Sunday, December 28, 2008

A Short Outline of 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.

From the 1st edition Pg 484:
“I believe that animals have 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 have 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 germinal vesicles, their cellular structure, and their laws of growth and reproduction. We see this even in so trifling a circumstance as that the same poison often similarly affects plants and animals; or that the poison secreted by the gall-fly produces monstrous growths on the wild rose or oak-tree. Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.”

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. "

A few years earlier, he had 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 famous 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 F. Wöhler, in his 1828 synthesis of urea, a "live" compound, from inorganic stock chemicals ("ON THE ARTIFICIAL PRODUCTION OF UREA" Annalen der Physik und Chemie, 88, Leipzig.)


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. Iris Fry,
2000 "The Emergence of Life on Earth: A Historical and Scientific Overview" (Rutgers University Press) 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. A bit more technical is J. William Schopf (editor), 2002 “Life’s Origin: The Beginnings of Biological Evolution” (University of California Press), but it is well worth the effort.

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 references here are:

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

Wilde, Simon A., John W. Valley, William H. Peck, Collin M. Graham
2001 “Evidence from detrital zircons for the existance of contenental crust and oceans on Earth 4.4 Gyr ago” Nature (letters) Vol 409:175-181


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)

Shapiro, R. (1988). Prebiotic ribose synthesis: A critical review. Origins of Life and Evolution of the Biosphere 18: 71-85.

Weber, A. L. (2001). The sugar model: Catalysis by amines and amino acid products. Origins of Life and Evolution of the Biosphere 31: 71-86.

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

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 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, which I think generalizes to other complex CHONSP molecules.

The 1986 Shapiro book is very out of date, and very popular with creationists. The 1999 Shapiro paper has also been answered to my satisfaction. 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.

(To follow when I get a bit more time)


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 3.8 billion (or more) years 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,

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.

Bernd R.T. Simoneit, Ahmed I. Rushdi and David W. Deamer
2007 “Abiotic formation of acylglycerols under simulated hydrothermal conditions and self-assembly properties of such lipid products” Advances in Space Research
Volume 40, Issue 11, 2007, Pages 1649-1656


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 are organized along a sugar backbone. I mentioned earlier that these sugars 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 chirality "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.

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 "racemization" because 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 attached to one another, or better yet, if they are also attached to a mineral, racemization 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 chirality 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? How did they get organized on a chiarl backbone? 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 advantage of L- amino acids will force the selection of D-ribose structured 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.

To repeat the 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.

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.

Ponnamporuma, Cyril, Carl Sagan, Ruth Mariner
1963 “Synthesis of Adenosine Triphosphate Under Possible Primitive Earth Conditions” Reprinted front Nature, Vol. 199, No. 4890, pp. 121-126 (This is more of historic interest, but recall that ATP is the energy carrier for all cells.)

Someone in an email 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 inconclusive. 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, and some are even less than 10 months old. This is in direct contrast to the selective use by creationist writers such as Jonathon Sarfati, or Jon Wells, who use a few out of date and refuted articles to puff up their nonsense.

So, there you have it.

Monday, December 15, 2008

Responding to Newspaper Editorials

I have cut back on posts to blogs, or BB sites in favor of replying directly in newspaper sites. It seems to me that there is a wider range of readers. Here is a comment I wrote this AM in response to former state Rep. Ken Mercer, now a member of the Texas State Board of Education. Mercer wrote an editorial in the San Antonio Express-News posted on-line 12/14/2008 8:48 CST. So far, the newspaper has not posted my comment.

“It is very interesting to read Mr. Mercer’s presentation of the Texas State Board of Education’s thinking about evolution. He immediately casts this as “ultra-liberals” versus “people of faith.” And I agree. He is clearly uninformed, even “willfully ignorant” as Apostle Paul might say, about the scientific and education issues. The only possible substance of his position is that of raw Rovian wedge issue politics. Mercer makes false and misleading claims about evolutionary theory. His use of “micro-“ and “macro-“ evolution are absurd, but typical of creationist polemics. If any freaks or monsters of Mercer’s imagination like a “dog-cat” existed, it would utterly DISPROVE evolutionary theory. We have direct evidence of new species emerging from old. This has been observed in nature, and in the laboratory. Only the willfully ignorant, or the politically motivated would say otherwise. Mercer then shifted to Ernst Haeckel. Haeckel was profoundly wrong in his theory of embryology. But, the actual historical record is that “Haeckel’s” drawings were largely the work of others- even by scientists who most loudly protested them. These are not “weaknesses in evolutionary theory.” I recommend to any honest person the recent biography of Haeckel by Robert J. Richards (2008 University of Chicago Press). Further, I have reviewed many recent high school biology textbooks, and when the contested illustrations were used it was as examples of a failed theory. As it happens, photographs are available that make the same case for common descent. The Piltdown hoax was not peer reviewed for “forty years,” as the actual “fossils” were kept away from critical examination. And, I must point out that it was scientists who uncovered the hoax- not politicians nor preachers. Since Mercer is so in favor of academic freedom, he will naturally halt his opposition to birth control, and medically accurate sex education for high school students. Unless that is he is a hypocrite. But at the end, I once again agree with Mercer, “An agenda that opposes both freedom of speech and academic freedom is unpatriotic, un-American, and unscientific.” And, I hope he changes his agenda soon. "


The lack of paragraphs is the defalt format of SA the site.




Up date: The comment was blocked due to an undocumented character limit. I posted it in three parts. This is the downside of newspaper comment sections- they are vary locally and are generally inconsistant.