Slashdot Mirror
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."
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.
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 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.
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.
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.
Support NYCountryLawyer RIAA vs People
'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...
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 ...
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
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...)
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.
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".
Jeremy
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...
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.
Support NYCountryLawyer RIAA vs People
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