Is Abiogenesis an hypothesis in distress?

Most every scientist recognizes that origin of life researchers have not solved the problem of how the first life came to be. An appeal to panspermia is really just kicking the can down the road.

My own interest is from the perspective of philosophy of science. I question whether origin of life research is even on the right track. It appears that the commitment to philosophical naturalism is so dominant among origin or life researchers that it is impossible for them to conduct their research using the normal standards of science. As a result, professional researchers in fields other than origin of life have written about the failures of these researchers.

An earlier conversation on Peaceful Science discussed some of these topics. It is well worth reading and can be found at:

@vjtorley began the discussion referring to criticisms of OOL research by James Tour of Rice University and Brian Miller. Dr. Miller also made a number of contributions to that discussion.

Here I would like to go into more detail of the criticisms leveled by James Tour and also begin discussion of the writings of Perry Marshall regarding information necessary for origin of life.

James Tour is a leading synthetic organic chemist. Perhaps his most interesting work is the nanocars he has synthesized. These little cars a little molecular machines. They have four little wheels (which I think are just one molecule in size) and two axles that turn, plus a chassis, a motor and a propeller. His first attempt to synthesize a motor for his nanocar worked, but not efficiently. It turned (IIRC) just 1.2 times per hour. Not functional. After more research, he thought perhaps it had one too many iron atoms (I believe it was iron). He couldn’t run a reaction that would remove that one atom, he had to begin from scratch. Sure enough, once finished the new motor turned at the rate of 100,000 revolutions per minute. That’s a tremendous improvement for just removing one atom.

This is important because most likely the earliest life had to have many such molecular machines to move things, such as waste products, around inside the cell. Tour criticized OOL researchers because he does not believe they are honest about the level of difficulty in the results they report or the unlikelihood such reactions could happen in nature. Specifically, he complains about the need for very exacting purifications otherwise the products and by-products of each synthesis will mix and create a useless goo. Is it possible that some separations could happen in nature? Yes, but it highly unlikely to get the level of purification necessary for even reaction much less the many, many reactions necessary for the origin of life.

Tour also complains about the assumption of just-in-time arrival of fresh and pure new chemicals for the next reaction. He also complains about the changing conditions for these reactions. Researchers change temperature from freezing cold to boiling hot and back again quickly in the lab. In nature, these kinds of changes take time and time is the enemy of clean reactions. Many of the products are highly reactive and will reactive with most any compound they contact during this change of temperature. Plus researchers also change atmospheric pressure from near zero to several atmospheric pressures. Most of this information is somewhat hidden from readers in footnotes or supplementary materials only a specialist might examine. Tour has also been critical of OOL researchers for their ignorance of CISS and quantum mechanics. Their research simply ignores that entire field.

Tour quotes Dostoevsky asking this very important question of OOL researchers - “Why is everyone here lying?”

http://inference-review.com/article/two-experiments-in-abiogenesis

Another non-OOL researcher who has entered the fray and deserves to be heard is Perry Marshall. Marshall is software expert and claims that biological information, whether encoded as DNA or RNA, is software code and requires a full communication system. He describes a communication has having an encoder, the code itself (DNA or RNA) and a decoder. If all three of these do not exist, then communication is impossible. All three need to be present inside the cell for the cell to function.

Marshall’s book Evolution 2.0 describes the problem OOL researchers are neglecting.

Marshall has offered a technology prize of up to $5 million for anyone who can explain this. Specifically, if you can produce a self-organizing digital communication system, he will write you a check for $100,000 and if it patentable then you can gain royalties of up to $5 million.

The judges are from Harvard, Oxford and Florida State University.

I think it’s clear that no one will ever be able to claim this prize. I cannot see how three different entities can self-organize an agreed upon code without intelligence. Perhaps you will accuse me of a lack of imagination and perhaps I’m guilty. But for the time being, I will continue to believe that certain things are impossible.

All of this brings me to the point. OOL research is in distress. No real progress has been made for a long time and indeed the more we learn the greater the difficulties of chemical evolution becomes.

More importantly, it is time for OOL researchers to do the right thing and to attempt to falsify the hypothesis that life can arise through natural processes without intelligence to guide the progress.

It seems to me that the desire for Peaceful Science can be a motivation for us to join together to call for OOL researchers to uphold the standards of science.

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That is the main sticking point in the article. I am not sure how they can do that. Isn’t the best they can do is say “We have no plausible natural explanation for the origin of life”?

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Exactly. That is 100% true. That means we do not know how the first life arose. If you feel the need to believe God directly created the first cell, that is certainly reasonable, even though it is unattested to in Scripture (unlike e.g. the de novo creation of Adam). Nothing in science disputes that belief. Science is silent on God’s action. This is one of those mysterious places in origins were maybe God acted.

That is quite a bit of common ground. It might go down hill from there…

As you may know, I’m friends with Dr. Tour. I’m pretty sure you are misreading him. He wrote this too, you know:

Pascal further writes in his Pensees 429 ,

This is what I see that troubles me: Nature has nothing to offer me that does not give rise to doubt and anxiety; if there is a God supporting nature, she should unequivocally proclaim him, and that, if the signs in nature are deceptive, they should be completely erased; that nature should say all or nothing so that I could see what course I ought to follow.

Though 350 years since Pascal penned his dilemma, as a modern-day scientist, I do not know how to prove ID using my most sophisticated of analytical tools.

An Axiom or a Hypothesis?

If Tour can’t prove ID, what makes you think you can? I think one reason is that you’ve missed a critical point about what abiogenesis is. It is not a hypothesis, it is an axiom. Science looks at different hypothesis of abiogenesis, and weights between them, but it does not consider things other than abiogenesis.

So without any doubt, abiogenesis is certainly not a hypothesis in distress, because it is not a hypothesis. It is an axiom. And it might be an incorrect axiom, but its all that science has because it does not consider God’s action. Methodological Naturalism, So Falsely Called. That doesn’t mean it is correct, but science is limited here.

As @Revealed_Cosmology puts it…

I’m not sure how they can do it either. Neither can Jim Tour. Neither can Perry Marshall.

Perry Marshall

A good friend of mine and @sygarte’s is mentioned.

Sadly, he is wrong on his facts. Biological information is not software code and does not require a communication system. Nonetheless, it is worth noting Perry Marshall has gone through a transformation (as I understand it) from ID to believing that this actually can be solved by natural processes.

How is that clear? Perry doesn’t agree with you.

The Ironic Parable

I don’t know Ron, Jim Tour has been clear that Intelligence can’t create life. He has a parable:

THE WORLD’S BEST synthetic chemists, biochemists, and evolutionary biologists have combined forces to form a team—a dream team in two quite distinct senses of the word. Money is no object. They have at their disposal the most advanced analytical facilities, the complete scientific literature, synthetic and natural coupling agents, and all the reagents their hearts might desire. Carbohydrates, lipids, amino acids, and nucleic acids are stored in their laboratories in a state of 100% enantiomeric purity.

Would the dream team—please—assemble a living system?

Take your time, folks, take a few billion years.

Nothing? Well, well, well.

Let us assume that all the building blocks of life, and not just their precursors, have been made to a high degrees of purity, including homochirality where applicable—the carbohydrates, the amino acids, the nucleic acids, and the lipids. They are stored in cool caves, away from sunlight, and away from oxygen. These molecules are indifferent to environmental degradation.

And let us further assume that they are all stored in one comfortable corner of the earth, not separated by thousands of kilometers or on different planets.

And that they all exist not just in the same square kilometer, but in neighboring pools where they can conveniently and somehow selectively mix with each other as needed.

Now what? How does the dream team assemble them without enzymes?

Very well. Give the dream team polymerized forms: polypeptides, all the enzymes they desire, the polysaccharides, DNA and RNA in any sequence, cleanly assembled.

Ready now?

Apparently not.

I entirely agree with him. Human intelligence cannot assemble life. That seems like pretty solid evidence that life does not appear designed, right? We cannot even create life with the best of our intelligence. It does not appear designed by any created being.

To be clear, God did design it, but we are not at all sure how. The way He makes things is very different than the way we make things. Which brings us right back to our common ground:

If you feel the need to believe God directly created the first cell, that is certainly reasonable. Nothing in science unsettles that belief.

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Joshua, thank you for a very thoughtful reply. I hope that my answers give you something to think about and discuss.

You write:

If Tour can’t prove ID, what makes you think you can? I think one reason is that you’ve missed a critical point about what abiogenesis is. It is not a hypothesis, it is an axiom. Science looks at different hypothesis of abiogenesis, and weights between them, but it does not consider things other than abiogenesis.

First, I have no connection to Discovery Institute, nor does James Tour or Perry Marshall. I’m certain that some of the work that comes out of Discovery Institute is good, but I don’t wish to be colored with the ID brush. It raises negative emotions in me.

Tour leaves open the possibility that a purely natural explanation for origin of life may be found, but he estimates it will take at least 350 years to do so. I think he’s being overly optimistic.

You call abiogenesis an axiom, but it is only an axiom to one who is committed to Philosophical Naturalism, that is, the belief that God does not exist or cannot be known to act in the material world. (Philosophical Naturalism is often confused with Methodological Naturalism, but Methodological Naturalism would never call abiogenesis an axiom.) I see no reason to hold such a view. In fact, I believe Philosophical Naturalism should be rejected because it is preventing science from making progress where progress is possible.

In place of Philosophical Naturalism, I propose (although I’m not the first to do so) the use of Regularism. Regularism is the belief that nature will always behave in the same way given the same situation. It is completely unbiased regarding the question of God’s existence or man’s ability to identify God’s activity in cosmological history. Because it is unbiased, it is able to pursue truth wherever it may lead.

You quote Pascal and I respect him, but science and philosophy have come a long way since the days of Pascal. We have Newton now and the law of cause and effect. Despite Hume’s skepticism regarding cause and effect, science is all about describing and quantifying causes and effects. By studying causes and effects, we have been able to determine a number of laws of nature. As a result, we can determine what nature is can do and what nature cannot do.

Philosophical Naturalism leads to the view that nature is all-powerful. But, if you think about it, that simply isn’t true. Nature is bound by natural laws. This should be obvious.

Let’s say for a moment that at some point in the future science is able to prove that nature is incapable of creating life through natural processes. In such a case, the “axiom” of chemical evolution is wrong but science has been hindered by the falsity of Philosophical Naturalism. In other words, science is stymied in origin of life studies rather than progressing. But there is a way to progress using Regularism and Laws of Nature.

If we can look at a particular effect somewhere in the cosmos and determine that natural processes could NOT produce that result (or that the result is unnaturally unlikely), well, I have a name for that. I call it a counter-natural cosmic event.

As I study cosmological history and the history of life, I see a number of counter-natural cosmic events. I intend to write a series of philosophy of science papers describing them. I can only see one explanation for them. If something isn’t natural, then it must be supernatural. I simply don’t know any viable third option.

Admittedly, there is a difficulty is charting a path to falsify the hypothesis of abiogenesis. But it is possible. If it isn’t possible, then abiogenesis should not even be considered a scientific hypothesis.

One of the first steps toward falsification might be to determine what level of odds would put the hypothesis beyond the realm of credibility. Do you think it would be possible for scientists to come to agreement on this? I’ve read one scientist who said one chance in 10^50 means it is theoretically impossible no matter how big the multiverse is. I’m not certain other scientists would agree, but I would be interested to know what other scientists think on this subject.

Another step would be more transparency in origin of life research. The research needs to be conducted in a natural setting, not just a lab. In a letter to a friend, Charles Darwin was the first to suggest that life arose “in a warm little pond.” At the time, the idea didn’t seem far fetched. No one knew how complex life is. But I think researchers would have a difficult time conducting their experiments in a watery pond-like setting. But it should be tried, both in fresh water and salt water. I think the water would dilute the chemicals and reactants and make the reactions far less efficient. And separations of the products and by-products would be very difficult in such a setting. As would the just in time delivery of the new chemicals for the next reaction. But if the reactions don’t work in a natural setting, then they really are not explanatory.

Do you see the point? The second step towards falsification would be to determine where these reactions and purifications could happen in a natural setting allowing only reasonable changes in temperature and atmospheric pressure. The types of reactions reported in the literature are only possible in well-controlled laboratories.

Then, of course, we still have the problem of the rise of a communication system. You claim that Perry Marshall has changed his view. Do you have a link for that? Because the website offering up to $5 million is still up and running. It appears to me that the challenge is still on. But if you are right, I would love to read where Perry has said that he has changed his mind and no longer sees DNA as a code.

No, I don’t think that is the best they can do. I give a couple of ideas on how to move toward falsification in my reply to Joshua. But one of them goes to identifying where these reactions and purifications could take place. I believe once researchers began to think about falsification that other ideas would become apparent to them.

Interesting. Okay, so you are not ID associated. James Tour, however, still is ID associated. Perry was, but no longer is (as I understand it). Also, the articles you linked to are from an ID associated publication by the way. But I’ll take your word for it. Sometime I want to know the story here.

Yup maybe he is.

Not true. I’m the counter example. I have no problem with God’s action in the world. I am not a philosophical naturalist. I even just argued for the de novo creation of Adam. In my scientific work, however, I rely on the long Christian theological tradition of methodological naturalism, though its called the wrong thing. I just know that science is not the whole story.

You work with students. It is critical you help them understand these distinctions, you could lead them into a whole ton of avoidable conflict. It does not appear you read the links I gave you. I hope you do. Three of the key ones:

The Rules of the Game

Methodological Naturalism, So Falsely Called

http://peacefulscience.org/tour-pascal/

Do you mind taking a look at those? To be clear, I see your proposals:

Except none of us have the authority to change the rules of science. It seems to be doing just fine as it is.

Except that is not philosophical naturalism.

Except that is not how science works. I can’t imagine how it could possibly do this.

Except, as a scientist, I cannot see how that is the case. That is just not what we do in science.

I know of no agreed upon case that satisfies that criteria.

The viable third option: “we have not yet understood or learned the explanation.” In a word, “ignorance.”

Nope. It is not possible to estimate the odds of an unknown process.

How much do you know about OOL of research? This does not make much sense. Our current “natural setting” is nothing like the “natural setting” billions of years ago on earth. Why would we try and run OOL experiments in the wrong setting?

Not really. I’m just not sure you know how science works. This is not how we do it.

Just ask him directly. He is very optimistic that someone will collect.

Oh, he still thinks DNA is an “information system.” He is wrong, in my view, but he still thinks that. The change is that he now thinks someone will eventually collect on his prize. He thought it was unsolvable, but now no longer.

Methodological naturalism does call abiogenesis an axiom. I’m not sure why you would disagree. In scientific work, we only consider natural processes. We only consider abiogenesis, not God’s creative act. Panspermia, sure, but that just postpones the abiogenesis question, as you rightly pointed out. By definition, no one is around to make that cell but God, and science does not consider God’s action. It is designed to study creation (that which is created) not the Creator.


@Ronald_Cram you seem like a smart guy who is well read. I appreciate that. I just think that science works differently than you know. You may really like the upcoming discussion on Divine Action with @rcohlers (Clinton Ohlers: Two Parables on Divine Action). This may clarify why exactly science can’t give you what you want, and why I’m not appealing to philosophical naturalism. Rather, I’m solidly in a theological tradition. It is the same tradition as Francis Bacon, James Tour, and Blaise Pascal. Maybe you can join us…

I suppose I haven’t come a long way from him. He is focused on Jesus. He sees Jesus as the center to which all tends, and all truth is found.

We know God only by Jesus Christ. Without this mediator all communion with God is taken away; through Jesus Christ we know God. All those who have claimed to know God, and to prove Him without Jesus Christ, have had only weak proofs. But in proof of Jesus Christ we have the prophecies, which are solid and palpable proofs. And these prophecies, being accomplished and proved true by the event, mark the certainty of these truths, and therefore the divinity of Christ.

I’m pretty happy with that view. All those who have claimed to know God, and to prove Him without Jesus Christ, have had only weak proofs. Now that I have the strong proof that God offers in Jesus, I have no need for weak proofs. Do you?

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For what’s it worth, no OOL researcher takes the “warm little pond” seriously anymore, it’s thermodynamically flat. And the overwhelming majority think panspermia fails as well. There has been great progress the last ten years. Especially out of the Yarus and Zagrovic labs.

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You might be right, but incredulity is not an argument.

This, however, is just false. There has been real progress, despite your doubts.

@T.j_Runyon is right. There has been a lot of progress in the last five years. We still do not know how the first life arose, but there has been progress in our understanding.

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Sorry, the quoting feature is giving me fits. You said: “It is the same tradition as Francis Bacon, James Tour, and Blaise Pascal. Maybe you can join us…”
I’d like to learn more about that tradition

Start here:

Then have fun next week here: Clinton Ohlers: Two Parables on Divine Action. The parables are scheduled to go up tomorrow or the day afterwards, so there are several days to think about them before we kick off the discussion.

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Whenever ID or Discovery Institute is mentioned, it is almost always with an element of derision or condescension. If one is painted with the ID brush, then no matter the strength of his evidence or how tightly his case is argued, it may be dismissed with an arm wave. I don’t want to be dismissed that easily. And neither do James Tour or Perry Marshall, which is why both have publicly stated they do not want to be associated with ID in capital letters. If you want to treat people fairly, never assume they are associated with ID or Discovery Institute.

No, Inference is not an ID-associated publication. They publish essays by a wide variety of authors, including Noam Chomsky. You can learn more about Inference here. http://inference-review.com/about

I’m not sure why you think James Tour is associated with Discovery Institute. He has never written an article for their publication. He’s not a fellow of the institute nor does he have any formal association that I know of. Tour did contribute to an anthology titled Theistic Evolution and this book had other contributors some of whom were from Discovery Institute and some who were not.

The same is true of Perry Marshall. He has never written an article for Discovery Institute’s website. He’s not a fellow nor does he have any official link.

I’m sorry, Joshua, but this shows confused thinking. I defined Philosophical Naturalism as “the belief that God does not exist or cannot be known to act in the material world.” If you believe that it is impossible to know that God has acted in the material world, then you are, by definition, a Philosophical Naturalist. I don’t see how it is possible to escape this.

Newton was certainly not a Philosophical Naturalist, perhaps not even a Methodological Naturalist. He hoped that his scientific endeavors would prove the existence of God, as he wrote in his famous letters to Dr Bentley. I don’t believe Newtonian gravity actually supports the existence of God, but the groundwork laid by Newton did make it possible for science to show God’s existence later on.

Just to demonstrate that Sean Carroll does not believe, as you do, that scientists are required to never consider the possibility of God, I will provide a quote from his appearance at the Greer Heard Forum when he debated Wiliam Lane Craig.

The quote begins 1:39:55 into the talk. I hope the time stamp works properly for you. I provide a transcript just below the URL.

“Some people try to sometimes say that science or naturalists start from an assumption of naturalism so they just simply won’t consider alternatives. I’m very happy to consider alternatives. I think if there was some phenomena in the world which really looked exactly like some religious tradition was saying should happen and was miraculous, was seemingly violating the laws of physics, what would scientists do in that situation? They would not say “We are not allowed to think about this because we agreed yesterday at faculty tea that the world is a natural world.” I think they would try to come up with the best explanation. If the best explanation is not naturalism, then I would buy that.” - Sean Carroll

Carroll goes on to say:

“In a proper, quantitative Bayesian probability analysis my prior for naturalism is higher than my prior for theism, but overwhelming evidence will always take care of that.”

Regarding my proposal to move away from Methodological Naturalism (because it so often slides into Philosophical Naturalism) to Regularism, you give a rather disdainful reply. Perhaps you are unaware of the growing philosophical unease with Philosophical Naturalism. I would suggest to you the following book, especially Chapter Three on Regularism by my friend Tom Gilson. The book is taken from “Proceedings of the 2016 Conference on Alternatives to Methodological Naturalism.”

Your next series of comments show that you are not taking my comments seriously. To say “I can’t imagine this” or “I can’t imagine that” or “science doesn’t work that way” doesn’t really help to advance the discussion. As I have made clear in this comment, Sean Carroll can imagine a situation in which it is possible for science to prove that something could not have happened through natural processes. The hypothesis that life arose from chemical evolution is one such situation. If it is not possible to disprove this hypothesis, then it is not scientific.

Regarding my proposal that OOL research be done in natural settings, I’m attempting to raise the bar. You ask:

But that is what is happening now. The reactions are being done in changing environments - from low temperature to high temperature back to low temperature and from low atmospheric pressure to high atmospheric pressure back to low - all with the goal of trying to improve yields with no thought as to how realistic these changing conditions are to early earth.

My proposal is to run the same experiments in conditions closer to the early earth and do it with a view toward falsifying the hypothesis. As you know, scientists have a responsibility to try to falsify their own work. It is not a task that humans love to do. That’s why I am also proposing that each research team try to falsify the work of other teams. Those who hold to DNA first can attempt to falsify the RNA World hypothesis, the metabolism first hypothesis and the cell membrane first hypothesis. The other teams can do the same.

There is no question in my mind that abiogenesis is falsifiable and would be falsified within a few short years if researchers actually held to the standards of science.

Regarding Perry Marshall, why not invite him here to discuss his book and his $5 million challenge. I think he would be willing to invest some time discussing his thoughts.

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3 posts were merged into an existing topic: Swamidass is Inescapably a Philosophical Naturalist

Joshua, I would like to clarify a couple of points. In one of your comments you said that James Tour was associated with ID. But on the blog you linked, you quote Tour:

“I (Dr. James Tour) have been labeled as an Intelligent Design (ID) proponent. I am not. I do not know how to use science to prove intelligent design although some others might. I am sympathetic to the arguments on the matter and I find some of them intriguing, but the scientific proof is not there, in my opinion. So I prefer to be free of that ID label.”

I think it is very clear that saying Tour is associated with ID is very unfair to him. He admits that he doesn’t know how to use science to prove intelligent design but “some others might.” He doesn’t claim it is impossible for science to prove that God exists. And I think Tour would be pleased if OOL researchers took their responsibility to test abiogenesis in an attempt to falsify it as welcome progress. Why don’t you invite him to participate in this thread and we can ask him?

My work is not related to showing a requirement for divine intelligence, although Perry Marshall’s work looks promising in that area.

My own interest has been in showing that certain events in history, specifically in cosmology and the origin of life, could not have happened through natural processes. I hope this clears up the earlier confusion.

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Umm. Everything you are asking of scientists they are doing

And it’s actually going the opposite way that you think it is…

No, they are not. I suggest you read the articles by Tour I linked above. The ones that were not printed in an ID-related journal.

Yes they are! Do you keep up with literature? Do you have private correspondence with OOL of researchers like I do? I can’t believe you said what you just said with a straight face.

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I notice that the level of discourse has devolved precipitously.

You’re right and I apoligize. Just tired of seeing work and people misinterpreted. I’m out

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Please read Tour’s essays and watch his video and then get back to me.