Wednesday, November 02, 2011

Jonathan M Flunks the Onion Test, Again

 
A few weeks ago I explained why Jonathan M is an IDiot [A Twofer]. The topic was junk DNA. Jonathan M had posted an article on Uncommon Descent where he claimed that The Onion Test is an argument in favor of junk DNA [Thoughts on the “C-Value Enigma”, the “Onion Test” and “Junk DNA”].

I explained, as politely as I could (not), that the onion test was not an argument in support of junk DNA. It's a "test" for those who think they can explain the presence of large amounts of supposedly functional DNA that looks a lot like junk. The "test" is to apply your reasoning to the genomes of various onion species to see if it makes sense.

Do you think that the excess DNA protects against mutations? Then why do some onions need a lot more protection than humans?

Do you think that the extra DNA can be explained by alternative splicing? Why do some onion species need more alternative splicing than others?

Do you think that most of the extra DNA is required for regulating gene expression? Then why do onions need more sophisticated regulation than humans?

This ain't rocket science. The description of the Onion Test is pretty easy to understand—unless, of course, you are an IDiot.

Jonathan M has taken another shot at attacking the Onion Test. This time his article appears on the official blog of The Discovery Institure: Why the "Onion Test" Fails as an Argument for "Junk DNA". The title sort of gives it away, doesn't it? We're still dealing with an IDiot.
Briefly stated, the often cited "onion test" observes that onion cells have many times more DNA than human cells do. And since the onion is considered to be relatively simple as compared to us, this discrepancy -- it is argued -- can only be accounted for if the preponderance of its DNA is, in fact, junk or non-functional. Let's see whether the concept really holds any water.
Let's go over this one more time. The Onion Test is a "test." (Look up the word "test" in the dictionary.) It's designed as a thought experiment to test a hypothesis about the possible function of large amounts of noncoding DNA. If you think you have an explanation for why most of the human genome has a function then you should explain how that accounts for the genomes of onions. Ryan Gregory knew that most so-called explanations look very silly when you try using them to account for genome size in onion species.

The Onion Test is not an argument in favor of junk DNA. It's a reality check on speculations about function.

Jonathan M still doesn't get it.

Are we surprised?


15 comments :

  1. I like how you're saying "We" as if people read your crap.

    I read J.M.'s Article and it actually made a lot of sense, had reasonably presented points, and facts to back up his logic. None of which is found in your article....

    You're just a cocky prick who thinks way too much of himself and his "logic"

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  2. He has a very superficial appreciation of a selected group of papers and likes to toss those references around to mask the absence of any real understanding of what's going on.

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  3. anonymous says,

    I read J.M.'s Article and it actually made a lot of sense, had reasonably presented points, and facts to back up his logic. None of which is found in your article....

    He's making the same points he's made before. Coincidentally, they are the same points I addressed in my review of Wells' book.

    If you aren't an expert in molecular biology and genomes, then how do you know whether his "facts" are facts and whether his article makes a lot of sense?

    I've shown you that his understanding of The Onion Test is wrong. If he gets that wrong, doesn't it cause you to wonder about the rest of what he says?

    Apparently not. You must be an IDiot.

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  4. What are you willing to bet "anonymous" is one of the DI's PR minions? It cracks me up how absolutely *none* of their well-paid flaks, Klinghoffer, Luskin, M, Wells or anyone else-- is willing to sign in here and challenge Larry. Or Ryan.

    And meanwhile, no comments are allowed at their own site. Tells you everything you need to know about their scientific credentials.

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  5. The more Ad Hominems used, the less trustworthy the writer regardless on the subject.

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  6. anonymous says,

    The more Ad Hominems used, the less trustworthy the writer regardless on the subject.

    From Wikipedia ...

    "An ad hominem (Latin for "to the man" or "to the person"), short for argumentum ad hominem, is an attempt to negate the truth of a claim by pointing out a negative characteristic or belief of the person supporting it. The ad hominem is normally described as a logical fallacy, but it is not always fallacious; in some instances, questions of personal conduct, character, motives, etc., are legitimate and relevant to the issue."

    I am not saying that Intelligent Design Creationists are wrong because they're IDiots. I'm saying they're IDiots BECAUSE they're wrong.

    You might have noticed that I take the time and effort to refute their pseudo-scientific arguements using scientific reasoning. Meanhwhile, the IDiots don't even bother to engage in the debate because their opponents are "Darwinists" and everyone knows you can't trust a Darwinist.

    ReplyDelete
  7. Anonidiot wrote: "You're just a cocky prick who thinks way too much of himself and his "logic""

    Oh look, it's cheap ad hominem time.

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  8. Do you think that the excess DNA protects against mutations?

    I'm not too sure how that would work as an explanation anyway. For all mutagens that work on a per-base rate (eg polymerase errors, or cosmic rays), they will hit just as many 'vital' parts of sequence if the genome consists of nothing but vital sequence, as if the vital parts were interspersed with lots of 'sacrificial' DNA. If someone was blindly strafing a battlefield, you'd lose the same proportion of n soldiers if they spread out with dummies in between them as if they stood shoulder to shoulder surrounded by fresh air. Only if the protective sequence was wrapped around the vital, or somehow 'deflected' errors, might there be an effect.

    Having less DNA would allow more care to be taken for a given replication time. Conversely, having lots of repetitive sequence seems to be a cause of misalignment mutations in meiosis.

    ReplyDelete
  9. The more Ad Hominems used, the less trustworthy the writer regardless on the subject.

    That's a meta-ad hominem! A neat little paradox for Philosophy Corner.

    Ad hominem: character X diminishes the authority of an individual on a subject. In your opinion character X is the use of ad hominems, applicable to any individual on any subject. You therefore use an ad hominem to diminish the authority of people using ad hominems...

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  10. Larry wrote: I'm saying they're IDiots BECAUSE they're wrong.

    Actually, I would rephrase the statement: "they're IDiots because they're systematically wrong". We are all wrong sometimes during our lifes, but those who repeatedly produce proven nonsense are either stupid or liars (of course, the options aren't mutually exclusive).

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  11. they're IDiots because they're systematically wrong. Even more so if they are wrong about the very same things they have been wrong before.

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  12. I just love jonathan m's entry on transcription factors:

    10% human genes ... 5% yeast ... 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.

    Right. Then 100% of the genes in some onions must be transcription factors (or in amebas). Why do they need such complex regulation? Which genes do the rest of the work?

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  13. I dont think anyone has pointed out that even in the Allium species with 'smallish' genomes only 2-5% is coding, the rest is non-coding- the majority of which is probably non-functional. So a closely related species that has 5 times the genome has at least 5x the amount of non-coding.
    I hate to bring this up but the IDers have missed an easy counter-argument to the Onion Test. Its not actually valid but it would persuade many in a standup debate.
    - Write off the Onion Test as recent whole genome duplications. Claim the original 1x genome had no 'junk' but the duplications do...and were not planned by the creator. Done. Now move on to CSI or IC etc etc.

    RodW

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  14. Negative Entropy wrote: Even more so if they are wrong about the very same things they have been wrong before

    That's what I meant by "systematically": it's about repeating the very same proven fallacies and not about producing an indefinite non-repeating sequence of nonsenses (obviously, the latter is yet not a really good sign...).

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  15. M. Dionis,

    I thought you meant that, but they can be systematically wrong, meaning wrong about anything they propose, and systematically wrong, meaning about the very same things. I just had to take that out of my chest.

    :-)

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