New York Times science writer defends the myth of junk DNA

_{Denyse O'Leary

March 7, 2015

'Junk DNA', Intelligent Design, News}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

Worries Carl Zimmer, a “No junk DNA” scenario could help creationists:

It’s no coincidence, researchers like Gregory argue, that bona fide creationists have used recent changes in the thinking about junk DNA to try to turn back the clock to the days before Darwin.

Zimmer is responding to the recent realization that there is very little junk DNA, and is apparently refurbishing and remarketing the concept, invoking of course the Sacred Name of Darwin:

The human genome contains around 20,000 genes, that is, the stretches of DNA that encode proteins. But these genes account for only about 1.2 percent of the total genome. The other 98.8 percent is known as noncoding DNA. Gregory believes that while some noncoding DNA is essential, most probably does nothing for us at all, and until recently, most biologists agreed with him. Surveying the genome with the best tools at their disposal, they believed that only a small portion of noncoding DNA showed any evidence of having any function.

But in the past few years, the tide has shifted within the field.

…

In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. “We don’t use that term anymore,” Collins replied. “It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, “turns out to be doing stuff.”

For Gregory and a group of like-minded biologists, this idea is not just preposterous but also perilous, something that could yield bad science. More.

Well bad Darwinism, anyway.

Bad creationists. Bad, bad. BAD!!

To see what Zimmer is up against, see also: Is “dark genome” becoming the new name for junk DNA?

“Researchers say junk DNA plays key role in brain development” and “Non-coding RNAs undermining the junk DNA concept?”

Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism. So even though “dark genome” makes more sense given all the functions now being identified, expect “junk DNA” to be defended in practice.

For an odd example of that, see “Nothing makes sense in evolution except in the light of junk DNA?”: “If ENCODE [a project that identifies functions] is right, then Evolution is wrong.”

And more recently, Furore over no junk DNA?

For background, see Jonathan Wells on the junk DNA myth

Pod: Richard Sternberg on “junk DNA”

More later. Meanwhile, why did Darwin’s faithful box themselves into this corner anyway? It would have been possible to construct a naturalistic theory of life in which there was no junk DNA. Readers?

Follow UD News at Twitter!

Comments

wd400:
So why to creationists and IDers have such a problem with junk DNA?
We shouldn't. However one has to be careful how one defines "junk". Then one has to remember tat unguided evolution can't even explain DNA's existence...Joe_{March 9, 2015
March
03
Mar
9
09
2015
06:40 AM
6
06
40
AM
PDT}

fifthmonarchyman: If we instead define function as something like “promotes diversity in a population” or “promotes the principle of plenitude in the grand sweep of life”. It's not hard to imagine that, if you squint real hard, anything might fall under that umbrella. Can you provide an empirical distinction so that we can test your hypothesis?Zachriel_{March 9, 2015
March
03
Mar
9
09
2015
06:11 AM
6
06
11
AM
PDT}

wd400 says If almost all the genome is functional we would expect the ~50 or so new mutations each of us have to be devistating. I say, Only if you define functional as “does something for us now”? If we instead define function as something like "promotes diversity in a population" or "promotes the principle of plenitude in the grand sweep of life". Then a genome that allows 50 or so mutations could be a very good thing. The point is course that perhaps you have too narrow an understanding of what it means to be functional. you say, Unless most of sequence space has biological function, and thus sequences are impervious to random changes. I say, What if an IDer was to hold that that functional sequence space is very sparse so that multiple changes are necessary to traverse the large barren patches. Then the ability of a genome to tolerate multiple mutations could be a very good thing. Your problem is your of idea of what qualifies as a valid function is vastly underdeveloped. you say, I suspect I am not the only person who finds it hard to extract meaning from your posts. I say, I never claimed to be the best communicator. Thank you for making the effort. Again I hope you find some one who will give you answers that will satisfy you. But I somehow doubt it will ever happen. Oh well, I guess you can continue with your current approach and see if you get a completely different result. Good luck with that peacefifthmonarchyman_{March 8, 2015
March
03
Mar
8
08
2015
07:12 PM
7
07
12
PM
PDT}

I suspect I am not the only person who finds it hard to extract meaning from your posts, fifth. Take this last post.
if they have function now then we are back to asking why mutations aren’t killing us. I say, Is not our continued existence beneficial to us? Use your head man
Your "answer" doesn't relate to the question at all. If almost all the genome is functional we would expect the ~50 or so new mutations each of us have to be devistating. Unless most of sequence space has biological function, and thus sequences are impervious to random changes, but an IDer can hardly hold that position!wd400_{March 8, 2015
March
03
Mar
8
08
2015
06:28 PM
6
06
28
PM
PDT}

wd400 asks, Is the function that all tansposons have “in principle” something that works now, or this future-function? I say, Is my air conditioner just functional in principle or does it have future-function depends on your perspective you say, If it’s future-function then no amount of research will find it I say, I'm pretty sure research could find the function in an air conditioner even before summer arrives. you say, if they have function now then we are back to asking why mutations aren’t killing us. I say, Is not our continued existence beneficial to us? Use your head man you say, If anyone want’s to try a coherent answer to the question above I’m happy to hear them. I say, I'm truly sorry you find my answers to be incoherent. That seems to be a pattern when we discuss stuff. It could not possibly be the result of your own self-defeating presuppositions so it must be me. ;-) I do hope you get an answer that will satisfy you. But I somehow doubt you will peacefifthmonarchyman_{March 8, 2015
March
03
Mar
8
08
2015
04:27 PM
4
04
27
PM
PDT}

You seem very confused now. Is the function that all tansposons have "in principle" something that works now, or this future-function? If it's future-function then no amount of research will find it (goodbye "science stopper" argument), if they have function now then we are back to asking why mutations aren't killing us. If anyone want's to try a coherent answer to the question above I'm happy to hear them.wd400_{March 8, 2015
March
03
Mar
8
08
2015
02:07 PM
2
02
07
PM
PDT}

WD400 says, WHen “highly functional” means not biologically functional, which is your claim! I say, How is increased space for mutational exploration not a biological function?? Are you honestly defining biological function to mean “does something for us now”? You say Some classes of DNA sequences are mostly junk, but noone is saying we should write-off all transposons as being junk and therefore uninteresting. I say, I'm claiming that all transposons are in principle functional if we have not found a viable function it means we have not looked hard enough or the original function has been lost. That is light years from the position the "perhaps there is some of this stuff that is not Junk so we can't write it all off." The first position tends to promote research the second not so much peacefifthmonarchyman_{March 8, 2015
March
03
Mar
8
08
2015
01:56 PM
1
01
56
PM
PDT}

How are “It’s highly functional” and “it’s not functional” compatible concepts
WHen "highly functional" means not biologically functional, which is your claim!
In the The Junk DNA framework any extra explorational space is purely coincidental. In fact selection would tend to minimize it over time.
People who don't know much evolutionary biology think this, but that's not the case. You'd expect selection is minimize junk when (a) The metabolic cost of replicating/transcribing DNA is a large part of an organism's energy budget (b) the effective population size is large (allowing efficient selection). Indeed, those two traits correlate strongly with genome size, which is one of the good arguments for junk DNA.
The reason that I don’t accept the Junk DNA framework is because it is a science stopper. If we assume no function we won’t look for a function. That seems like a pretty simple straightforward implication to grasp.
THis is... confused. Some classes of DNA sequences are mostly junk, but noone is saying we should write-off all transposons as being junk and therefore uninteresting.wd400_{March 8, 2015
March
03
Mar
8
08
2015
01:38 PM
1
01
38
PM
PDT}

WD400 says But this kind of conclusion is compatible with junk DNA as science finds it. I say, What?? How are "It's highly functional" and "it's not functional" compatible concepts??? In the The Junk DNA framework any extra explorational space is purely coincidental. In fact selection would tend to minimize it over time. This is a exactly the opposite of a view that sees such space as a functional part of the original design. Is egoism really so central to your worldview that the only functions that matter are ones that "do something for us now"? As for ID predicting function and ENCODE backpedaling. Surely you see how both could be true. The reason that I don't accept the Junk DNA framework is because it is a science stopper. If we assume no function we won't look for a function. That seems like a pretty simple straightforward implication to grasp. peacefifthmonarchyman_{March 8, 2015
March
03
Mar
8
08
2015
01:26 PM
1
01
26
PM
PDT}

It would be functional from the perspective of the designer. And since it is his design we are talking about that is the only perspective that matters in the end. But this kind of conclusion is compatible with junk DNA as science finds it. "The designer works in mysterious ways" might not be as satisifying an answer as the evolutionary one, but there is nothing incompatable with "these sequences do nothing for us now" and the ID position you lay out (that they are a kludgy design to allow future evolution). But if your answer is OK, I'm left wondering why are we told ID "predicted" that theses sequences would be shown to have biological function now, why IDists reprot every new transposon-associated function or lncRNA as evidence that the whole genome has function now (ignoring what a tiny proportion of the genome these cases add up to), and why did IDers so happily lap up ENCODE press releases but can't now adapt their views to match ENCODE's own backing away from that hype.wd400_{March 8, 2015
March
03
Mar
8
08
2015
01:01 PM
1
01
01
PM
PDT}

wd400 says But then the sequences are junk to us. I say, Do you have a mouse in your pocket? It would be functional from the perspective of the designer. And since it is his design we are talking about that is the only perspective that matters in the end. Zac says, So why does an onion needs much more DNA than a human? I say, I can only speculate. Finding the actual function will involve research. The problem with the whole "Junk DNA" framework is that it stifles that very research. peacefifthmonarchyman_{March 8, 2015
March
03
Mar
8
08
2015
12:55 PM
12
12
55
PM
PDT}

I wanted answers, not vague speculations. Perhaps on of the “functions” is to provide a space for mutational exploration. Could be (under ID, that's not really possible under the mainstream understanding of evolutoin). But then the sequences are junk to us. So why to creationists and IDers have such a problem with junk DNA? A problem so bad they are willing to swallow the ENCODE PR whole, but unable to accept that project's own walking back of their original claims?wd400_{March 8, 2015
March
03
Mar
8
08
2015
12:34 PM
12
12
34
PM
PDT}

fifthmonarchyman: The wood is equally functional in both instances it just performs different functions. You answered in the case of a violin. So why does an onion needs much more DNA than a human?Zachriel_{March 8, 2015
March
03
Mar
8
08
2015
12:27 PM
12
12
27
PM
PDT}

Wd400 says why an onion needs to much more DNA than a human? I say, You are assuming that DNA performs exactly the same function in both species. It's like asking why a forest needs more wood than a fine violin. It's a category mistake. The wood is equally functional in both instances it just performs different functions. You say, Or why the 50 or so mutations we each carry are not devestating, given you think they all fall in functional DNA? I say, Perhaps on of the "functions" is to provide a space for mutational exploration. peacefifthmonarchyman_{March 8, 2015
March
03
Mar
8
08
2015
12:16 PM
12
12
16
PM
PDT}

Which parts of the ENCODE scientists' post do you disagree with, humbled? I'd like to know what you think they've been "strong-armed" into lying about. Does anyone here who thinks junk DNA is "dead" want to explain why tey think that? Or why an onion needs to much more DNA than a human? Or why the 50 or so mutations we each carry are not devestating, given you think they all fall in functional DNA?wd400_{March 8, 2015
March
03
Mar
8
08
2015
11:53 AM
11
11
53
AM
PDT}

Seems those at ENCODE have been strong armed into doing damage control for the Darwin faithful. How dare they practise actual science, especially science that demolishes a key doctrine of Darwinian evolution.humbled_{March 8, 2015
March
03
Mar
8
08
2015
03:44 AM
3
03
44
AM
PDT}

There was a very interesting discussion with some of the ENCODE researchers on reddit: http://www.reddit.com/r/askscience/comments/znlk6/askscience_special_ama_we_are_the_encyclopedia_of/ Larry Moran: There's no question that the press has announced the death of junk DNA. Do you agree that you have demonstrated function for most of our genome? Encode researcher: ABSOLUTELY NOT: I do NOT think ANYONE has demonstrated function for most of our genome. In fact, ENCODE has not demonstrated function for ANYTHING because we published no functional studies. The only thing ENCODE has done is to find new regions on the genome that are correlated, in terms of their chemical signature (i.e. chromatin state of "openness", transcription factor occupancy, etc.), with other regions that have been proven functional by site-directed experiments. Correlated, no more and no less. And furthermore, it is even impossible to properly set thresholds for what is a real chemical signal and what is an artifact in these assays, as MH and I have discussed elsewhere in this thread. The 80% figure is almost certainly not even real chemical signatures. If you notice, 80% of the genome is the percent of the genome that is mappable so right now, I think the 80% figure simply means that if you sequence any complex genome-wide dataset deeply enough, you will eventually return the entire genome. It's just a signal-to-noise issue: if you keep looking, you'll eventually get all the noise possible: the entire mappable genome. Ewan knows this: in his blog, he says that he could either have said the 80% (low-confidence) figure or the more conservative 20% figure that we are more certain is actually telling us something that's more signal and minimal noise. But he chose the 80% figure in the end and the rest is history. Larry Moran: How much could still be junk in light of the ENCODE results? Encode researcher: Heck, all of it could still be "junk" by ENCODE results alone (and NOW when I say "junk", what I mean is that they don't have a direct effect on gene expression). First of all, the 80% figure could easily include more noise than signal because it was the informatically low-confidence set of called regions, so it's not even clear that what's in those 80% of regions are even what's in the cell. Second of all, it's unclear what many of these assays mean in terms of physical reality. For example, ChIP-Seq signal size is uncorrelated with factor occupancy or "function" as we currently understand it. Yes, we see signals where we know from other experiments that there is binding, but the seemingly most biologically important sites are not the largest signals. Therefore, the informatics thresholds are probably uncorrelated with degree of occupancy; they are only correlated with how certain we are they they are not simply an informatics artifact. Third, EVEN IF we believed that most of the regions we identify are real (i.e. there is occupancy there), as is likely the case for the more conservative 20% of the genome, that only means that that chemical signature is there -- it DOESN'T mean that this has anything to do with function. So yes, if you convert the 80% of the genome into a more conservative 20%, and then you say that you believe, say, only half of the regions identfied there are functional instead of "opportunistic" then that's 10% of the genome, which seems more in line with your estimations.goodusername_{March 7, 2015
March
03
Mar
7
07
2015
07:24 PM
7
07
24
PM
PDT}

fossil at 1: He is backing a dead horse, not a lame one. That gives pause for thought, no?News_{March 7, 2015
March
03
Mar
7
07
2015
05:27 PM
5
05
27
PM
PDT}

Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism.
Since the nature of DNA was not apparent until getting on for a hundred years after Darwin published his theory, it's stretching things to call it a "key argument for Darwinism". And the ENCODE researchers have been criticized for seriously overstating their case. Junk DNA is far from being a myth.Seversky_{March 7, 2015
March
03
Mar
7
07
2015
05:27 PM
5
05
27
PM
PDT}

In a Universe exquisitely fine tuned for Life, even "junk DNA" is pretty darn impressive. Respect the Junk.ppolish_{March 7, 2015
March
03
Mar
7
07
2015
05:18 PM
5
05
18
PM
PDT}

I am sorry but I have so little respect for Carl Zimmer it is pathetic. When I was taking a course in anthropology we were required to read a book of his on the subject and in it he presented a theory of why apes began to be bipedal that was beyond ridiculous, I mean really stupid - didn't make any real sense at all. Because of that I don't even bother to read what he has to say and I don't care what his education is or what his employment is and this article just adds to my assessment of the man.fossil_{March 7, 2015
March
03
Mar
7
07
2015
05:12 PM
5
05
12
PM
PDT}

You must be logged in to post a comment.

Leave a Reply