Microbiologist admits Darwinism’s shortcomings, says we should stick with it for now because …

PaV, as to Lizards: Phenotypic Plasticity - Lizard cecal valve (cyclical variation)- video http://www.youtube.com/watch?v=zEtgOApmnTA Lizard Plasticity - March 2013 Excerpt: So in this study, plasticity experiments were conducted. When the lizards were taken off a plant diet and returned to their native insect diet, the cecal valves in their stomachs began to revert within weeks. As the authors conclude, this pointed heavily to plasticity as a cause. We can infer that the this gut morphology likewise arose in similar fashion when coming into contact with the plant diet. http://biota-curve.blogspot.com/2013/03/lizard-plasticity.html bornagain77

wd400: Your response was respectful, substantive and fairly accurate. So, congratulations there. As to Lynch's book, I've not read it, though I remember reading an article by him covering some of the same ground. I will give it a look-over when I can. As to relaxing NS, you imply that the primary function of NS is 'negative' selection, and not 'positive' selection. I imagine you would rely heavily on 'neutral drift.' The problem with relying on 'neutral drift' is that when this is coupled to 'negative selection' the time frame for the right kinds of mutations is just way too long. Behe has documented this in a number of ways, as well as Axe and Gauger working with protein domains. But let's put all of this to a test. What do I mean? Well, in an experiment conducted in the latter half of the last century, a lizard was transplanted from one Adriatic Island to another. War broke out in the region. 35 years passed. When they went back, the lizards had grown larger, changed their behavioral patterns, and had slightly different jaws. But the biggest change of all was that "cecal valves" appeared in their digestive tract--obviously to deal with their changed habits and changed diet. The problem here is that everything happens so fast!! There is no way that either neutral drift, or NS, can explain so many large-scale changes occurring in so short a time. We have to have recourse to some other mechanism. The obvious choice would be that the changed diet and life habits (absence of predators and competitors) 'triggered' a response within their genome, likely brought about by "guided" mutations, and which, therefore, could take place rather quickly--within a generation or two. I forget how many lizards were transplanted; but it wasn't a whole lot. Let's say it was a 100. Let's say they mate 3 times a year. Let's say they produce four offspring, on average, in each mating. 50->400->1600 (yr 1)1600->6400->25600 (2nd yr.) I suspect the island couldn't handle 25,600 lizards, so the population would end up stabilizing itself, so that, effectively, you would have 3 x 4 x 25,600 offspring per each subsequent year. (36-2) x 307,200 = 10,444,800 offspring in the last 34 years, and roughly 92,000 the first two years, which can be ignored. So, "evolution" has 10.5 million (10^7) chances at the right mutation. And the probability of a particular mutation, at a particular spot on the genome is roughly 200/5 x 10^9, or 4 x 10^-8. So, if "evolution" needed ONE mutation at some particular spot along the genome, there wasn't enough time for that ONE mutation. If you bump up the island population to 100,000 instead of 25,600, then you end up with 40 million chances--still less than what is needed to overcome the rarity of a particular mutation occurring at a particular location within the genome. First of all, NS needs something (a mutation) to act upon. Here, there is the likelihood that not even ONE needed mutation occurred. So, NS is out---which is your position, more or less. That leaves 'neutral drift'. Well, let's say that because of "neutral" mutations over long generations of times, there are a whole lot of 'potentially beneficial' residues within the genome. But they were all there before the lizards were moved!! So that means that AT LEAST ONE MUTATION must occur for anything other than what you had before. And, as I've just demonstrate, there wasn't enough passage of time for even ONE mutation. Q.E.D. We no longer have any reason to consider either 'neutral drift', or NS, as the causative agents of the change which took place there in the Adriatic. You know, in physics departments throughout the USA, there are "string theorists" up the kazoo. Why? Because the scientific "establishment" was convinced that "string theory" was the answer for unifying the SM with GR (general relativity). But the LHC found no evidence of the kind of particles that "string theory" predicts. And, so, changes are occurring in physics departments. And physicists are beginning to deal with the fact that "string theory" is not the final solution to the above problem. This "natural" experiment in the Adriatic is enough evidence for sensible people to leave behind Darwinian theory. Are they? No. Are "string theorists" giving up? NO. Will they ever give up? Probably not. Will they eventually die? Yes. And then there will be a paradigm shift. I suspect something like this will have to happen in evolutionary biology. (Darwin more or less saw things just this way. He looked to the young to accept what was being rejected by almost the entire biological community at the time. And it worked. Hopefully, it can work again; but, this time with different results.) PaV

Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle - "Haldane's Ratchet" - Christopher L. Rupe and John C. Sanford - 2013 Excerpt: Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon "Haldane's Ratchet". http://media.wix.com/ugd/a704d4_47bcf08eda0e4926a44a8ac9cbfa9c20.pdf Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,, By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales. http://phys.org/news/2014-02-evolutionary-important-success.html This following headline sums up the preceding study very nicely: Fittest Can’t Survive If They Never Arrive – February 7, 2014 http://crev.info/2014/02/fittest-cant-survive-if-they-never-arrive/ The fate of competing beneficial mutations in an asexual population (Philip J. Gerrish & Richard E. Lenski) "As shown by Manning and Thompson (1984) and by Peck (1994), the fate of a beneficial mutation is determined as much by the selective disadvantage of any deleterious mutations with which it is linked as by its own selective advantage." http://myxo.css.msu.edu/lenski/pdf/1998,%20Genetica,%20Gerrish%20&%20Lenski.pdf bornagain77

wd400:

We also have population genetic evidence for mutation enttering populations are being rapidly pushed toward fixation.

"population genetic evidence"? I would think that science requires real world evidence. What we need is a way to model what mutations do. That is something beyond the piddly changes we observe. Changes in beak size does not explain the finch. Anti-biotic resistance does not explain bacteria. Moth coloration does not explain the moth. We need to be able to test the hypothesis that changes to genomes can account for the diversity of life starting from the first populations as Darwin saw it- simple prokaryotes. (Baraminology can easily explain the diversity of life starting from the originally Created Kinds) Only then could we determine if natural selection is up to the task. But thanks to the current state of biology being dominated by BWE, no one has any idea what makes an organism what it is and the evidence is against the "organisms are the sum of their genome"*

To understand the challenge to the “superwatch” model by the erosion of the gene-centric view of nature, it is necessary to recall August Weismann’s seminal insight more than a century ago regarding the need for genetic determinants to specify organic form. As Weismann saw so clearly, in order to account for the unerring transmission through time with precise reduplication, for each generation of “complex contingent assemblages of matter” (superwatches), it is necessary to propose the existence of stable abstract genetic blueprints or programs in the genes- he called them “determinants”- sequestered safely in the germ plasm, away from the ever varying and destabilizing influences of the extra-genetic environment. Such carefully isolated determinants would theoretically be capable of reliably transmitting contingent order through time and specifying it reliably each generation. Thus, the modern “gene-centric” view of life was born, and with it the heroic twentieth century effort to identify Weismann’s determinants, supposed to be capable of reliably specifying in precise detail all the contingent order of the phenotype. Weismann was correct in this: the contingent view of form and indeed the entire mechanistic conception of life- the superwatch model- is critically dependent on showing that all or at least the vast majority of organic form is specified in precise detail in the genes. Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes as Weismann’s “unambiguous bearers of information” or view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a small fraction of all known genes, such as the developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene- Michael Denton "An Anti-Darwinian Intellectual Journey", Uncommon Dissent (2004), pages 171-2

Se also Why Is A Fly Not A Horse?" * we are just what emerges from the interactions of the matter and energy of a fertilized egg (the environemnet wouldn't change what type of organism comes out) Joe

wd400: The calculations under drift and under selection would be different, right? Depending on the direction/extent of the selection pressure. Maybe you're just saying they are the same in this particular experiment due to the lack of selection? At any rate, I think I understand what you were saying, namely, that mutations being "rapidly pushed toward fixation" is indirect evidence of their beneficial nature. I think that is probably a reasonable inference (with the usual caveats around the concept of "beneficial" and what it might mean in a particular context). When I initially read your comment I thought you were referring to some other, unusual kind of push toward fixation, so that is all I was trying to clarify. Thanks, Eric Anderson

A couple of quick these, The experiment is in a mutation-accumulation lines, not populations. Because they go through such massive bottlenecks they are effectively free of selection. So, without negative selection the effects of mutation would indeed be ruinous. o you mean more rapidly than would be expected under normal genetic drift/neutral calculations? Or are you referring to beneficial mutations under selection? These are the same thing, I think? When a mutation arises then rapidly approaches fixation that's down to selection. Thankfully, that also produces unique signatures (the one I had in mind is loss of diversity around the focal mutation, since recombination doesn't have time to move other variants around). wd400

Thanks, wd400. After I wrote my comment #35, I thought I should have given more shrift to neutral mutations, because I realize some people, including you, view most mutations in that light. I agree that beneficial mutations can exist. Particularly if we divorce the concept of "beneficial" from concepts like "constructive" or "information-producing", etc. In nearly all cases known, we are dealing with a breakdown of a pre-existing system or protein. But, yes, in particular circumstances or specific environments, that breakdown could be beneficial by being the lesser of two evils. Sickle cell being the classic example; several others in the same vein. ----- Thanks for the link to the paper, I'll try to read through it completely when I get a chance. This sentence jumped out at me though (in the context of deleterious vs. neutral mutations we were discussing): "The net effect of accumulated mutations in D. pulicaria across all lines assayed was deleterious in 67.6% of the lines (proportion of significant negative slopes), neutral in 24.3% (proportion of non-significant slopes) and beneficial in 8.1% (proportion of significant positive slopes)." I take it that even if one were to argue that most mutations are "neutral" individually, that over time the cumulative effect is strongly detrimental. Indeed, if given more time and more accumulation, even their observed 24.3% would likely have partly tended detrimental. The 8% beneficial in this particular situation is interesting. I'll see if I can tell what additional meat they put on that statement. ----- Finally, you said: "We also have population genetic evidence for mutation entering populations are being rapidly pushed toward fixation." Do you mean more rapidly than would be expected under normal genetic drift/neutral calculations? Or are you referring to beneficial mutations under selection? Thanks, Eric Anderson

I've read The Genetical Theory of Evolution, but a long time ago. I really have no desire to measure-off our bookshelves. AS to the Fundamental Theorem of Natural Selection, I'm familiar with it. In his book Fisher was quite impresice in describing it, but it's a simple enough observation which formalises some of our intuitive feeling about the way natural selection works. Personally, and I differ from many other evolutionary biologists, I think the relaxation of selection is probably a major driver of complexity. You could read Lynch's The Origins of Genome Architecture to get a feel for this if you haven't already. Eric, In fact, for most species most mutations are near enoguht o neutral as to make no difference. In culutre and in well-adapted populations benificial mutants are rare enough that they can be excluded from most calculation. Which isn't to say tehy dont' exist. Here is one paper I read recently, which surprised me in that it had evidence for benifical mutations: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548015/ We also have population genetic evidence for mutation enttering populations are being rapidly pushed toward fixation. wd400

With respect to: "If you can say “mutations are mostly bad, so no driving adaptation” . . ." I have no doubt that wd400 knows more about population genetics than I do. This statement reminds me, however, of an introductory class I took on genetics and evolution. In the section on "Mutations as the source of genetic variation", the professor discussed bad mutations, neutral mutations, and beneficial mutations. He said most mutations are bad. No surprise there. Others are neutral, such as AAA -> AAG. [Note, it is not clear that these are purely neutral, but I'll go along for now.] We then talked about mutation rates, fixing in populations and so on. So far so good. The part that caught my attention, however, was a drive-by comment by the professor (missed, no doubt, by many students) that we would not be dealing with beneficial mutations because "they are so rare that it is not worth trying to calculate." But that is just an anecdotal experience from one class by one particular individual. Maybe wd400 has more hard data he can bring to the table to tell us about these beneficial mutations. How often do they happen? What is the rate? What observations allow us to draw this conclusion? Inquiring minds want to know. Eric Anderson

wd400: Have you read R.A. Fisher's "Genetical Theory of Evolution"? I have read what I consider the most important parts, including Chapter 2, on the "Fundamental Theorem of Natural Selection." Do you know upon what basis he derives this "theorem"? How many population genetics books have you read, or accessed? I've probably have seen many more than you have. I have four textbooks on "genetics" on my bookshelf. I've looked all over for plausible mechanisms in which NS can account for the rise in complexity that evolutionary theory requires. I have found none. By complexity, I simply mean that for any truly 'new' function to arise, proteins have to be involved. (I'm sure you would agree here.) And, any 'new' protein involves a tremendous number of bases, let alone nucleotides. Present evolutionary theory does not provide a plausible way in which NS can account for this quantum astronomical growth in complexity that is required. I'm afraid that the 'onus' is on Darwinists to provide such a mechanism. Common sense tells us they have not provided it. Please cite authorities, books, articles. Show me something. PaV

wd400,

If you can say “mutations are mostly bad, so no driving adaptation”

That claim actually has far more empirical weight than the converse. And if we're talking about adaptation of novel increasing functional complexity, what you quoted there is by all accounts, practically a law of nature. Your position to the contrary has no evidence whatsoever.

or “evolutionary theory is almost all about survival of the fittest” then you haven’t really engaged with evolutionary biology

Pretty obvious he is referring to proposed evolutionary mechanisms, (and I think you know that) in which case he would be correct again. Neo-Darwinists bow before the god of natural selection. This wasn't a technical treatise. It was simply a couple paragraphs summing up evo theory and its problems. You're just kicking up dust, wd400. Someone insulted your religion and you have to take a shot at him. lifepsy

wd400 @28:

If you can say “mutations are mostly bad, so no driving adaptation”

Actually, it's much worse than that. Almost ALL mutations are bad, IMO. I say this because Darwinists do not count all the mutations. They only count the ones that survive being repaired by the organism, which are a tiny fraction of the total. IMO, if living organisms did not have a gene repair mechanism, there would be no life to speak of. Mapou

Simple logic: on this Earth, as we know it, life can come only from life. We do not know how life originated, but once it did appear, it progressed from single-celled organisms to us complicated conscious humans. Darwin theory obviously does not tell us how evolution causes speciation, but it must have happened. That is why I believe in theistic evolution. Entirely natural processes don't seem capable of developing the complexity of living organic chemistry in the present human genome. turell

wd400, actually, contrary to how you think science works in the rarefied air you breath of the few enlightened Darwinian elite, the way science actually works the burden is on you to prove that Darwinism is realistically feasible. With no actual empirical grounding, nor rigid mathematical basis, supporting your grand Darwinian claims that all life arose by undirected Darwinian processes, then, as far as 'real' science is concerned, everything you say is complete rubbish: "On the other hand, I disagree that Darwin's theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?" (Berlinski, D., "A Scientific Scandal?: David Berlinski & Critics," Commentary, July 8, 2003) https://uncommondescent.com/intelligent-design/quote-of-the-day-8/ Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe Excerpt: "Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859." … http://biologicinstitute.org/2011/05/05/oxford-university-seeks-mathemagician/ bornagain77

wd400- please reference this alleged theory of evolution so we can all see what it says. Joe

You don't need to take courses, attend seminars or gain degrees to understand evolution (indeed, that's the very first point I made in this thread). But if you want you opinion to be taken seriously, and you actually want to change the way we understand evolution, then the honus is on you to understand the theory you are critiquing. If you can say "mutations are mostly bad, so no driving adaptation" or "evolutionary theory is almost all about survival of the fittest" then you haven't really engaged with evolutionary biology (I don't know how many times you we need to reprodice that quote of Laryr Moran confirming he agrees with that last point, btw). So, you are welcome to think what ever you want to about evolutionary biology. But if you want to make a meaningful critique of it as a science, and not the popular conception of evolution of your own misunderstanding of the field, then you will have to spend a little time understanding it. I don't think that's an unreasonable position. wd400

wd400, perhaps Richard Lewontin doesn't understand evolution either? Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) - Casey Luskin April 12, 2011 Excerpt: Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it--changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, "You know, we've tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I've told you about." This just appalled me. So I said, "Richard Lewontin, you are a great lecturer to have the courage to say it's gotten you nowhere. But then why do you continue to do this work?" And he looked around and said, "It's the only thing I know how to do, and if I don't do it I won't get grant money." - Lynn Margulis - biologist http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.html bornagain77

PaV:

I guess you don’t realize that lots of schooling is required to understand evolution. Years and years of training; books to read; seminars to attend. . . .

It is called "Special High Intensity Training. It is only when one is full of S.H.I.T. can one successfully promote evolutionism. Joe

wd400's claim that only the 'enlightened' highly educated Darwinists (of which he considers himself to be one) truly understand evolution is an interesting claim for him to make since every thuggish troll on the internet thinks he has full mastery of the deepest intricacies of evolution. I think the truth of the matter is far closer to this quote News highlighted the other day:

"You might think that a theory so profound would be laden with intimidating mathematical formulas and at least as difficult to master as Newton’s Mechanics or Einsteins Relativity. But such is not the case. Darwinism is the most accessible “scientific” theory ever proposed. It needs no math, no mastery of biology, no depth of understanding on any level. The dullest person can understand the basic story line: “Some mistakes are good. When enough good mistakes accumulate you get a new species. If you let the mistakes run long enough, you get every complicated living thing descending from one simple living thing in the beginning. There is no need for God in this process. In fact there is no need for God at all. So the Bible, which claims that God is important, is wrong.” You can be drunk, addled, or stupid and still understand this. And the real beauty of it is that when you first glimpse this revelation with its “aha!” moment, you feel like an Einstein yourself. You feel superior, far superior, to those religious nuts who still believe in God. Without having paid any dues whatsoever, you breathe the same rarified air as the smartest people who have ever lived." – Laszlo Bencze https://uncommondescent.com/intelligent-design/laszlo-benczes-reflections-on-darwin-day/

of note:

“For many years I have thought that it is a mathematical scandal that we do not have a proof that Darwinian evolution works.” Gregory Chaitin Active Information in Metabiology - Winston Ewert, William A. Dembski, Robert J. Marks II - 2013 Except page 9: Chaitin states [3], “For many years I have thought that it is a mathematical scandal that we do not have proof that Darwinian evolution works.” In fact, mathematics has consistently demonstrated that undirected Darwinian evolution does not work. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.4/BIO-C.2013.4

bornagain77

Nullasalus: By the way – does anyone else notice that when it comes to evolution, disagreement is always translated as ‘You don’t understand evolution!’?

It's a joke really. And every time I hear I'm reminded of the old retort: "I'll tell you the same thing I once told a stand up comedian at a strip club in Vegas: I didn't come here for the jokes." CentralScrutinizer

nullasalus:

It’s as if disagreement is literally unthinkable. You’re either all on the same page or you just don’t get evolution fundamentally.

I guess you don't realize that lots of schooling is required to understand evolution. Years and years of training; books to read; seminars to attend. . . . After all this preparation, you will finally understand that evolution is the "survival of the fittest." PaV

"You don't know how evolution works!" - Consensus science. A bit of a rummy affair what? Ho-De-Ho

@20. This is an important observation. Evolution is being taught to children, but the theory is in such a sad state that those with a college science education apparently don't understand it properly. Lock step conformity to a theory that can't be explained isn't science. dgw

By the way - does anyone else notice that when it comes to evolution, disagreement is always translated as 'You don't understand evolution!'? Larry Moran plays the card in the link I give. Everyone's playing the card with Kaz. Dawkins and company played the card with EO Wilson. EO Wilson arguably played it right back. Jerry Fodor got the same treatment for writing What Darwin Got Wrong. Thomas Nagel got the same. It's as if disagreement is literally unthinkable. You're either all on the same page or you just don't get evolution fundamentally. nullasalus

I’m sorry, but if someone drags out “most mutations with bad, so adaptaton can’t be the result of mutation” I think we can safely assume they have’t read or tought very deeply about evolution.

Kaz seems to be saying that evolution as we've been able to model it and study it in the lab is great at producing changes that are degrading or minor tweaks of function, but producing novelty is a blindspot. You may disagree, but it's not some obviously wrong statement.

Moran, I’m sure, doesn’t think anything about the “almost exclusive emphasis on selection in modern evolutoinary theory” since, as he clearly states there is no such thing.

Let's quote Larry again: The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there's more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don't understand evolution. nullasalus

wd400: I’m sorry, but if someone drags out “most mutations with bad, so adaptaton can’t be the result of mutation” I think we can safely assume they have’t read or tought very deeply about evolution.

That may be your opinion, but you never provide any substantial reasons to agree with you. But do feel free to provide any blow by blow description of how RV+NS is responsible for the development of any novel body plans, cell types, tissue types or organs... except for simplifications (less complex) or degenerative effects. (crickets) CentralScrutinizer

wd400, funny you always claim to truly understand evolution but by golly you never present any empirical evidence of it happening. (in fact I've found you being dishonest in the regards a few times),,, Would you like to try falsify the null hypothesis for functional information generation by material processes (Abel) or is that beneath your exalted opinion of yourself? bornagain77

I'm sorry, but if someone drags out "most mutations with bad, so adaptaton can't be the result of mutation" I think we can safely assume they have't read or tought very deeply about evolution. Moran, I'm sure, doesn't think anything about the "almost exclusive emphasis on selection in modern evolutoinary theory" since, as he clearly states there is no such thing. The popular undertsanding of evolution certainly focses mostly on selection. So, again, Thomas' mistake marks him out as someone who knows little about real evolutionary theory. wd400

The big point of Kaz Thomas' article seems to be this: there are very large holes in evolutionary theory, some of them to be practically expected given the scope of what it's trying to explain and the nature of the subject. Origins of novelty beyond the marginal would be one of those current holes, the Cambrian Explosion, the speed of evolution, the onset of human intelligence, etc. He didn't really seem to say anything groundbreaking here, much less false, but man - judging by the comments, some people are just furious. nullasalus

I disagree with the entire quoted text (which is why I quoted all of it). i.e. the argument that because most non-neutral mutations are deleterious, mutations can’t be the source of adaptation.

Great, so disagree with him. But that's not indicative of him being clueless about evolution, and by pointing out that most non-neutral mutations are harmful doesn't exactly put him at odds with ID proponents, or somehow make his ideas wrong.

There aren’t multiple definitions of speciation, and the species probldm is not about speciation but human’s ability to delimit species.

If you change what does or doesn't count as a species, you are trivially changing the definition of speciation, since you'd be making reference to different populations and standards for species. It looks like Kaz is going in an ID direction here, since most of what he wrote seems to be emphasizing the development of novelty.

I’m not sure what you are trying to prove by quoting Moran, who confirms the falsity of Thomas’ claim that “almost everything in evolutionary theory is based on ‘survival of the fittest’”.

Read Moran again. As I said, taking 'survival of the fittest' to mean 'natural selection', which does seem to be where Kaz was going with that, makes it clear what he was talking about - and that he wasn't wrong. What does Moran think of the almost exclusive emphasis on selectionism in modern evolutionary theory? You tell me. nullasalus

wd400 funny how no one really understands evolution except you and your Darwinian cohorts! As well, since you quoted it, do you have a problem with this claim?

"The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab."

Because that is exactly what we find!:

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

and:

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html Mutations and Darwinism - Dr Jerry Bergman - June 2013 - video http://www.youtube.com/watch?v=pfgiAWBluxE

In fact the top five supposedly 'beneficial' mutations of Lenski's LTEE, after 50,000 generations were combined and found to negative epistasis. This is NOT what you need to have your preferred hypothesis be true wd400! The reason why mutations are overwhelmingly detrimental, and we have such a hard time finding any truly beneficial mutations on there way to building things up wd400, is because of the 'poly-constraint' imposed by the poly-functionality' inherent within an organism. The following article is about the genome but the principle of poly-constraint due to poly-functionality is also extended to proteins:

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006

The primary problem that poly-functional complexity presents for neo-Darwinism is this: To put it plainly, the finding of a severely poly-functional/polyconstrained genome by the ENCODE study, and many other studies, has put the odds, of what was already astronomically impossible, to what can only be termed fantastically astronomically impossible. To illustrate the monumental brick wall any evolutionary scenario (no matter what “fitness landscape”) must face when I say genomes are poly-constrained by poly-functionality, I will use a puzzle: If we were to actually get a proper “beneficial mutation’ in a polyfunctional genome, then instead of the infamous “Methinks it is like a weasel” single element of functional information that Darwinists pretend they are facing in any evolutionary search, with their now falsified genetic reductionism scenario I might add (Shapiro, Nobel), we would actually be encountering something more akin to this illustration found on page 141 of Genetic Entropy by Dr. Sanford.

S A T O R A R E P O T E N E T O P E R A R O T A S Sator Square http://en.wikipedia.org/wiki/Sator_Square

Which is translated ; THE SOWER NAMED AREPO HOLDS THE WORKING OF THE WHEELS. This ancient puzzle, which dates back to 79 AD, reads the same four different ways, Thus, If we change (mutate) any letter we may get a new meaning for a single reading read any one way, as in Dawkins weasel program, but we will consistently destroy the other 3 readings of the message with the new mutation (save for the center). This is what is meant when it is said a poly-functional genome is poly-constrained to any random mutations.

Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637

In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark):

"Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010

Supplemental note:

Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information - Jonathan Wells - published online May 2013 Conclusion:,, Recent discoveries of multiple overlapping functions in non-protein-coding DNA show that the biological information in the genome far exceeds that in the protein-coding regions alone. Yet biological information is not limited to the genome. Even at the level of gene expression - transcription and translation — the cell must access information that is not encoded in DNA. Many different RNAs can be generated from a single piece of DNA by alternative splicing, and although some splicing codes occur in intronic DNA there is no empirical justification for assuming that all of the information for tissue- and developmental-stage-specific alternative splicing resides in DNA.,, even after RNA has specified the amino acid sequence of a protein, additional information is needed: Protein function depends on three-dimensional shape, and the same sequence of amino acids can be folded differently to produce proteins with different three-dimensional shapes [144–147]. Conversely, proteins with different amino acid sequences can be folded to produce similar shapes and functions [148,149]. Many scientists have pointed out that the relationship between the genome and the organism - the genotype-phenotype mapping = cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. So non-protein-coding regions of DNA that some previously regarded as “junk” turn out to encode biological information that greatly increases the known information-carrying capacity of DNA. At the same time, DNA as a whole turns out to encode only part of the biological information needed for life. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0009

bornagain77

I disagree with the entire quoted text (which is why I quoted all of it). i.e. the argument that because most non-neutral mutations are deleterious, mutations can't be the source of adaptation. There aren't multiple definitions of speciation, and the species probldm is not about speciation but human's ability to delimit species. I'm not sure what you are trying to prove by quoting Moran, who confirms the falsity of Thomas' claim that "almost everything in evolutionary theory is based on 'survival of the fittest'". wd400

In this case, it’s clear the author’s education has taught them almost nothing about evolutionary biology.

Really? The fact that he has doubts about the extent of what we know via evolutionary biology is enough to indicate that? He seemed to mostly bluntly say what is all too obvious when reading up about the field.

The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab.

Which part of this do you even disagree with? Are you saying most non-neutral mutations are beneficial? Via Nature: Mutational effects can be beneficial, harmful, or neutral, depending on their context or location. Most non-neutral mutations are deleterious.

Or someoe who doesn’t seem to know what speciation is

He does seem to know what speciation is. The fact that the word has multiple meanings doesn't really speak against him.

or thinks ” Almost everything in evolutionary theory is based on “survival of the fittest,”?

Insofar as he means it's historically been selectionist, Larry Moran seems to agree. Sayeth ID-hating Larry: The revolution is over and strict Darwinism lost. We now know that random genetic drift is an important mechanism of evolution and there's more to evolution than natural selection. Unfortunately, this blatantly obvious fact is not understood by the vast majority of people and teachers. There are even many scientists who don't understand evolution. Maybe it's not Kaz Thomas who doesn't know much about evolutionary theory, but his critics. nullasalus

wd400- evolutionary biology is mostly just a glossy narrative void of scientific rigor and detail. And truthfully it reads like Lamarkism- just look at the narrative of how the vision system allegedly evolved. It is all Lamarkism- all of it physical changes to the vision system that get passed down. Nothing on the molecular level wrt its evolution. Joe

I just read Coyne's "rebuttal"- what a joke. Coyne sez the BF came from the TTSS yet he doesn't say how the TTSS arose. He actually references Pallen and Matzke as if they demonstrated how a BF evolved via natural selection and/ or drift. The best part is Coyne's examples of natural selection in no way indicative of NS being a designer mimic nor creating something like a bacterial flagellum. Too funny... Joe

Seems like he has a bachelors degree in microbiology, then started a PhD and dropped it. So, not a microbiologists but not without trianing. Of course, we should judge articles but the quality of their arguments, not the credentials on their authors. In this case, it's clear the author's education has taught them almost nothing about evolutionary biology. Does teh ID movement really want to throw it's support by someone who can say something as uninformed at teh quoted text When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab. Or someoe who doesn't seem to know what speciation is, or thinks " Almost everything in evolutionary theory is based on "survival of the fittest,"? wd400

selvaRajan,

Kaz Thomas seems to be a technical writer and a software documentation professional.

According to his bio page at the OP's linked site: A graduate of the University of California at Irvine and Davis (with degrees in biology and microbiology) and a former University of California Regents Fellow, Thomas has taught biology, bacteriology, and laboratory physics at the college level. He was on the Inventions Committee at Novell, Inc. and is the holder of seven U.S. software patents. He has a long and varied background in technical writing (most recently serving as a Technology Evangelist for Adobe Systems) and is in love with the word heterodoxy. He seems to have about as much claim to be a microbiologist as Dawkins has to claim he's a scientist. If we're judging by current professions, Dawkins and Kas Thomas are both writers. And PZ Myers is a blogger who sometimes teaches. nullasalus

It looks like Kas was formerly a microbiologist. From his blog:

I guess I should have made clear, up front, that I have two degrees in biology: a B.S. from UCI and a master's in microbiology (summa cum laude) from UC Davis, where I was a Regents' Fellow. I took (and passed) qualifying exams for a Ph.D. One of the specialty areas I was examined in was molecular genetics.

Maybe being a microbiologist is like learning to ride a bike? JoeCoder

News, Kaz Thomas seems to be a technical writer and a software documentation professional. He is not a Microbiologist. Please check http://www.linkedin.com/in/kasthomas selvaRajan

I see that Jerry Coyne is the self-appointed chief inquisitor of all heresies against the Church of Darwin. Mapou

Now Darwin's followers are saying Thomas should be stripped of his degrees or should ask for his money back. Guy's got guts. Anyone know him? News

Boy, this article has Jerry Coyne and fellow Darwinian trolls having a fit in the comment section. :) As well they should be. The points that Dr. Thomas honestly admits to are all severe problems for Darwinism that have all been hammered away at for years by ID proponents:

The Trouble with Darwin by Kas Thomas - February 16, 2014 Excerpt: Darwin's landmark work was called The Origin of Species, yet it doesn't actually explain in detail how speciation happens (and in fact, no one has seen it happen in the laboratory, unless you want to count plant hybridization or certain breeding anomalies in fruit flies). Almost everything in evolutionary theory is based on "survival of the fittest," a tautology that explains nothing. ("Fittest" means most able to survive. Survival of the fittest means survival of those who survive.) The means by which new survival skills emerge is, at best, murky. Of course, we can't expect Darwin himself to have proposed detailed genetic or epigenetic causes for speciation, given that he was unaware of the work of Mendel, but the fact is, even today we have a hard time figuring out how things like a bacterial flagellum first appeared. When I was in school, we were taught that mutations in DNA are the driving force behind evolution, an idea that is now thoroughly discredited. The overwhelming majority of non-neutral mutations are deleterious (reducing, not increasing, survival). This is easily demonstrated in the lab. Most mutations lead to loss of function, not gain of function. Evolutionary theory, it turns out, is great at explaining things like the loss of eyesight, over time, by cave-dwelling creatures. It's terrible at explaining gain of function. It's also terrible at explaining the speed at which speciation occurs. (Of course, The Origin of Species is entirely silent on the subject of how life arose from abiotic conditions in the first place.) It doesn't explain the Cambrian Explosion, for example, or the sudden appearance of intelligence in hominids, http://bigthink.com/devil-in-the-data/the-trouble-with-darwin

Kas Thomas is a graduate of the University of California at Irvine and Davis (with degrees in biology and microbiology) and a former University of California Regents Fellow, Thomas has taught biology, bacteriology, and laboratory physics at the college level. bornagain77

Why it is an absolute disaster that the incomplete wrong theory of Darwin is allowed to continue as if it has no problems. Because finding God leads to a wonderful life. JDH