@pauluc: perhaps you could give us your analysis of this …

Comment on LSU memorandum confirms Educate Truth’s allegations by Sean Pitman.

@pauluc:

perhaps you could give us your analysis of this paper and how the data supports your creatonist perspective?

1. Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE. Comparative analysis of Alu repeats in primate genomes. Genome Res 2009 May;19(5):876-885.

What are the “actual facts” here?
What is the guesswork and what is the unproven axiom.
What is the creationist interpretation of this?

The facts:

SINEs, to include Alu repeats, are indeed short interspersed sequence elements of ∼300 nt in length, propagating within a genome through retrotransposition and account for ∼10% of the human genome sequence. They also have an impact on phenotypic change via alternative splicing, genomic rearrangements, segmental duplication, and expression regulation causing disorders like Hunter syndrome, hemophilia A, and Sly syndrome.

The guesswork:

The proposed evolutionary relationships over deep time based on nested hierarchical patterns is just-so story telling without scientific value. Such stories have no useful predictive value nor are they effectively falsifiable.

Part of the problem here is that the paper you reference treats SINE insertions as “homoplasy-free character states in cladistic analyses of primates.” The assumption isn’t true. According to Cantrell, et at., SINE insertions are simply not homoplasy-free phylogenetic markers since they are subject to hot-spot insertions independent of phylogenetic relationships.

Cantrell, Michael A. and others. 2001. An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion. Genetics 158:769-777.

In any case, there really are no “foolproof” genetic markers of common decent. All of the ones proposed so far to be foolproof have been shown to have significant flaws. The prediction that pseudogenes, transposons (SINEs and LINEs) and other shared mutational mistakes are conclusive evidence for common descent has not held up. For example, consider the following excerpt from David Hillis’ paper entitled, “SINEs of the perfect character.” published in the Proceedings of the National Academy of Sciences, 1999:

What of the claim that the SINE/LINE insertion events are perfect markers of evolution (i.e., they exhibit no homoplasy)? Similar claims have been made for other kinds of data in the past, and in every case examples have been found to refute the claim. For instance, DNA-DNA hybridization data were once purported to be immune from convergence, but many sources of convergence have been discovered for this technique. Structural rearrangements of genomes were thought to be such complex events that convergence was highly unlikely, but now several examples of convergence in genome rearrangements have been discovered. Even simple insertions and deletions within coding regions have been considered to be unlikely to be homoplastic, but numerous examples of convergence and parallelism of these events are now known. Although individual nucleotides and amino acids are widely acknowledged to exhibit homoplasy, some authors have suggested that widespread simultaneous convergence in many nucleotides is virtually impossible. Nonetheless, examples of such convergence have been demonstrated in experimental evolution studies.

Beyond this, the assumption that SINEs and other such sequences could not have originally served any beneficial purpose (i.e., that no reasonable designer would have deliberately included them within the primate genome) has also been shown to be false.

In a Science article by Wojciech Makalowski, the following comments are made that seem to echo what design theorists have been saying for a very long time:

Although catchy, the term “junk DNA” for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as genomic treasure.”

Makalowski, Wojciech. 2003. Not Junk After All, Science 300:1246-1247

As it turns out, a lot of beneficial and even critical functionality has been identified for SINEs, LINEs, pseudogenes, and other various kinds of genetic sequences that were once thought to be “Junk DNA”; remnants of mistakes of a long evolutionary history of trial and error. There are also sequences which don’t seem to have any function, yet remain identical between very different species.

For example, in May of 2004 Haussler and Bejerano used computers to compare the human genome with the mouse and the rat genomes. They were surprised to find long stretches of shared non-coding “junk” DNA that were exactly the same in humans and rodents.

“There were about five hundred stretches of DNA in the human genome that hadn’t changed at all in the millions and millions of years that separated the human from the mouse and the rat,” says Haussler. “I about fell off my chair. It’s very unusual to have such an amount of conservation continually over such a long stretch of DNA.”

Many of these stretches of DNA, called “ultraconserved” regions, don’t appear to code for protein, so they might have been dismissed as junk if they hadn’t shown up in so many different species. Haussler “confirmed that negative selection is three times stronger in these regions than it is for nonsynonymous changes in coding regions.” As far as Haussler is concerned, “It is a mystery what molecular mechanisms would place virtually every base in a segment of size up to 1 kilobase [i.e., 1000 bp] under this level of negative selection”. That’s 500 regions of DNA up to 1000 bp that are identical between rats and humans – up to 500,000 identical genetic sites in DNA?! What is also surprising is that these same regions largely matched up with chicken, dog and fish sequences as well; but are absent from sea squirt and fruit flies. Note that the last supposed common ancestor for all of these creatures was thought to live some 400 million years ago.

“From what we know about the rate at which DNA changes from generation to generation, the chance of finding even one stretch of DNA in the human genome that is unchanged between humans and mice and rats over these hundred million years is less than one divided by ten followed by 22 zeros. It’s a tiny, tiny fraction. It’s virtually impossible that this would happen by chance.”

Of course, this is in light of an interesting experiment described by Nóbrega et. al. in a 2004 issue of the journal Nature where the authors demonstrated that large-scale deletions (two large non-coding intervals: 1,511 kilobases and 845 kilobases in length for a total of 1,243,000 bp) of non-coding DNA could be tolerated by mice without any detectible functional effect. “Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis.” What is especially interesting here is that these particular non-coding sequences are conserved between humans and rodents. The authors argue that, “Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals.”

The problem here is the question of why such “disposable DNA” would be so conserved over many tens of millions of years? Functional or non-functional, it still poses a problem for standard evolutionary theory. If functional, it isn’t non-functional remnants of evolutionary trial and error history and fits well within design theory. If non-functional its high degree of conservation doesn’t seem to fit with the idea that many tens of millions of years have actually passed since the ancestral origin of either humans or rodents (or chickens, dogs, and fish).

Even so, those like Haussler and Nóbrega still believe very strongly that humans and rats do in fact share a common ancestor that lived a hundred million years ago or so. The idea that perhaps humans and rats might have actually been individually created, deliberately, does not even cross their minds.

In short, such patterns do not falsify the ID-only hypothesis since they do not even address the origin of high levels of functional information within the genomes of living things. Also, the age of various genomes is often calculated based on mutation rates that are actually calculated based on prior evolutionary assumptions. Real time studies of mutation rates have shown that these assumptions are off by as much as 20 or even 100 fold.

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

Then, there is also the problem of the rapid degeneration of the functional elements in the genomes of slowly reproducing species – humans, other primates, and all other mammals for that matter. All such gene pools are devolving, not evolving. They are declining in quality – i.e., they are headed for extinction at a fairly rapid rate.

http://www.detectingdesign.com/dnamutationrates.html#Detrimental

Such evidence calls into serious question the validity of these just-so stories of mainstream scientists when it comes to their explanation of the nested hierarchical patterns that they find in various genomes.

For more information on this topic see:

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

http://www.uncommondescent.com/intelligent-design/daniel-fairbanks-cherry-picks-data-on-pseudogenes-to-prop-up-common-descent/

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

LSU memorandum confirms Educate Truth’s allegations
@pauluc:

You wrote:

I do not even know what you mean by “ID-only”. Most scientists would understand ID as code for “We dont understand this except God did it”.

The ID-only hypothesis is the testable hypothesis that the phenomenon in question can only be explained by intelligent design on at least the human level of intelligence. In other words, the origin of the phenomenon in question is indeed not currently understandable using mindless mechanisms alone while being currently understandable using at least human-level design.

You go on to write:

Although the poperian model of science as hypothesis testing and a requirement for falsifiability is still the dominant understanding it is much more complicated than that… In summary however the theory suggests that a thesis such as quantum mechansisms, origin of life by evolution by common descent is surrounded by a group of agregated interrelated hypotheses. These might include Darwinian natural selection.

This argument is often used to suggest that certain peripheral elements of modern evolutionary theory may be challenged and even falsified, but the core truth of common descent remains intact as an unshakable fact of science.

Let me suggest to you that nothing is absolutely provable in science. Hypotheses, theories, and even the laws of science are not facts. They are explanations or interpretations of the facts that are potentially wrong. They are and must be open to testing and the potential of effective falsification. If they are not, they leave the realm of science and move into the realm of religious-style dogma or empirically-blind faith.

If the Darwinian mechanism of RM/NS is effectively falsified as having the creative potential to produce the qualitative functional diversity that we see in living things, beyond very low levels of functional complexity, you have a theory of common descent without a reasonable mindless mechanism. If only intelligent design is a known force that can reasonably explain the existence of such diversity of functionally complex information systems, what you have is creationism. The only argument left is over if the creation of life and its diversity happened slowly or rapidly.

It is for this reason that evolutionary scientists are clinging so desperately to the Darwinian mechanism – despite its very clear statistical limitations to very very low levels of functional complexity (even given trillions of years of time). They cling to this untenable mechanism because they simply do not want to accept the obvious implications that a lack of a viable mindless mechanism has – i.e., the need for a very intelligent designer. Also, the other suggested mechanisms, like your reference to a ratchet-like mechanism, are no more tenable than RM/NS and are, effectively, variations on the same basic theme.

Yet, you write:

Science could completely reject all darwinian mechanisms but the thesis of evolution would remain because of the absence of a better theory.

A theory of origins without a viable mechanism is a stack of cards. You know it, I know it, and pretty much all mainstream scientists know it. That’s why they don’t want to publicly acknowledge the very clear limitations of RM/NS.

Also, the underlying theory of common descent must also be falsifiable if it is truly a scientific theory. The ID-only hypothesis is very easily falsifiable. How about the theory of common descent? Not falsifiable? Really?

Again, if an idea is not effectively falsifiable, even in theory, it isn’t scientific. It really is as simple as that.

Your approach of pointing out the problems you see with some aspect of the evolutionary model completely misses this point. You are approaching science and knowledge from the approach to truth you hear from the pulpit and from fundamentalists like Bob Ryan. You cannot be a christian unless you believe in the literal creation. You cannot have a sabbath unless the literal creation is correct. There can be no second coming unless the creation is literally true. This is not the mindset outside the inclaves of fundamentalism. The pillar talk of people like this engender the idea that failure at a single point destroys the whole edifice. This does not pass the test of realism.

You don’t seem to understand my position. I repeat, yet again, that this isn’t a moral issue. One can be a very good Christian, living like Jesus lived, and not understand the truth of origins… and be saved in Heaven someday. The only reason why a correct understanding of origins is important is because it helps to provide a solid rational basis for the credibility of the Gospel message of hope here and now. While hope, by itself, doesn’t save anyone, it is nice to have hope here and now if one can find a solid basis for hope.

You cannot hope to change the scientific paradigm that is the thesis of evolution by pointing out even a multitude of errors or inconsistencies in the surrounding interrelated hypotheses without a compelling alternative core model. You have to provide both an overarching alternative to evolution as a thesis and to each of the surrounding interrelated hypotheses each of which provide support for the overall hypothesis.

If the foundational struts holding up any theory can be shone to be false, no other theory is needed to argue that the current theory is simply wrong. Thomas Edison, before his invention of the light bulb, came up with hundreds of false theories that looked great on paper, but just didn’t work when put to the test. The same thing is, or at least should be, true of any scientific theory.

Beyond this, I repeat, there is a very good well supported theory of origins to replace the modern theory. It is the Biblical model of origins that has the weight of empirical evidence.

Do you seriously want us to believe that geo biodiversity can be accounted for by a model of plate tectonics that suggests that in 6000 years south america moved >11000 km from Gwondanaland. This is incredible; minimal rate of nearly 2 Km per year! The constraints imposed on the model, a 6000 year earth history makes your task of credibility virtually impossible. But if you move away from the “about 6000″ of divine relevation you are on your own and well away from the mothership of the church.

Why do you think that a very rapid initially catastrophic movement of continents is so unreasonable and inconsistent with the currently available evidence? Why hasn’t there been more coastal erosion if the continents really did split up some 200 million years ago? That’s enough time to erode all continents on all sides more than 2,000 kilometers. And they still fit?

Consider that Japan just moved 12 feet to the east within minutes with just a 9.0 earthquake. What would happen if the Earth was hit by a large meteor 100 kilometers in diameter?

I don’t think you’re comprehending the degree of energy that was released during and even after the Noachian Flood.

You have a problem in that your core thesis that God created everything 6000 years ago was the dominant model some 150 years ago but this has been tested and progressively rejected as untenable because of accumulating evidence for the alternative model over the last 150 years.

The Biblical model wasn’t really rejected by mainstream science until Darwin proposed his RM/NS mechanism of origins. The uniformitarian model of geology, which is currently failing, also contributed to this drift from the Biblical model. If these models failed within mainstream science, the Biblical model would again gain dominance.

The real problem here is the secular mindset of many which think that any consideration of a Biblical model is inherently anti-scientific and irrational. That’s simply not true.

This does not to me seem the carefully ordered regular precise structure I would expect of intelligent design. If you suggest that we do not yet know but that all of this nonetheless reflect careful thought or that it reflects interference and corruption from the devil as David Read woudl suggest I would have to conclude that your ID concept is vaccuous has not explanatory value and is far from scientific.

Again, you’re basing your notion of intelligent design on how you would have done things. That isn’t the correct basis for determining if something can only be rationally explained via intelligent design. Just because a child’s soap box car might not fit your notion of an ideal design does not mean that it doesn’t clearly invoke the need for intelligent design.

This is why design-flaw arguments are meaningless – a red herring. Beyond this, you somehow think to question the designed origin of systems that are functionally complex on a level far beyond your own design capabilities. That, in itself, should give you pause – should cause you to think that you are perhaps being just a bit arrogant to think that you can effectively critique a system of function that you cannot come close to matching.

In contrast the evolutionary model of common origin and ancestory has extraordinary explanatory and predictive value. It predicts that changes between species will reflect this history of origin by descent from common ancestors.

The theory of common descent can only effectively explain, on the same level as intelligent design theory, the similarities between creatures. It cannot effectively explain the qualitative functional differences beyond very very low levels of functional complexity without invoking intelligent design.

So, you see, the failure of the mainstream theory of origins isn’t in explaining similarities. It is in explaining the differences.

I ask you to take any published analysis of a multigene family and ask the same questions. Do they objectively support order and design or are they best accounted for by contingency and chance with a mere modicum of selection.

Again, you’re looking at patterns of similarities. The same gene families with the same basic qualitative functionality can easily drift via mutations over time, very rapidly, while still maintaining the same basic type of functionality.

This is the reason why neutral, near neutral, or even evolution of the level of the same basic type of function isn’t a problem at all.

The problem is when you start talking about the origin of qualitatively unique types of functions within living things beyond very low levels of functional complexity. It is at this point that the mainstream theory of origins fails and the ID-only hypothesis comes into play.

5] I have dealt with “real science” and new models above but your statement

” … but on the functional aspects associated with the NHP that cannot be explained by any known mindless mechanism while being within the realm of the powers of intelligent design at a very high level.”

is a faith statement, a non-sequitur that does not get to the point of this dialogue which was why the genome is as it is and can you honestly say it is best accounted for by “design”.

It is not a blind-faith statement at all – devoid of the weight of empirical evidence. As already noted, there is no currently known viable mindless mechanism to explain the origin of the novel functional aspects of the NHP of the ToL beyond very low levels of functional complexity. It is at this point that the only known mechanism that can explain such qualitatively novel functional complexity is deliberate intelligence on at least the human level or beyond.

Sean Pitman
www.DetectingDesign.com


LSU memorandum confirms Educate Truth’s allegations
@pauluc:

You wrote:

Nowhere however do you answer the real question that was posed to David Read. You are implying that the creationist argument is correct simply because the alternative is deficient. I know this is the SOP but I had hoped that you would be proactive in telling me whey this data is best interpreted from a creationist perspective which was David Reads contention.

Nested Hierarchical Patterns (NHPs) can be explained by both common descent with mindless modification over time and by deliberate design. Many human designed systems, like object oriented computer programming for example, show NHPs.

So, how does one tell if a given NHP is the result of mindless mechanisms or the result of deliberate design? Well, one must actually investigate various features of the pattern itself to see if all of the features associated with the pattern can be adequately explained by any known non-deliberate mechanism. If some aspect of the pattern cannot be explained by a known non-deliberate mechanism, but is still within the realm of deliberate design, the ID-only hypothesis can rationally be invoked at that point. Once it is known that deliberate design was most likely involved with the production of at least some aspect of the NHP in question, it is also reasonable, at that point, to suggest that the overall NHP itself may have been deliberately designed as well.

In the case of living things, they are indeed generally arranged in a NHP – a “Tree of Life” (ToL) so to speak. Again, the NHP itself can be produced by mindless mechanisms or by deliberate design. So, what aspect of the ToL would be beyond the realm of any known mindless mechanism? – given that the NHP itself can be produced by mindless mechanisms?

As noted previously, the functional differences between living things and even subsystems within living things, beyond very low levels of functional complexity, can only be explained, at the current time, by intelligent design. There is no currently known mindless mechanism that can produce qualitatively novel functional information beyond very low levels of functional complexity.

Since every living thing demonstrates very high levels of functional complexity, the ID-only hypothesis can rationally be invoked to explain the origin of life. And, since many different types of living things have qualitative functional differences as well, these high level qualitative differences can also be most rationally explained by the ID-only hypothesis.

Once one demonstrates that intelligence was most certainly in play in the origin of numerous aspects of the ToL, one can also rationally propose that the overall NHP was also the likely result of deliberate design.

How can the apparently unplanned but cobbled together and functional mess that is the genome be best explained in a creationist framework? It cries out chance and contingency which is precisely what evolution would predict and why it is increasingly seen as the most compelling by most genome scientists. As you know you will not replace this dominant model by carping about minor or major deficiencies because in science you know a model is not replaced because it is deficient but because there is a better model.

Real science demands that models be at least theoretically falsifiable. That means that a particular model can be shown to be false even if there is no other model with which to replace the current model. A false model is a false model. It’s as simple as that.

Beyond this, your notion that the genome is a hodge-podge poorly planned jumbled mess is a view that is at odds with the currently emerging view of the genome – a fractal view if you like where the more closely it is investigated, the more and more intricate and complex it appears. What might initially appear to be a “mess” of circuits, wires, and microchips might later turn out to be a cutting edge supercomputer designed by the most advanced minds in computer science. The only reason why someone might initially interpret their work as a “mess” is because of the initial ignorance of the observer.

In other words, the concept of a “mess” is subjective – it is in the eye of the beholder. This “messy” notion of yours certainly isn’t objective science. Just because you wouldn’t do it that way doesn’t mean it wasn’t intelligently designed. And, if you can’t do as good yourself, you probably aren’t qualified to describe something as “a mess” or “poorly designed” to begin with. Richard Dawkins got into this embarrassing situation when he described the inverted human retina as an obvious example of poor design… later shown to be an ingenious design (to include the fairly recently discovered fiber-optic Mueller cells).

In light of your “poor-design” argument, consider the following thoughts of Erika Hayden on the intricacies of the genome and how clueless modern scientists have been in their understanding of it:

“We fooled ourselves into thinking the genome was going to be a transparent blueprint, but it’s not,” says Mel Greaves, a cell biologist at the Institute of Cancer Research in Sutton, UK. Instead, as sequencing and other new technologies spew forth data, the complexity of biology has seemed to grow by orders of magnitude. Delving into it has been like zooming into a Mandelbrot set — a space that is determined by a simple equation, but that reveals ever more intricate patterns as one peers closer at its boundary….

“It seems like we’re climbing a mountain that keeps getting higher and higher,” says Jennifer Doudna, a biochemist at the University of California, Berkeley. “The more we know, the more we realize there is to know.”…

Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. “Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive,” says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia.

Erika Check Hayden, Human genome at ten: Life is complicated, Nature 464, 664-667, Published online 31 March 2010

See also:

http://www.detectingdesign.com/pseudogenes.html#Fractal

The onus is on you to produce a better more compelling model. As Clausen has indicated they are currently lacking. For these published observations on the distribution of alu repeats you must show the superiory of you model not the inadequacy of the existing model. To be real science you must then go on to test the predictions of your model experimentally.

Again, real scientists don’t need a new model before they can question the validity of the current model. Beyond this, the basis of a new model is not based on the NHP of the ToL, but on the functional aspects associated with the NHP that cannot be explained by any known mindless mechanism while being within the realm of the powers of intelligent design at a very high level.

Sean Pitman
www.DetectingDesign.com


Recent Comments by Sean Pitman

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Thank you Ariel. Hope you are doing well these days. Miss seeing you down at Loma Linda. Hope you had a Great Thanksgiving!


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Thank you Colin. Just trying to save lives any way I can. Not everything that the government does or leaders do is “evil” BTW…


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Only someone who knows the future can make such decisions without being a monster…


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Where did I “gloss over it”?


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I fail to see where you have convincingly supported your claim that the GC leadership contributed to the harm of anyone’s personal religious liberties? – given that the GC leadership does not and could not override personal religious liberties in this country, nor substantively change the outcome of those who lost their jobs over various vaccine mandates. That’s just not how it works here in this country. Religious liberties are personally derived. Again, they simply are not based on a corporate or church position, but rely solely upon individual convictions – regardless of what the church may or may not say or do.

Yet, you say, “Who cares if it is written into law”? You should care. Everyone should care. It’s a very important law in this country. The idea that the organized church could have changed vaccine mandates simply isn’t true – particularly given the nature of certain types of jobs dealing with the most vulnerable in society (such as health care workers for example).

Beyond this, the GC Leadership did, in fact, write in support of personal religious convictions on this topic – and there are GC lawyers who have and continue to write personal letters in support of personal religious convictions (even if these personal convictions are at odds with the position of the church on a given topic). Just because the GC leadership also supports the advances of modern medicine doesn’t mean that the GC leadership cannot support individual convictions at the same time. Both are possible. This is not an inconsistency.