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Opposable Thumbs and Upright Walking Caused By "Junk DNA"
Posted by
Soulskill
on Sun Sep 07, 2008 10:25 AM
from the stranded-pairs dept.
from the stranded-pairs dept.
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."
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I for one .... (Score:5, Funny)
When shall we welcome our furry, opposable thumbed overlords. Could Douglas Adams had been right all along?
Furry overlords notwithstanding... (Score:5, Interesting)
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...)
Parent
Re: (Score:3, Insightful)
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... (Score:5, Insightful)
Parent
Re: (Score:3, Interesting)
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.
Just like the brain areas "you don't use" (Score:3, Insightful)
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" (Score:5, Informative)
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.
Parent
Call it "Dark DNA" (Score:3, Insightful)
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:Just like the brain areas "you don't use" (Score:4, Informative)
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.
Parent
Re:Just like the brain areas "you don't use" (Score:4, Informative)
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.
Parent
Re: (Score:3, Informative)
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: (Score:3, Informative)
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 [wikipedia.org] 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 distributio
Re:Just like the brain areas "you don't use" (Score:4, Informative)
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 [bioedonline.org] with no apparent ill effect to them or their progeny.
Parent
Re:Just like the brain areas "you don't use" (Score:4, Funny)
Does it share 90% of schematics with Core 2?
Parent
Re: (Score:3, Informative)
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.
RNA has short lifetime - hard to study (Score:3, Informative)
Re:Just like the brain areas "you don't use" (Score:5, Informative)
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 [washington.edu]. Please don't help it survive - it's time to let it die.
Parent
Re: (Score:3, Insightful)
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: (Score:3, Interesting)
Nuts. Galen, widely recognized as the father of modern medicine, thought the brain was used to cool blood (like a radiator). There
Re:Just like the brain areas "you don't use" (Score:5, Insightful)
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.
Parent
Re: (Score:3, Interesting)
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 reproduc
Re: (Score:3, Interesting)
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, b
Re:Just like the brain areas "you don't use" (Score:4, Insightful)
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.
Parent
Re:Just like the brain areas "you don't use" (Score:4, Informative)
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.
Parent
Gee, maybe JUNK DNA is a dumb idea (Score:5, Insightful)
Junk DNA doesn't exist. It's just DNA we don't understand.
RS
Re:Gee, maybe JUNK DNA is a dumb idea (Score:5, Interesting)
'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 [genomebiology.com]
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...
Parent
Re:Gee, maybe JUNK DNA is a dumb idea (Score:4, Interesting)
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.
Parent
Re: (Score:3, Informative)
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. [doe.gov] 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.
DNA fingerprinting (Score:5, Interesting)
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 (Score:4, Informative)
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.
Parent
Someone might want to tell these researchers... (Score:2)
god needs a better spam filter (Score:2)
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).
In other words... (Score:5, Funny)
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: (Score:3, Funny)
Re: (Score:3, Insightful)
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... (Score:5, Insightful)
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.
Parent
Re: (Score:3, Interesting)
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 system
"Junk" DNA (Score:4, Informative)
Re: (Score:3, Informative)
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.
DNA = Turing Machine Instructions (Score:5, Interesting)
Re: (Score:3, Informative)
No DNA is "Junk DNA" (Score:3, Insightful)
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).
Finally. (Score:4, Funny)
Lovely... (Score:4, Funny)
Re:Why not admit to ignorance? (Score:5, Interesting)
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.
Parent
Re:Junk is as Junk does. (Score:5, Insightful)
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.
Parent
Re: (Score:3, Funny)
Re: (Score:3, Interesting)
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: (Score:3, Informative)
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 o
Re: (Score:3, Informative)
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...
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