
This Biology Book Blew Me Away - Tomte
https://www.gatesnotes.com/Books/The-Vital-Question
======
dnautics
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 reductant, but as a facilitator
oxidation. This is biology's "great umpolung chemistry" moment.

2) The great oxidation catastrophe. Because oxygen, the oxidized poop of the
previous process is highly toxic, there was a huge exinction event across
pretty much all clades. But some of the emergent chemistry (disulfide bonds
e.g.) really enabled structural scaffolding that facilitated higher order
cellular structure. Mitochondria went into hiding inside of the reducing
environment of an proto-archaeal species and boom - eukaryotes.

3) The size and distance of the earth from the sun. Hydrogen at ambient
temperature achieves escape velocity. This means the net chemical trend over
billions of years was oxidizing. One wonders if this made the first two
chemical processes somewhat inevitable.

I'd also like to point out that thinking parsimoniously about energy from an
evolutionary standpoint is not necessarily productive. For example: There's a
lot of junk DNA (VNTRs, e.g.) which do not seem to be subject to aggressive
optimivation for energy.

~~~
danieltillett
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_ancestor](https://en.wikipedia.org/wiki/Last_universal_ancestor)

~~~
acqq
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?

~~~
wolf550e
They competed with modern bacteria and lost?

~~~
acqq
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.

~~~
lawpoop
Alternatively, maybe not everywhere, forever, but in tiny, microscopic niches
across the globe, not accessible to modern bacteria how would devour them in
an instant.

What are our chances of finding any of them?

------
rusanu
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](https://www.youtube.com/watch?v=UGxAB4Weq0U)
. Is made by the author and it covers the ideas of life origin exposed in The
Vital Question.

Also interesting his paper on the double-agent theory of aging:
[http://www.nick-lane.net/double-agent%20theory.pdf](http://www.nick-
lane.net/double-agent%20theory.pdf)

~~~
mg74
Would you recommend it as an audio book, or are the visuals essential?

~~~
rusanu
Can't rly answer since I have never ever tried an audio book, but I can tell
that imho there are important visuals every 4-5 pages or so.

~~~
mg74
Thanks, that's what I wanted to know

------
apo
I really like books that expose holes in scientific knowledge. Books that
attempt to fill in those holes with conjecture based on observation are even
better. This book does both very well.

However, I did notice some glaring factual errors relating to chemistry (my
speciality). Chapter 2 includes the passage:

> Second, and more telling, a major distinction between bacterial and archaeal
> membranes seems to be purely random - bacteria use one stereoisomer (mirror
> form) of glycerol, while archaea use the other. ...

This is false. Glycerol is _achiral_ \- devoid of stereochemistry. It is its
own mirror form.

What Lane may be talking about is lipid hydrolysis, in which functionality at
one of the two _prochiral_ oxygens of a lipid is cleaved preferentially, but I
haven't followed up on this yet.

Either way, Lane spins a scenario where the two main groups of organisms make
two different kinds of glycerol. This simply can't be true.

This isn't merely a minor technical error. Enantiomeric purity and the same
configuration of amino acids has been a hot topic in the origin of life
because the kind of scenarios that are supported there are quite different
than if various species used mixtures of amino acid stereoisomers or different
pure isomers.

~~~
jcranmer
My recollection had been that the D/L system of enantiomeric naming was
derived from glycerol. Upon looking it up, it seems the derivation is from
glyceraldehyde. I have no idea why I remember it being derived from glycerol,
and I suspect that the reason may be the same reason why Lane refers to
stereoisomers of glycerol.

------
rusanu
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.

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

[http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej...](http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201621a.html)

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.

------
niels_olson
> 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 forms of life are spontaneously occurring on the sea floor
all the time? By now the overwhelming majority of those new forms are probably
eaten by an existing critter, but in the early days, there were many, many,
many events. And, like he says, there were many, many times when one cell ate
another cell. I rather doubt it only succeeded to result in eukaryotes once.

~~~
civilian
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
don't matter. :)

But, I think the mistake you're making is a misunderstanding of how long this
early evolution takes, vs. how long it takes for life to spread around the
ocean. Abiogenesis is probably much slower than the time it takes for a
unicellular alkaline vent-dweller to occupy the globe.

And, as far as eukaryotes go, keep in mind that there was about a billion
years where there were only bacteria & archaea on the globe. 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.

~~~
red-indian
Horizontal gene transfer is well established. Existence of a small number of
common genes between two species does not necessarily indicate a common
ancestor.

~~~
civilian
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_.

~~~
frenchy
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?

~~~
civilian
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](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.

------
red-indian
I recommend these biology books:

Molecular Cell Biology - Lodish

[http://www.amazon.com/Molecular-Cell-Biology-Harvey-
Lodish/d...](http://www.amazon.com/Molecular-Cell-Biology-Harvey-
Lodish/dp/1464183392/)

Molecular Biology of the Cell - Alberts

[http://www.amazon.com/gp/product/0815344325/](http://www.amazon.com/gp/product/0815344325/)

~~~
forgotpwagain
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/...](http://www.amazon.com/Physical-Biology-Cell-Rob-
Phillips/dp/0815341636)

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

[http://www.amazon.com/Physical-Biology-Cell-Rob-
Phillips/dp/...](http://www.amazon.com/Physical-Biology-Cell-Rob-
Phillips/dp/0815344503/ref=dp_ob_title_bk)

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?

~~~
sn9
Alberts is the canonical cell bio text in most undergraduate biology programs.

Phillips is more of an introduction to biophysics, so would require some
degree of comfort with calculus and physics (e.g., classical mechanics, some
E&M, and some statistical mechanics). The preface says only calculus and
elementary physics is required.

------
itodd
Radiolab [as usual] did a great episode on this theory called Cellmates.

[http://www.radiolab.org/story/cellmates/](http://www.radiolab.org/story/cellmates/)

~~~
civilian
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.

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

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

~~~
civilian
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/](http://www.radiolab.org/story/rhino-hunter/)

------
ssivark
I haven't read the book, but I wish to make a subtle but important distinction
between 'energy' and 'entropy'.

Whenever we say energy in common parlance, we actually mean a source of _low
entropy_ (energy). From the perspective of physics, "life" is a non-
equilibrium process so the crucial input is low entropy stuff (fuel/food/etc),
which can be 'used' by the organism while converting that stuff to high
entropy waste.

As far as we know, energy is always conserved; strictly speaking there is
never an energy crisis. It's all about (low) entropy.

~~~
dredmorbius
You might also want to consider the terms exergy (available energy / free
energy), and emergy (input energy or energy memory).

 _Life exploits entropic gradients._ So do all complex dissipative systems,
evolving or otherwise. Such as economies.

Ilya Prigogine, Alfred J. Lotka, Howard and Eugene Odum, and Jeremy England
may be of interest.

------
keithpeter
OA title image was taken in the Micrarium at the Grant Museum of Zoology at
UCL. Open to the public and well worth a visit should you happen to live in
London. The whole place has a decidedly steam-punk feel with skeletons, brass
instruments, and handwritten labels.

[http://www.ucl.ac.uk/museums/zoology](http://www.ucl.ac.uk/museums/zoology)

[http://www.ucl.ac.uk/museums/zoology/about/collections/objec...](http://www.ucl.ac.uk/museums/zoology/about/collections/objects/micrarium)

Now, I shall have to get the book. I've not read much about biology and energy
since finding Schroedinger's _What is life_ in the library at school.

------
allisthemoist
If you are at all interested in the origin of life and the role of energy
therein, I cannot recommend any single source of knowledge more than the
following paper as it has literally changed my life:
[http://onlinelibrary.wiley.com/doi/10.1002/cplx.20191/abstra...](http://onlinelibrary.wiley.com/doi/10.1002/cplx.20191/abstract)

It is written by two of the most intelligent people I think I've ever come
across, Eric Smith, who is an external professor at the Sante Fe Institute,
and Harold Morowitz, who founded the Krasnow Institute for Advanced Study at
George Mason. Both men work in very disparate fields. Morowitz was a
specialist of biology, origin of life scenarios, and biochemistry while Smith
is a (brilliant) physicist and chemist. However, together they have assembled
an encompassing theoretical structure that I am confident will lead science
for several decades, once it is gradually integrated into other fields of
research - e.g., Jeremy England at MIT has looked at some of the same
thermodynamic phenomena using statistical physics (great article on his work -
[https://www.quantamagazine.org/20140122-a-new-physics-
theory...](https://www.quantamagazine.org/20140122-a-new-physics-theory-of-
life/))

Eric Smith actually did a video describing this work while at Sante Fe that is
worth a watch:
[https://www.youtube.com/watch?v=ElMqwgkXguw](https://www.youtube.com/watch?v=ElMqwgkXguw)

This is the first paragraph of the paper mentioned above:

 _Life is universally understood to require a source of free energy and
mechanisms with which to harness it. Re- markably, the converse may also be
true: the continuous generation of sources of free energy by abiotic processes
may have forced life into existence as a means to alleviate the buildup of
free energy stresses. This assertion – for which there is precedent in non-
equilibrium statistical mechanics and growing empirical evidence from
chemistry – would imply that_ _life had to emerge on the earth, that at least
the early steps would occur in the same way on any similar planet, and that we
should be able to predict many of these steps from first principles of
chemistry and physics together with an accurate understanding of geochemical
conditions on the early earth. A deterministic emergence of life would reflect
an essential continuity between physics, chemistry, and biology. It would show
that a part of the order we recognize as living is thermodynamic order
inherent in the geosphere, and that some aspects of Darwinian selection are
expressions of the likely simpler statistical mechanics of physical and
chemical self-organization._

~~~
djestrada
England's proof of an absolute lower bound on heat production during self-
replication is a central text in this discussion:
[http://www.englandlab.com/uploads/7/8/0/3/7803054/2013jcpsre...](http://www.englandlab.com/uploads/7/8/0/3/7803054/2013jcpsrep.pdf)

Other resources:

Bechtel (2010): Biological mechanisms: organized to maintain autonomy
[https://mechanism.ucsd.edu/research/bechtel.biologicalmechan...](https://mechanism.ucsd.edu/research/bechtel.biologicalmechanismsorganization.pdf)

Walker et al (2015): The informational architecture of a the cell
[http://arxiv.org/abs/1507.03877](http://arxiv.org/abs/1507.03877)

------
restalis
_" He makes a persuasive case that complex life must have the traits we see
today. And he argues that it would almost certainly develop the same way
everywhere. Which means that, if we find complex life on other planets, it
will quite likely share the same traits." "is so compelling that it’s hard to
imagine any other way"_

The explanation is just a hypothesis about the cellular structural evolution
of the living organisms we're having all around us. From what I understand
that was only one successful combination of cell structures working under a
given set of conditions. In another conditions another combination could have
formed the basis of later evolved complex life. Sure, the E.T. life would most
likely have similar composition of chemical elements (because of their
abundance in the universe, if nothing else), but I can't expect it to
necessarily have the same base structural cell model at their core. I think
Mr. Gates' fascination with related problems affected his disposition for
healthy criticism here.

------
jdimov10
"Why does all complex life—every plant and animal you can see—share certain
traits, like getting old and reproducing via sex? "

There are plenty of examples of asexual reproduction in plants and animals as
well as complex organisms never getting old.

------
mattdeboard
I like how not even the text loads on that blog if you have JS disabled.

------
jrcii
"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 biology? If this was a post about the software business that would be one thing. It's so ubiquitous I don't necessarily expect anyone to understand my point, but this strikes me as a form of worshiping money. Because he has money we care what he thinks about anything and everything. It's a more covert form of the absurdity in reading and caring about what some celebrity likes to eat for breakfast.

~~~
xrange
>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...

~~~
jrcii
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. Intuition is the product of micro-
observations and predictions calculated with this system. 3. Organic life
responds to its environment using a closed-loop feedback system that can be
modeled as a series of steps (Sense, Organize, Analyze, Decide, Execute) where
the Execute step changes the input in the Sense step.

~~~
igravious
Respect you putting up.

#1 Original. More importantly, I like it :) Game theory meets ideology. I
reckon that an multi-agent based simulation model with enough features could
test your hypothesis. I think sociology will get there in about a decade. If
you do this now you'll revolutionise a part of the field.

#2 Not original. Epistemological theories have this covered. Also, you're
blurring or at least not making distinct different kinds of knowing. Check out
phenomenology as well. Check out cognitive neuroscience. I know these are huge
areas but you seriously think nobody has thought about this following on from
McCullogh-Pitts? There's knowing how versus knowing that for a start. There's
knowing facts versus intuitions. Inductive reasoning has been studied.
Intuitionism is a thing.

#3 Not original. Cybernetics has this covered. Also, Your steps are far far
far too general.

~~~
fmoralesc
1 is not necessarily original. Filip Buekens et al have worked on a model that
constructs social institutions as emerging from incentivization structures
like those present in cooperative games.

See for example J. P. Smit, Filip Buekens and Stan du Plessis (2011) "What is
Money? An Alternative to Searle's Institutional Facts", Economics and
Philosophy 27(1), pp 1 - 22,
[http://journals.cambridge.org/action/displayFulltext?type=1&...](http://journals.cambridge.org/action/displayFulltext?type=1&fid=7977007&jid=EAP&volumeId=27&issueId=01&aid=7977005)

~~~
igravious
Interesting. Thanks.

Along related lines (I think): Author Fleischmann, Anselm.

Title A simple Luhmann economy market mechanisms that lead to the emergence of
the economy as proposed by Niklas Luhmann are explored by agent based
modelling

Imprint Saarbrücken : VDM Verlag Dr. Müller, 2008.

[https://library.ucc.ie/record=b2094907](https://library.ucc.ie/record=b2094907)

