ENCODE’s ‘junk DNA’ claims spark biological bunfight An overly-promotional – or perhaps merely badly-written – abstract in Nature has spawned a biology boffins’ bunfight. It started with this item, “An integrated encyclopedia of DNA elements in the human genome”, which makes the startling claim that the ENCODE project (Encyclopedia of DNA Elements) had data which “enabled us to …
“provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called 'junk' DNA”
Interesting. Do they specify what part of mass this is mean for? Ave marias? Partaking in the Blood of Christ ritual? Gobbling tasteless bread? Kneeling? Singing?
“provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called 'junk' DNA”
I don't think that this is a problem, nor should it be.
It's a sorry day when the scientifically divined truth of a matter is seen as less than idea, because it might give weight to unscientific thinking.
"It's a sorry day when the scientifically divined truth of a matter is seen as less than idea, because it might give weight to unscientific thinking."
Somewhat related is the idea that certain scientific positions should be accepted because of their political, ideological, or propagandistic utility. Three really obvious examples that spring to mind are: Leonard Susskind's assertion that string theory should be accepted and supported because it strengthens atheism; the underemphasis - sometimes to the point of complete denial - of the influence of genetics in human behavior; and the overemphasis - sometimes to the point of strict determinism - on the role of genetics in human behavior.
Examples both historical and contemporaneous could of course be multiplied ad libitum.
> God has a bad compiler, a self-written compression library and moreover codes bad dung when it comes to anything high-level.
Or was quite good at producing redundant, fail-safe solutions with built in monitoring. Yeah, those of us in IT can tell you how often that happens without intelligent design!
Creationist "comfort" is irrelevant. What would be an interesting study however, is to assess whether expecting "design" might actually accelerate scientific progress. While the genome project carried on, was there a negative impact on the progress of science due the assessment that lots of DNA is junk? Would more people have worked on DNA analysis if that assessment had not been made?
I'm not suggesting scientists should defer to a Church, but putting aside the study of all things pre-history, when it comes to hard science, does an atheist worldview impede scientific progress?
Would an expectation of order rather than chaos improve science?
/troll
"negative impact on the progress of science" - No! Because real scientists have never assumed the junk DNA is junk. If they had, then the Human Genome Project would have been a lot smaller - just sequence the exons. Junk DNA was always a bit of a problem for molecular biologists to explain, why would a highly-evolved organism carry around so much rubbish, so it was studied and there are competing theories.
<joke>I know! The junk is actually the Designer's source code comments, which proves the Designer wants us to re-engineer ourselves just as soon as we've learnt to read them!</joke>
The problem is we still have far too much prototype code in us. Too many layers to the logic, using doubles when a char would be sufficient, that kinda thing.
If only 3% of the DNA actaully does something outwardly useful then the remaining 97% must be there for background processes, considering the amount of defects with people I wouldn't be surprised if our DNA was compirsed of a state machine 20 layers deep.
$DEITY has a bad compiler, a self-written compression library and moreover codes bad dung when it comes to anything high-level.
Oh I don't know now, he (or she) seems to have got quite a good implementation of Inheritance and Polymorphism. And who would have thought that a dangling pointer could be so much fun.
However I doubt if $DEITY is a programmer:-
A mechanical engineer, an electrical engineer and a civil engineer were arguing over what type of engineer $DEITY was.
The mechanical engineer pointed to the body's intricate skeletal/muscular system and proudly stated that $DEITY must have been an mechanical engineer. The electrical engineer said that was ok but he felt that the brain and nervous system were of such incredible design and complexity that $DEITY had to be an electrical engineer.
The mechanical engineer and the electrical engineer both looked at the Civil engineer who was smiling at their discussion. "I suppose you think $DEITY was a civil engineer" they said.
"Of course" replied the civil engineer. "Who else would put a waste outlet next to a major recreational area"?
This could have been an interesting and informative article, but some key errors crept in early on:
1) "Noncoding DNA" does NOT mean "not *associated with* encoding protein strings"; rather it means "not encoding protein strings". As an analogy, only the characters in this article that make up the article's words would be the "coding" characters, while the title, formatting, HTML tags, ads and so forth would be "noncoding" characters, even though many of them are in fact "associated with" the article's text.
The results of this major study have not changed our estimates of the proportion of the genome that is non-coding, as the coding part remains a small fraction of the total. Rather, the study has attempted to assign some function to much of the non-coding part that previously had no known function assigned. Again, pushing our genome-as-Reg-article analogy, the study has identified some characters as parts of the title, others as formatting characters, others as indicating where ads should be placed, others as ad content, others as the first characters of every line, and more. Clearly, the initial functions in this list are potentially quite interesting to would-be genome/Reg-article decoders. The later functions I listed, such as those involved with serving ads, are indeed "functions", but unlikely to be significant for the function of the article. Finally, there are likely to be chunks of characters without any function for the article -- perhaps a bit of someone's debugging core dump that was accidentally pasted in, or old, now irrelevant, comments. The last is what everyone would agree on as true "junk" DNA; many would also argue that the genomic analogs of ads and their functional elements also belong in the evolutionary "junk" bin (in DNA, these include sequences such as integrated retroviruses, transposons, and so forth). A controversial aspect of the recent study is that it also includes many physical features of the DNA as potential functional regions; although in a limited number of cases, these have been associated with some clear function, it's unclear whether the association holds in general. In our analogy, this would correspond to sites such as the first characters of every line. These account for much of the difference between the 20% and 80% numbers.
2) Nobody (other than the article's author) suggested that "functional" "...means that even being replicated counts as a 'function'". Since essentially 100% of the DNA in the cell gets replicated when the cell divides, that would unhelpfully define 100% of the DNA as "functional" just because it exists! At least one knowledgeable commenter did tweet that the 80% number "...includes definitions of 'activity' barely more interesting than 'replicated'..." and it's that definition of "interesting" that causes all the controversy.
3) Scientists should not decide what results to publish based on whether Intelligent Designists (or even so-called climate denialists) will find succor in their results. What is, is; if someone finds that to be compatible only with creationism, that's the person's own issue, not that of society. Along those lines, I'd caution readers that the mere fact of even 100% of the genome having some function would not be evidence one way or the other in that specific controversy.
I always thought there were two possible explanations:
1.Life is all about DNA and we are just carriers. The 2% we know are useful are just the ones getting their hands dirty so all the rest can get on with the real work :)
2.The 98% is just filler. If damage is random then most damage would impact things that don't matter.
But I'm a programmer not a biologist so both theories are probably crap :D
The Creationists and the Evolutionists are both wrong.
If you wanted to create lifeforms you would be mad to do it in your own world because if they turn out evil they would destroy you, The solution is to create them in a simulation let them evolve and periodically make adjustments*. Exactly the same as we do with AI algorithms.
At the end of the process you delete all the bad ones and introduce the good ones to reality.
The Buddhists have been saying for a long time that this world is an illusion , maybe they're on to something.
The way things are going we may all soon find out..
*According to New Scientist Magazine a technical civilisation that started just one million years ago would by now have computers so powerful that they could simulate what we perceive as reality. So who knows what an intelligence that developed more than a billion years ago could do.
<-------- Zarathustra?
It is remnants of our Human Cylon/hominid ape/Human-Human blood being mixed successfully?
Or, possibly -- if there is a God/Supreme Being/Nature, whatever, he/she/it has a great sense of humor-- keep making findable the things that will confound, confute, and otherwise embarrass the stupid proseletysers and make look smart those who boldly and tirelessly TRY to REALLY, neutrally understand the world and its components and leave out the junk mystery, religion, and other mysticisms that are non-quantifiable except emotionally or for feel-good....
One example that could shut up a whole planet load of religious injectors is to ask rabid, homophobic types why HIV + controllers and HIV non-progressors and slow progressors exist. IF HIV were "God's Punishment for Homosexuality", just to use an example, then why to Non-Progressors, Controllers, and Elite Controllers exist? Probably to tell SOME humans through the continuum of humanity to just STFU!
Other examples could be why do some humans survive man-made poisons and yet others drop like flies. Why did some survive bubonic plague/black death and other massive "human eradicators", yet humanity was allowed to trundle on through time.
The DNA probably is far more useful than junk, filler, or any other negative connotation or assertion of uselessness. Besides, assuming humanity will continue on for another 5,000-15,000 years in need of bodies, there will always need to be useful stuff for scientists to find out about us. Otherwise, what is the point if we in short order learn all that there is to know?
If the creationists believe that non-coding DNA is really important, why don't they just pick a simple eukaryote, make a bunch of changes in its non-coding DNA, and see if they end up with a different organism? Seriously, it's a relatively easy claim to prove or disprove, just go ahead and test it!
Because (1) that would be far too much like doing real science, and (2) it might turn out to be their equivalent of Arago's Bright Spot.
Nick Matzke needs to get over himself and shut up already. Even if 100% of dna were found to be functional, that would NOT bolster "intelligent design." Look at things that ARE intelligently designed--things that we make and program--and you'll find everything from 100% utility to all sorts of fluff and superfluous crap. Evolutionary biologists have BEEN predicting that "junk" dna would eventually be found to have some function based on the theory that natural selection tends to prune useless features. I forgot who said it, but some scientist said that biologists shouldn't be afraid to use terminology or talk about research that makes creationists wet themselves. Creationism has been falsified for ages. Intelligent Design was proven in a court of law to be nothing but creationism in a cheap tuxedo.
It's a complete and utter failure of thinking. Even religious people who are willing to look at it objectively should see this, it's bad, it makes bad assumptions, it has no falsifiability, and it is promoted in the most intellectually dishonest way.
However, what it does mean is that when arguing with creationists (which can be fun and stimulating in its own way [i.e. if they say something stupid that you haven't heard before, it gives you something to investigate]) this will become a new argument. It doesn't have to be valid, but it gives them some firepower to convince the layman who can't be bothered to read anything except creationist dogma like Behe. It promotes a misunderstanding of science that is detrimental to the spread of knowledge through the populace, which is why creationism is so dangerous in general.
"It promotes a misunderstanding of science that is detrimental to the spread of knowledge through the populace, which is why creationism is so dangerous in general."
Fuck that. If you want to know what is really detrimental to the spread of knowledge, it's post-modernism and the sociology of science.
So 2% of the *whole* genome encodes *all* the working bits?
That means the organism is devoting 50x more than is necessary to it's DNA copying/checking/repairing budget.
This suggests over generations (Say a million years) individuals who did not "waste" all that energy would out compete others. There are only 2 possible conclusions.
a) The energy budget for this process as a % of cell metabolism is *so* small even being 50x too inefficient is not real burden
b) The other 98% (somehow) *justifies* it's being retained by being *useful*.
That would be what we laymen call a *clue*.
BTW a DNA codon is a 6 bit code which codes for 20 proteins. The *logical* design would assign 2-3 codes to *every* protein. Except it assigns 1 code to a start-of-protein message and 3 to an end-of-protein, neatly leaving 60 codes to give 3 options for each amino acid *except* that's not what happens and i n1 case the amino acid tryptophan is coded by *one* codon, so any mutation at this point *guarantees* a change in outcome.
The view of the DNA/RNA/Ribosome as a passive data storage system has been obsolete for some time. It's looking more like a database with embedded rules being actioned depending on modifiers.
Evolution (change in the frequency of genetic variants) is driven by two force: random drift and natural selection. The smaller a population is the great the stochastic effects of drift, and the lesser the effects of selection. Copying DNA really isn't that energy intensive in the scheme of things, so there isn't much pressure to reduce the amount of excess DNA. While indeviduals may do very slightly better with shorter genomes, this is completely out weighed by the massive effects of drift on a species with a population size as small as humans. If you look at orgnaisms with much larger populations, like bacteria, or flies even, they do have much more compact genomes (and much less intergenic space).
That was the first thing I was taught on my first day studying Biochemistry and Cell Biology at degree level, and it's always worried me that anyone could think that there's a huge amount of DNA that serves no purpose at all - it has structure, therefore it must also have function. Much like the oft-quoted claim that "we only use 10% of our brains", that stuff isn't there for no reason; if it was, there'd be an enormous metabolic advantage to any mutation that could drop it (and the burden of maintaining and replicating it). It would have always been better to say that it is DNA that we don't know what it does, rather than that it was "junk". (It's also the reason why I don't eat GM food: I don't think we understand DNA and the engineering of it nearly as well as the marketing departments of huge biochemical corporations claim we do when trying to sell their products. I think the technology should stay in the lab for another few decades at least.)
The article from 2009 might, too....
http://www.sciencedaily.com/releases/2007/04/070423185538.htm
" Gill Bejerano, PhD, assistant professor of developmental biology and of computer science at Stanford, found more than 10,000 nearly identical genetic snippets dotting the human chromosomes. Many of those snippets were located in gene-free chromosomal expanses once described by geneticists as "gene deserts." These sections are, in fact, so clogged with useful DNA bits - including the ones Bejerano and his colleagues describe - that they've been renamed "regulatory jungles."
"It's funny how quickly the field is now evolving," Bejerano said. His work picking out these snippets and describing why they might exist will be published in the April 23 advance online issue of the Proceedings of the National Academy of Sciences.
It turns out that most of the segments described in the research paper cluster near genes that play a carefully orchestrated role during an animal's first few weeks after conception. Bejerano and his colleagues think that these sequences help in the intricate choreography of when and where those genes flip on as the animal lays out its body plan. In particular, the group found the sequences to be especially abundant near genes that help cells stick together. These genes play a crucial role early in an animal's life, helping cells migrate to the correct location or form into organs and tissues of the correct shape."
More at the url...
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