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Does peer-reviewed research support a naturalistic origin of life?

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There was a recent debate between Dr. James Tour and Professor Dave, an atheist with a bachelors degree who makes YouTube videos. The atheist spent his entire opening speech attacking Tour’s character. When Tour asked him to show him origin of life chemistry, he refused. The atheist shuffled through papers he apparently found by Googling, and read the titles. When asked what was in them, he said that he couldn’t remember.

But I was trying to decide who won the debate. There was one place where the atheist claimed that the early Earth had no molecular oxygen. He needs that to be true, in order for the chemistry that creates the building blocks of life to work. So I thought I would talk about a paper that refutes that. After my argument, I’ll talk about another mistake that the atheist made in the debate. Based on those two mistakes, I concluded that the atheist was speaking errors either intentionally or unintentionally, and therefore lost the debate.

Here’s a paper published in the prestigious peer-reviewed science journal Nature, entitled “The oxidation state of Hadean magmas and implications for early Earth’s atmosphere”.

Evolution News explains what the paper is about.

Excerpt:

A recent Nature publication reports a new technique for measuring the oxygen levels in Earth’s atmosphere some 4.4 billion years ago. The authors found that by studying cerium oxidation states in zircon, a compound formed from volcanic magma, they could ascertain the oxidation levels in the early earth. Their findings suggest that the early Earth’s oxygen levels were very close to current levels.

[…]Miller and Urey conducted experiments to show that under certain atmospheric conditions and with the right kind of electrical charge, several amino acids could form from inorganic compounds such as methane, ammonia, and water. Several experiments have been done using various inorganic starting materials, all yielding a few amino acids; however, one key aspect of all of these experiments was the lack of oxygen.

If the atmosphere has oxygen (or other oxidants) in it, then it is an oxidizing atmosphere. If the atmosphere lacks oxygen, then it is either inert or a reducing atmosphere. Think of a metal that has been left outside, maybe a piece of iron. That metal will eventually rust. Rusting is the result of the metal being oxidized. With organic reactions, such as the ones that produce amino acids, it is very important that no oxygen be present, or it will quench the reaction. Scientists, therefore, concluded that the early Earth must have been a reducing environment when life first formed (or the building blocks of life first formed) because that was the best environment for producing amino acids. The atmosphere eventually accumulated oxygen, but life did not form in an oxidative environment.

The problem with this hypothesis is that it is based on the assumption that organic life must have formed from inorganic materials. That is why the early Earth must have been a reducing atmosphere. Research has been accumulating for more than thirty years, however, suggesting that the early Earth likely did have oxygen present.

[…]Their findings not only showed that oxygen was present in the early Earth atmosphere, something that has been shown in other studies, but that oxygen was present as early as 4.4 billion years ago. This takes the window of time available for life to have begun, by an origin-of-life scenario like the RNA-first world, and reduces it to an incredibly short amount of time. Several factors need to coincide in order for nucleotides or amino acids to form from purely naturalistic circumstances (chance and chemistry). The specific conditions required already made purely naturalist origin-of-life scenarios highly unlikely. Drastically reducing the amount of time available, adding that to the other conditions needing to be fulfilled, makes the RNA world hypothesis or a Miller-Urey-like synthesis of amino acids simply impossible.

If you read the paper’s abstract, it finds that molecular oxygen would have been present by the end of the Hadean era. The earliest signs of life we have are from just after the end of the Hadean era. So, its undeniable that molecular oxygen was present. Did professor Dave lie, or was he just ignorant? One thing for sure, he pronounced that there was no oxygen in the same confident, insulting voice that he used for the rest of his presentation.

OK, so with that out of the way, Professor Dave also cited a paper in the journal Science. And there is an article on Creation.com by Johnathan Sarfati, who has a PhD in chemistry, about that very paper.

His post says:

It’s likely that the media reports you mention were referring to the paper in Science journal by Tracey Lincoln and Gerald Joyce.1 Quite often, the media hype just doesn’t match what was actually discovered. To be fair, Joyce, a well known chemical evolutionist, made it clear that he and his Ph.D. student Lincoln had not produced life, despite the headlines.2 Much earlier, Joyce admitted:

“The most reasonable assumption is that life did not start with RNA … . The transition to an RNA world, like the origins of life in general, is fraught with uncertainty and is plagued by a lack of experimental data.”3

Joyce and Lincoln started off with a fairly long RNA molecule. Given that nothing like RNA appears in Miller–Urey experiments, this already shows unjustified interference from an intelligent investigator. In fact, not even the building blocks, ribonucleotides, appear in such experiments, and they do not spontaneously form RNA. In fact, there are numerous chemical difficulties with obtaining RNA by blind undirected chemistry, the only sort allowed on the hypothetical primordial earth, as chemical evolutionist A.G. Cairns-Smith points out in his book Genetic Takeover4 (see extract at Cairns Smith: Detailed criticisms of the RNA world hypothesis). And it’s a huge step from RNA to the genetic code, its major use today.

Furthermore, this paper didn’t demonstrate replication but ligation—joining two small RNA pieces, previously designed to be a match to the longer strand. So this research already assumed not just one but three RNA strands. For this to be relevant to chemical evolution, the two pieces just by chance had to have pretty close to the complementary base pairs of the first piece—natural selection could not be invoked before reproduction.

Furthermore, since polymerization is unfavorable, the RNA pieces must be chemically activated in some way. Note that a catalyst merely accelerates the approach to equilibrium; it doesn’t change it (see diagram and explanation in Dino proteins and blood vessels: are they a big deal?). The paper states that one of the two joining RNA strands has a triphosphate group on the end. This is very reactive, so would be an unlikely component of a primordial soup, and would not last long even if it appeared. So a supply of matching activated RNA pieces likewise shows unacceptable investigator interference.

See also Does ribozyme research prove Darwinian evolution? for a critique of an earlier Joyce paper on alleged ribozyme evolution, as well as Self-replicating peptides? which has many similarities to the recent Joyce claim.

Now Tour seemed to let this problem drop in the debate. It just seems that Professor Dave was assuming from the titles of the papers that they were relevant to the problem of life. Well, scientists always sound optimistic in their papers. I know, I had to write one for my masters degree thesis, and it was published. That’s why you have to look at the data and be skeptical. Sadly Dave wasn’t able to be skeptical. He wanted something to be true, so he just didn’t bother to interact with challenges to his view. The whole problem with the origin of life is that there are many counter-factual conditions, experimenter interferences, etc. that have to be done to make things work at all. Dave reads the titles of papers, but he just isn’t aware of how the experimenters have adjusted the experiments in ways that are not true to the conditions on the early Earth.

Dr. Tour lost his temper and shouted a lot during the debate, so I don’t think the debate is worth watching. However, if you want to watch a good debate on the origin of life, try this one between Dr. Fazale Rana vs Dr. Michael Ruse. And if you want to see a good explanation of the sequencing problem, check out this lecture by Dr. Stephen C. Meyer. (who has also debated atheists who didn’t lie, shout or insult him – and they even had doctoral degrees)

Polemics

Will computers and robots ever become self-aware?

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There is a very famous thought experiment from UC Berkeley philosopher John Searle that all Christian apologists should know about. And now everyone who reads the Wall Street Journal knows about it, because of this article. (Full text available at archive.md)

In that article, Searle is writing about the IBM computer that was programmed to play Jeopardy. Can a robot who wins on Jeopardy be “human”? Searle says no. And his famous Chinese room example (discussed in the article) explains why.

Excerpt:

Imagine that a person—me, for example—knows no Chinese and is locked in a room with boxes full of Chinese symbols and an instruction book written in English for manipulating the symbols. Unknown to me, the boxes are called “the database” and the instruction book is called “the program.” I am called “the computer.”

People outside the room pass in bunches of Chinese symbols that, unknown to me, are questions. I look up in the instruction book what I am supposed to do and I give back answers in Chinese symbols.

Suppose I get so good at shuffling the symbols and passing out the answers that my answers are indistinguishable from a native Chinese speaker’s. I give every indication of understanding the language despite the fact that I actually don’t understand a word of Chinese.

And if I do not, neither does any digital computer, because no computer, qua computer, has anything I do not have. It has stocks of symbols, rules for manipulating symbols, a system that allows it to rapidly transition from zeros to ones, and the ability to process inputs and outputs. That is it. There is nothing else.

Here is a link to the full article by John Searle on the Chinese room illustration.

By the way, Searle is a naturalist – not a theist, not a Christian. Now, let’s hear from a Christian scholar who can make more sense of this for us.

Here’s a related article on “strong AI” by Christian philosopher Jay Richards.

Excerpt:

Popular discussions of AI often suggest that if you keep increasing weak AI, at some point, you’ll get strong AI. That is, if you get enough computation, you’ll eventually get consciousness.

The reasoning goes something like this: There will be a moment at which a computer will be indistinguishable from a human intelligent agent in a blind test. At that point, we will have intelligent, conscious machines.

This does not follow. A computer may pass the Turing test, but that doesn’t mean that it will actually be a self-conscious, free agent.

The point seems obvious, but we can easily be beguiled by the way we speak of computers: We talk about computers learning, making mistakes, becoming more intelligent, and so forth. We need to remember that we are speaking metaphorically.

We can also be led astray by unexamined metaphysical assumptions. If we’re just computers made of meat, and we happened to become conscious at some point, what’s to stop computers from doing the same? That makes sense if you accept the premise—as many AI researchers do. If you don’t accept the premise, though, you don’t have to accept the conclusion.

In fact, there’s no good reason to assume that consciousness and agency emerge by accident at some threshold of speed and computational power in computers. We know by introspection that we are conscious, free beings—though we really don’t know how this works. So we naturally attribute consciousness to other humans. We also know generally what’s going on inside a computer, since we build them, and it has nothing to do with consciousness. It’s quite likely that consciousness is qualitatively different from the type of computation that we have developed in computers (as the “Chinese Room” argument, by philosopher John Searle, seems to show). Remember that, and you’ll suffer less anxiety as computers become more powerful.

Even if computer technology provides accelerating returns for the foreseeable future, it doesn’t follow that we’ll be replacing ourselves anytime soon. AI enthusiasts often make highly simplistic assumptions about human nature and biology. Rather than marveling at the ways in which computation illuminates our understanding of the microscopic biological world, many treat biological systems as nothing but clunky, soon-to-be-obsolete conglomerations of hardware and software. Fanciful speculations about uploading ourselves onto the Internet and transcending our biology rest on these simplistic assumptions. This is a common philosophical blind spot in the AI community, but it’s not a danger of AI research itself, which primarily involves programming and computers.

AI researchers often mix topics from different disciplines—biology, physics, computer science, robotics—and this causes critics to do the same. For instance, many critics worry that AI research leads inevitably to tampering with human nature. But different types of research raise different concerns. There are serious ethical questions when we’re dealing with human cloning and research that destroys human embryos. But AI research in itself does not raise these concerns. It normally involves computers, machines, and programming. While all technology raises ethical issues, we should be less worried about AI research—which has many benign applications—than research that treats human life as a means rather than an end.

When I am playing a game on the computer, I know exactly why what I am doing is fun – I am conscious of it. But the computer has no idea what I am doing. It is just matter in motion. The computer’s behavior is just the determined result of its programming and the inputs I supply to it. And that’s all computers will ever do. Trust me, this is my field. I have the BS and MS in computer science, and I have studied this area. AI has applications for machine learning and search problems, but consciousness is not on the radar. You can’t get there from here.

News

Does peer-reviewed research support a naturalistic origin of life?

4 Comments

So, on Friday night, there was a debate between Dr. James Tour and Professor Dave, an atheist with a bachelors degree who makes YouTube videos. The atheist spent his entire opening speech attacking Tour’s character. When Tour asked him to show him origin of life chemistry, he refused. The atheist shuffled through papers he apparently found by Googling, and read the titles. When asked what was in them, he said that he couldn’t remember.

But I was trying to decide who won the debate. There was one place where the atheist claimed that the early Earth had no molecular oxygen. He needs that to be true, in order for the chemistry that creates the building blocks of life to work. So I thought I would talk about a paper that refutes that. After my argument, I’ll talk about another mistake that the atheist made in the debate. Based on those two mistakes, I concluded that the atheist was speaking errors either intentionally or unintentionally, and therefore lost the debate.

Here’s a paper published in the prestigious peer-reviewed science journal Nature, entitled “The oxidation state of Hadean magmas and implications for early Earth’s atmosphere”.

Evolution News explains what the paper is about.

Excerpt:

A recent Nature publication reports a new technique for measuring the oxygen levels in Earth’s atmosphere some 4.4 billion years ago. The authors found that by studying cerium oxidation states in zircon, a compound formed from volcanic magma, they could ascertain the oxidation levels in the early earth. Their findings suggest that the early Earth’s oxygen levels were very close to current levels.

[…]Miller and Urey conducted experiments to show that under certain atmospheric conditions and with the right kind of electrical charge, several amino acids could form from inorganic compounds such as methane, ammonia, and water. Several experiments have been done using various inorganic starting materials, all yielding a few amino acids; however, one key aspect of all of these experiments was the lack of oxygen.

If the atmosphere has oxygen (or other oxidants) in it, then it is an oxidizing atmosphere. If the atmosphere lacks oxygen, then it is either inert or a reducing atmosphere. Think of a metal that has been left outside, maybe a piece of iron. That metal will eventually rust. Rusting is the result of the metal being oxidized. With organic reactions, such as the ones that produce amino acids, it is very important that no oxygen be present, or it will quench the reaction. Scientists, therefore, concluded that the early Earth must have been a reducing environment when life first formed (or the building blocks of life first formed) because that was the best environment for producing amino acids. The atmosphere eventually accumulated oxygen, but life did not form in an oxidative environment.

The problem with this hypothesis is that it is based on the assumption that organic life must have formed from inorganic materials. That is why the early Earth must have been a reducing atmosphere. Research has been accumulating for more than thirty years, however, suggesting that the early Earth likely did have oxygen present.

[…]Their findings not only showed that oxygen was present in the early Earth atmosphere, something that has been shown in other studies, but that oxygen was present as early as 4.4 billion years ago. This takes the window of time available for life to have begun, by an origin-of-life scenario like the RNA-first world, and reduces it to an incredibly short amount of time. Several factors need to coincide in order for nucleotides or amino acids to form from purely naturalistic circumstances (chance and chemistry). The specific conditions required already made purely naturalist origin-of-life scenarios highly unlikely. Drastically reducing the amount of time available, adding that to the other conditions needing to be fulfilled, makes the RNA world hypothesis or a Miller-Urey-like synthesis of amino acids simply impossible.

If you read the paper’s abstract, it finds that molecular oxygen would have been present by the end of the Hadean era. The earliest signs of life we have are from just after the end of the Hadean era. So, its undeniable that molecular oxygen was present. Did professor Dave lie, or was he just ignorant? One thing for sure, he pronounced that there was no oxygen in the same confident, insulting voice that he used for the rest of his presentation.

OK, so with that out of the way, Professor Dave also cited a paper in the journal Science. And there is an article on Creation.com by Johnathan Sarfati, who has a PhD in chemistry, about that very paper.

His post says:

It’s likely that the media reports you mention were referring to the paper in Science journal by Tracey Lincoln and Gerald Joyce.1 Quite often, the media hype just doesn’t match what was actually discovered. To be fair, Joyce, a well known chemical evolutionist, made it clear that he and his Ph.D. student Lincoln had not produced life, despite the headlines.2 Much earlier, Joyce admitted:

“The most reasonable assumption is that life did not start with RNA … . The transition to an RNA world, like the origins of life in general, is fraught with uncertainty and is plagued by a lack of experimental data.”3

Joyce and Lincoln started off with a fairly long RNA molecule. Given that nothing like RNA appears in Miller–Urey experiments, this already shows unjustified interference from an intelligent investigator. In fact, not even the building blocks, ribonucleotides, appear in such experiments, and they do not spontaneously form RNA. In fact, there are numerous chemical difficulties with obtaining RNA by blind undirected chemistry, the only sort allowed on the hypothetical primordial earth, as chemical evolutionist A.G. Cairns-Smith points out in his book Genetic Takeover4 (see extract at Cairns Smith: Detailed criticisms of the RNA world hypothesis). And it’s a huge step from RNA to the genetic code, its major use today.

Furthermore, this paper didn’t demonstrate replication but ligation—joining two small RNA pieces, previously designed to be a match to the longer strand. So this research already assumed not just one but three RNA strands. For this to be relevant to chemical evolution, the two pieces just by chance had to have pretty close to the complementary base pairs of the first piece—natural selection could not be invoked before reproduction.

Furthermore, since polymerization is unfavorable, the RNA pieces must be chemically activated in some way. Note that a catalyst merely accelerates the approach to equilibrium; it doesn’t change it (see diagram and explanation in Dino proteins and blood vessels: are they a big deal?). The paper states that one of the two joining RNA strands has a triphosphate group on the end. This is very reactive, so would be an unlikely component of a primordial soup, and would not last long even if it appeared. So a supply of matching activated RNA pieces likewise shows unacceptable investigator interference.

See also Does ribozyme research prove Darwinian evolution? for a critique of an earlier Joyce paper on alleged ribozyme evolution, as well as Self-replicating peptides? which has many similarities to the recent Joyce claim.

Now Tour seemed to let this problem drop in the debate. It just seems that Professor Dave was assuming from the titles of the papers that they were relevant to the problem of life. Well, scientists always sound optimistic in their papers. I know, I had to write one for my masters degree thesis, and it was published. That’s why you have to look at the data and be skeptical. Sadly Dave wasn’t able to be skeptical. He wanted something to be true, so he just didn’t bother to interact with challenges to his view. The whole problem with the origin of life is that there are many counter-factual conditions, experimenter interferences, etc. that have to be done to make things work at all. Dave reads the titles of papers, but he just isn’t aware of how the experimenters have adjusted the experiments in ways that are not true to the conditions on the early Earth.

Dr. Tour lost his temper and shouted a lot during the debate, so I don’t think the debate is worth watching. However, if you want to watch a good debate on the origin of life, try this one between Dr. Fazale Rana vs Dr. Michael Ruse. And if you want to see a good explanation of the sequencing problem, check out this lecture by Dr. Stephen C. Meyer. (who has also debated atheists who didn’t lie, shout or insult him – and they even had doctoral degrees)