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

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"

[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"

[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.

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: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: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: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.)