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James Shapiro at Fermilab: Richards Dawkins “lives in a world of fantasy”

Thought I’d whack the hornets’ nest with that deliberately provocative title.

But Dawkins isn’t the only person who can pack a lecture hall to capacity these days. Last Friday evening (1/22), molecular biologist James Shapiro of the University of Chicago spoke to a standing room-only (800+) audience in Ramsey Auditorium at Fermi National Accelerator Laboratory. His topic was “Evolution in the 21st Century,” and you can see his slides here. I don’t know if an audio file will eventually be made available, but here are some observations about the lecture and Q & A:

1. Shapiro mentioned ID a few times, always with sobriety — meaning he didn’t say “those ID people are dangerous anti-science theocrats” or other polemics of that tenor. Rather, he noted that his ideas about ‘natural genetic engineering’ helped to answer ID objections.

The implicit message was that the difficulties on which ID focused — e.g., the origin of new features rapidly — were real, and needed to be answered. Current theory was not adequate. Genes were not in the driver’s seat of life, he urged; rather, the organism was. Biology needs to understand how organisms intelligently modify their genomes in response to challenges. Genetic change is not random, but controlled.

2. Shapiro repeatedly contrasted his ideas with neo-Darwinism, and had nothing but scorn for Richard Dawkins, whom he said “lives in a world of fantasy.” He stressed that evolutionary theory needed mechanisms for very rapid, coordinated change.

3. During the Q & A, a man sitting just behind me asked — with unmistakable agitation — why Shapiro had frequently used the word “macroevolution.” The questioner protested that macroevolution was a concept dreamed up by creationists, so how could Shapiro use the term? Was Shapiro intending to “repurpose” macroevolution for his own ends?

Shapiro respectfully, but forcefully, disagreed. Macroevolution is not simply microevolution plus time. “Macroevolution,” he argued, “refers to when we have a major change in the nature of the organism. When a chordate changes into a vertebrate, that’s macroevolution. When one kind of plant changes into a flowering plant and the genome doubles at the same time, that’s what I would consider a macroevolutionary change.”

By contrast, Shapiro continued, “when a butterfly changes the pigment on its wings so it doesn’t get predated when it’s sitting on a city wall, that’s microevolution. That’s a small change. So I think the two changes can be distinguished from each other.”

“These are sudden events,” he concluded. “They can’t occur over many cell generations or many organism generations. They must occur within a single generation. Big changes can happen suddenly. How that all works, we don’t know yet. But we have to recognize that it must work suddenly and try and figure out what are the control processes and how does the complexity of the living cell allow these things to happen.”

The audience was enthusiastic, and didn’t want to leave; the moderator had to halt the Q & A to allow everyone to move to a reception in Wilson Tower.

Final note: it wouldn’t be fair to Shapiro, or to Dawkins for that matter, to leave the remark “lives in a world of fantasy” without explanation. So I strongly recommend the reader follow up with the paper, “Revisiting the Central Dogma in the 21st Century,” posted at Shapiro’s site. In particular, pay attention to the Boolean propositions featured on page 22.

In Shapiro’s estimation, Dawkins adheres thoughtlessly to the causal primacy of DNA, which is biologically nonsensical: DNA + 0 = 0.

Now Dawkins surely knows that naked DNA (or RNA) is going nowhere. But to come back to biological reality requires returning to the whole organism — see the list of Boolean propositions below, under “Contemporary picture” — which one can guess for Dawkins is uncomfortably close to ID or vitalism. Dawkins starts with naked replicators because they’re small, imaginably close to prebiotic chemistry, and don’t need a lot of extra machinery around.

Problem is, such entities would disappear on the early Earth more or less overnight.

Crick’s central dogma of molecular biology:

1. DNA –> 2X DNA
2. DNA –> RNA –> Protein –> Phenotype

• Contemporary picture of molecular information transfers:

1. DNA + 0 –> 0
2. DNA + Protein + ncRNA –> chromatin
3. Chromatin + Protein + ncRNA –> DNA replication, chromatin maintenance/reconstitution
4. Protein + RNA + lipids + small molecules –> signal transduction
5. Chromatin + Protein + signals –> RNA (primary transcript)
6. RNA + Protein + ncRNA –> RNA (processed transcript)
7. RNA + Protein + ncRNA –> Protein (primary translation product)
8. Protein + nucleotides + Ac-CoA + SAM + sugars + lipids –> Processed and decorated protein
9. DNA + Protein –> New DNA sequence (mutator polymerases)
10. Signals + Chromatin + Protein –> New DNA structure (DNA rearrangements subject to stimuli)
11. RNA + Protein + chromatin –> New DNA structure (retrotransposition, retroduction, retrohoming)
12. Signals + chromatin + proteins + ncRNA + lipids –> nuclear/nucleoid localization

SUMMARY: DNA + Protein + ncRNA + signals + other molecules: Genome Structure & Phenotype

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27 Responses to James Shapiro at Fermilab: Richards Dawkins “lives in a world of fantasy”

  1. Mr PaulN,

    Thank you for the report and helpful links!

    Problem is, such entities would disappear on the early Earth more or less overnight.

    I’m not sure what your comment is aiming to say. Naked replicators would disappear because of replacement by more efficient organisms or simply because they don’t work well enough to survive?

    Shapiro give a lot of credit to WGD (Whole Genome Duplication, I think), HGT, fusions, infections, etc that dump large amounts of already functioning DNA into cells. While these hybrids might not succeed in a fully populated ecology, an ecology with open niches (due to extinction events, changing geology, etc.) makes less demands in terms of functional level necessary to survive. Hence, rapid change.

    All good news for taking evolution to the next level of explanation, but where does it leave ID?

  2. For some reason this reminded me of Robert Shapiro’s prediction that we would understand the origins of life in the next five years. He made that prediction in 2006. With one year left that prediction doesn’t seem any more likely now than it did then.

    Of course the reason I am reminded of it is the name similarity and the new year.

  3. Very interesting. I’m glad he points out the problems with gradual evolution. I would love to find out how sudden changes are made so that I can breed a dog that has wings and can fly. Actually, I would not want that thing pooping on me.

  4. My guess is that the problem he has with ID is that he doesn’t understand that it is compatible with common descent.

  5. Big changes can happen suddenly. How that all works, we don’t know yet. But we have to recognize that it must work suddenly and try and figure out what are the control processes and how does the complexity of the living cell allow these things to happen.

    Notice the claim – big changes can happen suddenly, then the inevitable Darwinian standard line – “we don’t know yet”

    Oh well, at least we’re gettting rid of gradualism!
    But this answer is yet another shrug-off like Gould’s P.E.!

    What’s the diff? How are we advanced?
    A: We aren’t.

    I.e. Darwinists are slowly being forced
    to reject gradualism but they still refuse, without adequate reason, to accept the obvious.

    Once again I post the following paper,
    “Three subsets of sequence complexity and their relevance to biopolymeric information” by David L Abel1 and Jack T Trevors and a comment or two:

    Prescriptive sequences are called “instructions” and “programs.” They are not merely complex sequences. They are algorithmically complex sequences. They are cybernetic. Random sequences are maximally complex. But they don’t do anything useful. Algorithmic instruction is invariably the key to any kind of sophisticated organization such as we observe in any cell. No method yet exists to quantify “prescriptive information” (cybernetic “instructions”).

    Nucleic acid prescription of function cannot be explained by “order out of chaos” or by “order on the edge of chaos” [163]. Physical phase changes cannot write algorithms. Biopolymeric matrices of high information retention are among the most complex entities known to science. They do not and can not arise from low-informational selfordering phenomena. Instead of order from chaos, the genetic code was algorithmically optimized to deliver highly informational, aperiodic, specified complexity [164]. Specified complexity usually lies closer to the noncompressible unordered end of the complexity spectrum than to the highly ordered end (Fig. 4). Patterning usually results from the reuse of programming modules or words. But this is only secondary to choice contingency utilizing better efficiency. Order itself is not the key to prescriptive information.

    ———————-
    In physics, no empirical evidence exists, not even an anecdotal account, of Chaos, Catastrophe, maximum Complexity, order or pattern ever having produced sophisticated algorithmic function or cybernetic organization of any kind. A pulsar signal has abundant order and pattern. But it doesn’t DO anything useful. It contains no meaningful or functional message. It knows nothing of decision nodes or choice contingency. In biology, no rational or empirical justification exists for attributing linear, digital, encrypted, genetic recipes to stochastic ensembles OR to physical laws in any amount of time. Yet thousands of peer-reviewed papers exist in the literature on “self-organization.” How can denial of self-organization possibly be correct? The answer is that all of these papers are universally misdefining what is being observed. Self-ordering phenomena are being observed, not self-organization. But self-ordering phenomena do not measure up to the task of genetic programming.

    ———————–

    Artificial life investigators and most applied biologists accepted this reality early on. Steering is required to achieve sophisticated function of any kind. Much of the life-origin research community, however, continues to “live in denial” of this fact.

    – from Biosemiotic Research Trends

    Its all so very obvious but our Darwinist friends are still living in denial.

  6. Biology needs to understand how organisms intelligently modify their genomes in response to challenges

    I didn’t hear the lecture and haven’t even looked at the slides, but if genomes are “intelligently” modified by anything, and that is why rapid change happens, how is that not Intelligent Design? ID doesn’t mean “God did it”, it just means intelligence did it.

  7. Thanks, Paul, always enjoy your posts.

    ———–

    jehu, I didn’t remember that Robert Shapiro said OOL would be solved by the end of this decade. If he did, that is a real howler. Anyone with even a tenuous grasp of reality would have known that we weren’t even close on OOL.

    ———–

    uoflcard, when Shapiro says that “organisms intelligently modify their genomes” I don’t believe he is saying that they do so in the original meaning of the word “intelligence” (namely, to choose between contingent alternatives, which is the essence of specified complexity). What he really means is that in response to environmental and other factors, a pre-existing mechanism inside the organism naturally, and by force of chemistry and physics, causes changes in the genome. A very cool mechanism, to be sure, but not “intelligence” in any traditional sense.

    Of course the original design/source of such a mechanism would itself be evidence of intelligence, but that is a next order question from away what Shapiro means.

  8. Borne– Big changes can happen suddenly. How that all works, we don’t know yet.

    There is nothing wrong with saying that provided it isn’t followed up with something like “but ID can’t be right”

  9. 9

    At least Shapiro is appreciating the challenges given by ID proponents. This is the sort of attitude by Darwinists that we’ve been calling for, so we shoud be satisfied with (if not in agreement with) Shapiro.

  10. 10

    The real distinction between macro and microevolution is that macroevolution has never been observed. Microevolution has. That’s the distinction that is probably most helpful. Macroevolution is a theoretical extrapolation of observed microevolution.

    Anyway, I think it’s great we are fleshing out the central dogma, but DNA is still central to everything in the cell is it not? I don’t think this tendency some ID people have of disparaging the central dogma is going anywhere. ID’s best arguments are based on DNA. I don’t see a reason or need to pretend that DNA is not still the real driver in biology.

    1. DNA + 0 –> 0
    2. DNA + Protein + ncRNA –> chromatin
    3. Chromatin + Protein + ncRNA –> DNA replication, chromatin maintenance/reconstitution
    4. Protein + RNA + lipids + small molecules –> signal transduction
    5. Chromatin + Protein + signals –> RNA (primary transcript)
    6. RNA + Protein + ncRNA –> RNA (processed transcript)
    7. RNA + Protein + ncRNA –> Protein (primary translation product)
    8. Protein + nucleotides + Ac-CoA + SAM + sugars + lipids –> Processed and decorated protein
    9. DNA + Protein –> New DNA sequence (mutator polymerases)
    10. Signals + Chromatin + Protein –> New DNA structure (DNA rearrangements subject to stimuli)
    11. RNA + Protein + chromatin –> New DNA structure (retrotransposition, retroduction, retrohoming)
    12. Signals + chromatin + proteins + ncRNA + lipids –> nuclear/nucleoid localization

    Protein and RNA = coded for by DNA
    chromatin = DNA folded by proteins
    signal transduction = changes gene expression
    ncRNA = coded for by DNA
    Everything else in that list is about modifying DNA with stuff that was produced ultimately by DNA. I don’t see what the big deal is about the central dogma. One could just as easily criticize Meyer or Dembski for focusing too much on DNA and proteins.

  11. tragic mishap wrote:

    “Macroevolution is a theoretical extrapolation of observed microevolution.”

    That’s what Shapiro denied. He stressed that macroevolution is qualitatively different, as a process, from anything we see that we would describe as microevolution.

    tragic mishap also wrote:

    “Everything else in that list is about modifying DNA with stuff that was produced ultimately by DNA.”

    What evidence do you have that a cell is produced by DNA?

  12. 12

    Thanks for the post Paul Nelson.

    Over the past few years I have made it a point to read and re-read all of J. Shapiro’s work. I completely agree with the view that CY gave above in comment #8.

    What I am waiting for now is for the Darwinists who visit this site (and repeatedly exercise their spleens over religion) to line up on this thread and tell us just how Shapiro is FOS. Parse away.

  13. While Mr Shapiro’s tax dollar paid webpage of him looking into a microscope is some fine eye-candy, that academic paper of his is laced with darwinism and relies on literally cartoon depictions of just-so stories such as the “antiobiotic immunity” being inherited on page 10 by a microbe leaping out of a side alley and stealing from a passer-by microbe with no mention of where the passer-by’s genes come from. This is just the sort of slack pseudoscholarship which the socialist NCSE backs and ‘Expelled’ exposed, sending the darwinoid cockroaches scuttling for shelter. If this is the kind of “science” our tax dollars are going towards then I can only hope the Berlin wall of darwinism cracks sooner rather than later.

  14. 14

    Paul Nelson,

    “That’s what Shapiro denied. He stressed that macroevolution is qualitatively different, as a process, from anything we see that we would describe as microevolution.”

    So Shapiro then actually departs from extrapolating macroevolution from the evidence for microevolution. What evidence then, does he have left for macroevolution – since he apparently still holds to it?

    I’m of the understanding that the evidence for microevolution is what Darwinian evolutionists insist is the strongest evidence that evolution on a grand species-morphing scale is happening.

  15. Thought I’d whack the hornets’ nest with that deliberately provocative title.

    Paul,

    I believe that I have earned a reputation as the master of the DPT (Deliberately Provocative Title) at UD, and I will not reliquish that self-assigned title easily. (Just check out the number of replies to my DPT posts.)

    As a former militant atheist/materialist who finally realized that everything he believed about everything that matters was based on junk science and an incoherent and self-refuting philosophical commitment, I lay claim to the UD DPT crown.

  16. The questioner protested that macroevolution was a concept dreamed up by creationists, so how could Shapiro use the term?

    Wasn’t this canard popularized by talk.origins? I can’t believe there are still people who think it’s true.

    Microevolution in Relation to Macroevolution

    Darwin’s bridge between microevolution and macroevolution

    Macroevolution: The Morphological Problem

    Macroevolution is more than repeated rounds of microevolution

    Arguments over macroevolution versus microevolution have waxed and waned through most of the twentieth century. Initially, paleontologists and other evolutionary biologists advanced a variety of non-Darwinian evolutionary processes as explanations for patterns found in the fossil record, emphasizing macroevolution as a source of morphologic novelty.

  17. Biology needs to understand how organisms intelligently modify their genomes in response to challenges.
    So I guess the rodents that had to get off the ground when there were no trees around learned to grow wings real fast.

  18. “ Macroevolutionary processes are just the vector sum of microevolutionary processes in conjunction with large scale changes in geology and the environment ”

    “Just as in microevolution, basic evolutionary mechanisms like mutation, migration, genetic drift, and natural selection are at work and can help explain many large-scale patterns in the history of life. The basic evolutionary mechanisms — mutation, migration, genetic drift, and natural selection — can produce major evolutionary change if given enough time.”

    http://evolution.berkeley.edu/…..0_0/evo_48

  19. JohnnyB @4:

    My guess is that the problem he has with ID is that he doesn’t understand that it is compatible with common descent.

    You may want to check the tiltle of this web site.

  20. The basic evolutionary mechanisms — mutation, migration, genetic drift, and natural selection — can produce major evolutionary change if given enough time.

    And the evidence for this hypothesis is…?

    Here’s an anology. I have this mechanism that adds a single grain of sand to a pile of sand. If you just give it enough time, this mechanism can produce a major change to that sand pile. You should not be surprised to see that sand pile transformed into a fabulous ice sculpture.

    Um, no. It’s a mechanism. It adds one grain at a time. No major changes in view. Add all the time you want. If you want a major change, you need to change the mechanism.

  21. “the evidence for this hypothesis is…?”

    One piece of evidence is the observed micro rates of biological changes, expressed as ‘darwins’. These not only fit the micro observations, but the rates are beyond what is required in the more evidentiary fossils which line up lineages that are defined as being macro evolutionary changes.

    Would you prefer I cite some hominid fossils?

    Here’s an analogy. I have this mechanism that involves the upper layer crust plates which slide along the earth mantle at a very slow but predictive measurement. These small, cumulative, changes if given enough time, this mechanism can produce a major change to that crust plate. You should not be surprised to see that crust plates transformed into a fabulous mountains.

  22. 22

    Paul:

    That’s what Shapiro denied. He stressed that macroevolution is qualitatively different, as a process, from anything we see that we would describe as microevolution.

    And he said that the difference was the speed in which it occurs? That’s like saying breaking the speed limit is qualitatively different from not breaking the speed limit. There’s no point trying to define where the line is without speaking quantitatively. In fact, that’s exactly what ID is trying to do. I think Behe even called it an “evolutionary speed limit” in Edge of Evolution.

    I just don’t understand how you could make the case that macroevolution operates differently than microevolution. It’s still got to be some sort of mutation right?

    A qualitative difference could be information loss versus information gain, or at least, a change that was pre-specified by the existing information. Not sure how you could make a case for a qualitative difference from an evolutionary perspective is all.

    Paul:

    What evidence do you have that a cell is produced by DNA?

    All I’m saying is you can trace a line back to DNA from everything in the cell. I didn’t say DNA could produce a cell all by it’s lonesome, as in chemical evolution. It still makes perfect sense to me to think of DNA as the reference point for everything in the cell. The information in DNA can interact with the environment better that we thought, that’s all.

  23. Nakashima wrote:

    I’m not sure what your comment is aiming to say. Naked replicators would disappear because of replacement by more efficient organisms or simply because they don’t work well enough to survive?

    Szostak and others working on RNA World hypotheses argue that ribozymes with true self-replicating properties would need to be isolated (in vesicles or closed membranes) immediately, both to avoid well-known error catastrophe problems, but also to protect these relatively fragile molecules from chemical degradation. Put something inside a closed vesicle, however, and a new set of problems arise. What you’ll find — in the end, analytically — is you need something akin to a modern cell, if you’re going to have a cell at all.

    traqic mishap wrote:

    I just don’t understand how you could make the case that macroevolution operates differently than microevolution. It’s still got to be some sort of mutation right?

    Let’s take one of Shapiro’s examples of macroevolution which I didn’t cite in my report, namely, the endosymbiotic hypothesis for the origin of cell organelles (mitochondria and plastids). On the hypothesis (for mitochondria), an unknown prokaryotic cell engulfed a free-living alphaproteobacterium, and instead of digesting it, set up housekeeping with its new symbiont, soon-to-become organelle.

    “Engulfing” is an all-or-none event, if it works at all. Happens in one fell swoop, and in no sense is this event a mutation in DNA.

    Polyploidy — such as doubling of chromosomal number — isn’t a DNA basepair change, either, and it also happens in a single generation.

    tragic mishap also wrote:

    All I’m saying is you can trace a line back to DNA from everything in the cell. I didn’t say DNA could produce a cell all by it’s lonesome, as in chemical evolution. It still makes perfect sense to me to think of DNA as the reference point for everything in the cell.

    Then it should be possible to read the blueprint or plan for a cell from the DNA primary sequence, right? If “everything in the cell” is there in the nucleic acid, we should have a one-to-one mapping from DNA to cell structure and function.

    But we don’t. I encourage you to take a look at Franklin Harold’s The Way of the Cell (Oxford, 2001). Harold, a cell biologist, is not an ID advocate. He writes:

    So compelling is the siren song of DNA that most scientists take it for granted that the genome specifies, not only the primary structures of proteins and RNA, but the higher levels of cellular organization as well…Genes specify the cell’s building blocks; they supply raw materials, help regulate their availability and grant the cell independence of its environment. But the higher levels of order, form and function, are not spelled out in the genome. (p. 69)

    Harold titles the next chapter, “It Takes A Cell To Make A Cell,” which all evidence from cell biology shows to be the case, universally.

    Don’t get me wrong: DNA is an astonishing, absolutely critical molecule for life. But one cannot read off, from its sequence, how to construct even a single E. coli.

  24. Then it should be possible to read the blueprint or plan for a cell from the DNA primary sequence, right? If “everything in the cell” is there in the nucleic acid, we should have a one-to-one mapping from DNA to cell structure and function.

    Given environmental controls that should be theoretically possible, yes. For instance you could ask given this environment, this DNA will be accessed in this way, leading to this structure and this function.

    Genes specify the cell’s building blocks; they supply raw materials, help regulate their availability and grant the cell independence of its environment. But the higher levels of order, form and function, are not spelled out in the genome.

    He can’t possibly know this. We are still living in a field which has been focusing almost entirely on genes. An extremely large portion of the genome is not genes. What is the rest of it doing? We know its being transcribed, but beyond that we have very little idea what 95% of the functional genome does, not to mention a similar percentage of genes themselves which we know very little about. I’m not disputing that it takes a cell to make a cell. It’s just that cells are dynamic systems. Proteins degrade, cells die, material is continually being replaced. What you are telling me is that cells can replace and replicate in ways that do not reference DNA in any way. None of the examples you gave really do that. Prions are the only example of anything in biology that can actually do that, and even those are probably due to some genetic susceptibility.

    But one cannot read off, from its sequence, how to construct even a single E. coli.

    It’s actually worse than that. You can’t read off the structure of a single protein from it’s genetic sequence either. That is primarily a problem of a lack of computing power though. Given enough computing power it should be possible to do this. Or a better algorithm for making those kinds of predictions, which is IMO the single area where ID has the most scientific potential. Biologic is doing stuff like that right now from what I hear, using some language analysis program.

    I will try and check out that book, but there is still so much we don’t know about DNA. The first thing you would do to see what a software program does is learn the language, then look at the code. We have seen the code, but we don’t know the language yet.

    What it would take to convince me I suppose is if you could take out of a cell every last copy of a particular protein, insert a novel one in its place and observe the cell continue to make the new one instead of the old. You could for instance, remove an ubiquitin and replace it with a substantially different ubiquitin from a different species. I would hypothesize that the cell would simply continue making the old version of ubiquitin and the one you inserted might work but after all the copies you inserted degraded it would be replaced by the old version. With DNA you can do just that: Insert a new gene and the cell will start producing a new protein corresponding to the new gene.

  25. 25

    Forgot about this:

    “Engulfing” is an all-or-none event, if it works at all. Happens in one fell swoop, and in no sense is this event a mutation in DNA.

    Polyploidy — such as doubling of chromosomal number — isn’t a DNA basepair change, either, and it also happens in a single generation.

    But those things do not create new information. One is just copying the old information and the other is combining two different sets. There is no way those kinds of processes could change an invertebrate to a vertebrate. They are weird examples of organisms changing. It cannot possibly be the kind of mechanism behind the macroevolution Shapiro wants to explain.

  26. 26

    Paul, for what experiment would you and I have a different hypothesis? That would answer a lot of my questions I think.

  27. FermiLab AV Archive

    Shaprio slides from 1/22/10

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