignorance and you then assume that your unsubstantiated views must be correct.

    Where are we in terms of our agreements ?

    1] You accept that most or the species that exist today arose by a process of natural selection from ancestral populations. We have been over humans, hogs and canines and largely agree on diversification mechanisms except in the pace. I accept long periods you do not.

    2] You image that a population of 2 can generate sequence variation sufficient to generate species and genera in a period of 4000 years. In terms of the levels of diversity I am presuming that you do agree with David Catchpole of CMI who in Creation 2013 35(4):31 claims that 2 badgers went on the ark and generated a great diversity of species and genera within the Mustelidae family’

    “Also likely descended from that same pair are these nine non-American badger species: the European badger [Meles meles). the Asian badger (Meles leucurus), the Japanese badger (Meles anakuma), the hog badger (Arctonyx collaris——which lives in central and southeast Asia), the Chinese ferret- badger (Melogale moschata). the Javan ferret-badger (Melogale orientata), the Bornean ferret-badger (Melogale everetti), the Burmese fcrret—badger (Melogale personata), and the Vietnam ferret-badger (Melogale cucphuongenesis).
    These are ten different species but also four different genera."
    "But we haven’t exhausted the badger kind yet. The honey badger or ratel, Mellivora capensis, marks the 11th species and the 5th genus of badgers in the Mustelidae, which is sometimes referred to as the ‘weasel family’. Indeed, the honey badger itself is often described as ‘weasel-like’. In fact, it's highly likely that weasels and other members of the Mustelidae are also descended from the same ancestral pair as the badgers. That includes not ‘ just the likes of polecats and stoats (ermine) but also otters—recent genetic studies point to American badgers having become reproductively isolated from Eurasian badgers before weasels, ferrets and otters...."

    You image this diversity was by a process of mendelian inheritance where phenotype differences were selected by transmission of specific allelic variants from the gene pool present in 2 animals.

    3] I have a much more conventional view of population genetics and think that a gene pool in a population of 2 dooms to failure levels of diversity required for the observed speciation cannot exist in 2 animals except by a miracle. You do not think that any miracle was involved. I think it highly unlikely that there was such a genetic bottleneck and then this level of speciation except by miracles. You agree that almost all the genetic allelic variation present across the derivative species came from new mutations not present in the original pair but I would say the new mutation occurred in a viable population of hundreds if not thousands of animals and that speciation occurs in populations not in individual pairs.

    4] I think it likely that the same process that lead to speciation within genera or “kinds” also accounts for derivation of different families from common ancestors. You do not an propose there is an insurmountable barrier to that diversification at the level of families and above.

    5] You have proposed that it is at the level of 1000FSAAR but have not given me any example derived from the comparison of genomic sequences for specific genes.

    It is at this point that you would have a publishable paper if you compare genomic sequences between different mammalian species and document the 1000FSAAR systems that equate to the limits defining “Kinds” and the evolutionary limit. Statistical probability and islands of functional sequence as you admit is not novel or publishable. You have to have data and analysis that is novel and compelling.

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    • This is where your fundamentalism comes up agaisnt the realities of knowledge. You want it to be black or white, obvious and certain. It is not and there is great amounts of ignorance which motivates the scientific endeavour. Scientists admit ignorance and you then assume that your unsubstantiated views must be correct.

      You are ignorant about how the very mechanism of Darwinian evolution does its job at various levels of functional complexity? – but your still so sure that random mutations and natural selection must have been the mechanism that did the job somehow? – even though you don’t know how?

      Beyond this, how are my observations “unsubstantiated”? The observation that the ratio of potentially stable, not to mention beneficial, vs. unstable sequences in protein sequence space declines exponentially with each increase in the minimum size requirement has been published by several authors. This particular claim is not at all hypothetical. The question is, how are the resulting gap distances in sequence space crossable at various levels? No one has any idea – certainly not you. Yet, you are still most confident that your favorite mechanism is still up to the job. Really? How is this a “scientific” position when you have no reasonable idea how your mechanism works at various levels? – science based on complete ignorance? – based on “circumstantial evidence” as Rosenhouse argued? – circumstantial evidence that is entirely based on what a God would or wouldn’t do, not on what your mechanism can or cannot do? Please…

      Where are we in terms of our agreements ?

      1] You accept that most [of] the species that exist today arose by a process of natural selection from ancestral populations. We have been over humans, hogs and canines and largely agree on diversification mechanisms except in the pace. I accept long periods you do not.

      Exactly. You can add cats to that list since it seems likely to me that all cats, from lions to house cats, evolved from the same original parental gene pool very rapidly over just a few thousand years.

      2] You image that a population of 2 can generate sequence variation sufficient to generate species and genera in a period of 4000 years. In terms of the levels of diversity I am presuming that you do agree with David Catchpole of CMI who in Creation 2013 35(4):31 claims that 2 badgers went on the ark and generated a great diversity of species and genera within the Mustelidae family’

      “Also likely descended from that same pair are these nine non-American badger species: the European badger [Meles meles). the Asian badger (Meles leucurus), the Japanese badger (Meles anakuma), the hog badger (Arctonyx collaris——which lives in central and southeast Asia), the Chinese ferret- badger (Melogale moschata). the Javan ferret-badger (Melogale orientata), the Bornean ferret-badger (Melogale everetti), the Burmese fcrret—badger (Melogale personata), and the Vietnam ferret-badger (Melogale cucphuongenesis).
      These are ten different species but also four different genera."

      "But we haven’t exhausted the badger kind yet. The honey badger or ratel, Mellivora capensis, marks the 11th species and the 5th genus of badgers in the Mustelidae, which is sometimes referred to as the ‘weasel family’. Indeed, the honey badger itself is often described as ‘weasel-like’. In fact, it's highly likely that weasels and other members of the Mustelidae are also descended from the same ancestral pair as the badgers. That includes not ‘ just the likes of polecats and stoats (ermine) but also otters—recent genetic studies point to American badgers having become reproductively isolated from Eurasian badgers before weasels, ferrets and otters...."

      I'd have to look more closely at some of these relationships, but certainly a very wide range of phenotypic variations is possible in a very short period of time.

      You image this diversity was by a process of mendelian inheritance where phenotype differences were selected by transmission of specific allelic variants from the gene pool present in 2 animals.

      I believe that a great many novel alleles were produced by random mutations in very short order after the Flood - just at a low-level of functional complexity.

      3] I have a much more conventional view of population genetics and think that a gene pool in a population of 2 dooms to failure levels of diversity required for the observed speciation cannot exist in 2 animals except by a miracle. You do not think that any miracle was involved. I think it highly unlikely that there was such a genetic bottleneck and then this level of speciation except by miracles. You agree that almost all the genetic allelic variation present across the derivative species came from new mutations not present in the original pair but I would say the new mutation occurred in a viable population of hundreds if not thousands of animals and that speciation occurs in populations not in individual pairs.

      Of course speciation occurs in populations, not in individual pairs. Our only real disagreement here is if a viable population can start from a bottleneck of just two individuals. Clearly, it can. You assume that modern levels of detrimental mutations were present during the time of the Flood. This isn’t true. The gene pools at the time of the Flood had far less detrimental mutations, which would have allowed for an extreme population bottleneck without genetic meltdown and extinction.

      4] I think it likely that the same process that lead to speciation within genera or “kinds” also accounts for derivation of different families from common ancestors. You do not an propose there is an insurmountable barrier to that diversification at the level of families and above.

      Where did I draw the line at “families and above”? I draw the line at the production of novel protein-based systems that require 1000 specifically arranged amino acids and above. I haven’t drawn a line based on far more subjective taxonomic classifications. But, if I were to draw such a line within the taxonomic classification system, it would be at the level of Orders, not Families, since intra-family hybrids are known, whereas no viable intraordinal hybrids are known – as far as I’m aware. Examples of intra-ordinal hybrids, like crosses between a sand dollar and a sea urchin, are interesting in that they produce larvae that appear to share features of both parents, but don’t survive past the larval stage of development.

      5] You have proposed that it is at the level of 1000FSAAR but have not given me any example derived from the comparison of genomic sequences for specific genes.

      I’m not sure what you’re asking for here? What does a genomic comparison have to do with defining a level of functional complexity? Functional complexity is defined by the minimum number of specifically arranged residues required to produce the function in question. The greater the minimum requirement, the greater the level of functional complexity for that type of system – regardless of the sequences of other types of systems. This has nothing to do with genomic comparisons with other types of systems.

      It is at this point that you would have a publishable paper if you compare genomic sequences between different mammalian species and document the 1000FSAAR systems that equate to the limits defining “Kinds” and the evolutionary limit. Statistical probability and islands of functional sequence as you admit is not novel or publishable. You have to have data and analysis that is novel and compelling.

      It’s not that its “not publishable”, but that it’s already been published. The data already published in literature shows that the stable islands in sequence space get significantly farther and farther apart with each step up the ladder of functional complexity (due to an exponential decline in potentially beneficial vs. non-beneficial with each step up the ladder with a fairly uniform distribution of functional sequences within sequence space – contrary to Rosenhouse’s vision of sequence space). The conclusion that this would have an exponentially negative effect on the effectiveness of RM/NS should be published, but no one will publish this rather obvious observation because this observation clearly undermines the very basis of neo-Darwinism.

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  58. Sean Pitman: I also find it interesting that you don’t consider Matzke, in particular, an “expert” when it comes to understanding and explaining the evolutionary mechanism. He’s published some very popular papers on the topic… none of which address the problem of the exponential decay of beneficial sequences in sequence space with each step up the ladder of functional complexity. The only way that the mechanism of RM/NS could remotely do the job is if Rosenhouse’s vision of a nice line of closely-space steppingstones actually reflects reality – which it doesn’t.

    There is a difference between shooting off a response on website that has cited you mostly in a way that is dubious for context and responding in the literature. In the literature for one there will be citation of the relevant literature which you seem to discourage here. If you want his considered opinion you will publish where it will be seen and seriously considered. I suspect he knows more than you and enough to not consider himself the leading expert on mathematical modelling of sequence space. Blogs waste time and effort and for scientists and for most people the attention span is mercifully short.

    Anyway I have said more than enough for today. I am still waiting for your correction of the comments on the “seasonal induced genomic mutations in drosophila”.

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    • There is a difference between shooting off a response on website that has cited you mostly in a way that is dubious for context and responding in the literature. In the literature for one there will be citation of the relevant literature which you seem to discourage here.

      What I discourage is the blanket citing of dozens or even hundreds of articles which you haven’t actually read yourself. That’s called reference mining and is not helpful and would not be published by any journal in the form you like to post in this forum (citing a bunch of reference that supposedly support your position without any relevant quotes or summary or what the key argument is in your own words). What would be publishable, and what I want from you, are relevant quotes from pertinent papers that support your position – as well as your own explanation of the idea in play showing that you actually understand how and why the literature on the topic has any bearing on the conversation.

      If you want his considered opinion you will publish where it will be seen and seriously considered. I suspect he knows more than you and enough to not consider himself the leading expert on mathematical modelling of sequence space. Blogs waste time and effort and for scientists and for most people the attention span is mercifully short.

      Evidently you don’t know Nick very well. He wastes great deal of time on blogs – mostly on Panda’s Thumb and a few years back on Talk.Origins were we had numerous exchanges. And, if Nick actually did have a decent comeback for an argument, he would try to present it in a most exuberant manner to try to make his opponent look as ignorant and ill-informed as possible.

      Anyway I have said more than enough for today. I am still waiting for your correction of the comments on the “seasonal induced genomic mutations in drosophila”.

      What do I need to correct? Are you talking about seasonally-induced allelic variations in drosophila? – where the relative frequency of different types of alleles is affected by temperature changes? How is this a problem? Of course allelic frequencies can and do change quite rapidly in line with environmental changes. The same thing is true for peppered moths and Darwin’s finches. I really don’t see the issue here…

      And, while we’re talking about needed corrections, what about your unmodified claim that you’d recognize a highly symmetrical granite cube as a “blindingly obvious artifact of intelligent design (or “creative intelligence” if you prefer) only because of your brain’s ability for pattern recognition? Why not address how your brain figures out how the very same pattern expressed in different materials is or isn’t the result of deliberate design?

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  59. Sean Pitman: But, I do appreciate your admission that you personally have no idea why I’m wrong.

    As I said dubious for context. I think you will find I have repeatedly pointed out your abyssmal ignorance of populations genetics the inconsistency in your ideas about what is the limit of speciation and diversity, your parlous scientific model for post flood biology, your lack of clear delineation at the gene level of 1000fsaar limits and your hubris and disrespect of scholarship in assuming you alone have superior knowledge to any expert in any field despite an apparent lack of familiarity with peer review, the role of publication and the real processes of science.

    I do not really think that qualifies as having no idea on where you are wrong.

    I freely admit I could be wrong on many things and do not know much about the analysis of sequence space but I do have this nagging feeling that when confronted with the options one should usually bet on the favourite unless you have some additional or inside information. You can think that a syncophantic attitude to expertise if you want but I am familiar with inaccurate characterization.

    I am I guess most grateful that you do hold your views so strongly as it does prevent you following through on your promise to: [If I ever statement deleted because of familiarity]

    I just pray there was a little more charity toward scientists in Adventist institutions who honestly try to faithfuly serve God and the Adventist church while holding a different view of science than you.

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    • As I said dubious for context. I think you will find I have repeatedly pointed out your abyssmal ignorance of populations genetics

      Abyssal ignorance? What have I said about population genetics that is so abysmally ignorant? – that novel low-level alleles can be produce very rapidly? How is that wrong or ignorant of the facts?

      the inconsistency in your ideas about what is the limit of speciation and diversity

      What have I said that is inconsistent with regard to speciation and/or diversity? – that is inconsistent with the numerous ways that species are defined which can be inconsistent with each other?

      your parlous scientific model for post flood biology

      Flood biology? What is that? Are you talking about how animals could have traveled around the world after the Flood starting from a single point? You think that your model clearly falsifies the Biblical model of a universal Noachian Flood in this regard? How so?

      your lack of clear delineation at the gene level of 1000fsaar limits

      What is unclear to you about my delineation of functional systems that require a minimum of 1000 specifically arranged amino acid residues? What is unclear to you when I say that such systems do not evolve? – that there isn’t a single example of the evolution of any system at this level or beyond in literature?

      and your hubris and disrespect of scholarship in assuming you alone have superior knowledge to any expert in any field despite an apparent lack of familiarity with peer review, the role of publication and the real processes of science.

      I understand the role of peer review and publication just fine. I’ve actually gone through the process a few times myself. And, I do recognize its value. However, I do not see it as a requirement for effectively using scientific methodologies to discoverer truths about the world in which I live which may disagree with popular opinion. In this regard, I’m in very good company.

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  60. ” These are my ideas and I don’t care who else does or doesn’t agree.”

    Here lies solipsistic hubris that makes Dr. Pitman a god on to himself. He is not really interested in debating anything, only cherry picking what facts, theories and logic to support his unique brand of YEC. No fear, this is not science. And when we hear his plaintive cry: prove me wrong, let’s have compassion. True wisdom comes when understands that one is often wrong; and recognizes it. This applies to geniuses like Einstein and Hawkings. Science is greater than one person’s ideas. There is a reason why Dr. Pitman will not put his ideas to the test of experimentation or peer review. Einstein did. Darwin did. Not Pitman
    though and the reason is obvious.

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    • Science is greater than one person’s ideas.

      Really? So, you think Einstein or Galileo or Leonardo da Vinci or Newton, or even Darwin would have given up their ideas if they remained unpopular? These guys strongly believed in the individual ability to learn about the world around them using scientific methodologies and reasoning, regardless of what anyone else thought about their ideas or conclusions. It’s one thing to listen to those around you and consider carefully countering ideas, hypotheses and theories. It’s quite another thing to let others dictate your own individual opinion and interpretation of the data. Scientific breakthroughs that counter the paradigm of the day require individuals who are willing to disagree with the status quo – who will not buckle under peer pressure to conform or agree with popular opinion just because it is popular.

      Beyond this, neo-Darwinism is considered to be more than a science today. It is held in reverent awe as something holy and untouchable by most mainstream scientists. It’s fundamentals are never, or nearly never, questioned in literature. Those who have tried it have put their careers on the line to do so. My ideas against the very basis of Darwinism, the Darwinian mechanism itself, would never get published in any mainstream journal. Paul Cameron has himself stated very clearly that he would never publish my ideas in any science journal if it were up to him – because he doesn’t consider my ideas scientific even though he personally has no idea how to counter my ideas. Still, he wouldn’t publish them for others to try and offer countering evidence. Why not? Because, publication is considered to be a form of credibility in and of itself and no modern science journal wants to be seen to be giving any kind of credibility to intelligent design theories. It just isn’t the same today as it was even in Einstein’s day – and even Einstein’s ideas probably wouldn’t have become published without help from Max Planck.

      Before Einstein was famous, he was a nobody with nothing but an undergraduate degree. His very controversial paper probably would not have been published by anyone. So, Einstein first sent his paper to Prof. Max Planck. Surprisingly, Planck was intrigued by Einstein’s theories and he thought that they deserved to be published in the scientific journals. Planck then persuaded the editors of a local German physics journal, Annalen der Physik, to publish Einstein’s work – and so they did.

      In this first 1905 paper, Einstein presented his argument, including his now famous conclusion that E=MC^2, in a very short three-page paper entitled “Does The Inertia Of A Body Depend On It’s Energy Content?” The paper had no footnotes and not one single reference to support it.

      The scientific establishment went a bit bonkers.

      “Who does this Einstein think he is? How dare he contradict the fundamental principles of Newtonian physics. Where is his scientific evidence? What are his credentials for making such an assertion? This is preposterous….we can’t allow people just to say things like this without proof! How dare he…this idea should be given no credence at all!”

      “One Hundred Authors Against Einstein” was published in 1931. When asked to comment on this denunciation of relativity by so many scientists, Einstein replied that, “To defeat relativity one did not need the word of 100 scientists, just one fact.”

      Was Einstein being solipsistic? I think not…

      The same is true today. In order to falsify the ID or CI hypothesis for certain molecular machines, one doesn’t need to look to the opinion of the majority of scientists, but to the factual evidence that is currently in hand (not evidence that might be discovered in the future)…

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        • So, I’m a crackpot because I happen to agree with Einstein? – that a theory isn’t proved wrong or unscientific simply because the majority of scientists happen to disagree? – that some actual countering evidence is also required? That science isn’t a popularity contest? – or at least shouldn’t be? Who’s the crackpot here?

          However, I do appreciate your concern for my reputation ;-)

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  61. Sean Pitman: You’re very naive about how papers are chosen and published if you really believe that no one looks beyond PubMed or Scopus or ISI… especially when someone is obviously trying to challenge the very basis of neo-Darwinism in a submitted paper. Observations about IgE molecules simply don’t elicit the same gut reaction – and you know it.

    But you havent challenged the very basis of neo-Darwinism have you? You have not even submitted a paper? You are speaking confidently from a position of ignorance and relying on the unsubstantiated gossip in the literal creationism microcosm not at all speaking from experience or person knowledge. You have reviewed 1 paper. That does not make you an expert in any way. Which journal editors have you spoken to to get this information? Who have you personally spoken to about their rejection on the basis of the content rather the quality of their paper?

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  62. Sean Pitman: Paul Cameron has himself stated very clearly that he would never publish my ideas in any science journal if it were up to him – because he doesn’t consider my ideas scientific even though he personally has no idea how to counter my ideas.

    Please give me the citation for that. I have been for the last 3 years asking you to publish and have offered to help. Why because you havent done the science until it is published.

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    • I guess Leonardo da Vinci wasn’t a scientist then? or Galileo? Not even Darwin published his theory in a peer-reviewed journal… not a valid scientist?

      You also wrote:

      When J Exp Med, Nature or Science reviews a paper reporting experimental work and critiques it asking for more mechanism which they are want to do they never in my experience ask for explanation as anything but naturalistic explanation. I would agree with the journals that if it does not follow this convention it is not science and will not be published as science.”

      The problem, of course, is that most scientists do not consider a hypothesis of intelligent design (or creative intelligence as you put it) as the most likely explanation for the origin and diversity of life on this planet (beyond very low levels of functional complexity) to be a “naturalistic explanation” – even allowing for some form of naturalistic alien intelligence as the “creator”. Mainstream scientists are very concerned, for good reason, that such an admission would “allow the Divine Foot in the door.” And, therefore, even you seem to agree, that such a hypothesis of design simply isn’t going to get published in mainstream literature – not even if you were in charge of such a journal.

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  63. Sean Pitman: It’s not that its “not publishable”, but that it’s already been published. The data already published in literature shows that the stable islands in sequence space get significantly farther and farther apart with each step up the ladder of functional complexity (due to an exponential decline in potentially beneficial vs. non-beneficial with each step up the ladder with a fairly uniform distribution of functional sequences within sequence space – contrary to Rosenhouse’s vision of sequence space). The conclusion that this would have an exponentially negative effect on the effectiveness of RM/NS should be published, but no one will publish this rather obvious observation because this observation clearly undermines the very basis of neo-Darwinism.

    Indeed it is unpublishable because it lacks novelty. It is known. It generates a simple “so what?” You have to answer the so what with experimental data.

    I have repeatedly suggested what you need to do if you actually are interested explore the implications of your model.

    Lets go back to cats dogs and weasels.

    Within the classification of caniformia there is the suborder feliformia which includes
    Nandiniidae (asian civet cat)
    prionodontia (linsang)
    Felidae (cats in all their forms)
    Viverridae (African civet and African linsang)
    Hyaenidae (hyena
    herpestidae ( Mongoose )
    Eupleridae (malagasy civet)

    Within the other suborder Caniformia there are
    Canidae (Dogs wolfs jackals and coyotes)
    Ursidae (bears in all their forms)
    Pinnapedia (seals walruses and sea lions)
    musteloides (red panda, weasels ferrets , racoon, skunk )

    You accept that within these groups family or superfamily there was rapid diversification by mutation and natural selection of simple allelic changes. If that is so I cannot see why all the groups within the caniformia and within the feliformia could not have arisen over the conventional periods of geologica time (which you seem to readily accept). Further why could not the caniformia and feliformia have arisen by the same process of mutation and natural selection. So the anwer to your question and your accusation that I have no idea how natural selection and mutation works I would say simply that the process of mutation and natural selection that you readily accept as giving quite profound changes over 4000 years is capably over periods of 1000 times that of giving changes within orders by nothing more than simple allelic changes.

    But you say no there is a limit because of the theoretical model of sequence space and the conjecture that there is profound difference (structure of >1000 FSAAR between animals at the level of something like family or above.

    I have occam razor on my side in saying there is absolutely no reason to postulate such a barrier in the absence of evidence.

    Further your postulate of a barrier is not at all based on any empirical evidence but on one particular reading of a religious text. That has not been part of science.

    This is where your argument on 1000FSAAR has to be pitched if you expect to be taken seriously. You have to show what are the specific 1000FSAARs that occur between species which you claim cannot be related by descent because of such structures.

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    • Indeed it is unpublishable because it lacks novelty. It is known. It generates a simple “so what?” You have to answer the so what with experimental data.

      What experimental data would you suggest? A non-beneficial gap distance is the data. The implications of such a gap distance are obvious. No additional experimental data is needed to tell you that a mechanism of random mutations takes exponentially longer to get across such a gap distance (on average) with each linear increase in the gap distance. That conclusion, though very simple, completely undermines neo-Darwinism.

      You accept that within these groups family or superfamily there was rapid diversification by mutation and natural selection of simple allelic changes. If that is so I cannot see why all the groups within the caniformia and within the feliformia could not have arisen over the conventional periods of geologica time (which you seem to readily accept). Further why could not the caniformia and feliformia have arisen by the same process of mutation and natural selection.

      There would be no reason unless there are qualitatively functional differences within the different gene pools that require more than 1000 specifically arranged amino acid residues.

      So the anwer to your question and your accusation that I have no idea how natural selection and mutation works I would say simply that the process of mutation and natural selection that you readily accept as giving quite profound changes over 4000 years is capably over periods of 1000 times that of giving changes within orders by nothing more than simple allelic changes.

      That would be a great argument as long as such intraordinal changes never required the production of a qualitatively novel system of function that in turn required a minimum of more than 1000 specifically arranged amino acid residues.

      The question isn’t if you understand how RM/NS could produce low level changes, or even if all intraordinal differences are low level. The question is if RM/NS could produce qualitatively novel higher-level changes that require a minimum more than 1000 specifically arranged amino acids to work? You simply can’t address that question. And, that question completely undermines neo-Darwinism because such higher level functional differences obviously exist between many different species.

      But you say no there is a limit because of the theoretical model of sequence space and the conjecture that there is profound difference (structure of >1000 FSAAR between animals at the level of something like family or above.

      I have occam razor on my side in saying there is absolutely no reason to postulate such a barrier in the absence of evidence.

      The evidence is that qualitatively unique systems to exist in different gene pools that require a minimum of far more than 1000 specifically arranged amino acids. You do realize this, of course. You know full well that a bacterial flagellar motility system didn’t come out of thin air. It had to come from somewhere. And yet, this system requires several thousand specifically arranged amino acids to function as a motility system. How did such a system evolve at such a high level of functional complexity? You have no idea and Occam’s razor isn’t on your side here. If you’re going to invoke Occam’s razor, the most simple and obvious solution to explaining complex machines that require a significant number of precisely interacting parts is intelligent design. Your previous appeal to some kind of mystical “emergent” property of biological machines beyond “reductionist mechanics” is nonsense. They are machines in every sense of the word. And, such machines, if built of anything else, would be instantly recognized as being very similar to machines that humans build, and would therefore “have the appearance of design”. Even Richard Dawkins admits this much. He says straight up that biological machines look designed, but aren’t designed. Well, if they look designed, Occam’s razor suggests that the burden of proof is then on those who claim that they aren’t designed to show why they aren’t designed – to demonstrate a viable mechanism that could do the job.

      Well, sorry to say, you haven’t done that. And, there are very good reasons for this – such as the nature of sequence space beyond very low levels of functional complexity.

      Further your postulate of a barrier is not at all based on any empirical evidence but on one particular reading of a religious text. That has not been part of science.

      The Bible is not required to support my hypothesis of a statistical barrier to evolutionary progress beyond very low levels of functional complexity. Where did you get this idea? The limitation is based entirely on what is known about sequence space and the exponential decline of potentially beneficial vs. non-beneficial sequences with each step up the ladder of functional complexity. The Bible doesn’t even address such a concept nor does the Bible explicitly declare that any such limitations exist to speciation over any given period of time.

      This is where your argument on 1000FSAAR has to be pitched if you expect to be taken seriously. You have to show what are the specific 1000FSAARs that occur between species which you claim cannot be related by descent because of such structures.

      I already have. Start with what you know more about – like bacterial biomachines. Many such qualitatively novel biomachines exist between species that simply cannot be explained the Darwinian mechanism. If Darwinists would admit even this much, the whole game would be over – and they know it. You know it too.

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  64. Sean Pitman: The question is if RM/NS could produce qualitatively novel higher-level changes that require a minimum more than 1000 specifically arranged amino acids to work? You simply can’t address that question. And, that question completely undermines neo-Darwinism because such higher level functional differences obviously exist between many different species.

    What many different species and what changes define these limits? You are claiming something for which you have never providing any evidence beyond Behe’s flagella. You are continually reverting to the bacterial flagella but we are talking now about vertebrates and evolution of species where there is significant body of evidence in genomic sequence comparisons to inform a discussion, not about abiogenesis for which there is scan knowledge. What are these systems of high level complexity that seperate cats from dogs. I amprepared to take the “risky” approach and am going out on a limb in saying there are unlikely to be any such systems. There are certainly none in the literature on mammalian sequence comparison.

    Further as a theistic evolutionist cant I legitimately claim that God tinkers when there is any such problem and the schemata of neo-darwinian evolution remains intact. After all you accept Darwinian mechanism for origin of species within “kinds” but draw the line (arbitrarily I would contend) and do not accept it for the orgin of related “kinds”.

    I have suggested the experiment to test your model. Get out all the sequences comparisons between for example cats dogs and bears and tell me with specificity what are the highly complex systems of greater than 1000 FSAAR that separate them? Once you have the putative 1000 Fsaars that define this limit you can map its occurence across species. Then you might have some evidence to present that is an insurmountable barrier calling for intelligent design. Statistical models of islands drawn from your head is all very nice but just so much “so what” and removed from the reality of origin of species.

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    • What many different species and what changes define these limits?

      Changes don’t define anything. A level of functional complexity is defined by the minimum number of specifically arranged amino acid residues that are required to build the system in question. It’s like a 20-character sequence in the English language system that is made up of several words. If a certain type of beneficial function requires a sequence of words totaling at least 20 specifically arranged characters, that is the minimum structural threshold requirement to achieve that type of function. Such a 20-character sequence may be realized by a single point mutation to a pre-existing sequence. Or, it may be that the closest pre-existing sequence requires 12 mutational changes. However, the odds that the minimum number of require mutational changes will be just one or two changes decrease exponentially with each linear increase in the minimum size and/or specificity requirements. This is what creates the non-beneficial gap problem for higher and higher level systems in any language or coded message.

      So, whatever species happens to have a novel higher level system compared to any other species that does not have this system, it can be known that the one with the 1000 saar system did not evolve from any of the ones without it – because all such systems require “creative intelligence” to produce due to the statistical problems for all known non-intelligent mechanisms (just like the highly symmetrical granite cube that you yourself claim is a “blindingly obvious artifact” of creative intelligence – despite your stumble there when you mistakenly explained that conclusion of yours is somehow due to your brain’s teleological ability to detect design behind certain patterns wherever they may appear).

      You are claiming something for which you have never providing any evidence beyond Behe’s flagella.

      I’ve given you a great deal of evidence. It’s been demonstrated, quite clearly, that the ratio of beneficial vs. non-beneficial at the level of 1000 specifically arranged amino acids and beyond is exponentially lower compared to lower-level systems. It’s been shown, not surprisingly given the first observation, that any system that requires this minimum or greater is extremely isolated in sequence space. I’ve shown, in fair detail, that the proposed steppingstones for evolutionary pathways for such systems (published by Matzke in particular) are each far far to far apart in sequence space for the Darwinian mechanism to get from any one to any other of these “steppingstones” this side of trillions upon trillions of years of time. I’ve also shown that this is true for any system, any system at all (not just flagellar systems), that require more than 1000 specifically arranged amino acid residues to work. The problem doesn’t get easier for other systems. It remains the same.

      You are continually reverting to the bacterial flagella but we are talking now about vertebrates and evolution of species where there is significant body of evidence in genomic sequence comparisons to inform a discussion, not about abiogenesis for which there is scan knowledge.

      Why are you talking about abiogenesis here? Are you really this confused about flagellar evolution models and why they are so popular among evolutionists? Flagellar evolution models, like Matzke’s in particular, aren’t based on abiogenesis. They aren’t thought to spring into existence from nothing outside of a living thing. Obviously, it is thought that the flagellum evolved after the bacterium was already in existence. The problem, of course, is that given the pre-existence of homologies to all the required subparts to the bacterial flagellum, the evolution the flagellum by RM/NS would still be absolutely impossible. How is that? Because, the pre-existing homologous proteins in the bacterium are not homologous enough to produce the flagellar motility system. Very specific modifications are required. And, these required modification are too numerous, between every single proposed steppingstone, for evolution to actual happen between any one of these steppingstones this side of trillions upon trillions of years of time.

      Sequence comparisons are based on similarities, not the required differences needed to produce qualitatively novel systems. This is where Matzke gets all confused – just like you. He assumes that homology demonstrations for each protein within the bacterial flagellum (and other such machines) make the conclusion for evolution of the entire machine obvious. This is a mistaken assumption. A demonstration of homologies for the subparts of a system says absolutely nothing about the minimum number of required modifications needed before these subsystems will work together properly to form the larger more complex system.

      That’s the entire problem with these homology arguments – to include your homology arguments for animal relationships. Similarities say nothing about the minimum number of genetic changes that would be required to produce the qualitatively unique functional differences between different kinds of creatures. And, the minimum number of required differences increases with each increase in the minimum structural threshold requirement (i.e., with each increase in functional complexity).

      What are these systems of high level complexity that seperate cats from dogs. I am prepared to take the “risky” approach and am going out on a limb in saying there are unlikely to be any such systems. There are certainly none in the literature on mammalian sequence comparison.

      First off, why are you asking for examples of higher level differences between cats and dogs while completely ignoring the numerous examples of such between different kinds of bacteria? If you won’t accept the examples of the numerous complex biomachines that do in fact exist within different kinds of bacteria and which have been studied in great detail, if you call such machines magically “emergent” and label me a “reductionist” for thinking that they are actual machines, how is a discussion of cats vs. dogs going to solve or change anything for you?

      Further as a theistic evolutionist cant I legitimately claim that God tinkers when there is any such problem and the schemata of neo-darwinian evolution remains intact. After all you accept Darwinian mechanism for origin of species within “kinds” but draw the line (arbitrarily I would contend) and do not accept it for the orgin of related “kinds”.

      The problem is that you claim to have no empirical evidence for your theistic position. You can claim that God tinkers all you want, but you can’t have your cake and eat it too. Where is the evidence that such tinkering is required? Darwinists claim that it is not required, and they’re right, but only when it comes to very low levels of functional complexity. When it comes to higher levels, beyond 1000 saars, deliberate tinkering most certainly was required because no other known mechanism could have done the job.

      I have suggested the experiment to test your model. Get out all the sequences comparisons between for example cats dogs and bears and tell me with specificity what are the highly complex systems of greater than 1000 FSAAR that separate them?

      I’ve already done this for bacterial biomachines. If you won’t accept the demonstration on the bacterial level, a level which is far easier to study and for which far more is known, what’s going to make things any different if you are shown higher level qualitative differences between dogs and cats? Nothing. You’re just trying to dodge the obvious conclusion is all. If you are shown that such differences do in fact exist between dogs and cats, you’re going to simply ask for the differences between something else – like cows vs. whales, etc. It’s never ending and most disingenuous.

      Once you have the putative 1000 Fsaars that define this limit you can map its occurence across species.

      No you can’t. The limit of 1000 saars applies to any kind of qualitatively novel system that has this minimum structural threshold requirement. It is not a set sequence. There are many different kinds of systems all with very different sequences that all require more than 1000 specifically arranged amino acid residues (as is the case for any language/information system). Do you really not understand this very basic concept?

      Then you might have some evidence to present that is an insurmountable barrier calling for intelligent design. Statistical models of islands drawn from your head is all very nice but just so much “so what” and removed from the reality of origin of species.

      You wouldn’t be saying “so what” if you had any idea about what is actually happening in protein sequence space at various levels of functional complexity. You just have no idea…

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    • Pauluc,

      It would seem to me that a more appropriate test would be to map the requirements from a fish to man, find your inner fish so to speak.

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  65. Sean Pitman: However, I do appreciate your concern for my reputation ;-)

    Indeed I may well have been in error in underestimating your fame. The evolution crackpot index even has an entry for 100 points inspired by you.

    http://scienceblogs.com/evolvingthoughts/2006/11/11/the-evolution-crackpot-index/

    As one commentator suggests in outing you.

    “After spending zillions of moments wading through Sean Pitman’s neutral gaps before reaching the other side, I am very gratified that these Gaps are worth more than a full Pitman, 26^1.41345418475 = 100. ”

    I do worry that your dogmatic statements and polemic do not help to pursuade like a published study with measured and reasoned arguments would.

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    • What is unreasoned or unclear about the non-beneficial gap problem? It’s a very simple and straightforward observation. How is it that if there are exponentially fewer uniformly distributed targets in a given area that they will not therefore be exponentially harder to find by any random search algorithm? How is this a “crackpot” observation? Why are there no observed examples of RM/NS producing any qualitatively novel system that requires more than 1000 specifically arranged amino acid residues? (which is still at a very low sub-cellular level of functional complexity). Why is there an observable exponential stalling out of examples of evolution in action below the 1000 saar level of functional complexity? What solution have you or anyone else presented for this problem? I’d seriously like to know. Or is it easier to simply cover up your own lack of knowledge by calling the questions and observations of someone who’s challenging your position, “the most crackpot of all ideas that could possibly be presented with a maximum score of 100!”?

      As far as I understand the problem, it seems to me that my statements are quite measured and most generous to the Darwinian perspective. It is just that the significance of a situation where minimum non-beneficial gap distances increase linearly with each increase in the minimum structural threshold requirements for higher and higher level systems rapidly undermines any reasonable possibility of random mutations keeping up with this problem.

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  66. Sean Pitman: What experimental data would you suggest? A non-beneficial gap distance is the data. The implications of such a gap distance are obvious. No additional experimental data is needed to tell you that a mechanism of random mutations takes exponentially longer to get across such a gap distance (on average) with each linear increase in the gap distance. That conclusion, though very simple, completely undermines neo-Darwinism.

    Unfortunately this sort of dogmatic ill thought out statement is not taken seriously as is evident from responses to you at pandas thumb, pharyngula scienceblog and other sites.

    1] I have suggested the relevant experiments. Dont fixate on bacterial flagella and abstractions like sequence space. Most people dismiss it as a theoretical model disconnected from reality. Think mammalian evolution.

    2] It does not at all undermine neo-Darwinian evolution eather for theistic evolutionist or for you who accept completely a neo-Darwinian basis for speciation in post-flood biology

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    • Unfortunately this sort of dogmatic ill thought out statement is not taken seriously as is evident from responses to you at pandas thumb, pharyngula scienceblog and other sites.

      Interesting, given that you have no explanation for the rate of evolution at various levels of functional complexity.

      1] I have suggested the relevant experiments. Dont fixate on bacterial flagella and abstractions like sequence space. Most people dismiss it as a theoretical model disconnected from reality. Think mammalian evolution.

      Unfortunately, your suggested experiments aren’t relevant nor do you seem to understand the problem. Sequence space is not disconnected from reality. The sequence space issue is the entire problem for the Darwinian mechanism as far as I can tell. There simply is no other factor limiting this mechanism. And, biological machines, like bacterial flagella, are a perfect place to start evaluating the concept of evolution at various levels of functional complexity because so much is known about these machines and the underlying genetics. Your arguments about mammalian evolution are irrelevant because you’re not talking about specific systems with qualitative differences that have various minimum size and specificity requirements. It is also much much much harder to study mammalian evolution vs. bacterial evolution. The generation times alone for mammals are prohibitive for these kinds of experiments.

      2] It does not at all undermine neo-Darwinian evolution eather for theistic evolutionist or for you who accept completely a neo-Darwinian basis for speciation in post-flood biology

      This is nothing more than wishful thinking. Evolutionary ideas existed long before Darwin. Why then didn’t they catch on before Darwin came along? Because, no one had thought of a convincing naturalistic mechanism to explain the diversity of life – that’s why. As soon as it is recognized that the Darwinian mechanism is not viable beyond very low levels of functional complexity, neo-Darwinism would quickly lose its exalted position and popularity. And, according to Dawkins, it would be much harder to be an “intellectually fulfilled atheist”.

      Your repeated argument for post-Flood speciation as somehow being significant can easily be explained by evolution at very very low levels of functional complexity – which has never been a problem for either IDists or creationists.

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  67. Having read through all the recent exchanges I have to confess I am absolutely wrong as you suggested repeatedly. I thought you were actually interested in education and truth as your site advertises. That you grock the process of science and had some desire to communicate your ideas in the forum of science. Reluctantly I have to admit it does not appear so. I offered some advice as I do have a committment to education and science. I am clearly wasting my time here and am increasingly confident that your “my way only” approach to communication means you will never ever publish your work in the scientific literature. I will go back to my graduate students who do appreciate any help I can provide and are actually interested in doing good research and publishing their work for the world to read.

    Grace.

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  68. ” So, you think Einstein or Galileo or Leonardo da Vinci or Newton, or even Darwin would have given up their ideas if they remained unpopular?

    No, I think science would have discredited them if their ideas were not supported by observation and experimentation. Something you are not prepared to do other than blog speculate. Why do you think they are all revered today? They weren’t guys running around trying to prove the negative as you are doing.

    You see, you will need to gain some scientific support as Einstein, Galileo, Da Vinci and Darwin did (especially the latter on the origins of life) or else you’ll be forgotten as a religious ideologue. Notice how nobody attributes a religious bias to those greats of science, notwithstanding their religious beliefs? In fact Einstein was quite awed by the apparent design to the universe :)

    You keep talking about the weight of the science as your claim to being right. Where is your original work in that regard? Who weighs that science other than you? But you don’t care about that, or even what your fellow scientists think, which makes you a solipsist. Now, if ultimately you are elevated to the scientific pantheon as the other greats, I’ll be totally wrong and the world will hold you in such high esteem. That would not make me unhappy, because I will likely have witnessed a miracle! :)

    However, if ID is going to turn over macro evolution in won’t do it by default or back door, cloaked creationism. It will done by experimentation and the scientific method. But if you continue to allude to the miracles of the Bible being scientific, you are going to face ridicule from the Paulucs and Prof Kents of the Adventist world, let alone outside of that bubble. They understand the difference between the objective weight of the evidence – which cannot simply be solipsistically determined by one individual, no matter the source of the ideas – and faith.

    Oh, by the way, if you haven’t yet done so, I recommend you read Walter Issackson’s excellent biography on Einstein. I think you’ll find out Einstein had more than just ideas. If you don’t mind me saying so, I think he was a bit more skilled in math than yourself :)

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    • No, I think science would have discredited them if their ideas were not supported by observation and experimentation.

      Exactly, so why not at least try to do the same for my ideas, which are quite easily falsifiable?

      I know, you can’t do it yourself, but you’re quite sure that if I publish my ideas in a mainstream science journal that someone out there will know how to shoot my theory all to shreds. Right? This sounds like a no-brainer! Why not just published my ideas and test them against the big boys? It must be that I’m afraid to get shot down! and that’s why I don’t publish… Don’t you think?

      I guess that’s why I went on live radio to debate Jason Rosenhouse? – because I was afraid that he’d show me how silly my ideas are on public radio? – how the Darwinian mechanism is so clearly capable of creating all kinds of things regardless of their level of functional complexity? If I was so afraid of getting smashed to pieces by some of these Darwinian big shots, why take such public risks? – even in their own blogs and public forums? Why not just hide out in my own little ghetto?

      Come on now. You have to know that I’d love to be able to publish my ideas on the statistical limits to the Darwinian mechanism in a science journal like Nature or Science or any mainstream science journal. I really would. The problem, as I’ve already explained, is that no one is going to publish, in any mainstream science journal, any argument for intelligent design or creative intelligence (even if the intelligence were a “natural” intelligence like some kind of intelligent alien life form) as the origin of various kinds of biological machines. It just doesn’t happen these days without someone getting fired over it. So, the next best thing is to take the argument directly to them and challenge them in their own blogs, on the radio, and on television, etc. There’s nothing else I can do. My hands are tied.

      In any case, do let me know when you’re willing to reasonably define what it would take for you to recognize a phenomenon as a true “miracle” or when you’re able to present something, anything, that explains how the Darwinian mechanism of RM/NS can actually work beyond very low level of functional complexity.

      Until then, what are you really contributing here? What are you trying to say? – that you don’t know but someone else probably does? That you’re skeptical about everything and nothing could possibly convince you of the existence of God or any other designer of life? – not even if you were to personally witness some of the most fantastic miracles described in the Bible? Good luck with that… but you’re just fooling yourself in your efforts never to be tricked by anything. You’re missing out on a great deal that life has to offer.

      Still, I wish you all the best.

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  69. ” You’re missing out on a great deal that life has to offer.

    And perhaps you as well if your inquiry is not a free one but one shackled by religious beliefs inculcated at a young age.

    I wish you all the best as well and hope one day you will be able to examine reality without religious bias. Then you will know intellectual freedom without fear or promise of immortal reward.

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    • I have no fear, thanks to God and His mercy, and no one is free of bias – not even you. You’ve simply traded one religion for another. It is still possible that your current bias blinds you to what would otherwise be obvious.

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  70. @ Allen

    “Atheism is a religion just like anything else that is believed.”

    I agree. Any form of belief or non belief in God is a form of religion. It is beyond the realm of science to determine if there is ‘a’ god or not. What science can do and does do is cast doubt upon man created, cultural iteration(s) of god(s) – in other words: what is the likely nature of a creator.

    For example, one can argue the mere fact that we can conceive of a god means the possibility exists. Whereas an atheist would argue: if one cannot prove that creation emanated from any of the forms of god(s) that man worships, it proves they don’t exist.

    Deism, or ID being the modern form, is an interesting approach to the issue. Why? Because rather than just anthropomorphize God or attribute unknowm phenomena to a deity it looks at the potentiality of divine reason. But such presumed design is always subject to the cold, empirical, investigation of natural cause and effect and of course probematic theodicy – why would such turbulent universe ( at least our solar system) be designed for a creature made in God’s image. But of course Man is very inventive and imaginative in his rationalizations and myths- a bite of a forbidden apple figuratively representing off limits knowledge- and BAM: sin unravels the theretofore perfect yarn of bliss.

    Now highly intelligent men and woman – some scientists at that! – like Dr. Pitman understand all this. But faith and belief in a loving god and life hereafter is a potent panacea for all that ‘ails’ the human ‘soul’. “Whatever gets you through the night is all right, all right” And Dr. Pitman has often intelligently appealed to the potential yearning in myself in a compassionate manner. The problem is – in my humble estimation- the search for empirical truth must be totally divorced from wishful thinking or outcomes whatever they may be. When that happens in science – human integrity reigns and knowledge advances.

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