This Biology Book Blew Me Away
gatesnotes.com
gatesnotes.com
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.
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.
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.
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.
"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?
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.
What are our chances of finding any of them?
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.
Normally I don't think of water in either way ...
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.
Also interesting his paper on the double-agent theory of aging: http://www.nick-lane.net/double-agent%20theory.pdf
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.
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.
http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej...
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.
http://www.nature.com/nature/journal/v531/n7592/full/nature1...
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.
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.
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.
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.
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.
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.
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.
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.
The latter is highly, highly unlikely.
> 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.
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?
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.
We're not talking about two species, we're talking about two domains.
> 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.
You say it was change. Could have as well taken 0.5 or 2 billion years.
In another comment, /u/dnautics said it was because in the newly formed oxygen atmosphere, the mitochondria had to seek shelter inside other cells.
Who knows? At least the appearances of oxygen atmosphere and eukaryotic cells happened at about the same time.
https://en.wikipedia.org/wiki/Timeline_of_the_evolutionary_h...
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.
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.
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.
https://en.wikipedia.org/wiki/Timeline_of_the_evolutionary_h...
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.]
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...
per what unit volume? Or unit surface area?
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.
B: "Really? I don't like bourbon."
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.
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.
http://www.ucl.ac.uk/museums/zoology
http://www.ucl.ac.uk/museums/zoology/about/collections/objec...
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.
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...)
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
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.
Watching the video and tracking down the papers.
England's another discovery of the past couple of years, doing interesting work.
Other resources:
Bechtel (2010): Biological mechanisms: organized to maintain autonomy https://mechanism.ucsd.edu/research/bechtel.biologicalmechan...
Walker et al (2015): The informational architecture of a the cell http://arxiv.org/abs/1507.03877
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.
Molecular Cell Biology - Lodish
http://www.amazon.com/Molecular-Cell-Biology-Harvey-Lodish/d...
Molecular Biology of the Cell - Alberts
I think I have a subtle preference for Alberts, rather than Lodish in terms of text, but I think the Lodish illustrations are better.
At this point I think I have three copies of Alberts stashed in various closets and trunks.
This book great for people who want more than a pop-science book but less than a textbook.
http://www.amazon.com/Physical-Biology-Cell-Rob-Phillips/dp/...
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?
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.
There are plenty of examples of asexual reproduction in plants and animals as well as complex organisms never getting old.
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.
Surely you aren't going to leave us hanging without giving us a synopsis of the top three...
#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?
#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.
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&...
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.
Also, for you to win it is not necessary for others to fail :)