Sunday, May 22, 2011

Junk & Jonathan: Part 4—Chapter 1

I received a copy of the book a few days ago and this is my first posting on its contents. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

This is a very small book. There's only 114 pages of text—it's more like a large pamphlet than a book. If I'd read it from front to back in one sitting it would only have taken an hour or so. But I couldn't read it in one go because nobody can put up with IDiot rhetoric for that long!

Chapter 1 is The Controversy over Darwinian Evolution. It has nothing to do with junk DNA.

Wells begins by telling his readers that evolution is a fact. By that he means "microevolution." Wells doesn't believe in macroevolution or common descent and he even challenges the evidence for speciation. As usual, he supports his claims with selected quotations from scientists.
Sixty year after Dobzansky wrote this, biologists had still not observed the origin of a new species ("speciation") by natural selection. In 1997, evolutionary biologist Keith Stewart Thomson wrote: "A matter of unfinished business for biologists is the identification of evolution's smoking gun," and "the smoking gun of evolution is speciation, not local adaptation and differentiation of populations."
Wells is telling his readers that as long as biologists have not directly observed a new species forming then speciation has not been demonstrated. This rules out all evidence from the fossil record and all evidence from molecular phylogeny. Nice trick.

Problem is, there's lots of lots of evidence for speciation, including some examples where speciation has been caught in the act. Wells, like most IDiots, doesn't understand how evolution works. He seems to think that new species will form overnight and that all biologist have to do is keep their eyes open and record the examples.

I don't know for sure whether Wells intends to emphasize speciation by natural selection when he claims that, "biologists had still not observed the origin of a new species ("speciation") by natural selection." If that's his intent then it's true that there are very few examples of true speciation (biological species concept) that can be attributed directly to natural selection. As Jerry Coyne points out, reproductive isolation is mostly due to accident (random genetic drift) and not natural selection [The Cause of Speciation]. That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation. [UPDATE: Coyne and some commenters have corrected me. Coyne actually does think that most speciation is due to natural selection. I'll stick with Futuyma as my authority. He's much more open to the idea of speciation by random genetic drift (Evolution 2nd ed. p. 447)]

There are two possibilities here. Either Wells is deliberately misleading his readers by emphasizing that speciation must occur by natural selection or he's ignorant of modern evolutionary theory. Since most IDiots have a concept of evolution that dates back to the nineteenth century, I'll go with the second explanation. However, there's almost certainly an element of deception in his remarks since Jonathan Wells has a long history of deliberately misrepresenting evolution.

Theme

Genomes
& Junk DNA
So, Wells is dead wrong about the first point in his book. There's abundant evidence of speciation (and macroevolution) and, furthermore, modern evolutionary theory does not attribute speciation exclusively to adaptation (i.e. there's more to evolution than Darwinism).

The importance of Wells' rejection of macroevolution will become obvious later on in the book when he argues that Intelligent Design Creationism does not rule out common ancestry. He agrees that someone like Michael Behe can believe in common descent and still be a card-carrying IDiot.

By the way, Wells is clever enough to cover his bases in case speciation is ever observed.
Of course, even if scientists eventually observe the origin of a new species by natural selection, the observation would not mean that natural selection can also explain the origin of significantly new organs or body plans. But the fact that scientists have not observed even the first step in macroevolution means that "evolution's smoking gun" is still missing.
The rest of the chapter (three pages) is a re-hash of arguments Wells made in Icons of Evolution and elsewhere.
  • The Cambrian Explosion "contradicts Darwin's theory that major differences should arise only after millions of years of evolution ...."
  • Molecular evolution isn't accurate: "molecular evidence is plagued with inconsistencies." The rejection of molecular evidence as unreliable is going to cause problems for Wells later on since he relies on it for some of his arguments about junk DNA. As usual, the IDiots want to have their cake and eat it too.
  • Homology is a circular argument, according to Wells, so you can't use homology as evidence for evolution. That's correct. Similarity is the evidence and homology is the conclusion. This flaw in Wells' reasoning has been pointed out to him repeatedly over the past decade but he ignores all criticism and continues to use arguments that have been refuted.
  • The Haeckel drawings were fakes and, "The truth is that vertebrate embryos start out looking very different from each other, then they converge somewhat in appearance midway through development before diverging as they mature." This has nothing to do with junk DNA so I won't discuss the massive amount of embryological evidence for evolution.
Wells closes with,
So microevolution is a fact, supported by overwhelming evidence, but macroevolution remains an assumption, illustrated with icons that misrepresent the evidence or rely on circular reasoning. The icons are not science, but myth.
This sets the tone for the rest of the book. Even though it is filled with references to the scientific literature there's never any discussion of alternative hypotheses or conflicting data. This is not a book where the author wants to inform his readers about the exciting controversies and conflicts within science. This is a book where the author wants to promote creationism by attacking and misrepresenting evolution using faulty logic and untruths.

The next paragraph is quite interesting. He invokes the beliefs of Americans as support for his claims. Apparently they're much more perceptive that the typical evolutionary biologist. (I wonder what he thinks of Australians and Europeans?)
This may be one reason why—despite the Darwinists' near-monopoly over science education—most Americans still reject the doctrine that human beings evolved from ape-like ancestors by unguided processes such as random variation and survival of the fittest.
I think this means that Wells also rejects common ancestry. If so, it will mean that he can't use it to support any of his arguments later on in the book, right?

Finally, at the very end of the chapter we get to the point,
In the 1950s, neo-Darwinists equated genes with DNA sequences and assumed that their biological significance lay in the proteins the encoded. But when molecular biologists discovered in the 1970s that most of our DNA does not code for proteins, neo-Darwinists called non-protein-coding DNA "junk" and attributed it to molecular accidents that have accumulated in the course of evolution. Like peppered moths, Galapagos finches, Darwin's Tree of Life, homology in vertebrate limbs, and Haeckel's embryos, "junk DNA" has become an icon of evolution. But is it science of myth?
I've discussed Wells' ignorance of history in previous postings but, for the record, here are the facts.
  • By the 1970s molecular biologist were well aware of the fact that non-protein coding genes existed (e.g. ribosomal RNA genes, tRNA genes etc.)
  • By the 1970s molecular biologists knew of several functions of DNA sequences that weren't genes. Origins of replication and regulatory sequences were well-known but there were others.
  • Even in the 1970s no knowledgeable molecular biologist could ever defend the idea that all non-coding DNA was junk. (It's true that there were some stupid scientists who weren't aware of tRNA genes and regulatory sequences and made silly statement because of their ignorance but they don't count.)
  • By the 1970s junk DNA was a fact. The scientific controversy was over how much of our genome is junk. Is it the majority or only a small percentage?
  • By the 1970s knowledgeable evolutionary biologists were well aware of the fact that most of our genome was mutating and evolving as though most changes were neutral (genetic load arguments). This didn't mean that most of our genome was junk but it did mean that the sequence couldn't be important or we would never be able to tolerate the genetic load. This was not common knowledge among biologists—still isn't.
  • By the 1970s most molecular biologists were aware of the so-called "C-value paradox" where very closely related species have very different genome sizes. They correctly interpreted this to mean that the species with the large genomes probably didn't need all that extra DNA. (Up until now, Intelligent Design Creationists have not offered a reasonable answer to The Onion Test. Wells tries on Chapter 8.)
  • The proponents of large amounts of junk DNA in our genome would hardly ever have referred to themselves as "Darwinist" or "neo-Darwinists." In fact, they tended to be among those evolutionary biologists who opposed adaptationism and favored Neutral Theory and random genetic drift. Pluralist concepts were much more compatible with the idea of significant amounts of junk DNA than strict "Darwinist" interpretations of genome evolution.


49 comments :

  1. When I read the part about not observing speciation "by natural selection", my first thought was that Wells wanted to discount any examples of speciation by artificial selection. That way, he could claim that any evidence for new species arising during controlled selection experiments doesn't count. That wouldn't be "natural" selection, it would be artificial selection by intelligent agents (humans), thus proving ID.

    Also, I think Wells left himself a loophole on common ancestry. He says Americans reject the doctrine that human beings evolved from ape-like ancestors by unguided processes. That doesn't technically rule out that humans arose from ape-like ancestors due to direct interventions from the "Intelligent Designer" (wink).

    Of course, many (most?) Americans would reject that possibility as well....

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  2. Wells, like most IDiots, doesn't understand how evolution works.

    In one of his previous posts prof. Moran accused of "not understanding evolution" some scientists who published in "peer reviewed" about how our expaction and knowledge of how many genes there are in human has changed over time.

    Now there is a controversy regarding "group selection" - E.O.Wilson has brushed up the concept recently. The accusation of "not understanding evolution" between group selectionsts and "selfish gene" proponents are not rare.

    One wonders who is the guy who really "understand evolution."

    It would also help if prof. Moran has brought up some "speciation in action". I hope it would not be "ring species"?

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  3. I think this means that Wells also rejects common ancestry. If so, it will mean that he can't use it to support any of his arguments later on in the book, right?

    If Wells can show an inner contradiction of the theory of evolution his own opinion doesn't matter. He can use every part of the theory against the theory.

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  4. VMartin writes:

    The accusation of "not understanding evolution" between group selectionsts and "selfish gene" proponents are not rare.

    Having read some of your blog posts, I think if there is one thing on which group selectionists and selfish gene proponents might agree, it is that you don't understand evolution.

    Not that I claim to have any deep understanding of the subject myself, but anyone who thinks a bunch of different coloration patterns on ladybugs poses a problem for the theory of evolution is just not thinking clearly. (Consider the fact that when Darwin wrote he was fully cognizant of, and took into account, the multitude of variations available through artificial selection - i.e., animal breeding - and you will understand how ridiculous it is to say wide variability of form poses a challenge for evolutionary theory more than 150 years later.)

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  5. Ooh, ooh, what does Wells say about The Onion Test???? Does he even acknowledge genome size variation?

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  6. Larry --

    I was with you until the last point:

    Larry: The proponents of large amounts of junk DNA in our genome would hardly ever have referred to themselves as "Darwinist" or "neo-Darwinists." In fact, they tended to be among those evolutionary biologists who opposed adaptationism and favored Neutral Theory and random genetic drift. Pluralist concepts were much more compatible with the idea of significant amounts of junk DNA than strict "Darwinist" interpretations of genome evolution.


    There are lots of evolutionary biologists (and were by the 1970s) who would attribute much of the evolution of the noncoding part of the genome to random genetic drift and neutral mutation. But these same people see lots of natural selection (as well as some more neutrality) in the evolution of the coding sequences and their control sequences. They would argue that the changes in observable morphology (for example) reflect large amounts of natural selection. Your phrasing sets up an opposition between agreeing that lots of junk DNA exists and evolves neutrally, and saying that (say) the elephant's trunk is strongly affected by natural selection. Did you intend that?

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  7. Larry writes:


    The proponents of large amounts of junk DNA in our genome would hardly ever have referred to themselves as "Darwinist" or "neo-Darwinists."

    Sorry, Larry, but you are a Darwinist. You may claim that stochastic processes, like random genetic drift, are significant (Kimura's theory) but you don't believe that natural selection and adaption is not the driving force behind macroevolution.

    It is just that Darwinists want to have it both ways. They want to claim that evolution is the product of differential viability and that junk and waste is part and parcel of evolutionary change.

    If you are not a "Darwinist" then what are you? A Lamarckian?

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  8. Joe Felsenstein says,

    There are lots of evolutionary biologists (and were by the 1970s) who would attribute much of the evolution of the noncoding part of the genome to random genetic drift and neutral mutation. But these same people see lots of natural selection (as well as some more neutrality) in the evolution of the coding sequences and their control sequences. They would argue that the changes in observable morphology (for example) reflect large amounts of natural selection. Your phrasing sets up an opposition between agreeing that lots of junk DNA exists and evolves neutrally, and saying that (say) the elephant's trunk is strongly affected by natural selection. Did you intend that?

    No, I didn't mean that.

    What I meant was that most adaptationists are skeptical about the idea that a huge percentage of our genome is junk. They tend to be among those who argue for function.

    Most pluralists are more comfortable with the idea of massive amounts of junk in our genome because that doesn't conflict with their view of evolution.

    There is a genuine scientific controversty (as you well know) over the amount of our genome that's junk. All I'm saying is that the two scientific sides of that debate tend to split along the adaptationist/pluralist lines, as expected.

    What annoys me is when the IDiots claim that junk DNA was predicted by Darwinism and is used as evidence for Darwinism. I see "Darwinism" as equivalent to adaptationism (emphasis on natural selection) and the "Darwinist" view did not predict that most of our genome would be useless junk.

    Furthermore, if every nucleotide of our genome proved to be functional that would be powerful support for an adaptive explanation of evolution (i.e. Darwinism). This is not what Wells and the other IDiots say. They say that Darwinism required junk DNA and Darwinism will be discredited if the junk turns out to be useful.

    What is your position? You often tilt toward the adaptationist camp so you could serve as a test case. Do you think that more than half of our genome is useless junk that could be dispensed with?

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  9. See what I mean.

    Joe Felsenstein, the father of modern population genetics, wants to have his cake and eat it.

    On the one hand, he claims natural selection is active on the coding and regulatory sequences of DNA ( nobody would disagree) while not so concerned if relatively unimportant non-coding stuff clutter up the genome by way of random drift etc.

    But it doesn't work like that. Selection is all-pervading. If 50% of the genome were really useless, selection would whittle it down, as it has done in countless examples where even something functional imposed too high a metabolic cost on the organism.

    Moreover, as Felsenstein must surely realize, neutral evolution is most effective in small populations. I would argue that any real "junk" can only accumulate in relatively isolated populations. But is the maize plant, which is 70-80% made up of retrotransposons, a good example of this condition? I think not.

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  10. NickM asks,

    Ooh, ooh, what does Wells say about The Onion Test???? Does he even acknowledge genome size variation?

    Be patient. I'll get to it when I cover Chapter 8. Or, you could buy your own copy and find out—I know you're tempted even though it supports the Discovery Institute. :-)

    You can buy it on Amazon.com for only $9.75. I had to pay $14.94 (US) (=$14.41 Cdn).

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  11. kereng says,

    If Wells can show an inner contradiction of the theory of evolution his own opinion doesn't matter. He can use every part of the theory against the theory.

    Wells is making the case against junk DNA. Scientists argue that the presence of similar bits of junk DNA in the same locations in the chimpanzee genome and the human genome is evidence of common descent since there's no other reason for those useless bits to be in both genomes.

    Wells doesn't believe in common descent so he has to argue that this fact is irrelevant. (It would be nice if he could offer another explanation but he doesn't.) In this case, Wells doesn't accept the evidence of sequence conservation because he rejects the idea that chimps and humans have a common ancestor.

    On the other hand, later on in the book he tells us that certain non-coding parts of the genome are conserved and this is strong evidence for it being functional.

    Isn't that strange logic?

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  12. Bozorgmehr (Atheistoclast) says,

    If you are not a "Darwinist" then what are you? A Lamarckian?

    I'm a supporter of modern evolutionary theory with a pluralist worldview [Why I'm Not a Darwinist].

    Try and keep up. I know it's hard but you aren't making much of an effort.

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  13. I'm a supporter of modern evolutionary theory with a pluralist worldview

    No such thing as a "pluralist" in evolutionary biology and theory.

    All Darwinists, Dawkins included, attribute a lot to random drift and stochastic processes - especially at the molecular level.

    But, as Joe Felsenstein just remarked, the elephant didn't get its trunk (or the giraffe its long neck) by accident. There are 3 possibilities for this development:

    1) Darwinian natural selection

    2) Intelligent design

    3) Lamarckian acquistition

    I hope you can one day select option 2.

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  14. Larry said:What is your position? You often tilt toward the adaptationist camp so you could serve as a test case. Do you think that more than half of our genome is useless junk that could be dispensed with?

    I vote for much more than half being "junk" (having its sequence not constrained). Maybe 80-90%. I am impressed by the mutation load problem otherwise.

    Your terminology is controversial: I don't think the terms "adaptationist" and "pluralist" for this distinction are standard. They're your attempt to make the distinction, but they are yours. "Darwinist" is of course even more controversial: does it mean someone who thinks adaptation is generally explained by natural selection? Or someone who is a pan-selectionist with respect to the genome? Or, as the creationists would have their followers believe, someone who is a mindless follower of a long-dead guru? I'm the first kind of Darwinist but not the latter two.

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  15. I think that Larry's description of adaptationists being against junk DNA and neutralists being for it might be an adequate description of at least peoples' "instincts" in the 1960s and early 1970s. But once everyone admitted that lots of neutral evolution happened, I think the differences narrowed a lot, since everyone could see that only a small proportion of the genome was conserved.

    The above I think would describe the population of population geneticists, who know about mutation load and conservation and neutrality etc. A fair number of biologists writ large, especially molecular biologists, may still fit into the "naive instinctual adaptationist" category, which Larry often criticizes -- but which, ironically, undermines Wells's claim that Darwinian assumptions lead to the conclusion of junk DNA, when in reality in their most naive form, they lead to the opposite. (And, this naive adaptationist assumption is itself where a fair amount of the naive "all junk has function!" stuff in the press comes from.)

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  16. @NickM,

    If you read the scientific literature you'll see far more criticism of junk DNA than defenses. It's very easy to get the impression that most molecular biologists are very skeptical of the concept that most of our genome is junk.

    There are quite a few prominent scientists who write as though the concept of junk DNA has been discredited and those articles seem to get by peer review without any problems.

    The only data I have is a poll from several years ago: What Did Biologists Really Say About Junk DNA?.

    Maybe it's time for another one.

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  17. I'd say that there certainly are many molecular biologists who have a hard time believing that most of the genome is "junk". Part of the reason is that they think there must be all sorts of complex mechanisms hidden out there ... and needing millions of dollars of new grant money to discover.

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  18. Atheistoclast states:

    "Selection is all-pervading. If 50% of the genome were really useless, selection would whittle it down, as it has done in countless examples where even something functional imposed too high a metabolic cost on the organism."

    That doesn't necessarily follow. Depends on the fitness cost associated with excess DNA, as well as the rate at which new junk accumulates.

    Preventing the accumulation of junk is not without cost itself. Which costs more? Replicating extra DNA, or maintaining exquisitely high fidelity mechanisms to prevent or eliminate junk?

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  19. Larry:
    Or, you could buy your own copy and find out—I know you're tempted even though it supports the Discovery Institute. :-)

    DON'T. Just wait until used copies become available.

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  20. Yes, Larry - please set the gussied up electrician straight!

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  21. Bozer:
    If 50% of the genome were really useless, selection would whittle it down, as it has done in countless examples where even something functional imposed too high a metabolic cost on the organism.


    How high a metabolic cost is there for a genome that is 50% 'junk'?

    How did you calculate it?
    I have read (don't recall the source)that a typical cell expends more energy simply moving materials across their membranes in an hour than they do replicating their genomes once during their lifetimes, providing that they even divide.

    Does your calculated energy expenditure for a junky-genome being replicated outweigh the normal energy expendictures for a cell's housekeeping activities?

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  22. If in addition to surviving, you've got enough energy to play Nintendo, then you've got enough spare energy to evolve.

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  23. How about speciation by hybridization and polyploidy? It's not only been observed and well documented, but actually repeated experimentally.

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  24. A quibble: Jerry Coyne does not say that speciation is mostly due to drift. As his book (Speciation; Coyne & Orr) makes clear, reproductive isolation seem most often to be caused by selection, and drift takes much longer.

    What Jerry actually says is somewhat different: that the isolation does not result from selection *whose target is isolation*, but as a byproduct of different selection acting on geographically separated populations.

    So yes, speciation results from selection. But it's an accidental result of that selection, not its focus.

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  25. "most adaptationists are skeptical about the idea that a huge percentage of our genome is junk"

    Citation, as they say, needed. Whence do you pull such pronouncements?

    "You often tilt toward the adaptationist camp so you could serve as a test case. Do you think that more than half of our genome is useless junk that could be dispensed with?"

    I see Dr. Felsenstein has answered for himself, but as someone who Dr. Moran used to consider a rank 'adaptationist', I'll say: "sure". Evidence: pufferfish.
    I don't understand why this would surprise you. We adaptationists are not ignorant of molecular evolution, we just don't care much. Phenotypes are a lot more interesting to us.

    I am surprised to hear the (unsupported but several-sourced) claim that 'moleculr biologists' might be junk-DNA denialists as a group, though.

    "If 50% of the genome were really useless, selection would whittle it down, as it has done in countless examples where even something functional imposed too high a metabolic cost on the organism."

    Assumes facts not in evidence. The vast majority of a cell's energy budget is spent on ion transport and protein synthesis, and nothing else is evern close.

    Also, it's worth pointing out as a heuristic that even if large amounts of DNA are functionless junk at the molecular level, its accumulation could still have phenotypic consequences (e.g. cell size, metabolic rate) that could then be subject to selection.

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  26. Wasn't the big blue box with "Discovery Institute Press", a clue to anyone about what this book was?

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  27. In typical eukaryotes, the metabolic cost of DNA replication (only occuring periodically prior to cell replication) is then and only then about 2% of the cell's energy budget. Protein synthesis in comparison routinely accounts for ~75% of the cell's energy budget.

    N. Lane and W. Martin, The energetics of genome complexity, Nature 467 (2010)

    This information has previously been pointed out to Bozorgmehr, but he has somehow "forgotten".

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  28. John Harshman says,

    A quibble: Jerry Coyne does not say that speciation is mostly due to drift.

    I disagree. Read: The Cause of Speciation.

    Coyne can speak for himself but I interpret his writing to mean that the actual evolution of reproductive isolation is rarely due to selection, although he's very interested in the rare cases where this seems plausible.

    It's quite difficult to even imagine situations where geographically isolated populations could undergo selection for the inability to interbreed. The evolution of reproductive isolation is an accident due to fixation of certain alleles by random genetic drift [What Causes Speciaiton?].

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  29. If Wells can show an inner contradiction of the theory of evolution

    He can't.

    his own opinion doesn't matter

    LOL! In that case, we can ignore the vast majority of the book, especially the quoted part where he offers his disingenuous opinion as to why Americans reject evolution.

    He can use every part of the theory against the theory.

    Misrepresentation -- he's using his opinion about part of the theory against the theory.

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  30. The Cambrian Explosion "contradicts Darwin's theory that major differences should arise only after millions of years of evolution ...."

    The Cambrian "explosion" was, what, 50-100 million years long? So Darwin's guesstimate that it would take millions of years appears to be pretty good. Someone needs to tell the IDiots that "explosion" refers to the number of new species, not to the speed of their appearance.

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  31. But it doesn't work like that. Selection is all-pervading. If 50% of the genome were really useless, selection would whittle it down, as it has done in countless examples where even something functional imposed too high a metabolic cost on the organism.

    Actually I will even go one step farther. The cost is like your computer CPU, to use that as an example. If you have an ENIAC, you are limited by what it can access in memory (number of switches that existed), what it can access in storage (it didn't have any), and how much it can do at once (one thing, and one things only). If you have a quad core 64-bit processor... Well, lets put it this way, modern machines have terabyte drives, can, in theory, support close to a terabyte of RAM, and can run a lot of things at the same time.

    Now.. You will note there are limitations anyway. We can't cram enough cores into one to run *everything* you might ever install at one time. There is also, likely, a functional limitation on how big a single cell could get too (the size determining how much you can do at one time). Even the fact that we use quad cores, instead of just a really fast single core, is a limitation. We had to go multi-cellular to make it work, in effect. Even computers have such limits, so you can't ever get as much RAM as you can in theory use, for example.

    But, living cells have other limitations that computers don't. A lot of it has to be running, constantly, in parallel, and swapping of active and inactive stuff has to go one all the time, basically like a CPU swapping out data between various places. If you even *tried* to run a modern OS on an 8086 (1Mhz), it would take a year just to load, and another year to start an application. On a modern machine, you can do all of that *very fast*.

    But, here is the point. We have specialized stuff that helps. We have GPUs, to handle the graphics, we have FPUs, to handle math, we have special bits that provide easier data movement to and from the various places it needs to go. In short, even a modern quad core, without all that stuff, would be 100 times slower than it is.

    So, what does that have to do with DNA? Well, up to the physical limit, you can expand memory and storage without limit (size of the cell and nucleus). There is no certain idea as to what the upper limit is, though some things may have gotten close. But, to do this, you need power to push the system, and that comes from mitochondria. They give us what single cell organisms don't generally have. A power source that lets the thing be a quad core, lets it have 1 terabyte of RAM, lets it have 2 terabytes of storage, and lets it move all this stuff, without worrying about how much of it is useful or not.

    Now, look at your modern computer, as an organism. Instead of running 1-2 very specialized processes, with minimal, or even no, display, streamlined to do specific tasks, and where you have to be *very* careful that everything fits in the space available, you have mad variation in display, thousands of independent functions, etc. And, buried in all of that are office documents you never finished, notes you made and forgot about, bits and pieces of stuff that where once working, but got replaced, viruses that got in, etc. Piles of stuff that either does nothing now, but did at one time, or never did anything, or where experimental, or just change the color of the display cursor.

    Multi-cell organisms, with the inclusion of mitochondria, gained the equivalent of a Hemi engine, while the single cell organisms remained stuck with bicycle peddles. There is so much waste energy available that the effect is like loading 4 people in your car, instead of 2. Hardly enough to require worrying.

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  32. Larry, you are misreading Coyne. Even the quote you give in The Cause of Speciation", if you read closely, is a paraphrase of what I said (or, rather, what I said is a paraphrase of Coyne). Read his book. Selection is a much stronger cause of the sort of divergence that results in speciation than drift is. See especially Chapter 11, from which I quote: "There is now considerable evidence that natural ans sexual selection pay a role in speciation. This evidence derives from a wide variety of studies: laboratory experiments on divergent selection, molecular analyses, comparative contrasts, and, perhaps most important, case studies. In contrast, firm evidence for the role of genetic drift in speciation is rare. Indeed, it is hard to point to any examples other than chromosomal speciation in plants and mice, and unusual cases of shell coil-reversal in snails."

    And, later in the same paragraph: "It appears, then, that at least one important debate has been settled: selection plays a much larger role in speciation than does drift."

    You may not agree with Jerry (though I do), but let's not confuse his position. (Unless it's changed radically since 2005, and I'm unaware of any such change.)

    I repeat that you are missing the distinction between selection having speciation as an accidental byproduct (what Coyne is arguing for) and selection that is directly aiming for speciation. It's the former that is common, while the latter is rare.

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  33. If the non presence of junk DNA were evidence in favor of intelligent design (it's not, but bear with me), the scientific reaction would not be to write a novella of misrepresentation, weasel-wording, and Humpty-Dumptifying bent on reducing the definition of "junk DNA" to mean "no DNA at all".


    It would be to conclude that design played a significant role in the development of prokaryotes, but little or no role in eukaryotes.

    Without a narcissistic view of the importance of eukaryotes - and particularly a certain eukaryotic species - the conclusion that design played a significant role in prokaryotes, but not eukaryotes would be extremely interesting, but by no means cause to take up an ideological sword against the dragon of junk DNA.

    As has been observed before, the War on junk DNA is yet another way in which an unwarranted desire for specialness exposes itself.

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  34. Kahegi, thanks for the great explanation. I would add that the mitochondria is the far greater enabled than multicellularity. There are some single-cell eukaryotes that have lots of junk DNA. (There are some amoebas with more DNA than humans, for example).

    But among prokaryotes (no mitchondria) DNA replication really does eat up a significant chunk of the energy budget, and extra useless DNA really does constitute a competitive disadvantage. And guess what? Bacteria have virtually no junk DNA.

    This is true even for aerobic bacteria, even the close relatives of the putative ancestors of the mitochondria. What eukaryotes have that no prokaryote does is the ability to have lots of mitchondria at once, and to make more when energy demands go up.

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  35. amphiox says,

    But among prokaryotes (no mitchondria) DNA replication really does eat up a significant chunk of the energy budget, and extra useless DNA really does constitute a competitive disadvantage.

    It's really hard to calculate the metabolic cost of junk DNA, even in prokaryotes.

    About 80% of the genome of a typical bacterium is transcribed and during a single life cycle there will be several hundred transcripts produced from each gene (on average). That's a lot of nucleic acid—about one hundred genomes worth. And it doesn't even begin to account for all of the other things going on inside the cell.

    Every generation, for example, the cell has to double the amount of membrane and cell wall and that's much more costly than replicating a bit of extra DNA.

    We don't know exactly why bacteria have so little junk in their genomes but it's unlikely to be a simple matter of metabolic cost.

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  36. These are great posts Larry,

    But I think you've got Coyne wrong. He's quite clear the he means the genetic differences that underly reproductive isolation in "secondary contact" usually arise from selection in one or both nascent species during their physical isolation. Chapter 11 of Speciation if very explicit about this.

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  37. @David Winter and John Harshman,

    I stand by my statement about Jerry Coyne and speciation. You should read his posting Reinforcement and the origin of species.

    Populations that are geographically separated will evolve independently by natural selection and random genetic drift. Many studies have focused on natural selection as the mechanism of divergence because that's the most interesting example to most biologists.

    Whether or not these diverging populations become "species" depends on whether they evolve mechanisms that ensure reproductive isolation.

    As Coyne says,

    Genetic barriers aren’t thought to arise for the purpose of keeping species distinct. Rather, they are usually thought to be evolutionary accidents: geographically isolated populations diverge genetically under natural selection or other evolutionary forces like genetic drift, and that divergence leads to the evolution of genetic barriers (mate discrimination, the sterility of hybrids, ecological differences, etc.) as byproducts of evolutionary change.

    The "byproducts" aren't selected.

    Coyne is interested in those rare cases where reproductive isolation is actually an adaptation that occurs when the two populations are in contact. This is an exception to the rule.

    Now I understand the models involving epistasis where it's possible that the different alleles affecting reproduction may have been adaptive in both populations but those are special cases of the more general phenomenon.

    Why is so important to fight against the idea that reproductive isolation (true speciation) might just be an evolutionary accident?

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  38. @David Winter and John Harshman,

    I've heard back from Jerry Coyne and you guys are correct!

    Here's what Coyne says.

    I think you 've got me wrong on two accounts (you can post this if you'd like):

    1. When I say that speciation is often (not always) an "accident"--I mean that reproductive barriers are accidental byproducts of genes that diverged for other reasons. That is not genetic drift, but pleiotropy, and

    2. As we show in chapter 11 of our book (Speciation, by Coyne and Orr), the evidence is that most reproductive barriers resulted from genes that diverged by natural selection, not genetic drift. Hypothesis that reproductive isolation results from genetic drift are not supported by either theory or experiment. Thus, as far as we can see, speciation usually esults from natural selection, although the reproductive barriers may be pleiotropic byproducts of the genes that diverged by selection. That does not rule out the involvement of drift completely, but we know of very few cases where it is implicated (a chance in chirality of snails, from right- to left-handed coiling or vice versa, may be one such case).

    So I think you're mistaken in saying that I think speciation results largely from drift. I think this comes from your misinterpretation of what I meant when I say that speciation is a "genetic accident."


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  39. Larry,

    I've heard back from Jerry Coyne and you guys are correct!

    You say that as if it's a shock to find me correct in anything. I assure you that I have been correct on several previous occasions in my life also. I even like to think that I'm correct much of the time. Of course, much of the time I agree with you.

    So let this be a lesson to us all to read our sources carefully.

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  40. Homology is a circular argument, according to Wells, so you can't use homology as evidence for evolution.

    I suppose that Wells likewise dismisses all evidence of neutral molecular evolution garnered from the statistical study of homologous genes that have no selective advantage, while that dismissal of evidence supports his claim that God doesn't make junk DNA.

    (I have not read all the comments, so somebody might have already noted this.)

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  41. As has been observed before, the War on junk DNA is yet another way in which an unwarranted desire for specialness exposes itself.

    Actually its dumber than that. The people doing the whining think that the way to get a point across is to just whine more, and louder, and find some big names to support them. Worse, if you tell them, "Where is your peer reviewed work.", they respond with peer reviewed whining and demands that we recognize the authority of which ever big names they imagine they have found (even if they have to misrepresent, misunderstand, and misuse, without permission, those big names). The one thing they don't do, since they don't have labs, or research, is actually support there assertions, without relying on cherry picking research of people that actually are doing such detailed examination of genetics, by showing what all the DNA they insist isn't really junk actually *does*.

    They actually think that just making up hypothesis, or assertion, like, "its front loaded stuff for use later, or in the past", or, "it has to do something, so you can't be right", or, "some badly done math by someone that, at this point, doesn't even qualify as an idiot savant, says its not possible for it to happen!", constitutes science. They literally seem to think that all real researchers do all day is the same thing, i.e., sit on their asses, writing papers, and thinking, instead of actual work. Its like telling your accountant he is, "over paid, doesn't do anything, anyone could figure out your taxes, no matter how complicated they are, and the reason is because God wouldn't have designed the tax code, and the economy, if it wasn't intended to be 'simple'. After all, those out of work people, failed companies and gross inefficiencies are all just myths!" If someone said that, other than maybe a Libertarian, they would be dragged off to the nearest loony bin, or, at the bare least, no accountant would sell them services ever again, if the insulted one could stop it. But, its the same stupid argument we get from IDiots about DNA.

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  42. Kagehi says,

    ... peer reviewed whining ...

    I love it! Can I use it?

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  43. Why is so important to fight against the idea that reproductive isolation (true speciation) might just be an evolutionary accident?

    I don't think it is, and I even think the way in which we study speciation might bias the our estimates of how important selection is. I just wanted to point out you were saying something different than Coyne would.

    As to the idea that reproductice isolation is equal to "true speciation"... species can can remain quite distinct even with odd insertion of genes from another lineage, so I don't think we should tie species-hood on any one character (even if lack of gene flow makes species, it doesn't have to be the sine qua non of them.

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  44. john Harshman says,

    So let this be a lesson to us all to read our sources carefully.

    I did read my sources carefully. What I didn't read was his book on speciation where he apparently was more clear about his real position.

    BTW, I do remember one or two times when you were right and I was wrong. :-)

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  45. As to the idea that reproductice isolation is equal to "true speciation"...

    This is a "no-macro evolution" argument, and totally stupid. It basically argues that if we see species change enough they don't breed, that doesn't mean that a lizard, in a few million years, won't produce both other *drastically different* lizards, and birds. Its just another variation of "god of the gaps". "Ah, ha! You proved that speciation has happened, but not that speciation of *kinds* does, until you do that, God can still be hiding in there some place, making both seals and dogs out of their 46 million year old ancestor. So there!"

    The same question on that comes up over and over, and they have no answer, "Why, if you can prevent two new species from breeding via isolation, is it then somehow, according to you, impossible for additional changes to make them completely different, over tens of millions of years of such isolation?" The answer seems to be, invariably, "Well, just because I say so!"

    Oh, and yeah, Moran, you can feel free to steal my "peer reviewed whining". ;) lol

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  46. Dr. Moran posted:
    "I don't know for sure whether Wells intends to emphasize speciation by natural selection when he claims that, "biologists had still not observed the origin of a new species ("speciation") by natural selection." If that's his intent then it's true that there are very few examples of true speciation (biological species concept) that can be attributed directly to natural selection. As Jerry Coyne points out, reproductive isolation is mostly due to accident (random genetic drift) and not natural selection [The Cause of Speciation]. That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation. [UPDATE: Coyne and some commenters have corrected me. Coyne actually does think that most speciation is due to natural selection. I'll stick with Futuyma as my authority. He's much more open to the idea of speciation by random genetic drift (Evolution 2nd ed. p. 447)] "

    How in the world could Dr. Moran, who presents himself as an expert, get the part that is stroked out wrong?

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  47. Dr. Moran originally posted:
    "That's in line with modern evolutionary theory and Coyne should know because he's one of the world's leading experts on speciation."

    Then suddenly Dr. Moran reverses himself completely and just goes on.
    This is absurd.
    Whatever Dr. Moran thinks modern evolution theory is, it can turn into its opposite and nobody is supposed to notice.

    Do we need any better example of the bankruptcy of evolution theory thinking?

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  48. According to Dr. Moran
    "There are two possibilities here. Either Wells is deliberately misleading his readers by emphasizing that speciation must occur by natural selection or he's ignorant of modern evolutionary theory."

    The other possibility is that Dr. Moran does not have a clue about what constitutes "modern evolutionary theory". As we can see by his breathtaking reversal in his post.
    But then who does a have a clue about what constitutes "modern evolutionary theory"? Apparently Coyne, who is "one of the world's leading experts on speciation".
    doesn't know.

    But Dr. Moran continues blithely on his way - lecturing the rest of us.

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  49. What is called a "junk DNA" is also a record of mutations that appear to be associated with the origin of species.

    "Junk DNA" represents mostly families of repeats generated by transposable elements (TEs). Fixation of TEs by genetic drift in small populations may cause them to "drift apart" and become founder populations for new species.

    See:

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3183009/

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