The first research seminar of the International Laboratory of Statistical and Computational Genomics had been postponed almost a month due to COVID-19. In April, however, the event finally took place. Laboratory Head Vladimir Shchur discusses what life is like for scientists in self-isolation during the pandemic, what genomics is, and why gesturing is important when teaching online.
In the winter, when our new laboratory started up, I organized a virtual communication space for the entire team of staff and students on Slack. During that time, it was a convenient additional platform for maintaining the operation of the lab. When we transitioned online due to the pandemic, Slack suddenly became a crucial tool for us. We were already accustomed to communicating with each other through the platform, and we all actively used it. It immediately became clear that the current situation isn’t going to change any time soon and that it is important not to lose touch with each other. We started a channel called #coronalife, where, in relay-race fashion, staff and students post motivational messages with funny pictures. Thus, we have a forum for informal communication.
We are working as usual. Even before the lockdown, we regularly used Zoom to meet with our foreign colleagues, although, of course, not to the same extent as now. In addition to research seminars, we conduct weekly lab meetings at the laboratory for lab members - a format more common in England and the USA. A week ago, we held a lab meeting on Zoom, where all the team members met with our Academic Supervisor, Professor Rasmus Nielsen of Berkeley, and our international colleagues, Thorfinn Korneliussen (Copenhagen) and Russ Corbett-Detig (Santa Cruz, California). Since the meetings are in English, I asked Natalia Kudinova, a MIEM English instructor, to join us. Now we are organizing additional classes in technical English and the art of presentation, which we will also hold on Zoom.
Geographical borders have now been erased: in Moscow, Denmark, and California, we are all working remotely
The online format helps and even encourages us to foster closer collaboration between our employees, students, and colleagues from laboratories abroad. For example, the laboratories of Berkeley and Santa Cruz have more biologists, and we have more mathematicians. This is a great opportunity to engage in more interdisciplinary research.
In a short time, we have established a new way of working that is intensive and productive, and we have adapted to the new reality. Nevertheless, I am sure that without face-to-face interaction, science loses a lot. It’s not for nothing that we travel to conferences. You can of course read all the latest research in journals, but a lot of new and unexpected ideas are born in face-to-face conversation between colleagues. Often, these ideas grow into new joint projects. Personal contact is necessary, so it is not possible to move online completely.
Genomics is a young interdisciplinary science that attracts mathematicians, computer scientists, biologists, physicists, and others. We create mathematical models and use them to develop data analysis methods and apply them to experimental data.
Currently we are working on a joint project with Egor Prokhorchuk, Head of the Laboratory of Vertebrate Genomics and Epigenoimcs of the Russian Academy of Sciences. Using archeological excavation findings from the North Caucasus, we are analyzing the ancient DNA of a person who lived in the Early Bronze Age. We want to see whether historical and archaeological conclusions about the migration of peoples in this territory are consistent with genetic data. For example, when archaeologists unearth a new settlement, their findings may resemble an already known culture that existed elsewhere. What does this mean? Did this mixing occur due to trade? Or was there a full exchange between cultures, including interpopulation marriages? Or, perhaps, an aggressive tribe conquered and replaced the tribes living in this territory, and the new population completely replaced the original one. A mathematical analysis of ancient DNA can provide a clue as to which of these answers is closer to reality.
Thanks to sequencing technology (DNA extraction), we can study ancient genomes
In particular, when comparing the frequency of various genome patterns in people from different eras, we can understand which of these patterns have spread due to adaptation to changing environmental conditions. For example, variations of FADS genes, which help us digest fatty foods, appeared in northern peoples due to dietary adaptation.
One of the most famous examples of adaptation is the assimilation of lactose by the population of almost all of Europe. It is still unclear when and where this gene pattern appeared. Some studies show that in Northern Europe selection was significantly stronger than in the south. Other scientists, to the contrary, question the role of natural selection in the formation of this gene pattern. Thus, even in such a well-known example, many questions remain, and the scientific community has not yet come to a consensus. Nevertheless, an increase in the amount of genetic data available to us, both modern and ancient, provides new opportunities for studying evolutionary processes and the development of populations.
In April, we held our laboratory’s first research seminar. This is one of the main formats for our academic activity. I like to recall, for example, the seminars I took with Professor Vladimir Arnold when I was a student—his explosive manner of speaking and his fiery eyes.
Due to the Covid-19 pandemic, our first seminar was held later than planned, but in the end, we did hold this important event. I wanted my colleague from Skoltech, Dmitry Ivankov, to open the first seminar since he knows how to ignite audiences with his energy and talk about complex things in simple terms. Dmitry talked about what hinders us in using genotypes to predict phenotypes. This topic is the holy grail of evolutionary biology. Everyone dreams of getting a genome and its DNA sequencing into a computer and seeing the body that has this given genotype, with all its idiosyncrasies, special abilities, and diseases. It seemed to me that even participants who haven’t yet delved too deeply into issues of DNA, RNA, and epistasis (the dependence of the effect of the genetic variant on its context) appreciated the beauty and scale of Dmitry’s work.
However, at the same time, I understand that online formats are not as good as face-to-face contact when it comes to energy. The speaker doesn’t get enough feedback from the audience; without personal contact, people start to get distracted. We’re all learning how to keep our attention focused during online communication. In my own online classes with students, I’ve started asking everyone to turn their cameras on, and I try to adjust my camera so that students can see my hands and gestures, since this helps convey emotions and engage the viewer more effectively.
It so happened that at the last seminar of our academic retreat in Voronovo, we discussed how to motivate ourselves and our colleagues to stream their research seminars online. Now you do not need to motivate anyone. We are all online. This has its pros and cons. For example, now we have time to ‘go’ to events we ordinarily didn’t have time for before. At seminars and lectures of our laboratory, we are glad to see anyone and everyone—students and employees of any faculty and any university, as well as those who are just interested in science.
I hope that when the pandemic ends, all academic events will be accompanied by online broadcasts. It seems to me that this kind of hybrid mode will be very popular. At our seminars, we will definitely begin to do this.