Now, see, this is why you shouldn’t read a gadgets & fashion magazine for information on science. Wired has run an awful little article that breathlessly claims that junk DNA ain’t junk—it’s all got a purpose, because opossum junk DNA is different from human junk DNA (I know, that makes no sense at all, but there it is in the article).
Then, just to make it even worse, that non sequitur is followed up by bunch of “we knew it all along” quotes from creationists. And then they’ve got Francis Collins chiming in and saying that he doesn’t use the term “junk” because he thinks it’s all lying around in case there’s a future use for it. Gah. He’s supposed to know what he’s talking about; it sure doesn’t show whenever he opens his mouth.
Fortunately, Larry Moran shreds this one. In addition, one scientist who was quoted as saying something sensible in the article, T. Ryan Gregory, expands and clarifies his sole comment. It’s really too bad the writer didn’t spend more time with him than with Michael Behe.
I must be missing the argument here. I thought basic evolutionary biology/genetics says that non functional regions are more tolerant of mutations and so will diverge quickly. Doesn’t the fact that opossum junk DNA is very different to human junk support the idea that most of it does nothing, or did the article leave out that bit that would make this make sense?
The BBC is running a similar story – unrelated, but same (potential) conclusion.
Human genome further unravelled
Interesting debate, no doubt fertile material for those legions of ID quote miners out there.
Don’t IDists feel disconcerted that they pin so many hopes for proving the existence of the once almighty God on bits of junk DNA?
I have no idea whether some junk DNA might turn out to have a function. I’m not a biologist. But even if it did, how would that prove anything whatsoever regarding the existence of a supernatural deity?
I still don’t really understand the psychology of these people. At what point will they just give up? It must get pretty annoying to be proven wrong so many times. It would certainly upset me.
What a truely appalling article !
Also, surely the term junk depends on how you look at it ?
I thought that R.Dawkins’ book describes that a gene could be defined as “successful” if it “managed” to get passed into later generations and that was “it’s” primary “objective”.
Presumably if a gene doesn’t code for anything it’s unlikely to be acted upon by the processes of natural selection ?
Apologies, having properly read Larry Moran’s excellent posts, I see that my understanding of the term junk DNA was somewhat incorrect 8(
However, I can’t see how IDiots think that junk DNA can possibly support “intelligent” design, as surely a good designer would omit all the redundant stuff ?
“it makes no sense to explain the existence of non-coding DNA because it might someday prove useful. Evolution does not work that way. Elements might be coopted, but maintaining this option explains neither the origin nor the persistence of non-coding sequences.”
On the one hand you cannot select for something that might be useful. On the other hand if a sequence of genes that carried junk around turned out to be more successful because there was useful stuff there, could that make it more likely that junk would be accumulated?
How timely! The Washington Post (that famous science journal) has an article today on the front page about this very topic. Y’all probably know all about it, but I’m not in the genetics business and don’t have my ear to the ground. Apparently, many (29) papers are going to be published today elucidating a $42M project on stretches of “junk DNA” flanking active genes. Apparently, much of it is not junk at all, but overlapping genes, control elements, etc. Called Project Encode: http://www.genome.gov/10005107
Should be fun!
SG
Here’s my non-expert opinion:
Since junk DNA is supposedly not expressed, you cannot select for its contents, thus it is more likely than not to contain.. junk.
However, if the mechanisms that create junk DNA are beneficial, then an organism might be more likely to have some junk DNA in their genome because the mechanism would be selected for.
Its a quandry, for sure. I’m not even positive I got that partially correct. I only got a 3.2 in my genetics course in college :-(
G. Shelley said: “Doesn’t the fact that opossum junk DNA is very different to human junk support the idea that most of it does nothing…”
Yes.
“…or did the article leave out that bit that would make this make sense?”
Yes.
There are a ton of entertainingly stupid comments about this article over on Slashdot.
Personally, I dunno junk DNA from junk food, so it wouldn’t surprise me at all if there were some function there, but what that has to do with the FSM I don’t know.
I admit that I was surprised to see Collins make such a confused statement (twice, also to Reuters).
I have been compelled to blog on the ENCODE study and some of the not-always-very-scientific discussion of it:
Junk DNA gets wired.
“Because” versus “so that”.
More about ENCODE from Scientific American.
Brian,
You can have selection independent of the actual sequence if the sheer presence of non-coding DNA is relevant for some spacing or structural role, and you can have selection for or against the amount of DNA based on effects on cell cycles. You can also have selection against transposable elements if they insert into genes and cause mutations or other disruptions in the genome. So, it’s not simply a matter of non-coding = never under selection. The bigger problem is that you can’t have selection now for something that might be useful someday.
At what point will they just give up? It must get pretty annoying to be proven wrong so many times.
I’ve often wondered the same.
Sadly, however, I can report more directly that seeing them quoted again and again in the popular press despite their record of failure is definitely thoroughly annoying… Sorta like watching a supermarket tabloid run a self-styled ‘psychic’ making predictions for thye coming year, year after year after year, and never mind those predictions year after year after year are either (a) banally obvious, or (b) wrong.
The short memory of the public and of mass market editors is the most valuable asset of frauds everywhere.
Related note: Tom Tomorrow on Wired in 1995. Still a fairly good summary:
http://www.salon.com/12nov1995/comix/comix3.html
A while back, Wired seriously bungled a story about the Terrestrial Planet Finder, implying it was still going when it had in fact been defunded. I didn’t have high expectations of them before, but my hopes were certainly grounded after that.
Come to think of it, wasn’t it a story in Wired which coined “the New Atheism”? (The big difference being, like, selling more books.)
They’ve definitely got some dim bulbs over there.
T. Ryan Gregory says the following on his own site:
I wonder if the same kind of lossy compression turned sensible statements by Collins into silly nonsense, or if they were bad to start with. While it might sound crass, I think it’s worth suggesting that any science writer who goes out of their way to seek out creationist quotes is not a reliable information channel.
TR, thanks for the clarification. The only issue I have is with the last sentence. I think its too broad. In the case of junk DNA, the PRESENCE of junk DNA could be selected for, even if the CONTENTS can not be. That was the point of my rambling post.
The Guardian has it, too.
Collins gets complex specified information from The Lord concerning DNA delivered fresh each morning with bagels and coffee.
I am willing to open book on Behe pulling a Denton.
How much of that Guardian article is actually true? This bit in particular bothered me:
“Other sequences of genetic code are thought to be ‘on standby’, awaiting a time further down the evolutionary path when they will be beneficial to human beings.”
as it seems to contradict all established evolutionary theory as written, which makes me think that it must be a misunderstanding on the writer’s part. Can anyone clarify what’s being talked about there?
“Other sequences of genetic code are thought to be ‘on standby’, awaiting a time further down the evolutionary path when they will be beneficial to human beings.”
Well… it’s like this. Some is on standby waiting to be used later… some was going to be used but was bumped, and the rest is just on a really long layover.
Just to note:
This is very close to the ID crowd making an actual disprovable prediction. If it’s all designed, even the junk DNA, then junk DNA is more or less required to have a purpose, no?
Make the IDiots own the junk-DNA-has-a-purpose idea, is what I’m saying. And then document, document, document.
Complete ignorance question here, but wouldn’t ENCODE’s findings of all these new sequences have some implication for how we tune molecular clocks? I’m no expert in how we use those to date convergences, but it was my understanding that doing so required a whole bunch of assumptions about various seemingly non-coding areas and how much they change over time based on this.
Brian Thompson “In the case of junk DNA, the PRESENCE of junk DNA could be selected for, even if the CONTENTS can not be. That was the point of my rambling post.”
The amount of DNA can be selected for or against, certainly, but not because it may have consequences in the future. This is fundamentally incompatible with how natural selection operates. It is differential survival and reproduction among contemporary organisms within populations, and foresight is not involved.
ps: The Guardian report is nonsense pretty much from intro to end.
OK. I’ve had enough. I used to work on so-called junk DNA and did in fact find that some of it has function – in the regulation of gene expression for example. But the vast majority of it has not been observed to have any function at all, and the functional parts actually provide very strong evidence in favour of evolution. It really pisses me off that junk DNA is used again and again by IDists and their ilk. One of my papers is up on Reasons to Believe for this very reason. I’ve tried to get them to take it down, but nothing doing.
So here’s my plan. I’m going to write a blog post (expect it some time this weekend) explaining exactly why my paper actually supports evolution. Then I’m going to start emailing other people whose papers are on the same website and ask them to send me similar descriptions that I will then post on their behalf. I’ll also ask each person to email the Reasons to Believe website and ask for their paper to be removed. The posts will be collected under the label Reasons Not to Believe in Lies.
If one of your papers is up on Reasons to Believe, please let me know and we’ll get started.
Oh, and another thing – that same journalist interviewed a colleague and me last week for an article she’s writing about some of our company’s products. She was completely unprepared and hadn’t even visited our website before calling us. I haven’t seen the finished article yet and now I’m scared.
as it seems to contradict all established evolutionary theory as written, which makes me think that it must be a misunderstanding on the writer’s part. Can anyone clarify what’s being talked about there?
Or a complete mis-wording. I’m not an expert, so someone who is one can feel free to correct me…
Junk DNA *could* mutate into useful DNA.
Much junk DNA is junk because it misplaced a start or stop codon. The misplaced codon could mutate again and disappear (bringing back the original gene plus accumulated mutations), a mutation could provide a new codon in a position that produces a functional gene, or a mutation within the junk could provide a function.
What I’ve read makes me think that these scenarios are not very likely, but they would be technically possible.
But saying junk DNA could be useful to humans somewhere down the line if it happened to mutate into a functional gene seems a somewhat dubious argument for saying that junk DNA has a use in anything other than quite a tenuous sense. And certainly isn’t grounds for thinking that junk DNA is stockpiling genes-in-progress for the future, which it seems to imply. Science reporting in newspapers makes me sad.
MSBC has picked it up too- see
http://www.msnbc.msn.com/id/19214813/
Expect the experts at UD to harp on it for the months to come.
And certainly isn’t grounds for thinking that junk DNA is stockpiling genes-in-progress for the future, which it seems to imply. Science reporting in newspapers makes me sad.
In chorus, folks.. “Amen” ;-)
I was trying to show where the science is and how it was manipulated, not excuse the writer.
In a way I have some sympathy for these writers but the truth of the matter is that there is just too much information coming out recently for a general “science writer” to be able to grasp all the necessary detail. Editors need to employ people who actually know about the latest developments, not someone with some sort of undergraduate arts education level of scientific knowledge.
That said there can be no excuse for asking creationists what they think of the latest breakthroughs (what next, asking a flat earther their opinion about the next satellite that NASA sends up ?) or stating that junk DNA is being kept in unused storage in the body until some sort of Lamarckian mechanism decides it is useful.
Its rather sickening for us working in the field to hear the creationists crowing about this. Researchers in gene regulation have long known that non coding or sequences are important and have simply looked for more ways of defining the truly functional segments (which are still a very small percentage of the entire ‘junk’ DNA sequences).
One very useful method to do this is to look for evolutionary conservation and another is to look for the association of functional marks (such as the location of acetylated or methylated histone molecules) with particular sequences. Have the DI or any of the other crowin creationists suggested anything at all that has been useful in this regard ? Or have they actually lifted a single pipette to carry out a single experiment ?
I can’t see why the ID crowd would be so excited about the article. Junk DNA isn’t junk DNA, it is spare parts for future evolutionary developments. Well really, I doubt if that is why it is there, but it could well do so.
But wait a minute. Evolution doesn’t exist [for them]. So why should there be a junkyard full of wrecked DNA lying around just in case? Sort of a contradiction here, isn’t it?
Get used to hazy scientific articles. Between 20-25% of the US population still believes the sun goes around the earth, the model Copernicus disproved 400 years ago. Being a reality acceptor or rationalist is always going to be like being in a leaky boat. You have to keep bailing forever or else. You just have to hope that the wingnuts don’t toss you and the bucket over the side and sink the boat!
This talk of junk DNA being useful at some time in the future sounds more than a little like Greg Bear’s Darwin’s Radio where “junk DNA” suddenly starts being expressed; driving humans to the next “stage” of evolution.
In a $0.02 from the peanut gallery (I am not in any sense a molecular biologist):
I’ve heard very plausible arguments that DNA which does not code for proteins but is transcribed to RNA behaves in ways one would not expect with the “junk DNA” hypothesis. Although I think both the creationist and popular science articles rarely address this in an intelligent way, I saw an academic lecture at Caltech by John Mattick that convinced me that this is a legitimate field of inquiry.
Because this is sufficiently far outside my field, and I don’t have my notes handy, and it was over a year ago, take the following with an extreme grain of salt:
My recollection of his hypothesis is that he proposes that there is a large quantity of DNA which does not code for proteins, but which has been shown to be transcribed into non-coding RNA. He believes it should be investigated whether this RNA serves as a regulatory system for other mechanisms in some indirect way, such as blocking or enhancing the messenger RNA or similar. He suggested that the “central dogma” of gene->RNA->protein is considered the whole picture because it works so well, particularly in the E. coli and such, but he described a plausible (but not compelling) hypothesis that eukaryotes developed a separate control system that allowed a “digital” style of control for certain functions that is sufficiently different in expression than the protein production, and that this could have been largely overlooked by scientists because the direct genes-to-proteins results were so compelling that a lot of scientists started saying things like “it’s junk, get over it” as a dogmatic belief.
I have no idea if it will turn out that Mattick is a crackpot, but he seems to have fairly good credentials, he gives a good academic talk (as assessed by an ignorant computer scientist, anyway), and as far as I know he has no particular agenda other than to investigate this hypothesis scientifically and see how it fares.
I blogged a bit right after I went to the talk here which also has a link to the talk abstract. This was immediately after the talk, so it’s more likely to be untainted by the cobwebs of my mind.
I am not intimately familiar with the “proof” that junk DNA is junk. I’ve found that, at least to an educated layman, the assumptions leading to this conclusion sound exaggerated. I don’t know if that’s accurate, or if the science writers are picking up on the same issues I am, and I don’t see any way in which this debate has any bearing on creationism of any sort… I do think, though, that I’d love to hear Mattick’s theories and similar investigations of function in noncoding DNA discussed by developmental and molecular biologists who are more qualified than I am, rather than dismissed because a bunch of science writers and creationist wonks are responding to some recent pre-publication announcement.
Do you plan on discussing the article published in Nature on new understanding of “junk” DNA? I’m curious to understand more about it.
http://www.genome.gov/25521554
Large chunks of the junk just repeat and repeat. It’s hard to imagine that that stuff is gonna come in handy after a few mutations.
It’s not like knockout studies haven’t been conducted. You can delete a lot of this junk without negative consequences.
Let the folks at the Discovery institute be the ones to sequence the salamander genome if they think junk DNA is so special.
PZ,
I am missing something here. In your headline, or somewhere.
One commenter above noted: [there are] “stretches of “junk DNA’ flanking active genes. Apparently, much of it is not junk at all, but overlapping genes, control elements, etc.” .. which conforms to my limited understanding of genetics, i.e. there is important stuff going on outside of the start-stop codons.
But your headline “It’s junk. Get over it.” …
Maybe I am reading too much into that headline, … but I find it confusing.
Okay,
‘Junk’ is narrower than ‘non-coding.’
For anyone else who needs that refreshed or clarified , this post helps:
http://sandwalk.blogspot.com/2007/04/noncoding-dna-and-junk-dna.html
What I want to know: is it the same “junk” in each of us, as opposed to having completely random nucleotide sequences in different individuals?
I strongly suspect the former, that our ‘junk’ is just as similar as are our ‘functional’ bits between each individual.
I mean, if it is really superfluous, wouldn’t random mutations accumulate in the inactive regions precisely because they have no effect (the vast majority of the time) on anything? Functional genes that mutate will either kill the organism, or be kept because the are associated with a non-lethal functionality and they are assimilated ( functions might be maintained if they are associated to desirable traits).
Does this make sense so far?
To defend Wired in general, it was their article on ID a few years back that got me so pissed off with creationists that I went on to read a few books, think a lot, renounce my faith and get on the fast-track to hell. So, err.. thank, Wired!.
Yep. There’s coding DNA, about 3% of the genome. There’s regulatory DNA, which is maybe twice that. There are scattered stretches that have structural functions in the chromosome. But then the majority is literally junk: you can mutate it, you can delete it, you can add to it, you can juggle it, and it has no discernable effect on the phenotype. We can look at its origin, and it’s stuff like the products of reverse transcriptases and duplication errors.
That some of it has acquired functions is fine; we’ll discover more instances of that. You can also argue that just the bulk of it has effects — nuclear/cytoplasm ratio has a role in regulating cell size, so it could have a kind of generic function, like the styrofoam peanuts in a shipping crate. But it doesn’t change the fact that most of it doesn’t contain information in its sequence of relevance to the organism.
Have none of these idiots ever heard of transposons, gene duplications, and retroviruses? These all make junk DNA in various ways. Indeed, this “junk” often serves as a resource for future evolution, however this is (in some cases) precisely because much of it’s just junk lying around.
Of course we don’t know how much truly functionless “junk DNA” is lying about the nuclei. But we definitely know that some is, and there may be a whole lot.
Glen D
http://tinyurl.com/35s39o
I suspected that the “junk”, given the parsimony of the system, was “old” adaptive solutions that may have “new” uses when the “new” “old” challenge happens again. No teleology, just a frugal reserve for changes met before- “in principal”- sort of. The astounding rapidity of morphological change sometimes seen in “radiation” suggests a “reserve”. Not like organisms hadn’t met changing conditions before. Some of ’em got thru all of ’em until now. They’re all “rransitional” so far.
The actual Nature articles in question are here:
http://www.nature.com/nature/journal/v447/n7146/index.html
Wired reporters may be unclear on various concepts, but this seems like a pretty interesting and substantial set of results.
and Skeptic8’s comment about “frugal reserves” is interesting; I just finished Ward’s _Out of Thin Air_ book on oxygen and evolution, and was struck by how often we’ve had extinction and radiation events where the dominant body plans changed dramatically. perhaps under those conditions, animals that had vestigial remains of old systems were more apt to survive than those that were very aggressive at purging old, no-longer-used genes, since it was easier to adapt to catastrophic changes like extinction events if they retained a larger toolbox?
My DNA is going to have a tag sale next month and get rid of all its junk.
“When genes are conserved through natural selection, it’s usually because they have important functions. ”
They could just be selfish DNA. It could just be there to change the likelihood of recombination within a gene. Etc.
Finding something useful in a junkyard does not confirm the hypothesis that there is no junk in the junkyard. The idea that “evolutionists” are somehow threatened by such discoveries is a straw man. Many “evolutionists” are also surprised at the amount of DNA that seems non-essential…it seems wasteful, and increases the likelihood of events like translocations.
Here’s a relevant paper that deserves more attention:
Marcelo A. Nóbrega, Yiwen Zhu, Ingrid Plajzer-Frick, Veena Afzal and Edward M. Rubin (1994). Megabase deletions of gene deserts result in viable mice. Nature 431, 988-993.
And then they’ve got Francis Collins chiming in and saying that he doesn’t use the term “junk” because he thinks it’s all lying around in case there’s a future use for it.
*sigh*
his cognitive dissonance is getting worse.
and after he actually did a pretty nice job of detailing how the genetics of the human genome supported the ToE in his last book.
sure the “moral law” part of his book was completely fubar, but the genetics stuff in the first half was mostly quite good.
he’s become yet another victim of:
This is your brain….
This is your brain on religion.
any questions?
How can a brain surgeon be over a century out of date WRT our knowledge of how personality and the brain are intimately tied?
Frontal Lobe Syndrome in Childhood
Frontal lobe syndrome was first defined in 1868 by J. M. Harlow. Harlow particularly emphasized the personality and behavior change after a frontal lobe lesion. In the DSM-IV classification system, the main category titled “Personality Change due to a General Medical Condition” includes the conditions related to head trauma. For the child, particularly cerebral injuries associated with severe head trauma cause ordinary behavior changes as well as deviations in development.
…
Euphoria, excessive activity or socially destructive behavior (the condition characterized by disinhibition and impulsivity) may occur owing to injury of the orbitofrontal zone of the prefrontal cortex. Frontopolar injuries cause apathy, lack of interest, insensitivity, loss of motions or activities (Caine & Lyness, 2001).
This is just one small sample of course. What a quack!
Whoops! Posted the above to the wront thread, apologies…
>>However, if the mechanisms that create junk DNA are beneficial, then an organism might be more likely to have some junk DNA in their genome because the mechanism would be selected for.
I work with evolutionary algorithms and junk DNA can serve some purposes (though these probably do not carry over to biological evolution), in that, if you introduce a number of random mutations and the mutation rate is up too high the “organisms” will start breeding vast amounts of junk DNA to water down the mutation rate and protect the functional part of their genotype.
As for the article in question, it’s beyond pathetic. The fact that the code wasn’t preserved is evidence it’s junk! You can check diverse organisms find the code that is the same and thusly predict where you will find the coding DNA. Here’s an example from my own evolutionary algorithms. The following are the genotypes of related organisms:
**/++*4e-+c1d=89f1bd2k6f1h1b63i
**/+-*4e-a=1d=8828l53b7lckkfdj9
**/++*5e-%21d%84gjgfgdhd12506dj
**/++*4e-cb1dl8ghc4fili903l4a9j
*//+/*6e-=f1d$8ge177ca2d6j66d91
*-/+/+5e-77%d=8h908fibe6e611i5j
**/++*6e–%1d=8f0832bcj735a9lj3
**/++*5e-531d=9f2b6blka7a431ibk
**/++*4e-+71d=79f021kk6f1h1063i
Anybody want to take a guess at what the important bits are and what the junk DNA is? In fact, one can tell which bits are extremely important and which have a little bit of wiggle-room if you look closely.
Tatarize…the mutation rate in the GA would be mutations/string or mutations/text-character? From what you say, it sounds like you’d allow a certain number of mutations per string, regardless of the length of the string.
But in the biological realm, we’re talking about mutations per base pair…I don’t see how increasing the length of DNA would protect genes from point mutations. It may, however, decrease the number of crossing-over events within a gene.
As for your problem, I assume the “important” stuff is the stuff that repeats in different strings. But a lot of junk DNA is highly repetitive and conserved…and yet deleting it doesn’t seem to harm the organism. So the analogy breaks down there, no?
I am going to reply to, retract and apologise for my own post at #25:
We got the article back an hour after I wrote the above and were very happy with it. Sorry to be so hasty.
If they’re going to buy into the idea that’s it’s not junk, then I’d hope they’ll also buy into the fact that the article mentions that the sequences are conserved over hundreds of millions of years. That’s a bit longer than the IDC wingnuts’ figure of 6000 years.
However, knowing their usual tactics, they’ll cherry pick the bits that they think bolster their inane theories and ignore the inconvenient bits.
Labeling it as junk was probably a mistake, though.
I think you and Razib need to duke it out:
http://scienceblogs.com/gnxp/2007/06/it_werent_junk_after_all.php?utm_source=sbhomepage&utm_medium=link&utm_content=sublink
Collins’ quote, if genuine is appalling. I agree – this is an example of “your brain on religion”.
>>But in the biological realm, we’re talking about mutations per base pair…I don’t see how increasing the length of DNA would protect genes from point mutations. It may, however, decrease the number of crossing-over events within a gene.
Typically, it doesn’t. Although near the ends of the chromosomes they tend to have higher mutation rates and thus you would probably find more junk there to protect the important genes. My point wasn’t that it held over into biological evolution, it was that it could serve a purpose without doing anything.
This seems to be how you get secondarily winged stick insects.
However, pseudogenes don’t make up a very large part of junk DNA (45 % are retrovirus/transposon corpses alone!), and because pseudogenes are not under selection, they are free to accumulate mutations that would make them dysfunctional even if the start & stop codons all came back in the right positions, so you’re right it’s not likely, and indeed it doesn’t seem to be common.
This seems to be how you get secondarily winged stick insects.
However, pseudogenes don’t make up a very large part of junk DNA (45 % are retrovirus/transposon corpses alone!), and because pseudogenes are not under selection, they are free to accumulate mutations that would make them dysfunctional even if the start & stop codons all came back in the right positions, so you’re right it’s not likely, and indeed it doesn’t seem to be common.