A strong critique of the “arsenic paper”

June 7, 2011 • 5:35 am

I’ve rarely seen a critique this strong in the reviewed scientific literature.  It’s about Wolfe-Simon et al.’s paper in Science suggesting that a bacterium could incorporate arsenic instead of phosphorus in DNA and biomolecules.  Simon Silver and and Le T. Phung take strong issue with this in a piece in the “current controversies” section of FEMS Microbiology Letters, “Novel expansion of living chemistry or just a serious mistake?”  Simon and Phung suggest that although arsenic could have been taken up by the bacteria when they were grown in vitro, there is no evidence that it was sequestered in DNA or other places save perhaps in vesicles, where the desperate bacterium was trying to remove it.

Note, this is not post-publication peer review on a blog, but a critique in the published literature.  And it’s strong from the outset. Take a look at this abstract:

The recent online report in Science (Wolfe-Simon et al., 2010; http://www.sciencexpress.org) that a newly isolated bacterial strain can apparently replace phosphate with arsenate in cellular constituents such as DNA and RNA either (1) wonderfully expands our imaginations as to how living cells might function (as the authors and the sponsoring government agency, the USA NASA, claim) or (2) is just the newest example of how scientist-authors can walk off the plank in their imaginations when interpreting their results, how peer reviewers (if there were any) simply missed their responsibilities and how a press release from the publisher of Science can result in irresponsible publicity in the New York Times and on television. We suggest the latter alternative is the case, and that this report should have been stopped at each of several stages.

Some of the meat:

The questionable conclusion of the paper appears as an established fact in the abstract (first paragraph of the report): ‘arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins.’ There are no data to support this claim, which is repeated. . . . There is no reason to conclude (as the authors have in their penultimate sentence) that they have found life ‘substituting As for P’.

And the conclusion, which tries to exculpate two authors from participating in the paper’s hype (and, I believe, lay the blame for that hype at the door of Wolfe-Simon):

One caveat: we consider two of the senior-scientist authors, R.S. Oremland and J.F. Stolz, to be microbiologists who have contributed in major ways to the understanding of the environmental microbiology of arsenic in recent years (including three reports published in Science in the last 10 years and several in FEMS journals). These caused no antihype flak. We hope our long-term relationships can survive this entirely negative and uncompromising analysis of their new report, which would have been much better handled before publication (Obama style over a bottle of beer), rather than with the excessive Internet hype that the authors initiated and the controversy that developed on newspaper and journal pages. However, this is only a current example of a report, where basically no one who can form a detailed technical opinion believes the conclusions (except the authors), based on the data shown. It is a sad story, reminiscent of the quip: déjà vu – all over again!

Ouch!

___________

Silver, S. and L. T. Phung. 2011. Novel expansion of living chemistry or just a serious mistake? FEMS Microbiol. Lett 315:79-80.

Paula Kirby: Why I’m an atheist

June 7, 2011 • 4:54 am

Paula Kirby is rapidly becoming an eloquent voice for atheism.  You might have a look at her piece in yesterday’s Hibernia Times, “Atheism is the true embrace of reality.”  You won’t find any new arguments here, but it’s worth reading because it describes her personal odyssey from theism to atheism. She was a devout Christian until 2003—so devout that someone suggested she should be a nun.

Then she discovered that every Christian had a different conception of God, and, mirabile dictu, everyone’s conception of the deity comported with their own personality and predilections:

We all knew we were right, and we all based that knowledge on the personal relationship we had with him.  How could any of us possibly be wrong?

What was striking about these observations was that those of us whose personalities led us to embrace the world and other people in a spirit of openness, generosity, warmth and tolerance “knew” that God did the same. And those who lacked the confidence for that, and consequently saw the world as threatening and evil and bad, “knew” that God saw it that way, too.

This is why subjective experience cannot tell us anything about God.  Knowing what kind of god someone believes in tells us a great deal about that person – but nothing whatsoever about the truth or otherwise of the existence of any god at all.

And this brings us to something very important about atheism.  Atheism is not in itself a belief. Few atheists would be so bold as to declare the existence of any god at all utterly impossible.  Atheism is, quite simply, the position that it is absurd to believe in, much less worship, a deity for which no valid evidence has been presented.  Atheism is not a faith: on the contrary, it is the refusal to accept claims on faith.

Kitteh contest: Simon (RIP)

June 7, 2011 • 4:42 am

This is a sad coincidence: last week I wrote reader Bettina, telling her that I’d like to post her cat Simon today, and asking for any update she had.  She informed me on Sunday that Simon had just been killed by a dog.  This is happening entirely too often around here (the same fate met Huxley), and it makes me really sad.  So this post, written by Bettina, must serve as Simon’s memorial.  He was a tuff cat, and I’m sorry for his loss.

Simon was a cat with many lives.  He used his first life one winter when he was hit by a car, taking months to recover and keeping a limp in one back leg.  His next life was a paw that wouldn’t stop bleeding and needed stitches under anesthesia.  Then, he ran away while I was on vacation, and it took a month to find him.  Upon returning, he nearly died of illness caused by fleas.  Next, he developed an abscess the size of a ping pong ball on his face, which required surgery and tubes stitched into his cheek to help it drain.  He lost his life in a fight with probably a dog on 4 June of this year, and died outside in one of his favorite spots.  We (my boyfriend and I) always called him a grump because of his low tolerance for petting, puppies and kittens.  But he loved to follow his humans around the neighborhood, meowing loudly if we walked faster than his gimpy legs could match.  I loved him rubbing his face on my face, crying to be let out, and sneak attacking the dog from behind.  He was especially fond of jumping out of the bushes and rolling in the driveway when I came home, asking for scratches and attention.  He had a special personality, and I will miss him.


Sarah Palin: I was right about Paul Revere

June 6, 2011 • 11:06 am

Sarah Palin is never going to admit that she screws up about anything.  Remember her gaffe about Paul Revere last week, when she said Revere was riding to warn the British, firing shots and “ringing those bells” to let those dastardly British know they couldn’t take our arms?  The thing is, Revere wasn’t warning the British, he was riding, in secrecy, to warn Samuel Adams and John Hancock that their arrest by the British was imminent. And of course he neither fired shots nor rang bells.

But in an interview with Chris Wallace for Fox News, Palin held her ground:

“You realize that you messed up about Paul Revere, don’t you?” “Fox News Sunday” anchor Chris Wallace asked the potential 2012 presidential candidate.

“I didn’t mess up about Paul Revere,” replied Palin, a paid contributor to the network.

“Part of his ride was to warn the British that were already there. That, hey, you’re not going to succeed. You’re not going to take American arms. You are not going to beat our own well-armed persons, individual, private militia that we have,” she added. “He did warn the British.”

Oy vey!  But the funniest part is this: some of Palin’s minions went over to Wikipedia and tried to edit the “Paul Revere” entry to make her original gaffe look less embarrassing.  Here’s one change reported by PuffHo:

According to the revision history on the Wikipedia page, Palin supports [sic] attempted to add the line in italics below:

“Revere did not shout the phrase later attributed to him (“The British are coming!”), largely because the mission depended on secrecy and the countryside was filled with British army patrols; also, most colonial residents at the time considered themselves British as they were all legally British subjects.”That revision was deleted with the explanation “content not backed by a reliable sources [sic] (it was sarah palin interview videos).”

Go here to see the entire hilarious discussion between the Wikipedia editors and Palin’s fans.

Church cancelled due to lack of God

June 6, 2011 • 7:57 am

Via Brother Blackford, a funny column from the Onion:

The South—Parishioners of Pastor Theo Leobald’s First Congregational Church of Holy Christ In Heaven will not meet next Sunday morning for a coffee social and morning Bible study as they do every week, gathering in fellowship and offering thanks and praise to God on high. The reason for the cancellation? Simply the fact that, according to Leobald, God does not now, has never, and will never exist.

The Church of Holy Christ In Heaven will soon change its name to the Church of Imaginary Make-Believe Land.

When asked why he is convinced of God’s nonexistence, Leobald became visibly irritated with reporters.

“What’re you, an illiterate peasant? Aren’t you familiar with 20th century thinking at all? Christ, read a book, or maybe just think about the idea for a minute. Pretty ridiculous, huh?” he said.

When pressed, however, he sighed heavily, and explained that thousands of years ago, tribes of nomadic desert peoples made up God because, being incapable of scientific reasoning due to caveman-like existences, they had no other way of making sense of things like sunshine, rocks and pork-transmitted trichinosis.

“They made it all up, and they were ignorant, unwashed, half-naked pre-historic barbarians,” Leobald said. “So who are you gonna believe: Carl Sagan, and the pantheon of the world’s greatest scientific and intellectual minds, or some guy who measured wealth by how many goats he had?” . .

And lots more, including this:

For those who still want to worship, if not God, but just something, Leobald has started a Sunday morning group called The Church of Imaginary Make-Believe Land, where churchgoers will have their choice of nonexistent beings to submit to. Some of the worship selections include Poseidon, super-agent James Bond and fabled storybook character Peter Pan. “I’m worshipping Peter Pan,” Gladys Fye, 108, said. “I do so love his adorable little pointed green shoes. Oh, that Tinkerbell with her magic dust!”

It’s amazing that all this stuff is true, but seems so funny.

Politics and atheists: the good news and the bad

June 6, 2011 • 7:26 am

It seems like barely yesterday that Obama was elected, but everyone’s already getting juiced up about the 2012 elections.  Reader Sigmund called my attention to this new Pew survey of what voters are looking for in a political candidate.  (Note: if you download the pdf file, you’ll see that the date on the front page—June 2, 2010—is off by a year.)  The good news is that Obama is way ahead of any possible Republican candidate, and that no Republican candidate stirs much enthusiasm, even among Republican voters:

That, of course, will change as 2012 approaches.

The bad news is that, among traits that candidates could have, one of them is absolute political poison. You know which one it is:

“Not believing in God” is the worst trait of all, much worse than having had an extramarital affair.  The Pew report finds that this figure is “little changed from four years ago.”  America remains a nation deeply disapproving of atheists. (I wonder what the figures would be in Europe.)  The unchanged level of disapprobation is a bit disconcerting, but at least gives the lie to accommodationist claims that vociferous atheism is turning people off.  And we know that lack of religious belief is still increasing everywhere in America.

I wonder what the figures would have been if “Approves of Hitler” were a category!

The Sphenisciform Shuffle: how penguins keep warm.

June 6, 2011 • 5:41 am

Read with me, if you will, the opening paragraphs of a swell new paper in PLoS One (access free; reference at bottom) about how emperor penguins, Aptenodytes forsteri, keep warm in the Antarctic winters.  Just by filming the birds for 4 hours on a single day (August 3, 2008), the four researchers found an amazing group behavior.  (I see no sense in rewriting the authors’ perfectly clear scientific prose):

Emperor penguins are the only vertebrates that breed during the austral winter where they have to endure temperatures below -45o C and winds of up to 50 m/s while fasting. From their arrival at the colony until the eggs hatch and the return of their mates, the males, who solely incubate the eggs, fast for about 110–120 days. To conserve energy and to maintain their body temperature, the penguins aggregate in huddles where ambient temperatures are above 0o C and can reach up to 37o C.

(37o C is, of course, human body temperature, so it’s nice and warm in the groups.)

Each colony consists of a group of huddles, and in each one the penguins are tightly packed, and all facing in the same direction. The density of penguins can reach—get this—21 animals per square meter! (And these are not small birds: they weigh between 50 and 100 pounds and can be up to 4 feet tall.)  The picture below shows several huddles within a larger group:

Several emperor penguin huddles. Photo by Robyn Mundy.

More from the paper:

Huddling poses an interesting physical problem. If the huddle density is too low, the penguins lose too much energy. If the huddle density is too high, internal rearrangement becomes impossible, and peripheral penguins are prevented to reach the warmer huddle center. This problem is reminiscent of colloidal jamming during a fluid-to-solid transition. In this paper we show that Emperor penguins prevent jamming by a recurring short-term coordination of their movements.

The authors filmed the penguins on a single day, using time-lapse photography at a rate of one image every 1.3 seconds.  As the figure from the paper (below) shows, individuals were tracked using the characteristic yellow and white face patch of the breed. Note that the males in these huddles are incubating eggs (nearly all of them had one), and when they move they do so by waddling with the egg balanced on their feet.

Here’s the amazing thing the authors found: penguins keep the huddle “fair”, and move from the periphery to the interior (and vice versa), by episodic but coordinated waves of penguin shuffling:

The jammed state of the huddle is interrupted every 30–60 s by small 5–10 cm steps of the penguins (Fig 1C,1E, Movie S2, S3), reminiscent of a temporary fluidization. These steps are also spatially coordinated and travel as a directed wave with a speed of about 12 cm/s through the entire huddle (Fig. 1E). After the wave has reached the end of it, the huddle re-enters the jammed state. Interestingly the propagation speed of the traveling wave is comparable to the speed of the individual penguins during the step. This is analogous to the propagation of sound waves in an elastic entropic medium (gas or fluid) where typical molecular velocities are comparable to the velocity of pressure waves.

You will of course want to see what this looks like.  The links below go to the three movies from the paper (each between 1.5 and 4 minutes long), along with the descriptions.  DO NOT MISS THESE STUNNING MOVIES.

Movie S1. Huddle formation and occurrence of coordinated traveling waves. Time lapse recordings (full field of view) over 2 h (resolution reduced from 10 MP to 480 p), showing about half of the penguin colony during the aggregation and huddling process. At the beginning of the movie (~12 p.m. with temperatures above −35°C), only few penguins aggregated in smaller huddles. As the temperatures gradually fell, larger and more stable huddles formed until nearly all the penguins aggregated in one large huddle.

To see the Sphenisciform Shuffle in the next two videos, keep your eye on the penguins’ white face patches. You’ll see them advancing in a jerky but coordinated way as the penguins step forward.

Movie S2. Huddle formation and occurrence of coordinated traveling waves (detail). Time-lapse recordings (detail of S2 over 1 h) showing multiple huddles. The penguins in a huddle mostly face in the same direction which defines a rear end and a front end of the huddle. When a penguin joins the huddle, it does so by aligning itself first in the direction in which the other penguins are facing, and then moving closer to the huddle. As a result, penguins tend to join a huddle at its rear (trailing) end and leave it at the front (leading) end. During the periodic traveling wave, the huddles move in the forward direction (in the direction in which the majority of the penguins are facing).

The shuffling is most evident in this video:

Movie S3. Coordinated traveling waves in a densely packed huddle. 21 min sequence from S2 (detail corresponding to Fig. 1B) at reduced speed. The movie shows the travelling wave of small steps every 30–60 sec.

The authors show that this type of movement is not unique to penguins, but has been seen in locusts and fish schools, as well as in tissue-cultured cells. They also show that it resembles “fluid-to-solid gelation of short-ranged attractive colloids.”  But returning to the biology, the behavior raises two interesting questions:

  • Is this behavior evolved or learned, or a combination of the two?  Natural selection could of course favor this “altruistic” behavior since it’s to each penguin’s advantage to participate in a shuffle.  The time you lose being cold on the periphery is more than compensated for by the larger amount of time you spend inside the warm huddle.  (The behavior is not pure altruism, of course, for individuals gain rather than lose fitness by participating in the shuffle).  But what about cheaters, who don’t move along, or didn’t when the behavior evolved? They would benefit by never having to be on the periphery, but they could of course have been punished for such cheating by the other penguins. It would be very hard to test whether this behavior was hard-wired, since it would involve creating large huddles of naive, hand-reared penguins under artificial conditions, and then subjecting them to an artificial winter.
  • Mechanically, how does it work?  The authors note, “It is also unclear whether the traveling wave in a huddle is triggered by a single or few leading penguins and follows a well-defined hierarchy among group members, similar to the collective behavior in pigeon flocks. Modeling attempts with self-driven agents have explained collective behavior such as temporal and long-range spatial synchronization in bird flocks, fish schools or traffic congestion by evolutionary strategies and a small set of simple interaction rules between neighboring agents. Similar mechanisms may also apply to the collective behavior of penguins in a huddle.

You don’t need fancy machinery or DNA sequencers to discover amazing things about our world.  This senational behavior was revealed by four researchers armed only with a question and a video camera.

________

Zitterbart D.P., B. Wienecke, J. P. Butler JP, and B. Fabry. 2011. Coordinated movements prevent jamming in an emperor penguin huddle. PLoS ONE 6(6): e20260. doi:10.1371/journal.pone.0020260

Dawkins defends Darwin in Dublin

June 5, 2011 • 12:03 pm

Almost live from the World Atheist Convention in Dublin, which winds up today: here’s Richard Dawkins answering the questions of an annoying Muslim creationist.  Notice that Dawkins manages to avoid stridency despite the rudeness of the questioner, who implied that Dawkins really believes in creationism but won’t admit it.

h/t: via Grania Spingies