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  Topic: Abiogenesis discussion thread, No trolls please, we're adults< Next Oldest | Next Newest >  
Dr.GH



Posts: 1957
Joined: May 2002

(Permalink) Posted: Jan. 11 2007,17:21   

I put this together almost 2 years ago, and it need to be updated.  But, I think that you can still get a quick start on the relevant literature in primary journals.

Darwin's first edition of The Origin of Species made no particular mention of the origin of life. He does make some general observations in the conclusion of the sixth edition published in 1872. He writes,
 
Quote
"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,
 
Quote
"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.

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. The Emergence of Life on Earth: A Historical and Scientific Overview by Iris Fry, (2000 Rutgers University Press), is the best general reader book available on the topic. Even though it is only 5 years old, a second edition is warrented 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:

1) Composition of the Hadean/early Archean atmosphere.

The key reference(s) here is:

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).

There are a few 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&#65533;? 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&#65533;? 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."

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&#65533;? 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&#65533;? 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&#65533;? Astrobiology 1:133-142

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 collegues 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&#65533;? 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 eachother, since there are only a handfull 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 representitive 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:

Fuller, W. D., Sanchez, R. A. & Orgel, L. E. Studies in prebiotic synthesis. VI. Synthesis of purine nucleosides. J. Mol. Biol. 67, 25-33 (1972).

Robertson, MP, Miller SL.
1995 An efficient prebiotic synthesis of cytosine and uracil. Nature 375, 772 - 774 ()

Nelson K.E., Robertson M.P., Levy M, Miller S.L.
2001 Concentration by evaporation and the prebiotic synthesis of cytosine. Orig Life Evol Biosph Jun;31(3):221-229

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?

One major source seems to be from meteors.

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.

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&#65533;? 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&#65533;? Science, Vol. 293, Issue 5538, 2236-2239, September 21, 2001

Segre' D., Ben-Eli D. Deamer D. and Lancet D.
2001 “The Lipid World&#65533;? Origins Life Evol. Biosphere 31, 119-145.

So now that we got 'em, what do they do once they are 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


Pastuer 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) adn 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 or metal atom, 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&#65533;? 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.

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.

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.
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.
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&#65533;? 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

Someone asked why I posted so many references.

There are several reasons. First, that is how science is done, we build on the work of others.

Second, when we use referenced data to make a point clear we state the source of our information up front. Anyone can read these papers. If they want, they can argue that I have misread the article, or that the article itself has been refuted by more up-to-date
information.

Third, a common creationist claim is that there is no valid research on the origin of life, or that the research done is inconclucive. The references I have cited are evidence that these claims are false.

Fourth, except for some historical references, my sources are mostly less than 10 years old. This is in direct contrast to the selective use by creationist writers such as Jon Sarfati, or Jon Wells, who use a few out of date and refuted articles to puff up their nonsense.

So, there you have it.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
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