The Blog

Second chances of the professional sort

A little over a year ago I was invited to speak at a conference on Major Transitions in Evolution organized by an incredibly impressive group of students at the Universidad Nacional Autónonma de México. I couldn’t resist participating given the students, the venue, and because some intellectual heavy-weights in biology and evolutionary biology were taking part too. The event did not disappoint. You can see videos of the wonderful and wide-ranging lectures here. (If you are interested, mine is the first one at this link, starting at about 2 minutes and 45 seconds in.)

Of the other speakers attending, I was particularly excited to meet Bruce Alberts. He currently holds the Chancellor’s Leadership Chair in Biochemistry and Biophysics for Science and Education at the University of California, San Francisco, after serving as the Editor-in-Chief at Science from 2009-2013 and 12 years as the President of the National Academy of Sciences. In 2014 he was the lead author on a paper published in the Proceedings of the National Academy of Sciences about the systemic flaws in biomedical research, which, I feel, serves as a commentary about biology writ large. I really wanted to meet him in person.

By crazy chance, the very first night I arrived at the hotel, I went down to the restaurant to get something to eat. Who was sitting at a table there with his wife but Bruce Alberts! I went up and introduced myself, and they very kindly invited me to join them for dinner.

While I appreciate a lot of what we talked about, and the opportunity to meet him, I can’t quite shake my feelings about something he did later in the conference. He spoke with students and told them about how he had failed his PhD defense at Harvard University. I am likely mis-remembering the details, but he talked about how he almost didn’t get his PhD and thought his career was over before it had really even started. But, he got a second chance to defend, and look what happened…

Something about this story never sat quite right with me. Instead of seeming like an inspirational story to never-give-up, it felt more like a demonstration of his privilege. He could mess up big time, but he still got a second chance to make it right. I’m not at all convinced that this applies to women and under-represented groups of people in academia.

This crossed my mind again today when I read about Jonah Lehrer. He has a new book out called “A Book About Love.” At first, I was reading the review in the New York Times and was thinking it was a book I’d like to read.

But then I realized who he is. He’s the Columbia graduate, journalist who rose to prominence very quickly a few years back but blew it all by plagiarizing, fabricating Bob Dylan quotes, and other unethical things along those lines. On outline of what happened can be found on Wikipedia.

He breeched the foundation of intellectual/journalistic/academic ethics. How do you trust someone after that? This wasn’t just one little mis-step. He did repeated, calculated ethical breeches. As I have said many times in the past, you have complete control over your integrity, but once you lose it, you can’t ever get it back. I don’t think I can trust his research and writing, no matter how much remorse he claims.

But here he is. Featured in the New York Times. Back again.

Talk about the most amazing second chance ever.

Second chances. As I think through all of the people I have known personally or have known of in academia, anectodally, second chances are not equally distributed. A second chance is a  luxury not afforded to all. For people who are not traditionally seen as members of the academy, the rule seems to be more like one-strike-you’re-out. And the strike isn’t even necessarily due to one’s own actions.

I’ve always felt on the edge professionally, that one mis-step and my chances at a successful academic career would instantly drop to zero. It is very easy to fall off the edge. This fear is why I worked, I kid you not, 10-12 hour days, almost every day of every week for close to 10 years at the start of my career. (I would not recommend this for mental health reasons.) It worked though. Here I am, tenured, and at a well-respected institution. But I was also incredibly lucky, at the right place at the right time and working very hard — it takes both.  And I was forutnate. I never needed a second chance.

Luck and second chances, we don’t really have control over those. Senior people dole those out to the junior people they think are deserving of them.

It would be interesting to survey academics to see how many men & women, and whites & minorities who made it past tenure needed and were given a second chance. The null hypothesis is that second chances are evenly distributed. The alternative hypothesis, which I am inclined to see as the more likely, is that they are most definitely not.

School for Advanced Research, Santa Fe

Have you heard of the School for Advanced Research in Santa Fe? If not, I want to rectify that. From their “about” web page, it was established in 1907 “as a center for the study of the archaeology and ethnology of the American Southwest. Since 1967, the scope… has embraced a global perspective through programs to encourage advanced scholarship in anthropology and related social science disciplines and the humanities, and to facilitate the work of Native American scholars and artists.”

I was honored to take part in this mission in March of 2016 as a participant in the Advanced Seminar on Geospatial Approaches in Anthropology organized by Bob Anemone and Glen Conroy. I took part to share the satellite imagery-driven survey work Jackson Njau and I did in Tanzania, and other field work.

Photo from the SAR page about the seminar:
Photo from the SAR page about the seminar:

Ok, ok, I know some of you saw that photo and had the immediate reaction of “MAN-PANEL!” I get it. Men are starting to speak up and avoid events with such a crazy sex bias. But if you are the only woman, what do you do? Not go and let there be no representation? The composition of the group morphed a bit over the year in advance, so it wasn’t obvious until just before that it had become a man-panel. There are women who I could have suggested, but I didn’t notice early enough to speak up. I’ll pay more attention in the future.

But, I bring up the SAR seminar for a different reason.

See the guy standing behind me to the right? That’s Peter Ungar. He studies what he has dubbed “food prints”, which is a clever term that encompasses the scratches, pits, isotopes, and whatnot that food leaves on teeth. From this, he can figure out what long-extinct animals ate. It’s pretty neat work that you should check out, and maybe even buy one of his books!

Peter and I are, as you immediately see, both tooth biologists and have known each other since I was a graduate student. Over the last couple of years, we’ve talked for a few minutes as we’ve crossed paths at various conferences about why robust hominids have really robust teeth and what they used them for.

Background: There was a hominid living in eastern Africa and another living in southern Africa millions of years ago. They have huge molars and premolars, and very little incisors and canines. These features are associated with huge masticatory anatomy — the bones and muscle attachments of the jaws. We know they must have been eating an impressively difficult diet, but what was it? Did both species eat the same thing? Do they look similar because of shared ancestor or convergence?

From the “food prints”, it turns out that they were apparently eating different things. But, why would they have such similar shaped teeth if one of them was eating moreso leaves than the other?

The work I do brings a consideration of the underlying genetics to solving this conundrum.

From the developmental genetics research done on mice, lots of genes are involved in making cusps and configuring their placement on a molar. It is a complicated mechanism, and we scientists are still figuring it out.

In contrast, all of the genetics resarch to date suggests that the genetic mechanisms that influence whether or not a primate has thick or thin enamel is pretty simple. For example, my colleagues and I figured out that variation in molar enamel thickness doesn’t have any genetic correlation with tooth size or body size or anything else we could think of to test (see Hlusko et al. 2004 American Journal of Physical Anthropology “Genetics and evolution of primate enamel thickness: A baboon model”).  (By the way, that was an amazing paper to write — I should blog about that one of these days…)

Peter and I were pretty sure that these two huge-toothed hominid species look alike not because of adaptation to eating the same foods, but because of the underlying genetic architecture of dental variation. Both species had adapted to eating foods that were hard to process, although these were different types of foods. The simpler genetic architecture of enamel thickness in primates meant that thicker enamel could more readily evolve in response to the selective pressures of these more challenging diets. Pointy cusped teeth may be more ideal for eating leaves, but evolving them takes longer than does evolving thicker enamel because the underlying genetics is more complex.

And so, the first evolutionary response to these challenging diets were lineages with increasing enamel thickness. Had these creatures lived for millions more years, the leaf-eaters may have ultimately been selected to have pointy cusps good for leaf-eating.

What does this have to do with geospatial approaches in anthropology?

While we were both at the SAR seminar to talk about other aspects of our research, Peter and I got to delve into a much deeper conversation about genetic architecture and foodprints. A walk around Chaco Canyon solidified our ideas. We then skipped an afternoon walk around the beautiful SAR campus to sit at the wooden dining room table to sketch out the argument. We had a manuscript submitted within weeks, and just two days ago, our hypothesis was published as a Perspective (“Evolutionary Path of least resistance“) in Science.

This experience has reinforced to me the benefit of professional meetings, and especially, of the tremendous value in putting academics together for longer periods of time to contemplate and discuss. There are very few institutions that provide this kind of forum, and SAR is one of them. And, an important one at that. Thank you to the amazing SAR staff who made this possible, even though it is an off-shoot of the original intent of the seminar. The geospatial work is coming…

Eureka moments in science

I have found over the course of my 20 years in academia that there are times when scientific magic happens. These require just the right mix of colleagues, expertise, data in-hand, and time to think. You can’t force these, but you know when you are in one of them. The synergy is electric, you can’t stop thinking about the questions and how to solve them. You and your colleagues are on the same wavelength, almost reading each other’s minds but simultaneously challenging each other at every step. This kind of research chemistry is science  at its best (and also, when it is the most rewarding for those of us who do it).

Back in the spring of 2015 my lab was in the thick of one of these episodes. My then-postdoc Chris Schmitt (who is now a professor at Boston University), two of my graduate students (Tesla Monson and Marianne Brasil), and I met for hours at  a time, at least once or more like 2-3 times a week to synthesize the ~18 years of quantitative genetics I’d done on baboon dental variation, and try to figure out how to use these results to improve our understanding of the relationship between genotype and phenotype for primate dentitions. With large phenotypic data sets collected through a couple of National Science Foundation grants and from generous colleagues and published literature, we bantered back and forth. We ran more analyses than I care to remember, adjusted, and reassessed. Didn’t believe our results, tried something new. And we asked ourselves repeatedly, “what exactly are we really trying to find out, and is this analysis actually addressing that specific question?” It was exploratory research at its finest.

We ended up with a manuscript that combines data from developmental genetics, quantitative genetics, neontology, and paleontology, and in so doing, revealed a pattern in primate evolution that elucidates a major evolutionary event. I love this paper — it is what I envisioned doing 20 years ago as a first year graduate student (and advocated for in publication in 2004), yearning to apply a knowledge of genetic patterning mechanisms to hominid paleontology. Doing this well took a lot more background research than I realized it would take, but it is great to finally be here.

It has been quite an adventure trying to get this manuscript published, and we aren’t quite there yet. I’ll post about that later, once the journey finds its happy ending. For now, I wanted to talk about the process.

Did you notice what I did not mention in the description of how we did the research?

There is no eureka moment.

evo_67_1_coverI’ve commented on this before. At that time it was in regards to another magical collaboration that resulted in my lab’s cover article in Evolution (Grieco, Rizk, & Hlusko. 2013. A modular framework characterizes micro- and macroevolution of old world monkey dentitions. Evolution 67(1):241-59.)

The day after that paper was accepted for publication, I was coincidentally interviewed for The Leakey Foundation’s Dig Deeper series.

I direct your attention to the 2 minutes 52 second mark in the video, when I was asked if I’d ever had a eureka moment.

I am increasingly coming to the conclusion that in good science, at least in my scientific discipline, there is no such thing as a eureka moment. A good scientist may see an output of an analysis or find a fossil in the field that ends up being the key piece to solving a scientific puzzle, but the knee-jerk reaction is, or should be, one of skepticism. Not one of “yes! I did it!”

(In the field, we have the term “hominid fever”, which describes the condition you have when everything looks like a hominid. This can really be embarrassing. After hearing multilple stories of  paleontologists rushing off to make press announcements for “hominids” that turned out to be monkeys and carnivores, I am perhaps the most boring, unexcited fossil-finder. Just ask my grad student Whitney Reiner about the moment when she discovered a one-million-year-old hominid distal ulna at Olduvai Gorge). 

I get that a skeptical narrative of discovery doesn’t make good copy. Everyone loves the idea of a eureka moment.

But when we place so much emphasis on eureka moments, and when good scientists fib a bit to embellish their discovery story to make it more exciting for the press and social media, the public and other scientists start to believe that this is how it is supposed to happen.

Young scientists aren’t being taught the conservative approach. They aren’t being taught that skepticism is the foundation of good science. Uncertainty followed by a lot of hard work is good science. Immediately knowing the answer is not.

Ours is a field of discovery. But us more senior scientists need to be more clear that discovery means trying to disprove what you think you may have found. Only after you have exhausted all the ways you can demonstate that an interpretation is wrong, then you know you’ve likely discovered something new.

There’s no eureka moment in there, but if you are lucky, you just might get to have a 6-month long eureka experience. Like I did in the spring of 2015.

Kefir, family, and the evolution of our species

The other day, a new friend gave me an amazing gift: kefir that she’s cultured from grains that were given to her by a buddist nun.

These aren’t really grains at all, but a mixture of yeast and bacteria that live symbiotically and break down the lactose in milk. I’ve seen kefir in the grocery store, but never tried it. Honestly, I hadn’t really thought much about kefir at all.  But now, I’m intrigued, in large part because of the evolutionary history, the anthropology, and the touching guesture of friendship.

My family name, Hlusko (which I think should be spelled Hluško) is from eastern Europe, just a hop-skip-and-a-jump over the Black Sea from the Caucasus. Since the practice of Kefir fermentation comes from that part of the world, this is sort of like discovering a little piece of my long-lost family heritage. Well, close enough anyway, for me as a third-generation-removed American.

Milk fermentation has been an important part of pastoralist cultures because adult mammals (including humans) can’t typically digest the sugars in milk, i.e., lactose. Babies and young children can digest mama’s milk because they have an active LCT gene that produces lactase in the intestines, a protease that breaks down the lactose protein into more simple sugars as it moves through the digestive system. This gene stops being expressed as you age. Since most mammals only drink milk when they are young and nursing, the loss of lactase production in the body as they become adults is inconsequential. This is the usual condition across mammals. From what I’ve been able to discern from the literature, I think that the LCT gene stops being expressed in humans sometime around age 7.

(This mankes me wonder why we stereotypically give adult cats a big bowl of milk. I’m guessing they don’t really like it, but will have to experiment once I adopt another kitty, but that’s for another day.)

If your body doesn’t produce lactase, bacteria in your gut will break down the lactose you may consume for you. But, these bacteria produce gas as a by-product, which is not such a pleasant thing to have build up inside your body. The bacterial fermentation also leads to an increase in-flow of water into the intestines, which leads to diarrhea.

Over millions of years, there have been mutations in the genetic regulatory elements that turn the LCT gene on and off. Some of these mutations caused the LCT gene to continue being expressed long after childhood. In these people, their bodies could digest lactose long past the age when they’d needed this ability. But for the vast majority of human evolution, this kind of mutation was meaningless because they  didn’t consume milk once they’d been weaned.

But about 3,000 years ago, some populations of people started keeping animals such as cows, goats, and camels close to them, and then started to utilize their milk. The people who could easily drink/digest milk as adults had a significant food and liquid resource that wasn’t as easily available to other adults. They ended up healthier, and consequently, with more children surviving over time, and the trait rose in frequency in the population.

These adult milk-digesters are what we call lactase persistent, because they persist in the production of lactase into adulthood. It is a mutant phenotype. Being lactose intolerant isn’t an allergy or being sick at all. That is the typical mammalian condition.

The human cultural practice of using kefir to ferment milk makes the milk digestable for adults who don’t have a mutation that keeps their LCT gene functioning past childhood. Thanks to kefir, milk gets fermented before you drink it, rather than after, which is a much more pleasant experience for everyone invovled. Plus, it opened up another way that we can benefit from domesticated mammals. Given how much pastoralist people rely on their animals as the foundation of their entire economy, they don’t like to slaughter them all that often. Their regular subsistence from the animals usually comes in the form of blood and milk, and fermented milk products have proven to be another incredibly beneficial and important resource that these animals provide.

The selection for lactase persistence in humans happened at least four times, once in Europe  and three times in Africa (Tishkoff et al., Nature Genetics 2007 Jan;39(1):31-40), and the timing is remarkably correlated with adoption of pastoralism in those parts of the world. There has been a lot of work done exploring this in even more detail since Sarah Tishkoff’s team first discovered that there were multiple mutations effecting LCT expression, but she has been the leader in exploring genetic variation across SubSaharan Africa. For this reason, she’s one of my intellectual heroes. (Aside from her great science, she’s a really nice person to boot.)

The lactase persistence alleles are a classic example of convergence in humans, convergence that results from cultural shifts away from hunting and gathering towards animal domestication. And while the story is one that I am very, very familiar with, it was wonderful to merge a meangingul gift from a new friend to a cultural connection with my family’s heritage, and, to the evolution of my species. It doesn’t get much better than that.

Talking about evolution

I am a huge NPR fan, or perhaps, more like an NPR junkie of sorts. If I’m home, NPR is on the radio as my background noise.

One of the programs I really like is Shankar Vedantam’s Hidden Brain. This morning he was talking about a study on stress that found that people who dance together, with the same choreography, have a reduction in their perception of pain, as well as reduced stress. Neat stuff. The report was based on a study published in the journal Evolution and Human Behavior by Bronwyn TarrJacques Launay, and Robin I.M. Dunbar (article’s title is, “Silent disco: dancing in synchrony leads to elevated pain thresholds and social closeness”)

One thing in particular in Vendantam’s reporting caught my ear, and that was the language he used to describe evolution, and specifically selection for a particular trait.

Near the end of the short report, Vedantam says, “When experiences feel good, that’s usually a signal that they have served some kind of evolutionary purpose. So the brain evolved to find certain kinds of food tasty because eating those foods had survival value for our ancestors.

People use this kind of framing all the time, but I think it leads to a misunderstanding of evolution because it is backwards. The brain didn’t evolve itself a new characteristic in order to do better at the natural selection game.

Instead, there is naturally occuring variation in a population because mistakes are made in DNA replication during the process of reproduction (i.e., when sperm and egg cells are made).

If one variant leads to a behavior or a response that leads to the individual having more or healthier offspring compared to individuals who don’t have that variant, then over time, that variant will become more and more common.

The more accurate way to have said the second sentence would be, “People who got a psychological bump from eating foods that are particularly healthy tended to eat more healthy food. In the long-run, they were healthier and ended up with either healthier offspring, or more of them, or both. Over time, the genetic mechanism that underlies the psychological boost will have increased in frequency in the population as a consequence.”

Wordy, I know. But that’s evolution. There isn’t any intentional directionality to it.

The Wikipedia Project

This spring semester, 2016, I have had the joy of working with 10 amazing undergraduate students to develop an American Cultures Engaged Scholarship project for IntegBio 35AC Human Biological Variation.

Clockwise from top left: Bailey Ferguson, Olivia Downs, Maddie Zuercher, Nirali Rahul, Christy Hulett, Jacqueline Morales, Alyssa Case, Jun Sin, TJ Ford, Nathan Shin, and Leslea Hlusko.

IntegBio 35AC is a large lecture (300 students), lower division, non-majors biology class that addresses modern human biological variation from historical, comparative, evolutionary, biomedical, and cultural perspectives. It introduces students to the fundamentals of comparative biology, evolutionary theory, and genetics as it relates to their everyday lives — how they view the diversity of people around them.

With funding and support from the University of California Berkeley’s American Cultures Program and the WikiEdu Foundation, the eleven of us developed a month-long project that students in IntegBio35AC will participate in through their discussion sections starting in the fall of 2016. Each discussion section will edit a Wikipedia article about a topic related to the class. Every student will be trained to be a wikipedian, and will develop the skills (and hopefully the motivation) to share their Berkeley-gained knowledge with the world through the improvement of Wikipedia.

We edited three Wikipedia pages as a trial run-through of the project. To see what they did, compare this 2014 article on Natural Fertility, with this revised one from April 2016. This has had 925 page views since they started working on it.

Check out the students’ edits to the Race and Health page. Here’s what it looked like before they made their improvements: January 2016.  There have been 7,701 page views since they started their edits in February (138/day).

And the third article they edited, Transgender in Sport went from this in January 2016 to this in April 2016. In the two months since they started working on this article, there have been 2,499 page views.

Talk about impact.

In addition to developing this project, these students helped me re-think quite a bit of how we do assessment in the class. They convinced me to drop the three formal in-class exams and move to six on-line quizzes instead. We exchanged the final exam for the paper (which used to be due right before Thanksgiving break). This will give students more time to really delve into their topics, and GSIs will have more time to critique the papers thoughtfully.

I’m very grateful to Berkeley’s Center for Teaching and Learning for an Instructional Improvement grant that will pay for a graduate student to help implement all of these changes to our online course website over the summer. Many thanks to Austin Peck for helping me with this over the next month.

After having been through the formal teaching environment of IntegBio35AC together in the fall of 2015, and now having this much more informal, collaborative classroom experience together, these ten students have each earned a special place in my heart. It has been a really rewarding experience for me as a professor.  These students trusted me enough to provide very honest feedback and creative ideas for how to improve the class. I also learned a tremendous amount about how students interface with their coursework and the campus. While quite a lot has changed since I was in college, it also wonderful to be reminded of just how much doesn’t change from generation to generation. If you don’t believe me, check out the YikYak app.

These students will give a guest lecture to the Fall 2016 IntegBio35AC course to introduce the project and show the students what the beginning and end of the Wikipedia Project looks like. I’m eager to see how much next semester’s students enjoy what we’ve created!