Friday, September 21, 2012

Coyne's Silence on Junk DNA

Apparently, our DNA isn't so junky after all.

34 comments:

Crude said...

I think it's more complicated than that. Though the junk DNA side just lost the PR battle, clearly - the ENCODE people said that it's not junk, that's what was reported, and that's what people will remember. It's nice to be on the other side of a PR outcome for a change.

Right now there's a lot of behind the scenes bitching about what is and isn't junk DNA, how much of it is actually essential or useful to humans, etc, and both sides are screwing with their definitions. I think the whole debate is screwed up at this point.

Papalinton said...

Perhaps the reason is Coyne isn't aware he was under any obligation to respond to comment from the discredited Discovery Institute.

Papalinton said...

Here is the total sum of the Discovery Institute in its entirety. [How is that for double positive?] As the accmpanying article humorously illustrates it seems liile more tnan a 'Grand Idee' in search of relevance.

HERE IT IS

Crude said...

Linton,

A few things.

First, that idiot Coyne has considered it important to reply to Michael Behe at length in the past. I imagine part of the problem was that Behe went and got published in the Quarterly Review of Biology, something Dawkins and Myers have apparently forgotten how to do.

Second, the ENCODE results are, of course, not from the DI. What that post is asking isn't for Coyne to respond to the DI - they're asking for a response to ENCODE.

I normally just ignore you, since you're a hack. But this is a great opportunity to illustrate how, as usual, you don't even comprehend what you read. You should have brought up the real dispute - the differing definitions over what does and doesn't constitute junk DNA. But, oops, you're completely blind to that discussion.

Anyway, I'd say try to learn what's actually being discussed here and try to grasp it, but as I said in the past, that's way beyond you. Better google for a reply and paste the first line you see. Just don't plagiarize it, since you know you can't do that when I'm in the thread. ;)

Papalinton said...

Crude
Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

Interestingly, Behe's employer, LeHigh U, published this statement, in part:

" The department faculty, then, are unequivocal in their support of evolutionary theory, which has its roots in the seminal work of Charles Darwin and has been supported by findings accumulated over 140 years. The sole dissenter from this position, Prof. Michael Behe, is a well-known proponent of "intelligent design." While we respect Prof. Behe's right to express his views, they are his alone and are in no way endorsed by the department. It is our collective position that intelligent design has no basis in science, has not been tested experimentally, and should not be regarded as scientific."

Crude, I suspect Coyne is on firm ground in his commentary.

Crude said...

Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

Wonderful charge. Be a good boy and substantiate it.

Interestingly, Behe's employer, LeHigh U, published this statement, in part:

Yeah, the H isn't capitalized. And, contrary to what you imply, Lehigh did not publish this statement after Behe's article - that was years prior.

Funny - I pointed out that you don't comprehend anything. You google and paste. So what's your response to being corrected and shown that Coyne does, apparently, consider DI members as needing to be responded to?

You google and paste. ;)

Papalinton said...

Crude
" Second, the ENCODE results are, of course, not from the DI. What that post is asking isn't for Coyne to respond to the DI - they're asking for a response to ENCODE."

I don't think you or DI, or Victor for that matter have made the case for Coyne to respond to the DI. The DI is not a bona fide player in the marketplace of ideas. It seems even the Templeton Foundation, the quintessential religious institution whose charter seeks little more than attempt to buy science to prop up its religious agenda, shies away from the DI.

Crude said...

Linton,

You made a charge:

Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

Substantiate it. Or admit you can't.

I don't think you or DI, or Victor for that matter have made the case for Coyne to respond to the DI.

You have yet to make the case you're capable of understanding the issues being discussed here, much less being capable of giving much evaluation.

You've wanted attention for a while, Linton. Well, good news - in this thread, you have mine. We're going to find out just what you know about this specific issue, and ID in general.

And we're going to start with the charge you threw out. Let's see it get substantiated. You suggested that Behe's article got published basically by accident, due to poor review standards, and that said standards were tightened up after the fact in response to that.

I'd like to see evidence of this, thank you.

By the way, here's a snippet of one biologist's evaluation of Behe's article:

I think that while Behe’s summary of the results of these short-term lab experiments is generally accurate, one would be completely off the mark to extend his conclusions to evolution in general—that is, evolution as it has occurred in nature, be it in microbes or eukaryotes.

That would be Jerry Coyne.

Papalinton said...

" Lehigh did not publish this statement after Behe's article - that was years prior."
Does not make it any less relevant or pertinent, Crude.

You might also wish to read the following which places Behe's contribution in the Quarterly Review in the proper scientific perspective and context HERE

I know there is great store invested in Behe's ideas and in christian theists' attempts to keep his ideas afloat, but I am not sure it is ever going to be a productive exercise. Beheld has been sidelined in the science community not becsuse of his crazy stance on ID but lsrgely because he has yet to contribute any meaningful research in biology. That is the strength of it. His foray into 'irreducible complexity' simply put paid to any pretense his books were scientific treatises.

Victor's OP should be viewed as a humerous tongue-in-cheek little distraction, don't you think? You need to lighten up a bit, crude. ;o)

Crude said...

Does not make it any less relevant or pertinent, Crude.

Insofar as it was totally irrelevant given the context, Linton... ;)

You might also wish to read the following which places Behe's contribution in the Quarterly Review in the proper scientific perspective and context HERE

One last time, Linton. You made a specific charge. Here it is, again:

Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

You didn't say you disliked the article, you didn't say it was poorly written, you didn't even refer to the content. You said that the article was approved by a mistake in the vetting process, which was changed as a result of its publication. Two times I asked you to substantiate your charge. You didn't.

Because it never happened. You made it up, and didn't expect to be called on it. But you were - you tried to ignore it, that didn't work. So now, you're trying to change the subject.

Beheld has been sidelined in the science community not becsuse of his crazy stance on ID but lsrgely because he has yet to contribute any meaningful research in biology.

You may want to compare Behe's research and peer-reviewed work in the last decade compared to Dawkins' or Myers' before you play this game. ;)

You need to lighten up a bit, crude. ;o)

I am - I'm absolutely delighting in exposing that you're an idiot.

Oh, but wait, let me guess: you were just pretending. That bit about how Behe's article only got through because of a trip-up in the vetting process, which was then corrected? It was a schtick.

Here's your defense, Linton. Good job. ;)

Papalinton said...

" Well, good news - in this thread, you have mine. We're going to find out just what you know about this specific issue, and ID in general."

Get off the thread crude. Your 'attention' is uncalled for and frankly is a mark of boorish pious behaviour. What is there to know about ID that hasn't been so utterly and effectively and permanently determined by the Dover trial?

Who in their right mind gives a fig about about ID and the DI other than Bible crazies? Even the Texas board of education has dropped all the crap about ID, Christian creationism in its biology curriculum.

You will need more than the Bible, Apologetics and the traditions of Christian mythicism, indeed you will require no less than a miracle, to jump-start the fibrillating blood pump of christian superstition in the US.

Now be a good boy and run along and go pray to your [putatively] live lump of immaterialsm about how the naughty unbeliever is persecuting you.

You know full well ID is a dead cause. Heaven's above, get a grip.

rank sophist said...

Arguing with Papa is like fighting with wet cement. It's easy to win, but eventually you discover that you can't get out.

Syllabus said...

"Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process."

Really, guy, put up or shut up. Be a good empiricist and link to the place you got this information from.

Crude said...

rank,

It's easy to win, but eventually you discover that you can't get out.

Oh, I know. I'm not arguing with him. I'm using him to illustrate my points about him, and atheists like him. There's no getting through to the guy - right now he's squirming because, for the Nth time, he's been caught out as knowing diddly about what he talks about, even the very pages he links ad nauseum. But man, he can be made an example of.

I've ignored him for weeks, until his recent 'I'll go over to Feser's and show everyone how smart I am - oops, wait, they all think I'm a complete moron, even the atheists agree, let's try to forget that' schtick. But it's damn fun to prove he doesn't know what he's talking about when I can pull explicit evidence illustrating it.

Back to programming for me, for now!

William said...

A couple of comments:

When the human genome was sequenced, most medical commentators noted that there was no immediate benefit to the treatment of human diseases. One prevalent reason given, even back then, was that the DNA sequence was that of a "parts list" for the human body, like a list of the things used to build a house, lacking blueprint or instructions for use of the parts.

Where are those blueprints and instructions? In part, the part of junk DNA that isn't junk.

Second, there should be at least some evolutionary pressure to eliminate excessive DNA sequences, since they carry a metabolic cost and are a potential source of harmful mutation if wrongfully expressed. A modern non-ID Darwinist might think those would be reasons to contradict Coyne's predictions.

Papalinton said...

Here is a review of Behe's 'peer-reviewed' claims:

"What kind of scientist is Michael Behe?

A bad one, apparently:
Associate Professor Dr. David Lampe, of Duquesne University (Pittsburgh, Pennsylvania), did a review of Michael Behe's work from 1996 to 2005 to determine how productive he is as a scientist.[11] The study was based on how much work he had published in peer review journals, how many of his articles were referenced in further scientific research, and total number of publications. To establish a baseline, Lampe used Sean B. Carroll of the University of Wisconsin, who studies the developmental basis of evolutionary biology. He summarizes his findings thusly:
To summarize, Michael Behe has published 17 “items” since 1996,1 but only one of those items is a primary research paper related in any way to his ID research program, and that paper never mentions ID. His most important work, Darwin’s Black Box, has been cited 80 times, mostly negatively or else in non-science journals. Sean Carroll, by contrast has published 36 peer-reviewed papers and been cited a total of 1,508 times.
I conclude, based on the evidence, that Michael Behe is obviously not a scientist of the first rank and appears not to be doing any serious work at the present time. More to the point, ID creationism is not an important idea in science. Science is a meritocracy where ideas earn their place. Until ID shows it can be used as a productive idea to perform scientific work it should not be presented as a viable alternative to well-established evolutionary theory. Academic freedom issues are simply not germane in this context. Short-circuiting the normal process used to establish the scientific ideas we teach to students is simply dishonest.

Lampe's footnote in the original reads:
1 On October 10, 2005 I took a look at Behe's expert testimony for the Kitzmiller et al. vs. Dover Area School District trial on teaching ID in the public school classroom currently underway in Harrisburg, PA. In his expert testimony Behe lists a much longer curriculum vitae than the one I used above. It contains 56 items, instead of the 17 I found initially. None of this latter material was cited in the science citation search I used or appeared in my PubMed search. I must say, the longer list is highly unusual. Among the "extra" 39 publications there are:
. translations of Darwin's Black Box into 7 different languages (each cited as a new item);
. two web-based articles;
. 9 letters, critiques, or essays in conservative political or religious magazines (Crisis, First Things, American Spectator, National Review, and The Weekly Standard);
. one poster abstract;
. at least 6 more book chapters in overtly religious books;
. lots of other book reviews, letters, etc. One quickly loses track in here.
This is fine as far as it goes, but the nature of this material is very unusual for a scientist who claims to have an active research program in the science of intelligent design. It is not surprising to me that Behe would not list this latter work on his Lehigh website or that it is not cited by scientists. A great deal of it is material that is simply irrelevant on an academic scientific curriculum vitae. ID is supposed to be scientific and I think this other material really betrays the underlying motivation of ID creationism. A dispassionate person would reasonably conclude that Michael Behe is peddling ID creationism to a narrow constituency and relying on them to demand a change in school curricula. Unfortunately, salesmanship is no substitute for research. Indeed, I don't see how he has time to produce any data!!

My suggestion is "get back in the lab."


CONT.

Crude said...

Linton,

Here is a review of Behe's 'peer-reviewed' claims:

Not what was asked for.

Here's the theme of the thread at this point. Here's your claim:

Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

Substantiate, or - finally, and at this point awkwardly - retract. Otherwise, I'll just bookmark this thread as yet another piece of evidence in the Linton file. You know, along with the plagiarism, the 'you have to use methodological naturalism to find the supernatural!!!' schtick, your crashing and burning at Feser's blog within the span of a day, etc.

Substantiate or retract, Linton. ;)

Papalinton said...

CONT.
On the matter of ENCODE:

A little bit of overblown hype by DI and religionists everywhere, methinks:

See HERE

Birney dodges but Sparc nails it.
by T. Ryan Gregory, on September 10th, 2012
Ewan Birney has a new post up on his blog about reaction to the ENCODE publications and the associated media extravaganza last week. Unfortunately, it adds very little of substance to the discussion and most of the main criticisms are dodged again. But, the one redeeming feature of the post is the following comment left by “Sparc”, which nails the problem exactly:

IMHO the issue is not the precission of ENCODE’s definition of “function” but rather about the fact that ENCODE ignored the well established and defined concept of Junk DNA. It’s as if some geographer would define hills with height over base > 100m as mountains. This would transform the majority of the world’s surface into mountains. It is obvious that this wouldn’t make sense even if the given definition is very precise.

And see HERE


Crude said...

Here's the theme of the thread at this point. Here's your claim:

Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

Substantiate, or - finally, and at this point awkwardly - retract. Otherwise, I'll just bookmark this thread as yet another piece of evidence in the Linton file. You know, along with the plagiarism, the 'you have to use methodological naturalism to find the supernatural!!!' schtick, your crashing and burning at Feser's blog within the span of a day, etc.

Substantiate or retract, Linton. ;)

Papalinton said...

'Here is a review of Behe's 'peer-reviewed' claims:'

"Not what was asked for".


But you were clear in your claim of Behe's standing as a 'bona fide[?] scientist:

CRUDE: "You may want to compare Behe's research and peer-reviewed work in the last decade compared to Dawkins' or Myers' before you play this game. ;)"

Sorry crude, I know theists are clutching as hard as they might to tradition as civilization moves into the post-Christian phase. It is to be expected that theists become somewhat fearful and desperate mindful of the changing nature of their circumstances. The DI's somewhat manic challenge to Coyne re ENCODE is symptomatic of that rearguard action. You and Behe have had it good for some 1500 years of dominance of christian superstition but social and cultural evolution is inexorable. Once christian woo has been allowed to wind down toward optimal entropy, as it is clearly trending, society then will be able to pay closer attention to mitigating the more menacing and unpredictable manifestation of the christian doppelganger, Islam.

Crude, enjoy your brief moment in the sun. ["'It's nice to be on the other side of a PR outcome for a change."]


Crude said...

But you were clear in your claim of Behe's standing as a 'bona fide[?] scientist:

I said he's in better shape than Myers or Dawkins as of now. And, you're changing the subject.

Again:

Here's the theme of the thread at this point. Here's your claim:

Yes, the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process.

Substantiate, or - finally, and at this point awkwardly - retract. Otherwise, I'll just bookmark this thread as yet another piece of evidence in the Linton file. You know, along with the plagiarism, the 'you have to use methodological naturalism to find the supernatural!!!' schtick, your crashing and burning at Feser's blog within the span of a day, etc.

Substantiate or retract, Linton. ;)

Crude said...

Actually, why continue that.

Linton, you made it up. In a panick, confronted with evidence that didn't fit with your worldview, or worse, your performance, you quickly ad-libbed something. When you were called on it, you tried to blow past it. When I persevered, you tried to change the subject.

It works when you're in front of a class and control of the conversation, perhaps. Anywhere else? Not so much. ;)

You're intellectually bankrupt, Linton, and a liar besides. But hey, this was mostly known. I just love demonstrating the obvious every now and then.

Papalinton said...

"...., the sppearance of Behe's article in the Quarterly Review was itself a somewhat hot button issue which resulted in the Review instituting stricter guidelines for future eligibility for publication. The Review had gotten a little tardy in their selection process."

Yes crude, I have to humbly admit to just a teensy-weensy bit of hyperbole in the above off-the-cuff statement. Apparently it was indeed somewhat of a pleasant surprise that a paper from a creationist bio-chemist was published. Clearly he appeared capable of doing good science so long as he ditched the theo-woo. It is interesting to note that there has been a dearth of Behe contributions in the QRB or any other professional journal. Obviously the selection process works.

As far as Behe's paper is concerned, Paul Braterman, from the University of Glasgow and Professor Emeritus at the University of North Texas, notes:

"As you know by now, Behe has actually had a paper published in a peer-reviewed scientific journal (Behe M.J., Quarterly Review of Biology 85(4), 2010, 419-415). Well, not exactly a paper, more of a literature review. Well, not exactly a literature review, more a review of previous reviews, reinterpreting their findings according to his own criteria. The publication itself is shoddy piece of work. I have written numerous reviews myself, and would never have dreamed of basing them on earlier reviews, rather than my own up-to-date literature search. But let that pass."

I guess you can appreciate the context of Behe's article in the QRB having absolutely nothing to do with original research. The one time he is published in a science journal happens to be little more than an exercise in hanging onto the hem of lab coats of the many dedicated scientists who actually put in the hard yards of original research that formed the substantial body of his somewhat meagre offering.


Crude said...

Yes crude, I have to humbly admit to just a teensy-weensy bit of hyperbole in the above off-the-cuff statement.

And finally. There it is. Backed to the wall, the subject not being allowed to be dropped, you... say it was 'hyperbole'.

Linton, I know you're a guy who loves to use words that sound intelligent despite your not knowing the meaning of them, but when you say basically 'Oh, yes, that paper. The one that slipped through because of lax review standards, which were after the fact altered to make sure papers like that never are published again', and this never happened, it's not hyperbole. It's just plain wrong.

But, there's that intelligence of yours on display again. You can't say "I was wrong". So you talk 'embellishment' and 'hyperbole'. Which, of course, just morphs the 'liar' charge to 'bad liar'.

Well done, man. Truly, yours was a brilliant display.

That's sarcasm, Linton. And you may want to look up the word's definition before you use it. ;)

Papalinton said...

"You're intellectually bankrupt, Linton, and a liar besides,"

'Intellectually bankrupt', 'liar', all epithets that are indistinguishable from and interchangeable with atheism according your lexicon, crude. No surprises there. In fact I would have been surprised had you refrained from such standard christian fare. Just as Coyne is an idiot, and I'm a hack, and Dawkins is a hatemonger, to boot, it is really no great shake to envision wearing them as a badge of honor. After all what is there left for theists to express their impotent rage and discomfort at the inexorable progress of the phalanx of atheism in the world, now that the christian tale is increasingly being exposed for the superstitious mythos that it is. There is no question christian theism will be as the dodo into the future.

Papalinton said...

Rank
"Arguing with Papa is like fighting with wet cement. It's easy to win, but eventually you discover that you can't get out."

Germane to the notion of junk, arguing with bible crazies is like wrestling pigs in mud. You both get dirty but the pigs love it.

Papalinton said...

"Well done, man. Truly, yours was a brilliant display"

Well, of course it was. And I'm happy for you to notice. Regrettably it seems you have not the confidence in your own ability to express sarcasm without recourse to having to also explain it. That is emblematic of one unconfident in one's ability to communicate with sophisticated nuance. You would do well to momentarily lift your eyes from Aquinas et al and read more widely. It is good for your physical, mental and emotional health.

Crude said...

Blah blah, Linton. Once again, you look like a damn fool. Granted, I seemed silly for arguing with a fool, but a bit of silliness now and then's fun. ;)

But now, you're right back where you deserve to be: on my practical ignore list. To be rescinded the next time you make an ass out of yourself and I can have some fun pointing it out.

So, you know. See you later today. ;)

ozero91 said...

I think this is just the Higgs Boson thing all over again. It doesnt add much at all to the debate. Its still certain that less than 10% of the genome actually codes for proteins. The rest may have function, but that function is pretty mundane, such as protein binding sequences and regulatory elements.

cl said...

Yep, business as usual.

Papalinton said...

Crude
"But now, you're right back where you deserve to be: on my practical ignore list. To be rescinded the next time you make an ass out of yourself and I can have some fun pointing it out."

You should be thankful. Now you have a purpose to your life. At least I have answered your prayers, and with a strike rate much greater than the other guy.

Now that we have thoroughly dispatched Behe the 'scientist' and the grandiloquent Discovery Institute, the busy hub of theo-science, in downtown Seattle [see HERE], it seems there is little more to add to the debate on Coyne's apparent silence on junk DNA.

Bilbo said...

There's still a lot of debate about the significance of ENCODE's claims. Michael White, for example, still argues that most of our genome is still junk:

http://www.huffingtonpost.com/michael-white/media-genome-science_b_1881788.html

Meanwhile, regarding Behe, his review was peer-reviewed. The only proper way to diss his paper is by another peer-reviewed paper.

cl said...

Bilbo,

"There's still a lot of debate about the significance of ENCODE's claims. Michael White, for example, still argues that most of our genome is still junk:"

Yeah, I saw that, too, but arguments from incredulity don't have much sway on me, so I just chuckled and chalked it up to more human arrogance.

William said...

I find the entire debate, as it relates to theism, wanting.

If you want a real example of purported inefficiency, what about the amount of solar energy which does not act on our planet? Now THAT is purported inefficiency.

Accept that as a theist, and I grant junk DNA without a qualm.