Alternate Biochemistry
NASA has announced the discovery of a strain of bacteria that is not only able to live in an extreme environment loaded with the toxin arsenic, but is able to incorporate arsenic into its basic structure. The research is part of NASA astrobiology project – exploring the limits of life in order to infer the possible environments beyond earth in which life might exist.
Researchers were investigating bacteria in the harsh environment of Mono Lake – which has been without a supply of fresh water for 50 years and is loaded with arsenic. The discovery of so-called extremophiles – bacteria that have adapted to extreme environments – is nothing new. Bacteria are amazingly adaptable forms of life and have been found is very hot as well as cold environments, and in environments under high pressure and with high salinity. The ability to tolerate the presence of a toxin is interesting, but also not surprising given what has already been discovered about extremophiles.
What is entirely new with this discovery, however, is the fact that these bacteria, a strain (GFAJ-1) of a common type of bacteria called Gammaproteobacteria, appear to incorporate arsenic into their own biochemistry. In normal living cells phosphorous is used as part of the DNA and RNA backbone, in addition to being the energy transporting molecule (adenosine triphosphate), and being part of structural phospholipids. Arsenic is chemically similar to phosphate, and in fact that is partly the reason for its toxicity – it is very disruptive to normal biochemistry. These bacteria seem to have replaced phosphate with arsenic in some of these structures and molecules.
This is an important proof of concept – an alternate biochemistry in which arsenic replaces phosphate is possible.
This raises several interesting points. The one that NASA is primarily interested in is exobiology – life outside of earth. As the number of possible environments in which life can exist expands, so does the probable density of life in the universe and the chance that we will discover such life. The most common alternate biochemisty that I hear (whether in science fiction or speculation) is one in which silicon replaces carbon. Methane-breathers (using methane instead of oxygen for metabolism) is also common. Swapping arsenic for phosphorous now has to be added to the list.
Another interesting point is that “alien” life may exist on earth. So far, all life on earth that we have examined is biochemically similar and is clearly related – the result of one origin of life and subsequent evolution. But there is no reason why there cannot be multiple trunks to the tree of life on earth. Life may have arisen, or been seeded, multiple times. Clearly one origin now dominates, and may be exclusive, but there may be bacteria-like organisms on earth that are the remnants of other origins. Or, they may share a common origin with known life, but have branched off so much earlier than any known life that their biochemistry (even their DNA code) can be vastly different than anything known.
There are many thousands of species of bacteria that we have not yet fully investigated, so this possibility cannot be ruled out. We can conclude that if such a so-called shadow biome exists it must be rare, or else by chance alone we would have encountered it by now.
It can be argued that the discovery of extremophiles, especially this latest discovery, makes the discovery of “alien” bacteria on earth more unlikely because even in extreme environments bacteria that is related to the rest of life have pushed their way in. Perhaps the life that we know was so successful that it managed to invade every possible niche, crowding out any competitors.
Perhaps we will have to look beyond earth to discover the descendants of a truly independent origin for life. Such exploration is underway on Mars, and there are other candidates in our solar system, such as the moons Europa, Titan, and Enceladus. The primary way that we look for microbial life in such locations is by looking for the signs of biochemistry. This is precisely why NASA is interested in this research – they have to know what kinds of biochemistry to look for. This research may partly determine the kinds of experiments that future NASA probes will use to search for the signs of exobiology.
I posted on Steve’s other blog, but I’m guessing Steve is traveling in Australia and probably wrote that article last week, and just scheduled it to be posted today – before the news of how the paper/research may be flawed.
NASA may take a PR hit from both the hype of the announcement and the conclusions, but if it turns out that this report is based on flawed science techniques, then this is great example of the self-correcting of science.
Yep .. it was overhyped shoddy science. That said, NASA itself isn’t in a self-correcting mood right now.
And, I suspect NASA of budget-related motives on the hyping, too:
http://socraticgadfly.blogspot.com/2010/12/bad-or-at-least-breathless-science-by.html
Some readers may be interested in criticism of the paper from chemical and microbiological perspectives:
http://scienceblogs.com/webeasties/2010/12/guest_post_arsenate-based_dna.php
http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html
Aw
http://scienceblogs.com/webeasties/2010/12/guest_post_arsenate-based_dna.php
shit
http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html
Thanks for an excellent article. Could we keep skepticblog at this level of discourse? I think the miscalculation was to hype the finding. It reminded me of how the ardi fossil finding was hyped and then led to disappointment Someone is offering scientists bad PR advice.
I never saw anything disappointing with ardi – it’s a fossil with interesting characteristics. All the news stories were extremely annoying and just plain wrong though, so I doubt much of the public has a clue about what’s special about ardi. Maybe in this MTV world people think that making up fantastic (and wrong) stories to attract the ADHD audience for 3 seconds constitutes “science communication”.
To get back to the earth as we know it (smile), is Mono Lake “without a supply of fresh water…”??? Maybe not significant, but surely, there is some runoff that still does occur, i.e. Lake levels, tho extremely `briny’, do fluctuate, and some precip events do occur, even in that dry environment…??? In fact wasn’t there a brouhaha about Lake depletion with LA-DWP several years/decades ago about cutting off all streams/rivers into Mono so all water could instead be channeled via Owens Valley to the L. A. area???
On an unrelated note. How can we as readers reward excellent skepticblog articles like these. We as readers seem to reward the poor opinion articles by giving them traffic and punish good articles by agreeing with them. In fact, I would bet there is a strong negative correlation between the rating and traffic.
Any thoughts?
Good comment. I agree :-)
Why do so many scientists get trpped trying to prove their hypothesis? To prove your hypothesis, surely the easiest way is to go about disproving it, then if it still stands up, you are onto something!
Great article Steve, shame that it looks like the research may not hold up.
@Somite- After the last few largely commented upon blogs, I could not agree more, they look and read more like a political blog….
@most people here.
Imagine that, people debating over issues…. We skeptics can’t have debtate!!!!
if Shermer’s articles on politics, economics, human behavior and movies drive the most traffic, then he needs to keep it up. Maybe one day, the bulk of you will learn how to rationally and logically debate with those people who disagree with your own politics.
“Maybe one day, the bulk of you will learn how to rationally and logically debate with those people who disagree with your own politics”…said the master.
I’m sorry- because Shermer quotes patently unscientific nonsense in his posts (see Cool it! review)- it is my politics inquestion?
Please give me your definition of logic.
Wait, where’s the film review? Isn’t this a film review blog?
Wolf, no that would be
Michael Shermer’sJohn Stossel’s blog.@Oldskool:
The authors didn’t get tripped up trying to prove their hypothesis. The problem is that they didn’t try to *disprove* it.
Regarding the science itself:
In my mind, the biggest problem with the original paper, which few science bloggers are discussing, is that the evidence presented to support “growth” on arsenate with no added phosphate is weak and the methods are full of caveats. First, they use turbidity to follow growth. The change in turbidity they see is modest. Turbidity is affected by any light-scattering material in the culture. Given that there are known arsenic metabolisms that lead to mineral precipitation (see Newman et al. Appl. Environ. Microbiol. 1997 for an example), turbidity is not an accurate way to follow growth in this case.
The second method they use to measure growth is acridine orange staining. There are some reports in the literature that suggest that acridine orange accumulates in PHB. Based on their TEM images, it looks like the arsenate-treated cells are producing massive amounts of intracellular PHB. So, there is a good chance that the increase in acridine orange-stained cells is actually due to a change in their detection limit rather than an increase in cell number.
There are other methods routinely used by microbiologists to measure growth. One can plate for colonies and count them to get an indication of the number of cells in a sample. Or one can measure protein levels. For such an extraordinary claim, I am surprised the reviewers did not request these measurements.
Somite says, “Someone is offering scientists bad PR advice.”
Uh, Yeah. That is certainly possible, I suppose.
However, the horror can work the other way around too: somebody may have been offering NASA outreach folks some bad carrots that were dangled in front of their noses. And they nibbled if not chomped.
They have been known to snap up at most anything that smells potentially appealing…especially if it is well-seasoned with the flavor of mass-appeal.
Alas, that partition of NASA (and many science-engineering facilities as well as universities) have long since adopted the notion that everything can be treated as if it was a question of winning public acceptance.
The worst thing that ever happened to the practice of government or university-based science news releases is that they all jumped on the idiot bandwagon, especially around 15 – 25 years ago, ostensibly to ‘enhance’ and ‘stimulate’ the public’s appreciation of science. They went directly to the ‘experts’ of profit-making via sensationalism by employing the tricks and tricksters from Madison Avenue and Hollywood. Once that got entrenched, everything they ever tried to instill in the public in terms of a decent and sincere conveyance of science to the popular mind was lost. The public appreciation of the basic integrity of science, which was once well established throughout the 1950’s, ’60’s and well into the decade of the ’70s, was replaced by a mode that exchanged long-term integrity for the short-term ‘wow’ factor, as if science is all really a matter of STIMULATING the public rather than merely informing them.
That’s what ‘public outreach’ has done, and the consequences have been, and continue to be, absolutely disastrous.
And almost nobody ever bothers to look at this very real problem…quite possibly because the practice is now so well entrenched, and there are so many now employed who hearken from the market, that any examination of the problem is inevitably bounced back to these very personnel, who certainly have a tidy interest (amply funded by government and university moneys) to protect.
Meanwhile everyone sees the obnoxious growth of denialism in climate science and evolution, not to mention a precipitous deterioration of the public’s appreciation of what science is not only all about, but in a festering DISTRUST of science and scientists, cultivated by a growing cabal of jokers and crackpots who have gained considerably on the internet, all the while spending an exorbitant amount of effort and money to rectify this growing problem. It is quite clear from this perspective, even to those who gave them the job and consequent power, that those who are given the task to fix it have no incentive for doing so.
Anything as obtuse as science can and must be embellished! WHY? Because the MARKETING ETHIC is king! NOT because science might happen to be based on an ethical foundation such as honesty. That wouldn’t sell nearly as well.
Readers who are scientists: here’s the question: Who is largely given that task? Who is regularly given the responsibility for ‘educating the public’? I’ll give you three guesses, and if you can’t come up with the right answer, chances are you haven’t personally done a heck of a lot to help educate the public yourself. THAT important task is routinely given to the very same ‘marketing experts’ who have been specifically hired to do their thing and who have escalated the problem in the first place…straight out of your control, and that is truly shameful, indicative of an institutional absolution of your personal responsibility to engage the public with your work.
What bugs me on top of everything else is the incessant whining about how we need another Carl Sagan to help gain a proper public appreciation of science. BALONEY! I have had the honor of personally working with Carl, and the very last thing he would ever have suggested or advocated is that some ‘scientific messiah’ ought to take up the task of cultivating the public trust he worked so hard to establish. It may well be that he helped ‘commercialize’ science, but it seems entirely clear to me that his putative evangelism reached a heck of a lot more ordinary people than those in the scientific community (including the jealous)…who are quite content to rest easy, allowing the ‘hired experts’ to interpret their findings, suitably dumbing it down for what is supposed to be a proper level of public digestion, and doing next to NOTHING to engage the public on a personal level.
Most scientists are supposed to be teachers. Quit whining about how hard it is and start ACTING like it!
Meant best to say in the ninth paragraph:
“Meanwhile everyone in the scientific community who sees the obnoxious growth of denialism in climate science and evolution, not to mention a precipitous deterioration of the public’s appreciation of what science is not only all about, but in a festering DISTRUST of science and scientists, cultivated by a growing cabal of jokers and crackpots who have gained considerably on the internet, do next to nothing (quite contrary to pre-1979, when many more scientists were willing and able to personally engage newspapers and magazines to encourage them to get it right) all the while spending an exorbitant amount of effort and money to rectify this growing problem. It is quite clear from this perspective, even to those who gave them the job and consequent power, that these who are given the task to fix it have no profitable incentive for doing so.”
Many pardons.