Archive

Posts Tagged ‘astrobiology’

“Arsenic” Life, or: There Is TOO a Dragon in My Garage!

Note: This article was originally posted at Starship Reckless.

GFAJ-1 is an arsenate-resistant, phosphate-dependent organism — title of the paper by Erb et al, Science, July 2012

Everyone will recall the hype and theatrical gyrations which accompanied NASA’s announcement in December 2010 that scientists funded by NASA astrobiology grants had “discovered alien life” – later modified to “alternative terrestrial biochemistry” which somehow seemed tailor-made to prove the hypothesis of honorary co-author Paul Davies about life originating from a “shadow biosphere”.

As I discussed in The Agency that Cried “Awesome!, the major problem was not the claim per se but the manner in which it was presented by Science and NASA and the behavior of its originators. It was an astonishing case of serial failure at every single level of the process: the primary researcher, the senior supervisor, the reviewers, the journal, the agency. The putative and since disproved FTL neutrinos stand as an interesting contrast: in that case, the OPERA team announced it to the community as a puzzle, and asked everyone who was willing and able to pick their results apart and find whatever error might be lurking in their methods of observation or analysis.

Those of us who are familiar with bacteria and molecular/cellular biology techniques knew instantly upon reading the original “arsenic life” paper that it was so shoddy that it should never have been published, let alone in a top-ranking journal like Science: controls were lacking or sloppy, experiments crucial for buttressing the paper’s conclusions were missing, while other results contradicted the conclusions stated by the authors. It was plain that what the group had discovered and cultivated were extremophilic archaea that were able to tolerate high arsenic concentrations but still needed phosphorus to grow and divide.

The paper’s authors declined to respond to any but “peer-reviewed” rebuttals. A first round of eight such rebuttals, covering the multiple deficiencies of the work, accompanied its appearance in the print version of Science (a very unusual step for a journal). Still not good enough for the original group: now only replication of the entire work would do. Of course, nobody wants to spend time and precious funds replicating what they consider worthless. Nevertheless, two groups finally got exasperated enough to do exactly that, except they also performed the crucial experiments missing in the original paper: for example, spectrometry to discover if arsenic is covalently bound to any of the bacterium’s biomolecules and rigorous quantification of the amount of phosphorus present in the feeding media. The salient results from both studies, briefly:

– The bacteria do not grow if phosphorus is rigorously excluded;
– There is no covalently bound arsenic in their DNA;
– There is a tiny amount of arsenic in their sugars, but this happens abiotically.

The totality of the results suggests that GFAJ-1 bacteria have found a way to sequester toxic arsenic (already indicated by their appearance) and to preferentially ingest and utilize the scant available phosphorus. I suspect that future work on them will show that they have specialized repair enzymes and ion pumps. This makes the strain as interesting as other exotic extremophiles – no less, but certainly no more.

What has been the response of the people directly involved? Here’s a sample:

Felisa Wolfe-Simon, first author of the “arsenic-life” paper: “There is nothing in the data of these new papers that contradicts our published data.”

Ronald Oremland, Felisa Wolfe-Simon’s supervisor for the GFAJ-1 work: “… at this point I would say it [the door of “arsenic based” life] is still just a tad ajar, with points worthy of further study before either slamming it shut or opening it further and allowing more knowledge to pass through.”

John Tainer, Felisa Wolfe-Simon’s current supervisor: “There are many reasons not to find things — I don’t find my keys some mornings. That doesn’t mean they don’t exist.”

Michael New, astrobiologist, NASA headquarters: “Though these new papers challenge some of the conclusions of the original paper, neither paper invalidates the 2010 observations of a remarkable micro-organism.”

At least Science made a cautious stab at reality in its editorial, although it should have spared everyone — the original researchers included — by retracting the paper and marking it as retracted for future reference. The responses are so contrary to fact and correct scientific practice (though familiar to politician-watchers) that I am forced to conclude that perhaps the OPERA neutrino results were true after all, and I live in a universe in which it is possible to change the past via time travel.

Science is an asymptotic approach to truth; but to reach that truth, we must let go of hypotheses in which we may have become emotionally vested. That is probably the hardest internal obstacle to doing good science. The attachment to a hypothesis, coupled with the relentless pressure to be first, original, paradigm-shifting can lead to all kinds of dangerous practices – from cutting corners and omitting results that “don’t fit” to outright fraud. This is particularly dangerous when it happens to senior scientists with clout and reputations, who can flatten rivals and who often have direct access to pop media. The result is shoddy science and a disproportionate decrease of scientists’ credibility with the lay public.

The two latest papers have done far more than “challenge” the original findings. Sagan may have said that “Absence of evidence is not evidence of absence,” but he also explained how persistent lack of evidence after attempts from all angles must eventually lead to the acceptance that there is no dragon in that garage, no unicorn in that secret glade, no extant alternative terrestrial biochemistry, only infinite variations at its various scales. It’s time to put “arsenic-based life” in the same attic box that holds ether, Aristotle’s homunculi, cold fusion, FTL neutrinos, tumors dissolved by prayer. The case is obviously still open for alternative biochemistry beyond our planet and for alternative early forms on earth that went extinct without leaving traces.

We scientists have a ton of real work to do without wasting our pitifully small and constantly dwindling resources and without muddying the waters with refuse. Being human, we cannot help but occasionally fall in love with our hypotheses. But we have to take that bitter reality medicine and keep on exploring; the universe doesn’t care what we like but still has wonders waiting to be discovered. I hope that Felisa Wolfe-Simon remains one of the astrogators, as long as she realizes that following a star is not the same as following a will-o’-the-wisp — and that knowingly and willfully following the latter endangers the starship and its crew.

Relevant links:

The Agency that Cried “Awesome!”

The earlier rebuttals in Science

The Erb et al paper (Julia Vorholt, senior author)

The Reaves et al paper (Rosemary Rosefield, senior author)

Images: 2nd, Denial by Bill Watterson; 3rd, The Fool (Rider-Waite tarot deck, by Pamela Cole Smith)

Slouching to the Right of the Drake Equation

And what rough beast, its hour come round at last,
Slouches towards Bethlehem to be born?

— William Butler Yeats, “Second Coming”

The last few years have been heady for planet hunters. First the hot Jupiters; then the will-o’-the-wisp Glieslings and their cousins; and in the last year, the results from the Kepler mission which detected planetary systems in the low thousands; one of these is Kepler 22.

Kepler 22 is a G5 type star (our sun is G2, about 10% bigger and hotter) 600 light years away with a planetary entourage. For anyone who was in a sequestered jury room or a silently running nuclear submarine, what got splashed across the news media on December 5 was the confirmation that one of the Keplerings is a super-Earth (2.4 times the radius of our planet) that is solidly within the habitable zone of its primary – habitable defined as the region where water can remain liquid. It circles its primary in 289 days and its estimated average temperature is a balmy 22 C/75 F if (big if) it has an atmosphere thick enough for a mild greenhouse effect.

That’s what we know, and it’s important and exciting enough. Here’s what we don’t know, which makes the exclamations of “Twin Earth!” annoying: we don’t know its mass (though the wobble velocity puts an upper limit of 36 Earth masses on it), its composition, the composition of its atmosphere or if it has any moons. Equally annoying are the suggestions to name it The Christmas Planet or the barely less mawkish Hope, right down there with the naming of putative Gliese 581g something like Betty (not even Elizabeth, which at least would celebrate an unforgettable historic figure, plus several literary ones).

The Kepler findings are pinning down the still-loose middle terms of the Drake equation by strongly indicating that most suns have planetary systems, and most planets are of the small rocky variety. Of the approximately 2,000 systems Kepler tentatively identified, about fifty have planets within the habitable zone, of which perhaps ten are “Earth-like” (loosely defined).

Half a percent may not sound like much. But given the quarter trillion suns in our galaxy, the numbers mount up quickly. Plus, of course, the size and location of the newcomer inevitably raises expectations: if Kepler 22b is rocky and has decent amounts of water and a reasonably thick atmosphere, the probability of life moves into the “likely” zone. So it’s not surprising that the Allen Array turned its dishes in the direction of Kepler 22 (no requests for Warren Zevon yet, but the night is still young) – or that the concept art is coming in thick and fast.

It is a great pity that Kepler 22b is so far. Even expeditions with quasi-exotic propulsion systems (or exceptionally nice humans in flawless arkships) would take a long time to reach it. But the lengthening list of not-quite-Earths is a powerful enticement not to abandon the faltering beacon of space exploration. Once again, I will close with what I said about Gliese 581g:

“Whether [Kepler 22b] is so hospitable that we could live there or so hostile that we could only visit it vicariously through robotic orbiters and rovers, if it harbors life — even bacterial life, often mistakenly labeled “simple” — the impact of such a discovery will exceed that of most other discoveries combined. Unless supremely advanced Kardashev III level aliens seeded the galaxy like the Hainish in Ursula Le Guin’s Ekumen, this life will be an independent genesis, enabling biologists to define which requirements for life are universal and which are parochial.

At this point, we cannot determine if [Kepler 22b] has an atmosphere, let alone life signatures. If it has non-technological life, without a doubt it will be so different that we may not recognize it. Nor is it a given, despite our fond dreaming in science fiction, that we will be able to communicate with it if it is sentient. In practical terms, a second life sample may exist much closer to home — on Mars, Europa, Titan or Enceladus. But those who are enthusiastic about this discovery articulate something beyond its potential seismic impact on biology and culture: the desire of humanity for companions among the sea of stars, a potent myth and an equally potent engine for exploration.”

Image: 1st, one of the four Kepler 22b imaginings by space artist Ron Miller. 2nd, comparison of Sol and Kepler 22 (NASA/Ames/JPL).

Postscript: Immediately after my discussion of Kepler 22b, Christopher Jones interviewed me for Trek.fm. He asked me many interesting questions about the 100-Year Starship symposium, long-generation starships and the future of humanity on- and off-earth. You can hear the interview here.

The Agency That Cried “Awesome!”

Note: This is the second of two articles in which I discuss the NASA “arsenic bacterium” debacle. The previous one is Arsenic and Odd Lace.

“Those whom the gods wish to destroy they first make mad.” – Anonymous ancient proverb

In the 1961 film The Guns of Navarone, Greek resistance fighters and Allied demolition experts set out to destroy a nest of large cannons so that a rescue convoy can go through the straits the guns overlook. A young Greek who’s part of the mission goes after a group of Germans gunslinger-style, jeopardizing the venture. The Germans cut him to ribbons. When the mission members meet at their rendezvous point, his sister María (Iríni Pappás) says to his partner Andréas (Anthony Quinn, obligatory at that time whenever swarthy ethnics were required): “Tell me what happened.” Andréas replies: “He forgot why we came.”

María tries to keep her brother focused on the mission.

Last week, NASA administrators forgot why we came. They forgot the agency’s mission, they forgot science, they forgot their responsibility to their own people and to the public. Instead, they apparently decided that all publicity is good, as long as they don’t misspell your name.

Ever since I became fully conscious, I’ve dreamed of humanity exploring the stars. These dreams were part of the reason I left my culture, my country, my family and came over here, determined to do research. Every launch made my heart leap. I wept when I saw the images sent by the Voyagers, Sojourner negotiating Martian rocks. I kept thinking that perhaps in my lifetime we might find an unambiguous independent life sample. Then, at long last, astrobiology would lift off and whole new scientific domains would unfurl and soar with it.

Instead of that, last week we got bacterial isolate GFAJ-1. We got an agency which appears so desperate that it shoved experiments with inadequate controls into a high profile journal and then shouted from the rooftops that its researchers had discovered a new form of life (de facto false, even if the results of the increasingly beleaguered Science paper stand).

This is not the first or only time NASA administrators have been callously cavalier. Yet even though the latest debacle didn’t claim lives like the Challenger incident did, it was just as damaging in every other way. And whereas the Challenger disaster was partly instigated by pressure from the White House (Reagan needed an exclamation point for his State of the Union address), this time the hole in NASA’s credibility is entirely self-inflicted. Something went wrong in the process, and all the gatekeeping functions failed disastrously.

Let’s investigate a major claim in the Science paper: that GFAJ-1 bacteria incorporate arsenic in their DNA, making them novel, unique, a paradigm shift. Others have discussed the instability of the arsenate intermediates and of any resulting backbone. Three more points are crucial:

1. This uniqueness (not yet proved) has come about by non-stop selection pressure in the laboratory, not by intrinsic biochemistry: the parent bacterium in its normal environment uses garden-variety pathways and reverts to them as soon as the pressure is lifted. This makes the “novel life” claim patently incorrect and the isolate no more exotic than the various metallophores and metallovores that many groups in that domain (Penny Boston, Ken Nealson) have been studying for decades.

2. The arsenic-for-phosphorus substitution in the DNA is circumstantial at best. The paper contained no sequencing, no autoradiography, no cesium chloride density gradients. These are low-tech routine methods that nevertheless would give far more direct support to the authors’ claims. Density gradients are what Meselson and Stahl used in 1958 to demonstrate that DNA replication was semi-conservative. Instead, Wolfe-Simon et al. used highly complex techniques that gave inconclusive answers.

The Meselson and Stahl experiment

The reagents for the methods I just listed would cost less than $1,000 (total, not each). A round of sequencing costs $10 – the price of a Starbucks latte. In a subsequent interview, Oremland (the paper’s senior author) said that they did not have enough money to do more experiments. This is like saying that you hired the Good Year blimp to take you downtown but didn’t have enough money for a taxi back home.

3. Even if some of the bacteria incorporate arsenic in their DNA, it means nothing if they cannot propagate. Essentially, they can linger as poison-filled zombies that will nonetheless register as “alive” through such tests as culture turbidity and even sluggish metabolism.

NASA spokespeople, as well as Wolfe-Simon and Oremland, have stated that the only legitimate and acceptable critiques are those that will appear in peer-reviewed venues – and that others are welcome to do experiments to confirm or disprove their findings.

The former statement is remarkably arrogant and hypocritical, given the NASA publicity hyperdrive around the paper: embargoes, synchronized watches, melodramatic hints of “new life”, of a discovery with “major impact on astrobiology and the search for extraterrestrial life”. This is called leading with your chin. And if you live by PR, you cannot act shocked and dismayed when you die by PR.

As for duplicating the group’s experiments, the burden of proof lies with the original researchers. This burden increases if their claims are extraordinary. The team that published the paper was being paid to do the work by a grant (or, possibly, by earmarked NASA money, which implies much less competition). For anyone else to confirm or disprove their findings, they will have to carve effort, time and money out of already committed funds — or apply for a grant specifically geared to this, and wait for at least a year (usually more) for the money to be awarded. It’s essentially having to clean up someone else’s mess on your own time and dime.

Peer review is like democracy: it’s the worst method, except for all others. It cannot avoid agendas, vendettas, pet theories or hierarchies. But at least it does attempt judgment by one’s peers. Given the kernel of this paper, its reviewers should have been gathered from several disciplines. I count at least four: a microbiologist with expertise in extremophiles, a molecular biologist specializing in nucleic acids, a biochemist studying protein and/or lipid metabolism and a biophysicist versed in crystallography and spectrometry.

Some journals have started to name reviewers; Science does not, and “astrobiology” is a murky domain. If the scientific community discovers that the reviewers for the GFAJ-1 paper were physicists who write sciency SF and had put on the astrobio hat for amusement and/or convenience, Lake Mono will look mild and hospitable compared to the climate that such news will create.

Because of the way scientific publishing works, a lot of shaky papers appear that never get corrected or retracted. As a dodge, authors routinely state that “more needs to be done to definitively prove X.” Even if later findings of other labs completely contradict their conclusions, they can argue that the experiments were correct, if not their interpretation. Colleagues within each narrow domain know these papers and/or labs – and quietly discount them. But if such results get media attention (which NASA courted for this paper), the damage is irreversible.

People will argue that science is self-correcting. This is true in the long run – and as long as science is given money to conduct research. However, the publication of that paper in Science was a very public slap in the face of scientists who take time and effort to test their theories. NASA’s contempt for the scientific process (and for basic intelligence) during this jaw-dropping spectacle was palpable. It blatantly endorsed perceived “sexiness” and fast returns at the expense of careful experimentation. This is the equivalent of rewarding the mindset and habits of hedge fund managers who walk away with other people’s lifelong savings.

By disbursing hype, NASA administrators handed ready-made ammunition to the already strong and growing anti-intellectual, anti-scientific groups in US society: to creationists and proponents of (un)intelligent design; to climate change denialists and young-earth biblical fundamentalists; to politicians who have been slashing everything “non-essential” (except, of course, war spending and capital gains income). It jeopardized the still-struggling discipline of astrobiology. And it jeopardized the future of a young scientist who is at least enthusiastic about her research even if her critical thinking needs a booster shot – or a more rigorous mentor.

Quiros circus, Spain 2007

Perhaps NASA’s administrators were under pressure to deliver something, anything to stave off further decrease of already tight funds. I understand their position – and even more, that of their scientists. NIH and NSF are in the same tightening vise, and the US has lost several generations of working scientists in the last two decades. Everyone is looking for brass rings because it’s Winner Take All – and “all” is pennies. We have become beggars scrambling for coins tossed out of rich people’s carriages, buskers and dancing bears, lobsters in a slowly heating pot.

NASA should not have to resort to circus acts as the price for doing science. It’s in such circumstances that violence is done to process, to rigor, to integrity. We are human. We have mortgages and doctors’ bills and children to send to college, yes. But we are scientists, first and foremost. We are – must be – more than court jesters or technicians for the powerful. If we don’t hold the line, no one else will.

The paper: Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PCW, Anbar AD, Oremland RS (2010) A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. DOI: 10.1126/science.1197258.