Counterion Conundrum

(For Popkin's great Science News writeup, click here)
(Update - Also, Chemistry World!)

Update (11/13/13) - Blog buddy Lila Guterman of Science News has the inside scoop:
"An answer! Authors via @gabrielpopkin: cerium(III)chloride heptahydrate (99.9% pure) from Sigma (cat. nr. 228931-25G)"

~~

Fascinating news for the inorganic biochemistry fans out there: Scientists have ID'd a bacterium (Methylacidiphilum fumariolicum) living in highly acidic volcanic pools that seems to use rare earth metals in one of its enzymes. A multinational team modeled the enzyme with a variety of rare earth cores, and the bacterium appeared to selectively take them up in cell culture. Cool!

Just one small problem: What's the counterion?!?

My crack online reporting team has scoured the manuscript, finding only mentions of a mysterious Ce(III), along with triply-oxidized La* and Pr. Nowhere in the Supporting Information do they mention reagents used, and the reporter has confirmed that this subject wasn't broached.

Given the other salts the researchers added to the media, it's likely that they used either cerium (III) sulfate or cerium (III) chloride. However, Sigma-Aldrich sells no less than 10 different cerium (III) salts (Strem has over 20!), and I'm willing to bet they have markedly different bioavailability, oxidation potential, aqueous solubility...the works.

Readers, does anyone know what the cerium source is in this paper?** I certainly don't wish to draw unwarranted conclusions, but we're all still touchy over another recent dust-up having to do with a miraculous trace element.

Please let me know in the comments.

*IUPAC police: Throughout the paper, the authors refer to "Ln ions." Do you suppose they mean La (lanthanum)? Are elements abbreviated differently in other places?

**Interestingly, the authors note that their acidic growth media leached trace rare earths out of the glassware. I've never looked at that as a reaction contaminant, but I guess I'll have to start!

JLC to JPL: Huh?

Readers, help me out here: what am I missing about this NASA-JPL press release? (thanks to Phenomena for the tip). I mean, I grok where they're trying to go - investigating OOL chemistry through construction of a hydrothermal vent simulator - but the text feels all jumbled-up! For instance:

"Scientists with the NASA Astrobiology Institute's JPL Icy Worlds team have built this series of glass tubes, thin barrels and valves with a laser and a detector system"

Wait, they built it with a laser? (Must be for the spot-welds)

"They want to see if sending these two liquids through a sample of rock that simulates ancient volcanic ocean crust can lead to the formation of simple organic molecules such as ethane and methane, and amino acids, biologically important organic molecules. Scientists have long considered these compounds the precursor ingredients for what later led to chains of RNA, DNA and microbes."

Hang on just a second, that sounds rather confusing, NASA. I think you mean complex molecule generation paves the way for future complexity. Methane, ethane, and amino acids aren't going to spontaneously assemble into DNA. Ever.

That word, "ancient,"
I do not think it means what you think it means...

"This experiment has its roots in a theory from Russell in 1989 that moderately warm, alkaline hydrothermal vents at the bottom of the ocean could have hatched life about 4 billion years ago. The ancient ocean at these vents contains carbon dioxide, which provides the supply of carbon that could be reassembled into organic molecules."

"Ancient Ocean?" Is there a secret time-bubble hidden deep in the present-day mid-Atlantic? In case you're counting, they use the clunky 'organic molecules' some six times in the release.

"Scientists will alternately send the two solutions through a thin barrel of iron-magnesium-silica-volcanic-type rock that was synthesized by Shibuya..."

A what? A zeolite, maybe? There are so many qualifiers in that adjective conglomeration, I can't even figure out whether it's really a rock...

Source: NASA JPL

Also, PPE alert: If you're showing off your experiment, which is under pressure (100 atm) and heat (near to boiling), wear your goggles! We don't want Jyllian including you in the weekly round-up!

OK, maybe I'm being too harsh. In no way do I mean to impugn the actual science, which seems fascinating, just the strange retelling of it. 

But hang on, aren't these the same folks (NASA Astrobiology Institute) who wrote that "Extraterrestrial Life on Earth" presser just two years ago? We all know how that turned out. 

One would think they'd be very careful wording future releases.

RIP Fleischmann, "Cold Fusion" Creator

It's not every day my Google News feed proclaims a famous chemist's passing. So it was that the AP relayed the obituary of Martin Fleischmann, one half of the Fleischmann / Pons duo that first reported table-top, room temperature energy production from an electrochemical cell, dubbed "cold fusion." 

1989: At a University of Utah press conference, Fleischmann (r)
and Pons announce their results, two weeks ahead of publication.

The Fleischmann story provides a parable for the perils of overselling early results. Ironically, Fleischmann had already made quite a career for himself: he'd been made a Royal Society Fellow years before the cold fusion controversy.

I won't go too deeply into the scientific frenzy the scientists' impromptu press conference generated (see Curious Wavefunction for a recap). But the sage Santayana paraphrase "Those who don't know history are doomed to repeat it" seems apt, given the recent GFAJ-1 / 'arsenic life' debacle. Turns out, exciting results demand replication, and this publicity can bring more attention than you augured for. 

When the press calls, you'd better have the extraordinary evidence to back up your claims.

Arsenic Life Wrap-Up: The Good, the 'Not-So-Good'

"Arsenic Life," a hot-button issue for much of the past year, reemerged this week with two new papers, one propitious, and one, well...not so much.

GFAJ-1 bacteria
Source: nasa.gov

As covered by Curious Wavef(n), the first paper related Prof. Rosie Redfield's well-documented efforts coaxing the GFAJ-1 strain to flourish in arsenic-rich media, which, if successful, would imply arsenate linkages in the bacterial DNA. Redfield bursts the bubble nicely, utilizing multiple tools (LC-MS, cell growth assays, gels) to cast doubt on the earlier study, even mentioning that most of the detected arsenate could be washed away with distilled water.

Well, if timing is everything, then the second #arseniclife publication really missed the boat. Last week, a commentary appeared in the open-access online journal Biomolecules, bearing the epic title From Phosphorus to Arsenic: Changing the Classic Paradigm for the Structure of Biomolecules. Heavy stuff!

This summary takes the opposite tack, casting "Dr. Wolfe-Simon's discovery" as a fighting underdog - viewed skeptically today, but enshrined and glorified by future generations much like Copernicus or Darwin (both name-dropped inside). The prose shakes the reader with thrilling, emphatic statements, lines you might find in a rousing stump speech or an action movie. A few choice selections:

"...Some have died as a result
of these discussions..."
Image Credit: Silver Lining

"It is no surprise that this work has come under what some may consider a brutal attack in the past year; the proposed repercussions almost beg of it."

"...members outside of the scientific community may view the criticisms and other events that have transpired as superfluous, vindictive, and outright scathing." 

"...the implications of [arsenic life] have the potential to shake the foundation of biology as we have known it for centuries."

 "This discovery...would be absolutely groundbreaking to all of science."

You get the point. These excesses, coupled with a few cut-and-paste sources (N.B. Don't include "page-access" dates in references) and a passing remark to Wolfe-Simon's potential scientific martyrdom, complete the commentary. Yesterday, several Twitter denizens, led by the industrious Carmen Drahl, noted a very familiar vibe to this piece. To borrow a phrase from Derek and Leonid, it sounded suspiciously like a "term paper," final reports students submit to wrap up specific college courses.

My feelings, reading Paper #2
Source: Jobbing Scriptwriter

Was it? A very strong maybe. Check out this editorial, culled from the Colorado State University Journal of Undergraduate Research  (p. 16), scribed by the lead author. Bears a rather striking homology to the Biomolecules piece, sources* and all. The second author, currently an undergraduate at Boston University, may have interacted with the CSU authors at a conference, or perhaps on a summer REU.

As corresponding author, Prof. Mark Brown (CSU) would, I'd believe, have final say over the manuscript. Did he check it against the lead author's previous work? The journal's Author Information section mentions that five external reviewers must be named, although "...the Editor will not necessarily approach them."

So, to round up this bizarre publishing escapade, we have undergraduate authors submitting previous work in an open-access, loosely-reviewed, and barely-edited online journal, all with the benediction of a faculty member? Sounds dubious...much like arsenate linkages in DNA.

*Can someone please tell me where to find Ed "Young" at Discover Blogs? : )


Update, 6.8.12 - Commenter Stuart Cantrill (Editor, Nature Chemistry) points out on Twitter that the original piece also misspelled "phosphorous" in the title. Sigh.

Comic Homage

I've been a bit under the weather, so I've turned to an old stand-by: digging through the archives of my favorite webcomics. Bonus, when they contain scientific or chemical references.


So far today, I've made it through most of xkcd, and happened to finish Deborah Blum's Poisoner's Handbook last night. With some time on my hands, I figured a "mash-up" of the two might be in order.
(Cheat Sheet: check out this story about biochemistry, NASA, and "alien life" found here on Earth)

MESSAGE FROM THE FUTURE: BEWARE THE SUPER-TOXINS!