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The Emerging Complexity of the Genome

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Recently, a friend who thinks about (and has published on) the nature of the eukaryotic genome, said to me, “Paul, no one really knows what the genome is any more.” He went on to explain that the picture most biologists carry around in their heads, of the relationship of genes to organismal form and function — indeed, the very concept of the “gene” itself — had been seriously challenged by discoveries in comparative genomics and molecular biology within the past few years. How all this will shake out eventually, he said, is anyone’s guess. But the theory of evolution, he concluded, cannot escape the coming turbulence.

For an overview of some of the discoveries my friend had in mind, see this article from today’s Boston Globe. [Registration may be required.]

And welcome to the Golden Age of Biology. Without question, it’s now the most exciting science going. Unfolding astonishing vistas of puzzling data, theory nowhere in sight, hard creative thinking required.

Comments
Thanks, Paul. Great article. Regarding junk DNA, one might of course suspect some junk, even in the ID context (nobody should be surprised that a designed system can eventually run down or break). However, what does the consistent, rolling drumbeat of the evidence suggest? That the general trend is the more we understand (think mammalian eye, for example), the more we see a highly complex, astonishingly coordinated, well-regulated system, rather than junk. This is completely consistent with design and completely anathema to a blind, bumbling, cobbled-together assortment proposed by Darwin and his modern followers. It is interesting to see the science-stopping stranglehold of the old paradigm, even in the face of the kind of evidence outlined in the article. Look at Lander's statement: "Half of it may be doing something very useful. The other part may turn out to be, well, just junk . . ." Why would anyone take that view today? Perhaps because of a lifetime of indoctrination in the central dogma? I am willing to stand up and go on record with a different prediction: While there may turn out to be some non-functional DNA, the *vast* majority of DNA (more than 95%) will turn out to have biological function. Time will tell which of us is currect.Eric Anderson
September 24, 2007
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It is the joy of physics to find simplicity behind apparent cosmic complexity. It is the joy of biology to discover in the essential complexity of the biosphere, the greatness of the Mind behind it.idnet.com.au
September 24, 2007
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In answer to a challenge to show a prediction of ID that could be falsified I wrote this this morning: Almost all Junk DNA will be found to have purpose. That is a major ID prediction and one that has found substantial validation in the preliminary ENCODE study of 1% of the Human genome. The Theistic prediction for ID will predict that the complexity of the remaining 99% of the genome to be decoded will exponentially add to the impressive complexity we are currently finding and will definitely challenge man’s ability to comprehend it. Indeed, the complexity that will be found can be tentatively predicted to far far surpass man’s ability to comprehend it fully, since even a simple protein folding on itself takes a entire years worth of computing time on the world’s most powerful supercomputer. And now this quote from the Boston Globe article this afternoon: However none dispute that biology is at an extraordinary pivotal point - one in which the pace of discovery seems faster than the ability of even the most brilliant minds in the field to comprehend.bornagain77
September 24, 2007
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I am one who thinks that "junk DNA" is mostly not junk. I have been saying that for many years. There are those who use organisms such as the onion to say that complexity and genome size are unrelated and I concur with the logic of that conclusion in the few cases they specify. Then there are those who do experiments taking large segments of introns out of the geneome and find the organism is essentially working fine. Often a novel would still make sense with a chapter removed. These organisms may lose something that is hard to test for in the lab. I have had patients who have had brain surgery and lost fairly large clumps of brain tissue. I am unable to easily detect any deficiency. No one would claim that those parts of their brain were "junk". Either my testing is poor or there are alternative methods available to achieve a test result. Depending on the energy and resource cost of producing a long genome, it may be of no special disadvantage for some organisms to do better with duplicated sectors of genome. My take on junk DNA for many years has been that the so called genes code for the protein machines and building materials. That is relatively easy. They contain the hardware shop of the organism. The "junk DNA" contains the plans for constructing and maintaining organisms. It is hard enough to imagine bricks evolving, but very rarely we may find a rock shaped like a brick. It is even harder to imagine a factory being made of many bricks that are put in a special order in a form that makes a functioning brick factory without intelligent design. I suppose that is an argument from credulity and NDE does not have to be credulous. It has a special exemption from critical analysis.idnet.com.au
September 24, 2007
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A question about the human genome project, if you all don't mind: The article referenced speaks of the successful mapping of the entire human genome in 2003. And of course, since that time I've heard this claim dozens of times in the media, about how wonderful it is that we've managed to map the entire human genome. But, and pardon me for being so slow to ask this question, is that an accurate description of the human genome project? What do they really mean by "mapping" here? Because if they mean that they've figured out what genes-- in the 1.5% of the genome that actually codes for proteins--make what proteins, then pardon me if I'm not as impressed as I once was. I'm still impressed, mind you… but less so. Or does this "mapping" really just mean figuring out which genes code for proteins and which do not? Or does it mean just taking the human genome and 'reading' it so that we can see the entirety of the code, whether we understand what it means or not? Understand my question? Thanks in advance.TRoutMac
September 24, 2007
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DaveScot, there have definitely been a number of IDers who have loudly predicted that ID would reveal that much (most?) of the "junk DNA" would have value. See the strength of that prediction in Denton's "Nature's Destiny". He says that failure of the prediction will bring down ID. I would be surprised if there were no junk DNA. I know that when I compile a program, a significant number of functions get included in my compile just because they were in an object that I used some functionality of. But the 95% junk view is not a very "intelligently designed" view. Bottom line, significant IDers have said for a long time "there's value in that junk", and the darwinists have said the opposite, that "there cannot be value in that junk because there would be too many mutations per generation to be managed by RM+NS." The IDers said it, it proved to be true, it's a confirmed prediction.bFast
September 24, 2007
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I still fail to see how ID predicts no junk DNA. Random mutation definitely happens and if it's good at *anything* it's good at producing unorganized, non-functional crappola. It can produce crap out of nothing and it's even better at making crap out of stuff that wasn't crap to begin with.DaveScot
September 24, 2007
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This is squarely a confirmed prediction of the ID hypothesis. Such clear predicitive value should rightly move ID from spurious hypothesis to respected theory. Ah but the religion of darwinism would never allow that.bFast
September 24, 2007
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Dawkins disciples will argue that the discovery of ever greater complexity is evidence AGAINST ID, since the designer of all of this must necessarily be even more complex than the thing designed.russ
September 24, 2007
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"Science is just starting to probe the wilderness between genes," said John M. Greally, molecular biologist at New York's Albert Einstein School of Medicine. "Already we're surprised and confounded by a lot of what we're seeing."
I've said it before, and I'll keep on saying it: Darwinists are "surprised and confounded" all the time by real-life findings.
A slew of recent but unrelated studies of everything from human disease to the workings of yeast suggest that mysterious swaths of molecules - long dismissed as "junk DNA" - may be more important to health and evolution than genes themselves.
This is something long predicted by both panspermia and ID proponents. Which are the better, and more scientific, theories; the ones that accurately predict subsequent findings, or the ones that are consantly surprised by them?dacook
September 24, 2007
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