Category Archives: Thoughts about science

The circumcision decision

130913_medex_circumcisionbaby-jpg-crop-promo-mediumlargeIn my final class, I drew the students’ attention to this really excellent example of how to rationally think about evidence and reach a conclusion. I hope all SC200 graduates are now capable of assembling relevant data and thinking about it the way this author does.

I like his discussion because it leads him to a conclusion opposite to that reached by the Federal Government (CDC) and by the American Academy of Pediatrics, a professional body that should know a thing or two. I have no strong opinion on the author’s conclusion, but I sure do like his reasoning process.

I raised this particular topic because the majority of students will face this uniquely delicate decision in their not-too-distant future. As with so many decisions, they can take the easy route and accept the first bit of advice they hear from an authority figure like their mom, minister, medic or some moronic website — or they can think about it critically themselves. I really hope I empowered them to do that.

Why should we  teach science to nonscience students?

“What do we hope to accomplish?” asks Stuart Firestein in his interesting 2016 book Failure. I like his answer:

“Science has for the past four or so centuries provided more and better explanations about nature than anything in previous recorded history. Mostly it developed a strategy for finding stuff out and knowing whether to believe it or not.”      

As he says later in the book: “Science is the best method I know for being wary without being paranoid.”

Climate change change

Today I reviewed what Mike Mann had said in class about the evidence that climate change is real and mostly due to humans. Then I re-did the poll I took before Mike came to class. Last week, 39% of the students (n= 152 respondents) either didn’t know or disagreed with the statement The earth is warming mostly due to human activity. Today, it was 16% (n=132 respondents). So I guess that’s progress.

But that prompted some scary stuff on the comment wall:

There are bigger issues going on in the world that need our immediate attention. War, violence, the economy.
Climate change isn’t happening because humans are not superior to god’s will.
Climate scientists are going to hell because they are saying humans are superior to god’s will.
Everything that happens with global warming is due to nature and god, not humans. God is superior to us and determines what happens to earth.
I know global warming is fake because my uncle is a republican congressman and says so.

It’s always a little tricky to tell the comedy from the reality.

More constructively, I had a really good idea for a teachable moment. Following Mike Mann’s forceful presentation last class, I polled the class today:

132 respondents

132 respondents

And that gave me the opening to say that among the 100-500 climate or climate-related scientists on campus (a guess, based on estimating the post-docs and grad students as well as faculty), there was not one….NOT ONE… who would disagree with Mike’s summary of the evidence that climate change is happening and largely man made. That’s the extent of consensus on this. If I wanted to find a climate denier, I’d have to hunt among the non-scientists on campus, and even then probably only among the politically motivated. I pointed out that when TV news does balance, it’s not balance in any real sense. Just a scientist and some talking head. It looks 50:50 but that’s an incorrect impression.

I also used it as a moment to to say that if any of those 100-500 Penn State scientists could convincingly show that climate change was not happening or not man made (or a Chinese invention), that scientist would be famous. That’s why we can be pretty confident when they all agree. Everyone is trying to take down everyone else’s science.  When it stays standing, we have to start to think it might be right.

Well I thought it was a good teachable moment….

The Hunger in Our Heads

Much to my delight, one of the TAs just emailed asking for a copy of Class Test 1 because Angel’s review option only shows the questions, not the media article on which half the questions are based.

This means at least one student is reviewing their test performance, immediately after the test. At least one student has ceased control of their learning!!!. Awesome.

This is the article.  I found the message a bit surprising. Intellectual work makes us hungry — and the claim is that excise reduces that brain-induced hunger. I dunno. Surely adding exercise will add hunger? Maybe the article is describing another surprising thing we did not know about ourselves — or maybe the conclusion is just plain wrong.

The $100 challenge

Scientists are all over each other looking for flaws in ideas and data.  This is what makes science so powerful: relentless peer review. It’s why we can all be pretty confident about scientific consensus in fields we do not have technical expertise to assess, like climate change. Yet powerful forces in the (mostly US) public arena believe deeply that scientists can go horribly wrong because scientists go in for mass delusion or worse, mass conspiracy to get grant money (scientists could put together a conspiracy if they tried).  For a classic and truly frightening example of this, brace yourself and check this out.

I try various ways to get all this across in class. I talk about Lysenko and what he did to Soviet plant genetics (and hunger levels). Abetted by politicians, Lysenko was successful by negating the scientific process (not least by having scientific critics killed or imprisoned). I also talk about the trials and tribulations of Penn State’s very own Mike Mann, who has been harassed by politicians who think they know his science better than he or his colleagues do.

But to get the point across, I hit on a fabulous scheme. I said in class, and followed up in an email:

” I will give $100 to the first person who finds an example where bad, fraudulent, mistaken or incorrect science was first demonstrated by someone other than a professional scientist (e.g. a politician, lawyer, lobbyist, concerned parent). To play safe, the example should come for the 20th or 21st Century. I contend that the process of science (formal and informal peer review) does more to keep science honest than anything else. Be the first to prove me wrong and you are $100 richer!”

2015-12-01 15.02.16I thought that would be the end of it, as it had been when I made the same challenge before. But not this time!! Here is me losing my $100 in front of 300 students. After a spirited and very thoughtful Thanksgiving e-discussion with Isaac Will, I decided he had found a case. Dr Andrew Wakefield did terrible damage to public health by linking the MMR vaccine to autism in a paper in The Lancet. Many, many scientists subsequently showed with different data there was no link, and I believe that their scientific work was most important in debunking Wakefield’s mischief. But that still left Wakefield’s original data – all rather poor but nonetheless unarguably still there. Issac argued that investigative journalist Brian Deer showed just what crap it was.  He figured out that Wakefield had terrible financial conflicts of interest AND that his patients were not random cases but carefully chosen to try to show an MMR-autism link. Deer’s work demonstrated that Wakefield’s poor (shockingly poor) science was actually fraudulent. This led to the retraction of the paper by The Lancet. The story is well summarized here. In essence, Deer showed the only ‘data’ supporting Wakefield’s case was garbage, thereby taking the final study off the table. I felt Issac had a point: Deer indeed revealed important scientific weaknesses not discovered by scientists. So I became $100 poorer.

But oh, what a teachable moment. One case in over 100 years. Next year, I’ll post the $100 challenge again. Can anyone think of another case?

Class material

I post the slides and material I use in the classroom on Angel. Turns out the file for the second class was corrupted and couldn’t be opened. Only one student brought that to my attention, and then during the class test yesterday. Well, I guess that means at least someone is looking.


120327124746-deep-water-oil-coral-story-topChuck Fisher came to class Tuesday to talk about his marine research. Chuck is such an enthusiast, and has such great pics and yarns. Submersibles and cool animals and deep sea vents and black smokers and exploding oil rigs are all so visual. And Chuck does it so well.

He had a couple of messages for the students I really enjoyed. First, that he allowed his sense of fun to drive his career. Fun, people, NOT money. And so he’s had a ball, such a full life. It’s hard to tell non-scientists what motivates scientists; I barely understand it myself. Fame? Money? Curiosity? In my experience, fun is as good and as common a motivator as any. Second, that motivator led Chuck to useful stuff too, even though he never set out to do anything useful. He discovered animals which turned out to have a type of haemoglobin that is now used in artificial blood. His understanding of the ecology of deep sea vent communities in the Pacific has allowed him to advise deep sea mining companies – and the governments whose job it is to protect their chunk of ocean. And his technology and science made it possible to assess the damage the Deep Water Horizon explosion did to the Gulf fauna.

Student reaction after was very positive. I got the usual questions on the comment wall about whether this stuff will be in the exam (as Steve Jones once said, the question Professors most loath). But some students seemed inspired. Can’t ask more than that. Thanks Chuck.

An exercise in humility

Science is good at generating knowledge because it crowd-sources criticism. We humans are hopeless at finding fault in ourselves, but we are damn good at finding fault in others. Science exploits that. This is completely different from other realms of human endeavor (imagine politicians or lawyers or marketing people or religious leaders encouraging people to find flaws in their arguments).

But over the years I have struggled to get this across to students. Last year, I hit on what I hoped would be a powerful approach: follow in real time during the semester a paper of mine as it went through the peer review process.


It sure was powerful. I gave the students a grandstand view of the peer review process in action, and a close look at a few of the rigor hoops scientists have to jump though. But I accidentally provided a perhaps more important experience: a grandstand view of my anger, tears, fury, incredulity, humility, disagreements, disputes….in other words, an experience of science and the human condition. They seemed to revel in it. I will never forget the sound of the class groaning as I told them of the latest failure. Particularly because their groans got more emotional with each successive failure.
This was how it played out that semester.
Early August 2012, submitted to Science. Rejected without review.
Mid August, submitted to Nature. Rejected without review.
Early September, pre-submission inquiry to PLoS Medicine. Full submission encouraged.
Mid September, submitted to PLoS Medicine. Rejected without review.
Late September, pre-submission inquiry to PLoS Biology. Full submission encouraged.
End September, submitted to PLoS Biology. Rejected December 4: four negative reviews.
Well…, at least I was able to show the students some reviewer comments before semester end. When they last heard from me, the paper was in limbo. I told them I would email them in the Spring semester with the outcome. I should have been so lucky.
Late January, 2013, submitted to PNAS. Rejected without review early March.
Early March, pre-submission inquiry to PLoS Pathogens. Full submission encouraged.
Mid March, submitted to PLoS PathogensRejected May 23. Four largely positive reviews.
June 7, re-submitted to PLoS Pathogens. Rejected end June. Three largely positive reviews.

accepted.jpgJuly 4, resubmitted to PLoS Pathogens. Accepted July 10.

Yesterday, September 12, 2013, it got published.
And what happened to the paper in those intervening 13 months? Well, it mostly just got shorter. We dumped almost all the mathematics, which we will publish elsewhere, and we took out an experiment, which we will publish elsewhere. Otherwise, we changed the rhetoric a bit (adding a paragraph repeating what we had said before).
And now we wait to see whether anyone in the scientific community thinks the paper is as good as we do. Today, I emailed the SC200 class of 2012 to tell them how it all ended. And I think I will tell the class of 2013 this tale. I don’t have the heart to do another paper in real time.


Not freshmen, as one of my students puts it.

I went to two welcome functions for the class of 2017. The first was convocation, in the Bryce Jordan Center. I was straight off a plane from Scotland to Newark, and exhausted. But it was so energizing to see 9,000 young people raring to go. 
Convocation.jpgAnd then, next day, to see 900 new science students just thirsting for it.
ECoS Welcome.jpg
The class of 2017 includes my oldest son. All power to him and his classmates. I increasingly feel like it’ll all be ok if the world is in the hands of his generation.  


Today, the last proper class, I talked about why we sleep. Yet another profoundly important and interesting question science has so far failed to answer.

It occurred to me while putting the session together: I have taught the students much more about what science has failed to discover than what it has discovered. I did start with a couple of success stories: worm infections do reduce school performance, smoking is bad for you. And I added a couple more later on (Vaccine safety and efficacy, Bacteria cause gastric ulcers). 
But for the rest of semester, I reveled in ignorance, doubt, dispute and uncertainty. Prayer, GM safety, Doctors who kill, Dark matter, Dark energy, High fructose corn syrup, Genomic predictors of self, Why people can’t intuit probability, Autism, Gay animals, Climate projections, Nano-safety, Aliens, Battle of the sexes, Climate politics, Zombies, Microbiome, Immortality, Cancer, Obesity-causing viruses…so much darkness.
I bet none of the students ever had a science class oozing so much ignorance.