DNA, Phosphorus, and Arsenic

Most of you know that DNA strands have a sugar-phosphate background. The bases in each strand are covalently linked to each other by phosphodiester linkages between the 5′ and 3′ carbon atoms of the deoxyribose sugar.

Recently there has been a claim by NASA-funded scientists that a certain bacterium can replace those phosphates with arsenic. Close examination of the Science paper has revealed that, at most, a few percent of the phosphorus atoms are replaced and even that amount is challenged. It has become abundantly clear from reading the paper that the bacteria absolutely required phosphorus and sufficient quantities were present in the media as contaminants.

I've already linked to Rosie Redfield's critiques of the paper and the press conference. Now I want to add Carl Zimmer's take on the whole affair—the title tells all: "This Paper Should Not Have Been Published".

Carl raises an issue that has cropped up in many of the comments sections of various blogs. Is criticizing a scientific paper appropriate outside of the peer-reviewed scientific literature? Is it ethical to cast doubt on the integrity of scientists when questioning the quality of their science?

Felisa Wolfe-Simon¹ is the lead author of the study and she was the main spokesperson in the video below. Carl Zimmer asked her if she wanted to respond to the criticism of her paper and here's what she said, according to the Slate article,

"Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated," wrote Felisa Wolfe-Simon of the NASA Astrobiology Institute. "The items you are presenting do not represent the proper way to engage in a scientific discourse and we will not respond in this manner."

Carl asked some other scientists about this and the best quote comes from Jonathan Eisen,

But Jonathan Eisen of UC-Davis doesn't let the scientists off so easily. "If they say they will not address the responses except in journals, that is absurd," he said. "They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature."

My own impression of this fiasco is that the scientific authors of the paper can be accused of bad science and the lead author, Felisa Wolfe-Simon, is guilty of grossly misrepresenting her work at the press conference. There really can't be any excuse for that behavior if you want to call yourself a scientist. Those who think this is impolite and unethical are dead wrong. It's an absolute requirement of good science that we point out to the general public when scientists are behaving badly, otherwise we lose all credibility.

As you watch this video keep in mind that the bacteria absolutely require phosphate in the media in order to grow and that only a few phosphorus atoms, at most, are replaced by arsenic in DNA. If you think that's what Felisa Wolfe-Simon is telling you then you need to work hard on your listening comprehension skills.

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1. The name of the bacterial strain is GFAJ-1. Rumor has it that this stands for "Get Felissa a Job." I wonder how that's working out? Do you think the job offers are pouring in?

John Lennon (1940 - 1980)

 
John Lennon died on Dec. 8, 1980 when he was shot four times in the back by Mark David Chapman. His ashes were scattered by Yoko Ono in Central Park in New York at the site of the Strawberry Fields Memorial.

That was thirty years ago today. A whole new generation has grown up since then and I fear we are in great danger of forgetting what Lennon and The Beatles did to help change our culture for the better.

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The Value of Blogs

Many people have questioned the significance of blogs and bloggers. Some think that science blogs have no useful purpose and that they are undermining the peer review process of publication in scientific journals. Science journalists resent the fact that amateur writers can throw up something on a blog and claim that it's contributing to science education.

Over the years I've come to appreciate that science blogs do at least one thing that's new—they provide instant commentary on science news and that helps to serve as authoritative fact-checking. Science blogs monitor science journalism in the same way that political blogs monitor FOX news and the New York Times.

This role has been illustrated in spades over the past few days as we monitor the response to the NASA hype over bacteria that grow in the presence of arsenic. The weaknesses of the Science paper are now well-known thanks to many science bloggers. In the past, this kind of analysis would have had to wait for the publication of an appropriate critique in a scientific journal and that was very unlikely to happen for a number of very good reasons. Thus, in the past shoddy, over-hyped work got a free pass and science journalists who fell for the hype never even realized that they had been duped.

Read David Dobbs on Wired for a thoughtful analysis of the episode and the lesson we need to learn [Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?]. It's interesting that even Nature News got sucked into promoting the hype. This shows that even journalists at the premier science journals are not very skeptical.

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Arsenic and Bacteria

The blogosphere is not happy with the recent announcement by NASA of bacteria that are able to "thrive and reproduce using the toxic chemical arsenic." [NASA-Funded Research Discovers Life Built With Toxic Chemical]

This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth. The research is published in this week's edition of Science Express.

I read the paper (Wolfe-Simon et al., 2010) and I can assure you that nothing in that paper is going into my biochemistry textbook. I predict that a year from now we'll have forgotten about this discovery. I'm not even sure it's going to be confirmed but, if it is, the result is pretty trivial.

For a start, even the title of the paper is misleading. The title says "A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus" but all of the data show that there was phosphorus in the media and that the bacteria used it for growth and reproduction. This selected strain of bacteria incorporated more arsenic than non-selected species but it by no means did it replace all phosphate with arsenic. Only a few percent (at most) of the phosphorus atoms in DNA, for example, were replaced by arsenic.

The purpose of this posting it to alert you to a fantastic article by microbiologist Rosie Redfield at the University of British Columbia. I strongly urge that everyone read her take-down of the science paper [Arsenic-associated bacteria (NASA's claims)]. The problem is not just that a bad paper was published in Science—it's that the paper was so heavily promoted in the media. We've got to do better when it comes to educating the general public about science.

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Wolfe-Simon, F., Blum, J.S., Kulp, T.R., Gordon, G.W., Hoeft, S.E., Pett-Ridge, J., Stolz, J.F., Webb, S.M., Weber, P.K., Davies, P.C.W., Anbar, A.D., and Oremland, R.S. (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science Published Online 2 December 2010 [DOI: 10.1126/science.1197258]

Carnival of Evolution #30

 


The 30th version of Carnival of Evolution has been posted on The Scientific Life (Bob O'Hara).

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The Death of the Sniper Scientist

 

I've just discovered a new blog called Canadian Girl Postdoc in America. Check it out.

You can start by recommending your favorite science book [The One] but be sure to read the wonderful series on Slow Science: The Death of the Sniper Scientist.

The author is interested in evolution and population genetics and she has been blogging for three years! I think she likes plants.

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Students vs Icons of Evolution

 
I teach in a second year course on "Scientific Misconceptions and Controversies." In my part of the course we discuss creationism and evolution. The object is to learn to think rationally about the controversy.

Students have to read Icons of Evolution and write an essay analyzing the arguments in one of the chapters (their choice). They have no problem recognizing the flaws in the logic and the outright mistruths in that book. For typical university students with a rudimentary understanding of evolution it's like shooting fish in a barrel.

The Discovery Institute sees it differently but they must live on another planet.


Here's how David Klinghoffer describes Jonathan Wells in a recent posting on Evolution News & Views [Celebrating Ten Years of Icons of Evolution].

A Berkeley PhD in molecular and cell biology, Wells is among the most lucid and accessible scientist-writers devoted to the modern project of critiquing Darwin. When I say the book is sweetly reasoned, I don't only mean that it's well reasoned but that there's an appealing geniality, a sweetness, to the man's writing that stands out in contrast to the donkey-like braying of a Darwinian biologist Jerry Coyne, the sinister coilings of a Richard Dawkins, the ugly "humor" of a P.Z. Myers. Yes, you can get a sense of a person's character, and perhaps too his credibility, from the words he uses.

And here's an example of "sweet geniality" from page 234 of Icons.

What about scientists who knowingly make false utterances or misleading omissions but believe the overall effect is not misleading because they are teaching "a deeper truth"? Does the commitment to a supposed deeper truth excuse conscious misrepresentations? Such an excuse probably wouldn't help a stock promoter. Under federal law, a stock promoter is not justified in mistating the facts just because he or she deeply believes that a company is destined to prosper. The stock promoter commits fraud by misrepresenting the truth, regardless of his or her underlying beliefs. Shouldn't scientists be held to the same standard?

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it?

...

If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and they use their position of dominance to censor dissenting viewpoints.

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The Hitchens-Blair Debate: It's Was a Tie!

 

I thought Hitchens did a much better job that Tony Blair but it's hard to be unbiased. Here are the results of the poll before and after the debate.

On the question "Is Religion a Force for Good?"

Before the debate ...

Yes (Blair): 22%
No (Hitchens): 57%
Undecided: 21%

After the debate

Yes (Blair): 32%
No (Hitchens): 68%

Both speakers increased their numbers by about 10%. In simplistic terms, the undecided members of the audience split 50:50 on the question.

That's a tie by my calculation. The blogosphere is reporting this as a huge victory for Hitchens but it didn't seem that way in Massey Hall in Toronto. Just because Hitchens started out with 57% of the votes doesn't mean he won the debate. (Although I think he did.)

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Don't Mess with Rob Day

 
Rob Day, better known as Canadian Cynic, finally got tired of the malicious defamations posted by Patrick “Patsy” Ross on his blog The Nexus of Assholery. The result was an $85,000 judgment in Rob's favour—$10,000 in legal costs and $75,000 in punitive damages [Another Mudfish Beached]. Let's hope Patsy pays up before the police have to come knocking on his door.
This is one way to deal with bloggers and trolls who step over the line. Another way is to press criminal charges against those who post serious threats. I think the second way is better, if it's an option, and I'm looking forward to the time when some of the mentally deranged trolls are locked away in an institution without a computer. There are a few such trolls who may soon be getting a visit from the cops.

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Was Darwin Wrong?

 
I understand, and agree with, the basic sentiment behind this poster but I wish they'd chosen better examples. Charles Darwin was wrong about lots of things.¹

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1. But he's still the best scientist who ever lived.

Christopher Hitchens vs. Tony Blair

 
I couldn't get tickets to see the actual debate at Massey Hall in Toronto so I'm doing the next best thing by going to the beer party live streaming of the debate at CFI tomorrow night.

All the cool people will be there (wearing WiFi radiation protection).

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Starts: Friday, November 26th 2010 at 7:00 pm
Ends: Friday, November 26th 2010 at 9:00 pm
Location: Centre for Inquiry, 216 Beverley Street (just south of College and St. George)

Since the debate between well-known atheist and author Christopher Hitchens and former British Prime Minister Tony Blair sold out we will be screening the live video stream of the event at CFI Ontario.

In a world of globalization and rapid social change does religion provide the common values and ethical foundations that diverse societies need to thrive in the 21st century? Or, do deeply held religious beliefs promote intolerance, exacerbate ethnic divisions, and impede social progress in developing and developed nations alike? To encourage a far-ranging discussion on one of human kind's most vexing questions, the 6th semi-annual Munk Debate will tackle the resolution: be it resolved, religion is a force for good in the world.

$5, $4 for students and FREE for CFI Members.

Attendees are invited to stay after the debate to enjoy some food and drinks while they discuss who they thought won the debate!

$3 Beer!

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How to Protect Yourself from WiFi Radiation

A study by some Dutch scientists claims to have shown that WiFi kills trees [Study Says Wi-Fi Makes Trees Sick]. Combine that with the widespread myth evidence that WiFi radiation is harming school children [Sometimes School Trustees Make You Proud] and all of a sudden we've got a serious problem. University campuses are awash with WiFi radiation coming from sites in every building. If you are one of those people who think you're being harmed, I've come up with a simple solution—a tinfoil¹ hat to protect your brain. I have carefully researched the shape of this hat in order to maximize the desired effect. Wear it when you are at your desk studying, when you are in class, and when you're taking a break. Get all your friends to wear one too. Not only will this tinfoil hat protect you, it will also serve as a reminder to others that you are an intelligent person who cares about the environment. Here's a special note to parents of school age children who are worried about WiFi radiation in the public schools. It's easy to make a protective hat. Just roll up some poster board in the shape of a cone and cover it with tinfoil. Make sure your children keep the hat on while they are in school. Your children will rapidly gain the admiration and respect of the other students for being so scientifically literate.

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1. It's actually aluminum foil but who's counting? The photos were taken by Alex Palazzo who wishes to remain anonymous.

Rock Stars of Science

 
This poster is from Rock Stars of Science. There are six people in the photo: one of them is a rock star (I'm told) and five of them are famous scientists (I'm told).

Is this a good way to promote science? Martin Robbins doesn't think so: 'Rockstars of Science' should be 'Scientists of Rock'.

I could be wrong. Maybe this is a good way of reaching out to people. Maybe GQ's readers are getting out their dictionaries and picking through those descriptions, stopping occasionally to stare at the blurry, bearded interloper in the background of Bob's photograph. And maybe those readers are now more inspired by science as a result. If so, I'd like to see some evidence of it - maybe a poll of readers?

But I still can't help but feel that if you have to resort to rockstars make science cool, you're really not very good at communicating science. Because science is way cooler than rock stars.

You won't be surprised to learn that Chris Mooney likes this campaign and ERV doesn't. Jerry Coyne doesn't like it either. Does anyone notice a pattern here? ... The one person who isn't a scientist is the one who thinks he knows how to promote science.

So, who's behind this promotion? It's a company called GEOFFREY BEENE that I've never heard of. But don't take that lack of knowledge seriously because I'm a scientist and I'm definitely not cool.

Here's a video put out by the company. Is this mostly about science or is it mostly about the company exploiting their support for medical technology?

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Don't Mess with Skepchick!

 
Skepchick asked you to boycott movie theaters that were showing the anti-vaccine video promoted by Age of Autism [Let’s all go to the movies and save ourselves some lives]. Many of us posted complaints on the AMC website.

Yesterday Age of Autism and SafeMinds released the following statement as reported in the latest posting on Skepchick [Good guys win!]. Congratulations Skepchick!

SafeMinds was notified late yesterday afternoon that AMC Theaters has decided to block the SafeMinds Public Service Announcement (PSA) on influenza vaccines with mercury. The PSA alerts parents and pregnant women of the presence of mercury in most influenza vaccines and the ample availability of mercury-free alternatives. The CDC has declined to give a preference for the mercury-free versions, so it is important that the public is aware of its options. AMC’s advertising representative had reviewed and approved the PSA to run in AMC cinemas over the Thanksgiving weekend. A small group of vocal vaccine proponents dismissive of mercury concerns learned of the PSA and bombarded the AMC website, leading to the company’s decision to prevent its release. SafeMinds thanks its supporters who viewed the PSA and contributed to its efforts to educate the public to avoid unnecessary mercury exposure. Mercury in all forms is dangerous, especially to the developing fetus and infants, as referenced on the PSA website www.safemindsflu.org. SafeMinds will continue its mission to educate the public on this important healthcare topic.

BTW, the ad was NOT a public service announcement by any stretch of the imagination.

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Nobel Laureates Become Pseudoscientists

 
There are several well-known examples of Nobel Laureates in science who later become enamored with quackery. Orac mentions a few on his blog in The Nobel disease strikes again.

Can you guess who holds the record for the swiftest turn around from getting the Nobel Prize to endorsing quackery? (Hint: mentor of Richard Dawkins).

Of course this record only applies to scientists who became quacks after getting the Nobel Prize. That lets Kary Mullis off the hook.

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