Opposable Thumbs and Upright Walking Caused By "Junk DNA"

quinnlynn writes "A group of research scientists at Yale discovered that the evolution of opposable thumbs and upright walking in humans is due to changes in the genome in the areas still classified as "junk DNA." Quoting: 'Results from a comparative analysis of the human, chimpanzee, rhesus macaque and other genomes reported in the journal Science suggest our evolution may have been driven not only by sequence changes in genes, but by changes in areas of the genome once thought of as "junk DNA." ... Researchers have long suspected changes in gene expression contributed to human evolution, but this had been difficult to study until recently because most of the sequences that control genes had not been identified. In the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic "switches" to turn genes on or off.'" Yale has also recently completed sequencing the Trichoplax genome. Trichoplax has the simplest known animal genome, and it shares 80 percent of its genes (comprised of 98 million base pairs) with humanity. Professor Stephen Dellaporta was quoted saying, "We are [excited] to find that Trichoplax contains shared pathways and defined regulatory sequences that link these most primitive ancestors to higher animal species. The Trichoplax genome will serve as a type of 'Rosetta Stone' for understanding the origins of animal-specific pathways."

Comments

I for one ....

[ColdWetDog]

Sometimes these factoids scare the coffee out of me ...

... still unknown whether HACNS1 causes changes in gene expression in human limb development or whether HACNS1 would create human-like limb development if introduced directly into the genome of a mouse.

When shall we welcome our furry, opposable thumbed overlords. Could Douglas Adams had been right all along?

Re:I for one ....

[Anonymous Coward]

only if they have 42 limbs

Re:I for one ....

[neonsignal]

Wasn't it the mice who engineered the genome change in us? Just a little experiment. The dolphins were furious.

Re:I for one ....

[corrie]

It has nothing to do with 42. It has more to do with the mouse...

Go and actually read The Hitchhiker's Guide to the Galaxy. The movie version won't help you much here.

Just like the brain areas "you don't use"

[MarkusQ]

Every time early researchers solve part of a problem they seem to label the part they haven't solved as being unimportant or irrelevant.

You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

Find out how to read the DNA code used for a few percent of the genome (the codons to protein via RNA parts)? The rest must be junk.

When will we learn? Writing "Here there be dragons" at least had to benefit that it led future explorers to (correctly) assume that these places might have something interesting in them.

--MarkusQ

P.S. I can't do car analogies, but for the last fifty years or so we've known how to extract strings from the data segment and thought we understood "the" genetic code. Now it's turning out that all that "junk DNA" in the code segment actually has a significant regulatory role in deciding which strings get printed, and when. Who would have guessed?

Re:Just like the brain areas "you don't use"

[thermian]

Actually its been widely known that 'junk DNA' does have an active role for a long time. The big problem is identifying which bits of it are responsible for regulation/transcription.

The main problem with the public's perception, and indeed that of some scientists, is the continued use of the term 'junk DNA' when the concept it embodies has been thoroughly discredited.

For the moment a lot of work does discount area's of DNA for which there isn't enough background information, but that's more to do with the need to make progress on the bits we understand, rather than to avoid looking at the junk.

This is likely why so many people still think that Junk DNA is a thing that we actively avoid. It isn't.

Re:Just like the brain areas "you don't use"

[jdrugo]

You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

This old myth actually never had its origin in science, but was created and then spread through popular media. Please don't help it survive - it's time to let it die.

Re:Just like the brain areas "you don't use"

[zappepcs]

junk dna
theory of evolution
master/slave systems

People get pissy when I insist they use proper terminology when conveying ideas and information. I think those people ignorant, yet here we are suffering (again) because of bad terminology.

While the theory of evolution is correct, the multiple uses of the word theory give rise to confusion if not downright misinformation. I'm amazed that those involved with genetic research can know of the theory of evolution on the one hand and on the other assume that there is so much junk in our genome? Now we are stuck with their original gaff. If Darwin was right about evolution, then all that DNA stuff has to be there for a reason. Same with the 10% of the brain thing. It's all there for a reason, we simply do not yet know the reason.

Master/slave is one of those terms that is correct, and technically makes sense, but now we are pc and don't like those terms anymore so we have to use something else. I've seen huge threads arguing on that one. There are more examples of terminology problems, but the point is that using the correct terminology, and naming things with their future use in mind is important. The 'here there be dragons' idea is quite valid. Sounds a lot like 'somebody needs to document this code' to me.

Re:Just like the brain areas "you don't use"

[Daniel Dvorkin]

You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

Find out how to read the DNA code used for a few percent of the genome (the codons to protein via RNA parts)? The rest must be junk.

You'd have a good point ... except that no serious researcher in neuroscience or genetics has ever claimed either of those things.

Re:Just like the brain areas "you don't use"

[gregbot9000]

I am no Biologist but I have often wondered at thew high levels of successful evolution mammals can do compared to the relatively slow levels that reptiles and insects seem to have. The idea of "Junk DNA" being merely unused DNA would make a lot more seance then it just being nothing. I wouldn't be surprised if our ability to digest rotten meat, or our spine structure being different, or our forearms being longer were all still there. It would allow for much faster adaption if instead of reinventing new structures at random all our bodies had to do was express other "Junk" genes at random.

Re:Just like the brain areas "you don't use"

[Cyberax]

Not exactly. We _know_ that a large part of DNA (about 40%) is junk, because it consists of simple repeating sequences (LINEs and SINEs).

It might have some indirect functions (like working as a buffer for mutations), but it's junk by itself.

There's also a fair amount of inactive genes and other junk.

Re:Just like the brain areas "you don't use"

[iNaya]

AFAWK

Until we've correlated every function of the human body to a gene, how can we discredit any part of the sequence as doing nothing?

Re:Just like the brain areas "you don't use"

[Anonymous Coward]

I think the real question is, after they patent this portion of DNA will be no longer be able to use our thumbs legally?

Re:Just like the brain areas "you don't use"

[Cyberax]

Because we already know some things about the genome as a whole.

SINEs and LINEs do nothing - they only propagate themselves (http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element).

Inactive genes are just that - inactive. They can't be transcribed because they lack crucial parts.

However, some parts of the DNA which were first identified as a junk do have useful functions and are called 'non-coding DNA'.

Re:Just like the brain areas "you don't use"

[jhoegl]

We actually use 90% of our brains. It has been discovered that there is "grey matter" and "white matter". "Grey matter" is thought to conduct or transport data between the "white matter", which is the processing part of our brains. So in essence we have multiple processors, much like todays CPUs except our processors are more specific in what they process. AI is around the corner, you have your choice of fears, Matrix, Transformers, 8ft tall bears that shoot laserbeams from their eyes....

Re:Just like the brain areas "you don't use"

[jhoegl]

I read the "junk DNA" as being not active, but more a footprint or history of our evolution. Watch out creationists, for you may have come from a pile of poo!

Re:Just like the brain areas "you don't use"

[GuldKalle]

But if it's useless, it ought to be more prone to mutations, and should by this time end up as random noise.
Note: i am by no means an expert, I'd just like an answer if anyone out there knows,

Re:Just like the brain areas "you don't use"

[thermian]

Not exactly. We _know_ that a large part of DNA (about 40%) is junk, because it consists of simple repeating sequences (LINEs and SINEs).

It might have some indirect functions (like working as a buffer for mutations), but it's junk by itself.

There's also a fair amount of inactive genes and other junk.

No, we have no idea what a lot of it does, but its not junk, its just not fully understood. The term junk implies we know that it does nothing, but we do not know this for sure, and a lot of what we were sure was inactive now turns out to be active after all.

Also, we don't even know for sure if 'inactive' genes are really inactive or not. Its fiendishly hard to tell an 'active' gene from an 'inactive' one as it is. Inactive in this case meaning that it is sufficiently different in form from what we understand as being an active gene that we believe it may be one longer in use, or we haven't detected expression from it.

In fact there is no method currently capable of telling active genes from inactive ones with greater than 80/12 accuracy.

This means that when 80% of genes, in fact the promoter element, which is what we look for, have been correctly identified, 12% of DNA which is known not to be Genes have been incorrectly identified as being Genes.

And that's with labeled data that has been carefully prepared. Even allowing for labeling errors, that's not great accuracy, although its pretty good that we can do that well.

Applying the same technique to unlabeled DNA (such as a straight end to end search of someones DNA sequence), and its likely your level of accuracy will drop even more.

Re:Just like the brain areas "you don't use"

[Cyberax]

But some parts of genome are completely understood. SINEs and LINEs are retrotransposons - they just try to replicate inside your genome and they make the bulk of 'junk DNA'.

Re:Just like the brain areas "you don't use"

[moteyalpha]

A strange thing happened, I removed the junk data ( sync preamble ) from my floppy disk encoding and it quit working. I agree that SINEs and LINEs are less of a factor than others but a system is responsive to all its parts and until somebody makes a human clone with all the short and long repeats removed I assume that it does something, even if it just makes a different sync preamble or a getter ( to use a radio tube analogy ) for other junk.

Re:Just like the brain areas "you don't use"

[Cyberax]

We have an animal with almost none of DNA junk - it's the famous pufferfish. It seems that it doesn't cause them any problems.

Re:Just like the brain areas "you don't use"

[moteyalpha]

I have an 8085 SDK and it has no FPU and it seems to run fine.

Re:Just like the brain areas "you don't use"

[ColdWetDog]

Somebody else is beating you up about the 10% brain issue (although when you deal with people on a regular basis it's not hard to believe that 99.9995% of a human's brain isn't used much), you Darwinism leads me to jump on you about another pet peeve of mine.

If Darwin was right about evolution, then all that DNA stuff has to be there for a reason.

Charles Darwin was amazingly right on the broader picture of speciation and evolution. Not surprisingly, he got some stuff wrong. But nowhere does ol' Charley - or any other serious tract on evolution - require the perfection that your statement implies.

Many people (biologists included) look at highly evolved structures (and by this I am specifically not including television producers) and wonder about the complexity and intricacy of it all and use these concepts as some sort of metric for perfection. Evolution doesn't require this at all. All you have to do to be successful is to produce more of you than dies off for whatever reason. If you carry large quantities of DNA (or adipose tissue or whatever) that doesn't do anything useful but doesn't do anything harmful, then that's OK. If said stuff is a selective disadvantage, then it's not so OK but it might not be a problem in terms of the ability to create progeny. Stuff doesn't have to be there for a "reason". It can be neutral or only mildly deleterious and the critter survives.

That said, it may be that these piles of repetitive sequences interspersed with sequences that used to code for something but currently don't create a gene product or are used as a control sequence, serve as evolutionary reservoir to get spliced and diced by random processes and eventually create something that does help the organism survive.

Evolution only requires that the organism muddle through better than some other organisms. It doesn't require perfection and grace.

Re:Just like the brain areas "you don't use"

[JebusIsLord]

There is good reason for us to theorize that large portions ARE junk. We have useless vestigial organs (appendix, in-vitro gills and tails etc), because there is harmless genetic code for these things even though they're useless. It is an educated hypothesis that much of our DNA is similarly useless but harmless enough not to be selected against evolutionarily.

But agreed - a lot of it is just an "I don't know what this does". Lots of it WILL be found to be functional.

Re:Just like the brain areas "you don't use"

[Cyberax]

Does it share 90% of schematics with Core 2?

Re:Just like the brain areas "you don't use"

[JebusIsLord]

Lets say a feature evolves, and then is adapted for another use later on (feathered wings for catching insects, probably later evolved to aid in flight). Some of those insect-catching genes are now useless, so they either disappear or are simply turned off. Having a few extra genes doesn't hurt the host, so they don't disappear in later generations.

Another hypothesis is that much of the "junk" is actually left-over DNA from all the retroviruses our ancestors became immune to (and made it into their reproductive cells). Lots of these retroviruses are now extinct, making the DNA "junk".

Re:Just like the brain areas "you don't use"

[julesh]

You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.
[...]
You'd have a good point ... except that no serious researcher in neuroscience or genetics has ever claimed either of those things.

Yep. This should be modded up.

For example, the "unused brain" thing has never been reliably attributed to a real scientist. Basically, it was made up by the media.

OTOH, I do believe that many geneticists did originally believe that the so-called junk DNA served no useful purpose. See this article, which suggests that at least in the 1970s there was a common belief among geneticists that at least some DNA served no practical purpose other than to replicate itself. It wasn't until about 10 years ago that we started finding actual practical uses for the so-called junk DNA, so presumably that belief persisted at least until then.

It is, however, fair to say that it has never been scienctific consensus that all junk DNA is useless. But saying that no geneticist has claimed it would be foolish, as I'm sure enough digging will turn up at least some such claims: it was until relatively recently a plausible, if extreme, position.

Re:Just like the brain areas "you don't use"

[Gyga]

It's no more prone to mutations than the rest of your DNA, it undergoes the same replication process.

Re:Just like the brain areas "you don't use"

[zappepcs]

I read a story the other day where it is posited that about 8% of our DNA is retrovirus leftovers.

On the evolution and it not requiring perfection comments, lets look at it this way. Whether we see a reason for it's existence, it is there for a reason. Mother nature is rather good at not creating useless junk everywhere. If it is left over DNA and not actively used at this point in our being, you might think of it as junk in relation to what we require of our DNA right now, or at least as far as we know, but it was there for a reason. That reason might be no more significant than it was required to build the actual DNA that we don't call junk at some point in our past. We do not know enough about it to say that it is not required, or is useless junk.

There is as yet (to my knowledge) no definitive understanding how the junk DNA plays a part in the development of mutations here and there. Much of that 'junk DNA' may well be to prevent certain mutations from happening again. While what we know about DNA is important, what we don't yet know is MORE important. Since we are only just now beginning the business of growing things in the lab, we have a long way to go before we can definitively talk about what DNA is required and what is not. Given that all life on this planet shares a great deal of common DNA it is likely that any small change could affect whether or not we grow to be humans or something else that does not live. A thorough investigation of what the junk DNA does will entail something a bit more difficult than mapping the human genome. So, summary is: junk DNA == a lot of DNA that we know almost nothing about. What we do know is that the DNA we do not call junk DNA is stuff that we know about and understand somewhat.

We all have some leftover parts; Coccyx, appendix, and perhaps a few other things that are not actively being used that we understand. Men have nipples. All of this indicates that mammalian DNA has a common starting point in view of the biology of mammals in general. Do we know with any veracity if the junk DNA is related to non-human mammalian DNA? Is this evidence of a virus that mutated us to humans? Right now, we believe that there is only a very small percentage of difference in DNA between humans and primates etc. What if that junk DNA is part of the stuff that separates us by more than that? What happens to DNA under duress? That is to ask what happens when DNA is attacked by a virus? Does any of the junk DNA turn on? Is it turned off to stop us from being super-humans? Is it turned off because of some virus long ago that stops us from being much better than we are now? That is to question whether our current state is perfect, or as good as it can be? Perhaps unlocking the knowledge of the junk DNA will be the key to living 900 years, or seeing perfectly for life. The trouble is that we don't know what it does, and as humans our first thoughts are if we don't understand it, it must be for nothing, useless, waste material. I like to think differently about Mother Nature and evolution.

Sorry about the rambling.

Re:Just like the brain areas "you don't use"

[philspear]

I am no Biologist but I have often wondered at thew high levels of successful evolution mammals can do compared to the relatively slow levels that reptiles and insects seem to have.

I am a biologist, you've got that totally backwards (it's okay though, it's for counterintuitive reasons). By most evolutionary standards, the bugs own this planet. A famous geneticist named Haldane was asked once "knowing what you do about nature, what can you tell me about God?" He said "He has an inordinate fondness for beetles." They're incredibly diverse compared to mammals. Insects dramatically outnumber us and out breed us. And their evolution rate is extremely fast due to their extreme proliferation. Pioneering studies of genetics and evolution almost always involve Drosophila flies because you can get tens of thousands of generations in a research career (and genetic change to match that) wheras you could probably get at most two human generations and only hundreds of mice generations. As one last testament to the (evolutionary) superiority of insects: cockroaches have been here before we have and will undoubtedly survive after we have nuked ourselves off the planet, they might slow down for a generation, but they've far outspecialized mammals.

Keep in mind that evolution doesn't mean higher, smarter, faster, it just means more fit to their niche. A bigger brain has given us the power to make a civilization and big buildings, but evolutionary fitness is actually measured in how many offspring you have, since that's the goal ultimately in evolution, and bugs have us whipped there.

It would allow for much faster adaption if instead of reinventing new structures at random all our bodies had to do was express other "Junk" genes at random.

That is an accepted theory, one which the current results do support (I think, I haven't read the article.) It's also worth noting that plenty of times, non-junk DNA gets co-opted for different purposes. What appears to have happened fairly often is that a gene that's needed for something gets copied, so some organism has two functional copies of it, and then one is free to be changed slightly to different purposes. I don't know the statistics, but there are huge families of closely related genes which have different purposes but were at one point probably carbon copies that now do other things.

Re:Just like the brain areas "you don't use"

[HiThere]

It may be no more prone to mutation, but it's significantly less subject to selection pressure. There's always a tiny pressure, but in non-transcribed DNA it's usually below the noise-level, unless it does something like shape the folding (of the DNA) in a significant way. Even then it can usually be overruled by epi-genetic modifications, so the selection pressure on non-transcribed DNA is trivial.

Re:Just like the brain areas "you don't use"

[HiThere]

I don't think that you understand the theory of evolution.

Evolution predicts that much junk will be generated during the process of evolution...and that it will be cleared away at a rate related to how expensive it is to continue it's existence. It also predicts that this will be a stochastic process.

At a more basic level the question becomes "What is the proper theoretical level to assign the role of replicator?" Traditionally this was considered to be either the individual animal or the population. Recently (20 years) strong arguments have been made that the proper level is the gene. This has been confirmed, though not proven, by the discovery of transposons and various other genetic elements that appear to act as parasitic genes. Also by virus genes embedded into the DNA that appear to have melded into the normal code to produce useful-to-the-organism genetic code, and others that do things like alter the sex ratios in a manner that facilitates their propagation of multiple copies.

It's hard to see what proof would be possible. Confirmation is offered by some predictions based on that theory being confirmed and on many other observations that are more simply explained by considering the genetic code itself as the level at which evolution is occurring.

One would think that genetic programming might offer some clues, and, indeed, it does. In genetic programming one of the big problems is clearing away junk genetic codes as the generation progress. I'm not current, but when I last checked this problem had not been solved satisfactorily.

Re:Just like the brain areas "you don't use"

[MarkusQ]

You found out what 10% of the brain does (the sensory/motor areas)? The other 90% must not be used for anything.

Find out how to read the DNA code used for a few percent of the genome (the codons to protein via RNA parts)? The rest must be junk.

You'd have a good point ... except that no serious researcher in neuroscience or genetics has ever claimed either of those things.

Nuts. Galen, widely recognized as the father of modern medicine, thought the brain was used to cool blood (like a radiator). There has been a long line between where he was and where we are today, and pretty much every error that plausibly could be made has been, at some point along the way, by some serious researcher. For that matter, Roger Penrose, a Fellow of the Royal Society of London, claims that we don't use any of our brain to think with, and instead do some sort of funky thing with quantum gravity in our microtubules, which only he seems to understand. I think he's wrong, but you'd be hard pressed not to call him (or Galen) a serious researcher, unless you play the game of saying that people who weren't on the right track aren't serious researchers, which makes your claim trivially true, since no serious will ever have been wrong about anything.

--MarkusQ

Re:Just like the brain areas "you don't use"

[Anonymous Coward]

But Galen never said that only 10% of the brain are used to cool blood.

Re:Just like the brain areas "you don't use"

[MarkusQ]

This old myth actually never had its origin in science

From the first paragraph of the link you cite:

Perhaps it was the work of Karl Lashley in the 1920s and 1930s that started it. Lashley removed large areas of the cerebral cortex in rats and found that these animals could still relearn specific tasks.

Also, if you read my post again you'll see that I'm holding the 10% myth up as a well known example of bad use of partial knowledge. The point here is to question such cases when they come up, not to keep flogging them long after their dead, or (worse, IMHO) try to deny that they ever happened.

--MarkusQ

Re:Just like the brain areas "you don't use"

[CharlesEGrant]

A strange thing happened, I removed the junk data ( sync preamble ) from my floppy disk encoding and it quit working. I agree that SINEs and LINEs are less of a factor than others but a system is responsive to all its parts and until somebody makes a human clone with all the short and long repeats removed I assume that it does something, even if it just makes a different sync preamble or a getter ( to use a radio tube analogy ) for other junk.

At an abstract philosophical level you have a point, but by the same token you wouldn't let a doctor remove a wart from your finger, because we can't be sure that the wart doesn't play some unknown role in maintaining health. Practically, quite a bit of evidence shows that warts play no significant role in maintaining health, and can be removed safely. There is a LOT of evidence that LINEs and SINEs are simply 'scars' left by a parasitic attack, much like a wart. Large segments of "junk" DNA have been removed from mice with no apparent ill effect to them or their progeny.

Re:Just like the brain areas "you don't use"

[lawpoop]

SINEs and LINEs do nothing - they only propagate themselves.

C'mon -- you don't really know that they do nothing. Perhaps they're useful when winiding DNA into chromosomes, or have some larger scale structural purpose, rather than just coding genes.

Here's a quote from the very article you linked to:

"With about 1 million copies, SINEs make up about 13% of the human genome.[8] While previously believed to be "junk DNA", recent research suggests that both LINEs and SINEs have a significant role in gene evolution , structure and transcription levels[9]. The distribution of these elements has been implicated in some genetic diseases and cancers."

Re:Just like the brain areas "you don't use"

[moteyalpha]

You may be right. I had not seen that study , there is more recent anecdotal research and I think that more will be discovered. In that article from 2004 they stated it was not considered a complete proof and more recent research indicates otherwise. It would be interesting to see some research that started with what is considered essential DNA and then work forward from lethal levels to include other parts to identify essential parts as has been done with single celled organism. Technically speaking, the development of natural immunity to warts is in fact a positive effect. It is possible in nature that what is junk in one context is useful in another.

Re:Just like the brain areas "you don't use"

[Anonymous Coward]

...but evolutionary fitness is actually measured in how many offspring you have, since that's the goal ultimately in evolution, and bugs have us whipped there.

Evolution has a "goal"? That statement has some rather large implications.

Re:Just like the brain areas "you don't use"

[mysticgoat]

SINEs and LINEs do nothing - they only propagate themselves (http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element).
Inactive genes are just that - inactive. They can't be transcribed because they lack crucial parts.

idunno.

Bootstrap computer programs are very simple analogs to what goes on in a cell during telophase. Some bootstrap computer programs have long runs of NOP codes or other repetitive do-nothing structures, but if you cut them out, the system won't boot because it would then try to look for an MBR on the floppy before the drive's stepper motor is calibrated. Sometimes large, empty structures are built into the code itself, because it is sometimes more expedient to copy such things to an explicit area of ram as a pre-initialized, zeroed array than it is to explicitly allocate the space and use a loop to initialize it.

So I have some doubt that repetitive, simple structures in DNA have no function. I think a lot more needs to be learned about the context in which these portions of DNA are activated before these things we do not understand are dismissed as doing nothing.

Similarly, there were chunks of assembly language in the Apple ][ code that looked like scrap heaps of malformed opcodes, unless you realized that the system was jumping to the second byte of the first instruction, and in that context things made perfect sense. I don't think we know enough yet about the various ways that DNA is used, especially during the critical boot processes of telophase, to declare a gene inactive simply because it won't work with transcription RNA.

I think a better phrasing than "do nothing", or "inactive" is "we don't understand".

Re:Just like the brain areas "you don't use"

[jc42]

[F]or the last fifty years or so we've known how to extract strings from the data segment and thought we understood "the" genetic code. Now it's turning out that all that "junk DNA" in the code segment actually has a significant regulatory role in deciding which strings get printed, and when. Who would have guessed?

Anyone with a background in computer software, for starters.

Consider the page you're reading now, which is in HTML. It's full of all this junk called "tags", which don't appear in the final product on your screen. Some of the tags (such as <HEAD>) totally prevent any text content from appearing in the window (though a <TITLE> tag's content may appear outside the window in its title bar). There may be CSS and/or JavaScript text that doesn't appear on your screen. All this is "junk", pure space-wasting filler, if what you're after is the text content. We can even explicitly include out-of-band "junk" in the form of <!-- HTML comments -->.

If you want to see an even better analogy to DNA, rename a handy .doc file as .txt, and look into it with a plain-text editor. Unlike HTML, where the "junk" stuff is readable, the "junk" parts of a Word doc are binary gibberish that doesn't resemble text in any human language, under any encoding. And if the .doc file has been edited, you're also likely to see fragments of the deleted text, marked as deleted by the "junk" control fields, but still preserved in the file.

DNA has been understood for half a century as a kind of biological "memory". It's parallels to computer memory are obvious. In those few decades, we have devised uncountable ways of encoding data, most of them involving direct parallels to "junk DNA" in the form of fields that tell the software how to parse and interpret the "non-junk" data fields.

Meanwhile, it has become clear that Ma Nature has used vaguely similar encoding schemes for several billion years. And Her encodings are every bit as messy, confused, and full of relics as any of our simple-minded data encodings.

And, like Microsoft, Mother Nature didn't provide documentation for the internals. I wonder if She considers the encoding scheme proprietary?

Re:Just like the brain areas "you don't use"

[philspear]

Grr... pick at my phrasing will you? You see what I meant right? We consider ourselves the pinacle of evolution only because we have a different set of standards. Evolutionary success is better measured in reproductive successes. We're losing to other mammals in that reguard, mammals as a whole are the losing team when compared to things like insects.

And I neglected to mention that this whole multicellular thing is by evolutionary standards a massive failure. Bacteria are by far the dominant mode of life on this planet.

Re:Just like the brain areas "you don't use"

[Lost Race]

So we shouldn't deny that it ever happened, even if it never happened? Lashley never said the brain was 90% unused. Oh noes, I'm a denier!

Re:Just like the brain areas "you don't use"

[CTachyon]

Kind of a bad example. Penrose is a mathematician who focuses on big-picture physics (relativity and cosmology). Beyond his speculation on "quantum consciousness", he is not recognized as an expert in either neuroscience or quantum mechanics. I put as much stock in Penrose talking about consciousness as I would in a neurosurgeon talking about his pet sub-theory of Big Bang nucleosynthesis.

Exited?

[Anonymous Coward]

"We are exited [sic?] to find that Trichoplax contains..."

Gee, maybe JUNK DNA is a dumb idea

[Ralph Spoilsport]

I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

Junk DNA doesn't exist. It's just DNA we don't understand.

RS

Re:Gee, maybe JUNK DNA is a dumb idea

[Jeff DeMaagd]

Junk DNA doesn't exist. It's just DNA we don't understand.

As far as I understand it, the term was a complete misnomer. Maybe the people that coined the term used it as specific jargon meaning something, if so, they didn't seem to understand how it might be misleading.

Re:Gee, maybe JUNK DNA is a dumb idea

[OriginalArlen]

Yeah, that would totally rock. You'd end up with some hideous blasphemy, like a sort of cross between Sarah Palin and Cowboy Neil. Or perhaps Cthulhu.

Re:Gee, maybe JUNK DNA is a dumb idea

[RDW]

'I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.'

Well, Nature has (sort of) done this experiment already. The Fugu (pufferfish) genome has a highly 'compressed' genome, with about the same number of genes as mammals, but a much smaller complement of non-coding DNA:

http://genomebiology.com/2002/3/9/comment/1012

So it's certainly possible for an 'advanced' species to survive without the 'burden' of much of this material (obviously the regulatory elements are still required, but a lot of the highly repetitive stuff seems to be dispensable). Of course the 'junk DNA' may still confer evolutionary advantages (as the linked article put it: 'it may in fact be the clay from which evolution fashions morphogenetic changes'), and perhaps it says something that mammals have in general evolved in what most of us would regard as a much more interesting way than pufferfish...

Re:Gee, maybe JUNK DNA is a dumb idea

[mpe]

I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

Unless you also modified the host's DNA as well it might well do nothing. Chickens have genes for growing teeth and long tails, which are simply switched off.

Junk DNA doesn't exist. It's just DNA we don't understand.

Some of it probably is actually junk. Where DNA performs no function at all there is no evolutionary effect to weed out harmful mutations. Though it's possible that many mutations of an "obsolete" gene may result in something useful.
If DNA is observed which dosn't vary much between individuals (or even species) then that tends to imply that it functional (possibly even very important). Even if we currently have no idea what that function actually is.

Re:Gee, maybe JUNK DNA is a dumb idea

[mikael]

Would being underwater shield fish (and their DNA) from the mutation causing effects of radiation and other factors in the environment? Although, there was a research study that showed there were something like a million virus particle per litre of sea water.

Re:Gee, maybe JUNK DNA is a dumb idea

[SoupIsGoodFood_42]

I agree. It's a pretty stupid term that was probably never intended to be an official name, or whatever you call it. I wish they would hurry up and change it to something more meaningful, because it's one of those things that is going to cause a huge amount of misconception (if it hasn't already).

Re:Gee, maybe JUNK DNA is a dumb idea

[jannesha]

I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

Would you be satisfied if it was done in a mouse instead? Because that's already been done. These researchers removed 2.3 million bases from the 2.7 billion-bp genome, and could find no defects in the resulting mice. I totally agree that "we don't know what it does" != "it has no function". But some of it, clearly, really is just junk. --jjj.

Re:Gee, maybe JUNK DNA is a dumb idea

[Grimxn]

Surely the most adaptable creature (genome) is one that is "programmed" (has evolved) to be able to adapt rapidly when circumstances require it? We assume that DNA codes for a static equilibrium - "this is how your children will be", however, a really well evolved species would have the built in ability to adapt when things got tough. The "code" that did this would appear meaningless in the context of static equilibrium.

Of course, for that to have been an evolutionary advantage, our ancestors would have had to have lived through many long periods where circumstances changed. :)

Re:Gee, maybe JUNK DNA is a dumb idea

[Anonymous Coward]

Just like java programs have evolved in what most of us would regard as a much more interesting way than assembly programs? Sorry, it doesn't add up.
I'd rather have an optimized DNA, thank you.

Re:Gee, maybe JUNK DNA is a dumb idea

[Culture20]

I'd love to see the results of removing Junk DNA from a human's genome, and then pump it into an egg and grow it up all normal like and see what kind of walking cancer emerges.

In the year 9595, a race of deformed turkey was genetically developed by chicken scientists as revenge against his bird brother. [...] The chickens became a master race through a freak accident involving radiation, [Junk DNA from a human's genome,] and interestingly enough, to me, marshmallows.

Re:Gee, maybe JUNK DNA is a dumb idea

[Ralph Spoilsport]

oh balderdash. How much did they test the mouse? sure It probably lived its miserable mouse life in its miserable mouse cage, but:
what was its affect?
Do you think they tested for how nice it was, or how friendly it was, or how smart it was? Probably not. They probably tested it to see if it would eat and shit properly, and live a statistically reasonable length of time in its nasty little mouse cage.

What was its preference in flavours?
Do you think it preferred sunflowers over millet or was it really fond of quinoa? Do you think they tested for that? Probably not.

Was it outgoing or shy or psychotic?
They probably couldn't tell. Did it have ADD? Probably never tested for it.

No, it's not just junk. And the test you're describing was purely to see if removing a set of DNA resulted in something other than a still birth or a giant furry virus, by comparison to the finessed set of criteria I'm looking at.

No, it's not junk. What it is, we don't know, but when we investigate, we find meaning. And saying they found no defects is meaningless. John Wayne Gacy was a perfectly functioning human. He just liked to KILL PEOPLE AND EAT THEM. Was it genetic? Probably not. But the ability to do so, by definition, had to be. (as opposed to say, antelope...)

RS

Re:Gee, maybe JUNK DNA is a dumb idea

[Anonymous Coward]

Silly, everyone knows it goes "In the year 9595
I'm kinda wondering if man's gonna be alive
He's taken everything this old earth can give
And he ain't put back nothing".

Re:Gee, maybe JUNK DNA is a dumb idea

[Anonymous Coward]

This can only mean one thing -- OpenBSD has the least cruft.

Re:Gee, maybe JUNK DNA is a dumb idea

[jannesha]

I'm going to assume that you didn't RTFA, so I'll fill in some details about which you speculate:

A variety of features were analyzed, ranging from viability, growth, and longevity to numerous other biochemical and molecular features.

The authors admit:

"An important caveat, however, is that no matter how detailed our analyses, our ability to test for a particular characteristic in mice is limited. All we know is that, in the time frame examined, there were no detectable changes in the specific features that we studied."

Now, this work, performed at Lawrence Berkeley National Laboratory, was published in Nature. [subscription required] It's hardly balderdash.

There's plenty of rational explanations for the presence of Junk DNA. For one example, retrotransposons commonly insert themselves and then are silenced by the host genome...it's an easier way to deal with them than deletion. But they remain. Sometimes (rarely) they can lead to new beneficial genes, but by and large they are just junk.

I'm still in agreement that just because we don't know what it does, we shouldn't assume that it does nothing. I really don't understand what you're trying to say about John Wayne Gacy, but it sounds like a bit of a Reductio ad Hitlerum.

Re:Gee, maybe JUNK DNA is a dumb idea

[Lost Race]

... mammals have in general evolved in what most of us would regard as a much more interesting way than pufferfish...

Yeah, some of us would regard it that way. Those of us who are mammals, anyway.

So what is this?

[Adam Hazzlebank]

Yea, I didn't RTFA. Is this stuff sRNA/ncRNA something like that? Does it look like it forms secondary structure? Someone smart reply please. :)

Re:So what is this?

[Anonymous Coward]

Yea, I didn't RTFA. Is this stuff sRNA/ncRNA something like that? Does it look like it forms secondary structure? Someone smart reply please. :)

Maybe.

Why not admit to ignorance?

[Anonymous Coward]

I have always found it irksome when biologists claim that a high percentage of our DNA is just junk (do-nothing) DNA. It's as though they were saying "we of course know what it does: It does not do anything".
Why not say "we don't know what it does, if anything at all"?

Re:Why not admit to ignorance?

[Adam Hazzlebank]

I have always found it irksome when biologists claim that a high percentage of our DNA is just junk (do-nothing) DNA. It's as though they were saying "we of course know what it does: It does not do anything". Why not say "we don't know what it does, if anything at all"?

Most of them do, "Junk DNA" is a handy phrase and one that's been picked up by the media, the majority of Biologists are quite open minded on the subject. The fact that a lot of it is translated in to RNA even lends wait to the argument that it is of functional value. Aside from that things like telomeres (the ends of DNA that get eaten away as the replicates) and centomeres would be labelled as "junk" even though they have obvious functional value. Most scientists just use "junk" as a synonym for "non-protein coding" as a kind of shorthand.

Re:Why not admit to ignorance?

[IndustrialComplex]

My argument against 'junk' DNA and similar things; If it costs energy to do, then there is likely a reason it is being done. Otherwise, we would probably see it 'phased' out due to natural selection pressures.

Re:Why not admit to ignorance?

[Adam Hazzlebank]

My argument against 'junk' DNA and similar things; If it costs energy to do, then there is likely a reason it is being done. Otherwise, we would probably see it 'phased' out due to natural selection pressures.

Having unused DNA around could give you an evolutionary advantage. A higher mutation and duplication rate will let you adapt quickly to changes in the environment.

For example, an inexact duplicate of a gene is created. This then mutates in to something useful giving you a selective advantage. A lot of the time those duplicates will be useless, but sometimes they will be useful.

Re:Why not admit to ignorance?

[ColdWetDog]

Having unused DNA around could give you an evolutionary advantage

Or it might not be enough of a disadvantage to be a problem. Or both.

Mouse Embryos != Human Embryos

[Nymz]

The article mentions tests on mouse embryos, but if we are trying to find information about humans development and human DNA, then shouldn't we use human embryos? As long as the tests can be completed before the 24th week (Yale is in Connecticut) or 28th week (New York is nearby) then there shouldn't be a problem.

For those that would cowardly moderate this discussion troll, it's the 21st century. If a mom (in the very same state of Connecticut) can force her 14 year old daughter to have three abortions in six months time, then why can't a scientist, who is a professional, that is going to follow strict guidelines, do the very same thing but for an honorable purpose.

Re:Mouse Embryos != Human Embryos

[Fyz]

I salute your 19th century soapbox rant about the 21st century! You sir, are the epitomy of human evolution!

Re:Mouse Embryos != Human Embryos

[gardyloo]

Interesting.

    Perhaps the moderation as "troll" is because you state that the "mom forced her child to have three abortions in the span of six months" (the article only says that the first one was forced by the mother), but what of the man having sex with his 14-year-old "girlfriend" and the girl who got pregnant three times? Bravo for selective outrage.

Re:Mouse Embryos != Human Embryos

[stranger_to_himself]

The article mentions tests on mouse embryos, but if we are trying to find information about humans development and human DNA, then shouldn't we use human embryos? As long as the tests can be completed before the 24th week (Yale is in Connecticut) or 28th week (New York is nearby) then there shouldn't be a problem.

I'm not sure but I think IVF embryos can be used for research once they are no longer needed. Thing is it's much easier to actually get mouse embroys, even without the ethical implications.

Also the recent fuss in the UK about making human/animal hybrids has been trying to get around this, by putting human DNA which is easy to get into eggs from other animals.

Re:Mouse Embryos != Human Embryos

[Nymz]

I salute your 19th century soapbox rant about the 21st century! You sir, are the epitomy of human evolution!

Is that your best defense, for a continued use of mouse embryos over human embryos?

Re:Mouse Embryos != Human Embryos

[stranger_to_himself]

I salute your 19th century soapbox rant about the 21st century! You sir, are the epitomy of human evolution!

Is that your best defense, for a continued use of mouse embryos over human embryos?

The best defense is that mouse embryos are a lot easier to make and are a reasonable human model for a lot of purposes.

I don't know how you would harvest human embryos but I can't imagine it's pleasant or particularly safe. Also in humans it's hard to do research on early stage embryos because often people don't know they're pregnant until it's too late. For example we only know about the prevalence of chromosomal abnormalities between about 12 weeks and birth, there's no way to find out how many conceptions are lost before then.

Re:Mouse Embryos != Human Embryos

[Nymz]

Perhaps the moderation as "troll" is because you state that the "mom forced her child to have three abortions in the span of six months" (the article only says that the first one was forced by the mother), but what of the man having sex with his 14-year-old "girlfriend" and the girl who got pregnant three times? Bravo for selective outrage.

Here's another article that cites an AP report that describes the mothers involvement. As for "selective outrage", I'm as concerned as the next person about statuary rape, but rape is a crime and not relevant to D&X (intact dilatation and extraction).

Re:Mouse Embryos != Human Embryos

[Nymz]

The best defense is that mouse embryos are a lot easier to make and are a reasonable human model for a lot of purposes.

You are correct for that testing stage, and thanks for the on-topic reply for this controversial subject. But like testing for new drugs, the early stages are virtual simulations, the middle stages have animal testing, and the final stages involve human trials.

Re:Mouse Embryos != Human Embryos

[Nymz]

Also the recent fuss in the UK about making human/animal hybrids has been trying to get around this, by putting human DNA which is easy to get into eggs from other animals.

The rabbit-human hybrids are a promising tool for studying diseases, and testing drug therapies for those diseases. If the law is clear on when human life begins, then there should be no ethical impediments.

Re:Mouse Embryos != Human Embryos

[mpe]

The article mentions tests on mouse embryos, but if we are trying to find information about humans development and human DNA, then shouldn't we use human embryos?

Mice and humans share rather more than 80% of their DNA. For the kind of studies involved it may be a case of "any mammal will do". Since humans tend to be difficult (and expensive) to use as test subjects researchers tend not to do so unless they have to.

As long as the tests can be completed before the 24th week (Yale is in Connecticut) or 28th week (New York is nearby) then there shouldn't be a problem.

If you are using mice then you could easily be working with the grandchildren of the mice you started off with.

Re:Mouse Embryos != Human Embryos

[BrokenHalo]

I'm as concerned as the next person about statuary rape

I wouldn't be. I would have thought it might be a bit of a detumefying experience, though those statues might not notice... ;-)

Re:Mouse Embryos != Human Embryos

[Nymz]

Mice and humans share rather more than 80% of their DNA. For the kind of studies involved it may be a case of "any mammal will do".

Not according to the article:

However, Noonan stressed that it is still unknown whether HACNS1 causes changes in gene expression in human limb development or whether HACNS1 would create human-like limb development if introduced directly into the genome of a mouse.

Re:Mouse Embryos != Human Embryos

[stranger_to_himself]

I don't think the law can ever be clear because there is no single time at which human life begins. Even conception (which is probably the closest to an actual event) is not the start of life for your first cell, that was created when your mother was still a foetus.

Politicians seem to go for viability as a cut off, which seems reasonable, but that keeps moving earlier and earlier. Personally I would go for about ten weeks, but that isn't based on anything more scientific than a gut feeling.

Also I think the law should be driven by ethics, not the other way around!

Re:Mouse Embryos != Human Embryos

[Nymz]

I don't think the law can ever be clear because there is no single time at which human life begins.

Legal Definition
The Supreme court decided that viability would be the determiner of the earliest "potential life" at around the 28th week, with Roe vs Wade in 1973.

Even conception (which is probably the closest to an actual event) is not the start of life for your first cell, that was created when your mother was still a foetus.

Well, technically an egg is alive, just like a rabbit is alive, or a carrot is a living thing, but they aren't human things. The difference is ethically we can kill and eat a rabbit, but not a human.

Science Definition
Conception is the fusion of gametes to produce a new organism of the same species. That new organism, produced by process of conception, is indeed the start of a life.

Also I think the law should be driven by ethics, not the other way around!

I agree, our laws should be based upon our ethics. We write and enforce laws that protect our lives and property, because we value our lives and property.

Re:Mouse Embryos != Human Embryos

[gardyloo]

Even gargoyles gargle!

Re:Mouse Embryos != Human Embryos

[Nymz]

I'm as concerned as the next person about statuary rape I wouldn't be. I would have thought it might be a bit of a detumefying experience, though those statues might not notice... ;-)

I blame the gene responsible for poor spelling, because I have to use the spell checker so often, that I don't word check the spell checker. ;-)

Re:Mouse Embryos != Human Embryos

[Mr. Slippery]

Conception is the fusion of gametes to produce a new organism of the same species. That new organism, produced by process of conception, is indeed the start of a life.

The sperm and egg are both alive before conception. No life is created at conception; life started billions of years ago and is an ongoing process.

And let me point out that conception can ultimately result in the production of multiple organisms of the parent's species. Unless you want to argue that identical twins (or even identical triplets or quadruplets) are the same organism?

Life is just an interesting chemical reaction, of little ethical relevance. What is relevant is consciousness and personhood; these are things generated by the brain. A fetus, or even a newborn, does not have sufficient brain development to be possessed of either.

We understand that the end of complex brain activity is the true end of a person; we ought to understand that the start of complex brain activity is the true start of a person. There isn't a single moment when it happens, any more that than there was a single moment when the Earth formed out the protoplanetary cloud of dust and gas.

Re:Mouse Embryos != Human Embryos

[Mr. Slippery]

If the law is clear on when human life begins, then there should be no ethical impediments.

Surely you don't believe that question of ethics are settled by legal decisions? Did the Dredd Scott case make slavery ethically ok?

(To be clear: I know a lot of "pro life" people use Dred Scott as some sort of code word. I'm not one of them.)

And the question is not when human life begins; human life began thousands of years ago, with the first organism of genus Homo. The question is when does the personhood of an individual begin.

Re:Mouse Embryos != Human Embryos

[Nymz]

The sperm and egg are both alive before conception.

I said that.

No life is created at conception; life started billions of years ago and is an ongoing process.

Ok, you disagree with the accepted definition of conception, that I posted. Perhaps this was the point you should have shared your own definition.

And let me point out that conception can ultimately result in the production of multiple organisms of the parent's species.

No, conception has never been shown to do that, citation required.

Unless you want to argue that identical twins (or even identical triplets or quadruplets) are the same organism?

No, identical twins are formed when a zygote divides, and not during conception, stop saying that unless you are going to provide a citation.

Life is just an interesting chemical reaction, of little ethical relevance. What is relevant is consciousness and personhood; these are things generated by the brain. A fetus, or even a newborn, does not have sufficient brain development to be possessed of either.

So a newborn baby can't make a conscious decision to move his arm or turn his head, and he can't feel pain or cry either? Those actions are observable characteristics of conscious behavior. Perhaps if decided to move his arm and bitchslap you, would that meet your definition? ;-)

Re:Mouse Embryos != Human Embryos

[Nymz]

Surely you don't believe that question of ethics are settled by legal decisions? Did the Dredd Scott case [slashdot.org] make slavery ethically ok?

I never said or implied the ethics of anything would ever be settled. What I did say is there should be no ethical impediments once the law is made clear. What that means is that people may exercise their free speech, and they may protest, but they may not limit the rights of others.

Re:Mouse Embryos != Human Embryos

[crashfrog]

then why can't a scientist, who is a professional, that is going to follow strict guidelines, do the very same thing but for an honorable purpose.

Because it's really not that necessary. Mouse embryos work just fine - and you can do research on them unencumbered by the moral objections of laypeople - because the mouse genome is around 95% the same as ours.

On a genetic basis, mammals are basically mammals. At some point, we'll exhaust the applicability of the mouse genome to the human genome, and we'll have to do the research you describe to answer some final, minor questions; but we're nowhere near that point yet.

Quite frankly it's a lot easier to work on model organisms like mice, or fruit flies, or what have you.

Re:Mouse Embryos != Human Embryos

[Nymz]

Because it's really not that necessary.

I assume you meant well when repeating that reasonable sounding cop-out,
and I assume you read the article even though you missed the following quote describing that it is necessary:

However, Noonan stressed that it is still unknown whether HACNS1 causes changes in gene expression in human limb development or whether HACNS1 would create human-like limb development if introduced directly into the genome of a mouse.

While part of me wishes there were easy answers, I think it's prudent to assume there aren't.

Re:Mouse Embryos != Human Embryos

[Mr. Slippery]

I never said or implied the ethics of anything would ever be settled. What I did say is there should be no ethical impediments once the law is made clear.

A complete non sequitur. The law - clear or unclear - has no impact on what is or is not ethical.

Re:Mouse Embryos != Human Embryos

[Mr. Slippery]

Ok, you disagree with the accepted definition of conception, that I posted. Perhaps this was the point you should have shared your own definition.

Your definition, whether "accepted" or not, is meaningless. In the moment before conception, you've got living tissue; in the moment after, you've got living tissue. Saying that "life begins at conception" is meaningless.

No, conception has never been shown to do that, citation required.

What, you need a citation on the existence of identical twins? Here ya go. One incident of conception can ultimately result in multiple organisms.

So a newborn baby can't make a conscious decision to move his arm or turn his head,

Correct.

Those actions are observable characteristics of conscious behavior.

No, they are not. I can make an unconscious robot that moves its arm and makes crying noises. An amoeba can extend a pseudopod; an insect can move its legs. None of these are the actions of conscious, self-aware beings.

Consciousness arises as an organism with a complex brain interacts with its environment. A fetus or neonate has not yet significantly interacted with its environment, and its cortical development is still rudimentary, with synapses still forming.

As noted here, "By birth, only the lower portions of the nervous system (the spinal cord and brain stem) are very well developed, whereas the higher regions (the limbic system and cerebral cortex) are still rather primitive. The lower brain is therefore largely in control of a newborn's behavior: all of that kicking, grasping, crying, sleeping, rooting, and feeding are functions of the brain stem and spinal cord."

Re:Mouse Embryos != Human Embryos

[Knara]

Aside from the largely similar genome, lab mice are preferable because they serve as a form of control. They are bred to be (as much as is possible) more or less a homogeneous population, so that variations can be more easily ruled out in experiments.

This would likely be more difficult to do with humans, though probably not impossible. When combined with various ethical considerations present in our current society, they do the job well.

Re:Mouse Embryos != Human Embryos

[crashfrog]

Well, look. It's not legal obstacles that stand in the way of that research; it's that we don't yet know enough to start that research.

There actually is a procedure for doing experiments on human cultures, tissue, and even individuals.

DNA fingerprinting

[Anonymous Coward]

In defense of DNA fingerprinting it is often stated that the databases only store non-coding DNA, so there is no risk that someone might be able to centrally deduce possible health problems and other traits which could negatively affect the individual. How does that argument hold up now?

Re:DNA fingerprinting

[Anonymous Coward]

well the fingerprints are afaik just that; like a hash or checksum...
there isn't a billionth of the dna data in a genetic fingerprint as opposed to a full sequence.

Re:DNA fingerprinting

[brit74]

Anonymous coward is right: DNA fingerprinting doesn't store or show genetic sequences. It would be impossible to determine a person's exact genetics or genetically-based health problems based off of a DNA fingerprint.

Re:DNA fingerprinting

[julesh]

In defense of DNA fingerprinting it is often stated that the databases only store non-coding DNA, so there is no risk that someone might be able to centrally deduce possible health problems and other traits which could negatively affect the individual. How does that argument hold up now?

I'm not sure where the statement you're questioning came from, but my understanding of DNA fingerprint databases is that they don't actually store DNA base-pair sequences at all, but merely a list of the distances between certain marker sequences. Imagine taking a text document, counting the length of each paragraph, and summarising it by saying how many of each length there is. With long enough documents you're unlikely to find exact matches, but the numbers don't tell you anything actually useful about the contents of the file.

Re:DNA fingerprinting

[laddiebuck]

Yes, or to put it more compactly, a hash is stored.

Someone might want to tell these researchers...

[Chineseyes]

monkeys DO have opposable thumbs.

Re:Someone might want to tell these researchers...

[Anonymous Coward]

Someone might want to tell these researchers... monkeys DO have opposable thumbs.

Only old-world monkeys, like the rhesus macaque which was mentioned in the summary. New world monkeys lack opposable thumbs. I'm sure the researchers already know this. I'm sure they also know the difference between apes and monkeys. Was your post a joke or are you trying to make some point that I'm too dumb to see?

Junk is as Junk does.

[erexx23]

I don't understand it therefor it must be junk!
Perfectly scientific.

Re:Junk is as Junk does.

[goose-incarnated]

I don't understand it therefor it must be junk! Perfectly scientific.

Most scientists do not actually do this. Most reporters, on the other hand, do.

Re:Junk is as Junk does.

[Anonymous Coward]

Ignore him. He and the others have a need to feel they are smarter than scientists, and see obvious things that the "scientific worldview" causes the eggheads to miss.

This kind of anti-intellectualism is common in America. People hate to think that scientists may be people just like them - maybe a bit smarter, on average, but not geniuses all. They just have a dedication to learning and apply it, something most people are too lazy to do, so they just act like they "know better" than scientists. The appeal to "common sense" lets them hide their jealousy of scientific achievement.

Re:Junk is as Junk does.

[erexx23]

I noticed I received a Troll for this and ouch! I completely see this now
- I was being sarcastic... sorry!
What I meant was, what a perfectly non-scientific 'word' or phrase.

Constant verification and review is always a good part of science.

Re:Junk is as Junk does.

[oldhack]

The excuse of blaming the "dumb mainstream media" is getting pretty thin. Maybe the scientists should point out the limits of their findings and what they mean by "junk" or "dark", etc., if only so to shut up slashdot smarta**es. Fat chance - marketing principle applies everywhere?

Re:Junk is as Junk does.

[bhiestand]

The excuse of blaming the "dumb mainstream media" is getting pretty thin. Maybe the scientists should point out the limits of their findings and what they mean by "junk" or "dark", etc., if only so to shut up slashdot smarta**es. Fat chance - marketing principle applies everywhere?

Your timing is incredible! How, exactly, would scientists communicate with the public? What do they do when the mainstream media intentionally misrepresents scientific quarrels?

Fear Looms Over Scientist's Experiment to Uncover Secrets of 'Big Bang' was a front page article on FoxNews.com today. Aside from the title, which implies "Arrogant Scientist Thinks He Knows It All", the text of the article is 100% misleading. Here are some good quotes, emphasis mine:

A British physicist has claimed he can explain the secrets of the Big Bang Theory, but his controversial experiment has scientists believing he could bring about the end of the world, the U.K.'s Daily Mail reported.

Evans' ambitions, however, have brought widespread concern among scientists who say the experiment could create a shower of unstable black holes inside the Earth, and subsequently bring destruction to the planet.

The Daily Mall then went on to make some indirect ad hominem attacks on the lead researcher because he "is so relaxed about his job, he wears shorts to work".

Anyone who has been watching the story or knows anything about it knows that the crackpot doomsday theories have been thoroughly debunked ad nauseum.

Perhaps "dumb mainstream media" should focus on reporting the actual facts, as already reported by scientists in their published, peer-reviewed papers, rather than intentionally distorting them to create sensationalist headlines to further their ideological goals? Since we know they won't do that, people like you should turn your criticism on those who deserve it.

Disclaimer: FOX News can not be said to have not known the facts in this case. They displayed an Associated Press report about the LHC in June 2008 which accurately represented both sides of the debate in a more honest manner.

god needs a better spam filter

[thermian]

Well he must do if all this junk is getting through and messing with his creations.

So anyway god, I suggest you start using spamhous's new 'creation guard' anti DNA spam list. Its the state of the art for protecting all your 'miracles of life'(tm).

I wonder, how do they run the tests

[Anonymous Coward]

git bisect start
git bisect good human
git bisect bad chimpanzee ./configure && make clean && make

In other words...

[pushing-robot]

In the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic "switches" to turn genes on or off.

...Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff — preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

Re:In other words...

[$RANDOMLUSER]

Heh. Good point. I know that a lot of my code that's been around for a long time may contain as much as 30% commented out code, not to mention all the stuff in #ifdef blocks.

Re:In other words...

[Daniel Dvorkin]

Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff -- preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

[Sigh] Every time a biology story is posted on /. it seems like we get a bunch of posts along the lines of "dumb biologists, any techie would have figured that out a long time ago!"

Please don't confuse the reality with the dumbed-down versions that appear in the popular press or the even more dumbed-down summaries. Bioinformatics, which is what I do, has been an established science for over a decade, and I can assure you that computer scientists have been working with biologists for a lot longer than that. Most of the obvious computational analogies have already been thought of -- and most, unfortunately, have had to be discarded. Despite some of the superficial similarities, genomes are not programs, at least not in the way CS people use the word. They're more like a collection of heuristics, and even that way of thinking about things breaks down when you start looking at the details.

I'm more on the CS/math/stat side of things, and my colleagues on the bio side are often mystified by what I do -- but I'm equally often mystified by what they do. Both CS and biology are tremendously complex fields, and if you think you can arbitrarily apply lessons learned from one field to the other, you will almost always turn out to be wrong. Biologists and computer scientists can learn a lot from working with each other; work in one field very often leads to advances in the other; and by all means (he says, with a healthy dollop of self-interest) the areas of collusion should continue to grow. But thinking that there's some natural equivalence in one field to what you know from the other is simply a mistake.

Re:In other words...

[pushing-robot]

For what it's worth, I was aiming for funny — not insightful.

But as time goes on, I predict that the two fields will become very closely linked, as we continue to develop machines that imitate biology (and vice versa).

Re:In other words...

[Daniel Dvorkin]

Fair enough, and I admit I'm a bit touchy on the subject.

No doubt there will be a close link, but I think the division will always be a pretty strong one. I'm deeply skeptical about the potential of "DNA computing" and the like (although I'd be happy to be proven wrong!) and I suspect we will mostly be analyzing biological data with computers, rather than doing computational things that produce direct biological results, for quite some time. The fundamental difference, of course, is that biological systems evolved while computational systems are designed ...

Re:In other words...

[Anonymous Coward]

You're probably kidding, but the big difference is that biological processes are usually massively parallel and interdependent, while programs are primarily sequential or can easily be described as such.

Even a sequential, programming-language-like system that is slightly DNA-like but with lots and lots of helpful hints and things famiiar to programmers built in is actually quite challenging to reverse engineer.

Re:In other words...

[Anonymous Coward]

"But thinking that there's some natural equivalence in one field to what you know from the other is simply a mistake."

Physics is based on math. Chemistry is based on physics. Biology is based on chemistry.

To say that there is not some natural equivalence in one field to what you know from another is simply a mistake.

Re:In other words...

[julesh]

a lot of my code that's been around for a long time may contain as much as 30% commented out code, not to mention all the stuff in #ifdef blocks.

You know, getting rid of all that stuff is what version control systems are for.

Re:In other words...

[oldhack]

...Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff -- preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

Let's not use a $10M cruise missile to knock out a $10 tent.
(Damn, I wish that wasn't a BS.)

Re:In other words...

[Anonymous Coward]

What's the opposite of reductionism? "Increasionism?"

Re:In other words...

[Anonymous Coward]

Haha.. increasionism would be good.

I guess i should have listed that in the opposite direction, though I'm a little lisdexic i guess.

-k

Re:In other words...

[Anonymous Coward]

'Holism' is probably the closest term we have to an antonym of reductionism. 'Partism' doesn't exactly roll off the tongue.

Anyway, just because two fields are reducible to the same fundamental base (in the abstract), doesn't mean they have anything in common. Chinese cooking and Italian cooking both use noodles and sauce, but knowing how to cook one doesn't mean you automatically know how to cook the other!

Re:In other words...

[mlush]

In the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic "switches" to turn genes on or off.

...Biologists discover "flags". Seriously, these guys should just bring a programmer on-staff — preferably assembly, as decoding the arcane secrets of all Earth life should be a breeze for anyone whose day job involves the x86 instruction set.

I'm glad you got you +5 funny (and not insightful), but I'm going to try for the double and try and explain why Biology is hard

Imagine a tech startup company that have just written a 'hello world' demo script (first life)... Then the whole IT department resigns enmass leaving only the Pointy Haired Boss to run the operation.

There is a market for boxes that say "hello world" and they sell quite well but the PHB knows there are other markets (aka ecological niches) to exploit

Rather than getting in new programmers the PHB (who has lots of time on his hands and no understanding of programming) randomly messes with the code, randomly altering/adding/deleting characters, copy pasting whole chunks round.... but he dosn't just mess with the code he also messes with interpreter the operating system and in extreme cases the hardware, creating millions of different products

He then tests the code by putting it on a web site and seeing what sells. He does not understand why it sells (just it must be slightly better than other products) so he bins the ones that don't sell and uses the sellers as the basis for the next round of diddling (even the ones that only sold once)

The important point here is that he does not know how his products work or even what they do! He just knows that which sell. So he could have had a hello world that became a terminal emulator then into a spread sheet and thence to a mail server. The second important point is that there is is code reuse, but (mostly (1)) only within a product line so there could be several mail server products that work in completely different ways (Dolphin and sharks swim but share an ancestor ~420 Million years ago so have a vastly different biology).

Evolution has produced the ultimate legacy system, vast complex of undocumented, uncommented spaghetti code, containing massive stretches of commented out code that is vital to the system, written in an undocumented programming language that can subtly differ from species to species that exploits every 'neat little hack', every spooky action at a distance, and the very fuzzyest of Logic

I'm not saying that programmers have no place in biology (quite the opposite!), it just takes them a while to appreciate the full complexity of the problem

(1) actually there is code reuse between product lines (ie lineages) bacteria swap DNA all the time and virus can become part of your DNA

Re:In other words...

[Anonymous Coward]

Some people don't get a joke (and have no idea on how complicated the x86 instruction set is).

"Junk" DNA

[quinnlynn]

I probably should have clarified in the post but "Junk" DNA is a misnomer though still the most commonly used term for the part of the human genome (over 90% of it) that we don't know the uses for. The word "junk" isn't used in the sense that the DNA there is worthless and should be discarded. More like a junk drawer. There's a bunch of stuff over there that doesn't seem to belong to anything but we know that a lot of it probably does, so scientists keep testing around in there to see what goes where.

Re:"Junk" DNA

[wisebabo]

Hmm... I thought the term "Junk" DNA referred to the fact that a lot of it (all?) seems to be made up of long repeating sequences like AAAAAAAAA or ACACACACAC or something else that seems pretty 'worthless" like ending sequences that aren't at the end of anything. Also I thought that they saw "skeletons" of viruses (from retrovirii that became permanently embedded in our DNA) and broken and incomplete copies of functional genes. But then IANABiologist.

Re:more proof that evolution is wrong!

[DanielLC]

It says a Trichoplax shares 80% of its DNA with humanity. Humans have 3 billion base pairs, and Trichoplaxes have 98 million. Thus, humans only share (9,800,000*80%)/3,000,000,000=2.6% of their DNA with a Trichoplax.

DNA = Turing Machine Instructions

[Laxori666]

We'll eventually discover that DNA is just instruction tape for a type of turing machine which generates our entire body as its output. As we all know, Turing machines require lots of repetitive instructions to operate because they're so limited in their actions.

Re:DNA = Turing Machine Instructions

[sydbarrett74]

There was a fascinating talk on TED.com by Paul Rothemund saying exactly that.

Re:DNA = Turing Machine Instructions

[Anonymous Coward]

So then, is cancer like an infinite loop of cell generation?

while(true)
{
    cells++;
}

Re:more proof that evolution is wrong!

[stranger_to_himself]

It says a Trichoplax shares 80% of its DNA with humanity. Humans have 3 billion base pairs, and Trichoplaxes have 98 million. Thus, humans only share (9,800,000*80%)/3,000,000,000=2.6% of their DNA with a Trichoplax.

It says Trichoplax shares 80% of its genes with humanity. What I guess it means is that 80% of Trichoplax genes have a human ortholog (ie a gene with a sufficiently similar function and sequence).

Call it "Dark DNA"

[Colin Smith]

Apparently 90% of the universe is made of some weird useless stuff. Might as well use the same term for stuff we don't understand.
 

Re:Call it "Dark DNA"

[moteyalpha]

And all things that are not yet discovered could be called 'dark inventions'. I can imagine that the extra load of SINEs and LINEs could act to slow the replication process of the cell to make cell replication slower and more stable or that it could change the synchronization of different parts or act to increase the diffusion distance between one part and other.

Re:Call it "Dark DNA"

[Anonymous Coward]

I think we already do. It's called "God".

No DNA is "Junk DNA"

[moxley]

Saying that any DNA is "Junk DNA" is like saying that all dark matter in the universe (which we don't quite yet fully understand) is "Junk Matter."

It's the sort of misnomer that has no place in science IMO.

It always blows my mind when I think about things like this, how people think that at this point in our development that humans are the be all end all, that we understand everything there is to understand - it's such bullshit. I am not saying that our science and advancements aren't incredible and amazing; they are - I am only saying that it is incredibly foolish to think we know everything..about anything really... (in the natural world especially).

Re:No DNA is "Junk DNA"

[Pedrito]

Saying that any DNA is "Junk DNA" is like saying that all dark matter in the universe (which we don't quite yet fully understand) is "Junk Matter."

You're absolutely right. Right now, the term "junk DNA" is just sort of a way of filing it as "unknown function", but the term "non-coding DNA" is probably the more accurate term to describe it.

It's been hypothesized for some time that some of this non-coding DNA is used for morphological guidance of development. That is, some of the coding specifies why we look like we do. Why we have 10 fingers, 10 toes, 2 arms, 2 legs, and no big horn sticking out of our foreheads.

While there are genes that describe how to create and maintain the cells that make up the stomach, for example, there are no genes that describe the shape of the stomach or how it connects to the intestines and esophegous or that control where it is in the body. It makes a great deal of sense that this information is in the non-coding regions.

You're right, we don't know everything, but we know a great deal and the rate at which we're learning has grown exponentially in the past 30 years. The Human Genome Project has completely revolutionized biology. I suspect it won't be too long before we map out the function of the non-coding regions.

Re:No DNA is "Junk DNA"

[CharlesEGrant]

It always blows my mind when I think about things like this, how people think that at this point in our development that humans are the be all end all, that we understand everything there is to understand - it's such bullshit. I am not saying that our science and advancements aren't incredible and amazing; they are - I am only saying that it is incredibly foolish to think we know everything..about anything really... (in the natural world especially).

I think the term "junk DNA" was chosen to be provocative rather then dogmatic. We'd figured out the basic process of how DNA gets translated into proteins, and we'd observed that in bacteria almost all of the genome is in the business of coding proteins, but then we found that in eukaryotes only a small fraction of the DNA directly codes for proteins. The question immediately arose: if it doesn't code for proteins what does all that junk do? It was immediately recognized that some of the "junk" played a role in regulation of gene expression, but there is a godawful lot of it. Some of it is clearly the detritus left behind from attacks by parasites like retro-viruses and transposons. Bacteria get by without much "junk" and large segments of the "junk" DNA can be removed from mice with no apparent ill affect, even to the offspring. Why would something so apparently useless be so ubiquitous? Calling it "junk" just emphasizes the paradox.

Re:No DNA is "Junk DNA"

[Sj0]

It appears to me that some aspects of DNA have meta-functions. Over generations they will facilitate useful mutations, by functioning as a piece of code which modifies the DNA, but don't have a local effect on the organism.

the other 20%

[v1]

Trichoplax has the simplest known animal genome, and it shares 80 percent of its genes (comprised of 98 million base pairs) with humanity.

I get the impression by this that the 80% or so roughly defines the basic "building blocks", things like how to make a kidney or blood cell or even a midochondria, and the remaining 20% is more of a blueprint of how to take the blocks to build a given animal in shape and behavior. The shape of the skeleton, layout of the circulatory system, etc.

Re:the other 20%

[tehdaemon]

You need the Wikipedia entry on Trichoplax. They are really simple.

Also, this is 80% of Trichoplax's DNA is also in human DNA, not the reverse. Trichoplax's DNA is about 98 million base pairs, humans are around 3 billion... 80% of 'hello world' is also in the linux kernel, for a comparison...

T

Sigh. It's not junk.

[Anonymous Coward]

The "junk DNA" meme doesn't seem to want to go away. Assuming you don't have access to Science magazine where the paper and a perspective were published last week, here are two links that might help.

First, John Hawks has an excellent summary of what the research did, with links to other excellent summaries:

http://johnhawks.net/weblog/reviews/genomics/evo-devo/prabhakar-2008-hacns1-selection.html

Second, Carl Zimmer does a great takedown on the "Junk DNA" meme.

http://blogs.discovermagazine.com/loom/2008/09/05/science-writers-need-science-history/

Finally, where did upright walking get into the picture? Nobody I know of (at least nobody who can be presumed to know what they're talking about) is saying that.

John Roth

Finally.

[ari wins]

I'm glad I can now scientifically justify why I like a little junk in the trunk.

Re:Finally.

[StormReaver]

"I'm glad I can now scientifically justify why I like a little junk in the trunk."

There should be a moderation option, "-1, Too Much Information".

Re:Finally.

[Anonymous Coward]

You must be catholic.

"Conserved junk DNA" is the state machine

[Anonymous Coward]

State machines are understood in considerable depth in the EE world, practically, theoretically, mathematically.

Biologists need to learn about state machines and start applying those concepts to biological transformations, e.g. development of egg through all of the phases of embryo and infant to adult.

That is unlikely, instead they will re-invent the concepts, new terminology, no math, ...

Re:more proof that evolution is wrong!

[expatriot]

From the link (I know ...)
âoeTrichoplax placozoans are animals that have only four body cell types and no structured organs. They represent descendents of the oldest multi-celled animal, perhaps older even than sponges,â said author Stephen Dellaporta, professor of molecular, cellular and developmental biology at Yale.

So this seems to say that the simple animal shaares basic instructions on how to make cells.
Humans obviously have additional DNA for making organs.

Lovely...

[DelitaTheFridge]

Our DNA has a goddamn registry.

Re:Lovely...

[Anonymous Coward]

Don't worry, we'll soon evolve dna.conf

"Junk" DNA = Boolean switches?

[Anonymous Coward]

Maybe the "junk" is where the high level action is, a pattern of boolean switches controlling the the "identified" DNA which would be roughly equivalent to subroutines tailored to specific jobs. The latter would be easier to identify than a pattern of booleans.

Furry overlords notwithstanding...

[BrokenHalo]

This is hardly new. It has been recognised for some time that so-called "junk" DNA is nothing of the sort, but is almost certainly associated with gene expression to some degree.

The cool thing here (and what, I hope, will keep me in a job for a while) is trying to work out how.

(The fun aspect of molecular biology is that so much changes even over the course of a 4-year degree course... - and to think I nearly went into maths, where I wouldn't be doing anything remotely cutting-edge until PhD level...)

Re:Furry overlords notwithstanding...

[Sique]

It has been recognised for some time that so-called "junk" DNA is nothing of the sort, but is almost certainly associated with gene expression to some degree.

So basicly the known 26000 genes are somewhat of a coding library with wellknown functions, and the "junk DNA" is the actual program code calling those functions?

Re:Furry overlords notwithstanding...

[frieko]

I would say it's more like 50 year old COBOL air traffic control program that's been patched thousands of times by different people. Nothing is where it should be or done the way it should be, no guidelines were followed, but somehow it still manages to compile because each incremental change was tested before patching the source tree. (Hopefully someone can convert this to a car analogy for me.)

Re:Furry overlords notwithstanding...

[tsa]

When I learned about junk DNA at University in the very eary 1990s I thought the theory was rubbish. Now it turns out I was right. That is a good feeling.

Re:Furry overlords notwithstanding...

[Nightlight3]

The genes are more like global variables, while the auto variables and the actual code is in the "junk" DNA. Our scientific priesthoods (in any field) behave exactly like the ancient Egyptian priesthoods who, after figuring out a bit of a pattern behind calendar seasons, star constellations and Nile cycles, declared themselves all-knowing about everything there is, on earth and in heavens, before and after death. Among others, they declared brain as unimportant organ used only for cooling.

The worst offenders nowdays are public health "scientists" who pick out from vast patient databases (using statistical software which is a mysterious magic wand for most of them) some correlations on self-selected subjects, which could mean anything, then hand-pick one possible explanation as the "real" one (coincidentally, it is always the one benefiting financially the most their sponsors, pharmaceutical industry), declare pompously "science has spoken, debate is over" and then use it to drive policies, regulations and medical expenditures. Their "science" invariably ends up in more control over your life, worse health for you and your family (e.g. recent rapid rise of autism, asthma, allergies, obesity, diabetes, dialysis...) and more money going from your pocket to theirs and of their sponsors.

Re:Furry overlords notwithstanding...

[tsa]

Maybe you can see it as a Fat32 filesystem that has been used for a long time after the most important programs were put on it. Many files are all over the disk now because of fragmenting.

Re:Furry overlords notwithstanding...

[BotnetZombie]

A picture says more than a thousand words.
Here, have a look

Re:Furry overlords notwithstanding...

[AndresCP]

Like a balloon and ... something bad happens!

Re:Furry overlords notwithstanding...

[Anonymous Coward]

Let's hope not, I hope my cars are better designed than that...

Re:Furry overlords notwithstanding...

[Anonymous Coward]

And who is the driver of the car? God.

There you go.

Re:Furry overlords notwithstanding...

[Keebler71]

close.... but with a layer of encryption.

Re:Furry overlords notwithstanding...

[Anonymous Coward]

No, no: car analogies are for computers. You're in uncharted territory.

Re:Furry overlords notwithstanding...

[5of0]

Does anyone else find it humorous that said picture was hosted on funnyjunksite.com, given the subject at hand?

Nobody?

Okay, sorry to have wasted your time.

Re:Furry overlords notwithstanding...

[Anonymous Coward]

That's a decent analogy, but rather than 50 year old COBOL program, go with about a couple of million years.

Hey, Wait

[Slartibartfass]

In before Godwin's.

you call that junk?

[jtgd]

...the evolution of opposable thumbs and upright walking in humans is due to changes in the genome in the areas still classified as "junk DNA."

Well then, I guess they'll have to change their classification of "junk DNA"

Re:you call that junk?

[EmagGeek]

"Well then, I guess they'll have to change their classification of "junk DNA""

I'm sure they'd rather condemn humanity's ability to use tools and stuff than admit they were wrong.

One man's junk is...

[Zarf]

... another man's ... well... umm... man.

George Carlin

[phrostie]

wasn't George Carlin that said

"ever notice how your junk is stuff and everyone elses stuff is junk?"

Re:George Carlin

[Bob-taro]

wasn't George Carlin that said "ever notice how your junk is stuff and everyone elses stuff is junk?"

Yes, only George didn't say "junk".

RNA has short lifetime - hard to study

[peter303]

Some of the "junk DNA" is transcribed into non-protein-coding RNA. RNA does its business, then decays in minutes. New technologies are discover its new roles.

Re:junk reporting

[Migraineman]

While the science folks tend to be reasonable, the members of the press aren't. They expect "hard answers," and tend to get all pissy if scientists haven't figured everything out yet. Their editors don't like storied that contain lots of "we don't know," so I'm sure they're more than willing to fill-in the gaps as necessary.

I can also envision a situation where someone gets completely frustrated at the members of the press for repeatedly asking the same inane questions, and finally resorts to calling something "junk" just to get the reporters off his case. I've watched enough of the NASA briefings to know that most of the reporters haven't a clue about what they're reporting. Using the term "junk DNA" could easily be a sarcastic dig at the reporters, since they probably won't get it.

Evolutionary Biology Is Junk?

[Anonymous Coward]

It's the sort of misnomer that has no place in science IMO.

Well, junk DNA is a prediction of evolutionary biology. Are you saying that EB is junk? ahahaha...

by way of analogy

[Anonymous Coward]

Genomes are to biology what Knuth's "The Art of Computer Programming" is to programming.

Evolutionary Biology Predicted Junk DNA

[Anonymous Coward]

Junk DNA is a prediction of evolutionary biology. Intelligent Design theory, on the other hand, predicts that there can be no such thing as junk DNA because an intelligent designer would not purposely design junk. So the OP is right; this is more proof that evolution is wrong. What do evolutionists have to say to that? ahahaha...

Re:Evolutionary Biology Predicted Junk DNA

[Firehed]

What do evolutionists have to say to that? ahahaha...

Once species' trash is another species' treasure. Duh.

Re:Evolutionary Biology Predicted Junk DNA

[protobion]

er, unfortunately you don't understand evolution.
Junk DNA is so called because WE cannot assign any function to it yet. That doesn't mean it doesn't have a function - biologists are well aware of that. At most, finding a trait regulated by the "junk DNA" automatically elevates that part of the genome to a non-junk status. That is the point. In fact, this is what is done regularly as the functions of various regions of DNA are identified. Evolution, by the way makes no prediction for the presence or absence of "useless" DNA. On one hand, the useless DNA may serve as a mutational playground, while putting up an energy cost for maintaining such a playground. As will all cases in evolution, there is an optimization problem for a cell to between mutational flexibility and natural selection for energy efficiency. Clearly then ,the optimum is heavily cell-type and environment dependent.

"Junk DNA"

[LuYu]

Maybe life uses those "junk DNA" sequences as experimental. The most radical changes could be included at the end of the strands, and those would cease to be copied first, killing only a few.

you owe the researchers an apology

[philspear]

Every time early researchers solve part of a problem they seem to label the part they haven't solved as being unimportant or irrelevant.

Maybe it's different for different sciences, but in cell or molecular biology that is not the case. Most papers I read specifically adress the unknowns in the discussion section, usually a one line thing that amounts to "we don't understand why this happened in our experiments, but it is very important" or "This helps but it isn't the complete picture, we still need to do X, Y, and Z." Other times they suggest hypotheses or models that are not supported yet by the literature and say those should be tested next.

Part of the reasons they point this out is because typically the lab that published the paper is going to be putting out research on that soon, intends to look at it, and/or is genuinely intrigued by it. Nearly all answers in science raise more questions than they answer if you're doing it right at this stage.

What you may be confused by is that the meat of the article is going to be about parts the researchers HAVE figured out and want the world to know. It would be totally backwards for most of the research article to be focused on what isn't yet known. "Yeah, our evidence supports the idea that so called 'junk' DNA probably gave rise to some of our features, heres a picture supporting that, but lets focus on what we don't know, you can ask us the next time you see us how we determined this junk DNA gave us thumbs if you're really interested. How about the rest of it though? I wonder what it does. Mystery!"

It also might be that you're reading the dumbed down article linked to instead of the actual primary literature, IE the stuff a journalist wrote instead of the researchers. The actual article (probably requires a subscription, but here http://www.sciencemag.org/cgi/content/full/321/5894/1346) focuses on this one example that they DO know about already (I just skimmed it myself). And indeed if you can't access the article yourself I can tell you they do explicitly point out what they dont' know without saying it's unimportant or irellevant. Quite the opposite.

The role of CENTG2 in limb development has not been evaluated. Mouse Gbx2 is expressed in the developing limb, but Gbx2 null mice have not been described as showing abnormal limbs (25). The potential impact of humans pecific changes in the expression of these genes on limb development thus remains to be explored.

The article also does you one better and suggests strategies for further studies, using their study as an example

Independent of these considerations, our study suggests that adaptive nucleotide substitution altered the function of a developmental enhancer in humans, and illustrates
a strategy that could be used across the genome to understand at a molecular level how human development evolved through cisregulatory change

The researchers are far from arrogantly assuming they know all that is important. They know better than anyone the limitations of their research. It's the journalists and non-scientists who are trying to make it sound like a complete picture, since that's the better story.

JUNK is not the same as TRASH

[Latinhypercube]

How can you label something Junk unless you know what it is for ? Have they experimented with removing all the Junk dna and tried to develope an animal like this ? It seems totally absurd that nature would leave intact 95% of our dna as junk.(http://en.wikipedia.org/wiki/Junk_DNA) Isn't this like a 5 year old kid running into a library and designating 95% of the books as junk, because they do not understand it. Much like memory, I'm sure that although much of this dna may not be necessary on a day to day basis, it co-exist to support other more important dna in a more complex and interconnected manor.

Intelligent Designer Does Not Design Junk

[Louis Savain]

Junk DNA is a prediction of evolutionary biology. Intelligent Design theory, on the other hand, predicts that there can be no such thing as junk DNA because an intelligent designer would not purposely design junk. So the OP is right; this is more proof that evolution is wrong. What do evolutionists have to say to that? ahahaha...

Why was the parent modded down as flamebait? Is it because it is telling an inconvenient truth to the atheist moderators on Slashdot? I think so.

It is true that junk DNA is a prediction of evolutionary biology. And it is true that ID predicts that there is no junk DNA for the simple reason that an intelligent designer does not design junk.

You just can't take the truth when it contradicts your Darwinist/atheist agenda.

Re:Intelligent Designer Does Not Design Junk

[Anonymous Coward]

Actually, it's cause it doesn't prove evolution wrong... it just changes the theory of evolution.

Re:Intelligent Designer Does Not Design Junk

[bunratty]

Huh? What prediction of evolutionary theory has been falsified? My understanding is that it is a theory precisely because it has failed to have been falsified.

Re:Intelligent Designer Does Not Design Junk

[renegadesx]

Why was the parent modded down as flamebait?

For the same reason that your post is modded funny (it would be troll or flamebait otherwise). Especially considering it doesnt "disprove" evolutionary biology in the slightest and everyone here knows it.

Even if it was a creationist posting (which I doubt, the ahahaha kind of gives it away) he knew he was flaming when he wrote that posting it on /. of all places.

The so called "junk DNA" being not really junk is old news, saying it "disproves" evolutionary biology is just like a typical creationist troll trying to "disprove it" giving the scientific side no added information as if its been dogmatic since Darwins time.

The scientific model is one that ALWAYS changes however slight with *shock horror* new discoveries and new information we are always working on.

The reason why creationists are viewed as stupid is they argue without any understanding at what they are trying to disprove. Essensially trolling with an army of strawmen, and yes I have encountered that MANY times and it is very fustrating.

I get the sneeking feeling that you are trolling too, considering that you were modded "funny" instesad of "insightful" leads me to think that I am not alone in that assumpsion

One Scientist's Junk Is a Creationist's Treasure

[Louis Savain]

One Scientist's Junk Is a Creationist's Treasure

DNA is a program and OS

[mlwmohawk]

Every time I see DNA stuff discussed I think it looks more and more like a program. There are areas that are "code" and there are areas of "data."

The "junk DNA" may simply be static constants or variables used by the rest of the DNA. If you were to look at the static load area on an embedded system you'd call it junk because it seems to do nothing. It has illegal operands. But it has a purpose, it turns things on/off, defines their behavior, etc. Sound familiar?

I think biologists focusing on DNA should take a computer science course.

Re:DNA is a program and OS

[Anonymous Coward]

You have no idea what you're talking about, so stop embarrassing yourself.

Better yet, read up on some biology instead of projecting your computer paradigms where they don't fit.

Re:DNA is a program and OS

[mlwmohawk]

You have no idea what you're talking about, so stop embarrassing yourself.

Better yet, read up on some biology instead of projecting your computer paradigms where they don't fit.

Well, I'm not a molecular biologist, true, but the constant emergence of computer-like analogies coming from the study of DNA certainly gives one pause to consider if not postulate the similarities between the two.

Re:DNA is a program and OS

[CharlesEGrant]

The analogies with computer software were obvious back in the early sixties when the genetic code was first figured out. It turns out they are mostly just vague metaphors, and aren't terribly useful in accounting for any of the details of how biology actually works. Computer science is useful in sorting out how the biology works, and there are thousands of computer scientists working in molecular biology. Statistical models like Hidden Markov Models, Baysean Networks, and Support Vector Machines are where most of the work is being done. Check out PLOS Computational Biology, one of several journals that are devoted to the intersection of computer science to and biology.

Re:DNA is a program and OS

[brit74]

No, genetics is not like computer programming. (I studied both biology and computer science in college.) If they seem that similar, it's because human beings tend to describe and understand new things using concepts that they already know.

Re:DNA is a program and OS

[mlwmohawk]

No, genetics is not like computer programming. (I studied both biology and computer science in college.) If they seem that similar, it's because human beings tend to describe and understand new things using concepts that they already know.

Thats all well and good, but you offer no factual debate or argument to support your claim. You offer only an appeal to some supposed expertise, which isn't even extensive nor is it validated.

In common terms, "if it looks like a duck, and it quacks like a duck, we should at least consider the possibility that we have a duck." I'm not suggesting that DNA, as a program, has executional states as a linear computer, but there are startling similarities to computer program operation.

So, I ask you how are they different and why? Support your statement.

Re:DNA is a program and OS

[CharlesEGrant]

So, I ask you how are they different and why? Support your statement.

The most obvious difference is that there is no genetic equivalent to a CPU. If you want to be poetic, there are rough genetic equivalents to stored memory, disk drive heads, hash tables, p-code, and garbage collection, but these are only poetic analogies, they don't provide any insight into how the biology actually works. In fact if you take them seriously they'd probably mislead you. People make the same sort of analogies between computers and large corporations. It's cute, but it's only a metaphor, not a mechanism. Some computer science concepts have been very useful in analyzing biology (Shannon information for example), but the superficial analogies don't get you anywhere.

Re:DNA is a program and OS

[mlwmohawk]

these are only poetic analogies, they don't provide any insight into how the biology actually works

While I hear what you are saying, I think you are looking at it as if I'm saying that DNA works like a computer, I said it works like a program and OS. Which is subtly different.

There are definitely commonalities to how "programs" work to how DNA works. No central CPU is required. Are the underlying mechanics similar, no, of course not. There, never the less, exists similarities.

Re:DNA is a program and OS

[CharlesEGrant]

There are definitely commonalities to how "programs" work to how DNA works.

So you've said, but you haven't provided any examples. If you could provide some specifics, I could explain where they fall down.
You're coming into an area of research that's over 50 years old, and as I've said, there are thousands of computer scientists working in the field.

mod-parent up.

[Anonymous Coward]

"If DNA is observed which dosn't vary much between individuals (or even species) then that tends to imply that it functional (possibly even very important). Even if we currently have no idea what that function actually is."

This is the fundamental flaw with most of what is taught about "non-coding" or "junk" dna.

Terminology decoder says:

[Anonymous Coward]

"JUNK" = pseudo scientist speak for "we cannot explain this one" and "it goes against all of our foregone conclusions".

Now REAL scientists would state it as "Here is a DNA sequence we found that we think is related to opposable thumbs and walking upright, but we have not fully unravelled its secrets."

Re:This Was Predicted by Intelligent Design

[Anonymous Coward]

Actually programming is often much more like evolution than intelligent design.

Surprised?

[db32]

Given the current state of affairs how is anyone surprised that the piece that separates humans is considered "junk"? Seems perfectly logical to me.

two areas where the opposabe thumb comes in handy:

[davidsyes]

Sex and Medicine. For sex, use your "junk DNA" imagination.

For medicine:

http://www.taut.com/reposable.asp

Obviously,

[Anonymous Coward]

God put the junk DNA there to test us!

Re: computational systems are designed

[neonsignal]

You haven't been exposed to the source code of Windows have you? Are you one of these people who conceal their irrational belief in the Almighty Bill Gates by talking about intelligent design? Next you will be telling us that all of the flaws are deliberate! :-)

Ancestors?

[PhilHibbs]

In what sense is some little grub that is alive today my ancestor? It may be remarkably similar to something that lived billions of years ago, but it's no more my ancestor than CowboyNeal is.

Re:Ancestors?

[Weedlekin]

"In what sense is some little grub that is alive today my ancestor?"

And why is it assumed to be an ancestor just because it has less genes than any other animal that they've sequenced? Coral polyps have more genes than humans, and we also share large numbers of the same ones, but this doesn't mean corals evolved from humans.

Re:Ancestors?

[mfnickster]

If you RTFA, you may notice the following quotes:

"Trichoplax placozoans are animals that have only four body cell types and no structured organs. They represent descendents of the oldest multi-celled animal, perhaps older even than sponges," said author Stephen Dellaporta, professor of molecular, cellular and developmental biology at Yale.
[...]
"Trichoplax shares over 80 percent of its genes with humans," said Dellaporta. "We are exited to find that Trichoplax contains shared pathways and defined regulatory sequences that link these most primitive ancestors to higher animal species. The Trichoplax genome will serve as a type of "Rosetta Stone" for understanding the origins of animal-specific pathways."

So evidently the good Professor is not suggesting that Trichoplax is a human ancestor - when he says "these most primitive ancestors," he is talking about the "oldest multi-celled animal" he mentioned above, of which Trichoplax is a representative descendant.

Obviously, he could have been clearer about that!

Re:Ancestors?

[Weedlekin]

The point I'm trying to make here is that the claim about placazoans (which only have one member species) being descendants of the first multi-celled animals isn't based on any supporting evidence at all, except in the sense that all multi-celled animals, including placazoans, evolved from a common ancestor. Soft-bodies creatures rarely leave any fossil evidence, so there aren't any known placazoan fossils, and although this doesn't mean that they weren't among the earliest multi-celled creatures (absence of evidence isn't evidence of absence), there's no current proof that they existed at that time.

Re:Ancestors?

[Anonymous Coward]

Oh, okay - you didn't specify that.

I was just addressing the misperception in the GP that they were claiming this organism is a human ancestor!

Isn't all DNA "Junk DNA"?

[Anonymous Coward]

Touch my junk, and you'll get my DNA.

The Rats of NIMH

[drwho]

The Rats of NIMH, or the mice of HACNS1? I wonder if we gave rats opposable thumbs and perhaps some FOXP2 work...and voila! a new labor force for working in those jobs that "Americans don't want to do".

Survivers Survive

[geoffrobinson]

Since there aren't many useful predictions that can be made with the theory, it would be extremely difficult to falsify.

Re:Survivers Survive

[johanatan]

Yep, so if you demarcate science by (among other popular things) falsifiability, then Darwinism is *not* science. At best, it is crackpot pseudo-science.

Re:Survivers Survive

[mfnickster]

Yep, so if you demarcate science by (among other popular things) falsifiability, then Darwinism is *not* science.

Read, and be enlightened:

http://www.talkorigins.org/faqs/evolphil/falsify.html

At best, it is crackpot pseudo-science.

Oh. Never mind.

Re:Survivers Survive

[Anonymous Coward]

My comment was mostly tongue in cheek. It's the same argument Darwinists give to exclude ID. But, there's two important points they miss:

1 - Whatever criteria you choose (falsifiability, etc) to demarcate science either includes or excludes both Darwinism and ID at the same time.
2 - Demarcating science is futile. Philosophers of science long ago gave up on it, but scientists have apparently not gotten the memo.