Wednesday, October 12, 2011

A Twofer

A few weeks ago David Klinghoffer criticized science bloggers for only going after "extremely marginal and daffy creationists." He challenged us to take on the "real scientists" like Jonathan M. [A Reason to Doubt the IDiots]

Today you're in for a treat, dear readers, 'cause I'm going to respond to a daffy creationist who happens to be Jonathan M. It's a twofer!

The subject is junk DNA, a subject that's almost guaranteed to bring out the worst in IDiot rationalization [Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”].

Jonathan M wants to discuss the "Onion Test" that was originally proposed by Ryan Gregory as a way of assessing the validity of arguments against junk DNA. Here's the original link: The Onion Test. And here's how Ryan describes it.
The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?
Note that the Onion Test is for people who think they have a functional explanation for the vast amount of putative junk in our genome. What Ryan is suggesting is that such proposals should be able to account for the huge genome of onions as well as the huge genome of humans.

Let me give you some examples. Some people suggest that we need a big genome in order to protect our genes from mutation. If that's true then why do onions need five times more DNA? Some people suggest that we have big genomes because we're so complex and we need huge amounts of regulatory sequence. If so, why do onions need more?

Keep in mind that the Onion Test is "... a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA."

Let's see how Jonathan M handles the discussion.
Briefly stated, the “onion test” (which originates with T. Ryan Gregory) observes that onion cells have many times more DNA than we do. And since the onion is considered to be relatively simple as compared to the human, this discrepancy can only be accounted for within the context of the view that much of its DNA is, in fact, junk. This phenomenon is also known as the “C-value enigma”, and describes the lack of correlation (among eukaryotes) with respect to genome size and organismal complexity.
No, Jonathan, that's not quite right. The Onion Test is a test for those people—like Jonathan Wells—who think that most of our genome has a function. He's supposed to "test" his speculation to see if can explain onion genomes. The Onion test is not about proving the existence of junk DNA and its not about explaining the C-Value Paradox [Genome Size, Complexity, and the C-Value Paradox].
Theme

Genomes
& Junk DNA
This whole argument for junk DNA seems to rest on the critical assumption that having seemingly excessive amounts of repetitive DNA has no positive bearing on an organism’s physiology. But this assumption has been invalidated by the scientific evidence.
I hate to break it to you Joanathan M, you being such a great scientist and all, but the Onion Test is not an argument for junk DNA. It's a test of possible functional explanations. (Didn't I mention that already?) Jonathan M has completely misunderstood the Onion Test. Would it surprise you, dear readers, to learn that Jonathan Wells also flunks the test [Junk & Jonathan: Part 11—Chapter 8]. This isn't rocket science.

One correlation which has been established is that highly-expressed genes tend to have short introns (Castillo-Davis et al., 2002), a likely reflection of the selective-pressure on transcriptional economy with respect to very highly expressed genes.
This is correct. And very highly expressed genes don't have any introns. But introns only make up 25-30% of the genome. The largest category of junk is defective transposons.

Let's assume that the presence of junk DNA as intron sequences is selected in order to slow down transcription. Why do onion cells need so much more junk DNA. And why do related species of onion differ so greatly in their genome sizes? What's that got to do with introns?
Perhaps some of the C-value enigma can be accounted for in terms of alternative splicing and alternative polyadenylation. Alternative splicing allows a single form of a pre-mRNA transcript to be spliced into a number of different forms by skipping exons or by recognizing alternative splice sites, as shown in the diagram above. It is known that the level of alternative splicing exhibited in humans (about 60%, with an average of 2 or 3 transcripts per gene) is much higher than that for C. elegans (about 22%, with less than 2 transcripts per gene).
I don't agree with the facts. I don't think it's true that most human genes produce multiple functional copies of mRNA by alternative splicing.

But let's assume that it's true. Let's assume that a large fraction of putative junk DNA is there because it promotes alternative splicing. Why do onion cells need so much more alternative splicing and why do related species of onion differ so much in their need for alternative splicing? That's what the Onion Test asks.
Approximately 10% of human genes code for transcription factors (a special class of protein which binds to specific sequences of DNA, namely, enhancers or promoters which are adjacent to genes which they regulate the expression of). In contrast, only about 5% of yeast genes code for transcription factors. When coupled with a much larger network of transcriptional enhancers and promoters, such a difference could result in a much larger set of gene expression patterns. This could lead to a non-linear increase in organismal complexity (see Levine and Tjian, 2003).
I don't even understand the point. Is Jonathan M saying that a huge percentage of our genome is devoted to regulatory sequence? If so, why do onions need so much more regulatory sequence? (The actual amount of regulatory sequence amounts to no more than 1% of the genome. That still leaves 90% junk.)
The graph shows a clear quantitative correlation between cell volume and DNA content. The trap into which the “junk DNA” advocate has fallen — as he so often does — lies with the (erroneous) assumption that all functions associated with DNA are sequence-dependent. But this need not universally be the case (in fact, it has long been shown not to be). This correlation holds not only true of vertebrate animals, but also for plants and unicellular eukaryotes (protozoa). It has been suggested by many that DNA possesses a structural role in controlling nuclear volume, cell size and cell-cycle length. With increased cell size comes selective pressure for a corresponding increase in nuclear volume.
There seems to be a correlation between cell size and genome size. Is this cause or effect? Why did some species of onion undergo selection for increased cell size while their close relatives did not? The Onion Test is a reality check on this type of explanation but Jonathan M doesn't get it.
In summary, to point to the C-value paradox — or the so-called “onion test” — as evidence for the preponderance of junk or nonsensical DNA within animal genomes is based on several critical assumptions which are contradicted by recent data. The common naive supposition that having a larger genome size is neither here nor there in terms of organismal physiology has been shown to be untenable. With the ever-increasing expansion of our knowledge of the nature and functional inter-relatedness of the genome, those who choose to continue using the “junk DNA” argument as a club with which to beat intelligent design should find these facts disconcerting.
Hey, Jonathan M! Did you hear that "whooshing sound" when you were writing this posting? That was the sound of a point going over your head.1

UPDATE: Denyse O'Leary has found this posting [Biochemist Larry Moran responds to Jonathan M’s junk DNA post]. So far, the comments on Uncommon Descent just confirm my conclusion that Intelligent Design Creationists are IDiots. I'm waiting for a "real scientist" like Jonathan M to weigh in and explain why he misrepresented the Onion Test. (It's interesting that Denyse didn't make any editorial comment. Usually she defends her fellow IDiots. Maybe she realizes that Jonathan M blew this one?)


1. whoosh

71 comments :

  1. Holy crap,

    In summary, to point to the C-value paradox — or the so-called “onion test” — as evidence for the preponderance of junk or nonsensical DNA within animal genomes ...

    Two things I didn't know:

    1. That the C-value paradox was the same as the onion test.

    2. That onions were animals.

    Wow, I learned something new. These IDiots might be on to something ...

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  2. Thanks for clarifying this, Larry. I was aware of the posts but haven't had time to deal with it. You've explained it as well as I could in any case.

    People seem to be hung up on either the onion specifically (I could have chosen any of thousands of species to compare) or the term "universal function", which could be one or several functions that make most non-coding DNA functional for organisms. Of course, most people propose only one function at a time anyway, but this is not really relevant to the central point.

    Also, it's somewhat amusing that the post seeks to school me on the relationship between genome size and cell size. :-)

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  3. I like the fugu test. It's only problem is that a creationist might claim that humans are much more complex than fugu (how, exactly) and thus need more DNA. The proper response would be to ask whether other species of puffer are as complex as humans, then.

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  4. Ryan -- glad you are following this! IIRC, the differences in genome size between these particular onions are not due to mere polyploidy, do I have that correct? Cheers!

    Also -- I don't know if you've read Wells's book yet, but there is a great brief discussion of the onion test -- great because he embarassedly brushes past it so quickly. Maybe he hopes readers won't notice...

    Nick

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  5. Let's assume that a large fraction of putative junk DNA is there because it promotes alternative splicing.

    That would be something of a head-scratcher. If different versions of a gene are necessary, why not just have different segments of DNA for each? If that's what junk is 'for', I bet you'd use less DNA overall, over having multiple edits (which are prey to a single mutation affecting them all).

    Then we have an apparent drive to keeping lumps of sequence-irrelevant genome to control the cell cycle.

    So basically we seem to have a portion of the genome driven to exquisite economy, and a whole mass of crap that renders that design feature wholly unnecessary.

    I suspect multiple designers, and not enough meetings at the project planning stage!

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  6. @Alan. I think Jonathan M is making a "point" along the lines of, a cell needs X amount of DNA (pull out favourite correlation with cell size/metabolism/whatever). We, the blind and stupid, look at what is functional (proteins etc.), F, and assign the rest as junk, J, where J = X - F. Alternative splicing and complex regulation reduces the need for functional DNA F and therefore increases J (as X = F + J) because he seems to assume that X is set for some reason.

    The thing I don't get is that, even if there IS some reason for the total genome size relating to "physiology", why does that make ID any less wrong? Given that multicellular organisms regulate both cell size and metabolism without changing their own genome sizes, there are obviously more elegant solutions to this problem. Making and packaging a load of extra DNA just for filler does not seem to be particularly "intelligent" to me. If there is a selective advantage for a particular genome size, evolutionary theory still provides a better explanation.

    (I'd actually be happier if there was a reason for maintaining large genomes once they had evolved. It MUST present a pretty large energetic load on an organism like a human, with a trillion cells. Why aren't large deletions selected for, reducing our genome size? Or is it just that crap is leaking into our genome as fast as selection can remove it? It still looks like evolution, though, especially when you see what the "junk" is made up of. Even if there is some kind of selection on the whole, the junk is still junk that can be mutated or deleted, you just can't delete too much of it.)

    Perhaps God created certain species, like Allium cepa, as a playground (or molecular safari park) for transposable elements? Everyone loves transposable elements! (Do the larger genomes have more TEs? Too much reading, not enough time! Can anyone recommend a good recent review on this stuff?)

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  7. I wonder why the IDiots are so down on junk DNA? I write computer programs, which I guess makes me an intelligent designer, and my hard drive is full of little test programs, half-finished projects, etc, etc. I wouldn't think junk DNA was a problem for ID theory unless the alleged designer was omniscient and infallible, and ID theory isn't about God, right?

    Anyway, it's funny that so-called Intelligent Design Theorists show no interest whatsoever in how intelligent design actually works as a process, and concentrate on bashing evolution.

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  8. @NickM

    Yes, these onions are all diploids. I checked that before choosing onions as the main example.

    I am aware of Wells's book but haven't gotten around to discussing it yet. He just skips over details or conflates different topics. Not all that worthy of a response relative to other items on my to do list.

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  9. @cabbagesd'abbattement

    (I'd actually be happier if there was a reason for maintaining large genomes once they had evolved. It MUST present a pretty large energetic load on an organism like a human, with a trillion cells. Why aren't large deletions selected for, reducing our genome size?

    I think that MUST is debatable. It's those trillion cells that are the load, whatever it takes to make them. For one organism to 'undercut' another - "I'll make those trillion cells for 5% less" - there has to be a market in which that pricing is rewarded in increased output.

    The cells that matter, the germ line, can be replicated up to quorum in a couple of weeks. Then they sit there, for bleeding ages! Resources are poured into building a ruddy great soma. The evolutionary battle would be between the rival somatic colonies that surround these slumbering germ cells, and presumably there are opportunities for selective tuning of the resources that go into their construction. But why should those with deletions leave more offspring than those without? The kind of deletion that would make much difference - chucking away a whole chromosome, for instance - isn't really on. And these super-lean genomes are going to have to undergo a successful meiosis at some point.

    If food is not limiting, I think that the leaner individuals will simply excrete more nitrogen.

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  10. @Alan. I think Jonathan M is making a "point" along the lines of, a cell needs X amount of DNA (pull out favourite correlation with cell size/metabolism/whatever). We, the blind and stupid, look at what is functional (proteins etc.), F, and assign the rest as junk, J, where J = X - F. Alternative splicing and complex regulation reduces the need for functional DNA F and therefore increases J (as X = F + J) because he seems to assume that X is set for some reason.

    Yes but, if the "physiology working group" had created a role for an X-base genome, the "protein production committee" seems to have completely wasting its time reusing segments of F to minimise that fraction of it. I don't see why F has to be so much smaller than X, even if we accept the bones of the argument. There seems to be unnecessary 'headroom' in the system, from a design pov, which could have been put to work making multiple proteins in a less error-prone manner than alt-splicing without coming anywhere near breaching X. Conclusion: not really evidence of the kind of top-notch single-intelligence design asserted.

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  11. @cabbagesofdoom

    What Neil said. With the addition that selection works within a generation (roughly). So, if there is one genome that's 95% and another that's 94.9% junk, I can't see the differences mattering too much.

    If the marginal cost of preventing the accumulation of junk is small in each generation then we expect it to add up and up.

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  12. @Alan: You are right, of course, it is not a "must" scenario as I made it sound. [Note to self: don't post comments before morning caffeine is imbibed!]

    I still think that the energetic load must be big in absolute terms; I think a kb of DNA has about 100 histones on it, so a 1kb deletion would save 3000 trillion bases of DNA (assuming 3 trillion cells) and 300 trillion histones. Of course, though, the important thing is whether this could be seen by selection.

    If this energetic load was all that mattered, each kb deletion would give a selective advantage of approx. 1/3,000,000 if my maths is correct. This needs to exceed 1/4N to be under selection, where N is the effective population size. So N = 750,000 / L, where L is the length of the deletion in kb. There is evidence that a deletion of approx 1Mb +/- can be tolerated in mice (http://www.nature.com/nature/journal/v431/n7011/full/nature03022.html), so *if* this could also happen in humans and be otherwise neutral, it would need an effective population size of 750, which is very small.

    That just leads the question of what proportion of the cell's energy budget goes into DNA+histones and what proportion of total fitness is determined by total energy budget, E. I have no idea what this is likely to be but it means that N = 750,000 / (E x L). I think the effective population size of ancestral humans is thought to be in the range 10,000-100,000, so if E x L is greater than 75 then selection should see it. For a 1Mb deletion, this means that 7.5% of total fitness must be determined by DNA+histone load. This seems quite high to me, so perhaps it's not that surprising at all that the junk hangs around! (Maybe someone with a better handle on cellular metabolism can estimate how much of the energy budget is spent on DNA + histones, although I suspect that energy as a proportion of fitness is anyone's guess?)

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  13. @David. I agree. A careless aside on my part. My main point is that even if genome size was shown to be under selection, it still wouldn't make ID any more likely or evolution any less likely.

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  14. @Alan: Don't get me wrong... I don't think Jonathan's point makes any sense. That's just the only way I can rationalise his comment as explaining more "junk" DNA. Unless, of course, he is worried about introns being called "junk" and trying to give them functional significance and thus reduce "junk". I don't know. It's hard to follow his meandering "logic", especially when he seems to be trying to simultaneously argue that junk isn't junk and that junk is there for a reason.

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  15. Is it not possible that the large genome size of onions (in contrast with the human species) is the result of several rounds of whole-genome duplications? From a rational teleological perspective, introns pose no real problem, 'cause the original, first introns in ancient onions may have been functional, but after whole-genome duplication occurred in that ancient lineage, the duplicated introns would have become functionless since there would be little selective pressure to preserve their sequence identity. This answers the "onion test" from a rational intelligent design perspective. Note that whole-genome duplication is a recognized "evolutionary force in animals, fungi and other organisms...especially plants."

    (From: "Ancestral polyploidy in seed plants and angiosperms.")

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  16. "I hate to break it to you Joanathan M, you being such a great scientist and all,"

    Why is it that this generation of adults still act like they are in high school? Wait maybe I don't want to hear the answer to that!

    Even if you were right, you still come off as a child. Whatever happened to mutual respect?

    Whatever happened to dignity and honor?

    Whether Jonathan is wrong or right should still be handled in a civil matter.

    If this is what the brainiacs have now amounted too I now understand why this world is slowly falling apart.

    Sandwalk I'm going to be honest with you, I don't care if it is an ad-hominem. Someone desperately needs to bring this to your attention.

    *you need to learn the ways of honor and respect*

    You talk about Jonathan like he peed in your Cheerios, but I'm unsure if you are one to admit your faults or just say he deserved it, blah, blah, blah

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  17. Anonymous,

    Ad hominem does not mean insult. Let me repeat: ad hominem does not mean insults. Let me repeat: ad hominem does not mean insults. Let me repeat: ad hominem does not mean insults. Let me repeat: ad hominem does not mean insults. Let me repeat: ad hominem does not mean insults.

    I hope you got it. Now look it up and you might understand why those are not the same. (If I do the homework for you, you will not learn anything.)

    I can't talk for Larry, but I would have been much more insulting than him. Professional liars like the IDiots do not deserve the most minimal respect. I know that it is much more elegant to let the insult form itself in the clear bashing of their shit by showing it to be shit, but I am not English (those guys know how to insult with the arguments, rather than tell the insults themselves), so I stick with what I know.

    Also, it is much more elegant and mature to be able to listen to the arguments despite the insults embedded than avoiding insulting in the first place. If I am insulted, and I can show them to be wrong, then the insult bounces back. You should also be able to take the insults when you deserve them.

    Note, for instance, that I said I learned that onions are animals from this Jonathan M ass-hole. That was no sarcasm, that was a direct insult. Still, I don't mind insulting the guy in much less unambiguous terms (as you can see). I feel actually quite well.

    Finally, I feel more inclined to think that someone is "childish" when they worry too much about "mutual respect" and such shit, rather than listen to what was said otherwise.

    Grow up already.

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  18. Anonymous -- is it too much to ask that someone like JonathanM get themselves well-educated on a topic before announcing to the world that the scientific community has gotten huge parts of basic science horribly wrong?

    All of us in the scientific community have to work very hard to make any real progress at all, and if someone overturns some widely-accepted notion, it doesn't happen because of thinking up half-baked objections over breakfast, it happens because of extremely careful, extremely well-informed, extremely detailed research.

    When someone comes along and declares that all/most junk is functional and that scientists were idiots for thinking otherwise, and yet is unaware of the huge variability in genome size (it's not just onions, it's thousands of species) -- and furthermore when they push this on journalists, school children, etc., it's damned annoying.

    If someone like JonathanM wants our respect, they've got to do "due diligence" in their research before trying to convince the public.

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  19. @Cabbages of Doom

    I suspect that energy as a proportion of fitness is anyone's guess?

    Yes - and this is likely to be highly circumstantial. If everyone is adequately fed, the fact that - for example - some individuals absorb 5% more through their gut than others is not going to have much impact at all. But when times are lean, the fitness of the better absorbers goes up. This kind of thing makes the mathematics tougher, because you try to keep fitness as some kind of function - uniform, or frequency-dependent, say.

    If we had a small population, and held food at the cusp of starvation, we may see selective fixation of deletions. But the larger populations get, the less likely that those extreme conditions will hold for long enough to get fixation - every time food becomes plenty, selection is relaxed, the advantage dissipates and new additions can drift in.

    There's also bias against deletion to factor in. If deletions are caused by misaligned recombination, meiosis is offering up equal numbers of shortened and extended gametes. But fewer of the shorter will be viable.

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  20. @Alan: Don't get me wrong... I don't think Jonathan's point makes any sense. That's just the only way I can rationalise his comment as explaining more "junk" DNA.

    No, I know! I was just taking the "if (as he says) the genome as a whole betrays Design, then ..." stance, which leads to the unexplained curiosity of vast amounts of X-supporting DNA, with a tiny fraction of F cowering in a corner of it. If I were designing it (and X a real optimum), I'd make F bigger, and make better use of the swathes of X-F at my disposal.

    Unless, of course, he is worried about introns being called "junk" and trying to give them functional significance and thus reduce "junk".

    I think that's the case. But rather than using 25% of the genome to support introns and alt-splices, a better Design approach might be to have no introns and use that space to supply the various direct transcripts instead. It's costly to make all that RNA then chuck it (referring back to your 'energetic cost' point), and this method is error prone in editing and has greater mutational sensitivity. Get rid of introns and there's room for about a dozen variants per gene, without impinging on anything in intergenic space. I think you'd only need 2 or 3 to cover the known alt-splice spectrum. But hey, I'm not telling the Designer his business!

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  21. Genomicus writes:

    From a rational teleological perspective, introns pose no real problem, 'cause the original, first introns in ancient onions may have been functional, but after whole-genome duplication occurred in that ancient lineage, the duplicated introns would have become functionless since there would be little selective pressure to preserve their sequence identity. This answers the "onion test" from a rational intelligent design perspective.

    So let me get this straight: Duplicating a genome and consequently making formerly functional DNA superfluous is "rational intelligent design"? So you think an architect who designs you a 4-story house when you only really want and need 2 is making an intelligent design decision?

    I suppose perhaps that does answer the onion test. It's apparent some humans need less intelligence than our tangy relatives.

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  22. @Genomicus. A couple of quick points:

    1. Humans have undergone at least two rounds of genome duplication in the past. Not sure about onions but suffice it to say that, no, genome duplication does not explain the C-value paradox. (Fugu, for example, has undergone an extra duplication versus human but has a smaller genome.)

    2. You describe an evolutionary process, not Intelligent Design. The former is a much better explanation for observations of genome duplication (and subsequent genes losses and sub/neofunctionalisation) than the latter. An Intelligent Designer could just design the organism with the genes and complexity it needs in the first place.

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  23. Jud:

    "So let me get this straight: Duplicating a genome and consequently making formerly functional DNA superfluous is "rational intelligent design"? So you think an architect who designs you a 4-story house when you only really want and need 2 is making an intelligent design decision?"

    Well, you're mis-characterizing my position. What I am saying is this:
    that the original eukaryotes had fully functional introns, consistent with the intelligent design hypothesis, but then as the eukaryotes evolved through non-teleological mechanisms, some of those eukaryotes had whole-genome duplications, resulting in a loss of function of the duplicated introns. This answers the onion test, effectively, from a rational intelligent design approach. The first introns were fully functional, but evolutionary tinkering lead to a loss of function for duplicated introns.

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  24. cabbagesofdoom:

    "Humans have undergone at least two rounds of genome duplication in the past. Not sure about onions but suffice it to say that, no, genome duplication does not explain the C-value paradox. (Fugu, for example, has undergone an extra duplication versus human but has a smaller genome.)"

    Yea but how is this relevant? That humans have undergone whole-genome duplications is irrelevant to the thesis that onions have undergone more whole-genome duplications than humans. Whole-genome duplication does indeed answer the onion test, when we're talking about introns.

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  25. cabbagesofdoom:

    "You describe an evolutionary process, not Intelligent Design. The former is a much better explanation for observations of genome duplication (and subsequent genes losses and sub/neofunctionalisation) than the latter. An Intelligent Designer could just design the organism with the genes and complexity it needs in the first place."

    You are belaboring the obvious: that whole-genome duplication is an evolutionary process. This doesn't influence my argument though. In a teleological perspective, the first introns were fully functional; those functional introns were duplicated by non-teleological mechanisms, leading to a loss of function of the duplicated introns. If A represents the first, functional introns, then A is duplicated producing B, which are the duplicated, ultimately functionless introns.

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  26. @Genomicus,

    Your irrational speculations have nothing to do with the onion test. You are assuming that Jonathan M interpreted the test correctly. This means that you did not read my post.

    I'm wasting my time telling you this, right?

    If you were capable of reading for comprehension you probably wouldn't be an IDiot in the first place.

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  27. @Genomicus: Fugu vs human is highly relevant. The "onion test" is not just about onions.

    Whole genome duplication leaves traces. If the C value paradox could be explained by WGD, I think the Gregory lab (or others) would have a paper entitled: "Whole genome duplication solves the C value paradox" (Or something similar.) Some of the variation in genome size is undeniably due to WGD but certainly not all.

    (And I still don't buy the argument that the original introns are well explained as a feature of "Intelligent Design". 1. Not all introns are involved in alternative splicing. 2. Many genes are regulated perfectly well without introns. 3. It's far from self-evident that alternative splicing is "better" than multiple single-exon genes. Easier to evolve? Yes. Better design? No.)

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  28. Hmmm. I tried to take Jonathan M up on a point in one of his articles, on an ancient fully aquatic whale. It never surfaced.

    I was critical of his interpretation - that all modern whale features had no time to evolve between land ancestors and this early whale - but shouldn't honest scientists be open to criticism? Indeed, should they not welcome it?

    Of course, the UD policy is quite clear, and I accept that they need moderation - I'm not really whingeing about that post. I felt I was polite, but I could be wrong; maybe it came across as contentious. But it undermines the respect that they seek, if challenges to ID are not allowed to be viewed by the blog's natural audience. I don't know how Nick Matzke and Elizabeth Liddle do it - either have the patience, or get through the Guardians at the Gates:

    "Potential Trouble – newly registered users go on this list at least for their first comment and if you are an ID-critic you’ll probably stay on it."

    If one can't comment on points of 'serious science' with bloggers like Jonathan M, it doesn't help Klinghoffer's case.

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  29. cabbagesofdoom,

    IDiots, like most apologists, while imbeciles at times, learn rhetorics quite well. One of the things they do, is count with our natural human incapacity to actually pay attention to more than a few items at a time. Which makes us go behind red-herrings very easily.

    Here genomicus managed to make you forget what the onion test is about. Just re-read Larry's main post, and you will see that WGD followed by massive loss of functions does not answer the question posed in the onion test. It just offers a mechanism for increasing amounts of junk DNA. Albeit with an unjustified magical being at the beginning of the story. Genomicus, of course, must be happy that you went behind the "arguments," rather than scratch your head and first note that the crap was not really answering the onion test at all, and that you missed the huge problem that genomicus' "propositions" consist on moving the designer wherever necessary in order to keep the idea of a designer alive regardless of junk DNA. It is obvious that for genomicus, what counts is if there is a space to hide the designer. Just demonstrating that it is just creationist stubbornness. Think of such phrases as "well, god could have used evolution!" and you will see what's going on.

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  30. @Negative Entropy: I'm intrigued as to which of my comments led you to that conclusion. As far as I am concerned, I was pointing out that WGD does not answer the Onion Test. (And arguing that introns themselves are better explained by evolution than ID - it isn't a place for a "designer" to hide.) I obviously expressed myself badly. Don't worry, though - Genomicus neither made me forget what the onion test was about nor bewitched/befuddled me with ID red herrings.

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  31. Larry Moran:

    You are right, and I was wrong. After re-reading your post, I realize that the onion test is for those who think that they have come up with a universal function for "junk" DNA.

    That blunder of mine, however, doesn't really rebut my view of how the original introns would be functional in a telic perspective.

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  32. Hey cabbagesofdoom,

    Well, Genomicus bewitched/befuddled me and almost made me go after a red-herring or two, just as many apologists have done before. Good thing that I did not answer right then.

    Best!

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  33. @Genomicus: A telic perspective of introns will, by definition, assign a function to the original introns. Only the original introns, though, I notice. As your theory appears to make no new predictions about distributions or functions (and lack thereof) for contemporary introns, it would seem unnecessary, untestable and, therefore, unscientific. Contriving a being to set things in motion and then observe from the sidelines in a fashion that is indistinguishable from non-existence has zero explanatory power.

    You are free to believe in such a thing and can, no doubt, generate scenarios of such beings that are consistent with observed data. Unless such a theory offers some additional explanatory power, however, you cannot expect scientists to take it seriously. In fact, your situation is much worse than this; by positing the existence of a Designer, I think that you totally eliminate the need for introns at all. I am aware of no classes of biological function for which introns are either necessary or sufficient. Equally, I am not aware of any specific scenarios in which introns would be the design option of choice if one was not shackled by evolutionary processes.

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  34. cabbagesofdoom:

    You raise some interesting points, but given that my view doesn't explicitly answer the onion test, I'm not sure that Prof. Moran would approve of us going off on a bit of a tangent on this thread.

    By the way:
    "As your theory appears to make no new predictions about distributions or functions..."

    Well, actually, my view isn't a theory at all. I'd say it's a hypothesis, but that might be debatable.

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  35. Genomicus,

    It is refreshing to see someone on your side admitting to an obvious mistake. Now I wonder how much would it take to show you why putting a god-designer wherever you please adds nothing to science nor to understanding anything about biological systems. But I rather not push it.

    I am perplexed. There might be hope for you to understand the scientific side. Even if you don't get to agree with godless evolution at least you might understand why we don't see the need for any gods anywhere. I will not be holding my breath though.

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  36. Negative Entropy:

    Well, firstly, I'm not sure how 'god' got into this discussion. Do we speak of gods when we discuss the engineering of an automobile? Not really. Nor do we mention any deities when we speak of the design plan behind robotics. And the same should be true when we discuss biological origins. I am indeed a teleologist, in that in my view features of life do suggest that a rational mind were behind their origin. But I do not believe that a deity was the engineer (or engineers) of those features of life. Why? Because I do not know who the rational mind(s) was. No intelligent design proponent does. You seem to assume that I believe in a deity in the first place. But, in my mind, the question of the existence (or lack thereof) of deities is no more relevant to biological origins than the question of the existence of flying saucers. Distressingly, many (but not all!) intelligent design proponents do indeed seem to imply that a deity must have "dunnit."

    ReplyDelete
  37. Negative Entropy:

    Anyways, my preliminary ramblings aside, I actually do not add an intelligent designer wherever I please. There's some stuff in biology that intelligent design adds little to (conversely, there's some stuff in biology that intelligent design can add to). But I think that the telic hypothesis can actually add something to the intron discussion.

    Consider that:

    a. Introns aren't found as often in bacterial genomes as in eukaryotic genomes. This has some interesting implications for the front-loading hypothesis. Perhaps, as Mike Gene has suggested, introns facilitated the evolution of metazoan life.

    b. Given that introns are readily found in eukaryotes, this makes me suspect that the original introns were in some way linked to the complexity of organisms. This means that the original introns were indeed functional, which is what we would expect from the telic hypothesis.

    The above two scenarios are testable, incidentally.

    ReplyDelete
  38. a. Introns aren't found as often in bacterial genomes as in eukaryotic genomes. [...] Perhaps [...] introns facilitated the evolution of metazoan life.

    I think the issue here is most likely the relaxation of selection against genome expansion (ie, a similar issue to the rest of junk; lack of restraint rather than positive advantage). Bacteria are selected to replicate quickly. Eukaryotes are much more leisurely about it, multicellular eukaryotes even more so. The more investment is put into a large long-lived soma, the less the drag of extra DNA becomes, even though you seem to multiply up the cost by the number of cells.

    b. Given that introns are readily found in eukaryotes, this makes me suspect that the original introns were in some way linked to the complexity of organisms. This means that the original introns were indeed functional, which is what we would expect from the telic hypothesis.

    Again, the complexity of organisms goes up in tandem with the increase in somatic cell numbers, and I think that that is the underlying explanation of the pattern. Cells in a multicellular colony have different constraints from those with nothing but a cell membrane between them and the rest of the biosphere. And even single-celled eukaryotes are multicellular colonies of a sort. Although possessed of only one copy of their genome, they harness multiple mitochondria in its support.

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  39. Genomicus writes:

    You seem to assume that I believe in a deity in the first place. But, in my mind, the question of the existence (or lack thereof) of deities is no more relevant to biological origins than the question of the existence of flying saucers.

    Then your mind needs to expand a bit. ;-) Non-deity designers simply change the venue, they don't at all answer the question of biological origins. That is, if a non-deity helped design life on Earth, that simply moves the question of biological origins to the designer's home planet. Thus, the question of the existence of deities surely *is* relevant to biological origins.

    What you are left with, in the absence of some magic fellow-in-the-sky simply zapping It All into existence, is a regression of designers. As you go back in time, you must eventually reach a first designer and natural processes that gave rise to he/she/it.

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  40. If someone were to find the first hundred digits of pi encoded into the junk DNA of some organism, that would be evidence of design. If another scientist then predicted that the next hundred digits of pi would be found in the immediately adjacent junk DNA, and this prediction were confirmed, it would be almost impossible to deny ID.

    So it is possible to imagine scientific confirmation of ID. It is therefore wrong to think of ID as a necessarily unscientific hypothesis. Commenters here who suggest otherwise , how would you defuse this example?


    Hmmm. It’s possible to imagine scientific confirmation of anything. If that makes the thing itself scientific, then … yeah. :0) Still, I think your example falls into the ‘information trap’. You illustrate a kind of ID that almost wants to be found – its purpose is not to support biological function, but to use DNA as an informational notepad that says “LOOK! OVER HERE! DESIGN!”. We already know that genetic information can be 'intelligently' encoded - we build oligonucleotides by the ton, and could insert them in genomes at the drop of a hat. We could, if perverse enough, encode and insert the digits of pi. So ID exists, and science could conceivably confirm it in that artificial instance. We would nonetheless expect to be supplied with the methodology in order for that confirmation to be ‘scientific’. Someone could hope to offer something to the scientific method, but until that hope is realised, I’d be inclined to withhold judgement. I don't think science has boundaries, but it does have standards. The perennial complaint is that those standards get to be defined by scientists.

    When it comes to the biologically functional, I don’t think biology offers the kind of traction science would need to make the design distinction. We’re not talking about vertebrae spelling out “Kilroy was here”, but about structures that are so functionally useful, or apparently improbable, that Kilroy must have been there!

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  41. Genomicus,

    Sorry, but if you are going to start by denying that IDiots are trying to push a god by disguising their deity as a nameless "intelligent designer" then we are starting with the left foot. You know that ID is a way to disguise creationism, and saying things like "Because I do not know who the rational mind(s) was. No intelligent design proponent does" you are lying openly and shamelessly (I added the bold font to highlight the point where you lie the most openly).

    My ramblings aside, your "telic hypothesis" adds nothing to the intron discussion. Design is not the only way in which introns could have been "functional at the beginning" (where you seem to mean "functional to the organisms bearing them"), and thus claiming a god there does not help understand anything. We know of natural mechanisms producing functional stuff. Thus, you are putting a god there just for the sake of having a god somewhere.

    Then, if introns, selfish DNA, and junk DNA "facilitated" the evolution of metazoans and other multicellular organisms, it does not mean that they did such thing "on purpose" or "by design." Just like, if viruses "invented" DNA, as some have proposed, it does not mean that viruses did such thing for the sake of all life forms that would follow.

    Since Alan Miller also answered your "points," all I add to finish this is that there are serious philosophical problems with your "telic" propositions. Just take a careful and honest look.

    Adios.

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  42. Allen Miller wrote

    I suspect multiple designers, and not enough meetings at the project planning stage!


    Multiple Designers Theory.

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  43. Alan Miller:

    I think the issue here is most likely the relaxation of selection against genome expansion (ie, a similar issue to the rest of junk; lack of restraint rather than positive advantage). Bacteria are selected to replicate quickly. Eukaryotes are much more leisurely about it, multicellular eukaryotes even more so...

    Well, that's interesting but introns may have indeed facilitated metazoan evolution. Your explanation for why introns aren't as prevalent in bacterial genomes is consistent with the telic hypothesis.

    Again, the complexity of organisms goes up in tandem with the increase in somatic cell numbers, and I think that that is the underlying explanation of the pattern. Cells in a multicellular colony have different constraints from those with nothing but a cell membrane between them and the rest of the biosphere.

    This is the underlying explanation for what pattern? I didn't mention a pattern. I just said that introns are more prevalent in eukaryotic genomes than bacterial genomes, hinting that introns have some functional link with organismal complexity. And a functional link is what the telic hypothesis predicts.

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  44. Jud:

    Non-deity designers simply change the venue, they don't at all answer the question of biological origins. That is, if a non-deity helped design life on Earth, that simply moves the question of biological origins to the designer's home planet.

    Yea but you're assuming two things: (a) that the intelligence(s) must be either biological or supernatural; (b) that I am proposing that intelligence is needed to generate intelligence.

    The initial intelligence need not be biological or supernatural. In one of his sci-fi stories, Arthur C. Clarke mentioned an intelligence built on patterns of electricity. It's a fictional story, I know, but it shows that intelligence is not limited to biology.

    This brings me to my second point: intelligence is not needed to generate intelligence. Chance might be able to do the trick. There may be dozens of ways intelligence can come about. To assume that the only two options are either non-teleological evolution of "godunnit" is assuming that we know all the possible ways that intelligence can arise.

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  45. Negative Entropy:

    You know that ID is a way to disguise creationism, and saying things like "Because I do not know who the rational mind(s) was. No intelligent design proponent does" you are lying openly and shamelessly (I added the bold font to highlight the point where you lie the most openly).

    You accuse me of "lying openly and shamelessly." That's a pretty serious charge, but let's see how well it holds up to scrutiny. Let's begin with the statement in which you say I lied the most openly:

    No intelligent proponent knows (who the designer is). You're saying that's a dishonest statement. But I'd like to know which intelligent design proponents knows for a fact who the intelligent designer is and how this ID proponent figured out with scientific data who the designer is. By saying that the above statement is false, you're saying that some ID proponents do know who the designer is. But this means that there is indeed a designer, and you yourself say that there is no designer of biology. I'd like to see you resolve this contradiction that you've placed yourself in by accusing me of making a false statement.

    Gracias.

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  46. (Allan) Bacteria are selected to replicate quickly. Eukaryotes are much more leisurely about it, multicellular eukaryotes even more so...

    (Genomicus)Well, that's interesting but introns may have indeed facilitated metazoan evolution.

    Yeah, may have. But I would reject outright any notion of 'front-loading'. One has to see a removal of the selective constraint on genome expansion before the agents of expansion can creep into the genome - unless they bring some balancing advantage with them. Introns predate multicellularity.

    Your explanation for why introns aren't as prevalent in bacterial genomes is consistent with the telic hypothesis.

    What, someone wanted bacteria to have limited capacity for genome expansion? So they put them in a little bubble with an external energy-generation membrane, and only gave them two replication forks, and surrounded them by other cells that were racing for the same metabolites? Sorry, no sale!

    (Allan) Again, the complexity of organisms goes up in tandem with the increase in somatic cell numbers, and I think that that is the underlying explanation of the pattern.

    (Genomicus) This is the underlying explanation for what pattern?

    The pattern that introns are rarest in bacteria, and most prevalent in multicellular eukaryotes. A pattern consistent with decreasing constraint on genome expansion.

    hinting that introns have some functional link with organismal complexity. And a functional link is what the telic hypothesis predicts.

    Introns have a link (whether functional or not) with something about eukaryotes, I will grant you. They have multiple replication forks, linear chromosomes, meiosis (ancestrally or currently), mitosis, greater size, mitochondria, a cytoskeleton, histone, compartmentation, a non-energetic cell membrane ... Some, many or all of these may be responsible for their susceptibility to genome expansion. Complexity? Well, they are by no means all 'complex' in the way you mean.

    I don't deny that intron-enabled alt-splicing may be a mechanism for differential expression of genes in tissues. But that does not mean that that is what introns are 'for'. Evolution is a bodger.

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  47. Genomicus writes:

    Yea but you're assuming two things: (a) that the intelligence(s) must be either biological or supernatural; (b) that I am proposing that intelligence is needed to generate intelligence.

    A bit more creative than usual, but sorry, it's not getting you out of your quandary.

    The initial intelligence need not be biological or supernatural. In one of his sci-fi stories, Arthur C. Clarke mentioned an intelligence built on patterns of electricity. It's a fictional story, I know, but it shows that intelligence is not limited to biology.

    Simply substitute "natural" for "biological". Intelligence must arise in either a natural or "un-" (super-) natural fashion.

    This brings me to my second point: intelligence is not needed to generate intelligence. Chance might be able to do the trick.

    Sure. Which means that all the objections raised to evolution on the basis of probability (both valid probability calculations and the bogus math used by ID folk) apply in spades to chance creation of intelligence. Which is more likely to appear from your basic chemical soup, something on the scale of an RNA molecule, or something on the scale of you and I? And if you wish to talk of hypothetical electromagnetic energy intelligences, then do you contend the relevant probabilities (for gradual evolution from simpler constructs vs. intelligence "poofing" into existence) are any different in that situation? This is leaving aside, of course, the fact that there really is no good reason for engaging in such rank speculation in the first place, with evolution being as well-confirmed as it is on multiple scientific fronts.

    So we're back to this: Even if, though it is plainly unnecessary, one wished for some particular reason to move the origins of Earth's biota off Earth, evolution would still be an infinitely more sensible explanation than intelligence suddenly poofing into existence full-blown.

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  48. Genomicus,

    I thought you played the semantics very well, and expected that answer. But, semantics aside, you know very well that ID is an attempt at disguising belief in whatever version of the Christian gods the cdesign proponentsists hold. Also, many of them claim to know that their versions of such god indeed exist. So, even after your careful semantics, you are still lying. Only lying very carefully (maybe I should retract the "openly").

    I noted too that you were careful here: But I do not believe that a deity was the engineer (or engineers) of those features of life. You say that you don't believe, not that no cdesign proponenstsists believes ... So, this indicates that you are smart enough to understand that, despite we are distracted by this red-herring, what you propose if philosophically unsound.

    I think we are both adults here. Why play such games instead of you openly admitting whatever is behind your stance to put "teleology" at whichever point is left after semi-admitting that there might be junk DNA. It certainly is unnecessary and sounds just like "god could have used evolution."

    No hay de que.

    (You were not careful enough on this one, but I imagine you could not help yourself to giving this a rhetorical twist: Well, firstly, I'm not sure how 'god' got into this discussion. You know well that "gods" got into the discussion from the beginnings of the hiding the true cdesign proponentsists intentions to push their gods into the science classroom. Even if that meant to go into the hypocrisy of calling their gods an "intelligent designer.")

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  49. Negative Entropy:

    I thought you played the semantics very well, and expected that answer. But, semantics aside, you know very well that ID is an attempt at disguising belief in whatever version of the Christian gods the cdesign proponentsists hold.

    Yes, I agree with you the the intelligent design movement is largely motivated by the creationist creed. But this does not mean that every single proponent of intelligent design as a biological hypothesis (instead of as a movement) is a creationist or believes in a deity. So, if you are discussing biological origins with me you can drop the "god-designer" line because I oppose any attempt to get gods into science.

    Also, many of them claim to know that their versions of such god indeed exist. So, even after your careful semantics, you are still lying. Only lying very carefully (maybe I should retract the "openly").

    I have defended my position that I am not lying, and you have not shown exactly how I lied. Note that I did not say that "no intelligent design proponent claims to know who the designer is." I said that no intelligent designer knows who the designer is. The former statement is dishonest, while the latter is perfectly true. Do you think that some ID proponents do know who the designer is? If so, then please, please tell me who knows (not claims to know) who the designer is. If you cannot do that, then of course your charge that I was lying is well, false.

    You know well that "gods" got into the discussion from the beginnings of the hiding the true cdesign proponentsists intentions to push their gods into the science classroom.

    I still don't know how gods got into this discussion with me because I do NOT believe that some deity was the designer.

    Hasta la vista.

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  50. Genomicus writes:

    I still don't know how gods got into this discussion with me because I do NOT believe that some deity was the designer.

    That's fine. Would I be correct in assuming that "some deity" = "any supernatural cause"? That is, you believe whoever or whatever the designer was, it was constrained within natural laws, including the manner of its origin?

    If the answer to that is affirmative, then it seems to me you're stuck with the fact that an evolutionary, step-wise origin of a designer from simpler beginnings is infinitely more likely than an entity of such intelligence and capabilities poofing into existence full-blown. Which in turn raises the issue of why you would ever wish to believe in a hypothesis that would necessitate such an infinitely unlikely entity, in preference to the far more likely on its face, and far more scientifically well-confirmed, theory of evolution.

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  51. Genomicus,

    You insist on the semantics of those phrases. I said I noted that you were careful enough. I note too that I wasn't. But, among adults, or at least among adults who have learned to think, we know that we don't arrive at truths by who has committed the highest number of semantic mistakes. We know that rhetorics is not a way to get at truths, but rather to win debates. We know that winning debates is not the same as arriving at truths too. Got it? Rhetorics and "winning" debates is fine when your audience is stupid and you are a snake-oil salesman (or an apologist, which is practically the same).

    I agree that by mere syllogisms not all ID "proponents" would be creationists, but experience shows that all of them might be. You claim not to be, and I sure don't believe you for a second. I can't know for sure, but the way you push "telic" hypotheses with the wrong examples, and the wrong logic, and the way you play the "apologist," (concentrating on semantics and rhetoric, moving the "designer" around, omitting or ignoring or misrepresenting what evolution would actually predict--as you do in your blog, et cetera), tells me I might just be right.

    So, again, I think now that not only you are smart enough to notice the mistakes in your "telic" hypotheses. I also think you know, but you rather pretend not to. I also note that the honesty you displayed about your mistake with the onion test was just bait and switch. That's also my usual experience with apologists. You did not disappoint.

    Sayonara.

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  52. I am an ID advocate but consider myself open-minded and willing to try to understand other viewpoints. But I do not find The Onion Test all that forceful, mainly because it has absolutely nothing to do with investigating the validity of the original claim.

    From the original description:

    "Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?"

    If I have a proposed function for some non-coding DNA, why should I be obligated to explain why some organisms have disproportionately more or less non-coding DNA due to the same function? I'd much rather talk about the validity of the proposed function. It is unfair to say that a proposed function "fails" because the theorist cannot subsequently explain why an onion needs 5x's more non-coding DNA than a human due to the given function.

    From Larry Moran's original post:

    "Let me give you some examples. Some people suggest that we need a big genome in order to protect our genes from mutation. If that's true then why do onions need five times more DNA? Some people suggest that we have big genomes because we're so complex and we need huge amounts of regulatory sequence. If so, why do onions need more?"

    Who cares? As an objective observer, I would want to comprehend the argument(s) for big-genomes-protect-against-mutation and the evidence presented in favor of it, and likewise would want to comprehend the argument(s) against the same theory, along with evidence that demonstrates its falsehood. i.e., science. Where does the Onion Test fit into that? I don't see how. (And btw, I have zero opinion on that specific example)

    A more speculative opinion I have on this is that TOT seems to make a rather simplistic biological assumption, that any proposed function for non-coding DNA should behave in a simple, positively related way to genome size, like

    f=bx or f=bx^2

    where:

    f --> amount of non-coding DNA due to proposed "universal" function

    and

    x --> genome size

    If the last 2 centuries of biology has taught us anything, it is to not underestimate the complexity of biology. I personally do not think we are anywhere near the bottom of the rabbit hole (your opinion may differ, but it would be only that). So I tend to take simplistic biological assumptions with a grain of salt.

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  53. Also, I don't really care too much about the "junk DNA" argument, anyway. Even assuming that the genome really is 90% junk, to me it's like unearthing the most complex piece of equipment ever witnessed and arguing about whether or not the dirt around the device was designed. Who cares? Look at the rest of it! It's amazing! And we haven't even figured most of it out yet!

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  54. Negative Entropy:

    Whatever. I'm not playing semantics: I am merely defending myself against the outrageous claim that I was "openly and shamelessly lying." Or is defending oneself against false accusations considered a rhetorical strategy?

    That said, if there is something wrong in my telic hypotheses, then I change them. If not, but if someone thinks there is something wrong with them, then I respond. But it's obvious that you have your mind made up about me. That's fine with me. I am not interested in winning talking points, really, despite what you may think. Anyways, I'm not going to waste any more of my time trying to convince someone like you who actually thinks that I may be a creationist and/or inspired by the creationist creed.

    Take care!

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  55. Jud:

    No, I do not think the intelligence is supernatural.
    What makes you think that the chance origin of non-biological intelligence is less probable than the non-teleological origin of say, the bacterial flagellum?

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  56. Genomicus writes:

    What makes you think that the chance origin of non-biological intelligence is less probable than the non-teleological origin of say, the bacterial flagellum?

    We can get back sometime to talking about the flagellum, for which there's a quite sensible evolutionary pathway. But for right now, let's concentrate on your misunderstanding (avoidance?) of my point.

    Whether you think intelligence first came about biologically, electromagnetically, or otherwise, it is always infinitely more likely that the intelligence was the end product of something that began small and simple, than that anything sufficiently complex and organized to be intelligent simply sprang into being full-blown.

    So the appropriate comparison is not between electrical and biological structures, it is between simpler and more complex electromagnetic phenomena, or between simpler and more complex biochemical phenomena.

    Is it more likely, if one speculates that intelligent electromagnetic entities exist, that they developed gradually from quite simple electromagnetic entities, or that they poofed into existence all at once? Surely the answer must be the former, from someone who thinks a rotating hair on a bacterium's butt is a bridge too far.

    The central point remains: Intelligence in whatever form - biological, electromagnetic, what-have-you - is infinitely more likely to have developed gradually from simpler structures, than to have spontaneously sprung into existence full-blown. After all, any improbabilities involved in the coming into existence of simpler structures is multiplied by many, many orders of magnitude in the case of something so vastly more complex and organized as to manifest intelligence. Then the question is, since intelligent entities spontaneously springing into existence is so utterly unlikely, why do you engage in rank speculation about such a thing occurring in preference to 150 years of careful, conscientious scientific work confirming evolution?

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  57. uoflcard writes:

    Who cares?[About the onion test.] As an objective observer, I would want to comprehend the argument(s) for big-genomes-protect-against-mutation and the evidence presented in favor of it, and likewise would want to comprehend the argument(s) against the same theory, along with evidence that demonstrates its falsehood. i.e., science. Where does the Onion Test fit into that? I don't see how. (And btw, I have zero opinion on that specific example)

    I'm lost in admiration. In the space of a few sentences you manage to express 4 utterly different assessments of the Onion Test. You -

    - Don't care about the Onion Test

    - Want to comprehend the arguments for and against the functional necessity of big genomes (the Onion Test is just such an argument, against functional necessity of a big genome in humans)

    - Don't comprehend the argument being made by the Onion Test

    - Have no opinion on the Onion Test

    So you don't care, you want to understand, you don't understand, and you have no opinion. Oh, and also, in the very next comment you say you don't care at all about the whole "Junk DNA" argument, after having spent the previous comment discussing it. Whew! If that's the sort of "logic" you've brought to the table when assessing evolution, no wonder you believe in ID.

    I don't think the Onion Test is at all difficult to understand. I might spend some time trying to explain it, but if you say you don't care about the whole subject of junk DNA anyway (which raises the question of why you've commented twice in a thread about it), I suppose I'd be wasting my time with you, wouldn't I?

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  58. Genomicus,

    Because "science" says so. ;) The Theory of Natural Evolution: It's always changing, but it's always right.

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  59. uoflcard,

    Read Asimov's "The relativity of wrong".

    http://chem.tufts.edu/AnswersInScience/RelativityofWrong.htm

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  60. uoflcard writes:

    The Theory of Natural Evolution: It's always changing, but it's always right.

    One could say exactly the same thing about the theory of gravitation, quantum physics, or any other well-confirmed scientific theory that is always incorporating new facts. Do you think gravity is not a fact because of that? Or nuclear fission or fusion, or any of the other consequences of quantum physics?

    These things are plainly factual, aren't they? And so is evolution. So you see just how effective your "reasoning" is in poking holes in evolution.

    Thanks for playing, try again sometime. Certainly hope you're prepared to do better than your first couple of efforts.

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  61. Jud:

    "Whether you think intelligence first came about biologically, electromagnetically, or otherwise, it is always infinitely more likely that the intelligence was the end product of something that began small and simple, than that anything sufficiently complex and organized to be intelligent simply sprang into being full-blown. "

    Quite right. So your point is what? That the hypothetical electromagnetic intelligence would have evolved? I have absolutely no problem with that.

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  62. Genomicus writes:

    Quite right. So your point is what? That the hypothetical electromagnetic intelligence would have evolved? I have absolutely no problem with that.

    My point is that it's more than a little odd that you see no problem with the concept of evolution of hypothetical electromagnetic intelligences based on no evidence whatever, but when it comes to biological evolution solidly grounded in tens of thousands, perhaps hundreds of thousands, of studies by careful, conscientious scientists over 150 years, there you draw the line. Or to put it more succinctly, the more evidence, the less you believe. Seems rather contrary.

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  63. @The Other Jim: thanks for that Asimov link. I've not seen that one before. Great stuff!

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  64. @Jud: Can you recommend an account/summary of flagellum evolution that is particularly good/clear? I was about to poke around for one and I'm feeling lazy!

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  65. Can you recommend an account/summary of flagellum evolution that is particularly good/clear?

    Not "dumbed down," reasonably well detailed, perhaps a little long and technical if the thought is to persuade IDers, but quite good for those who accept the fact of evolution and are looking for a survey:

    http://home.planet.nl/~gkorthof/pdf/pallen_matzke.pdf

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  66. Arguing that junk DNA must exist because an onion has way more DNA than a human does is absurd. It should be obvious that not all the information required to make a human being is contained in human DNA.

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    Replies
    1. Oh PLEASE clarify this one. I have my popcorn ready...

      Delete
  67. Replies
    1. So to paraphrase, you are saying DNA content is irrelevant because we need to eat vitamins?

      Delete
    2. Looked at your post -an interesting idea - but you've really mixed up "ideas" and "materials". Vit K (or iron as used in haemoglobin) are materials not "plans." Think of building a building - the DNA is the blueprints. If you told someone that not all the information was contained in the blueprints because bricks were being brought into the building site from outside they would look at you like you were nuts.

      The vit K is used to help fold proteins - but all the "information" about those proteins would still be there without the Vit K, the proteins simply couldn't be fully "built."

      Delete
  68. Dear Mr Moran,

    Picking up an old thread, we now have evidence that MOST of the DNA in a mammalian genome has a function ...
    http://www.nature.com/nature/journal/v489/n7414/pdf/nature11247.pdf

    I will be interested in your response to this.
    Stefan Gillies

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