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Chemical Evolution

June 30, 2014

Evolution of modern plants and animals is easily seen in the progression of forms in the fossil record. Most significant was the Cambrian explosion, about half a billion years ago, in which many new life forms appeared, evolved, and flourished. The fossil record also informs us that sometimes a body plan just doesn't make sense, and those organisms become extinct.

There were organisms before the Cambrian, in the aptly-named Precambrian. The actual origin of life (abiogenesis) is thought to have occurred long before the Cambrian. Evidence of bacteria dated to be about three and a half billion years old has been found in Western Australia, as I wrote in a previous article (Bacterial Microfossils, January 8, 2014).

At its base, life is a chemical reaction, and the field of molecular evolution tracks the chemical changes that have occurred in organisms during evolution. Elucidating the chemistry of early life, even before the appearance of fossil shapes in the geological record, is the subject of chemical evolution.

Chemical Evolution is the title of a 1969 book by Melvin Calvin (see photo).[1] Calvin, who was awarded the 1961 Nobel Prize in Chemistry, had a lengthy tenure at the University of California, Berkeley, where he did research in this topic.

Cover of 'Chemical Evolution' by Melvin Calvin

From the Preface to Chemical Evolution by Melvin Calvin

"The study of chemical evolution is based upon the assumption that life appeared on the surface of the earth as a result of the normal operation of the laws of physics and chemistry. This implies that there must have been a period of time in the earth's history that encompassed the transition between a non-living molecular population on its surface and a population of molecular aggregates that we would call living."

(The cover of my wife's copy.)


Calvin was one of the first exobiologists, for the simple reason that the chemical pathways to life on Earth can occur elsewhere, as well. Calvin was an attendee at the first conference on interstellar communication at Green Bank, West Virginia, in 1961. Also in attendance were Carl Sagan, Frank Drake, Giuseppe Cocconi and Philip Morrison. Cocconi and Morrison had published their influential paper, "Searching for Interstellar Communications", just two years earlier.[3] Calvin's Nobel Prize was announced while he was at this conference.[2]

One interesting sidelight on the founding of exobiology was the pushback by traditional evolutionists. Darwin Medal winner, George Gaylord Simpson, objected to how exobiology was draining funds away from traditional studies. Simpson is quoted as saying that exobiology was a "science that has yet to demonstrate that its subject matter exists!"[3] Simpson's conservative views can be seen, also, in his rejection of continental drift.

How far removed from the inorganic are the living? Not that far. In 1965, Sol Spiegelman and his colleagues were able to reduce the complexity of a large, naturally-occurring and replicating RNA molecule to just 218 nucleotides.[4] This molecule is known as the Spiegelman Monster. Further work has identified even smaller replicants.

There's one hypothesis of the origin of life that's always piqued my interest as a materials scientist. In this scenario, mineral surfaces acted as templates for the regular arrangement of organic structures. As proposed in the clay hypothesis, these minerals could have been small crystallites in clay.

It's been observed that nature follows the maxim, "If it ain't broke, don't fix it." Many chemical reactions of life have persisted from its start. In a previous article (Precambrian Protein, August 26, 2013), I wrote about the molecular evolution of the protein, thioredoxin. This enzyme has several metabolic functions in cells, and it is used by nearly every species, from bacteria to humans. Research indicates that only small structural changes have occurred in thioredoxin from the time of the last common ancestor.[5-7]

Escherichia coli

A scanning electron micrograph of Escherichia coli bacteria.

(Photomicrograph by Rocky Mountain Laboratories, NIAID, NIH, via Wikimedia Commons.)


Nature does optimize some of its reactions while preserving their purpose. Research published at the end of last year by chemists at the University of Iowa (Iowa City, Iowa) shows that dihydrofolate reductase was optimized in its transition from bacteria to humans, but its essential dynamics have been preserved.[8-9] The dihydrofolate reductase enzyme is an important enzyme. It exists in nearly every organism, since it assists in DNA biosynthesis and cell replication.[9]

In their study, the Iowa chemists used information obtained from bioinformatics to synthesize forms of the enzyme intermediate between the bacterial and human types to follow the path of evolution. They found that the bacterial enzyme is just as effective at its task, the only difference being that evolution designed the human enzyme to act much more quickly.[9]

References:

  1. Melvin Calvin, "Chemical Evolution," Oxford University Press, 1969, ISBN 0-19-855342-0, 278 pp. (via Amazon).
  2. Steven J. Dick And James E. Strick, "The Living Universe - NASA and the Development Of Astrobiology," Rutgers University Press, New Brunswick, New Jersey, 2004 (via archive.org).
  3. Giuseppe Cocconi and Philip Morrison, "Searching for Interstellar Communications," Nature, vol. 184, no. 4690 (September 19, 1959), pp. 844-846.
  4. S. Spiegelman, I. Haruna, I.B. Holland, G. Beaudreau and D. Mills, "The Synthesis of a Self-propagating and Infectious Nucleic Acid with a Purified Enzyme," Proc. Nat. Acad. Sci., vol. 54, no. 3 (September 1, 1965), pp. 919-927.
  5. Alvaro Ingles-Prieto, Beatriz Ibarra-Molero, Asuncion Delgado-Delgado, Raul Perez-Jimenez, Julio M. Fernandez, Eric A. Gaucher, Jose M. Sanchez-Ruiz and Jose A. Gavira, "Conservation of Protein Structure over Four Billion Years," Structure, August 8, 2013, DOI:10.1016/j.str.2013.06.020.
  6. Simon Redfern, "Resurrected protein's clue to origins of life," BBC News, August 8, 2013.
  7. 'Digging up' 4-billion-year-old fossil protein structures to reveal how they evolved, Press Release, Cell Press, August 8, 2013.
  8. Kevin Francis, Vanja Stojkovic and Amnon Kohen, "Preservation of Protein Dynamics in Dihydrofolate Reductase Evolution," The Journal of Biological Chemistry, vol. 288, no. 50 (December 13, 2013), pp. 35961-35968.
  9. Gary Galluzzo, "UI researcher studies evolution on the molecular level," University of Iowa Press Release, December 13, 2013.

Permanent Link to this article

Linked Keywords: Evolution; plant; animal; fossil record; Cambrian explosion; extinction; extinct; Precambrian; abiogenesis; bacteria; Western Australia; chemical reaction; molecular evolution; Melvin Calvin; Nobel Prize in Chemistry; University of California, Berkeley; research; atrobiology; exobiologist; Earth; academic conference; interstellar communication; Green Bank, West Virginia; Carl Sagan; Frank Drake; Giuseppe Cocconi; Philip Morrison; evolutionist; Darwin Medal; George Gaylord Simpson; funding of science; conservatism; conservative; continental drift; inorganic chemistry; life; living; Sol Spiegelman; self-replication; replicating; RNA; molecule; nucleotide; Spiegelman Monster; hypothesis; ; materials science; materials scientist; mineral; surface; pattern; template; organic compound; clay hypothesis; crystal; crystallite; clay; nature; Bert Lance; If it ain't broke, don't fix it; protein; thioredoxin; enzyme; metabolism; metabolic; cell; species; bacteria; human; protein structure; structural change; common descent; last common ancestor; scanning electron micrograph; Escherichia coli bacteria; Wikimedia Commons; chemist; University of Iowa (Iowa City, Iowa); dihydrofolate reductase; DNA; biosynthesis; bioinformatics; chemical synthesis; synthesize; Melvin Calvin, "Chemical Evolution," Oxford University Press, 1969, ISBN 0-19-855342-0, 278 pp.; Steven J. Dick And James E. Strick, "The Living Universe - NASA and the Development Of Astrobiology," Rutgers University Press, New Brunswick, New Jersey, 2004.

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