The Building Blocks of Microbial Evolution

It was an honour and a pleasure to participate last week in the Society for General Microbiology Annual Conference in Birmingham.

Two sessions were of special interest, and did not overlap. These were The building blocks of microbial evolution and Mitochondria and related organelles in microbial eukaryotes. The conference also had fascinating plenary and prize lectures.

Good to meet old friends and colleagues, and make new ones. Good, too, to see such progress in understanding fundamental problems.

My presentation in Birmingham, on 30 March, was entitled Anoxygenic photosynthesis and the archaean world. In it, I presented my hypothesis for the events that caused the transition from anoxygenic to oxygenic photosynthesis, and from the Archaean to the Proterozoic aeon. This was also the subject of A redox switch hypothesis for the evolutionary origin of oxygenic photosynthesis, which I gave on 24 March to the 2015 Iron–Sulfur Proteins Meeting at the MRC National Institute for Medical Research, Mill Hill.

I am optimistic that I can see a means by which to test this hypothesis, as it is outlined in The origin of atmospheric oxygen on my research web page.

International Convention Centre, Birmingham
International Convention Centre, Birmingham

The Many Worlds Interpretation

Sober reflection may be required after my paean of praise for physicists in the post In Our Time, The Photon.

Too many worlds is a thought-provoking Aeon article by Philip Ball.

Nobody knows what happens inside quantum experiments. So why are some so keen to believe in parallel universes?

Apparently there is a strongly held view that simplicity and elegance trump falsifiability, and there are an indefinite number of parallel universes in which everything that can happen does happen. The problem is that we are inhabit just one of these, and can know nothing of any of the others.

Scientific method: Defend the integrity of physics by George Ellis and Joseph Silk (Nature, 16 December 2014) proposes that physics is becoming undermined by untestable theory. Any hypothesis is only as good as the evidence that supports it.

As card-carrying Popperian, I am with Ellis and Silk. However, all seem to agree that the Copenhagen model won’t do. The question is: what can we put in its place?

I have nothing to offer. However, important questions about the nature of reality and of ourselves clearly coincide in deciding how to interpret quantum mechanics.

I still wish I were a physicist. I have consistently sought unifying principles in biology, biochemistry, and evolution, while believing that nothing can advance understanding if it fails to make predictions about observations that could, in principle, demonstrate that it is false. I act on the assumptions that we all inhabit the same single World, and that we can, if we are honest with each other and ourselves, share our experiences of it, thus increasing our understanding; pushing forward the boundaries of knowledge; seeing more deeply into nature. The alternative seems absurd. And, in fact, dangerous.

Nevertheless, both physicists and biologists eventually run up against the insight that there is a problem in understanding how we can know things in the first place. There, I am endorse Philip Ball’s closing comment.

Here, after all, is a theory that seems to allow everything conceivable to happen. To pretend that its only conceptual challenge is that it leads to scenarios like the plot of Sliding Doors (1998) shows a puzzling lacuna in the formidable minds of its advocates. Perhaps they should stop trying to tell us that philosophy is dead.

In Our Time, The Photon

What an informative and inspiring edition of BBC Radio 4 – In Our Time, The Photon on 12 February.

Steve Jones sometimes refers to biologists as having “physics envy”. I suffer from this. Steve suggests it is because biologists know that physicists are cleverer than they are. Hard to know. However, as a group, physicists use terms clearly and consistently, and don’t waste time on trivial disagreement. They seem to wish to understand each other, and always strive to know how the world really is.

I’d intended to write on my own experience as a guest, last May 15, on In Our Time. BBC Radio 4 – In Our Time, Photosynthesis. I’ll try to get back to this. Just for now, let me record that Melvyn Bragg – surely the perfect host and chairman – wrote:

I think it was John Allen who said that the United States aerospace industry is giving quite substantial support to research into photosynthesis. The reason that NASA is interested is because they are looking for ways in which they can identify on the surface of planets what may be the origins of life as we know it. Seems a terrifically oblique way to subsidise science, but in my view, the more oblique the better. John ended the programme with a wonderful quotation from Priestley about the practical discovery of photosynthesis. It was, he said, as a result of Priestley’s curiosity. All of Priestley’s research was curiosity-driven. Again and again research has been curiosity-driven.

I’ve picked up from academics over the past few years a feeling, sometimes of sadness, sometimes approaching despair, that that sort of research – i.e. intellectual curiosity, knowledge for the sake of knowledge – is not in favour at the moment. Why on earth have we become a box-ticking, bureaucratic, over-managed society wherever you look? Why don’t we follow the talent, instead of (as in the case of universities and elsewhere) driving the talent out because of ways of managing which only make sense in some sterile boardroom…?

How strongly I agree.

How clearly is Melvyn’s last point illustrated by subsequent events.

Sir Paul Nurse on Conjectures and Refutations

BBC Radio 3 – The Essay, The Book that Changed Me, Sir Paul Nurse on Conjectures and Refutations

Broadcast Friday 23 Jan 2015 22:45

My own revelation of the insight of Karl Popper came from second-year tutorials with Colin McClare, a lecturer in Biophysics at King’s College London. I had the temerity to argue with my tutor. He won. He was right.

I began with The Logic of Scientific Discovery, and read it from cover to cover. Conjectures and Refutations came next.

It continues to amaze me that so many people responsible for making decisions on science, funding, and research priorities seem not to have understood that “Hypotheses are nets – he who casts will catch”.

And that the purpose of every experiment is to test an hypothesis.

Evidence of sustained activity

Partly as a follow-up to Not extinct

30 May. “The redox switch hypothesis for the first cyanobacterium – and for the advent of free molecular oxygen”. Physics Across Disciplines Colloquium. School of Physics and Astronomy, Queen Mary University of London, UK.

Fascinating half-day meeting. Thanks to the organisers. What a splendid department that must be. Would have loved further contact.

17-18 September. Plastid Preview 2014. Session chair. University of Kent, Canterbury, UK.

A mixed bag in the latest episode of this longstanding annual meeting. The emphasis seems to have moved away from plastids to such topics as biofuels. On which subject I am in full agreement with Hartmut Michel and the late and much missed David Walker. For many reasons, not just its reasoned appraisal of our options for renewable energy, I recommend Brian Cox’s wholly splendid BBC Two – Human Universe, What is our Future? As I write, there are “4 weeks left to watch”. I’d love to drive a Tesla.

9-11 October. “Mitochondrial genome function and maternal inheritance”. Session “The Oocyte”. Tecnobios Procreazione Symposium 2014. Rome, Italy

Extraordinary meeting. I don’t know where the idea of inviting me came from – someone must have tracked down my e-mail address from Allen and de Paula, Biochem Soc Trans 2013, and invited me to speak to its title. There was interest in my presentation, including by clinicians, with offers of collaboration and requests to send samples for analysis. I also stood in as chairman for a session that ended with a presentation, by Mats Brännström, Gothenberg, on the first demonstrably fully successful human uterus transplant, reported the week before in Lancet. Later he asked me about our source of mitochondria, but seemed rather to lose interest when I told him it was fruit fly, zebrafish and jellyfish. Throughout the meeting there was simultaneous translation. The translation from Italian into English was fluent and idiomatic, including phrases such as “the trick is”. I don’t know how they do that. I have no idea how well my presentation rendered into Italian. A speaker from Yale University was particularly enthusiastic about our work so I introduced him, by e-mail, to the lead experimentalist, while making clear the contributions of all co-authors to our three most relevant 2013 papers. If only these opportunities had come a year or two earlier, or if I still had the immediate prospect of entering into collaboration. I’ll just have to keep trying.

14 October. Geobiology Research Seminar. “Accidents and eons. How coincidence and free oxygen changed the World forever ”. Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.

What can I say? If ever anyone refers to a research-led university, just ask them “Do mean like Caltech…?” 900 students in total. Almost all buildings are named laboratories, prefixed with the name of a benefactor, or Nobel prize winner, and suffixed with the name of an branch of scientific enquiry. Imagine the change of mindset required for “The Joseph Priestley Laboratory of Chemistry” or “The G. E. Fogg Laboratory of Biology”. The Caltech campus is superb. The guest house – The Athenaeum – has busts of Einstein and Pauling on the stairs. I spent Tuesday morning talking with a young faculty member recently granted tenure, and three ferociously bright lab members. Outstandingly good questions, which made me think. I am not sure I convinced anyone about the redox switch hypothesis. I tried. I reflect this means there is something left for me to do. Under extreme jet-lag I also met my friend Michael Russell and his wife, Liz, on Monday night. In some sort of apologetic tone think I said something like “That’s all very well for someone over here in paradise…”

16-17 October. “Why keep genomes?”. National Academy of Sciences’ Sackler Colloquium co-sponsored with the Canadian Institute for Advanced Research. “Symbioses Becoming Permanent: the Origins and Evolutionary Trajectories of Organelles”. Beckman Center, Irvine, California, USA.

Two days of mostly great science, and thought-provoking ideas. Highlights included a closing talk from a philosopher-of-science from Sydney, Maureen O’Malley. I could write much more. The NAS will apparently post video recordings on-line in due course.

28-29 October. “Redox and proton-motive homeostasis”. 2nd Conference of Network of Researchers on Horizontal Gene Transfer and the Last Universal Cellular Ancestor. University of Leeds, UK.

See this blog’s Leeds meeting of NOR on HGT and LUCA.

Coda. I suppose this is more of a real blog, while too much for one post. I have still to write to say thanks to many named or alluded to, above, as well as to other participants, all of whom it was a pleasure to meet. Also to hosts who were generous in the extreme. As evidence of sustained activity, there is much more, and more in the pipeline.