Tuesday, 12 November 2013

The not-green ocean

That the ocean is blue and not green is evident, yet the reason for this is not as silly as one would think.

In fact planktonic algae are not as abundant as they could could be, if it were not for phosphorous and iron limitation. If life could survive off air and the minerals in sea water alone, the ocean would be as green as a rainforest —or whatever colour the photosynthetic pigment of this hypothetical life were to be. Light gives power, carbon can be fixed from carbon dioxide and amino groups can be obtained from nitrogen gas —with some trouble—, while phosphorus tends to be insoluble so comes from rocks: there are no rocks on the open ocean surface.

There is a counter-intuitive phenomenon called eutrophication where, when nitrogen and/or phosphorus get dumped into a river or lake, an algal bloom occurs, which blocks the light to the bottom of the watermass and the decomposing dead alga result in oxygen deprivation. This just show how some elements are the rate limiting step for a green watermass. Adding nutrients before the tipping point, results in a more lush ecosystem. There are a lot of pipe-dreamy talks of phosphorous and iron fertilisation of the oceans to combat CO2 levels: forest occupy only 7% of the planets surface, whereas oceans occupy 71%, so there is a lot of carbon fixing that could be going on that isn't. What interests me, however, is how could Nature overcome the issue.

Ammonia causes eutrophication because it is limiting as nitrogen fixation is neither simple or cheap, but it can and is made, albeit slowly. The major issue is the fact that splitting N2 costs 4 pairs of high energy electrons and O2 quenches the reaction in nearly all nitrogenases.

Whereas strategies to avoid oxygen sensitivity in nitrogenases can (and maybe has) evolve, phosphate and iron limitation is an insurmountable issue.

Iron is a big problem, for starters no iron means no heam and no iron-sulfur clusters, which catalyse several complex reactions, including that of nitrogenase. The problem is actually greater as except for alkali metals, there are a few parts per billion or less of most metals. The reactions vary, but not many of them could be substituted by hypothetical delocalised pi orbitals, other larger elements and similar. So the metal dependence is unavoidable.
Also, it is a fairly safe guess that life will not evolve to be phosphorous-less any time soon: the genome (DNA) needs it, the transcriptome (RNA) needs it and the cellular energetic currency (ATP) needes it. The best evolution can do is to streamline the genome to the bare minimum. There is a lot of talk about nucleic acid analogous with carbon-based backbones, most which do not form helices but tangled messes —hey, they are still amazing. So engineering such a phosphorous-free organism is out of the realm of what is current feasible in synthetic biology and more in the realm of science fiction. Plus, if the oceans were dominated by a (planet-saving) spooky GM organism, prince Charles would never shut up.
I am not aware of any other oxygenated multivalent ions that would fit the bill or that have even been tested, for example nitrate-backboned DNA would be very explosive, whereas sulfate-backboned DNA would be neutrally charged, but the question if an element other than phosphorous would work is pretty cool and is comparable to the debate of the fictional arsenic bacterium.
If there were some non-phosphorous system that did form helices… the genome would still be different, requiring new polymerases and XNA-binding proteins. The transcriptome would be different as RNA would not fold making riboswitches, tRNA and other quirky RNA structures unusable. The transcription machinery would have to be fully proteinaceous. The energy storing bond would have to be something different (acetyl-CoA or something radically new)... but rather cool.

Thursday, 5 September 2013

Conferences (NZSBMB)

Report for the NZSBMB

Conferences are about learning. And from them I have learnt a lot, not only in terms of scientific knowledge, but also in terms of common sense.
I went to two conferences in July, namely SMBE 2012 (Society for Molecular Biology and Evolution) in rainy Dublin —Ireland was rightfully called Hibernia, the land of winter, by the Romans— and the Gordon Biocatalysis 2012 conference in sweltering Rhode Island.
The first thing I learnt was that three successive red-eye flights are a bad idea regardless of cheapness and of how well-travelled one is as no amount of travelling can make one prepared for it. Another thing I learnt was that when the airhostess insists a poster-tube be given to her for stowage one should behave like a tigress protecting her cubs, lest one want it inexplicably sent to Denver…
The lab I work in studies enzyme evolution via promiscuity, which means that we scare evolutionary biologists by talking about kcat and KM values and enzymologists by talking about selection pressures. Therefore, I went to two conferences, one for each side. The work I presented as a poster was the change of various enzymatic activities (main and promiscuous) of an enzyme across different lineages.
The SMBE is a big conference, which is not necessarily a good thing. There were six parallel sessions, which nominally means one could go to relevant ones and avoid the irrelevant ones and within the first day I mastered the art of flitting from one session to the other. However, I soon found out that some sessions I was very keen on were full to (EU fire-code) capacity. A further side effect of parallel session is that often one has to make a tough choice between two interesting talks, whereas at other times one has to choose from a series of utterly uninspiring talks.
In addition to talks, there were the poster sessions, where I presented my newly reprinted poster. Many complicated factors are at play in the (unappreciated) art of poster placement in a hall. The main factor that determines whether a passer-by stops to read a poster is not due to the content although a QR code can help, but due to the presence of other readers (nucleators). Therefore, due to the queues, being close to the bar is probably one of the best places to attain this phenomenon. And next to the bar was exactly were my poster was.
My second conference, the Gordon Biocatalysis conference, was diametrically opposite: it was small, which meant it was a good environment to easily interact with other participants, both students and faculty. The talks were longer (i.e. not crammed) and all were fascinating. I left the conference having met many really smart and nice people, having learnt a lot about the frontiers of research and having been awed by what the future holds in store.
I did however learn another piece of common sense, namely to not make promises that cant be kept: I promised Wayne, my supervisor, I would not do anything embarrassing, yet I did so twice. In a first instance, there was a discussion of Star Trek that degenerated into a biggest trekkie competition, which I unfortunately won by having been wearing star trek themed socks. Then during a free afternoon, I let out a bellowing scream when a volleyball flew towards me referred to by others as my Klingon battlecry. Not my finest hour

Thursday, 1 August 2013

Phylogenetic clunkiness

Writing a bacterial phylogenetics paper is probably the most agonizing type of paper to write due to the clunkiness of the language. But it's not the jargon that make life hell, it's the missing jargon that make it hard. The quantity of jargon actually make life a bit easier, but the lack of some blatantly useful words makes it painfully clunky and stuffy.
Reading a phylogenetics paper is generally visually painful due to the frequent usage of italics and "quote" marks. A phenomenon that I once read described aptly as a "typographic circus" by someone on a Wikipedia talk page. The italics are for taxa described validly according to the bacteriological code, whereas quotes are reserved for candidate taxa which have not been validated yet —the bugs exist, but nobody has done the paperwork. Nevertheless, the aesthetic problem is trivial compared to the lexal ones…
One such problem is the lack of trivial names (common names).
Only a few groups of  bacteria have trivial names and for some reason in microbiology, unlike botany, scientific names are rarely "trivialised", a process of making an English word for a member of a taxa, for example, a crustacean is a member of the family Crustacea and a bromeliad is a member of the genus Bromelia.
The most notable exceptions are a proteobacterium (a member of the phylum Protobacteria), an enterobacterium (a member of the family Enterobacteriales) and a pseudomonad (a member of the genus Pseudomonas). This is a shame as it circumvents the repetitive clunkiness and stuffiness. Taxonomic names, after all, are labels for the group, which can adopt a metaphorical usage to denote one of its members, primarily due to the quirkiness of the Latin name: for example, a group of sheep is a flock, but calling a single sheep a flock would sound awkward, whereas calling a sheep an Ovis sounds less weird, just technical. However, the phrase "a member of the" becomes really trite really quickly, one alternative is to use the word sp. (species), but it is still a bit weird: is the supposed to be the indefinite article "an" before Ovis sp.? A further perk is that a trivial name often allows adjectives to be formed, which is much nicer to read than a noun used adjectivally or "of the".
This last note is related to another problem with the Latin grammar of the nomenclature: all higher ranked names are plurals in Latin whereas there is only one of them (there are several members). In Latin (and other romance languages) collective nouns are plurals, whereas in English they are generally singulars (grammatical concord), but can be treated as plurals in informal speech (notional concord), e.g. the Alps is a mountain range (grammatical concord), the band are playing (notional concord). It does seem like a minor nuisance, but it gets really knotty when describing relationships and last common ancestors… on the plus side though the pride in the "look at my fancy Latin" is pretty nice.