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An exercise in humility

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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, 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.
July 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 much darkness.

I bet none of the students ever had a science class oozing so much ignorance.
One of the objectives of the course is to explain to the class why people become scientists. It is not the long training, low pay, endless hours or poor job security. I failed miserably to give a good answer in previous years. I got colleagues to post explanations, and the answers are good but its hard to get students to read the blog, and it made no impact when I read them out last year.

So I tried a different tack. I got a talented film student, Tristan Buckley, to make a film to explain. This is what he produced. I showed it in class Thursday. You could have heard a pin drop.

$100 says...

I was talking in today's class about how political pressures can come on scientists, using the very local example of Mike Mann. If you are a climate change denier, you need his hockey stick to go away. It will go away only if it is wrong. This means many politicians and political operatives criticize the science behind it, even though the majority of climate scientists accept that it broadly correct. If you are a climate change denier, you get out of that one by saying that there is a conspiracy among climate scientists to stay silent about the truth in order to get grants.

I think it is really important to get across to my class that scientists can't do conspiracies. We are an extremely competitive bunch who make our reputations by finding flaws in other peoples' reasoning - the bigger the flaw, the more we can over turn, the better. In fact, I go one stage further. I assert that scientists are better at rooting out incorrect science than anyone else.

Which led me to challenge the class: $100 to the first class member who can name a non-scientist whose insights have led to a scientific consensus being over turned. I can think of lots of scientists who have overturned a scientific consensus.  I can't think of a single politician, religious leader, snake oil salesman, mystic, rock star, lawyer... who has done that.


Are we alone?

Tuesday, I did a class on whether there is life elsewhere in the universe. The students think this is one of the most interesting questions in science

I did it in two chunks.  The first concerns the bit career scientists are involved with: the search for life in our solar system (e.g. Curiosity), the search for Goldilocks planets elsewhere in the Milky Way (e.g. Kepler) and the efforts to listen (e.g. SETI). And of course the Drake equation.

The second chunk is about whether we are being visited: flying saucers, UFOs, Roswell, Alien Abductions and the like. The students are much more interested in this part. I only think about it for this class - and it strains my very being to do so. The main educational benefit is that it helps shape a discussion about what counts as meaningful evidence. 

There is interesting irony here. Eye witness accounts of alien abduction, deeply believed by the abductees themselves, are deeply disbelieved by almost every credible scientist. Yet in other aspects of life, equally deeply believed eyewitness accounts are enough to put people on death row.

There are other ironies. There is not a jot -- not a jot -- of evidence there is life elsewhere, but many scientists are spending a lot of money, much of it federal tax dollars, looking for it. In contrast, there are hundreds (?I can't find a reliable number) of US citizens who say they have been abducted by aliens visiting earth. That's a lot of evidence.Yet so far as I can tell, there is no credible scientific effort investigating that evidence. Of course, that's because, by and large, deeply held personal experiences are not very accessible to the rest of us. If I could go see for myself, then the investigation is on. Otherwise, there is nothing. It is just like religious experience: strong evidence to those who have the experience. Nothing to someone with a different experience. That doesn't make it wrong. It makes it inaccessible.

The final irony struck me during class. I am trying to get the students to think about the nature of evidence, to think decide for themselves what to make of eye witness accounts and grainy shots of strange objects in the sky.  And the Comment Wall lights up with texts from the students asking what I believe.

As if that matters. Three quarters of the way through semester, and there is still is no right answer folks. You have to think for yourselves.

The good things

I had a staggeringly bad day. I am fighting the NIH over deeply unnecessary red tape. It's been a shock to me how much worse the bureaucracy is in America compared to any where else I have lived (NZ, UK, Germany). Even buying and selling a car privately, which I did yesterday, involves way more bureaucracy than it does in those other countries. I am also trying to deal with bad chemistry between key people in my working life. And there are ongoing discipline problems in the class (which I will blog about when they are sorted).  

But, four good things happened today, and sanity requires I focus on those. I can tell you about three of them.

(1) It looks like we turned up Marek's disease virus in the farm samples we got Wednesday.  Very good news for us; very bad news for the farmer involved.

coffee-cup.jpg(2) I had a breakfast coffee with one of the SC200 students. She is highly motivated about the course, loves the critical thinking aspect, and is enjoying the topics I am teaching (these are the vehicles I use for getting across hard concepts). She is a theater major, and we had a very interesting discussion about performance art. My sort of teaching is performance art. Clearly, she had not thought about teaching like that before, though she got it as soon as I raised it. She made me think it would be really great to do a class (be student) in Professorial Theater 101. I wonder what we could do for PSU teaching if we got into that.

(3) I talked with Eberly College of Science Dean Mary Beth Williams (1, 2about Gen Ed teaching. She and I are trying to change the world, starting at Penn State. She now tells me that in conjunction with Chris Long in Liberal Arts, she wants to go rogue. To really push the boundaries. To behave very, very unorthodox (in this context we can do bad grammar). To push the university (American education?) into something really new. Something really good. And really brave. To really extend our students--and our faculty. Hallelujah. I bet the University doesn't have the balls for this. She does.

And I note that somehow, she does this all the time to me. I am cripplingly busy. And she wants to push me harder. She never once says "Andrew, I know you are busy but..". She just says: here's a vision. She doesn't even have the decency to ask: "wanna run with it?'.

Calming chickens

I spent the morning on chicken farms. We have an EEID grant to look for Marek's disease virus in Pennsylvania. MDV has evolved to become seriously nasty. We're working on the possibility that vaccines made it so. To me, it's a fascinating question (although I have no deep understanding of why). And the context is fabulous. The efficiency of the poultry industry is mind blowing. It is incredible what smart people and market forces can achieve. Chickens used to be more expensive than oysters. Now...  If humans can make chickens dirt cheap, and go to the moon, how come we can't do simple things, like Middle East peace?

Even better though, think about the scene from the virus' perspective. Broiler chickens (the ones we eat) exist for 6-7 weeks, with maybe 30,000 birds of identical genotype and phenotype all in a single room. No wonder merry evolutionary hell is let loose.

Aviagen Trip 043.JPGBut today, none of that coolness mattered. It was just really nice to be out with proper scientists Patty and Dave in a relaxed setting. And the nature of the work - sampling dust - is lovely. After a few hours, things are done, targets reached, and everyone is happy. It is never like that when you are teaching or running a research group. Always there is something you could do better, faster, more efficiently. Its enough to drive you mad.

Does God exist?

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In class today, I talked about the question of whether prayer heals.  This question very naturally lends its self to scientific experimentation.  I based the class about one such study [Leibovici (2001) Effects of remote, retoactive intercessory prayer on outcome in patients with blood stream infection: randomised controlled trial. British Medical Journal 323: 1450-1.pdf].  It's a great hook to get across lots of stuff, like the difference between faith (where no data will change your mind) and science (where data makes a difference). It also illustrates hypothesis testing, experimental design, chance, third variables and a whole lot of other good stuff, not least the sheer beauty of the randomized controlled trial.

But it is a challenge as a teacher because you have to tread very, very carefully.  The students are tense discussing this, feelings run strong, and it would be easy to ruin lives or crush their interest in science.  But what gets me is the sheer audacity of the Lebovici's hypothesis. He asserts that "we can not assume a priori that time is linear, as we percieve it, or that God is limited by linear time, as we are". So in his study, the praying happened after the clinical outcomes had already happened.

This is an astoundingly strong test of the hypothesis.  I for one would be totally, totally impressed if praying for peoples' health after the event made a difference. Not least because it is the perfect double blind.  Nobody in the study can have known there would be a study because there wasn't one until 4-10 years after the people were sick. The students find it very hard to accept this notion at all.  But if God is all powerful....

Last year I was asked if this was a test for the existence of God.  Obviously I dodged the question. Sensible teachers should. But as I age, taking risks in the classroom seems interesting.  So I polled the students.

Poll Everywhere

I didn't say in class.  Not my place.  But I disagree with that majority.  If praying for patient health retrospectively actually works, so that a randomly chosen group of patients actually got out of hospital earlier if they were prayed for: what other explanation could there be?  Of course, if it doesn't work, there could be tons of reasons.  Not least that God doesn't play this sort of ball.

Peer review

For two years now, I have been pondering how to teach my students about peer review. Love it or hate it, peer review is an essential part of science. Expert scrutiny makes a huge difference. The review process is why you can trust scientific papers more than, say, the latest political diatribe. It is why I trust what climate scientists say, even though I cannot judge climate science myself.

How to show students the power of this system? I tried just saying it when I first did the course in 2010.  The students glazed over. Last year I showed the students a couple of reviews I had got. They seemed slightly more interested.

So this year, I am going to go the whole hog. I am going to do the review process in real time.  We've just finished the best paper I have ever written. Conceivably, it is the best paper I will ever write (I hope not), and it concerns drug resistance, one of the most important topics of the age. It got bounced from Science two weeks ago - unreviewed. I wept. We've since sent it off to Nature. I am sure I will be crushed again. Since this story is likely to run all semester, I figure I can involve the students in the emotional roller coaster. With luck they will learn about the review process, and the essential negativity of science - and that scientists are humans who get really, really emotional about rejection.

I am slightly scared about this experiment. Not normal to bare my soul in front of 178 young people.

Noted added after class: This soul-bearing approach actually seemed to work as a teaching device. The students seemed engaged in the review process. The tragic thing was that the form letter rejection from Nature arrived a few hours before the class, which I duly reported to the students, the saga continues. I wonder if it will be done by semester end. Hopefully, whatever happens, there will be lots of teachable moments.

The Responsibility

This is the time in semester when I still have the energy and enthusiasm to really feel the burden of this course.  The students are busy writing their introductory blog entries, where they have to explain why they are not science majors, and why they are doing my course. The main goal of the exercise is to make sure they can work the blog, but what gets revealed are woeful tales of the failure of K-12 science education (some particularly disturbing examples: 1, 2, 3, 4, 5).

The burden to rectify this falls to me. I do worry whether I am up to the task. I need to get the students to really appreciate the passion, the joy and the beauty.  And as importantly, I need to get them to appreciate the power: why science reveals so many incredible things that other wise elude humanity. I also need to encourage the students (give them permission?) to start using the scientific process in their everyday lives. Rational skepticism is the key to critical thinking, and making their world and mine better.

I am more than normally worried about this responsibility because I am reading This Will Make You Smarter, edited by John Brockman of Brockman asked some of the leading scientific communicators of the age to answer the question: What scientific concept would improve everybody's cognitive toolkit? I got the book to mine it for material for the course, but it turns out that I already cover everything. The really sobering thing is that the book makes the course seem more important than even I imagined. The extraordinarily eloquent contributors are screaming out: empower non-scientists.

Up to the task Read?

Indian summer

I got back from India yesterday, in time to start SiOW 2012 tomorrow. I wish I could take the class on a trip to India. The places we work - the places where malaria is - are not the places tourists go. Yet among the trash and the smells and the grime and the very poor, there are advertisements for schools and colleges that offer math and science as a way out. And while we were there, the Indian prime minister was talking enthusiastically about investing in science as a way to maintain the phenomenal growth of the last decade. It is such a contrast to the Presidential campaign happening here.  The Indians see math and science the way Americans did in the 1950s.  I wonder whose century the 21st Century will be.

Basant Nagar beach.jpg
One of our field sites: Basant Nager, Chennai, S. India


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During the class session with the Dean on the Penn State scandal, one of the students asserted that professors with tenure teach less well.  

I was a bit shocked. I had never thought about it much, but my instinct was that the reverse would be true: faculty striving for tenure would put less effort into teaching because they have other things to do. It's very hard to get tenure if you haven't got serious grants, but grant success has become the hardest task in the business. To teach well, you just have to be better than the gal/guy down the corridor. To get a grant, you have to be among the best in the world. 

On top of that, your application has to be completely perfect, guaranteed to work and so incredibly well written that not a single one of the many reviewers will be in the slightest way offended or bored. The National Science Foundation forces scientists to show how their science will impact teaching. I can't help think that the system itself bleeds out the time, energy and enthusiasm that generates the very teaching excellence we all want.  

The Dean answered the student by saying that .... 

American education

From a beautiful article in this week's Time magazine from Fareed Zakaria, one of Time's many great journalists (italics mine):

time cover.png

"I went through the Asian educational system, which is now so admired. It gave me an impressive base of knowledge and taught me how to study hard and fast. But when I got to the U.S. for college, I found that it had not trained me that well to think. American education at its best teaches you how to solve problems, truly understand the material, question authority, think for yourself and be creative. It teaches you to learn what you love and to love learning. These are incredibly important values, and they are why the U.S. has been able to maintain an edge in creative industries and innovation in general."

Many of my students are hungry for American education at its best and work hard on my attempts to offer it. This is indeed so the point of it all. I agonize about whether I am pushing them hard enough at this. And how to reach the other students, for their own good and for everyone else's. Zakaria's article appears in an issue of Time which is asking where the American dream went.

Something wrong with rest of world

A very entertaining correspondent in New Zealand sent me this. 

Evolution and GDP.jpg


We had science writer Faye Flam from the Philadelphia Inquirer in class today. She does investigative science journalism and writes a column on evolution and an extremely stimulating blog. Faye said so explicitly many things which I feel the need to dance around.  Fabulous.

Since we had a professional blogger in the room, I asked the class what they've found hardest about the blogging they've had to do for this course. Rachel said she hated the uncertainty in things: when she is researching a blog post, she just wants certainty. Faye laughed. Tough.

I think no interesting problem in science has certainty. It's a failure of K-12 education that students expect otherwise. If we had certainty about things, there wouldn't be scientific problems. 

But this desire for certainty reminded me of a post on Faye's blog.  A reader argued that certainty is precisely what is good about creation stories, and more generally about religion.  You can really get certainty.  

My late mother-in-law always said she felt sorry for me. She got the answer to everything on Sunday. I was stuck with trying to make sense of it all myself.

The Full Monty

Today I gave the class the Monty Hall problem.  I like it because most people choose the wrong solution and it is extremely hard to explain the right solution without mathematics (ie the toolkit of science). The verbal explanations are somehow so unsatisfactory. Try this nonsense for example, which is technically correct Hollywood gibberish [mind you, Kevin Spacey does define professor cool].

The reaction of one of my PhD students when I told her what I was going to do: 

Oh my God, you're not going to Monty Hall them! 
Do you have any idea the emotion that will generate? Paul Erdos didn't get this problem and was vitriolically angry about it until it finally clicked. My husband and I nearly got divorced over it (he didn't mention that Monty knows what's behind the doors and will always choose to reveal a goat, then he refused to believe that those conditions mattered). You're in a country where people may be armed... ARE YOU COMPLETELY INSANE????? 

which, when I explained I escaped alive, was followed by:

....but were they genuinely not worked up about it? It made me blindingly angry, and when I brought this up once at a party as an amusing story, the point being how funny it was that this maths problem produced such passion, two people at the party almost came to blows about it. These were neighbours, not maths geeks. Also really annoyed husband's brother, husband's best friend.....  so what the hell is wrong with your Penn State students? Are they dead?

Well no, but I could not decide what the students made of it. Is it just too weird to wrap your head around a pointless problem that is (by the professor's own admission) very hard to wrap your head around?  Next class I'll discuss why it is so hard for people to wrap their head around it.  Shame no one understands that either.  At least there are some hypotheses.

The failed objective

Thumbnail image for Thumbnail image for Thumbnail image for Thumbnail image for einsteinwiki.jpgI dumped one of the course objectives from last year. 

Norm Freed, the now retired Dean who assigned me this course, rightly argued that a course objective should be to explain to non-scientists why science so impassions scientists.

That it does impassion is clear.  But why?  I have no explanation that will work on an 18 yr-old non-scientist.

Answers on a post card.

How lousy is non-science?

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Perhaps the most important implication of the gross inefficiencies of medical science actually lies beyond science.  If just 2% of medical ideas generate positive benefits, and as many generate harm as help, think what the hit rate must be in fields of human inquiry where experimentation and hard inference are impossible.

Think economics.  Whole chunks of politics.  And law.  Policy makers must be really groping in the dark.

More humility.

Another of Dean Larson's pearls came after he had told the students that when they were born, we thought the stuff in the universe was star dust.  Today, we think that less than 5% of the the universe is star dust; what constitutes the remaining 95+% is mysterious (the physicists, who can get away with such things, call it 'Dark').
The lesson the Dean drew:  "Humility in the face of persistent great unknowns is the true philosophy that modern physics has to offer"  -- Joseph Silk, Cosmologist.

So while biologists were decoding genomes and building new life forms, the astronomers and cosmologists were discovering ignorance on a vast scale. Physicists have been ahead of the curve so far, so there is probably a lesson in this for those of us with more earthly concerns.

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