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I’d like a straight yes or a straight no, Professor Moran


Professor Moran has been kind enough to grace us with his presence on my post, Bad math: Why Larry Moran’s “I’m not a Darwinian” isn’t a valid reply to Meyer’s argument. But he hasn’t answered a simple question I posed to him, regarding Dr. Stephen Meyer’s comments on the neutral theory of evolution in his book, Darwin’s Doubt (Harper One, 2013).

In his discussion of the neutral theory of evolution, Dr. Meyer focuses on the ground-breaking work of Dr. Michael Lynch. Meyer argues that the neutral theory is incapable of accounting for the origin of new animal body plans, because it is built on faulty mathematical assumptions (bolding mine – VJT):

Michael Lynch, a geneticist at Indiana University, … proposes a neutral or “non-adaptive” theory of evolution in which natural selection plays a largely insignificant role…

Lynch argues that in small populations, animal genomes will inevitably grow over time as nonprotein-coding sections of DNA (as well as gene duplicates) accumulate due to the weakness of natural selection. He thinks that these neutral mutations drive the evolution of animals…

Lynch does argue in one paper that neutral evolutionary processes can generate new complex adaptations – adaptations requiring multiple coordinated mutations – within realistic waiting times. In particular, writing in a recent paper with colleague Adam Abegg of St. Louis University, he argues that “conventional population genetic mechanisms” such as random mutation and genetic drift can cause the “relatively rapid emergence of specific complex adaptations.”…

But some things are just too good to be true, and it turns out that Lynch and Abegg made a subtle but fundamental mathematical error in coming to their conclusion. Appropriately, perhaps, the first person to demonstrate that Lynch’s incredible claim was problematic was Douglas Axe… In the end, he traced Lynch and Abegg’s claims to two erroneous equations, both of which were based on erroneous assumptions. In essence, Lynch and Abegg assumed that organisms will acquire a given complex adaptation by traversing a direct path to the new anatomical structure. Each mutation would build on the previous one in the most efficient manner possible – with no setbacks, false starts, aimless wandering, or genetic degradation – until the desired structure or system (or gene) is constructed. Thus, they formulated an undirected model of evolutionary change, and one that assumes, moreover, that there is no mechanism available (such as natural selection) that can lock in potentially favorable mutational changes on the way to some complex advantageous structure….

Yet nothing in Lynch’s neutral model ensures that potentially advantageous mutations will remain in place while other mutations accrue. As Axe explains, “Productive changes cannot be ‘banked,’ whereas Equation 2 [one of Lynch’s equations] presupposes that they can.” Instead, Axe shows, mathematically, that degradation (the fixation of mutational changes that make the complex adaptation less likely to arise) will occur much more rapidly than constructive mutations, causing the expected waiting time to increase exponentially.
(2013, pp. 321, 322, 327-328)

Lynch and Abegg’s paper, “The rate of establishment of complex adaptations” (Molecular Biology and Evolution 27: 1404-1414, doi:10.1093/molbev/msq020) can be found here. Dr. Douglas Axe’s critique of their paper, which is titled, “The limits of complex adaptation: An analysis based on a simple model of structured bacterial populations” (BIO-Complexity 2010(4):1-10, doi:10.5048/BIO-C.2010.4) can be found here.

The question I put to Professor Moran, in a comment on my thread, was very straightforward:

Are you claiming that Dr. Axe and Dr. Meyer have misconstrued the nature of random genetic drift?

Sadly, I’m still waiting for an answer. In case Professor Moran missed it or accidentally overlooked it, I’m posting it here again. I’d appreciate it if Professor Moran would be kind enough to answer with a straight “Yes” or “No.”

The reason why I’m asking this question is a very simple one. Professor Lynch is an eminent scientist: he is Distinguished Professor of Evolution, Population Genetics and Genomics at Indiana University, Bloomington, Indiana. He has also written a two volume textbook with Bruce Walsh, which is widely regarded as the “Bible” of quantitative genetics. In 2009, he was elected to the National Academy of Sciences.

For his part, Dr. Douglas Axe is the director of the Biologic Institute. His research uses both experiments and computer simulations to examine the functional and structural constraints on the evolution of proteins and protein systems. After obtaining a Caltech Ph.D., he held postdoctoral and research scientist positions at the University of Cambridge, the Cambridge Medical Research Council Centre, and the Babraham Institute in Cambridge. He has also written two articles for the Journal of Molecular Biology (see here and here for abstracts). He has also co-authored an article published in the Proceedings of the National Academy of Sciences, an article in Biochemistry and an article published in PLoS ONE.

There’s no getting around it. One of these scientists has made a bad mathematical mistake. Either Professor Lynch made a bad mistake in the article he co-authored with Adam Abegg (Department of Mathematics, St. Louis University), arguing that “conventional population genetic mechanisms” such as random mutation and genetic drift can cause the “relatively rapid emergence of specific complex adaptations” within realistic waiting times, or Dr. Axe made a terrible blunder in the paper he wrote, critiquing Lynch and Abegg’s flawed assumptions. As far as I can determine, neither Lynch nor Abegg have responded to Dr. Axe’s critique, which was written in 2010. Nor has any other evolutionist of note that I’m aware of. For that reason alone, I’m inclined to believe that Dr. Axe got it right and that Lynch and Abegg are wrong.

But if that’s the case, then Professor Moran owes Dr. Meyer an apology. He has accused Meyer of ignoring the neutral theory of evolution and focusing his attack on Darwinism. However, if Meyer’s rebuttal of the neutral theory, which is based on Dr. Axe’s work, is scientifically sound, then Meyer has dealt a knock-out blow to the neutral theory. That isn’t what I’d call “ignoring” a theory.

If, on the other hand, Professor Moran believes that Dr. Axe’s mathematical argument regarding the speed of neutral evolution is fundamentally flawed, then why has he never said so on his blog, and why has he never explained the fallacy to his readers?

I'm not qualified enough to critically analyze Axe's equations. But there are people qualified to do so. What Axe should have done is to present his case in their midst by submitting his work to a proper scientific journal and subjecting it to peer review. But he opted for the easy route by publishing it in his own journal where nobody is going to question it! I wouldn't consider such a paper a scientifically valid publication. Evolve
Evolve: I see this, "wouldn't get past peer review," argument every so often. To me, it looks like an argument from personal ignorance paired with unwavering faith. If one could explain why something wouldn't get past peer review, one wouldn't need to make a bald assertion. Yet one obviously has faith that there is someone somewhere who could explain the challenge away. Phinehas
It suggests that he knew his claims wouldn’t get past proper peer review. LoL. Fool. Mung
Vincent Torley, If Axe was right, why didn't he publish his article in a mainstream journal instead of in Bio-complexity - which is a creationist journal of which Axe himself is the Managing Editor! See: http://bio-complexity.org/ojs/index.php/main/about/editorialTeam It suggests that he knew his claims wouldn't get past proper peer review. No serious scientist considers articles in Bio-complexity worthwhile, and Lynch may not have responded due to that reason alone. Evolve
I wrote this back in 2010. Paul Nelson had an OP on this paper. Here's what I wrote:
This thread is already on page 2. That’s a shame since this is an important paper. Just a few brief comments. Axe’s paper treats the paper by Lynch and Abegg first, and then he develops his own model based on the “island model” of Kimura and Marauyama. In his treatment of L&A’s paper, Axe points out that their neutral model, based on an equation they derive, using an approximation for the presence of a cell with the complex adapted allele present that is independent of the number of bases (“d”) needed for this complex adapted trait, is counterintuitive and doesn’t make much sense. L&A say that (ut)^d, when ut << 1, u being the mutation rate and t the time in generations, can basically be considered as u^-1. Axe remarks that if you ignore d in such a way, then it is no surprise that d has no effect on the time to fixation of the complex trait. Briefly, let's assume ut is .01. Then (.01)^10 (that is, 10 base changes) is 10^-20, whereas u^-1 is, per L&A, 10^-6. Does it really make any sense at all that whether it is one base change needed, or 10 base changes needed, that the evolutionary process happens in roughly the same time frame? Axe, having come up with his own model, compares his equations for the maladaptive and neutral cases to L&A's maladaptive and neutral cases. L&A's neutral case doesn't show a step-like increase in time to fixation per added base change needed, while Axe's and L&A's maladaptive equations do. Axe would conclude that L&A's neutral case equation gives odd results, ones that are not very believable. I think it is fairly clear that L&A have made a mistake in their approximating procedure for the neutral case. As to Axe's model, his model is very similar to Behe and Snoke's model, save for the fact that B&S's model has the maladaptive mutations crippling the organism, which Axe says, per studies conducted, doesn't really happen. Thus, Axe comes up with the possibility of more base changes for the maladaptive case. Nevertheless, he only ends up with a high-end possibility of six base changes using his neutral model. This represents about 3-6 a.a. changes, substantially higher than Behe and Snoke's limit of about 2-3 a.a. Yet, as Axe points out, this limitation on base change substitutions per Darwinian mechanisms, throws into question any Darwinian explanation for novel protein foldings, and, thus, Darwinism itself. Axe's model seems quite realistic. So, once again, Darwinian capabilities for evolutionary change have been demonstrated to be remarkably limited.
Vjtorley, Let me offer you a word of advice, which I almost always hate to do. Morans, Coynes, Dawkinses and the rest do not give a damn what the truth is, because of a "god syndrome". It is very addictive and it makes people do crazy things. In short, it is the power to dictate what others are supposed think and believe according to THEIR WAY OF THINKING, often supported with imaginary evidence. Just ask them about the evidence for the origins of life and eukaryotes. You know the answer already but is it scientifically viable? KevNick
Further to REC, and the charge of 'ad hominem'. What he writes is truly ironic, because it is his posts, not mine, that are textbook versions of ad hominem fallacy. I have pointed out that students appraise Moran's classes poorly. REC then attacks the character of the students. He suggests they are not real students. He thinks they are lying about being his students because in fact they are 'malicious asses' who hold a failed 'worldview'. THIS is what ad hominem IS. He rejects the charge made by the students, and therefore attacks their character. He impugns their honesty. They MUST be lying, because he doesn't like what they said. I hope that REC now has a better understanding of a term he used in error. soundburger
Dr. Moran says that he mischaracterizes ID proponents as "Creationists" and calls them "IDiots" because they mischaracterize him as a "Darwinist," which he says he isn't. However, ID defines Neo-Darwinism as unguided evolution, which is consistent with Dr. Moran's position, even though he emphasizes the role of genetic drift and de-emphasizes the role of natural selection. I have raised this issue with Dr. Moran in the past, but he has no response. How, then, can he think he is being intellectually honest when he appears to know that what he says is untrue? StephenB
REC, by all means DON'T 'waste your time' with me, but it is clearly you, not I who lacks reading comprehension skills. The OP asks him to defend his response. Though you are using a typical, hyper literal dodge to avoid it, the post is asking Moran to do more than simply say yes or no, but to explain his reasons for doing so. My defense of ad hom? Again, do you understand what the term means? It appears that you do not. His students are 'malicious asses'? What nonsense. They are not criticizing him because of their 'worldview'; that you think so is downright bizarre. Look, here is the link, see for yourself. http://www.ratemyprofessors.com/ShowRatings.jsp?tid=39948 soundburger
soundburger: "And besides, what IS his argument? He just wrote ‘Yes’. This is typical of Moran. He thinks he is being cute by giving a one word, essentially meaningless, response to a lengthy challenge." Original Post: ".... I’d appreciate it if Professor Moran would be kind enough to answer with a straight “Yes” or “No.” I don't think I'll spend my time on someone who lacks basic reading comprehension skills, thanks. I mean, his response is demanded by the TITLE of this post. I love your defense of your ad hom: I don't have a argument to make, so my attack on the person isn't a fallacious argument. Gorgeous. "Or do you imagine that people only pretend to be his students in order to log on and criticize him there? Why would they do that?" Because they are malicious asses whose worldview has been left behind, and they are so powerless they have no other recourse. REC
REC, I have no debate with Moran, so I am not using ad hominem to diminish the strength of his argument. I assume you know what the term means. And besides, what IS his argument? He just wrote 'Yes'. This is typical of Moran. He thinks he is being cute by giving a one word, essentially meaningless, response to a lengthy challenge. You have no idea what 'rate my prof' is, do you? Are you calling his students fools for not liking his classes? Or do you imagine that people only pretend to be his students in order to log on and criticize him there? Why would they do that? Can't they just criticize his views on religion, or junk DNA, for example? Why pretend to be his students? But seriously, if you like, go there yourself and take a look. The comments almost certainly come from students, and some of them are really funny in addition to being scathing. Finally, and does this even need to be said? - someone who continually refers to those he disagrees with as idiots and kooks, and is unfailingly contemptuous towards them should be considered fair game in the, what you refer to as 'ad hominem' department. soundburger
"As far as I can determine, neither Lynch nor Abegg have responded to Dr. Axe’s critique, which was written in 2010. Nor has any other evolutionist of note that I’m aware of. For that reason alone, I’m inclined to believe that Dr. Axe got it right and that Lynch and Abegg are wrong." Which presupposes those evolutionary biologists have heard of Axe, or consider his critique worth responding to. I have actually cited Axe in my reviews, but only on his older and excellent primary data, from which he concludes: "Since attainment of crude function is the critical initial step in evolutionary innovation, the relatively scant requirements contributed by the hydrophobic core would greatly reduce the initial hurdle on the evolutionary pathway to novel enzymes." How he turns his back on his own data is anyone's guess. @2: Again, the hilarity of this site. Weren't you all howling about ad hominem attacks the other day? And any fool can set up a rate my professor or amazon account--and there are plenty of fools who despise Larry Moran. REC
Two comments ... First, thanks to Professor Moran for participating here. That's a "straight yes". I'd hope he would explain further but at least we know there's a disagreement with Dr. Axe's argument. Second, some praise for Bio-Complexity. I've read several papers there and the scientists offer excellent clarity in their writing. In this case, Dr. Axe does a very fine job in explaining the mathematics and the concepts involved. I would think Lynch and Abegg would respond to it - especially since it is featured in Darwin's Doubt. I also find it hard to believe that Meyer and Axe got this wrong - it seems pretty clear that the model in the Lynch paper is incorrect.
Specifically, of all the possible evolutionary paths a population can take, the analysis of Lynch and Abegg considers only those special paths that lead directly to the desired end—the complex adaptation.
That's either true or false -- as the OP indicated. Silver Asiatic
Alas, I fear you will get nowhere with Larry Moran. He is a stubborn, arrogant, blowhard. He goes almost instantly for the facile, the cruel, the smarmy. If you look him up on Rate My Prof (if it is still there), you will see that he scores abysmally low, and that most of the students who comment talk about his pomposity and arrogance, even his preference for showing off how smart he is to actually teaching. If you look up his textbook on amazon, again, you will see mostly complaints and a low ranking. It hurts to write this, but truly, this is a man who deserves it. He deserves to be called out and exposed for his arrogance and nastiness towards those he disagrees with. His own site is mostly populated with sycophants, as is Jerry Coyne's. He doesn't seem to have much going for him other than immeasurable self-certitude and his place, such as it is, among the New Atheists. But his students, pity them, view him differently. soundburger
Yes Larry Moran

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