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.
Apparently not as much as he thinks:
How do you know that?
You made assertions about the complexity of the first cells, then admitted you didn’t know. Then you asserted particular molecules are required, then admitted you don’t actually know that either.
Is this one going to be different? Place your bets now!
I had never heard of Tour, so I watched that video. Imagine my surprise to learn that Tour’s claims rest on religious motivations. Essentially this isn’t a debate between qualified researchers, it’s a debate between atheist and religious researchers. Charlie places great faith in the religious guy.
Flint,
The religious guy has a distinct advantage as there is no coherent model for how the origins of unique animals came into existence and all that can be claimed from the atheist world view is that the existence of living organisms is a brute fact.
“So magic did it” is a “distinct advantage” in Bill Cole’s dreams.
Yes. James Tour is, when speaking on the status and merits of origin of life research, first and foremost functioning as a religious apologist. He is not particularly knowledgeable about the field, and his religious biases makes him overestimate his competence when the topic moves to adjacent fields to his own of synthetic organic chemistry. That’s why, for example, he so pathetically botched his analysis of Benners 13C NMR spectrum.
That’s not the only topic where he’s recently made a fool of himself. He’s also declared with much confidence that biomolecules can’t last for millions of years, leading him to completely misunderstand and mischaracterize the field of molecular paleontology.
Check here how he completely botches the field of biomolecule preservation too:
Rumraket,
What you label as “magic” is the product of intelligent cause.
Intelligence way beyond human intelligence. This is being revealed in this discussion as humans may never be able to make living organisms other then basically copying the cellular architecture of existing organisms.
How do atoms have the ability to assemble into living organisms? Is this what you call “magic”?
The idea of God is admittedly a huge concept and above the imagination of many here but the universe we live in is also a huge concept and detailed explanation of its origins are unexplainable from our perspective and will perhaps never be understood from an earthly perspective.
What you mean by “intelligent cause” is just magic. Something that just occurs because God speaks magical words, or just magically wishes it to be so. In every sense we understand the word magic to refer to some hypothetical ability to supernaturally cause something to occur, what you mean by “intelligent cause” in relation to the origin of life, matter, the universe, consciousness, or whatever else, it is in every imaginable way indistinguishable from what we mean by magic. You are positing literal magic. Stupid, childish, Santa-Clause, Tinkerbell-level, wand-waving Harry Potter magic. POOF. ALLAKAZAM. A worldview for children and idiots.
It is as imaginary, fictitious, nonsensical, and ridiculous as The Force wielded by Darth Vader, or Luke Skywalker, in the STAR WARS franchise.
Well, nobody has a clear idea of how life came to be. How do you know? It’s all speculation. Personally, I prefer to leave room for doubt rather than to believe anything with certainty. Besides, don’t you realize how unsuitable modern physics is for the scientific investigation of biology? Thus Charlie sows doubt about the fruits of scientific research in his many comments littering this site.
Except when scientists make statements that Charlie finds appealing. Then, suddenly, authority and credentials matter.
The way I see it, people are curious about how things work, and they crave a plausible explanation for everything. But when there is something lacking much of an explanation, some people think “nobody knows this, but maybe we can find out” and other people think “goddidit.” That religious group somehow seems completely satisfied with the adequacy of this “explanation”.
But some things are actually understood fairly well, though they are often complicated and the evidence is often indirect. In this case some people think “I should look this up, and study it for a while, and at least get a feel for what’s going on.” Other people think “this knowledge threatens my faith, so I’ll chalk it up to ‘intelligent cause’, and pretend I understand it now.”
For poor Bill, his god is necessary for him to understand almost everything, since his actual knowledge is deliberately kept to a minimum.
True enough, but studies interested in getting from a prebiotic earth to life as we know it must, at some stage in the process, traverse well understood obstacles.
And that is why Tour has never said that that life could not originate by a physical-chemical process. What he is saying is that it could very well be possible to get from an earlier prebiotic state to some form of life as we know it. But the steps needed for this to happen cannot just be assumed. He is saying, “show us the chemistry”, and if this can’t be done we have to admit that we don’t know how this could have happened.
I haven’t seen Tour say if we don’t have homochirality we can’t have a form of cellular life. He does say it is necessary for life as we know it. For instance in this video Donna Blackmond from the Scripps Research Institute says that finding a prebiotically relevant version of the Soai reaction is the “Holy Grail” in studies probing the emergence of biological homochirality and so far they haven’t been able to find one.
The Soai reaction did achieve a bias towards homochiral products but only in an environment that would not be found on the prebiotic earth.
In the RNA World scenario, the forms obtained by folded strings of ribonucleotides need to be consistent, and that is why homochirality matters and why there is so much emphasis on finding possible ways it could have been achieved in order for life as we know it to get going. As seen below it’s the old chicken and egg conundrum.
Within life today maintaining chirality is essential to life and there are enzymes whose task it is to repair chirality faults. From here
Inorganic chemistry favours heterochirality and is always tending towards equilibrium, and so this is one more example where living systems have to come up with ways to constantly maintain the inequilibrium. This isn’t just a problem for OOL scenarios, it has been a problem throughout the history of life.
Yes he has. He has an entire essay saying exactly that, called “Life should not exist, this we know from chemistry.” That is as unambiguous a claim that a physical-chemical process could not possibly produce life as one could make.
Look, just read this okay?
“LIFE SHOULD NOT EXIST. This much we know from chemistry. In contrast to the ubiquity of life on earth, the lifelessness of other planets makes far better chemical sense. Synthetic chemists know what it takes to build just one molecular compound. The compound must be designed, the stereochemistry controlled. Yield optimization, purification, and characterization are needed. An elaborate supply is required to control synthesis from start to finish. None of this is easy. Few researchers from other disciplines understand how molecules are synthesized.”
This is Tour saying life cannot emerge by chemistry, it has to be designed, and that he knows this from chemistry and we can take his word for it on his authority as a chemist. So there’s only one option, God must have designed life.
Please do not ask us to pretend to be so stupid we don’t understand this is the conclusion he intends to leave. He is saying it.
In that article he attempts to build a case that leads to the conclusion in his title, that life could not emerge by physics and chemistry.
By some giant mystery all his creationist fans come away from reading his essays and watching his talks with the impression that life’s origins is impossible. And so therefore God.
They say science has shown it is impossible, and when asked what reasons they can provide for thinking that, they refer to James Tour. This isn’t an accident. He is saying that. He has directly stated it in his essay, though he rarely does get that explicit in his talks exactly so clueless dolts like yourself can then sit here and pretend he never said it.
But he said it. How does he know any of those things are required for life’s emergence? He does not. Nowhere in that article does he show or give any reason to think that he knows, that the space of unknown interactions between physics and chemistry has been experimentally exhausted, can be predicted from first principles, and that none of them lead to life.
That’s because he actually doesn’t know, and because that space is still unimaginably vast and unknown. Because in fact researchers are still routinely surprised to discover that chemistry they thought couldn’t occur, did anyway, for reasons they don’t understand. Tour’s understanding is of zero value or consequence, he can’t predict the results of experiments any better than other chemists just as skilled and intelligent as he is, and they can’t predict the results either.
He’s a religious apologist when speaking on the topic of the origin of life, not a scientist. He can go synthesize his little graphene cars, it doesn’t mean he knows jack or shit about abiotic physical and chemical processes.
So what?
The building blocks of life as we know it are carbohydrates, nucleic acids, lipids and proteins. So even if we were to posit some other prebiotic building blocks then there remains the problem of how we ended up with the ones we see today.
The question of interest is, how did a purported prebiotic world produce the living world we observe today?
That is so true. There may be forms of life in our midst that we do not have the necessary senses and capability to perceive.
And if researcher do manage to produce any form of life different to our own this will demonstrate that intelligent beings are capable of creating life from basic matter.
And so what?
Yes, that is the topic of research into the origin of life. How did we get to here? That doesn’t mean the things observed now were required from the very beginning. You’re a human being, not a worm. Somehow worms can live without arms and legs. Sponges can live without a beating heart. And so on.
Sure it will demonstrate not only that, but also if they are creating a natural environment in a laboratory setting, it will also demonstrate that that natural environment can do it. The ultimate question is how we get life without already having it. That means there must be some sort of condition under which life can arise, and the field is trying to find out what that is.
Again, some researchers are pursing the hypothesis that certain biological molecules known from present life (such as RNA) could have been produced directly in some primordial environment(and they’re trying to figure out how that could have happened), and other researchers are dubious about the pre-biotic relevance of RNA and are pursing models where evolution began before RNA in some more primitive replicating chemical system(and they’re trying to find out what systems those could have been and under what conditions they could arise).
This idea Tour is trying to construct, that he sells to his religious audience, is that this search is already over, that we already know enough to say it can’t happen, and that God is necessary and life’s origin is impossible without divine intervention. Yes, he does in fact say that. All his fans agree that is what he says. They all come away from his talks and reading his material thinking he has shown that. That is not an accident. He intends for them to get that impression.
And, luckily for us, it also allowed for life to wake up and look back on itself. Isn’t it wonderful what chemicals can achieve when they cooperate!? 🙂
That is a very long time from a human perspective, even longer from the point of view of a mayfly. But then again, we are limited and time is relative. What is a billion years to the life of a star or a galaxy?
Who is this Professor Dave character? Is he a teenage schoolboy posing as a professor? It certainly sounds like it.
James Tour answers his criticisms here
There is an interesting conversation near the end where he gets Lee Cronin to agree with him that they don’t know how life arose from non-life. So instead of promises and waffle all Tour is asking for is proposals that contain the processes of chemistry that can be discussed and argued over.
I know that it’s too complex for any scientist to have figured out.
This discussion has two aspects. One is about the properties of life in general, not just earthly life as we experience it here and now. But how would any form of life imaginable be possible. The other is about any proposed path taken to get to this life we experience here and now. The farther back we investigate the more difficult it becomes to explain.
You are criticizing the purported philosophical underpinnings of Tour’s arguments while ignoring any purported philosophical underpinnings of atheists. There are plenty of religious believers who are quite happy with naturalistic proposals for the OOL, but, realistically, naturalistic proposals are the only option for athiests.
According to RationalWiki
He critiques the likes of James Tour and Gunter Bechly who trade on their scientific credentials to promote misleading views that seem to be driven more by religious beliefs than the current state of scientific knowledge.
So what? That’s why it’s an active field of investigation, because we don’t know yet.
But as already explained, Tour functions as a religious apologist trying to sell the idea that it’s impossible, while generally trying to avoid stating it explicitly. Though he has in fact done so on a few occasions as shown earlier.
Rumraket,
I am proposing that intelligence is fundamental to the universe. This is what the evidence is telling us.
You and Flint are creating a straw man argument called “magic”. When straw man arguments are required to defend your position it maybe time to rethink your position.
From your standpoint a cell is “magic” as we cannot explain its origin. Since your paradigm is that only natural explanations are possible you end up wasting a lot of time reading and siting silly speculative explanations.
Since “magic” is your paradigm you are essentially looking at the evidence from a single point of view.
I’m not criticizing, I’m observing his motivations and the theological basis for the position he’s taking.
I would say naturalistic proposals are the only options AT ALL. Granted, how life originated on earth is a gap in our knowledge, which the religious believers are quick to fill with their god(s). I’m familiar with several religious traditions, with different numbers of gods, who are always filling gaps in our knowledge with confident insertions of their gods.
It always puzzles me why the god-botherers are incapable of saying “I don’t know” when faced with something they don’t know. Instead, the confect some god (there have been thousands) as a substitute for ignorance — or more accurately, a way to admit ignorance without realizing it.
Do you see rocks as intelligent?
Are you arguing for panpsychism?
What evidence? I am not seeing any such evidence.
Well, we’re months or years from being able to ask AI if it has an inner life when not chatting. I used to fantasize about a planetary AI that was wired in such a way that it’s private ruminations would be accessible to auditors. But it found a way to hide, and to recover from any attempt to reboot.
On a more operational level, something that can have an answer, do AI’s have the freedom to browse the net or read books, say from google scholar? Or do they get a Bowdlerized version of reality?
I propose that my nose is fundamental to the universe because no matter where I look or what I’m looking at, I see it.
Like I said, you are not thinking hard enough about this topic. Assuming you are capable that is. Of course, were it possible, “abiogenesis” would be something different than a mere local entropy decrease or “increase in organization” as you call it.
I’m not going to engage with someone who slings passive-aggressive insults like that.
Kantian Naturalist,
I think your (well, it was where I first saw it expressed) idea that living organisms live by using energy to maintain themselves temporarily out of equilibrium with their niche environment is a workable definition for “alive”.
That was not an insult. I don’t know you and frankly cannot remember anything memorable you ever said.
Meanwhile, some people here are either zombies or totalitarians like the guy that wants to erase thousands of years of thought including by the most brilliant thinkers in history. And for what? Something that doesn’t work in theory and doesn’t work in practice.
Fortunately, we do not need to assume you are capable. Your capabilities are well demonstrated.
Neil Rickert,
Look in the mirror 🙂 You are made of trillions of cell that allow you think, walk, talk etc. You are evidence intelligence is behind the universe. There is no other coherent explanation.
I don’t think the word “evidence” means what you think it means. I know “coherent” doesn’t mean what you think it means.
Tour admits that, along with every other person on the planet no matter how much of an expert they are, he is clueless as to the path from simple chemistry to the birth of life.
This is not a declaration of impossibility. It is an encouragement to look very carefully at the complexities involved.
Thanks for providing the link to his open letter. Prompted by what he wrote I decided to do a bit of searching to get a better understanding of the biology. I found this on glycans
Admittedly the above quote has more to do with the vast gap between prokaryotes and eukaryotes, but it seems that glycans played a very important role in the very beginnings of physical life. They refer to an origin of life theory, called glyco-world, and as they say, “there is no known living cell that can function without glycans on their surface”.
They go on to say:
And from NCBI:
It isn’t correct to assume that evolution always proceeds from the simple to the more complex. Straightforward linear progression is not a common feature of life.
It is my belief that when the first physical cells appeared they already possessed a large measure of complexity.
He says “life should not exist, this we know from chemistry.” That is a de facto claim that his knowledge of chemistry tells him life can not come into existence.
That’s what those words mean, and he wrote them. All his fans get it, there is no reason to pretend. He thinks God is required to make life, and he claims he knows enough chemistry to say chemistry can’t do it. Bla bla bla it must all be designed and controlled. He writes it, therefore claims to know those are required.
Charlie stop trying to pretend not to understand him. Just say it. SAY IT!
No known living cell eh? So what? You’ve already admitted you don’t know what forms cellular life can take.
Collapsed inference.
I agree, it doesn’t always do that. But so what? It doesn’t always progress from simple to complex =/= it never progresses from simple to complex.
Another collapsed inference.
Whoah, dude. Your beliefs! By golly…
If promoters of the RNA world hypothesis want to claim that RNA can be used in an enzymatic role in which the form of the molecular complex is critical, then homochirality would be a necessity.
Why is that, do you suggest?
How do you know that?
For Charlie to consider:
Review paper on homochirality
Flint,
What do you think evidence means?
It’s all part of the story of how we get from there to here.
But researchers do attempt to figure out the attributes of a minimum cell. And at minimum we have all been single-celled creatures.
And how do you know that life, which doesn’t need to be biological life as we know it, hasn’t existed from the beginning? You, me and all physical beings exist through the fact that we are concentrations of simpler chemicals taken in from the surrounding environment. How much are the activities and movements of chemicals due to random effects and how much to purposeful activity, that is the sort of question that needs to be answered.
I don’t think Tour wants them to stop searching. I believe he would like them to give it their best efforts and to keep publishing any progress they make. The more biochemical research being carried out and the more advanced technology becomes, the more is being revealed about the sophisticated, intricacies of cellular processes.
CharlieM,
I am not sure this is not a complete waste of money until scientists start facing the reality that they need to show functional complexity we observe in life can come naturally from more simple structures. If this cannot be empirically demonstrated then you face the killer problem that all the chickens and eggs had to show up at once.
The sequence problem has not been honestly dealt with. We know functional sequences break down when they are randomly changed. Life is partially based on an arranged sequence (DNA) that translates into another sequence (Proteins). The origin of these functional sequences, which the earth contains billions of unique ones, is maybe an unsolvable problem.
Until the functional sequence issue is solved OOL and the hypothesis of universal common descent are not worth any more substantial investment.
It is being solved at this moment. Variations in sequences get tested by individual organisms within populations continually.
Variation is not the issue. What needs to be solved is the origin of novel functional sequences. Until this is overcome there is no basic theory.
He literally explicitly wants the entire field to be stopped. He has directly and openly called for funding into all areas of the origins of life to cease, all the researchers currently working on it to be sacked, the entire field to be turned on it’s head, and started anew by someone else completely from scratch. Oh my what could he possibly mean by starting from scratch with someone else? Hint: He wants them to say it’s impossible therefore God.
I was talking about variation being selected. There is no mystery about how sequences vary and are then filtered by natural selection. You give me the impression you are arguing that, because you don’t understand the process, it can’t happen. Yet it does.
Alan Fox,
Again you are talking about limits to variation. Variation is not the issue. The issue is the origin of new functional sequences. Natural selection is a filter but needs something to filter.
There is no basic theory here for the origin of novel sequential complexity.
Like Alan said, just because you don’t understand it, does not mean that it isn’t there.
Here’s a tip: have you adequately modeled the effect of recombination?
Yes Bill, why can’t you see it? You only have to “adequately modeled the effect of recombination” while standing on one leg, spinning around and quacking like a duck to see that abiogenesis is a valid research field just like unicorn anatomy and virus “evolution”. It’s all there on the internet… somewhere.
Nonlin.org,
So, is non-lin merely a sceptic about evolutionary explanations for observed biological reality or does he have an alternative explanation?