Keib’s tree of heaven
September 15, 2007, 4:53 pm
Filed under: Trees

Keib's Tree of HeavenToday, because I am an idiot, I turned up at Keib Thomas’s memorial celebration at Southwark Cathedral exactly 24 hours late. This would probably have amused Keib. It saddened me a bit. Then I came home and saw this tree in the glorious not-quite-summer sun and thought I’d put a little memorial here.

Keib was a community activist who did a great deal to make life better for all sorts of people in Southwark and the Borough, and a wonderfully gentle presence. He used to live just along the road from our house in Greenwich, above Halcyon Books; for a long time he was justKeib Thomas the-guy-who-looks-like-David-Crosby to me, but we got to know each other, stopping to chat now and then when we saw each other. That all came about after I somehow enlisted his help in taking down the Tree of Heaven in the overgrown back garden next door, a tree that was feasting on sunlight that should have been feeding the plants Nancy was growing in our passageway. Getting to the tree through the garden’s clutter and kibble was in fact the hard bit; dismantling it with a hand saw was easy — the wood was so soft it was like cutting butter. I took off branches two, three metres tall. But as Keib knew and told me, the tree would return. And as you can see it has made a good start.

I think we both knew, too, that people and trees differ in this — that when the time comes we do not return, or, for that matter, go on. While he was active with interfaith groups Keib had no religious beliefs himself (he thought their absence positioned him well as a go-between). But such knowledge, in the context of Keib’s time having come far too soon, is hard. Happier to look at the tree, breathe deep of the air he and it shared and which everything yet to come will share in too, and indulge in a little Kipling:

They will come back—come back again, as long as the red Earth rolls.
He never wasted a leaf or a tree. Do you think He would squander souls?

Picture of Keib from SAVO website

Sky Rashby
September 14, 2007, 7:23 am
Filed under: Uncategorized

The terrible thing about the molecular evidence on early photosynthesis discussed here is that the young man who was the lead author, Sky Rashby, a grad student at Caltech, took his life shortly before it was published. At the end of the paper his co-authors write:

With profound sadness we record that Sky Rashby passed away on
August 25, 2007, while this manuscript was in press. This is his work
and his first scientific publication. We mourn the tragic loss of this
talented young scientist and compassionate individual.

Sky Rashby and Crystal GammonI’m not quite sure why it says first scientific publication, as he seems also to be an author on this discussion of whether we might be able to deduce the presence of photosynthesis from the spectra of other planets without knowing the details of the pigments involve. These are questions that have become more widely speculated on in the past year or so — a pair of big papers in Astrobiology, discussed by John Raven in a News & Views piece in Nature (subscription required) — touching as they do on both the theoretical question of what the limits to photosynthesis are and the practical question of what we will be able to say about alien biospheres when or if we detect them. Rashby was definitely looking at some of the key questions concerning photosynthesis in a planetary context.

There’s an account of Sky from the Topanga Messenger here, and a website put together by friends and family here. There’ll be a memorial service on the 22nd of September. His death has obviously been a terrible shock to those who worked with him and taught him, as well as those who grew up with him and loved him. I never knew the man, but he was shaping up as a contributor to debates that fascinate me and working with people I’ve met and will meet again, which is why I feel the diminishment that comes from all such sadnesses more strongly in this case. As an outsider there’s not much more to say with ending up sounding like the pastor at the beginning of The Big Chill; I just hope the people left behind find the healing they need.

Image from Crystal Gammon and the Remembering Sky website

Evidence and early oxygen
September 14, 2007, 7:01 am
Filed under: Earth history, Warning: contains molecules

There’s an interesting paper in Proceedings of the National Academy of Sciences this week which adds a small new twist to a great double-headed mystery concerning the beginning the history of photosynthesis on earth (which thus comes pretty near the middle of Eating the Sun: it’s a book with a rather arcane relation to chronology.) When did photosynthesis of the oxygen producing persuasion start, and why did the oxygen produced not immediately turn up in the atmosphere?

There’s pretty hard-to-doubt evidence that the earth’s atmosphere did not have a significant amount of oxygen in it on a permanent basis before about 2.45 billion years ago. (Some people do manage to doubt this, but they have to work fairly hard in order to do so — most people in the field accept it.) At the same time, shales dug out of a borehole in Australia contain various chemicals that suggest a) that there were cyanobacteria, which produce oxygen, living 2.7 billion years ago and b) that some other creatures were using this oxygen for their own metabolic needs. There are persistent rumours of similar results from even older shales, but as far as I know they haven’t actually made it to publication.

This creates a seeming paradox: how can it be possible to have a biosphere that produces oxygen through photosynthesis and at the same time see no oxygen in the atmosphere. And how can such a state of affairs go on for at least 250 million years, and quite possibly a lot longer. The bottomline of most of the answers to this conundrum is that there was enough other stuff — organic carbon and reduced gases from the mantle — for the oxygen to react with that it could never build up stably in the atmosphere. Only when the supply of this “other stuff” was changed, through some mixture of an increased rate of burial of organic carbon, a lessened flux of reduced gases from the mantle, and an increased oxidation of the atmosphere as a whole due to the escape of hydrogen into space, did it become possible for oxygen levels to rise, at least a little. This fascinating interplay between life and the planet it enlivens is gone into in some detail in the book: David Catling has provided a helpful pdf update on the state of the debate for those who want more.

The new paper, Biosynthesis of 2-methylbaceriohopanepolyols by an anoxygenic phototroph (PNAS doi/10.1073/pnas.0704912104), comes out of the labs of Alex Sessions and Dianne Newman at CalTech, of and from which many good things are heard. The lead author is Sky Rashby, for more on whom see this post; also on the team is Roger Summons of MIT, who with colleagues published the evidence for cyanobacteria at 2.7 billion years ago (Newman has just moved to MIT, too). To some extent this new paper challenges that evidence, in that it removes one strand from it. Cyanobacteria make chemicals called 2-methyhopanes, and until now nothing else has seemed to do so, and so the presence of those chemicals in the ancient shales seemed good evidence for cyanobacteria. The new paper shows that a bacterium called Rhodopseudomonas palustris also makes the molecules in question. R. palustris is a photosynthesiser, too — but not an oxygen producing one (there is a wide range of bacteria that use sunlight this way without producing oxygen). So the idea that there were cyanobacteria present long before there was atmospheric oxygen can no longer rely on the methyhopanes for support.

At first blush, this might seem to give comfort to those who, like Joe Kirschvink, also at Caltech, want to argue that oxygen-producing photosynthesis led to the oxygenation of the atmosphere directly — that an evolutionary transition led directly to a geological one, as outlined in this PNAS paper. But the methyhopanes aren’t the only evidence for an earlier origin. What was particularly interesting about the 2.7 billion year old shales Summons and his colleagues studied was that they contained both what seemed to be evidence of oxygen producing cyanobacteria and what seemed to be evidence of oxygen consumption, in the form of molecules called steranes. Producing steranes is thought by most people to require oxygen. And so it’s not special pleading to say that while cyanobacteria are no longer the only possible source for the 2.7 billion year old 2-methyhopanes, the oxygen requiring steranes in the same sample make them the most likely source, and pretty much require that something photosynthetic somewhere was producing oxygen at the time. (There is also, as I understand it, evidence elsewhere that oxygen-requiring methane eating bugs were around before the oxygen hit the atmosphere. Not all methane eaters require oxygen — but some do, and apparently there are molecular markers that can tell you which sort was present where.)

So the idea of a lag between the evolution of oxygen production and the arrival of free oxygen in the atmosphere has at worst only taken a minor knock; from what I can gather most people in the field are still fairly convinced on the matter. It would take a second dramatic finding — for instance evidence that the steranes in the 2.7 billion year old samples are contaminants — to really throw things into doubt. As far as I know there is no indication that any such second shoe is about to drop.

Meanwhile, the molecules involved in this identity parade may well prove interesting in and of themselves. The fact that they are present in two different photosynthetic bacteria suggests that they might have a photosynthetic purpose of some sort. What that might be remains to be seen, though there are already some theories. If the genes for the pathway that makes the stuff can be found, then it might be possibleto be more definitive about which bugs use it and under what conditions.




Review: Ian Finlayson in The Times
September 10, 2007, 1:51 pm
Filed under: Reviews received

A capsule review in the “Nonfiction in short” column in Saturday’s Times. In toto:

Unless you recently took GCSE biology, when did you last think about photosynthesis? Although Morton admits that the molecular machinery of photosynthesis is not a regular bar-room topic, he urges it upon our attention as a crucial process that creates oxygen, energy and living matter from sunlight water and carbon dioxide. An understanding of photosynthesis is even more vital now that we are dealing with the new carbon cycle and climate changes that resulted from the Industrial Revolution.

Georgina Ferry’s Max Perutz book
September 9, 2007, 3:34 pm
Filed under: Books

Occupied as I am at present with thoughts of books, I thought I might offer a few short reviews of things I’ve read recently that are at least vaguely relevant. Georgina Ferry’s Max Perutz and the Secret of Life is one such — a lovely biography of the molecular biologist who not only solved the structure of haemoglobin but also figured outPerutz book cover how it worked. In fact, that second part is one of the book’s delights; Perutz’s most imaginative work, producing a theory of how the affinity which haemoglobin displays for oxygen differs depending on how much oxygen it is already carrying, is one of the few examples I can think of of a scientist doing his or her best work after already having received a Nobel prize.

Georgina captures a person, a place (Cambridge from the 40s to the 70s) and an intellectual transition (the creation of molecular biology) very well, it seems to me. Perutz comes across as a determined plodder more than a mercurial genius, a fussy man (spectacularly and remarkably unselfconciously so when it came to his food), probably a bit pompous and on occasion cantankerous, but well meaning, well liked and well disposed, with a great willingness to commit to his insights. In part, as the book shows, he was lucky — lucky in taking on the seemingly impossible goal of working out protein structures at just the time when it was going to become possible, and lucky in ending up at the right place to carry the goal out, Bragg’s Cavendish Laboratory. At the same time, he went out of his way to try and ensure the occasions for other peoples’ luck, setting up an inspired minimalist management structure at the Laboratory for Molecular Biology that allowed all the big brains to feel unfettered while encouraging a wonderful cross pollination of ideas.

You also have to feel fond of man who when asked for some of his Nobel-prize-worthy seed by the Repository for Germinal Choice replied

Let me tell you that I am small, bald, short-sighted and cross-eyed, that my testes have been exposed to X-rays these 44 years…and that I am plagued by multiple allergies and crippled by back trouble. This shows that the winning of the Nobel Prize does not necessarily go with other desirable genetic traits.

The bad back led him often to stretch out prone during seminars while still playing an active role, thus lending a new meaning to the idea of questions from the floor.

I usually read biographies by way of the index, starting off with an event or relationship or idea I’m curious about, reading on for a bit, then when bored going back to the index and looking for something new. In this book’s case, that meant starting off with the lovely David Keilin, a mentor to Max as he was earlier to Robin Hill (who’s the anchor for the Cambridge parts of Eating the Sun). My justification for this — which let’s face it is probably just an attention-deficit thing, at heart — is that human lives are not intrinsically story-shaped (and merely writing that phrase reminds me that sometime soon I need to get myself a copy of Ann Wroe’s deeply non-linear Shelley book) and that the traditional parents-birth-education-etc biography thus traps itself in an unsatisfactory template. But after starting this book with the Cambridge stuff I found it so interesting and agreeable that I went pretty much straight through to the end and then went back to the beginning and read all the developmental stuff I normally avoid, and quite enjoyed that too, seeing Max growing up and climbing mountains and getting a crush oh his lab partner and seeing Nazis start to exert their power in his homeland and, on returning to Austria for a holiday, being “refreshingly vulgar, a very agreeable contrast to my usual life in England”. And seeing him fall in love not just with women but also with England and Cambridge. I believe Perutz once said that a man’s country was not the one he happened to be born in, but the one he chose to die in, and this book explains a lot about how that choice shaped the life of this impressive and oddly endearing man.

Review: Jon Turney in The Independent
September 7, 2007, 11:08 am
Filed under: Reviews received

A very generous review of Eating the Sun by Jon Turney in The Independent. Here’s the conclusion:

What begins as an essay on an under-appreciated part of the history of science turns into something richer and more ruminative. The result has everything you could possibly want from a popular science book. There is wonder here, and intellectual excitement; clear explanation and lyrical writing; and much new insight into how the world works, linking the very small and very large.

It even finishes with an unfashionably optimistic take on global warming. Now that we understand the natural nanomachinery that captures solar energy, Morton reckons, it is only a matter of time before we can redesign it to generate fuel – subtly engineered, like leaves, to recycle carbon. Research funders should feel a duty to take heed. Everyone else can read Morton’s fascinating book for pleasure.

For comparison and edification, should you wish either, here is the review of Mapping Mars by the same pen from the same pages.

Amazingly frequent occurrence anatomised
September 6, 2007, 9:39 am
Filed under: Warning: contains molecules

There’s a fascinating paper in this week’s Nature (Lindell et al, Nature, 449, pp 83-86 (2007) doi:10.1038/nature06130) dissecting what must be one of the most frequent fatal biological interactions in the world: the infection of the photosynthetic bacterium Prochlorococcus Med4 by the virus, or “phage”, P-SSP7.

This sounds pretty obscure, but it is a commonplace thing. In fact it is unimagineably commonplace. Prochlorococcus is perhaps the most plentiful organism on the planet — the average millilitre of surface seawater contains about 100,000 of them. A quick and doubtless very dirty calculation suggests that thereProchlorococcus are more prochlorococcus in the earth’s oceans than there are atoms in your head (sources wiki, madsci, guesswork). In parts of the ocean that are nutrient poor (which is a lot of the ocean) these peculiarly small bacteria — sometimes called picoplankton — dominate primary photosynthetic production.

And while doing so they get a lot of viral infections — perhaps 2-3% of the entire population is torn apart by phages every day (that figure is actually from a paper about synechococcus, but I’m happy to go with orders of magnitude here). This all means that a virus infects one of these bacteria a trillion times every nanosecond. And this process, or rather something functionally very similar, has presumably been happening at a similar rate for billions of years.

As I said, unimagineably commonplace.

So what goes on? A team at MIT and other institutions (including Debbie Lindell, now at the Technion, Penny Chisholm, the scientist who first discovered prochlorococcus, and George Church, high-throughput sequencing guru) has looked into the problem by stopping the process of infection at various stages (by flash freezing the bacteria involved) and then looking to see what genes were being transcribed when.

The virus forces the bacterium to produce copies of itself; if it didn’t, it would be a very poor virus. And the way it gets to work is very familiar, in that it is very like the job that the phage T-7 does on lab favourite E. coli. The deep similarities between the strategies used in the gut (natural habitat of E coli) and the open ocean on bacteria that live in entirely different ways is, the authors point out, remarkable.

At the same time as it’s doing this, though, the virus is also transcribing a small set of genes which, though carried in the viral genome, describe proteins that are used by the bacterial metabolism. One of these proteins is D1, which is the protein at the heart of photosystem II, the molecular machine that strips electrons from water using sunlight and thus drives the whole photosynthetic process. The other proteins are also involved in photosynthesis and the cell’s ability to handle its energy. By making more of these proteins, the virus is giving the bacterial cell an energy boost — at exactly the time that it is also requiring the cell to make copies of teh viral genome, which uses a fair amount of energy.

Meanwhile, control of the genomes having been taken over by the virus (and there’s an ablative absolute unknown to Caesar) most of the bacterial genes are shut off to some extent, meaning the proteins the bacteria would normally be making to keep itself in business don’t get made. But though the activity of 1,716 genes gets turned down this way, the expression of 41 others actually goes up, some immediately after infection, some about two hours later.

Some of this is the bacteria’s attempt to do something about the infection. Some may be caused by the phage for its own purposes. Some of it may be things that were once adapatations against infection but which the virus has evolved to welcome, even to promote. The story is particularly involved with the hli gene family. These genes do something (not entirely clear to me what) to help photosynthesis along and allow the bacteria to deal with high light conditions. They get turned on when the phage first strikes — and then copies carried by the phage itself get turned on. What’s more, some of the versions of hli genes seen in bacterial genomes seem to have been acquired from phages and then put to bacterial use.

This is all fascinating (at least to me). And as the authors say, further work on these lines will probably have implications for understanding how bacterial photosynthesis works at an ecological level and what factors limit it. But it also seems to hint at something bigger or stranger. It is very hard for us to see this other than in terms of one thing attacking another. Its almost impossible to describe without terms of agency on the part of the players. But reading about it in this detail brings with it a sense in which teh infectuion almost feels like a thing in itself — a process to be described in its own terms, not as a struggle between two players. I suppose this feeling is linked to the ideas that drive “systems biology” — that there is a system here, phage+bacterium, that is its own thing, and can’t be reduced to two complex components, that evolves in its own way.

I’ve no idea whether that idea has much use or room for expansion; and it carries a vaguely Cronenbergy vibe I’m not necessarily on for. It just felt hard to avoid. The paper is fascinating regardless.

Image: Lawrence Berkeley Labs