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Sunday, December 19, 2010

"Junk DNA" now rehabilitated as "dark matter"

Slowly, but surely, the junk DNA creeps down from the attic, up from the basement, and in from the shed:
Shining a Light on the Genome's 'Dark Matter'

Elizabeth Pennisi

Science 17 December 2010: Vol. 330 no. 6011 p. 1614 | DOI: 10.1126/science.330.6011.1614 (paywall)

It used to seem so straightforward. DNA told the body how to build proteins. The instructions came in chapters called genes. Strands of DNA's chemical cousin RNA served as molecular messengers, carrying orders to the cells' protein factories and translating them into action. Between the genes lay long stretches of “junk DNA,” incoherent, useless, and inert.

That was then. In fact, gene regulation has turned out to be a surprisingly complex process governed by various types of regulatory DNA, which may lie deep in the wilderness of supposed “junk.” Far from being humble messengers, RNAs of all shapes and sizes are actually powerful players in how genomes operate. Finally, there's been increasing recognition of the widespread role of chemical alterations called epigenetic factors that can influence the genome across generations without changing the DNA sequence itself.

The scope of this “dark genome” became apparent in 2001, ...
So the ID guys were right ... oh, wait, they can't be right. It's not in the script.

Heard a rumour that one of the ID theorists is writing a book on the uses of junk DNA. Can't be true, of course.

See also: Junk DNA: Darwinism's last stand?

Now junk DNA assists evolution

Hat tip: David Tyler

No satellite hookup needed for this show, if the sky is clear

NASA Science News for Dec. 17, 2010

Northern winter is beginning in a special way. On Dec. 21st, the winter solstice, a lunar eclipse will be visible across all of North America.
The luster will be a bit "off" on Dec. 21st, the first day of northern winter, when the full Moon passes almost dead-center through Earth's shadow. For 72 minutes of eerie totality, an amber light will play across the snows of North America, throwing landscapes into an unusual state of ruddy shadow.
The eclipse begins on Tuesday morning, Dec. 21st, at 1:33 am EST (Monday, Dec. 20th, at 10:33 pm PST). At that time, Earth's shadow will appear as a dark-red bite at the edge of the lunar disk. It takes about an hour for the "bite" to expand and swallow the entire Moon. Totality commences at 02:41 am EST (11:41 pm PST) and lasts for 72 minutes.
If you're planning to dash out for only one quick look - it is December, after all - choose this moment: 03:17 am EST (17 minutes past midnight PST). That's when the Moon will be in deepest shadow, displaying the most fantastic shades of coppery red.

FULL STORY here. And here's the lunar eclipse photo gallery.

Entertain children the old-fashioned way. Don't buy them something. Show them a wonder that belongs to everyone. Then give the money to children's education in developing countries.

He said it: Should evolutionary theory evolve?

Sure, in any direction consistent with an outmoded materialism. And how grand a vision is that?
There’s no need to formally revisit the Modern Synthesis, argues Douglas Futuyma, an evolutionary biologist at the State University of New York at Stony Brook, because evolutionary theory is flexible enough to incorporate well-substantiated new ideas as they arise. “I think the evolutionary synthesis has already been extending itself almost continually for the last few decades,” he says. “I’m not saying that there’s nothing interesting [in the Extended Synthesis]. I just think the self-conscious labeling of it as a new point of view or a challenge to the old, most people don’t buy."
Most dare not buy any new approaches. No as long as they can stumble to the pay wicket through a mass of contradictions and contrary evidence.

Nothing can contradict a poorly supported idea, of little substance to begin with, and fixed on place by a solid block of iron rice bowls. Nothing but facts, which matter little in an environment where students must pay for this guy's textbooks.

Origin of life in hot water? Scalding water?

Discovery Institute advises,
Is the Origin of Life in Hot Water?
Is origin of life chemistry in hot water? So it seems according to a new paper in the Proceedings of the National Academy of Sciences. The authors address the conundrum of origin of life chemists between the rate of (un-catalyzed) organic reactions and the lack of time available for these reactions to occur. From the article (note: an enzyme is a biological catalyst):

Whereas enzyme reactions ordinarily occur in a matter of milliseconds, the same reactions proceed with half-lives of hundreds, thousands, or millions of years in the absence of a catalyst. Yet life is believed to have taken hold within the first 25% of Earth's history. How could cellular chemistry and the enzymes that make life possible, have arisen so quickly?" [Internal citations omitted]

Indeed this is one of the problems with origin of life scenarios, particularly those scenarios that presume a metabolism-first world (as opposed to an RNA-first world). The half-life of certain reactions without a catalyst can be millions of years, but studies show that the emergence of early bacteria could be dated as far back as 3.5 billion years (see ENV post on a cold origin of life and Schopf, J. William, "The First Billion Years: When Did Life Emerge?" Elements vol 2:229 (2006) for more on this). This means there was a limited amount of time for fundamental biological reactions to occur. Reaction kinetics can be prohibitive. However, the authors of this paper have a theory to solve the reaction kinetics problem.
Do they? I bet you are going to go right ahead and spoil my illusions again,
Evil Discos. And to think I am just getting over the disappointments created by the primordial soup, the primordial pizza, and the chemical minestrone.

The trouble with all these "food fight" origin scenarios is the assumption that if a big enough mess gets made, order and information will happen naturally. As if.


Just up from the quote mine: When biology actually does make sense, ...

A friend writes to say,
One frequently quoted line in biology is Dobzhansky's (1973):

"Nothing in biology makes sense except in the light of evolution."

It was refreshing, however, to read John Dupre's footnote to this quotation:

"Actually I suspect that much of molecular biology would make perfectly good sense if biological organisms had been deliberately designed by God or Martians. And arguably molecular biology is currently a more active field (though not, perhaps, a theory) than is the study of evolution." (1)

It's nice to hear a bit of balance being brought to this overused dictum!

(1) Dupre, J. (2001) In defence of classification. Stud. His. Phil. Biol. Sci. 32(2):203-219.

Find out why there is an intelligent design controversy:

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