Saturday, April 01, 2017

The Vital Question, by Nick Lane

Nick Lane's The Vital Question seeks to explain why all eukaryotes share a large number of traits that are completely absent from all bacteria and other simple organisms. As Lane says in his opening page

All complex life shares an astonishing catalogue of elaborate traits, […]. Why, if all of these traits arose by natural selection, in which each step offers some small advantage, did equivalent traits not arise on other occasions in various bacterial groups?

Life arose around half a billion years after the earth's formation, perhaps 4 billion years ago, but then got stuck at the bacterial level of complexity for more than a billion years, half the age of our planet. […] In stark contrast, all morphologically complex organisms […] descend from that singular ancestor about 1.5—2 billion years ago. This ancestor was recognizably a 'modern' cell, with an exquisite internal structure and unprecedented nanomachines encoded by thousands of new genes that are largely unknown in bacteria. There are no surviving evolutionary intermediates, no 'missing links' to give any indication of how or why these complex traits arose, just an unexplained void between the morphological simplicity of bacteria and the awesome complexity of everything else.

Lane claims that this gap in our understanding should be glaringly obvious, and the scientific community should be struggling mightily to fill it in, but (he says) few are working on it, and fewer are talking about it as an important item on the agenda.

Lane's argument is that the combination of bacteria and archaeon that allowed the formation of eukaryotes happened once, and must have quickly evolved to have mitochondria, cilia, and to rely on sex for reproduction, and that all complex life descended from that single event. One of the surprising things is that eukaryotes didn't replace their ancestors; even though they have enough advantages that all complex life descends from that single event, there are still plenty of opportunities for the ancestral forms. The explanation Lane presents is that there's a delicate balance in the energy economy in bacteria and archaea, which doesn't allow the cells to grow much larger, and puts serious constraints on what kinds of mechanisms can be powered inside the cell. When that single archaeon engulfed a bacteria and turned it into the primal mitochondrion, the energy balance changed, and it became possible to store energy and distribute it around the cell, which made it possible to power more kinds of mechanisms, which led to the explosion in the variety of life and ways of living.

The usual story is that the environment changed (the Great Oxygenation) which enabled more styles of living. But what you'd expect if that was the cause would be a separate explosion from every kind of living creature, while what we really see in the evolutionary record is that when there are events like this (the cambrian explosion, e.g.) they radiate from a single progenitor, which tells us there was a significant discovery in that line that enabled the new directions of evolution.

Lynn Margulis' research shows that the form of modern eukaryotes derives from a series of mergers of adjacent bacteria and archaia. (One of the .sig lines I use refers to this) Lane says that while her results hold up, the mergers all occurred in a single line of descent, and all existant eukaryotes radiated out from the same end point of the serial events. Apparently none of the intermediate forms were good platforms from which to generate new life forms.

There are some simpler organisms (giardia among them) that are like eukaryotes in many ways, but lack mitochondria. They have long been viewed as an intermediate evolutionary point between archaia and eukaryotes, but modern phylogenetics (tracing the descent via gene similarity) shows that they're actually descended from eukaryotes, and merely discarded some of the internal structure because it wasn't needed in the environmental niches they occupied. This buttresses Lane's contention that all plants, animals, algae, fungi and protists share a common ancestor.

The common ancestor stored its DNA in a nucleus with a double membrane. The cell itself has a membrane with pores that were inherited by all the branches of its descendants. All the DNA has telomeres as well as introns which are spliced out using common machinery before proteins are built. The golgi apparatus, the form of the cytoskeleton, mitochondria, lysosomes, peroxisomes, the endoplasmic reticulum and the intra-cellular signaling mechanism are also common.

If you're interested, Lane goes into a lot of detail on his hypothesis on the energetic mechanisms that could have led to the evolution of the mitochondrial pathway starting from deep sea hydrothermal vents, where hydrogen and oxygen are bound in a way that can produce positive energy when the bonds are broken. I mostly understood it as I read it, but I'm going to have trouble doing it justice. Here's a precis of the argument; ATP is the end product, and is both stable and easy to extract energy from. A simple mechanism that can produce ATP has the effect of making many energy consuming processes possible.

Hydrothermal vents at the ocean bottom ("black smokers") are places where constantly renewed magma is in contact with sea water, which results in hot acidic water. Lane picks out nearby "alkaline vents" (also on the ocean bottom, but not where magma is exposed) as the plausible site for metabolism to arise. The alkaline version is rich in dissolved hydrogen, accompanied by "other reduced gases including methane, ammonia and sulphide". The rock is riddled with micropores from micrometers to millimeters in size. The flow of warmed sea water is relatively slow, so there's plenty of time for percolation and reaction. There are eddies in the flow, which allows reactive products to accumulate and concentrate locally. Before the Great Oxygenation, the most common gas in both the atmosphere and the ocean was CO2. In this environment, CO2 will react exergonically (releasing energy) with H2 to form CH4 (methane), but it needs a catalyst.

Lane considers it a crucial clue that all living cells drive their energy metabolism via proton gradients across thin membranes. To expand that, the claim is that the production of ATP always happens in the presence of cell membranes that separate proton-rich from proton-poor regions of a cell, and require a constant supply of H2 on the low-density side, and produces ATP on the high-density side. On the low density (alkaline) side, the H2 donates an electron, which is gobbled up in the production of ATP. Both of these reactions happen spontaneously.

Lane then describes a path via which permeable membranes (which don't benefit from better pumping) could evolve to be more selectively permeable, which would allow better pumping to be a benefit. This change makes it possible for the cell to escape from the natural proton gradient, since it can sustain its own internal gradient. Lane hyphothesizes that once selective permeability arises, archaea and bacteria evolved different membrane pumps (evidenced by the fact that they use steroisomers of glycerol) and split into evolutionarily distinct lines.

I'm not sure I explained that very well, but this felt like the first time I've read an explanation of basic cell metabolism that presented a mechanistic picture of the benefit of ATP (stores energy in an easily-extracted form), how the production of ATP is paid for energetically (proton gradients maintained by membranes and selective pumping), and why these designs are fundamental to the difference between bacteria, archaea, and eukaryotes, and eventually lead to the development of chloroplasts as an alternate energy source. Lane gives an explanation at a similar mechanistic level of what happens during apoptosis (programmed cell death; also conserved across the eukaryotes!)

Lane also argues that anti-oxidant supplements interfere with the apoptosis pathway, and thereby reduce health. He presents this as the currently accepted scientific viewpoint, though it's news to me. I need to do more research here.

I learned a lot of biology from this book, and thoroughly enjoyed it.

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