Nick Matzke posted Entry 2649 on October 18, 2006 10:35 PM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2643

Carl Zimmer has a post up about his new article in the November 2006 issue of National Geographic. The article surveys recent research on the origin of multicellularity, segmentation, the vertebrate head, eyes, limbs, feathers, flowers, and the new kid on the block…the flagellum! And he even bases it on Pallen and Matzke 2006. Mark Pallen is interviewed – unfortunately there is nothing about the Genomic Dub Collective, but I’m sure that’s destined for ReggaeTimes.

Famed flagellum researcher Howard Berg is also interviewed. Sadly, there is nothing about the ID movement’s frequent claim that one of the spiffy design features of the flagellum is that it is “water-cooled” – a claim which they usually attribute to Berg (googling “water-cooled flagellum” brings up only ID/creationism websites). In my humble opinion, a fish has a far stronger claim to being “water-cooled”, given that the heat-retention capabilities of nanometer-scale molecular system are essentially nil (I read once that the heat energy radiates away dissipates in picoseconds at that scale). Someone should ask him about that some day.

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Comment #140330

Posted by Torbjörn Larsson on October 19, 2006 10:15 AM (e)

“I read once that the heat energy radiates away in picoseconds at that scale”.

Friction and heat transfer is different for nanoscale devices. I found a discussion with references confirming picosecond order cooling for proteins @ http://www.iscid.org/boards/ubb-get_topic-f-18-t… .

http://www.pnas.org/cgi/content/full/100/3/874

Although we have focused on ATP synthesis, we note that the results are also of interest for the mechanism of the gamma-subunit rotation during hydrolysis by F1-ATPase. The dissipation of the energy from an exothermic reaction (ATP/H2O to ADP/Pi), which is on the subnanosecond time scale in proteins” (With thanks to yersinia.)

Comment #140331

Posted by Gerard Harbison on October 19, 2006 10:32 AM (e)

I read once that the heat energy radiates away in picoseconds at that scale

I’ll put on my physical chemistry pedant’s hat, and say it conducts away, and on a time scale more like nanoseconds. Energy loss by radiation at infrared wavelengths is many orders of magnitude slower.

Comment #140336

Posted by Torbjörn Larsson on October 19, 2006 11:13 AM (e)

Gerard, I immediately regretted saying “picosecond order” about (one) subnanosecond dissipation observations. I stand corrected.

Comment #140346

Posted by Nick (Matzke) on October 19, 2006 12:17 PM (e)

Durn PT commentators, always checking my facts.

I too was thinking of those quotes on ISCID (since, surprise surpise, I was yersinia):

http://www.pnas.org/cgi/content/full/100/3/874

Although we have focused on ATP synthesis, we note that the results are also of interest for the mechanism of the gamma-subunit rotation during hydrolysis by F1-ATPase. The dissipation of the energy from an exothermic reaction (ATP/H2O to ADP/Pi), which is on the subnanosecond time scale in proteins (45), would be far too rapid to contribute directly to the gamma-subunit rotation, which is on the millisecond time scale.

[and ref 45 says: ]

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cm…

Proc Natl Acad Sci U S A. 1986 Dec;83(23):8982-6.

Molecular dynamics simulations of cooling in laser-excited heme proteins.

Henry ER, Eaton WA, Hochstrasser RM.

In transient optical experiments the absorbed photon raises the vibrational temperature of the chromophore. In heme proteins at room temperature conversion of a 530-nm photon into vibrational energy is estimated to raise the temperature of the heme by 500-700 K. Cooling of the heme is expected to occur mainly by interacting with the surrounding protein. We report molecular dynamics simulations for myoglobin and cytochrome c in vacuo that predict that this cooling occurs on the ps time scale. The decay of the vibrational temperature is nonexponential with about 50% loss occurring in 1-4 ps and with the remainder in 20-40 ps. These results predict the presence of nonequilibrium vibrational populations that would introduce ambiguity into the interpretation of transient ps absorption and Raman spectra and influence the kinetics of sub-ns geminate recombination.

So it sounds like molecular-scale cooling occurs primarily by conduction, and this process occurs in a matter of picoseconds?

This has got me confused:

Gerard, I immediately regretted saying “picosecond order” about (one) subnanosecond dissipation observations. I stand corrected.

Doesn’t going below one nanosecond put you into picoseconds?

Comment #140353

Posted by David vun Kannon on October 19, 2006 1:14 PM (e)

A nice article, though the section on bacterial flagella was the weakest, IMHO.

One of the sources Carl ever so helpfully references at the end of his blog entry is “The unicellular ancestry of animal development.” Developmental Cell 2004. which seems to shed a bit of light on flagellar evolution in the section “The Flagellar Synthesis Constraint”.

If some flagella share MTOC structures with other intracellular processes, where is the argument that they are irreducibly complex? Similarly, if bacteria can dismantle flagella when attached to surfaces (as I think is hinted at by Niehoff in Language of the Life) there would seem to be plenty of opportunity to develop flagella from simpler systems and co-option.

Comment #140380

Posted by wamba on October 19, 2006 3:37 PM (e)

I’ve got that issue waiting at home. I can’t wait to see if they use the “fair and balanced” approach, with interviews of Minnich and Behe. Methinks Zimmer knows better.

Comment #140456

Posted by Torbjörn Larsson on October 19, 2006 8:37 PM (e)

“Doesn’t going below one nanosecond put you into picoseconds?”

Sure, but it 999 picoseconds is still on the order of (one) nanoseconds.

I thought only the best was good enough for PT, so I was aiming to be precise. ;-)

Comment #140547

Posted by Nick (Matzke) on October 20, 2006 1:53 AM (e)

If some flagella share MTOC structures with other intracellular processes, where is the argument that they are irreducibly complex? Similarly, if bacteria can dismantle flagella when attached to surfaces (as I think is hinted at by Niehoff in Language of the Life) there would seem to be plenty of opportunity to develop flagella from simpler systems and co-option.

You are getting your flagella confused. Flagella are like animal wings, there are three different kinds that are non-homologous. See Table 3 of the Big Flagellum Essay or the wikipedia article.

The Pallen and Matzke article is the latest on bacterial flagellum evolution. This article is the latest on eukaryotic flagellum (=cilium) evolution.

Comment #140678

Posted by Gerard Harbison on October 20, 2006 10:21 AM (e)

Nick:

Cooling of a heme by heat transfer to the rest of the protein is a good bit faster than cooling of an entire protein by transfer to the solvent. Heat conduction is very non-linear.

The IDers are right only to the extent that on the length scale of biological molecules, under normal conditions, everything is water-cooled with near perfect efficiency! If you take a completely synthetic platinum catalyst on finely divided carbon, it too will be perfectly solvent cooled!

Actually, the discussion got me thinking that if you ran a diffusion-controlled enzyme fast enough, by overloading it with substrate, back-of-the-envelope calculations indicate you might get a detectable, non-equilibrium heating of the active site. Overheating an enzyme might be interesting enough to make the experiment worth trying.

So while ID might not lead to a research program, if you take the assertions of IDers and invert them, you might come up with something interesting! It’s sort of the reverse mask of a scientific theory!

Comment #140727

Posted by Torbjörn Larsson on October 20, 2006 1:55 PM (e)

“So while ID might not lead to a research program, if you take the assertions of IDers and invert them, you might come up with something interesting!”

So are they the devil’s advocate or (scientists) useful idiots?

Comment #140843

Posted by Gerard Harbison on October 20, 2006 9:42 PM (e)

So are they the devil’s advocate or (scientists) useful idiots?

The second, with the privoso they’re not particularly useful…

Comment #140849

Posted by 'Rev Dr' Lenny Flank on October 20, 2006 9:54 PM (e)

Yep. Just idiots.

Comment #140858

Posted by Gerard Harbison on October 20, 2006 10:27 PM (e)

Aaargh, that was proviso, not priviso!

Comment #141423

Posted by Carl Zimmer on October 24, 2006 12:21 PM (e)

Grady, what’s your point? Does my not being a scientist somehow make my article automatically wrong on all counts–despite the fact that it is based on interviews with leading scientists in these areas, and despite the fact that the staff of National Geographic then carefully checked the accuracy of the article with scientists? If, as a non-scientist, I write, “Gravity is an attractive force between aggregates of matter,” does gravity cease to exist?

Comment #141609

Posted by Joe McFaul on October 26, 2006 12:57 PM (e)

“Carl Zimmer is not a scientist.”

No, the Discovery Institute got all the good ones: Jonathan Witt, Casey Luskin, Bruce Chapman and John West.

Carl’s ability to translate technical scientific language into terms understandable to other non-scientists like me is a rare gift.

Comment #141622

Posted by Anton Mates on October 26, 2006 2:24 PM (e)

Grady wrote:

Carl Zimmer is not a scientist.

Many National Geographic writers aren’t.

Out of curiosity, any relation to Colleen Grady?

Comment #141660

Posted by Michael Suttkus, II on October 26, 2006 8:06 PM (e)

Well, I wouldn’t bring up National Geographic given it’s checkered record with regard to science…

Still, “He’s not a scientist” is nothing but an empty ad hominem. Especially given that everyone on the other side forfeited their right to be called scientists the day they put conclusion before fact.

Comment #145964

Posted by Joseph Alden on November 22, 2006 3:49 PM (e)

Nice try Carl.

Your data was very amusing, yet also typical of most evos propaganda pimps. Let’s review your delusional rants.

First, you quote Sean Carroll’s lame example of a building appearing to be constructing itself, because if one walks by late in the day, they wouldn’t see all the workers, etc. etc.
One small problem.
Those workers are utilizing the blueprints of an “intelligent designer”, i.e. an architect, to get everything correct. They don’t just show up each day & start pounding nails, welding sheet metal and pouring concrete. Thousands of specific details are required, for little things like proper weight distribution, among others.
Sorry, your regurgitation of Mr. Sean therefore becomes bogus.

Second, you also make a lame attempt at another classic evos “ fairy tale “ ; the evolution of the eye. Hey Carl, if an easily detached retina disproves ID, then I’ve got even more ammo for your next rant. Share with your NG readers this example. If Nick whacks Lenny over the head, with say, a Louisville slugger, poor Lenny most likely becomes worm food, within a few days. Therefore, since ID did not mandate a football helmet, for each human skull, this proves ID cannot exist, right ? The eyeball HAS to have come into existence by mere chance, right Carl ? NOT !
Somehow, you & your evos in-breds got the notion that Intelligent Design always has to dictate perfection. Not quite. We have automobiles that get recalled, planes that crash, people that become ill and die, etc. etc. Just because something is not perfect, does not mean it wasn’t designed.

Next, you also made a failed attempt, at solving the mysteries of the plant kingdom. Here’s another classic evos double-standard. You say that flowers have established into existence for themselves, “ brilliant pigments and sweet nectars to lure insects, blah, blah, blah.” However, we have a slight problem Carl. Mr. Gary Hurd of Talk Origins, says plants have no ability for intelligent thought or cognitive reasoning. They cannot possibly know of animals and insects looming about. Therefore, your point becomes pointless. Thus the evos propaganda becomes, once again, nothing more than idiot’s logic.

Here’s a thought Carl. Since you’re not a valid scientist, you might suggest to your fellow in-breds at NG, to add a cartoon section to the magazine. This may better suit your writing ability. Cheers.

Comment #146024

Posted by Steviepinhead on November 22, 2006 4:16 PM (e)

Bleh.

Uh, maroon, the plants don’t have to “know” that there are animals and insects out there. Those plants who do get nibbled or who don’t achieve pollination won’t have as many descendants as do those whose heritable variation “happened” to construct phenotypes that were less likely to be eaten or more likely to be pollinated.

This is all pretty simple stuff, yet it has managed to elude your mental grasp.

Perhaps too many plants among your ancestors have interfered with you own ability to mentate.

Comment #146030

Posted by stevaroni on November 22, 2006 5:08 PM (e)

you & your evos in-breds got the notion that Intelligent Design always has to dictate perfection. Not quite. We have automobiles that get recalled, planes that crash

God doesn’t design planes, trains and automobiles. Those are built by mortals, who are, by definition, fallible.

In your model, God does design people. I don’t know what kind of God you envision, but one who builds such demonstrably flawed probucts “in His image” does not encourage me.

Comment #146045

Posted by Anton Mates on November 22, 2006 6:58 PM (e)

Joseph Alden wrote:

Somehow, you & your evos in-breds got the notion that Intelligent Design always has to dictate perfection. Not quite.

Can you please tell us something that either Intelligent Design or Unintelligent Design does dictate?

Comment #153587

Posted by Charles Tharp IV on January 6, 2007 12:41 PM (e)

Sean Carroll, a biologist at the University of Wisconsin–Madison, likens the body-building genes to construction workers.

The way I think this analogy should read is like this.

“If you walked past a construction site at 6 p.m. every day, you’d say, Wow, it’s a miracle—the building is building itself, evolving out of nothing. But if you sat there all day and saw the workers and the tools, the blue prints, the architects, engineers, supervisors, and every one else adding their intelligence to the overall design, you’d understand how it was put together. We can now see all the prior planning, workers and the machinery. And the same machinery and workers can build any structure as long as they are given a new set of blue prints developed by intelligent architects and engineers.”

A limb, a feather, or a flower is a marvel of intelligent design, but not a miracle as you may have attributed to the building before correctly interpreting all the evidence.