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This Biology Book Blew Me Away

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Re: This Biology Book Blew Me Away

#71

Post by niels_olson »

civilian wrote: post #31
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.

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 .

In a resource constrained world, where a lot of energy is being spent on other things (like fighting), certain fundamentals may well get highly optimized, and indeed outright stolen.

Re: This Biology Book Blew Me Away

#72

Post by siyer »

acqq wrote: post #63
searine wrote: post #12

Earlier quoted context omitted.

Classics. I think I have a subtle preference for Alberts, rather than Lodish in terms of text, but I think the Lodish illustrations are better. At this point I think I have three copies of Alberts stashed in various closets and trunks.

Looking in the Amazon description, 6.6 pounds each?

And you feel every ounce of those when reading them. Most good versions of this class of book are this heavy (typically prescribed for the late 'undergrad'/first year grad introductory class reading). The neuroscience equivalent (Kandel, Schwartz, Jessell) is 8.7 pounds, with very thin pages.

Re: This Biology Book Blew Me Away

#73

Post by civilian »

niels_olson wrote: post #56
civilian wrote: post #46

Earlier quoted context omitted.

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. Regard…

That's some highly biased writing you just quoted. Rather than respond here, perhaps I shall at some point write a more detailed essay. But for the time being, re-read that with an eye toward how many times he sets up a strawman and then knocks it down saying "there's no evidence". Seriously? Did you do a lit search before you reposted someone else's writing? For example: no evidence of primordial soup? Go diving muc…

I'm quoting the author of the book that this thread is discussing, this isn't a random cherry-pick. :)

Craig Venter wasn't sailing around the world 3 billion years ago.

//edit

okay, so, I was trying to explain what the state-of-the-research was, and what this book says. I used to think that the RNA-world hypothesis was also the most likely! You have a good understanding of biology, and you're smart enough to make decent arguments, but you just aren't up to date.

I don't think anything I say will persuade you. You should go read The Vital Question and publish in a journal when you prove Nick Lane wrong.

Re: This Biology Book Blew Me Away

#74

Post by sampo »

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…

> A billion years! Why did it take so long to form a eukaryote then? It's because it's very x 10^9 unlikely to happen.

You say it was change. Could have as well taken 0.5 or 2 billion years.

In another comment, /u/dnautics said it was because in the newly formed oxygen atmosphere, the mitochondria had to seek shelter inside other cells.

Who knows? At least the appearances of oxygen atmosphere and eukaryotic cells happened at about the same time.

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

Re: This Biology Book Blew Me Away

#75

Post by sampo »

niels_olson wrote: post #68
btilly wrote: post #47

Earlier quoted context omitted.

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 per what unit volume? Or unit surface area?

I think they mean per planet.

Re: This Biology Book Blew Me Away

#76

Post by untilHellbanned »

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 might have better ideas as you understand them in your head, but the actual words you use to communicate with other humans matter. These don't say that much. In contrast, Nick Lane's are intriguing.

Re: This Biology Book Blew Me Away

#77

Post by untilHellbanned »

jrcii wrote: post #4

"Nick reminds me of writers like Jared Diamond, people who develop a grand theory that explains a lot about the world. He is one of those original thinkers who makes you say: More people should know about this guy’s work." I have original ideas that explain a lot about the world but no one cares because Bill Gates didn't tell everyone to listen to me. * Can anyone remind me why we care what Bill Gates thinks about bi…

Your asterisked point about Bill Gates I 100% agree with. Your ideas vs. Nick Lane's, not as much.

Re: This Biology Book Blew Me Away

#78

Post by frenchy »

civilian wrote: post #31
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.

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 .

I have no particular side on this debate, nor am I an expert, but wouldn't the current state still be possible if the recipients of the gene transfer out-competed all the other variants in its lineage?

Re: This Biology Book Blew Me Away

#79

Post by astazangasta »

danieltillett wrote: post #32
astazangasta wrote: post #25

Earlier quoted context omitted.

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.

If horizontal gene transfer was common and rampant at the outset of life, then a fundamental fact of evolutionary descent was not true at that point. This means there may NOT be a LUCA, but several progenitor organisms that each contributed to a portion of eventual life. E.g. there are four features ABCD. We may have descendants that are AB, BC, CD, AD, without having any creature that was ABCD.

Re: This Biology Book Blew Me Away

#80

Post by civilian »

frenchy wrote: post #78
civilian wrote: post #31

Earlier quoted context omitted.

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 .

I have no particular side on this debate, nor am I an expert, but wouldn't the current state still be possible if the recipients of the gene transfer out-competed all the other variants in its lineage?

I'm really kicking myself for saying "a few" genes are shared between archaea & bacteria.

> The proteins that archaea, bacteria and eukaryotes share form a common core of cell function, relating mostly to transcription, translation, and nucleotide metabolism. https://en.wikipedia.org/wiki/Archaea#Genetics

It's really more like hundreds or thousands of genes. And they're around the foundations of translating DNA to RNA and RNA to amino-acid chains.

And we share the genes that are related to DNA maintenance and translating DNA to proteins.

The idea is that, without these shared genes, horizontal gene transfer doesn't even make sense. There would be no shared genetic code. The nucleotides used might not even be the same. Amino-acids have right-handed chirality (which is probably related to our DNA having left-handed chirality). If life independently evolved it would probably use amino acids and nucleotides, but there's no guarantee that the handedness would be the same, or that the genetic code would be the same.

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