The Answer to Chickens and Eggs
One regret I have regarding the demise of Uncommon Descent is being unable to continue discussion with Upright Biped, a regular at UD who believed he had an argument against the natural evolution of the genetic code, which I refer to as his “semiotic hypothesis”.
Whilst wrapped up in impenetrable jargon and idiosyncratic prose, it is/was quite a simple argument: that the first organisms could not evolve the genetic code without already having the metabolism in place and vice versa, an insoluble chicken-and-egg conundrum.
Upright Biped first publicized his idea in 2011, and it was the subject of an OP by Elizabeth Liddle (owner of this site) in October 2011.
I didn’t get involved much at the time, as discussion seemed to stick at the semiotics, whereas I thought Upright Biped’s best point was it would be impossible for a genetic storage system to evolve prior to metabolism and equally for heritable metabolic pathways to evolve without a genetic storage system. A classical chicken and egg issue.
In 2005, I encountered the late Robert Shapiro (over his alleged peer review of Mike Behe’s Darwin’s Black Box) who was a sceptic on RNA World, and he influenced me to adopt the same view. Anyway, Upright Biped continued sporadically to promote his idea at Uncommon Descent and elsewhere without much success, yet I thought the “which first, genetic code or metabolism” conundrum was a strong argument.
Not least due to the input from erstwhile TSZ regular, Allan Miller, I have since changed my mind about RNA World and now find it a plausible idea, and there is more and increasing evidentiary support for RNA World than I knew of in 2005 and 2011.
The brilliant thing about RNA World is that RNA can act as a gene, in that it can and does act as a template for replication and also RNA is capable of being a catalyst, a ribozyme, the RNA equivalent of a protein enzyme. Indeed, RNA is the catalytic heart of cellular metabolic “machinery” that synthesizes proteins, the ribosome. No chickens and no eggs, and critically, no genetic code needed.
I should put in a word for Nick Lane here, whose UCL research group have published many papers on the origin of life from a biochemical standpoint. I recently bought his book, Transformer: The Deep Chemistry of Life and Death, which I recommend as a good summary of the current state of play without being overly technical. There’s a good video of a recent talk here for a recent overview.
I’ve contributed a fair few comments to Uncommon Descent over the years, and been banned a few times, culminating in my disappearance under the pseudonym, Aurelio Smith, back in 2015, since when I’d been content to lurk until, last year I noticed Upright Biped addressing comments to an ID sceptic, JVL, promoting his semiotic argument again. JVL is a mathematician and Upright Biped seemed to have fixated on JVL to the extent of harassing him. So I registered under the pseudonym, Fred Hickson, and added my 2¢.
Unfortunately, force majeure has prevented the discussion with Upright Biped continuing so I hope he’ll consider joining us here.
Thanks for that. I’m sure I’ve visited this site of his before. It’s is full of lots of very interesting and useful information and he does a good job of putting things across, although he does seem to be a little preoccupied with James Tour.
Do we need to be religious apologists to note that from all that we observe life comes from life and the most basic unit of life is the cell. Any cell owes its existence to the fact that it can ingest non-living matter. The substances that pass through the living body maintain its form, but they are not the primal cause of that form. Form outlasts material substance. Look at your fingerprints, layers of dermis are in a constant flow of shedding and renewal, but the form of the fingerprints remain.
What reasons could there be for widely distributed relatively simple dead matter to coalesce into an organized form with recognizably living traits? One reason could be that they just happened to come together serendipitously. Another is that they could be coalescing into a pattern in a way reminiscent of sand taking up a form on Chladni Plates as seen below.
The whole reflected in the parts. The face of the frog demonstrates a principle that could be applied to life as a whole. Instead of concentrating research efforts on particle interactions, perhaps we should be thinking more in terms of the relationship between fields and particles.
I think this second option is worth pursuing. Especially when, as you say, it is an active field of investigation, and we don’t know yet how it happens.
Chladni plates now that’s magic! 🙂
I already tried that. He responded that the “biological reality” you speak of has in fact never been observed. This is basically his standard reply to any attempt to inform him of anything he rejects. I think he may be a bot, and not a very sophisticated bot at that.
Good question. My opinion is, yes we DO need to be religious apologists to believe that the very first life must be pretty much the same as anything alive today – after 3 billion years of evolution! This is why I proposed earlier that if we could take 1000 biologists back in time and keep sampling as we moved forward, we’d reach a time when half of the biologists would agree that something qualified as “alive”. I wonder if life at that 50%-agreement point would even remotely resemble a modern cell. Perhaps it would take another half a billion years before all 1000 biologists agree as to what sort of proto-life reached the point of being unquestionably alive.
I envision even the simplest possible RNA molecule as something that took a billion years to appear.
Could it be that he is motivated by his love of chemistry eagerness to search for truths?
I take it you are familiar with the old Indian tale of the “Six Blind Men and the Elephant”. This tale does not prove that elephants don’t exist.
Then why does Tour keep saying, “We don’t know”?
Yes, he believes it takes more than chemistry to create life.
But I do know what forms living cells as we know them can take.
Why would I disagree with your statement above? I haven’t inferred there is no simple to complex progression. We have only to look at each of our progressions from single cell to multicellularity to see a direction from relatively simple to complex.
Yes, we all have beliefs. My beliefs are formed by the information I have gained and how consistent I see it fitting reality.
No.
You mean, while he’s busy assuring us that natural forces and materials could not possibly have produced life without help? He seems to “know” this.
But what if he’s wrong?
Sheesh! Living cells as we know them have been evolving for over 3 billion years. Do you suppose that, just possibly, life as we know it today bears no resemblance to proto-life 3 billion years ago?
You are taking what cells look like today, assuming the precursor to the modern cell looked and worked the same, and being as amazed as Tour that anyone in their right mind would think such a cell would just kind of coincidentally form all at once and nothing first.
Reality 3 billion years ago wasn’t what it is today, and you cannot honestly force-fit unknown chemistry from back then into today’s life.
Because any enzymatic use of an RNA polymer to enable replication of the protocell would require the string to be folded in a consistent way. Even if it did chance upon a functional enzyme heterochirality of the nucleotides would inevitably fill up the protocell with more useless globules of RNA than it could handle.
Thanks, I’ll take a look.
Maybe you are right. But researching this area might throw up many surprising or unexpected results and if the private sector is willing to invest in the research, I’m all for letting them do it. Although I agree that public money would probably be better used elsewhere.
Okay, but I can see his point. I can understand his frustration about the general narrow-mindedness in this area of research.
I envision complex life being in existence from the beginning, but in a form that was too subtle to leave any deposits that were course enough to fossilize. And the more primitive simpler life forms are the ones that condensed into hardened forms the earliest. But their premature hardening laid the foundations for the later forms to appear.
Uh huh, right. Research in this area is exploring every remotely possible way life could have started except by magic. Tour wants to throw all those avenues away and start with magic ONLY. Anything else is “narrow minded”? I understand that for you, any non-god-based research, of any sort whatsoever, is “narrow minded”, but I don’t know how god-based research would be operationalized.
Why? You don’t seem able to even conceive of anything simpler that what has resulted from 3 billion years of evolution, so it MUST have been 3-billion-year evolved from day one, it just didn’t leave any traces. Right. And you say others are narrow minded!
(And I think you meant coarse, not course)
Required to? Why? Besides, given an aqueous environment with temperature between limits, ditto pH, RNA molecules will take up
consistent conformations.
What evidence supports that claim?
That sound decisively dogmatic.
That more is needed than building blindly from simple molecular precursors is a good working assumption until it can be demonstrated that they alone are sufficient.
We can’t directly observe all of natural history, so what we happen to be able to observe right now is not capable of telling us the full range of natural phenomena. We know there are numerous natural phenomena we have not directly observed but we can know they occurred in the past by inference.
That is a matter of definition. I think it is all good to define life as being cells, but that definition alone doesn’t tell us there is no pathway by which cells can emerge, or that there aren’t forms of cellular life possible that are much simpler and intermediate stages on the way to cells as we know them.
There could be reasons in physics? You know, in the same way there are physical reasons we get things like stars, planets, fire, hurricanes, etc.
The fact that life exists and is a physical phenomenon should cause us to think there are such physical reasons.
Exactly. There are physical circumstances under which those patterns in sand emerge. The same could be true about the origin of life, and as you say it is a topic of active research what those physical conditions could be.
But religious apologists say it’s all already over, that a solution will never be found because they think it’s impossible and God is required. They have no idea. We can see from the reasons they state, that they have no idea. All they can do is appeal to our current ignorance. They can state no principle in physics or chemistry that would prevent there from being a natural, physical-chemical process by which life could originate.
Well I’m glad if you don’t disagree, but many of your posts read rather mealy-mouthed to me. On the one hand you seem to both do the appeal-to-ignorance sort of fallacy (we only know of cells coming from cells, for example), yet at the same time you admit we are largely ignorant of the range of possible natural phenomena that could be described as cells, and about the range of possible natural processes that could give rise to them.
I don’t know what you’re trying to achieve in this discussion but I get the distinct impression you want to on the one hand argue for some sort of God-like intelligence being involved at the origin of life, yet at the same time you are recurrently forced to admit you actually can’t go that far from the many fallacious appeals to ignorance and hasty generalizations we get from religious apologists.
Because he wants to create a space for his belief in God, and he considers natural explanations for certain phenomena to encroach on that space. Like many religious believers he probably sees this tension and thinks something along the lines of “If God is not required to create life, or human beings, then what reason is there even to believe in Him?” And he probably doesn’t really like the SoPhIsTiCaTeD ThEoLoGiAn waffle about God creating the natural processes and then went hands-off. It’s not the sort of God he needs in his life. He needs and wants a God that takes a direct interest in his life and steers and guides things in direct and undeniable ways. In the end, he wants proof. Something tangible and obvious, not sophisticated philosophical waffling about with God being active in the distant past and then took a 13.7 billion year vacation.
And then there’s the whole crap about politics and morality. He’s a conservative, and he probably sees a connection between his conservative religious values and his religion, and he probably thinks the secular society he lives in has all sorts of immoralities in it. And all the usual stuff. The God the religious conservatives want is THE GIGACHAD testosterone male bearded dude that boldly and unapologetically creates by divine fiat, and will come and slay sinners some day and make smug, latte-drinking liberals cry and beg for forgiveness. Not this silly feminized crap that subtly set up a game of dominoes.
Look, all we need to do is go on the internet and see what religious conservatives say to each other. We can read it in the wedge document, we can hear what they say on podcasts, read it on forums and so on. This is all connected to them. Society, politics, religion, science. They despise the modern world, with people being openly gay, trans, sexually promiscuous, needing safe spaces, having mental disorders, and all that. Back in the old day women stayed in the kitchen, took care of the children, and the REAL MEN went and got the food. Oh lawd look at how girls today have numerous sexual partners by the time they’re 20. Look at how men say they’re women. And they do drugs and watch porn, and have abortions. Bla bla bla bla.
Then experiments that demonstrate life can be generated from chemistry alone will show that he is wrong.
Then some OOL researchers need to broaden their field of enquiry, because they keep trying to build polymers from the same building blocks that make up the molecules of life today. Yes, I’m sure that the diverse forms of life that inhabit the planet today are unlike anything that would have been present 3 billion years ago. But in what way do you think the building blocks have differed?
The first cells would have the same problems to overcome as modern prokaryote cells have. They would need to have a protective membrane that allowed for the selective exchange of materials, would need to be in an environment that provided a source of nutrients to use to supply energy and building material, would need to be able to replicate. If living systems were completely different from those of today, they would have needed to be able to converge on life as we know it or we would not be here today.
In what way would chemistry have been different back then? When do you think amino acids, nucleotides, RNA polymers, phospholipids and such like first appeared? Do you think any of them predated life as we know it?
In no way at all. The regularities of this universe do not vary with time.
“Chemistry” has two meanings:
One: the rule-set that governs how different molecules interact. This is invariant.
Two: the molecular environment, usually with regard to solvents, redox, pH, and temperature. This varies.
Let’s not confuse the one with the other.
Sure thing. All we have to do is replicate the precise environmental conditions at the time evolution began. Which we don’t know and probably can’t know.
Modern organisms have an enormously different environment, which presents totally different problems. Things like the makeup of the atmosphere, the length of the day/night cycles, the availability of nutrients, the presence of competitors, etc.
Why do you think my opinion matters? My own mental model, not necessarily accurate in any way, requires two things: the ability to replicate, and the replication producing something close enough to what replicated to continue the chain of replication. How close “close enough” is, I don’t know. But given those two requirements, what necessarily follows is evolution. Once evolution starts, the agencies of survival (the chain continues) and selection (the replicants that continue the chain are no less, and often more, successful at keeping the chain going) come into play. Evolution is a chain reaction.
I wouldn’t expect the initial replicants to resemble modern cells, I wouldn’t expect the most primitive self-replicators to require all those ingredients necessary today. I wouldn’t expect this process to continue on the first try – it might take thousands of tries. I wouldn’t expect any biologist to regard this process as producing “life” for probably hundreds of millions of years. I doubt anything we would regard today as a “cell” would emerge for most of that time.
DNA_Jock,
Well, sure. Was someone confusing the inherent properties of matter and energy in this universe with the the state of play under particular circumstances of temperature, pressure etc?
It happens, I guess. 😉
Wasn’t he the guy who was denied tenure because he had never published any original material, had never had a student get a PhD, and claimed the denial was because of discrimination against his religious faith? Maybe I should run out and buy the book proving that Adam and Even were real historical people?
Unless the fine structure constant varies. 🙂
It is indeed that Dr Guillermo Gonzalez. He of The Privileged Planet.
petrushka,
Is the jury still out on it?
I imagine the physical aspect of life from 3 billion years age to have been a great deal more simple than it is today. There were no conscious physical beings, no multi-cellular life, no evidence of technology. And do not imagine the single celled organisms then to be like any extant prokaryotes.
(And I think you meant coarse, not course)
Yes, of coarse I did. 🙂 Thanks for pointing my error out.
Because the effectiveness of enzymes depends on taking up specific forms. And if the nucleotides are not homochiral, the forms they take up will not be consistent.
If the RNA world hypothesis proposes strings of RNA being constructed and folded within a membrane it will also need to propose a way that ineffective RNA clusters are excreted or disassembled.
What evidence supports any claim that RNA strings can faithfully assume functional shapes?
The article at your link says the prosecutor is still searching for evidence, but hasn’t found any. Physics is fun because you can argue about the origin of existence without touching on religion.
They will not be consistent between each time they are constructed if we assume they’re constructed by random polymerization of a racemic mix of monomers. Is that the only possible option by which to get ribozymes?
Interestingly non-homochiral structures can nevertheless adopt structures and perform biochemical functions.
Yes. So what?
What other forms would OOL researchers propose for the origin of life? How would the original life form shield itself from the surrounding environment? How would it gather material so as to maintain some sort of replication? How do you propose physical life got started without some sort of separation from the surrounding environment? Any separate entity that we can imagine, I would class as a cell.
There are no laws of physics or chemistry which accounts for the teleology evident in life, let alone consciousness.
It is the interpretation of the patterns of vibrations which gives meaning to the physical activity. Physics and chemistry can describe all the physical movements of the spoken word, the vibrations in the air and its transmission through the tympanic membrane and sensory nerves. But physics and chemistry do not give any of this meaning.
The answer, “God did it”, was considered unsatisfactory to Perry Marshall, who most of us will be familiar with. So he decided that religious apologists were of no help. But neither were there adequate answers as to how life began in the first place coming from neo-Darwinists and those looking towards physics and chemistry. And so he decided to do his own research. Some of his reading material is mentioned here.
And his challenge arising from this hasn’t been met so far.
I think Lee Cronin was going to submit something in an attempt to meet the challenge but I don’t know any more than that. Did he put something forward and if so what became of it? I don’t know.
The standard proposal is that the cause or causes of the emergence of life lies in the more basic, simpler molecules and processes present in the early earth. I am putting forward an alternative proposal on the origin of life. In my opinion the cause can be found in a more subtle, extremely complex realm which exists above the physical as we know it. Physical life didn’t spring haphazardly from the less complex. it “condensed” from a more complex source which is outside the limits of the five senses and their extension available through technology.
Why would this be any less worth considering than the standard account?
Or it could just be that he looked at the processes that were supposed to have somehow combined to turn random mixing into living systems, and he might have thought to himself, “others might believe in these highly improbable series of events, but don’t ask me to believe this was how it happened.” It may be incredulity, but, with our ever expanding understanding of living systems, it is a justified incredulity. No cell would function without the bustle of highly complex, purposeful activities taking place within it.
Why would underlying physics and chemistry suddenly give rise to such purposefulness?
Highly relevant to this discussion:
https://en.wikipedia.org/wiki/Autocatalytic_set
Order is free. If order is lunch, then there is a free lunch.
Gosh, I see that piece I wrote about Upright Biped’s semiotic theory was from 12 years ago!
Well, I still stand by it I think.
With regard to RNA world: Not sure I was aware then of the Szostak lab’s work on the importance of lipid vesicles that tend to let short peptide chains in and not longer chains out:
https://molbio.mgh.harvard.edu/szostakweb/researchVesicles.html
I do think it’s an elegant idea.
I see Sabine Hossenfelder is the subject of a thread at Pandas Thumb. I haven’t taken much notice of her as she is a declared strict determinist, which position I find rather odd, but I’m tempted to get her book. If Matt Young’s review is accurate (and I’ve no reason to think not) it might be up
my street. Yours too?
Yes, I like Jack Szostak. In one exchange at Uncommon Descent, his name was brought up (in relation to aminoacyl tRNA synthetases) prompting me to email him. He replied very civilly, attaching a paper he thought relevant. (He also was fine with being quoted):
Dear Alan,
The origin of the aaRS enzymes is an important issue, because obviously coded protein synthesis by the ribosome could not have evolved if the aminoacylated tRNAs did not already exist. The paper you noted shows that RNA enzymes (ribozymes) could act as aaRSs, so that helps to some extent, in the sense that the evolution of a set of aaRS ribozymes could have evolved in the RNA World, that early phase of life prior to the evolution of coded protein synthesis. But why would aaRS ribozymes have evolved if there was no ribosomal machinery to use their products (aminoacylated RNAs) to make proteins?
One possible answer, which my lab is exploring, is that aminoacylated RNAs had some early function, prior to their use as substrates for the ribosome. For example, aminoacylation may have facilitated the assembly of early ribozymes. If aminoacylated RNAs had some such early function, there would have been a selective pressure for the evolution of aaRS ribozymes. I have attached pdf’s of two of our papers on this subject. We’re still working on this, and exploring related questions, such as the function of the first peptides.
As with all of the so-called chicken-and-egg paradoxes in the origin and evolution of life, the answer comes from breaking down the evolutionary process into a series of smaller steps, all of which can happen sequentially.
Best wishes,
Jack
The papers:
Radakovic 2021 (PDF)
Radakovic et al. 2022
This seems confused (not sure whose confusion):
Dennett’s position is that whether or not the universe is deterministic or not is irrelevant to the question of free will.
There is plenty of confusion in the world about “random” vs “unpredictable”, but then there is also plenty of confusion about the word “random” itself! In some context it means “unmodelled”. In others it means “stochastic”. In others it means “drawn an equiprobable distribution.
I’m with Dennett – I don’t think the question as to whether we have free will or not hangs on whether the universe is “deterministic” or not, but in what people mean by “unpredictability”.
And I would argue that the hidden assumption when people talk about whether something is “predictable” is that the concept of predictability is a property of the predictable-thing, not a property of the predictor. By leaving the predictor out of the equation, I’d argue we miss the very agent whose “free will” is under debate!
And as “free will” is about the actions we choose based on our predictions about the outcomes, it’s a really key omission!
Why should the birth of physical life on earth begin with entities such as lipids and coalescing nucleotides or amino acids? I think this is the preferred explanation because these things are substantial and tangible. We can imagine simple materials interacting and gaining in complexity until a point is reached when reproduction occurs. And this fits well with materialistic assumptions.
What if the physical complexity of life preceded any condensation into a liquid, gel or solid form? Concerning fields, we know that the geomagnetic field acts as a barrier between the earth and its environment. In like manner the beginnings of physical life could have involved “cells”, not as we know them today, but as field-like containers allowing processes within to be shielded from the disruptions of the external environment. In this scenario, energy precedes matter at life’s beginnings.
Why should physical life have begun forming and complexifying with the states of matter in their grossest densification?
There’s no scientific answer to the question “why?”, Charlie.
You could be correct. Perhaps life began in an environment which was principally more aeriform and energetic, than liquid and solid.
True. But for continued replication a fair bit of consistency is required.
A better question is surely: why shouldn’t it?
I mean, if there’s a plausible explanation as to how life got started in terms of known physics and chemistry, we don’t need to posit some other explanation, just as we don’t need to posit anything other than known physics and chemistry for lightning, or tornadoes, or volcanoes, or the sun rising and setting – all phenomena that people have in the past attributed to non-physical processes.
Which is not to say that having a “natural” causal explanation for something is an argument against “super-natural” causation . It just means that we don’t have to appeal to a “super-natural” causation to account for it.
And even theologically – nobody (I don’t think) limits divine creative power to things we can’t explain “naturally”. If there’s an omnipotent creator deity, we can surely grant him/her the credit of being able creating a “natural” system that will bring all these things about, without having to reach in and tweak bits from time to time to make sure life, for instance, emerges as envisaged.
tbh this is my biggest beef with ID or indeed any argument that infers a creator deity from the lack of a “natural” explanation for some phenomenon. It seems to reduce the deity to a less-than-competent creator!
Why not a deity capable of creating a system that Just Works? Works so well that it gives rise to creatures capable of gaining an inkling as to Just How?
I think, of a genuinely omniscient and omnipotent creator, we can say “no creator was required at all”.
I’m not sure she is a strict determinist. She has a video dealing withe the possibility that some constants (fine structure??) might be evolving (in the original sense of the word, unrolling). She has opinions, but I don’t think she is dogmatic about anything. She is a bit caustic toward particle physicists that want to spend zillions of dollars looking for particles for which there is no evidence.
I believe there has always been animosity between experimentalists and theorists. Don’t know if that’s what she is talking about.