From Vent Chemistry To Biochemistry

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Description of Workshop

This workshop is dedicated to a subset of topics supported by NSF FIBR grant NO. 0526747: “From geochemistry to the genetic code”. In this first workshop under the grant, we are gathering world experts on the chemistry and biota of deep-ocean hydrothermal vents, organosynthesis in geochemistry, in cells, and in the laboratory, metabolic networks and mechanisms of catalysis, and the emergence of macromolecules from a small-molecule organic substrate. The purpose of the meeting is to understand whether core metabolic pathways as they exist in modern organisms are likely to have formed as prebiotic states of network order in the chemistry of hydrothermal vents, and to examine the key difficulties in replicating their emergence in the laboratory. Several of the invitees are leaders on aspects of this problem, approached from premises different from the ones held by those of us on the grant. We hope that their insights, criticisms, and alternative approaches will significantly broaden our thinking about the topic. The workshop also serves as an intensive meeting for the members of the grant from different universities, and fulfills the proposed activity of one intensive weeklong workshop per year, to be augmented by smaller sessions involving subsets of the grant participants.

A specific subtopic of the meeting will be what is known about vent chemistry. What are the inorganic species and chemical environments of vents, what metabolic pathways are used by extant biota, and what inferences can we draw from these about favored species or modes of existence?

A second subtopic will be the analysis of “unsupervised” chemical networks as models of prebiotic organosynthesis. The goal is to predict, given inorganic inputs and a characterization of the environment (temperature, pH, availability of mineral catalysts or compartments), which if any pathways are the attractors in the most general network of allowed reactions, and what if any role modern intermediary metabolites play in such networks. A number of the invitees are experts in the use by modern organisms of phosphates, metal sulfides or other chelated metals, and other energetic or catalytic mechanisms that may have inorganic counterparts relevant to pursuing this question with laboratory experiments.

A final subtopic will be the emergence of macromolecules from prebiotic metabolic networks, and the transfer of information between the networks and macromolecular structures that may take on regulatory functions over them (specifically, the emergence of translation and coding for RNA or protein enzymes). This problem is central to the emergence and form of the genetic code, and the possibility that metabolic patterns may have survived the transition to be imprinted on the modern code.

Proposed Schedule and Topics

First four days are a workshop for all participants on the transition from geochemistry to the first emergence of biochemistry. Each day divided into morning and afternoon sessions, with two one-hour presentations per session and extended discussion time between presentations. General workshop is open to all SFI personnel.

Topics will include:

  1. Summary of current understanding of the geochemistry, biota, and biochemistry of hydrothermal vents and their fauna. Concerns are energetic and reactive inorganic species relevant to the earliest emergence of biochemical pathways, and indirect evidence for these from the pathways used by extant organisms. Related topic is a survey of the use of phosphates, metal sulfides, and chelated metals by modern organisms relevant to their possible use in mineral form.

  2. Relation of inorganic inputs to likely primordial organosynthesis,

  3. The relation of extant or plausible vent-synthesized organics to intermediary metabolites used by modern reducing organisms.

  4. The vent environment as a source of mineral catalysis, compartments, temperature, salinity and pH gradients, and other possible substitutes for the macromolecular catalysts, compartments and gradients maintained by modern cells.

  5. Statistical analysis of unsupervised chemical networks.

  6. The emergence of coding and the transition from metabolic networks to macromolecular regulation.

Chemical Reaction Network Theory Bibliography I and II (note Mikulecky 2001 )