Origin of Life

We conduct both theoretical and empirical research to address how adaptive evolution got started prior to the emergence of genetic encoding in RNA. Our theoretical work studies chemical reaction networks with a focus on autocatalytic motifs (subnetworks that have the capacity for collective stoichiometric increase in all their members) and the ecological relationships among these motifs. The guiding principle is that the earliest mode of evolution resembled ecological succession where the “species” accumulating over time are not biological species but autocatalytic motifs. With collaborators in physics, math, and computer science, we are using mathematical analysis and stochastic modeling to explore the capacity of chemical ecosystems to show multistability, respond to selection, and accumulate complexity in spatially explicit environments.

Our empirical research entails assembling plausible prebiotic chemical microcosms and looking for quantitative evidence of autocatalysis and evolution-like dynamics. Our main method is chemical ecosystem selection, a strategy for keeping prebiotic mixtures out of equilibrium by recursive dilution with a fresh “food” soup. Changes over time are tracked with high-performance liquid-chromatography mass-spectrometry and other methods to look for non-linear dynamics. Additionally, we have interests in the origins of compartmentalization and the emergence of functional biopolymers (peptides and RNAs).

A minor, additional focus is on the origin of eukaryotes: a unique evolutionary event that resulted in a quantum leap in cellular complexity. It is quite clear that eukaryogenesis entailed the merger of an archaeal host with the bacterial progenitors of mitochondria, but how that symbiosis proceeded and how it yielded the characteristic structure of eukaryotic cells remains less well understood. The widespread assumption used to be that the nucleus and endomembrane system emerged from outside-in, via invaginations of the bounding plasma membrane. We argued in 2014 that eukaryotes originated from the inside-out when the archaeal ancestor extruded the original plasma membrane into extracellular structures that ultimately transformed into the outer nuclear membrane, endomembrane system, and eukaryotic plasma membrane. The inside-out model has gained increasing support thanks to new data from Asgard archaea.

figure shows examples of the final configuration of stochastic simulations of chemical ecosystems

The figure shows examples of the final configuration of stochastic simulations of chemical ecosystems with two mutually inhibiting autocatalytic cycles (red and blue) on a 2D-surface. Heat-maps show snapshots of hexagonal reaction-diffusion arrays of diameter 39 for different chemical diffusivity values. Each site was seeded with 10 member molecules of each cycle. The top row shows relative dominance of the two cycles. The middle row summarized the extent to which pixels are dominated be one cycle (white) or contain members of both cycles (purple). The bottom row summarizes the average difference in composition between each pixel and its four neighbors. The results show that system complexity is maximized at intermediate diffusion rates.


Origin of life publications

Plum, A. and BaumDA. (2023). ACEs in spaces: ACEs in spaces: Autocatalytic Chemical Ecosystems in Spatial Settings. ArXiv: https://arxiv.org/abs/2212.14445

Peng, Z., Linderoth, J., BaumDA. (2022). The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life. PLoS Comput Biol 18(9): e1010498. https://doi.org/10.1371/journal.pcbi.1010498

Vincent, L., Colón-Santos, S., Henderson J. Cleaves II, Baum, D. A.*, Maurer, S. E. * [co-corresponding author] 2021. The Prebiotic Kitchen: A Guide to Composing Prebiotic Soup Recipes to Test Origins of Life Hypotheses. Life 11(11): 1221.

Peng, Z., Plum, A., Gagrani, P., and Baum, D. A. 2020. An ecological framework for the analysis of prebiotic chemical reaction networks. J. Theoretical Biology 507:1-15.

Vincent,  L., Berg, M., Krismer, M., Saghafi, S., Cosby, J., Sankari, T., Vetsigian, K.,  Cleaves, H. J. III, and Baum, D. A. 2019. Chemical Ecosystem Selection on Mineral Surfaces Reveals long-term dynamics consistent with the spontaneous emergence of mutual catalysis. Life. 9(4), doi:10.3390/life9040080

Mizuuchi, R., Blokhuis, A., Vincent, L., Nghe, P., Lehman, N., and Baum, D. A. 2019. Mineral surfaces select for longer RNA molecules. Chemical Communications 10.1039/C8CC10319D

Baum, D. A. 2018. The origin and early evolution of life in chemical complexity space. Journal of Theoretical Biology. 456: 295-304.

Baum, D. A. and Lehman, N. 2017. Life’s late digital revolution and why it matters for the study of the origins of life.  Life 7(3), 34: doi: 10.3390/life7030034

Baum, D. A. and K. Vetsigian. 2016. An experimental framework for generating evolvable chemical systems in the laboratory. Origins of Life and Evolution of Biospheres, 47:481–497.

Baum, D. A. 2015. Selection and the origin of cells. Bioscience 65: 678-684.

***Prospective Origin of Life Student?***