Saturday, March 30, 2013

Learning About Evo-Devo

We talked about evolutionary developmental biology (evo-devo) in my class last week. The main issue is whether the proponents of evo-devo are making a substantive contribution to evolutionary theory. Is evo-devo going to be part of an extended modern synthesis, and, if so, how? My own view, which I express to the class, is that the discoveries of developmental biology pretty much confirm what Stephen J. Gould wrote in Ontogeny and Phylogeny back in 1977.
What, then, is at the root of our profound separation? King and Wilson argue convincingly that the decisive differences must involve the evolution of regulation: small changes in the timing of development can have manifold effects upon a final product "Small differences in the timing of activation or in the level of activity of a single gene could in principle influence considerably the systems controlling embryonic development. The organismal differences between chimpanzees and humans would then result chiefly from genetic changes in a few regulatory systems, while amino acid substitutions in general would rarely be a key factor in major adaptive shifts." Differences in regulation may evolve by point mutations of regulatory genes or by rearrangement of gene order caused by such familiar chromosomal events such as inversion, translocation, fusion, and fission. Studies of banding indicate that at least one fusion and ten large inversions and translocations separate chimps and humans.

Stephen J. Gould (1977) Ontogeny and Phylogeny, Harvard University Press, Cambridge Massachusetts, USA pp. 405-406
This helps us understand the history of life, especially the evolution of animals, but it doesn't contribute to evolutionary theory.

PZ Myers is teaching a developmental biology course and his students are dealing with three take-home questions this weekend [What I taught today: O Cruel Taskmaster!]. I'd like to reproduce two of them here since they're very relevant to the debate over the importance of evo-devo.
Question 1: One of the claims of evo devo is that mutations in the regulatory regions of genes are more important in the evolution of form in multicellular organisms than mutations in the coding regions of genes. We’ve discussed examples of both kinds of mutations, but that’s a quantitative claim that won’t be settled by dueling anecdotes. Pretend you’ve been given a huge budget by NSF to test the idea, and design an evodevo research program that would resolve the issue for some specific set of species.
I'd like my students to keep in mind Richard Lenski's ongoing evolution experiment in E. coli. Recall that evolution of the ability to grow on citrate depended mostly on mutations that changed the regulation of citrate utilization genes.

Since we have many examples of mutations that affect regulation of gene expression in bacteria, yeast, and other single-cell organisms, why do the proponents of evo-devo think they're on to something special when they look at development in animals? What is there about the evolution of "form" that changes our views on evolution?
Question 2: Every generation seems to describe the role of genes with a metaphor comparing it to some other technology: it’s a factory for making proteins, or it’s a blueprint, or it’s a recipe. Carroll’s book, Endless Forms Most Beautiful, describes the toolbox genes in terms of “genetic circuitry”, “boolean logic”, “switches and logic gates” — he’s clearly using modern computer technology as his metaphor of choice. Summarize how the genome works using this metaphor, as he does. However, also be aware that it is a metaphor, and no metaphor is perfect: tell me how it might mislead us, too.
Before answering PZ's question about Sean Carroll and metaphors, I'd like my students to remember the quotation I gave them in class. Discuss the use of hyperbole and metaphor in this context.

The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades, a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and function. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.

This book tells the story of this new revolution and its insights into how the animal kingdom has evolved. My goal is to reveal a vivid picture of the process of making animals and how various kinds of changes in that process have molded the different kinds of animals we know today and those from the fossil record.

Sean B. Carroll Endless Forms Most Beautiful: The New Science of Evo Devo, W.W. Norton & Co., New York (2005) p. x
I'd also like Sandwalk readers to keep in mind the recent ENCODE publications. They talked extensively about genetic circuits and regulation. In fact, their major "finding" was the idea that our genome is full of regulatory elements; so many, in fact, that most of what we thought was junk DNA is actually part of a a vast control circuit. Has this emphasis on a multitude of switches and controls been misleading or is it turning out to be correct?

I would ask a third question. The evolution of toolkit genes (i.e. transcription factors) make it possible to evolve many different body plans with only a small number of mutations. It helps explain the Cambrian explosion. Given our current understanding of evolution, is it possible to select for a evolution of a toolkit that has this potential for future evolution? Explain your answer.


73 comments :

  1. ... is it possible to select for a evolution of a toolkit that has this potential for future evolution?

    No. Selection operates on what's available in the here and now, not on what may or may not happen in the future.

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    1. Do you rule out any selection for evolvability? It seems to be one of the main "contributions" of evo-devo.

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    2. If there existed a means that allowed for more rapid adaptation (evolvability), then I could envision a scenario (a rapidly changing environment) where that would be selected for. Which is, sort of, the opposite of my previous answer.

      I'm not a biologist, either.

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    3. Lee Altenberg presented a computer simulation, using Stuart Kauffman's NK model, in which the system was allowed to alter K, the number of other genes a gene interacted with. A low K meant more evolvability. And the population did in fact evolve toward more evolvability. Having it do so is not necessarily an argument that an evolving population magically prepares itself for future events.

      He has also presented mathematical theory predicting this behavior. The (very good) paper is in a symposium volume but can be downloaded here.

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    4. It seems to me that the main questions on selection for evolvability would be whether evolvability has a cost and over what time scale any advantages or costs operate.

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    5. I think the message of Lee's paper is that if, in a population, some genotypes can move towards having less tangled interactions of genes, that the improved fitnesses are more likely to be found in those genotypes, so that ordinary individual selection can then alter the shape of the fitness surface. So the advantages can operate over a short time scale.

      That said, the issue of costs is a serious one, but not fatal.

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    6. Do you rule out any selection for evolvability? It seems to be one of the main "contributions" of evo-devo.

      I read Sean Carroll's books a while ago, and as a layperson I'm quite sure I did so with less understanding and retention than you have, Dr. Moran. I have to say, though, what you talk about as a "main 'contribution'" is not something I took away from my reading. Rather, a point I took away (which may be related to what some people would call "evolvability") is that changes in regulatory genes may have a better chance - still low, but better - of creating changes that allow survival than changes in coding genes.

      I will also say that as a layperson, having read so much in the popular science press about coding genes, the role played in evolution of new forms by changes in regulatory genes was something new and informative to me, though I assume it was neither to people familiar with the field.

      Joe Felsenstein raises an interesting issue. I hadn't thought about your question that way. I'd liken this to various species of microorganisms having developed the property of raising mutation rates under certain stresses. Of course the IDiots, Shapiro, et al., would see some guiding hand there. But I do think it's interesting that the survivability odds may apparently favor (or at least not be terribly much against) genes that permit flirting with error catastrophe rather than standing pat under these environmental stresses.

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    7. Separate to any benefit accruing to mutators, a passive constraint is provided by the mechanism of 'perfection'. Even if the optimum mutation rate was zero, genes could not get there because the mechanism of 'improvement' is mutation. It also starts to cost more, since care takes time. Like near-light-speed travel, the closer you get the harder it becomes.

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  2. Probably I don't understand the essence of the matter, but why not? Genome expansion by genes only intermittently useful and not generally deleterious. I'm thinking of certain bacteria (often soil bacteria) that have relatively large numbers of non-essential genes (including regulatory genes) that enable exploitation of wide range of carbon sources even though many of these carbon compounds are probably only rarely encountered. Changing environmental conditions could make many of these genes quite essential at some point and their continued presence in genome means they are subject to random mutation that may impact the range of activity (of the proteins) over time as well. Could this not be applicable to diploids as well?

    But as I say, I may be misunderstanding the matter, and may have just embarrassed myself with this answer. :) I'll live I guess.

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  3. Re the evolution of toolkit genes: What you can say, I think, is that genes that act early in development, or in particular zones along embryo gradients, can be co-opted as timers and inducers of later features that arise through mutation. This toolkit, if I understand it correctly, does not seem to be selectable. However, once the kit arose, natural selection may have favored alterations.
    On the other hand, mechanisms that promote short-term ‘evolvability’, such as crossing-over, modest mutation rates, sexual reproduction vs. parthenogenesis, etc., can be selected when they confer an immediate reproductive advantage on the genes (s.l.) responsible.

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  4. The last quoted writer said there's been a revolution in biology and that NO scientist would of though our bodies and insects come from the same genes in operation.
    There's a bigger revolution saying there is a common blueprint to biology and genes only represent a parts department used by the creator to organize biology as was done in physics.
    Biology is just extremely complicated physics.
    Its not from chance dancing with mutations.
    creationism would of predicted a common foundation in genetics holding up biology.

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    1. In my experience, creationism "would of" predicted whatever we see, but only after we see it. In fact you can find a lot of creationist references to the idea that homologous features have completely different genetic mechanisms, usually citing a single paper by Gavin de Beer. They were really happy to make that paper into a disproof of evolution and a prediction of creation, right up to the time it turned out not to be true.

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    2. Byers: creationism would of predicted a common foundation in genetics holding up biology.

      This is patently false. Creationists for many decades have lied and continue to lie about biochemical similarities to make it appear that humans are NOT biochemically similar to animals.

      If creationism "would of" predicted a common foundation in genetics, why have creationists lied about biochemical facts for decades to make the common foundation disappear?

      Creationist lies could not make that common foundation disappear, no matter how hard they tried.

      Remember how creationists Henry Morris and Gary Parker lied about a long list of chemicals, claiming that they were NOT more similar between human and chimp?

      Remember how creationist Duane Gish lied about the protein that was most similar between humans and the bullfrog?

      Or how creationist and jailed fraudster Kouznetsov lied about so-called "creatinine kinase"?

      If the creationist hypothesis really is "Common Design implies Common Designer", why do creationists keep lying to make the design appear UNcommon!?

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    3. There is no deception but errors in conclusions can occur.
      Creationism does teach a common blueprint from a designer would presume like physics in biology of creatures.
      We all have two eyes, butt, legs etc.
      We are all off the same rack.
      yet it would be this way is a creator was behind it.

      Yes many YEC creationists have tried to show differences between us and primates.
      its a wrong idea that this is needed.
      People uniquely do not have our own body but are renting another creatures body. No descent however. This because we uniquely were made in Gods image.
      It is undesirable and vain to seek much difference between people and apes.
      We should be very close inside and out because we are using the same type of body.

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  5. Larry what do you mean when you say "theory" in that evo-devo doesn't contribute to evolutionary theory? Do you mean that, so far, it's been descriptive but hasn't provided an overarching new mechanism of evolutionary change? Just wondering.

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  6. Diogenes.

    Remember how scientists lied about Piltdown man....
    Remember how scientists lied about Junk DNA
    Remember how scientists lied about GM foods being bad
    Remember how scientists lied about some bacteria living in arsenic
    Remember how scientists lied about global warming.....

    What's your point? Do only creationists lie? People lie and we all do it! I think researchhas shown that every person lies to himself about 400 times a day, could that also be a lie?

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    1. Andre,

      Remember how scientists lied about Piltdown man....

      No, I remember that Charles Dawson was an amateur antiquary without a college degree who perpetrated the fraud by himself. Even if we call him a "scientist", that's scientist, singular, not scientist, plural, as you try to sneak in.

      One might blame other scientists for being fooled by Dawson, but most were denied access to the "fossil", and of those who saw it, some were not fooled and denied its authenticity.

      That's about one evolutionary fraud per century, as compared to the DOZENS of creationist frauds just in the last 50 years. DOZENS.

      Remember how scientists lied about Junk DNA

      Who? I certainly can prove CREATIONISTS lied about Junk DNA. Over here I nailed Casey Luskin to the wall over his lies about Junk DNA, until ENV got in the last word and closed comments in fear.

      Which scientists (not creationists) specifically do you say lied? Please cite the article in the peer-reviewed literature revealing which scientists "lied about Junk DNA."

      Remember how scientists lied about GM foods being bad

      Who, specifically? What journal article in the peer-reviewed literature? A bunch of ooga booga holistic types lied about GM foods being bad. I don't know any scientists who did.

      Remember how scientists lied about some bacteria living in arsenic

      Listen, you idiot, they actually do live in arsenic. The controversy was whether they incorporate it into their DNA structure.

      If you were not an idiot, you would know that when the "arsenic life" paper came out, it was TRASHED by scientists. Few scientists were fooled.

      You know who was fooled? Elizabeth Pennisi, a non-scientist and journalist at Nature, who later went on to sell "The Death of Junk DNA" and is commonly CITED BY CREATIONISTS.

      Remember how scientists lied about global warming.....

      Who? In what peer-reviewed journal article? I certainly know corporations, politicians, and global warming skeptics (most of whom are not scientists) lied.

      Why don't you watch Potholer54's many videos showing how warming skeptics lie outright? Potholer54 has many such videos showing how warming deniers lied.

      What's your point? Do only creationists lie?

      My point is that the rate of scientific fraud is hundreds of times higher with creationists-- and I can back that up-- but their scientific achievements are nil.

      Creationists have discovered NO important extinct species or fossils, but they promoted numerous frauds and fakes. Indeed, essentially all of their original, positive claims are frauds or hoaxes or gross incompetence.

      There was the Paluxy River human fraudprints amid dinosaur tracks, which Carl Baugh named "Humanus Bauanthropus", after himself; the "black skull" of Freiberg, actually made out of coal; the Calaveras skeleton fraud; Carl Baugh's "Humanus Davidii", which was actually a prehistoric fish's tooth; Clifford Burdick's "Moab Man" of the Cretaceous; Wilder-Smith's "Phenanthropus mirabilis" of the Carboniferous ("footprints" outlined with chalk); Carl Baugh’s and Donald Chittick’s “Coso Artifact” (actually a 1920’s spark plug for a Model T); Kent Hovind's and Jack Chick's "New Guineau Man", wholly invented; "Meganthropus", photoshopped pictures of Biblical giants; the Castanedolo and Olmo fossils, real enough, though their geological strata were dishonestly identified by creationists; Burdick's pre-Cambrian pollen; and the Ica Stones from Peru, to name a few. Also, there are usually about 2-3 fraudulent claims of the discovery of Noah's Ark per DECADE.

      The fraud rate must be compared against their rate of actual achievement and discovery, which is ZERO.

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    2. And Andre,

      since you inserted yourself into my argument with Byers, why don't you address the question I directed at Byers:

      If the creationist hypothesis really is "Common Design implies Common Designer", why do creationists keep lying to make the design appear UNcommon!?

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    3. Who is the designer? That is a good question.... stuff don't appear to be designed as you and your ilk maintain, they are in fact designed, by who? Good question....

      As for your rant that creationist supposedly lie more, here go have fun with some crooked scientists...


      www.retractionwatch.com

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    4. Andre asks:
      Who is the designer? That is a good question....

      Andre, that is NOT the question I asked.

      Here is the question I asked:

      Me: If the creationist hypothesis really is "Common Design implies Common Designer", why do creationists keep lying to make the design appear UNcommon!?

      I demonstrated that that in fact happens with a few links above, and I can link to many more.

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    5. Beats me, I don't have a problem with common ancestry or common design, it all depends on the evidence...,

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  7. One last thing, a trillion cells each having about a 100 000 chemical reactions per second every second is pretty fantastic engineering don't ya think because you have to be an IDIOT to believe that any natural process, especially the random mutation and natural selection kind you love so much could have done this...... Chance did it? No chance!!!!! You hold onto that miracle you believe in for as long as you like.....

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    1. Andre, look at any picture of a snowflake, with its sixfold symmetry, and ask yourself if chance could make such a structure. Of course it couldn't, because the laws of physics and chemistry are not random.

      One last thing, a trillion cells each having about a 100 000 chemical reactions per second every second is pretty fantastic engineering don't ya think

      Enormously less reliable than a 1980's calculator. At least that can do long division and logarithms in a microsecond, and does not believe in spooks, deities and angels.

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    2. The laws are not random..... Where did the laws come from?

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    3. Almost forgot, a snowflake is not a living cell nice try.....

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    4. Diogenes wrote:

      "Andre, look at any picture of a snowflake, with its sixfold symmetry, and ask yourself if chance could make such a structure. Of course it couldn't, because the laws of physics and chemistry are not random."

      I'm not sure if scientists can fully explain the nature and origin of the ice nuclei, which are necessary to induce freezing of cloud droplets at temperatures about -40°F (-40°C).

      I'm not sure if scientists can even fully explain rain?

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    5. Kevin,

      What exactly do you mean by "the nature and origin of the ice nuclei"? I suspect that you are assuming something gratuitously here, but I rather ask before trashing your question.

      Explain rain? Seriously? What? Are you looking for a quantum mechanical "explanation"? I learned about rain in pre-kindergarden school, so really, what the hell are you talking about?

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    6. Andre,

      The laws are not random..... Where did the laws come from?

      Who cares. Maybe that's just because. If believers don't think that the question: "where did your god come from?" is valid, why should I assume that the question is valid for natural laws?

      Almost forgot, a snowflake is not a living cell nice try.....

      Why nice try? Do you really think that nature works differently inside living things compared to outside of living things? Do you really think that the chemistry within living cells you were talking about is not chemistry somehow?

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    7. I'm not sure if scientists can even fully explain rain?

      Fully or not, at any rate they can explain it way better than non-scientists can.

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    8. Kevin Bryan wrote: I'm not sure if scientists can fully explain the nature and origin of the ice nuclei, which are necessary to induce freezing of cloud droplets at temperatures about -40°F (-40°C).

      And this Watchtower Society page says: Recall God’s question: "Have you entered into the storehouses of the snow?" Many think of clouds as the storehouses of snow. Can you imagine going to these storehouses to inventory snowflakes in their infinite variety and to study how they came to be? A science encyclopedia says: "The nature and origin of the ice nuclei, which are necessary to induce freezing of cloud droplets at temperatures about -40°F (-40°C), are still not clear."—Psalm 147:16, 17; Isaiah 55:9, 10. [Emphasis mine.]

      It also has similar quotes about the mysterious origin of rain, concluding thus:

      In simpler terms, scientists have offered detailed theories, but they really cannot fully explain rain. Yet, you know that the vital rain falls, watering the earth, sustaining plants, making life possible and pleasant.

      So, Negative Entropy, you can see what Kevin is driving at. It isn't quantum mechanics for sure.

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    9. Hell of a catch, Piotr.

      Clearly, scientists can't explain a damn thing. When my son says, "Daddy, why is it raining?" I'll say "God makes it so" and when he asks me any other possible question, "Daddy, why X Y Z?" I'll say again "God makes it so," and soon, to be sure, he'll stop asking.

      If you want to see one of the top 10 stupidest things I've ever heard from a creationist (and I've heard a lot), there's this thread in which creationist JRS insists that no scientist has ever or could ever make water molecules by combining hydrogen and oxygen.

      He is challenged by some knowledgeable people, linking to videos of scientists making hydrogren burn. But for creationists, seeing is not believing. You have to read that thread to believe it.

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    10. Yeah sure, you're really not different from a rock, I mean just the other day I heard that very same rock perform Beethoven's 9th symphony. Yes they are not much different for sure your ability to not distinguish is uncanny, good job!!!

      I want to know where the laws come from, you should care about that, because like it or not every law does indeed have a law giver.

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    11. Andre,

      Sometime ago I called you an imbecile, and you insisted that I should apologize. Now you give me this rhetorical crap?

      I didn't say that life is no different to a rock, I asked if you really thought that natural laws changed inside living things. After all, on the one hand you mention hundreds of thousands of chemical reactions inside cells, implying that you understand that those reactions are actually, ahem, chemical. Next you reject snow flakes as examples of organization happening all by itself because snow flakes are not cells. Do you see your contradiction at all? Either you accept that chemistry happens inside cells, or you reject that chemistry happens inside cells. Either you accept that physics happens inside cells, or you reject that physics happens inside cells.

      Your wanting to know where natural laws come from comes with an unwarranted assumption: that these laws had to come from something else (though now you tell me that you "know" that there's a law-giver per law, I never had a polytheist arguing around before). Well, I don't assume so. I rather ask if there's good reason to think that natural laws need to come from something else. Maybe they are just what they are and that's that, maybe not. But I see no reason why your question should be answered before we could reject the notion of "law-givers," whose origin I do know: your "law-givers" come from primitive human imagination. They have evolved from imagining volcanoes and thunder and the sun and stars and more as anthropomorphized-huge-and-prone-to-anger beings.

      I hope you have the brains to distinguish between your meaningless and contradictory rhetoric and my explanations.

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    12. NE writes,
      "Maybe that's just because. If believers don't think that the question: "where did your god come from?" is valid, why should I assume that the question is valid for natural laws?"

      This is an excellent question and it strips things right down to the bare bones. This is not a scientific issue at all. For either side. This isn't even about science.
      It is about believers and non-believers choosing sides, framing their philosophy to match, and using or disregarding 'science' as it suits them.

      NE, whether you realize it or not, that is probably the least scientific thing you ever wrote, but very nicely atheistic. ;)

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    13. Of course there is chemistry in us how else will we be able to function? Point here though, we are more than just chemistry unlike rocks...... That is the part that science is having a problem with,because it is not reducible to anything material.

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    14. It's both hilarious and sad to see people actively REVEL in their ignorance.

      "We don't know X and we are PROUD we don't know X, therefore a magic man dun it".

      No Andre, we aren't "more than just chemistry". You'll be able to point out a reaction that takes place in a human tissue that defies physical and chemical law now, won't you? No?

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    15. Rumraket, it is actually you who is being hilarious. Of COURSE we are 'more than just chemistry', because chemistry behaves as it does/exists at all because of the laws of the universe Andre mentions. This is not even an issue that should be contested.
      Your question itself gives that away, when you write '...defies physical and chemical LAW..."

      So you are back to the same question, where do the laws come from and why are they there?
      And your answer, although it might appear more 'logical' if (and only if) someone is committed to a materialistic viewpoint, is no more 'scientific' than Thomas Aquinas writing about angels.
      You are committed to a philosophically atheistic outlook, which is fine. But it isn't scientific.

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    16. I have to wonder if atheistic biologists, like Larry, and their 'fans' like Rumraket ever find it a bit curious that they find themselves knowledgeable about the ONE field that seems to disprove God to them. People study architecture just as hard and just as dedicatedly as people study biology. Same for music. But you don't see music blogs or architecture blogs by atheists practitioners trying to use their field to back up their beliefs. They COULD, if they wanted to.
      Same for professional sports. For example, if a great athlete like Lebron James were an atheist, he might say something like, "Well, I know a lot of people are out there praying for us to win, or praying for us to lose, but all I ever see is me and my teammates going out there and doing the best we can, win or lose. It's our effort and the effort of our opponents; no god(s) necessary."
      We NEVER see that; why not?
      Why biology、why the theory of evolution? Bio-atheists seem to find it merely curious, a quirk perhaps, that Alfred Russell Wallace did the same type of fieldwork (at least as much if not more) as Darwin, arrived at a nearly identical hypothesis, and felt convinced that in all that he observed the presence of what he called 'Mind' could be detected. And Darwin, in a private letter, excoriated him for this. Why? Why was Darwin so insistent that his theory be necessarily materialistic/atheistic? Wallace's stature in the world of 'science' fell considerably, but he stuck to his guns. And this has gone on ever since.
      For all the 'skepticism' you folks pride yourself on, you seem oddly unwilling to apply it to your own beliefs.
      YOU think that biological discoveries point to atheism. But this is a philosophical position, NOT a scientific judgement.
      But, please, don't let me stop you. By all means keep on killing god if it makes you happy.

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    17. @Andyboeger
      Andre intentionally tried to distinguish us from rocks, which to him really ARE "just chemistry" apparently. So it's not about natural law, it's because Andre Gross thinks there's something magical going on inside living human/organismal tissue that doesn't or could't take place in rocks. So my quesion to poor, confused little Andre is what it is he thinks living organisms do, which defies the "just chemistry" of rocks or other "inanimate" matter.

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    18. andyboeger said...
      I have to wonder if atheistic biologists, like Larry, and their 'fans' like Rumraket ever find it a bit curious that they find themselves knowledgeable about the ONE field that seems to disprove God to them.

      Actually, you are making the claim that biology disproves god(s). They are claiming that what is known does not require god(s) as part of the explaination.

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    19. Well, Rumraket, obviously Andre's answer will be related to the concept of consciousness. You will then argue, as you always do, that consciousness is nothing other than brain chemicals doing certain things. It is a fruitless, unprovable argument.

      But it would be interesting to learn exactly WHY you find his answers 'hilarious' and 'sad'. By your very own reckoning, all that is happening is that the chemicals in HIS brain are doing something different than the chemicals in YOUR brain, related to this one simple point (in most other respects we can assume they act much more similarly). Why is it hilarious and/or sad that different chemicals doing different things in different, very temporary organisms, lead to people coming to different ideas about life? It is all just your judgement, and that, as well, is just your brain chemistry doing something.

      So laugh and cry all you want at his comments. You certainly have no overarching reason to, but then again, nobody can stop you either.

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    20. The Other Jim writes, 'Actually, you are making the claim that biology disproves god(s). They are claiming that what is known does not require god(s) as part of the explaination.'
      Good. So you are fine with all the atheistic biologists, from Richard Dawkins on down, just coming out and admitting that their science is their science, and their atheism is their atheism, and they have no real valid reason to place the two alongside each other as if they were a set?
      Because I'd be really happy if they did.
      Architects could just go on being architects, pro athletes could just go on being pro athletes, and biologists could go on being biologists, and if any of them want to talk about how ridiculous the notion of God is, they could just leave their profession out of it. Sounds really good to m.

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    21. So you are back to the same question, where do the laws come from and why are they there?

      For the beginnings of an answer we can read high energy physics papers on the Arxiv, or still better obtain sufficient education to really understand where the research is going. Or we can indulge in "reasoning" that is generally ignorant of the knowledge that has been accumulated in the past 100-odd years of that research.

      On that score I'll "take the awe of understanding over the awe of ignorance any day," thank you. (Hat tip to Douglas Adams for the quote.)

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    22. Jud, by all means do the research. And be in awe of it. I don't think all that many people are actually in 'awe' of ignorance, but Douglas Adams does set up a very nice strawman, just the same.

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    23. Douglas Adams wrote,
      "I have to reply that I really do mean Atheist. I really do not believe that there is a god - in fact I am convinced that there is not a god (a subtle difference). I see not a shred of evidence to suggest that there is one. It's easier to say that I am a radical Atheist, just to signal that I really mean it, have thought about it a great deal, and that it's an opinion I hold seriously. "

      I believe him. I believe he thought a great deal about it, and that it's an opinion he holds seriously. Well, I have also thought a lot about the existence of an intelligence (generally referred to as 'god') underpinning and giving rise to this universe, believe in it, and it's an opinion that I hold seriously.

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    24. Architects could just go on being architects, pro athletes could just go on being pro athletes, and biologists could go on being biologists, and if any of them want to talk about how ridiculous the notion of God is, they could just leave their profession out of it. Sounds really good to m.

      Of course, architects and athletes don't have to deal with the equivalent of creationists. If there were hoards of people trying to force architecture schools to teach that bridges are held up by a miracle of God and structural engineering has nothing to do with it, I bet you'd see architects getting quite involved in the issue of God.

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    25. lutesite, yes, that is an excellent point. But it does go both ways.

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    26. Architecture, music and athletics do not deal with the history of life on Earth and the origin of humans. Biology does, so it naturally comes under attack by those who used to have the monopoly on explaining where we came from -- conservative religious leaders, biblical literalists, door-to-door preachers (who now seem to prefer virtual doors to real ones, especially if it's raining), etc. They don't care a rat's butt about architecture, music and athletics, but regard life and the place of man in the universe at their turf. I visit science blogs in order to learn something. IF I were interested in waging a guerrilla war against IDiots, I'd visit their blogs, which I never do. But they come thick and fast here just to try to spoil other people's fun. I was looking forward to an interesting discussion in this thread. Instead, I see the usual crap posted by Andre, a Jehovah's Witness on the unfathomable mystery of the rain, and everybody going off at a tangent as a result of the distraction. Jolly good show: discussion wrecked, point scored by IDiots.

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    27. Piotr, that is too clever by half. You make it sound as if this is just some 'innocent science blog' without considering its host, Larry Moran. He as you know is every bit as much of a 'militant atheist' as he is a biology professor. He wrote on this very site, a couple months ago, (ironically to Andre) that he always thought that most theists are stupid.
      He has written that he sees science and religion as being inherently antithetical. He has written that he wants to 'change society' and that he wants to see a 21st century based on reason and science.
      It is hardly curious that his site would attract opponents to his worldview. You need look no farther than the man himself, and certain fans of his who absolutely hate religion, to wonder why you can't just come here to have a nice chat about genes and mitochondria.

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    28. So what? In this thread Larry did not even allude to religion, theism, ID, creationism or any such topic. It did not stop the f***ing creotard Byers from launching a troll attack half an hour after the first poster, or others from following suit.

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    29. @ piotr

      "I visit science blogs in order to learn something. IF I were interested in waging a guerrilla war against IDiots, I'd visit their blogs, which I never do. But they come thick and fast here just to try to spoil other people's fun"

      Creationists infestation of scientific debates and their attempts to derail them is a serious and an infuriating problem. I wish they would be thrown out, not necessarily from the site itself, but from those threads which disseminate valuable scientific information, so those of us who want to learn something can do so without constant incessant disruption.

      Basees

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    30. @andyboerger

      lutesite, yes, that is an excellent point. But it does go both ways.

      Really? It goes both ways? I was not aware that there were cabals of scientists attempting to legislatively force Christian churches to teach evolution and Big Bang cosmology instead of the Genesis creation myth. I had no idea. That really must stop. I don't know how I never heard about it.

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    31. lutesite, your sarcastic answer speaks volumes. Surely you don't think that all, or even most, theists want the ten commandments or whatever taught in place of evolution?
      And yet blogs like this make no distinctions. Anyone who believes in god is equally deluded, and according to someone like steve oberski, equally 'culpable'.
      An excellent case in point, and not because she is any way exceptional, is my niece. A high school biology teacher. As appalled as you are by the thought of creationism being taught in science classes. Her mom, my sis, works for the diocese, and she herself was married recently in a Catholic church.
      But there are folks who post here who consider her to be a deluded fool first, and secondly a science teacher on the same side as you in terms of keeping creationism out of science classes.
      So if you don't know what my comment means, then I can only assume that you haven't considered it fully.

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    32. Andy,

      I have to say that I have never feared philosophy. I used to despise it, because the view we get about philosophy includes, for example, philosophers who take a sophist such as Plantinga seriously at least in terms of having to deal with such an ass-hole. It might be that the exercise of figuring out how the sophism was constructed is part and parcel with being a philosopher, but I am would be much happier if he was regarded for what he is, an ass-hole, and told so, rather than having philosophers writing articles refuting his shit, as if an academic article was necessary. Then there's this stupid idea that some have that philosophy can be done in empty space. But I digress.

      I don't choose sides, I don't frame my philosophy to match, and I don't use or disregard 'science' as it suits me. Furthermore, note that my position is much more "comfortable" than the theist, and that's at the core, arguably perhaps, of science: I don't use imaginary beings to fill in gaps of knowledge. Theists do. They pretend to pass their imaginary beings for reality. I just don't. Should there be evidence for super beings, then I would consider them. Therefore the atheist and the theist positions are not the same at all.

      You said to someone else something to the effect of challenging your beliefs. Well, how do you think I got into atheism? I was raised a believer. A Christian. Reality mismatched my beliefs time and again, until the logical conclusion came to me. You might not find science as something that proves gods wrong because the one you seem to believe is much less compromised by anything than the Christian god would be. But sure you would understand that if Genesis is false, then we can conclude easily that the Christian god is false. I know, there's many different versions of the Christian god, but depending on compromise, most of them, if not all, are easily refuted by reality. The same goes for many other gods. I use the Christian one(s) as example because of familiarity.

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    33. All I can say to you "skeptics" keep believing in your miracles that dead matter just come alive....... It is really funny that this chance event has not happened again in 4 300 000 000 years, and yet I know someone personally that has won the lotto twice...... But life just poofing magically into existence...... nothing yet, and I won't be holding my breath, life only comes from life....... good luck with your fairy tale.

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    34. Jud, by all means do the research. And be in awe of it. I don't think all that many people are actually in 'awe' of ignorance, but Douglas Adams does set up a very nice strawman, just the same.

      Sadly, because of a misspent youth (got a law degree), I don't have the math and physics chops to do the research myself. But my point is that I am far, far more interested in hearing from people doing hard work and making serious headway on these issues than I am in hearing from people who have not done the work. How fascinating would you find repeated airing of opinions on gardening by a non-gardener? That's the same way disquisitions on "where do the laws come from" strike me when aired by those who've done none of the long, hard work that would make their opinions on these matters valuable and informative to others.

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    35. Jud

      Andy gave you some good advice, make the effort and do the research yourself, you will learn a few things about just so stories that have being doing the rounds.

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    36. Andy gave you some good advice, make the effort and do the research yourself, you will learn a few things about just so stories that have being doing the rounds.

      And I responded to Andy that research into the relevant areas (examples being inflation, multiverses, and the part of string theory referred to as "the landscape") are beyond my abilities. Are you saying you are conversant with the mathematics required to perform actual research in these areas, and have found from the math that the research reported in academic journals contains "just so stories"? What specific articles (and please point out the mathematical errors)?

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    37. Jud

      Just two questions.....

      1.) We are unable to see outside this universe, how do you or anyone else know that there are other universes other than this one? What evidence is there?

      2.) What does math have to do with non-evidence?

      Lastly, I have an engineering background.

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    38. The Salem Hypothesis strikes again....

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    39. Anyway, to question (1), we do not know that multiverse theory is correct. Rather, it is a prediction of some of the cosmological models of the universe:

      http://discovermagazine.com/2011/oct/18-out-there-welcome-to-the-multiverse#.UVtNwVfNlS0

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    40. Jud asks, "How fascinating would you find repeated airing of opinions on gardening by a non-gardener? That's the same way disquisitions on "where do the laws come from" strike me when aired by those who've done none of the long, hard work that would make their opinions on these matters valuable and informative to others."

      Jud, I completely sympathize. Because for the many who have done the 'long, hard work' of meditation, reflection, spiritual study and so forth in order to improve ourselves and increase our sense of appreciation and gratitude for our existence, and as a result attained insights that clearly make us better people, not only in the way we treat others but how we are treated by others, etc. to be told that our way of life is 'deluded' and 'stupid' from people who are sure that we are making it all up, that our beliefs are no different than fear of the dark and dying, that there is a direct line of evolution from throwing people into volcanoes to how we live, to have our beliefs likened to the 'tooth fairy' and 'spooks', to be 'slam-dunked' with 'who designed the designer?', etc. etc., from people whose opinions on these matters are neither valid NOR informative, the feeling that you express is exactly and precisely the same.
      So I sympathize.

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    41. Just two questions.....

      1.) We are unable to see outside this universe, how do you or anyone else know that there are other universes other than this one? What evidence is there?

      Read The Inflationary Universe by Alan Guth for an explanation written for a lay audience of how what is known about the development of the early universe implies a multiverse.

      2.) What does math have to do with non-evidence?

      You're kidding, right? Before the mathematics of relativity, how would Sir Arthur Eddington have known that his observations of Mercury were evidence of light being bent by gravity? Heck, how would he have known to look at Mercury in the first place? Observations become evidence only if there is a hypothesis to prove or disprove, and the hypotheses that provide descriptions of the origins of the universe sufficiently cogent and detailed to prove or disprove are intensely mathematical.

      Lastly, I have an engineering background.

      What is the most ridiculous thing you've ever heard a non-engineer say about an engineering issue you've been involved with?

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    42. for the many who have done the 'long, hard work' of meditation, reflection, spiritual study and so forth in order to improve ourselves and increase our sense of appreciation and gratitude for our existence, and as a result attained insights that clearly make us better people

      And made you so much more humble, too.

      Just wondering if all this meditation and self-reflection has sharpened your sense of irony. I mean, seeing as how you're complaining that some people turn everything into a contest between religion and atheism, in yet another in a long series of threads on scientific subjects (in this case the contribution of evo-devo to evolutionary theory) where you've shoehorned in multiple comments about religion versus atheism.

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    43. It is interesting to learn that you think that one lacks humility for merely saying they are better now than they were before.
      I find this rather odd. Are you not better now than you were before, and has some discipline not helped you get there? If not, I feel sad for you.
      If so, just admit it and be happy about it. I won't consider you to be arrogant for doing so.

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    44. ...and Jud, as for 'irony', my two initial responses here were to comments made by Rumraket and Negative Entropy. The discussion had already moved beyond a scientific topic and had Rumraket calling Andre 'hilarious' and 'sad'.
      So I'm terribly sorry for having lowered the level of discourse.

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    45. Jud

      The most ridiculous has to be Dawkins; "Things appear to be designed for a purpose but is in fact not"


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    46. Lutsuite

      Yes a prediction that is untestable.... Where is the edge of our universe? Have we been able to see past it to know that they exist? This is not science, it will never be, and here is why.... It is not observable, it is not testable and it is not repeatable. It is Not science, its metaphysics.

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  8. Well, Larry, your answers are an acceptable start to addressing the questions -- I'm hoping my students will also take a critical approach. But you'll need to flesh them out with a little more substance if you hope to earn an A in the class.

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    1. I'm wasn't going to write a complete answer. It would have taken too long and I would have missed the Easter bunny, the Men's World Curling championship, and the opening episode of season 3 of Game of Thrones.

      I agree that you are a "Cruel Taskmaster!"

      P.S. Does anyone get an "A" in your course? :-)

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  9. Negative Entropy, just to touch on the points you most recently brought up in response:

    I agree that some theists 'use imaginary beings to fill in the gaps of science'. I don't believe that would be the majority, however.
    I think there are many theists in the western world with a reasonable education who are comfortable with the idea that science will continue to make extraordinary findings about this universe, and still consider those discoveries strictly contained within the 'magesterium' of the natural world, of which they do not consider god a part. So the conflict isn't there for all theists, although it is there for the bible thumpers, of course.
    For most theists, and I think this should be true for most atheists as well (despite the best efforts of Richard Dawkins and company), belief in god is neither 'scientific' nor 'unscientifc', but rather 'ascientific' in exactly the way the letter 'a' is used in 'atheism'. Belief in god isn't, for most believers, a theory they are toying around with, consciously or unconsciously. It is something else, and science, by its nature, isn't out to get that which it is, although some atheistic scientists decidedly are.
    There ARE 'fundamentalist' atheists who wish to drive religious beliefs out of this world. There are many, many more fundamentalist Muslims and Christians who want to force their beliefs on others. In both cases, demonization of ones perceived enemy is part and parcel of the assault.

    I had similar experiences to you, by the way. But I wouldn't say it was science, per se, that bumped up against my beliefs. Just common sense. I was way too young to have much scientific knowledge, but it was obvious that the stories in the bible were just made up. So, again, I think it is somewhat of an exaggeration, and one which is very much in vogue these days, to say that science is playing any kind of major role in changing theists into atheists. It's generally not the people making the most noise, whether on fundamentalist Christian side, or the 'skeptic' side, who are having the most influence. That's why they need all that noise.

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  10. I am not a biologist, but is it not the case that the ultimate consequence of evodevo is that environmenataly induced changes in phenotype can be selected and inherited?

    If this was the case, then doesn't it follow that evodevo would bring to the modern sintesis the questioning of the Weismann's principle and the gene as the unit of evolution?

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