The non-believers review of “The Case for Faith” – Objection #3, part 2

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On abiogenesis:

This section begins with a short discussion on Darwin’s speculative remark about life forming spontaneously in “some warm little pond”. Bradley comments:

But simultaneous with the publication of Darwin’s Origin of the Species, Francesco Redi demonstrated that meat that was kept away from flies never developed maggots. Then Louis Pasteur showed that air contains microorganisms that can multiply in water, giving the illusion of spontaneous generation of life. He announced at the Sorbonne in Paris that ‘never will the doctrine of spontaneous generation recover from the mortal blow of this simple experiment.’.. But then in the 1920s, some scientists said they agreed with Pasteur that spontaneous genesis doesn’t happen in a short time frame. But they theorized that if you had billions and billions of years — as the late astronomer Carl Sagan liked to say — then it might really happen after all.” (p.132-133)

Fortunately, Bradley doesn’t try to play the game that a lot of creationists try — claiming that Pasteur proved abiogenesis can’t happen, as if atheists must deny the results of Pasteur’s experiment. The idea of abiogenesis is that the formation of life is unlikely, but given lots of time and all the surface area of planets all over the universe, some fortunate accident happens. That’s a very different situation than the tiny beaker and short time-frame of Pasteur’s experiment. To use an analogy, abiogenesis says that if you buy a bunch of lottery tickets each week, then over a long period of time, you’ll eventually win the jackpot. Creationists argue that Pasteur proved that no one wins the lottery: go out and buy one ticket, and when you don’t win, it proves that no one ever wins.

Additionally, oxygen prevents the formation of organic chemicals. Earth’s early atmosphere had very little oxygen, but modern earth has a lot of oxygen – produced by photosynthesis. This is another way Pasteur’s experiment is limited: it’s evidence against spontaneous generation inside the modern, oxygen-rich atmosphere. I should reiterate that Strobel doesn’t make this creationist argument, but it’s a common claim among creationists in general. For example, Answers in Genesis: “Pasteur’s work should have dealt the death blow to the idea of spontaneous generation. But spontaneous generation is an essential part of the theory of evolution.” (Link)

I remember being taught in school about [Miller-Urey's] landmark experiment in which he recreated the atmosphere of the primitive earth in a laboratory and shot electricity through it to simulate the effects of lightning. Before long, he found that amino acids — the building blocks of life — had been created. I can remember my biology teacher recounting the experiment with an infectious enthusiasm, suggesting it proved conclusively that life could have emerged from nonliving chemicals.
…
Bradley: “For a while, evolutionists were euphoric. But there was a major problem with the experiment that has invalidated its results.”

I had never been taught anything in school about the Miller experiment being fatally flawed. “What was the problem?” I asked.

“Miller and Oparin didn’t have any real proof that the earth’s early atmosphere was composed of ammonia, methane, and hydrogen, which Miller used in his experiments. They based their theory on physical chemistry. They wanted to get a chemical reaction that would be favorable, and so they proposed that the atmosphere was rich in those gases. Oparin was smart enough to know that if you start with inert gases like nitrogen and carbon dioxide, they won’t react.”

My eyes got wide. This was a devastating critique of Miller’s experiment. “Are you saying that the deck was stacked in advance to get the results they wanted?” I asked, incredulity in my voice.

“Essentially, yes,” he replied.

“What was the real environment of the early earth like?” I asked.

“From 1980 on, NASA scientists have shown that the primitive earth never had any methane, ammonia or hydrogen to amount to anything,” he said. “Instead, it was composed of water, carbon dioxide, and nitrogen — and you absolutely cannot get the same experimental results with that mixture. It just won’t work. More recent experiments have confirmed this to be the case.”

“So the scientific significance of Miller’s experiment today…,” I began, prompting Bradley to finish my sentence.

“… is zilch,” he said. “When textbooks present the Miller experiment, they should be honest enough to say it was interesting historically but not terribly relevant to how life actually developed.” (p.134-136)

First of all, they accuse Miller and Urey of “stacking the deck” – to put it more bluntly: cheating – to get their results. It’s as if they want to undermine their credibility as scientists. But, is it cheating if they didn’t know what the early atmosphere was actually like? Bradley says it was known from the 1980s that “the primitive earth never had any methane, ammonia or hydrogen” – but the Miller-Urey experiment happened in 1953.

Second, Miller-Urey’s experiment was not significant simply as a model of the formation of organic molecules on a primitive earth, but it’s significant because it shows the formation of organic molecules using nothing but some simple molecules plus energy. It established an example of blind forces creating organic molecules. (And it explains the discovery of organic molecules on meteorites, like the Murchison meteorite: “[It] was found to contain common amino acids such as glycine, alanine and glutamic acid but also unusual ones like isovaline and pseudoleucine… A complex mixture of alkanes was isolated as well which was similar to that found in the Miller-Urey experiment.”) IDists/creationists never seem to notice that the Miller-Urey experiment also provides a counterexample against their “second law of thermodynamics” argument against evolution.

Third, there have been some recent claims that the early atmosphere did contain methane and ammonia.

Fourth, despite Bradley’s unequivocal statement that “you absolutely cannot get the same experimental results with [the mixture of water, carbon dioxide, and nitrogen]. It just won’t work.”, recent experiments have done exactly that. Jeffrey Bada (origin of life researcher) has shown that the addition of iron or carbonate minerals (limestone) to that mixture allows amino acids to form. He discovered that an atmosphere of H20, CO2, and N2 created nitrates that destroyed amino acids and turned the water acidic, which prevented new amino acids from forming. The addition of iron and carbonate minerals (as would’ve existed on earth) neutralized the nitrates and acid, allowing the amino acids to form again – just as in the Miller-Urey experiment. (Source)

This is one of the problems with Intelligent Design in general: they claim that such-and-such cannot happen by naturalistic forces, therefore God must’ve done it. The problem is that the “naturalistic forces cannot do X” argument – while it has some usefulness, it’s an unstable argument because even well-educated people (with PhDs in this case) can be wrong about the limitations of naturalistic forces. (Hmm, wasn’t Bradley the guy that Strobel described earlier as “a scientist concerned with accuracy… making sure to acknowledge nuances and not overstate his conclusions”?) Every once in a while, reality will come and smack you upside the head a few years after you claim nature can’t do X. And when a group (IDists/creationists) has a desire for something to be inexplicable so that they can insert their god explanation, then there is a tendency to rush to that conclusion prematurely. Heck, I see lots of cases where IDists/creationists will say such-and-such is inexplicable by naturalistic forces even when it it demonstrably untrue.

Strobel and Bradley then move on to the problem of getting the right amino-acids together to form something “living” – it can “process energy, store information, and replicate”.

“Essentially, you start with amino acids. They come in eighty different types, but only twenty of them are found in living organisms. The trick, then, is to isolate only the correct amino acids. Then the right amino acids have to be linked together in the right sequence in order to produce protein molecules…. It would be unguided by any outside help. And there are a lot of other complicating factors to consider.”

“Such as what?”

“For instance, other molecules tend to react more readily with amino acids than amino acids react with each other. Now you have the problem of how to eliminate these extraneous molecules. Even in the Miller experiment, only two percent of the material he produced was composed of amino acids, so you’d have a lot of other chemical material that would gum up the process.

“Then there’s another complication: there are an equal number of amino acids that are right- and left-handed, and only the left-handed one work in living matter. Now you’ve got to get only these select ones to link together in the right sequence. And you need the correct kind of chemical bonds — namely, peptide bonds — in the correct places in order for the protein to be able to fold in a specific three-dimensional way. Otherwise, it won’t function.
…
“In the same way, perhaps one hundred amino acids have to be put together in just the right manner to make a protein molecule… Now you have to bring together a collection of protein molecules — maybe two hundred of them — with just the right functions to get a typical cell.” (p.137-139)

I might also add that even if this unlikely scenario was correct, the result would be an organism composed of only animo-acids. Because there is no heredity molecule (DNA or RNA), this “organism” would be incapable of producing offspring – so it would be a short-lived sterile little curiosity.

Over the next ten pages, Bradley then considers (and dismisses) some ideas people have come up with to overcome the difficulties of abiogenesis:

(1) Random chance caused all these organic molecules to be in the right place at the right time. Given the number of combinations involved, Bradley dismisses this.
(2) “Chemical Affinity” – that there is some inherent attraction between the right pieces that cause them to fall together in the right sequence because of chemical bonding preferences.
(3) Self-Ordering tendencies – like water molecules spiraling down a drain, organic molecules order themselves somehow.
(4) Seeding from space – life emerged somewhere else and was brought here (e.g. by a meteor), but this doesn’t explain the initial start or why life was able to form elsewhere.
(5) Vents in the ocean – hot vents provided a place for life to begin and he says it might’ve provided an unusual energy source for early life, but that the heat would’ve likely destroyed organic molecules.
(6) Life from clay – that clay was a substrate that helped organic molecules connect together. Bradley dismisses this possibility saying that clay wouldn’t help the amino-acids link up in the correct sequence.

From the standpoint of probability, the scenario outlined by Bradley would be unlikely to produce even the smallest bacteria (Carsonella has only 182 genes and 160,000 nucleotides) or virus (the Bacteriophage MS2 virus has a genome of only 3569 nucleotides). From the standpoint of probability, both are well outside the possibility of spontaneous generation. (Assuming we allow any two nucleotides to work in each position, then a string of 3569 nucleotides has 2.37 x 10^1074 combinations.) Bradley hammers this point home:

“[T]he mathematical odds of assembling a living organism are so astronomical that nobody still believes that random chance accounts for the origin of life. Even if you optimized the conditions, it wouldn’t work. If you took all the carbon in the universe and put it on the face of the earth, allowed it to chemically react at the most rapid rate possible and left if for a billion years, the odds of creating just one functional protein molecule would be one chance in a 10 with 60 zeros after it.” (p.141)

Now, the argument is a pretty good one, and I’m not surprised that people called this chapter one of Strobel’s strongest. Except one thing: with all the details and counterarguments Bradley goes into, it’s easy to forget to ask the question: “Do scientists think that pathway outlined by Bradley is the one that explains how life came from non-life?” The answer is “No”. The Miller-Urey explanation outlined by Bradley fell out of favor with abiogenesis researchers in the early 1980s. Instead, they favor some different scenarios. This graph sums up the situation pretty well:

Bradley has argued against abiogenesis the same way that all creationists do: calculate the probability of jumping form simple molecules to a fully-functioning organism, and ignore the fact that abiogenesis researchers don’t believe things happened that way.

It’s worth saying that abiogenesis is still a mystery. There are a number of theories (and the Origin of Life entry at wikipedia has summaries of them). There has been some interesting discoveries on the spontaneous formation of fatty-acid vesicles (which would act like simple cell-walls), and also how clay helps RNA form chains (albeit, random chains), and the discovery that RNA can act as both a hereditary molecule and as an enzyme like proteins (ribozyme).

Some people have proposed that early life was composed of RNA, and the RNA acted both as the hereditary molecule and did the job of proteins. The downside to this theory is that RNA doesn’t form well spontaneously from simpler chemicals, so it’s a mystery how to get enough of these molecules around to form chains and replicate.

From Discover Magazine’s article on Jack Szostak’s research into RNA-based origins of life:

In the early 1980s Tom Cech, then a young biologist at the University of Colorado at Boulder, uncovered evidence that RNA does more than simply relay messages from DNA to proteins. In an experiment that earned him a Nobel Prize, he found that a single-celled creature named Tetrahymena possessed some RNA molecules that could act like simple enzymes. These molecules, which came to be known as ribozymes, twisted into a complicated snarl that allowed them to hack themselves apart. In other words, RNA could carry information like DNA and carry out biochemistry the way proteins do.
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Szostak decided to expand his research on the RNA world: He set out to find a simple way to enclose his ribozymes… They began by experimenting with fatty acids. These molecules, which make up the bulk of cell membranes, were likely to have been floating in the prebiological oceans of Earth. A number of nonbiological reactions can give rise to fatty acids; they’ve even been found in meteorites. Fatty acids also have the fortunate habit of being naturally attracted to one another, forming sheets that eventually curl in on themselves and create bubbles.

Hanczyc and Fujikawa began studying the bubbles, known as vesicles, to see if they could grow and divide like cell membranes without the help of a lot of cellular machinery. In the 1990s Italian chemist Pier Luigi Luisi figured out how to make vesicles grow by adding loose fatty acids to their solution; gradually, some of the molecules slipped into the vesicles and expanded them. Hanczyc and Fujikawa spent three years perfecting the process to make it more efficient. “Right now, 90 percent of the material we add gets incorporated into the vesicles we already have,” says Hanczyc.
…
One afternoon in the summer of 2002, Szostak was sitting in his office when Hanczyc and Fujikawa walked in with a vial of murky liquid. His students had added a kind of clay known as montmorillonite to their solution of fatty acids. Somehow the clay sped up the rate of vesicle formation 100-fold. “We spent years working on getting the growth and division stuff to work. That was a pain,” says Hanczyc. “But the clay worked the first time.”

Clay had already proved to be potentially important in the origin of life. In the 1990s biochemist James Ferris of Rensselaer Polytechnic Institute showed that montmorillonite can help create RNA. When he poured nucleotides onto the surface of the clay, the montmorillonite grabbed the compounds, and neighboring nucleotides fused together. Over time, as many as 50 nucleotides joined together spontaneously into a single RNA molecule. The RNA world might have been born in clay, Ferris argued, perhaps the clay that coated the ocean floor around hydrothermal vents.

“The thing that’s interesting is that there’s this one mineral that can get RNA precursors to assemble into RNA and membrane precursors to assemble into membranes,” says Szostak. “I think that’s really remarkable.”

As Hanczyc and Fujikawa analyzed their new vesicles, they made an even more remarkable discovery. Some of the grains of [clay] actually wound up inside the vesicles. Their next step was obvious. “It was very straightforward,” says Hanczyc. “You just mix the RNA with clay, and mix it with the fatty acids, and voilà, you have RNA on the clay particles inside the vesicles.” (Discover Magazine: What Came Before DNA?)

A theory about the first metabolism is that inorganic matter (iron monosulfide) formed the first catalysts, forming the first metabolism. (And life still uses the same inorganic chemicals found near underwater vents as catalysts, hinting that they may be on to something.) Later, genetic material come along and regulated, refined, or piggybacked on these metabolic pathways.

The slow trickle of hydrogen and carbon dioxide through such [thermal underwater] chambers and across the iron sulfide catalyst promotes formation of acetate, according to Russell and Martin. Acetate is a key intermediate in virtually all biosynthetic pathways, and in modern cells, enters these reactions tethered to sulfur. In modern bacteria, the two enzymes that make acetate depend on a catalytic core of iron, nickel, and sulfur, arranged almost exactly as they are in the free mineral itself. “In other words,” Russell and Martin have written, these enzymatic metal clusters “are not inventions of the biological world, rather they are mimics of minerals that are indisputably older, and which themselves have catalytic activity in the absence of protein” (Public Library of Science: Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks)

Some think they might’ve discovered the first metabolic cycle based on thermal underwater vents, sulfur, and requiring only two enzymes:

While other microbes make methane from carbon monoxide, this particular species (one “Methanosarcina acetivorans”) also produces acetate–better known as vinegar. Ferry and House, in collaboration with Barry Karger at Northeastern University, showed how carbon monoxide is converted to acetate in a biochemical pathway that includes a well-known pair of enzymes, called Pta (”phosphotransacetylase”) and Ack (”acetate kinase”). The two researchers realized that, in the presence of minerals containing iron sulfides, acetate could have been catalytically converted to a sulfur-containing derivative called an acetate thioester. Attached to the mineral surface, a “protocell” containing primitive forms of these two enzymes could then have generated biochemical energy by converting this derivative back to acetate. Excreting acetate would have completed the cycle. “Our paper,” House suggests, “contains a very sensible early metabolism.” “It is quite possible,” Ferry says reverently, “that this could be the first metabolic cycle.” (Methane-belching bugs inspire a new theory of the origin of life on Earth)

The basic idea behind modern abiogenesis research is that a simple system came into place (much simpler than the ‘whole living organism’ described by Bradley, and certainly not containing 200 genes), and slowly built into something more complicated.

The discovery that clay helps RNA form chains, and causes fatty acids to pinch-off into small vesicles containing those RNA chains is one of discoveries that comes out of the blue. That’s one of the interesting things about abiogenesis research – something won’t be forming the way scientists want – but then they discover that a material found in nature does the job. It was reminiscent of the discovery that limestone or iron could help water, carbon dioxide, and nitrogen form amino acids. These kinds of “out of the blue” discoveries makes me think the abiogenesis possibility isn’t the shut-case Bradley makes it out to be.

In the end, it’s still a mystery. It might be like lightning, planetary movement, or the origin of the species – stuff that used to be mystifying and attributed to God, but ultimately had a naturalistic origin. But, it would be an assumption to jump the gun and say the origin of life is like those other things. I still have to admit that I still feel a little bit uneasy seeing abiogenesis presented in museums as if it’s a known fact.

Additional information:
Discover Magazine: What Came Before DNA?
Public Library of Science: Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks
Methane-belching bugs inspire a new theory of the origin of life on Earth
TalkOrigins: The Origin of Life
TalkOrigins: Lies, Damned Lies, Statistics, and Probability of Abiogenesis Calculations

But, back to Strobel – Bradley goes on to describe the “dismal” state of the origins-of-life research, quoting various researchers, saying that pessimism pervades the entire field. (And I’m not familiar enough with the field to gauge how accurate Bradley describes the feelings of researchers, although I have already noted a number of discoveries earlier in this article — most of them made since the publication of Strobel’s book.)

Time after time, origin-of-life scientists have come up empty when they’ve tried to theorize how chemicals could evolve into matter.
…
“What does one do with this scientific stalemate?” I asked Bradley.

“That depends a lot on one’s metaphysics,” he said. “Shapiro, whom I highly respect, says there must be some physical laws we haven’t discovered yet which will eventually show us how life arose naturally. But there’s nothing in science that guarantees a natural explanation for how life began…”

“Then what,” I said, “is your own best hypothesis?”
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“If there isn’t a natural explanation and there doesn’t seem to be the potential of finding one, then I believe it’s appropriate to look at a supernatural explanation. I think that’s the most reasonable inference based on the evidence.”
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“What prevents more scientists from drawing that conclusion?”

“Many have reached that conclusion. But for some, their philosophy gets in the way. If they’re persuaded ahead of time that there isn’t a God, then no matter how compelling the evidence, they’ll always say, ‘Wait and we’ll find something better in the future.’ But that’s a metaphysical argument. Scientists aren’t any more objective than anybody else. They all come to questions like this with their preconceived ideas.”
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“So you think the facts point convincingly towards a Creator?”

“Convincingly is too mild a term,” he replied. “The evidence is compelling. ‘Convincing’ suggests it’s a little more likely than not; ‘compelling’ says you have to really work hard not to get to that conclusion.” (p.149-152)

Maybe it’s just my agnostic/atheist position, but I don’t think Bradley has compellingly shown that the origins-of-life question is unanswerable. It would be compelling if I actually believed Bradley’s pathway for life: that all 200 genes would have to be simultaneously and spontaneously present for life to exist. The way the issue is presented in the book makes it seem persuasive, but looking at external sources makes Bradley’s whole presentation look rather narrow and overly pessimistic.

Further, regarding the entire Intelligent Design movement in general: the only reason they’re looking inside the sciences for evidence of God is because God is so ridiculously absent from every other part of our world. Because God isn’t doing miracles, and because the “resurrected” Jesus isn’t walking around talking to people today (as the gospels allege he did after his crucifixion) they have to look into probabilistic arguments in chemistry. Having come up with no evidence in the real world, they have to look through a microscope to find their ever-elusive evidence of God.

Then, Bradley then makes a rather odd argument called “reasoning by analogy”, where he quotes astronomer John F.W. Hershel:

“If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself.” (p.153)

He then goes on to make the argument that DNA is composed of words and information, like a written language. Because written language has an author, how can we deny that DNA must also have an author?

“Now, when we see written language, we can infer, based on our experience, that it has an intelligent cause. And we can legitimately use analogical reasoning to conclude that the remarkable information sequences in DNA also had an intelligent cause. Therefore, this means life on earth came from a ‘who’ instead of a ‘what’.”

Undeniably, it was a powerful and persuasive argument. (p.154)

Wow. And Strobel is impressed with that “analogical reasoning” argument? It seems really poor to me, and sounds like a recipe for creating crackpot theories. For example, we’ve all heard the metaphor that the brain is like a computer. Now, all computer viruses are written by people (usually maliciously). Reasoning by analogy, we conclude that all illnesses of the mind are therefore be products of malicious entities (demons or malicious people). Of course that’s ridiculous. The whole “analogical reasoning” idea is just a rhetorical device to get the reader thinking along a particular path and then changing the situation, knowing their mind will follow a similar path. You sort of wonder how much he knows about the mechanism of evolution with that argument. Evolutionary systems are quite capable of producing and optimizing sequences of DNA. (And ID promoters almost always show that they are ignorant of this simple evolutionary mechanism.)

And just to be clear, Bradley isn’t simply talking about the DNA inside the first organism, but he’s talking about the DNA in all of life on earth. To say that all DNA must be the written words of an Intelligent Designer is a ridiculous argument when you understand how evolutionary mechanisms can produce useful DNA.

“In other words, what is encoded on the DNA inside every cell of every living creature is purely and simply written information.” (p.153)

“Each cell in the human body contains more information than in all thirty volumes of the Encyclopedia Britannica. It’s certainly reasonable to make the inference that this isn’t the random product of unguided nature, but it’s the unmistakable sign of an Intelligent Designer.” (p.155)

Further, if we assume all DNA was coded by the great designer in the sky, then we must also conclude that HIV, malaria, tapeworms, flesh-eating bacteria, smallpox, leprosy, rabies, and so on are also created by God. (And Behe did take the step of saying that malaria was designed – though most IDists distance themselves from that disturbing claim.) Or would Bradley suddenly substitute “demon” in place of “Intelligent Designer” in that case? Although, if that were true, you’d think those demons would be a whole lot better at spreading drug-resistant HIV, bringing back the extinct strain of influenza that killed 20 million people around the end of World War 1, or returning smallpox to the earth (it caused 500 million deaths in the 20th century, but was eradicated by a worldwide vaccination campaign and hasn’t been seen since the 1970s).

Bradley then continues to turn the “we don’t know” into irrefutable evidence that “goddidit”:

“Despite all their efforts, they haven’t even come up with a single possibility [for the origin of life] that even remotely makes sense. And there’s no prospect they will. In fact, everything is pointing the other way — in the unmistakable direction of God. Today it takes a great deal of faith to be an honest scientist who is an atheist.” (p.155)

I also can’t help wondering – even if we accepted everything Bradley has written here, why is his “Intelligent Designer” unmistakably God? Theoretically, it could be an alien race. Although, if we accept Bradley’s arguments – it would be an alien race with a biology not like our own (thus avoiding the same origin-of-life issues).

Strobel then concludes that the idea of a naturalistic explanation for life is based on seems-persuasive-but-isn’t-really evidence. As for Strobel’s question, “why does the persuasive evidence of science compel so many to conclude that the unguided process of evolution accounts for life?” (p.27), well, he never attempted to find out what that persuasive evidence was, or why people believe it. The closest he came to answering that question was quoting Behe saying that many people, “just don’t want there to be anything beyond nature”, and that he (Strobel) “was more than happy to latch onto Darwinism as an excuse to jettison the idea of God so [he] could unabashedly pursue [his] own agenda in life without moral constraints.” (p.126)

The next objection Strobel is going to tackle? “If God is morally pure, how can he sanction the slaughter of innocent children as the Old Testament says he did?”

Next: The non-believers review of “The Case for Faith” – Objection #4, part 1

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