Tuesday, June 08, 2010

Jonathan Wells Weighs in on Alternative Splicing

You can read his contribution at Evolution News & Views (sic): The Fact-Free “Science” of Matheson, Hunt and Moran: Ridicule Instead of Reason, Authority Instead of Evidence.

What I find so interesting is the willingness of Wells and Sternberg to believe whatever they find in the scientific literature. (Yeah, right.) In this case, they've found a few papers claiming that the vast majority of human genes exhibit alternative splicing. They claim this refutes the idea that introns are mostly junk.1

Do they really believe everything that's published in the scientific literature? I don't think so. They are very selective in what they believe. They only believe the papers that criticize evolution or support their belief in intelligent design. That's why they have no credibility. That's why they deserve ridicule. That's why reasoning with an Intelligent Design Creationist is a waste of time.

Don't believe me? Try reading Icons of Evolution by Jonathan Wells. It's the example we use in my course to illustrate how NOT to do science.

Here's Wells standing up for his friend ...
So why are Matheson and Moran so sure that huge portions of introns don’t have functions? According to Matheson, it’s because “Larry Moran and I clearly know a whole lot more about molecular genetics” than Sternberg.

A more naked appeal to authority would be hard to find. It sounds like an undergraduate trying to score points in a late-night bull session (“I know all about that; I took a course in it…”), not a college professor engaged in a scientific debate.

But Matheson didn’t stop there. He demeaned Sternberg by calling him “poor Richard.” He also claimed that Sternberg is “disastrously clueless” because he doesn’t understand “the important and very basic distinction between a transcript and an intron.” Since every undergraduate biology student learns that an intron is a segment of DNA, while a transcript is a segment of RNA encoded by DNA, this last jibe is on a par with Moran’s insult that Sternberg can’t do elementary arithmetic. And it is equally unjustified.
Here's what undergraduates learn when they read what I wrote in my textbook. Maybe I should send copies to Wells and Sternberg?
Internal sequences that are removed from the primary RNA transcript are called introns. Sequences that are present in the primary transcript and in the mature RNA molecule are called exons. The words intron and exon also refer to the regions of the gene (DNA) that encode corresponding RNA introns and exons. Since DNA introns are transcribed, they are considered part of the gene.


1. I'm ignoring the fact that Sternberg's calculation assumed that every intron in a gene must be alternatively spliced. That assumption is/was not based on anything in the scientific literature but it's unlikely that Sternberg will admit his error.

13 comments :

  1. {groan}

    In his ENV piece, Wells states:

    Yet Hunt cited no scientific literature, just as Moran cited none to support his assumption that only one intron per gene may be involved in alternative splicing.

    Actually, a 2008 article in Science reported 94,241 splice junctions in human messenger RNAs. Since each splice requires two junctions, and humans probably have between 20,000 and 25,000 genes, this suggests an average of 2 introns per gene involved in alternative splicing.


    In the paper Wells cites, it says:

    We observed 95% of the splicing events expected in this data set, given the current sequencing depth (Table 1) (16). We identified 4096 previously unknown splice junctions in 3106 genes, mostly called by single reads and unique to one cell type (Table 1). Many of these junctions were associated with actively transcribed genes exhibiting more exons than average, pointing to rare splicing events. Approximately 6% of all splice-junction reads identified AS events (6416 junctions in 3916 genes HEK and 5195 junctions in 3262 genes in B cells) (table S9).

    In other words, there were fewer than 2 alternative splice junctions per gene that was subject to alternative splicing. (This is not surprising – one only needs one altered junction to get a different splicing event. This is another basic mistake that the ID crew makes.) And, on average, one alternative intron per gene subject to AS.

    Incredibly, Wells, like Sternberg, thinks that all introns are alternatively spliced - that’s the only explanation for why he claims that all 94,000+ splice junctions correspond to alternatively-spliced introns. Even though the authors of a paper cited by Wells state clearly that the true number is 6% of this. (Readers should understand that there is overlap between the events seen in HEK and 3262 cells, hence the apparent discrepancy that a sharp reader may pick up.)

    Wells makes an error even more grievous than this – he talks authoritatively about a paper even though he’s only scanned the abstract. Do this in class and you don’t do very well. Try it in a qualifying exam and you end up failing. Try it in a thesis defense and …

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  2. A more obvious false assumption that the ID crew is making is a sort of ID counter-part to the fallacy of assuming that these introns in humans arose through natural selection by default.

    Even if you have introns involved in humans in some particular gene if you look at eukaryotic diversity of that gene it is unlikely to be alternatively spliced throughout all of those organisms. Alternative splicing is a secondary trait cobbled together after the fact.

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  3. Wow. This is ... just a complete non-answer.

    Wells is griping that the people arguing the opposite side of Sternberg and Meyer basically simply mocked them and provided no sources or arguments against them. The reply here:

    "Do they really believe everything that's published in the scientific literature? I don't think so. They are very selective in what they believe. They only believe the papers that criticize evolution or support their belief in intelligent design. That's why they have no credibility. That's why they deserve ridicule. That's why reasoning with an Intelligent Design Creationist is a waste of time."

    First, if there are papers that disagree over some of the numbers and conclusions, the same charge could be made against you. And it also wouldn't seem to be a bad thing, since if there are disagreements everyone's going to have to pick what they think is the right one, and then they can argue over the reasons they like one over another.

    Of course, you could be vulnerable to that charge IF YOU'D GIVEN ALTERNATIVE SOURCES. But you didn't. You simply tossed out the numbers you liked -- and adjusted them -- with no sources, even though seemingly Sternberg, at least, gave some. Thus, you can actually be accused of making stuff up. I'd rather be accused of cherry-picking than making stuff up.

    And the defense of "I know what I'm talking about" is, in fact, a "Trust me, 'cause I'm an authority". Which is a logical fallacy.

    See, if you aren't willing to show them wrong, attacking them solely on the basis of ridicule or other beliefs of theirs is, in fact, a logical fallacy called "ad hominem". If you really think reasoning with them is a waste of time, don't reason with them. However, the issue is that if they are willing to give sources and you aren't, and I'm an innocent bystander and thinking critically, who do you think I should believe?

    As for Rent's comment, you don't defend yourself from a charge that you didn't give any sources by looking something up in one of the sources provided by your opponents and saying "They got it wrong". You also don't give yourself any credibility by taking a claim where he calculates two and essentially seemingly saying "Well, it's less than two, but probably more than 1", as if that really matters all that much, and not showing how. It looks like you're nitpicking for things you can call wrong so that you can try to discredit them, but I fail to see why that's so important as to allow you to "groan" over it.

    And the thing is, I'm probably over-educated. If I can't see why it matters, most people not in science won't either.

    Maybe that explains why you guys aren't making much in-roads with common, every day people against creationism.

    Now, to sum up, I don't think mocking is all that useful a debate tactic, but I concede that in some cases it might be reasonable to think that it might be useful in support of an argument. I don't think it is, but I concede that it's not irrational think it might in those cases. However, mockery and ridicule IN LIEU OF ARGUMENT is never useful. It's okay to call someone stupid as you tear down their arguments with excellent examples and cites of proper data and evidence, but it's never okay to do that WITHOUT providing that evidence and argumentation. If you do the latter, that's a pure ad hominem argument. And for that, you should be ashamed.

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  4. I must apologize for saying "Rent" instead of Hunt. I have no idea why I kept associating his name with Rent instead of Hunt. Sorry about that.

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  5. Yes, Allan, that is clearly why evolutionary theory isn't making inroads into the general public – because Larry didn't give citations to scientific papers that our very intelligent and scientifically literate public will then go read and understand. Certainly it's not because evolutionary theory contradicts Genesis, or that ET, especially regarding arcana such as introns and entrons, can be difficult to understand, or even that most people, intelligent or otherwise, simply don't have much time to learn anything at all about it (50% of the American public read NO books last year). Why, if only every single anti-creationist statement had 100 or more links attached, surely—

    Oh wait, I just gave a 'non-answer' - I guess creationism must be more scientifically viable than I thought!

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  6. Allan writes:

    "And the defense of "I know what I'm talking about" is, in fact, a "Trust me, 'cause I'm an authority". Which is a logical fallacy."

    Actually, it is not a logical fallacy. It may not be a convincing answer, but if one actually does possess expertise in the subject under discussion, then writing "Trust me" is not a fallacious argument.

    The argument from authority, better stated as the argument from false authority, is what, for example, Wells does when he wriotes about pretty much anything.

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  7. Anonymous the first: Putting aside that I didn't mean to imply that it was the only reason, but I do think it helps. And your comments are precisely why. Let's face it, most of the people that you're trying to reach with this are not going to be experts in any scientific field, let alone biology. So they aren't going to know the answers and even if you gave them the papers they likely wouldn't understand them if they read them. So, knowing this, if you see a debate that has an impact on something you believe but is in a field you are not an expert in, what do you do?

    Imagine that you read the debate, and see one side outline their calculations, give quotations from papers and reference papers. And the other side simply says "You're wrong because you don't know what you're talking about", asserts the differences, and provides no references. Imagine that you're someone who has no particular reason to trust or distrust either side or the people involved. Who, evaluating this objectively, would you consider to be acting more properly intellectual or scientific?

    Anonymous the second: "Trust me, 'cause I'm an authority" is ALWAYS an example of the fallacy of the argument from authority. Trusting an authority -- at least provisionally -- is not, but making an argument from "He's an authority" as opposed to presenting the relevant evidence is, in fact, the fallacy of appeal to authority. Particularly when the other side is at least appearing to be trying to provide actual evidence.

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  8. Allan C Cybulskie says,

    Imagine that you read the debate, and see one side outline their calculations, give quotations from papers and reference papers. And the other side simply says "You're wrong because you don't know what you're talking about", asserts the differences, and provides no references. Imagine that you're someone who has no particular reason to trust or distrust either side or the people involved. Who, evaluating this objectively, would you consider to be acting more properly intellectual or scientific?

    Now imagine that both sides actually agree on the references or are at least willing to accept them for the sake of making a more important point. That was the case in my posting.

    Imagine that one side says the following: there are about seven introns per gene on average and 90% of genes exhibit alternative splicing. That means that at least 90% of all introns are alternatively spliced.

    Imagine that the other sides says this is incorrect. They say there may only be one intron per gene that's alternatively spliced so the minimum number is much less.

    Who do you believe?

    Did you see any references supporting the claim that every intron is alternatively spliced?

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  9. Allan C Cybulskie says,

    First, if there are papers that disagree over some of the numbers and conclusions, the same charge could be made against you. And it also wouldn't seem to be a bad thing, since if there are disagreements everyone's going to have to pick what they think is the right one, and then they can argue over the reasons they like one over another.

    Of course, you could be vulnerable to that charge IF YOU'D GIVEN ALTERNATIVE SOURCES. But you didn't. You simply tossed out the numbers you liked -- and adjusted them -- with no sources, even though seemingly Sternberg, at least, gave some. Thus, you can actually be accused of making stuff up. I'd rather be accused of cherry-picking than making stuff up.


    I take some of your points quite seriously even though it wasn't the main issue I was objecting to.

    The frequency of alternative splicing is a very controversial topic. It's not possible to cite one or two references that settle the issue. One camp says that the vast majority of human genes are alternatively spliced and the other camp says that most of the data is artifact. According to them, the real percentage of alternatively spliced genes is much lower.

    I really don't care which side you support or which side Sternberg and Wells support. I think it's an interesting and exciting debate.

    However, I do care about whether you are aware of the controversy or are completely ignorant of its very existence. When you cite one or two papers supporting one of the positions then go on to base important calculations on those citations, then that indicates to me that you don't understand the field.

    Sternberg could have said something like this ...

    "There are several papers in the scientific literature claiming that 90-95% of human genes are alternatively spliced. While this data has been challenged, let's assume, for the sake of argument, that it's correct and do some calculations about the function of introns based on this maximum number."

    That would have been the correct thing to do if you know the field. Don't you agree?

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  10. I'm not counting Sternberg blameless either. I do think he should have probably been more careful about his numbers. Which, BTW, I actually DID comment on earlier (adjusting the 7.6 down to 4 because it seems that neither side had provided any empirical evidence to show whether it was 1 or 7.6, and both seemed unlikely). I don't think Sternberg is right. I think he's probably wrong. I agree with you that he should have said that. So, then, can we agree that he should have said things differently, and you should have as well?

    Again, I'm not a biologist and, bluntly, don't really even LIKE biology (my least favourite science and I try to avoid it whenever possible). I would definitely not know what I was talking about on this issue. But, unfortunately, that also means that I don't know which of the two of you DOES know what he's talking about. That's where sources and clear expressions of what's going on are so important; if I COULD check out what you mean, I feel better about it (or, at least, won't take sides).

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  11. Oops. I missed your first post somehow.

    But, in that thread, I did show you what I'd do: Neither of you provided empirical evidence, it probably isn't always all or always only 1, so with no way to tell I re-estimate by making it a random number between 1 and all, and using the average of that, which I calculated -- possibly incorrectly -- as about 4 (3.5 if you round down instead of up), get that number, and say "Is that significant?"

    I don't even really care about the whole ID part, to be honest, since I don't really see how having DNA that used to be useful but isn't now or might be useful in the future or just will never be useful again really says anything one way or another on this. Seems easy to reconcile with both design and non-design evolution.

    I also would like to say that I didn't mean to ignore your comment about taking some of my points seriously. I do appreciate that, and if something I say here can strike a chord, it'll do a bit to relieve my growing annoyance at all sides in this whole mess.

    Which, BTW, is probably the biggest motivation behind my making the comment in the first place.

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  12. Allan:

    "Anonymous the second: "Trust me, 'cause I'm an authority" is ALWAYS an example of the fallacy of the argument from authority. Trusting an authority -- at least provisionally -- is not, but making an argument from "He's an authority" as opposed to presenting the relevant evidence is, in fact, the fallacy of appeal to authority."

    Sorry, really really thinking that you are correct does not actually make you correct:

    Fallacy: Appeal to Authority

    Also Known as: Fallacious Appeal to Authority, Misuse of Authority, Irrelevant Authority, Questionable Authority, Inappropriate Authority, Ad Verecundiam
    Description of Appeal to Authority

    An Appeal to Authority is a fallacy with the following form:

    1. Person A is (claimed to be) an authority on subject S.
    2. Person A makes claim C about subject S.
    3. Therefore, C is true.

    This fallacy is committed when the person in question is not a legitimate authority on the subject. More formally, if person A is not qualified to make reliable claims in subject S, then the argument will be fallacious.
    [http://www.nizkor.org/features/fallacies/appeal-to-authority.html]

    appeal to authority

    The appeal to authority is a fallacy of irrelevance when the authority being cited is not really an authority. E.g., to appeal to Einstein to support a point in religion would be to make an irrelevant appeal to authority.
    [http://www.skepdic.com/authorty.html]



    You are not alone in too broadly applying the concept - Wiki, and a number of other easily accessible sources do the same thing.

    As I wrote before, 'Trust me, I'm an authority" may not be a convincing argument, but it is not fallacious reasoning. Were Larry, say, a philospher, or a theologian, or a mathematician, or a physicist, and he claimed 'Trust me on the questions of genetics, I'm a theologian or great repute' - now THAT would be a classic appeal to authority of the fallacious type, which, I should not need to point out, is among the primary forms of argument emanating from anti-evolutionists these days.


    I should also point out that Larry did not, in fact, engage in such a position in the first place.

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  13. Well, posting on-line sources about it -- while admitting that some sources disagree -- doesn't make you right either. So let's skip all this and go straight to the reasonable way to settle it: by proving it.

    Let's take what my formulation of the appeal to authority is:

    1. Person A is an authority on subject S.
    2. Person A makes claim C about subject S.
    3. Therefore, C is true.

    Note that this is yours without the "claimed to be" attachment. So, in order for me to show that this is a fallacy, I have to prove the argument invalid, in that the premises can be true while the conclusion is false. If I can do that, it's a fallacy, and if I can't, then it isn't.

    Note as well that I leave the "the person isn't an authority" out, but that if this is the form of the appeal to authority that I'm using, then that isn't a fallacy, since it isn't a case where all the premises are true and the conclusion false, but a case where one of the premises is, in fact, false (1, to be specific). That makes the argument false, but not a fallacy. If this was a valid argument, the form would be right and it would be valid, but not sound, if the person was not an authority.

    So, let's look at this. Let's imagine that A is an expert in a field S, and makes a claim C. Now let us also imagine that a month later, new evidence is discovered -- even by A -- that reveals that C is actually not the case; the authority -- and field -- were incorrect about C. Plugging that into the logical form above:

    1) is true; A was and still is an authority in S.
    2) is true; A made C.
    3), the conclusion, is false; C was not true.

    The premises are true, the conclusion false, therefore the argument is invalid, therefore it is a logical fallacy.

    Now, as most sources do say, informally we should -- and do -- trust authorities. And so, in general, we do prefer an authority over non-authorities. What the fallacy essentially says, though, is that you can't use authority to settle an argumentative dispute, or to refute evidence or argumentation. So, someone who makes a claim C when asked "Why do you believe C?" is perfectly okay to say "A told me" (if they are a valid authority; if they aren't I agree that it carries no argumentative weight). But if someone else is providing evidence or argumentation for why C is incorrect, it isn't okay to simply stand on "A says it's true". A might be wrong, even about C's in their field. At that point, you have to provide WHY A says it's true, so that the arguments and evidence can be assessed.

    As for whether that was done, I'm always concerned with comments that sound like "He doesn't know what he's talking about" without providing sources and evidence. At least it deserves an admonishment to provide such.

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