This Biology Book Blew Me Away • Hacker News Board

Re: This Biology Book Blew Me Away

#21

Post by lumpypua » Wed, May 18, 2016, 8:27 PM UTC

dnautics wrote: post #10

lumpypua wrote: post #6

Earlier quoted context omitted.

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.

Re: This Biology Book Blew Me Away

#22

Post by rusanu » Wed, May 18, 2016, 8:28 PM UTC

dnautics wrote: post #2

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 re…

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).

Re: This Biology Book Blew Me Away

#23

Post by red-indian » Wed, May 18, 2016, 8:30 PM UTC

civilian wrote: post #20

niels_olson wrote: post #3

> All complex life on earth shares a common ancestor, a cell that arose from simple bacterial progenitors on just one occasion in 4 billion years. This strikes me as a commonly held but deeply flawed origin story, and a close read suggests Gates doesn't buy it either, but fell into the literary trap of writing it anyway. If we believe the first form of life occurred on the sea floor, why shouldn't we believe that new…

If you had read the book, you would know that Archaea and Bacteria both share some genes. Not many genes, but a few genes that are very fundamental. And not even the genes we were expecting to be the "minimum viable product" for life. Nick Lane thinks that the evidence is for there being a common ancestor between Archaea and Bacteria too. The genetic evidence backs it. Your intuition and suspicious about bias just do…

Horizontal gene transfer is well established. Existence of a small number of common genes between two species does not necessarily indicate a common ancestor.

Re: This Biology Book Blew Me Away

#24

Post by [deleted] » Wed, May 18, 2016, 8:33 PM UTC

dnautics wrote: post #2

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 re…

[deleted]

Re: This Biology Book Blew Me Away

#25

Post by astazangasta » Wed, May 18, 2016, 8:33 PM UTC

niels_olson wrote: post #3

> All complex life on earth shares a common ancestor, a cell that arose from simple bacterial progenitors on just one occasion in 4 billion years. This strikes me as a commonly held but deeply flawed origin story, and a close read suggests Gates doesn't buy it either, but fell into the literary trap of writing it anyway. If we believe the first form of life occurred on the sea floor, why shouldn't we believe that new…

This theory is now widely questioned. I recommend this paper by W. Ford Doolittle on the subject: http://www.pnas.org/content/104/7/2043.short - also, "Uprooting the Tree of Life", http://www.ncbi.nlm.nih.gov/pubmed/10710791.

Basically, the argument is that horizontal gene transfer must have been such a huge part of life at its inception that the notion of a "LUCA" is confused, and we must expect to find a disgusting mess at the root of the tree of life.

Re: This Biology Book Blew Me Away

#26

Post by lumpypua » Wed, May 18, 2016, 8:33 PM UTC

rusanu wrote: post #19

I have read The Vital Question, after hearing about it from BillG's blog. And it did blew me away. I immediately read also Oxygen, by same author, and I found it equally interesting (it goes in more detail on some topics, but some of the ideas in Oxygen are superseded by his later books). If you can spare an hour, I recommend this video: https://www.youtube.com/watch?v=UGxAB4Weq0U . Is made by the author and it cover…

I'd also like to recommend Power, Sex, Suicide by the same guy, Nick Lane.

It's an absolutely amazing book that explains the origins of mitochondria, why they're necessary for complex life (and this means that complex life is exceedingly rare in the universe), and all sorts of effects the differing genomes of mitochondria and cells have: fertility, aging, and a bunch of other ones.

If you're interested in cellular biology, read this guy.

Re: This Biology Book Blew Me Away

#27

Post by danieltillett » Wed, May 18, 2016, 8:38 PM UTC

dnautics wrote: post #2

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 re…

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

Re: This Biology Book Blew Me Away

#28

Post by niels_olson » Wed, May 18, 2016, 8:44 PM UTC

red-indian wrote: post #23

civilian wrote: post #20

Earlier quoted context omitted.

If you had read the book, you would know that Archaea and Bacteria both share some genes. Not many genes, but a few genes that are very fundamental. And not even the genes we were expecting to be the "minimum viable product" for life. Nick Lane thinks that the evidence is for there being a common ancestor between Archaea and Bacteria too. The genetic evidence backs it. Your intuition and suspicious about bias just do…

Horizontal gene transfer is well established. Existence of a small number of common genes between two species does not necessarily indicate a common ancestor.

It would seem to me that bacteriophages alone sort of ruin the idea of a phylogeny with a single root.

Re: This Biology Book Blew Me Away

#29

Post by rusanu » Wed, May 18, 2016, 8:44 PM UTC

I have a question for the HN molecular biology aficionados: Where can I find some good critique of Nick Lane's ideas? He sure convinced me, but I would like to see what the experts say about it.

Re: This Biology Book Blew Me Away

#30

Post by lumpypua » Wed, May 18, 2016, 8:45 PM UTC

red-indian wrote: post #23

civilian wrote: post #20

Earlier quoted context omitted.

If you had read the book, you would know that Archaea and Bacteria both share some genes. Not many genes, but a few genes that are very fundamental. And not even the genes we were expecting to be the "minimum viable product" for life. Nick Lane thinks that the evidence is for there being a common ancestor between Archaea and Bacteria too. The genetic evidence backs it. Your intuition and suspicious about bias just do…

Horizontal gene transfer is well established. Existence of a small number of common genes between two species does not necessarily indicate a common ancestor.

They're not looking at things like antibiotic resistance, they're looking at genes core to biological function like cell membrane proteins and ribosomes—and those look like they came from a common ancestor. So, your options:

1. Common ancestor.

2. Not common ancestors, but with enough random chance common biochemistry that this core function gene could be usefully used by the new microbe, and is functional enough in the new host that it isn't ejected immediately, and managed to stay functional and evolve past the original core function gene in terms of fitness so that original core function gene could be ejected, and the original core function gene did get ejected and the microbes with the new core function gene managed to outcompete all the microbes with dual core-function genes.

The latter is highly, highly unlikely.