Evolution of an Irreducibly Complex System – Lenski’s E. Coli

"CHartsil is confused. All that happened with Lenski’s experiment is that the E coli could now utilize citrate in an oxygen-rich environment. They already had that ability in the an anaerobic environment." That was already pointed out. It didn't have the ability in an aerobic environment. "An IC system did NOT evolve via unguided processes." It was dependent on multiple changes in multiple systems and cannot function without all of said changes. It's IC "No new genes were formed. An existing gene was duplicated and put under the control of a different promoter, ie a promoter that was on in the presence of O2." It's a new gene head to tail opposed to the other. "Thus, Behe explains that the precise genetic mechanisms that allowed E. coli to uptake citrate under oxic conditions are not known. But Behe goes further and points out that the citrate-metabolizing E. coli strains really aren’t anything new, and that previous investigations suggest that the ability of the E. coli to uptake citrate under oxic conditions might result from molecular loss-of-function:" Except it WAS already known, a head to tail duplication and a novel regulatory module. That's the point. It's new information that is reliant on other, also new information. "The change was not information-rich It’s not clear that natural selection produced this change Function was diminished or lost rather than gained" It can now metabolize a food source in an entirely new environment. As the generations pass, it only becomes more prominnet It was due to a duplication. Also, evolution is not directional.CHartsil

February 25, 2015

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kairosfocus @85 on the other thread writes: F/N part 2: Let’s continue, sect 6: ______________ >>Section 6: Another Bogus Claim of “Novel Function Arising Through Mutation and Selection” In this section, we: • Understand why Dennis Venema’s citation of Joseph Thornton’s steroid research does do not demonstrate a “fascinating case of a novel function arising through mutation and selection” • Review the multiple responses to Thornton’s research from leading ID proponents (all ignored by Venema) who found the changes were not information-rich, not necessarily produced by natural selection, entailed diminishment rather than gain of function, and well within the ‘edge of evolution’ • See that Venema undercuts his own claims by admitting, “Steroid hormones are a closely related molecules — it’s not too surprising that slightly different molecules fit into a related group of protein receptors” In the case of Richard Lenski’s Long Term Evolution Experiments (LTEE) with E. Coli bacteria, we saw that Dennis Venema of BioLogos cited purported examples of natural selection increasing specified and complex information — but intelligent design (ID) proponents had long before critiqued these examples. For example, Lenski’s LTEE had been critiqued by Michael Behe when they first came out in 2008, and then later in Behe’s 2010 paper in Quarterly Review of Biology. Venema, however, discussed none of these critiques. But Venema has a second empirical example he cites to supposedly show the Darwinian evolution of what he calls “CSI on Steroids.” Citing research co-published by University of Oregon biologist Joe Thornton in 2006, Venema calls this “a second fascinating case of a novel function arising through mutation and selection.” But here too, ID proponents had extensively critiqued the experiment when it was first published. And again, Venema failed to discuss or respond to any of these prior arguments from ID proponents. It’s hard to ignore responses from the ID camp to Thornton’s research since there are so many of them. These responses were all published back in 2006 when Thornton’s research was first published: Michael Behe on the Theory of Irreducible Complexity How to Explain Irreducible Complexity — A Lab Manual Paul Nelson on Debating the Controversy That Doesn’t Exist Bruce Chapman on the Science Stories that Fizzled (and the One that Might Have Been) CSC Director Stephen C. Meyer Responds to Research on Irreducible Complexity Casey Luskin: Science Plays Politics, but Implies Behe and Snoke (2004) Supports Irreducible Complexity and ID After All Many of these responses will be discussed below. Venema claims that Thornton’s research shows “a second fascinating case of a novel function arising through mutation and selection.” As we will see, if by “novel function” Venema means “diminishment of function,” then perhaps he is correct. As a brief and cursory summary of problems with the Thornton et al. research, consider the following points: The Thornton et al. research cited by Venema merely found that an alleged precursor enzyme could potentially perform two functions, and then supposedly lost the ability to perform one of those functions. At worst it shows loss-of-function through two mutations. At best, this is an example of small-scale change, which the research of ID proponents like Michael Behe readily concedes is possible. Because Thornton et al.’s research only supported small-scale evolution, which ID proponents don’t question, Behe wrote in response: “This continues the venerable Darwinian tradition of making grandiose claims based on piddling results. There is nothing in the paper that an ID proponent would think was beyond random mutation and natural selection. In other words, it is a straw man.” Christoph Adami reviewed Thornton et al.’s research in Science, claiming it refuted ID. The research was also puffed in the New York Times as addressing intelligent design after the authors issued a press release entitled “Evolution of ‘Irreducible Complexity’ Explained,” purporting to be a direct response to “[a]dvocates of Intelligent Design.” Whether they are right or wrong, this is amusing since we see ID-critics debating over the scientific controversy that they claim does not exist. The authors’ press release gave a retroactive confession of ignorance, admitting that “[h]ow natural selection can drive the evolution of tightly integrated molecular systems … has been an unsolved issue in evolutionary biology.” Yet in the New York Times article, Thornton commented that “There’s no scientific controversy over whether this system evolved. The question for scientists is how it evolved.” So before this study they didn’t know how it evolved, yet somehow they knew it did evolve. It sounds like they are assuming the truth of Darwinian theory rather than testing it. Before the paper was published, Thornton had stated on his website that his “goal is to illustrate how a complex, tightly integrated molecular system — one which appears to be “irreducibly complex” — evolved by Darwinian processes.” After ID-theorist Paul Nelson pointed out that this implied that Thornton saw irreducible complexity as a legitimate scientific challenge, the words “irreducibly complex” magically disappeared from Thornton’s website. The episode demonstrates that ID raises legitimate scientific challenges of interest to Darwinian evolutionary biologists, even as they sometimes deny that fact for political reasons. In sum, this study doesn’t show how Darwinian evolution scales Mount Improbable, as Dawkins has put it. It simply shows that neo-Darwinism can get you the last 10 yards up the mountain after you’ve already spent 10 hours hiking. It’s an exercise in what Behe called “making grandiose claims based on piddling results.” But there’s much more to say in response to this research. Since much of the work responding to it has already been done, the best thing is simply to quote from some of these responses: Response 1: Michael Behe’s comments: The bottom line of the study is this: the authors started with a protein which already had the ability to strongly interact with three kinds of steroid hormones (aldosterone, cortisol, and “DOC” [11-deoxycorticosterone]). After introducing several simple mutations the protein interacted much more weakly with all of those steroids. In other words, a pre-existing ability was decreased. That’s it! The fact that this extremely modest and substantially irrelevant study is ballyhooed with press releases, a commentary in Science by Christoph Adami, and forthcoming stories in the mainstream media, demonstrates the great anxiety some folks feel about intelligent design. In the study the authors wished to see if two related modern proteins called the glucocorticoid (GR) receptor and mineralocorticoid receptor (MR) could be derived from a common ancestral protein. Using clever analysis the authors made a protein that they thought represented the ancestral protein. That protein binds several, structurally-similar hormones, as does modern MR. They then introduced two amino acid changes into the protein which are found in modern GR. The two changes caused the ancestral protein to bind the different kinds of hormones anywhere from ten- to a thousand-fold more weakly. That protein bound aldosterone about three-fold more weakly than cortisol. The authors note that modern GR (in tetrapods) also binds aldosterone more weakly than cortisol. So perhaps, the thinking goes, an ancestral gene that could bind both hormones duplicated in the past, one copy accumulated those two mutations to become the modern GR, and the other copy became modern MR. [...] Here are number of comments in response: 1) This continues the venerable Darwinian tradition of making grandiose claims based on piddling results. There is nothing in the paper that an ID proponent would think was beyond random mutation and natural selection. In other words, it is a straw man. 2) The authors (including Christoph Adami in his commentary) are conveniently defining “irreducible complexity” way, way down. I certainly would not classify their system as anywhere near IC. The IC systems I discussed in Darwin’s Black Box contain multiple, active protein factors. Their “system”, on the other hand, consists of just a single protein and its ligand. Although in nature the receptor and ligand are part of a larger system that does have a biological function, the piece of that larger system they pick out does not do anything by itself. In other words, the isolated components they work on are not irreducibly complex. 3) In the experiment just two amino acid residues were changed! No new components were added, no old components were taken away. 4) Nothing new was produced in the experiment; rather, the pre-existing ability of the protein to bind several molecules was simply weakened. The workers begin their experiments with a protein that can strongly bind several, structurally-very-similar steroids, and they end with a protein that at best binds some of the steroids ten-fold more weakly. (Figure 4C) 5) Such results are not different from the development of antibiotic resistance, where single amino acid changes can cause the binding of a toxin to a particular protein to decrease (for example, warfarin resistance in rats, and resistance to various AIDS drugs). Intelligent design proponents happily agree that such tiny changes can be accomplished by random mutation and natural selection. 6) In the “least promising” intermediate (L111Q) the protein has essentially lost its ability to bind any steroid. In the “most promising” intermediate protein (the one that has just the S106P alteration) the protein has lost about 99% of its ability to bind DOC and cortisol, and lost about 99.9% of its ability to bind aldosterone. (Figure 4C) 7) Although the authors imply (and Adami claims directly) that the mutated protein is specific for cortisol, in fact it also binds aldosterone with about half of the affinity. (Compare the red and green curves in the lower right hand graph of Figure 4C.) What’s more, there actually is a much larger difference (about thirty-fold) in binding affinity for aldosterone and cortisol with the beginning, ancestral protein than for the final, mutated protein (about two-fold). So the protein’s ability to discriminate between the two ligands has decreased by ten-fold. 8) One would think that the hundred-fold decrease in the ability to bind a steroid would at least initially be a very detrimental change that would be weeded out by natural selection. The authors do not test for that; they simply assume it wouldn’t be a problem, or that the problem could somehow be easily overcome. Nor do they test their speculation that DOC could somehow act as an intermediate ligand. In other words, in typical Darwinian fashion the authors pass over with their imaginations what in reality would very likely be serious biological difficulties. 9) The fact that such very modest results are ballyhooed owes more, I strongly suspect, to the antipathy that many scientists feel toward ID than to the intrinsic value of the experiment itself. 10) In conclusion, the results (and even the imagined-but-problematic scenario) are well within what an ID proponent already would think Darwinian processes could do, so they won’t affect our evaluation of the science. But it’s nice to know that Science magazine is thinking about us! Behe’s point (10) is especially noteworthy since Venema writes about Thornton et al.’s research that “Over and against these lines of evidence, however, the Intelligent Design Movement claims that such novelty is inaccessible to random mutation and natural selection.” But Behe has made it clear that these kinds of modest loss-of-function changes are exactly the type of changes we might expect from Darwinian evolution. So Venema is misrepresenting the claims of the ID movement. In fact, Venema undercuts his own argument that this research represents significant novel CSI by admitting that: “Steroid hormones are a closely related molecules — it’s not too surprising that slightly different molecules fit into a related group of protein receptors.” This research does not demonstrate that natural selection and random mutation can produce functional, information-rich genes and proteins because what was produced was not information-rich. If anything, function was diminished or lost rather than gained. Response 2: Stephen Meyer’s Comments: The Bridgham et al. study published in Science is trivial. ID theorists have long known that a few mutations can slightly alter an existing protein fold. What we question is whether mutation and selection are sufficient to search the enormous combinatorial space of possibilities necessary to finding fundamentally new protein folds and structures. This study does nothing to allay our skepticism on that score. Contrary to what the authors assume receptor-hormone pairs do not constitute irreducibly complex systems. The receptor-hormone pair is only a small component of a signal transduction circuit that regulates other complex physiological processes. For such pairs to have any selective or functional advantage many other protein components have to be present, including the other components of a signal transduction circuit and the physiological processes that such circuits regulate. If this is the best that Michael Behe’s critics can do after ten years of trying to refute him, then neo-Darwinism is in deep trouble. The really interesting thing about this paper is not the science it contains–its scientific results are trivial–but the sociological dynamics surrounding the publication of these papers. The AAAS has repeatedly insisted there is no scientific controversy about intelligent design. Now Science, the AAAS flagship journal, publishes two articles taking positions on a controversy that the AAAS says doesn’t exist. Will Science now allow Michael Behe to respond or will it only publish articles about the controversy which claim that ID is wrong? Response 3: “How to Explain Irreducible Complexity — A Lab Manual”: Another response to the Thornton et al. research came from various Discovery Institute authors in a fun piece titled How to Explain Irreducible Complexity — A Lab Manual: What [Bridgham/Thornton et al.] do say, however, is biologically meaningless. A Tutorial in Evolutionary Theory To understand why, we need a brief primer in fundamental evolutionary theory. Natural selection preserves randomly arising variations only if those variations cause functional differences affecting reproductive output. Since Bridgham et al. tell their story by invoking natural selection (see below), the system whose origin they claim to explain must have a selectable function for it to qualify as irreducibly complex. Indeed, given that natural selection favors only functionally advantageous variations, Behe has made clear that “function” in a biological context necessarily means a selectable functional advantage, for an obvious reason: a system of well-matched parts that performs a function can’t lose that function unless it possesses one to begin with. Unfortunately, these receptor-ligand pairs do not meet Behe’s definition of irreducible complexity for an equally obvious reason: receptor-ligand pairs do not by themselves confer any selective functional advantage. Indeed, in Bridgham et al.’s scenario, the function undergoing natural selection is not simply MR-aldosterone binding, but electrolyte homeostasis, the complex physiological regulation of essential cellular ions such as potassium or calcium. The novel receptor MR evolved, they write, “because it allowed electrolyte homeostasis to be controlled” (p. 100). Natural selection is acting, therefore, not on MR-aldosterone binding alone. Indeed, it cannot, because unspecified binding confers no functional advantage. But that is what Bridgham et al. do not seem to understand. They think they are explaining the origin of a single receptor-ligand pair, the mineralocorticoid receptor (MR) protein and the steroid hormone aldosterone. But that is biological nonsense. It is nonsense, moreover, strictly on the grounds of evolutionary theory itself. Let’s suppose the newly-evolved cellular receptor, MR, interacts with a hormone ligand, aldosterone. This is a novel relationship. Now, will natural selection preserve it? Who knows? Without more information — that is, without more details about the cellular or organismal effect of that novel binding — the bare function “aldosterone binds to MR” is biologically vacuous. Compare: Pound a nail, we tell you. Where and why? you ask. Never mind that, we say, just go pound a nail. So you hammer a three-penny nail through the power supply of this blog’s server. In any case, the receptor-ligand pair by itself is certainly not irreducibly complex. These pairs represent only small components of complex physiological processes such as metabolism, inflammation, immunity, and electrolyte homeostasis. For such pairs to have any selective advantage as part of the regulation of larger physiological processes, many other protein components have to be present. In particular, all the other components of a complete signal transduction circuit have to be present, as well as the component parts of the physiological process that such circuits regulate. (Even the ligand aldosterone itself doesn’t exist apart from a separate enzyme that produces it, and Bridgham et al.’s gene duplication scenario does not account for the origin of this necessary component either.) Bridgham et al. appear to grasp the need for more details (albeit in a distressingly loose way) because both early and late in their paper they specify the functional role of MR. The receptor “is activated by aldosterone to control electrolyte homeostasis” (p. 97) they note, and evolved “because it allowed electrolyte homeostasis to be controlled” (p. 100). Thus, in Bridgham et al.’s scenario, the actual system undergoing natural selection is electrolyte homeostasis, not simply MR-aldosterone binding. There’s a good reason for that: as noted, the function “aldosterone-MR binding,” considered in isolation, cannot be a target for natural selection. Try it, if you think it can. You’ll quickly find that you are floating in biological limbo. Aldosterone binds to MR…MR interacts with aldosterone…MR and aldosterone…OK, enough of that. Why does MR interact with aldosterone? Hello? Can we get an organism here? Back to Biological Reality So — is the physiological system of electrolyte homeostasis, of which both MR and aldosterone are small parts, irreducibly complex? Maybe. Take a look at a physiology textbook, or even any review paper on steroid or receptor biochemistry. Bridgham et al. don’t say much about the complexity of electrolyte homeostasis, however, because they are unaware that they have completely misunderstood the relevant unit of selection in their scenario. They write (p. 98): It is not obvious how the tight aldosterone-MR partnership could have evolved. If the hormone is not yet present, how can selection drive the receptor’s affinity for it? Conversely, without the receptor, what selection pressure could guide the evolution of the ligand? By Bridgham et al. ‘s own account, however — although they don’t realize it — natural selection is not acting at this level (the MR-aldosterone relationship alone) at all. To have any selectable function, many more components need to brought into the story. Genuine irreducible complexity re-emerges, and will be quite unexplained by the Bridgham et al. scenario. Response 4: My Own Comments: [L]ook at the bottom line of what this research really found: Adami highlights that the lock and key fit of the glucocorticoid enzyme with the cortisol substrate is based upon the specificity of merely two amino acids, where the precursor molecule was also functional (lacking those 2 mutations). In other words, one enzyme might have evolved into another via 2 mutations. This would appear to be a fairly simple system–and, assuming it did evolve in this fashion, an unimpresive example of evolution. Two meager mutations (something which even Behe and Snoke’s (2004) simulations found could evolve under mutation and selection) is not an impressive evolutionary leap and there seems no reason to assume that many enzyme-substrate interactions might not require the simultaneous substitution of many more amino acid residues in order to function, vastly decreasing the likelihood of their evolution. (In fact, this research would not address the origin of complex molecular machines requiring many interacting parts, like the bacterial flagellum.) Even if we grant that this present system is “reducibly complex” (with regards to at least 2 meager amino acids, that is), why should we assume that all the other enzyme-substrate interactions in biology follow suit? The last two commentaries combine to make two important points: First, the fact that one precursor enzyme could potentially perform two functions, and then lost the ability to perform one of those functions, does not imply that all biologically functional enzymes can evolve in this fashion. Second, we must keep in mind that the research of Bridgham/Thornton et al. involved intelligently directing mutations in these enzymes. Since they did not identify specific selective advantages, intelligent agents were doing the selection in a goal-directed fashion, hoping to select for future function. This is important when we consider the research of Axe (2010), discussed in Section 3 above. Axe found that when there is no selective advantage to a given mutation, it has a much smaller chance of becoming fixed in a population.[3] Thus, while a series of intelligently directed mutations might lead back to a functional ancestor, Bridgham/ Thornton et al. have not demonstrated that this pathway is likely to have been followed under natural conditions. Venema stated that “If any natural mechanism can be shown to produce “functional, information-rich genes and proteins,” then intelligent design is no longer the best explanation for the origin of information we observe in DNA.” But in this example we have seen that: The change was not information-rich It’s not clear that natural selection produced this change Function was diminished or lost rather than gained In fact, Venema undercuts his own argument that this research represents significant novel CSI by admitting in a comment that: “Steroid hormones are a closely related molecules — it’s not too surprising that slightly different molecules fit into a related group of protein receptors.” ID proponents would say the same thing, which is why this research does not demonstrate that a “natural mechanism can be shown to produce ‘functional, information-rich genes and proteins.’” >> _______________ In short the story is by no means the slam dunk one sided case as has been presented. KFEric Anderson

February 25, 2015

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kairosfocus @84 on the other thread writes: F/N: On the Lenski counterexample to IC claim, I suggest a glance at CL’s remarks in Sect 5 here (and onwards) in response to Venema: http://www.discovery.org/a/17571 Let me clip Sect 5, as a first example: ______________ >> Section 5: Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information In this section, we: • Understand why Venema’s citation of Lenski’s “Long Term Evolution Experiments” do not demonstrate that “Complex, specified information can indeed arise through natural mechanisms” • Review Michael Behe’s 2010 paper in Quarterly Review of Biology which investigated Lenski’s research and found that “mutations were decreasing or eliminating the protein’s function” • Investigate why Lenski’s E. coli bacteria that evolved the ability to uptake citrate under oxic conditions didn’t evolve anything new and likely experienced loss-of-molecular function Some critics of intelligent design (ID) misunderstand ID as a denial of natural causes. For example, we have recently seen how theistic evolutionist Dennis Venema wrongly suggests that, in both a scientific and theological sense, ID denies natural causes. Venema imports this misunderstanding into his proposed methods of testing ID, suggesting that if we find natural causes doing anything, then ID is refuted. Venema writes: “any natural mechanism that can be shown to produce information would render [Stephen Meyer's] argument that information only arises from intelligent sources null and void.” Dennis Venema’s argument collapses into this: ‘if Darwinian evolution can do anything, then ID is wrong.’ But this is not how we test ID, for ID readily allows that natural selection and random mutation can effect some changes in populations. The right question is not ‘Can natural selection do anything?’ but rather ‘Can natural selection do everything?’ With this in mind, let’s analyze Dr. Venema’s discussion of Richard Lenski’s Long Term Evolution Experiments (“LTEE”) with E. coli. Where’s the Behe? Before discussing the LTEE, it’s important to note that from the beginning of his series for BioLogos on evolution and the origin of information, Venema didn’t just purport to critique Stephen Meyer’s arguments in Signature in the Cell. Rather he referred to rebutting the entire “Intelligent Design Movement” or what he called (following Judge Jones?) the “IDM.” But if Venema is going to critique the entire “IDM” using Richard Lenski’s “Long Term Evolution Experiments,” then Venema should discuss the most relevant literature of the “IDM” that discusses those experiments. He doesn’t do that. In Venema’s discussion of the LTEE, there is no mention of a 2010 peer-reviewed scientific paper written by the most prominent biochemist in the “IDM,” published in a prominent biology journal, extensively critiquing Lenski’s LTEE. Venema fails to note and discuss Michael Behe’s December 2010 paper in Quarterly Review of Biology (QRB), which extensively discusses and critiques Lenski’s Long Term Evolution Experiments. Instead, Venema critiques the writings of Stephen Meyer, who hasn’t commented on Lenski’s LTEE because they weren’t relevant to his arguments in Signature in the Cell about the origin of life. By misrepresenting Meyer’s thesis as being refuted by evidence of the power of natural selection, Venema creates a straw man. Meanwhile he ignores the substantive critiques by leading ID proponents of the very evidence he raises. Vague Discussions vs. Precise Discussions of Lenski’s LTEE As an initial salvo regarding Lenski’s LTEE, Venema writes: [T]here were many possible genetic states of higher fitness available to the original strain, and random mutation and natural selection had explored several paths, all leading to a higher amount of “specified information” — information that specifies increased reproduction and survival in the original environment. All this was by demonstrably natural mechanisms, with a complete history of the relevant mutations, the relative advantages they conferred, and the dynamics of how those variants spread through a population. The LTEE is at once a very simple experiment, and an incredibly detailed window into the inner workings of evolution. But what exactly was the “specified information” that increased? What new function was gained? Where did natural selection and random mutation produce functional, information-rich genes and proteins? Venema doesn’t say what new functions arose, what changed, or what information was gained. His claim that natural selection produced “specified information” is vague. By contrast, in critiquing claims that the LTEE has produced something new, Behe’s 2010 Quarterly Review of Biology paper was anything but vague: By examining the DNA sequence of the E. coli in the neighborhood surrounding the IS [insertion sequence] elements, the investigators saw that several genes involved in central metabolism were knocked out, as well as some cell wall synthesis genes and several others. In subsequent work, Cooper et al. (2001) discovered that twelve of twelve cell lines showed adaptive IS-mediated deletions of their rbs operon, which is involved in making the sugar ribose. Thus, the adaptive mutations that were initially tracked down all involved loss-of-FCT. Several years later, when the cultures had surpassed their 20,000th generation, Lenski’s group at Michigan State brought more advanced techniques to bear on the problem of identifying the molecular changes underlying the adaptation of the E. coli cultures. Using DNA expression profiles, they were able to reliably track down changes in the expression of 1300 genes of the bacterium, and determined that 59 genes had changed their expression levels from the ancestor, 47 of which were expressed at lower levels (Cooper et al. 2003). The authors stated that “The expression levels of many of these 59 genes are known to be regulated by specific effectors including guanosine tetraphosphate (ppGpp) and cAMP-cAMP receptor protein (CRP)” (Cooper et al. 2003:1074). They also noted that the cellular concentration of ppGpp is controlled by several genes including spoT. After sequencing, they discovered a nonsynonymous point mutation in the spoT gene. When the researchers examined ten other populations that had evolved under the same conditions for 20,000 generations, they found that seven others also had fixed nonsynonymous point mutations in spoT, but with different substitutions than the first one that had been identified, thus suggesting that the mutations were decreasing the protein’s activity. The group then decided to concentrate on candidate genes suggested by the physiological adaptations that the cells had made over 20,000 generations. One such adaptation was a change in supercoiling density; therefore, genes affecting DNA topology were investigated (Crozat et al. 2005). Two of these genes, topA and fis, had sustained point mutations. In the case of topA, the mutation coded an amino acid substitution, whereas, with fis, a transversion had occurred at the fourth nucleotide before the starting ATG codon. The topA mutation decreased the activity of the enzyme, while the fis mutation decreased the amount of fis gene product produced. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) If you weren’t following all the technical language, here’s what’s going on: For the first 20,000 generations of Lenski’s LTEE, very little happened. There were a few molecular adaptations observed, yet whenever we understood their molecular basis, they involved the knocking out of genes, or decreasing protein activity — in essence, a decrease in specificity. Behe summarizes: The fact that multiple point mutations in each gene could serve an adaptive role — and that disruption by IS insertion was beneficial — suggests that the point mutations were decreasing or eliminating the protein’s function. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010) (emphasis added).) Unlike Venema’s discussion, Behe’s is precise, giving multiple examples and detailed descriptions of the types of changes observed in Lenski’s LTEE. And Behe found that the types of changes taking place in the E. coli tended to decrease or eliminate protein function. Before getting into a discussion of the citrate-using strain of E. coli, Behe closes with another specific example that involved decreasing gene activity in Lenski’s LTEE: In an investigation of global protein profiles of the evolved E. coli, Lenski’s group discovered that the MalT protein of the maltose operon had suffered mutations in 8 out of 12 strains (Pelosi et al. 2006). Several mutations were small deletions while others were point mutations, thus suggesting that decreasing the activity of the MalT protein was adaptive in minimal glucose media. Looking at Table 3 of Behe’s QRB paper, not a single example of an adaptive mutation in Lenski’s LTEE entailed a gain of a new molecular function. In fact, over the course of his entire paper, Behe goes further and explains that most of our known examples of molecular adaptations in bacteria entail “loss-of-function” mutations. Somehow, Venema doesn’t discuss any of these findings. E coli. Could Uptake and Metabolize Citrate Before Lenski’s LTEE Later, when referring to a different stage of the LTEE, Venema claims that a new function did arise in Lenski’s E. coli bacteria during the experiments: the ability of E. coli to metabolize citrate. Venema claims that “One of the defining features of E. Coli is that it is unable to use citrate as a food source,” but after a series of mutations “bacteria that use citrate dominate the population.” According to Venema, these experiments show “Complex, specified information can indeed arise through natural mechanisms.” Yet Venema leaves out important details, creating an inaccurate impression. As we’ll discuss below, normal E. coli already have machinery to uptake and metabolize citrate, so the general fact that Lenski’s bacteria showed this ability is really quite unremarkable. Unfortunately, Venema’s readers on the BioLogos will never hear that. They also won’t learn that Michael Behe has written extensively about Lenski’s research, showing that the machinery for E. coli to uptake and metabolize citrate already existed in these bacteria. This isn’t an entirely new biochemical pathway. Venema fails to note that normal E. coli already have the ability to uptake and metabolize citrate. They just can’t normally uptake it under oxic conditions; Lenski’s bacteria evolved the ability to uptake it under oxic conditions used in the experiment. Then the E. coli used their normal metabolic pathways to use citrate as a food source. Behe made this point while commenting on these claims soon after they were first published in 2008: Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a “citrate permease” which can transport citrate from outside the cell through the cell’s membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (Michael Behe, Amazon Blog, “Multiple Mutations Needed for E. Coli” (June 6, 2008).) Likewise, Behe’s recent 2010 paper in Quarterly Review of Biology provided an extensive critique of claims that Lenski’s LTEE showed the evolution of a new pathway that could metabolize citrate. Venema doesn’t cite or mention Behe’s QRB paper, but it too explains that E. coli already had the ability to metabolize citrate. Behe explains: Recently, Lenski’s group reported the isolation of a mutant E. coli that had evolved a Cit+ phenotype. That is, the strain could grow under aerobic conditions in a culture of citrate (Blount et al. 2008). Wild E. coli cannot grow under such conditions, as it lacks a citrate permease to import the metabolite under oxic conditions. (It should be noted that, once inside the cell, however, E. coli has the enzymatic capacity to metabolize citrate.) The phenotype, whose underlying molecular changes have not yet been reported, conferred an enormous growth advantage because the culture media contained excess citrate but only limited glucose, which the ancestral bacteria metabolized. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) Thus, Behe explains that the precise genetic mechanisms that allowed E. coli to uptake citrate under oxic conditions are not known. But Behe goes further and points out that the citrate-metabolizing E. coli strains really aren’t anything new, and that previous investigations suggest that the ability of the E. coli to uptake citrate under oxic conditions might result from molecular loss-of-function: As Blount et al. (2008) discussed, several other laboratories had, in the past, also identified mutant E. coli strains with such a phenotype. In one such case, the underlying mutation was not identified (Hall 1982); however, in another case, high-level constitutive expression on a multicopy plasmid of a citrate transporter gene, citT, which normally transports citrate in the absence of oxygen, was responsible for eliciting the phenotype (Pos et al. 1998). If the phenotype of the Lenski Cit+ strain is caused by the loss of the activity of a normal genetic regulatory element, such as a repressor binding site or other FCT, it will, of course, be a loss-of-FCT mutation, despite its highly adaptive effects in the presence of citrate. If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) Thus, previous research suggests that the adaptation which allowed these E. coli to uptake citrate under oxic conditions might be caused “by the loss of the activity of a normal genetic regulatory element.” Here’s what is likely going on here: Under normal conditions, E. coli can metabolize citrate; after all metabolizing citrate is an important step in the Krebs cycle, a pathway used by virtually all living organisms when creating energy. But under oxic conditions, E. coli lack the ability to transport citrate through the cell membrane into the cell. E. coli can do this under reducing conditions, but under oxic conditions E. coli can’t normally uptake citrate. If Lenski’s citrate-using E. coli are like previous E. coli which were discovered uptaking citrate under oxic conditions, then it seems likely that the bacteria underwent a mutation that knocked out the regulation mechanism of a citrate-transport gene, causing over-expression, allowing the E. coli to uptake citrate under oxic conditions. In other words, the machinery for both transporting and metabolizing citrate was already present in these bacteria. But a series of knockout mutations broke the regulation of pre-existing citrate transport mechanisms, causing over-expression of a citrate transport gene, allowing citrate to be transported under both oxic and anaerobic conditions. If this is the case, then clearly this example of Darwinian “evolution” entails the loss of a molecular function, not the gain of a new one. And there was no wholesale acquisition of the ability to metabolize or, as Venema put it, “use” citrate. In fact, as Behe notes, we don’t really yet understand the precise molecular mechanisms that caused these E. coli to be able to uptake citrate under oxic conditions. So as far as we can tell, these changes entailed the origin of no new functional genes or proteins but might have resulted from a broken regulatory mechanism. We have not seen that natural selection and random mutation can produce functional, information-rich genes and proteins, and Venema is wrong to suggest otherwise. Contra Venema, this example hardly shows the Darwinian evolution of a “new function,” especially since E. coli already had the ability to uptake and metabolize citrate. Venema claims that CSI has arisen, but if we don’t even know what mechanisms were involved in this change, how does he know that it is new CSI? What do Lenski’s LTEE Really Tell Us? In his QRB paper, Behe goes on to explain that to date, the known adaptations that have occurred in Lenski’s LTEE are either modification-of-function or loss-of-function changes: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) Behe’s paper further suggests that when there are several kinds of potential adaptive mutations that might occur, loss or modification of function adaptations will be far more common than gain-of-function adaptations. He concludes: Even if there were several possible pathways by which to construct a gain-of-FCT mutation, or several possible kinds of adaptive gain-of-FCT features, the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) The sort of loss-of-function examples seen in the LTEE will never show that natural selection can increase high CSI. To understand why, imagine the following hypothetical situation. Consider an imaginary order of insects, the Evolutionoptera. Let’s say there are 1 million species of Evolutionoptera, but ecologists find that the extinction rate among Evolutionoptera is 1000 species per millennium. The speciation rate (the rate at which new species arise) during the same period is 1 new species per 1000 years. At these rates, every thousand years 1000 species of Evolutionoptera will die off, while one new species will develop–a net loss of 999 species. If these processes continue, in 1,000,001 years there will be no species of Evolutionoptera left on earth. If Behe is correct, then Darwinian evolution at the molecular level faces a similar problem. If, all other things being equal, a loss or modification of function adaptation is generally 100-1000 times more likely than gain of function adaptations, then eventually an evolving population might run out of molecular functions to lose or modify. Neo-Darwinian evolution cannot forever rely on examples of loss or modification-of-function mutations to explain molecular evolution. At some point, there must be a gain of function. Vaguely Appealing to Vast Probablistic Resources Won’t Work Venema closes his post on the LTEE by saying: “what the IDM claims is impossible, these ‘tiny and lowly’ organisms have simply been doing — and it only took 15 years in a single lab in Michigan. Imagine what could happen over 3,500,000,000 years over millions of square miles of the earth’s surface.” But vague appeals to vast eons of time and huge population sizes are unconvincing. You just have to do the math. As David Abel reminds us: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.” … One chance in 10200 is theoretically possible, but given maximum cosmic probabilistic resources, such a possibility is hardly plausible. With funding resources rapidly drying up, science needs a foundational principle by which to falsify a myriad of theoretical possibilities that are not worthy of serious scientific consideration and modeling. (David L. Abel, “The Universal Plausibility Metric (UPM) & Principle (UPP),” Theoretical Biology and Medical Modelling, Vol. 6:27 (Dec. 3, 2009).) In the case of E. coli and citrate, the bacteria already had the ability to uptake and metabolize citrate, and simply found a way to transport it under different conditions. It’s likely this occurred by overexpressing pre-existing transport mechanisms. Does this imply that anything and everything “could happen over 3,500,000,000 years over millions of square miles of the earth’s surface”? Well, ID proponents aren’t interested in making vague and ambiguous appeals to vast amounts of probabilistic resources. They want to test these questions, and follow the evidence where it leads. As discussed here, ID proponents have asked just how long it takes to evolve traits that require multi-mutation features. A multi-mutation feature requires multiple mutations to be present before there is any advantage given to the organism. Doug Axe’s research makes assumptions very generously favoring Darwinian evolution. He assumed the existence of a huge population of asexually reproducing bacteria that could replicate quickly — perhaps nearly 3 times per day — over the course of billions of years. Yet even here, complex adaptations requiring up to six mutations with neutral intermediates can become fixed. Beyond that, things become implausible. If only slightly maladaptive intermediate mutations are required for a complex adaptation, only a couple (at most two) mutations could be fixed. If highly maladaptive mutations are required, the trait will never appear. Axe discusses the implications of his work: [T]he most significant implication comes not from how the two cases contrast but rather how they cohere — both showing severe limitations to complex adaptation. To appreciate this, consider the tremendous number of cells needed to achieve adaptations of such limited complexity. As a basis for calculation, we have assumed a bacterial population that maintained an effective size of 109 individuals through 103 generations each year for billions of years. This amounts to well over a billion trillion opportunities (in the form of individuals whose lines were not destined to expire imminently) for evolutionary experimentation. Yet what these enormous resources are expected to have accomplished, in terms of combined base changes, can be counted on the fingers. (Douglas D. Axe, “The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations,” BIO-Complexity, Vol. 2010(4):1-10.) If Axe is correct then we cannot always assume, as Venema seems to do, that sufficient probabilistic resources exist to produce complex features we see in life. Summarizing Venema’s Argument Regarding the LTEE In short, Venema’s argument regarding the LTEE collapses into common misconceptions about ID, which go something like this: (1) ID holds that Darwinian evolution cannot do anything. (2) If Darwinian evolution can do something then it can do anything. (3) Lenski’s experiments show Darwinian evolution can allow E. coli bacteria to evolve a “new function” of metabolizing citrate. (4) Therefore ID is wrong, and given enough time, Darwinian evolution can do anything we “imagine.” At each step in his argument, the facts and/or the logic is wrong: Regarding (1): In fact, ID does not hold that Darwinian evolution can’t do anything. Rather it claims that natural selection can do some things, but not everything. ID proponents readily acknowledge (as Behe has) that “if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it.” The problem comes when multiple mutations are required to produce some new structure — and as Axe’s research shows, this is where Darwinian evolution typically gets stuck. Regarding (2): Darwin-defenders have a long history of over-extrapolating from the data. ID is scientifically cautious and concludes that no one single experiment can show that Darwinian evolution can do everything we ask of it. A single experiment showing the ability of Darwinian evolution to do X simply shows the ability of Darwinian evolution to do X; it doesn’t necessarily show Darwinian evolution can do Y, Z, and A, B, and C, etc. ID says we need to test hypotheses carefully and not over-extrapolate from observed data. Regarding (3): In fact Lenski’s experiments did not show the Darwinian evolution of an entirely new function. E. coli bacteria already had the ability to uptake and metabolize citrate, and the experiments simply showed they evolved the ability to uptake it under oxic conditions. This very likely required the loss of a molecular function. Regarding (4) ID proponents do not think it is wise or scientifically accurate to vaguely invoke vast eons of time or vast population sizes to document the alleged power of Darwinian evolution. ID cautions that Darwinian evolutionists often assume that there are sufficiently vast probabilistic resources to accomplish any task imaginable, but that assumption might not be valid. Rather than simply assuming, Doug Axe’s research finds that adaptations requiring more than six neutral mutations, or two maladaptive mutations, to provide a functional advantage would not arise in the history of the earth. Subsequent research by Axe and Ann Gauger suggests that it would not be uncommon for Darwinian evolution to face obstacles that exhaust the probabilistic boundaries as found by Axe’s research. In 2011, they published research in BIO-Complexity that found at least seven mutations (probably many more) would be necessary to convert one protein into a supposedly closely-related protein. While Darwinians may (or may not) claim that this was a real evolutionary pathway, it’s the type of pathway that is often claimed to have been traversed by natural selection over the course of life’s history. The fact that this simple conversion required more mutations to produce a new function than would be allowed under Axe’s mathematical models shows that there may be real obstacles to the Darwinian evolution of new proteins. Venema’s citation of Lenski’s LTEE certainly does not show otherwise.>>Eric Anderson

February 25, 2015

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Joe @83 on the other thread writes: CHartsil is confused. All that happened with Lenski’s experiment is that the E coli could now utilize citrate in an oxygen-rich environment. They already had that ability in the an anaerobic environment. An IC system did NOT evolve via unguided processes. No new genes were formed. An existing gene was duplicated and put under the control of a different promoter, ie a promoter that was on in the presence of O2.Eric Anderson

February 25, 2015

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