Epigenetics Evolution Evolutionary biology Genetics

Spetner’s Non-Random Evolutionary Hypothesis

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Note: This is a guest post by Virgil Cain. I have left it as is, with just a couple of typographical corrections. See my brief comments and caveats at the end.

—–

By Virgil Cain

In 1997, “Not By Chance” by Lee Spetner was published. In it he argued for a “non-random evolutionary hypothesis” which had a mechanism of “built-in responses to environmental cues” at its heart. Some mutations happened just when they were needed. And some happened at just the right place to be effective. And even others, called transposons aka jumping genes, carried within its DNA coding sequence the coding for two of the enzymes required for it to be able to move around.

A transposon has in it sections of DNA that encode two of the enzymes it needs to carry out its job. The cell itself contributes the other necessary enzymes. The motion of these genetic elements about to produce the above mutations has been found to be a complex process and we probably haven’t yet discovered all the complexity. But because no one knows why they occur, many geneticists have assumed they occur only by chance. I find it hard to believe that a process as precise and as well controlled as the transposition of genetic elements happens only by chance. Some scientists tend to call a mechanism random before we learn what it really does. If the source of variation for evolution were point mutations, we could say the variation is random. But if the source of variation is the complex process of transposition, then there is no justification for saying that evolution is based on random events. (Dr Lee Spetner “Not By Chance” page 44)

Barbara McClintock was laughed at when she elucidated her discovery of jumping genes for the simple reason they have the characteristics of being under some control.

The “non-random evolutionary hypothesis” applies to individuals- individuals do evolve, ie change at the genetic level.

Enter 2006 and the publication of “Evolution in Four Dimensions” by Eva Jablonka and Marion J. Lamb and the elucidation of epigenetics, ie “built-in responses to environmental cues”. I couldn’t stop thinking about “Not By Chance” wondering if Lee Spetner had read it and if he felt vindicated by it. Organisms are designed with different levels of possible variation. For example there is a possible variation with how the existing genes get expressed and another is changing the actual genes such that it changes the proteins. Change the regulation of the gene or change the gene itself. Lenski’s E. coli changed the regulation of a gene by duplicating it and putting it under control of a promoter that allowed for it to be expressed in an aerobic environment. It was an environmental factor, the presence of O2, which repressed the gene. It was another environmental factor, the presence of citrate, which made getting that gene expressed beneficial.

“Evolution in Four Dimensions” is a good book to have around. They describe experiments of microsurgery onParamecium. A piece of the cortex was cut out, rotated 180 degrees and reinserted. The offspring inherited the change. (Lamarck 101)

Then came 2011 and the publication of “Evolution: A View from the 21st Century” by James A. Shapiro (a colleague of Dr. McClintock) and even more support for the “non-random evolutionary hypothesis” and “built-in responses to environmental cues”. Again I wondered about Dr Spetner and if he was reading this book too. The book starts out talking about “Sensing, Signaling, and Decision Making in Cell Reproduction” and has a table of “Examples of Targeted Genetic Engineering”. Of course he thinks it all evolved because obviously that is what evolution does or maybe due to coercion from fellow U Chicago Professor Jerry Coyne that is what he had to say to prevent being attacked. But I digress, the book is well worth the read and there is evidence that some mutations happen just when they are needed. They are not random with respect to fitness; it is the organism doing some rearranging to stay fit.

In 2014 Lee Spetner’s “the Evolution Revolution”- Why Thinking People are Rethinking the Theory of Evolution” was publisged and although he doesn’t cite “Evolution in Four Dimensions” he does cite Jablonka’s work on epigentics. He does cite both Shapiro’s work and the book “Evolution: A View from the 21st Century”.

Moving along, Lee Spetner cites several cases in which evolution happened much too rapidly to be accountable for genetic accidents and [instead] have all the appearances to have been triggered by the environment:

1- Studies on daisy and daisy-like plants and their seed dispersal mechanisms. On the mainland the seeds are packaged such that the wind can carry them great distances- little white fluff-balls floating endlessly on a warm summer’s breeze. But on a small island that isn’t a good strategy. Once transplanted from mainland to small island they lose that seed-dispersal ability in just a few years – Cody & Overton (1996) “Short Term Evolution of reduced dispersal in Island Plant Populations” Journal of Ecology 84(1): 53-61

2- Rhagoletis pomonella– went from feeding solely on hawthorn, to apples and onto cherries, roses and pears. Studies show the hawthorn and apple flies differ genetically

3- Guppies- Cichlid fish prey on large mature guppies and killifish prey on small immature guppies. When cichlids are their main predator in the environment the guppies mature earlier and have many small offspring which evade the cichlids. When killifish are their main predator the guppies mature late and have fewer but larger offspring which can evade the killifish. He cites several papers that have Reznick as one of or the main contributor

4- Lizards and rapid evolution- Losos (2001) “Evolution: A Lizard’s Tale” Scientific American 284(3): 64-69; Losos and Schoener (1997) “Adaptive differentiation following experimental island colonization in Anolis lizard”Nature 387: 70-73; and other articles by Losos and/ or Schoener

5- Finches- Lee Spetner was here on UD and posted this one See here

He reiterates his hypothesis is different, in that with his, individuals do evolve.

—–

Comments by Eric Anderson:

We have been discussing this issue, largely as a result of this thread. Specifically, wd400 claimed that there are no examples of genetic change that are non-random with respect to fitness, a key assertion of Neo-Darwinian theory. As a result, I invited Virgil Cain to draft a brief OP on Spetner’s new book, as Spetner discusses several examples of genetic change that are non-random with respect to fitness.

I would note a couple of additional points, to help avoid side roads and irrelevancies.

First, my original OP and the points raised therein stand largely independent of whether there are non-random genetic changes. I raised it as an open issue and as one of the things that Reznick had perhaps not considered. Second, on a related thread wd400 made a statement suggesting that heritability of a trait somehow demonstrates that the trait could not have arisen in response to environmental factors. This is clearly incorrect and demonstrates confusion about the issue at hand, which is how the trait arose, not whether it can be subsequently inherited. Third, I would note that the finch beaks discussed in the other thread are in interesting example, but perhaps not the most compelling example. Don’t get hung up on the finch beaks in determining whether there are any examples of non-random genetic change.

While there are other interesting issues at play, on this current thread I would ask that commenters focus on the specific issue at hand:

Are there genetic changes that are non-random with respect to fitness?

45 Replies to “Spetner’s Non-Random Evolutionary Hypothesis

  1. 1
    Eric Anderson says:

    While there are other interesting issues at play, on this current thread I would ask that commenters focus on the specific issue at hand:

    Are there any examples of genetic changes that are non-random with respect to fitness?

    A claim has been made that there are none. Spetner provides several examples to challenge that Neo-Darwinian claim. Let’s keep the discussion focused on this issue.

  2. 2
    Virgil Cain says:

    Just to note- all of the above changes occurred within several generations. It is that factor that leads to the inference that the changes are non-random.

  3. 3
    wd400 says:

    wd400 made a statement suggesting that heritability of a trait somehow demonstrates that the trait could not have arisen in response to environmental factors.

    Heritability has a precise meaning in biology and what I’m saying in that post should be clear to anyway who can read it and the OP.

    All these appear to simply be examples of rapid adaptation.

  4. 4
    Mapou says:

    Great article. Does Spetner explain where this genetically programmed ability to adapt to environmental cues comes from?

  5. 5
    Mapou says:

    wd400:

    All these appear to simply be examples of rapid adaptation.

    Which, we all know, RM+NS cannot do since the combinatorial explosion kills it.

  6. 6
    Virgil Cain says:

    All these appear to simply be examples of rapid adaptation.

    Absolutely, and too rapid for natural selection to produce

  7. 7
    Virgil Cain says:

    Mapou:

    Does Spetner explain where this genetically programmed ability to adapt to environmental cues comes from?

    I will look but it seems to me he accepts a Special Creation of sorts

  8. 8
    Eric Anderson says:

    wd400:

    All these appear to simply be examples of rapid adaptation.

    Well, of course. But that doesn’t answer the question. The question is, what is the cause of the rapid adaptation. Apparently it is not random-with-respect-to-fitness mutations. That is the issue.

  9. 9
    wd400 says:

    Apparently it is not random-with-respect-to-fitness mutations

    Why would you think that?

  10. 10
    Eric Anderson says:

    Two points:

    (a) Spetner has outlined several examples of genetic changes that appear to occur in response to environmental change. As just one example, he cites several studies showing that “in the presence of lactose, adaptive mutations activating a dormant gene encoding an enzyme that will hydrolyze lactose in E. coli are of a kind different from mutations that occur in the absence of lactose.” (We might also note the presence of that “dormant” gene, which is just a little too convenient from a Neo-Darwinian perspective.)

    (b) The changes that take place in essentially all the examples Spetner cites occur too rapidly to themselves be the random mutations in question. Now we could adopt a completely undemonstrated and essentially circular position and claim, “Well, yes, but the machinery that responded to those environmental changes was initially produced by random-with-respect-to-fitness mutations.” Not very satisfactory. Indeed, we would do well to turn your question around and ask why in the world someone would think that significant biological changes, including key genetic changes required for survival in specific environments, are the result of random-with-respect-to-fitness mutations.

    —–

    Again, do random mutations occur? Sure they do. In rare cases can they provide a fitness advantage in specific situations? Yes. Is there evidence for other genetic changes that occur other than at random? Yes; and the evidence is growing.

    The “random mutations drive everything” claim is based on ignorance and naive assumptions about what can be produced by such a process. It cannot possibly be demonstrably true as a matter of current knowledge. We are just scratching the surface in terms of biological knowledge, so at best such a claim functions as a placeholder for our ignorance. Worse, it often functions as an impediment to consideration of new evidence, as in your case. Additionally, as we learn more, the claim inevitably stands on the wrong side of the evidentiary trend. It cannot, by definition, become more solid. It can only become weaker as we learn more about what is actually going on in biology.

  11. 11
    wd400 says:

    Well, I guess (a), in addition to not being mentioned above, is a reference to Cairns’ “adaptive mutation” studies. They don’t provide any evidence that mutation is anything other than random with respect to fitness.

    For (b) the examples above most likely involve selection acting on standing variation, or perhaps phenotypic plasticity. You will have to provide a much better argument than “sometimes adaptation is fast” if you want to prove mutations are no random with respect to fitness.

    The rest of your post is just noise, as far as I can tell.

  12. 12
    Virgil Cain says:

    Random mutation is just noise. And yet you think it does significant things.

  13. 13
    Mapou says:

    wd400, it’s not random because only a subset of the genetic sequences are mutable. The moment you limit the search space, you are no longer in RM+NS LA-LA land.

  14. 14
    Virgil Cain says:

    Thanks Eric- I didn’t post what he said in the first book. This is a paper Spetner references:The origin of mutants

    Nucleic acids are replicated with conspicuous fidelity. Infrequently, however, they undergo changes in sequence, and this process of change (mutation) generates the variability that allows evolution. As the result of studies of bacterial variation, it is now widely believed that mutations arise continuously and without any consideration for their utility. In this paper, we briefly review the source of this idea and then describe some experiments suggesting that cells may have mechanisms for choosing which mutations will occur. (bold added)

  15. 15
    mike1962 says:

    Mapou: wd400, it’s not random because only a subset of the genetic sequences are mutable. The moment you limit the search space, you are no longer in RM+NS LA-LA land.

    That reminds me of the old Disneyland car ride. When I was a little kid I couldn’t wait to get on that ride so I could “steer” the car. Was I allowed to actually steer it? Yes, within certain boundaries. The car was actually attached to a track rail that limited the steering of the car. I could definitely “steer” the car within limits, but I could not drive the car off the track. Darn!

    Random mutations are “random”, but they seem to be random in the same way the Disneyland car is random. There is a limit to the mutation. As you say, only a subset of the genetic sequences are mutable. That means it’s random but it’s not really random. It’s not random in the strongest sense of the term.

    https://www.youtube.com/watch?v=FVcBLbQh5xI

    If you graphed out the steering movements of each driver, you would have a macro level graph that was the virtually identical for every driver, and a micro level graph that was completely different for every driver, no two drivers would be the same in the whole history of Disneyland. Wild micro randomness within very strict macro limits.

    P.S. even the atomic level and quantum level randomness is not really random in the strongest sense of the term. This is demonstrated by that fact that over time the distribution of the results will become more and more even. The greater the time, the smoother the distribution. What hidden hand makes sure that happens in our universe?

    Nobody knows.

  16. 16
    Vy says:

    @mike, this kinda says the same thing too (assuming I understood it correctly):

    This nonhomogeneous distribution of variation suggests that multiple mutational hits at certain sites are common, an observation that challenges the fundamental assumption of the infinite-sites–mutation model. The nonrandom patterns of recombination and mutation suggest that randomly chosen single-nucleotide polymorphisms may not be optimal for disequilibrium mapping of this gene

    It may be one gene discussed but based on all the “[non]evolution-in-action” experiments, it seems pretty general to me.

    And it seems a lot of the evo biologists are going Lamark.

    Or not. Who knows with these people.

  17. 17
    Mapou says:

    mike1962,

    Great analogy. Metaphors are the best teaching tools there is.

  18. 18
    Zachriel says:

    mike1962: Random mutations are “random”, but they seem to be random in the same way the Disneyland car is random. There is a limit to the mutation.

    Do you have evidence for this assertion?

    mike1962: only a subset of the genetic sequences are mutable.

    That is incorrect. While some areas of a genome are mutational hot spots, no area of the genome is immune from mutation. However, some mutations may be deleterious and quickly weeded out of the population, if that is what you mean; but that’s just evolution.

  19. 19
    Mapou says:

    ZAchriel @18,

    Man, get a clue and a backbone. Mutations do indeed happen everywhere in the genome but most mutations are immediately repaired. Most genes and sequences are perfectly conserved over millions of years.

    Stop spewing lies, Croteau.

  20. 20
    mike1962 says:

    Zechriels: Do you have evidence for this assertion?

    Evidence of non-random mutation rates suggests an evolutionary risk management strategy

    Nature 485, 95–98 (03 May 2012)

    A central tenet in evolutionary theory is that mutations occur randomly with respect to their value to an organism; selection then governs whether they are fixed in a population. This principle has been challenged by long-standing theoretical models predicting that selection could modulate the rate of mutation itself1, 2. However, our understanding of how the mutation rate varies between different sites within a genome has been hindered by technical difficulties in measuring it. Here we present a study that overcomes previous limitations by combining phylogenetic and population genetic techniques. Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases. Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection. Our observations suggest that the mutation rate has been evolutionarily [sic] optimized to reduce the risk of deleterious mutations. Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. The findings have important implications for our understanding of evolution and the control of mutations.

    http://www.nature.com/nature/j.....10995.html

    Beside the above, the genome overall itself is a limiting factor. What can be mutated is limited by what currently exists. Mapou is correct when he says that mutations do indeed happen everywhere in the genome but most mutations are immediately repaired. Most genes and sequences are perfectly conserved over millions of years. This is not a randomly mutating system in the strongest sense of the term. Like the Disneyland car ride, it is wild randomness at the micro level within tightly constrained limits at the macro level.

  21. 21
    PaV says:

    wd400:

    An italian lizard was transplanted to a Croatian island, where, in less than 36 years, it developed cecal valves in its digestive system, increased the size of its jaw, changed its behavioral patterns, and accomodated itself to the presence of a nematode in its hindgut.

    How many amino acid changes did this take?

  22. 22
    Virgil Cain says:

    If it was an Italian lizard then the mechanism was “badda-bing, badda-boom” and the amino acids were changed to protect the innocent. 🙂

    We could tell ya which amino acids but then we would have to kill ya- knowwadImean?

  23. 23
    PaV says:

    I didn’t know that NS had an Italian accent! 🙂

    Or perhaps you’re asking yourself, when a body is thrown into the Hudson River, does it drift neutrally?

  24. 24
    PaV says:

    When a body is thrown into the Hudson River, does it drift neutrally?

  25. 25
    Zachriel says:

    mike1962: “the variation is not random

    That’s right. There are a number of known biases in mutations, however, mutations are still random with respect to fitness. Moreover, the entire genome is subject to mutation, contrary to your previous statement.

  26. 26
    Vy says:

    That’s right. There are a number of known biases in mutations, however, <strong.mutations are still random with respect to fitness.

    You’ve made that claim so many times that I’m starting to realize it’s most likely a knee-jerk reaction.

  27. 27
    Zachriel says:

    Vy: You’ve made that claim so many times that I’m starting to realize it’s most likely a knee-jerk reaction.

    Not at all. Mike1962 claimed the paper contradicted that mutations are random with respect to fitness, and also that some areas of the genome are not subject to mutation. The paper supports neither contention. The difference between Vy and mike1962 is that mike1962 tries to support his position.

  28. 28
    bFast says:

    PaV, “When a body is thrown into the Hudson River, does it drift neutrally?”

    We cannot critique the Darwinian model if we can’t understand it. This is a good example to illustrate “random with respect to.” There is nothing about the Hudson River that was modified with dead bodies in mind. Therefore, the flow of the Hudson is “random with respect to dead bodies”. That said, if a good forensic scientist examines a discovered dead body, he can use the characteristics of the river to calculate possible entry points and entry times. Ie, the river has a pattern of influence on the flow of the body. By the same token, there are patterns within nature, and within mutations. These patterns are, to some extent (though to much less extent than the Hudson River) not random. However, the neo-Darwinian model says that these patterns were not engineered with genetic development in mind. Their characteristics are there, how they influence mutations can be analysed, but they are not there to help out mutations.

    Consider the Hudson again. If there were a problem of bodies floating down the river, law enforcement may span the river at certain locations with very coarse mesh net — a net that captures human body sized things, but not smaller stuff. This would be non-random with respect to dead bodies. It would be put there with dead bodies in mind. If the nature of the non-Randomness in biology could be demonstrably shown to have been put there for the purpose of driving mutations, then neo-Darwinism would no longer be able to claim that RM is “random with respect to genetic mutations.”

    Some time ago there was a very well-though discussion on this board with Dr. MacNeill. He enhanced RM (he actually insisted on RV, random variation) with “non-foresighted”. This is an excellent therm. If foresight can be demonstrated in mutations, then RV is no longer universal.

    Bottom line, please you guys, give up the “its not chi-square random” bs. (Don’t know what chi-square is, google it.) That is not required for neo-Darwinism to be correct. Rather foresight must be demonstrated to challenge the theory. It is foresight that Spetner points to. It is foresight that “the third way” points to, but in the case of the third way at lease, it is the foresight of the organism, foresight that was purported to have been developed via RV+NS.

  29. 29
    Vy says:

    Mike1962 claimed the paper contradicted that mutations are random with respect to fitness

    The paper supports neither contention.

    You are yet to show that. So far all you’ve done is claim “There are a number of known biases in mutations, however, mutations are still random with respect to fitness without objectively supporting it.

    The difference between Vy and mike1962 is that mike1962 tries to support his position.

    Is this coming from the same guy that ignored my questions, gave non-answers and gave answers to imaginary questions in the other thread?

    Yeah, sorry but I don’t have the time to buy crayons and glitter to explain things to you.

  30. 30
    Zachriel says:

    Vy: You are yet to show that.

    Mike1962 quoted the relevant sections. The paper shows that mutation rates vary across the genome, but doesn’t show they are non-random with respect to fitness. Furthermore, the paper explicitly states that mutations occur across the genome.

    Vy: So far all you’ve done is claim “There are a number of known biases in mutations, however, mutations are still random with respect to fitness“ without objectively supporting it.

    See Lederberg & Lederberg, Replica Plating and Indirect Selection of Bacterial Mutants , Journal of Bacteriology 1952.

  31. 31
    Virgil Cain says:

    Random with respect to fitness is meaningless gibberish and a distraction in a debate on whether or not they are guided or just happenstance occurrences. It is also difficult, if not impossible, to demonstrate such a thing.

    That is why the OoL is key to this debate. If the OoL was intelligently designed then it is a given life was designed with the ability to adapt. Only if the OoL was just an emergent property, say of small porous rocks around ocean vents (not black smokers), would we say that the mutations are happenstance occurrences.

    We know bacteria can and do communicate. For all we know they are checking on the fitness of the population and making sure that all misadventures they can account for are accounted for. And seeing that bacteria had been exposed to molds in nature that would be a source of misadventure and something they would have covered.

  32. 32
    Vy says:

    The paper shows that mutation rates vary across the genome, but doesn’t show they are non-random with respect to fitness.

    Read it:

    A central tenet in evolutionary theory is that mutations occur randomly with respect to their value to an organism; selection then governs whether they are fixed in a population. This principle has been challenged by long-standing theoretical models predicting that selection could modulate the rate of mutation itself

    Clear? Moving on . . .

    See Lederberg & Lederberg, Replica Plating and Indirect Selection of Bacterial Mutants , Journal of Bacteriology 1952.

    Has as much value as claiming the Lenski experiments prove your assertion: none.

  33. 33
    Vy says:

    That is why the OoL is key to this debate. If the OoL was intelligently designed then it is a given life was designed with the ability to adapt. Only if the OoL was just an emergent property, say of small porous rocks around ocean vents (not black smokers), would we say that the mutations are happenstance occurrences.

    To the evodelusionist, “we don’t how the OOL got started or how it started but since we know god didn’t do it, probablymaybecouldness must’ve done it so it is independent of evolution” is a good cop out.

  34. 34
    Vy says:

    “… got started or how it …”

    it should read “why”

  35. 35
    tommy hall says:

    seems like non-random mutation to me……

    http://www.sciencedaily.com/re.....121627.htm

    “Environs prompt advantageous gene mutations as plants grow; changes passed to progeny”

  36. 36
    bFast says:

    tommy hall, very good find! “but actually influences helpful mutations.” Yes, that sounds like non-random wrt fitness.

  37. 37
    Robert Byers says:

    A observation would be that surely people had non random genetic change in changing our skin colour and many attributes of our bodies. However I guess evoltionists would say that was from evolution also. No one saw it but people back in the day.
    It could only be that bio changes comes from innate triggers.
    It should be figured out ,somehow, without having to watch it happen like lizards and so on.

  38. 38
    PaV says:

    bFast:

    Why are you taking seriously a comment that was made completely in jest?

  39. 39
    PaV says:

    wd400:

    Again, how many amino acid changes do you think it took to get lizards to from cecal valves, grow larger jaws, change their territorial behavior, change their eating habits, and accommodate nematodes in their hind gut?

  40. 40
    Zachriel says:

    Vy: “This principle has been challenged by long-standing theoretical models predicting that selection could modulate the rate of mutation itself

    That is correct. Please note that the authors say the differential rates may be an evolutionary adaptation. In any case, the mutations, when they occur, are still random with respect to fitness.

  41. 41
    Virgil Cain says:

    Why does Zachriel think its opinion is actual evidence?

  42. 42
    Vy says:

    Virgil, I wonder why too. I bet it has something to do with differing opinions between its multiple selves.

    The version that posts those kind of comments has a Yoda Complex issue.

  43. 43
    Vy says:

    Please note that the authors say the differential rates may be an evolutionary adaptation

    Evodelusionary adaptation my foot.

    Anyways, just like I said the last time, the claims of madmen do not affect the logical interpretation of reality.

    In any case, the mutations, when they occur, are still random with respect to fitness

    Opinionated and harebrained kneejerk assertion.

  44. 44
    PaV says:

    wd400:

    We await.

  45. 45
    tommy hall says:

    Btw……Not By Chance was a monumental eye-opener for me personally. Literally life altering. So a big, hearty thank you to Dr Spetner for writing this book.

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