Reconstructing Ancient Life: The Phylogenetic Tree, Nitrogen Fixation, and the Translation Machinery as Life's Oldest Computer

Batu Kachar, an astrobiologist, discusses the profound insights gained from studying the phylogenetic or evolutionary tree of life, emphasizing that Earth is the only known place to study biology. By reverse-engineering ancient gene sequences and proteins, researchers can reconstruct ancestral life forms and environments, despite the inherent "fogginess" of looking billions of years into the past. Kachar highlights that the most significant biological innovations, such as the emergence of the first cells, photosynthesis, eukaryotes, and the oxygenation event, occurred in the early history of life, long before the appearance of larger, more complex organisms.

The conversation delves into the study of modern "survivors" like bacteria (cyanobacteria, E. coli, diazotrophs) to infer the characteristics of ancient life. A key focus is nitrogen fixation, a singular evolutionary invention crucial for life as we know it, which converts atmospheric nitrogen into usable ammonia. This process, mediated by the nitrogenase enzyme, is contrasted with the multiple pathways for carbon fixation. The human-engineered Haber-Bosch process is mentioned as a modern abiotic equivalent, underscoring the fundamental importance of nitrogen to biological systems and its significant impact on human civilization.

Kachar elaborates on the translation machinery, describing it as the "oldest computational device of life" and a "chemical decoding device" that is central to all cellular life. This complex system integrates chemical, physical, informatic, computational, and biological principles to convert mRNA sequences into functional proteins. It operates with remarkable precision and resilience, capable of functioning even in cell-free environments. The discussion highlights the genetic code's degeneracy, where 64 possible codon states encode only 20 amino acids, providing a crucial redundancy that allows for errors without compromising the integrity of the biological message.

The episode draws parallels between deciphering the genetic code and reconstructing ancient human languages, where modern forms provide clues to ancestral states and environments. The universality of the start codon and the robustness of the genetic code are presented as fundamental aspects of life's operating system. By understanding these core mechanisms and the interplay between geology and biology, researchers aim to unravel the mysteries of life's origin and evolution, implicitly informing the broader search for life beyond Earth by identifying essential biological attributes.

"you can study chemistry you can study Physics you can study geology anywhere in the universe but this is the only place you can study biology this is the only place to be a biologist that's it"

"phytogenetic trees could be one of the most uh romantic and beautiful Notions that can come out of biology it shows us a way to depict the connectedness of life and all living beings with one another"

"the fun stuff is what what thing is boring I think that the the phase that's well at least two different times in the geologic history one is the first life uh past origin of Life how did first life look like"

"biology is you you basically study with study the survivors broadly speaking yeah and you're trying to pitch the sort of put together their history based on whatever you can recover today what makes biology fascinating also let it erased its own history in a way"

"humans don't like their ancestors they rarely invite them over for dinner yeah right that bacteria is in your dinner bacteria is in your gut but today is helping you for dinner"

"there's just one mechanism that Evolution invented to convert it is so far we know there's there's only one nitrogen fixation pathway as opposed to say carbon you can find up to seven or eight different carbon based microbes invented to fix carbon that's not the case for nitrogen it's a it's a singularity across geologic time"

"I cannot think of it no it's it's it's essential to Life as we know you you and I are having this conversation because life found a way to fix nitrogen"

"it is on a very unique subsystem of cellular life in comparison to I would say metabolism and we used to um you know when we are thinking about cellular life we think of cell as the basic units or the building block but from a key perspective that's uh not the case that one may argue that everything that happens inside the cell serves the translation and the translation Machinery"

"it's like a printer I would divide it into actually even four more additional steps or disciplines than what would it take to study it by the way you described it it's a chemical system it's the compounds that make it up are chemicals it's physical it's uh tracks the energy to make its job to do its job its own informatic what is processed are the bits it's computational the discrete states that the system is placed when the information is being processed that's itself is computational and it's biological it's a there's variability and inheritance that come from imperfect replication even and infer imperfect computation"

"the computers don't have don't link information to function right they are not tightly coupled nowhere close to what translation or the way translation does it"

"there are 500 different amino acids life can choose right it's narrowed it down to training we don't know why a lot of people think about this genetic code is quite fascinating right"

"this may seem like a waste but informatically it's important because it's abundant and it is uh redundant right so so this code degeneracy you see this in that's implemented by this translation missionary inside the cell so it means we can make errors right you can make errors but the message will still get through"