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The Evolution Paradigm Shift

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The Evolution Paradigm Shift

Postby Twain Shakespeare » 08 May 2012, 02:28

“Given the exemplary status of biological evolution, we can anticipate that a paradigm shift in our understanding of that subject will have repercussions far outside the life sciences. . . . How such an evolutionary paradigm shift will play out in the physical and social sciences remains to be seen. But it is possible to predict that the cognitive (psychological) and social sciences will have an increased influence on biology, especially when it comes to the acquisition and processing of information.”

–James A. Shapiro, Evolution: A View from the 21st Century

No conclusions about what is here, only about what is not.

the key passage in the interview I link-posted is....

Suzan Mazur: I went through the book over the weekend. It’s very thoughtful the way you’ve put it together. Would you describe your theory, which involves cells speaking to one another — cognitively, informationally. You say in reality the “gene” is “not a definite entity” — it’s “hypothetical in nature.”

James Shapiro: There are three components there.

(1) As I say in the book, cells do not act blindly. We know from physiology and biochemistry and molecular biology that cells are full of receptors. They monitor what goes on outside. They monitor what goes on inside. And they’re continually taking in that information and using it to adjust their actions, their biochemistry, their
metabolism, the cell cycle, etc. so that things come out right. That’s why I use the word cognitive to apply to cells, meaning they do things based on knowledge of what’s happening around them and inside of them. Without that knowledge and the systems to use that knowledge they couldn’t proliferate and survive as efficiently as they do.

(2) We’ve learned a great deal about hereditary variation through molecular genetics studies. I was personally involved in this back in the late 60s and 70s and since then we’ve learned about a wide variety of biochemical systems that cells use to restructure their genomes as an active process. Genome change is not the result of accidents. If you have accidents and they’re not fixed, the cells die. It’s in the course of fixing damage or responding to damage or responding to other inputs — in the case I studied, it was starvation — that cells turn on the systems they have for restructuring their genomes. So what we have is something different from accidents and mistakes as a source of genetic change. We have what I call “natural genetic engineering.” Cells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change.

This is consistent with what Barbara McClintock first discovered in the 30s when she was studying chromosome repair and then later in the 40s when her experiments uncovered transposable elements. All of these natural genetic engineering systems are regulated or sensitive to biological inputs. That sensitivity is what we’ve learned about cell regulation in general. As I say, cells don’t act blindly, and they don’t act blindly when they change their genomes.

(3) So if genetic change is not a series of accidents and not a series of necessarily small changes, then how does it work out in evolution? That’s where the DNA record from genome sequencing comes in and confirms what many of us had argued for a long time: namely, all of these systems of genetic change, of natural genetic engineering, have played a major role in evolutionary change. We have a new view of how cells operate in evolution, which is much more information technology friendly.

I think the first blog I put out was quoting a December 2011 paper where they went through the human genome using the 29 mammalian genomes that had recently been aligned. The authors concluded that, at a minimum, there were 280,000 different components, defined functional elements in the genome, that came from mobile genetic elements.

The point is that natural genetic engineering systems have played major roles in evolutionary change. We also see in the DNA record that evolutionary change has not just been a slow accumulation of random changes.

A good way of summarizing this is to compare the genome to storage systems in computers. The conventional view is that the genome is a read-only memory (ROM) system that changes only by copying errors. Incorporating what we have learned at the biochemical level about the cellular and molecular processes of DNA change, we can formulate a fundamentally different view. The contemporary idea is that the genome is a read-write (RW) storage system that changes by direct cell activity. How cell control circuits guide that change activity is the scientific issue of the moment.


http://www.counterpunch.org/2012/05/07/ ... -shift/See More
The Evolution Paradigm Shift » Counterpunch: Tells the Facts, Names the Names
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The Evolution Paradigm Shift
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Twain Shakespeare
 
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