The Blog

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.

I’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.

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.

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 Tarr, Jacques 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.

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.

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!