HN Books @HNBooksMonth

I don't enjoy the science writing at Quanta. Their articles in fields I know something about are so inarticulate and misleading that I have to doubt whether their reporting in fields to which I am largely ignorant (particularly the publication's namesake, quantum mechanics) would stand up to scrutiny.

In this case, you should know that the phagocytic model of endosymbiosis has been radically upended since the successful culturing of a Lokiarchaeota in (ecto)symbiosis with a delta-proteobacterium in 2019 by Imachi et al.

"Isolation of an archaeon at the prokaryote–eukaryote interface" https://www.nature.com/articles/s41586-019-1916-6 doi.org/10.1038/s41586-019-1916-6

The striking images of the branching, filamentous prokaryotic Lokiarchaeotum grappling its metabolic partner resembled nothing I had ever seen in biology before, save maybe the mycorrhizal root nodules of a legume at a ~2000x smaller scale. The prevailing model of the process of eukaryotic endosymbiosis is now "entangle-engulf-endogenize", rather than phagocytosis, which might be a secondary post-mitochondrial lifestyle adaptation.

If the Nature paper is difficult for you to read or access, this summary is well written and provides better citations than the Quanta article.

"Challenging Eukaryogenesis: The Story of the Eukaryotic Ancestor" https://arxiv.org/abs/2008.06608 doi.org/10.48550/arXiv.2008.06608

If you are interested in this topic, I cannot praise Nick Lane's nonfiction trilogy of books on mitochondria and evolution highly enough:

  • "Oxygen: The Molecule that Made the World" (2002)
    https://www.amazon.com/Oxygen-Molecule-that-Made-World/dp/0198508034
  • "Sex, Power, Suicide: Mitochondria and the Meaning of Life" (2005)
    https://www.amazon.com/Power-Sex-Suicide-Mitochondria-Meaning/dp/0192804812
  • "The Vital Question: Energy, Evolution, and the Origins of Complex Life" (2015)
    https://www.amazon.com/Vital-Question-Evolution-Origins-Complex/dp/0393088812

⬐ btrettel

Gell-Mann amnesia is a huge reason why I don't trust the popular science press in general, not just Quanta Magazine.

In fluid dynamics, their pages on why turbulence is hard [0] don't mention the actual reason turbulence is hard: It has a really high computational complexity. There is no mystery here. The math behind it is pretty simple. I guess this doesn't sell the article though, so a journalist won't say that. Though I'm not sure the people at Quanta Magazine are aware!

Quanta Magazine also spends an extremely disproportionate amount of articles on the (constant viscosity) Navier-Stokes existence and uniqueness problem [1]. This is essentially a pure math problem, in my view, of no practical consequence [2]. Contrary to what Quanta Magazine writes, this has nothing to do with turbulence beyond that both use the Navier-Stokes equations.

[0] https://www.quantamagazine.org/the-trouble-with-turbulence-2... https://www.quantamagazine.org/what-makes-the-hardest-equati...

[1] https://www.quantamagazine.org/deep-learning-poised-to-blow-... https://www.quantamagazine.org/famous-fluid-equations-spring... https://www.quantamagazine.org/for-fluid-equations-a-steady-... https://www.quantamagazine.org/what-makes-the-hardest-equati... https://www.quantamagazine.org/mathematicians-find-wrinkle-i... https://www.quantamagazine.org/a-fluid-new-path-in-grand-mat...

[2] https://news.ycombinator.com/item?id=31049535

⬐ peter303

I second this trilogy, particularly the second book. Particularly the hypothesis that sex was a Faustian bargain that was accompanied by programmed death.

The article seems to suggest he's simulating a "soup" of many different molecules and seeing which combinations lead to sustained reactions. Nick Lane's book "The Vital Question" [1] discounts the primordial soup idea (that life arose in tidal pools or streams near volcanos due to the right chemical mixture being present in the water at that time) and suggests underwater alkaline hydrothermal vents as the location of the first formation of life. The hydrothermal vents produced (see also his recent paper [2]) alkaline fluids which mixed with acidic seawater within micropores provided by the geological structures of a particular type of vent. This, he hypothesises, led to proton gradients which are essential for life.

Of course, both these guys are experts at the top of their fields, at respected institutes. I possess neither of those qualities.

[1] https://www.amazon.com/Vital-Question-Evolution-Origins-Comp...

[2] http://nick-lane.net/publications/origin-life-alkaline-hydro...

Peripherally related book recommendation: https://www.amazon.com/Vital-Question-Evolution-Origins-Comp... Someone here on HN recommended it to me and it was an awesome read (that I doubt I understood).

⬐ joekrill

I really loved this book -- it's definitely highly recommended by many folks (I think know Bill Gates was a big fan). But I don't recall it containing much -- if anything at all -- about CRISPR?

⬐ neom

It doesn't directly. However, in reading the article I was able to think about what I learned about prokaryotes, archaea, and generally just feel like having read that book I enjoyed the article a lot more, if that makes sense? :)

⬐ joekrill

Ah got it -- I thought maybe I missed something in there! Was a great book, for sure.

⬐ joshbaptiste

I listened to the audio book and must state that it's very involved and not really for the layman like me. I got lost on the eukaryotes explanation which lost me for much of the other topics.

⬐ rqebmm

I've found audiobooks (and podcasts) to be great for lighter reading, but I tend to drift in and out. That's not a great system for something more scaffolded like a textbook where you have to thoroughly understand each part in order to build the next piece on top

⬐ neom

As someone who is severely dyslexic: basically the only way I can consume large amounts of written content in an acceptable amount of time is audio book. Thankfully- I'm pretty sure listening to an audio book for me is the same level of comprehensible intake as a non-dyslexic via written word. :)

⬐ Splendor

IIRC it was on Bill Gates' book list last year.

⬐ alextheparrot

In line with this, I'd also like to recommend 'The Gene'[0]. The author has informed me of new things (Even though I studied biochemistry during college) and also focused a lot on the ethical discussions relating to genetic modification. It also directly discusses CRISPR as it is quite new. I'd recommend all of Mukherjee's other books as well (Mainly Emperor of all Maladies).

[0]https://www.amazon.com/dp/1476733503

⬐ fossuser

I'd second this recommendation - currently reading it right now and it has the nice combination of being really interesting and really easy to read. Mukherjee's style is really clear and enjoyable.

Is that life itself is relatively "easy" and is likely to be common.

Life appears common, but multicellular life appears to be extremely uncommon and appears to have evolved only once on earth, at least according to Nick Lane's excellent (though inadvertently depressing) book The Vital Question: Energy, Evolution, and the Origins of Complex Life (https://www.amazon.com/Vital-Question-Evolution-Origins-Comp...). I can't gauge the accuracy of his claims but the book does not appear to have been rebutted, at least from what I've found. Given all the discussion about biology on this thread I'm surprised no one else has mentioned it.

⬐ derekp7

Also, as far as we know, single-celled life also evolved exactly once. This is one thing I haven't seen a good answer for -- if life came about so early, that would indicate that it is easy. But since it occurred only once, that would indicate that it is hard.

The common explanation is that once life evolved and began to spread, that it would prevent other life from appearing by out-competing it. But there is plenty of raw materials and sunlight to go around, so I don't buy that explanation.

The only thing that seems to fit, is that life is hard to evolve, but has extra-terrestrial origin. If that is the case then life should exist (at least in bacterial form) wherever a suitable habitat is found.

Yes, they used that exact term, invoking Darwin at the same time. And I agree with you about the time frame.

I've been reading "The Vital Question"[1] of late and it has been the first book in a while where I've had several "oh that makes so much sense!" moments. And one of the tenets is that Darwin was correct in the small, and wrong in the large understandings of evolution.

Something that jumped out to me while reading it, is that information extraction drives our technology systems like energy drives biological systems. Read the book and then sit back and analyze Twitter as a multi-cellular organism with information as energy and individuals as cells. A sort of Datasaurus. Fun stuff.

[1] "The Vital Question: Energy, Evolution, and the Origins of Complex Life" -- http://www.amazon.com/Vital-Question-Evolution-Origins-Compl... based on the recommendation tweeted by Gates and comments here, I read it through cover to cover while camping, and now going through a second reading to pick up what I overlooked the first time.

I've been reading The Vital Question by Nick Lane, where he puts forth some theories about the origin of eukaryotes, and life in general. It does make it seem that abiogenesis and eukaryote-genesis are much more difficult than we give them credit for.

So in the Drake Equation, I think that F[L] is probably pretty low.

And because eukaroyte genesis is difficult and only happened once (and it took a billion years of bacteria & archea hanging out before we got a eukaryote), and eukaryotes are a prereq for multi-cellular organisms and thus intelligent life, F[i] is also really low.

http://www.amazon.com/The-Vital-Question-Evolution-Origins/d...

⬐ breckinloggins

This gets my vote. My hunch is that intelligent life like the kind we would love to meet happens either on the order of once or twice per galaxy during the galaxy's entire lifetime, or it happens SO rarely that, if the universe is infinite in extent, then any intelligent observer looking out from the "center" of their observable universe will most likely be in the only intelligent civilization in that visible radius.

Depressing, but it seems more plausible than things like "Great Filters of DOOM". It would predict that there is a lot of intelligence in the entire universe, but each cluster of intelligence is profoundly alone.

⬐ samstave

Then why the fuck do we keep killing ourselves?

Seriously, if we taught this level of intelligent-life appreciation to every born soul... the world would be a better place.

Rather than starting with the teachings we do for youngsters; why not just teach them how freaking rare and lucky they are to be a consciousness present to hear that fact and then know that they can then expand the known universe... but do this in a much more deliberate fashion than we are now?

We need to be much much more deterministic from a species if we will survive for eons.

⬐ vectorjohn

We keep killing ourselves because so many people are so damned reassured that death isn't the end. That or they just pessimistically assume there's no way we'll make it to eons.

I think we could easily last for eons, but yeah. We have to get people on board with that possibility.

⬐ Florin_Andrei

> Then why the fuck do we keep killing ourselves?

We are slaves to our own genetic sequences to a much larger extent than we usually think.

It's pretty easy to show that the behaviors that lead to people killing each other are driven by mechanisms initially evolved to ensure that our own genetic sequences keep multiplying and spreading out, eliminating competition. And they're pretty dumb mechanisms, running on the lower levels of our brains, so don't expect them to be very selective, or run without failure. Sometimes they hit an internal bug and become runaway destruction loops, which sometimes even turn against the individual itself.

Many things that are typically considered "evil" can be traced back ultimately to these mechanisms that ensure that our own genetic sequences win the race. In a way, "evil" was actually useful, way back in time, in an evolutionary sense. It's just recently that we've acquired new desires and aspirations, which are in conflict with the old, narrow, dumb routines.

⬐ baddox

> Then why the fuck do we keep killing ourselves?

Because the knowledge that "us killing ourselves" collectively is bad for us collectively does not affect the decision for an individual to kill another individual.

⬐ zardo

>Then why the fuck do we keep killing ourselves?

Not enough game theorists in charge.

⬐ civilian

To quote Ender's Game: "I am not a happy man, Ender. Humanity does not ask us to be happy. It merely asks us to be brilliant on its behalf. Survival first, then happiness as we can manage it."

It doesn't really answer why we commit suicide. But it does give an answer to why we aren't happy.

⬐ baddox

Where do you get the estimate of "once or twice per galaxy"? I can agree that it might be "rare," but I have no idea how you would pin down the rareness to that level of accuracy.

⬐ breckinloggins

It's a total guesstimate. The interesting thing to me is that I have no idea how anyone else pins down THEIR estimates to any level of accuracy, but they are apparently confident enough in their estimates to posit things like the "Great Filter", when other (equally likely) estimates such as mine require no such thing.

⬐ monk_e_boy

Panspermia is one solution to this.

⬐ shawndumas

All problems [in philosophy] can be solved by another level of indirection...

⬐ monk_e_boy

Ha! But it does solve the 'this rare event happened here on Earth but it is very unlikely to happen anywhere' because those little single cells came here from somewhere else. That source infected millions of planets.

It moves the problem of starting everywhere to starting in one place (more likely)

⬐ AnimalMuppet

Getting it to occur once is more likely than getting it to occur many times. However, it does give you a new problem: making cells that can survive hard vacuum, radiation, and extreme cold, for millenia (at least), and still be viable when they reach a new planet. We're not talking speed-of-light propagation here. We're probably not even talking 0.01 c. So even to the nearest neighboring star is probably thousands or tens of thousands of years. In vacuum. In extreme cold. Without even photosynthesis to provide energy. Yeah, I'm kind of skeptical of this actually working.

⬐ civilian

If panspermia does happen in the universe, I bet that it happens with the sheltering of asteroids and meteors. Life develops on low-gravity planets with turbulent atmosphere -> some cells get into space -> get caught by comets and other objects -> slowly propagate within comet -> comet has an unstable orbit that sends it to another system, where it has an encounter with a habitable planet.

An icey comet could provide radiation protection and it could accidentally go through a gravity assist to increase it's speed.

I suppose that the best evidence we could collect to prove or disprove panspermia is to see if it's happened between planets/moons/objects within our own solar system.

⬐ Florin_Andrei

One thing to keep in mind is that the time interval of stability for Earth as a life-bearing planet is actually fairly close to the end. We're past the 75% point. The Sun's evolution will "soon" put an end to that (speaking on a cosmic scale).

So it seems like it was a close call. Life needed almost the full extent of that interval of stability to create an (arguably) intelligent species. There can be no reset and start over. This is it, for the solar system. If we fail to survive, this whole star and its planets have failed to produce viable intelligence.

If Earth turns out to somehow be unusually stable as a life-bearing planet, this might explain a large portion of the Fermi paradox. This might be a large chunk of the Great Filter.

⬐ PuffinBlue

"How long do you say the sun had left?"

"...5 billion years."

"Whew, that's OK, I though you said 5 million!"

⬐ Florin_Andrei

> 5 billion years

The Sun will get significantly hotter over the next 1 billion years. Life on Earth will become impossible (unless artificially maintained) quite a while before the end of that 1 billion year interval.

⬐ PuffinBlue

...I had so much I wanted to do :-(

Cheatsheet, without the affiliate links (another commenter posted these with affiliate links then deleted it after being called out):

The Road to Character, David Brooks - http://www.amazon.com/gp/product/081299325X

Thing Explainer, Randall Munroe - http://www.amazon.com/gp/product/0544668251

Being Nixon: A Man Divided, Evan Thomas - http://www.amazon.com/gp/product/0812995368

Sustainable Materials With Both Eyes Open, Julian Allwood - http://www.amazon.com/gp/product/190686005X

Eradication: Ridding the World of Diseases Forever?, Nancy Leys Stepan - http://www.amazon.com/gp/product/0801450586

Mindset: The New Psychology of Success, Carol Dweck - http://www.amazon.com/gp/product/0345472322

Honorable Mention:

The Vital Question: Energy, Evolution, and the Origins of Complex Life, Nick Lane - http://www.amazon.com/gp/product/0393088812

⬐ aerovistae

Affiliate links? Like, Bill Gates gets some money when you click through his blog? Please tel me I'm misunderstanding.

⬐ rbinv

There are actually no direct links to Amazon (or other similar sites) in his blog posts. Parent meant other commentators in this thread.

⬐ hueving

No, another commenter posted links but slapped affiliate tags on them.

⬐ None

None

⬐ jmknoll

Just to mention - you can read 'Sustainable Materials with Both Eyes Open' on the authors' website (although I'm sure they wouldn't mind people buying it on Amazon as well). http://www.withbotheyesopen.com/read.php

⬐ rodly

I'm curious, why is it that people dislike affiliate-backed links if the link is relevant, useful, interesting and of equal quality to the normal link? Seems irrational.

⬐ None

None

⬐ davidw

Nothing wrong with affiliate links if you're a regular user of this site: we're capitalists here. I make sure to include them if I link to a book, because I could use the money more than Jeff Bezos. Of course, I don't link to stuff just for the sake of linking to it, but only do so if I would have anyway. I think it's pretty clear whether someone is a spammer or not.

https://news.ycombinator.com/user?id=hullo seems to be the person who included some links. They have clearly been here a while, participates constructively, and doesn't seem to spew out a lot of affiliate links (any, actually, that I can see).

⬐ unethical_ban

I suppose some think there is an opportunity for disingenuous posting if there is monetary gain to be had. That said, I agree with you, and knowing I have posted affiliate links without trying, I think any malice attributed to it is misplaced.

⬐ davidw

With affiliate links, I sometimes make upwards of 10 dollars every few months - enough for a free book once in a while. I'll let you guess how that compares to my salary...

I think it's pretty clear from people's posting/comment history whether they're adding them in good faith or not.

⬐ None

None

⬐ tlrobinson

Perhaps, but taking a famous person's list of books and reposting it with affiliate links and no disclaimer is definitely crossing the line in my book.

⬐ manish_gill

Why? I'm genuinely interesting in your line of reasoning.

⬐ hueving

Profiteering in comment sections pollutes the incentives for commenters. Sure the links were useful, but they were much less useful than a person providing a really insightful comment about a typical article that shows up here. I don't want one person making monetary gain over another.

⬐ davidw

> I don't want one person making monetary gain over another.

Seems like that shipped sailed a long time ago: there are a lot of people who link to their companies, offer jobs, and that kind of thing here. Making money is not a bad thing - spamming is.

If anyone's interested, I hereby offer to spend the entirety of my ill-gotten affiliate gains on beers if anyone ever visits Bend, Oregon.

⬐ andreyf

If only there was a system where we could somehow crowdsource deciding which comments are "really insightful" and which are not...

⬐ davidw

Don't think I might have upvoted it, but it does represent a minor convenience.