Would you like to start the New Year with a free copy of The Design Matrix? While last month's winner had to find Santa, this month we'll need something to symbolize the New Year "“ like a baby!

So here is what you need to do:

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HERE

Oh, and Hoppy New Year, Everyone!

The debate about evolution and intelligent design eventually comes down to demands for evidence. Yet evidence is simply data that are interpreted in the light of previous experience and belief. What's more, evidence comes in different flavors. For example, the type of evidence that might be used to guide a police investigation may not suffice as "evidence" in the context of a court room trial. In fact, an investigator is likely to look at the data differently from a defense lawyer. The investigator may initially rely on lower standards of evidence to follow up hunches and be sensitive to cliues. The lawyer will insist on the highest possible standards to defend his client.

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Cells keep a close watch over the transcriptome "“ the totality of all parts of the genome that are expressed in any given cell at any given time. Researchers at the Salk Institute for Biological Studies and the University of Missouri-Kansas City teamed up to peel back another layer of transcriptional regulation and gain new insight into how genomes work.

Converting the "genetic blueprint" into molecular building blocks requires two basic processes: transcription, which copies the information from DNA into RNA transcripts and takes place in the cell's nucleus, and translation, where the RNA serves as a template to manufacture proteins outside the nucleus.

But before transcripts can guide protein synthesis or take on regulatory functions, they have to undergo a strict mRNA surveillance system that degrades defective, obsolete, and surplus transcripts. In their study, published in the Dec. 28 issue of Cell, the scientists zoomed in on a specific subclass of transcripts that are under the control of the exosome, a molecular machine in charge of controlled RNA degradation.

"We found evidence for widespread exosome-mediated RNA quality control in plants and a "˜deeply hidden' layer of the transcriptome that is tightly regulated by exosome activity," says Joseph R. Ecker, Ph.D., professor in the Plant Biology Laboratory and director of the Salk Institute Genomic Analysis Laboratory"¦"¦"¦"¦"¦ "It is likely that these RNAs that are usually "˜deeply hidden' become important for genome function or stability under some circumstances", adds co-first author Julia Chekanova, an assistant at the University of Missouri-Kansas City. "We need to do more work to figure out what these circumstances are."

HERE

Those who have read The Design Matrix might appreciate the significance of these recent observations:

The cobbling together of life from synthetic DNA, scientists and philosophers agree, will be a watershed event, blurring the line between biological and artificial — and forcing a rethinking of what it means for a thing to be alive.

"We're heading into an era where people will be writing DNA programs like the early days of computer programming, but who will own these programs?" asked Drew Endy, a scientist at the Massachusetts Institute of Technology.

"I see a cell as a chassis and power supply for the artificial systems we are putting together," said Tom Knight of MIT, who likes to compare the state of cell biology today to that of mechanical engineering in 1864. That is when the United States began to adopt standardized thread sizes for nuts and bolts, an advance that allowed the construction of complex devices from simple, interchangeable parts.

If biology is to morph into an engineering discipline, it is going to need similarly standardized parts, Knight said. So he and colleagues have started a collection of hundreds of interchangeable genetic components they call BioBricks, which students and others are already popping into cells like Lego pieces.

From here

There will be plenty of ho ho's once Santa gets time to read.

It looks like The Design Matrix has even caught the attention of Nick Matzke, former Public Information Project Director at the National Center for Science Education (NCSE) and who was profiled in the November 2006 edition of Seed magazine as a "revolutionary mind." Matzke, not surprisingly, did not like it at all:

I've read it. It's basically a case study in what smoking ruins were left of ID after the ARN forum debates of 2000-2003, which is where PCP degradation, cytosine deamination, and most of the other inconvenient-to-ID examples that Mike Gene discusses in his book were brought to his attention for the first time. Basically unparsimonious wishful thinking is all that's left once you've admitted, as Mike Gene does, that ID isn't science, that IC systems can evolve, and that natural selection is an effective design mimic. Basically all he can do is hide his IDer way back in the origin of life, ignore all the evidence that even the Last Common Ancestor was the product of a lot of evolution, and then try a few cheap tricks like asserting that cooption is a "pure chance" thing (wrong) and therefore taking the massive evidence of cooption as evidence for his emergency-backup completely-baffling-how-it-could-possibly-work ID option, front-loading, instead. I may get up the gumption to slay the slain one more time sometime this break, but no promises.

Okay, I need to fill in some details. I showed up to give a seminar and told the crowd I had no more copies of the DM to hand out. Things quickly got out of hand. And if you'll notice, a Teacher in the crowd was able to exploit the ensuing chaos to assault me. I'm thinking that next time, I might need a disguise.

[HT: ChristopherSaint]

Here

In Dec 2005, Seth Shostak, from the SETI Institute, wrote an article that attempts to distance SETI from Intelligent Design. I highly recommend this article, as it helps us see how a scientist goes about trying to detect non-human design.

Shostak makes the mistake of building his analysis around a straw man that circulates as media buzz. In his mind, ID is simply about trying to prove the existence of God and magic with complexity and then forcing children to learn this argument:

Finding evidence of complexity (the Nixon physiognomy) in a natural setting (the spud), and inferring some deliberate, magical mechanism behind it all, would be a leap from the doubtful to the divine, and in this case, Norm feels, unwarranted.

Cliff, however, would have some sympathizers among the proponents of Intelligent Design (ID), whose efforts to influence school science curricula continue to swill large quantities of newspaper ink. As just about everyone is aware, these folks use similar logic to infer a "designer" behind such biological constructions as DNA or the human eye. The apparent complexity of the product is offered as proof of deliberate blueprinting by an unknown creator"”conscious action, presumably from outside the universe itself.

Since Shostak relies on this superficial perspective to discredit ID, I find his critique to be rather irrelevant. So let's turn to something more interesting.

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