Home » Darwinism, News » What do readers make of claims for neutral evolution?

What do readers make of claims for neutral evolution?

As in Carl Zimmer’s recent Scientific American article here.

The scenario that Gray proposes for the evolution of RNA editing goes like this: an enzyme mutates so that it can latch onto RNA and change certain nucleotides. This enzyme does not harm the cell, nor does it help it—at least not at first. Doing no harm, it persists. Later a harmful mutation occurs in a gene. Fortunately, the cell already has the RNA-binding enzyme, which can compensate for this mutation by editing the RNA. It shields the cell from the harm of the mutation, allowing the mutation to get passed down to the next generation and spread throughout the population. The evolution of this RNA-editing enzyme and the mutation it fixed was not driven by natural selection, Gray argues. Instead this extra layer of complexity evolved on its own—“neutrally.” Then, once it became widespread, there was no way to get rid of it.

David Speijer, a biochemist at the University of Amsterdam, thinks that Gray and his colleagues have done biology a service with the idea of constructive neutral evolution, especially by challenging the notion that all complexity must be adaptive.But Speijer worries they may be pushing their argument too hard in some cases. On one hand, he thinks that the fungus pumps are a good example of constructive neutral evolution. “Everybody in their right mind would totally agree with it,” he says. In other cases, such as RNA editing, scientists should not, in his view, dismiss the possibility that natural selection was at work, even if the complexity seems useless.

Gray, McShea and Brandon acknowledge the important role of natural selection in the rise of the complexity that surrounds us, from the biochemistry that builds a feather to the photosynthetic factories inside the leaves of trees. Yet they hope their research will coax other biologists to think beyond natural selection and to see the possibility that random mutation can fuel the evolution of complexity on its own. “We don’t dismiss adaptation at all as part of that,” Gray says. “We just don’t think it explains everything.”

Uh, no. Thoughts?

Is this serious inquiry or the Emperor’s lapdogs at play?

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32 Responses to What do readers make of claims for neutral evolution?

  1. an enzyme mutates so that it can latch onto RNA and change certain nucleotides. This enzyme does not harm the cell, nor does it help it—at least not at first.

    So basically, it evolved, and spread through the population, with no help at all from natural selection.

    What are the odds of that?

    It never ceases to amaze me how we can be told over and over that evolution isn’t a random process, but when you really need to explain something difficult, neutral evolution, and drift, and “it just happened – that’s all” are taken seriously.

    …especially by challenging the notion that all complexity must be adaptive.

    But that notion has been challenged repeatedly already, so nothing new here. So now we have just another tool in the evolution smorgasbord to be hauled out when needed to protect the theory from disconfirmation. (HT: Walter ReMine)

    “We don’t dismiss adaptation at all as part of that,” Gray says. “We just don’t think it explains everything.”

    You don’t say.

  2. Most evolution happens outside of positive selection as a matter of principle:


  3. It’s interesting that evolutionists themselves are coming to realize the problems with evolution by adaptation more and more.

    I can see this type of neutral evolution working very rarely in very simple cases where the new feature/ability can be evolved by one mutation. However, the chances that neutral evolution will result in an overall positive effect on the organism is vanishingly small I would think. After all, this is the same thing Dr. John Sanford is claiming. Only he says that the build up of these neutral mutations leads to an insurmountable problem for the organism. And I think his view has data to back it up.

    I see this idea of neutral evolution by gray as a tacit admission of the problem of mutations under the radar of natural selection. As Sanford shows, it has an overwhelmingly negative effect. The chances of any neutral mutation just happening to set the organism up for its next step forward in the evolutionary process – well lets just say it would take a lot of faith to believe in that.

    So adaptive eviction is not sufficient to explain evolution, but certainly this idea is way out there as well. That leaves us with two broken processes. Two I sufficient processes do not solve the problem!

    Even if by wild chance, this could have happened a few times, he opens up a fatal can of worms for evolution as Dr. Sanford shows.

  4. The chances of any neutral mutation just happening to set the organism up for its next step forward in the evolutionary process – well lets just say it would take a lot of faith to believe in that.

    Faith in Intelligent Design!

  5. Mung,

    There is still a knee-jerk reaction by most molecular biologists to presume any feature of a genome is there for some functional reason (c.f. ENCODE, rush to call every RNA transcript a function etc etc). So pointing out complexity can arise without selection is an important thing to do, I think.

    In terms of the probability of a new variant fixing without selection. It’s always the same one over the (effective) population size. So any particular mutation is unlikely to make it, but in time it’s inevitable that some will (and in fact, they’ll fix at the per-individual mutation rate). If you take the typical creationist approach to probablity – pre-specify some specific outcome as being required and work back to see how likely that looks exceeding improbable. But, of course, there was no pre-specification, and there are many many other pathways that could have generated similarly improbably outcomes for anyone that found them to wonder at.

    Constructive neutral evolution is a field still in development, but it’s one that should be taken seriously.

  6. As to wd400′s seemingly ‘blind faith’ claim in constructive neutral evolution:

    “Constructive neutral evolution is a field still in development, but it’s one that should be taken seriously.”

    Besides the concession that they really have no clue how complexity arises, since selection is removed from the picture with neutral evolution, it Seems this is the exact same dog that couldn’t hunt before,,

    Michael Behe on the theory of constructive neutral evolution – February 2012
    Excerpt: I don’t mean to be unkind, but I think that the idea seems reasonable only to the extent that it is vague and undeveloped; when examined critically it quickly loses plausibility. The first thing to note about the paper is that it contains absolutely no calculations to support the feasibility of the model. This is inexcusable. – Michael Behe

    A few notes on how the ‘neutral’ theory came about in the first place:

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video

    At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno’s work in the late 1950’s, 60’s through the early 70’s:

    What Is The Genome? It’s Not Junk! – Dr. Robert Carter – video – (Notes in video description)

    Berlinski, with his usual penetrating wit, comments on the neutral theory here:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.

    A few more quotes:

    Ann Gauger on genetic drift – August 2012
    Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter.

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.

  7. wd400:

    There is still a knee-jerk reaction by most molecular biologists to presume any feature of a genome is there for some functional reason (c.f. ENCODE, rush to call every RNA transcript a function etc etc).

    Funny, I was JUST thinking about ENCODE. It’s true!

    Why is it that ID opponents are quick to grasp at the slightest hint of “functionality” in a polypeptide, but so vehemently oppose the ENCODE findings?

    Don’t the “odds” I asked about depend in some way on just how many mutations were required to reach this new state of complexity? I mean, if it was a simple, they wouldn’t call it complex, would they?

    And after the first mutation, it has to get fixed, via drift. And that takes time. And then a second one has to come along that will, by some fortuitous means not yet well understood when combined with the first and some as yet unspecified number of future mutations, produce some new complexity that wasn’t there before, and that too has to get fixed. And that takes time. And all the while neither of these two can get lost or changed or we’re back to square one. Wash rinse repeat. And as we add more mutations to the scenario the odds that the prior ones get changed go up, after all, there’s no selection to favor them. It’s just pure dumb luck. Blind search at it’s finest.

    I’d just love to see a realistic model of this scenario.

  8. Why is it that ID opponents are quick to grasp at the slightest hint of “functionality” in a polypeptide, but so vehemently oppose the ENCODE findings

    I can only speak for myself. The ENCODE findings are what they are – the problem is in the interpretation that every transcribed section of DNA is a functional gene. I’ve never grasped at function in a peptide. They do something or they don’t really.

    In terms of the odds. Let’s talk about a specific example, like subfunctionalization. That is

    1. Gene duplication
    2. Loss of some functional region in each daughter gene
    3. Maintenance of orginal gene’s functions across the two daughter genes.

    This process increases complexity (more interacting gene products in the pathway) almost _has_ to happen eventually. Genes are being duplicated frequently, and this will usually have little or no fitness effect. Thus, gene duplicates will fix at the mutation rate.

    Mutations will keep popping up in the daughter genes. Since there is a back up copy of this gene, there is no selection pressure to maintain its function so amino-acid-changing mutations, which would usually be selected against, will fix at the mutation rate. Once that mutation is fixed, the other daughter gene is required and we are back to negative selection to conserve the function

    That’s the verbal model, you can turn it into a mathematical one and you see it playing out in genome sequences. But it should be clear that you get an increase in complexity of the genome with neutral models.

  9. And other than conjecture what actual empirical evidence do you have that it is even possible? Is it something like this:

    Problem 1: Offsetting the cost of gene expression

    Axe and Gauger observe that “The most widely accepted explanation for the origin of new enzymes is gene duplication and recruitment.” However, they cite experimental work showing that a duplicate gene is much more likely to be silenced (because of the costly resources expended in transcribing and translating it) than it is to acquire a new function. So the first obstacle is as follows:

    First obstacle: Because gene expression is costly, it cannot be assumed that weakly converted enzyme functions isolated by laboratory selection would provide net selective benefit in wild populations.

    In their view, intelligent design provides a better explanation because such innovations require a goal-directed cause that looks beyond immediate fitness costs that go along with preserving a non-advantageous duplicate gene. Thus, they derive the

    First principle: Innovations are more like investments than quick cash. They must be well implemented to offset their cost, and even then the benefits tend to accrue over a long period.

    - See more at: http://www.evolutionnews.org/2.....FmIaY.dpuf

    Mmmm, imagination instead of science wd400?

  10. As far as I can tell it’s Axe and Gauger doing the imagining

    However, they cite experimental work showing that a duplicate gene is much more likely to be silenced (because of the costly resources expended in transcribing and translating it)

    I should like to see their cited sources. Seems very unlikely to be true in Eukaryotes (but might explain why bacteria are so good and what they do and Euks are so junky)

    In any case. There is much evidence for gene duplication. They should do some science and stop imagining…

  11. Funny wd400, you, as usual, didn’t bother to cite any empirical evidence FOR your position but are, once again, making bald face assertions. Someone might get the impression you are less than forthright (better at least do a literature bluff dude!)

    Can Random Mutations Create New Complex Features? A Response to TalkOrigins – Casey Luskin June 22, 2012
    Excerpt: the (talkorigins) page suggests searching for “gene duplication” on PubMed to find “more than 3000 references” on the topic. These papers, we’re meant to assume, show how evolutionary mechanisms can create new information. But a survey of major review articles on gene duplication I published here on ENV in 2010 revealed that the studies never established that mutations could have produced the complex features in question. After taking a close look at this literature, I found:
    The NCSE’s (and Judge Jones’s) citation bluffs have not explained how neo-Darwinian mechanisms produce new functional biological information. Instead, the mechanisms invoked in these papers are vague and hypothetical at best:

    *exons may have been “recruited” or “donated” from other genes (and in some cases from an “unknown source”);
    *there were vague appeals to “extensive refashioning of the genome”;
    *mutations were said to cause “fortuitous juxtaposition of suitable sequences” in a gene-promoting region that therefore “did not really ‘evolve’”;
    *researchers assumed “radical change in the structure” due to “rapid, adaptive evolution” and claimed that “positive selection has played an important role in the evolution” of the gene, even though the function of the gene was unknown;
    *genes were purportedly “cobbled together from DNA of no related function (or no function at all)”;
    *the “creation” of new exons “from a unique noncoding genomic sequence that fortuitously evolved” was assumed, not demonstrated;
    *we were given alternatives that promoter regions arose from a “random genomic sequence that happens to be similar to a promoter sequence,” or that the gene arose because it was inserted by pure chance right next to a functional promoter.
    *explanations went little further than invoking “the chimeric fusion of two genes” based solely on sequence similarity;
    *when no source material is recognizable, we’re told that “genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors” because they are simply “hypermutable”;
    *we even saw “a striking case of convergent evolution” of “near-identical” proteins.

    To reiterate, in no case were the odds of these unlikely events taking place actually calculated. Incredibly, natural selection was repeatedly invoked in instances where the investigators did not know the function of the gene being studied and thus could not possibly have identified any functional advantages gained through the mutations being invoked. In the case where multiple mutational steps were involved, no tests were done of the functional viability of the alleged intermediate stages. These papers offer vague stories but not viable, plausibly demonstrated explanations for the origin of new genetic information.
    I haven’t gone through all “3000 references” cited by TalkOrigins. Neither, in all likelihood, has the author of the TalkOrigins page. But my strong suspicion is that if you went through many of those pages, you’d reach the same conclusion.
    This 3000-unnamed-paper citation bluff — and much other material on this TalkOrigins page, are not to be taken seriously.

    Evolution by Gene Duplication Falsified – December 2010
    Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.

  12. Incredibly, natural selection was repeatedly invoked in instances where the investigators did not know the function of the gene being studied and thus could not possibly have identified any functional advantages

    Ha! If you know the first thing about molecular evolution this is a pretty embarrassing mistake by Luskin. There are many way to measure the effect of selection that don’t require any knowledge of the selected residues function.

  13. wd400, if on the off chance you ever do decide to become honest, (I do believe in miracles by the way), This following article will give you a primer on how far off the mark Darwinists are from having any actual empirical support for there ‘ahem’ theory:

    Hopeless Matzke – David Berlinski & Tyler Hampton – August 18, 2013

  14. wd400, doesn’t it ever bother you that atheists like you are so conceded? You never offer any actual empirical evidence for you position and always go on about how much smarter you are than everyone else:

    How atheists became the most colossally smug and annoying people on the planet – August 2013

    its pretty sickening to tell you the truth. Tell you what smart guy, why don’t you be the first ‘oh so much smarter than everybody else’ atheist to put your money where your mouth is a show us just one molecular machine arising by Darwinian processes:

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe – 29:24 mark of following video

    Also of note, Dr. James Tour, who builds the most sophisticated man-made molecular machines in the world,,,

    Science & Faith — Dr. James Tour – video

    ,,will buy lunch for anyone who can explain to him exactly how Darwinian evolution works:

    Top Ten Most Cited Chemist in the World Knows That Evolution Doesn’t Work – James Tour, Phd. – video

  15. BA,

    You were doing so well at writing your own sentences for a bit there. I don’t reply to the link spam, but I’m honest, I’ve given you examples of the evolution of molecular machines by Darwinian methods (RNA enzymes) and I’m happy to provide evidence for particular claims. But I’m not going to dance on command, or answer each new item from the Gish gallop.

    This was a thread about constructive neutral evolution. Mung wanted to know what a model of complexity increasing without positive selection would look like, I presented them with a verbal version of one such model. The term subfunctionalization should be enough for anyone wanting to read more details into how thie model works and find what evidence there is to support it’s role in evolution.

  16. wd400, now this is interesting, after you put me down (right after I noted how conceded you were) you then claimed to be honest :) which is laughable to anyone who has dealt with you on UD, but you then you go all out and claim to have actual empirical evidence for purely Darwinian processes creating a molecular machine. REALLY???

    Well do not be so bashful wd400, Dr. Behe, Dr. Tour, Dr. Axe and a host other DRs., will be very interested in your proof. Present it, and let’s be done with all this debate!,,, Remember no intelligence is allowed to generate the sequences beforehand!

  17. correction: right after I noted how conceited you were,,

    there were other mistakes in my post, but I want to make sure you get that word,,,

  18. Seriously BA? You’re so desperate to insult me you need to respell the post and bold then term?

    Anyway – if you can point out where I’ve been dishonest let me know. As to the molecular machine. I previously pointed out this one . A sequence original created by in vitro evolution was modified to generate a new function by Darwinian methods.

    Now, I’m sure you’ll find something wanting in this. I’m very unlikely to reply.

  19. For anyone who wants a good laugh, here is the experiment that wd400 is trying to sell as Darwinian processes generating a molecular machine.

    Biologic Institute Announces First Self-Replicating Motor Vehicle – Doug Axe -
    Excerpt: The humble truth is that the catalytic RNAs simply join two pre-made halves together by making a single new chemical bond. [2] What’s more, the molecular structure for accomplishing this joining is built into the precursors in such a way that 1) wrong ends cannot be joined, and 2) the energy for the correct joining is pre-supplied.

    How reasonable is it to call something so carefully set up “self-replication”?

    It all boils down to the question of what is doing the work of making the replicas. If it isn’t really being done by the things being replicated, then it isn’t really self-replication. Living systems have fully earned that title by actually doing the work. But in the RNA demonstration, as in the Jeep one, the real work occurred behind the scenes. For the Jeeps it happened at a sophisticated assembly plant in Ohio. For the RNAs it happened on a sophisticated oligonucleotide synthesizer, supplied with the requisite reagents and programmed by people who went to great lengths to identify RNA base sequences that would work.

    To get an idea of how little was actually being accomplished (comparatively speaking) by the RNAs themselves, we should see how the total number of chemical bonds in the complete RNAs compares to the number made (one) during “self-replication”. Ignoring hydrogen atoms, which don’t join atoms up into large molecules, each complete RNA molecule had over 1,600 specific chemical bonds. Except for the final one, all of these bonds were pre-made in the process of making the precursors.

    So, advertising this as “self-replication” is a bit like advertising something as “free” when the actual deal is 1 free for every 1,600 purchased. It’s even worse, though, because you need lots of the pre-made precursors in cozy proximity to a finished RNA in order to kick the process off. That makes the real deal more like n free for every 1,600 n purchased, with the caveats that n must be a very large number and that full payment must be made in advance.

  20. wd400, You ask me to point out where you have been dishonest?

    that would be post 18 wd400! :)

  21. No. You asked for a molecular machine produced via Darwinian processes. You got one (of many such examples). Axe’s article is (a) not very informed and (b) apparently about the origin of life, not the question you asked.

  22. wd400, make that 18 and 21 that you have been dishonest in.

    your cite:

    Self-sustained Replication of an RNA Enzyme
    Tracey A. Lincoln and Gerald F. Joyce – Feb 2009

    Dr. Axe’s cite:

    Self-sustained replication of an RNA enzyme.
    Lincoln TA, Joyce GF. – Feb 2009

    As to the ‘man behind the curtain’ that wd400 pretends nobody can see,

    “the real work occurred behind the scenes. For the Jeeps it happened at a sophisticated assembly plant in Ohio. For the RNAs it happened on a sophisticated oligonucleotide synthesizer, supplied with the requisite reagents and programmed by people who went to great lengths to identify RNA base sequences that would work.

    Keep trying wd400, you may become as sleazy and dishonest as Matzke yet! :)

  23. BA,

    I don’t know why you’re so commited to insulting me and presuming bad faith on my part. It’s, to say the least, not very helpful.

    Read the paper, you’ll see the function in the starting RNAs was generated by in vitro evolution. You should read a bit more about these sorts of experiments, it turns out functional RNA molecules are quite common in sequence space (much more so than peptides).

  24. wd400, it is not an insult to point out that you are dishonest since you are in fact being dishonest, just as it is not an insult for me to call an alcoholic an alcoholic since anyone who drinks constantly is an alcoholic. The actual damage is done when the alcoholic himself denies that he is an alcoholic and continues to destroy his life and the lives of others who depend on him! Whether you are lying to yourself or to us I do not know for sure, so I cannot say it is ‘bad faith’ on your part. But I highly suspect that it is ‘bad faith’ on your part since, though you are certainly not as smart as you presume yourself to be, you seem, none-the-less, smart enough to be aware of your gross misrepresentation of the evidence. For instance, in the paper you referenced, in response to me asking you for empirical evidence of a molecular machine generated by purely Darwinian processes, you blatantly ignore all the behind the scenes work that was done by the ‘intelligent’ experimenters in order to make this very simple reaction work:

    “For the RNAs it happened on a sophisticated oligonucleotide synthesizer, supplied with the requisite reagents and programmed by people who went to great lengths to identify RNA base sequences that would work.”

    Needless to say, chemists going to great length to set up a single particular reaction is far from purely Darwinian processes generating a molecular machine.

    You know wd400, admitting you have a problem is the first step in recovery! :)

    As to the pathetic evidence wd400 presented to us for a single reaction ‘molecular machine’ and what actually needs to be explained by purely Darwinian processes:

    Bacterial Flagellum – A Sheer Wonder Of Intelligent Design – video

    Biologist Howard Berg at Harvard calls the Bacterial Flagellum
    “the most efficient machine in the universe.”

    Souped-Up Hyper-Drive Flagellum Discovered – December 3, 2012
    Excerpt: Get a load of this — a bacterium that packs a gear-driven, seven-engine, magnetic-guided flagellar bundle that gets 0 to 300 micrometers in one second, ten times faster than E. coli.
    If you thought the standard bacterial flagellum made the case for intelligent design, wait till you hear the specs on MO-1,,,
    Harvard’s mastermind of flagellum reverse engineering, this paper describes the Ferrari of flagella.
    ” Instead of being a simple helically wound propeller driven by a rotary motor, it is a complex organelle consisting of 7 flagella and 24 fibrils that form a tight bundle enveloped by a glycoprotein sheath…. the flagella of MO-1 must rotate individually, and yet the entire bundle functions as a unit to comprise a motility organelle.”
    To feel the Wow! factor, jump ahead to Figure 6 in the paper. It shows seven engines in one, arranged in a hexagonal array, stylized by the authors in a cross-sectional model that shows them all as gears interacting with 24 smaller gears between them. The flagella rotate one way, and the smaller gears rotate the opposite way to maximize torque while minimizing friction. Download the movie from the Supplemental Information page to see the gears in action.

  25. wd400,

    Either you are ignorant or dishonest- Scientists created those RNAs- darwinian processes had nothing to do with it. Also no new function evolved.

    As for gene duplication, please tell us how it was determined that gene duplication is a blind and undirected chemical process.

  26. BA,

    You asked for a molecular machine arrived at by Darwinian processes at you go one. As I’ve already said, the function of the starting sequences was also uncovered via in vitro evolution, so the text have copied from Axe’s and bolded is not relevant.

    Of course, as expected, you shifted the goal posts and now want molecular machines to arise without humans setting up the experiment (or something?) and one machine is not enough, you want the bacterial flagellum to arise from nothing (as if that was the position evolutionary biology supported). Between that and your rudeness you’ve amply shown why you aren’t worth bothering with, so I’ll take my leave here.

  27. wd400 what is interesting in all this is the paltry evidence you are more than willing to accept as evidence that randomly colliding molecules, all by their lonesome, can generate the unfathomed levels of complexity we are finding in life. The gulf between what you have shown us (even ignoring the intelligent chemists in the background guiding the process to a desired goal) and what needs to be explained is a chasm that easily spans the width and time of the universe. For instance:

    Just finding a functional protein it is estimated:

    The Case Against a Darwinian Origin of Protein Folds – Douglas Axe – 2010
    Excerpt Pg. 11: “Based on analysis of the genomes of 447 bacterial species, the projected number of different domain structures per species averages 991. Comparing this to the number of pathways by which metabolic processes are carried out, which is around 263 for E. coli, provides a rough figure of three or four new domain folds being needed, on average, for every new metabolic pathway. In order to accomplish this successfully, an evolutionary search would need to be capable of locating sequences that amount to anything from one in 10^159 to one in 10^308 possibilities, something the neo-Darwinian model falls short of by a very wide margin.”

    Signature In The Cell – Review
    Excerpt: Even if you grant the most generous assumptions: that every elementary particle in the observable universe is a chemical laboratory randomly splicing amino acids into proteins every Planck time for the entire history of the universe, there is a vanishingly small probability that even a single functionally folded protein of 150 amino acids would have been created.

    “a very rough but conservative result is that if all the sequences that define a particular (protein) structure or fold-set where gathered into an area 1 square meter in area, the next island would be tens of millions of light years away.”
    Kirk Durston

    And those are estimates based on the assumption that the universe is friendly to natural processes searching sequence space for functional proteins, yet in reality we find:

    Abiogenic Origin of Life: A Theory in Crisis – Arthur V. Chadwick, Ph.D.
    Excerpt: The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment. A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.

    Moreover, even if we found a functional protein by natural processes, the probability that we would be able to generate novel binding sites with it so that it might interact with different proteins in new and unique ways, (as is required in a Darwinian scenario), is, for all practical purposes, zero:

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    This ‘lack of flexibility’ in generating novel protein-protein binding sites agrees with what Dr. Axe and Gauger found for transitioning an existing functional protein into another similar protein of a slightly different function:

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.

    Moreover, because of differences in population sizes and reproduction rates, the problem is only exponentially exasperated for humans to accomplish any meaningful evolutionary novelty:

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    Excerpt: The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.

    Is There Enough Time For Humans to have Evolved from Apes? Dr. Ann Gauger Answers – video

    Those are the brute honest facts wd400, and as any fair minded person can see, it will take far more than a pathetic literature bluff from you to overcome those facts as to the severe limits found for Darwinian processes!

  28. In my first post I wrote:

    But that notion has been challenged repeatedly already, so nothing new here.

    wd400 offers an example, gene duplication with subsequent divergence.

    He at least implies that the same model would be applicable to the scenario outlined in the OP. But is it really the same scenario?

    wd400, are you saying there’s really nothing much new in the Gray proposal? There’s already a well know mechanism and model of what he is proposing?

    And isn’t a functional gene something that is at least presumably already complex?

  29. Thank God this thread was created by a real News person. Else I’d have to be worried that my obviously trollish posts would be deleted by someone posing as News.

  30. Mung,

    Subfunctionalization is just an acessable example or a process where complexity increases without any positive selection. You’d asked for an idea of the odds of netural processes adding up to somthing complex, and I thought it was a nice example of how even events that are very rare per-gene per-individual nevertheless happen all the time.

    I’m not saying the constructive neutral evolution crowd don’t have more than subfunctionalization to offer, just that it’s an example of their ideas. To that you can add the study of intrinsic biases in mutation, or the number of interactions proteins and RNAs have whether they are related to function or not. And of course there are population genetic arguments.

    Functional genes are complex, of course. But the point is not to explain all complexity, just how lineages get more complex.

  31. wd400:

    Subfunctionalization is just an acessable example or a process where complexity increases without any positive selection.

    Even the choice of term, subfunctionalization, tells the story.

    How do you propose to quantify the increase in complexity? Remember, I’m looking for a model or how to create one.

    Presumably the duplicated gene already codes for a functional protein, an entity that is by all accounts complex. Which means it already folds, and already performs some function. Even in your scenario you have avoid turning the product into something that does not fold, or find another fold strictly by neutral mutations.

    So I honestly don’t think you are giving me an option that is in any way analogous to that presented by the OP. But I’m willing to listen.

    I’m not saying the constructive neutral evolution crowd don’t have more than subfunctionalization to offer, just that it’s an example of their ideas.

    I say that they have something completely different to offer. Am I wrong?

    Others maintain that as random mutations arise, complexity emerges as a side effect, even without natural selection to help it along. Complexity, they say, is not purely the result of millions of years of fine-tuning through natural selection—the process that Richard Dawkins famously dubbed “the blind watchmaker.” To some extent, it just happens.

    Decidedly different. IMO.

    Even the title seems to suggest something contrary to your scenario (unless Zimmer is just using poetic license):
    The Surprising Origins of Evolutionary Complexity

    If the origins of complexity are by pure random search, then Darwinism is dead. My question is, how do we model it. How do we test it? IS it even remotely plausible?

    Poofery dressed up in the finest scientific garb!

    Unlike standard evolutionary theory, McShea and Brandon see complexity increasing even in the absence of natural selection. This statement is, they maintain, a fundamental law of biology—perhaps its only one. They have dubbed it the zero-force evolutionary law.

    By the way, I saw their book on Amazon some time back and didn’t even think I wanted to waste money on it. Maybe now I’ll at least have to take a look.

    Darwinism (supposedly) gave us a plausible “design without a designer.” But now we find out that not even natural selection is required to give us “the appearance of design.’

    Heck, it’s a fundamental law of biology. Great for ID! Teleologists rejoice!

  32. wd400:

    You asked for a molecular machine arrived at by Darwinian processes at you go one.

    Liar. Genetic engineering does not = darwinian processes and the “machine” you linked to was engineered.

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