Emergence and the Origin of Life?

by Sean Pitman:
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The following discussion is from a Spectrum article by Dr. Mailen Kootsey.  Dr. Kootsey is a physicist who has “multidisciplinary expertise”, to include appointments in departments of Physics, Physiology, Computer Science, Biomedical Engineering, and Biology.

His article is entitled, “Emergence and Origins of Life”.  In this article he tries to explain how complex biosystems can be produced, not only by random mutations and natural selection, but by a property active within the universe known as “emergence” – a creative force that is not dependent upon random mutations or natural selection at all.

 

In early discussions of evolution, the only hypothesized source of changes was random variations in genes, combined with natural selection. Intelligent Design proponents have attacked this hypothesis by calculating the astronomically small probability of the necessary subunits of a complex system coming together all at once [1]. These calculations have some problems because they ignore the possibility that the subunits come together in stages rather than all at once.

While it is true that complex systems may be built from smaller pre-existing subsystems.  It is not true that this can be done via the mechanism of random mutations and natural selection beyond very low levels of functional complexity.  The problem is that at higher and higher levels of functional complexity the minimum number of required modifications for the subsystems to properly come together to form a new more complex system increase in a linear manner.  With each linear increase in the required number of mutational changes to cross the non-beneficial gaps in sequence/structure space, the odds of success decrease exponentially.  This is the key problem with the creative potential of random mutations and function-based selection.  There’s an exponential stalling effect with each step up the ladder of functional complexity – regardless of the existence of pre-formed subsystems within the gene pool.

 

But, the recognition of emergence opens a whole new type of explanation for the origin of existing complex systems: complexity can also be the result of the selection process of emergent laws, a natural part of the universe. Natural laws of emergence can choose configurations from the vast number of possible combinations, a choice that is not dependent on randomness and does not require multiple generations and vast lengths of time or natural selection.

The problem is that the “emergence argument” cannot explain the creation of biomachines because the very same parts, depending upon orientation relative to each other, can produce many different types of biomachines and organelles and even organ systems.  Unlike the water molecules in a snowflake, these machines are not pre-determined by the inevitable orientation of subparts in certain predictable ways under certain environmental conditions – but are dependent upon a very specific order and organization of the underlying building blocks that is defined by a pre-established set of coded instructions – detailed instructions that are not contained within the building blocks themselves.  Systems like this cannot be explained by “emergence” of the type Dr. Kootsey is talking about.  They can only be explained by intelligent design beyond very very low levels of functional complexity.

 

A species of African termites, when grouped together in a site with suitable soil available, construct a mud structure several feet high with internal ventilation and favorable orientation to the sun [2]. These termites have no leadership structure and no internal blueprint from which to work, yet similar colonies always construct mounds of similar size, shape, and functionality. After extensive study, scientists realized that they were studying a complex system that, given the right environment, always resulted in the production of similar mounds. The components of this system are the individual termites with very simple sensory organs and neural responses. Their simple characteristics, when multiplied in a group and added to an environment, create a complex system that produces a structure of remarkable architecture – hardly predictable from the properties of a single termite!

Forget about the enormous amount of information that is contained within the genetic programming of all living things for a moment – to include termites.  After all, termites are genetically programmed to produced a certain kind of nest in certain environments.  That is why they don’t create beehives and why bees don’t produce termite nests – regardless of environmental conditions.

Beyond this, the “emergence” in this case is based on the same subparts (termites) doing a certain “emergent” task regardless of their orientation relative to each other.  The subparts (the termites in this case) are not required to be in a specific arrangement relative to each other to achieve the “emergent” effect.

Compare this to a rotary bacterial flagellum where the motility function of this micro-machine is dependent upon the specific order and orientation of the different kinds of amino acids within the machine.  Without this specific order the motility function would not be realized.  And, this order is not “emergent” in that it is not automatically produced by simply placing the proper number of amino acids in the “proper environment”. There is no proper environment that will cause these parts to know what to do without the coded instructions contained within the DNA of the organism. They simply will not self-assemble themselves to form this or any other “emergent” function, at this level of complexity, without pre-existing genetic instructions that tell them how to specifically arrange themselves in order to achieve this collective functional ability.  And, the genetic instructions will also not “self-assemble” without the input of deliberate intelligent design.

This is key to understanding the limits of naturalistic mechanisms – limits that are very limited indeed and cannot explain much of anything beyond very very low levels of functional complexity (i.e., nothing that requires more than 1000 specifically arranged characters).

For further discussion of this topic see:

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

 

58 thoughts on “Emergence and the Origin of Life?

  1. Thanks, Sean, for your excellent response!

    Describing emergence as a creative force is an attempt at crediting nature for what God does or has done in the past. Trying to negate the evidence of design in nature is the epitome of foolishness. This is the result of insisting in the use of the so called methodological naturalism, which precludes any credit to a Creator.

    I can understand why those who prefer to ignore a Creator would resort to such extreme lack of common sense, but I can’t figure out why those who by their membership in a Christian organization would waste their time with such nonsense.

    Why would a believer in a Creator invest so much time in pretending that nature and the laws of nature could be explained without the intervention of a Creator or a Designer?

    Christian scientists already have the answer to the question of intelligent design. Why pretending that they don’t?

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  2. Excellent article. My good pard shows that he isn’t scared to tackle opposing views, even within the Adventist ranks. I presume Dr. Kootsey is an Advenist from his cv?

    Now about that ole tail on the bug and whether it can be broken down into smaller parts. Isn’t it true that the Type III Secretiry System is similar to the protein structure of the flagellum?

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    • Yes, the TTSS system is very similar to a structure of 10 proteins out of the 40 or so proteins that form the rotary flagellum. It’s like removing the engine of a car and having the lights or radio still work. It is very easy to remove parts from a system while maintaining the function of various subsystems. However, doing the reverse cannot be done with the same ease.

      It is not just as easy to randomly add parts to a system to produce a more complex system that requires a greater minimum number of parts. Why not? Because, adapting parts that used to work in other systems doing other jobs to work together requires various small modifications. The greater the minimum part requirement for the more complex system the greater the number of these required modifications to get the subparts to work together properly. And, with each linear increase in the number of required modifications, the amount of time required to achieve these modifications, via random mutations, increases exponentially.

      Sean Pitman
      http://www.DetectingDesign.com

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  3. The following exchange is taken from a discussion on the Spectrum blog – Sean Pitman

    Are we back to Magic?

    Stuart Kauffman, “I wish to say that life is an expected[?], emergent [define?] property of complex chemical reaction networks.”

    What chemical reactions simple allow digital code to appear??? Kauffman does not deal with the mechanism for this non-sense but posits that this is so. Where is the lab work demonstrating this spontaneous generation??

    Kauffman calls this “natural magic.” In a lecture at MIT he stated,

    “Life bubbles forth in a natural magic beyond the confines of entailing laws. This allows us to be “reenchanted” with nature and find a way beyond modernity.”

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    • Your comments are spot on. We creationists aren’t the one’s appealing to magic beyond design abilities and intelligence that we ourselves are capable of producing to at least some degree. Rather, the Darwinists are the ones who have been reduced to such mindless appeals to magic where things “poof” into existence for no apparent reason – without any guidance from any kind of intelligent designer or even any rational laws of nature which are actually known or apparently testable or discoverable by any empirical means…

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      • Alchemy was once called “science,” but today we know it as the “magician’s trick.” All life was magic to our ancestors who had no understanding or control of what they observed: rainbows, volcanoes, earthquakes; all were attributed to gods or mysterious forces.

        Today, scientists seek to tear apart the atom and understand “how” things function. They have explanations for much that was previously unknown. Why should we dismiss their findings only in certain areas? We eagerly greet their new discoveries if offering cures for dreaded diseases, but dismiss those that are counter to our religious beliefs. Religion is not antithetical to science, nor should it be; they must work together rather than attempt to destroy the other.

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        • I certainly agree that useful religion and true science have the same Source and therefore should be in harmony. However, when scientists start arguing for the magical appearance of biological complexity by appeals to some mystical kind of “emergence”, that’s not science or useful religion. That’s just blind faith in some kind of naturalistic philosophy.

          It’s fine to try to discover the limits of what naturalistic mechanisms can explain. However, to define science as “methodological naturalism”, in a way that rules out any ability to detect the activities of intelligent design of any kind behind various features of living things, isn’t scientific or empirically rational. And, it isn’t consistent with other mainstream sciences that are based on the ability to detect intelligent design behind various phenomena – to include forensic science, anthropology, and even SETI science.

          How long should SETI scientists look for some mindless “raw” force of nature to explain the types of radio signals that currently have no known natural explanation? – before they can rationally conclude that such signals would indeed be very good evidence of true artefacts of intelligent design?

          You see, just because somethings that where once thought to require intelligent design are now known to be produced by mindless natural forces doesn’t therefore mean that everything can therefore be explain by mindless “raw” forces of nature. Such a conclusion is based on a non-falsifiable logical fallacy, not valid science.

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      • because it (allegedly) magically happened only some 6000 yrs ago…isn’t the YEC “magic” harder to believe than the philosophically labeled “magic” alluded to by scientists which took mega years to happen as the evidence in the rocks shows?

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        • Four billion years might seem like a long time to some, but it is the tiniest drop in the bucket compared to the time that would be required for even a small subcellular biomachine, like a rotary bacterial flagellum for example, to be produced by any known “raw” force of mindless nature. The production of any machine at this level of functional complexity is extraordinarily unlikely to be produced by random mutations and function-based natural selection, or any other mechanism like “emergence”, this side of trillions upon trillions of years of time.

          Intelligent design, on the other hand, can and does produce such machines in real time in very short order.

          So, which theory is most rationally and statistically tenable? Certainly not your theory of a few billion years of randomness and chaotic interactions guided by mindless natural mechanisms. Such a notion is truly magical – not at all “scientific”.

          Such just-so story telling might be entertaining, but these stories are not demonstrable. There are no examples of evolution in action, by emergence or RM/NS, producing any such machine beyond very very low levels of functional complexity. And, statistically, these stories are absolutely untenable. The only thing left to hold them up is an appeal to some mystical magical process – not science.

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  4. Nick Samoljok wrote “This is the result of insisting in the use of the so called methodological naturalism, which precludes any credit to a Creator.”

    Funny, Sean Pitman actually advocates methodological naturalism as a way of validating God’s existence. According to him, any a priori assumption regarding GOd’s existence or the Bible’s accuracy is blind faith. God adheres to his own natural laws; Satan cannot contravene those laws; and we can therefore trust what science informs us (until the science itself becomes colored by blind faith, which he insists atheists do all the time).

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    • Unlike methodological naturalism (a philosophical position that attributes everything, ultimately, to mindless “raw” forces of nature) the Bible itself argues that nature herself speaks eloquently for the existence of her Creator and His creative power:

      The heavens declare the glory of God; the skies proclaim the work of his hands. – Psalms 19:1

      For since the creation of the world God’s invisible qualities–his eternal power and divine nature–have been clearly seen, being understood from what has been made, so that people are without excuse. – Romans 1:20

      The God of the Bible does not appeal to or expect blind or “a priori” belief or faith in His existence or His character, but offers up abundant evidence as a basis for an intelligent trust in His existence, His character, and in the credibility of His Word, the Bible.

      In any case, the concept of fideism has already been extensively discussed in this forum and there is no need to rehash it all…

      Sean Pitman
      http://www.DetectingDesign.com

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  5. “Yes, the TTSS system is very similar to a structure of 10 proteins out of the 40 or so proteins that form the rotary flagellum.”

    “Because, adapting parts that used to work in other systems doing other jobs to work together requires various small modifications.”

    In other words pard, the bacterial flagellum is not irreducibly complex because the TTSS is likely a simpler precursor or component part right? Which means that the bacterial flagellum in its own right can not proven to be intelligently designed. It likely evolved from the coupling of simpler biological machines with small modifications and they in turn from even smaller machines or molecules. I think the mistake you are making is to calculate the odds in linear fashion of the end product formed step by step instead of looking at the odds of smaller biological machines hooking up at random and then being naturally selected.

    The Krebs Cycle is another example of a combination of smaller precursor cycles combining. This is where both your assumptions and math fail you in my layman’s estimation as you advised me to make and not rely on the experts! 🙂

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    • In other words pard, the bacterial flagellum is not irreducibly complex because the TTSS is likely a simpler precursor or component part right? Which means that the bacterial flagellum in its own right can not proven to be intelligently designed.

      That’s just the point! The motility function of the rotary bacterial flagellum is not reducible below its minimum structural threshold requirement. Below this threshold level, you will not be able to achieve the motility function to any useful degree. In other words, you can’t produce a rotary bacterial flagellum with just 100aa or even 1000aa – regardless of how they’re put together. Rather, such a system requires coding for several thousand specifically arranged amino acid residues, within a couple dozen different structural proteins, at minimum, before the rotary flagellar motility function can be realized.

      Now, as far as evolvability is concerned, it matters not if smaller subsystems might still retain their functionality (like the radio still working in your car when the engine is taken away). The higher level system, and it’s minimum structural threshold requirements, will not be evolved regardless of what lower level systems exist that might be put together in novel ways to form higher level systems. Why not? Because, too many non-selectable modifications would be required to do the job beyond very low levels of functional complexity.

      You don’t seem to understand the concept of minimum structural threshold requirements. You have this popular but mistaken idea that if any smaller functional system can be found within the larger system that the larger more complex system can therefore easily evolve via the simple linking together of smaller systems. Well, that’s just not true. It isn’t nearly as simple as you imagine to get smaller systems to link up properly. And, it gets exponentially more and more difficult to get this to happen with each linear increase in the level of functional complexity (i.e., minimum structural threshold requirements).

      It likely evolved from the coupling of simpler biological machines with small modifications and they in turn from even smaller machines or molecules.

      That certainly is the evolutionary story of how it “likely” happened. Your problem is that you haven’t sat down and calculated the odds like I asked you to do – nor have you read my argument on why this story becomes exponentially less and less tenable with each step up the ladder of functional complexity. Why not at least read through the statistical argument that falsifies this story of yours?

      I think the mistake you are making is to calculate the odds in linear fashion of the end product formed step by step instead of looking at the odds of smaller biological machines hooking up at random and then being naturally selected.

      Not true. I do in fact calculate the odds of “smaller biological machines hooking up at random” to form selectably beneficial higher level systems. That’s exactly the kind of odds I’m talking about. I’m not talking about evolving something completely from scratch! – not at all. Take whatever smaller systems you want. Put them into the same gene pool, and calculate the odds that they will randomly mutate so that they can attach themselves together in the proper manner to form higher level systems.

      What are the odds? Well, the odds are pretty good when your talking about very small systems – comparable to 3-letter words and such. However, the odds of anything hooking up to produce a system that requires more than 1000 specifically arranged characters (amino acid residues in this case) are extraordinarily unlikely this side of trillions upon trillions of years of time.

      Please do actually try to read through the argument and/or do a little of the math yourself.

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

      The Krebs Cycle is another example of a combination of smaller precursor cycles combining. This is where both your assumptions and math fail you in my layman’s estimation as you advised me to make and not rely on the experts!

      First off, the Krebs Cycle is an enzymatic cascade. It is not a machine that requires a specific 3D orientation of all of its parts in order to function. Such cascading systems are not much more complex, statistically speaking, than the most complex single protein part in the cycle. In other words, such enzymatic cascades are not like a flagellar motility system were all of the parts are required to be in a specific orientation relative to all of the other parts at the same time for the function in question to be realized. In fact, one can remove most of the enzymes from the cascading system without a complete loss of the same basic type of selectable function – energy production for the cell. This is not true of the flagellar system where a removal of the minimum part requirement will result in a complete loss of the motility function.

      Now, please, do some actual math…

      Sean Pitman
      http://www.DetectingDesign.com

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  6. As bible Christians, we have the “luxury” of appealing to a creator God who is beyond a scientific “proof”. We can even call it “spiritual magic” if we please.

    You evolutionists have no such luxury. Since you demand “proof” by way of science, we agree. Where is your proof? We are waiting……..!!!!

    But you have none, and you know it. All you can say is, “We don’t believe what the bible says, but we have no viable alternative.”

    All you can do is stumble all over yourselves and each other with massive doses of affirmation of your unbelief in the bible. You have nothing for the bible believing Christian community, but expect us to be impressed by your total inability to give us any viable alternative.

    So, your view is an insult to a bible believeing Christian. We freely admit there is no scientific “proof” that there is a “god” who can create. But we believe what we accept is a far better alternative with a rational basis for acceptance by way of ID, by a being who is able to create. The systematic order of all we see and can investigate affirms this conclusion.

    We don’t claim we can explain all their is to know about God. or, how He can create. So what? We don’t need to. But you “need” to prove your view since you claim there can be no “magic” in creation. And as soon as you admit some aspect of “magic”, you have just negated your whole reason to oppose the God of the bible.

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  7. “That’s just the point! The motility function of the rotary bacterial flagellum is not reducible below its minimum structural threshold requirement. Below this threshold level, you will not be able to achieve the motility function to any useful degree. In other words, you can’t produce a rotary bacterial flagellum with just 100aa or even 1000aa – regardless of how they’re put together. Rather, such a system requires coding for several thousand specifically arranged amino acid residues, within a couple dozen different structural proteins, at minimum, before the rotary flagellar motility function can be realized.”

    Isn’t ATP synthase a smaller, molecular, rotary motor found in the membranes of all bacteria? Is so is the rotary function of the bacterial function truly not reducible?

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    • Isn’t ATP synthase a smaller, molecular, rotary motor found in the membranes of all bacteria? Is so is the rotary function of the bacterial function truly not reducible?

      ATPsynthase is a complex machine that requires a minimum of several thousand specifically arranged amino acid residues. The same thing is true for rotary flagellar motility.

      Of course, the current wild-type systems can be reduced without a complete loss of the motility function (or ATPsynthase function). However, there is a structural limit below which further reduction is impossible. For rotary flagellar motility, this structural limit, this minimum structural threshold requirement, is several thousand (over 5000aa) specifically arranged amino acid residue positions.

      It is this minimum structural threshold limit that defines the “functional complexity” of a system and is the basis for determining its evolvabilty in a given span of time.

      Sean Pitman
      http://www.DetectingDesign.com

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  8. Howdy Pard

    I’ve been doing a lot of reading about that rebellious little molecular machine ATP Synthase. Looks like this ubiquitous little critter might provide some evidence between the common ancestry between Cyanobacteria and chloroplasts. Just wondering if you have done any math on the odds of ATP Synthase evolving from smaller subunits and the rotary motor of the bacterial flagellum evolving from ATP synthase?

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    • Have you done the math? or are you just accepting the stories without any statistical analysis on the odds of subsystems coming together to form larger more complex systems?

      As you know, I have done the math. I’ve given you the link to the statistical argument on my website several times now. Where is your statistical argument? I’ve failed to see you even try to present evidence along these lines…

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  9. “ATPsynthase is a complex machine that requires a minimum of several thousand specifically arranged amino acid residues. The same thing is true for rotary flagellar motility.”

    So what you are tellin’ me pard is both these two little rotary molecular engines are not related in origin but designed by the same feller? Hmmm… wonder why he designed two for the same rotary function? Bit redundant don’t ya think? I don’t think we need too much advanced math to ponder that one pard.

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    • So what you are tellin’ me pard is both these two little rotary molecular engines are not related in origin but designed by the same feller? Hmmm… wonder why he designed two for the same rotary function? Bit redundant don’t ya think? I don’t think we need too much advanced math to ponder that one pard.

      First off, these two very different machines have very different functions which require very different designs. One machine produces ATP, the energy currency of the cell, while the other produces motility. Why would anyone expect that such systems would require the exact same design?

      Secondly, since when is redundancy evidence that something is not designed? Lots of things humans design contain redundancies. Yet, they are still clearly designed.

      Sean Pitman
      http://www.DetectingDesign.com

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  10. “Such just-so story telling might be entertaining, but these stories are not demonstrable. There are no examples of evolution in action, by emergence or RM/NS, producing any such machine beyond very very low levels of functional complexity. And, statistically, these stories are absolutely untenable. The only thing left to hold them up is an appeal to some mystical magical process – not science.”

    I’m sorry Dr. Pitman, but I’m struggling with your logic. Are you saying you have demonstrable proof that the world was created in six days about 8000 years ago? You call evolution a just so story but how does this differ empirically from biblical creation?

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  11. In the Spectrum article, Kootsey wrote, “These termites have no leadership structure and no internal blueprint from which to work . . .” I took the phrase, “no internal blueprint from which to work” to mean that the mound-building behavior is not genetically programmed, or least not known to be genetically programmed. If in fact the termites are genetically programmed to produce this type of mound under certain conditions–as you say in your piece–then there is no mystery and no need to invoke the murky concept of “emergence” to explain the mounds.

    Does anyone know whether there’s been any genetic research done on these insects to try to explain the mound-building behavior?

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  12. “We freely admit there is no scientific “proof” that there is a “god” who can create.”

    I agree with you on that one and don’t begrudge your faith whatsoever, just like I don’t begrudge the faith of Catholics, Buddhists, Baptists, Muslims, Hindus, Jews… Faith is the free choice of the individual while Science needs to meet the objective standards of its discipline.

    You understand the danger of ID to the faith crowd and your concern is well warranted.

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  13. “No. I’m saying that the weight of evidence is most consistent with the Biblical account – to include evidence that living things require intelligent design and that the age of life on this planet is young.”

    Right, so because you can’t specifically demonstrate or prove biblical creation you rely on your subjective weight of the evidence. But when it comes to evolution, you acknowledge micro evolution, you acknowledge that RMNS works at a certain level, you know that DR. Ben Clausen of the GRI has stated that there is no viable scientific young earth or young life model. Yet you call evolution the just so story. Hmmm….seems like you have a bit of a double standard there, pard!

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    • Right, so because you can’t specifically demonstrate or prove biblical creation you rely on your subjective weight of the evidence.

      The “weight of evidence” is the basis of science. You do realize that nothing is absolutely provable in science? All there is as a basis for scientific belief is the “weight of evidence” or “predictive value” of a hypothesis or theory.

      But when it comes to evolution, you acknowledge micro evolution, you acknowledge that RMNS works at a certain level,

      Of course. It is the extrapolation from lower-level examples to higher-levels of evolution that isn’t scientifically or statistically rational or tenable or demonstrable. In other words, it isn’t scientific.

      you know that DR. Ben Clausen of the GRI has stated that there is no viable scientific young earth or young life model.

      I know he says this and believes this, but I think he is wrong. There is a very good young-life model – the Biblical model. This model has the weight of evidence clearly on its side for those who take the time to candidly consider it.

      Yet you call evolution the just so story. Hmmm….seems like you have a bit of a double standard there, pard!

      I’m asking from you just what I would ask from anyone proposing a rational hypothesis or theory – including myself. I’m not asking anything from you that I’m not willing to do myself.

      For example, I’ve done the statistical analysis and calculations for random mutations finding novel beneficial sequences within various levels of sequence space. Where have you presented any relevant calculations or mathematical analyses of any kind to support your arguments for the creative potential of RM/NS? – anything beyond just-so story telling?

      I’m sorry, but you seem to be the one with the double standard here…

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  14. Pard,

    I cited you a mathematical study as to the plausibility of evolution, you just don’t agree with it, which of course is your right. But please don’t say I didn’t supply it or the cited study is just so story telling.

    It seems to me that the subjective weight of the evidence for the individual is worth very little until such time as it is adopted my a majority of scientists as being correct. And I agree that Science is always falsifiable. Might evolution be wrong? Certainly, but no credible scientific theory, according to the scientific community, has come along to replace it yet, including ID. And frankly I’m glad of ID hypotheses, because they are challenging cause and effect natural mechanisms and making them meet the grade.

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    • I’ve asked you for the math that addresses function-based selection (i.e., natural selection). Your cited study doesn’t explain how a function-based selection mechanism can produce much of anything beyond very low levels of functional complexity. This paper doesn’t even address the concept of function-based selection. So, I ask you yet again, where’s your math? Where is anything beyond just-so story telling to support your assertion that natural selection is the fantastic creative force you claim it to be?

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  15. In the Spectrum article, Kootsey wrote, “These termites have no leadership structure and no internal blueprint from which to work . . .” I took the phrase, “no internal blueprint from which to work” to mean that the mound-building behavior is not genetically programmed, or least not known to be genetically programmed. If in fact the termites are genetically programmed to produce this type of mound under certain conditions–as you say in your piece–then there is no mystery and no need to invoke the murky concept of “emergence” to explain the mounds.

    Does anyone know whether there’s been any genetic research done on these insects to try to explain the mound-building behavior?

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  16. “Such just-so story telling might be entertaining, but these stories are not demonstrable. There are no examples of evolution in action, by emergence or RM/NS, producing any such machine beyond very very low levels of functional complexity. And, statistically, these stories are absolutely untenable. The only thing left to hold them up is an appeal to some mystical magical process – not science.”

    I’m sorry Dr. Pitman, but I’m struggling with your logic. Are you saying you have demonstrable proof that the world was created in six days about 8000 years ago? You call evolution a just so story but how does this differ empirically from biblical creation?

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  17. “ATPsynthase is a complex machine that requires a minimum of several thousand specifically arranged amino acid residues. The same thing is true for rotary flagellar motility.”

    So what you are tellin’ me pard is both these two little rotary molecular engines are not related in origin but designed by the same feller? Hmmm… wonder why he designed two for the same rotary function? Bit redundant don’t ya think? I don’t think we need too much advanced math to ponder that one pard.

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    • So what you are tellin’ me pard is both these two little rotary molecular engines are not related in origin but designed by the same feller? Hmmm… wonder why he designed two for the same rotary function? Bit redundant don’t ya think? I don’t think we need too much advanced math to ponder that one pard.

      First off, these two very different machines have very different functions which require very different designs. One machine produces ATP, the energy currency of the cell, while the other produces motility. Why would anyone expect that such systems would require the exact same design?

      Secondly, since when is redundancy evidence that something is not designed? Lots of things humans design contain redundancies. Yet, they are still clearly designed.

      Sean Pitman
      http://www.DetectingDesign.com

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  18. “We freely admit there is no scientific “proof” that there is a “god” who can create.”

    I agree with you on that one and don’t begrudge your faith whatsoever, just like I don’t begrudge the faith of Catholics, Buddhists, Baptists, Muslims, Hindus, Jews… Faith is the free choice of the individual while Science needs to meet the objective standards of its discipline.

    You understand the danger of ID to the faith crowd and your concern is well warranted.

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  19. “No. I’m saying that the weight of evidence is most consistent with the Biblical account – to include evidence that living things require intelligent design and that the age of life on this planet is young.”

    Right, so because you can’t specifically demonstrate or prove biblical creation you rely on your subjective weight of the evidence. But when it comes to evolution, you acknowledge micro evolution, you acknowledge that RMNS works at a certain level, you know that DR. Ben Clausen of the GRI has stated that there is no viable scientific young earth or young life model. Yet you call evolution the just so story. Hmmm….seems like you have a bit of a double standard there, pard!

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    • Right, so because you can’t specifically demonstrate or prove biblical creation you rely on your subjective weight of the evidence.

      The “weight of evidence” is the basis of science. You do realize that nothing is absolutely provable in science? All there is as a basis for scientific belief is the “weight of evidence” or “predictive value” of a hypothesis or theory.

      But when it comes to evolution, you acknowledge micro evolution, you acknowledge that RMNS works at a certain level,

      Of course. It is the extrapolation from lower-level examples to higher-levels of evolution that isn’t scientifically or statistically rational or tenable or demonstrable. In other words, it isn’t scientific.

      you know that DR. Ben Clausen of the GRI has stated that there is no viable scientific young earth or young life model.

      I know he says this and believes this, but I think he is wrong. There is a very good young-life model – the Biblical model. This model has the weight of evidence clearly on its side for those who take the time to candidly consider it.

      Yet you call evolution the just so story. Hmmm….seems like you have a bit of a double standard there, pard!

      I’m asking from you just what I would ask from anyone proposing a rational hypothesis or theory – including myself. I’m not asking anything from you that I’m not willing to do myself.

      For example, I’ve done the statistical analysis and calculations for random mutations finding novel beneficial sequences within various levels of sequence space. Where have you presented any relevant calculations or mathematical analyses of any kind to support your arguments for the creative potential of RM/NS? – anything beyond just-so story telling?

      I’m sorry, but you seem to be the one with the double standard here…

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  20. Pard,

    I cited you a mathematical study as to the plausibility of evolution, you just don’t agree with it, which of course is your right. But please don’t say I didn’t supply it or the cited study is just so story telling.

    It seems to me that the subjective weight of the evidence for the individual is worth very little until such time as it is adopted my a majority of scientists as being correct. And I agree that Science is always falsifiable. Might evolution be wrong? Certainly, but no credible scientific theory, according to the scientific community, has come along to replace it yet, including ID. And frankly I’m glad of ID hypotheses, because they are challenging cause and effect natural mechanisms and making them meet the grade.

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    • I’ve asked you for the math that addresses function-based selection (i.e., natural selection). Your cited study doesn’t explain how a function-based selection mechanism can produce much of anything beyond very low levels of functional complexity. This paper doesn’t even address the concept of function-based selection. So, I ask you yet again, where’s your math? Where is anything beyond just-so story telling to support your assertion that natural selection is the fantastic creative force you claim it to be?

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  21. Thanks, Sean, for your excellent response!

    Describing emergence as a creative force is an attempt at crediting nature for what God does or has done in the past. Trying to negate the evidence of design in nature is the epitome of foolishness. This is the result of insisting in the use of the so called methodological naturalism, which precludes any credit to a Creator.

    I can understand why those who prefer to ignore a Creator would resort to such extreme lack of common sense, but I can’t figure out why those who by their membership in a Christian organization would waste their time with such nonsense.

    Why would a believer in a Creator invest so much time in pretending that nature and the laws of nature could be explained without the intervention of a Creator or a Designer?

    Christian scientists already have the answer to the question of intelligent design. Why pretending that they don’t?

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  22. “Yes, the TTSS system is very similar to a structure of 10 proteins out of the 40 or so proteins that form the rotary flagellum.”

    “Because, adapting parts that used to work in other systems doing other jobs to work together requires various small modifications.”

    In other words pard, the bacterial flagellum is not irreducibly complex because the TTSS is likely a simpler precursor or component part right? Which means that the bacterial flagellum in its own right can not proven to be intelligently designed. It likely evolved from the coupling of simpler biological machines with small modifications and they in turn from even smaller machines or molecules. I think the mistake you are making is to calculate the odds in linear fashion of the end product formed step by step instead of looking at the odds of smaller biological machines hooking up at random and then being naturally selected.

    The Krebs Cycle is another example of a combination of smaller precursor cycles combining. This is where both your assumptions and math fail you in my layman’s estimation as you advised me to make and not rely on the experts! 🙂

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    • In other words pard, the bacterial flagellum is not irreducibly complex because the TTSS is likely a simpler precursor or component part right? Which means that the bacterial flagellum in its own right can not proven to be intelligently designed.

      That’s just the point! The motility function of the rotary bacterial flagellum is not reducible below its minimum structural threshold requirement. Below this threshold level, you will not be able to achieve the motility function to any useful degree. In other words, you can’t produce a rotary bacterial flagellum with just 100aa or even 1000aa – regardless of how they’re put together. Rather, such a system requires coding for several thousand specifically arranged amino acid residues, within a couple dozen different structural proteins, at minimum, before the rotary flagellar motility function can be realized.

      Now, as far as evolvability is concerned, it matters not if smaller subsystems might still retain their functionality (like the radio still working in your car when the engine is taken away). The higher level system, and it’s minimum structural threshold requirements, will not be evolved regardless of what lower level systems exist that might be put together in novel ways to form higher level systems. Why not? Because, too many non-selectable modifications would be required to do the job beyond very low levels of functional complexity.

      You don’t seem to understand the concept of minimum structural threshold requirements. You have this popular but mistaken idea that if any smaller functional system can be found within the larger system that the larger more complex system can therefore easily evolve via the simple linking together of smaller systems. Well, that’s just not true. It isn’t nearly as simple as you imagine to get smaller systems to link up properly. And, it gets exponentially more and more difficult to get this to happen with each linear increase in the level of functional complexity (i.e., minimum structural threshold requirements).

      It likely evolved from the coupling of simpler biological machines with small modifications and they in turn from even smaller machines or molecules.

      That certainly is the evolutionary story of how it “likely” happened. Your problem is that you haven’t sat down and calculated the odds like I asked you to do – nor have you read my argument on why this story becomes exponentially less and less tenable with each step up the ladder of functional complexity. Why not at least read through the statistical argument that falsifies this story of yours?

      I think the mistake you are making is to calculate the odds in linear fashion of the end product formed step by step instead of looking at the odds of smaller biological machines hooking up at random and then being naturally selected.

      Not true. I do in fact calculate the odds of “smaller biological machines hooking up at random” to form selectably beneficial higher level systems. That’s exactly the kind of odds I’m talking about. I’m not talking about evolving something completely from scratch! – not at all. Take whatever smaller systems you want. Put them into the same gene pool, and calculate the odds that they will randomly mutate so that they can attach themselves together in the proper manner to form higher level systems.

      What are the odds? Well, the odds are pretty good when your talking about very small systems – comparable to 3-letter words and such. However, the odds of anything hooking up to produce a system that requires more than 1000 specifically arranged characters (amino acid residues in this case) are extraordinarily unlikely this side of trillions upon trillions of years of time.

      Please do actually try to read through the argument and/or do a little of the math yourself.

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

      The Krebs Cycle is another example of a combination of smaller precursor cycles combining. This is where both your assumptions and math fail you in my layman’s estimation as you advised me to make and not rely on the experts!

      First off, the Krebs Cycle is an enzymatic cascade. It is not a machine that requires a specific 3D orientation of all of its parts in order to function. Such cascading systems are not much more complex, statistically speaking, than the most complex single protein part in the cycle. In other words, such enzymatic cascades are not like a flagellar motility system were all of the parts are required to be in a specific orientation relative to all of the other parts at the same time for the function in question to be realized. In fact, one can remove most of the enzymes from the cascading system without a complete loss of the same basic type of selectable function – energy production for the cell. This is not true of the flagellar system where a removal of the minimum part requirement will result in a complete loss of the motility function.

      Now, please, do some actual math…

      Sean Pitman
      http://www.DetectingDesign.com

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  23. Nick Samoljok wrote “This is the result of insisting in the use of the so called methodological naturalism, which precludes any credit to a Creator.”

    Funny, Sean Pitman actually advocates methodological naturalism as a way of validating God’s existence. According to him, any a priori assumption regarding GOd’s existence or the Bible’s accuracy is blind faith. God adheres to his own natural laws; Satan cannot contravene those laws; and we can therefore trust what science informs us (until the science itself becomes colored by blind faith, which he insists atheists do all the time).

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    • Unlike methodological naturalism (a philosophical position that attributes everything, ultimately, to mindless “raw” forces of nature) the Bible itself argues that nature herself speaks eloquently for the existence of her Creator and His creative power:

      The heavens declare the glory of God; the skies proclaim the work of his hands. – Psalms 19:1

      For since the creation of the world God’s invisible qualities–his eternal power and divine nature–have been clearly seen, being understood from what has been made, so that people are without excuse. – Romans 1:20

      The God of the Bible does not appeal to or expect blind or “a priori” belief or faith in His existence or His character, but offers up abundant evidence as a basis for an intelligent trust in His existence, His character, and in the credibility of His Word, the Bible.

      In any case, the concept of fideism has already been extensively discussed in this forum and there is no need to rehash it all…

      Sean Pitman
      http://www.DetectingDesign.com

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  24. Excellent article. My good pard shows that he isn’t scared to tackle opposing views, even within the Adventist ranks. I presume Dr. Kootsey is an Advenist from his cv?

    Now about that ole tail on the bug and whether it can be broken down into smaller parts. Isn’t it true that the Type III Secretiry System is similar to the protein structure of the flagellum?

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    • Yes, the TTSS system is very similar to a structure of 10 proteins out of the 40 or so proteins that form the rotary flagellum. It’s like removing the engine of a car and having the lights or radio still work. It is very easy to remove parts from a system while maintaining the function of various subsystems. However, doing the reverse cannot be done with the same ease.

      It is not just as easy to randomly add parts to a system to produce a more complex system that requires a greater minimum number of parts. Why not? Because, adapting parts that used to work in other systems doing other jobs to work together requires various small modifications. The greater the minimum part requirement for the more complex system the greater the number of these required modifications to get the subparts to work together properly. And, with each linear increase in the number of required modifications, the amount of time required to achieve these modifications, via random mutations, increases exponentially.

      Sean Pitman
      http://www.DetectingDesign.com

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  25. The following exchange is taken from a discussion on the Spectrum blog – Sean Pitman

    Are we back to Magic?

    Stuart Kauffman, “I wish to say that life is an expected[?], emergent [define?] property of complex chemical reaction networks.”

    What chemical reactions simple allow digital code to appear??? Kauffman does not deal with the mechanism for this non-sense but posits that this is so. Where is the lab work demonstrating this spontaneous generation??

    Kauffman calls this “natural magic.” In a lecture at MIT he stated,

    “Life bubbles forth in a natural magic beyond the confines of entailing laws. This allows us to be “reenchanted” with nature and find a way beyond modernity.”

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    • Your comments are spot on. We creationists aren’t the one’s appealing to magic beyond design abilities and intelligence that we ourselves are capable of producing to at least some degree. Rather, the Darwinists are the ones who have been reduced to such mindless appeals to magic where things “poof” into existence for no apparent reason – without any guidance from any kind of intelligent designer or even any rational laws of nature which are actually known or apparently testable or discoverable by any empirical means…

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      • because it (allegedly) magically happened only some 6000 yrs ago…isn’t the YEC “magic” harder to believe than the philosophically labeled “magic” alluded to by scientists which took mega years to happen as the evidence in the rocks shows?

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        • Four billion years might seem like a long time to some, but it is the tiniest drop in the bucket compared to the time that would be required for even a small subcellular biomachine, like a rotary bacterial flagellum for example, to be produced by any known “raw” force of mindless nature. The production of any machine at this level of functional complexity is extraordinarily unlikely to be produced by random mutations and function-based natural selection, or any other mechanism like “emergence”, this side of trillions upon trillions of years of time.

          Intelligent design, on the other hand, can and does produce such machines in real time in very short order.

          So, which theory is most rationally and statistically tenable? Certainly not your theory of a few billion years of randomness and chaotic interactions guided by mindless natural mechanisms. Such a notion is truly magical – not at all “scientific”.

          Such just-so story telling might be entertaining, but these stories are not demonstrable. There are no examples of evolution in action, by emergence or RM/NS, producing any such machine beyond very very low levels of functional complexity. And, statistically, these stories are absolutely untenable. The only thing left to hold them up is an appeal to some mystical magical process – not science.

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      • Alchemy was once called “science,” but today we know it as the “magician’s trick.” All life was magic to our ancestors who had no understanding or control of what they observed: rainbows, volcanoes, earthquakes; all were attributed to gods or mysterious forces.

        Today, scientists seek to tear apart the atom and understand “how” things function. They have explanations for much that was previously unknown. Why should we dismiss their findings only in certain areas? We eagerly greet their new discoveries if offering cures for dreaded diseases, but dismiss those that are counter to our religious beliefs. Religion is not antithetical to science, nor should it be; they must work together rather than attempt to destroy the other.

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        • I certainly agree that useful religion and true science have the same Source and therefore should be in harmony. However, when scientists start arguing for the magical appearance of biological complexity by appeals to some mystical kind of “emergence”, that’s not science or useful religion. That’s just blind faith in some kind of naturalistic philosophy.

          It’s fine to try to discover the limits of what naturalistic mechanisms can explain. However, to define science as “methodological naturalism”, in a way that rules out any ability to detect the activities of intelligent design of any kind behind various features of living things, isn’t scientific or empirically rational. And, it isn’t consistent with other mainstream sciences that are based on the ability to detect intelligent design behind various phenomena – to include forensic science, anthropology, and even SETI science.

          How long should SETI scientists look for some mindless “raw” force of nature to explain the types of radio signals that currently have no known natural explanation? – before they can rationally conclude that such signals would indeed be very good evidence of true artefacts of intelligent design?

          You see, just because somethings that where once thought to require intelligent design are now known to be produced by mindless natural forces doesn’t therefore mean that everything can therefore be explain by mindless “raw” forces of nature. Such a conclusion is based on a non-falsifiable logical fallacy, not valid science.

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  26. Howdy Pard

    I’ve been doing a lot of reading about that rebellious little molecular machine ATP Synthase. Looks like this ubiquitous little critter might provide some evidence between the common ancestry between Cyanobacteria and chloroplasts. Just wondering if you have done any math on the odds of ATP Synthase evolving from smaller subunits and the rotary motor of the bacterial flagellum evolving from ATP synthase?

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    • Have you done the math? or are you just accepting the stories without any statistical analysis on the odds of subsystems coming together to form larger more complex systems?

      As you know, I have done the math. I’ve given you the link to the statistical argument on my website several times now. Where is your statistical argument? I’ve failed to see you even try to present evidence along these lines…

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  27. “That’s just the point! The motility function of the rotary bacterial flagellum is not reducible below its minimum structural threshold requirement. Below this threshold level, you will not be able to achieve the motility function to any useful degree. In other words, you can’t produce a rotary bacterial flagellum with just 100aa or even 1000aa – regardless of how they’re put together. Rather, such a system requires coding for several thousand specifically arranged amino acid residues, within a couple dozen different structural proteins, at minimum, before the rotary flagellar motility function can be realized.”

    Isn’t ATP synthase a smaller, molecular, rotary motor found in the membranes of all bacteria? Is so is the rotary function of the bacterial function truly not reducible?

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    • Isn’t ATP synthase a smaller, molecular, rotary motor found in the membranes of all bacteria? Is so is the rotary function of the bacterial function truly not reducible?

      ATPsynthase is a complex machine that requires a minimum of several thousand specifically arranged amino acid residues. The same thing is true for rotary flagellar motility.

      Of course, the current wild-type systems can be reduced without a complete loss of the motility function (or ATPsynthase function). However, there is a structural limit below which further reduction is impossible. For rotary flagellar motility, this structural limit, this minimum structural threshold requirement, is several thousand (over 5000aa) specifically arranged amino acid residue positions.

      It is this minimum structural threshold limit that defines the “functional complexity” of a system and is the basis for determining its evolvabilty in a given span of time.

      Sean Pitman
      http://www.DetectingDesign.com

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  28. As bible Christians, we have the “luxury” of appealing to a creator God who is beyond a scientific “proof”. We can even call it “spiritual magic” if we please.

    You evolutionists have no such luxury. Since you demand “proof” by way of science, we agree. Where is your proof? We are waiting……..!!!!

    But you have none, and you know it. All you can say is, “We don’t believe what the bible says, but we have no viable alternative.”

    All you can do is stumble all over yourselves and each other with massive doses of affirmation of your unbelief in the bible. You have nothing for the bible believing Christian community, but expect us to be impressed by your total inability to give us any viable alternative.

    So, your view is an insult to a bible believeing Christian. We freely admit there is no scientific “proof” that there is a “god” who can create. But we believe what we accept is a far better alternative with a rational basis for acceptance by way of ID, by a being who is able to create. The systematic order of all we see and can investigate affirms this conclusion.

    We don’t claim we can explain all their is to know about God. or, how He can create. So what? We don’t need to. But you “need” to prove your view since you claim there can be no “magic” in creation. And as soon as you admit some aspect of “magic”, you have just negated your whole reason to oppose the God of the bible.

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