In praise of rudeness

You may have heard that the replicability of much biomedical research has been called into question, in particular by the Ioannidis paper in 2005 that demonstrated that a heck of a lot of junk got into print, largely as a consequence of statistical noise being treated as significant, for a host of reasons. It was a bit of a wake-up call (unfortunately, most people just rolled over an smacked the snooze button), but one person who is on full alert is Dan Graur. Graur is being impolite again, and has a recommendation to improve the problem.

Interestingly, the rate with which junk claims are published in the field of experimental physics is nowhere near the stratospheric rates that are found in biology and medicine. Why the difference? Dr. Ioannidis thinks that there are two reasons for the difference. First, it seems that in the biomedical research community there exists an aversion to publish negative results, especially negative results of failed replications.

Second, it seems that there are sociological differences between the physics community and the biomedical community. In physics, there seems to be a higher “community standard for shaming reputations.” If people step out of line and make unsubstantiated claims, they are shamed in public.

Wait — I have to call a foul on the play. The Ioannidis paper certainly does say the first difference, but the second…nope. The quoted phrase about shaming doesn’t appear anywhere in the source Graur links to — I’d like to see where it came from.

I’m inclined to agree with it, except that I don’t have any evidence of any public shaming going on in the physics community. I’d like to know more about how physicists police their own than is given here.

This is the abstract from Ioannidis — you can easily see that there is a focus on removing bias and better statistics, there isn’t anything about using shame as a tool.

There is increasing concern that most current published research findings are false. The probability that a research claim is true may depend on study power and bias, the number of other studies on the same question, and, importantly, the ratio of true to no relationships among the relationships probed in each scientific field. In this framework, a research finding is less likely to be true when the studies conducted in a field are smaller; when effect sizes are smaller; when there is a greater number and lesser preselection of tested relationships; where there is greater flexibility in designs, definitions, outcomes, and analytical modes; when there is greater financial and other interest and prejudice; and when more teams are involved in a scientific field in chase of statistical significance. Simulations show that for most study designs and settings, it is more likely for a research claim to be false than true. Moreover, for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this essay, I discuss the implications of these problems for the conduct and interpretation of research.

But don’t let that stop Graur, he’s on a roll!

In biomedicine, the search for truth is no longer a virtue, politeness is. According to an editorial in Nature Methods that singled out our work for criticism, one should avoid “harsh and offensive words” at all costs. “Civility in discourse is essential,” proclaim the editors of Nature Methods. Do not shame reputations! Well… by not shaming reputations, we have built a field of study where bombast thumps substance, and where wasters of public money are rewarded. By paying attention to “manners” we have prostituted science to a degree where “most published research findings are false.”

Rudeness has nothing to do with science. Science is not about abiding by a code of behavior put forward by Miss Manners. In criticizing ENCODE, our style of writing was meant to bring to the attention of the public a problem generated by the ENCODE propaganda barrage.

Face it, ENCODE for creationists was like “water memory” for people believing in homeopathic medicine. ENCODE deserved the same treatment as the “water memory” paper that was published in Nature by Jacques Benveniste. ENCODE needed to be shredded to pieces in a manner similar to the way Great Randy [the Amazing Randi] shredded “water memory.” The Great Randy [the Amazing Randi] was so rude, that his criticism was likened by Benveniste to a “Salem witch hunt.”

In science, sometimes a strong rude voice is needed to fight self-promotion and self-delusion. My favorite example of a rude voice concerns Theodor Roosevelt and his refutation of Abbott Thayer’s theory on all coloration in nature being “concealing” (e.g., the famous flamingoes in the sunset). Thayer’s book was shredded to pieces by Theodor Roosevelt (one year after completing his presidency). I wish my mastery of the English language would allow me to emulate Roosevelt’s viciousness. Alas, English is my third language.

We need strong and impolite voices to fight “stem cells created by acid baths,” “cold fusion,” “arsenic-based life,” and other feats of self delusion. People still believe that Svante Pääbo sequenced ancient DNA from an Egyptian mummy in 1985. Why? Because there were no strong and impolite rebuttals. Every criticism was whispered and “soto voce.” Science has become a collection of Yes Men (and Women) afraid of the big shots and their own shadows.

I agree, and I’d like to see more vigorous responses to the boring lot of trivial phenomenology that is cluttering up some of the journals I like to read. We’re getting to a point where the literature is swamped with kipple that could benefit from some housecleaning, and a little less emphasis on publishing for the sake of publishing. But we rely so often on the quantity of articles published as a metric for academic success, rather than the quality.

But I’d also like to see a stronger analysis comparing the literature in physics and biomedicine — is it really that different?

Missing the point of Giordano Bruno

I’m seeing a lot of silly carping about Neil deGrasse Tyson’s Cosmos — almost all of it is focused on the story of Bruno told in the first episode. The apologists for religion are upset: how dare a science program point out the poisonous influence of religion? Bruno wasn’t really a scientist anyway, so he shouldn’t count! Peter Hess of the NCSE offers up a good example of apologetics.

Unfortunately, the series premiere risks squandering that opportunity through a combination of misleading history and reliance on an antiquated narrative of inevitable conflict between science and religion—and the Catholic Church in particular—that simply is not borne out by the facts. A generation of careful scholarship has given us a nuanced and sophisticated understanding of the long, rich, and complex relationship between religion and the sciences. This latest Cosmos reflects none of that historiography, presenting us instead with what is quite literally a cartoon version of the life story of someone who was not a scientist. Missing were the stories of Catholic astronomers such as Copernicus [delayed publication out of fear; only saw his ideas in print on his deathbed; book was prohibited by the Catholic Church in 1616] and Galileo [tried by the Vatican, forced to recant, spent the end of his life under house arrest], Protestants such as Brahe [Brahe was a geocentrist — a geoheliocentrist, actually] and Kepler [Did you know his mother was tried and imprisoned for witchcraft?] and Newton[Also a mystic, Bible-prophecy walloping, fanatical religious person], or Fr. George Lemaître, proposer of the Big Bang.

Whenever I see one of these guys throw out noise like a nuanced and sophisticated understanding of the long, rich, and complex relationship between religion and the sciences, I want to ask…what was nuanced and sophisticated about setting a human being on fire? I also think his list of famous scientists overlooks an important trend: between Copernicus and Lemaître, we are seeing the steady triumph of science over religion, that we see the Church forced to reduce the severity of its enforcement of dogma in the face of the overwhelming success of science in accurately describing the world. The Church was dragged kicking and screaming into an era where you don’t get to murder people for disagreeing with your dogma.

It is odd therefore that Cosmos focuses almost exclusively on the marginal case of Giordano Bruno. Of course, I am not defending Bruno’s persecution and death—no decent human being now would ever condone burning a person alive for any reason. Moreover, in 2014 we view legitimate theological dissent very diffferently than did our ancestors.

But the circumstances were quite different 400 years ago. According to the 16th century Italian legal code and the customs of Renaissance politics, Bruno was judged by an ecclesiastical court to be an obdurate heretic for refusing to cease in promulgating his theological ideas. As such he was deserving of capital punishment and was turned over for execution by the civil arm in Rome. In the 21st century we inhabit a very different era, a religiously pluralistic age of largely secular states in which the nature and exercise of authority are vastly different than they were in Post-Reformation Italy.

Is anyone else getting that queasy feeling, like when you read about William Lane Craig justifying the murder of babies by ‘Israeli’ soldiers? Hey, it was OK to set people on fire in 1600! Why are you complaining?

I agree that we live in a very different era in the 21st century. Give the credit to secularism, rationalism, and the Enlightenment, though, because fucking religion fought every progressive change every step of the way, with liberal religion dogging along by discarding parts of the religious nonsense of previous generations.

I don’t think it odd at all that the series brought Giordano Bruno to the fore. This is not at all a show for scientists, but to bring a little bit of the awe and wonder of science to everyone. I think it was a good idea to use a non-scientist as an example of how dogma oppresses and harms everyone. Bruno was an idealist, a mystic, an annoying weirdo, a heretic, and for that, the Catholic Church set him on fire.

Do I need to repeat that? Bruno was tortured to an agonizing death for his beliefs. Full stop. Don’t even try to rationalize that.

Furthermore, Neil deGrasse Tyson’s own words, transcribed by Wesley Elsberry, are crystal clear on the point he was making.

Giordano Bruno lived in a time when there was no such thing as the separation of church and state, or the notion that freedom of speech was a sacred right of every individual. Expressing an idea that didn’t conform to traditional belief could land you in deep trouble. Recklessly, Bruno returned to Italy. Maybe he was homesick, but still he must have known that his homeland was one of the most dangerous places in Europe he could possibly go. The Roman Catholic Church maintained a system of courts known as the Inquisition, and its sole purpose was to investigate and torment anyone who dared voice views that differed from theirs. It wasn’t long before Bruno fell into the clutches of the thought police.

The Church maintained an Inquisition to torture people who didn’t follow Catholic dogma in thought. Let’s not hide that fact. Let’s not pretend it was OK because it was 400 years ago. Let’s not say it was irrelevant because many of their victims, like Bruno, were not scientists. I think it’s a rather important point that the progress of science requires that we not set people who disagree with us on fire.

Wesley makes a very good point at the end.

The point “Cosmos” was making was more basic. At the level of telling people about science, we don’t need a lot of historical nuance about the Inquisition: what they did was so far out of bounds of the way discourse needs to be handled that simply noting the historical divergence is sufficient. “Cosmos” did that, plainly told people they were doing that, and, sadly enough, a lot of people of otherwise lofty intellect managed not to take the point.

I will also disagree with Hess. There is a conflict between science and religion. Somehow, these people think that the historical evidence of people leaving behind their antiquated religious ideas and gradually adapting to a more secular view of the world is evidence that religion and science are compatible.

You know, I’d heard this vague euphemism that the church “immobilized his tongue” to prevent Bruno from speaking heresy on the way to the stake, but I didn’t know how. The answer was provided in the comments:

[on the way to the stake, Feb 19, 1600] As the parade moved on, Bruno became animated and excited. He reacted to the mocking crowds, responding to their yells with quotes from his books and the sayings of the ancients. His comforters, the Brotherhood of St. John, tried to quiet the exchange, to protect Bruno from yet further pain and indignity, but he ignored them. And so after a few minutes the procession was halted by the Servants of Justice. A jailer was brought forward and another two held Bruno’s head rigid. A long metal spike was thrust through Bruno’s left cheek, pinning his tongue and emerging through the right cheek. Then another spike was rammed vertically through his lips. Together, the spikes formed a cross. Great sprays of blood erupted onto his gown and splashed the faces of the brotherhood close by. Bruno spoke no more. … as the fire began to grip, the Brothers of Pity of St. John the Beheaded tried one last time to save the man’s soul. Risking the flames, one of them leaned into the fire with a crucifix, but Bruno merely turned his head away. Seconds later, the fire caught his robe and seared his body, and above the hissing and crackling of the flames could be heard the man’s muffled agony.

Yeah, that’s what the apologists want to dismiss as irrelevant.

Cosmos: Thumbs up!

It’s off to a good start, and I quite enjoyed the first episode. It was maybe a bit heavy on the simplifications and the eye-popping graphics, but I’m seeing it as a tool to inspire a younger generation to get excited about science again, so I think that actually is a good thing.

It’s also impressive that a strongly pro-science program (and one that took a few shots at Catholic dogmatism) was on broadcast television, and even on Fox. I was getting exasperated with the too-frequent commercial breaks, but I think that’s the price we pay for getting wider dissemination to the public, rather than to just us privileged few who can afford cable and/or buying the DVDs.

I don’t mean to be neglecting the blog today

But I’m neglecting the blog today. I’m finally at #scio14, and it’s busy busy busy. So far today I’ve been in sessions on reaching diverse audiences and on doing better at serving differently abled communities, because I’d like to do both, and this afternoon there’s stuff on media and networks and who knows what that will keep me engaged.

It’s actually refreshing to be here–it really is a diverse group, and there are lots of younger people (I feel like the crotchety old fogie…oh, wait, I always feel like that). My goal this weekend is to dispel a little bit of my disillusionment with online communities and get inspired again, and this is a good place to do that. So I’m just making little notes on ideas that can give me fresh eyes and change up what I do…and I hope, do it better.

You’ll forgive a little mild distractedness for that, right?

Glad you couldn’t make it

I just got back from our Cafe Scientifique meeting, and it was a fabulous success: attendance was over 60 (which is why I’m glad you couldn’t make it — it was standing room only as it was) and we had a good representative sampling of the Morris community.


I don’t know what the secret of drawing everyone in was. We did make much flashier signs this month, but also the topic might have been it: Carrie Eberle from the USDA lab in town gave a talk on foraging crops for bees that hit the sweet spot in appealing to farmers, gardeners, science people, and everyone who likes honey. And it was a very good talk.

I’m back from the Creation Science Fair!

And I don’t have a lot to say. If you were looking for horrifying tales of creationist stupidity and extravagant inanity, it wasn’t here — it was a fairly typical range of posters, of the same sort you’d see at a public school science fair. Some were descriptive, some were about experiments; some were mundane, some were a bit out there; some you could tell Mom & Dad did most of the work, some were clearly driven by the passion of the students; some were rather poor, some were really good examples of kid science. The only difference between this and a secular science fair was the requirement to include a Bible verse on the poster.

There were about 2 dozen exhibits in a hallway on a Christian bible college, so it was on the small side. It was fairly busy, though, with lots of adults having conversations with the kids.


I actually came out of it fairly optimistic. The organizers might want to skew the kids towards their bizarre mythology, but in practice, the kids were having none of it; they were playing with pulleys or breeding rabbits or testing water quality or talking about bees, and it was all about the evidence. Whether they like it or not, these kids are being given the tools to kick their tired Christian ideology to the curb. Give ’em time. Let them keep thinking. Creationism is unsupportable by the honest application of the tools they are learning.

Also, surprisingly, the Bible verses on each poster were extremely encouraging. Nobody was testing biblical nonsense at all — there were no hypotheses, even, derived from the Bible. The overwhelming impression was that the kids had an idea they wanted to test first, and then, after the fact, slapped on a verse that somehow related to the experiment that they’d done. They were either non sequiturs or amusingly inappropriate. Take, for instance, this one:


That’s right: this student just compared the absorbency of diapers to Jesus. I hope they think this through and that the true meaning of the Bible becomes apparent to them.

This was another one I appreciated. The Bible says “fear and dread” of people will be upon all the birds and beasts, so this kid’s idea was to test whether that hypothesis was true by seeing if he could tame birds.


The result: yes, he could. Therefore, the Bible is false. Oh, wait, he didn’t actually say that.

Anyway, good work, kids. Keep ignoring the Bible or debunking it!

The cuddliest artificial genetic mutant ever

The food science blog Biofortified is running a kickstarter to encuten genetically modified organisms with Frank N. Foode™ plushies. Give to help promote informed food choices and get soft fuzzy rewards!

One of the secondary inducements are mini-maize seeds, that allow you to grow tiny corn plants in your home. I am surrounded by kilometers of vast corn fields — corn and soybeans, corn and soybeans, corn and soybeans, everywhere. Not tempting at all. But maybe some of you more urban readers need a tiny reminder of where your High Fructose Corn Syrup and ethanol and popcorn and an awful lot of the carbohydrates in your diet come from.

They aren’t making the mini-maize seeds part of the rewards any more: you can get them for free!