Big Biology

What are network motifs, and how and why do they matter to biological networks?

On this episode, we talk with Uri Alon, systems biologist at the Weizmann Institute of Science, about biological networks. In the early 2000s, Uri discovered some of the fundamental characteristics of these networks and, since then, has worked to understand networks across different levels of biological organization. His work shows that, from genes to whole organisms, networks are filled with repeating patterns of connections known as network motifs, such as feedback and feedforward loops. We talk about how the motifs arise and what they mean for the performance and evolution of the systems in which they’re embedded. Moving farther afield, we also talk about how scientists can productively move into new areas, and how Uri teaches early-stage scientists to leap confidently into the unknown. And a bonus: Uri sings and plays guitar for us!

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Why do humans look so different from one another? Why do we have different types of hair and different skin colors? And what do these traits have to do with the concept of race?

On this episode, we talk with Tina Lasisi, incoming professor at the University of Michigan, about variation in human hair structure and skin color. We talk about why such variation may have evolved, and how biologists are studying it. We also discuss the implications of her work for the concept of race. Tina encourages scientists and the public to be curious about (rather than afraid of) human diversity, as it’s an obvious part of our world that should be understood from multiple perspectives, including biological.

Also be sure to check out the Preprints in Motion podcast here!

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Happy holidays from the Big Biology team! As a bonus episode this week, we are sharing Art's recent interview with James Fodor on The Science of Everything podcast. Art and James discuss various topics in evolution and genetics, covering material that spans years of Big Bio conversations.

Enjoy, and see you next year!

What’s the smallest number of genes that cells need to grow and reproduce? Is it possible to synthesize minimal genomes and insert them into cells? What do minimal genomes teach us about life?

In this episode, we talk to John Glass, leader of the Synthetic Biology Group at the J. Craig Venter Institute. Over the past decade, Glass and colleagues developed techniques for manipulating and synthesizing entire bacterial genomes. Starting with Mycoplasma bacteria, which have very small genomes, they determined the minimal number of genes (473!) required to support life. They experimentally confirmed this number by synthesizing genomes from scratch, containing just the essential genes, and putting them into other bacteria whose genomes were removed. Cells in this lineage, called JCVI-syn3.0, grow and divide approximately like wildtype cells do.

We talk with John about how they pulled it off and what this minimal genome tells us about life more generally. We also chat about the functions of essential genes and what so-called non-essential genes may do in the wild. Finally, we touch on what if anything minimal genomes say about the origin of life and on the group’s ongoing efforts to synthesize entire cells – not just genomes! – from scratch.

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How will we find life beyond Earth? Can we use a molecule's complexity to distinguish life from non-life?

A common way to search for extraterrestrial life is to look for signs of complex organic molecules on other moons and planets. One trouble with this approach, though, is that lots of complex molecules can arise from inorganic processes. To be sure that complexity indicates life, we also need to distinguish forms of complexity that could only be produced by information-rich processes – things that must be alive.

On today’s show, we talk with astrobiologist Sara Walker about this idea in relation to a new theory, called assembly theory, that she and colleagues are currently developing. Assembly theory characterizes the complexity of objects, including molecules, by how many steps are required to make them – the more steps, the higher the object’s complexity index. This perspective reorients our attention from the traits of objects that make them complex to the historical sequence of events that must have occurred to create them. Sara proposes that this idea provides natural ways to think about a large set of interesting processes, including how information is manifest and used in living systems, the creative roles of natural selection in evolution, and the ever present problem of understanding levels of selection.

This was Sara’s second appearance on the show, check out her first episode here.

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What hidden life lies at the bottom of the deep ocean? How do so many species survive and even thrive with so little light and food and at such pressure?

In this episode, we talk to Helen Scales, a marine biologist, writer, and broadcaster who has written the essential guidebook to the deep ocean titled “The Brilliant Abyss”. On our way to the bottom of the sea, Helen recounted her journey from academia to writing and shared some of the lessons for others looking to dive into science communication. She also introduced us to some of her favorite species and their unique adaptations for surviving at extreme depths as well as several threats that the deep ocean faces. Technology has not only opened up this ecosystem to exploration but also to exploitation. Helen lays out the current state of ocean conservation and offers some hope and advice to those looking to protect the planet's largest habitat.

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What is eco-evo-devo? How can ants help us understand the evolution of development?

There are 20 quadrillion ants in the world, and they come in lots of different shapes and sizes. We even see big differences within colonies, like ants in the genus Pheidole which have different castes: workers, soldiers, and, in some species, super soldiers. Super soldiers are the muscle-y brutes of the ant world that grow huge heads to defend the colony and attack large food items, like other insects. This variation is all due to developmental plasticity – the same ant genotype produces distinct phenotypes depending on the environment of their early lives.

On this episode, we talk with Rajee Rajakumar, a professor at the University of Ottawa, who studies Pheidole ants to understand the interactions between their genes, their developmental environments, and their phenotypes. Rajee is also a HUGE ant fan! We talk with him about his 2018 paper in Nature about the mysterious organs that control these differences in development, and amazingly, how these organs could be socially regulated via pheromones.

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What happens when potential fraud is detected in research papers on major medical issues?

In this episode, we talk to Charles Piller, an investigative journalist who published a shocking story in Science magazine in July this year laying out compelling evidence for misconduct in multiple journal articles on Alzheimer’s disease. This misconduct appears to have occurred in recent papers involving the experimental drug, simulfilam, as well as older, foundational papers in Alzheimer’s research.

Charles’s story focuses on the sleuthing of Matthew Schrag, a neuroscientist and physician at Vanderbilt University who studies Alzheimer’s disease himself. In an extensive (even heroic) effort, Schrag identified over 100 potentially manipulated images in multiple major research papers. We talk with Charles about the consequences of those seemingly fraudulent images for the field and for public trust in science. We also talk about the potential consequences for whistleblowers like Schrag, and what journals and funding agencies are doing to support integrity in basic research.

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Can genes in single species act as keystones in ecosystems? What is AOP2, and how does it affect community composition and persistence?

In this episode, we talk to Matt Barbour, a professor at the University of Sherbrooke, about “keystones” in biology. You’re probably familiar with the keystone species concept, but Matt’s research focuses on whether genes can play a similarly fundamental role in an ecosystem. In an incredible set of experiments, Matt and his colleagues used simple experimental food webs to find that the stability of these miniature complex systems was strongly associated to the genotype at one specific locus in the plant, Arabidopsis thaliana, called AOP2. The particular genetic variant led to complete breakdown of community stability, imbuing that gene with a keystone-like function.

We talk to Matt about his recent publication in the journal Science and discuss how results from his simple lab setup relates to keystone effects in natural communities.

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How much coffee should we drink? Is there a scientific way to have a healthy, happy life? And how do we distinguish scientific sense from nonsense?

In this episode, we talk with author and University of Alberta professor Timothy Caulfield about decision making and misinformation in the modern world. A surprising number of “common sense” decisions that people make in their daily lives are not actually backed by strong scientific evidence, and Tim strives to debunk these in his recent book, “Relax, Dammit!: A User's Guide to the Age of Anxiety”.

Among other things, we discuss with Tim how often we should check email, and how risky it really is for kids to walk to school. We also talk about how science communication can be used to curb misinformation, and Tim shares his dos and don’ts for effective scicomm.

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