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Culture War Roundup for the week of June 5, 2023

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I have connections to people doing research into the origins of life, and frankly the probabilisty-based arguments against natural biogenesis are very weak.

  • Cosmological fine-tuning isn't an argument against natural (or at least materialistic) origin because it runs into the anthropic paradox. If the universe were fine-tuned to create life, the same arguments must hold to show that it was fine-tuned to create humanity, and to create you. After all, just as a universe supporting life like us is improbable, so is your specific combination of genes and experience fantastically improbable. Any number of chance encounters (even a half-second delay in your father's ejaculation) could have resulted in a different sperm meeting that egg, and you simply not existing. Nonetheless, we also know that no fine-tuning of sperm selection was involved in the process, and God was not necessary: we can choose sperm in the lab and force a baby to happen. We can even tune the genetics of nonhuman individuals for appearance, health, and personality, and it is only ethics that keeps us from doing that to humans.

  • If you look at a specific origin of life it looks fantastically improbable, but there are a lot of demonstrations that the "minimal replicating natural system" is probably a lot smaller than a protein, let alone a full cell. All that would be required is a set of amino-acids that are stable at the temperature and pressure of oceanic vents, and which catalyze the creation of themselves. (The technical term for this is an autocatalytic set.) It has been shown that proteins are unnecessary: RNA can catalyze its own replication (http://dx.doi.org/10.1038/s41586-019-1371-4), and peptides (https://www.nature.com/articles/s41586-019-1371-4) and amino acids (https://pubs.acs.org/doi/10.1021/acscentsci.9b00520) can arise from chemical environments with very simple precursors (HCN and H2O are all you need for amino acids to arise). The search for a minimal amino acid set with the ability for self-replication is ongoing, but if any such set occured even once in the billion-year history of oceanic vents, then it would have become the primary chemical makeup of its environment. Such a set would not even need to be very efficient at first; in an environment without RNAase it only needs to self-catalyze faster than its thermal breakdown, and evolution does the rest. FOOM.

  • There is also circumstantial evidence to suggest this happened. The synthesis of amino acids and sugars is more favorable at 85C in the environment of certain porous and hydrogen-rich rocks, and this environment is preferred by certain extant microorganisms (https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2021JG006436). Most recently, I heard about a manuscript showing that of the 402 proteins which have been highly conserved in bacterial metabolism, 380 of them are highly stable at the pressure, temperature, and pH of these mineral-emitting thermal vents. (Unfortunately, I can't find it. Edit: Maybe ThenElection finds it below.)

Most recently, a friend told me about a manuscript showing that of the 402 proteins which have been highly conserved in bacterial metabolism, 380 of them are highly stable at the pressure, temperature, and pH of these mineral-emitting thermal vents.

Perhaps this? 355 instead of 380.

http://complexityexplorer.s3.amazonaws.com/supplemental_materials/3.6+Early+Metabolisms/Weiss_et_al_Nat_Microbiol_2016.pdf

The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life’s origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA’s physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway, N2-fixing and thermophilic. LUCA’s biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations. The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains. LUCA inhabited a geochemically active environment rich in H2, CO2 and iron. The data support the theory of an autotrophic origin of life involving the Wood–Ljungdahl pathway in a hydrothermal setting.

So one also has to wonder why a deity would create life in the place most likely for life to form from a naturalistic abiogenesis event instead of somewhere else.

Turns out there is another paper. Will try to send you a link by the weekend.

Oh thanks! I don't know if that's the paper that they were describing, but it sounds similar. Great find!

I think our priors on "the universe was fine-tuned to create me" should probably be lower than "the universe was fine-tuned to create life"?

Yeah, it's very important for this to know just how hard it is to get a minimal RNA self-replicator. Without a sense of that, it's hard to evaluate the relative probabilities. But, of course, the anthropic principle would just mean that it would happen somewhere in the universe, not even somewhere in the observable universe, so this part is probably less relevant.

I wasn't sure whether to put this as a reply to OP directly or someone like you, but I'll try here since you seem somewhat knowledgeable about these things.

I'm not at all an expert in these things, but my understanding was that natural biogenesis from soup-of-weird-chemicals to moderately complex single-cell life forms was pretty straightforward and plausible to happen naturally. I understand this was believed to have happened within a few million years of it being physically possible, i.e. soon after the Earth formed and cooled down enough to have liquid water. The things that was more of a head-scratcher in the how in the world did this happen without divine intervention was the jump to multi-cellular life.

How does a cell that evolved to be all about itself and it's direct descendants ever decide to team up with several other cells, which all abandon their individuality and dedicate themselves to the survival of a higher-order organism? Now that seems more like a touch of a higher power. While single-celled life originated (spontaneously?) fast, the first multi-celluar organisms took billions of years to appear AIUI, and it's off to the races after that.

Apart from what other users have brought up, there's also the fact that experiments in multicellularity appear very early on in the fossil record. Our oldest evidence for it consists of macrofossils that were discovered in the Franceville basin in current-day Gabon, in what would have been a shallow oxygenated delta at the time, and which have been dubbed the "Francevillian biota" or "Gabonionta". They are dated to 2.1 Ga, in the early Paleoproterozoic.

The emergence of this biota follows the Great Oxidation Event approx 2.4-2.1 Ga, an event where cyanobacteria caused a mass extinction by producing oxygen, something which is toxic to many anaerobes. The interaction of free oxygen with cellular components produces an oxygen radical called a "superoxide anion" which is capable of triggering a chain of destructive reactions in the cell. Aerobes are only capable of withstanding this because they possess enzymes called superoxide dismutase which essentially "neutralise" the superoxide anion (and if exposed to too much oxygen can still experience hyperoxia).

Before then, Earth had a reducing atmosphere practically free of oxygen, and the GOE changed the environment into an oxidising atmosphere, with oxygen levels being as high as 10% of their present atmospheric level by the end of the GOE. And it also seems that oxygenation is a factor which is a prerequisite for the development of large multicellular organisms. Only aerobic respiration can produce enough energy for a complex metabolism, and although there are some exceptions, few multicellular life forms are anaerobic.

The Francevillian biota are surprisingly complex considering how early they appear. There are a number of forms the fossils take. Some look like elongated pearl-strings that end in a "flower". Others look like really bulbous nipples. They exhibit patterns of growth determined from the fossil morphologies that are suggestive of intercellular signalling and thus of mutually synchronised responses that are the hallmarks of multicellular organisation, and there's also evidence that they were capable of moving around in search of food resources - there are string-like tracks at the site which might represent mucus trails.

A particularly striking feature of the Francevillian biota is that they are isolated in time. No structures similar to them are known from earlier times and the biota are conspicuously absent from the overlying layer of black shale. It is notable that their disappearance also seems to roughly correlate with an occurrence called the Shunga event. What caused it hasn't been conclusively pinned down, but it involves the creation of one of the oldest known petroleum deposits on Earth, indicating the demise of a massive primitive biomass. The Shunga reserves in the Lake Onega region of Russia alone preserve up to 25 × 10^11 tonnes of organic carbon, and deposits of about the same age and having similar carbon isotope chemistry have been found elsewhere in northwest Russia, as well as North America, Greenland and West Africa, indicating that this was a global event. The organic blooms associated with the Great Oxidation Event abruptly cease, and oxygen levels drop back down to pre-GOE levels.

In short, these fossils seem to represent a first experiment in megascopic multicellularity that arose during a period of oxygenation and subsequently died off when the environment shifted against them. This seems to indicate that multicellularity can start developing relatively quickly, and part of the reason why there was a delay is because the first experiments in multicellularity were abruptly stopped in their tracks.

Which raises the question as to what would've happened had the extinction not occurred. This was a very crucial point in the evolution of life and small changes in the initial state of a system can lead to huge downstream ramifications, so how different would life be today if they had been able to develop?

Unfortunately I don't think theism is required to explain that. The evolution of cooperation, predation, parasitism, communication, etc ("social behavior") is expected in any sufficiently complex resource-contrained environment, just as a result of game theory combined with selection. Once cells land on strategies of cooperation where they are sacrificing their own reproduction to provide resources for their siblings (in the style of the selfish gene), it isn't a big jump to multicellular organisms. According to Wikipedia, multicellularity has evolved independently at least 31 times, and complex multicellularity at least 6 times (https://en.wikipedia.org/wiki/Multicellular_organism). Since it has happened so many times, two things must be true: (1) it wasn't spectacularly improbable and (2) the genetic lines of each of those mutations has remained competitive enough to survive to this day.

I'll admit that the evolution of sexual reproduction has me stumped, though. I'm sure someone has written papers on it, and there's probably a Wiki on it, but I kind of want to puzzle over it first.

I think your understanding is incorrect. Evolving multicellular organisms once you already have unicellular organisms is probably much easier than abiogenesis; it has in fact happened multiple times independently. Multicellularity has evolved independently at least 25 times in eukaryotes, and also in some prokaryotes, like cyanobacteria, myxobacteria, actinomycetes, Magnetoglobus multicellularis or Methanosarcina.

How does a cell that evolved to be all about itself and it's direct descendants ever decide to team up with several other cells, which all abandon their individuality and dedicate themselves to the survival of a higher-order organism?

The same reason multicellular organisms evolve social behaviors - your relatives share a high proportion of your genes, so it is adaptive for genes to code for traits that improve your relatives' survival and propagation.

Indeed, most unicellular beings reproduce asexually, so they share 100% of genes with their kin, barring new mutations. Most instances of primitive multicellularity derive from cells dividing but remaining physically connected, so all cells in the colony are genetically identical.

Your first two links are to the same place.

From the Wikipedia article on abiogenesis:

“The prevailing scientific hypothesis is that the transition from non-living to living entities on Earth was not a single event, but a process of increasing complexity involving the formation of a habitable planet, the prebiotic synthesis of organic molecules, molecular self-replication, self-assembly, autocatalysis, and the emergence of cell membranes. Many proposals have been made for different stages of the process“

That sounds very complicated. Many different parts are involved with many different mechanisms, which had to be in place at the right time in many different stages.

Your first bullet point only functions as an explanation of fine tuning if we assume in advance that the (or “a”) multiverse hypothesis is true. It’s unlikely that I would result from my parent’s act of conception, but billions of acts of conception were happening before I was conceived. But we don’t have an analogous knowledge of there being billions and billions of universes with different parameters and physical laws, exhausting enough of the possibilities to eventually create life.

Should I explain why I find the multiverse hypothesis less plausible than theism as an explanation of fine tuning, or do you already agree with me that it is?

Your second bullet point calls for some subject matter expertise that I obviously don’t have. You mention that RNA can be self-catalyzing. I suppose this raises the question of “just how hard would it be to create RNA by chance circumstances.” How complex is RNA in terms of number of parts and mechanisms?

To your third bullet point, I’m not as surprised that organisms which were already created in such environments can now live in them as I am by the suggestion that they were created in the first place. I agree that this is evidence in favor of their possibly being created in them, though, of course, because if it was impossible for an organism to live in such an environment, it would be impossible for them to be created in them. But anyway, I’m not sure this is a strong item of evidence in favor of abiogenesis and don’t weight it very heavily.

I don’t understand this sentence:

“ of the 402 proteins which have been highly conserved in bacterial metabolism, 380 of them are highly stable at the pressure, temperature, and pH of these mineral-emitting thermal vents.”

What are proteins “which are highly conserved in bacterial metabolism?” And why is this significant?

I would love to chat with your friend, please consider giving me a point of contact. (If it matters, I’m not a Christian, I’m a weak, almost-reserving-judgement-but-not-quite deist with a sense that there is something to the cosmic fine tuning argument for life.)

Your first bullet point only functions as an explanation of fine tuning if we assume in advance that the (or “a”) multiverse hypothesis is true. But we don’t have an analogous knowledge of there being billions and billions of universes with different parameters and physical laws, exhausting enough of the possibilities to eventually create life.

No it doesn't depend on a multiverse at all. (Does all statistical reasoning require multiverses to exist?) It only requires a belief that the universe we see is one example of the set of all possible (imaginable) universes.

It’s unlikely that I would result from my parent’s act of conception, but billions of acts of conception were happening before I was conceived.

You don't seem to be understanding the implications of the anthropic principle. For every human that is conceived, there are billions of sperm which are thrown out, and there are even more (billions upon billions upon billions(*A)) of potential genetic combinations which could happen but don't. Had the sperm which became you not fertilized the egg which became you, you would just not exist to have this conversation. Full stop. The probability that you in particular would exist is just too small. The number of possible humans is of similar magnitude to the number of atoms in the universe.

(A) The human genome has 3,054,815,472 base pairs, and two random humans might differ by up to 0.6% of their genome, so we can say that two random humans are separated by about 18M base pairs, whereas the rate of mutation in human DNA is ~2.5×10^(−8) per base per generation, so each human will have about 76 new mutations. To simplify a bit (assuming mutations are evenly distributed, which they are not, but you will see that it doesn't matter), this means the possible range of single mutations that are still considered human is bounded between 4^76 = 5.7 x 10^45 (all mutations between humans occur on the same 76 nucleobases) and 18M choose 764 (any of 76 mutations could occur anywhere in the genome). Either way, the number of possible humans is really big, so if you were not born when you were born, you would never have been, at least not in our light cone.

Your second bullet point calls for some subject matter expertise that I obviously don’t have. You mention that RNA can be self-catalyzing. I suppose this raises the question of “just how hard would it be to create RNA by chance circumstances.” How complex is RNA in terms of number of parts and mechanisms?

This was addressed by ResoluteRaven below. The answer appears to be "not very hard", and that was also the gist of the paper I linked above about combining HCN and H2O to make amino acids.

if it was impossible for an organism to live in such an environment, it would be impossible for them to be created in them. But anyway, I’m not sure this is a strong item of evidence in favor of abiogenesis and don’t weight it very heavily.

This is poor logic, because it can be continued ad infinitem to explain anything inconvenient for your position, and makes your position unfalsifiable. (You might say it proves too much. If your position is unfalsifiable, then it is not testable. To put it another way, suppose that 50 years from now scientists were to demonstrate abiogenesis in the lab. You could still argue that they merely discovered the method by which God created life. How convenient, considering it would also the method by which life could have arisen without a God at all.

In the modern day, I've heard creationists arguing on behalf of the position that the earth is only 6,000 years old. When confronted with the fact that fossils can be dated to millions of years ago, they fall back to the argument that if fossils appear to have been buried for millions of years, they must have been placed in the rock formation by an intelligent designer to appear that way, so as to trick modern-day humans. This argument can of course be extended to argue that everything before any arbitrary moment in the past has been retconned, and God just created a world to look convincingly old. If your Designer is all-powerful, I guess that might make sense to you, but it is equally valid to suppose that the Designer didn't do much more than set some parameters on the Big Bang and press a button to see what would happen.

What are proteins “which are highly conserved in bacterial metabolism?” And why is this significant?

I hate to be trite, but another commenter below has explained this already. I may suggest that if this topic matters to you (or is truly critical to maintaining your faith), then you try reading the first few chapters of a textbook on molecular biology for the relevant background. You don't have to read very far. I got to chapter 3.

I would love to chat with your friend, please consider giving me a point of contact.

I'm really sorry, but my friend has spent an inordinate amount of their career arguing against intelligent design. Probably about as much time as they have spent doing biological research. Given that the return to humanity is much higher if they spend their time doing research, I really don't want to provide them access to more ideas from intelligent design.

No it doesn't depend on a multiverse at all. (Does all statistical reasoning require multiverses to exist?) It only requires a belief that the universe we see is one example of the set of all possible (imaginable) universes.

It does require it, I think.

One draw from a haystack vs 100000000000000 draws will have different chances of hitting the needle.

If only one universe exists, and most possible universes are very non-conducive to life, it should be surprising to us that we exist, since that seems so unlikely. At that point, we should be looking for explanations that might make it more likely, like multiverses or theism, or it being necessary that the universe be that way, or actually, most universes are conducive to life after all. But we can't just say that in worlds where we woke up it would look like worlds where we might be able to wake up, because the really surprising thing here isn't that but why the hell did we wake up at all, if we are indeed in the only universe, which should by every expectation be very hostile to life. (note, I'm assuming those two things, not asserting them here)

How complex is RNA in terms of number of parts and mechanisms?

RNA is composed of one sugar molecule (ribose) and 4 nucleotides in various arrangements. These have all been found in meteorites, indicating that they are likely abundant throughout the universe. I would expect them to come together spontaneously, possibly even within those meteorites themselves shortly after they formed while they still contain pockets of liquid water.

What are proteins “which are highly conserved in bacterial metabolism?” And why is this significant?

To a biologist, "highly conserved" means something between "very old" and "nearly unchanged from the earliest times," depending on context. In this case it is closest to the latter. The oldest proteins being stable in hydrothermal vent conditions being evidence that bacteria originated from there is similar to how linguists can determine the homeland of a proto-language by the words for animals and plants that are shared across all its descendants (e.g. if the word for "pine tree" is shared by all of them but not "palm tree" then they probably didn't come from the tropics).

The minimally replicating natural system would need:

  1. Some way of reproducing dynamically in response to mutations. It can’t just be able to reproduce itself perfectly, but otherwise not at all; it needs an information carrier that can vary the assembly instructions in ways that would result in multiple different possible viable offspring. Otherwise, evolution would’ve never happened, because there would only have ever been one organism, or the one organism would have died very early on.

  2. Some machinery for assembly of parts,

  3. a way of reading the instructions,

  4. An outer membrane that holds all of this stuff together,

  5. A way to catalyze it’s own chemical processes

How is RNA sufficient for all of the above?

RNA molecules capable of replicating themselves and other RNA molecules are already known to be possible. The beauty of RNA is that it can both carry information and also catalyze chemical reactions, including the synthesis of other RNA's, and the oldest bit of active chemical machinery within our cells (the ribosomes) use RNA rather than amino acids for their key activity (protein synthesis).

Mutations will occur spontaneously because the replication is inherently imperfect, for RNA more so than for DNA because the molecules are less stable, so it's not something that needs to be accounted for separately. A membrane is not strictly necessary as long as all the components are close enough together. Nearly all of the cellular machinery still works if you take it out of the cell and this is commonly used in the biotechnology industry when we only care about one or two enzymes and not the whole system.

The trick with the anthropic argument is that it doesn’t rely on multiverses or even infinities. Just that A -> B. Given that we are making observations and philosophy instead of choking on vacuum, we must be in conditions that support such activities. It doesn’t explain why you were born to your specific parents, but it does argue that those parents can’t be virgins.

I think it would require multiverses. Yes, it proves rather trivially that you are in the kind of universe in which life exists, but it doesn't provide reasoning for why we should expect that universe to exist. A multiverse should be capable of providing the second, assuming that the multiverse is the sort of multiverse that can do that, I would think?

People mean different things by “the anthropic principle” so let me clarify what you have in mind. Sometimes the idea is supposed to challenge the fine tuning argument by pointing to the multiverse and invoking the law of large numbers. That argument works if you have some reason to think the multiverse exists and is more probable and theoretically virtuous than theism.

But I also hear much more naive and confused sounding appeals to the anthropic principle. For example, sometimes people seem to be suggesting that because a phenomenon involves the creation of observers, the phenomenon requires no explanation, which is silly. Imagine if I prayed for a parachute while falling from a plane, one spontaneously manifested out of thin air and deployed to save my life, and I reflected afterwards about why that happened. I conclude, “well, I wouldn’t be here to ask the question in the first place if that didn’t happen, so there must be no explanation needed.”

Or imagine saying the theory of evolution is dispensable because “if it didn’t happen we wouldn’t exist. We wouldn’t be here to wonder about it if not, so what is there to explain?”

I’m not trying to use the Anthropic principle as an argument for any process over another. No, it’s a refutation of the fine-tuning premise in general. Good conditions aren’t evidence for or against an intelligent designer.

That means I have to answer “no” to your question, because we’d have to see the “seeming improbability” no matter how it came about.

Suppose you were sentenced to death by firing squad but a thousand marksmen ten feet away missed their shot. Would you say you don’t have to explain how this happened (by design, presumably—a conspiracy not to kill you), because being in a position to ask it requires already existing?

If this is still supposed to be about the unlikeliness of abiogenesis, then this analogy would only make sense if you believed that the conditions necessary for the arising of life happened only once in the entire history of the universe. Then it really would be a miracle.

But it's more like there are a bajillion people about to be executed, each with their own thousand-strong firing squad and we know that at least one of them survived. With so many tries, one of them could have gotten super lucky. (And of course, we don't really know how many marksmen you need to postulate to match the probability of abiogenesis happening in some small volume of the primordial soup at a particular point).

(If it's about the wonder of the fact that our universe can support life at all, then I'm fine with answering "I dunno" while insisting that there's no justification for jumping from "I dunno" to "therefore, God.")

This is correct.

The level of analogy for which he makes sense would be ways the physical laws of the universe itself is fine-tuned for life. As long as there are no varying-laws multiverses, then there's only one, not a bajillion.

I'll also note that the firing squad example makes this more complicated to me. I was reminded of Joe Carlsmith's SIA vs SSA series on anthropics, which I don't remember well enough to be able to give truly informed opinions.