Genes, Environment, and Pattern Generation

I’m dipping my toe into the toxic vat of YouTube once again. I’m considering a weekly science story on that medium, and here is my first effort. Pardon my lack of showmanship and video skills, but maybe those will evolve over time.

Hey, if anybody is interested, I’d be willing to do a video hangout to discuss this specific topic later this week. Contact me if you want to argue!

Good science is done on Puerto Rico

People are still trying to simply survive in Puerto Rico, so your first efforts to help should be directed at more general causes. But in addition, universities and labs have been disrupted by the hurricane, and it’s going to take time and money to get the science flowing again. The Society for Developmental Biology is coordinating efforts to help developmental biologists on the island get back on their feet, so here’s a place where you can contribute:

In view of the extensive damage caused by Hurricanes Irma and Maria to the laboratories of our colleagues in Puerto Rico, the Society for Developmental Biology has set up a relief grant program in order to facilitate the continuation of research programs in those labs or at another temporary host location. We come to you to ask for help matching (or surpassing) SDB’s seed funds ($20,000) to the program. This will allow us to provide a higher level of assistance beyond SDB’s current capacity. You may earmark your contribution via SDB’s website on the donation page, by clicking Puerto Rico Relief Fund.

Investigators at institutions located in Puerto Rico who are currently conducting research projects in developmental biology may apply for a grant. Priority will be given to current SDB members. Funds may be used for replacement of organisms, reagents, supplies, travel to host lab by PI or his/her trainees, core facility usage fees at host institution, etc.

The Human Story Retold Through Our Genes

Now there’s an ambitious title: Adam Rutherford’s A Brief History of Everyone Who Ever Lived. It’s a substantial book, but I would have thought it would have had to be a bit longer to cover everyone, and really, a biography of every individual who ever lived would probably get a bit repetitious.

Fortunately, this isn’t a collection of actuarial tables and obituaries. It’s something much more useful: a description of how we know what we know about humanity, from the perspective of genetics, with a solid awareness of the limitations and capabilities of such an approach. That’s helpful — one of our big problems right now is the abuse of genetics by the ignorant to advocate for an impossibly deterministic and racist view of human history. This book counteracts that by describing the methodology accurately, and you’ll learn a lot by reading it. But don’t panic, it’s not a textbook — it does tell the stories and is a good read.

If you doubt me, a revised chapter has been made freely available, A New History of the First Peoples in the Americas, just for us provincial Americans (the full book has a far more global perspective). This one focuses on some of the historical and scientific controversies around efforts to pigeonhole American Indians into one ill-fitting racial category or another.

The idea that tribal status is encoded in DNA is both simplistic and wrong. Many tribespeople have non-native parents and still retain a sense of being bound to the tribe and the land they hold sacred. In Massachusetts, members of the Seaconke Wampanoag tribe identified European and African heritage in their DNA, due to hundreds of years of interbreeding with New World settlers. Attempting to conflate tribal status with DNA denies the cultural affinity that people have with their tribes. It suggests a kind of purity that genetics cannot support, a type of essentialism that resembles scientific racism.

The specious belief that DNA can bestow tribal identity, as sold by companies such as Accu-Metrics, can only foment further animosity—and suspicion—toward scientists. If a tribal identity could be shown by DNA (which it can’t), then perhaps reparation rights afforded to tribes in recent years might be invalid in the territories to which they were moved during the 19th century. Many tribes are effective sovereign nations and therefore not necessarily bound by the laws of the state in which they live.

When coupled with cases such as that of the Havasupai, and centuries of racism, the relationship between Native Americans and geneticists is not healthy. After the legal battles over the remains of Kennewick Man were settled, and it was accepted that he was not of European descent, the tribes were invited to join in the subsequent studies. Out of five, only the Colville Tribes did. Their representative, James Boyd, told The New York Times in 2015, “We were hesitant. Science hasn’t been good to us.”

Data is supreme in genetics, and data is what we crave. But we are the data, and people are not there for the benefit of others, regardless of how noble one’s scientific aims are. To deepen our understanding of how we came to be and who we are, scientists must do better, and invite people whose genes provide answers to not only volunteer their data, but to participate, to own their individual stories, and to be part of that journey of discovery.

A book about human genetics with a humanist perspective? That debunks 19th century dogma about race and intelligence? Yeah, it’s good. I’ve been trying to think of ways I could fit it into my already packed-full genetics course, or whether I could offer a non-majors course that incorporated it as a text.

But at least I can tell you all that you need to read it.

There will be a test. Not that I’ll be giving it, but rather that our entire culture seems to be testing you on this subject right now. You should read the book so you can answer it correctly.

What are we going to do about the Nobels?

Ed Yong points out the problems with the Nobel prize: they don’t reflect how science is actually done, they tend to reinforce an archaic notion that scientists work alone and have “Eureka!” moments, they are arbitrary in picking which of the many scientists who contributed to a discovery get the award, and when they make those arbitrary choices, they tend to be biased towards male establishment scientists. It also adds an excessive luster to recipients — it’s for a single discovery, but you’re set for life if you get one, and it gives people who had a singular insight, for which their prize was justly deserved, an unwarranted authority on all too many things. That’s how we get a Watson, a Shockley, a Mullis.

He doesn’t mention another problem, though: the narrowness of the categories. You cannot win a Nobel prize for mathematics, or computer science, or evolutionary biology. Not even biology: all the great work in my field has to be warped to fit a category called “physiology and medicine”, which the Nobel committee does (after all, they’ve managed to award developmental biology a few times), but still, it forces us to look at the world of science through a specifically focused 19th century slit.

Rosbash, Young, and Hall, who won for their work on the molecular basis of circadian rhythms, did great work and should be acknowledged. But thanks to the arcane rules of the prize — no more than three people, who all must be alive — there is an army of researchers who also contributed to the work, and will be ignored. Among those contributors was the late Seymour Benzer, a real scientist’s scientist, who made amazing discoveries in the arcane fields of phage genetics and neurogenetics and of course, circadian rhythms. It’s not that Benzer was neglected — he had awards out the wazoo — but that a life of sustained effort and scientific discipline does not get the ultimate award (it’s also bothersome that there is an “ultimate award”) and won’t get the public attention he deserved.

I don’t know what to do about it, though.

The Nobel prize is the result of a wonderfully successful PR campaign that does a good job of highlighting good science…but it also contributes to the public perception of all worthy endeavors as being kind of like a horse race. It’s not what they did or how they got there or where we go to next, it’s all about who got to the finish line first and who gets to wear the shiny gold medal. You can’t exactly abolish them — they’re the outcome of a committee and an endowment, and people have every right to honor scientists — but it would sure be nice if those honors could be spread around more to everyone who deserves them, rather than being concentrated to create an artificial scientific elite.

Bottom line is that we aren’t and shouldn’t do anything about the Nobels. We should have more ways to recognize scientific accomplishment, though, and the media should be able to notice the science happening all around them instead of celebrating gold disks handed out every October.

Teams of Memes, bursting from the seams

Image courtesy of the googles.

Daniel Dennett’s From Bacteria to Bach and Back is a lengthy and winding journey. It is characterized (including by its publisher) as a general explanation of the evolution of minds and various peculiar mental functions, consciousness and language being the two most hotly discussed by philosophers, but there’s a better way to read it. As its best, the book is a tour of Dennett’s personal philosophical repertoire, illustrating how ideas from his books and papers fit together.

Dennett’s general theory of the development of genetics stems from his broad theory of memes, where a meme is any informational entity that can be transmitted and replicated. The rough idea is that minds are meme-machines in the way that organisms are gene-machines (in Dawkins’ analogy of the gene’s-eye-view). This is a fruitful analogy, in some respects, though I think it can and should draw some skepticism from readers. I’ll return to those worries later.

The basic building blocks of Dennett’s view are indicated by gestures and short explanations, which is a challenge since he’s spent so much time discussing and arguing for them elsewhere in his work. In any case, there are really two that it is important to understand.

[Read more…]

A food science scam

Where’s the data on this sign’s effect on spelling?

Brian Wansink has a problem. First, he’s been jiggering his data until he gets a statistically significant result, which to me means that none of his conclusions are to be trusted. Then, he was reworking these thinly significant results into multiple papers, taking watery gruel and sliming the literature with more noise. And now he’s accumulating more retractions as his shoddy research practices are exposed.

I’m just increasingly appalled at the crap that is earning him tens of millions of dollars of research funds. It’s cartoonishly superficial. Let’s put goofy names on the food in school lunchrooms!

The most recent retraction — a rare move typically seen as a black mark on a scientist’s reputation — happened last Thursday, when JAMA Pediatrics pulled a similar study, also from 2012, titled “Can branding improve school lunches?”

Both studies claimed that children are more likely to choose fruits and vegetables when they’re jazzed up, such as when carrots are called “X-Ray Vision Carrots” and when apples have Sesame Street stickers. The underlying theory is that fun, descriptive branding will not only make an eater more aware of the food, but will “also raise one’s taste expectations,” as the scientists explained in one of the papers.

You know, I believe this actually does work — I have no doubt that creative labeling can draw the attention of kids (and adults!). But would it make a significant difference in kids’ eating habits? Don’t you suspect that there would be a bit of a backlash? Kids aren’t stupid. They’re going to see right through this game fairly quickly, and a trivial relabeling is going to have only a transient effect. And they’re paying 30,000 schools up to $2000 each to try out these labeling strategies! Is it worth it? I don’t know. And you still can’t trust Wansink’s work.

People are finding inconsistencies in the papers, statistical errors, and outright statistical abuse. What can you say about a paper that decides p=0.06 meets the criterion for signifcance, and further, miscalculated the p value in the first place?

In a blog post, Brown expressed concern about how the data had been crunched, and confusion about how exactly the experiment had worked. He noted that a bar graph looked much different in an earlier version. And, he pointed out, the scientists had said their findings could help “preliterate” children — which seemed odd, since the children in the study were ages 8 to 11.

In yet more scathing blog posts, Anaya and data scientist James Heathers pointed out mistakes and inconsistencies in the Preventive Medicine study, “Attractive names sustain increased vegetable intake in schools,” which claimed that elementary school students ate more carrots when the vegetables were dubbed “X-ray Vision Carrots.”

Worse…when those mistakes were pointed out, Wansink discovers that all the original data for those papers is ‘missing’. How convenient.

Wansink runs something called the “Food and Brand” lab. You can guess from just the name that he’s encouraging corporate support, and I suspect that’s a big part of the problem — this lab isn’t about science, it’s about reinforcing economic values for the benefit of their corporate collaborators.

She had me at “rivers of maggots”

Christie Wilcox writes about the ecological experiment asking what happens to the environment of a mass die-off, done by dumping 6 tons of dead pigs in a heap in a forest. It’s impressive. The scavengers swoop in and proliferate, and you literally do get heaving, writhing rivers of maggots pouring off the rotting mass.

There is video at the link. I decided not to imbed it since I didn’t know if all of my readers would have finished lunch yet.