What’s it like to use a supercomputer? UAB researcher Jeff Morris has a surprising analogy.
“It’s kind of like playing the guitar,” he laughs. “It’s pretty easy to do something productive pretty quick when you start, but obviously you can improve over a lifetime of usage.”
Morris, an associate professor of biology at UAB, is one of the more than 1,000 researchers who use the massive computational power of UAB’s Cheaha supercomputer to assist them with their work. The state’s fastest supercomputer, Cheaha provides UAB researchers conducting projects in fields ranging from neuro-imaging to dance with access to high-speed calculations and image processing — essentials when surveying large amounts of data or conducting complex simulations.
In Morris’s case, that looks like sequencing and re-sequencing the genetic material of 500 generations of algal bacteria. For a different experiment, sequencing 12 genomes would have taken about 150 days/genome without Cheaha; sequencing of all 12 took 10 days on Cheaha. Morris’ lab used a total of 5,288.285 CPU hours on Cheaha last year.
Morris’s passion for marine microbiology has driven his career to some incredible places. He first became interested in algae as an undergraduate working on stream monitoring. Later, as a postdoc at Michigan State University, Morris developed the concept that launched his career and which he calls the “Black Queen Hypothesis.”
“(The Black Queen Hypothesis is) this process of evolution where you predict that organisms will evolve to lose certain functions if the products of those functions have a tendency to leak out into the environment where other members of the community can have access to them,” he says.
Put another way, the Black Queen Hypothesis describes an equilibrium process in which the function-performing organisms, or “helpers,” in a given environment come to a point of mutual coexistence with nearby function-dependent organisms, or “beneficiaries.” The process allows both groups to thrive by creating and maintaining diversity in the overall population.
His paper publicizing the hypothesis has been cited hundreds of times. For Morris, the success of the Black Queen Hypothesis was confirmation he was doing something useful that was appreciated by other people. “It definitely made an impact,” he says.
That impact continues to direct his research today. The ideas behind the Black Queen Hypothesis form the basis of his current experiments to understand the effects of acid buildup on the marine food chain.
Since 2013, Morris has been funded by the National Science Foundation NSF to conduct research on the impact of ocean acidification on marine phytoplankton, or algae. His most recent experiment involved culturing hundreds of phytoplankton, sequencing their genomes, then subjecting groups of them to increasing levels of aqueous carbon dioxide — for the equivalent of a century. The goal is to see how projected increases in the acidity of seawater by 2100 will affect the microscopic algae that form the foundation of the ocean’s food chain.
“The idea is they’re going to adapt to the new environment, and they’re going to do that through genetic mutations,” he says. “They’re going to get better at growing in whichever environment that you have them in.”
Once the physical trials were completed, Morris’s team sequenced the genomes of all of the generations of bacteria again and compared them to the initial reference sequences of the first generation’s genetic information to determine just what mutations had occurred. The analysis is ongoing but has already yielded some interesting results.
“We’re still in the process of analyzing this — I just got done with the process of analyzing the genomes a few months ago — but you can see clearly there are some genes which are hugely more likely to mutate under future conditions,” Morris says. “So what are they? What sort of metabolic pathways are targets of natural selection under those conditions, and what does that tell us about what the future oceans are likely to look like?”
Morris’s enthusiasm for marine microbiology is infectious. It’s easy to overlook the fact that while his research relies on living phytoplankton, the bulk of the analysis is carried out in the digital realm of the supercomputer — a disconnect that Morris sees as one of the main areas for improvement in his field.
“What I really would like to see is maybe getting a little bit away from the very applied side of it and have more biologists think about the computing itself,” he says. “We have these huge computer-intensive things that we have to run … but it’s just sort of an unknown mystery what’s going on inside of it.”
Morris says he hopes scientists in his field seek opportunities for “more direct collaborations with computer scientists.” For students, Morris advises aspiring biologists to consider taking computing classes to supplement their studies. The combination of lab experimentation and computing that underlies modern biology can be “difficult and stressful in a lot of ways, but if you love it and it’s what you’re good at and it’s all you really want to do, you’ll do it,” he says.
And he emphasizes that the challenge isn’t faced alone: “One of the great things about it is that you get to be around other people who are like that as well. Your whole life is built around talking about science and talking about deep things, which I think is rewarding in its own way.”