A biochemist’s view of life’s origin reframes cancer and aging
quantamagazine.org
quantamagazine.org
Looking forward to reading Lane's work and seeing how it compares. I'm particularly interested in hypotheses and theories about abiogenesis and I remember being struck by the elegance of the Wächtershäuser paper when I first read it, even if it was over my head at times. Hoping for a similar feeling here!
Made me wonder: if the theory was true, how would this change our view of life being created on other planets?
1. Oceans were absolutely saturated with reactive metal complexes, particularly including iron. A billion years later oxygen poisoning started, and it all oxidized and precipitated out, but life was established by then and (some) survived the catastrophe. So, the chemical environment was very different than is easy to reproduce today, and full of stuff that would have catalyzed all kinds of reactions that go very slowly without.
2. Oceans were also absolutely lousy with nucleic and amino acids, and random RNA sequences. An RNA that copies other RNAs it bumps into was nothing special, but when two of them bumped, suddenly in a (geological) eye-blink the entire ocean was teeming with their highly-optimized descendants, along with any other RNAs that proved helpful to have around. Natural selection was already hard at work, no cells or genes needed.
So that is the environment that life arose in, utterly unlike anything found anywhere today. Any random drop of water that got caught up in a membrane would be full of those RNAs that had proven most useful at copying, and also all those random catalytic metal complexes.
I gather that nowhere in the natural world do we find any cellular process that creates a membrane from scratch; all everywhere grow from bits pinched off from membranes already on hand. Arguably, what is really essential to species is being made of bits extended from the first membrane that wrapped enough replication machinery to do the whole process inside. It would need to have been better at allowing loose nucleic acids in than letting assembled RNAs out. Life is bags of water and stuff that pack the bag with catalyzed reaction products and can extend the bag as it fills up. When a lobe gets pinched off with enough stuff inside, off it goes.
Later there would be genes, and metabolism.
I can recommend the author's book 'The Vital Question', which dives into some hypotheses addressing precisely these considerations in much more detail.
The major problem is concentration. Even if you invoke geological timescales and a favourable redox environment, concentrations of reactants would be rapidly diluted in the ocean. Since there are quite a few dehydration reactions in the synthesis of oligonucleotides (like RNA) and proteins, when diluted in the ocean, the plentiful water drives the equilibrium back towards the starting materials. Without some mechanism to accumulate the reactants to form the first R/DNA, it remains an open question how the process got started.
There used to be a homeostasis-first theory—to compete with the metabolism-first and oligonucleotide-first theories—but it hasn't gained a lot of traction as an independent theory.
Catalysis lowers the activation barrier, sure, but you still have to contend with the thermodynamic equilibrium in the absence of the catalyst, in addition to subsequent degradation by light, etc.
> ocean full or random stuff that we can't actually imagine today
We probably can't ever really know what was in the Earth's ocean before life, but quite a bit of research has been put into figuring out some plausible conditions and then testing the hypothesised pathways put forward by the leading theories under said conditions.
All this is to say, yes, clearly abiogenesis occurred, but there are major gaps in the leading theories that are interesting and testable. I don't think it's very useful to gloss over the details, even if in the end the best we can hope for is a plausible pathway given a specific set of assumed conditions.
I imagine one that splits a molecule could work only or mostly in the one direction, if to go the other way would require both constituent parts to come together at the same time. But that is an example favoring entropy.
What would one that favors assembling molecules look like? A ribosome seems like the extreme example; those don't disassemble proteins. But is a much simpler example very unlikely?
I don't want to minimize the gaps on our knowledge. We don't know how any macromolecule polymerization occurred. But I also don't want to maximize the gap. Those kinds of reaction are completely mundane and occur on a huge variety of environments. The fact that we don't know what environment it was doesn't mean it's an outwordly phenomenon. And adding just a few of those mundane reactions is enough for life to appear.
(Anyway, I question your certainty about the concentration of water on our primordial oceans. Abiogenesis research usually uses a model of water origins that gives a precise estimation for its amounts, but not only we know that this model is wrong - water is cycled by geologic means like any other mineral - but we also do not have anything with near that amount of precision to the other substances that composed it.)
On a more germain topic, this is a more attractive theory to me, though I don’t buy the criticism of the “just happened on the surface” argument: the fact that we see the result of some random selection doesn’t make it more or less likely — the same would apply to the formation of our planet!
The first part of my comment was more a lighthearted comment on magazine photography + a little brain quirk.
I just finished 2005's "Power, Sex, Suicide: Mitochondria and the Meaning of Life", which sets the foundations for some of the thesis in this article while trying to identify just how mitochondria got wrapped up with eukaryotes.
I should revisit some of his earlier works, but I get the feeling some of the questions about gaps in knowledge & research in those books would be covered off and answered in his later works. (I could be totally off the mark there, however.)
How the Krebs cycle powers life and death - https://www.youtube.com/watch?v=vBiIDwBOqQA
Why is Life the Way it Is? https://www.youtube.com/watch?v=gLcWfecmZhE
[0] https://www.livescience.com/turtles-dont-age
[1] https://blogs.unimelb.edu.au/sciencecommunication/2019/10/13...
https://www.preposterousuniverse.com/podcast/2022/05/23/198-...
also on YT https://www.youtube.com/watch?v=9IZ_CVu2M68
First, cell membranes channel electrical charges between external acidic environment with interior basic environment to catalyze hydrogenation of hydrogen on a carbon skeleton.
Well, that's succinct. But also, that layering is perhaps a recapitulation of acidic oceans on top of basic on top of basic mineral floors, so that cells have the same schematic layout as oceans on planets, with the sea floor as catalytic membrane.
Beautiful
Metabolism before genes makes perfect sense. Defining life is silliness as far as I'm concerned, but DNA is a very specific mechanism of reproduction whereas metabolism is more universal basic concept. Or so it seems to me...
Whoever wanted to disambiguate vs Kings College in 1836 presumably.
Birkbeck college which is also a constituent of the university of london (like UCL) is a contemporary and focussed on technical education for working people, with teaching at night so they could both work, and study. It also has Jeremy Bentham in it's DNA.
(worked at UCL in the 80s. my mum went to the slade school of art there in the 1940s. its a great place)
Well I’ll be damned… they actually put his remains on display. How gruesome.
https://www.smithsonianmag.com/smart-news/philosophers-dress...
ancient times - Oxford and Cambridge universities come into being, composed of multiple independent and mostly equivalent colleges (ie all teaching the full range of subjects)
1826 - London University founded
1829 - King's College founded
1836 - London University and King's College combine to form the University of London, comprising two colleges roughly on the Oxbridge model; London University is renamed to University College
University College may be a silly name, but what else would they have called it? London College? Hardly better.
Note that University College, Oxford and University College Dublin are called that for completely different reasons.
In the UK, a university is a collection of semi-independent colleges, each with their own students and faculty and their own departments for all the various subjects. A university college is the founding college in a university. (University College London is a constituent college of the University of London.)
So the name might sound comically redundant to Americans, but it makes sense in the British system.
"What team are you?" "Manchester" "Where do you come from?" "Manchester"
"What team are you?" "The Angels" "Where do you come from?" "The Angels"
no they're not, generally colleges focus on teaching and undergraduate programs, and universities revolve around research and graduate schools. In some cases, there are colleges within universities, particularly in ye olde schools.
I think it is probably very common for Universities to have college faculties. They also often have Halls, Lodges, Schools, and so on, under the main University umbrella.
Generic tangents are much less interesting than specific responses to an article (or specific tangents!) because the more generic a claim, the more that (1) there is less that is meaningful to be said about it, and (2) the more repetitive it is. That's a really bad combo for a site that's trying to be good for curiosity.
https://hn.algolia.com/?dateRange=all&page=0&prefix=true&que...
After that, anyone is free to conclude that we don't know where it comes from, or a designer did it, and who is this designer. But darwinian evolution is dead as a "science".
The reason phylogenetic trees can be so thorough is because evolution is real.
- a computer code that makes a full functionnal self-replicating cell (DNA is a code even for darwinian evolutionnists) - a kind of cd-rom to store the code - a kind of cd-rom reader to read the code - a kind of cd-rom printer to reprint the code for the next generation - a kind of 3D printer to interpret the code and manufacture the proteins - and of course 1 billion times more complicated than that - keep in mind that a functionnal protein has 1/10^500 or so to appear by pure chance in a mutation (the universe has 10^80 particles)
Nike Lane theory and others are "just so stories", there is no science neither any proof behind it. How an engineer can accept this ? This is just pure faith in a materialistic kind of creationism. Look at the flagelle rotary engine architecture, Michael Behe Intelligent Design theory, and Pr James Tour lectures on YT.
These are two different things though, separated by maybe as much as one billion years.
Structures in living systems often came about by such a process. Features that had made intermediate forms adaptively useful are not in evidence, but sometimes appear in related species, or in embryonic development. Evolution cannot plan for the future, but it is happy to discard what is not useful anymore. It is our challenge to imagine the structures discarded, and how they were useful in that form, and scientists' to find evidence preferring one path of development over others.
Anyone can give up and say "God did it" on any day. Others do not give up, and biology as it stands today is a product of not giving up. We might wonder how it could have got here, but it too has come through many intermediate forms, with much since discarded.
Also the identical solutions that appear in different species are named "convergent evolution" (e.g. the eye of vertebrates and cephalopods); it is by no way a validation of gradual evolution because chance could not build the exact same solutions. It is on the contrary a proof of design (reuse of building blocks)
"Irreducible complexity" is specifically what the arch principle answers. The uncompleted arch along with everything holding it up is of immediate value, as it is, for maximizing reproductive fitness; it is our task to understand how. Later, the completed arch has value as, possibly, something entirely else, where the scaffolding did not and fell away.
Nature doesn't care what the arch or its intermediate forms were "for". Any structure may be used in any way that aids fitness (or, often, not). Insects' extra wings become protective wing covers. Legs that were once fins may walk instead of swimming, or fly, or type. T. rex's arms, and ostrich's, waggle uselessly.
The evolution of eyes has been traced from eye spots through to completed eyes, and each intermediate stage is in fact better for reproductive fitness than the previous one. The form of eyes is dictated by their use, but human eyes' present form is decidedly inferior to squids'. (Ask your God about that?) It has lately turned out that the basis for eyes was already in the last common ancestor of squids and us. It has been a very long time since eyes were a persuasive example. Maybe read up?
About the eye, which common ancestor to squids and vertebrates is it ?
You are aware that all species that existed 500 million years ago are extinct, leaving only their descendants? That would include our common ancestor, leaving squids, and us, and fruit flies. (Some coeval species left fossils, though probably not that one.) But the gene that places our eyes, inserted into a fruit fly chromosome at a place dictating growth of a body part, grows an eye there. A fruit fly eye, of course.
Careful: claiming software you wrote is divinely inspired will not go over well at code review, particularly if you insist it doesn't need to pass tests.
So, a series of not-excessively-harmful monkey-patches accumulate under stringent testing to significant improvement. We don't need to guess about that: it has been demonstrated by laboratory experiment, which you may read all about if you care to. Or don't, and continue parroting Behe's sterile talking points long after they have been thoroughly discredited.
It is not 'pure logic' because your analogy is flawed - biological systems are not arches or mousetraps. Imagine a system as a triangle of three components that all rely on each other. The vertices of the triangle are component (proteins, organs, whatever) and the edges are 'dependencies' of some kind.
Now add a fourth component, dependent on some (or all) of the others. Now remove some of the edges until you have a square (or 4-cycle). Now this system is 'irreducible' as breaking the dependent links breaks the cycle.
Essentially, all biological systems have a 'chain' of previous versions that were functional and evolvable into the next version. This is only possible because these systems have redundant parts, and flexible associations. For example, many proteins 'moonlight' as alternate roles within an organism.
"Since biochemistry darwinists have to work and to prove now!" - This sentence doesn't even make sense. It is Intelligent Design advocates like Behe that are making the claim that these systems "could not" have evolved.
As another commenter said, this is the 'Argument from Ignorance' : "We do not know how it evolved so it could not have!". We know the structure of biological systems in more and more detail. We know how they change at the smallest level. The theory is fairly basic : redundant, self-assembling, flexible systems can change through gradual evolution.
Gould would talk about 'rewinding' the tape of history. There's no way to go back in time and see for sure what previous systems looked like. However that in no way means the tape itself does not exist.
Nature has no problem building an arch through a long series of small changes, no keystone required.
The creative power of randomly mutated code is, again, easily verified.
Changing a single bit in computer code is very likely to have an arbitrarily large, commonly fatal effect. Changing a single base in a gene rarely does. But a lot of bases changed is likely to have some effect; the more changes, the more effect.
What critics of natural selection always miss is that the set of small changes between one state and another, in a breeding population, do not need to happen one after the other. It could take hundreds of steps, but they all may exist scattered through the population at the same time, and can over just a few dozen generations propagate to all, when conditions favor that; or even fewer if lacking most is fatal.
Bacteria need a lot more generations to evolve, because they don't swap genes around much. But their generations are very short. Some mutations they do swap around, particularly antibiotic resistance, and ability to infect a new host, via plasmids. Anthrax normally lives in soil, but picks up virulence genes from plasmids it happens upon.