> a system with primordial chemicals could generate self-replicating reactions and structures - you could figure that out by looking in a mirror

Only if you require no evidence, and no verifiable, independently confirmed experiments to back up your claim. What you said is basically the scientist's version of intelligent design at this point.

You are a large bag of molecules. You self replicate and generate a variety of structures. You are great evidence that complex systems arise out of simple phenomena. Wolfram's initial explorations dealt with this in particular. This is also the reason for developing systems like Conway's game of life. Simple rules. Complex outcomes.

The pumice stone you use to scrub yourself with has a particular distinctive pattern to it, not caused by life, but rather by volcanic and non-biological forces. When you wash your hands with soap and water in front of that bathroom mirror, the you construct a reversed lipid bi-layer, a self organizing structure that occurs as a result of polarity. This set of forces is the same as those that self-organizes your cell walls.

I think there's plenty of evidence. You just need to do a bit of learning to understand what you're seeing.

There have been plenty of experiments showing that the building blocks of life will spontaneously self-assemble under the right conditions. We have now confirmed that comets and other bodies in space contain complex molecules such as hydrocarbons.

There are also plenty of experiments demonstrating that certain structures self-assemble and even "replicate" (for some definition of replicate) under the right conditions, purely as a function of their molecular structure.

There is no conclusive proof... but certainly everything we've discovered to date supports abiogenesis of life given the right conditions and a few 100 million years for many trillions of attempts. It is likely that the first "life" wasn't life as we would define it, more like a prion: a self-replicating molecule built out of amino acids dumped on Earth from meteorite and comet impacts. The first true "life" was probably exceedingly simple and lived off chemical reactions around hydrothermal vents.

No conclusive proof? No proof at all.

Go and listen to James Tour and his video on the problems of just getting the right pre-life chemical synthesis to occur. He is a organic chemist (one of the top in the world) and he talks about each of the incompatible processes between each step.

I would be more inclined to take his word for it than a biologist (of any stripe). Abiogenesis seems to be the least likely scenario in the formation of life (as in close to 0 as to make no difference) irrespective of the amount of time that is allocated.

> Abiogenesis seems to be the least likely scenario in the formation of life

Yet we know it happened, because life exists, and it didn't spring from magic so it must have sprung from non-life. Random chance is a hell of a search algorithm, abiogenesis is simply the inevitable outcome randomly trying every possible combination over hundreds of millions of years. There are no more likely scenarios.

Just because we know something is, does not mean know why. You make a very broad leap to say that there are only two possibilities - magic and abiogenesis - and that one of those possibilities doesn't exist.

There are three broad classifications of philosophical belief - the universe is all there is and there is no non-physical component, that the universe is and has a non-physical component (it is alive, etc) and that there is a creator who is separate from the universe and that creator made the universe.

Within that context, the three can be split into two variations, the universe (with or without a non-physical component) is eternal (steady state or cyclic) and an eternal creator who has made a finite lifespan universe.

Abiogenesis can arise in one of those three variations, in the other two, either the universe creates life as apart of its functionality (its non-physical attributes) or there is a creator that has designed and set in motion life.

Please note that abiogenesis is a completely different subject to any evolutionary model that people may subscribe to.

You can argue all you like about the variations above but you cannot use science to determine the "truth" of which variety you personally believe in. That is a metaphysical/philosophical/religious debate that is outside of the domain of science.

So, where does that leave us in this discussion? Well, it says that you have not given much thought to your point of view in such a way that you are able to logically argue its merit. In which case, I would suggest that you might like to flesh out your arguments because as they stand, the arguments you present are extremely weak and illogical.

His point was that we know it happens because we exist, it's that we don't know how it happened.

There's no well understood theory of abiogenesis. For something to be a theory it must be supported by repeatable experiment and/or repeatable observation. The difference between hypothesis and theory is very important.

There are many good hypotheses on abiogenesis but until someone demonstrates rudimentary repeatable abiogenesis in the lab without "hand-holding" interventions then it's not a theory. (Or alternately finds a way to observe strong evidence for abiogenesis and how it occurred in the fossil record in a reproducible way that is specific enough to rule out other explanations for the same data.)

That's not correct. There's no scientific theory of abiogenesis, because we haven't elucidated the entire pathway and developed falsifiable methods of determining which of the various models is correct, but there certainly is a theory of abiogenesis.

In fact, the theory is so well developed that there isn't really a competing scientific explanation to explain how life ultimately arose other than through abiogenesis. The area of research has been fairly fertile, to the point that many of the findings in that field have spun off into their own areas of research, from their original pursuit of the origins of life.

If there is no scientific theory of abiogenesis then there can be no theory so well developed that there is no competing scientific explanation. If it isn't science in the first place, it can't be science in the second place.

Abiogenesis and evolution as complementary ideas and its competition of intelligent design are philosophical standpoints attempting to portray themselves as science. They are metaphysical.

A simple example of one of the current evolutionary ideas is that there is much "junk" dna within each lifeform. If this is so, then with the current technology, we should be able to edit this "junk" dna out of the chromosomal dna structure and still be able to have fully viable lifeforms that breed true and are fully compatible for the pre-edited lifeforms. if there is 80% "junk", we should be able to edit this 80% out with no ill side-effects. If it turns out that we can't edit this "junk" out without causing non-viability or ill side-effects that that dna was not "junk" in the first place.

Over all the hundreds of millions of species existing on this planet, we should be able to find all sorts of species that are in transition forms (having partially functional organs or forms) today. You can make all sorts of claims about what has happened in the past, especially when you cannot actually test those living organisms in the lab.

That isn't true. Feel free to tell me what the alternative theories that constitute competition to abiogenesis. The alternatives are pretty much 1) a deity or 2) some mythical life force assembled things.

Abiogenesis has a ton of evidence behind it, but we do not have the entire chain of conditions and reactions required to go from primordial molecules to actual fact. Much in the same way that 'AI' vanishes, as we develop evidence and establish facts that support abiogenesis, they become standard biology, chemistry or physics.

Compare the argument for abiogenesis in the 1800s to the one today. We've discovered the mechanism for generating our species from single celled life forms, we've determined that RNA have intrinsic catalytic ability, we've developed robust theories of non-equilibrium reaction processes.

As for your statement about junk DNA, you have a very limited understanding of what that actually refers to. Junk DNA refers to non-coding dna. We know those areas can influence chromatin structure, contain regulated control sequences which influence gene expression, contain splicing sequences, etc.

As for your last paragraph, you make it very clear you don't understand the subject you're talking about. I suggest doing more than reading pop science books and picking up a volume on molecular biology. It will clear up what I imagine are a legion of misconceptions you have about what we know.

What is not true? You made one statement then you made a contradictory statement.

It matters not that neither of the alternatives that you supplied are palatable to your thinking processes. You cannot prove the veracity of your belief system by any scientific method as they are metaphysical in nature.

As I pointed out above, try listen to James Tour and you will see much of your "ton of evidence" is really evidence. It is conjecture and may have some evidential value, but on the basis of actual processes, the "evidence" just doesn't stack up.

We have in no way discovered the mechanism for turning single celled lifeforms into our species. If we had, we should have no problems in doing this from any sample of single cell lifeforms other than our own. We can't and we don't.

I don't consider any of the dna to be junk. I am using the definitions as promulgated by those who ascribe to the idea of "junk" dna. By your own definition as given above, this means that the relevant "junk" dna is not "junk".

As for my last paragraph, it is a consequence of the evolutionary model. You can argue that it is not a consequence of the model but then you would be arguing against the evolutionary model itself. Since I took a great deal of interest in this area in my younger days and I would read as many of the published experiments as I could. What got me looking at this further was the discrepancy between the reported results of these experiments and the purported conclusions reached by the experimenters.

My last sentence is accurate, if you cannot test and reproduce the outcomes/results then it is just conjecture. So with those comments, what is your background, interest and expertise in these areas?

I don't think an extended back and forth will be very fruitful at this time.

You have very large misconceptions about what we know, because you've approached the subject to look at a point of interest without understanding the context of the evidence we have. It's laudable that you're looking into things, but you have clear, demonstrable, gaps in your knowledge. It's as if you're trying arguing against the existence of rocks by pointing at pebbles and erosion while forgetting you're standing on a mountain littered with boulders.

I know this message must come off in an abrasive manner, and I do apologize. That isn't the intent. It is just difficult to show you precisely where you're wrong with the finite time I have available to me. I can't be your personal tutor for the natural sciences, but I feel an obligation to future readers to put your comments in context.

If you're serious about learning about the subject, pick up a molecular biology textbook and start reading, or audit a few 101 level courses at your local university. Molecular biology is great because you will get a huge bang for your buck in terms of understanding the natural world with your very first few classes!

>to the point that many of the findings in that field have spun off into their own areas of research, from their original pursuit of the origins of life.

That sounds fascinating. Can you give some examples?

Your general description is correct, but your specific application is not; because you've implicitly in the latter limited empirical confirmation such as to juatify the label theort to direct observation or indirect observation that admits no other explanation. Neither is required, and the latter would move it beyond theory to irrefutable fact, as an observation “that is specific enough to rule out other explanations”, obviously, rules out all other explanations.)

> The big question isn't, and wasn't, whether a system with primordial chemicals could generate self-replicating reactions and structures - you could figure that out by looking in a mirror.

OK, we knew that, but what are the precise conditions under which it is more or less likely to happen? Understanding that requires a mathematical theory of exactly how self-replicating patterns form under the laws of thermodynamics, which is what this line of work is aiming to provide.

It's a cute paper telling biochemists things they already knew. The biochemical sciences aren't discovering entropy for the first time.

The premise this work adopts doesn't add to our understanding of complex chemical systems. Believe me, there are plenty of computational chemists in the world.

There is no THE theory of abiogenesis.

The main question for me is abiogenesis.

How did the first self-replicating things evolve?

It seems that the kolmogorov complexity of the simplest quines in most languages is relatively high. One would imagine that, in terms of chemistry, the kolmogorov complexity of something that can self-replicate and also evolve with mutations which do not prevent the replication from taking place over generations - ie resilience - is too high to have arisen by mere chance.

Be wary of anthropic bias. If this universe didn't happen to support life, then we wouldn't exist here to observe it. Perhaps there are other universes with different laws of physics, and we would exist in one of them instead. And even in our own universe, there are many trillions of planets. Yet we only know of one that has evolved life. The fact that we observe life here tells us nothing about how probable it is.

In fact as far as we can tell, life is extremely rare. We've only found one instance of it forming on it's own. And it can only exist in a very tiny space between the earths crust and the upper atmosphere (and only in very small quantities in most of that space.) We haven't found self replicating systems on other planets or deep within the earth.

So any theory that posits "life is an inevitable outcome of thermodynamics" is almost certainly wrong. It's a theory that can't be falsified, and has no predictive power. A more interesting theory would be one that can explain why our specific planet and our specific laws of physics support life. Why do exist here instead of somewhere else?

As far as we can tell intelligent life is extremely rare. The not too distant universe could be well-populated with simple unicellular life (or just individual self-replicating molecules). It may be that self-replicating molecules form relatively easily but the jump to more complex life forms is exponentially more rare; but that would be more a question about the power of Darwinian selection than England's theory.

Also, England's theory never says "life is an inevitable outcome of thermodynamics," Jeremy England said that. There's a big difference. As it stands the theory says nothing about self-replication, it merely predicts chemicals forming seemingly-rare (with respect to the full chemical space) ordered structures. And his theory does have predictive potential and the simulated results in his PNAS paper support his predictions. It's certainly experimentally falsifiable: put a bunch of chemicals together that can form bonds, if you have an approximate understanding of the chemical space, you test apply an appropriate energy source, and see if the resulting chemicals occupy a surprisingly rare part of that space as predicted.

But I do agree that your question "Why do [we] exist here instead of somewhere else?" is one of the more interesting questions.

England's theory tells you that once you get close to a certain free energy basin you will access its optimal minimum. To my understanding it is silent about how you get "close enough"

Yep it seems to be rare, thus falsifying the theory that England is developing.

And by the way, can't multiverse thinking be invoked pretty much anytime to explain anything?

"Oh we have fine tuning that is a knife's edge 1 part in 10 to the 127th"

"Yeah well maybe we have even more universes."

That's not real science. That's actually digging your heels in and saying "there is nothing beyond what we already found and understand". How will you go about testing this?

The multiverse isn't falsifiable. It's philosophy, not science.

>And by the way, can't multiverse thinking be invoked pretty much anytime to explain anything?

That's exactly the problem I've always had when it comes up.

Anthropic bias doesn't explain anything. It just says that you can't use your own existence as evidence of something. Because if you didn't exist, you wouldn't be able to make the opposite argument. It's basically just a wider application of survivorship bias. It works whether or not there are actually other universes (although the existence of other universes definitely makes it more intuitive to understand.)

By itself that may be true. As they say, "painting the target around the arrow" proves nothing.

But what if the target was there before? Then you have to explain how the arrow hit it so perfectly. There is a difference.

The difference is, is there anything special about the target's placement?

One can argue that alternative universes where soups of particles didn't give rise to life are all uninteresting.

You can of course say that life is needed to make the judgment for what is interesting.

But are you sure there is no sense in which the target can be said to have been painted before the arrow was fired? It all rests on that.

> In fact as far as we can tell, life is extremely rare.

As far as we can tell, right. Given our extremely narrowed view on the vast universe I'd say we've seen literally nothing yet. I'd not be surprised if life is not rare at all. It may only be rare in the tiny fraction of space that we know about.

When we first sent probes to other worlds, many people seriously expected to find life. The first astronauts on the moon were quarantined for weeks afterwards. Instead it seems like the vast majority of space is dead.

There may be lots of other planets like Earth, sure. But that's a very different claim than "life is an inevitable outcome of thermodynamics". At best it's "life is an inevitable outcome of very specific conditions that happened to exist on ancient Earth and Earth-like planets, under specific combinations of chemicals and temperature..." You need a lot more than just thermodynamics to have life.

It's probably entirely possible to create a self replicating machine using only components found on the surface of the moon. In fact that's been a serious research project of NASA for a long time. But such a machine will never form by chance, because the probability is so incredibly small. And so the moon is lifeless.

> and only in very small quantities in most of that space

It depends on how you define quantity. Total biomass may be low in proportion to crust, sure. But fully one fifth of the atmosphere is being maintained in a clearly unstable state (free oxygen!) by something. There's no way an alien would look at a spectrograph of our atmosphere and think anything but "it's alive".

Chance is not 'mere'. Whatever you think high complexity is, is just as well a low complexity to a different perspective. We are only slightly more remarkable than dirt, and over 4.5 billion years of chemical history, I don't see what you're basing your objection on.

Why are you certain that _self_ replication would be a necessary condition for "life-ish" chemistry to start happening, and to start evolving?

I expect chemical metabolisms pre-dated organisms, and purely metabolism based replicators pre-dated stored instruction replicators.

Can you elaborate on this and describe a complete picture of what you think happened?

Certainly not a complete picture. More of an unfinished amaetur impressionist water color.

But something along the lines of the dynamics seen in reaction diffusion systems.

Once you have a "metabolism" where interacting chemicals produce one another, you have a system that can sustain itself on it's reactants.

In a mess of random reactions, order will emerge through feedback effects, chemicals that are used up are used up, those that are replenished will increase in concentration.

Various regions will have different ratios, and different impurities giving a landscape in which versions of the metabolism may specialize or interact. ... Some regions produce molecules that self assemble into things like walls and membranes. ... RNA, likely around as a component the whole time, at some point it is specialized into an information medium role.

Stir continuously, simmer for 1-billion years or until it photosynthesizes.