152 thoughts on “The Biology of the Baroque”

  1. Summary of Jerry Coyne’s takedown of Noble:

    1. What we mean by “random” is that mutations occur regardless of whether they would be good for the organism. (Shapiro says this, if you actually read his book)

    2….when we map adaptations in organisms, they invariably turn out to be changes in the DNA

    3. ….adaptive methylation, such as “parental imprinting”, in which the father or mother contributes differently methylated DNAs that do different things in the zygotes and offspring, is based on instructions in the DNA itself

    4. I know of not a single adaptation in organisms that is based on such environmentally-induced and non-genetic change.

    5. For an adaptation to become fixed in a population or species, it must be inherited with near-perfect fidelity. And that is not the case for all environmentally-induced modificatons of DNA. They eventually go away.

    6. … those big jumps or horizontally-transmitted changes in DNA must still obey the rules of population genetics. They are equivalent to mutations, but they’re just BIG mutations.

    7. Further, we can make “diploid hybrid species” in the lab by hybridizing two species and letting their mixed and somewhat incompatible DNA sort itself out over several generations. What you can get is a non-polyploid hybrid species that is reproductively isolated from both parental species—that is, a new lab-produced species.

  2. petrushka,

    1. What we mean by “random” is that mutations occur regardless of whether they would be good for the organism. (Shapiro says this, if you actually read his book)

    Mayr disagrees. He says random means happenstance, as in accidental. What Coyne says is meaningless.

    2….when we map adaptations in organisms, they invariably turn out to be changes in the DNA

    So being a human must not have been an adaptation as no one has mapped that to changes in the DNA

  3. Frankie:
    petrushka,

    Mayr disagrees. He says random means happenstance, as in accidental. What Coyne says is meaningless.

    This is not disagreement. Happenstance IS regardless of whether they would be good or bad for the organism.

    So being a human must not have been an adaptation as no one has mapped that to changes in the DNA

    Changes from what? The DNA differences between humans and chimps has been mapped in complete detail, right down to the last base pair.

  4. Flint,

    Happenstance IS regardless of whether they would be good or bad for the organism.

    But whether or not it is god or bad for the organism doesn’t make it happenstance

    The DNA differences between humans and chimps has been mapped in complete detail, right down to the last base pair.

    Yes and we still don’t know what makes a chimp a chimp nor a human a human. Evolutionism needs that to be the sum of the genome yet no one has ever made that connection. Genomes may influence and control development but genomes do not determine what will develop.

  5. Frankie:
    Flint,

    But whether or not it is god or bad for the organism doesn’t make it happenstance

    Why not? Random with respect to benefit is random, whether or not you call it “happenstance.”

    Yes and we still don’t know what makes a chimp a chimp nor a human a human.

    Of course we do.

    Evolutionism needs that to be the sum of the genome yet no one has ever made that connection. Genomes may influence and control development but genomes do not determine what will develop.

    Of course the connection has been made. Of course genes determine what will develop. Of course these genes have been compared, not just between humans and chimps, but now that it’s fast and (relatively) cheap to sequence entire genomes, a huge number of detailed comparisons is being done.

    If you wish to raise valid objections, your statements must be correct.

  6. Flint,

    Random with respect to benefit is random, whether or not you call it “happenstance.”

    It isn’t random if it was directed by the organism


    Yes and we still don’t know what makes a chimp a chimp nor a human a human.

    Of course we do.

    Of course we don’t. That is why geneticist Giuseppe Sermonti wrote the book “Why is a Fly Not a Horse?”

    Of course genes determine what will develop.

    Evidence please. I can quote geneticists who say otherwise.

    If you wish to raise valid objections, your statements must be correct.

    Your statements aren’t correct

  7. To understand the challenge to the “superwatch” model by the erosion of the gene-centric view of nature, it is necessary to recall August Weismann’s seminal insight more than a century ago regarding the need for genetic determinants to specify organic form. As Weismann saw so clearly, in order to account for the unerring transmission through time with precise reduplication, for each generation of “complex contingent assemblages of matter” (superwatches), it is necessary to propose the existence of stable abstract genetic blueprints or programs in the genes- he called them “determinants”- sequestered safely in the germ plasm, away from the ever varying and destabilizing influences of the extra-genetic environment.

    Such carefully isolated determinants would theoretically be capable of reliably transmitting contingent order through time and specifying it reliably each generation. Thus, the modern “gene-centric” view of life was born, and with it the heroic twentieth century effort to identify Weismann’s determinants, supposed to be capable of reliably specifying in precise detail all the contingent order of the phenotype. Weismann was correct in this: the contingent view of form and indeed the entire mechanistic conception of life- the superwatch model- is critically dependent on showing that all or at least the vast majority of organic form is specified in precise detail in the genes.

    Yet by the late 1980s it was becoming obvious to most genetic researchers, including myself, since my own main research interest in the ‘80s and ‘90s was human genetics, that the heroic effort to find information specifying life’s order in the genes had failed. There was no longer the slightest justification for believing there exists anything in the genome remotely resembling a program capable of specifying in detail all the complex order of the phenotype. The emerging picture made it increasingly difficult to see genes as Weismann’s “unambiguous bearers of information” or view them as the sole source of the durability and stability of organic form. It is true that genes influence every aspect of development, but influencing something is not the same as determining it. Only a small fraction of all known genes, such as the developmental fate switching genes, can be imputed to have any sort of directing or controlling influence on form generation. From being “isolated directors” of a one-way game of life, genes are now considered to be interactive players in a dynamic two-way dance of almost unfathomable complexity, as described by Keller in The Century of The Gene- Michael Denton “An Anti-Darwinian Intellectual Journey”, Uncommon Dissent (2004), pages 171-2

    Chapter VI “Why is a Fly not a horse?” (same as the book’s title)

    ”The scientist enjoys a privilege denied the theologian. To any question, even one central to his theories, he may reply “I’m sorry but I do not know.” This is the only honest answer to the question posed by the title of this chapter. We are fully aware of what makes a flower red rather than white, what it is that prevents a dwarf from growing taller, or what goes wrong in a paraplegic or a thalassemic. But the mystery of species eludes us, and we have made no progress beyond what we already have long known, namely, that a kitty is born because its mother was a she-cat that mated with a tom, and that a fly emerges as a fly larva from a fly egg.”

  8. Sexuality has brought joy to the world, to the world of the wild beasts, and to the world of flowers, but it has brought an end to evolution. In the lineages of living beings, whenever absent-minded Venus has taken the upper hand, forms have forgotten to make progress. It is only the husbandman that has improved strains, and he has done so by bullying, enslaving, and segregating. All these methods, of course, have made for sad, alienated animals, but they have not resulted in new species. Left to themselves, domesticated breeds would either die out or revert to the wild state—scarcely a commendable model for nature’s progress.

    (snip a few paragraphs on peppered moths)

    Natural Selection, which indeed occurs in nature (as Bishop Wilberforce, too, was perfectly aware), mainly has the effect of maintaining equilibrium and stability. It eliminates all those that dare depart from the type—the eccentrics and the adventurers and the marginal sort. It is ever adjusting populations, but it does so in each case by bringing them back to the norm. We read in the textbooks that, when environmental conditions change, the selection process may produce a shift in a population’s mean values, by a process known as adaptation. If the climate turns very cold, the cold-adapted beings are favored relative to others.; if it becomes windy, the wind blows away those that are most exposed; if an illness breaks out, those in questionable health will be lost. But all these artful guiles serve their purpose only until the clouds blow away. The species, in fact, is an organic entity, a typical form, which may deviate only to return to the furrow of its destiny; it may wander from the band only to find its proper place by returning to the gang.

    Everything that disassembles, upsets proportions or becomes distorted in any way is sooner or later brought back to the type. There has been a tendency to confuse fleeting adjustments with grand destinies, minor shrewdness with signs of the times.

    It is true that species may lose something on the way—the mole its eyes, say, and the succulent plant its leaves, never to recover them again. But here we are dealing with unhappy, mutilated species, at the margins of their area of distribution—the extreme and the specialized. These are species with no future; they are not pioneers, but prisoners in nature’s penitentiary.—geneticist Giuseppe Sermonti in “Why is a Fly Not a Horse?”

  12. CharlieM,

    If you haven’t done so already you should watch this video by Denis Noble.

    Yes, I’m familiar with Noble. Lizzie’s a fan. I’m not.

    God though, why are Creationists always directing people to read the arguments of someone else? Someone who thinks evolution true, no less. ie, that someone else fundamentally disagrees with the Creationist? I’m supposed to argue with Noble, who is not present, while you look on with an indulgent smirk?

    Naked genes are not inherited, the entity that is inherited is the fertilized cell which contains the genes. You and me as oirganisms began as a single cell. The cell is passed over from mother to offspring and the genes could do nothing without this cell. Even when single celled organisms divide you cannot say that the genes alone were inherited because the cytoplasm and cell wall is also shared between the daughter cells.

    Cytoplasm is made by genes. The fact that a portion of the cytoplasm in a given cell is not made by the gene copies that reside in that cell is immaterial. Cytoplasm turns over pretty quickly. None of your mother’s or father’s cytoplasm remains in you. All that remains is the genes, template-copied down the generations.

  13. Allan Miller,

    Cytoplasm is made by genes.

    The proteins in the cytoplasm are encoded by genes but do the genes also make the gel? Do you have a reference for your claim?

  14. Well, it looks like Denton isn’t at all alone.

    “In this remarkably insightful and ambitious book, Wagner argues that homologies are real: they are not just surviving similarities between related organisms that have not yet been erased by selection and drift, and they shape evolutionary trajectories by organizing the flow of variation to selection. He develops a synthesis of adaptationist and structuralist perspectives on evolution that is both conceptually rich and empirically grounded.” — Kim Sterelny, author of The Evolved Apprentice: How Evolution Made Humans Unique

  15. Mung: I don’t need the NCSE to tell me why a fly isn’t a horse.

    You do if you believe that Giuseppe Sermonti has anything to tell you.

    Winston Ewert clearly needs me to tell him “Why a Bug is not a Weasel.” Hopefully I’ll get that done… this year. Shoveling shit is not nearly as easy as blowing it out your ass. At least I know now that a few people get the pun.

  20. Frankie:

    The proteins in the cytoplasm are encoded by genes but do the genes also make the gel? Do you have a reference for your claim?

    Ooh, what a gotcha! And pasta is not made by people, but by pasta makers. If you are aware of a cytoplasmic component that does not have a genetic origin (even if made via protein), do tell. Well, water, I suppose, and some dissolved salts. Yeah, what a victory.

  21. Mung: Well, it looks like Denton isn’t at all alone.

    Either Denton is in the mainstream (in which case his title should be, Evolution, A Theory Making Steady Progress), or he is wrong about the lack of explanations.

  22. Allan Miller:
    Frankie:Ooh, what a gotcha! And pasta is not made by people, but by pasta makers. If you are aware of a cytoplasmic component that does not have a genetic origin (even if made via protein), do tell. Well, water, I suppose, and some dissolved salts. Yeah, what a victory.

    LoL! The solution is the bulk of the cytoplasm and the proteins couldn’t do anything without it.

  23. Tom English: You do if you believe that Giuseppe Sermonti has anything to tell you.

    Winston Ewert clearly needs me to tell him “Why a Bug is not a Weasel.” Hopefully I’ll get that done… this year. Shoveling shit is not nearly as easy as blowing it out your ass. At least I know now that a few people get the pun.

    I would believe Sermonti over any evolutionist. That is a given.

  24. Tom English:
    Breaking News. Discovery Institute to publish Why a Horse Is Still Not a Fly.

    No the next book will be “Why Evolutionists are Assholes”

  25. petrushka: Either Denton is in the mainstream (in which case his title should be, Evolution, A Theory Making Steady Progress), or he is wrong about the lack of explanations.

    Evolution isn’t a theory and five year olds have explanations too. And they are on the same level as evolutionary explanations

  26. Frankie: Evolution isn’t a theory and five year olds have explanations too. And they are on the same level as evolutionary explanations

    I notice you never seem to talk about ID or the entailments of ID, just about what evolution is not and curses.

    Inference to best explanation says, um, what?

  27. Frankie: The solution is the bulk of the cytoplasm and the proteins couldn’t do anything without it.

    And I’ll add the unspoken and therefore Jesus for you.

    But so what? I think you’ll find if you simply say what you said there but then add another sentence that explains why the previous sentence supports ID you’ll be much more convincing in your arguments.

    As it stands, you might as well have added ‘and if the planet never formed, no proteins at all’ as all you’ve said is a statement of fact. It neither confirms nor disconfirms evolution or ID.

    You keep forgetting to add the argument bit when you are making an argument! Please try harder.

  28. petrushka: Either Denton is in the mainstream (in which case his title should be, Evolution, A Theory Making Steady Progress), or he is wrong about the lack of explanations.

    I’d say Denton is the one who lacks explanation altogether.

    Denton is the one who imagines, basically, that a Designer picks the shape of the leaves because Designer just grooves on the shapes.

    What kind of pointless “explanation” is that? With that “explanation”, life could have consisted of anything. Ugly, beautiful, functional, arbitrary, shaped, shapeless, plain, baroque: anything could have been what the Designer grooved on.

    Once you accept the idea that god twiddles its little fingers and draws out the edges of the maple leaf — just because it thinks those look prettier — then anything goes. What about plain boring straight leaves of grass? Yep, them too, god the artist twiddles its little fingers and creates bajillions of flat plain leaves because it thinks they make a good background for other items. Or whatever.

    Can’t easily figure out why something in biology appears the way it does? Don’t bother trying to explain it: god the artist wanted it that way.

    That’s not any ways equivalent to what un-goddy biologists like Wagner do with the evidence of structure, form, and development controlled by heritable genes.

  31. petrushka: Either Denton is in the mainstream (in which case his title should be, Evolution, A Theory Making Steady Progress), or he is wrong about the lack of explanations.

    I’m not sure that’s an “either/or”. And it isn’t clear which “mainstream” is being referenced.

    Denton seems to see the theory of evolution as “an historical narrative describing a series of contingent events”. Perhaps all creationists see it that way. I see the theory as an account of ongoing processes, rather than as an historical narrative. I do think that different perspective makes a huge difference.

  32. Neil Rickert: Denton seems to see the theory of evolution as “an historical narrative describing a series of contingent events”. Perhaps all creationists see it that way. I see the theory as an account of ongoing processes, rather than as an historical narrative. I do think that different perspective makes a huge difference.

    I see evolution as a regular process that amplifies the effects of some contingent events.

  33. Mung,

    Actually, Allan complains because I do it too much.

    No I don’t. I complain at reams of copy-paste (especially if I’ve seen the same shit a dozen times).

  34. Mung,

    Aren’t there some reactions that produce water molecules?

    I believe so. There are processes that produce elements too. Your point?

  36. So, is Frankie saying that because atoms aren’t manufactured by genes, that’s what gives cytoplasm some kind of privileged status, a reflexive dominance?

    Just the usual bizarre claptrap. A cell divides, each daughter gets approx 50% of the material in it. The rest comes from outside, imported by proteins that are made by genes, or manufactured inside, ditto. Divides again, same thing happens. Pretty soon there are none of the original cytoplasm molecules left.

    Conversely if you have a sexual species you have cytoplasm from two parents, four grandparents, 8 great grandparents … How come we don’t burst? Which one wins in the Great Cytoplasmic Lottery? (hint: it’s none of ’em)

    In short, how in hell does cytoplasm supplant genetics in inheritance?

  37. Allan Miller: I believe so. There are processes that produce elements too. Your point?

    You think everything in the cytoplasm can be accounted for by genes. Except perhaps water. And salts. The water in the cytoplasm probably comes from genes too. The salt probably does as well. That’s my point.

  38. Do people here just not follow a line of reasoning unless it’s all right there in front of them from start to finish?

  39. Mung,

    Do people here just not follow a line of reasoning unless it’s all right there in front of them from start to finish?

    When the reasoning is as bad as yours typically is, we need to see it laid out explicitly. It’s often hard to reconstruct the long series of mistakes that lead you to your erroneous conclusions.

    When we’re dealing with better reasoners (who are also typically better communicators), it’s easier to fill in the blanks.

  40. petrushka:
    Summary of Jerry Coyne’s takedown of Noble:

    1. What we mean by “random” is that mutations occur regardless of whether they would be good for the organism. (Shapiro says this, if you actually read his book)

    And that is also how Denis Noble uses the term. In fact in the paper that Coyne references Noble writes:

    Randomness cannot therefore be defined independently of asking ‘random with respect to what’? I will use the definition that the changes are assumed to be random with respect to physiological function and could not therefore be influenced by such function or by functional changes in response to the environment. This is the assumption that excludes the phenotype from in any way influencing or guiding genetic change.

    You continue:

    2….when we map adaptations in organisms, they invariably turn out to be changes in the DNA

    Few would argue that phenotypal changes are accompanied by changes in the DNA. It is obvious that any change in proteins must involve changes in DNA.

    3. ….adaptive methylation, such as “parental imprinting”, in which the father or mother contributes differently methylated DNAs that do different things in the zygotes and offspring, is based on instructions in the DNA itself.

    These researchers from the University of Tsukuba. are not so sure of themselves:

    The mechanisms for imprinting are not fully understood, but they involve modifications to the DNA that are removed and then reset ‘de novo’ during the creation of eggs and sperm. These modifications are termed epigenetic modifications, as the DNA sequence itself is not altered.

    In one example epigenetic tagging depends on whether or not a mother rat licks and grooms her offspring. We can agree that DNA is involved. But can you tell me in what way is this based on instructions in the DNA?

    4. I know of not a single adaptation in organisms that is based on such environmentally-induced and non-genetic change.

    I do not disargee that changes in organisms involve genetic changes, but correlation does not equal causation. For example, there is a correlation between the form of this sentence and changes in the circuitry of the computer I am using, this does not mean that the computer’s circuitry is the cause of the form that this sentence takes.

    5. For an adaptation to become fixed in a population or species, it must be inherited with near-perfect fidelity. And that is not the case for all environmentally-induced modificatons of DNA. They eventually go away.

    This does not challenge the point that Noble was making DNA is not the sole transmitter of inheritance and that information does not just flow in one direction as was originally conceived in the Modern Synthesis.

    6. … those big jumps or horizontally-transmitted changes in DNA must still obey the rules of population genetics. They are equivalent to mutations, but they’re just BIG mutations.

    And you know that these major changes are random with respect to the effect on the organism how?

    7. Further, we can make “diploid hybrid species” in the lab by hybridizing two species and letting their mixed and somewhat incompatible DNA sort itself out over several generations. What you can get is a non-polyploid hybrid species that is reproductively isolated from both parental species—that is, a new lab-produced species.

    And what exactly is this supposed to refute in anything that Noble said? Where did he say that we have not been able to produce new species? In fact in the video he talks of an experiment which crosses a carp and a goldfish and obtains an adult which has traits of both.

  41. i notice that Coyne does not even mention Noble’s examples of genetic networks. Does he have any arguments trying to refute Noble on these?

    Here is something I found from Science Daily
    Scientists map changes in genetic networks caused by DNA damage

    Using a new technology called “differential epistasis maps,” scientists have documented for the first time how a cellular genetic network completely rewires itself in response to stress by DNA-damaging agents.

    If you cannot see that this is difficult to explain from a gene centric point of view then I don’t know what else to say.

  42. Goldfish are a species of carp. There are many species of carp. This is a category error, like saying we’re crossing a dog with a mammal.

  46. Charlie: really complicated science babble; therefore goddidit.

    What a really original idea. I wonder why no one ever thought of that one.

    How do we know that mutatations are random with respect to fitness?

    I dunno, maybe by running a controlled experiment with sealed populations for 30 years or so.

    Alternatively, one could take a steaming pile of creationist bullshit and pretend it is an opinion.

  47. Flint:
    Goldfish are a species of carp. There are many species of carp. This is a category error, like saying we’re crossing a dog with a mammal.

    Did you watch the video? If you did you will have noticed that the parent fish were different species. So it’s like saying we’re crossing a dog with a mammal other than a dog.

  48. petrushka:
    Charlie: really complicated science babble; therefore goddidit.

    What a really original idea. I wonder why no one ever thought of that one.

    How do we know that mutatations are random with respect to fitness?

    I dunno, maybe by running a controlled experiment with sealed populations for 30 years or so.

    Alternatively, one could take a steaming pile of creationist bullshit and pretend it is an opinion.

    When in doubt hit them with the “what you are really saying is goddidit” retort. I am afraid it is you who gets 0 out of 10 for originality.

    “How do we know that mutatations are random with respect to fitness?”

    Please read what I wrote. I’m surprised that Flint hasn’t picked you up for saying that mutations are big jumps or horizontally-transmitted changes in DNA.

  49. Mung,

    You think everything in the cytoplasm can be accounted for by genes. Except perhaps water. And salts. The water in the cytoplasm probably comes from genes too. The salt probably does as well. That’s my point.

    Your point is wrong, then. Much water and salts come in/out through passive mechanisms, though there is obviously a relation, because active transport of one can cause passive transport of the other. But in neither case are the molecules made by the cell’s genes.

    Cells spend a fair bit of energy evacuating these things, and a fair bit more bringing them in.

    Do people here just not follow a line of reasoning unless it’s all right there in front of them from start to finish?

    If people don’t understand your point, it is not always their fault.

    In this case, your clarified point seems irrelevant, which may be why I didn’t get it. What proportion of the water molecules in a cell come directly from genetically-mediated reactions? [eta: via RNA/protein, I feel the need to add for the benefit of certain parties who might think I’m saying genes perform reactions].

  50. CharlieM,

    Did you watch the video? If you did you will have noticed that the parent fish were different species. So it’s like saying we’re crossing a dog with a mammal other than a dog.

    If you’re crossing one species with another, and the offspring are fertile, they aren’t really different species, biologically speaking, even if we choose to name them so (dumb archetypal essentialists that we are). You can cross dogs with jackals.

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