Archive for the ‘Origins of Life’ Category

Robert Shapiro, 1935-2011

Wednesday, August 3rd, 2011

I was saddened to learn of the recent death of Robert Shapiro, Professor Emeritus of chemistry at New York University.  Although I went to NYU and essentially lived in the chemistry department, I cannot recall meeting him in my time as an undergrad.  It’s a shame, because he was one of the few professors in the field of origin-of-life chemistry—my favorite subject of research.

I continue to be amazed that OoL research is not more popular among chemists.  The mystery of how life originated on Earth roughly four billion years ago has got to be the greatest question in our planet’s history, and the answer all but certainly falls within the exclusive purview of chemistry—physics is too impractical to solve the problem, and by the time you get to biology, the problem has long since been solved.

Shapiro wrote what is by far my favorite book about the origin of life, Origins: A Skeptic’s Guide to the Creation of Life on Earth.  When people ask me what book they should read to get a taste of the problem, I tell them that just about any popular book on the subject is a fine first read, but they should be sure to read Shapiro’s book next.  I think it’s best to get a taste of the romanticism of the field and listen to the proponents’ sales pitches for the main theories before experiencing how Shapiro tears them apart. Origins is a bucket of cold water best tossed on someone after a long, warm shower—it stings, but it is also invigorating.

I was glad to finally meet Shapiro when he visited Harvard to give a talk in 2008.  True to form, he delivered a lecture poo-pooing the idea that RNA or DNA could have been important in the origin of life—a gutsy prospect considering RNA-OoL proponent (and eventual Nobel laureate) Jack Szostak was at Harvard and sure to be in the audience.  But that’s the thing I loved about Shapiro—he seemed to live to identify problematic ideas and call them out with vigor.  As more and more chemists join the ranks of those who oversell their work, I think that it’s great when respected chemists stand up and share their skepticism about the value of an idea, discovery, or line of research.  While many professors are happy to grumble in private, very few are willing to criticize their colleagues publicly.

Felisa Wolfe-Simon Does NOT Get It

Thursday, June 16th, 2011

Cupcake Kid (see Fig. 1) reminds me that I have yet to comment on the recent developments regarding the arsenic-based life paper.  I feel entitled to do so, as (i) it continues to be a major story in chemistry, (ii) I worked on origin-of-life chemistry as a graduate student, and (iii) this blog ran one of the first critiques of the initial report.

You will recall that the original study was published online in December amidst a crapflood of publicity.  First, the authors and NASA held a preposterous press conference to trumpet their results.  Soon afterwards, they were bowled over by a second wave of press regarding the shoddiness of the study.  This backlash from the scientific community caused Science to delay publishing the paper in print until earlier this month so they could run it alongside eight technical notes with peer-reviewed criticism of the study.

I’ve already talked about the original paper and some of my personal interactions with Dr. Wolfe-Simon.  Now, I’ve also had the chance to look at the technical comments, the authors’ response, and some of the secondary coverage online.  Sadly, nothing has changed.

Elizabeth Pennisi of Science Insider (here) and Derek Lowe at In the Pipeline (here) have already summarized the main arguments in the technical notes and the counterarguments of the authors.  My personal view is that the paper has been so severely compromised scientifically that it is practically worthless.  I’m not saying that there isn’t potentially something interesting about the GFAJ-1 bacterium; there probably is, but discerning this information is going to require experimental work that is more careful than what Wolfe-Simon reported.

Just about the easiest way for my scientific respect for someone to drop to zero is by catching him either (i) acting like he knows something that I know he doesn’t, or (ii) saying something I know to be dead wrong and insisting that he’s right.  It’s like someone trying to bluff you with their hole cards showing.  In this vein, what I find truly ghastly about Dr. Wolfe-Simon’s actions is that she seems to show absolutely no contrition whatsoever.  Practically every critique presented to Wolfe-Simon is met with a riposte.  I expected to see at least a few statements along the lines of “yeah, we should have done that experiment” or “yeah, we should have been more careful.”  Alas, were there any?  And even if all of Wolfe-Simon’s retorts are valid—I don’t believe they are—some of the critiques are so obvious that they should have been anticipated and addressed in the original paper.

I do not agree with the common sentiment that “this is how the system is supposed to work”.  This whole evolution has been a farce, and it is not how the system is supposed to work.  Yes, continued work in a field is supposed to be undertaken to confirm or correct original ideas, but a study as flawed as Wolfe-Simon’s should never have been published in Science in the first place.  The most obvious problems and omissions should have been ironed out by peer review.  For a paper as manifestly flawed (or incomplete—take your pick) as Wolfe-Simon’s to be published in a top-tier journal, something went wrong.  But I’ll agree that once such a mistake has been made, the (informal) backlash and (formal) technical comments are probably the best way to mitigate the damage.

What is also absurd is that in the face of a hurricane of criticism from nearly all of the heavy-hitters in the origin-of-life community, Wolfe-Simon seems to be taking credit for catalyzing how the system is supposed to work and pushing science forward at a faster rate.  Listen to what she told C&EN:

Wolfe-Simon, who works at NASA’s Astrobiology Institute and the U.S. Geological Survey in Menlo Park, Calif., tells C&EN she thinks the controversy has primed the scientific process. “We’ve been able to gain so much because of discussion and collaboration,” she says. “This is moving science forward faster.”

Stop and think about that sentence so you can fully appreciate the stupidity of it.

What planet does this woman live on?  This is like a serial killer taking credit for increasing vigilance in a victimized neighborhood.  Yes, all of the uproar has moved Wolfe-Simon’s study forward faster than she was capable, but only because she shamelessly trumped it up to the point that others felt compelled to deal with it.  All of the attention paid to her study has robbed scientists’ time and attention from more interesting areas.  The uproar has also jerked around the public and the press.

The manner in which Wolfe-Simon has dealt with the media is comical.  First, she participated in a dreadful press conference to promote the work, and the media blitz quickly backfired when it brought with it the magnified scrutiny of the scientific community.  Then Wolfe-Simon decided to lie low and not answer questions from the press, saying that she “wanted to be able to have that discourse in the scientific community, as a record”.  But look at what has transpired in the interim:  She gave a public TED lecture in March and provided extensive commentary for a rising-star advice piece in the June edition of Glamour magazine.   She also appeared in a profile in Time magazine as one of the 100 most influential people in the world.  As an excuse to avoid the (unwanted negative) press, she said in December that she “really wanted to get back home and back into the lab”.  But as Rosie Redfield and others point out, Wolfe-Simon’s response to the technical comments contained no new experiments.  Jeez, Louise!

The press needs to stop treating Wolfe-Simon so respectfully and start treating her with the suspicion that she deserves.  She is doing damage to the scientific community and to the public—if not by continuing to promote shoddy science and misinformation, at the very least by wasting everybody’s time.

Sadly, Wolfe-Simon just does not get it.

Photo credit:  Carolyn Patterson

Albert Eschenmoser and I Had Arsenic for Lunch

Wednesday, December 8th, 2010

Chemical Ed VomitsWow…there has been a lot of criticism of the “arsenic-based life” paper.  A lot.  There’s so much that I’m not even going to try to link to all of it.

As you know, I’m a pretty affable person.  I never have a bad word to say about anyone, and the last thing I would do is kick someone while she’s down.  That’s just not my style.  Consequently, I’m not going to tell you about the time I had lunch with Dr. Felisa Wolfe-Simon a couple of years ago when she was a postdoc at Harvard.

You see, a good deal of my graduate work was in the field of origin-of-life chemistry.  I was a fellow of the nascent Origins-of-Life Initiative at Harvard and participated extensively in the program.  I am fascinated by the challenge of the problem and believe that the matter of how life originated on Earth is the second greatest mystery in the planet’s history.  (The first is how the arsenic paper made it past the editors of Science.)

A couple of years ago, the great Albert Eschenmoser came to give a talk at one of the monthly Origins Forums at Harvard.  Thanks to the largess of the director of the initiative, I snagged an hour with Prof. Eschenmoser and the honor of taking him to lunch.

I invited my partner-in-OoL-crime to the chat, and after the two of us had a nice discussion with Eschenmoser about our research, we were joined by a fourth person for lunch: Dr. Felisa Wolfe-Simon.

My knowledge of FWS was limited.  I knew her only as the girl with hot pink hair who asked a lot of questions at OoL talks.  I think there should be a strict limit of two questions per person per seminar, unless I need to go to the bathroom, in which case there should be a one-question limit.  And short of trying to gain employment as a marker buoy in Boston Harbor, I can think of no good reason to dye one’s hair magenta.  Whatever.

Lunch was short…and uncomfortable.  At one point, FWS brought up trying to incorporate arsenic into DNA.  (Remember, this was years ago.  I assume it was before she started her work at Mono Lake.)  FWS said she wanted to make DNA with arsenic atoms as the backbone.

Eschenmoser asked if Felisa had any experience in synthetic chemistry.  She responded that she had none, at which point Eschenmoser recommended that she not undertake this work as it would be very synthetically challenging.  FWS’s response was that it might be a good thing for her to have no synthetic experience: with no knowledge of the challenges, she would not be daunted by such a hard task.

I love when people justify ignorance…of anything.  And I didn’t think she was joking.  I buried my gaze into my avocado sushi roll and occasionally exchanged uncomfortable glances with my labmate.  In the words of John McEnroe…you CANNOT be serious!  Did she not know to whom she was speaking?  This was Albert Eschenmoser, a titan of organic chemistry.  I felt embarrassed that I was even involved in this conversation…and in the chemistry building at the finest university in the world.  Ugh.

Eschenmoser took her comment at face value and went on the reinforce the point that this task would require extensive synthetic skill.  Lunch was over quickly after that.  My labmate said he would never forgive me for wasting his time.  I can’t blame him.

What does all of this mean?

1) I am a jerk.  Sorry.

2) Wolfe-Simon is not an organic chemist or anything close to one.  I have no trouble understanding the lack of attention to detail in the chemistry presented in the Science paper.

3) Wolfe-Simon has been looking for arsenic-based biomolecules for quite some time.  I don’t want to try to read too far into the tea leaves, but sometimes when you are really looking hard for something, you think you’ve found it when you haven’t.  She missed some obvious experiments, but my guess/hope was that she didn’t do so maliciously with an intent to deceive.  She is one of the most enthusiastic, effervescent scientists I have ever encountered.   I think that she may have been so excited to have found what she was looking for that she got a little ahead of herself.

Still, I don’t condone this behavior from an experienced scientist.  Regardless of whether her conclusions stand, the work is shoddy.  What really bugs me is that papers like these end up harming the field of prebiotic chemistry.  I have said before—on blogs and in seminars—that prebiotic chemistry does not get the attention the subject deserves.  One of the big reasons it doesn’t is because chemists don’t respect the field.  People trumpet the simplest results as major discoveries and chew up space in Science and Nature that would probably best be left for less sexy but more robust results.  This paper is going to do nothing but reinforce this image, and that’s a damn shame.

Preliminary Thoughts on the “Arsenic-Based Life” Paper

Friday, December 3rd, 2010

This is indeed an interesting paper.  I have some questions about it; maybe I am misreading things.  Pardon the terseness.  I’ll update this post later this weekend.

1.  What was the source of the arsenate used in the growth media?

I can’t find the vendor/product information in the paper or the SI.  I am inclined to agree with Steve Benner and his suspicion that there may be sufficient phosphate in the “–P” media to support growth.  Life has a nice ability to concentrate/pick out what it needs.

2.  How could you think that arsenic is in the backbone of the DNA?

This paper shows that arsenic(V) esters hydrolyze in water in seconds.  The authors hypothesize that the bacterium has mechanisms for coping with this, but how does that explain the fact that they see a nice, clean gel (with a single band) of the isolated DNA?  Shouldn’t that band streak like the Dickens?

3.  “Arsenic possesses a similar atomic radius [to phosphorus]”?

Is 15 picometers (P: 100 pm, As: 115 pm) really that similar?  That seems like miles to me (on the atomic scale).  It is bound to have profound implications for bond strength and molecular structure.

4.  Title:  “Using Arsenic” [vs. “Tolerating Arsenic”]

I am not convinced the data presented support the conclusion that these organisms are “using” arsenic.  It will definitely be interesting to see if future work can isolate and characterize biomolecules from this organism that include covalent bonds to As.  Regardless, this paper is interesting because it presents an organism that is very tolerant of arsenic.

The Universe: Spaceship Earth

Wednesday, July 11th, 2007

I just finished watching The Universe: Spaceship Earth on The History Channel. As someone intimately involved in origin-of-life research, I’d give it a B for accuracy. As an unabashed fan of TV documentaries, I’d give it a C+ for entertainment value. Fortunately, an episode of Ice Road Truckers came on immediately afterward to cleanse the palate.

The first twenty minutes of Spaceship Earth were a pretty solid introduction to the formation of the solar system and planetary accretion. The only gripe I had was that the producers seemed to heavily favor the water-from-comets theory over the water-from-volcanic-outgassing theory, where the debate in the community isn’t nearly so one-sided.

The program soon moved into the development of life, and that’s where the wheels came off. They used the origin of life as a tease, like, “we’re going to tell you how life originated after you watch these fabulous commercials.”

“This will be interesting,” I thought, “Here’s comes the chemistry; I wonder what they’ll focus on. Prebiotic soup? RNA world?”

Nope. Boy, was I disappointed. After a two-minute segue that implied the Earth was seeded by life from an asteroid (the panspermia theory), the discussion quickly moved to photosynthetic bacteria (which now magically existed). What a cop out. I suppose we chemists have made little progress in solving the problem, but the producers really provided a disservice to their viewers by resorting to using panspermia as a bridge from physics to biology.

As if the handwaving wasn’t bad enough, obvious errors soon followed. At one point, a professor being interviewed said that the first bacteria had a lot of gases like H2S and CH4 to use and a little CO2. Hmmm. If 96% of the atmosphere is a little, then I guess he’s right.

The discussion quickly moved into thermophilic and extremophilic bacteria being potential models for early life, then into some simple evolution. The last 10-15 minutes of the hour-long program focused on the boring and played-out story of how the global climate is changing and that humans are probably to blame.

Overall, I guess it was OK. They could have included some interesting OoL chemistry, but until we have a more compelling and complete story, I suppose producers are going to be reluctant to talk about it. Bottom line: If you’re looking for something good on TV, watch Ice Road Truckers, Copa America action, U-20 World Cup action, or le Tour instead of a Spaceship Earth re-run.