Origin of life and Abiogenesis resources

[Monad]

This thread is for resources, links and references on theories of and evidence for abiogenesis and on the early origins of life including the origins of biological evolution itself. It will be stickied and will also contain links to threads of interest on the subject.

The first 2 posts are from the original thread by Gary Hurd containing a set of references on the Origins of life he compiled. The original thread is here:

http://www.talkrational.org/showthread.php?t=9976

[Monad]

I put this together nearly 4 years ago, and it needs to be updated. None the less, for your friend confused about the origin of life:

Darwin's various editions of The Origin of Species made little mention of the origin of life. He does make some general observations in the concluding chapter. He writes in the Sixth Edition (1872),

"I believe that animals are descended from at most only four or five progenitors, and plants from an equal or lesser number.

Analogy would lead me one step further, namely, to the belief that all animals and plants are descended from some one prototype. But analogy may be a deceitful guide. Nevertheless all living things have much in common, in their chemical composition, their cellular structure, their laws of growth, and their liability to injurious influences."

And,

"No doubt it is possible, as Mr. G.H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so, we may conclude that only a very few have left modified descendants."

And a bit later, "Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual. When I view all beings not as special creations, but as the lineal descendants of some few beings which lived long before the first bed of the Cambrian system was deposited, they seem to me to become ennobled. "

The final sentence in the first edition, "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." was slightly modified in the Sixth to clearly indicate that the "Creator" was responsible for the origin of life. Some scholarly studies claim that Darwin regretted making this concession to his publishers.

Charles R. Darwin, in a 1871 letter to the botanist Joseph Hooker wrote, "It is often said that all the conditions for the first production of a living organism are present, which could ever have been present. But if (and Oh! what a big if!) we could conceive in some warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, etc., present, that a protein compound was chemically formed ready to undergo still more complex changes, at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed. "

Later in the same letter, he observed,

"It is mere rubbish thinking at present of the origin of life; one might as well think of the origin of matter."

The theory of evolution is an explanation of the diversity and distributions of life forms, not the initial origin of life. This is an active area of research called “abiogenesis,” “astrobiology,” or simply origin of life (OOL). It is obviously part of the larger scientific project to understand the universe, but is not fundamental to evolutionary theory.

The general interest books on the origin of life (OOL) typically start with a lengthy discussion of the historical theories of life. Beginning with the Greeks and working our way toward the present, there are three most significant events: the invention of the microscope, the synthesis of urea , and the experiment by Pasteur in 1862.

All the early thought on the origin of life can be reduced to a theory of spontaneous generation of life, or the creation of life by supernatural external agency. The invention, and improvements to the microscope between 1590 and 1674 CE profoundly changed mankind's conception of life and its complexity. This seemed to many as support for the spontaneous generation of life notion, as these microscopic life forms were thought as the simple "seed" for latter complex life. Anton van Leeuwenhoek's discovery of sperm also added to this "support" for the spontaneous generation theory.

There was also the thought that the organic "stuff" of life was completely different from "inorganic" or mineral matter. Known as "vitalism," this concept was shown to be false by Wühler in 1832 when he made urea, a "live" compound, from inorganic stock
chemicals.

The most popular argument that creationists like to cite against results from modern origin of life research is that Pasteur demonstrated that the "spontaneous generation" theory was invalid. However, we should be quite clear that the Pasteur experiments showed that complex life forms do not form spontaneously. They did not address the origin of life as we currently understand the concept.

The growing interest in the search for extra-terrestrial life as fueled more productive research on OOL in the last 15 years than has ever been done in history. is the best general reader book available on the topic. It is eight years old, and a second edition is warranted to bring her presentation up to date.

There are quite a list of specifics that go into origin of life research, and very few research groups go far with more than a few. Just to list the key areas as I see them: Argument:
1. The late Hadean Earth had a neutral to reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun. Highly reduced oasis existed at hydrothermal vents and other mineral rich locations,
2. Under those conditions, phospholipids, amino acids, nucleic bases, and pentoses readily form (augmented by extraterrestrial sources such as cometary delivery) and are concentrated by freezing and evaporation as well as mineral surface plating, and encapsulation,
3. Amino acids spontaneously form short (8 to 20 aa’s) racemic peptides, and random RNAs with as few as 2 types of nucleic bases have enzymatic activity. Spontaneous phospholipid vesicles sequester these peptides as transmembrane pores, and along with enzymatic RNAs plated to mineral grains such as montmorillonite, calcite, and metal sulfides.
4. Electron potential differences are exploited from transmembrane pores to form adenine triphosphate, establishing the first metabolism,
5. These ancient first cells were racemic, using both L- and D- amino acids because they were readily available,
6. Biological and geochemical events reduced the availability of D- aa's,
7. These ancient cells evolved racemases to maintain/sustain their existing metabolic pathways as attested by L- to D- amino acid racemases found even in humans. Ergo: The chirality "problem" in OOL isn't a problem.


1) Composition of the Hadean/early Archean atmosphere.

The key reference(s) here is:

Feng Tian, Owen B. Toon, Alexander A. Pavlov, and H. De Sterck
2005 "Hydrogen-Rich Early Earth Atmosphere" Science 13 May 2005; 308: 1014-1017; published online 7 April

Genda, Hidenori & Abe, Yutaka
2003 “Survival of a proto-atmosphere through the stage of giant impacts: the mechanical aspects” Icarus 164, 149-162 (2003).

Holland, Heinrich D.
1984 The Chemical Evolution of the Atmoshphere and Oceans, Princeton Series in Geochemistry Princeton University Press

Holland, Heinrich D.
1999 “When did the Earth’s atmosphere become oxic? A Reply.” The Geochemical News #100: 20-22 (see Ohmoto 1997 )

Kasting, J. F., J. L. Siefert,
2002 “Life and the Evolution of Earth's Atmosphere” Science 296:1066

Pepin, R. O.
1997 "Evolution of Earth's Noble Gases: Consequences of Assuming Hydrodynamic Loss Driven by Giant Impact" Icarus 126, 148-156 (1997).

Tian, Feng , Owen B. Toon, Alexander A. Pavlov, and H. De Sterck
2005 "A Hydrogen-Rich Early Earth Atmosphere" Science 13 May; 308: 1014-1017; published online 7 April 2005


There are others, but anyone reading those above will get the basics. The result is that there was a reducing atmosphere, and ocean system with highly reducing oases. A recent paper:

Rosing, Minik T. and Robert Frei
2003 U-rich Archaean sea-floor sediments from Greenland – indications of >3700 Ma oxygenic photosynthesis" Earth and Planetary Science Letters, online 6 December 03

presents data that suggest there were very early oxygenic life forms in marine basins that most likely (to me anyway) were wiped out.

So, with a reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun, we can ask the next question which is,

2) What was the source for "organic" molecules?

The classic paper was of course Stanley Miller's 1953 paper

Miller, Stanley L.,
1953 “A Production of Amino Acids Under Possible Primitive Earth Conditions” Science vol. 117:528-529

With a bit more information included in:

Miller, Stanley, Harold C. Urey
1959 “Organic Compound Synthesis on the Primitive Earth” Science vol 139 Num 3370: 254-251

Miller showed that a very simple set up that mimicked some key asspects of the early Earth could rapidly produce amino acids, among other things.

This result has been one of the most often repeated (and confirmed) experiments I have ever encountered. In spite of this, creationists regularly claim that it is invalid. Jonathan Wells, a fellow of the creationist "Discovery Institute" claims to have refuted the Miller/Urey experiment (and all of what he called Darwinist "icons." Wells himself has been exposed as a very shallow thinker.

But, the atmosphere is not the only synthesis location. For example

Amend, J. P. , E. L. Shock
1998 “Energetics of Amino Acid Synthesis in Hydrothermal Ecosystems” Science Volume 281, number 5383, Issue of 11 Sep , pp. 1659-1662.

Blank, J.G. Gregory H. Miller, Michael J. Ahrens, Randall E. Winans
2001 “Experimental shock chemistry of aqueous amino acid solutions and the cometary delivery of prebiotic compounds” Origins of Life and Evolution of the Biosphere 31(1-2):15-51, Feb-Apr

Chyba, Christopher F., Paul J. Thomas, Leigh Brookshaw, Carl Sagan
1990 "Cometary Delivery of Organic Molecules to the Early Earth" Science Vol. 249:366-373

Engel, Michael H., Bartholomew Nagy,
1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838.

Matthews CN.
1992 Hydrogen cyanide polymerization: a preferred cosmochemical pathway. J. Br. Interplanet Soc. 45(1):43-8

Schoonen, Martin A. A., Yong Xu
2001 “Nitrogen Reduction Under Hydrothrmal Vent Conditions: Implications for the Prebiotic Synthesis of C-H-O-N Compounds” Astrobiology 1:133-142
Creationist liars also like to insist that without a reducing atmosphere, there could be no amino acid production. I think it was totally fitting that the last publication of Stanley Miller, 55 years after his ground breaking article, demonstrated that under a neutral atmosphere, or even with trace free oxygen, ample amino acids could form in the presence of common minerals such as calcite.
H. James Cleaves & John H. Chalmers & Antonio Lazcano & Stanley L. Miller & Jeffrey L. Bada 2008 "A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres" Orig Life Evol Biosph 38:105-115

So amino acids are easy and plentiful on a pre-life (abiotic) Earth.

But, we need more than just amino acids- sugars, nucleic acids, and lipids are also needed. I'll take those next.

Let's see.. I guess this is

2a) amino acids
2.b) sugars

Why do we need sugars? Well, the biggest reason is that without five carbon sugar our building life form can't make a "memory" like RNA or DNA. I'll get to the details later. First, where are the sugars?

Weber AL.
1997 Prebiotic amino acid thioester synthesis: thiol-dependent amino acid synthesis from formose substrates (formaldehyde and glycolaldehyde) and ammonia. Origins of Life and Evolution of the Biosphere 28: 259-270.

{I know the title says "amino acid" but sugar is in there. Hint: formose is a kind of sugar. }

Cooper, George, Novelle Kimmich, Warren Belisle, Josh Sarinana, Katrina Brabham, Laurence Garrel
2001 Carbonaceous meteorites as a source of sugar-related organic compounds for the early Earth Nature 414, 879 - 883 (20 Dec 2001) Letters to Nature

Cody, George D., Nabil Z. Boctor, Timothy R. Filley, Robert M. Hazen, James H. Scott, Anurag Sharma, Hatten S. Yoder Jr.
2000 “Primordial Carbonylated Iron-Sulfur Compounds and the Synthesis of Pyruvate” Science v.289 : 1337-1340

Sephton, Mark A.
2001 Meteoritics: Life's sweet beginnings? Nature 414, 857 - 858 (20 Dec ) News and Views

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia)

Stanley Miller, and colleagues suggested an earlier substitute for sugar in :

Lazcano, Antonio, Stanley L. Miller
1996 “The Origin and Early Evolution of Life: Prebiotic Chemistry, the Pre-RNA World, and Time” Cell vol 85:793-798

Nelson, K. E., M. Levy, S. L. Miller
2000 “Peptide nucleic acids rather than RNA may have been the first genetic molecule” PNAS-USA v.97, 3868-3871

There are many more articles, but the bottom line reads "We got sugar."

OK, I'll do nucleic acid bases next. There aren't many that are used on Earth, just five.

There are a large number of creationist's books and web sites that claim there is some huge stability problem with nucleic acid base synthesis. This is a nice demonstration of how creationists copy each other, since there are only a handful of creationists with the education to even understand what this means. None that I know of have actually done research in the directly relevant area. Their claims generally can be traced back to a legit scientist, Robert Shapiro. Two of his representative publications are:

Shapiro, Robert
1986 "Origins: A Skeptics Guide to the Creation of Life on Earth" New York: Summit Books

Shapiro, Robert
1999 Prebiotic Cytosine Synthesis: A Critical Analysis and Implications for the Origin of Life. Proceedings of the National Academy of Science 96 (8): 4396 *Side reactions make cytosine synthesis unlikely, but see Nelson et al (2001)

The 1986 book is very out of date, and very popular with creationists.

The 1999 Shapiro paper has also been answered. Levy and Miller raise a question of their own in:

Levy, M and Miller, S.L.,
1998 The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38,

But, like superior scientists, they answer the questions they raise.

The following are a selections of research articles that address the pre-biotic origin of nucleic acid bases:


For our fans following along at home, there are aspects of nucleoside synthesis in the earlier referenced papers as well.

So, we got plenty of nucleic acid bases.

2c) lipids.

Lipids are the stuff of membranes, they are what keeps inside in, and outside out. Today they are made by simple cells and moved up the food chain. So where did they come from 3.7 billion years (or so) ago?

Likely sources were meteors, and hydrothermal vents;

Deamer, D. W.
1985. Boundary structures are formed by organic components of the Murchison carbonaceous chondrite. Nature 317:792-794.

Deamer, D. W., and Pashley, R. M.
1989. Amphiphilic components of carbonaceous meteorites. Orig. Life Evol. Biosphere 19:21-33.

W. R. HARGREAVES, S. J. MULVIHILL & D. W. DEAMER
1977 “Synthesis of phospholipids and membranes in prebiotic conditions” Nature 266, 78 - 80 (03 March)

D.E. Epps, E. Sherwood, J. Eichberg, and J. Oro
1978 “Cyanamide Mediated Syntheses Under Plausible Primitive Earth Conditions: V. The Synthesis of Phosphatidic Acids” J. Mol. Evol. 11,279—292.

Rushdi, Ahmed I., Bernd R. T. Simoneit
2006 “Abiotic Condensation Synthesis of Glyceride Lipids and Wax Esters Under Simulated Hydrothermal Conditions” Origins of Life and Evolution of Biospheres Volume 36, Number 2: 93-108 / April,

Krishnamurthy, R., Pitsch, S. & Arrhenius, G. 1999 Mineral induced formation of pentose-2,4-bisphosphates. Origins Life Evol. Biosph. 29, 139-152 ().

Dworkin, Jason P., David W. Deamer, Scott A. Sandford, and Louis J. Allamandola
2001 “Self-assembling amphiphilic molecules: Synthesis in simulated interstellar/precometary ices” PNAS 98: 815-819

Pizzarello, Sandra, Yongsong Huang, Luann Becker, Robert J. Poreda, Ronald A. Nieman, George Cooper, Michael Williams
2001 “The Organic Content of the Tagish Lake Meteorite” Science, Vol. 293, Issue 5538, 2236-2239, September 21, 2001

Segre' D., Ben-Eli D. Deamer D. and Lancet D.
2001 “The Lipid World” Origins Life Evol. Biosphere 31, 119-145.

So now that we got 'em, what do they do once they are together on Earth?

They make things.

Martin M. Hanczyc, Shelly M. Fujikawa, and Jack W. Szostak
2003 Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division Science October 24; 302: 618-622. (in Reports)

D.W. Deamer
1997 "The First Living Systems - A Bioenergetic Perspective", ; Microbiology and Molecular Biology Reviews, 61(2): 239; June

Chakrabarti, A.C., R.R. Breaker, G.F. Joyce, & D.W. Deamer
1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 ( December)

Khvorova A, Kwak YG, Tamkun M, Majerfeld I, Yarus M.
1999. RNAs that bind and change the permeability of phospholipid membranes. Proceedings of the National Academy of the Sciences USA 96:10649-10654.

Yarus M.
1999. Boundaries for an RNA world. Current Opinion in Chemical Biology 3:260-267.

Walter P, Keenan R, Scmitz U.
2000. SRP-Where the RNA and membrane worlds meet. Science 287:1212-1213.



So far, we have amino acids, riobose and/or other 5 carbon sugar substitutes (pentoses), we have lipid membranes which encapsulate mineral particles and "organic" molecules. This is without any needed "interventions" and is purely the result of ordinary chemistry.

But, there are more things that need to happen before there is life on Earth.

Point 3) formation of complex systems

3a) Chirility

Pasteur discovered that most amino acids came in two forms which can be identified by how they refract light. We label theses L- (for levo or left) and D- (for dextro, or right). The interesting thing is that life on Earth uses the L form of amino acids, and hardly ever uses the D- form. A solution of just one form is called "chiral" and a mix of forms about 50/50 is called racimic. The kinds (L or D) are called enantomers.

The nucleic acid bases I mentioned earlier are also found in L- and D- forms, only in this case life on Earth only uses the D- form.

Creationists like to present this as a profound mystery that is supposed to "prove" that they are correct. I want to mention a neat instance where both left and right amino acids are used in a living thing. It is very rare, but it does happen. Next time a creationist claims to be an "expert" and that amino acid chirility "proves" something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclucive L- amino acids.

Before we go forward another couple of basic chemical facts need to be added to the discussion. First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racimization" becuse eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attatched to one another, or better yet, if they are also attatched to a mineral, racimization can be very slow. Very, very slow.

This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form. The advantage comes from a surprising direction: outer space.

Cronin, J. R. & Pizzarello, S.,
1999. Amino acid enantomer excesses in meteorites: Origin and significance. Advances in Space Research 23(2): 293-299.

Service, RF,
1999. Does life's handedness come from within? Science 286: 1282-1283.

Antonio Chrysostomou, T. M. Gledhill,1 François Ménard, J. H. Hough, Motohide
Tamura and Jeremy Bailey
2000 "Polarimetry of young stellar objects -III. Circular polarimetry of OMC-1" Monthly Notices of the Royal Astronomical Society Volume 312 Issue 1 Page 103 - February

Michael H. Engel and Bartholomew Nagy,
1982 "Distribution and Enantiomeric Composition of Amino Acids in the Murchison Meteorite", Nature , 296, April 29, , p. 838.

Jeremy Bailey, Antonio Chrysostomou, J. H. Hough, T. M. Gledhill, Alan McCall, Stuart Clark, François Ménard, and Motohide Tamura
1998 Circular Polarization in Star- Formation Regions: Implications for Biomolecular Homochirality Science 1998 July 31; 281: 672-674. (in Reports)

Chyba, Christopher F.
1997 Origins of life: A left-handed Solar System? Nature 389, 234- 235 (18 Sep 1997)

Engel, M. H., S. A. Macko
1997 Isotopic evidence for extraterrestrial non- racemic amino acids in the Murchison meteorite. Nature 389, 265 - 268 (18 Sep) Letters to Nature

That should do for that. The next question is can the advantage of L- amino acids be conserved in the formation of more complex molecules called "peptides?" Yep.

Schmidt, J. G., Nielsen, P. E. & Orgel, L. E. 1997 Enantiomeric cross-inhibition in the synthesis of oligonucleotides on a nonchiral template. J. Am. Chem. Soc. 119, 1494-1495

Saghatelion A, Yokobayashi Y, Soltani K,
Ghadiri MR,
2001"A chiroselective peptide replicator",
Nature 409: 797-51, Feb

Singleton, D A,& Vo, L K,
2002 “Enantioselective Synthsis without Discrete Optically Active Additives” J. Am. Chem. Soc. 124, 10010-10011

Yao Shao, Ghosh I, Zutshi R, Chmielewski J.
1998 Selective amplification by auto- and cross-catalysis in a replicating peptide system. Nature. Dec 3;396(6710):447-50.

And there seems to be other L- selction advantages as well. For example:

Hazen, R.M., T.R. Filley, and G.A. Goodfriend.
2001. Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality. Proceedings of the National Academy of Sciences 98(May 8):5487.

So chirility doesn't seem to be a big problem. This is far different from the way creationists present this. They cite a few out of date reports and then falsely claim that chiral life is impossible by natural means. I want to mention a neat instance where both left and right amino acids are used in a living thing. It seems very rare, but it does happen. Next time a creationist claims to be an "expert" and that amino acid chirility "proves" something supernatural, you can gob-smack-em. The protein is called Gramicidin A and it has 8 L-amino acids, 6 D-amino acids, and one glycine which is an amino acid that is neither L- or D- in its structure. I have found that even many biologists will bet an "adult beverage" that all proteins are exclusive L- amino acids.

But what about the nucleic acid bases? A new paper has just laid out the next step:

Ricardo, A., Carrigan, M. A., Olcott, A. N., Benner, S. A.
2004 "Borate Minerals Stabilize Ribose" Science January 9; 303: 196 (in Brevia)

Pizzarello, Sandra, Arthur L. Weber
2004 Prebiotic Amino Acids as Asymmetric Catalysts Science Vol 303, Issue 5661: 1151, 20 February 2004

It turns out that the selective advatage of L- amino acids will force the selection of D- nucleic acids, and the whole reaction can proceed under common, natural conditions.

There are larger arguments for a racemic origin of life.
Edward Trifonov (2004) confirmed two ideas, that the earliest amino acids were those easiest to form abiotically, that codons and aa's organized contemporaneously to form short ogliomers (what he didn't cite was the notion that oligomers can form spontaneously, are "selected" merely by being stable, and that RNAs (or Lacanzo and Miller's PNAs) imprint and replicate "successful" short peptides.) Trifonov wrote, "The amino-acid chronology itself is a quintessence of natural simplicity and opportunism: use first those amino acids that are available. When done with all codons, take from those amino acids that have too many."
The fact is that there are a growing list of short proteins with D- aa's, (most of the ones I know of are bacterial membrane components but there are also examples from yeasts to humans). Add to this, most bacteria have evolved enzymes that convert L-aa's to D-aa's for the same Miller/prebiotic amino acids. Again even we humans have enzymes to use D-aa's. Argument:
8. The late Hadean Earth had a neutral to reduced atmosphere and ocean system, a shallow, hot crust and a UV rich, "cold" sun. Highly reduced oasis existed at hydrothermal vents and other mineral rich locations,
9. Under those conditions, phospholipids, amino acids, nucleic bases, and pentoses readily form (augmented by extraterrestrial sources such as cometary delivery) and are concentrated by freezing and evaporation as well as mineral surface plating, and encapsulation,
10. Amino acids spontaneously form short (8 to 20 aa’s) racemic peptides, and random RNAs with as few as 2 types of nucleic bases have enzymatic activity. Spontaneous phospholipid vesicles sequester these peptides as transmembrane pores, and along with enzymatic RNAs plated to mineral grains such as montmorillonite, calcite, and metal sulfides.
11. Electron potential differences are exploited from transmembrane pores to form adenine triphosphate, establishing the first metabolism,
12. These ancient first cells were racemic, using both L- and D- amino acids because they were readily available,
13. Biological and geochemical events reduced the availability of D- aa's,
14. These ancient cells evolved racemases to maintain/sustain their existing metabolic pathways as attested by L- to D- amino acid racemases found even in humans. Ergo: The chirality "problem" in OOL isn't a problem.

Trifonov, Edward N. 2004 "The Triplet Code From First Principles" Journal of Biomolecular Structure & Dynamics, ISSN 0739-1102 Volume 22, Issue Number 1,

Babbitt PC, Mrachko GT, Hasson MS, Huisman GW, Kolter R, Ringe D, Petsko GA, Kenyon GL, Gerlt JA.
1995 "A functionally diverse enzyme superfamily that abstracts the alpha protons of carboxylic acids." Science. 1995 Feb 24;267(5201):1159-61.

Nathalie Chamond, Maira Goytia, Nicolas Coatnoan, Jean-Christophe Barale, Alain Cosson, Wim M. Degrave and Paola Minoprio
2005 "Trypanosoma cruzi proline racemases are involved in parasite differentiation and infectivity." Molecular Microbiology Volume 58 Issue 1 Page 46 - October 2005

Alexander Jilek, Christa Mollay, Christa Tippelt, Jacques Grassi , Giuseppina Mignogna, Johannes Müllegger, Veronika Sander, Christine Fehrer, Donatella Barra and Günther Kreil
2005 "Biosynthesis of a D-amino acid in peptide linkage by an enzyme from frog skin secretions" Published online before print March 9, 2005, PNAS | March 22, 2005 | vol. 102 | no. 12 | 4235-4239

Yamashita, Tatsuyuki, Ashiuchi, Makoto, Ohnishi, Kouhei, Kato, Shin'ichiro, Nagata, Shinji & Misono, Haruo
(2004) "Molecular identification of monomeric aspartate racemase from Bifidobacterium bifidum." European Journal of Biochemistry 271 (23-24), 4798-4803.

Ian G. Fotheringham, Stefan A. Bledig, and Paul P. Taylor
1998 "Characterization of the Genes Encoding D-Amino Acid Transaminase and Glutamate Racemase, Two D-Glutamate Biosynthetic Enzymes of Bacillus sphaericus ATCC 10208" Journal of Bacteriology, August 1998, p. 4319-4323, Vol. 180, No. 16

K. Y. Hwang, C.-S. Cho, S. S. Kim, K. Baek, S.-H. Kim, Y. G. Yu and Y. Cho
1999 "Crystallization and preliminary X-ray analysis of glutamate racemase from Aquifex pyrophilus, a hyperthermophilic bacterium" Acta Cryst. (1999). D55, 927-928




Well, we have all the pieces. Our planet was formed from massive collisions of planetoids that had undergone independent evolution and weathering which retained much of their atmospheres to add to the growing planet Earth. We have amino acids, sugars, nucleic acid bases, lipids and minerals under an anoxic to reducing atmosphere and ocean with a thin hot crust and a UV rich cold Sun. Plus, remember that the Moon is closer and orbiting faster producing massive tidal flows compared to modern times.

Will these combine to make any thing?

Yep, they sure will:

Ferris JP, Hill AR Jr, Liu R, and Orgel LE. (1996 May 2). Synthesis of long prebiotic oligomers on mineral surfaces [see comments] Nature, 381, 59-61.

Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR.
1996 “A self-replicating peptide.” Nature Aug 8;382(6591):525-8

A.C. Chakrabarti, R.R. Breaker, G.F. Joyce, & D.W. Deamer
1994 Production of RNA by a Polymerase Protein Encapsulated within Phospho-Lipid Vesicles Journal of Molecular Evolution 39(6): 555-559 (1994 December)

Smith, J.V.
1998 Biochemical evolution. I. Polymerization on internal, organophilic silica surfaces of dealuminated zeolites and feldspars Proceedings of the National Academy of Sciences of the United States of America 95(7): 3370-3375; March 31, 1998

Smith, J.V., Arnold, F.P., Parsons, I., Lee, M.R.
1999 “Biochemical evolution III: Polymerization on organophilic silica-rich surfaces, crystal- hemical modeling, formation of first cells, and geological clues” Proceedings of the National Academy of Sciences of the United States of America 96(7): 3479-3485; March 30, 1999

Blochl, Elisabeth, Martin Keller, Gunter Wächtershäuser , Karl Otto Stetter
1992 “Reactions depending on iron sulfide and linking geochemistry with biochemistry” PNAS-USA v.89: 8117-8120

Dyall, Sabrina D., Patricia J. Johnson
2000 “Origins of hydrogenosomes and mitochondria: evolution and organelle biogensis.” Current Opinion in Microbiology 3:404-411

Huber, Claudia, Gunter Wächtershäuser
1998 “Peptides by Activation of Amino Acids with CO on (Ni,Fe)S Surfaces: Implications for the Origin of Life” Science v.281: 670-672

Imai, E., Honda, H., Hatori, K., Brack, A. and Matsuno, K.
1999 “Elongation of oligopeptides in a simulated submarine hydrothermal system“ Science 283(5403):831–833.

Lee DH, Severin K, Yokobayashi Y, and Ghadiri MR,
1997 Emergence of symbiosis in peptide self- replication through a hypercyclic network. Nature, 390: 591-4

Ekland, EH, JW Szostak, and DP Bartel
1995 "Structurally complex and highly active RNA ligases derived from random RNA sequences" Science 21 July 1995: Vol. 269. no. 5222, pp. 364 - 370

Reader, J. S. and G. F. Joyce
2002 "A ribozyme composed of only two different nucleotides." Nature vol 420, pp 841-844.

[Monad]

http://www.teach12.com/ttcx/CourseDe....aspx?cid=1515

The course is called The Origin of Life by professor Hazen, it is quite good, possible for download via torrent, but if you have the extra money, the teaching company is a good place to spend it.

It's only 35 dollars for the download.

Sorry if I'm not supposed to post here.

[Monad]

NB Hazens work is oft cited in abiogenesis research - especially in relation to the origins of biochemistry and mineral evolution. e.g.:

http://ammin.geoscienceworld.org/cgi.../93/11-12/1693

[Monad]

Some links on Russell and Martin's model of biochemical and cellular evolution in alkaline geothermal vent systems:

Original thread here:

http://www.talkrational.org/showthread.php?t=21313

I think I just read one of the most interesting papers I've read in a long time. Things really fall into place regarding the origins of life. I'm sure some are familiar with Wächtershäuser's hydrothermal vent model of abiogenesis. Well Russell and Martin have proposed a model that builds on his ideas but overcome some of the challenges (such as the intense heat) and it really makes a lot of sense. The full paper is here:

On the origin of biochemistry at an alkaline hydrothermal vent

http://rstb.royalsocietypublishing.o.../362/1486/1887

the thing I like about it is that it's a metabolism first model that nevertheless provides the basis for integrating early replicators into the mix and in fact gives them a mechanism for why and how they would integrate. Unlike the hot hydrothermal vents (black smokers) in Wächtershäuser's model, Russell and Martin focus on the more recently discovered alkaline vent systems that are associated with subduction zones such as here:

http://en.wikipedia.org/wiki/Lost_Ci...othermal_field)

as well as being far cooler than the black smokers these vent systems provide a number of other catalysis for the development of complex organic biochemistry:

1) The structures formed by these vent systems create millions of micro-caverns which "provide a means of concentrating newly synthesised molecules, thereby increasing the chance of forming oligomers;
2) the steep temperature gradients inside the hydrothermal vent allow for establishing "optimum zones" of partial reactions in different regions of the vent (e.g. monomer synthesis in the hotter, oligomerisation in the colder parts);
3) the flow of hydrothermal water through the structure provides a constant source of building blocks and energy (chemical disequilibrium between hydrothermal hydrogen and marine carbon dioxide);
4) the model allows for a succession of different steps of cellular evolution (prebiotic chemistry, monomer and oligomer synthesis, peptide and protein synthesis, RNA world, ribonucleoprotein assembly and DNA world) in a single structure, facilitating exchange between all developmental stages;
5) synthesis of lipids as a means of "closing" the cells against the environment is not necessary, until basically all cellular functions are developed."

quote from here: http://en.wikipedia.org/wiki/Iron-sulfur_world_theory

6) In addition these zones are far more stable and last much longer than the black smokers so would have provided a more stable and indeed protected environment for early life to evolve in.

[Monad]

Another paper by Martin and Russell:

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.

http://rstb.royalsocietypublishing.o...6-8ac56e3053a9

basically what they seem to be saying (it's complicated but Lane summarises it for people like me that don't get all the biochemistry) is that the vent system facilitated the development of mineralised semi-cellular systems but that didn't have the ability to replicate outside of the vent system. So the LUCA was not a free living cell but part of a mineralised cellular complex. Within these systems there were several pathways that favoured the development and concentration of more complex molecules (including a reversed Krebs cycle) and precursors to ATP such as acetyl thioesters and acetyl phosphate. They postulate that these conditions also favoured the emergence of simple RNA type molecules which became populations of "viral" like self replicating proto lifeforms "infecting" the mineralised protocells (and eventually some of them combining with them in a form of symbiogenesis). I'm still trying to get my head around it all myself but they have quite a lot of evidence for their arguments including from studies of current vent systems and from analysis of the important differences between the ways that bacteria and archaea replicate DNA.

[Monad]

http://www.ncbi.nlm.nih.gov/pubmed/15764708

A mechanism for the association of amino acids with their codons and the origin of the genetic code.

http://://www.ncbi.nlm.nih.gov/pubme...gdbfrom=pubmed

Evolution of the genetic triplet code via two types of doublet codons.

http://://www.ncbi.nlm.nih.gov/pubme...les&logdbfrom=

The triplet genetic code had a doublet predecessor

Also worth reading some of the work on how the DNA replication system evolved at least twice:

http://nar.oxfordjournals.org/cgi/co...act/27/17/3389

[Monad]

Overview of the hydrothermal vent theory

http://www.plosbiology.org/article/i...l.pbio.0030396

[Monad]

Michael Russell's home page:

http://www.gla.ac.uk/projects/originoflife/

with lots of downloadable papers:

http://www.gla.ac.uk/projects/origin...f_articles.htm

I've picked out some of the more juicy papers:

The Alkaline Solution to the Emergence of Life: Energy, Entropy and Early Evolution

http://www.gla.ac.uk/projects/origin...etica_corr.pdf

Inorganic Complexes Enabled the Onset of Life and Oxygenic Photosynthesis

http://www.gla.ac.uk/projects/origin...PS2%202008.pdf

The rocky roots of the acetyl-CoA pathway

http://www.nordita.dk/conference/Ast...l+Martin04.pdf

This one is an awesome piece of biochemical/geochemical detective work

and this one is a more accessible overview:

http://www.gla.ac.uk/projects/origin...rev%202008.pdf

[Monad]

On the origin of genomes and cells within inorganic compartments

http://www.molevol.de/publications/135.pdf

A juicy quote:

Archaebacteria and eubacteria sharply differ not only by
virtue of their unrelated membranes and cell walls but
also by the equally dramatic disparity of their DNA
replication machineries [47,48]. Surprisingly, the central
components of these systems (DNA polymerases, primases
and replicative helicases) are either unrelated or, at least,
not orthologous in archaebacteria and eubacteria [44,49–
52]. This contrasts the basic unity and conservation
among the major proteins of the translation and transcription
systems [53]. Thus, LUCA is inferred to have had
an advanced translation system that resembled modern
ones in its principal features, but lacked a doublestranded,
replicating DNA genome, possessing an RNAbased
replication system instead [44,47,53].

However, several other components of the DNA
replication machinery, such as the sliding clamp plus the
clamp loader ATPase and the DNA ligase, as well as
enzymes of DNA precursor biosynthesis – ribonucleotide
reductase and thymidylate kinase – are homologous in all
prokaryotes, which led to the proposal that LUCA had a
retrovirus-like replication cycle [44] (Figure 1). Because
RNA molecules are fragile compared with DNA, and no
RNA virus with a monopartite genome O30 kb has been
described [54], it has been suggested that the genome of
LUCA consisted of a set of co-inherited RNA segments,
each coding for one or a few proteins [44]. The retroviruslike
genetic cycle of LUCA would account for a set of
multiplying, competing, functionally diversifying and
recombining molecules without demanding the complexity
of a fully fledged prokaryotic genome.

[Monad]

William Martin's homepage and an extensive list of publications from his lab and co-researchers

http://www.molevol.de/lab/martin.html

http://www.molevol.de/lab/publications.html

That's an extensive and impressive list so I've picked out a few that seem most pertinent to this thread's subject:

Getting a better picture of microbial evolution - en route to a network of genomes

http://www.molevol.de/publications/177.pdf

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

http://www.ncbi.nlm.nih.gov/pubmed/1...?dopt=Abstract

Hydrothermal vents and the origin of life

http://www.molevol.de/publications/174.pdf

The origin of mitochondria in light of a fluid prokaryotic chromosome model

http://www.molevol.de/publications/151.pdf

Evolutionary biology: out of thin air (origins of photosynthesis)

http://www.molevol.de/publications/154.pdf

Martin W, Dagan T, Koonin EV, Dipippo JL, Gogarten JP, Lake JA: The evolution of eukaryotes.

http://www.ncbi.nlm.nih.gov/pubmed/1...?dopt=Abstract

(Damn can't access that! - looks good)

Introns and the origin of nucleus-cytosol compartmentalization (!!!)

http://www.molevol.de/publications/138.pdf

The missing link between hydrogenosomes and mitochondria

http://www.molevol.de/publications/134.pdf

Archaebacteria (Archaea) and the origin of the eukaryotic nucleus.

http://www.molevol.de/publications/136.pdf

On the origin of genomes and cells within inorganic compartments

http://www.molevol.de/publications/135.pdf

That's just a few - Xmas has come again There are several I have already posted above but it is clear Martin, Russell and Koonin are in the forefront of some very exciting research into several aspects of the origins of life including:

• Abiogenesis - from inorganic to organic pathways including origins of cells, ATP/energy pathways and Krebs cycle
• Origins of Archaea and Eubacteria
• Origins of viruses
• The role of lateral gene transfer and endosymbiosis in early evolution
• Origins of photosynthesis
• Origins of mitochondria
• Origins of the Eukaryote nucleus

and that all these strands come together to form a very consistent and plausible whole

Links to dedicated pages giving an overview of subjects:

• endosymbiosis and endosymbiotic gene transfer
• the origin and evolution of anaerobic energy metabolism in eukaryotes
• the evolution and compartmentation of biochemical pathways in eukaryotes
• the general process of plant evolution as viewed with molecular markers

[Monad]

Did DNA replication evolve twice independently?

http://nar.oxfordjournals.org/cgi/co...act/27/17/3389


More on Eugene Koonin:

http://en.wikipedia.org/wiki/Eugene_Koonin

http://www.ncbi.nlm.nih.gov/CBBresearch/Koonin/

His publication list (very long and impressive - should raise some eyebrows):

http://www.ncbi.nlm.nih.gov/sites/en...rm=koonin%20ev

[Monad]

Martin Nowak has also been doing some interesting work on what came before evolution - i.e. the transition from non life to life and evolution.

Life is based on replication and evolution. But replication cannot be taken for granted. We must ask what there was prior to replication and evolution. How does evolution begin? We have proposed prelife as a generative system that produces information and diversity in the absence of replication. We model prelife as a binary soup of active monomers that form random polymers. ‘Prevolutionary’ dynamics can have mutation and selection prior to replication. Some sequences might have catalytic activity, thereby enhancing the rates of certain prelife reactions. We study the selection criteria for these prelife catalysts. Their catalytic efficiency must be above certain critical values. We find a maintenance threshold and an initiation threshold. The former is a linear function of sequence length, and the latter is an exponential function of sequence length. Therefore, it is extremely hard to select for prelife catalysts that have long sequences. We compare prelife catalysis with a simple model for replication. Assuming fast template-based elongation reactions, we can show that replicators have selection thresholds that are independent of their sequence length. Our calculation demonstrates the efficiency of replication and provides an explanation of why replication was selected over other forms of prelife catalysis.

Prelife catalysts and replicators

http://rspb.royalsocietypublishing.o...1674/3783.full

Prevolutionary dynamics and the origin of evolution

http://www.pnas.org/content/105/39/14924.full.pdf+html

enjoy

[Monad]

Some additional models of inorganic "scaffolding" for the origins of the first proto life:

Clay montmorillonites as catalysts for RNA polymerisation


http://www.sciencemag.org/cgi/content/full/302/5645/618

Some good references and links to more papers at the end of this one

also

http://geology.gsapubs.org/content/33/11/913.abstract

[Monad]

The original thread for this is here:

http://www.talkrational.org/showthread.php?t=20792

Unintelligent Design
A monstrous discovery suggests that viruses, long regarded as lowly evolutionary latecomers, may have been the precursors of all life on Earth

http://discovermagazine.com/2006/mar...lligent-design

New giant virus discovered:

http://www.physorg.com/news179588551.html

Redefining viruses: lessons from Mimivirus

Didier Raoult & Patrick Forterre

http://www.nature.com/nrmicro/journa...micro1858.html

Didier Raoult & Patrick Forterre are key figures in this research. Some additional papers by Forterre are found here (some in French):

http://en.scientificcommons.org/patrick_forterre

http://www-archbac.u-psud.fr/labhome/pforterre/epf.html

Also this in English:

http://www-archbac.u-psud.fr/Meeting...reilles_e.html

[Monad]

At one time Crick argued the exact pattern of the triplet genetic code was a "frozen accident" and had no specific reason for its sequence. However since then many studies have revealed clues to the origins of the genetic code hidden in the code itself - particularly in the types of amino acids most favoured:

http://www.ncbi.nlm.nih.gov/pubmed/2650752

http://www.ncbi.nlm.nih.gov/pubmed/15764708

[Monad]

Eric Murphy provided this link to a series of lectures on Abiogenesis and Evolution:

http://www.rockefeller.edu/evolution/

[Monad]

http://www.pnas.org/content/early/20...64106.abstract


Summary and link courtesy of RedRuth:

Originally Posted by RedRuth

Endosymbiosis is the the theory that some eukaryotic organelles (mitochondria and chloroplasts) were originally alphabacteria that were engulfed by other bacteria and established a symbiont relationship. (These types of symbiotic relationships are also studied in insects, they’re not unique to this event) So, mitochondria used to be free living organisms and there is plenty of evidence to back this theory up.
Over time some if not most of the genes that were encoded by the symbiont genome moved from the mitochondria to the host nuclear genome (there’s very good evidence for this as well). But this poses a problem, how do the proteins synthesised in the cytosol get into the mitochondria, protein targeting is a complicated and important system. So originally the engulfed mitochondria could survive in the cytosol of the host without any protein import machinery but as soon as genes were moved to he nucleus and deleted from the mito genome they become essential. So how do proteins get into mitochondria. There are are basically 3 complexes that do the job depending on where the protein is destined. Bearing in mind that mitochondria have a double membrane. There is also a short signal peptide at one of the ends of proteins destined for the mitochondria.

TOM - Translocates proteins through the outer membrane into the space between the membranes. The protein can go 1 of two ways now. It can either use the

SAM - Which organises membrane proteins into the outer membranes if that’s where they belong or

TIM - Which translocates proteins through the inner membrane.

There are also accessory proteins and chaperones involved but it’s the tranlocating complexes that we’re interested in.

The SAM complex has a direct bacterial homologue (Omp85 protein) which organise membrane proteins into the outer membrane of bacteria that have double membranes - like the one’s that mitochondria evolved from. This would explain why proteins destined for the outer mito membrane translocate through the membrane then back into it from the inter membrane space instead of being directly organised/folded into the membrane from the cytosol side. This is analogous to what would happen in a double membrane bound bacteria.

The paper is about looking for bacterial homologues of the TIM complexes, that is the translocation complex on the inner membrane of the mito. The authors found possible homolgues for two of the core components of complexes in alpha-proteobacteria and called them TIMA and TIMB, they don’t have a role in protein translocation. They then did experiments to show that both proteins are located in the inner membrane of the bacteria they were found in (this membrane is analogous to the inner membrane of the mitochondria) and that the 3D structure of TIMA resembles that of it’s mito homologue TIM44. TIMB has something called a J domain at one end which seemed comparable to the J domain of its mito homologue TIM14

They then did some experiments to see if TIMB could be converted to function as mitochondrial TIM14. They did this by changing one amino acid in the J domain which is crucial for forming a complex and put this domain from TIMB onto the part of TIM14 that directs the protein to the mitochondria to make a chimeric protein. They then knocked out TIM14 in yeast and put this chimeric protein in to see if it could functionally complement the TIM14, which it did. This shows that part of the TIMB protein can, with one amino acid change, function as TIM14 meaning it could have been co opted from its function (by gene duplication and divergence) to form part of the TIM complex.

So that’s the experimental part of the paper. In the discussion they speculate that a complex between TIMA TIMB and the amino acid transport LivH could have formed a proto TIM complex in the inner membrane. They also look for and find a ‘stripped down’ version of the TOM complex as proof of principle that less complex translocation complexes can function. So, all in all an interesting paper that sheds some light on the possible evolutionary origins of the mitochondrial protein import system.

Discussion here:

http://www.talkrational.org/showthread.php?t=18617

and here:

http://www.talkrational.org/showthre...light=Clements

[Monad]

http://www.molevol.de/publications/154.pdf

On the evidence for the origins of the photosynthetic molecular "machine"

Going to post some more on the evolution of photosynthesis - seems there have been some major breakthroughs. Firstly Russell (again) and Allen (who is a leading light in photosynthesis research) had predicted that certain inorganic minerals such as manganite would prove to be precursers of the part of the photosynthesis pathway that splits oxygen from water (the photosynthesis pathway in modern organisms is in 3 main parts - a manganese based part that splits water to release oxygen and 2 photosynthesis systems that work together). Russell and Allen argue that organisms initially used manganese to protect them from the strong UV rays in the early Earth - a process that in itself would create surplus electrons that could be used to do work.

Mackinawite ([Fe>>Ni)S]), greigite
(NiS2[Fe4S4]S2Fe) and a tunnel manganite
(CaMn4O8) similar in structure to hollandite were
minerals that enabled the onset of chemosynthesis
and, later, of oxygenic photosynthesis – the two
events to make the greatest impact at the surface of
our planet. The inorganic complexes contributing
to the growth of such minerals – ([FeS2Fe]4H2O;
[Fe4S4]2+/1+; [Fe3S4]+1/0; NiFe5S8, CaMn4O8 as well
as HP2O7
3−) – were later sequestered by small
organic molecules (initially polypeptides or
carboxylate groups) to become active centres of
the enzyme precursors that initially catalyzed the
primary reactions of energy conversion and nutrient
cycling. Examples of such adventitious cooptions
were to produce (i) pyrophosphate ‘eggs’ in successive
main chain NH peptide nests; (ii) protoferredoxins
as thiolated metal sulfide eggs in peptide nests;
(iii) precursors to carbon monoxide dehydrogenase
(CODH)/acetyl CoA synthetase (ACS) as a Nipeptide
and a thiolated egg in a peptide nest and
(iv) the precursor to the active centre of the OEC by
periplasmic carboxylates and hydroxyls adjacent to
RC II in a protocyanobacterium.

Inorganic Complexes Enabled the Onset of Life and Oxygenic Photosynthesis

http://www.gla.ac.uk/projects/origin...PS2%202008.pdf

More to come

[Monad]

Nick Lane has written several very interesting and readable books summarising and synthesising a a lot of recent research (including Russell and Martin's and Koonin's) on the origins of life:

Life Ascending: The Ten Great Inventions of Evolution

http://www.amazon.co.uk/Life-Ascendi...2171752&sr=1-1

Oxygen: The molecule that made the world

http://www.amazon.co.uk/Oxygen-molec...ref=pd_sim_b_1

Power, Sex, Suicide: Mitochondria and the meaning of life

http://www.amazon.co.uk/Power-Sex-Su...2171752&sr=1-2

Lane has also done original research and contributed papers on the origins of life - his bibliography is here (with a number of downloadables):

http://www.nick-lane.net/Nick%20Lane%20Publications.htm

[Monad]

http://www.talkrational.org/showthread.php?t=21436

The scientists show that prion variants constantly arise in a particular population. These variants, or "mutants", are believed to differ in the way the prion protein is folded. As a consequence, prion populations are, in fact, comprised of multiple sub-strains.
This, Weissmann noted, is reminiscent of something he helped define some 30 years ago - the evolutionary concept of quasi-species.
The idea was first conceived by Manfred Eigen, a German biophysicist who won the Nobel Prize in Chemistry in 1967. Basically stated, a quasi-species is a complex, self-perpetuating population of diverse and related entities that act as a whole. It was Weissmann, however, who provided the first confirmation of the theory through the study of a particular bacteriophage - a virus that infects bacteria - while he was director of the Institut für Molekularbiologie in Zürich, Switzerland.
"The proof of the quasi-species concept is a discovery we made over 30 years ago," he said. "We found that an RNA virus population, which was thought to have only one sequence, was constantly creating mutations and eliminating the unfavorable ones. In these quasi-populations, much like we have now found in prions, you begin with a single particle, but it becomes very heterogeneous as it grows into a larger population."
There are some unknown dynamics at work in the prion population that leads to this increased heterogeneity, Weissmann added, that still need to be explored.
"It's amusing that something we did 30 years has come back to us," he said. "But we know that mutation and natural selection occur in living organisms and now we know that they also occur in a non-living organism. I suppose anything that can't do that wouldn't stand much of a chance of survival."

Weismann is also important because he was the first to prove the existence of a quasi species. This concept was developed by Manfred Eigen who also developed the concept of the hypercycle which ties back into the work on the origins of biochemistry because hypercycles are thought to be one way that self organisation can lead to protolife.

http://www.iscid.org/encyclopedia/Hypercycles

http://www.biologie.uni-hamburg.de/b-online/e41/41b.htm

Eigen's bibliography is here:

http://www.mpibpc.mpg.de/groups/eige...ns/german.html

[Monad]

Just linking across to this comprehensive site on abiogenesis:

http://abiogenesisevo.blogspot.com/

[SteveF]

http://www.springerlink.com/content/b418465308240147/

[Monad]

http://www.talkrational.org/showthread.php?t=23152