Environment and Ecology, Science, Science and Society

Fresh out: extraterrestrial life _not_ discovered!

You can thank the rampant speculation caused by NASA’s press release for this blog post’s title1.

[UPDATE: There’s now a lot of controversy over the paper, which a number of microbiologists says it’s not, um, terribly good…]

Very, very tough little bacteria
Very, very tough little bacteria

And the thing is, the discovery in question is a really awesome and important one.  But it’s also a pretty technical one, and I imagine will leave a lot of people saying something along the lines of ‘meh’.

The discovery is, of course, that scientists have found a strain of bacterium2 which is able to use arsenate instead of phosphate in its biological bits and processes.  To understand why this is awesome, some background…

Background (to be skipped by those who know it)

All of the organisms we’ve come across on earth are made up of the ‘big 6′ - hydrogen, oxygen, carbon, nitrogen, sulphur and phosphorus.  Without any of these, an organism loses its fundamental livingness, and is instead simply a great steaming (or not), pile of failed biochemistry.

If I were in front of a periodic table, I should now point at the element Phosphorus.  With a long wooden stick.  Phosphorus is used in cells in a variety of interesting and essential ways: it forms the backbone of DNA, and is also the ‘P’ in ADP/ATP, the molecules which serve as cells’ energy reservoirs/factories.  Oh, and it’s a heap of other important things as well, including stuff like, you know, proteins.

More pointing at the periodic table now!  Another fascinating thing is that this most marvellous table is not some random agglomeration of elements.  Oh no.  Its structure allows us to make some rather interesting inferences.  For example, elements in a column have a lot in common with each other, and can often substitute for each other in biological processes.  Which is why some critters can use tungsten instead of the very-fun-to-say molybdenum.

Or they can use cadmium instead of zinc.

Or copper instead of iron, for the carrying of oxygen (which is why the blood of some mollusks and bug-type things is green).  Interestingly enough, this substitution breaks the ‘same column’ rule - anyone know why?

And, of course, it’s led to much hypothesizing that it may be possible for life to use silicon instead of carbon3, or, possibly, arsenic instead of phosphorus… The most biologically common form of phosphorus is phosphate, which behaves similarly to arsenate in a number of ways.  The thing is, though, that while arsenic can be substituted for phosphorus in the early steps of some biological pathways, it’s just sufficiently different that later arsenic-based metabolites are unstable.  Which is why it’s toxic: it knocks biological processes over.

Kids: do not try eating arsenic at home (or anywhere else, for that matter)

Main story (those who tuned out, feel free to tune back in)

Right, so!  Some scientists, including NASA people, went out to a lake in eastern California, enchantingly called Mono Lake.  Why?  Well, they were on a treasure hunt.  Or, to be more precise, a bacterium hunt.  Mono Lake is far saltier than usual, alkaline (the opposite of acidic), and contains much higher levels of arsenic than usual as well.  A good place to look for arsenic-using beasties.

They took some of the lake’s sediment and, through various mysterious processes known only to microbiologists (and anyone who cares to read the paper)4, they isolated bacteria from said sediment, and set them to growing in two different mediums - one containing arsenate but no (or very little) phosphate, and one containing phosphate but no arsenate (the control).  And they counted how many bacteria grew.

Now, one would expect the bacteria in the control medium to grow just fine.  That’s what they’re there to do.  But, oh joy!  The bacteria in the arsenate-containing medium (now to be called the As+ group) grew too!  Interestingly, they had a far larger intracellular (‘inside the cell’) volume than did their control friends.  This was due to a number of large vacuoles6 inside the cell ,which the authors theorised might be helping the bacteria to stabilise arsenic toxicity.

They then looked at the cells themselves, to seeing whether the As+ group had actually incorporated arsenic into its structures and functions.  And it had!7 There were clear indications that arsenic had been incorporated into DNA - the As+ group had high levels of arsenic and low levels of phosphorus in its DNA fraction, whereas the control group had low levels of arsenic, but high levels of phosphorus.  It also looks like the As+ group had incorporated arsenic into other of its biomolecules, including proteins and small molecular weight metabolites.

To sum up, then: yes, the beasties certainly prefer phosphorus to arsenic, and grow better in it.  But that’s not the point: it’s the first time anything has been shown to be able to grow without phosphorus!

Feeling the urge to say ‘meh’

Of course, this discovery is very exciting to microbiologists, organic chemists and so forth.  But why would the rest of the world care? A couple of reasons, but let’s tackle the obvious, NASA-promoted one.

Currently, the search for extraterrestrial life hinges is predicated on the assumption that such life will be comprised of the ‘big 6′.  This finding suggests that that may not be the case at all, which in turn expands the scope for our search, by increasing the possible ways in which life might be built.

Which is awesome :)

Secondly, it suggests that even life on earth may have come up with some other interesting solutions to the problem of information storage (currently, we’re most familiar with DNA), and we haven’t been looking hard enough for them.  Which is also pretty exciting.

And so there you have it.  The actual science behind all the hoo-ha.  And some pretty fascinating stuff it is, too.  Congratulations to the lake-wading scientists behind it!

Oh yeah, and you can see some excellent comment on the research, from Kiwi scientists, here.

UPDATE: Something of a rant about embargo breakers.  Thanks to The Sun and The Daily Fail for breaking the embargo on this story yesterday.  What you did was spoil the fun, and hard work of everyone else who had been working on this, and were abiding by the rules.  And you wonder why journalism gets knocked for having low integrity…

‘NOTHER UPDATE: photos from the NASA press conference can be seen here.


1 I mean, seriously, what were they thinking?  They must have known this would cause an absolute sh*tstorm of wild theories.  I’m a huge fan, but this seem a little bit pot-stirring of them…

2 GFAJ-1 of the Halomonoadaceae, to be precise

3 Yes.  Silicon-based life.  Crunchy, and potentially sparkly.  Also, of course, we know that computer chips still use silicon /looks around meaningfully

4 I have.  I’m not going to go into the details, as I fear they will induce snoozing in many of my readers.  My descriptions of the methods used are, therefore, something of a simplification.

5 Phosphate is the most commonly occurring form of phosphate.  Arsenate behaves similarly to it in many ways.

6 A ‘cavity’ inside a cell, surrounded by a single membrane, which contains water, food or other compounds (including waste byproducts from metabolism)

7 UPDATED NOTE: on the recommendation of a commenter, I’d like to stipulate that ‘high’ here is a relative term: it’s a matter of proportionality.  For the full nitty-gritties, read the paper.



Felisa Wolfe-Simon, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E. Hoeft, Jennifer Pett-Ridge, John F. Stolz, Samuel M. Webb, Peter K. Weber, Paul C. W. Davies, Ariel D. Anbar, Ronald S. Oremland (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus Science : 10.1126/science.1197258

  • Pingback: Tweets that mention Fresh out: extraterrestrial life _not_ discovered! | misc.ience -- Topsy.com()

  • http://www.sticknz.net Peter Kerr

    Well explained, thanks

  • aimee whitcroft

    Cheers :)

  • Brendan Moyle

    I agree- excellent explanation that made it sound like a lot of humour in it too.

    Likewise, didn’t appreciate the NASA pot-stirring either. Was wondering if there was some upcoming funding decision they were trying to influence. It’s a very cool discovery with big astrobiological consequences. But, mmm, not a great delivery.

  • aimee whitcroft

    Yeah, I was wondering the same thing. On the other hand, NASA’s _always_ looking for more money, being as perennially cash-strapped as they are…

    So yes - awesome discovery, but poor delivery could lead to a bit of a backlash. Will be interesting to see what happens :) I really enjoyed science writer Ed Yong’s tweet this morning:

    “You know what gets me about the NASA thing? I had to be the “measured” one. I want to be the excited, awed one but that rug was pulled out.”

    Indeed. I retweeted it.

  • http://www.stevekass.com stevekass

    You write:

    “They then looked at the cells themselves, to seeing whether the As+ group had actually incorporated arsenic into its structures and functions. And it had! There were clear indications that arsenic had been incorporated into DNA – the As+ group had high levels of arsenic and low levels of phosphorus in its DNA fraction, whereas the control group had low levels of arsenic, but high levels of phosphorus. It also looks like the As+ group had incorporated arsenic into other of its biomolecules, including proteins and small molecular weight metabolites.”

    The actual story isn’t so compelling. The As+/P- group did NOT have high levels of arsenic. They had levels that were slightly higher than the As-/P+ group, but hardly high. They were only high when considered as a ratio to the P levels, which were 99% depleted in that group. But of that 99% lost phosphorus, little, if any, was replaced with arsenic. (See Table S1 of the supplementary materials, which is more revealing than Table 1 of the paper: http://www.sciencemag.org/cgi/content/full/science.1197258/DC1 )

    Also, while there was evidence to support the hypothesis that arsenic had been incorporated into DNA, there was NO evidence to suggest that the As+/P- was distinct in this regard. For all we know, there’s just as much arsenic in the DNA of the As-/P+ group (and in wild bacteria as well). We have no clue if or how an occasional As-for-P replacement affects the biochemical processes. See page 3 of the article. The authors failed to look at that question. There’s no scientific reason they didn’t report results for the same “synchrotron X-ray studies” on both groups. In fact, they should have, because those results would have been a critical test of their hypothesis.

    Either they ran the tests, but the results invalidated their hypeworthy hypothesis (and were therefore suppressed), or they didn’t run the tests (in which case it’s hard to believe their primary goal was scientific truth - to evaluate a hypothesis).

    Call me cynical, but if I had to guess (and the lead author’s “Iron Lisa” website gives me no pause), I’d say the authors (and Science Magazine) valued publicity, even if it’s mostly hype and confabulation, over scientific truth.

    Steve Kass

  • aimee whitcroft

    Fair enough. As I said - I simplified q bit to get the message across. ‘High’ is an extremely relative term without putting numbers and proportions to it - the point I was making was that there was a discernable difference.

    And yup, read pg 3 (read it a coupla times, in fact) - again, simply trying to portray, as simply as possible, what is said. I’m happy to add a note, however, specifying that ‘high’ was meant proportionally…

  • Pingback: Saturday snippets | Code for Life()