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Thursday, June 14, 2007

DNA Oops

Oops, it turns out that scientists didn't know what they were talking about with regard to junk DNA. This really is a radical change in the long-held scientific consensus:
"We're finding that a lot of the genome is as mysterious as 'dark matter' in physics; we know it is out there doing something. The challenge is to find out what and why," said Thomas D. Tullius , professor of chemistry at Boston University and one of the ENCODE researchers. "There were huge surprises; this research has upset a lot of thinking about how the genome works."

He added in an interview: "There now appear to be thousands of places in the genome that were long thought to be useless or meaningless, but which we now see to have a functional role. But we don't really understand what that role is."

Most startling, according to researchers, is that some areas of the genome looming as crucial are regions that don't contain specific instructions for making proteins. That recognition amounts to a sea change in basic biology.
It certainly does. Among other items, it calls into question very basic tenets of evolutionary gene studies based on gene "clocks" and it calls into severe question the statement that we share almost all of our DNA with our closest primate relatives. It's so radical that it's hard to construct a parallel. Something on the order of geologists holding a press conference and announcing that the world is flat after all. This isn't really new because the individual studies have been piling up. This is rather the admission of a shift into a new consensus.


Evolutionary psychologists have posited that the "extra" genome is somehow involved in memory. For example, if you stub your toe, how does it know to deal with an infection that had previously only been in your nose? The cells in the toe must "remember" somehow, but how? Where? It can't be neurotransmitters coming from the nervous system because the initial information substances come from the toe.

Anyway, there seems to be intergenerational memory that the body has, too. This, too, is unexplained.

It is hubris for evolutionary scientists to be so certain about things like primate relatives. We know less about the human body than we know about the ocean and we don't know much about the ocean.
In a way, it's inspirational. The age of great discoveries isn't over yet.

But yes, we have a long way to go in understanding the world, and how life interacts with it.
Timely post--echoed in the cover story of this week's Economist:

Ever since the human-genome project was completed, it has puzzled biologists that animals, be they worms, flies or people, all seem to have about the same number of genes for proteins—around 20,000. Yet flies are more complex than worms, and people are more complex than either. Traditional genes are thus not as important as proponents of human nature had suspected nor as proponents of nurture had feared. Instead, the solution to the puzzle seems to lie in the RNA operating system of the cells. This gets bigger with each advance in complexity. And it is noticeably different in a human from that in the brain of a chimpanzee.

If RNA is controlling the complexity of the whole organism, that suggests the operating system of each cell is not only running the cell in question, but is linking up with those of the other cells when a creature is developing. To push the analogy, organs such as the brain are the result of a biological internet. If that is right, the search for the essence of humanity has been looking in the wrong genetic direction.
Carl - the stupidity of using animal eggs to create stem cells is obvious by what you write. I have been shocked in reading about such research. There is RNA and mitocondrial DNA involved in the cell outside the nucleus. Given the really bad results shown in human trials using embryonic stem cells, embryonic human/animial stem cells seem to be a lot like upgrading from an axe to a chainsaw.

I don't think journalists do a very good job in writing about these initiatives.

There are theological implications as well. The Buddhists aver that life resides in the whole organism. They seem in fact to be correct. Also, it makes one think again about the Catholic church's insistence that life begins at conception. That appears to be true.

The "consensus" explanation of how genes work doesn't explain how living organisms work or develop. I agree with you that the description of the network is closer to reality.
ed in texas

Yeah, I had wondered how long it would take for this to go the way of 'you only use 10% of your brain'. Just think, you're a rational biologist, and a believer in natural selection as a driver in evolution. But you also believe that DNA strings are mostly irrelevant, when competition for rescources would favor jettisoning excess baggage, so to speak.
You also understand that highly complex creatures, such as upper primates, share massive amounts of chromosone structure with lesser flora, such as tomato plants.
The spirit of Victor Frankenstein is alive and well, and they think hubris is a flavor of Ben&Jerry's.
Thats the way science works, you blow up old hypotheses as new information comes along.

Your flat earth analogy doesn't fly... a decrepit explanation would still require evidence.
But the flat earth hypothesis was formed on the basis of what was most obvious - top the mountain range, and see another rolling scene of plains below....

Yes, all sorts of widely accepted scientific hypotheses have become the superstitions of yesteryear. That's the virtue of science, but I am not sure that our ascientific culture truly understands that.

The next 10 or 15 years in biology is going to be very exciting. The phenotype/genotype neat split of my youth is already a tattered flag. Neo-Lamarckism is already raising its head.
This page has relevant info

See especially CB 130. This is a change in emphasis from genetics to epigenetics, not a discovery of epigenetics.

"Among other items, it calls into question very basic tenets of evolutionary gene studies based on gene "clocks" and it calls into severe question the statement that we share almost all of our DNA with our closest primate relatives."

No, neutral mutations still happen at the same rate and genes still propagate through a population at different speeds depending on if they are selected for or against. It just adds a different level at which changes can occur at. We still share most of our protein coding genes with great apes but the regulatory genes (those that control how long bones should grow to or how much hair should grow where or how big a liver should be) are able to change at faster rates since the effects of them changing are less likely to cause fatal mutations than knocking out or changing a gene that codes for a crucial protein.

Has anyone ever wondered why the results of genetic dating (there are several different and independent methods of doing this) are so consistent with the results from anatomical, fossil and geological, radioisotope studies and lines of evidence? There are minor adjustments to the picture on occasion but for all lines of evidence to give the same general picture should require some kind of explanation should it not? And to blame it on a huge conspiracy or fear of the elite ignores the fact that so many scientists from different cultures with different religious views all conspire to trick everyone. This is not some computer climate model that requires one to know the code to be able to evaluate it. This is the sum total of huge amounts of experiments, observations and analysis by vast numbers of scientists at scales from the nuclear physics up to genes and proteins, to single cellular organisms, to work by zoologists and botanists and population biologists and geologists. Even computer science has demonstrated the ability of random changes and automated selective pressures to produce novel and complex results.

As for the fact that cells are running chemical "operating systems" (more like software on a DNA computer but I will go with your analogy) having anything to do with the moral status of a cell, all cells are running such software and are constantly changing their state based on signals from other cells and the environment. Human beings are not reducible to chemical states of single cells. A person is a person due to the emergent properties of billions of cells.
Snake Oil Baron - (that's a great screen name!!):

Regarding genetic "clock" studies: First, the postulated population crash to about 10,000 individuals kind of strips out information. Second, if these areas are of more use than previously thought, then natural selection could be stripping out the mutation clock. Third, population swamping and immunological selection might be more of a factor than we are willing to grant. Fourth, I have been amazed out how small the samples are in such studies.

If anything, I think that paleontology is coming up with more varied fossils and a more confusing picture of human evolution. These studies are one lens, but only one lens, and all the possible mathematical paths are not being checked. The two studies that I tried to look at in detail seemed to me to be skewed by assumptions that fit the other evidence. Money is always a factor, but it would have been better to select a much larger sample size and use four or five non-coding regions.

If you look at very modern history, the population crash in the Americas has not really been explained. There seems to be evidence that it might have been occurring before significant European incursions, although European diseases certainly cut a swath.

Consider what that did, and think of the possible interactions between early human populations crossing in the tropical zones. It may be that the heuristics used have been a bit lousy scientifically.
A better lousy link. Comment 34 especially.

I am suggesting that the assumed "conversion" of evidence is at least capable of being skewed to fit current ideas.
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