Comment by dnautics | Hacker News Reader

Comment by dnautics | Hacker News Reader

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Two biology events (not sure this book covers) that are completely underestimated.

1) evolution of cyanobacteria as a freak merger of green-sulfur and purple photosynthetic bacteria. Well, biological historians DO understand the importance of this, but the reason why the chemistry is important is not well appreciated. Cyanos use water as a reductant - as an electron donor. Normally one does not think of water as a reductant, but as a facilitator oxidation. This is biology's "great umpolung chemistry" moment.

2) The great oxidation catastrophe. Because oxygen, the oxidized poop of the previous process is highly toxic, there was a huge exinction event across pretty much all clades. But some of the emergent chemistry (disulfide bonds e.g.) really enabled structural scaffolding that facilitated higher order cellular structure. Mitochondria went into hiding inside of the reducing environment of an proto-archaeal species and boom - eukaryotes.

3) The size and distance of the earth from the sun. Hydrogen at ambient temperature achieves escape velocity. This means the net chemical trend over billions of years was oxidizing. One wonders if this made the first two chemical processes somewhat inevitable.

I'd also like to point out that thinking parsimoniously about energy from an evolutionary standpoint is not necessarily productive. For example: There's a lot of junk DNA (VNTRs, e.g.) which do not seem to be subject to aggressive optimivation for energy.

I am not too sure we know how Cyanobacteria arose (I did my Ph.D. on them) nor how mitochondria arose. Given how rampant horizontal gene transfer is I doubt we ever will.

I think the most interest question in this early biology is why LUCA is so complex [1]. We have a massive gap between abiotic processes and the first organism we know anything about. What happened.

1. https://en.wikipedia.org/wiki/Last_universal_ancestor

Thanks. There are some hints to "why" on the page you link to:

"Before high fidelity replication, organisms could not be easily mapped on a phylogenetic tree. Not to be confused with the Ur-organism, however, the LUCA lived after the genetic code and at least some rudimentary early form of molecular proofreading had already evolved. It was not the very first cell, but rather, the one whose descendents survived beyond the very early stages of microbial evolution."

And the question that fascinates me is "where are these primitive forms"? Even if the original forms evolved since, why can't we find at least some "improved" forms that use these more primitive principles than the ones we're accustomed to?

And the question that fascinates me is "where are these primitive forms"? Even if the original forms evolved since, why can't we find at least some "improved" forms that use these more primitive principles than the ones we're accustomed to?

This is a really good question. It is possible that some of these primitive lifeforms still exist (deep underground would be my best guess) but for technical reasons we can’t easily find them.

We have two basic ways of find living microorganisms: 1. We can either grow them in culture, or 2. We can look for genetic markers that can be amplified using techniques like PCR. If these primitive micro-organisms grow slowly (say divide once a year) then we will never find them in culture (we already know the microorganisms that live deep underground grow at this sort of speed). The genetic marker approach requires that the primitive organism have the same genes as all modern organisms (ribosomes normally). If they don’t have these genes then we won’t find them using our current approaches - they could be there and we just miss them.

If I was Bill Gates rich I would spend some of my money sponsoring deep earth microbiologists to look for cells that appear to be maintaining an energy gradient, but which don’t have ribosomes.

They competed with modern bacteria and lost?

Yes, I'm aware of that hypothesis. But everywhere, forever?

It can also be we'll never know, as the life on Earth apparently existed for so long, billions of years, since the times the whole Earth was completely different than we know now (from the life's point of view).

Which is also fascinating, as on the Universe level we can actually observe the glow of the Big Bang, which happened much earlier.

Alternatively, maybe not everywhere, forever, but in tiny, microscopic niches across the globe, not accessible to modern bacteria how would devour them in an instant.

What are our chances of finding any of them?

Extinction is only a macro-phenomenon?

We don't know the exact mechanism (endosymbiosis vs. hgt, for example) - which is why I said "freak merger" to keep it vague, but correct me if I'm wrong, but it's pretty clear that PSI comes from purple and PSII comes from green sulfurs, by homology.

Agreed. This is why origin of life scenarios are so fascinating!

Oxygen, a previous book from Nick, cover these topics in great detail. The Vital Question deals with events that long predate the cyanobacteria, the Great Oxygenation Event and how we avoided oceans evaporating into space under UV radiation (at least the first chapters of the book, rest of it covers mostly origin of eukaryotic cell).

Yes, this book and the author's previous books cover exactly those topics among others. Nick Lane is a fucking awesome writer.

It's not the events themselves that are underestimated- it's the details.

Do the books specifically address using water as a reductant? My experience is that not even scientists in the field (I worked at reprogramming hydrogen-producing enzymes) have a full appreciation of how bizzare that is.

My chemistry background is pretty weak so I don't know if it touches the specific points you're curious about, but there's a pretty extensive discussion of electron transport and what all the mechanisms we see in the world today tell us about how life began to harness it. He ends up using the discussion to make the argument that all life in the universe likely uses redox chemistry for energy. Made sense to me anyway.

> He ends up using the discussion to make the argument that all life in the universe likely uses redox chemistry for energy.

If that's the conclusion, it's trivially true, since basically you can assign a redox value to every chemical transformation using the nernst equation.

The interesting thing is that IMO the resistance to the conceptual framework behind the way that the mitochondrion works was because it was hard for biochemists to picture the proton motive force (concentration gradient) as a redox potential (it truly is one) because it seemed more physics-ey than biochemistry-ey. Peter Mitchell cleared that up amidst quite a bit of controversy. He had to go to the lengths of setting up an independent research institute to get the work done.

You should read the book and tell us whether it lives up to your standards. If so, then we know that the book is a particularly valuable contribution.

Normally one does not think of water as a reductant, but as a facilitator oxidation.

Normally I don't think of water in either way ...

1) rust 2) if you do the basic transformation (addition of water to alkene, https://www.khanacademy.org/science/organic-chemistry/alkene...) biochemically and chemically speaking you usually assign an integral oxidation change of 0, but in reality, the alcohol is slightly higher oxidization state than the alkene.

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