Pharyngula

Luskin on gene duplication

Casey Luskin has to be a bit of an embarrassment to the IDists…at least, he would be, if the IDists had anyone competent with whom to compare him. I tore down a previous example of Luskin’s incompetence at genetics, and now he’s gone and done it again. He complains about an article by Richard Dawkins that explains how gene duplication and divergence are processes that lead to the evolution of new information in the genome. Luskin, who I suspect has never taken a single biology class in his life, thinks he can rebut the story. He fails miserably in everything except revealing his own ignorance.

It’s quite a long-winded piece of blithering nonsense, so I’m going to focus on just three objections.

  • First, Luskin tries to trivialize gene duplication, a strategy that Michael Egnor also followed.

    Yet during the actual gene-duplication process, a pre-existing gene is merely copied, and nothing truly new is generated. As Michael Egnor said in response to PZ Myers: “[G]ene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is ‘It’s just like gene duplication. Plagiarism is new information- you said so on your blog!’”

    This isn’t right, on many levels. Copying a pre-existing gene does create new information … but it’s just a small amount. Luskin can’t be serious in considering this a weakness: evolutionary biology would predict only small changes at any one time. If a process produced a massive increase in the information content of the genome in a biologically functional way (that is, not just the production of random noise), then we’d have to say that you’ve found evidence for Intelligent Design. A succession of small genetic changes is what we expect from evolution and genetics, and that’s what we see.

    The plagiarism problem Egnor invents is nonsense. The primary problem with plagiarism in the classroom is that it is unethical, and represents the appropriation of ideas from another source without acknowledgment. If a student were to quote a source wholesale while providing full attribution, it would not be considered plagiarism…although the student would be failed for failing to demonstrate any understanding of the material or providing any significant new insight. We expect our students to demonstrate intelligence, after all; duplication is not a product of intelligence.

    And again, whoosh, this will fly over their heads: the processes we describe in evolutionary genetics exhibit incremental increases in information in the absence of intelligent input — contrary to the expectations of the IDists.

  • It wouldn’t be a creationist article without a quote-mine, and Luskin obliges. You’d think they’d learn, someday … whenever I see somebody at the Discovery Institute quote something from the scientific literature, I know to immediately check the source, and I am never disappointed. They always mangle it. Here’s Luskin in action:

    A recent study in Nature admitted, “Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown.” (Ilan Wapinski, Avi Pfeffer, Nir Friedman & Aviv Regev, “Natural history and evolutionary principles of gene duplication in fungi,” Nature, Vol. 449:54-61 (September 6, 2007).) Yet the crucial question that must be answered by the gene duplication mechanism is, exactly how does the duplicate copy acquire an entirely new function?

    Oh, dear. That sounds like an awful admission, doesn’t it? Would you be surprised to learn that it’s very much like the infamous quote from Darwin, where he admits that the evolution of something as complex as the eye seems absurd, but then goes on to explain how it happened? That’s exactly the case here. Luskin has pulled out the first two sentences of the abstract, where the authors set up the problem they are about to address, and throws away the rest of the work where they go into detail on the evolutionary histories of orthologues in fungal genomes. Here’s the full abstract.

    Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.

    Tsk, tsk. It’s an interesting paper that documents the details of a number of cases of gene duplication and divergence, and Luskin ignores it all (I suspect because he lacks the competence to understand it) to imply the paper is about our failure to understand the processes. I just mentioned that my primary concerns with student work are that they demonstrate good citation ethics and that they show understanding; Luskin has just failed on both counts. He has misrepresented the sense of a paper and he has shown that he doesn’t understand the work. A student who turned in that kind of shoddy effort to me would get an immediate “F”.

  • Finally, Luskin shows that not only does he fail to understand the duplication part, but he hasn’t got much of a grip on the divergence part, either. He invents a silly challenge of his own.

    So here is my “Information Challenge”: For the sake of the argument, I will grant that every stage of the evolutionary pathway I requested above will survive, and thus I’ll give natural selection every possible benefit of the doubt. What I need is a step-by-step mutation account of how one sentence evolved into the other wherein the sentence remains functional – i.e., it has comprehensible English meaning – at all stages of its evolution. In short, I request to see how:

    “METHINKSDAWKINSDOTHPROTESTTOOMUCH”

    can evolve into:

    “BUTIMSUREDAWKINSBELIEVESHEISRIGHT”

    by changing the first sentence one letter at a time, and having it always retain some comprehensible English meaning along each small step of its evolution. This seems like a reasonable request, as it is not highly different from what Darwinists are telling me can happen in nature.

    No, it has some significant differences. The genetic code is degenerate — there are many synonyms in the ‘language’. Much, but not all, of a protein is going to be tolerant to a fairly wide range of amino acid substitutions. That means that in this analogy, the simulation ought to tolerate a great many misspellings, and that many of the words ought to be dispensable as far as generating meaning. In addition, evolution isn’t trying to drive one amino acid sequence to another specific amino acid sequence; selection is only going to work for retention of general functionality. English has too much specificity to work in this analogy. If he said he had a text string with a lot of gibberish containing the words “DAWKINS” and “PROTEST”, and he wanted to see a step by step series of shifts that turned it into a string with some other gibberish that conserved “DAWKINS” and evolved the word “RIGHT”, and that slight misspellings in the intermediates were acceptable, he’d probably declare the exercise trivial and too easy — but that’s exactly what happens in the evolution of proteins. It’s not pre-specified, it’s fault-tolerant to a degree, and it’s not that big a deal.

    And furthermore, we already have the real thing. Not an analogy, not a guess, but a “step-by-step mutation account” of how one functional protein evolved into another protein with a different function, by a process of gene duplication and divergence. He might try reading Ian Musgrave’s summary of the evolution of the cortisol and aldosterone receptors. It’s cool stuff, it describes exactly what he demands in a real protein, and the degree of detail goes right down to the order of single amino acid changes. It’s perfect.

    Of course, we also know exactly how the IDists react when scientists do provide explanations in terms of tiny incremental changes. Suddenly, the details become “piddling”, and they ignore them. I expect Luskin will do the same.

Pathetic in his ignorance, appalling in his dishonesty, and disgraceful in his unwarranted arrogance … that’s Casey Luskin. It’s really a mark of the growing desperation of the Discovery Institute that they are constantly dragging out this pipsqueak lawyer to lecture the public on biology.

Comments

  1. #1 djlactin
    October 1, 2007

    Evolution news and views does not allow comments (surprise!), so none of the sheep have any idea how vapid these ‘statements from “authority”‘ actually are. Here’s a thought:

    Perhaps we (you; somebody; not me– i don’t have the skills) needs to set up a blog/website that compiles all of the rebuttals to their inanity.

    And I nearly spewed my juice when I spotted this at the bottom of the Evolution News and Views website:

    cut
    “The misreporting of the evolution issue is one key reason for this site.”
    paste.

    So true!

  2. #2 katie
    October 1, 2007

    Honestly? He probably gave up on that article the second he saw the words “comprehensive” and “unbiased”. Completely foreign to him, I’m sure.

  3. #3 David Marjanovi?
    October 1, 2007

    What’s missing from your explanation is mutation. After a gene has duplicated, one of the copies is under reduced selection pressure and can mutate — and mutation equals new information. The duplication merely makes it possible to add information instead of substituting it.

  4. #4 Lynn David
    October 1, 2007

    The misreporting of the evolution issue is one key reason for this site.

    EvolutionNews.org sure got that right! They mean it literally!

  5. #5 John Morales
    October 1, 2007

    David (#4), doesn’t duplication alone represent an increase in “information” (in the sense of redundancy)?

    If I give someone two copies of an instruction manual, they can lose one copy (all the original information) and still retain all the original information.

  6. #6 June
    October 1, 2007

    Duplication is an essential first step, if you want to modify an original without changing it.

  7. #7 David Marjanovi?, OM
    October 1, 2007

    OK.

  8. #8 Bob Lane
    October 1, 2007

    You close with this paragraph:

    Pathetic in his ignorance, appalling in his dishonesty, and disgraceful in his unwarranted arrogance … that’s Casey Luskin. It’s really a mark of the growing desperation of the Discovery Institute that they are constantly dragging out this pipsqueak lawyer to lecture the public on biology.

    Mostly accurate rhetorical description, but what does the rebuttal gain by the name-calling epithet “pipsqueak”?

  9. #9 Zeno
    October 1, 2007

    So Luskin actually cites Egnor as a way of supporting his argument.

    How persuasive.

  10. #10 pete
    October 1, 2007

    Well done in pointing out the errors that stalk all the papers similar to this, there is no shortage of amnesia and selective bias on display.

  11. #11 TomS
    October 1, 2007

    May I suggest that the real problem with the plagiarism example is that the concept of “information” used by the creationists is incoherent or useless. Of course, there are paradoxes of “information” when dealing with such a concept. One might, for example, say that plagiarism does represent “increased information”, in the sense that at least the student has chosen which source to reproduce. The student might be given some credit for chosing a relevant or reliable source.

  12. #12 Fishbone McGonigle
    October 1, 2007

    Mostly accurate rhetorical description, but what does the rebuttal gain by the name-calling epithet “pipsqueak”?

    A bit of rhetorical flourish, perhaps?

    At any rate, who cares? Ooooooooooh, PZ called Luskin a “pipsqueak.” Pass the smelling salts and the clutching-pearls, as I fear I am getting the vapors.

    Or something.

  13. #13 BobApril
    October 1, 2007

    but what does the rebuttal gain by the name-calling epithet “pipsqueak”?

    Entertainment value. At least, I enjoyed it. The rebuttal proper does not include the last paragraph, nor, indeed, the first – those would be the introductory and summary paragraphs. Noting the Oxford definition, I’d say the epithet is amply supported by the evidence presented.

  14. #14 J-Dog
    October 1, 2007

    Bob Lane- Have you ever SEEN or HEARD Casey Luskin? No? Then shut up. Pipsqueak in this instance is not an epithet, it is a description. Luskin is the very embodiment of the “pipsqueak”. Small in stature, high in voice, small in mind = pipsqueak. It would also be accurate to describe his as a lying weasel shill for his DI Moony Masters.

    HTH :)

  15. #15 Jud
    October 1, 2007

    Couldn’t read Luskin’s piece after the first sentence: “In Part I, I demonstrated that specified complexity is the appropriate measure of biological complexity.”

    Appropriate measure, eh? Great, and what are the units of this measure?

  16. #16 No One of Consequence
    October 1, 2007

    I know his challenge is meaningless, but its also a common word game. It certainly seems possible, with a little help from a few thousand pharyngula friends.

    ME THINKS DAWKINS DOTH PROTEST TOO MUCH.
    BETH INKS DAWKINS; DOTH PROTEST TOO MUCH
    BETH INKS DAWKINS; DOTS PROTEST TOO MUCH
    BETH INKS DAWKINS; BOTS PROTEST TOO MUCH
    BE THINES DAWKINS; BOTS PROTEST TOO MUCH
    BE THINES DAWKINS; BETS PROTEST TOO MUCH
    BE THINES DAWKINS; BETI PROTEST TOO MUCH

    BUT IM SURE DAWKINS BELIEVES HE IS RIGHT

  17. #17 386sx
    October 1, 2007

    At any rate, who cares? Ooooooooooh, PZ called Luskin a “pipsqueak.” Pass the smelling salts and the clutching-pearls, as I fear I am getting the vapors.

    Why don’t they just have some scientists do the science writing over there? They can’t be that hard to find. (Oh yeah I keep forgetting they don’t like science.)

    May I suggest that the real problem with the plagiarism example is that the concept of “information” used by the creationists is incoherent or useless.

    All they have is analogy this, analogy that, blah blah. But no real stuff.

    “Imagine for a moment, if you will, that if the Cambrian explosion was little teeny trucks and busses, then evolution can’t do that!!!”

  18. #18 slpage
    October 1, 2007

    I think that one of the biggest problems in these “information” arguments that ID information mongers either do not understand or purposeully gloss over is the fact that there is no 1-to-1 phenotypic or physiological change for each and every mutation, regardless of typw, whether it si a pointmutation or a segmental duplication.

    Most point mutations do nothing, but some can be lethal. Some gene duplications do nothing. Others, by virtue of the increased expression of their product, can have major phenotypic of physiological consequences. The IDcreationist information mongers just place ALL mutations – in this case, gene duplications – in one basket and want to be able to directly apply their idiosyncratic post-hoc definitions in an all-encompassing manner.

    A gene duplication does not add “new” information according to their concocted definiton? well, gee, it must not be important then.

    This is why whenever I have the opportunity, in my classes I explain the limits of the language and computer analogies so that at least my students will be able to tell when they are being lied to by these people.

  19. #19 SOB
    October 1, 2007

    Hey J-Dog, have you ever SEEN Bob Lane? No? Then I would advise you not to piss him off.

  20. #20 minimalist
    October 1, 2007

    Wouldn’t gene duplication that results in the duplicate being under a different promoter count as ‘information increase’? Particularly if that promoter is part of a signal transduction cascade, or somesuch. At the very least, suddenly that protein becomes part of the suite of genes up- (or down-) regulated by the signal, even if it doesn’t do much that’s relevant to the signal.

    By the fuzzy definition alluded to be IDiots (which seems to be “stuff that does stuff… and stuff”), that has to count as some sort of information increase.

  21. #21 windy
    October 1, 2007

    Duplication does not even need to be the first step in the dance:

    Allelic divergence precedes and promotes gene duplication

  22. #22 Graculus
    October 1, 2007

    By the fuzzy definition alluded to be IDiots (which seems to be “stuff that does stuff… and stuff”), that has to count as some sort of information increase.

    The trick to getting them to shut up is to demand that they produce a metric. If you can’t measure it, then you can’t use it in math.

  23. #23 PZ Myers
    October 1, 2007

    What I mean is that gene duplication produces copies that are very nearly identical to the original; we can see exactly where the new version came from. No intelligence is required, just error.

    What would support ID is the appearance of a novel gene, with multiple functions and complex regulation, and no antecedents — an abrupt increase in functional complexity that didn’t come from error.

    Allopolyploidy is a good example of a case where we do see a sudden jolt upward in the information in the genome…but we can also see where the information came from and can explain it very simply, without invoking a designer.

  24. #24 David Marjanovi?
    October 1, 2007

    Appropriate measure, eh? Great, and what are the units of this measure?

    The Timecube? :->

    But can those liberal athiest scientists tell us WHICH copy? Bet they can’t.

    Of course not. It’s random. :-)

  25. #25 David Marjanovi?
    October 1, 2007

    Appropriate measure, eh? Great, and what are the units of this measure?

    The Timecube? :->

    But can those liberal athiest scientists tell us WHICH copy? Bet they can’t.

    Of course not. It’s random. :-)

  26. #26 Graculus
    October 1, 2007

    If you use Kolmogorov complexity, then it is an easy exercise that C(xx) > C(x) for infinitely many strings x.

    A straight duplication would, IIRC, increase the KC by exactly one instruction, no matter how much is duplicated (gene, chromosome or entire karotype), so it is a very small increase in KC. But, again, KC doesn’t actualy speak to “meaning”, that is, to functionality.

  27. #27 SEF
    October 1, 2007

    Re #4, #8, #9 (and any others I missed!)

    It’s not just that duplication allows mutation to modify one copy (or its control switches). The mere duplication itself can make a significant difference in practice. Having more of a particular gene product around can shift the balance in any interactive competitive promotion and inhibition process. That can cause knock-on effects during development of a organism as well as changes in ongoing cell operations. Something might end up longer (dog’s nose) or stronger or more rapid (neurone firing?) or wider (butterfly spots?) or finer (in divisions).

    Aha! I thought one of these was probably already on Pharyngula.

  28. #28 Jeffrey Shallit
    October 1, 2007

    No, Graculus, your argument just shows that C(xx) <= C(x) + c, where c is the cost of adding a “duplication” routine. (The <= arises because you don’t know that there might be a shorter way to get to the duplicated string without actually duplicating it.) The exercise I am referring to asks you to show that C(xx) > C(x) for infinitely many x. Perhaps it is not completely trivial; most of my students can usually solve it.

  29. #29 Brownian
    October 1, 2007

    Just a thought, but perhaps one of the benefits of us New Atheists (y’know, the ones who don’t politely pantomime the sign of the cross after grace at family dinners) like Dawkins, Hitchens, Harris, and others, is that they attract the attention of scientishes (get it?) like Luskin, leaving those actually doing work in the trenches alone.

  30. #30 PZ Myers
    October 1, 2007

    Hey, I should put that tandem repeat article up here today…especially since I’m swamped with work. Thanks for reminding me!

  31. #31 JD
    October 1, 2007

    Casey Luskin has a B.S. and M.S. in Earth Sciences from UC-San Diego and has been affiliated with the Scripps Institution for Oceanography Paleomagnetics Laboratory (an article on paleomagnatism on the Snake River Plain of Idaho in 2004).

    So? How is that relevant? He’s not a biologist. He holds no degrees in the life sciences. Only the one publication on a completely unrelated field? So apparently he wasn’t even competent in that and has since left to become a lawyer.

    As a lawyer, even Luskin knows he couldn’t testify as an expert on these matters. He’d be eliminated on the first question.
    Opposing counsel: Mr. Luskin are you a biologist?
    Luskin: No.
    Opposing counsel: Your honor please excuse this utterly ignorant person from the courtroom. He is completely unqualified.
    Judge: Mr Luskin, you are recused. Buh bye.

  32. #32 Brian
    October 1, 2007

    Perhaps I’ve lost the plot entirely, but when these nincompoops say things like:

    “[G]ene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is ‘It’s just like gene duplication. Plagiarism is new information- you said so on your blog!’”

    aren’t they making the fundamental mistake (intentionally or no) of stripping context from the science?

    If the paper in question is to be viewed as a genome, then gene duplication would be more like a paragraph repeated within the paper. Clearly the original paper and the new paper with the repeated paragraph are different in terms of their information content, even if the repetition doesn’t function any differently than its twin.

    Small accumulated changes and misspellings over time, especially of selected key words, could alter the meaning of the paragraph entirely, while others would leave its meaning largely unaffected.

    Thus their own objection, once corrected for that loss of context, provides a relatively simple/simplistic analogy for showing how gene duplication changes information content.

  33. #33 JRF
    October 1, 2007

    There was an article published only a few weeks ago about gene duplication alone having a direct and very visible effect on a species.

    http://www.physorg.com/news108572275.html

    Blasted link doesn’t appear to be working. For those too lazy to copy and paste into their address bar, humans carry extra copies of the salivary amylase gene, allowing us to break down starch much more effectively than apes. Our diet has since changed accordingly. So, if Luskin is to be believed, a whole species gained an almost entirely new food source based on “no new information?”

  34. #34 JD
    October 1, 2007

    The usage of “information” by the IDiots is most charitably described as “inchoate”, but *we* have to know better, just so we can rip them a new one.

    What exactly IS their usage? I’ve never seen them given a specific, quantifiable definition that would have any scientific meaning whatsoever. I think discussions of “information” with them are futile without a working, agreed upon, objective definition. It’s a disservice to even grant the ID proponents any credibility on this subject by referring to information as if they have defined it. They haven’t. Any rebuttal to their articles should point this out every time.
    One should view this as an ignostic does the existence of god. Any discussion is pointless until a definition is provided otherwise you might as well argue about the color of Saturday.
    Because the IDiots proposed the inclusion of “information” into the debate I want a specific definition of it with a step-by-step method for determining it. Tells us how much “information” does a litter of water have and how is that measured value different from those for a litter of carbon dioxide or a litter of oil or a litter of DNA. When done, then will talk.

  35. #35 JD
    October 1, 2007

    Argh, damn US language spellcheck in my previous post auto-changed litre to litter. Please substitute as appropriate. Or not, it still kinda works. I suspect everyone here get it; it’s the ID proponents that will have difficulty with that “information” :P

  36. #36 Brownian
    October 1, 2007

    you might as well argue about the color of Saturday

    I’ll bet the synesthetes know what colour it is.

  37. #37 Hank
    October 1, 2007

    But can those liberal athiest scientists tell us WHICH copy? Bet they can’t.

    Of course not. It’s random. :-)

    Both of them and none of them, at the same time.

    This is the reason why I love reading the stuff over here at scienceblogs. Not only are (many) of them lots of fun, they’re also occasionally highly informational in an informal sense.

    And that’s from an engineer in the making.

  38. #38 JD
    October 1, 2007

    you might as well argue about the color of Saturday

    I’ll bet the synesthetes know what colour it is.

    I bet they don’t (particularly if it’s a Sunday :P).

  39. #39 Steve LaBonne
    October 1, 2007

    What exactly IS their usage? I’ve never seen them given a specific, quantifiable definition that would have any scientific meaning whatsoever.

    Well, of course not. 1. They (and I specifically include the Isaac Newton of Information Theory) aren’t smart enough to do any such thing. 2. All they want from “information” anyway is to be a handy-dandy set of movable goalposts.

  40. #40 Graculus
    October 1, 2007

    It's mutations that introduce the new information...

    In Shannon theory the mutations reduce information. “Information” is used in a very specific way that has little to do with the way we usually use the word.

    In Shannon, “cat”, “dog” and “sxt” all contain the exact same amount of information, that is, they are all three letters long. Meaning (function) has absolutely no place in Shannon. In Shannon if you change “sxt” to “set” you have reduced the amount of information because it is not exactly the same as the original (even if the change increases functionality/meaning), Shannon is completely self-referential and devoid of any metric for functionality.

    Genes do not work like this at all, which is why Shannon shouldn’t be used for this purpose.

  41. #41 Brain Hertz
    October 1, 2007

    @ 58

    also:

    3) Specifying an actual definition of the kind of “information” they’re talking about would immediately lead to the conclusion that no magic is required in creating it. That’s why the “Isaac Newton of information theory” likes his definition fuzzy…

  42. #42 AlanWCan
    October 1, 2007

    If a process produced a massive increase in the information content of the genome in a biologically functional way…then we’d have to say that you’ve found evidence for Intelligent Design. Who wants to bet this comes back to haunt PZ (I even nicely quote-mined it for you).

  43. #43 Brain Hertz
    October 1, 2007

    In Shannon, “cat”, “dog” and “sxt” all contain the exact same amount of information, that is, they are all three letters long. Meaning (function) has absolutely no place in Shannon. In Shannon if you change “sxt” to “set” you have reduced the amount of information because it is not exactly the same as the original (even if the change increases functionality/meaning), Shannon is completely self-referential and devoid of any metric for functionality.
    Genes do not work like this at all, which is why Shannon shouldn’t be used for this purpose.

    I respectfully disagree with your opening quote… the words you quote do not contain the same amount of information, assuming that the first two are constrained to be words in the English language (which is the point I was making originally).

    If, in the third “word”, the constraint to be a valid word is removed, whereas the first two must be valid words, it has a greater information content. It has nothing to do with meaning, but with whether each letter is an independent observation of some stochastic process, and the nature of the distribution function.

    Back to my original point: two copies of the same thing, constrained to be identical, do not contain exactly twice the amount of information as one copy…

  44. #44 JD
    October 1, 2007

    If a process produced a massive increase in the information content of the genome in a biologically functional way…then we’d have to say that you’ve found evidence for Intelligent Design.
    Who wants to bet this comes back to haunt PZ (I even nicely quote-mined it for you).

    Alan, I noticed that too and it’s exactly why I think it’s a mistake to ever grant, or least give the impression, that ID has a working definition of “information”. I don’t know what “the information content of the genome” even is, let alone how it is measured and determined.

  45. #45 TomS
    October 1, 2007

    Because the IDiots proposed the inclusion of “information” into the debate I want a specific definition of it with a step-by-step method for determining it. Tells us how much “information” does a litter of water have and how is that measured value different from those for a litter of carbon dioxide or a litter of oil or a litter of DNA. When done, then will talk.

    I quite agree. Except that … well, let’s get to freshman chemistry … their concept of information: is it an extensive or an intensive property? Among other basic questions to ask about it.

  46. #46 Ian
    October 1, 2007

    “Mostly accurate rhetorical description, but what does the rebuttal gain by the name-calling epithet “pipsqueak”?”
    (Bob Lane, commenter #11)

    It’s what you get when you mutate “Casey Luskin”….

  47. #47 Bulman
    October 1, 2007

    Here’s an easy way to boil down the whole duplication isn’t new information.

    If I duplicate the number 1, but no new information is gained, then 11=1. (This also means that I would very much like to borrow $11 dollars from you.)

  48. #48 Brain Hertz
    October 1, 2007

    Bulman,
    the information introduced by duplication isn’t zero, but it isn’t as much as double.

    If I have random variables x1, x2,…. representing independent observations of the same distribution, the sequence:

    x1, x2, x3, x1, x2, x3

    does not contain twice as much information as the sequence:

    x1, x2, x3

    an increase in the genetic information in the scenario being discussed is only in the fact of there being one additional copy being made as compared to 2 or three.

  49. #49 Chris
    October 1, 2007

    Actually, in such a short example it *does* contain twice as much information: the information required to explain what duplication is would be much longer than the information required to simply double the sequence. Sometimes the best compression is no compression – not just because there is no pattern, but also potentially because the pattern doesn’t permit savings greater than the cost of using it.

    We’re used to cheating on the complexity of operations like repetition because we come with brains pre-loaded with certain operations. But in any rigorous complexity metric you have to include the decoding procedure as part of the complexity, which means you have to get into some pretty long sequences before their complexity is genuinely less than their length.

  50. #50 MarkH
    October 1, 2007

    Slam Dunk. Nice PZ.

  51. #51 Graculus
    October 1, 2007

    The amount of data clearly doubles, of course.

    In Shannon “information” and “data” are synonymous to a large degree.

    Yes, you could use KC, or Shannon. Whichever you use doesn’t change the answer, though.

    Oh yes if does matter, because both of these use very strict and very particular definitions for “information” and “complexity”. In fact, another name for Kolmogorov Complexity is “algorithmic complexity”. Doubling can only add, at most, one instruction to the algorithm that describes it.

    Anyways, you can’t just go around re-defining terms, that’s what the IDiots do with this stuff. You don’t randomly call electron bonding “gravitation”, do you? Shannon information and KC is very specific in what it measures, and doesn’t match what the colloquial meanings are.

    The amount of new information is not equal to that contained in the region being duplicated. If you select some region at random, to add information equal to its information content would require you to add another region of the same size with its contents selected independently at random, with the same distributions and interdependencies as the original.

    But that wouldn’t be Shannon information (if it’s equal size then the amount of information is equal, no matter what the content), and you don’t have a metric for *that*.

  52. #52 Keith Douglas
    October 1, 2007

    It seems that these guys don’t want to admit (or just don’t get) that duplication by itself is not what allows for new genes and ultimately new protein synthesis – it is presumably duplication followed by mutation in one of the duplicates, no? (Well, I suppose there might be an “end effect” too.)

  53. #53 Brain Hertz
    October 1, 2007

    The amount of data clearly doubles, of course.

    In Shannon “information” and “data” are synonymous to a large degree.

    I disagree. Very much so. The amount of data sets an upper bound on the amount of information, but not the lower bound.

    Yes, you could use KC, or Shannon. Whichever you use doesn’t change the answer, though.

    Oh yes if does matter, because both of these use very strict and very particular definitions for “information” and “complexity”. In fact, another name for Kolmogorov Complexity is “algorithmic complexity”. Doubling can only add, at most, one instruction to the algorithm that describes it.

    Anyways, you can’t just go around re-defining terms, that’s what the IDiots do with this stuff. You don’t randomly call electron bonding “gravitation”, do you? Shannon information and KC is very specific in what it measures, and doesn’t match what the colloquial meanings are.

    Excuse me? Where above did I state that information and complexity were the same thing?

    My statement is pretty clear, and I stand by it: namely, if you choose for some reason to substitute “complexity” for “information” (which wasn’t me, btw, I was responding to the substitution), it doesn’t change the answer to that particular question. I wasn’t suggesting some kind of equivalence. In which matter, you seem to be agreeing with me in your first paragraph above, by the way: my statement was that irrespective of whether you look at information or complexity, simply copying the message doesn’t double the information (or complexity).

    As for the definitions, I’m sticking with Shannon’s definition of information (which is where we started). I certainly agree that you can’t mess with the definitions as Billy Dembski likes to do (I commented on this earlier in the thread, in fact).

    But that wouldn’t be Shannon information (if it’s equal size then the amount of information is equal, no matter what the content), and you don’t have a metric for *that*.

    I’m not sure what you mean. If you aren’t trying to measure information by Shannon’s metric, what are you using?

    In any case, I very much disagree that you can measure the information by looking at the size of the message. You need to know the properties of the process that generated it. If not, what is the procedure you would use to calculate the information contained in the data?

  54. #54 Brain Hertz
    October 1, 2007

    ugh… thought I’d fixed all the blockquote errors in preview… I guess not. The fifth and sixth paragraphs above should be blockquoted.

  55. #55 Pete Dunkelberg
    October 1, 2007

    amount of information in a duplication …
    in strings of 0 and 1, compare

    0
    to
    00

  56. #56 John Phillips
    October 2, 2007

    Ironically, Luskin’s centre is called the IDEA or the Intelligent Design and Evolution Awareness centre. I say ironic as I see no actual Awareness of what Evolution is and definitely no signs of genuine intelligence from him or his fellow IDiots. And to those complaining or concerned about us mean atheists using such terms as IDiots, it is not an ad hominem when it is an accurate description culled from an examination of their own words and actions.

  57. #57 mark
    October 2, 2007

    Luskin is remarkably stupid. His puerile post shows not only a lack of insight, but also also that he is totally unacquainted with the literature. His “challenge” is readily addressed. What? Everyone has noticed this? The only significance of his antics, then, is that he seriously misleads uninformed persons who happen to read his work.

  58. #58 JM Ridlon
    October 2, 2007

    Luskin is writing a third part…can’t wait. I also noticed the quote-mine:
    http://sciencethegapfiller.blogspot.com/2007/09/luskin-quote-mine.html

    As well as a stunning misunderstanding of Shannon Information on Luskin’s part, which Dawkins explained in plain English.

    http://sciencethegapfiller.blogspot.com/2007/09/methinksluskinisconfusedaboutshannoninf.html

  59. #59 Eisnel
    October 2, 2007

    I’m sorry if this is something that’s already been discussed in the comments. Also, I’m not a biologist, so I can’t claim to understand genetics too much.

    Couldn’t Luskin’s “Information Challenge” be solved using something like gene duplication? What if the whole word sequence underwent a duplication event, and the duplicated part mutated while the first part stayed intact?

    METHINKSDAWKINSDOTHPROTESTTOOMUCHMETHINKSDAWKINSDOTHPROTESTTOOMUCH
    … (millions of years of mutations) …
    METHINKSDAWKINSDOTHPROTESTTOOMUCHGWYFLQWOPCKDFQGRMYRQKPLZRPDJFXBIO
    … (millions more years of mutations) …
    METHINKSDAWKINSDOTHPROTESTTOOMUCHBUTIMSUREDAWKINSBELIEVESHEISRIGHT

  60. #60 No One of Consequence
    October 3, 2007

    I solved Luskins challenge in 43 mutations.

    Results here along with an explanation of who would understand each mutation.

  61. #61 John Morales
    October 3, 2007

    #96, that is a most impressive display of applied geekery.

  62. #62 No One of Consequence
    October 3, 2007

    I’ll take that as a compliment.

    What can I say, I like word games, etc. and that seemed like a fun one.

  63. #63 Dan Cardinale
    October 4, 2007

    That was great. But you know, if an ID’er saw it, they’d play the “see, it has a designer!” card. Wouldn’t expect them to get the point…