Thursday, December 01, 2016

Learning about modern evolutionary theory: the drift-barrier hypothesis

Many evolutionary biologists are engaged in research that focuses on large organisms that are (presumably) adapting to a local environment. These "field biologists" are mostly concerned with rapid evolutionary changes. Those kind of changes are almost always due to natural selection. Many of these biologists are not interested in molecular evolution and not interested in any process other than natural selection.

Unfortunately, this promotes an adaptationist mentality where all of evolution is viewed through the filter of natural selection. This is the view criticized by Stephen Jay Gould and Richard Lewontin back in 1978 when they presented the Spandrels paper at a Royal Society meeting in London (UK).
Gould, S. J. and Lewontin, R.C. (1979) The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme. Proc. R. Soc. Lond. B 205:581-598. [doi: 10.1098/rspb.1979.0086
I believe there was a substantive change in our view of evolution back in the late 1960s and early 1970s. That's when the results of evolution at the molecular level were first being published. It lead to the development of Neutral Theory, Nearly-Neutral Theory and a growing appreciation of the importance of random genetic drift. Modern population genetics was able to cope easily with this new view of evolution.

It seems to me that most evolutionary biologists missed the revolution. That's why they're stuck with a 1950s view of evolution—one that only recognizes natural selection as a mechanism that changes allele frequencies in a population. That was the dominant perspective at the most recent Royal Society meeting in London a few weeks ago. Ironically, the participants were advocating the overthrow of the Modern Synthesis (1950s version) but they did not want to overthrow the view that adapationism is the only perspective. In fact, most of the changes they proposed were hyper-adaptationist.

Nothing in biology makes sense except in the light of population genetics.

Michael Lynch
It's been almost half-a-century since this new perspective on evolutionary theory was proposed. Many evolutionary biologists now know that deleterious alleles can be fixed in a population by random genetic drift. They know that natural selection isn't all-powerful; in fact, most beneficial alleles are lost before they ever become fixed. They know the probability of fixation by natural selection depends on the effective population size—the probability is greater in large populations the probability that deleterious alleles will be eliminated by natural selection depends on the effective population size—the probability is greater in large populations. Furthermore, for alleles that are only slightly beneficial, the power of natural selection to fix them in small populations is neutralized by stochastic effects (random genetic drift). Alleles with slight beneficial effects are far more likely to become fixed in large populations. [see comments] They know that effectively neutral alleles are common and they regularly become fixed in a population by drift.

There have been many vocal proponents of this view over the past few decades but their voices tend to be drowned out by the advocates of natural selection and the appearance of design. That's what attracts the attention of the general public, scientists in other fields, and even evolutionary biologists.

The overwhelming emphasis on natural selection in the media, and even in the scientific literature, has stalled the revolution and led to a situation where the vast majority of scientists have a flawed view of evolution. We see this in the universities where our students are often taught evolution by the very scientists I described in the opening paragraph. I'm particularly sensitive to this because I'm getting ready for my course on molecular evolution next semester and I know my most important task will be to correct the misconceptions of my students.

Michael Lynch has been trying to educate his fellow scientists, and the rest of the world, for the past few decades. His latest attempt is a paper in last month's edition of Nature Reviews: Genetics where he promotes the Drift-Barrier Hypothesis. He does this in the context of understanding mutation rates but the idea is generally applicable to all examples of evolution.
Lynch, M., Ackerman, M. S., Gout, J.-F., Long, H., Sung, W., Thomas, W. K., and Foster, P. L. (2016) Genetic drift, selection and the evolution of the mutation rate. Nature Reviews Genetics, 17:704-714. doi: 10.1038/nrg.2016.104

As one of the few cellular traits that can be quantified across the tree of life, DNA-replication fidelity provides an excellent platform for understanding fundamental evolutionary processes. Furthermore, because mutation is the ultimate source of all genetic variation, clarifying why mutation rates vary is crucial for understanding all areas of biology. A potentially revealing hypothesis for mutation-rate evolution is that natural selection primarily operates to improve replication fidelity, with the ultimate limits to what can be achieved set by the power of random genetic drift. This drift-barrier hypothesis is consistent with comparative measures of mutation rates, provides a simple explanation for the existence of error-prone polymerases and yields a formal counter-argument to the view that selection fine-tunes gene-specific mutation rates.
Let's look at Michael Lynch's view of evolution. This won't be new to most readers of Sandwalk but maybe it will stimulate some of you to reconsider your old-fashioned, adaptationist, view of evolution.

The question we're considering is: Why doesn't natural selection reduce the mutation rate to zero?. It seems reasonable to imagine that since some mutations are harmful, evolution should select for populations with the lowest possible mutation rate. The standard answer to the question is to imagine there are physical constraints on the accuracy of DNA replication preventing the evolution of a perfect DNA polymerase. This explanation doesn't hold up to close scrutiny as I pointed out in my earlier blog post.

Furthermore, the overall mutation rate—expressed as the number of mutations per generation—depends not only on the accuracy of DNA replication (and repair) but also on additional features such as the number of cell divisions required for formation of the germ cells. In humans, for example, the mutation rate could be substantially reduced by reducing the number of sperm cells made in males. Why hasn't that happened?

The answer depends on understanding the relationship between natural selection and random genetic drift. The two processes compete with each other and the winner is influenced by the size of the population. In small populations, a beneficial mutation can easily be lost by drift before it becomes established in a population. In larger populations, on the other hand, it's harder to lose the beneficial mutation by accident so eventually selection will win out and the beneficial allele becomes fixed by natural selection.

This is the essence of the drift-barrier hypothesis described in Lynch's latest paper by using a very nice figure.


The figure shows the probability of achieving adaptation (trait performance) as a function of the size of the population. Improvements by natural selection are impeded by downward pressure due to the stochastic effects of random genetic drift (blue arrows). This is very effective in small populations. Selection is represented by upward pressure (red arrows) and this is increasingly effective in large populations. However, "perfection" can never be achieved in any reasonable population as the selection coefficient becomes smaller and smaller. This is the drift barrier to adaptation.

The "drift-barrier hypothesis is described in Sung et al. (2012) (see also, Lynch, 2011),
... the drift-barrier hypothesis predicts that the level of refinement of molecular attributes, including DNA replication fidelity and repair, that can be accomplished by natural selection will be negatively correlated with the effective population size (Ne) of a species. Under this hypothesis, as natural selection pushes a trait toward perfection, further improvements are expected to have diminishing fitness advantages. Once the point is reached beyond which the effects of subsequent beneficial mutations are unlikely to be large enough to overcome the power of random genetic drift, adaptive progress is expected to come to a standstill. Because selection is generally expected to favor lower mutation rates as a result of the associated load of deleterious mutations, and because the power of drift is inversely proportional to Ne, lower mutation rates are expected in species with larger Ne.

The consequences are modeled in simulations of mutation rate evolution (below). When the initial mutation rate is high (red, black) there will be a decrease in the mutation rate until a point is reached where improvements are impeded by the drift barrier. When the initial mutation rate is low (blue) the rate will increase because the deleterious effects of increasing the number of mutations are below the threshold imposed by the pressure of drift. The result is a steady-state mutation rate that is far from perfection.

The important point here is not the evolution of mutation rates. It's the idea that drift and selection are both operating in natural populations and you can't understand one without taking into account the other. This is a point that needs to be publicized. We need to get out the message that's there's more to evolution that just natural selection. We need to convince science writers that modern population genetics provides a much better explanation of biological phenomena than just blind allegiance to the old-fashioned Modern Synthesis of Ernst Mayr and his colleagues.

Here's what you need to know in order to understand modern evolutionary theory. The first quotation is from the preface to The Origins of Genome Architecture (pages xiii-xiv). The second quotations are from the last chapter (page 366 and pages 368-369).


Contrary to popular belief, evolution is not driven by natural selection alone. Many aspects of evolutionary change are indeed facilitated by natural selection, but all populations are influenced by nonadaptive forces of mutation, recombination, and random genetic drift. These additional forces are not simple embellishments around a primary axis of selection, but are quite the opposite—they dictate what natural selection can and cannot do. Although this basic principle has been known for a long time, it is quite remarkable that most biologists continue to interpret nearly aspect of biodiversity as an outcome of adaptive processes. This blind acceptance of natural selection as the only force relevant to evolution has led to a lot of sloppy thinking, and is probably the primary reason why evolution is viewed as a soft science by much of society.

A central point to be explained in this book is that most aspects of evolution at the genome level cannot be fully explained in adaptive terms, and moreover, that many features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics. However, even if such support did not exist, there is an important reason for pursuing nonadaptive (neutral) models of evolution. If one wants to confidently invoke a specific adaptive scenario to explain an observed pattern of comparative data, then an ability to reject a hypothesis based entirely on the nonadaptive forces of evolution is critical.

The blind worship of natural selection is not evolutionary biology. It is arguably not even science.

Michael Lynch
Despite the tremendous theoretical and physical resources now available, the field of evolutionary biology continues to be widely perceived as a soft science. Here I am referring not to the problems associated with those pushing the view that life was created by an intelligent designer, but to a more significant internal issue: a subset of academics who consider themselves strong advocates of evolution but who see no compelling reason to probe the substantial knowledge base of the field. Although this is a heavy charge, it is easy to document. For example, in his 2001 presidential address to the Society for the Study of Evolution, Nick Barton presented a survey that demonstrated that about half of the recent literature devoted to evolutionary issues is far removed from mainstream evolutionary biology.

With the possible exception of behavior, evolutionary biology is treated unlike any other science. Philosophers, sociologists, and ethicists expound on the central role of evolutionary theory in understanding our place in the world. Physicists excited about biocomplexity and computer scientists enamored with genetic algorithms promise a bold new understanding of evolution, and similar claims are made in the emerging field of evolutionary psychology (and its derivatives in political science, economics, and even the humanities). Numerous popularizers of evolution, some with careers focused on defending the teaching of evolution in public schools, are entirely satisfied that a blind adherence to the Darwinian concept of natural selection is a license for such activities. A commonality among all these groups is the near-absence of an appreciation of the most fundamental principles of evolution. Unfortunately, this list extends deep within the life sciences.

....

... the uncritical acceptance of natural selection as an explanatory force for all aspects of biodiversity (without any direct evidence) is not much different than invoking an intelligent designer (without any direct evidence). True, we have actually seen natural selection in action in a number of well-documented cases of phenotypic evolution (Endler 1986; Kingsolver et al. 2001), but it is a leap to assume that selection accounts for all evolutionary change, particularly at the molecular and cellular levels. The blind worship of natural selection is not evolutionary biology. It is arguably not even science. Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.

Natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.It should be emphasized here that the sins of panselectionism are by no means restricted to developmental biology, but simply follow the tradition embraced by many areas of evolutionary biology itself, including paleontology and evolutionary ecology (as cogently articulated by Gould and Lewontin in 1979). The vast majority of evolutionary biologists studying morphological, physiological, and or behavioral traits almost always interpret the results in terms of adaptive mechanisms, and they are so convinced of the validity of this approach that virtually no attention is given to the null hypothesis of neutral evolution, despite the availability of methods to do so (Lande 1976; Lynch and Hill 1986; Lynch 1994). For example, in a substantial series of books addressed to the general public, Dawkins (e,g., 1976, 1986, 1996, 2004) has deftly explained a bewildering array of observations in terms of hypothetical selection scenarios. Dawkins's effort to spread the gospel of the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, and because more people have probably read Dawkins than Darwin, his words have in some ways been profoundly misleading. To his credit, Gould, who is also widely read by the general public, frequently railed against adaptive storytelling, but it can be difficult to understand what alternative mechanisms of evolution Gould had in mind.


Lynch, M. (2011) The lower bound to the evolution of mutation rates. Genome Biology and Evolution, 3:1107. [doi: 10.1093/gbe/evr066]

Sung, W., Ackerman, M.S., Miller, S.F., Doak, T.G., and Lynch, M. (2012) Drift-barrier hypothesis and mutation-rate evolution. Proc. Natl. Acad. Sci. (USA) 109:18488-18492. [doi: 10.1073/pnas.1216223109]

91 comments :

  1. I 100% agree. too bad there aren't many books that explain modern evolutionary theory to all those non-experts! ;)

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  2. This is all nice and dandy Larry but just like the the supporters of natural selection, or any other mechanism of evolution, the post lacks one fundamental element-evidence.

    Evolutionist have been promoting their own ideas about the mechanism of evolution for decades while wasting tax payers money and confusing the public instead of providing experimental evidence for their claims.

    I gotta be honest with you Larry, I can't see any difference at all between the many evolutionary ideas on how evolution works, or supposed to work, and the dispute between the Young and Old Earth Creationists. Until at least some real evidence is on the table, if I were Donald Trump, I would cut off all the funding for Darwin nonsense research until such evidence, or the prospect of it, is in view. It's about time to end this nonsense in evolutionary science and hold people accountable not only for their claims, but even more so for how they spend the hard-earned tax-payer money.

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    1. The paper is chock full of evidence. Why don't you read it?

      There's really not much point in discussing "evidence' with you if you think Young Earth Creationists have it.

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    2. Larry

      i have not seen evidence that genetic drift can cause macro-evolutionary change. Mind to provide evidence for this assertion, Larry ?

      development , body shape, and phenotype of organisms depends on
      epigenetic factors,
      Membrane targets and patterns
      Cytoskeletal arrays
      Centrosomes
      Ion channels, and
      Sugar molecules on the exterior of cells (the sugar code)
      Gene regulatory networks
      and various codes, several times mentioned here
      RNA methylation
      DNA dinucleotide methylation
      DNA CpG island methylation
      histone methylation
      chromatin remodeling
      DNA coiling
      microRNA regulation
      alternative splicing

      No gene sequence alterations in the list, because
      - Deletions, insertions and frameshift mutations are misinterpretations of the alternative splicing mechanism
      - Retrogenes and genetic recombinations are misinterpretations of the alternative splicing mechanism
      - RNA based gene duplications are misinterpretations of the alternative splicing mechanism

      So, what do you have left for supporting the idea that genetic change alone fits the bill ?
      DNA of every organism gets only degraded, little by little.

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    3. "i have not seen evidence that genetic drift can cause macro-evolutionary change. "

      You also haven't seen an immaterial divine mind, supernaturally wish the entire cosmos into existence. Yet you believe that with the staunch conviction of a psychotic.

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    4. Objection: We have never observed a being of any capacity creating biological systems and life.
      Answer: We do not need direct observed empirical evidence to infer design. If investigators know that someone was deliberately killed, is their conclusion invalidated because they don't yet know exactly who did it and how?
      When a detective arrives at the crime scence, and sees a bullet in the chest of the victim, and no arm nearby that could be a hint to suicide, the detective can with a degree of certainty conclude the victim was shot in the chest and killed. So its a murder crime scence.
      Same when we observe the natural world. It gives us hints about how it could have been created. We do not need to present the act of creation to infer creationism / Intelligent design.

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    5. Otangelo cluelessly shoots himself in the foot:

      Objection: We have never observed a being of any capacity creating biological systems and life.
      Answer: We do not need direct observed empirical evidence to infer design. If investigators know that someone was deliberately killed, is their conclusion invalidated because they don't yet know exactly who did it and how?


      Exactly! And, by the same argument, we don't need to directly observe the emergence of all species thru macroevolution to know that this occurred.

      The problem for your side is that what you claim to be "empirical evidence to infer design" doesn't exist. All you have are false claims, logical fallacies, and the blind belief in the inerrancy of religious scriptures.

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    6. Otangelo,

      "No gene sequence alterations in the list, because"

      Huh? How are changes in DNA sequence due to indels (including retrotransposition) not alterations? They are by their very definition an alteration, and they are also naturally occurring processes.

      If you don't think that the mechanisms of evolution (both selection and drift) can produce macroevolution, then please point to a single genetic difference between humans and other apes that these mechanisms can not produce. If you can't, then you have failed to support your argument.

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    7. Eric

      the difference between chimps and humans is said to be small. But the morpholoigical differences are hudge. Why is that ?

      I suggest you google: Chimps, our brothers ?

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    8. "the difference between chimps and humans is said to be small. But the morpholoigical differences are hudge. Why is that ?"

      Because that's how genetics work. Relatively minor genetic changes have large phenotypical effects. Even so, why is the morphological differences "hudge"? How do you quantify morphological change? Can you put a number on it?

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    9. Eric asked for one single genetic difference, Otangelo. Just one. Is that really too much to ask?

      Delete
    10. OG claims that deletions, insertions, frameshift mutations, retrogenes, genetic recombinations,and RNA based gene duplications are all misinterpretations of the alternative splicing mechanism.

      And yet, when we compare DNA sequences we can see these differences. Alternative splicing happens to RNA after it has been transcribed from DNA, but these differences are in the DNA, before alternative splicing.

      Yet another observation consistent with the hypothesis that OG does not know what he is talking about.

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    11. You also haven't seen an immaterial divine mind, supernaturally wish the entire cosmos into existence. Yet you believe that with the staunch conviction of a psychotic

      Well Mikkel, I'm not sure who claims to have seen the immaterial divine mind to bring cosmos into existence but you aren't as insane as someone who brings it up.

      If you need a realistic comparison between the two sides, just imagine you are talking to Jerry Coyne himself just in a different dimension.

      Why don't you explain how it is possible that the universe began highly organized (don't want to say perfect because of you know who)? Almost perfect. Don't give me the typical bs "science doesn't but it will" bs. I want it now, since you make your outrages claims NOW.

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    12. V -- Is it a fact that the universe began highly organized? Almost perfect? What standard would you use to assess that? There's no need to explain it unless it's true, but it is true??

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    13. It is true that the universe began in a state of extremely low entropy. Whether that is what Velhovsky means by "highly organized", I doubt even he knows. The question of why the universe once existed in such a state is an interesting one, but not one for which "goddidit" provides anything resembling a meaningful answer.

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    14. I don't go to comedy clubs anymore.

      When my wife asked me why, I said that materialists are much, more funny than any stand-up comedians I know.

      Above are typical examples of materialists who made up their mind no matter what evidence is or will be available.

      I have not doubt about that because I have seen it with epigenetics and "junk DNA".

      I call them The Goddiditers, because whenever they have not even one piece of evidence to support their beliefs, for what they call science, they cloak the issue with excuses, distractions or pure ignorance:

      "Yeah, scientists have not figure out how life began, so god did it". That is a typical response.

      Unfortunately, you will never see a link to an experiment or two that proves or convinces you or more so convinced them that "the accident-did-it". No way! I'm almost 100% sure that if there was such an experiment, I would have been linked many, many times over even if it was a promise of proving biogenesis.

      Why would a fairly large group of people, the majority of whom is well educated, would stick to a belief that has no evidence, "no hope of evidence any time soon"-not my words?

      It just boggles my mind what the screwed-up the society it is.

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    15. Larry wrote:

      " When you look at the big picture you see that evolution is good at producing things that work. "

      Of course evolution is this amazing mechanism that permits organisms to adapt to the environment. This is a process, amazingly created.

      But keep arguing and insisting that evolution is the universal mechanism to explain biodiversity despite the fact that it has been shown by mainstream science that a holistic aproach is required that includes epigenetics, is miopic and shows willful ignorance to say the least.

      Proponents of naturalism are lucid and bright to point out when a proponent of ID makes inaccurate assertions. Why do they not use their intelligence to recognize the shortcomings of naturalism, but use all their efforts to defend a explanation that is obviously false ?!

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    16. This comment has been removed by a blog administrator.

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    17. Hey Otangelo, in another thread you mentioned there is no proof for god (s). Well done.
      You then continued to state something (there's more than the naturalistic world as we see it), but you accidentally forgot to back this statement up with evidence.

      Would you be so kind to give proof of this holistic, non naturalistic world?

      In the following post you cite 3 papers which somehow are evidence for front loading? The first link is a nice paper, but you forgot to add this bit, directly after the sentence of your citation:
      "For example, modification of DNA can help organisms distinguish self DNA from foreign DNA(8). In bacterial species, DNA methyltransferases have co-evolved with a partner restriction enzyme that shares the same sequence preference. Since only host DNA is methylated, this system allows for degradation of foreign DNA by the corresponding restriction enzyme."

      Anyway, do tell where they mention (evidence for) front loading? Or pre-programming as you like to call it??

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    18. Ed

      do they need to mention it explicitly ?

      as for the evidence for a designer you ask for:

      google : 125 Arguments for God's Existence

      you can pick any of the arguments listed there. I will be more than happy to discuss any of it.....

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    19. Ah yes, gems like: "The fact that the physical universe had a beginning, means it had a cause."

      I asked you in a previous thread to show evidence of this cause. Furthermore, I asked you to provide evidence only your god/ designer is in fact the cause of this cause. I checked the thread I asked you to answer this and you failed to post an answer. Perhaps you'd like to give it a try?

      Anyway, first you admit there is no evidence for god(s), now you say there are 'arguments in favor of a god(s)', but arguments <> evidence.
      A lawyer can argue in court his client is innocent, but he needs facts and evidence to back up his claims.

      Back to the papers you cite, there is no mention of front loading/ pre-programming in these papers. So how come you think you can link these papers in support of your argument??

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    20. Ed

      Evidence does not equal proof. Evidence is what we observe in nature. That evidence points in my view to design/creation as the best explanation of origins of the natural world. If you disagree, feel free to point out, what kind of evidence that would convince you that a creator is required, and specially, what about you make a own case , and point out, why you think naturalism is the best explanation or our existence ?

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    21. Otangelo, what is the reason that you won't answer Ed's very clear and reasonable questions and, instead, try to change the subject?

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    22. Ed,
      I don't recall you providing any evidence as to how the universe could have begun without a cause and extremely organized without intelligence involved. Please refresh my memory.

      BTW: I got your answers just in case your're thinking I'm reneging like you have lol

      Delete
    23. Nice job of begging the question, Velhosky.

      There is no evidence that "intelligence" is needed in order for physical processes to demonstrate organization. And quantum physics demonstrates that things can come into existence uncaused.

      Delete
    24. Hey Velhovsky, do you remember this question I asked you regarding your claims?
      "Hey Velhovsky, you wrote:

      "I can make an argument that what you call the fact for evolution-common descent-I will call common design. I can present facts that will show that your "fact(s)" are just a collection of wishful thinking without any scientific or experimental evidence. "

      Well, I'd say the stage is all yours, I'm really interested in this argument supported by the facts you mention."

      Still waiting for your answer. Want to give it a try now?

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    25. Velhovsky:
      "Ed,
      I don't recall you providing any evidence as to how the universe could have begun without a cause and extremely organized without intelligence involved."

      Why should I, it's your claim there should be intelligence and cause. It's up to you to provide the evidence to support the claims.

      "BTW: I got your answers just in case your're thinking I'm reneging like you have lol "

      Well fire away with the evidence you have for intelligence and cause. I'm interested, perhaps you might even convert some one to this god...

      But you know Velhovsky, up 'till now you've pulled many a claim out of your high hat, but for some mysterious reason when asked for evidence for your claims, you never answer. Except by adding new claims which you also never substantiate. Why is that Vel?

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    26. Otangelo wrote:
      "If you disagree, feel free to point out, what kind of evidence that would convince you that a creator is required,"
      No, once again YOU need to provide the evidence to convince me, because it's your claim. Until you provide one (1) single shred of evidence of this cause and intelligence, the current scientific consensus (even with all it's remaining questions) fit the evidence found. And yeah, you can claim 'we don't know everything yet, so there might be evidence for a designer in the next 10 years', but then your claim becomes a god of the gaps fallacy.

      Want to try providing evidence for:
      "The fact that the physical universe had a beginning, means it had a cause."

      Or can we expect another dodge?

      Delete
    27. Ed

      nice dodging all on your side, congrats. I gave you 125 reasons to believe in God, but you keep asking for evidence....

      Its your turn now...

      Asking to provide positive, compelling evidence that points to the fact that the natural world can have a origin by its own, is not the same as to ask for evidence that God does not exist. If atheists are going to argue that adequate answers exist without the need for God, they are at least going to have to provide sufficient naturalistic explanations.

      Proponents of naturalism hope to one day learn how nothing magically can turn into something, or how we can reach now from eternity, how randomness can finetune hundreds of physical parameters to make life possible, how life can emerge from non-life randomly, and produce millions of species with the ability to evolve , and conscient intelligent minds can emerge from matter.....

      Delete
    28. Otangelo the Hypocrite writes,

      nice dodging all on your side,

      ...to the sound of dozens of exploding Irony Meters.

      Delete
    29. Otangelo:
      "Asking to provide positive, compelling evidence that points to the fact that the natural world can have a origin by its own, is not the same as to ask for evidence that God does not exist."

      I'm not asking for evidence that your designer (so it's god then?) doesn't exist. I'm asking you to give positive evidence of the intelligence and cause you claim to have caused "The fact that the physical universe had a beginning, means it had a cause." exists. Thus, I'm only asking for positive evidence to support your claim.

      You point me to a list of 125 reasons to believe in your god, the first reason on the list you've used many times already as proof of existence of your god/ designer.
      Perhaps now it's time to mention the fact you've admitted there's no proof for god(s). But at the same time you argue the designer is (your) god(s) and proof to believe in your god(s) is this list of 125 'reasons'.

      And you're actually surprised people don't understand your (failed attempts at) logic?

      Anyway, want to try again? Or should we settle on the conclusion that your claim "The fact that the physical universe had a beginning, means it had a cause." is just a claim, a statement pulled out of thin air?

      Delete
    30. Ed

      either a)you do infact not understand my posts, or b) behave as if you do not understand them. I guess its case b.

      I call it God, creator, intelligent designer, whatever. Why does it matter ?! The positive evidence is the fact, the universe exists, and had a beginning. That points to a cause. Are you sure you want to debate with me such kind of basic logical things ?

      I provided 125 reasons and arguments for Gods existence. I did not mention the identity. Thats not the point. And again: I have no absolute, conclusive, empirical proof for Gods existence. I have alraid said that. What do you not understand about that fact ? Proof does not equal evidence. Once more: What do you not understand about that ? There is no failed logic. Arguments aren''t proof either. They are just, as it sais, arguments. Arguments, that can be false, wrong, or compelling, convincing etc. But they do not constitute absolute proof.

      I am asking YOU to try again. You have been unable to provide a more convincing alternative to the origin of the universe. You have not many.....

      Again. Its your turn. People that read this must think how patient i am. Indeed.

      Delete
    31. As usual, Otangelo, your problem is not just that you are ignorant of basic facts. It is that you do not know how to use logic.

      The natural processes by which life arose, or thru which the universe began, remain unknown. That does not mean that supernatural processes become the correct explanation by default.

      To use an analogy you have used before, yourself: Suppose a murder has been convicted and, while there are several likely suspects who may have committed it, there is not yet enough evidence to charge any particular one of these. If we used your "reasoning" in this situation, the police would have to conclude the the murder could only have been committed by God, thru supernatural means they are unable to describe. Is that how you'd like our law enforcement to work?

      Delete
    32. Otangelo, well done:
      " Arguments, that can be false, wrong, or compelling, convincing etc. But they do not constitute absolute proof. "

      Thanks, that's all I needed to know.
      Anyway, I don't think there's much use in continuing here, you refuse to answer a simple question to support your claims.

      You've just pulled "The fact that the physical universe had a beginning, means it had a cause." out of thin air and at the same time you've presented it many times as evidence for (a) god(s)...

      Delete
    33. Ed

      The Kalaam Cosmological argument has been propagated by W.L.Craig for over 30 years, and he has debated it in depth with the formemost astrophysicists, cosmologists, and philosophers of science. And it stands as one of the pilars and strongest arguments that favour a theistic world view.

      If you want to educate yourself ( which i doubt you will ) , you can read the paper:

      The Existence of God and the Beginning of the Universe

      My challenge stands. Pick ANY of the presented 125 arguments i listed, and provide better explanations based on natural mechanisms, and we talk......

      Delete
    34. The Kalaam Cosmological argument has been propagated by W.L.Craig for over 30 years, and he has debated it in depth with the formemost astrophysicists, cosmologists, and philosophers of science. And it stands as one of the pilars and strongest arguments that favour a theistic world view.

      LOL! Seriously? That hoary old pile of fallacies is the best you have? Then we're pretty well done here.

      Watch what happens when Craig tries to pull that argument, as well as all his others, with an actual cosmologist, Sean Carroll. Craig gets so badly destroyed, he almost seems on the verge of tears by the end:

      William Lane Craig and Sean Carroll | "God and Cosmology" | 2014 Greer Heard Forum

      If you just want to watch the excerpts devoted to the Kalam:

      https://www.youtube.com/watch?v=g5iiHV4yo7M

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    35. Otangelo wrote:
      "
      My challenge stands. Pick ANY of the presented 125 arguments i listed, and provide better explanations based on natural mechanisms, and we talk......"

      Dude, seriously?!? You claim these arguments are proof of god(s), it's up to you to provide evidence in favor of your claims. Do you really have trouble understanding this? Should I try translating in Chinese and then you'll understand???

      Until you provide scientific evidence, and not the 'evolution can't do this, thus goddidit' crap which is basically the basis of the majority of your 125 arguments, we're done.

      Craig gets his ass handed back to him it seems, and that's the best pillar of theistic world view... Wow!
      I'd opt for Norse creation myths if I were you, at least the cow Audhumbla is licking a *pillar* of icy salt.

      Delete
    36. Ed

      you are a fool like Larry Moron.

      Get a life.

      Delete
    37. You 125 Arguments are not evidence for God. All they are, are attempt to refute scientific theories. Even if these attempts weren't laughably inept failures (which they are) they wouldn't prove the existence of God.

      Another logic fail from Otangelo.

      Delete
    38. I read OG's 125 proofs of God. Not fun. It's clear that OG has read a lot of science articles or at least the relevant press releases. He quotes from them. If scientists disagree about something, it can't happen. Therefore, God. If one scientist disagreed in the past but the problem has been solved, OG doesn't notice. Sometimes the whole argument is, "This is too complex to happen, therefore God." In fact, much of this could be summed up as we don't know how life began, therefore God or irreducible complexity, therefore God. He proves the Big Bang didn't happen, then uses the Big Bang as evidence for God. Here's relatively brief example of the type of logic, if one can call it that:

      10.The argument from transitional fossils
      The evidence of the words of Charles Darwin
      1. “As by this [evolution] theory, innumerable transitional forms must have existed. Why do we not find them in the fossil record? Why is not all nature in confusion instead of being, as we see them, well-defined species?”—Charles Darwin (1866)
      2. Even the few transitional forms claimed by scientists to be good ones are very questionable and what to say about not finding innumerable transitional forms.
      3. The work of a designer and his creation is obvious. All men call him God.
      4. God exists.

      You should go there and read 106, The argument of the universe as a big juggling exhibition. Amazing.

      The presentation of the 125 arguments does have a certain rhythm to it, a semi formal ritual pattern.

      And no, OG, I do not plan to discuss any of these arguments with you. Observing them was enough.

      Delete
  3. "They know the probability of fixation by natural selection depends on the effective population size—the probability is greater in large populations."

    I hope this is just a typo. The probability of fixation of a mutant allele decreases as population size increases. Since the expected number per generation in which any mutation occurs increases linearly with population size, the rate at which alleles with s>0 get fixed increases with larger population size, because the probability of fixation does not shrink as fast as this number increases (and conversely the rate decreases for s<0 as the probability of fixation goes down faster than the increase of the expected number. For s=0 these effects cancel each other out and you get the approximate molecular clock).

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    1. Perhaps you could help me out by writing a short phrase (like I did) that would convey the main point to a diverse audience like Sandwalk readers? There are times when I appreciate your nitpicking but there are times when it is not helpful. Maybe I just should have said something a bit more accurate in just a few more words. Can you suggest such a phrase?

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    2. Huh? The probability of fixation for a beneficial mutation is a matter of not getting lost, not going to zero, because once an allele's numbers are far enough from zero, it has essentially no chance of getting lost. So this hardly depends at all on population size, which is why the approximation 2s is often used. For a neutral allele, the probability of fixation is simply the starting frequency, which is 1/N (haploids) for a new mutation. This probability decreases linearly with population size, obviously.

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    3. FYI, Simon is conflating probability of fixation with rate of origin-fixation in the sentence that begins "Since the expected number".

      Larry, the simplifying statement that you want to make about selection and population size could be expressed as an effect on the probability of fixation of *deleterious alleles*, but it is more easily stated as a greater tendency to eliminate deleterious variants. There is a relentless rain of deleterious mutations in every population, and in small populations this can result in puddles and occasional floods, whereas in large populations, the rain is channeled efficiently into the gutter and drains away without causing any problems.

      That metaphor could be improved.

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    4. Thanks Arlin (and Simon),

      I get what you are saying. I'll change the statement to read: the probability that deleterious alleles will be eliminated by natural selection depends on the effective population size—the probability is greater in large populations.

      I've always had a bit of a problem with those calculations. Perhaps you guys can help me out?

      If a new allele arises with a selective advantage of 0.01 in a homozygous population, then what's the selective disadvantage of the existing allele? If the probability of fixation of the new allele is always close to 2% regardless of population size then doesn't that mean that the existing now-deleterious allele will always become fixed with a probability of 98%? Doesn't that mean that fixation of the deleterious allele in such situations is independent of population size?

      Also, I was trying to convey the idea that there's a competition between selection and drift such that when s is very low the allele becomes effectively neutral in small populations. Would I be correct to add? ...

      Furthermore, for alleles that are only slightly beneficial, the power of natural selection to fix them in small populations is neutralized by stochastic effects (random genetic drift). Alleles with slight beneficial effects are far more likely to become fixed in large populations.

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    5. I'm going to give a numerical example, but I'll be quite imprecise: Let's say you have a population and in each generation you have (on average) 10000 detrimental mutations, 20000 neutral mutations and 5000 beneficial mutations. Of these 400 detrimental ones, 600 neutral ones and 450 beneficial ones eventually get fixed. Now you double the population size. You get twice as many of each type of mutation, so it's 20000 detrimental mutations, 40000 neutral mutations and 10000 beneficial mutations. You end up with 350 detrimental ones, 600 neutral ones and 500 beneficial ones getting fixed. We can note that for the neutral ones the probability of fixation dropped by 50%, but the increase in population size also caused twice as many neutral mutations to occur and these effects cancel each other out. We can also note that while there were twice as many detrimental mutations, their chance of fixation dropped by more than half, resulting in less fixations than in the smaller population. And for the beneficial ones their chance of fixation dropped as well, but by less than half, which was more than offset by their increased number, leading to more fixations.

      I think for the simple two allele case the best option is to go with Kimuras version of s, because it has the neat property that if there are two alleles and one has a selection coefficient of s, the other one has a selection coefficient of -s. The 2s approximation is mathematically derived by letting the population size go to infinity in a particular way (there are alternative ways of letting the population size go to infinity which yield fixation probabilities of 1 if s>0 and 0 otherwise and ways to make the probability of fixation go to 0 for everything regardless of selection coefficient). I think it's usually more helpful to build intuition using Formula 8 from Kimura (1962) u=(1-e^(-4Nsp))/(1-e^(-4Ns)) and the analog for clonal haploid organisms u=(1-e^(-Nsp))/(1-e^(-Ns)); (p=1/2N and 1/N for novel mutants respectively).

      I can't really comment on how to convey the idea that there's a competition between selection and drift - you know my opinion that treating them as separate "things" or "processes" is often misleading. And I now have to warn you that the annoying type of nitpicking is coming up, because effectively neutral means that 2Ns is small (generally <1). So of course if s and N are small 2Ns become small, but they aren't really independent variables. It's a bit like saying "If the number of wheels is very small, bicycles and tricycles become effectively unicycled".

      Delete
  4. "...not even science." Ouch. So those natural selection biologists were not doing science? Keep it under your hat!
    Has those insisting natural selection is over blown really won their spurs.?
    Why is there such misunderstanding? How can creationists be blamed for not understanding evolutionism if evolutionist biologists have important, to be noted, gaps in understanding??
    Natural selection doesn't work at important levels or very much.
    Other mechanisms are needed by more thoughtful people and the future is with these people.
    That evolutionism is seen as a soft science is not the fault of natural selection biologists!
    its seen as soft by the public because its not able to prove its conclusions by excellent proofs. So its seen as speculative. Its about past and gone processes and events regardless of accuracy in conclusions.
    People, in common sense, understand this. Its like history and has its problems in proving its conclusions.
    Hard sciences are hard because the proof is excellent. Hard!!

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  5. yawn.
    Molecular evolution? genomics? Sure, all about drift. Fine.
    But what evidence have you got that drift is important in the evolution of phenotypes? Of organisms that have to survive and reproduce in their environments, and the physiological systems and behaviors that they use to do so?
    Oh, bupkiss? huh.

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    1. Some humans can roll their tongues and others can't. The phenotypic difference is genetic. The onus is on adaptationists to prove that this phenotype is adaptive.

      There are many phenotypic differences between populations/species that have not been explained by natural selection. In the absence of proof of adaptation, the default explanation is drift. We've discussed the differences in appearance of Asian and African elephants, for example, and the differing patterns of stripes on African zebras. I also wrote a blog post on the differences in the number of needles in clusters on different pine trees.

      The example I use in class is the heritable phenotypic differences between individual students. Do you think that all those differences, such as height, shape of the nose, colour of the eyes, length of your fingers etc., are under selection? Can you prove it?

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    2. Height of students? Well, a 1-inch-tall student would have low fitness, as would a 100-foot-tall student. Or do you think those differences too are neutral?

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    3. Clearly, the shape of my nose is perfectly designed because it holds up my spectacles so well.

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    4. I spend a lot of time looking for differences among taxa that will aid in their identification. Such differences are everywhere, and many of them seem unlikely to have adaptive benefits.

      In grasses, ligules can be membranous, of hairs, or membranous with hairs on top, and they all seem to work. Ligules can be long or short. One species has glumes cut straight across, with all veins equal, and a relative has pointed glumes, with some veins longer than others. Vestigial rachillas can be long, short, or absent. In another group, nectaries can be round or crescent-shaped, and insects seem to like both alternatives. Anther colors vary. Bracts may be herbaceous, scarious-margined, or entirely scarious. And so forth. These differences are genetic.

      You can imagine that these details make some adaptive differences, maybe, sometimes. But are all the differences among species really adaptive? I doubt it. I think that many of these differences get fixed early in the evolution of a taxon, for some reason or none at all, and just stay that way.

      Of course, these not-particularly-adaptive traits may become useful in some cases, as in certain Carex sedges where the vestigial rachilla is long and bent and functions as a hook. I doubt the other variations on rachilla length really matter. Just neutral phenotypic variation.

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  6. I wasn't aware of the drift-barrier hypothesis, and always thought the reason mutation rates don't evolve to 0 was because without mutation to generate new variation, the capacity for adaptation would be so close to 0, that any species with a too low mutation rate would eventually go extinct when the environment changed.

    On this view, the only reason all life isn't extinct is that by sheer chance it would be unlikely for all environments to remain static for so long that they could all evolve a practically perfect mutation rate.

    I have a hard time imagining how one could observationally distinguish between the two scenarios (drift-barrier vs adaptation-for-evolvability) after the fact.
    The irony of invoking an adaptive hypothesis to explain why natural populations are still capable of adapting isn't lost on me :)

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  7. "I believe there was a substantive change in our view of evolution back in the late 1960s and early 1970s. That's when the results of evolution at the molecular level were first being published. It lead to the development of Neutral Theory, Nearly-Neutral Theory and a growing appreciation of the importance of random genetic drift. Modern population genetics was able to cope easily with this new view of evolution."

    I get what you are trying to say, but this is not how the history and the theory actually unfolded. The understanding of molecular evolutionists is very much shaped, not by neo-Darwinism, but by the neo-mutationist thinking developed in the 1960s under the influence of biochemists like Anfinsen, Zuckerkandl, Dayhoff, and so on, later formalized in origin-fixation models in 1969 (Kimura and Maruyama, King and Jukes).

    Classical population genetics was not set up to "cope easily with this new kind of evolution" but instead was set up to reject it. New thinking had to be developed, and new formalizations to go along with it. Simpson, Mayr and Dobzhansky all tried to marginalize what came to be called "molecular" evolution. If the results of molecular sequence comparisons had fit perfectly with the old theory, we would have just called it "more evolution", but it was so obviously different, so it was seen as a different kind of thing, and was christened "molecular" evolution. Think about it.

    If thought leaders had taken "molecular" evolution seriously, it would have been seen as a repudiation of the extrapolationist gambit of macroevolution = microevolution underlying the Modern Synthesis. The claim was that everything we know about near-term evolution is consistent with evolution as the smooth selection-driven shifting of allele frequencies within an abundant "gene pool" from one multi-locus optimum to another (with no need to consider new mutations), and that nothing bars us from extrapolating from "shifting gene frequencies" to long-term evolution.

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  8. Thank you for this.
    Your complaint about the way the theory is presented is so nice, I have the same ones.
    There is hope for a doubter yet!
    I just have to get more familiar with population genetics, obviously.

    Thanks again.

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  9. Larry (and Michael), nice write-up. I agree with most of the details of the argument (a cogent description of important details in modern evolutionary theory), and I understand the frustration with people who argue on the topic without understanding the basics of it. However, I also want to argue for a more positive view. Progress over the last few decades is leading towards a much more detailed, accurate, and nuanced understanding of the mechanics of biology and the evolutionary process (whether we are talking about development, genomes, transposable elements, regulatory control, physiology or neurobiology). This is really exciting. People are going to stumble as they take new information on board (e.g., the conference you recently went to), and they are going to tend to be excited more by natural selection (perhaps overly excited) because of its importance in evolutionary design. Perhaps we can forgive them and simply work to make everyone's understanding more complete at the same time that we all share in the excitement of understanding evolutionary mechanics better (including mutation, drift and draft).

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  10. My reaction to this article is a bit like my reaction to articles about junk DNA. Have scientists ever said that every phenotypic difference between species and through time is adaptive?

    This isn't meant to be a rhetorical question. I also understand that Gould wouldn't have written about spandrels if neutral phenotypic change was a prominent mechanism in the historical development of the theory. But just how staunchly adapationist were theorists in the past?

    I do strongly agree with the idea that we don't start with a phenotypic change and then work backwards to find an adaptive rationalization for that change. Much of the problem stems from affirming the consequent:

    If P, then Q. Q, therefore P.

    Natural selection produces phenotypic change. We see phenotypic change, therefore natural selection. While the first statement is true, the second is not.

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    1. Have scientists ever said that every phenotypic difference between species and through time is adaptive?

      We could quibble about details but many scientists actually believe that the effects of neutral alleles are confined to molecular changes that have no effect on phenotype.

      It's hard to find any scientist who's crazy enough to declare that every single phenotypic difference must be under selection but some have come very close.

      The adaptationism controversy is quite different. It is concerned with whether, given that we're dealing with a phenotypic effect big enough to see and ask questions about, we should assume that it is the product of natural selection. The biochemist's "neutral mutations" are more than neutral. As far as those of us who look at gross morphology, physiology and behavior are concerned, they are not mutations at all. It was in this spirit that Maynard Smith (1976) wrote: "I interpret 'rate of evolution' as a rate of adaptive change. In this sense, the substitution of a neutral allele would not constitute evolution ..." If a whole organism biologist sees a genetically determined differences among phenotypes, he already knows he cannot be dealing with neutrality in the sense of the modern controversy among biochemical geneticists. Richard Dawkins in The Extended Phenotype 1982 p. 32

      He still holds this view today. Here's what he wrote in The Greatest Show on Earth (2009).

      As it happens, it is probably true to say that most mutations are neutral. They are undetectable by natural selection, but detectable by molecular geneticists; and that is an ideal combination for an evolutionary clock.

      None of this is to downgrade the all-important tip of the iceberg—the minority of mutations that are not neutral. It is they that are selected, positively or negatively, in the evolution of improvements. They are the ones whose effects we actually see—and natural selection "sees" too. They are the ones whose selection gives living things their breathtaking illusion of design. But it is the rest of the iceberg—the neutral mutations which are in the majority—that concerns us when we are talking about the molecular clock.

      As geological time goes by, the genome is subjected to a rain of attrition in the form of mutations. In that small portion of the genome where the mutations really matter for survival, natural selection soon gets rid of the bad ones and favors the good ones. The neutral mutations, on the other hand, simply pile up, unpunished and unnoticed—except by molecular geneticists.


      His idea is that neutral alleles are confined to insignificant changes in DNA sequence that are only visible to molecular geneticists.

      He and I have debated this issue over the past two decades and he's well aware of the controversy. He knows that many of us believe neutral alleles can affect phenotype. That's why he also adds the following, in the same book ...

      It is also possible (although "ultra-Darwinists" like me incline against the idea) that some mutations really do change the body, but in such a way as to have no effect on survival, one way or the other.

      As a general rule, the idea that all visible phenotypes are under selection is just an unstated, and unquestioned, assumption of most adaptationists. They will only back off (a little bit) if they are challenged to defend that view.

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  11. I've always had trouble seeing how mutation and selection could account for the complexity of eukaryotes, particularly all the multiprotein complexes that do the job of single proteins in bacteria.
    I think neutral mutations can cause non-functional protein interactions which sometimes become functional and are honed by selection. Didnt someone propose something like this in the lit? (Stoltfuz?)

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  12. DARWIN'S RESEARCH ASSOCIATE'S 1897 SOLUTION

    Beginning with an address to the Linnean Society four years after the death of his mentor, Darwin's young research associate, George Romanes, developed a view of evolution that is recognized neither by the modern synthesists nor the "third way" extended evolutionary synthesists. His clearest account is in his 1897 masterpiece, the third volume of his series entitled "Darwin, And After Darwin."


    Romanes' view was taken up and further developed by William Bateson and Richard Goldschmidt, and in the 1980s was adopted by both Stephen Jay Gould and Richard Dawkins (transiently); albeit neither cited the earlier work.


    Gould disavowed the viewpoint in his 2002 magnum opus. However, considerable evidence supporting Romanes' view had accumulated before Gould's sadly premature demise in that year, and more has accumulated subsequently.

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  13. Of course drift is one of the key mechanisms of evolution. We use the concept of drift all the time in our research, be it in the context of lineage sorting or loss of genetic diversity in small and fragmented populations.

    But there is a good reason why so many focus on adaptation in their research and public communications: There is indeed an appearance of design, it needs an explanation, and surely genetic drift is not its explanation.

    I mean, just look at the creationism debate, so often had on this very site. When some creationist goes "but how could something like the human eye evolve?", surely the answer will not be "through genetic drift", right?

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    1. The appearance of design can be overemphasized to the point where it impedes understanding. When I look at human bodies, for example, I see just as much evidence of poor design as I do of good design. When you look at the big picture you see that evolution is good at producing things that work. They are good enough to do the job but an intelligent designer, if she exists, could do a hell of a lot better.

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    2. It is generally agreed that no human being is perfect or designs things perfectly and yet we are intelligent.

      Even suboptimal designs require a designer. The Newcomen steam engine was not nearly as efficient or practical as Watts’ steam engine, but no one in his right mind would suggest on that basis that Newcomen’s engine self-assembled by random chance. Second, some designs that may look suboptimal to us are actual optimal e.g. the panda’s thumb; the panda uses his “thumb” (actually a specialized bone in the wrist) for near continuous grasping of bamboo. If it had used an opposable thumb to do so, as proponents of naturalism suggest as a superior design, it would almost certainly suffer from permanent carpal tunnel syndrome. Third, what we see now is the world as marred by the curse upon sin. For all we know, people as created may have been able to synthesize every necessary vitamin, but some of those abilities may have subsequently been lost due to genetic corruption and drift. Furthermore : Since Genesis history includes the origin of sin and death, it is crucially foundational to the logic of the gospel: a good world, ruined by sin, to be restored in the future.

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    3. No doubt about that, but is that not largely because adaptation works by tinkering as opposed to drift? Obvious examples are the trade-off with the birth canal, our knees and the laryngeal nerve. Again it would be hard to say "they are that way because of drift". They are that way because bodies are build through following developmental pathways that can only be changed to a small degree.

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    4. When you look at the big picture you see that evolution is good at producing things that work.

      Evolution explains adaptation of organisms to the environment, which is a pre-programmed process. It does not explain biodiversity. Nor the origin of life.

      Larry, what role does epigenetics play to make a organism ?

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    5. So let me get this clear, Otangelo: You acknowledge Larry's point that, if the human body was "designed", its designer committed several blunders that could easily be improved upon by a mere human designer.

      The puzzling thing here is that pretty well all of you creationists identify this "designer" as God, a being whom you believe to be infallible, omniscient and omnipotent. How do you guys reconcile this? Or is it just that you are so accustomed to speaking out both sides of your mouths that you no longer even notice when you do it?

      (Bringing up the idea of "original sin" does not save you, since any reasonable and objective assessment would conclude that that was a major design flaw that indicates negligence and incompetence on the part of the designer.)

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    6. Lutesuite, I agree. I've long thought that "original sin" story was a classic example of poor design and blame shifting.

      God creates humans, sets them in a wonderful place, gives them free will, and tells them not to eat fruit of one tree, which is not fenced. Then he's angry at THEM after he set them up to do it.

      (Fully accepting that interpretation of the story was a milestone in my personal spiritual growth. I think spiritual is the right word.)

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    7. Larry: "They are good enough to do the job but an intelligent designer, if she exists, could do a hell of a lot better."

      Whatever designer decided to place the testickes outside the body should be shot. Especially if he was also responsible for humans designing boys' bikes with that damned horizontal crossbar.

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    8. How do you guys reconcile this? Or is it just that you are so accustomed to speaking out both sides of your mouths that you no longer even notice when you do it?

      Got to be the latter. In another thread, Otangelo didn't even notice he was claiming at one and the same time that there were descendants but no ancestors. ("Front loading" but no common ancestry.)

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    9. "God creates humans, sets them in a wonderful place, gives them free will, and tells them not to eat fruit of one tree, which is not fenced. Then he's angry at THEM after he set them up to do it."

      Not to mention threatening them with death when they had no experience at all with the concept.

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    10. judmarc

      let me put that straight for you: I believe the designer created each of its kind, with inbuilt or front loaded mechanism of adaptation. So in the beginning there were were not just one ancestor, upon which all life diversified, but many , various of them.

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    11. @Lee Witt: Not to mention threatening them with death when they had no experience at all with the concept.

      Remember that JHVH placed two trees in the centre of the garden, the tree of life and the tree of knowledge. Obviously you don't need the tree of life, unless you are otherwise subject to death. Also, when JHVH threw A&E out of the garden, his explicitly given reason was lest they eat of the tree of life. Because with both the capacity to acquire knowledge, and immortality, they would be superior to the gods.

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    12. Jim Roberts.
      Not superior to God but living forever as evil rebellious beings would be a problem. Yes they were thrown out of the garden, probably not Eden however but only Eden;s garden, to be not allowed to eat of the second important tree.
      Why the tree of life if no death?? I don't know the historic scholarly reason .Probably it just reinforced a concept.
      Paradise lost!

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    13. Let me put that straight for you: I believe the designer created each of its kind, with inbuilt or front loaded mechanism of adaptation. So in the beginning there were were not just one ancestor, upon which all life diversified, but many , various of them.

      Ah, thanks for clarifying that for us. So, then, we must find ancestors of each of these "kinds" throughout the entire fossil record. Correct? So where are these ancestors? Are rabbits a "kind"? If so, then the fossil record should abound with Pre-Cambrian rabbits, if your "theory" is correct. Where are they? Are bumblebees a "kind"? Are banana plants? Sea sponges? Giraffes? Whales? Dandelions? Creationists? If so, then we should find the "ancestors" of all these "kinds" in the earliest levels of the fossil record, all "front loaded" with the genetic "information" needed to microevolve into what they are today.

      So isn't it just a bit strange that not a shred of existence exists for anything that even remotely resembles these ancestral "kinds"? Very odd. It's almost as if you're just spewing fabricated bullshit that has nothing to do with reality.

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  14. DNA can be altered due to epigenetic or immune system based reasons. These changes usually cause faulty genes that need to get hided from transcription machinery. This is done by histone methylation and it can be observed as chromatin remodeling, chromatin packaging and even chromosome loss.

    Increase of structural or functional complexity measured by growth of genetic information growth has never been observed. We can only observe variation and adaptation caused by intelligent and created mechanisms. The evolutionary theory is a dangerous heresy.

    http://sciencerefutesevolution.blogspot.fi/2016/12/can-evolution-produce-new-structures.html

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    1. Wow. That's even dumber than the articles on AiG.

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    2. "Increase of structural or functional complexity measured by growth of genetic information growth has never been observed."

      What a silly thing to say. Anybody can see that mutations can accumulate and produce new genes, or alter existing genes so they perform new functions.

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    3. I know. I don't understand what goes on in these people's heads. It's as if there were people around saying gravity's a lie because no one has ever observed something falling down.

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  15. Lets's have an example. Adaptation causes epigenetic alterations in the genome of organisms. Methylated cytosines are prone to to turn into thymine, hydroxymethylated cytosines tend to turn into guanine. The immune system associated genes can experience alterations too. Do these changes lead to large scale evolution? No. Absolutely not. Here's a couple of examples. First, the Canidae lineage. See what has happened to number of chromosomes after intensive adaptation:

    Wolf 78 chromosomes
    Bat-eared fox 72 chromosomes
    Gray Fox 66 chromosomes
    Fennec Fox 64 chromosomes
    Bengal Fox 60 chromosomes
    Kit Fox 50 chromosomes
    Tibetan sand fox 36 chromosomes
    Red Fox 34 chromosomes

    Another example is the Madeira mouse, who has lost almost half of its chromosomes just in 500 years. The reason for this phenomenon is obvious; the cell hides faulty genes by histone methylation and this leads to chromatin remodeling, chromosome packaging and finally to chromosome loss.

    You can look at the human genome and find almost one million SNPs in there. What do they cause? Over 10,000 genetic diseases and disorders.

    The evolutionary theory is a big lie.

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    1. See, here's how science works, Tomi: Form a hypothesis that leads to predictable observations. Then see if the observations made are consistent with the hypothesis.

      Science does not involve stringing together a bunch of words, whose meaning you do not understand, into nonsensical gobbledygook.

      HTH.

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    2. Tomi Aalto wrote:

      Here's a couple of examples. First, the Canidae lineage. See what has happened to number of chromosomes after intensive adaptation:

      Wolf 78 chromosomes
      Bat-eared fox 72 chromosomes
      Gray Fox 66 chromosomes
      Fennec Fox 64 chromosomes
      Bengal Fox 60 chromosomes
      Kit Fox 50 chromosomes
      Tibetan sand fox 36 chromosomes
      Red Fox 34 chromosomes


      A dramatic trend. On the other hand, you could write down those present-day species in the opposite order and get an equally dramatic trend:

      Here's a couple of examples. First, the Canidae lineage. See what has happened to number of chromosomes after intensive adaptation:

      Red Fox 34 chromosomes
      Tibetan sand fox 36 chromosomes
      Kit Fox 50 chromosomes
      Fennec Fox 64 chromosomes
      Bengal Fox 60 chromosomes
      Gray Fox 66 chromosomes
      Bat-eared fox 72 chromosomes
      Wolf 78 chromosomes

      which seems to show the chromosome count rising!

      Neither order tells us about what happened in a "lineage". Aalto's other generalizations are equally bogus.

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    3. Oops, sorry, I got the Fennec Fox and the Bengal Fox out of the desired order. Which just goes to show that the only biological process going on in these lists is the commenter editing them. Any of the 40,320 possible orders is equally valid.

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    4. In the dog family, chromosomes have been rearranged repeatedly, with changes in both gene order and chromosome number. In the cat family, however, all species (domestic cats, lions, tigers, caracals, etc.) have 38 chromosomes except a lineage of South American cats that have 36. Gene order shows few rearrangements. The South American cats have the same genes, but two small chromosomes seen in the more widespread cats have fused, lowering the chromosome count.

      The difference in chromosome evolution between cats and dogs proves . . . what about the occurrence of evolution?

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  16. The argument that adaptations could only based on selection and not on drift is an old but bad one. Adaptions were probably never build by only one mutation. That is, positively selected, neutral and even deleterious mutations could be involved during the evolution of an Adaptation. In addition, the selection coefficient of a molekular character often changes because of mutations occuring later on.

    So, each adaptation probably had evolved by Interaktion of selection AND drift. Andreas Wagner's work ("The origin of evolutionary Innovation") clearly point to that.

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  17. Larry,

    I realize that you are out there to defend the orthodoxy of Neo-Darwinism, or whatever is left out of it, that you still cling to.

    Sooner rather than later you, and the very few supporters of your Darwin-cracy will have to face the facts. Here is an example of an experimental evidence on epigenetic inheritance in mammals (one of of many documented) that reaches beyond the genome.

    Yup Larry.

    You should read it Larry because there are tens of experimental pieces of evidence that contradict your version of the theory of evolution and its predictions.

    I was not even going to mention your buddy J. Coyne Larry because he simply hanged himself in one of his last posts about epigenetics:

    https://whyevolutionistrue.wordpress.com/page/4/

    Here is why:

    Epigenetics: The sins of the father
    The roots of inheritance may extend beyond the genome, but the mechanisms remain a puzzle.

    http://www.nature.com/news/epigenetics-the-sins-of-the-father-1.14816

    BTW: there are now tens, if not hundreds of experiments that prove your theory of evolution wrong and J.Coynes as well. At least the part where you both omitted or disregarded epigenetics.

    I hope you have some answers before you retire and walk away from this mess you and your buddies like J.Coyne created.

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    Replies
    1. Interesting article. It shows some intriguing potential of serious study of epigenetics to increase our understanding of adaptations. It also shows that the field is in very early stages. Failure to replicate lab studies and reliance on those big association of study of humans are both problems. Some recent studies, including the mouse study reported, suggest there is something to this.

      However, epigenetic changes, like phenotypic plasticity in general, are dependent on genetics. The basic evolutionary processes remain. Whether epigenetic changes are an occasional embellishment on these processes or a significant contributor to change remains to be seen.

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    2. bwilson295,

      Please tell me you have not lost your mind!
      If you didn't, which I think I should fairly assume, how are you going to explain this faith of yours by not Darwinian shit, by random evolutionary changes? Do you realize what load this shit carries?

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    3. Don Quixote, As far as I can tell, I have not lost my mind.

      I see massive evidence that random genetic changes cause differences in reproductive success (natural selection) and that this combination of random and non-random processes produce the amazing biodiversity we see today.

      Discussion with people who assume that accepting evolution results from blind faith (like their own in whatever alternative they believe in) or who refer to evolutionary theory as shit are generally not productive. My participating in such a discussion would not be useful.

      If you want to understand why I would accept such a thing, you should start by reading Coyne's book Why Evolution Is True, which lays out the evidence and reasoning well.

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  18. It’s interesting to see that those that do have a clue seem nevertheless quite confused, myself included. For example, in the following article about the null hypothesis in evolution, the author creates a list* with sequences where substitutions are more abundant then in coding regions. He then claims that this is an example of neutral theory. I am convinced instead that the fact that coding regions harbour less substitutions then non coding regions is consistent with selectionist theory. So who is right here?

    I cite the important part in the article:

    ...Notably, if most of the sequence divergence between species is due to neutral evolution, then one should expect more changes in functionally less important sequences...

    * In protein sequences, conservative changes—substitutions of amino acids that have similar biochemical properties and are therefore less likely to affect the function of a protein—occur much more frequently than radical changes.
    * Synonymous base substitutions (i.e., those that do not cause amino acid changes) occur almost always at a much higher rate than nonsynonymous substitutions.
    * Noncoding sequences, such as introns, evolve at a high rate similar to that of synonymous sites.
    * Pseudogenes, or dead genes, evolve at a high rate, and this rate is about the same in three-codon positions.
    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. After all, if most substitutions were adaptive, as argued by selectionist theory, one would expect fewer substitutions in DNA regions where changes have little or no effect on phenotype (e.g., pseudogenes, noncoding sequences, synonymous sites) than in functionally important regions.



    http://www.nature.com/scitable/topicpage/neutral-theory-the-null-hypothesis-of-molecular-839

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  19. This (Lynch et al.) is a very interesting article. But how on earth can you write a paper on the drift barrier with 112 references, and not a single citation of Tomoko Ohta's work?

    Or am I missing something that make's Lynch's concept of the drift barrier fundamentally different from Ohta's near neutrality?

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