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This Biology Book Blew Me Away

gatesnotes.com

41–50 of 107 posts

Re: This Biology Book Blew Me Away

#41

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.

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…

There's a whole body of literature on how quickly a pile of nucleic acids can self-assemble and self-select to end up with a functioning ribosome. I'm pretty sure we're talking time scales of less than months. More like 10s or hundreds of hours. There's a lot of molecules in the ocean. For example, the water content of the ocean is about 4 x 10^46 water molecules. How frequently are valence electrons available for reaction, per second? A billion? The number of possible configurations over a billion years reels the mind.

Re: This Biology Book Blew Me Away

#42

> 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…

I've thought this too - if the conditions for life existed at one point on the planet the chance they didn't exist at some other point seems infinitesimal. Down-thread someone argued that the subsequent genesis events would fail to produce new "roots" of the tree of living things. However, if the new roots fill a different niche (eg geographically), or quickly mutate to fill a different niche; or if the earlier roots evolved to higher forms that operate in a different niche then that objection doesn't seem so strong.

Weigh that idea against the possibility of life elsewhere: if life only started once on Earth where the conditions for life to be created were perfect then the chances of life occurring elsewhere, life that follows the same forms at least, is surely so close to zero that we shouldn't ever expect to find extra-terrestrial life similar to forms on Earth? [It's not a watertight argument, I can see 2 flaws right off, but it's an interesting suggestion as a corollary to the "single terrestrial genesis event" idea.]

Re: This Biology Book Blew Me Away

#43

Earlier quoted context omitted.

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.

How would you reconstruct the phylogeny to see through that mess? We're not even talking about computational complexity yet. Simply, how do you see through a random number of random DNA fragments being inserted in random places of random genomes at random intervals over a billion years?

Re: This Biology Book Blew Me Away

#44

> 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…

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

Re: This Biology Book Blew Me Away

#45

> 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…

The economical (Occam's Razor) explanation of the patterning of life on earth, based on genetic studies, is that all current living things share a common ancestor. That's what the quoted sentence says, and what you wrote doesn't show that the quoted sentence is a "deeply flawed origin story".

Economy is not a fundamental principle of physical law. I recommend you try to work up from thermodynamics. Start by asking yourself how many molecules of water are in the ocean, and how frequently they vibrate.

Re: This Biology Book Blew Me Away

#46

Earlier quoted context omitted.

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…

There's a whole body of literature on how quickly a pile of nucleic acids can self-assemble and self-select to end up with a functioning ribosome. I'm pretty sure we're talking time scales of less than months. More like 10s or hundreds of hours. There's a lot of molecules in the ocean. For example, the water content of the ocean is about 4 x 10^46 water molecules. How frequently are valence electrons available for re…

From Nick Lane's article "How did LUCA make a living? Chemiosmosis in the origin of life" http://www.nick-lane.net/LAM%20BioEssays.pdf

> The concept of organic soup is nowadays closely allied to the idea that the origin of life and the origin of replication are the same thing. Natural selection remains the only mechanism known in which more complex forms can evolve, and natural selection requires a replicator. Regarding the nature of that replicator, there is currently no viable alternative to the idea that some kind of ‘RNA world’ existed, that is, there was a time before proteins and DNA, when RNA was the molecular basis of both catalysis and replication. Some elements of the RNA world concept are almost certainly correct. However, there is a strong version of this theory which states that RNA was once the only catalyst as well as the only replicator and so all the basic chemistry of life was invented by RNA.(4) This ‘RNA first’ theory is difficult to accept from the standpoint of the biochemistry of modern cells. For example, many essential enzymes are metalloproteins that contain mineral centres, such as iron-sulphur clusters, at their heart.(5) There is every reason to believe that such clusters, with the structures of inorganic minerals like greigite,(6,7) have more ancient roots even than those of RNA.

> The recent abiotic synthesis of nucleotides using UV radiation and phosphate to purify intermediates(8) seems to lend support to the idea that the primordial oceans became a warm broth filled with nucleotides, which spontaneously polymerised into RNA, able to catalyse its own replication as well as organic transformations that ultimately yielded cells with lipid membranes, proteins and DNA – a purely Haldanian distillation, eight decades after Haldane’s essay. But the fact that nucleotides can be synthesised in ‘warm pond’ conditions hardly makes an oceanic RNA world more likely; by the same measure, the circumstance that amino acids can be present in some meteorites does not mean that life must have arisen in outer space. Setting aside the absence of geochemical evidence that a primordial soup ever existed, there are grave difficulties with the soup theory. To give a single example, polymerisation into RNA requires both energy and high concentrations of ribonucleotides. There is no obvious source of energy in a primordial soup. Ionizing UV radiation inherently destroys as much as it creates. If UV was the primordial source of energy, why does no life today synthesise ATP from UV radiation? Worse, every time an RNA molecule replicates itself, the nucleotide concentration falls, unless nucleotides are replenished at an equal rate. UV radiation is an unlikely energy source for rapid polymerisation and replication, and an unpromising initiator of natural selection

The ocean's not as warm or as concentrated as the experiments you're referencing.

Re: This Biology Book Blew Me Away

#47

> 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?

Once a cell has formed, through the miracle of exponential growth its descendants will quickly suck up available nutrients until you run out of some key nutrient, and then it can never happen again.

Suppose that that formation of a viable cell was a 1 in a million year event. It would be essentially inevitable over a hundred million years. But the time from happening once to impossible is a lot, lot, lot less than a million years...

Re: This Biology Book Blew Me Away

#48

Earlier quoted context omitted.

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.

How would you reconstruct the phylogeny to see through that mess? We're not even talking about computational complexity yet. Simply, how do you see through a random number of random DNA fragments being inserted in random places of random genomes at random intervals over a billion years?

Hmmm I see what you're saying. It's a mess but I optimistically think it's still something we will be able to tease out, by looking at many genes in a genome.

FWIW, It was recently estimated that 2% of core genes per genome are from HGT. https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_ev... It makes HGT fairly identifiable and gives us a lot of non-transfered genes to work with when reconstructing a tree.

Re: This Biology Book Blew Me Away

#49
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_anc…

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?

Re: This Biology Book Blew Me Away

#50

> 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…

I've thought this too - if the conditions for life existed at one point on the planet the chance they didn't exist at some other point seems infinitesimal. Down-thread someone argued that the subsequent genesis events would fail to produce new "roots" of the tree of living things. However, if the new roots fill a different niche (eg geographically), or quickly mutate to fill a different niche; or if the earlier roots…

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