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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."
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.
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.
A learning experience is one of those things that say, 'You know that thing you just did? Don't do that.' - D. Adams
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.
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.
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.
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.
There was a fascinating talk on TED.com by Paul Rothemund saying exactly that.
'He who has to break a thing to find out what it is, has left the path of wisdom.' -- Gandalf to Saruman
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'.
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.
A learning experience is one of those things that say, 'You know that thing you just did? Don't do that.' - D. Adams
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.
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
Laws are horrible moral guides, moral guides make even worse laws.
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.
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.
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.
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.
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.
I think we've pushed this "anyone can grow up to be president" thing too far.
Actually, it's cause it doesn't prove evolution wrong... it just changes the theory of evolution.
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.
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."
Computers are useless. They can only give you answers.
-- Pablo Picasso