Monday, January 17, 2011

The Hierarchy of Evolutionary Apologetics: Protein Evolution Case Study

A common retort from evolution’s defenders is that all those scientists can’t be wrong. Is it conceivable that so many scientific papers and reports, with their conclusions about evolution, are making the same mistake? Before answering this we first must understand the hierarchy of the evolution apologetics literature. At the base of the pyramid are the scientific papers documenting new research findings. Next up are the review papers that organize and summarize the state of the research. And finally there is the popular literature, such as newspaper and magazine articles, and books. Across this hierarchy evolutionists make different types of claims that should not be blindly lumped together. Yes, there are problems across the spectrum, but they tend to be different kinds of problems.

Background: The Hierarchy of Evolutionary Apologetics

Scientific papers document important and perfectly legitimate research. The results are usually presented carefully and rarely are they exaggerated. And it is difficult to find such papers claiming that evolution is a fact.

These papers do, however, discuss the results strictly in terms of evolution. No matter how unlikely evolution is given the results, they are interpreted as though evolution were the only explanation. Problematic results, and they are common, are not allowed to suggest epistemological challenges. They may only pose theoretical problems.

The authors cannot suggest that we may not, after all, know evolution to be a fact. They may only point out our ignorance of how it is supposed to have occurred. In all of this it is difficult to avoid misrepresentations of the research results, but such blunders are limited by the narrow scope of such papers.

Review and survey papers, on the other hand, do make more expansive evolutionary claims. These review papers draw on the vast body of research literature to organize and summarize the state of the research. They draw broader conclusions, and when discussing the subject of evolution these papers are more likely to make obviously unsupportable evolutionary claims.

Finally the popular literature is the next step beyond the review papers. If the review papers are summaries for scientists, the popular literature provides summaries for the non scientific audience. It is here that the dogmatic, sweeping evolutionary claims are most prevalent. Evolution must be a fact, all the scientific evidence unquestionably supports and proves evolution, doubters have nothing but nefarious motivations, there is war between science and religion, and so forth.

In terms of sheer magnitude, the first category—the narrowly focused research papers—dominates the literature. And here there is far less speculation and far more technical detail. Problems do arise in the evolutionary interpretations of the results, but such speculation is a minor part of the paper.

But like toxic pollutants that accumulate and reach increasing concentrations at higher levels of the food chain, the speculation becomes amplified in the review papers, and then even more so in the popular literature. Like a morphing rumor, what begins as tentative and unlikely speculation of how evolution might account for problematic findings ultimately becomes yet another evolutionary proof text in the popular literature.

So when evolutionists argue that those scientific papers and reports cannot all be wrong, we might agree with them. The technical details of the scientific research are certainly not wrong. True, there are misrepresentations of science when the results are force fit into evolution, but the far more egregious misrepresentations of science are found as one moves up the hierarchy of the evolution literature.

Case study: Protein evolution

Imagine a choppy ocean filled with waves for as far as the eye can see. Meanwhile the sky is dotted with an occasional jet airliner flying far above. This scene gives an idea of what science is telling us about protein evolution. A protein consists of hundreds of amino acids glued together in a long sequence. Because nature uses 20 different amino acids, the total number of possible sequences is astronomically huge. For a protein with 300 amino acids in all, for instance, there are 20^300 (roughly equal to a one followed by 390 zeros) different possible sequences.

It is an ocean of possibilities. But the vast majority of these possible amino acid sequences are worthless to evolution. Not only are they essentially dysfunctional themselves, but even as evolutionary starting points they don’t lead to much better designs. If you evolve a typical randomly selected amino acid sequence, you can improve the design a bit, but the search quickly stagnates.

Like the choppy ocean, the protein function landscape seems to be filled with a great many swells. Evolution can move up from the bottom of a swell to the top of a nearby wave, but this is only a minor improvement in the protein function. Go any further and evolution would fall into the neighboring swell, leaving it no better off than when it started.

Very rarely, in this seemingly endless sea of minor ups and downs, an extremely efficient, functional protein punctuates the protein function landscape. Here the landscape rapidly shoots up into the sky. This is not a gradual rise leading to these lofty and tiny regions of functional proteins. Rather, the landscape abruptly rises to heights far above the ocean’s surface. Like the jet airliners flying far above the ocean, proteins appear to be rare events in an otherwise non descript landscape.

Several types of protein studies point to this conclusion. Some of these studies begin with random amino acid sequences and attempt to evolve them toward nature’s proteins or something like them. These studies show that only minor functionality can be evolved from random starting points. Nature’s marvels, or anything like them, are so astronomically rare evolution would never find them using its blind, adaptive walk. (This is to say nothing of how the machinery for such a search could have evolved in the first place.)

Other studies begin not with a random amino acid sequence, but rather work backwards from a known protein. These studies show that proteins are quite sensitive. The function of a typical protein exponentially degrades as random mutations are introduced.

Whether we start at the beginning or the end, the science tells us that the protein function landscape is not one of smooth funnels leading to fantastic molecular machines, as evolution would expect.

And as it seems to be with so much of biology, when scientists work with nature’s designs some fascinating engineering can be done. Just as the design of a jet aircraft can be adjusted and augmented to meet a new performance requirement, so too proteins can be adapted to meet desired properties. And just as engines or other components can sometimes be swapped between aircraft, so too proteins are marvelously modular, allowing for new designs to be created by mixing and matching.

Unfortunately evolutionists routinely conflate such design engineering with evolutionary possibilities. Proteins are adaptable, so can’t they gradually evolve? Proteins are module, so can’t they just swap designs when gradualism fails? The science contradicts such conclusions, but evolutionists are driven more by their theory than by the data. Here are two examples.

An example research paper

In this research paper, evolutionists investigated how proteins might have evolved. They attempted to demonstrate the evolution of a virus—a molecular machine consisting of several proteins—in the laboratory. To simplify the problem they started with all but a small part of the virus intact. They randomized the amino acid sequence of one part of one of the viral proteins, and they repeatedly evolved that randomized segment in hopes of reconstructing the entire virus.

What they discovered was that the evolutionary process could produce only tiny levels of functionality (in this case the virus’ ability to infect a host). Their evolved sequences showed no similarity to the native sequence which is supposed to have evolved. And the best virus they could produce, even with the vast majority of the virus already intact, was several orders of magnitude weaker than nature’s virus.

The reason their evolutionary process failed was that the search for better amino acid sequences, that would improve the virus’ ability to infect the host, became too difficult. A possible evolutionary explanation for these disappointing results is that in such a limited laboratory study, the evolutionists were simply unable to reproduce what the vast resources of nature could produce. Perhaps in the course of time evolution could evolve what the evolutionists could not do in the laboratory.

But the results refuted even this fall back explanation. In fact, the evolutionists would not merely need an expanded study with more time in the laboratory, they would need more time than evolution ever had—many times over. The number of experiments they would need to conduct in order to have any hope of evolving a virus that rivals nature’s version is difficult to compute. But it is at least 10^70 (a one followed by 70 zeros).

And yet, there it is. This relatively short sequence of amino acids exists as part of of the virus, with its fantastically high infection capabilities. And of course this is not merely a problem for a part of one protein, in one virus. It is a problem for all life, for proteins are crucial molecular machines throughout biology.

But not surprisingly the evolutionists interpreted their results according to their theory. The majority of the paper presents the detailed scientific results. There is no misinterpretation or exaggeration, until that is, the discussion of the implications for evolution. The evolutionists write:

Such a huge search is impractical and implies that evolution of the wild-type phage must have involved not only random substitutions but also other mechanisms, such as homologous recombination.

Homologous recombination? It would be difficult to imagine a more unlikely explanation. Homologous recombination is a complex genetic mechanism assisted by finely-tuned proteins. It is circular to recruit such a mechanism for the initial evolution of proteins—for no such mechanism is likely to have existed. And that is putting it mildly.

And even if homologous recombination could somehow have been in play, it wouldn’t help anyway. For while this is a clever mechanism for the swapping of nature’s protein modules, it does not help when used with sequences that are nowhere close to solving the problem. Jumping from one ocean wave to another doesn’t improve the odds in finding the astronomical, one-in-10^70, longshot.

The evolutionists found that it is impossible for evolution’s gradual search to solve the problem, even for the single module they were experimenting with (and all the other modules in the virus already at their native sequences). But if repeated attempts by evolution are going to fail, then the mixing and matching of those errant attempts will not help either. They merely represent another blind attempt. Unfortunately, it is unscientific conclusions such as these that inform the next level up in the apologetics hierarchy.

An example survey paper

This survey paper is entitled “Exploring protein fitness landscapes by directed evolution.” The paper discusses both the engineering problem of creating new proteins and its implications for how proteins evolved in the first place. For the most part this survey paper is a helpful and accurate summary of the relevant scientific findings at the time. The enormous complexity of the problem, and even the challenges for evolution are clearly stated. Here are several examples from the paper:

Notwithstanding significant advances, a molecular-level understanding of why one protein performs a certain task better than another remains elusive. This state of affairs is perhaps not surprising when we remember that a protein often undergoes conformational changes during function and exists as a dynamic ensemble of conformers that are only slightly more stable than their unfolded and nonfunctional states and that might themselves be functionally diverse. Mutations far from active sites can influence protein function. Engineering enzymatic activity is particularly difficult, because very small changes in structure or chemical properties can have very significant effects on catalysis. Thus predicting the amino acid sequence, or changes to an amino acid sequence, that would generate a specific behavior remains a challenge, particularly for applications requiring high performance (such as an industrial enzyme or a therapeutic protein). Unfortunately, where function is concerned, details matter, and we just don't understand the details. …

Although the distance between any two sequences is small (that is, equals the number of mutations required to interconvert them and is therefore ≤ L), this high-dimensional space contains an incomprehensibly large number of possible proteins. For even a small protein of 100 amino acids there are 20^100 (~10^130) possible sequences, or more than the number of atoms in the universe. Searching in this space for billions of years for solutions to survival, nature has explored only an infinitesimal fraction of the possible proteins. …

The vast size of sequence space makes it impossible to characterize (or even model) more than a minute fraction of this fitness surface. Despite this, several important features have emerged from accumulated experimental studies. The first is the low overall density of functional sequences: the vast majority do not code for any functional protein, much less the desired protein. …

Because most mutations are deleterious, the probability that a variant retains its fold and function declines exponentially with the number of random substitutions, and random jumps in sequence space uncover mostly inactive proteins. Thus new functions are extremely difficult to obtain without altering some aspect of the search. One approach is to create a new starting point, a parent protein with at least some minimal function, and improve that by directed evolution. …

An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries. …

Furthermore, natural evolution works on a different fitness landscape, and it is unclear how the protein fitness assayed during directed evolution is related to the organismal fitness that natural evolution optimizes.

These passages discuss some of the difficulties in using protein engineering as evidence for evolution, and some of the contradictory evidence protein engineering has produced. Unfortunately, none of this is interpreted outside of the evolutionary framework, and in fact the paper goes well beyond, and against, the scientific data in elaborating the evolutionary narrative:

Millions of years of life's struggle for survival in different environments have led proteins to provide diverse, creative and efficient solutions to a wide range of problems, from extracting energy from the environment to repairing and replicating their own code. …

Evolution, however, had no difficulty generating these impressive molecules. …

Evolution is unique because it works at all scales, from molecules to ecosystems — no other engineering design algorithm can make that claim. A simple algorithm of mutation and artificial selection has proved effective for everything from the selective breeding of plants and animals to discovering self-replicating nucleic acid sequences. …

Among the large number of mutational trajectories between a starting point and a solution, smooth uphill paths can often be found. …

Despite the vast size of sequence space and the complex nature of protein function, the Darwinian algorithm of mutation and selection provides a powerful method to generate proteins with altered functions.


This is the apologetics message of the paper that informs the popular literature. Whereas the research paper’s undefendable, non scientific statements were limited, now in the survey paper they frame the narrative from beginning to end. Evolution, one way or another, must have happened, so the evidence must support it. There can be no contradictory evidence.

To make this story sound scientific, the paper equivocates on evolution. It conflates the protein engineering findings that nature’s proteins can adapt with the evolutionary narrative:

Despite their complexity and finely-tuned nature, proteins are remarkably evolvable: they can adapt under the pressure of selection, changing behavior, function and even fold. …

Biological components and systems have shown a remarkable ability to adapt under the pressure of artificial selection, an evolvability that very likely reflects their own history of natural selection. …

Even the earliest directed evolution experiments noted how rapidly proteins could adapt to new selective pressures, indicating the ready availability of smooth uphill paths in the fitness landscapes. …

This simple uphill walk on a fitness landscape in sequence space works because proteins are wonderfully evolvable and can adapt to new conditions or even take on new functions with only a few mutations.

Proteins are remarkably evolvable along smooth uphill paths because, after all, their adaptation under artificial selection reflects their own history of natural selection? Of course the adaptation of native proteins proves no such thing. It is yet another rehearsing of Darwin’s flawed logic that animal husbandry and breeding provide a peek into the mechanisms of change that, by the way, created all of biology. Religion drives science and it matters.

96 comments:

  1. Hunter:

    This is the apologetics message of the paper that informs the popular literature. Whereas the research paper’s undefendable, non scientific statements were limited, now in the survey paper they frame the narrative from beginning to end.

    This is correct. The narrative was framed in the light of evolutionary theory. Alas, if only there were a competing theory in light of which the narrative could have been framed…

    Evolution, one way or another, must have happened, so the evidence must support it. There can be no contradictory evidence.

    What contradictory evidence should have been discussed in the paper?

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  2. Thanks for an excellent summary Dr. Hunter

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  3. Cornelius Hunter: Homologous recombination? It would be difficult to imagine a more unlikely explanation. Homologous recombination is a complex genetic mechanism assisted by finely-tuned proteins.

    Recombination is the primitive state. In the primodial environment, the trick is to prevent rampant interactions.

    Cornelius Hunter: And even if homologous recombination could somehow have been in play, it wouldn’t help anyway. For while this is a clever mechanism for the swapping of nature’s protein modules, it does not help when used with sequences that are nowhere close to solving the problem.

    Recombination of already functional proteins means recombining working motifs and patterns. Evolution which includes recombination works quite differently from evolution with point-mutation alone.

    Cornelius Hunter: Jumping from one ocean wave to another doesn’t improve the odds in finding the astronomical, one-in-10^70, longshot.

    The analogy doesn't apply to recombination. There are vast numbers of multidimensional slopes that are not represented in a naïve fitness landscape.

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  4. Cornelius,

    ----------------------------
    They draw broader conclusions, and when discussing the subject of evolution these papers are more likely to make obviously unsupportable evolutionary claims.
    ----------------------------

    Shouldn't that be 'unsupported' claims. The evidence may be there but isn't, not that the evidence will never be there. That would be an unsupportable claim.

    An excellent translation into good science. What in your opinion should they say: 'nature' instead of 'evolution'?

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  5. Evolutionists at best rely on an unobserved astronomically impossible lottery win as their defense. Funny that they can't see the problem with that.

    ReplyDelete
  6. Tedford the idiot said...

    Evolutionists at best rely on an unobserved astronomically impossible lottery win as their defense. Funny that they can't see the problem with that.


    Stupid Creationists at best rely on a ridiculous and unsupported strawman argument claiming evolution needs an unobserved astronomically impossible lottery win to happen.

    Everybody in the science community can easily see the problem with that.

    ReplyDelete
    Replies
    1. Hahahaha! http://americanloons.blogspot.com/2013/11/786-cornelius-hunter.html

      Delete
  7. This comment has been removed by the author.

    ReplyDelete
  8. Thorton,

    The only people who truly understand science are the ones like Neal that have nothing to do with it. To gain real understanding of something you must remove yourself from it and view it from the outside. That's why Neal understands science, reason, and rationality so much better than you and I: he is removed from them and so has the proper perspective for true understanding.

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  9. Cornelius wrote:

    It is yet another rehearsing of Darwin’s flawed logic that animal husbandry and breeding provide a peek into the mechanisms of change...

    Are you seriously claiming that the results of breeding experiments don't have anything to say with regards to natural selection? If that is the case, then why would any experiment have anything to say about the way things work?

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  10. Venture Free,

    Now that's a Poe and a half.

    ReplyDelete
  11. Homologous recombination? It would be difficult to imagine a more unlikely explanation. Homologous recombination is a complex genetic mechanism assisted by finely-tuned proteins.

    It is a "complex mechanism" as a repair system that fixes broken DNA strands. But it is a very common accident just because it is very easy for a DNA strand to separate and find another, similar, DNA strand. Curious that Cornelius would not know that homologous recombination happens by accident in PCR cycles. No assistance from any other proteins required.

    It is circular to recruit such a mechanism for the initial evolution of proteins—for no such mechanism is likely to have existed. And that is putting it mildly.

    The authors were not talking about "initial" evolution of proteins, but generic evolution. Still, as I said, homologous recombinations are accidents waiting to happen.

    Misguided religion drives Cornelius' pseudoscience, and it matters.

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  12. Negative Entropy:

    ===
    Curious that Cornelius would not know that homologous recombination happens by accident in PCR cycles. No assistance from any other proteins required.
    ===

    I see, so evolution had PCR. And was it serendipity that evolution had available to it a macromolecule that could swap like that?

    Also, how does homologous recombination solve the 10^70 search problem?

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  13. Cornelius,

    Excellent post. Judging by the response I think this topic totally destroys the specious arguments for evolution. Thank God God has supplied us intelligence to discover the wonders of his creative works. We have suffered long enough from the scientists who attempt to destroy our faith. It is not us that are ignorant, but them.
    .

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  14. Hunter:

    Also, how does homologous recombination solve the 10^70 search problem?

    From the cited review by Philip A. Romero and Frances H. Arnold:

    "An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries [73-75] (FIG 3a). It has been shown that mutations made by homologous recombination are much less disruptive and generate functional proteins with much higher frequency than random mutations [56] (FIG 3b). Methods based on homologous recombination direct crossovers to regions of high sequence identity and are generally limited to sequences that are very similar (more than 70% identity) [75], whereas various sequence-independent methods can recombine at random [76, 77] or user-specified sites [78, 79]. Recombining homologous proteins by choosing crossovers based on structural information allows construction of libraries of chimeric proteins that simultaneously exhibit a high level of functionality and significant genetic diversity [80]. In all cases, the chimeric proteins inherit the best (and worst) residues the parents have to offer, in new combinations not observed in nature."

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  15. Venture Free, I think Peter has you beat on the sarcasm meter. At least, I think he's being sarcastic. Poe's Law, y'know.

    There is a surprising dearth of comments on this article though.

    ReplyDelete
  16. Derick

    There is a surprising dearth of comments on this article though.
    ---
    It's so quiet I can hear my GM rusting.

    ReplyDelete
  17. Cornelius,

    I see, so evolution had PCR. And was it serendipity that evolution had available to it a macromolecule that could swap like that?

    PCR was an example of how easy it is for accidental homologous recombination to occur. Nice try at a cop out though.

    Also, how does homologous recombination solve the 10^70 search problem?

    How do you know it is a 10^70 problem? Even if so, how about we first solved some 10^13 problems? Recombine two solutions at 10^13 and you get what? 10^26? If you recombine two of these 10^26? 10^52? recombining those solutions at 10^52? 10^104? How many recombinations so far? Three?

    Oh the power of recombination. You know, the first time someone made the experimental evolution that contained recombination I did not believe the speed either. We were going so slow by random mutation and selection, and those guys would get results in a few days just by adding recombination. Then Frances Arnold (who you cited here) recombined a couple of her mutants, and got great results too. Then I worked out the numbers. No way to deny it. Both the numbers and the experiments said it quite clearly.

    Arrivederci!

    ReplyDelete
  18. C,

    I see that Pedant also gave you some answers on the recombination part. Thanks Pedant!

    ReplyDelete
  19. Negative Entropy,

    You're welcome, but credit is due to Dr Hunter, who cited the Romero & Arnold review in his OP. (Maybe he missed the part I quoted.)

    ReplyDelete
  20. Has homologous recombination been seen to create new proteins in nature, or just in the lab? I'm just asking.

    ReplyDelete
  21. Hey natschuster,

    Has homologous recombination been seen to create new proteins in nature, or just in the lab? I'm just asking.

    In nature, new new new proteins, I don't know. But new functions in duplicated proteins, yes, quite frequently.

    ReplyDelete
  22. Pedant,

    You're welcome, but credit is due to Dr Hunter, who cited the Romero & Arnold review in his OP. (Maybe he missed the part I quoted.)

    An honest mistake on his part, I am sure. I don't think an oversight like this could possibly be part of the anti-evolutionary narrative.

    :-)

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  23. NG:

    Has it been seen to happen? Or do they find proteins that kinda look like other proteins, and assume that it happened? I'm just asking.

    ReplyDelete
  24. Hi again natschuster,

    (That was quick.)

    It has been both observed and deduced. "Assumed" is not the proper way to describe it, it is more that given the data the recombination is deduced if the whole thing points to that explanation.

    If we found, say, two similar proteins, then we might assume that they are homologous (if similar beyond what could be expected by chance), but that one or both of them had suffered homologous recombination would not be testable/deducible from that alone. We need more homologous proteins and their genes to test for the possibility that there was homologous recombination.

    ReplyDelete
  25. Hi Hunter,

    This is genious. A blog administrator deleted a comment from me in which I explane my standpoint that there is no conflict between creationism, evolution, religion and science. I wrote about how all of them can be next to one another without any problem and even complement each other.

    Well, I understand.....

    Never mind. It defeats the purpose of the whole discussion correct?

    I am currious how long this poste will be up and if it will even appear for a little bit.

    We will see.

    This is experimental (I am a scientist), so please don't think I am angry or what. I am just conducting an experiment.

    ReplyDelete
  26. By the way, emil, it was good of you to speak up and not let this incident pass unscrutinized.

    ReplyDelete
  27. There were two removed.

    One as pedant said above (I actually don't remember any more what that was about) I had quite some not even showing up. Some of it I blaim on my slow internet connection that I have at home. I am not worried about that. This problem is on my end.

    However, the second one was on January 15th
    New Genes: Putting the Theory Before the Evidence
    There it just sayes something like comment removed by an administrator. Nothing else. No reason no nothing.

    However, Hunter sort of responded mysterically with saying someplace completely out of space January 17th.

    "I agree it is fascinating...."

    This sort of fits to what I think is my mysterically dissapeared comment.

    The question is what is fascinating:
    - how biology works?
    - doing research in biology and often find yourself (myself) wondering about how things possibly could have evolved?
    - how people tend to just jump to some conclusion if they don't have an answer?
    - how one can get people to endlessly discuss the "conflict" between evolution and creationism while getting nowhere?
    - how those who think that evolution is real can possibly hang on to that one?
    - how those who do think that creasionism is real but evolution not can possibly hang on to that one?
    - how it can be possible to be religious and at the same time realize that evolution is real?

    I don't know. Would be interesting to know though.

    ReplyDelete
  28. This comment has been removed by the author.

    ReplyDelete
  29. I had to correct myself. There were fare to many spelling mistakes. Sorry....

    In regard to homologous recombination and protein sequence similarities.

    There are millions of proteins we still have no idea about how their function. In practice, if one stumbles over a "new" sequence of a protein and there is the suspicion that this protein might be of importance, the following method is used to find its function:

    1. Run the sequence through a search program with the goal to find similar sequences of known proteins with known function.

    2. Compare which parts of the protein are similar to known proteins and which are not.

    3. Based on known functional subunits of known proteins with known function and based on similarities/differences between known and the unknown protein, make a good guess about the function of the newly discovered protein.

    4. Test your function hypotheses via appropriate experiments.

    This works quite well. It works so well that this is a standard method to uncover the function of newly discovered proteins. Can somebody give me a reasonable explanation why this works so well that does not involve evolution? I mean one that does not involves believing that God (Creator) exists?

    The good thing with evolution is that it neither requires the believe no disbelieve in the existence of God (Creator).

    Somebody said something like: Scientists taking faith away with evolution.
    Neither evolution nor scientists are taking faith away. Creationism does.

    ReplyDelete
  30. Oh, just another thought, but who cares….

    You think that all Scientists think that what we think today about evolution is THE TRUETH?

    Let me tell you this: Evolution, from a Scientific standpoint is nothing else than a theory that makes quite some sense in the light of what we think we know today about how things work in our world. However, I bet that a thousand years from now people will laugh at us like we wonder how people possibly could have thought that the world is flat.

    There is no THE TRUTH in science. It is what we currently think how things work according to reasonable scientific evidence. Who knows what is actually THE TRUTH? I don’t. Maybe there is somebody who does….. Who knows….

    What I do know though is that I personally can’t say with good feelings that there is scientific evidence for that God does exist even though I might believe that God does exist.

    Therefore, creationism is out of question from a scientific standpoint because it is missing the very ground on which it is build.

    Well, who knows what we will find in future. Maybe I am right and the world is an imaginary correction camp for angles who misbehaved and they are send to this place to learn how to do better. I must have done something badly wrong then….

    Yes, my brain cracked…..

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  31. I understnad that proteins can be very different yet still be called homologous. They can have an amino acid sequnce that is up to 20% different and still be called closely homologous. Is there more involved than simply reshuffling the modules?

    ReplyDelete
  32. emil

    Well, who knows what we will find in future. Maybe I am right and the world is an imaginary correction camp for angles who misbehaved and they are send to this place to learn how to do better. I must have done something badly wrong then….
    ---
    You may be right about angels,emil.Just look at Pedantski's picture.He must be one of them.

    ReplyDelete
  33. In general homologous simply means that it is thought to be derived from a common ancestor. It even doesn't have to have similar function, but often does. Homologous as itself doesn't say anything about what happened so that they ended up having different sequences.

    In contrast, analogous has similar function, but is not derived from a common ancestor.

    The way how people differentiate between homologous and analogous is the kind of similarity/difference between the sequences.

    Many proteins have particular sequence parts that are highly conserved. Those conserved parts are found over and over again in other proteins which are then thought to be homologous.

    Other proteins might have similar function but do not have the same specific conserved parts which is then interpreted as that they are not homologous but analogous.

    That means it is not only important how high the percentage of similarity/difference is but where exactly the similarities/differences are found within the sequence.

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  34. A little story off-track, Science in practice: (hopefully nobody reads this who knows me otherwise I identify myself – who cares – have fun if I do).

    I just started doing electrophysiology (intracellular recording). Well, in order to do this, I need to have microelectrodes that are capable of pinching into a cell without destroying it. Well, the way of making such seemingly impossibly small hallow needles is using an electrode puller. I never did this before.....good luck. Well this thing has 5 variables each of which has a range of several hundred different settings. That makes - let me think. An unbelievable huge number of possible settings, but only a few of them will yield in useful electrodes.

    Well, there are suggested settings. However, with our puller none of them got me anywhere even close to a useful electrode.

    So, a reasonable non-scientist probably would have given up at this point because statistically it is impossible to find a useful setting within a person’s lifetime. So, why bother trying?

    Well, I am a scientist, so I tried anyway. It took me about one week until I gave up on one kind of glass. Oh, I forgot there are not only different puller settings. There are also different kinds of glass one can use to do this.

    Well, today my brain finally completely cracked and I tried a different glass. It took me almost the whole day getting some useful electrodes and at the end of the day I managed to get a couple of my first intracellular recordings.

    Now, one wonders why it is hard to convince scientists to drop evolution? We experience it happening ……

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  35. Pedant:

    ========
    From the cited review by Philip A. Romero and Frances H. Arnold:

    "An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries [73-75] (FIG 3a). It has been shown that ..."
    ======

    This is referring to native proteins, not random sequences.

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  36. Derick Childress:

    ===
    Venture Free, I think Peter has you beat on the sarcasm meter. At least, I think he's being sarcastic. Poe's Law, y'know.
    ===

    Well then perhaps you could explain to us how proteins evolved. What are we missing?

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  37. Negative Entropy:

    ===
    PCR was an example of how easy it is for accidental homologous recombination to occur. Nice try at a cop out though.
    ===

    It is not a cop out. What is easy in PCR is not necessarily easy in a warm little pond, or ocean vent, etc. In fact, this is an example of how evolutionists inappropriately marshall properties of biology for support for their theory.


    ===
    How do you know it is a 10^70 problem? Even if so, how about we first solved some 10^13 problems? Recombine two solutions at 10^13 and you get what? 10^26? If you recombine two of these 10^26? 10^52? recombining those solutions at 10^52? 10^104? How many recombinations so far? Three?
    ===

    No, sorry, it doesn't work like that.


    ===
    Oh the power of recombination. You know, the first time someone made the experimental evolution that contained recombination I did not believe the speed either. We were going so slow by random mutation and selection, and those guys would get results in a few days just by adding recombination. Then Frances Arnold (who you cited here) recombined a couple of her mutants, and got great results too.
    ===

    No, again, this is with native sequences.


    ===
    Then I worked out the numbers. No way to deny it. Both the numbers and the experiments said it quite clearly.

    Arrivederci!
    ===

    Just add water.

    ReplyDelete
  38. emil:

    ===
    Hi Hunter,

    This is genious. A blog administrator deleted a comment from me in which I explane my standpoint that there is no conflict
    ===

    Next time please explain your position without the language.

    ReplyDelete
  39. emil:

    ===
    There were two removed.
    ===

    Only one was removed. Perhaps Google got the other (don't use hyperlinks, just paste in the address, otherwise Google will likely delete the comment).

    ReplyDelete
  40. Hunter:

    Pedant:

    ========
    From the cited review by Philip A. Romero and Frances H. Arnold:
    "An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries [73-75] (FIG 3a). It has been shown that ..."
    ======

    This is referring to native proteins, not random sequences.


    I suppose you consider this a problem, but you don’t explain. Is it a problem because two random sequences are unlikely to have enough homology to favor recombination? That doesn’t apply here, because the sequences in question are no longer random.

    My quote from Romero/Arnold addressed your earlier question about the Hayashi phage paper: "Also, how does homologous recombination solve the 10^70 search problem?" This “problem” is the difficulty of progressing from an earlier smooth fitness climb, mediated by point mutations, through a looming rugged fitness landscape. At that point in the experiments, there had been several rounds of mutation and selection, so the sequences under study were no longer random. See Fig. 2B.

    ReplyDelete
  41. Cornelius:

    "It is not a cop out. What is easy in PCR is not necessarily easy in a warm little pond, or ocean vent, etc. In fact, this is an example of how evolutionists inappropriately marshall properties of biology for support for their theory."

    An organism have to actively fight against spontaneous recombination. When it fails it causes chromosomal instability and is associated with cancer. Thus the difficulty is not for recombination to happen, it's not to happen too often.

    By the way, there are many examples of gain-of-function caused by gene fusion: bcr-abl comes to mind.

    Charles.

    ReplyDelete
  42. Cornelius,

    this is an example of how evolutionists inappropriately marshall properties of biology

    So you think partially duplicated DNA strands will not attach to similar (homologous) counterparts? It is thus inappropriate to think that A will pair with T and G with C? Wow, these evil evolutionists truly.

    No, sorry, it doesn't work like that.

    So combining solutions doesn't potentiate the search? Are you sure Mr. Computational Biologist?

    No, again, this is with native sequences.

    Really? So other homologous sequences won't recombine because they are not native?

    This sure is a revelation. A will not attach to T nor G to C unless they are in native sequences. Thanks Cornelius, I always thought those pairings were due to the physical and biochemical properties of these molecules. How foolish of me. Native sequences have magic embedded, and only then can DNA sequences recombine. Thanks for opening my eyes!

    ReplyDelete
  43. Hey natschuster,

    I understnad that proteins can be very different yet still be called homologous. They can have an amino acid sequnce that is up to 20% different and still be called closely homologous. Is there more involved than simply reshuffling the modules?

    I don't think scientists would call these closely homologous. "Homologous," yes, but not "closely." For scientists to accept proteins at such low identity values as homologous, the stats have to make sense overall. In other words, because of the properties of the amino-acids, and the sequences of their genes you might infer that they have diverged long ago, but still their similarity (not just identities, but also conservation of amino-acid properties, and identity at key positions) could convince you that they are in the same protein family. Other times, yes, there can be reshuffling of modules, but the 20% identity refers only to the alignable sections (the sections that can be homologous). If, on top of the stats scientists find the proteins to be involved in similar functions, then the case for homology gets stronger.

    ReplyDelete
  44. negative entropy probably know this.

    Just to make it even more redicules for non-biologists.

    Two DNA strands even combine if they do not completely "fit". That means combining two DNA strands does tollerate some "mistakes" and A or T can tollerate a C or G just fine within a sequence that is otherwise very similar and there are not too many of those "mistakes".

    We do know about this because some of the techniques used in genetics only work because alignment (attachment) of non-perfectly matching DNA is possible (refere to any high level science genetics book).

    Also, our body actually "uses" this to prevent unwanted proteins from being translated by producing another little bit of RNA that matches a part of the unwanted protein RNA and attaches to the protein RNA and with this prevents it from being translated but instead destroyed. The sequences at which the RNA align do not need to be perfectly the counterpart. About the same is enough.

    This mechanism is thought to have originally evolved as a protection mechanism against viruses. Today this mechanism is used in research to sielence gene expression.

    ReplyDelete
  45. Oh, sorry for the non-fancy language.

    I could use all sorts of fancy words for techniques, methods, and mechanism. I try not to do this by purpose but instead try writing things so that people who have no knowledge about this stuff can read and understand it - as an basic educational thing.

    Though, I am happy to answer questions about how all those specific things are called in a more scientific fashion with fancy words if somebody is interested to know more about it.

    ReplyDelete
  46. Derick Childress

    ----------------------------
    Venture Free, I think Peter has you beat on the sarcasm meter. At least, I think he's being sarcastic. Poe's Law, y'know.
    ------------------------------

    Another vacuous entry. It is clear that you have no conception of this subject. Please don't put word's in my mouth. Your comments have nothing to do with the science of this post.

    I have to wonder what motivates a person like you to continuously come up with such obvious misinformation. I know that gay rights activists are very vocal in the blogosphere. There are on a mission to keep the scientifically bankrupt notion of evolution as the current mindset to ensure Christian doctrine is not followed by society. That seems to be your goal at any cost, and the goal of many of those who argue as you do. We all know Cornelius' views. Are you a gay rights activist?

    .

    ReplyDelete
  47. Charles sayed:

    "An organism have to actively fight against spontaneous recombination. When it fails it causes chromosomal instability and is associated with cancer. Thus the difficulty is not for recombination to happen, it's not to happen too often."

    He is absolutely correct. There is a whole bunch of mechanism that prevent mistakes from happening or fix mistakes if they happened.

    Citation out of the text book: Molecular Biology of the Cell: "without those repair mechanism spontaneous DNA demage would rapidly change DNA sequences"

    existing repair mechanisms are:

    - mismatch repair
    - nucleotide excision-repair
    - repair by homologous recombination
    - base excision repair
    - double-strand break repair

    To prevent DNA replication mistakes at the first place, there are several check-point and proofreading mechanisms that prevent mistakes or might even stop DNA replication all together if something is wrong.

    citation out of the book above:
    "....about 1 mistake is made for every 10^9 nucleotides copied. this fidelity is much higher than one would expect, on the basis of the accuracy of complementary base-pairing. The standard complementary base pairs are not the only ones possible. For example, with small changes in helix geometry, two hydrogen bonds can form between G and T in DNA. In addition, rare tautomeric forms of the four DNA bases occur transiently in rations of 1 part to 10^4 or 10^5. If the DNA polymerase did nothing special when a mispairing occured between an incoming deoxyribonucleoside triphosphate and the DNA template, the wrong nucleotide would often be incorporated into the new DNA chain, producing frequent mutations...."

    The three steps that give rise to high Fidelity DNA synthesis are:

    - 5' -> 3' polymerization error per nucleotide polymerization: 1 X 10^5
    - 3' -> 5' exonucleolytic proofreading error 10^2
    - strand-directed mismatch repair error 1 X 10^2

    total error: 1 X 10^9

    Without that, the error would be be much higher.

    Current research suggests that there are even mechanisms we still don't know yet because there are certain bacteria which do not express the required enzymes for known repair mechanisms but still can repair or prevent DNA damage. So, there is still much to learn on this subject.

    This means, DNA change is dramatically slowed down by nature...

    Isn't that something?

    ReplyDelete
  48. Hunter:

    There is something that bothers me especially with this poste and I think I should express this.

    With your new poste you accuse scientists to talk about evolution when they should not talk about it (is this summary correct?).

    Well, in the past you "shredded" several well written and supported scientific papers in the light of evolution while the authors did not even marginaly metion evolution with one world at all.

    Many could have easily explained their findings in the light of evolution. Well, they didn't for what ever reasons. And - you then used their "failing" of discussing their work in the light of evolution to shredder their papers often in an absolute mean and non-scientific way.

    Some of them can even be so proud and of themselfs to have you as one of the first persons who cited their papers which is a real accomplishment in my eyes.

    How does this make sense?

    Is there anything scientist can do right? Or, is it all only about critical thinking and finding a ways of senseless destroying everything that happens not to fit your own personal oppinion? With other words politics?

    I just don't understand the rationality behind all this.

    ReplyDelete
  49. emil,

    I just don't understand the rationality behind all this.

    There is no rationality. Search the web for the "discovery institute" (DI) and for "cdesign proponentsists".

    It is mostly about disguising creationism as science. Since that has failed time and again, Cornelius, who works for the DI, seems to be testing the waters of accusing evolution of being either religion, or religiously-motivated.

    But search and make your own mind about it.

    ReplyDelete
  50. Now I think nasty but....

    If Cornelius and compenion succeed in accusing evolution of being a religion or religiously-motivated then they can go ahead and can ban it from being tought at school to children in the US because no religion must be tought at school. And this applies to everything that is associated with evolution.

    But, what happens then with Biology? Biology can't get around evolution. Wouldn't that be the death of science education all together? What would a teacher be allowed to answer if a child woud ask the question how bacteria become immune against antabiotics? What is the goal?

    I will look those things up.

    ReplyDelete
  51. Oh, in regard to trying to put a ban on evolution. This even would apply to computer science.

    Can sombody explain me why if evolution "can't" work do computerscience people use the known mechanisms of evolution to develop evolutionery (genetic) algorithms that mimic evolution to develop a search algorithms that allow find good solutions for problems which can't be solved otherwise due to an overwhelming amount of possibilities?

    I personally worte one time such a program and it worked like a charme. Well, Biologists have a huge advantage of writing such a programm because they now how evolution works. I was the only Biologist in the higher level computer science class and I rocked.

    Our goal was to use this program to find a good solution for a problem that otherwise could not have been solved because mathematically our solar system would have given up on us before the computer could have come to a solution using any other straight forward conventional search programm.

    With this program it took a couple of hours at longest to come to a good solution. It realy does work. Yes it was statistically impossible but this is what evolution is about. Allowing the "impossible" to happen within a reasonable time period.

    It seems like that even computer science people (no offence, I love computer science) obviously already came to understand Biology better than Creationists (ever will)?

    So, even in a high level artificial intelligence class you can't get around evolution.....

    ReplyDelete
  52. Hi,

    now it also makes sense why my comments disapeared because they were exactly about why evolution has nothing to do with religion and why religion and science/evolution are so different and why there is no conflict between them. I should try writing this again but this time a bit more carefull and see if it will disapear again....

    Most likely somebody is working right now very hard on finding good arguments against my arguments...

    Sorry for making so much trouble.

    Too bad that I don't have a copy of it.

    ReplyDelete
  53. "What contradictory evidence should have been discussed in the paper?"

    I thot there was plenty of contradictory evidence in the article. It was just ignored. Darwinists just ratchet up the level of their unswerving faith in the creative power of random non-directed forces whenever that happens.

    Pedant again says:
    "This is correct. The narrative was framed in the light of evolutionary theory. Alas, if only there were a competing theory in light of which the narrative could have been framed…"

    Just because materialism cannot come up with a decent feasible theory doesn't mean we have to settle for Darwinism and force any and everything to conform to it. That shows how insecure evolutionists are. Can't admit to even the possibility that evolution might not be true. It is a fact no matter how many seemingly insurmountable problems exist.

    ReplyDelete
  54. Pedant:

    #################################

    ========
    From the cited review by Philip A. Romero and Frances H. Arnold:
    "An approach to making multiple mutations that is used extensively in nature is recombination. Naturally-occurring homologous proteins can be recombined to create genetic diversity within protein sequence libraries [73-75] (FIG 3a). It has been shown that ..."
    ========

    This is referring to native proteins, not random sequences.

    I suppose you consider this a problem, but you don’t explain. Is it a problem because two random sequences are unlikely to have enough homology to favor recombination? That doesn’t apply here, because the sequences in question are no longer random.
    #################################

    The OP does discuss this a bit. What science is indicating is that random sequences as starting points are unlikely to evolve to sequences that are native (or sequences with comprable functionality). But native sequences as starting points, OTH, are quite adaptable.

    Yes, you can take random sequences as starting points and evolve them a bit, but you're nowhere close to native functionality. To use the fruitful results of recombination of native sequences as evidence that recombination can save the day in evolving from a random starting point is an unsupported argument. These are two different cases.

    ReplyDelete
  55. Charles:

    ##################
    "It is not a cop out. What is easy in PCR is not necessarily easy in a warm little pond, or ocean vent, etc. In fact, this is an example of how evolutionists inappropriately marshall properties of biology for support for their theory."

    An organism have to actively fight against spontaneous recombination. When it fails it causes chromosomal instability and is associated with cancer. Thus the difficulty is not for recombination to happen, it's not to happen too often.
    ##################

    My point was simply that whether in the cell or in a carefully designed laboratory setup, benefiting from recombination is easier than in a scenario where proteins are first evolving. This would go along with all the other problems with the evolution of the cell. I'm not saying this is impossible, but it is not obvious that recombination is going to be effective where proteins are first evolving. Your comments about associated instabilities don't seem to counter my point. In fact, they seem to support my second point about the serendipity implied by this evolutionary narrative. IOW, let's say it is true that proteins began to evolve (somehow), and the adaptive walk stagnated early on as it would have, and then recombination saved the day (somehow). All this calls for quite a bit of serendipity: DNA had the right properties to support recombination--just what was needed; dilution mechanisms did not spoil the experiment; the instabilities you mention did not wreak havoc, etc.

    ReplyDelete
  56. Negative Entropy:

    =======
    "this is an example of how evolutionists inappropriately marshall properties of biology"

    So you think partially duplicated DNA strands will not attach to similar (homologous) counterparts? It is thus inappropriate to think that A will pair with T and G with C? Wow, these evil evolutionists truly.
    =======

    That was not my point. One of the themes of biology is life's remarkable adaptability. Evolutionists inappropriately use this as evidence for the origin of life and the species. Recombination is an example of this.


    =======
    No, sorry, it doesn't work like that.

    So combining solutions doesn't potentiate the search? Are you sure Mr. Computational Biologist?
    =======

    In evolving from a random sequence, first you need a random sequence and a means for reproducing it. Next, you'll need the means for selecting tiny amounts of functionality that wouldn't make a significant difference for the organism. But even then, the adaptive walk will stagnate rather early. And there is no evidence that what little sequence signal you have at that point is headed toward a sequence sliver with native-like functionality (more below). In fact, the virus paper we discussed showed the stagnated sequences had no relation to the native sequence. And if there are many different sequence slivers with native-like functionality, then it is unlikely that your two sequences, that will undergo recombination, would be headed toward the same sliver, anyway. And even if they were, the recombination would not know where the sequence signal is in the nascent sequences. The recombination that evolutionists refer to is with fully functional sequences.


    ===
    How do you know it is a 10^70 problem? Even if so, how about we first solved some 10^13 problems? Recombine two solutions at 10^13 and you get what? 10^26? If you recombine two of these 10^26? 10^52? recombining those solutions at 10^52? 10^104? How many recombinations so far? Three?
    ===

    One problem here is that evolving a tiny bit of function from a random sequence is not done by taking the sequence a tiny bit toward a fully functional sequence. It is not as though the way to get 1% functionality is to get an alanine at the 10th residue because the fully functional has an alanine at the 10th residue. Depending on the particular random starting point, 1% functionality may be attained in ways unrelated to any fully functional sequence.

    So then when you stall, it is not as though you are on your way toward a sequence with native-like functionality. So recombination of two such sequences doesn't suddenly move you that much further toward a sequence with native-like functionality.

    Folks the point here is not that science disproves evolution. As usual evolution dwells in the shadows, dealing with speculative scenarios, heroic mechanisms and contingent events that occurred long ago when no one could see it. There is much we do not understand and perhaps there is a way for all this to have occurred. But what science does tell us is that the theory is not likely. And yet evolutionists insist it is a compelling, unavoidable, fact.

    ReplyDelete
  57. Hunter:

    Yes, you can take random sequences as starting points and evolve them a bit, but you're nowhere close to native functionality.

    You’ve said that before, but it’s no more cogent now. You make an historical objection about an evolutionary history that is not directly accessible to us. But when it comes to mechanisms. today’s researchers don’t have to reproduce the entire evolutionary history of a protein to hypothesize a plausible scenario for how they might have evolved, based on experimental data. That hypothetical scenario is subject to further testing, of course.

    If you have a testable alternative scenario in mind, please discuss, by all means.

    To use the fruitful results of recombination of native sequences as evidence that recombination can save the day in evolving from a random starting point is an unsupported argument. These are two different cases.

    It’s a plausible argument, based on currently known properties of genes and proteins.

    ReplyDelete
  58. tokyojim, quoting Pedant:

    "What contradictory evidence should have been discussed in the paper?"

    I thot there was plenty of contradictory evidence in the article.


    Please identify that contradictory evidence.

    Just because materialism cannot come up with a decent feasible theory...

    Thanks for admitting that.

    ... doesn't mean we have to settle for Darwinism and force any and everything to conform to it.

    You don't have to settle for evolutionary theory or conform to it (whatever "conforming" might mean). But for anyone who wants to approach biology scientifically (materialistically), it can't be ignored (in the absence of an alternative decent feasible materialistic theory).

    That shows how insecure evolutionists are. Can't admit to even the possibility that evolution might not be true.

    You just told us that there isn't a competing theory. While we wait for one, there are plenty of entailments of the theory evolution for us to work on.

    It is a fact no matter how many seemingly insurmountable problems exist.

    The fact of evolution derives from evidence: the fossil record, comparative anatomy, comparative molecular biology and comparative genomics, among other things. But we have much more to learn about possible mechanisms underlying that evidence. For those who care about such things, it's an exciting prospect.

    ReplyDelete
  59. Cornelius:

    "Your comments about associated instabilities don't seem to counter my point."

    Cancer cells acquire many novel properties through shuffling of their genomes. They get more and more resistant against the body natural defenses and against therapy. They can divide faster and faster and start proliferating in different tissues, etc... This is something that no normal cell can do, and it's all acquired by natural means. Genomic instability is an important actor, as it offers the possibility to fusion different genes.

    So, yes, it is possible to acquire novel functions through recombination. The challenge, as I said in my earlier post, is to avoid accumulating them too fast.

    ReplyDelete
  60. Cornelius:
    "IOW, let's say it is true that proteins began to evolve (somehow), and the adaptive walk stagnated early on as it would have, and then recombination saved the day (somehow). "

    You seem to think that recombination is a complex mechanism. High fidelity DNA repair using homologous recombination is a complex mechanism, but not recombination in itself. Double-strand breaks can generate cohesive ends on non-homologous DNA fragment that will stick together, and it will act as a primer for the DNA polymerase that will complete the fusion.

    Recombination was here from the beginning of DNA replication, as were mutations. Where there is DNA replication, recombination is almost unavoidable. Protein didn’t begin somehow to evolve! Changes tend to accumulate naturally; the difficult part is limiting the rate at which they happen.

    ReplyDelete
  61. Cornelius,

    That was not my point. One of the themes of biology is life's remarkable adaptability. Evolutionists inappropriately use this as evidence for the origin of life and the species. Recombination is an example of this.

    Nice trick putting origin of life next to origin of species. This is truly funny. Let me then list of biological processes inappropriately used by "evolutionists":

    Life's remarkable adaptability is due to variation and selection (and recombination). According to what you are saying, it is inappropriate to even think that life in the past has had variability and that environments have selected from such variability. Despite advantageous variability has been proven to arise by mutation, it is inappropriate to think that mutations in the past have provided variability. That we today can see the process in the lab: namely random mutations plus selection (and recombination), to provide new functions, stabilities, et cetera does not mean this was possible in the past. Surely life in the past had no variability, was incapable of recombination, and environments were unable to select anything. Thus, species cannot originate in the way we have witnessed them to originate today. Thanks for setting that straight Cornelius. Thinking that life was life in the past, and that biological processes and other natural processes were the same in the past is just ridiculous. Those evil evolutionists. For evolution as in common descent to be true, it would have to rely on specific processes to evolution. It has no right to rely on known processes no matter how convincing they appear to be.

    Now that we killed the ridiculous idea that species could arise in the past from previous populations through selection from variability, which can be increased by mutation and potentiated by recombination, there is no reason to try and destroy that other idea about origin of life. Right? If species cannot originate why should we bother with origin of life.

    By the way, black holes, how can they say black holes come from loads of matter and thus gravitational forces? They misappropriate gravity to believe the religion of black holes. They have to find their own processes those evil black-hole-ists.

    Man, we have lots of religions disguised as science, to debunk because they use today's natural processes as their basis. Those idiots!

    ReplyDelete
  62. Cornelius,

    So then when you stall, it is not as though you are on your way toward a sequence with native-like functionality. So recombination of two such sequences doesn't suddenly move you that much further toward a sequence with native-like functionality.

    Because you say so and regardless of what the experiments and the molecular record might say.

    Folks the point here is not that science disproves evolution.

    !?

    As usual evolution dwells in the shadows,

    How dare she! How dare evolution happen by misappropriating processes that don't belong to her! Who does evolution think she is?

    dealing with speculative scenarios, heroic mechanisms and contingent events that occurred long ago when no one could see it.

    Such as natural variation, selection, and recombination, all which could not have existed in the past.

    There is much we do not understand and perhaps there is a way for all this to have occurred. But what science does tell us is that the theory is not likely. And yet evolutionists insist it is a compelling, unavoidable, fact.

    Just because variation, selection, recombination and mutation work today in nature and in the lab. Just because taxonomy looks as if there is lots of common descent, just because biogeographical data also support such ridiculous idea, just because different lines of molecular evidence also point towards such ridiculous idea, just because ... Those evil evolutionists! So much misappropriated data!

    ---

    On that other front, I was just realizing, cosmologists have misappropriated gravity not just in their religion of black-hole-ism, but also to support the religion of ellipsicism. How dare they! That gravity works here on Earth does not mean it works for the planets and the Sun. That someone can use the equations that calculate the parable described by a cannon ball to inappropriately calculate an elliptical orbit around the Sun does not make gravitation true for the solar system. Those evil ellipsicists!

    So much to do! So many mistakes!

    ReplyDelete
  63. Charles,

    So, yes, it is possible to acquire novel functions through recombination. The challenge, as I said in my earlier post, is to avoid accumulating them too fast.

    Cancer's remarkable adaptability shows that cancer was designed by an intelligence. You cannot misappropriate these variation/adaptation mechanisms to support evolution. Sorry, but no.

    Recombination was here from the beginning of DNA replication, as were mutations. Where there is DNA replication, recombination is almost unavoidable. Protein didn’t begin somehow to evolve! Changes tend to accumulate naturally; the difficult part is limiting the rate at which they happen.

    No, no Charlie, if there was nobody to see it, it didn't happen. Man you are so slow.

    ReplyDelete
  64. Negative entropy,

    And - I am pretty sure somebody is already working on some sort of chemistrism as well following the same pattern.

    ReplyDelete
  65. emil,

    And - I am pretty sure somebody is already working on some sort of chemistrism as well following the same pattern.

    I truly hope so. I have heard of the religion of spectrism. They think that because substances have a telling pattern of light absorption they can detect those substances in a more complex sample. Those evil doers. Lots of work to do. Too many religions coming out of misappropriated processes and data. We have to keep a watchful eye.

    And don't get me started on computer scientisms and mathematisms!

    ReplyDelete
  66. Cornelius,

    you do know what Sober means when he says evolution has a low likelihood, don't you?

    ReplyDelete
  67. negative entropy,

    I just had an enlightment. Religion is taking things that work today and believing that they worked in the past as they do now correct?

    Then, it is also Religion to believe that things that do work now will work in the future.

    We must not foget to fight the evil hypothesisms. They are actually the most evil of all.

    ReplyDelete
  68. You know why they are the most evil of all?

    They do go undercover among all the others: evelusionisms, mathemathisms, computer sciencisms, spectrisms, ellipsicists, black-holists and the many others that are out there.

    ReplyDelete
  69. This comment has been removed by the author.

    ReplyDelete
  70. If I understand correctly, recombination works because it takes preexisting functioning modules and recombines them. But what keeps the modules intact during the recombining? What process if any, makes sure that the breaks in the chromosomes don't happen in the middle of the modules?

    ReplyDelete
  71. Pedant:

    ===
    "But what science does tell us is that the theory is not likely."

    For the theory to be unlikely, there would have to be a competing theory that better fits the evidence.
    ===

    As if the scientific claims of evolutionists are not silly enough, evolutionists follow with these silly philosophical claims. But this is a standard response.

    ReplyDelete
  72. Negative Entropy:

    ======
    "So then when you stall, it is not as though you are on your way toward a sequence with native-like functionality. So recombination of two such sequences doesn't suddenly move you that much further toward a sequence with native-like functionality."

    Because you say so and regardless of what the experiments and the molecular record might say.
    ======

    No, the experiments say this. To be sure there is much science does not know about the relationships between sequence and function, but what the science is indicating is that starting from a random sequence, it is difficult to evolve to sequences with native-like functionality.

    ReplyDelete
  73. Hunter:

    As if the scientific claims of evolutionists are not silly enough, evolutionists follow with these silly philosophical claims. But this is a standard response.

    So, when Copernicus hypothesized that the sun, not the earth, was the center of the solar system, based on his own observations, and subsequent observations supported his hypothesis better than the alternative, he was making a silly scientific claim. And he was followed by other silly astronomers, like Galileo, making silly philosophical claims about the likelihood of heliocentrism. And Galileo’s promotion of his silly philosophy brought him before the Inquisition, which confirmed his silliness.

    Yes, the request for a better hypothesis is a standard response because science, like the legal system, is based on evaluation of competing hypotheses in light of evidence.

    ReplyDelete
  74. natschuster,

    You are correct, there would be a problem.

    However, (it looks like that) there are regulation mechanisms that prevent recombination between unmatched strands.

    Examples are:

    Regulation of Mitotic Homeologous Recombination in Yeast: Functions of
    Mismatch Repair and Nucleotide Excision Repair Genes (2000)

    RecQ helicases and topoisomerases: components of a conserved
    complex for the regulation of genetic recombination (2001)

    Those papers are free. You can pull them and make up your own mind. There are many more papers about this subject (even very nice reviews). Unfortunately, many of them are not free which bothers me greatly by the way. I can get them, but that doesn't help.

    Also, there are different types of recombinations. In order to get a good idea about the whole thing it is neccessary to be much more detailed than simply talking about "recombination".

    ReplyDelete
  75. Pedant:

    ===
    So, when Copernicus ...
    ===

    You made the standard evolutionary protectionist claim that for evolution to be unlikely, there would have to be a competing theory that better fits the evidence. And now, as a defense of this pretzel logic, evolutionists use the standard evolutionary example of heliocentrism's victory over geocentrism. This is yet more pretzel logic since the example doesn't work work as evolutionists want it to.

    First, one does not need a counter explanation to know that an explanation is unlikely. When your explanation produces a long list of false predictions, and with each passing false prediction you add more epicycles, then you have an underlying problem. Compared to Darwin's theory, evolution today is a Rube Goldberg machine of special explanation tacked onto special explanation, each adding yet more serendipity to the theory.

    Evolutionists argue this mountain of scientific testimony is merely a research problem, not a theoretical problem, because they believe god never would have designed this world. The underlying foundation of evolutionary thought is metaphysical, and so when challenged evolutionists will always refer to their foundational "truths." Creation / design must be false, and so evolution, one way or another, must be true.

    How it happened may be unknown, but that it happened must be a fact. And so the standard evolutionary response to the massive scientific problems is "so what's your theory?" In the mind of evolutionists their theory cannot be judged to be unlikely without an alternative. Such an alternative would cause a restructuring to their foundation, and they would then rethink the problem accordingly. But lacking such an alternative, evolutionists rest on their sure foundation. Theology is still queen of the sciences.

    The Rube Goldberg machine of evolution is somewhat like the Rube Goldberg machine of geocentrism from centuries past. The preference for heliocentrism over geocentrism was largely due to the formers less complex formulation. Any theory can account for the data if you allow for enough special explanations. Geocentrism was quite accurate, but required a great many epicycles to do so.

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  76. Cornelius wrote: But what science does tell us is that the theory is not likely.

    Pedant wrote: For the theory to be unlikely, there would have to be a competing theory that better fits the evidence.

    A theory can have a low likelihood without any comparison to other theories*. For example, the likelihood of the existence of polar bears given evolution is miniscule (given ID, it can't even be calculated). However, given some more assumptions, such as the existence of other bears and an environment that is white and cold, the likelihood of evolution goes up drastically. Methinks that Cornelius sometimes ignores such assumptions.


    *I'm assuming here that we are talking about likelihood in the Bayesian sense. At least, Cornelius seems to use the term that way.

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  77. natschuster,

    How much do you know about the process of genetic recombination? I mean do you know when and where it can happen, which different types there are, and how we know that it does happen?

    I mean this mechanism is highly complex. Everybody who studies something that is related to Biology usually has to take some sort of Genetics class. But even in those classes they only scratch the surface. Higher level molecular cell biology classes or genetics classes are usually only taken by people who either are working on a PhD in Biology or do this for fun and even then those classes do not teach everything that is out there and only those who actually go into the field of genetics or molecular biology or teach themself for some reason end up getting a good picture. So, nobody who has trouble following what they are talking about here has to feel bad about it. It clearly does not belong into the box of common knowledge.

    However, in order to be able to sort out what is actually going on, one first needs to aquire the knowledge that is needed to make good judgements about validity or invalidity of statements.

    So, if you got lost, don't worry. What you can do is first, use any good cyclopedia for to find simple definitions about the specific terms. Then (and only after that, otherwise it will be overwhelming) take a good (beginner) text book either about genetics of molecular biology of the cell and go deaper into the material. While doing this, write down questions that came up into your mind. Not everything that we know is explained in text books. Usually they are several years behind our current knowledge.

    Then, look for higher level books or find scientific articles that address your questions. Start with reviews. They are usually most easily to read. From there, take the citated articles that seem to adress your questions best. You can also use internet or library search to find articles that cited the articles that are cited within the review.

    Do not only read one article or book about any particular subject but at least two or three. If they match then it is fine. If they don't then you found something scientists do not agree with one another, which is common. Go from there.

    This is what we tell our students to do if they need/want to find specific scientific information.

    Make up your own mind by studying the subject and don't just believe what somebody tells you.

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  78. I forgot,

    And, if your sit in front of two different oppinions on something such as: evolution can't work vs. evolution is real, collect articles from both sides, validate them for their scientific methods and evidence and consistancy, and keep tracking your questions down in both directions - not just one.

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  79. Hunter sayed:

    "Evolutionists .... , because they believe god never would have designed this world. The underlying foundation of evolutionary thought is metaphysical,"

    Hunter, there might be some religion that calles itself Evolutionist and the foundation of this religion might be to believe in the non-existance of God. Though, I never came across even one of them among those who think that evolution is real.

    Fact is that evolution as a scientific theory that does neither require believing in the existance nor the non-existance of God. This theory stands on its own. It is absolutely independent on any sort of religious believe system.

    There are thousands of scientists who do think that evolution is real and at the same time do believe in the existance of God as part of their religious believe system and they have no problem with that.

    There are also thousands of scientists who think that the scientific theory of evolution is valid while they have all sort of other religious believe systems such as Budism, Hinduism, and many others with all sort of ideas about how to explain the existance of our world on a metaphysical level and they have no problem with that.

    None of them have any problem with being religious and at the same time thinking that evolution is a valid scientific theory. You might not be able to do that and I feel sorry for you. But, this doesn't mean it is true for everybody on this world.

    In fact, it is not true for many many many people and I am one of them and I realy can't understand where the problem is.



    Hunter

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  80. emil:

    So homologous recombination that can result in improved protein function is, probably, not random. It seems like it is controlled by prexisting mechanisms. We aren't sure what these are, or how they work. This is sort of what Dr.
    Hunter was saying above.

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  81. Hunter,

    and, who is next on your list of being accused of having religious motivations beneath their well suported scientific theories?

    The Physicists or the Chemistrists?

    Are we allowed to do anything that does not require believing in the existance of God at the end if things would go according to what you have in mind?

    Something is here badly up-side down.

    It reminds me of something.

    There was once a very famous person..... who sayed in his famous book someting like: It is
    fascinating what one can make people due and believe with good propaganda. It is indeed the most powerfull wheapon of all.

    He even described his propaganda strategies in his book in great detail. Everybody supposed to have read it and they all still fall for it.

    You told me that it is fascinating.
    Yes, it is.

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  82. Dr Hunter,

    Thank you for your lengthy response, which held no surprises at the current epicycle of our discussion of what qualifies as science. Since I can't think of anything new to say, I will shut up on that topic for the time being.

    I will add that despite distractions about whether recombination is a key element of protein evolution and whether evolution is an adequately explanatory theory, we should not lose sight of the fact that the two papers that you cited in your original post demonstrate the creative power of repeated rounds of reproduction with variation (whether random or directed) followed by selection (whether by the environment or by human design). We thank Darwin for those insights, which can't be found in any theory of special creation.

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  83. Hawkes:

    A theory can have a low likelihood without any comparison to other theories*. For example, the likelihood of the existence of polar bears given evolution is miniscule (given ID, it can't even be calculated).

    I am glad to be corrected, but I don't get it. I should think that given special creation, the probability of polar bears (or anything under the sun) would be unity. How did you compute that miniscule probability of polar bears given evolution?

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  84. Hey natschuster,

    If I understand correctly, recombination works because it takes preexisting functioning modules and recombines them. But what keeps the modules intact during the recombining? What process if any, makes sure that the breaks in the chromosomes don't happen in the middle of the modules?

    Well, there two kinds of recombination. Homologous and "non"-homologous.

    Hum, I don't know how much knowledge to assume. So, let me see. Normally DNA is double stranded, and one strand binds to the opposite strand, each strand has a strong affinity to the other. If you have two copies of a gene, when a DNA strand of one breaks, It will have the tendency to pair with either its original pair, or into the pair of the other gene, thus recombining. Now, when two genes are very similar, but bear different mutations, this process can combine two mutations. If these mutations were selected before, their combination improves the characteristic that selected the two mutants in the first place. This is well established by experiment, and, as I told you before, also observed in nature, and inferred.

    Non-homologous recombination is also due to similarity of DNA. Only that pairing happens against much smaller pieces of DNA that are similar to the free strand by chance (there is a higher probability for small DNA strands to be similar than for longer ones for obvious reasons), thus combining, as you suggest in your question, different modules. There is no mechanism avoiding the recombination at the middle of a "module." But "module" is a human concept to try and understand these things. If a complete piece of protein were necessary for this recombination to be a success, then a faulty recombination will just die away, while correct ones will prevail. Though we see more success of "complete" module exchange than incomplete, we also see a few incomplete ones. Meaning that this module thing is not perfect. If only modules were perfect we would have an easier job to do.

    Anyway, I hope this helps.

    Best!

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  85. Hey again natschuster,

    So homologous recombination that can result in improved protein function is, probably, not random.

    The recombination is random. Say two mutant versions of a gene get selected for giving an advantage. Recombination between these two versions would result in a much better gene for whatever that advantage was. So selection takes away the randomness.

    It seems like it is controlled by prexisting mechanisms. We aren't sure what these are, or how they work. This is sort of what Dr.
    Hunter was saying above.


    The controlled mechanism is for the recombination that repairs accidental breaks in DNA. Recombination happens all by itself otherwise. All you need is similarity in DNA strands. For instance, when I learned some techniques in molecular biology one thing we were warned about was the possibility for recombination messing up our experiments.

    Have a great week.

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  86. Pedant:

    I am glad to be corrected, but I don't get it. I should think that given special creation, the probability of polar bears (or anything under the sun) would be unity. How did you compute that miniscule probability of polar bears given evolution?

    I didn't calculate it. I put my finger up in the air and estimated that given some sort of primordial cell sometime in the past, the likelihood that there would now be a thing such as a polar bear would be miniscule. I'm sure we could try to get a better value by estimating the likelihood of eukaryotes arising, followed animals, mammals and so forth (please fill in intermediate and subsequent stages if you would like). At the end of the day, however, I'm sure that you'd agree that there is a pretty slim chance that we would end up with polar bears.

    I'm not 100% sure how special creation would fare here. Sure, an omnipotent designer could easily make polar bears, but should we expect it? For example, does the Bible say that God wanted to make polar bears? I know for a fact that ID says nothing about the designer, so under to ID, we can't even begin to estimate the likelihood in question.

    Now, it is possible that your are not talking about likelihoods at all, but rather about probabilities (the two have specific meanings in bayesianism). Here, we are talking about the probability of your hypothesis given some observation. But I don't think that this is what Cornelius was talking about. His claim that evolution is unlikely tends to pop up when he discusses the likelihood of common ancestry over separate ancestry. This discussion comes from Sober's book "Evidence and Evolution" and Sober definitely talks about likelihoods.

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  87. Hawks,

    Thanks for taking the trouble to clarify your application of Bayesian probability to the evolution of polar bears. Having reviewed what little I know about the Bayesian approach, I recall that one must start with a prior probability, which in your case was pulled out of thin air. (From where else could one pull it?) Sorry if I took you too seriously.

    Therefore, I find the idea of applying Bayesian reasoning to the likelihood that evolution is an adequate explanatory theory ludicrous, and I assume that your tongue was firmly planted in your cheek in your two posts about this. At least I hope that was the position of your tongue.

    You went on to say:

    I'm not 100% sure how special creation would fare here. Sure, an omnipotent designer could easily make polar bears, but should we expect it? For example, does the Bible say that God wanted to make polar bears? I know for a fact that ID says nothing about the designer, so under to ID, we can't even begin to estimate the likelihood in question.

    Since, given special creation, we already know that God could have made polar bears and anything else on any given Thursday, I find at least as ludicrous the application of Bayesian reasoning to what we might have expected if we might have lived in a universe lacking polar bears or anything else.

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  88. Pedant,

    There was nothing tongue in cheek what-so-ever. It seems like your understanding of bayesian probabilities is sorely lacking, however.

    First of all, you don't start with prior probabilities when estimating likelihoods. You start with prior probabilities when estimating posterior probabilities.

    Just to give you an idea of the difference between the two: There are essentially two probabilities in bayesianism as it applies here: (1)likelihood, the likelihood of getting an observation given a hypothesis. (2) Posterior probability, the probability of your hypothesis given a certain observation. Sober uses the example of the observation that you have noises coming from the attic and the hypothesis that there are gremlins bowling up there. The likelihood here is very high, since bowling gremlins would be expected to create a lot of noise. The probability, however, is very low since noises from the attic are rarely made by gremlins bowling.

    Now, Cornelius has been talking about likelihoods, i.e. the likelihood of getting an observation given a certain hypothesis.

    So, why is it ludicrous to say that evolution would be unlikely to make polar bears? Even when not comparing evolution to other theories?

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  89. Hawks:

    There was nothing tongue in cheek what-so-ever. It seems like your understanding of bayesian probabilities is sorely lacking, however.

    Evidently my 30-second scan of the Wikipedia article didn’t bring me up to speed.

    But your explanation of the distinction between “likelihood” and “posterior probability” was most helpful.

    Now, Cornelius has been talking about likelihoods, i.e. the likelihood of getting an observation given a certain hypothesis.

    Are you sure that’s what he’s been talking about? I thought that the particular line he’s been following in this thread is that the evidence in hand contradicts evolution. “Failed predictions” and all that.

    So, why is it ludicrous to say that evolution would be unlikely to make polar bears? Even when not comparing evolution to other theories?

    I can see how a multitude of hypotheses, including that there are gremlins in the attic, makes hearing noises upstairs likely. But how does the hypothesis that evolution occurred make polar bears or anything else unlikely?

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  90. Addendum:

    I also can see that evolution does not predict the existence of polar bears. If that is what is meant by "unlikely," then I get it. That would be one of an infinity of failed predictions, I suppose.

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  91. Pedant,

    Are you sure that’s what he’s been talking about?

    I can't say I'm sure. Judging by the words he's written, it sure sounds like it. He has, as far as I can remember, consistently talked about how likely evolution is when referring to Sober's writings regarding common ancestry versus separate ancestry (Sober rightly points out that although the likelihood of common ancestry is low, it is still WAY higher than separate ancestry). Sober himself, when discussing these issues, is talking about likelihoods. Therefore, I thought I could assume that Cornelius meant the same thing. However, what he actually means... well, that might be another thing altogether.

    I can see how a multitude of hypotheses, including that there are gremlins in the attic, makes hearing noises upstairs likely. But how does the hypothesis that evolution occurred make polar bears or anything else unlikely?

    Think of it like this: if we were to replay the tape of life, i.e. if we were to go back in time to the first replicating cell, would you expect everything to look like it does now? Would you expect to see multicellular organisms? Would you expect to see eukaryoutes? Would you expect to see animals? Would you expect to see mammals? Would you expect to see polar bears? If your answer to the last question is "no", then the evolution of polar bears is unlikely. Please note (and this is a point that I think Cornelius fails to grasp) that when you say that a hypothesis is unlikely, you say nothing about it's probability. This is why you have to compare two (or more) hypotheses against each other. A hypothesis that is less unlikely (or more likely) than another stands a better chance of being correct (this is a bit simplified, obviously).

    P.S. just to reiterate something I wrote in an earlier post: we don't have to start with a simple primordial cell sometime in an unspecified past in order to estimate the likelihood of an observation under evolution. We could also start with using some assumptions such as the existence of bears that were not polar X years ago. We could also add assumptions about the existence of cold climates and white snow in the past that could select for something akin to polar bears. In such a scenario, the likelihood of evolution goes up quite considerably. What one has to do when doing this, is to be careful when selecting which assumptions to use - and no, you don't select them simply because they support your conclusion - you have to have independent evidence for them. See Sober's very good, if sometimes hard to understand, article "What is wrong with Intelligent Design?"
    (http://philosophy.wisc.edu/sober/what%27s%20wrong%20with%20id%20qrb%202007.pdf)

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  92. Hawks:

    Pedant,

    "Are you sure that’s what he’s been talking about?"

    I can't say I'm sure. Judging by the words he's written, it sure sounds like it.
    .

    Ambiguity, equivocation, and moving goalposts are vital weapons in the rhetorical arsenal of evolution denialists.

    He has, as far as I can remember, consistently talked about how likely evolution is when referring to Sober's writings regarding common ancestry versus separate ancestry (Sober rightly points out that although the likelihood of common ancestry is low, it is still WAY higher than separate ancestry).

    Sober is using contrastive reasoning. I believe that Hunter once called such reasoning a logical fallacy, but I don't have the reference. In any case, he finds such reasoning perverse, as shown by his comments in this thread.

    Sober himself, when discussing these issues, is talking about likelihoods. Therefore, I thought I could assume that Cornelius meant the same thing. However, what he actually means... well, that might be another thing altogether.

    Evasion is another weapon in the rhetorical arsenal of evolution denialists.

    Think of it like this: if we were to replay the tape of life...
    ... Would you expect to see polar bears?


    As I said above, I agree that evolution does not predict the existence of polar bears.

    Please note (and this is a point that I think Cornelius fails to grasp) that when you say that a hypothesis is unlikely, you say nothing about it's probability. This is why you have to compare two (or more) hypotheses against each other. A hypothesis that is less unlikely (or more likely) than another stands a better chance of being correct (this is a bit simplified, obviously).

    There you go again with your infernal contrastive reasoning. That pretzel-twisting evolutionist logic mocks true Baconian-Hunterian empirical science.

    See Sober's very good, if sometimes hard to understand, article "What is wrong with Intelligent Design?"
    (http://philosophy.wisc.edu/sober/what%27s%20wrong%20with%20id%20qrb%202007.pdf)


    I enjoyed rereading Sober's essay. But I have to remind you that it's full of that detestable contrastive reasoning.

    So, if I now understand you correctly, you've been saying that Hunter is correct in claiming that the likelihood of the theory of evolution can be determined in the absence of an alternative theory. However, that tells you nothing about its probability of being true, which requires comparison with other theories. That would make Hunter's objection trivial.

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  93. Pedant,

    That would make Hunter's objection trivial.

    I sure think that it is. I haven't exactly been the only one to ask Cornelius to propose an alternative to evolution that has a higher likelihood. But then, as you say, Cornelius doesn't like contrastive thinking...

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  94. Thanks, Hawks, I enjoyed our chat.

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