Slinging it further -- the arsenic bacteria saga continues

Well, we're not gone traveling yet -- and the arsenic bacteria saga continues.   Naturally enough, for a paper whose publication was preceded by such hype -- and followed by such immediate, justified skepticism.  Today's Science has an interview with Felisa Wolfe-Simon, the principal author of the paper that made such a splash a few weeks ago, and engendered such immediate skepticism, for many reasons, including that the experiment was inadequately controlled.  In brief, Wolfe-Simon is exhausted, and still hoping to collaborate with others who can confirm, or not, the findings she reported.  But being a true-blooded product of our culture, naturally she defends her results (graduate schools must train people to say a lot of things, but never "I was wrong!").

We won't go into any detail about the arguments here, because that's already being done much better elsewhere than we could do but we did want to include links here to some of that give-and-take, since we did post on the subject when the paper first came out.  Microbiologist Rosie Redfield's posts on  her blog, including the most recent very detailed response here, and reader comments, are of particular interest, as she goes point by point through the original paper, as well as the authors' attempts to answer skepticism, which they do here.

So far, without the additional carefully done experimental results that doubters are hoping to provide and/or analyze, it looks to us as though, at best, the jury is still out on these arsenic bacteria, and at worst, the original experiments were poorly carried out, poorly interpreted, and poorly reviewed.

And, as we said when we originally commented on this work, even if it were solid science, it doesn't say anything about life in space.  So NASA's Baloney campaign on its behalf should remain pilloried -- and it was NASA, not Wolfe-Simon who got the hype engine going on this one.  NASA seems to be good at engineering, but they should stay out of the basic biology business.  NSF should fund that.  'Astrobiology' is, if anything, a political wing of theirs, and Congress should remove its funding.  We know several good scientists who feed at that trough, but they'd still do good work funded in more conventional ways.  A truly disinterested panel could go through the current portfolio, transfer what's worthy to NSF, and put the rest to rest.

Science baloney is not new.  Legitimate as well as bogus scientists have long known that they can get ahead by dissembling, self-promotion, and puffing up their work in order to get attention, support, publication, or sales.  It's always up to the community to purge and self-police.   These days, the media (including many journals and even funding agencies) flood us with such puffery.  That we will not likely restrain over-claims should not stop us from resisting it, in the name of good science.

Peering over Peer Review

We all like to flatter ourselves about the deep insights that we publish in 'peer reviewed' journals.  Peer review means that a couple of people who (an Editor thinks) are qualified have looked at a submitted paper and said it's OK to publish in the journal in question.

Peer review has important purposes:  done at its best, it can spot errors, help with clarity of expression, and weed out trivial or irrelevant results.  In part this keeps science at least somewhat honest, and can serve to avoid total Old Boy network exclusion of competing ideas.  If we have to have standards for publication, and to judge scientists for grant support, tenure, promotion and the like, this is a reasonable way to do it.

But like anything, it can become an insider's snob system that either still supports the Old Boys or is exclusive, especially of maverick ideas.  As it grew over the years, peer review like any other system, became vulnerable to gaming by savvy investigators.  And because an ever-growing set of journals have to keep cranking out the pubs, the standards simply can't be kept that unbiased quality uniformly high.  Even with no ill intent, reviewers are far too overloaded to pay close attention to papers they review (and the same goes for grant peer review).  And to end all, perhaps, there is a proliferation of online journals some of which are like vanity press: in the pretense (sometimes justified) of avoiding the creativity stifling of peer review, almost anything submitted gets published....with the pretense of peer review in the ability of readers to comment, blog-style.

Meanwhile, free-standing social networking (like MT and other blogs) has become an important source of views and information, and an outlet for skepticism, circumspection, and different perspectives.  It is not entirely trustworthy, because bloggers like anyone else have their perspectives and agendas (but of course so do the peer reviewers that editors choose -- among whom many are bloggers).  But it's not useless and a careful blog-reader can (and should) judge the reliability.

A paper in Nature reviews the recent storm of complaint about what is increasingly being characterized as over-stated (at best), the story on arsenic based life, shows the state of play.  We immediately jumped on this paper here in MT for both scientific reasons and because this seemed more like NASA advertising than carefully presented science.  We think we were justified  in criticizing the story because it was far from a complete demonstration of what the media hype said it was biologically, and because despite NASA-hype it was irrelevant to any serious question about whether there were Little Green Men out there beyond Hollywood.  So in a sense ours was a meta-criticism: not of the primary work, but of the unjustified extension of it as if it had astrobiological implications.

Many others in the blogosphere, probably the most visible being Carl Zimmer over at The Loom, have seized on the paper, and some have noticed problems with the chemistry itself, that we are not competent to have noticed.  We said the paper itself, in Science, seemed reasoned in terms of overclaiming.  Perhaps even Science was vulnerable to the Big Story self-promotion and failed to obtain adequate peer review.

But there's more because the Nature commentary was as much about the legitimacy of blogosopheric reaction as it was about the science itself.  And the expected reaction, in our culture, is immediately to milk this for more self-gain:  (1) NASA and the authors, who have clammed up in the face of this clamor (contrary to their courting of attention initially), want studies to confirm their results....in other words, please pass out more money.  We would oppose that because the work even if well done would have no real 'astrobiology' research.   (2) Nature noted that they encourage online discussion of such issues, that is, use of their blog site and subscriptions to their journal.

Both Nature and NASA are vested interests.   It's hard not to have self-interested motives these days, and perhaps we shouldn't harp on them.  But they do bring to attention changes in the system by which scientific findings gain credence. The blogosphere that needs nurturing in this context is not one controlled by a commercial journal, but the independent, non-vested, free-for-all of the internet, where there is no control for PR-spinning or profit motive. 

The blogosphere is peer review, of a heterogeneous kind but perhaps not so much worse than stuffy professional expert-controlled peer review.  One need not pee over peer review to ask how more democratic and openly rather than covertly the social wheels are turned to decide what should see the light of day.

Arsenic and Old News?

Alien life!!

"Arsenite...[incorporates into DNA] in the place of phosphate in the nucleotides during the synthesis of DNA."  

You've seen this story all over the web in the last few days.  Alien life!  Life on other planets!!  NASA is revived!   Mars men get ready, 'cause here we come!

But, in fact, is that really the story?

The report was published in Science Express this week and written about in the NYT  -- and everywhere else you look:

Scientists said Thursday that they had trained a bacterium to eat and grow on a diet of arsenic, in place of phosphorus — one of six elements considered essential for life — opening up the possibility that organisms could exist elsewhere in the universe or even here on Earth using biochemical powers we have not yet dared to dream about.

 “There is basic mystery, when you look at life,” said Dimitar Sasselov, an astronomer at the Harvard-Smithsonian Center for Astrophysics and director of an institute on the origins of life there, who was not involved in the work. “Nature only uses a restrictive set of molecules and chemical reactions out of many thousands available. This is our first glimmer that maybe there are other options.”

NASA, naturally enough, with its PR army always at the ready to instantly toot its own horn, didn't miss this juicy chance:

NASA-funded astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

So some bacteria were artificially selected to eat arsenic.  What's the big deal here?  Is this a big deal?

Caleb Scharf, an astrobiologist at Columbia University who was not part of the research, said he was amazed. “It’s like if you or I morphed into fully functioning cyborgs after being thrown into a room of electronic scrap with nothing to eat,” he said.

Oh, that's it!  It is a big deal!  The bacteria morphed into cyborgs!  Or rather, the arsenic insinuated itself into the bacterial DNA, by replacing phosphates in some of the nucleic acids.  Is that a big deal?

That quote we started with?
It turns out that that quote with which we lead this post, in red, the one about arsenite incorporating into DNA, the big finding that NASA is touting, is from a paper published in 1980 -- 30 years ago -- about the health effects of arsenic and how and why it's so toxic. To humans.  Give humans enough arsenic and they die, but we can survive lower levels.  Kind of like bacteria.  And that 1980 paper cites a 1974 paper, Petres, J., D. Baron and I. Kunick, Untersuchungen fiber arscnbedingte VerKndenmgen der Nueleinsauresynthase in vitro, Derm. Mschr., 160 (1974) 724--729 -- ok, it's in German, but it's still knowledge that's out there.)


Something largely new, worth knowing--important, even!
It's long been known that Arsenic is chemically similar to Phosphorous and can substitute in many biomolecueles, like protein and DNA, and their reactions.  This is freshman chemistry.  It has also been known that the arsenic alternatives are less stable than those involving phosphorous in these compounds and reactions.

What this new study showed was that these particular bacteria, chosen because they had already adapted to a high-aresenic environment, could be induced by artificial selection pressure to incorporate arsenic into their basic biomolecules.  The study is a careful, sophisticated demonstration of this fact. The authors clearly state that the bacteria were already adapted--in the normal evolutionary way--to high-aresenic environment.  What they then did was gradually feed a serially transferred culture of these bugs to increasing concentrations of arsenic and little or no added phosphorous.  The bacteria that survived were able to substitute the arsenic for some, at least, of their biofunctions (including use to synthesize DNA).

This is worthy of publication in a major journal, and even newsworthy as showing the degree to which already adapted simple organisms can adapt further to a slowly changed environment.  It shows the potential power of evolutionary adaptation, and the degree to which life could, in some ways, function in an arsenic, phosphorous-deprived environment.

But this is not a new life form, any more than a giraffe is a new life form.  The idea that there is life that doesn't function exactly as we do is not new.  After all, we have found anaerobic life, life in extremely hot, cold, salty etc. conditions on Earth.  In most every way, these are ordinary bacteria and this is ordinary evolution followed by very carefully imposed artificial selection. 

Were they happy?
And those little bacteria?  They were much much happier when given phosphorus again after their arsenic bath.  As the authors say, the bacterium "is not an obligate arsenophile and it grew considerably better when provided with P" [phosphorus] -- which means that it would not have survived natural selection in the presence of both chemicals.

Indeed, this study doesn't provide a scrap of evidence that such forms could evolve into stable complex life forms de novo without the help of strong, intentional, teleological and hence totally non-Darwinian evolution.  Maybe it's possible, but this study shows nothing more than that bioreactions can occur, under some particular conditions, with the incorporation of arsenite in a complex cell already adapted to an arsenic environment.  We aren't chemists so can't say how much this study furthers, if not really revolutionizes, ordinary biochemistry.  The paper basically says nothing about life in NASA-land.   That was almost entirely PR hyperbole--the usual self-promotion (not, we note, by the authors in their paper, though they were funded by NASA).  

This paper can stand on its own legs as an interesting finding in biochemistry, or even a demonstration of the power of natural or artificial selection....but is there anything new here that wasn't already known in the 1974 German paper?  Perhaps the latter (we don't read German well enough to judge) was an in vitro reaction rather than one occurring in a whole organism.  If so, if this is a new finding about DNA synthesis in vivo, then responsible news media should just say that without all the ballyhooing and showmanship.

Do we know anything new about alien life?
As to alien life, what does this add?  Let's now assume that the study shows that, in principle, life could exist without phosphorous and with arsenic.  It has long been argued (wholly hypothetically, but let's not quibble about that either) that if there are billions of rocky planets in the universe (and, perhaps it's trillions, and perhaps there are many universes) and if even only a tiny fraction of those planets  have classical earth-life conditions, then just statistically there must be thousands of planets with life that has at least some similarities with our own.  That doesn't mean they use DNA with RNA intermediates, have brains or lipid cell membranes (or cells, for that matter).  But even assuming that is statistically possible, it may exist on at least some planets somewhere out there. The larger space is, the more of these there statistically would be, on the basis just of probability.  Of course such numbers games are fun, but prove nothing.

So what about the arsenic finding?  Suppose, say,  it doubled the fraction of planets that would have this additional life-possible make-up.  By playing the same numbers game, this would just raise the hypothetical number of planets with life on them by, say, a factor of two.  It doesn't change a single thing we've thought or known before.  Even if we assumed that the new result showed that arsenic could work.

It also doesn't raise by any serious amount the likelihood we'll find such planets, that we'll talk to the little green arseno-Men who live on them, or anything else.

Are we condemned to live in a world in which everything has to be boasted about, or turned into  entertainment?  Is it OK for science to be turned into fun in this way?  Or is it irresponsible? 

Science is interesting in its own right, and we know that, left alone, it will lead, if unpredictably, to increased and interesting knowledge, and improved standards of living.  But the hype-route obviously isn't working to make a population that's more deeply understanding of science.  It makes a population that (in the US) largely doesn't even 'believe' in evolution, and perhaps increasingly can't tell fact from fiction.