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This Biology Book Blew Me Away

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Re: This Biology Book Blew Me Away

#31

Post by civilian »

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.

Of course horizontal gene transfer exists, but that's also a discrete event that we can track. And a horizontal gene transfer event is one directional-- We wouldn't have a world where all archaea and all bacteria share fundamental genes, we'd have a world where some archaea have some freak bacteria genes.

We're not talking about two species, we're talking about two domains.

Re: This Biology Book Blew Me Away

#32

Post by danieltillett »

astazangasta wrote: post #25
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 disgustin…

Horizontal gene transfer is underestimated by biologists, but I am not sure in what sense LUCA is confused. I would not call the root of the tree of life a disgusting mess, just fuzzy.

Re: This Biology Book Blew Me Away

#33

Post by Symmetry »

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 we believe the first form of life occurred on the sea floor, why shouldn't we believe that new forms of life are spontaneously occurring on the sea floor all the time?

I'd be very surprised if such spontaneous life could compete against life with millions of years of evolution behind it. As to eukaryotes, them arising seems to be a much more unlikely proposition so I'd be surprised if it happened more than once given that it took an order of magnitude more time to happen once the conditions were right.

https://en.wikipedia.org/wiki/Timeline_of_the_evolutionary_h...

Re: This Biology Book Blew Me Away

#34

Post by ska »

civilian wrote: post #17
itodd wrote: post #7

Radiolab [as usual] did a great episode on this theory called Cellmates. http://www.radiolab.org/story/cellmates/

Was it a great episode? I felt like they added a lot of silly soundclips and used a lot of bad analogies. And per usual, you can almost literally hear the gears in Robert Krulwich's head grinding.

A: "These guys make a great bourbon old fashioned."

B: "Really? I don't like bourbon."

Re: This Biology Book Blew Me Away

#35

Post by throwanem »

jrcii wrote: post #13
xrange wrote: post #11

Earlier quoted context omitted.

>I have original ideas that explain a lot about the world Surely you aren't going to leave us hanging without giving us a synopsis of the top three...

1. The evolutionary advantage of cooperative problem solving is what gives rise to the human tendency to self-identify with mutually exclusive groups of every scope including political territories, religions, sports teams, etc. and in turn some of the largest aspects of human culture. 2. Our concept of knowledge, which is based on prediction from past observations, is rooted in the design of our nervous system. Intui…

You're claiming those ideas as original?

Re: This Biology Book Blew Me Away

#36

Post by civilian »

niels_olson wrote: post #28
red-indian wrote: post #23

Earlier quoted context omitted.

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.

How so?

I will happily agree that bacteriophages & HGT ruin the idea that phylogenetic tree can be a perfect tree-- our phylogenetic tree has many undirected cycles in it.

Re: This Biology Book Blew Me Away

#37

Post by forgotpwagain »

red-indian wrote: post #5

I recommend these biology books: Molecular Cell Biology - Lodish http://www.amazon.com/Molecular-Cell-Biology-Harvey-Lodish/d... Molecular Biology of the Cell - Alberts http://www.amazon.com/gp/product/0815344325/

For the HN audience, Physical Biology of the Cell may also be another useful perspective/introduction.

http://www.amazon.com/Physical-Biology-Cell-Rob-Phillips/dp/...

Re: This Biology Book Blew Me Away

#38

Post by niels_olson »

Symmetry wrote: post #33
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 we believe the first form of life occurred on the sea floor, why shouldn't we believe that new forms of life are spontaneously occurring on the sea floor all the time? I'd be very surprised if such spontaneous life could compete against life with millions of years of evolution behind it. As to eukaryotes, them arising seems to be a much more unlikely proposition so I'd be surprised if it happened more than once g…

Perhaps at a species level it may haven't happened many times, that is, a species of bacteria was ingested, or took harbor in, a larger cell. But if it worked once, it worked thousands if not millions of times.

Re: This Biology Book Blew Me Away

#39

Post by civilian »

ska wrote: post #34
civilian wrote: post #17

Earlier quoted context omitted.

Was it a great episode? I felt like they added a lot of silly soundclips and used a lot of bad analogies. And per usual, you can almost literally hear the gears in Robert Krulwich's head grinding.

A: "These guys make a great bourbon old fashioned." B: "Really? I don't like bourbon."

I just don't like how they talk about certain science topics, it's really... simple. I really enjoyed their episode on the Galapagos, and "The Rhino Hunter" http://www.radiolab.org/story/rhino-hunter/

Re: This Biology Book Blew Me Away

#40

Post by jessriedel »

rusanu wrote: post #29

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.

I strongly second this request. The best I could find was this Nature article

http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej...

which disputes Lane's claim that bacteria size is limited because ATP production putatively only scales with the area of the cell membrane (necessitating eukaryotes with mitochondria):

> It has previously been pointed out that the plasma membrane serves as the only region for ATP synthesis in bacteria, and since this surface area scales sublinearly with volume it will be outpaced by anything that is proportional to volume (Lane and Martin, 2010). Previous analyses have thus suggested that bacteria are becoming less efficient on a per-protein or per-gene level (Lane and Martin, 2010). However, the surprising superlinear scaling of metabolic rate and the sublinear scaling of both genome size and protein content lead to an increasing efficiency for both components. Figure 4a gives the power per gene as a function of cell size showing that it is increasing superlinearly across bacteria....Thus, it would seem that bacteria are not limited by an energetic efficiency challenge but rather by an energetic surplus that demands ever faster rates of biosynthesis and eventually leads to a space limitation via the packing of ribosomes as discussed earlier.

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