Evolution Evolutionary biology Genetics

The Death of Neutral Theory

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In today’s Nature, we find this article:
“Synonymous mutations in representative yeast genes are mostly strongly non-neutral.”

They investigated what effect “synonymous, nonsynonymous and nonsense” mutations involving “21 endogenous genes” would have on yeast. The fitness levels of synonymous and nonsynonymous fell in equal (though not ‘identical’) measure–around 75%.

I don’t have access to the article itself, only the abstract. The abstract begins thusly:

Synonymous mutations in protein-coding genes do not alter protein sequences and are thus generally presumed to be neutral or nearly neutral[1,2,3,4,5]

1 through 5 are citations. Who are they: Kimura, King and Jukes, Nei and Kumar, Li and Dan Graur. The heavyweights of neutral theory.

The abstract ends:

The strong non-neutrality of most synonymous mutations, if it holds true for other genes and in other organisms, would require re-examination of numerous biological conclusions about mutation, selection, effective population size, divergence time and disease mechanisms that rely on the assumption that synonymous mutations are neutral.

In the Phys.Org press release, one of the authors is quoted saying:

“Since the genetic code was solved in the 1960s, synonymous mutations have been generally thought to be benign. We now show that this belief is false,” said study senior author Jianzhi “George” Zhang, the Marshall W. Nirenberg Collegiate Professor in the U-M Department of Ecology and Evolutionary Biology.

“Because many biological conclusions rely on the presumption that synonymous mutations are neutral, its invalidation has broad implications. For example, synonymous mutations are generally ignored in the study of disease-causing mutations, but they might be an underappreciated and common mechanism.”

I can hardly wait to see what Larry Moran says at his Sandwalk blog.

I have often made fun of those who hold to the Neutral Theory in the non–Kimuran sense. My problem with the idea of everything being ‘neutral’ was that, hypothetically, anything can become anything. There’s no start nor finish to this process. I thought it was extravagant; instead, it was just wrong. Modern techniques–the use of Crisper to make mutant genes, has now allowed us to see how NT is a ‘dead-end.’ We can only hope that evolutionary biologists can see this. But there’s really no reason for such hope, is there?

The authors tell us that there’s no reason to believe that what they found in yeast won’t be found in other eukaryotic species, but that this will have to be tested to confirm that this ‘dead-end’ generally holds. I’ll bet on it holding in most families with few, if any, exceptions. We’ll see. Science progresses (while Darwinism ebbs).

25 Replies to “The Death of Neutral Theory

  1. 1
    bornagain77 says:

    Moran will just blow this off like he did the ENCODE results which found widespread functionality across the genome.

    Of related note:

    Synonymous (“Silent”) Mutations in Health, Disease, and Personalized Medicine: Review – 2012
    Excerpt: In contrast, a synonymous mutation does not delete or substitute one amino acid for another; thus the protein produced by both the normal gene and the mutant have the identical amino acid sequence. However, it can reduce the amount of a specific protein the cell makes or cause the structure of the protein to be distorted in a manner that disrupts its functioning in the body.,,,
    The CBER authors compiled a list of synonymous mutations that are linked to almost fifty diseases, including diabetes, a blood clotting disorder called hemophilia B, cervical cancer, and cystic fibrosis.
    http://www.fda.gov/BiologicsBl.....271385.htm

    Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. – Jan 2013
    Excerpt: Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides.,,,
    Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles
    http://www.ncbi.nlm.nih.gov/pubmed/23293005

  2. 2
    hoosfoos says:

    From a 2014 Cell paper:

    Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

    Here, in an analysis of >3,000 cancer exomes and >300 cancer genomes, we present robust statistical evidence that this is indeed the case: that synonymous mutations must frequently contribute to cancer. These silent mutations in exons may act through diverse molecular mechanisms, and they are often associated with changes in splicing.

    The DOI is Open Archive: 10.1016/j.cell.2014.01.051

  3. 3
    Belfast says:

    I think it is more possible that Professor Moran will ignore it.
    Under the heading of “Silent Mutations and Neutral Theory”, he wrote, “Neutral Theory and random genetic drift explains variation and it also explains molecular evolution and the (approximate) molecular clock. There are no other explanations that make sense and nobody has offered a competing explanation since Motoo Kimura (1968) or Jack King and Thomas Jukes (1969) published their papers almost fifty years ago.”
    It’s difficult to crab back from such a positive statement.

  4. 4
    bornagain77 says:

    To add a little background information to this, it is interesting to note that neutral theory effectively falsified natural selection as a major player in evolution.

    As Moran himself quoted Austin Hughs as saying, ‘Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.’

    Austin Hughes and Neutral Theory – Laurence A. Moran – June 19, 2017
    Excerpt: Originally proposed by Motoo Kimura, Jack King, and Thomas Jukes, the neutral theory of molecular evolution is inherently non-Darwinian. Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.
    http://sandwalk.blogspot.com/2.....heory.html

    Even Richard Dawkins himself finds the claim that chance alone, all by its lonesome, can explain life to be “absolutely inconceivable”.

    In the following video Richard Dawkins states that, “it cannot come about by chance. It’s absolutely inconceivable that you could get anything as complicated or well designed as a modern bird or a human or a hedgehog coming about by chance.’

    4:30 minute mark: “It cannot come about by chance. It’s absolutely inconceivable that you could get anything as complicated or well designed as a modern bird or a human or a hedgehog coming about by chance. That’s absolutely out.,,, It’s out of the question.,,,
    So where (does the appearance of design)) it come from? The process of gradual evolution by natural selection.”
    Richard Dawkins – From a Frog to a Prince – video
    https://youtu.be/ClleN8ysimg?t=267

    To put it even more bluntly than Richard Dawkins did, Jay Homnick states, “Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident… you have essentially “lost your mind.”

    It’s Really Not Rocket Science – Granville Sewell – November 16, 2015
    Excerpt: “It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. It strikes me as urgent to insist that you not allow your mind to surrender the absolute clarity that all complex and magnificent things were made that way. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident… you have essentially “lost your mind.”
    Jay Homnick – American Spectator 2005
    http://www.evolutionnews.org/2.....00911.html

    Thus, with Natural selection being tossed to the wayside by population genetics via ‘neutral theory’, as the supposed explanation for the ‘well designed’ things we see in life, Evolutionists, such as Moran, did not accept such a devastating finding as an outright falsification for their theory, as they should have done, but instead are now reduced to arguing that the ‘well designed’ things we see in life are, basically, the result of pure chance with natural selection now playing a very negligible role if any role at all.

    Contrary to what proponents of neutral theory may want to ‘religiously’ believe to the contrary, with natural selection out of the way as the supposed ‘designer substitute’,,,

    Darwin’s Influence on Modern Thought By Ernst Mayr – November 24, 2009
    Excerpt: Every aspect of the “wonderful design” so admired by the natural theologians could be explained by natural selection.
    https://www.scientificamerican.com/article/darwins-influence-on-modern-thought/

    Darwin’s greatest discovery: Design without designer – Francisco J. Ayala – May 15, 2007
    Excerpt: “Darwin’s theory of natural selection accounts for the ‘design’ of organisms, and for their wondrous diversity, as the result of natural processes,”,,,
    Darwin’s Explanation of Design
    Darwin’s focus in The Origin was the explanation of design, with evolution playing the subsidiary role of supporting evidence.
    http://www.pnas.org/content/104/suppl_1/8567.full

    ,,, with natural selection cast to the wayside as the supposed ‘designer substitute’, then the explanation for that ‘appearance of design’ in life does not default to chance, all by its lonesome, as the supposed explanation for the ‘wondrous diversity’ of life, (as Evolutionists such as Moran want to hold), but instead the explanation reverts back to the original intuitive assumption that the ‘wondrous diversity’ and complexity of life must be designed,

    As Richard Sternberg states, “Darwinism provided an explanation for the appearance of design, and argued that there is no Designer — or, if you will, the designer is natural selection. If that’s out of the way — if that (natural selection) just does not explain the evidence — then the flip side of that is, well, things appear designed because they are designed.”

    “Darwinism provided an explanation for the appearance of design, and argued that there is no Designer — or, if you will, the designer is natural selection. If that’s out of the way — if that (natural selection) just does not explain the evidence — then the flip side of that is, well, things appear designed because they are designed.”
    Richard Sternberg – Living Waters documentary
    Whale Evolution vs. Population Genetics – Richard Sternberg and Paul Nelson – (excerpt from Living Waters video)
    https://www.youtube.com/watch?v=0csd3M4bc0Q

    Of supplemental note to ‘the death of neutral theory’:

    The Neutral Theory in Light of Natural Selection – Andrew D Kern, Matthew W Hahn
    Molecular Biology and Evolution, Volume 35, Issue 6, June 2018
    Abstract:
    In this perspective, we evaluate the explanatory power of the neutral theory of molecular evolution, 50 years after its introduction by Kimura. We argue that the neutral theory was supported by unreliable theoretical and empirical evidence from the beginning, and that in light of modern, genome-scale data, we can firmly reject its universality. The ubiquity of adaptive variation both within and between species means that a more comprehensive theory of molecular evolution must be sought.
    https://academic.oup.com/mbe/article/35/6/1366/4990884

  5. 5
    Fred Hickson says:

    Goodness me, I’m feeling faint. I have to admit I’m in agreement with PAV, Bornagain77, Richard Dawkins and Darwinism and in disagreement with Austin Hughs (who he?) if BA’s quote is correct:

    Darwinism asserts that natural selection is the driving force of evolutionary change. It is the claim of the neutral theory, on the other hand, that the majority of evolutionary change is due to chance.

    There can be no adaptive change without selection.

  6. 6
    ET says:

    Fred Hickson still doesn’t understand that natural selection is a process of ELIMINATION.

  7. 7
    ET says:

    DaveScot provided an article that says synonymous mutations cause problems due to timing issues. It seems cells do NOT have an equal mix of tRNAs. So, if the tRNA that is replacing another is rare, it causes issues with the timing and the protein doesn’t fold properly. This is also in the book the “Design of Life” Dembski and Wells. So, yes, we have known that those mutations aren’t always neutral for years.

  8. 8
    bornagain77 says:

    FH, but the point is that Moran and company ARE correct about the inadequacy of Natural Selection.

    i.e. Natural Selection IS found, via population genetics, to be grossly inadequate as the supposed ‘designer substitute’.

    For instance, the ‘waiting time problem’,

    The waiting time problem in a model hominin population – 2015 Sep 17
    John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner
    Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,,
    Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information.
    While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man.
    It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years.
    http://www.ncbi.nlm.nih.gov/pm.....MC4573302/

    Moreover, it doesn’t take a PhD in mathematics to understand why Natural Selection is grossly inadequate as the supposed ‘designer substitute’.

    In order to explain the ‘appearance of design’ we see in life, Natural Selection would have to operate at the molecular/genetic level.

    The GS Principle (The Genetic Selection Principle) – Abel – 2009
    Excerpt: The GS Principle, sometimes called “The 2nd Law of Biology,” states that selection must occur at the molecular/genetic level, not just at the fittest phenotypic/organismic level, to produce and explain life.,,, (Yet) Natural selection cannot operate at the genetic level.
    http://www.ncbi.nlm.nih.gov/pubmed/19273248

    Yet, Natural Selection cannot possibly operate at the genetic level but can only select at the whole organism level.

    This presents an insurmountable problem for Darwinists.

    This insurmountable problem for Darwinists is clearly illustrated, and easily understood, with what is termed the ‘Princess and the Pea’ paradox.

    Dr. John Sanford goes over the easy to understand “Princess and the Pea” paradox in the following video at the 8:14 minute mark:

    Dr. John Sanford: Genetic Entropy and the Mystery of the Genome – video
    https://youtu.be/eY98io7JH-c?t=495

    The easy to understand lesson of the “Princess and the Pea” paradox is that Natural Selection can only select for an entire organism and cannot possibly ‘see’, and/or select for, individual nucleotides that are buried underneath the many layers of mattresses that selection, i.e. the Princess, is sleeping on.

  9. 9
    Silver Asiatic says:

    The term “non-neutral” is the nice way to say “harmful”. Or even more, “strongly harmful” – and therefore damaging to evolutionary claims that they’re just neutral.

    But in a study scheduled for online publication June 8 in the journal Nature that involved the genetic manipulation of yeast cells in the laboratory, University of Michigan biologists show that most synonymous mutations are strongly harmful.
    https://phys.org/news/2022-06-silent-genetic-mutations-neutral-broad.html

    Synonymous mutations are part of the “niche” that the organism has to fight against in order to survive.

  10. 10
    PaV says:

    BA77:

    Very nice post @5. Lays things out clearly and dramatically.

    Let’s not forget that this article is published in the journal Nature. Nature is for the most part, or has been, the enforcer of Darwinian orthodoxy and so here is an article that explodes a rival to Darwinian thought–as Fred Hickson wants to point out. Now the problem with this is that without Neutral Theory, Darwinism is dead!!

    How can that be? How can I make such a statement? Easy. The whole reason that the Neutral Theory came into existence were a set of experiments utilizing gel electrophoresis–cutting-edge technology in the late 60’s, that demonstrated that contrary to neo-Darwinian orthodoxy, there was an incredible level of genetic polymorphism. This meant that organisms would necessarily have to be “purifying” countless alleles and with each allele needing correction countless numbers of the species would have to die, termed ‘genetic load.’ This came from Haldane’s calculations done in the 50’s. Faced with this dilemma, Motoo Kimura developed his Neutral Theory, a theory that was at once opposed by neo-Darwinists. That was over 50 years ago.

    Summing up, the neutral theory was meant to “save” Darwinian orthodoxy and, so, with the seeming “death of the neutral theory” now being spotlighted by Nature, the unintended consequence (something that seems to have been forgotten about) is that neo-Darwinism falls flat. It fails as an explanatory theory.

    It’s almost like Nature took a shot at the Neutral Theory and then was killed by the ricochet. Interesting times.

  11. 11
    bornagain77 says:

    PaV, “It’s almost like Nature took a shot at the Neutral Theory and then was killed by the ricochet.”

    🙂 🙂
    LOL

  12. 12
    chuckdarwin says:

    SA states:

    The term “non-neutral” is the nice way to say “harmful”. Or even more, “strongly harmful” – and therefore damaging to evolutionary claims that they’re just neutral.

    The terminology isn’t that important. Neutral Theory always acknowledged that the bulk of mutations could be deleterious. One could argue persuasively that this finding, if it holds, bolsters the role of NS since NS is very efficient at stripping out deleterious mutations at the phenotypic level before they become fixed at the molecular level.

    Try as it might, ID just can’t seem to get that stake through the heart of NS.

  13. 13
    Silver Asiatic says:

    CD

    Or is it that “try as they may, evolutionists cannot get a theory that works”?
    Aside from the fact that strongly harmful mutations will cause a higher mortality rate, this still won’t help increase the number of beneficial mutations needed in the time required.

  14. 14
    chuckdarwin says:

    At least they have a theory. Science has always been about trial and error. Beats “design, a/k/a God, did it.”

  15. 15
    relatd says:

    CD at 14,

    Aliens did it? Who created the aliens? They are accidents too?

  16. 16
    bornagain77 says:

    CD: “Try as it might, ID just can’t seem to get that stake through the heart of NS.”

    Yet, seeing that NS is not even defined in a rigorous, i.e. ‘scientific’, manner, then, getting a ‘stake through the heart of NS’ is very similar to trying to nail Jello to the wall.

    Darwin’s Theory of Natural Selection Has Left a Legacy of Confusion over Biological Adaptation
    Brian Miller – September 20, 2021
    Excerpt: Evolutionary biologist Robert Reid stated:
    “Indeed the language of neo-Darwinism is so careless that the words ‘divine plan’ can be substituted for ‘selection pressure’ in any popular work in the biological literature without the slightest disruption in the logical flow of argument.”
    Robert Reid, Biological Emergences: Evolution by Natural Experiment, PP. 37-38 (2009)
    To fully comprehend the critique, one simply needs to imagine attempting to craft an evolutionary barometer that measures the selection pressure driving one organism to transform into something different (e.g., fish into an amphibian). The fact that no such instrument could be constructed highlights the fictitious nature of such mystical forces.
    https://evolutionnews.org/2021/09/darwins-theory-of-natural-selection-has-left-a-legacy-of-confusion-over-biological-adaptation/

    Evolutionary Fitness Is Not Measurable – November 20, 2021
    The central concept of natural selection cannot be measured. This means it has no scientific value.
    Excerpt:,, to measure something, it needs units. How is fitness to be measured? What are the units? Physicists have degrees Kelvin, ergs and Joules of energy and Faradays of electricity, but do 100 Spencers on a Haeckl-o-meter equal 10 Darwins of fitness?
    ,,, The term “fitness” becomes nebulous when you try to pin it down. Five evolutionists attempted to nail this jello to the wall, and wrote up their results in a preprint on bioRxiv by Alif et al. that asked, “What is the best fitness measure in wild populations?” (One might wonder why this question is being asked 162 years after Darwin presented his theory to the world.)
    ,,, The authors admit that their results do not necessarily apply to all living things. (they state),
    “A universal definition of fitness in mathematical terms that applies to all population structures and dynamics is however not agreed on.”
    Remember that this statement comes over 162 years after evolutionists began talking about fitness. If you cannot define something, how can you measure it? And if you can’t measure it, is it really scientific?,,,
    https://crev.info/2021/11/evolutionary-fitness-is-not-measurable/

    As Professor of Zoology John O. Reiss himself honestly admitted, “The rigor of this approach, however, is lessened because there is as yet no universally agreed upon measure of fitness; fitness is either defined metaphorically, or defined only relative to the particular model or system used. It is fair to say that due to this lack, there is still no real agreement on what exactly the process of natural selection is. This is clearly a problem.”

    Where is the purposelessness of evolution? – 23 March 2012,
    Excerpt: The only way variation is seen as random is that it is random in respect to the effect variation has on fitness.
    The major problem with this is that the precise meaning of fitness has not been settled. There is still a major debate about what exactly fitness is supposed to mean (see this post for more on this issue).
    John O. Reiss notes also make the following interesting remark:
    “The rigor of this approach, however, is lessened because there is as yet no universally agreed upon measure of fitness; fitness is either defined metaphorically, or defined only relative to the particular model or system used. It is fair to say that due to this lack, there is still no real agreement on what exactly the process of natural selection is. This is clearly a problem.”
    Without a proper definition of fitness, we can’t really say what natural selection is in the first place. Also, without a proper definition of fitness we can’t really make any sense of how variation can be random relative to fitness in the first place.,,,
    https://www.news24.com/MyNews24/Where-is-the-purposelessness-of-evolution-20120322

    i.e. As the late Stephen Jay Gould himself once honestly admitted, NS functions far more in the realm of fantasy, i.e. of imaginary just-so story telling, than it functions in the realm of real empirical science.

    Sociobiology: The Art of Story Telling – Stephen Jay Gould – 1978 – New Scientist
    Excerpt: Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers “Just So stories”. When evolutionists study individual adaptations, when they try to explain form and behaviour by reconstructing history and assessing current utility, they also tell just so stories – and the agent is natural selection.
    Virtuosity in invention replaces testability as the criterion for acceptance.
    https://books.google.com/books?id=tRj7EyRFVqYC&pg=PA530

  17. 17
    Silver Asiatic says:

    CD @14

    If there’s evidence for design, then that beats trial and error without it.

  18. 18
    bornagain77 says:

    CD: . “One could argue persuasively that this finding, if it holds, bolsters the role of NS since NS is very efficient at stripping out deleterious mutations at the phenotypic level before they become fixed at the molecular level.”

    Yet the real world is not nearly as kind to CD’s imaginary speculations as he hopes it to be.

    Can Purifying Natural Selection Preserve Biological Information? – May 2013 –
    Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford
    In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,,
    http://www.worldscientific.com.....08728_0010  

    Kimura’s Distribution
    http://dl0.creation.com/articl.....-white.jpg

    Correct Distribution
    http://dl0.creation.com/articl.....-white.jpg

    Dr. John Sanford Lecture at NIH (National Institute of Health): Genetic Entropy – Mutation Accumulation: Is it a Serious Health Risk? – 2018 video
    https://www.youtube.com/watch?v=eqIjnol9uh8

  19. 19
    Fasteddious says:

    Perhaps I don’t understand all the terminology, but it seems to me that this discussion conflates two different types of “Neutral Theory”
    – one type says that synonymous codons that call for the same amino acid in a protein are neutral;
    i.e. the same protein results with either codon.
    – the other says that most mutations in a gene are neutral vis-a-vis natural selection;
    i.e. changing some amino acids at random has little effect on the protein function and hence,
    the survival (or reproductive success) of the organism.
    While these two may be related, they are not the same thing. The article in question appears to be about the first type (synonymous codons), while much of the subsequent discussion is about the second type (neutral evolution).
    Please correct me if I’m wrong.

  20. 20
    PaV says:

    BA77:

    Excellent posts BA77. Very illuminating of the topic of this thread.

    Fasteddious:

    Your number (1) is the same as your number (2). Neutral mutations–synonymous substitutions–occur that leave the function of the protein unchanged (apparently), and thusly, NS is unable to “see” these different forms. This solves Kimura’s problem from the late 60’s of so many polymorphic amino acid sites in the genome, each needing preferential ‘death’ of organisms within that species–which, of course, is unsustainable. Hence Kimura’s Neutral Theory.

    Here, discovered only because of modern laboratory techniques that enable gene modification via the use of Crisper, the authors show that while on the surface these polymorphic versions of proteins don’t seem to matter, they do indeed matter and cause a loss of fitness to the organism. So, they’re NOT neutral. NS can “see” them.

  21. 21
    PaV says:

    Chuckdarwin@12:

    The terminology isn’t that important. Neutral Theory always acknowledged that the bulk of mutations could be deleterious. One could argue persuasively that this finding, if it holds, bolsters the role of NS since NS is very efficient at stripping out deleterious mutations at the phenotypic level before they become fixed at the molecular level.

    But that’s what I’ve pointed out: that the journal, Nature, the historical guardian of NS and hence neo-Darwinism, is very glad to present an article that seems to shoot down what is being said by biologists who hold to the

    But when you say that “Neutral Theory always acknowledged that the bulk of mutations could be deleterious,” I think you’re just making it up. Otherwise, you have neutral theorists holding onto an obvious contradiction: “we say that most mutations are neutral; that is, NS doesn’t see them. But, of course, they could always really be ‘deleterious.’ You can’t have your cake and eat it too. How about some intellectual honesty.

    CD@14:

    At least they have a theory. Science has always been about trial and error. Beats “design, a/k/a God, did it.”

    You’re setting up a false dichotomy here: either there is a completely ‘material’ cause for what we see in the fossil record, OR, “God did it” and there’s no more to be said about it.

    Who was Gregor Mendel? He was a priest, a canon in Switzerland. He was a man of God. Yet it is from him that comes the only true law at work in biology that we know of: Mendelian genetics.

    Did he say: “Oh, the reason that so many species exist is that God made each and every one of them.”? No, he used “trial and error” to determine that variation of traits exist contemporaneously in each population.

    Likewise, today’s scientist has simply to say: “Biological diversity is the result of some kind of intelligent design. How can I discover the rules of this intelligence.” And then you use “trail and error” to get at these rules.

    The history of science is littered with men (and women) who came up with ideas that proved pivotal and they did so by simply asking the question: How might God have done this?

    Here’s Darwinism (basically Fisher’s ‘Fundamental Theorem of Natural Selection’): the rate of increase in fitness is inversely proportional to the rate of death. And on this, we build the entirety of biological diversity? Really? Does the fossil record support such a contention? Not even Darwin thought so.

  22. 22
    chuckdarwin says:

    PaV/21 claims:

    But when you say that “Neutral Theory always acknowledged that the bulk of mutations could be deleterious,” I think you’re just making it up. (emphasis added)

    Really, PaV?

    It must be stressed that the neutral theory of molecular evolution is not an anti-Darwinian theory. Both the selectionist and neutral theories recognize that natural selection is responsible for the adaptation of organisms to their environment. Both also recognize that most new mutations in functionally important regions are deleterious and that purifying selection quickly removes these deleterious mutations from populations. Thus, these mutations do not contribute—or contribute very little—to sequence divergence between species and to polymorphisms within species. Rather, the dispute between selectionists and neutralists relates only to the relative proportion of neutral and advantageous mutations that contribute to sequence divergence and polymorphism. (emphasis added) (<https://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839//)

  23. 23
    chuckdarwin says:

    PaV/21
    Having a problem with the Nature link, hopefully this works: https://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839/

  24. 24
    PaV says:

    Chuchdarwin/23:

    These quotes come from the section of the link you quoted from.

    Right before the quote:

    All of these observations have been widely confirmed with the genomic data that are now available (Figure 1). These observations are consistent with the neutral theory but contradict selectionist theory.

    Right after the quote:

    Analysis of genomic sequence data reveals that there is no “all or nothing” answer to this dispute.

    Your quoted section simply lays out the “dispute” that still exists today. The “observations . . . widely confirmed with . . . genomic data . . . are consistent with the neutral theory but contradict selectionist theory. There are two sides to this debate. Nature has taken one side.

    But, as you can see from another quote taken from the very beginning of your link, neutral theory “contradicts” selectionist theory–that is, that NS “selects” variations that arise.

    The neutral theory holds that most variation at the molecular level does not affect fitness and, therefore, the evolutionary fate of genetic variation is best explained by stochastic processes.

    By the way, @21 , I wasn’t trying to imply that you were being dishonest. I thought rather that the “making things up” had to do with just not knowing where the “dispute” actually stood. 🙂

  25. 25
    chuckdarwin says:

    PaV/24
    I appreciate your explanation that you weren’t implying that I’m simply pulling stuff out of thin air. I’ve been called a lot of names on this blog, but irrespective of that, I think I’ve been diligent at sourcing my comments.

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