Shapiro, Evolution and Theology Part 2

In general I find Shapiro’s views very exciting and well worth disseminating as widely as possible. I think that his theory of Natural Genetic Engineering has the capability of finally unseating the rigid doctrinaire paradigm of neo Darwinism, with its overly simplistic and outdated view of the mechanism of evolution. If there is one universal rule that governs biology, it is that nothing is ever simple. Shapiro’s NGE is complex and chaotic enough to be true.

I see the biggest problem with NGE to be semantic. Shapiro likes to say that NGE replaces natural selection as the creative driver of evolution, the real source of major evolutionary change, the engine of innovation in biology. The problem is that this statement is incorrect on a few grounds. First, natural selection is not the source of variation in neo Darwinism either. So it’s a mistake to compare NGE to NS. What is correct is that NGE may be more important than random mutations (mostly point mutations or small deletions or insertions) in the creation of novel biological entities, and that therefore, the model of slow accumulation of small genomic changes must be modified to include major leaps of huge changes in genomes, which have very dramatic phenotypic consequences. Second, natural selection is still a critical component of evolutionary change, since whether the genome has undergone a single base change or large chromosomal rearrangement, there will be no fixation of this mutagenic event unless it has some selective advantage. Shapiro acknowledges this grudgingly by stating that there must be some purifying selection to weed out detrimental changes, but that really isn’t quite right.

While this is a minor complaint about the NGE theory, it does form the basis for most of the attacks on it by neo Darwinians. They defend natural selection (which is a safe strategy) while the real target that Shapiro should be going after, random mutations as the universal source of variation, is not discussed.

The other aspect of NGE that often gets less attention than it should is that all of the mechanisms by which such drastic and dramatic re-engineering of genomes take place are in response to extreme environmental stress. Under normal conditions, cells do not suddenly duplicate their whole genomes, or hybridize parts of their genomes with DNA from viruses or plastids. But cells do respond to all kinds of shocks, including massive DNA damage (from radiation or damaging chemicals) starvation, changes in salinity, osmotic pressure, temperature and so on.

So NGE is a stress response, and it is very valuable therefore as an explanation for evolutionary explosions following major environmental shocks like extinction events. As Shapiro says, in between these large and rapid changes, fine tuning (or micro evolution) by slow random mutations must certainly continue to improve the fitness of species, according to the standard synthesis.

I see all of this as the start of a new evolutionary theory, which does not supplant Darwin’s great idea, but refines it and gives it much stronger explanatory power. I am confident that given the evidence we have already, and that which is accumulating continuously, NGE will replace standard Neo Darwinism as the standard scientific model in a matter of a few years. (It might go faster if James Shapiro would simply change his rhetorical position and leave natural selection alone. Its random mutation that is the issue, Jim).

And what does this mean for Christian theology and the evolution/faith debate? I think it means a lot. The NGE idea has no direct theological implications. It does not fill a gap in knowledge with proof of divine intervention. But as Christians, that isn’t what we are, or should be looking for. What we do need are answers to questions about God’s role in creation, assuming we accept modern scientific data, and the truth of Biblical inerrancy. These are huge questions, and there will not be a single answer. But I think that NGE and similar ideas do point the way to a new theory of evolution that is both essentially Darwinian, and Christian. This would be a theory that is consonant with the great theological lessons of Genesis and the New Testament.

The general idea (clearly most of it remains to be worked on) is that God rules the biological universe on Earth through his dominion over the Earth. The rain, lightening, cosmological events, floods, droughts, all the events we still, in our secular world, call “Acts of God” are the very sources of stress that trigger the NGE mechanisms which lead to major and dramatic evolutionary leaps. Planetary disasters, like the Cretaceous asteroid strike, led directly to a tremendous explosion of mammalian evolution. In other words, the Neo Darwinian model of steady, automatic, random mutation, leading to slow accumulation of tiny changes, a model that requires and admits of no input from the outside, is much more difficult to reconcile with the concept of an actively  creative divine force in shaping life on Earth. In contrast, the NGE model, with its clear dependence on dramatic environmental stressor events (global or local), seems to be quite well accommodated to the concept of God having an active, continuous role in biological creation.

The flood story is symbolic and paradigmatic of this approach. What is interesting is that while God caused the flood to punish mankind, Genesis makes it quite clear that this was a general extinction event. Only a small number of living creatures (two of each kind) survived. The Bible tells us that this environmental catastrophe had an effect on all of life, exactly what we know has happened many times in terrestrial history. What the flood account teaches us in the context of a Christian evolutionary theory is that God’s actions upon the Earth, even His destructive actions, are part of his creative power, and with Shapiro’s NGE idea, we can begin to make the connection between that power and the reality of biological evolution.

Sy Garte

About Sy Garte

Dr Sy Garte earned his Ph.D. in biochemistry from the City University of New York, where he also holds a bachelor’s of science degree in chemistry. In addition to publishing more than 200 scientific publications in genetics, epidemiology, the environment and other areas, Dr. Garte is the author of Where We Stand: A Surprising Look at the Real State of Our Planet (Amacom) and Genetic Susceptibility to Environmental Carcinogenesis (Kluwer) and is co-editor of Molecular Epidemiology of Chronic Diseases (Wiley).
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30 Responses to Shapiro, Evolution and Theology Part 2

  1. Jon Garvey Jon Garvey says:

    Thanks Sy. Much food for thought.

    Two things that strike me from this immediately. The first is the concept that evolution becomes a messy series of processes, rather than a simple intuitive theory as Darwin proposed. In other words, it’s a history of life, not so much a science of life: the science is in the detailed processes, just as it is in human history. Only something bigger explains why things are as they are.

    The second thing is that, being such, Christians are forced to confront the biblical God of universal Providence again. The aloof Deist clockmaker might have coped with a bit of chance and an overarching natural selection. But if every stage in life, from the indeterminate quantum molecular event to the chaotic asteroid strike, is subject to contingency, then if God is to be considered Creator at all, he must necessarily govern all those events. It simply becomes superfluous to leave bits of the process “free” – in the sense of random.

    The line “God wouldn’t cause a volcanic winter” is shown up as a rather parochial attempt to tame the God of Abraham, Isaac and Jacob, and of our Lord.

    The comparison you make with the Flood is valid for the reasons you say, though I see that particular event as having primarily anthropocentric theological significance compared to, say, the K-Pg event, whose significance was evolutionary. Nevertheless, one lesson to be drawn from the comparison is that, whilst the Flood might be seen as a sledgehammer solution to evil, in fact God used it as a precision tool to preserve one family. So God’s providence does not merely determine an unstable orbit for an asteroid, but the precise effects it will have from its point and time of impact.

    • Lou Jost says:

      You said “…Evolution becomes a messy series of processes, rather than a simple intuitive theory as Darwin proposed.”

      As Sy himself says, the new mechanisms do nothing to shake the simple intuitive theory proposed by Darwin. Sy rightly says “I see all of this as the start of a new evolutionary theory, which does not supplant Darwin’s great idea, but refines it and gives it much stronger explanatory power.”

      Your comments about the flood, and Sy’s, suggest you may believe it really happened. I hope I am misreading you both. Surely you do not believe this….

  2. Lou Jost says:

    Sy, your criticism of Shapiro’s statements about natural selection are well-put. It is hard to understand why Shapiro would tie such an albatross around his own neck.

    Also, we have known for many decades that mutation rate per base is partly under evolutionary control. There are hotspots of mutation, and wide variation in mutation rate from chromosome to chromosome, and among loci within a chromosome. One could say, then, that mutation was not thought to be random (in the popular sense, as “equiprobable”) even in the neo-Darwinian synthesis. So again here, as with his criticism of natural selection, Shapiro is overstating his “revolution”.

    Randomness is a central issue here. The concept of randomness in neo-Darwinian theory is not really contradicted by modern findings, though it does need to be refined. The randomness which the theory posits is randomness with respect to the future fitness of the mutation (or genetic reshuffling). The products of natural genetic engineering are still random in that sense: the particular change actually produced in a cell’s genome is largely stochastic. The change may happen at locations where variation is most likely to increase fitness, but the particular change produced may or may not help increase fitness. There is no evidence for irreducibly-teleological causation, which is the form of non-randomness that would impact neo-Darwinism.

    Evolutionary biologists are excited about the novel mechanisms of genome change being uncovered over the last few decades, but they aren’t quite as revolutionary as some would like us to believe.

    Finally, I had to do a double-take when you seemed to say that you think the Bible is inerrant. But that is surely a topic for another day….

    • Sy Garte Sy Garte says:

      Lou

      I cant argue with anything you stated, but there is an important part of Shapiro’s paradigm that you didnt mention. And that is the kinds of mutations that he is talking about are different in character from the single nucleotide mutations of Neo Darwinism, and some of them, especially those resulting from horizontal gene transfer and whole genome duplication, have rapid and dramatic effects on phenotype. This suggests that important drivers of large scale evolutionary change (like the origin of vertebrates) do not result from slow accumulation of small changes, but from abrupt wholesale alterations of many systems. In other words, a mechanism for Gould’s punctuated equilibrium, which has been rejected by the purest of the neo Darwinians.

      I always thought that Gould’s case for PE was strong from an evolutionary point of view, but weak in its absense of mechanism. That is now changed. Of course, I expect you would agree with me, that real Darwinism can be easily accomodated to these data, but the dogmatic views of the “Modern Synthesis” defended by Coyne and co. will need to be radically modified. So far, Coyne isnt buying it.

      And yes, that is a topic for another day.

      • Lou Jost says:

        Sy, those things aren’t quite as new as you suggest. For example, whole genome duplication as a route to instant speciation has been known since the early 1900s, particularly in plants. My plant breeder friends have been inducing whole-genome duplication in their kitchens for decades. No one who worked out the modern synthesis of genetics and evolution was unaware of it. So I not only agree with you that the standard theory of evolution can accommodate these findings, I’d go further and argue that it always has accommodated them. Note, for example, that Jerry Coyne discusses the importance of whole genome duplication (polyploidy) in plant speciation on p 185-6 (Kindle edition) of “Why Evolution is True” (2009), and notes that about 70% of plant species have a genome duplication event in their evolutionary history. He’s not trying to minimize or hide these things, and there is no reason to. Note also that his book predates Shapiro’s, and most other scientific books on speciation in the last half-century would also have discussed this process .

        • Sy Garte Sy Garte says:

          Here is a quote from Coyne’s blog

          “In fact, we know of no evidence for mutations occurring nonrandomly or “adaptively”, i.e., that the occurrence of mutations is somehow biased in a direction that makes them more likely to be favorable when they arise, particularly when the environment changes in a way that requires favorable mutations to fuel adaptive evolution. There has been some controversy about the occurrence of “adaptive mutation” in bacteria, but that’s died out because there’s simply no evidence that the phenomenon occurs.”

          Dead wrong, Im afraid, the evidence is quite clear, and there is now a large body of literature including several review articles documenting the existence and widespread occurrence of adaptive mutations. This is what I mean by a non scientific, dogmatic stance of many neo Darwinians, such as Coyne.

          • Lou Jost says:

            We may be caught up in the ambiguity of the concept of randomness, as I mentioned in my original comment. I think Jerry is arguing against the teleological view I described. I don’t think he is denying that the probability of a mutation could change under stress. Rather, the mutations themselves are not biased to be adaptive. Readers can judge for themselves:
            http://whyevolutionistrue.wordpress.com/2012/04/07/jim-shapiro-continues-his-misguided-attack-on-neo-darwinism/

            • Sy Garte Sy Garte says:

              Alright, lets get into this a bit deeper. On the one hand we have the standard model as described by Luria and Delbruck first in 1944, which became dogma. Bacteria undergo random mutations all over the genome. This happens at every cell division. When a stress is introduced (either a poison or a loss of nutrient) millions of the bacteria die, but a few lucky ones who happened to have just the right mutation in the just the right gene survive, because they can (thanks to the preexisting mutation)metabolise an alternative nutrient, or neutralize the toxin. That is random mutation model.

              What Coyne claims (incorrectly) has no evidence is a different phenomenon. After the introduction of the stress, nothing happens for days. There seem to be no survivors. And then there is a rapid growth of many colonies. When the genomes are examined, it turns out that these surviving bacteria had a 5 fold or more high rate of mutation specifically in the very genes that are involved in the stress (either metabolic genes or detoxifying genes). It appears as if the bacteria knew which genes to hyper mutate (that isn’t the case, there are other reasons related to structure function that make that happen) in order to save its life.

              So, is that random? Neither Shapiro nor I are suggesting that some supernatural force helped the bacteria survive. But while there might have been many mutations in the targeted genes and only the beneficial ones were selected, (everyone agrees with that) the targeting itself of a particular region of the genome for hypermutability, and the right region at that, belies the idea that any mutation resulting from the stress (and not preexisting) could be called random according to the standard model of Luria and Delbruck.

          • Sy Garte Sy Garte says:

            And btw, Lou, I am assuming you are familiar with that post attacking Shapiro, from April 2012, since you commented on it.

            • Lou Jost says:

              Yup, I remember that thread. You and I both agree with him on some of his points.

              I don’t know enough of the literature on adaptive mutation to say how much evidence there is or isn’t for it, but as I said earlier, we’ve known for decades that mutation rate is partly under evolutionary control and varies from place to place in the genome. That is a kind of nonrandomness, but evolutionary theory had no problem absorbing it. The newer twist is that the local mutation rates might also vary in time due to stress. As long as the mutations are not teleologically directed, this also does not cause a problem for evolutionary theory. I think you agree with that. The process has no theological ramifications. It would have such ramifications if the mutations could be shown to be irreducibly teleological.

            • pngarrison says:

              In reference to Sy’s longer post above, it would seem plausible that the cell might increase the odds of a useful mutation by having a mechanism that ups the mutation rate only in genes that are being transcribed under the stress condition. Transcription-coupled repair or the increased susceptibility of transiently single stranded DNA during transcription would be possible contributors to “targeted” mutation. Thus if the cell already has a way of sensing the particular stress and inducing transcription of particular genes in response, then focusing mutation on genes being transcribed might be a way of inducing a mutant that can detoxify a related but new toxin (or metabolize a new sugar.)

              However, this assumes that a mechanism already exists to couple the stress to the transcription of particular genes. If a cell doesn’t already have such a mechanism, how can it know what genes to target? This seems to limit the scope of what is possible with such a scheme.

  3. GD GD says:

    Sy,

    I am not a biologist, so I hope you will be patient with me as I ask these questions:

    1 – An example is given in which bacteria have been subjected to a ‘death’ and ‘mass extinction’, and after this, a mutated version is reported/observed in abundance, and the cause for this is considered natural selection. If I understand this experiment correctly, it is anything but “natural” – it is a contrived experiment with the aim of subjecting a batch of bacteria to specified conditions. Additionally, is the data obtained that would prove that every single bacteria in that batch had identical genetic material, and one or two survived? Can this experiment be ‘quenched’ at the point of mutation, and this event clearly mapped out; just how long was the extinction, and what time is required for mutation?

    I ask these questions with this in mind – when any scientific experiment is carried out, in which the sample size is reduced to ‘extinction’ (below detection limits), we would go to enormous lengths to evaluate the limits of our laboratory/experimental methods and equipment. I cannot see how bio-experiments can achieve the detection limits of other sciences (e.g. ppb).

    2 – You suggest that enormously disruptive events in the past may be a form of ‘natural selection’. While my criticism of NT is more to do with its semantics (lack of mathematical definition such as found in established scientific laws), and not with a concept of natural events impacting on the planetary system, I would ask, “Do you have any repeatable method by which any form of NT (emphasis on natural) may be tested?

    Btw, I find your treatment of biological variation and time related evolution interesting.

    • Sy Garte Sy Garte says:

      GD

      If I understand your first question correctly, the answer is yes, the experiments are contrived to test a hypothesis, as is done throughout science. But the term “natural selection” still applies to such kinds of experiements, even if the conditions are not what would be found in the natural environment.

      It is highly unlikely that all the bacteria had the same genetic material. Those that had pre existing mutations in just the right place might survive, and those kinds of experiments were how the random mutation concept was first formuated. And yes, it is possible to determine exactly what happened at each point of time, and that timing and the characterization of the kinds of mutants that are found in the rare survivors are what gave credence to the idea of later targeted, non random directed mutations as a response to stress.

      Your other questions, especially regarding mathematical treatment of selection, and experiments regarding that are a bit beyond my capacity to respond here. They are worth an entire discussion on their own.

      • pngarrison says:

        The classic paper that established that (at least under some conditions) the mutations are not induced by the conditions was published in 1943, long before molecular genetics and the ability to determine what mutations had occurred. The conclusion was based on calculation of expected probability distributions for the number of resistant mutant colonies with a number of replicate bacterial cultures. One hypothesis predicted a Poisson distribution, the other a much broader distribution. A biologist probably wouldn’t have conceived of such a mathematical approach, but Max Delbruck had trained as a physicist. The paper is available here:
        http://www.genetics.org/content/28/6/491.full.pdf+html

        • GD GD says:

          Thanks for the paper by LURIAS AND M. DELBROCK; it is very interesting, as the authors have considered the many difficulties in establishing a quantitative understanding of the events that are associated with the destruction of bacteria when exposed to a virus.

          As I have stated on many occasions, I do not depend or refer to Darwinian thinking in my research, and thus I am more interested in hearing of the discussions/ debates related to theological methods proposed in response to Darwin, and not so much the ‘state of the bio-sciences’. In particular, I want to see any convincing experimental results that would conclusively lead to a law of natural selection. One important point regarding these types of experiments is this: not all relevant factors have been tested, or perhaps are testable. To illustrate this, I offer a simple example, as stated in this paper, “…putting the lower limit of integration not at time zero, when the cultures were started, but at a certain time to , prior to which mutations were not likely to occur in any of our experimental cultures.” And further down, we have, “While we have thus obtained a relation permitting an estimate of the mutation rate from the observation of a limited number of cultures, this relation is in no way a test of the correctness of the underlying assumptions and, in particular, is not a test of the mutation hypothesis itself.”

          Simply stated, the hypothesis that the experimental conditions meet the criteria that the virus can kill all of the bacteria is un-testable, because all of the bacteria have not died. Consequently, the hypothesis is, the batch of bacteria consisted of those that would die, and those that would not (resistant); the experiment would seek data that would give insights on the proportion of resistant bacteria in the batch. They then try to equate resistant with mutations; I cannot see this as anything other than an assumption, and certainly not an experimentally determined fact.

          The authors understand this and have discussed a method which seeks to estimate the number of resistant bacteria, and so I am not criticising the methodology nor technical merits of this paper. It does however, highlight the very real difficulties faced when trying to meet the criteria that “… NS is a law of science”. The observations are from extremely complicated systems, and this makes a direct, scientifically verifiable cause-effect studies that lead to NS very difficult.

          I am reminded of numerous cases where humans have introduced a relatively innocuous species in a large area (e.g. frogs in Queensland) because these people claimed studies had “conclusively” shown the behaviour was predictable based on Darwinian Theory. The result has been an ecological disaster that has defied all attempts to contain or eradicate.

          • Lou Jost says:

            GD, this is the same argument you have pursued in BioLogos, denying that natural selection is a scientific concept. I gave you extensive mathematical examples showing how natural selection works, and others gave real examples, but you are now back to the same sort of statements you made there. As I suggested before, you should at least read a basic text on this subject before you try to criticize its fundamental concepts. Natural selection is well-understood and can be expressed as a stochastic mathematical law. The same discussion is going on right now in BioLogos with Roger S. See the excellent comment by Paul Lucas in
            http://biologos.org/blog/science-and-the-truth-project-part-1
            comment 83524. Though he and I disagree on many things, he is exactly right about this.

            Your blaming the Australian frog problem on Darwinian theory is also bizarre. If anything, a Darwinian would have pointed out the danger of introducing a robust alien species to that evolutionarily-isolated continent, where its competitors and predators had low phylogenetic diversity.

            • GD GD says:

              Lou,

              I have studiously avoided responding to you at BioLogos – I want the same in this forum. We have disagreed on many points and it is indeed bizarre to repeat that. And by the way, the advice in Australia is provided by the CSIRO, who would be as aware of Darwinian thinking as you and others – this is the banality I find from Darwin’s disciples – they are never wrong, and if other scientists only knew Darwin what they know, boy oh boy, wouldn’t it be fun?

              So how about you send respond to other people and leave my comments out of your endless responses.

          • Lou Jost says:

            When you say something bizarre about science that I think is wrong, I will respond, if I have the time. That is what comments are for.

            • GD GD says:

              If you insist on making a nuisance of yourself and chose me for this, at the very least have the decency to read what I have written – you remind me of fanatics who insist they know what others think and believe – my remarks were that no-one thought or believed these frogs would become a literal plague (the latest seems to be these pests follow rainfalls to the south and may become a plague in the southern states) – based on the best scientific knowledge available, which includes that of biologists. How would a nut case like you conclude that I am blaming anyone or anything.

            • Lou Jost says:

              GD, you said “How would a nut case like you conclude that I am blaming anyone or anything.”

              Mainly I concluded that you blamed Darwinian theory for the ecological disaster because you said so:

              “…These people claimed studies had “conclusively” shown the behaviour was predictable based on Darwinian Theory. The result has been an ecological disaster…”

      • GD GD says:

        Sy,

        At the risk of being pedantic, if the bacteria do not contain the same genetic material, then the experiments start with a heterogeneous sample. I seems highly improbable that such work could establish an event that is directly related to the impact of the external factor (extinction, or what have you), on some sort of reaction (mutation) to that event. It would show that a portion of the sample would respond differently – thus a contrived experiment (not in a bad way, simply the only way that it may be done). This does not detract from testing a hypothesis, but it does show the tentative nature of the test(s).

  4. James says:

    Hi, Sy.

    Another good and thoughtful post. I am glad to see you here on Hump, where you are giving more expansive discussions than you have given on BioLogos — it enables everyone to see more clearly where you are coming from and where you are headed. I’m glad that Jon brought you in here.

    It has always struck me that, while Shapiro himself is not apparently a theist, his model is more compatible with standard theism than the classical neo-Darwinism of Mayr, Dobzhansky, Gaylord Simpson, etc. In the classical neo-Darwinism changes “just happen” to organisms, and they adapt as best they can; in Shapiro’s view organisms have, as it were, a toolkit for self-repair and self-modification, even radical self-modification. This isn’t exactly teleology in the sense of a straight arrow guiding the evolutionary process to Goal X, but it does give living things an ability to chart a course, so to speak, amid the seas of fortune. One can imagine God as having imbued life with this ability from the beginning, in order to facilitate future development.

    Regarding Shapiro and natural selection, I agree with you that attacking natural selection per se is not necessary to make his point; but could it be that he is targeting “natural selection” because extreme selectionists like Dawkins imagine selection to have more than a merely filtering, but indeed a creative, role? And isn’t Shapiro’s point that the “creativity” in evolution doesn’t come primarily from the selection part of the process, but from the amazing ability of the organism to re-engineer its own genome under certain circumstances? If all that variation can produce is relatively trivial changes, then only a slow process of natural selection over hundreds of generations is going to do anything “creative”, and natural selection therefore becomes the center of attention in evolutionary theory; but if variations can under some circumstances be colossal (due to natural genetic engineering), then the role of selection will in many cases be almost tautologous.

    To make the point with a crude analogy, if a flintlock rifle overnight gave birth to a machine-gun, it is pretty obvious that the tribe with the machine-guns is going to conquer the tribe with the flintlock rifles in one generation. Figuring out what will be “selected” is a no-brainer. If organisms can drastically modify their own genomes in response to environmental stress, then the larger creative leaps in evolution — such as major morphological changes — will take place in large measure on the initiative of the organism, not as a result of things entirely outside the control of the organism, such as accidental mutations or the crude death-dealing of natural selection.

    To be sure, Shapiro could modify his language here and there, to say that he is not against natural selection per se, but only thinks that its creative role is more limited than NDE imagines. That might make his ideas more acceptable to some evolutionary theorists. But that’s more of a rhetorical matter. I think the issue of substance still remains, and I think that the difference between Shapiro and someone like Coyne or Dawkins remains. They imagine the process of evolution quite differently. I’m old enough to remember reading popular-science expositions of evolution (many of them written by scientists) from the 1960s and 1970s, and there is no doubt that Shapiro’s conception of evolution is quite different from what was then the standard idea that the scientists were eagerly promulgating among the masses. I look forward to the time when the Isaac Asimovs and Carl Sagans of the future will be spreading the ideas of Shapiro (and Newman and others) instead of the ideas of Mayr and Dobzhansky.

  5. Lou Jost says:

    “… if variations can under some circumstances be colossal (due to natural genetic engineering), then the role of selection will in many cases be almost tautologous.” You are assuming that these colossal variations are usually going to be favorable. That is not true. While all re-arrangements of the parts may not all be equiprobable– natural selection can lead to NGE mechanisms that conserve the barrel, for example, while allowing lots of mixing in the trigger and firing pin areas. But NGE is still going to make a lot of garbage. Natural selection (with drift) will be the main determining factor for the fate of these products.

    • James says:

      Sorry; I was speaking in shorthand, and misled you. Yes, of course many of the large variations may be deleterious to the organism, and therefore will be “selected against.” I didn’t mean to imply that the majority of such changes would be beneficial. What I meant was that, when they are beneficial, “selection” doesn’t have any truly “creative” work to do.

      If, for example (a fantasy example, I know, and beyond what Shapiro is talking about, but I exaggerate to make the point) a lizard could give birth to a bird (let us suppose, in a world in which there are yet no birds or flying mammals to compete with this bird, but in which there are lots of tasty flying insects which lizards cannot easily capture but birds can), then “natural selection” will operate and the new “bird kind” will multiply. But the truly creative work in such a case is done by whatever internal organismic activity generates the flight apparatus within one generation; natural selection merely says, after the fact: “Good stuff!” And that’s quite different from Dawkins’s view, which is that selection is a designer-substitute, actively working with variations in order to produce great novelty.

      Dawkins’s view only makes sense if “selection” constantly hones tiny incremental changes, so that it is the constant, ongoing combination of selection plus variation which does the creative work, not variation alone. If really useful major changes can occur without incremental steps, then the ongoing coaching, prodding, censoring etc. of “selection” is — at least in those cases — not needed.

      Think of teaching slow versus bright students. A slow student, who can only learn in little tiny steps, may become competent only with constant coaching and feedback, struggling on test after test, or essay after essay, week after week, and needing to be steered in the right direction on a regular by the teacher. In such a case, it is clear that the teacher’s constant response to the student’s daily effort is a crucial cause of the student’s final success; the teacher and initially poor student as it were “co-create” the later good student through a long and painful process. But the super-bright student, who from day one gets perfect on all tests or writes essays well beyond grade level in vocabulary, style, and concept, and who from the start, even prior to any guidance from the teacher, is clearly thinking way ahead of the course — for that student, the teacher needs to do very little but simply record the student’s excellence for purposes of certification. The teacher isn’t the “creator” of the good student in such a case.

      So sure, selection — the testing of major changes — will take place even in Shapiro’s model of evolution. But regarding such rapid major changes — if they occur for the reasons Shapiro gives — then when they are useful, “natural selection” has little of a “creative” role in pushing evolution forward. It’s more like the schoolteacher assigning the “A” grade to the student who was already “A” material before the teacher ever walked into the classroom.

      I’m not saying that Shapiro does or should give zero importance to natural selection; I was merely providing a plausible reason why he would de-emphasize it, in comparison with evolutionary theorists who have a strong Darwinian bent. The de-emphasis would be a logical consequence of the much greater role he gives to the organism’s capacity to generate major change quickly out of its own internal resources, without having to wait for chance sequences of useful mutations, spread out over hundreds or thousands of generations, to “happen” to its genome.

      • Sy Garte Sy Garte says:

        Thanks James. I think that is a good rebuttal to my own concerns about Shapiro’s seemingly less than total reverence for the power of selection. The kinds of phenotypic improvements he is talking about leave little for selection to do, in comparison to the more subtle changes of random mutations. That makes sense, but I think Shapiro should be more explicit on this point.

  6. Lou Jost says:

    That’s a good explanation. I and most biologists (Dawkins too, probably) would agree that the creative work at the level of the individual was done by the accidental changes that made the bird. The size of the changes doesn’t seem terribly relevant; I think this would also be the generally agreed-upon analysis even for tiny changes.

    Natural selection works to change populations, not individuals, and in that sense it might be considered a creative process too, as it changes a population. It can even create novelty by causing two independent innovations, initially in separate individuals, to spread through a population, producing a new population whose members possess both innovations.

  7. Sy Garte Sy Garte says:

    png

    Yes, that is precisely the mechanism that is believed to occur with stress directed mutations. Increased transcription of the target gene allows for loop structures and other DNA alterations that increase the probability of mutation, and even if most of the mutations are deleterious or neutral, the higher the mutation rate the more likely that one cell will escape due to a positive outcome. And you are right that this only works when there exists a target gene, whose mutagenesis can overcome the stress. But SDM is only one of the many NGE approaches in Shapiro’s scheme, and he doesnt put much stress on it (sorry for the pun).

    • Lou Jost says:

      Some of the most elaborate genetic engineering mechanisms that Shapiro and others talk about are in somatic cells such as those related to the immune response. For the sake of readers who are not geneticists, I’ll note that these mechanisms don’t affect evolution directly, since they do not produce changes that are inherited.

      • Jon Garvey Jon Garvey says:

        Lou

        Surely (ie, Shapiro explicitly states that) his point on the immune system is that since the immune system has developed to employ hypermutation at targeted sites towards a specific physiological end (ie survival from attack), then it’s more than probable that it has found ways to harness the forces at work in evolution to give better-than-random results, at least. So the immune system is a predictor of evolutionary mechanisms.

        Evolution them, would be at least in part, a physiological response rather than a purely passive process. He doesn’t think of it in in terms of physiology as such, but others do (notably Dennis Noble, J Scott Turner).

        • Lou Jost says:

          I know Shapiro knows that. But non-geneticists get the mistaken idea that these complex mechanisms are now part of the known repertoire of evolution.

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