Science is hard, therefore God

I took another peek into the nonsense the Discovery Institute is currently peddling. It’s depressingly shallow, a lot of motivated reasoning and twisted use of the evidence. For instance, Kirk Durston has an article titled Could Atheism Survive the Discovery of Extraterrestrial Life?, which, as an atheist who would be thrilled to pieces if we discovered alien life of a completely independent origin, seems peculiar.

Here’s his argument, though. The origin of life on Earth is a hard problem (agreed). Current models, as he understands them, suggest that it was an event of exceedingly low probability, so low that it was extremely lucky that it happened here, but it would be extremely unlikely that it would also happen in multiple places in our universe. Therefore, logic dictates the existence of a supernatural creator. It’s simply, I don’t understand this, therefore god. It also flops inelegantly into a common creationist theme that there are only two possible models, and if I find a weakness in yours, my model is automatically correct, even if my model has even more flaws, which I conveniently ignore.

The centerpiece of these kinds of articles is usually some juicy admission from real scientists that we don’t understand every detail of the origin of life, therefore, ha ha, god exists! It’s annoying, because this is how science works, by identifying problems and working to solve them, and creationists love to pervert that methodology into some kind of admission that science is failing and wrong. They never seem to notice, either, that the only way they can steal some credibility is by quoting the scientific literature, or rather, misquoting it.

Durston provides us with a prime example of this tactic.

A 2011 article in Scientific American, “Pssst! Don’t tell the creationists, but scientists don’t have a clue how life began,” summarized our lack of progress in the lab. Of course, there are plenty of scenarios, but creative story-telling should not be confused with doing science, or making scientific discoveries. With regard to “thousands of papers” published each year in the field of evolution, as Austin Hughes wrote, “This vast outpouring of pseudo-Darwinian hype has been genuinely harmful to the credibility of evolutionary biology as a science.”

Evolutionary biologist Eugene Koonin, meanwhile, calculates the probability of a simple replication-translation system, just one key component, to be less than 1 chance in 10^1,018 making it unlikely that life will ever spontaneously self-assemble anywhere in the universe. His proposed solution is a near-infinite number of universes, something we might call a “multiverse of the gaps.”

So three sources: Horgan, Hughes, and Koonin. Is he reporting their work accurately?

He comes closest with his interpretation of Horgan’s article. It is very pessimistic, and is describing the failings of the RNA world hypothesis.

But the “RNA-world” hypothesis remains problematic. RNA and its components are difficult to synthesize under the best of circumstances, in a laboratory, let alone under plausible prebiotic conditions. Once RNA is synthesized, it can make new copies of itself only with a great deal of chemical coaxing from the scientist. Overbye notes that “even if RNA did appear naturally, the odds that it would happen in the right sequence to drive Darwinian evolution seem small.”

This is true. Does anyone believe in a pure, straight RNA world anymore? Not that I know of. The evidence is clear that RNA played a bigger catalytic role in the distant past — we can find vestiges of that role in our cells even now — but the answer is going to be more complicated than just “RNA did it”. And of course, “RNA didn’t do it” doesn’t imply that God did it.

Unfortunately, Horgan’s alternative is panspermia, which even he doesn’t believe.

Of course, panspermia theories merely push the problem of life’s origin into outer space. If life didn’t begin here, how did it begin out there? Creationists are no doubt thrilled that origin-of-life research has reached such an impasse (see for example the screed “Darwinism Refuted,” which cites my 1991 article), but they shouldn’t be. Their explanations suffer from the same flaw: What created the divine Creator? And at least scientists are making an honest effort to solve life’s mystery instead of blaming it all on God.

I also think he is too pessimistic and doesn’t seem to be aware of the breadth of origin of life research. The recent ideas from Martin and Lane about chemistry and proton gradients have been a breath of fresh air, and reveals the flaw in creationist dismissals of our current understanding — we are constantly learning new things, and what seems like an unsolvable problem now may become a trivial obstacle with further discoveries. It’s one of the virtues of not constraining your search space to the pages of a single old book.

The Hughes article gets a prize for being the most egregiously distorted of the three. For one, it’s not about problems in origin of life studies at all — it’s about poor statistical analyses and over-reliance on adaptive hypotheses. Read the abstract; does this sound like a guy who is questioning evolution?

Sequences of DNA provide documentary evidence of the evolutionary past undreamed of by pioneers such as Darwin and Wallace, but their potential as sources of evolutionary information is still far from being realized. A major hindrance to progress has been confusion regarding the role of positive (Darwinian) selection, i.e., natural selection favoring adaptive mutations. In particular, problems have arisen from the widespread use of certain poorly conceived statistical methods to test for positive selection (1, 2). Thousands of papers are published every year claiming evidence of adaptive evolution on the basis of computational analyses alone, with no evidence whatsoever regarding the phenotypic effects of allegedly adaptive mutations. But it would be a mistake to dismiss Yokoyama et al.’s (3) study, in this issue of PNAS, of the evolution of visual pigments in vertebrates as more of the same. For, unlike all too many recent papers in the field, this study is solidly grounded in biology.

Hughes also does not propose god as an alternative. We’ve got a better option, one that’s actually supported by the evidence.

As well as natural selection, nonselective (or “non-Darwinian”) mechanisms may play a role in the origin of adaptive phenotypes. The most important non-Darwinian process is chance fluctuation in gene frequency or genetic drift, which can lead to the fixation of selectively neutral mutations (those with no effect on fitness) or sometimes even of slightly deleterious mutations. Kimura coined the term “Dykhuizen-Hartl effect” to describe an originally neutral mutation that later becomes adaptive in a changed environment, including a changed biochemical environment resulting from other amino acid replacements in the same protein.

You know how every time I criticize evolutionary psychology for failing to understand that there’s more to evolutionary biology than just selection, I get a swarm of indignant responses that I must be a creationist? This is the same thing. Hughes is properly pointing out that other forces can drive evolutionary change and criticizing the scientists who seem unaware of that, and for that, Durston thinks he’s a creationist ally…or at least, someone whose words can be twisted to pretend he’s an ally.

What about Koonin? This one is interesting, because Koonin is a brilliant thinker and theorist, and always seems willing to take on sacred cows. His book, The Logic of Chance: The Nature and Origin of Biological Evolution, actually does have a chapter on the mathematical probability of the origin of life, and he does use that 10-1,018 number (but not for the origin of a single component: his point is the coevolution of the multiple components of the transcription and translation apparatus is a difficult problem). It is! In the book, Koonin does suggest that a Multiple Worlds hypothesis might offer an out, but I found that as unconvincing as panspermia or worse, the god did it hypothesis.

The heart of his argument, though, is the power of the Darwin-Eigen cycle. That is, in a replicating system, there is selection for better fidelity of replication, which allows increases in size and complexity by drift, which is then refined further by selection. The existence of this effect means you can get this constant escalation of complexity and information in cells by the interaction of 3 components, fitness, genome size, and replication fidelity. He’s actually making a powerful argument against another key component of creationist ideology, that you can’t get increases in information without a designer. It’s inherent in the system!

However, he also points out that before the Darwin-Eigen cycle can start chugging along, it needs to cross a threshold. You need some minimal genome size, which you could imagine coming together by chance, but you also need some minimal fidelity — if every generation is randomized, the cycle is not going to be able to get a grip — and that requires functionality that is not likely to arise by pure chance processes. Koonin has no problem as a scientist pointing out that you need a certain threshold of complexity to get the engine of selection and drift going, and recognizes that the emergence of a translation system to convert RNA sequences to protein is a crucial, and difficult breakthrough. That chapter in his book is explaining that this really is a hard problem.

But note that Koonin does not argue that the only alternative is a god — gods make no appearances in the book. Nor does he advocate giving up. Maybe there is a solution, he just hadn’t thought of one in 2011.

So, here’s a paper from 2007, “On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization” which Durston does not cite, which proposes pathways by which the breakthrough could have been made.

The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a “frozen accident” or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.

We describe a stepwise model for the origin of the translation system in the ancient RNA world such that each step confers a distinct advantage onto an ensemble of co-evolving genetic elements. Under this scenario, the primary cause for the emergence of translation was the ability of amino acids and peptides to stimulate reactions catalyzed by ribozymes. Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing.

The authors are Yuri Wolf and Eugene Koonin.

So Durston is incorrect to assume that Koonin gave up with a feeble multiverse of the gaps hypothesis. That a scientist acknowledges the difficulty of an interesting and complex problem is not a prelude to surrendering and going to church; that’s the creationist solution.

It also produced a very interesting paper.

A gathering of freethoughtbloggers

We’re doing this again, only this time I’m planning ahead a bit more. At 3pm Central, I’ll be hosting a few more of the bloggers on this network — exactly who will be a surprise.

We’ll go live at 3 or thereabouts. I think you can also do a text chat here with us.

Our guest was Matt Herron of Fierce Roller, and we talked about the evolution of multicellularity (a very cool subject — he works on Volvox, which is right there on the boundary between colonial and multicellular organisms), a little bit about weird creationist ideas, and a bit about social justice in the science community. Check out his blog!

Strikes in spaaace!

Great moments in labor history I was unaware of: did you know the Skylab astronauts went on strike?

Then it turns out that NASA is a bad boss.

More details here; the eventual outcome was that NASA never let any member of that mutinous crew fly into space again. (NASA isn’t alone, since Arianespace also has a messy labor history.)

They don’t understand logic or science

The Discovery Institute is still singing the same tune. It’s revealingly tone-deaf, too. David Klinghoffer champions falsification as a key strategy, and he doesn’t even understand it.

Want to falsify the theory of intelligent design? Here’s one way.

Show with a convincing computer simulation – no cheating allowed — that the infusion of biological information in the Cambrian explosion could occur absent the intervention of a guiding intelligence: artificial life in a variety as we see in the Cambrian event, but without design.

He starts out with an interesting proposal: falsify his favored theory. That’s how science works. We propose a hypothesis, and then we batter it about trying to find the flaws and identify tests that would evaluate whether our proposal actually works. I read that and thought that finally we were going to see a testable claim about Intelligent Design creationism.

No such luck. Read the next sentence, and he isn’t taking a critical look at ID creationism: he announces that we have to come up with a test to prove our theory is possible. That isn’t a falsification test! It’s the opposite of falsification — we have to prove every detail of evolutionary theory is true, or he gets to claim his bullshit idea is true.

Wesley Elsberry takes on the bizarre infatuation of creationists with binary models. This is good stuff.

There is nothing in falsification about how validating some other concept makes a concept false. This is a popular misconception in antievolution circles, though, as one finds this particular mistake in the output of various high-profile “intelligent design” creationists. It is a long-running misconception, a zombie pseudoscience if you will, as I was pointing this out directly to William Dembski and Michael Behe at a conference in 2001, and it continued to put in appearances from them later.

One might wonder why IDC advocates have such trouble with this. I think that it follows from confusing and conflating their “two-model” worldview with an actual concept in philosophy. The “two-model” view was a component of “scientific creationism” that has propagated through the various renamings that have followed it. The “two-model” view states that there are only two possible models, creationism or evolution, and evidence against one is evidence for the other. In other words, that one’s likelihood of belief in one can be bolstered by reducing one’s likelihood of belief in the other. Or, putting it in the terms that likely led to the confusion, the falsity of one model attests to the truth of the other. This whole notion is rank nonsense, and has been exposed as rank nonsense for decades. For example, Francisco Ayala, as a witness in the McLean v. Arkansas case in 1981 was questioned about the soundness of the “two-model” view by an unfortunate lawyer named Williams. Ayala said, “Surely you realize that not being Mr. Williams in no way entails being Mr. Ayala!” Judge Overton in his decision also noted the inherent problems with what he termed “a contrived dualism”. This was referenced in the Kitzmiller v. Dover decision as well, where it was noted that the same erroneous argumentation had been carried forward to that case.

I also take exception to creationist’s constant focus on “computer models”. Computer models are useful tools for assessing some ideas, but they’re no substitute for real data…especially when the events you’re pursuing are not simple, and have a million different equally valid ways of producing a result. Again with the binary thinking: Cambrian evolution will not be described with a “yes” or a “no”.

I’m also going to call shenanigans on his assumptions. The Cambrian was not an “event”. It was a long, multi-million year series of events, and it was driven by multiple phenomena. There was the pre-Cambrian bioturbation revolution, in which the evolution of worms with hydraulic skeletons drove massive turnover of nutrients in sediments; there was the gradual increase in atmospheric oxygen, which made more energetic organisms possible; there was a long history of evolution of animal lineages before the Cambrian that set the stage with breadth and depth of diversity. How do you “simulate” all that on a computer? And why bother, because you know creationists like Klinghoffer will simply reject any result that shows an increase in complexity without an infusion of biological information (whatever that means) as cheating?

Most importantly, no one with any sense or competence would carry out such a simulation to falsify creationism, an endeavor with no reward, since they’ll just move the goalposts as they always have.

Can you breed a Chihuahua and a Great Dane?

In this conversation yesterday, a common question came up: can you breed a Chihuahua and a Great Dane? It seems like it ought to be doable in one direction, if you cross a tiny little Chihuahua male to a large Great Dane female, but the question is what will happen if you cross a Great Dane male to a Chihuahua female — does the female swell up with giant puppies inside her until she looks like a watermelon with four tiny legs sticking out to the side, and then she explodes? That’s the cartoon version, anyway. I threw out my general recollection that no, fetus size is maternally regulated, so that doesn’t happen at all, but I didn’t recall any specifics, and said I’d look them up.

I did. It turns out there’s nothing but anecdotal bogosity out there on the interwebs. A lot of people cite this blog post from Ponderings from Pluto.

“It took a lot of trial and error,” said Marty Samson, a canine researcher with the University of South Texas. “At first, we tried having a Great Dane impregnate a Chihuahua, but that didn’t work: the puppies’ heads were bigger than the Chihuahua mother. We tried to deliver the puppies through Caesarian section four weeks early, but they were not viable enough to survive on their own.”

Neither the Great Mexicans/Chi-dane-danes nor their Chihuahua mother survived, leading Samson to conclude the only way to breed the dogs was to have a male Chihuahua mate with a female Great Dane.

Samson’s team had to erect a ladder for the male to climb since, even with the female Great Dane laying on the ground, his climbing on top of her was similar to an adult man having to climb a small structure.

Hey, everyone! It’s a satire site. It’s fake news. It even says so on the blog. I decided to check it out anyway, just in case. First problem: There is no such thing as a University of South Texas. There is a South Texas College, a Texas Southern University, a University of Texas Southwest, etc. But nope, sorry, we can’t ask the IRB at a fictional university to explain what they were thinking to allow this experiment.

I went further and checked PubMed, and there actually was an MD Samson who published a couple of papers in veterinary journals in the 1980s. They were not breeding experiments.

Other people cite Reddit (ugh, please). Nope, this is garbage, too. I also checked Snopes, just in case, but no joy.

It seems that either the experiment has not been done (purebred dogs are expensive, and owners are usually solicitous about breeding them appropriately; it’s also quite likely that this kind of research might be frowned upon as pointless), or it has been done and failed. It’s entirely possible that the two breeds are not interfertile. Or it may have been done, and the results were mundane and uninteresting, and not at all noteworthy.

I’m going to guess at the latter likelihood. I hit the developmental biology textbooks, and while it didn’t have the specific Chihuahua/Great Dane cross, Ecological Developmental Biology did describe a similar experiment in horses. Shetland ponies are small horses, less than 4 feet tall at the shoulder. Shire horses are huge draft horses. What if you cross them? The reciprocal crosses have been done, and no female Shetland ponies were exploded in the process. This diagram summarizes the results of the crosses.

The answer is simple: fetal size is regulated by the mother, and the foals are always of a size appropriate to the maternal breed. That makes sense; growth would be limited by the availability of maternal nutrients. The size of the offspring in different crosses are also correlated with uterus and placenta size. There is also evidence from human children.

When the same woman has borne children with different men, the birth weights of the babies are usually similar. However, when the same man fathers children with different women, the birth weights are often very different.

The final answer: the definitive experiment either has not been done or has not been reported in a credible source, but on the basis of other experiments, I’d predict that a Chihuahua mother would give birth to Chihuahua-sized puppies, no matter how big the father dog.

It’s a tried and true solution!

When a conservative party has trouble meeting the demands of a progressive future, they never consider compromising with the liberals: they always reach back and compromise with the most backward idiots they can find. The Tories in the UK fail to form a majority in the recent election, so what do they do? Revise their policies to be more in line with the electorate? Don’t make me laugh. They decide to form a coalition with the crazies. The DUP. Ian Paisley’s rotting corpse. This party:

It reminds me of how the Republicans in the US are making hay with an unholy union of Libertarians and the Religious Right. It just leads to greater decay.

Shorter David Brooks

The Driftglass report on Brooks’ latest: We can’t investigate Trump because look at all the misery caused by investigating the Clintons!

Instead, Mr. Brooks turns the entire Republican attempted-coup-by-impeachment scheme — from Whitewater through Blue Dress — into a more-in-sorrow-than-in-anger cautionary tale about the consequences of investigating presidents generally:

If past is prologue, this investigation will drag on for a while. The Clinton people thought the Whitewater investigation might last six months, but the inquiries lasted over seven years. The Trump investigation will lead in directions nobody can now anticipate. When the Whitewater investigation started, Monica Lewinsky was an unknown college student and nobody had any clue that an investigation into an Arkansas land deal would turn into an investigation about sex.

This investigation will ruin careers far and wide. Investigators go after anybody they think can yield information on the president. Before the Whitewater investigators got to Clinton they took down Arkansas Gov. Jim Guy Tucker, Webb Hubbell, Susan and Jim McDougal, and many others.

But of course, The Past can only be prologue for those who remember it fully and clearly. So how perfectly ironic it is that doing this very thing — remembering The Past fully and clearly — is also the greatest single existential and financial threat to Conservatism generally, and to Mr. David Brooks’ ability to afford his new multi-million dollar Capitol Hill retreat specifically.

The media are trying desperately to exonerate Republicans and blame the Democrats for our current situation — and I agree in part with the latter, because the Democratic party has lost its soul in a mad scramble for corporate dollars — but we cannot allow this kind of selective amnesia. The Republican party is a treacherous swamp of greed and treachery, and the people who voted for Trump are…

I would say much worse things about David Brooks.