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This Biology Book Blew Me Away

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Re: This Biology Book Blew Me Away

#51

Post by dnautics »

danieltillett wrote: post #27
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_anc…

We don't know the exact mechanism (endosymbiosis vs. hgt, for example) - which is why I said "freak merger" to keep it vague, but correct me if I'm wrong, but it's pretty clear that PSI comes from purple and PSII comes from green sulfurs, by homology.

Re: This Biology Book Blew Me Away

#52

Post by mg74 »

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author, and I found it equally interesting (it goes in more detail on some topics, but some of the ideas in Oxygen are superseded by his later books).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…

Would you recommend it as an audio book, or are the visuals essential?

Re: This Biology Book Blew Me Away

#53

Post by dnautics »

lumpypua wrote: post #21
dnautics wrote: post #10

Earlier quoted context omitted.

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.

> He ends up using the discussion to make the argument that all life in the universe likely uses redox chemistry for energy.

If that's the conclusion, it's trivially true, since basically you can assign a redox value to every chemical transformation using the nernst equation.

The interesting thing is that IMO the resistance to the conceptual framework behind the way that the mitochondrion works was because it was hard for biochemists to picture the proton motive force (concentration gradient) as a redox potential (it truly is one) because it seemed more physics-ey than biochemistry-ey. Peter Mitchell cleared that up amidst quite a bit of controversy. He had to go to the lengths of setting up an independent research institute to get the work done.

Re: This Biology Book Blew Me Away

#54

Post by baakss »

throwanem wrote: post #35
jrcii wrote: post #13

Earlier quoted context omitted.

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?

Are you suggesting they're not? Where did he plagiarize them from if so? He can't exactly prove they're original, but you could prove they have at least been said before, if not plagiarized.

Re: This Biology Book Blew Me Away

#55

Post by acqq »

forgotpwagain wrote: post #37
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/...

Thanks! The second edition has the preview on the Amazon too:

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

Looks worth the money, based on the pictures. However, as I browse through the text, the tone of the explanations seems to be a little casual, and the book more concentrating on "counting" than explaining the details presented with the pictures?

Otherwise it seems to be "what you get when a physicist gets to write about cells," is my impression right? It seems that Lodish and Alberts are better starts to learn the biological aspects?

Re: This Biology Book Blew Me Away

#56

Post by niels_olson »

civilian wrote: post #46
niels_olson wrote: post #41

Earlier quoted context omitted.

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. 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 much? Craig Venter brings back genes unseen by man just driving his boat through the Indian Ocean and this guy waves his hands saying there's no evidence of primordial soup?

Re: This Biology Book Blew Me Away

#57

Post by wolf550e »

acqq wrote: post #49
danieltillett wrote: post #27

Earlier quoted context omitted.

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…

They competed with modern bacteria and lost?

Re: This Biology Book Blew Me Away

#58

Post by snowwrestler »

niels_olson wrote: post #45
tokenadult wrote: post #14

Earlier quoted context omitted.

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.

Didn't Feynman win a Nobel Prize for showing that particles are always most likely to take the most efficient path?

Anyway, Occam's razor is about preferring theories, not physical laws. If two theories match a given set of observations, there is no objective reason to prefer one over the other. But it is easier to work with a simpler theory, so scientists prefer it out of self-interest.

Put another way, if there is no way to distinguish between a LUCA and continuous abiogenesis that looks exactly like a LUCA, then there's no reason to care that continuous abiogenesis might be occuring.

But if you believe there is a way to prove that continuous abiogenesis is occuring, then by all means conduct the observation and publish it.

Re: This Biology Book Blew Me Away

#59

Post by okket »

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…

There is also his "Why is Life the Way it Is?" talk he held last year at the Royal Institution.

https://www.youtube.com/watch?v=gLcWfecmZhE

Re: This Biology Book Blew Me Away

#60

Post by acqq »

wolf550e wrote: post #57
acqq wrote: post #49

Earlier quoted context omitted.

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…

They competed with modern bacteria and lost?

Yes, I'm aware of that hypothesis. But everywhere, forever?

It can also be we'll never know, as the life on Earth apparently existed for so long, billions of years, since the times the whole Earth was completely different than we know now (from the life's point of view).

Which is also fascinating, as on the Universe level we can actually observe the glow of the Big Bang, which happened much earlier.

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