UPDATES, NOTES, AND WEB PAGES FOR CHAPTER 1
Updates
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Page 4. Age of the Universe.The Universe is about 13.7 billion years old, give or take a billion or two. So the Solar System (and the Earth, of course) are relatively young on that sort of time scale. The Universe should exist for another 24 billion years or so), but our Sun will have self-destructed long before that, leaving only a white dwarf.
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Page 8. Making sugars in a Miller-type experiment. Press release. This is a paper from Steven Benner's lab in Florida. Sugars have been difficult to form in prebiotic experiments (I skipped over this point in the text.) Benner has cracked this problem. It turns out that in the presence of borate minerals such as borax, riboses (sugars that are vital components of RNA) form and persist. Borates form as natural minerals in desert basins, in Death Valley, for example. You need evaporation to concentrate them in layers, but serious desert lake beds are not rare on Earth, now or then. This is a neat demonstration that pre-biotic synthesis of important organic materials is still being improved in the lab, and therefore looks more and more likely to have happened on Earth. The paper itself, Ricardo, A., et al. 2004. Borate minerals stabilize ribose. Science 303, p. 196 will soon be available on the Web to everyone.
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Page 9. Making peptides from amino acids.
A paper in October 2004 reported that the volcanic gas carbonyl sulfide, COS, helps peptides to form from amino acids. It's a real stretch to say, as John Roach does twice in the National Geographic piece, that there have been no plausible ways to form peptides until this study. That's a gratuitous piece of misinformation. The paper is in Science and is now freely available on the Web. Leman, L, et al. 2004. Carbonyl sulfide-mediated prebiotic formation of peptides. Science 306: 283-286.
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Page 10. Jack Szostak and the evolution of protocells. There is major progress in solving this problem in the laboratory. The new experiments apply directly to conditions on the early Earth. These three sites include two fine essays by Carl Zimmer from 2004, both in Discover magazine:
Mini-Essays and Comments.
Reconstructing the Origin of Life
Experiments on the Origin of Life
Organic Compounds
Producing organic chemicals in an atmospheric haze that might have fed early organisms. National Geographic News The paper is published in PNAS.
Amino Acids
Peptides
Making peptides: a new paper in late 2004 showed that carbonyl sulfide, a gas with the formula COS, strongly encouraged amino acids to form into short chains (peptides) (see update above).
Chirality
: see mini-essay
The Naked Gene
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Altman and Cech started it all by discovering the catalytic power of RNA, in "ribozymes". Here is an account of the work, for which they won a Nobel Prize.
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News article in the New York Times, reviewing the RNA world as seen in April 1999.
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The RNA World (the world of the naked gene.
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Essay by Leslie Orgel, 1997, originally written for Scientific American, on RNA and the RNA world
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More support for ribozymes in an RNA world, May 2001: Press release from MIT
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RNA is more resistant to breakdown than we thought: this makes the "RNA world" concept more likely. Press release about a paper in Nature Genetics, September 2005.
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Christian de Duve, a noted cell biologist, believes that there was likely a precursor to RNA. Essay written for American Scientist, September 1995. [The arguments are biochemically complex, but reasonable.]
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A genetic code with only two letters? This is not theory: they have been synthesized. Nature news service, December 18, 2002, took it off open access. The paper is in Nature.
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DNA is made from TNA in a lab experiment.
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Jack Szostak and the evolution of protocells. See update above.
Kitty Litter: Clay Surfaces
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Another nice paper on prebiotic chemistry from the laboratory of Jack Szostak, referred to in the update for page 10. Montmorillonite clay increased the rate of forming lipid membrane-vesicles by about 100 times. Bits of clay ended up (with RNA attached to them) *inside* the vesicles. The paper was in Science accompanied by a commentary. The commentator says that the experiments simulate *alkaline* hot springs on the ocean floor. But remember that the Szostak group didn't say that! the commentator did, and then went on to push some of his own ideas.
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A nice piece of trivia: The invention of kitty litter.
Liposomes
The First Cell
Life To Be Made in the Laboratory?
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In early 1999 a proposal was announced that sounded optimistic but not unrealistic: it would set out to create life in the laboratory, but using a template provided by analyzing one of the most simple living bacteria. Here are some news reports:
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Report of the announcement
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A reaction..
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Perspective from the New York Times, December 14, 1999.
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The problem in my view is that these folks are playing with a potentially dangerous bacterium. Here is my sardonic reaction (probably tasteless too). It looks as if TIGR no longer sells the stuff, probably because of 9/11. But you can get hold of samples.
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Craig Venter will try to build a cell. Carl Zimmer wrote this for Science in February 2003. The team built a known virus, several thousand bases long, by gluing together pre-selected short chains of nucleotides. But it only took two weeks. The next step, they say, is making a cellular genome. It would be at least 300,000 bases long, and that's not a cell but a genome. Nevertheless, the techniques are in place. Scary. Craig Venter and his group have already done a quick-and-dirty human genome (Venter's, according to gossip), and a complete dog genome (Venter's poodle). You can't make up stuff like this! Hubris.
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On the other hand, you could try playing with DNA bases that don't exist in nature... On the road toward artificial life? Originally published in the New York Times, July 24, 2001.
Methanogens and Archaea. Web links.
The first living thing; and LUCA, the Latest Universal Common Ancestor of Life on Earth
The reference list for Chapter 1, Fourth Edition, with associated Web links
Last updated March 3, 2006.
Links last checked September 30, 2005.
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