The meeting circuit

Some people expressed surprise that I was at the Midwest Zebrafish meeting. They have meetings about zebrafish? How weird. Only not. What I find weird is that people are unaware of this mundane part of the science experience, so I thought I’d briefly explain it.

Every sub-sub-discipline does this. There are zebrafish meetings, fly meetings, worm meetings, mouse meetings, bat meetings. There are meetings dedicated to specific diseases. There are meetings for organs and tissues: brain meetings, kidney meetings, hair cell meetings, enteric nervous system meetings, ear meetings. There are meetings dedicated to the mechanisms of vomiting. There are meetings with 50 attendees, others with 30,000. They are going on in every city of the country all the time. We are right there under your nose.

Why do we hold these meetings?

  • Practice. It’s part of student training.

  • Networking. Bringing together people with similar interests is a great way to make connections.

  • Sharing new ideas. Sometimes an experiment might not be right for publication, so you get feedback on preliminary results.

  • Inspiration. We learn all kinds of cool stuff we can try in our labs.

  • Good times. You know how nice it is to hang out with weirdos with the same interests?

Who gets to go? Anyone. They’re open to anyone willing to pay for registration (which may be a few hundred dollars). You don’t want to go. It’s all very esoteric. This is where we let it all hang out: talks are wall-to-wall high-density jargon in which we assume everyone knows all the basics, or even the advanced stuff. It’s great, but lay people will be bored or lost. This stuff is often so rarefied and narrow that not even science journalists will be interested. It’s often condensed down to 12 minute talks — kind of like blipverts for the most technical stuff.

Sometimes people might wander by the hotel we’re having it in — it happened last night. The poster session for the meeting was held in the atrium, and we had a couple of people stop by and ask what it was all about. That’s great! We had a nice conversation and showed off some of our videos. Most scientists are happy to talk to anyone about the weird stuff we’re doing.

Now you know what it’s all about. Tomorrow I get to go home after an intense weekend…and I get to repeat it again in July.

They scam horses, don’t they?

Hey, veterinarians have to be pretty smart and disciplined to even be in that career, so it’s nice to see how many of them have to be rigorous and skeptical. Here’s an example of the universal problem of quackery explained by a vet:

One reason that many products and treatment methods remain on the market is because of this simple, and not entirely irrational, thought process: “I tried it, my horse got better, so it works!” Unfortunately, even when a horse’s problem improves following treatment, this, by itself, often cannot prove that the therapy was responsible for the improvement. Here’s an example. In other times, people did rain dances when the weather was dry and occasionally, it must have rained. Thus, they kept on dancing. That’s the same bit of logic I’m talking about as applied to determining whether treatments really work, or not.

There are some ethics involved here, as well. I believe that people who provide treatments and therapies for animals have a moral and ethical obligation to prove, first, that they are safe and, second, that they are effective prior to selling them to horse owners (NOTE: Not everyone agrees, as evidenced by the buckets of BS that are currently being peddled). It’s usually not that hard to demonstrate that a therapy doesn’t do any harm to an animal – the treatment is given, the animal doesn’t die, and there you go. Proving that it’s effective can be quite another matter, even if effectiveness is easy to claim.

This is a very common psychological exploit. Most organisms do have natural healing abilities; I’ve noticed over the years that if I have a cut, it magically heals, even though I don’t understand everything that is going on. Unscrupulous humans are able to hover over that ongoing process and claim that they’re the ones responsible for activating the magical healing power, even when they’re not, and there isn’t anything magical about it. We’re usually quite eager to have wounds and disease go away, so we’re psychologically willing to accept the ‘aid’ of said unscrupulous guru.

It’s especially potent for problems that have a variable progression, like cancer or back pains.

And it works on horses, too. Well, not actually on horses, but on gullible horse owners, who often have a deep emotional and financial investment in their animals. Once you’ve got the horse folk convinced, it’s an easy jump to bilking humans over human diseases.

My favorite example is Tellington TTouch, a kind of psychic massage therapy.

[TTouch] is a bodywork and training method based on circular movements of the fingers and hands all over the body. The intent of the TTouch is to activate the function of the cells and awaken cellular intelligence — “turning on the electric lights of the body.” The TTouch is done on the entire body, each circular TTouch complete within itself. It is not necessary to understand anatomy to be successful in speeding up the healing of injuries or ailments, or changing undesirable habits or behavior.

And, according to the unqualified and untrained woman who peddles this crap all over the world, it cures just about everything. Stress, migraines, depression, arthritis, stroke…it even enriches your relationships!

That’s a pretty impressive list of accomplishments for a system of touching rituals made up by one person based entirely on her own intuition. Unsurprisingly, however, there is absolutely no reliable evidence to support any of these claims. The TTouch web site claims, “We have also gathered a rich legacy of anecdotal evidence to support the effectiveness of TTouch to enhance personal wellness and quality of life” without any apparent recognition that this is meaningless in terms of validating the claims made for the treatment.

Unfortunately, the reason it’s my ‘favorite’ quack therapy is that it is heavily promoted by my university (well, one branch of my U — the backward and problematic Twin Cities branch) at the Center for Spirituality and Healing, the ongoing embarrassment thriving at the heart of one campus in this system. I’m looking at the long, long list of faculty and staff associated with this disgrace and thinking about how the science division at my campus is understaffed, and how all across the university we could use more support for the social sciences and humanities and arts, and how our students keep facing tuition increases, and right there is a fine piece of useless fat that could be cut away, and the loss would immediately benefit the University of Minnesota.

It’s a clear example of bad thinking doing actual harm.

I don’t know whether this is cause for optimism or despair

Doug Erwin argues that we’re not in the middle of a 6th mass extinction. It’s not because we haven’t decimated life on planet Earth; it’s because if we were, the catastrophe would be immense, and we ain’t seen nothin’ yet.

“People who claim we’re in the sixth mass extinction don’t understand enough about mass extinctions to understand the logical flaw in their argument,” he said. “To a certain extent they’re claiming it as a way of frightening people into action, when in fact, if it’s actually true we’re in a sixth mass extinction, then there’s no point in conservation biology.”

This is because by the time a mass extinction starts, the world would already be over.

“So if we really are in the middle of a mass extinction,” I started, “it wouldn’t be a matter of saving tigers and elephants—”

“Right, you probably have to worry about saving coyotes and rats.

“It’s a network collapse problem,” he said. “Just like power grids. Network dynamics research has been getting a ton of money from DARPA [Defense Advanced Research Projects Agency]. They’re all physicists studying it, who don’t care about power grids or ecosystems, they care about math. So the secret about power grids is that nobody actually knows how they work. And it’s exactly the same problem you have in ecosystems.

The good news is that we aren’t dead yet! The bad news is that when the end comes, it will be rapid and non-linear and unimaginably devastating. Just to put it in perspective, this is small potatoes compared to a real mass extinction:

For instance, it stands to reason that, until very recently, all vertebrate life on the planet was wildlife. But astoundingly, today wildlife accounts for only 3 percent of earth’s land animals; human beings, our livestock, and our pets take up the remaining 97 percent of the biomass. This Frankenstein biosphere is due both to the explosion of industrial agriculture and to a hollowing out of wildlife itself, which has decreased in abundance by as much as 50 percent since 1970. This cull is from both direct hunting and global-scale habitat destruction: almost half of the earth’s land has been converted to farmland.

The oceans have endured a similar transformation in only the past few decades as the industrial might developed during World War II has been trained on the seas. Each year fishing trawlers plow an area of seafloor twice the size of the continental United States, obliterating the benthos. Gardens of corals and sponges hosting colorful sea life are reduced to furrowed, lifeless plains. What these trawlers have to show for all this destruction is the removal of up to 90 percent of all large ocean predators since 1950, including familiar staples of the dinner plate like cod, halibut, grouper, tuna, swordfish, marlin, and sharks. As just one slice of that devastation, 270,000 sharks are killed every single day, mostly for their tasteless fins, which end up as status symbol garnishes in the bowls of Chinese corporate power lunches. And today, even as fishing pressure is escalating, even as the number of fishing boats increases, even as industrial trawlers abandon their exhausted traditional fishing grounds to chase down ever more remote fish stocks with ever more sophisticated fish-finding technology, global fish catch is flatlining.

Related concept: error catastrophe. One of the properties of organisms and food webs is that they’re surprisingly robust — you can punch holes in them and take out pieces and they just keep going until suddenly, the network can’t compensate and the whole thing just collapses. We’re cheerfully battering whole ecosystems and cheerfully telling ourselves how tough and resilient the world is, and it’s true…until one last damaging blow causes an abrupt disintegration.

Oh, did I say I didn’t know whether to be optimistic or despairing? I lied. I know which one I feel most.

Not for entomophobes

The Star Tribune has an article on 5 nasty Minnesota bugs to watch out for this summer. It’s not particularly useful. Top of the list: ticks and mosquitos, as if you can live here without knowing that. People who visit Minnesota unprepared for ticks and mosquitos are exsanguinated and stripped of their flesh in mere minutes, and don’t have time to open the local newspaper. You should see the charnel pit at the airport, it’s a great tourist attraction.*

Other problems with the article: each of the Bad 5 are accompanied by a full-color closeup photo. Yeah, like the people who are worried about bugs will be able to read the text with mandibles and way too many eyes staring at them.

Also, one of their ‘villains’ is…the house centipede. Why? They even admit that they’re harmless.

Nasty factor: They’re not harmful, but they rank high on the “ick!” scale. “People get weirded out by them because they have the long legs and they move really fast,” Hahn said.

How to protect: You can easily squash them. Or just ignore them.

‘high on the “ick!” scale’ is not a legitimate reason to squash an innocent living creature. Why are they even listed here? I think maybe sensationalist ickiness was the primary criterion.

I could write a shorter version of the article. For pests like mosquitos, ticks, and flies, use DEET and protective clothing and don’t go strolling through tall grass. For wasps, leave them alone. For other insects and spiders, learn to appreciate their contributions to the ecosystem and stop squashing them with that stupid “ick” excuse.

*I’m lying about the charnel pit. Of course it’s not a tourist attraction, it smells terrible.

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.

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.)