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.
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.
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?
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?
This is a really good question. It is possible that some of these primitive lifeforms still exist (deep underground would be my best guess) but for technical reasons we can’t easily find them.
We have two basic ways of find living microorganisms: 1. We can either grow them in culture, or 2. We can look for genetic markers that can be amplified using techniques like PCR. If these primitive micro-organisms grow slowly (say divide once a year) then we will never find them in culture (we already know the microorganisms that live deep underground grow at this sort of speed). The genetic marker approach requires that the primitive organism have the same genes as all modern organisms (ribosomes normally). If they don’t have these genes then we won’t find them using our current approaches - they could be there and we just miss them.
If I was Bill Gates rich I would spend some of my money sponsoring deep earth microbiologists to look for cells that appear to be maintaining an energy gradient, but which don’t have ribosomes.
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.
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.
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.
Oxygen, a previous book from Nick, cover these topics in great detail. The Vital Question deals with events that long predate the cyanobacteria, the Great Oxygenation Event and how we avoided oceans evaporating into space under UV radiation (at least the first chapters of the book, rest of it covers mostly origin of eukaryotic cell).
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.
1) rust
2) if you do the basic transformation (addition of water to alkene, https://www.khanacademy.org/science/organic-chemistry/alkene...) biochemically and chemically speaking you usually assign an integral oxidation change of 0, but in reality, the alcohol is slightly higher oxidization state than the alkene.
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 covers the ideas of life origin exposed in The Vital Question.
I'd also like to recommend Power, Sex, Suicide by the same guy, Nick Lane.
It's an absolutely amazing book that explains the origins of mitochondria, why they're necessary for complex life (and this means that complex life is exceedingly rare in the universe), and all sorts of effects the differing genomes of mitochondria and cells have: fertility, aging, and a bunch of other ones.
If you're interested in cellular biology, read this guy.
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.
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.
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.
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.
The Vital Question advocates a theory that mitochondrial endosymbiosis was critical to origin of eukaryote. Recently some evidences emerged that mitochondria was a late acquisition, casting doubts to the theory.
> 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.
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.
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?
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.
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.
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 the new host that it isn't ejected immediately, and managed to stay functional and evolve past the original core function gene in terms of fitness so that original core function gene could be ejected, and the original core function gene did get ejected and the microbes with the new core function gene managed to outcompete all the microbes with dual core-function genes.
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.
> 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.
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?
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.
I mean, at this point you have to define what an 'ancestor' is then. HGT kinda breaks the rules of what an ancestor is. With us, it's a little easier, we have tons of genes and a few viral infections don't break the concept of ancestor. When you have 100 genes total, 75 of which are from HGT, 10 from viruses, and 15 from the mother cell, who can be called the ancestor then? Remember, this was WAY back when too. Modern prokaryotes have some complex stuff to deal with all this, the first million generations did not (maybe). In that early soup, the basic concepts of what life is today don't have relevance. What is a mother cell anyways? Was it really gene transfer, or was that just what they all naturally did all the time? ETC.
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.
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...
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.]
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?
Many people don't seem to understand just how incredibly different the environmental conditions on Earth were when life was first ramping up. Those conditions not only no longer prevail, but the world is also full of competitors that weren't there in the beginning.
Also, we probably haven't cataloged 10% of the life forms on our ocean floors yet. There's still a lot to learn, and there will be surprises.
Continuing abiogenesis may very well be occuring (in the very few locations that may still resemble the beginning), but at what complexity are we defining "life" when asking this question? Simple spontaneous assembly of RNA precursors? Something more fully fledged?
In any case, the problem isn't even competitors that have evolved since then - it's the existence of complex metabolism. All of the "ingredients" you would need for abiogenesis to occur are now consumed by established organisms, ripping down the molecules for their own energy needs before they can catalyze into a more complex form.
Life as we know it doesn't have room for the earliest products of abiogenesis anymore. Whatever form our earliest genetic ancestors may have taken, Earth's present-day micro-biosphere is simply too ubiquitous and too ravenous.
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.
> Nobel Prize for showing that particles are always most likely to take the most efficient path
I only have a BS in physics, so do please correct me, but the path integral formulation of quantum mechanics helps predict particle behavior but doesn't say anything is most likely to happen all the time. Indeed, it requires considering how often very absurd things happen.
> it is easier to work with a simpler theory, so scientists prefer it out of self-interest
Thermodynamics is definitely simpler than any phylogenetic analysis trying to peer backward through a graph with many, many cycles in it. But thermodynamics requires accepting the possibilities of just how many times some very unlikely event might happen.
I simply meant that there are no data to show that any current living thing derives from a different earliest ancestor from all of the other currently living things. You are welcome to show me a counterexample if you know of one.
If scientists are biased at all, they're biased against life being hard; generally the party line is that it is easy. The standard line is that life arose once because all the evidence seems to point to the fact that all observable life comes from the same line, not because they can't conceive of any alternative.
It is still thought that there could be a slight possibility of a different life line still alive in some extreme environment, which we would have a hard time observing with our existing tools; e.g., if it was not built on DNA then some of the tooling we use to detect small amounts of otherwise-unknown life might not work. But to the best of my knowledge this is just speculation with no current concrete evidence.
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 disgusting mess at the root of the tree of life.
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.
Horizontal gene transfer is still rampant - actually it is a far better way to mix genes than sexual reproduction and it is probably why microbes rule the world.
LUCA is an imaginary organism that captures the features that all known living organisms share - almost certainly the history of decent of each gene in modern organisms is different.
>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?
I'd be very surprised if such spontaneous life could compete against life with millions of years of evolution behind it. As to eukaryotes, them arising seems to be a much more unlikely proposition so I'd be surprised if it happened more than once given that it took an order of magnitude more time to happen once the conditions were right.
Perhaps at a species level it may haven't happened many times, that is, a species of bacteria was ingested, or took harbor in, a larger cell. But if it worked once, it worked thousands if not millions of times.
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.
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/
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.
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.
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...
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...)
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.
Ooh, thanks! You've managed to combine my most and least favoured institutions here. I'm finding the Santa Fe Institute's research (and researchers) fascinating. GMU, OTOH, strikes me as automatically suspect due to its extreme pollution from Koch-funded Libertarian ideology, though I realise that doesn't infect all researchers or departments.
Watching the video and tracking down the papers.
England's another discovery of the past couple of years, doing interesting work.
"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.
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?
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.
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.
"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.
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.
#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.
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.
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.
#3 seems like a decent model, but is the model actually consistent with how "all organic life" functions? And what is the distinction between Organize&Analyze and Analyze&Decide and Decide&Execute?
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.
At least from an etymology perspective, analyze should come before organize. My version is Anticipate->Sense->Decide->Understand but I think it's not mine exclusively.
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.
Bill Gates is into biology because (A) he's curious and (B) his foundation pursues innovations in diverse fields all of which are not software. I don't know if he writes his own copy or not but I appreciate these reviews and TIL Nick Lane's books sound awesome and I did not know that before.
Also, for you to win it is not necessary for others to fail :)
We don't necessarily care what he thinks but we are made aware of what he thinks so when he mentions a book people are going to talk about it. What's the alternative? Ignore him because he's rich? Treat every media outlet like some photocopied fanzine publishing the random thoughts of random people with no reputation for anything?
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.