Tuesday, December 7, 2010

An Astrobiology tempest: Arsenic Life?

Is this an SEM Image of the first known lifeform to use a different biochemistry from the rest of us?

So many interesting things to mention about the recent findings of (partially) Arsenic-based life in Mono Lake, CA. First of all there's the discovery itself, detailed in a paper by Felisa Wolfe-Simon over at Science Magazine. But there's also something to be said about the way that NASA has handled the media surrounding the discovery. Additionally, in the week since the announcement, we've had some serious backlash by bloggers, including particularly pointed remarks by fellow science blogger, and microbiologist Rosie Redfield over at RRResearch. Some seem to think that "research paper review by blog" is a good thing and a sign of the times, but is it a substitute for the peer review process? Most troubling of all are the questions being raised in some spheres about the scope of NASA's astrobiological work and the worth of the planetary sciences. After all, they argue, what's Space got to do with studying pond scum on a lake in California?

For ease of use, I've subdivided my comments below.

1. Background on CHONPS and the Biochemistry of Life

Most of these themes have been covered in detail elsewhere, so I'll talk a little about highlights and aspects that have received less attention. Something that other sites seem to be missing is background, so I'll go into some detail here. In order to understand why life using Arsenic is so important, we need to go back to the periodic table. One of the fascinating things about the periodic table is its predictive power. By organizing elements in columns by the number of electrons in their outer shell, you are describing how those elements interact chemically. So, for instance, all the hallogens (Fluorine, Chlorine, Bromine, Iodine, etc) or the noble gasses (Helium, Neon, Argon, etc) get grouped together because they have similar properties. For many applications, you could swap Neon and Argon and get similar results because of this.

Periodic Table of the Elements, Source: http://blog.richmond.edu/openwidelookinside/archives/1675

So what about life? Well, we know that most living matter is made up of six chemical elements, collectively called CHONPS (Think "Chomps" with an "N") which stands for Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus and Sulfur (though DNA and RNA require no Sulfur, it is common in other biomolecules). One of the reasons that life is abundant on Earth is because many of these elements are themselves abundant. But could life use a different chemistry, with substitutions for each of these elements? After all, Silicon (directly below Carbon) has been hypothesized as a possible basis for different biochemistries for years (The astrobio head at NASA even brought up Star Trek's example of the Horta at the news conference).

What we find is that there may be a big gap between 'Possible' and 'Probable.' The reason for that is that the elements do change as you go down the periodic table. And so that while fluorine can be used as a poison gas, chlorine is safe for disinfecting bathrooms and your pool, while using liquid bromine in the lab risks little other then a bit of a headache (if handled properly). We even put Iodine on wounds since it does more damage to microbes than to us. In the same way, we find that Silicon, while sharing many similarities with Carbon, is much less versatile with fewer possible molecules. Similarly, Arsenic, which lies below Phosphorus on the periodic table is also less versatile, despite the similarities.

2. Alternate Biochemistries

However, could you generate life with Silicon or Arsenic? Possibly, but it would not be favoured over Carbon or Phosphorus under terrestrial conditions unless they were in very short supply. Even in Mono lake, where our friendly bacterium lives, we don't find sufficiently low levels of phosphorus to make this possible and as a result, in the wild, the bacterium in question does not actively incorporate Arsenic into its biomolecules. But what it does do is tolerate very large concentrations of Arsenic. That's a pretty special property. For most terrestrial organisms, Arsenic acts as a poison because its similarity to phosphorus. Since the body's chemistry is fine-tuned, Arsenic's subtelly different properties throw off our biochemistry to a lethal extent. The same thing would happen if you drank heavy water, but since our bodies contain much more water than phosphorus, the amount required to be lethal is much greater.

What Felisa Wolfe-Simon hypothesized, was that tolerance to Arsenic was a first step on the road to actually creating viable biomolecules out of Arsenic. And so, in the lab, they breed the bacteria from Mono lake in solutions successively more concentrated in Arsenic and less concentrated in Phosphorus. The whole time, they observed the bacteria happily dividing and growing, and when they processed their final samples, they found Arsenic inside of the cells, possibly incorporated into the biomolecules. This could be huge. Phosphorus is used to build the sugary backbone of DNA, allowing life to store information for procreation. But more interesting to me was the possibility of replacing the phosphate groups in ATP, the cell's energy storage molecule, with arsenate to form ATAs. Since ATP can be abiologically created, and can be polymerized to form self-catalyzing molecules like RNA, this opens up a whole new pathway for the initial evolution of life.

3. Is it Astrobiology?

So why is this astrobiology? Well, for those of you familiar with the topic (I have a primer here) you'll recall that one of the goals of astrobiology is to determine what environments elsewhere in the universe might be suitable for life. These constraints are set by the only kind of biology we know, our own. As such, the study of our bacterial cousins that can live in unusual environments increases the number of different environments where we know that life is possible. We call these creatures "extremophiles" because they love extreme environments. And in their diversity they never cease to amaze. We have bacteria that can survive an interplanetary trip (steptococcus), live at pressures of over 10,000 times atmospheric (e coli), in water above boiling (pyrolobus fumarii), even inside of nuclear reactors (deinococcus radiodurans).

But the common thread here is that all these extremophiles are based on the exact same biochemistry that powers you and I. If we were to discover an organism that used something other than CHONPS, all bets are off. That's exciting for astrobiologists.

4. Was it Hyped?

But is it exciting for the public in quite the same way? NASA thought so, and therefore deliberately released a vague teaser for the press conference. For us scientists, the nature of the discovery was fairly obvious. Felisa Wolfe-Simon was the lowest ranking scientist on the panel - that's usually a good hint that she's there to present her own work and not comment on someone else's. And Felisa had only published a couple of papers prior to the conference, both dealing with Arsenic biochemistry and mono lake in particular. Her last publication is particularly portentious and was entitled "Did life also choose Arsenic?"

But at the same time, I can see why the public went wild. Astrobiology is something that excites the human mind, and the first thing that it usually suggests is LGMs (little green men) or extraterrestrial life forms of a lower order. When the discovery was revealed to be something more prosaic and technical, other blogs screamed "hype!" While NASA could have done a better job with the teaser, they did get it noticed and the topic talked about. However, I would hate for this to be another example of crying wolf.

On the other side, it seems that we have more work to do in educating the public and particularly news agencies who disseminate information on scientific discovery. Rumours ran the gamut in the days leading up to the press conference, some of which could be easily debunked. One particularly prominent one suggested that bacteria had been found on Titan. Unless those bacteria were larger than 350m wide (the smallest Cassini-SAR spot size) there's no way that could have been true.

5. Controversy and Peer Review

One big question is whether any publicity is necessarily good publicity? Besides the folks crying "Hype!" we also have a number of professional scientists, most prominently Rosie Redfield, publicly denouncing the work described by the paper on Blogs. Rosie wrote what was (in my opinion) a needlessly harsh criticism of the work and by implication the researcher who performed it. However, she does raise legitimate concerns. As has been said before about ALH84001, the infamous Martian Meteorite, extraordinary claims require extraordinary evidence, and Rosie suggests that in this case due diligence was not done. Further, she suggests that the officials at NASA and the editors of Science, the highest impact factor and most reputable scientific publication in North America, are scientifically corrupt since they allowed the publication of such a shoddy piece of work.

Now I'm no biochemist, so I don't really have much to add to the discussion of legitimacy. However, I should point out a few things. FIrst, Science limits articles to 2500 words, which is not a lot of space to discuss methods, results and implications. Second, the article did pass peer review, most likely by three reviewers. This is not an easy process for even the most straightforward of papers, and I really hesitate to cast aspersions on the reviewers or the editors (again, I'd like to see more than "I feel this paper is crap, therefore the fact that it got published means peer review is corrupt") without more information. I should note that since this is the broad field of astrobiology, it is hard to find three experts able to cover the entire topic, so it's possible that the techniques were only lightly reviewed compared to other areas. As well, articles on the bleeding edge of Science are typically contentious, and what seems like two groups with intractable disagreements and unreconcilable positions may actually hide a broader agreement Take a look at the divisive debate over the value of the Hubble Constant, if you doubt that.

As a bulwark against this sort of thing, peer review is a system that has worked well, though it has its faults, and everyone loves to complain about it. As Winston Churchill once noted, Democracy is the worst form of government out there except for all the others. I think Felisa is justified in refusing to be goaded into getting into a shouting match on the internet, and to wait for Rosie to put her comments in a scientific letter. At the very least, it will give her another 2500 words in which to expand on her original work. That's as it should be. If we only had a press release or a conference abstract the methodology wouldn't be out there for all to see, and people would be screaming about that instead.

6. Damage Done?

Who are the winners in this whole affair? Well, NASA certainly got publicity - but it wasn't exactly the kind they were aiming for. Likewise, the furor which continues to fester on the internet probably was not what Felisa had in mind. A 1st author paper in Science is the sort of thing that can make a career for a postdoc - but the exposure risks serious damage to your career if it is believed that you have slipped shoddy work through the system. I can't say I envy being in Felisa's shoes right now. At the same time, there are some seriously big names on that Astrobiology panel at Headquarters and on the paper. If I had some doubts about my work, but my more experienced colleagues and my contacts at NASA were telling me that I had done a great job, I too would likely err on the side of trying to publish.

As for Rosie, her blog postings have been picked up by the CBC, partially due to the vitriol. She is preparing to submit a letter to Science and I wish her well with that. If she's right, this is also something that could make her career by creating for her a reputation as an independant-minded scientist with superior critical thinking. However, she's further along in her career than Felisa (I don't know if she's tenure-track or not) so she has less on the line. She also seems to be taking the tack that due to the high profile nature of a publication like Science, anyone who submits should be prepared for the attention.

As for the programatic damages, the combination of perceived hype and controversy has many wondering if Astrobiology is something that NASA should be doing. That's seriously dangerous talk in a year with a Congress searching for cutbacks to make. As well, I have to worry about Planetary Science. I get told all the time that we are all dilettantes, and that you could create a better exploration program by hiring only terrestrial specialists. This certainly doesn't help that perception.


  1. I dont think so if there is..


  2. welll - this is very long....and i skimmed most of it (I must be candid)

    but particularly on the peer review/public debate note:

    let's see if I can get my thoughts straight on this matter. I believe that scientists should absolutely be questioning the research of their peers. The professional peer review process is designed to do this, but that doesn't mean the debate is over. If another scientist reads the paper and wants to offer criticism, they should be more than welcome too. The emails of the PI's are put on the papers for a reason. Almost any scientist on the planet would be happy to discuss their latest paper and perhaps take in a new view, or try and convince you why their findings are significant.

    So in that way I believe what has happened across the internet is good. What has not been good is the apparent anger some have felt. This doesn't mean you have to sugar coat your feedback, you just shouldn't be boarding on making fun of another scientist.

    John I think i have what im trying to say. 'review by blog' as a sign of the times...i think this is good. BUT in no way as a replacement for ACTUAL professional peer review. Blogging is a faster way of waiting to meet the researcher at a conference so you can discuss their findings, and what you think of them. But i think if you want to be taken seriously, you have to give more serious criticism...and less outright name-calling.

    did that mental-vomit make any sense?

  3. You make a good point Jesse. What we need to be careful of is that blogging about science and publishing about science don't get conflated together. Peer review is a process, and while no one argues it's perfect, it's the best we've got. It assures us that at least a couple of folks, nominally unconnected to the research and knowledgeable in its methodology have checked things over thoroughly.(Side note: I hope to address and demystify the process a little in a future post.)

    Does that mean that everything that gets published is solid gold? No. Sometimes things do fall through the cracks. However, you have to have trust that any scientific publication, and certainly one as prestigious as Science, would have done their best due diligence. So I'm with Phil Plait on this one, hoping that calmer heads prevail: http://blogs.discovermagazine.com/badastronomy/2010/12/07/arsenic-and-old-universe/ .

    We all know that it's possible to poke small holes in just about any scientific paper. Anything on the bleeding edge is always going to have some uncertainty. As well we often forget that journal publishing isn't just about recording facts for posterity. It's also about getting information out to other researchers so that they can develop their own opinions and tests. Rosie seems to be suggesting that this result was not ready for prime time, but when would it be? Never have I met a reviewer who didn't want to see more data. It took Mumma 6 years to make his Martian Methane data completely bulletproof. As a postdoc, Felisa doesn't have that kind of time.

    So we need to be careful to tread lightly, I think. Because in the public's mind a Journal article is no different from a blog post or a newspaper article and too many people see science as no more than an opinion. If everyone chimes in about how the work is shoddy, then we won't get the kind of scientific debate that we need to have on this.

  4. Update: RR letter to science posted here http://bit.ly/dY7Nu8 and a response from Felisa posted here: http://www.ironlisa.com/gfaj/

  5. Updater: Longer response from Felisa posted here: http://ironlisa.com/gfaj/GFAJquestions_Response_16Dec2010.pdf