"We will focus on the cell because that is the most basic unit of life."....

This seems an arbitrary cut-off to just start with prokaryotes as it ignores the virus. Though virus are not deemed to be life in a traditional sense they are certainly not proteins but use RNA to reprogram other cells.

I see virus as a more basic unit within the context of abiogenesis and Evolution.

You may want to revise what you know about viruses, e.g. here: http://en.wikipedia.org/wiki/Virus

Bert

Rumraket wrote:Basically, what we want is to explain how a molecular system capable of undergoing darwinian evolution arrived. If we can produce such a system under plausible abiotic conditions, I think we would consider the problem solved. Complex systems are easily evolvable by darwinian means, but extremely difficult to make by simple abiotic chemistry. It has to start somwhere.

You are right. This is all we need.
...but we don't have it.

bert wrote:You may want to revise what you know about viruses, e.g. here: http://en.wikipedia.org/wiki/Virus

Bert

I have - the article points this out to when it says "(hypothesis that)....viruses played a central role in the early evolution, before the diversification of bacteria, archaea and eukaryotes and at the time of the last universal common ancestor of life on Earth..." (it cites Forterre P, Philippe H. The last universal common ancestor (LUCA), simple or complex?. The Biological Bulletin. 1999;196(3):373–5; discussion 375–7. doi:10.2307/1542973. PMID 11536914)

My point was that it matters little how life functions today in cells but how life evolved. It seems logical that the progression from atoms to simple organic compounds through amino acids would not then jump to cells. Cells are vastly complex made up of many compounds. It just seems too magical a step.

The horizontal gene transfer mechanism that virus have today is a more probable basis for accumulating the information in the genomes of all other life. Ergo the mechanisms of virus today should be closer to the mechanism of abiogenesis than "cells".

It's a little difficult to get around the atheist scientists who simply won't go away with their stupid disbelief in the simple facts of creation. And it's all so neatly explained by god-inspired goat herders.

To quickly get back to my earlier question of course I would think that it would take more than one chemical reaction to cause life to occur. I'm fascinated by this topic, why would anyone want to dismiss the beauty of that first moment when some very basic life form began reproducing itself, by saying that life emerged as we know it today with the wish of an imaginary being's word instead?

I'm amused when people point out to me that evolution cannot account for the complexity of the eye, because that's exactly what evolution does. That first spark of life had to go through so many transformations before a rudimentary eye evolved, which became the eye of the most complicated visual arrangement of insects and animals like the chameleon, so why would anyone want to believe that "goddidit" simply because they're too stupid to comprehend it's complicated evolution.

Agrippina wrote:

The_Metatron wrote:

Agrippina wrote:I'm bookmarking to read this thread later

Excellent, I suspect I'll be availing you of your prowess.

This is a very interesting thread and thank you for the mention on the first page.

I wish I had the time and the mental capacity to study the two ancient languages. It would be infinitely easier to study ancient sources if I were able to do that. The problem is that in my search for a general knowledge of everything that attracted my attention in my youth, and coming to formal education rather late in life, I wasted a lot of time that would have been well-spent had I rather revived my school Latin. Too late now so I have to depend on English translations and the collective intellect on this forum which sometimes boggles the mind.

Classical Latin and Classical Greek (I'll abbreviate these simply as 'Latin' and 'Greek' from now on) are two languages requiring a lot of care in their teaching. It's almost ridiculously easy to teach these languages badly. Which is why you'll find that teachers of the Classics, as they were once known, rely upon the development of something like 1,000 years of rigorous pedagogy in the field. Indeed, for much of that 1,000 year period, Latin and Greek were mandatory entry requirements for every university in Europe, and scholarly discourse was conducted exclusively in Latin until the late 18th or early 19th centuries.

This is one of the reasons why Linnaeus chose Latin and Greek as the basis for his classification system - when he was alive, Latin and Greek were still mandatory languages of scholarly discourse, and choosing those languages ensured rapid, universal acceptance of his system. Additionally, since Linnaeus intended that scientific names should be, wherever possible, descriptive of the organisms in question, and Latin and Greek possess rich vocabularies, it occurred to Linnaeus that choosing these languages would make this task relatively simple. Of course, he considered this to be the case in an era when insect biodiversity was still largely unexplored, and the existence of 350,000 species of beetle now known to science has long since tested those vocabularies to breaking point. When you're faced with an entire drawer containing 300 species of extremely similar, small dark brown beetles, and you have to find unique, unambiguous names for them all, the ingenuity taxonomists have to resort to is considerable.

As a consequence, you'll find that some of the original intentions of Linnaeus have fallen a little by the wayside, with respect to names being descriptive, because in the world of insect taxonomy, there are simply too many species. First, taxonomists started using the names of mythological characters in scientific names, on the understanding that a well-versed scholar would understand what attributes of those mythological characters were allegedly exhibited by the species in question. The Genus Dryas, for example, refers to wood nymphs in Greek mythology, and informs the astute reader of the taxonomic literature that the butterflies in question are forest dwellers. Likewise, the Small Tortoiseshell butterfly here in the UK belongs to the Genus Aglais, which is a reference to Aglaia, one of the Three Graces, an allusion to the fact that this is a highly colourful and attractive insect. In the case of the Small Tortoiseshell, its specific name points to another trick taxonomists used to expand the remit of Linnaeus' system - the full scientific name is Aglais urticae, and Urtica is the botanical Genus containing the Nettles. Consequently, urticae refers to the fact that the butterfly's larval foodplant is the common Stinging Nettle, Urtica dioica. You'll find that quite a few Lepidoptera in particular are named with reference to their foodplants: Catocala fraxini, a moth known commonly as the Clifden Nonpareil, feeds upon the leaves of Ash trees in the larval state, and Fraxinus is the botanical Genus that Ash trees belong to.

Likewise, geographical references appear in taxonomic names - usually ending in "-ensis", though some also end in "-icus" just to spread a little confusion among the neophytes. The Cichlid fish Geophagus braziliensis is a case in point - its taxonomic name translates directly as "earth eater from Brazil", referring to its habit of digging for invertebrates in sandy substrates. Another fish with a geographical taxon is the Characin fish Astyanax mexicanus, which as its name suggests, hails from Mexico. Quite why the fish was also named after the son of the King of Troy from the Iliad is unknown to me at this juncture, but I suspect that a reading of the relevant literature will soon turn up the reasons for this. As a short tangential diversion, this fish exists both in the form of surface dwelling populations, and cave dwelling populations that have lost their eyes over millennia about which I have said much in various other sections of the forum, and the eyeless form was originally given its own taxonomic name, until it was recognised that it was an eyeless form of Astyanax mexicanus. This taxon, now deprecated, was Anophthichthys jordani, the Generic name translating as "fish with no eyes", and it's a pity that the rules for zoological nomenclature don't permit that taxon to persist.

Serendipitously, Anophthichthys jordani allows me to introduce another taxonomic habit, one that has become firmly entrenched since the early 20th century - that of naming organisms after various scientists of note. Originally, such an honour was bestowed upon other taxonomists, so you'll find dozens of tropical Lepidoptera named after various butterfly researchers, or persons connected thereto in some manner, for example, this little lot:

Ornithoptera rothschildi

Euphaedra edwardsi

Euploea westwoodi

Poritia hewitsoni

Indeed, I could wax lyrical about taxonomic curiosities for hours, but there are other parts of your post to address, so I shall do that now!

Agrippina wrote:I have a question about the origin of life that I've always wondered about and especially because of where I live and what I observe in nature here. I appreciate that life in some form already exists in what I observe, but I just wonder whether it couldn't be simply explained in that way. And it's this: couldn't the origin of life, the very first spark, simply have been that the spark already existed in the air and that a combination of exactly the right chemical reaction caused it to happen? When we have a bout of torrential rain, as we have had this week, and in the dark corners of my garage where the water collects, little growths of smelly mold (or mildew, black algae or whatever it is) emerge within a very short time. Could it not simply have been the exactly correct humidity, water, material and a chemical reaction with the dust that sparked off the first burst of life?

Ah, abiogenesis. A subject I've had much fun with, courtesy of the scientific papers.

The scientific hypothesis is as follows. Once Planet Earth had formed, had shed the heat accumulated during the Late Heavy Bombardment, and acquired an atmosphere and liquid oceans, conditions were very different to those present now. First, the atmosphere contained virtually no oxygen - this was to appear later - and the atmosphere consisted principally of nitrogen, carbon dioxide, some hydrogen (though this was slowly lost to space, being the lightest of the constituent gases) and possibly some methane as well - these conditions comprise what is called the 'prebiotic Earth'. This atmosphere, however, still had weather systems of the sort we observe today, including thunderstorms, and lightning discharges in the atmosphere provided the energy input for a series of chemical reactions that led to the first simple organic molecules relevant to life. The famous Miller-Urey Experiment established that this process could produce amino acids, for example, which are the basic building blocks of proteins, and more recent work by Leslie Orgel and others has established that those initial amino acids could have formed short peptide chains, catalysed by a gas called carbonyl sulphide, which is emitted in quantity by erupting volcanoes. However, those molecules aren't the whole story, and are considered to be of importance later in the picture.

Among the other organic molecules that have been demonstrated to form under prebiotic conditions, when those conditions are replicated in the laboratory, are nucleotides. These are the basic building blocks of RNA and DNA, two molecules of central importance to the genetics of every living organism present today. The hypothesis that enjoys the greatest favour currently, is that RNA was the first genetic molecule, DNA being a later arrival, and that the first true replicators were simple strands of RNA that were formed by appropriate chemical reactions, catalysed by montmorillonite clay substrates in shallow parts of the primordial oceans. There are, I hasten to add at this juncture, other mechanisms postulated for RNA formation, but I'll leave those aside for the moment - suffice it to say that I have the relevant scientific papers in my collection.

Now, it has been demonstrated in the laboratory, that certain RNA strands possess an interesting property - they are autocatalytic under prebiotic conditions. This means that they catalyse the formation of yet more identical RNA strands from a solution of nucelotides within which they are present. Indeed, self-replication of these special strands of RNA, called autocatalytic ribozymes, has again been demonstrated in the laboratory, and I have a good number of papers on this subject, not to mention papers demonstrating that once autocatalytic ribozymes exist, their replication, whilst of a high fidelity, is imperfect, and that as a consequence, once these replicating ribozymes exist, evolution can start to influence its effects upon the outcome of said replication, because, as another excellent paper by Gerald F. Joyce demonstrates, a population of such ribozymes can be subject to differential replication success dependent upon ambient chemical conditions - in short, selection pressures appear within populations of these ribozymes.

However, we need something more than just RNA, if we're going to start building cells. Say hello to another class of molecules, known as lipids. Lipids are, in effect, the generic class of molecule to which fats belong, and certain lipids possess interesting properties. Phospholipids, for example, are polar molecules, with a hydrophilic, water-soluble functional group attached to a hydrophobic functional group that repels water. When these molecules are present in a reasonable concentration, they can arrange themselves spontaneously into structures. Indeed, all you need to do with a jar of suspended phospholipids, is shake the jar, and the phospholipids will self-assemble into structures known as micelles, bilayer sheets and liposomes, all three of which appear in modern cells.

What's even more interesting about some of these lipid structures, is that they can encapsulate other molecules whilst they are forming, and once formed, they act as filters, allowing some molecules to pass from one side of the structural boundary to the other, whilst forbidding other molecules from doing so. This selective osmotic capacity is again a central feature of modern cells. So, it is hypothesised that the first protocells were extremely simple in structure, consisting of liposomes encapsulating replicating RNA ribozymes. It's at this point that we reach the cutting edge of extant research, which is now aimed at constructing model protocells of this sort in the laboratory, and determining how they behave. There is also some work to be done on the matter of self-assembly of protocells from lipid/RNA solutions, but again, this work us now underway, and several interesting research papers covering model protocell work are also in my collection.

From this point, the active areas of research include determining how proteins became coupled to all of this, and how protocells evolved to utilise amino acids and short protein strands to perform simple metabolic tasks. Once that research is complete, and we have a handle on how these processes could have taken place, we'll be well on the way to establishing a robust framework for the origin of life.

Of course, there are some unanswered questions, but that's the whole point of the research in the field, to answer those questions, once the empirical means become available. Which, of course, means that those unanswered questions are of no comfort to mythology fetishists.

Agrippina wrote:I have no knowledge of chemistry, so to even pretend that I could explain what I'm asking in better terms than the above would be just nonsense, so I apologise if it sounds odd, or vague. I think sometimes that like with the "Big Bang" which we are now told wasn't that big and possibly didn't even bang, couldn't life's beginnings have been just a chemical reaction and not an earth-shattering "I'm here and ready to party!" kind of little almost nothing?

Indeed, as I've just expounded above, the scientific hypothesis is that chemistry formed the basis of the origin of life, not least because we have evidence in abundance that life is, in effect, chemistry writ large. Chemical reactions by the billion are taking place in you body right now, ranging from glucose metabolism via adenosine triphosphate in your muscles, to liberate the energy required for them to function, through to the differential exchange of sodium and potassium ions in your neurons to facilitate their generation of an electrical signal, through to the wonders of DNA transcription and translation, all of which are nothing more than intricate chemical reactions. Since we have such a vast body of evidence for chemical reactions taking place in living organisms (the whole of the pharmaceutical industry is founded upon this basic fact, for example), it's perfectly reasonable to hypothesise that chemical reactions were responsible for life coming into existence in the first place. Once again, no magic needed, and no magic man needed.

Agrippina wrote:Anyway, this is a terrific thread and I'm intrigued to keep reading, I have learned so much from all of you. Thanks Stijn for directing me here.

We who take delight in these topics welcome your arrival. It gives us the opportunity to share our scientific (and other) passions.

Cali, if you do not mind me asking, what do you do for a living? because I love hearing from you and it is a blessing to be able to read your intellectual postings.

Thank you for that lovely long reply Cali.
My reaction when I read this:

Indeed, as I've just expounded above, the scientific hypothesis is that chemistry formed the basis of the origin of life, not least because we have evidence in abundance that life is, in effect, chemistry writ large.

was a big "yesssssss!"
I love it when I get an idea and someone who knows tells me I'm on the right track.

Now I need to get the correct citations from you so that I can make a short statement to this effect when I say this is my paragraph about how it all began:

The first signs of microscopic life appeared around 3.7 billion years ago. Even though there is not yet a formal explanation for what sparked life to begin, we can safely say that the complexity of life was not instigated by the hand-waving of a deity invented by humans.

Agrippina wrote:I love it when I get an idea and someone who knows tells me I'm on the right track.

Yes, I knew it would be best left for Cali to tell you.

I recently had a visit fron a Jehovah's Witness. Something made me want to engage him so a twenty minute debate ensued. And I lost. I was told that gravity cannot be demonstrated, that there are various types of evolution and that morality did not exist before The Ten Commandments. I was also told that his son had a degree in physics and I should engage him. He said that he knew my house was built by someone even though he did not know him and by implication this was evidence for a Creator, because the Universe is his creation. It probably was a good idea that I did not engage his son as he might have well and truly destroyed any arguments I used. I think he gave me some literature, but I haven't read it. They will return again as they are regular visitors round here. Next time I think I will show a bit more respect. They are usually two West Indian ladies, one young and one old.

surreptitious57 wrote:I recently had a visit fron a Jehovah's Witness. Something made me want to engage him so a twenty minute debate ensued. And I lost. I was told that gravity cannot be demonstrated,

Perhaps you should have dropped something heavy on his foot and then ask if gravity was demonstrated to his satisfaction.

My thoughts exactly.

klazmon wrote:

surreptitious57 wrote:I recently had a visit fron a Jehovah's Witness. Something made me want to engage him so a twenty minute debate ensued. And I lost. I was told that gravity cannot be demonstrated,

Perhaps you should have dropped something heavy on his foot and then ask if gravity was demonstrated to his satisfaction.

I should have let him be, but I have a tendency to open mouth before engaging brain.

Agrippina wrote:Now I need to get the correct citations from you so that I can make a short statement to this effect when I say this is my paragraph about how it all began:

The first signs of microscopic life appeared around 3.7 billion years ago. Even though there is not yet a formal explanation for what sparked life to begin, we can safely say that the complexity of life was not instigated by the hand-waving of a deity invented by humans.

You want citations Agrippina? Be prepared for a LONG list!!!

I'll cover these in alphabetical order, along with some relatively brief commentary on the contents of the papers. Here's some appropriate citations:

A Combined Experimental And Theoretical Study On The Formation Of The Amino Acid Glycine And Its Isomer In Extraterrestrial Ices by Philip D. Holtom, Chris J. Bennett, Yoshihiro Osamura, Nigel J Mason and Ralf. I Kaiser, The Astrophysical Journal, 626: 940-952 (20th June 2005) - this paper covers empirical determination of mechanisms required to form the aming acid glycine, under the conditions extant in deep space (specifically, in cometary ices).

A Production Of Amino Acids Under Possible Primitive Earth Conditions by Stanley L. Miller, Science, 117: 528-529 (15th May 1953) - this is THE paper by Stanley Miller, in which he determined that it was possible to form amino acids simply by having electric discharges pass through prebiotic gases.

A Rigorous Attempt To Verify Interstellar Glycine by I. E. Snyder, F. J. Lovas, J. M. Hollis, D. N. Friedel, P. R. Jewell, A. Remijan, V. V. Ilyushin, E. A. Alekseev and S. F. Dyubko, The Astrophysical Journal, 619(2): 914-930 (1st February 2005) {Also available at arXiv.org] - another paper covering the matter of glycine synthesis in interstellar space.

A Self-Replicating Ligase Ribozyme by Natasha Paul & Gerald F. Joyce, Proc. Natl. Acad. Sci. USA., 99(20): 12733-12740 (1st October 2002) - First of many papers covering the existence of sef-replicating short strands of RNA (autocatalytic RNA ribozymes), and analysis of the behaviour thereof.

A Self-Replicating System by T. Tjivuka, P. Ballester and J. Rebek Jr, Journal of the American Chemical Society, 112: 1249-1250 (1990) - demonstration of the existence of autocatalytic organic reactions in other molecules, in this amino-adenosine.

Activated Acetic Acid By Carbon Fixation On (Fe,Ni)S Under Primordial Conditions by Claudia Huber and Günter Wächetershäuser, Science, 276: 245-247 (11th April 1997) - empirical demonstration of the ability of sediments containing certain mineral ions to catalyse organic reactions under the conditions present around deep sea hydrothemral vents, thus allowing for the formation of necessary building blocks under those conditions.

An Asymmetric Underlying Rule In The Assignment Of Codons: Possible Clue To A Quick Early Evolution Of The Genetic Code Via Successive Binary Choices by Marc Delarue, The RNA Journal, 13(2): 161-169 (12th December 2006) - demonstration of the evolvability of the genetic code during the "RNA world" stage, involving assignments of codons based upon specific classes of chemical reaction.

An Expanded Set Of Amino Acid Analogues For The Ribosomal Translation Of Unnatural Peptides by Matthew C. T. Hartman, Kristopher Josephson, Chi-Wang Lin and Jack W. Szostak, PLoS One, 2(10): e972 DOI: 10.1371/journal.pone.0000972 (October 2007) - demonstration that new variations of the genetic code can be produced in vitro, and exotic amino acids incorporated into the genetic code via appropriate chemical manipulation.

Attempted Prebiotic Synthesis Of Pseudouridine by Jason P. Dworkin, Origins of Life and Evolution of the Biosphere, 27: 345-355 (1997) - investigation of the mechanisms of synthesis of pseudouridine, a modified base found in the RNA molecules of a number of modern living organisms.

Autocatalytic Aptazymes Enable Ligand-Dependent Exponential Amplification Of RNA by Bianca J. Lam and Gerald F. Joyce, Nature Biotechnology, 27(3): 288-292 (March 2009) - demonstration that an extended class of RNA molecules can replicate under appropriate conditions, dependent upon the ligands that they react with, and that these can be harnessed for a variety of medical diagnostic applications.

Carbonyl Sulphide-Mediated Prebiotic Formation Of Peptides by Luke Leman, Leslie Orgel and M. Reza Ghadiri, Science, 306: 283-286 (8th October 2004) - demonstration that amino acids can form peptide chains in prebiotic ocean conditions, coutesy of catalysis by carbonyl sulphide, a volcanic gas that is readily soluble in water, and which improves the rate of peptide formation to the extent that 80% yields can be obtained at room temperature in under 24 hours.

Catalysis In Prebiotic Chemistry: Application To The Synthesis Of RNA Oligomers by James P. Ferris, Prakash C. Joshi, K-J Wang, S. Miyakawa and W. Huang, Advances in Space Research, 33: 100-105 (2004) - empirical demosntration in the laboratory that RNA molecules can be synthesised under prebiotic conditions by catalysis on montmorillonite clays, and that under certain conditions, RNA molecules consisting of more than 40 bases can be synthesised catalytically in this manner.

Cations As Mediators Of The Adsorption Of Nucleic Acids On Clay Surfaces In Prebiotic Environments by Marco Franchi, James P. Ferris and Enzo Gallori, Origins of Life and Evolution of the Biosphere, 33: 1-16 (2003) - another empirical demonstration that nucleic acids can be formed by catalytic reactions on montmorillonite clay surfaces under prebiotic ocean conditions.

Chemistry for the Synthesis of Nucleobase-Modified Peptide Nucleic Acid by R. H. E. Hudson, R. D. Viirre, Y. H. Liu, F. Wojciechowski and A. K. Dambenieks, Pure Appl. Chem., 76(7-8) 1591-1598, 2004 - empirical demonstration that alternative nucleic acids exist, and that these could be formed under prebiotic conditions.

Coevolution Of Compositional Protocells And Their Environment by Barak Shenhav, Aia Oz and Doron Lancet, Philosophical Transactions of the Royal Society Part B, 362: 1813-1819 (9th May 2007) - development of a chemically realisable model for protocells, that can be tested via computer simulation in order to determine the likely behaviour of protocells formed via the relevant processes.

Computational Models For The Formation Of Protocell Structures by Linglan Edwards, Yun Peng and James A. Reggia, Artificial Life, 4(1): 61-77 (1998) - computer modelling of lipid self-assembly and its relevance to protocell formation.

Conditions For The Emergence Of Life On The Early Earth: Summary And Reflections by Joshua Jortner, Philosophical Transactions of the Royal Society Part B, 361: 1877-1891 (11th September 2006) - review paper covering the mutliple approaches to the question of the origin of life, from prebiotic chemistry, through to the genetic manipulation of model organisms in the laboratory to create a 'minimal' cell.

Coupled Growth And Division Of Model Protocell Membranes by Ting F. Zhu and Jack W. Szostak, Journal of the American Chemical Society, 131: 5705-5713 (2009) - empirical demonstration of the validity of a model for protocell division without loss of protocell contents, facilitating future research into actual replicating protocells.

Darwinian Evolution On A Chip by Brian M. Paegel and Gerald F. Joyce, Public Library of Science Biology, 6(4): e85 (April 2008) - empirical demonstration that RNa molecule populations undergo Darwinian evolution when subject to relevant chemical selection pressures, in a manner that can be replicated in a well-equipped school laboratory.

Early Anaerobic Metabolisms by Don E Canfield, Minik T Rosing and Christian Bjerrum, Philosophical Transactions of the Royal Society Part B, 361: 1819-1836 (11th September 2006) - demonstration that theories about the metabolic processes of the earliest true cells are consistent with isotopic measurements of extremely ancient strata of the relevant age.

Efficient And Rapid Template-Directed Nucleic Acid Copying Using 2′-Amino-2′,3′-dideoxyribonucleoside-5′-Phosphorimidazolide Monomers by Jason P. Schrum, Alonso Ricardo, Mathangi Krishnamurthy, J. Craig Blain and Jack W. Szostak, Journal of the American Chemical Society, 131(40): 14560-14570 (16th September 2009) - empirical demonstration that encapsulated nucleic acids inside lipid vesicles can replicate, and thus form the basis for model protocells in laboratory investigations.

Emergence Of A Replicating Species From An In Vitro RNA Evolution Reaction by Ronald R. Breaker and Gerald F. Joyce, Proceedings of the National Academy of Sciences of the USA, 91: 6093-6097 (June 1994) - production of a replicating RNA species via in vitro evolution from a population of RNA molecules.

Enzymatic Synthesis Of DNA On Glycerol Nucleic Acid Templates Without Stable Duplex Formation Between Product And Template by Ching-Hsuan Tasi, Jingyang Chen and Jack W. Szostak, Proceedings of the National Academy of Sciences of the USA, 104(37): 14598-14603 (11th September 2007) - demonstration in the laboratory that nucleic acid synthesis using glycerol nucleic acid (GNA) could have provided a pathway from RNA to DNA.

Evolution And Self-Assembly Of Protocells by Ricard V. Solé, The International Journal of Biochemistry & Cell Biology, 41: 274-284 (2009) - demonstration that the protocell formation problem may be easier to solve than previously thought, concentrating upon mechanisms for coupling metabolism and container.

Evolution Of Amino Acid Frequencies In Proteins Over Deep Time: Inferred Order Of Introduction Of Amino Acids Into The Genetic Code by Dawn J. Brooks, Jacques R. Fresco, Arthur M. Lesk and Mona Singh, Molecular and Biological Evolution, 19(10): 1645-1655 (2002) - determination of the likely sequence of insertion of amino acids into the genetic code, based upon analysis of the behaviour of present day transcription systems, and simulations taking into account the differential chemistry of certain classes of amino acid.

Experimental Models Of Primitive Cellular Compartments: Encapsulation, Growth And Division by Martyn M. Hanczyk, Shelley M. Fukijawa and Jack W. Szostak, Science, 302: 618-622 (24th October 2003) - empirical demonstration in the laboratory, that montmorillonite clays catalyse the formation of lipid vesicles from micelles, thus facilitating protocell formation in a prebiotic environment, including the encapsulation of any RNA molecules formed catalytically on the same montmorillonite substrates.

Formation Of Bimolecular Membranes From Lipid Monolayers And A Study Of Their Electrical Properties by M. Montal and P. Mueller, Proceedings of the National Academy of Sciences of the USA, 69(12): 3561-3566 (December 1972) - systematic investigation of the behaviour of lipid bilayers, and how they can be formed from less complex lipd structures.

Formation Of Protocell-Like Structures From Glycine And Formaldehyde In A Modified Sea Medium by Hiroshi Yanagawa and Fujio Egami, Proceedings of the Japan Academy, 53: 42-45 (12th January 1977) - demonstration that structures resembling hypothesised protocells could be produced in prebiotic open oceanic conditions.

Formation Of Protocell-Like Vesicles In A Thermal Diffusion Column by Itay Budin, Raphael J. Bruckner and Jack W. Szostak, Journal of the American Chemical Society, 131: 9628-9629 (2009) - demonstration that thermal diffusion columns associated with hydrothermal vents could have accelerated the formation of protocells.

From Volcanic Origins Of Chemoautotrophic Life To Bacteria, Archaea And Eukarya by Günter Wächtershaüser, Philosophical Transactions of the Royal Society of London Part B, 361: 1787-1808 (7th September 2006) - review paper covering the hypothesis that metabolism of iron and sulphur, as seen in very ancient bacterial and archaeal lineages, could have formed the basis for the modern domains of life.

Functional Information And The Emergence Of Biocomplexity by Robert M. Hazen, Patrick L. Griffin, James M. Carothers and Jack W. Szostak, Proceedings of the National Academy of Sciences of the USA, 104 supplement 1: 8574-8581 (15th May 2007) - demonstration that functional information of the sort needed for the development of metabolisms could have emerged from simpler chemical antecedents.

Generic Darwinian Selection In Catalytic Protocell Assemblies by Andreea Munteanu, Camille Stephan-Otto Attolini, Steen Rasmussen, Hans Ziock and Ricard V. Solé, Philosophical Transactions of the Royal Society Part B, 362: 1847-1855 (2007) - demonstration that several different protocell models of varying initial complexity all undergo Darwinian evolution.

Homochiral Selection In The Montmorillonite-Catalysed And Uncatalysed Prebiotic Synthesis Of RNA by Prakash C. Joshi, Stefan Pitsch and James P. Ferris, Chemical Communications (Royal Society of Chemistry), 2497-2498 (2000) [DOI: 10.1039/b007444f] - demonstration that homochiral synthesis of RNA occurs on montmorillonite clay substrates, resulting in chiral selection for particular enantiomers.

How Life Began On Earth: A Status Report by Jeffrey L. Bada, Earth & Planetary Science Letters, 226: 1-15 (22nd July 2004) - review paper covering a number of relevant abiogenetic hypotheses, and their applicability to the origin of life problem.

Hyperthermophiles In The History Of Life by Karl O. Stetter, Philosophical Transactions of the Royal Society Part B, 361: 1837-1843 (11th September 2006) - demonstration by molecular phylogeny that hyperthermophilic bacteria and archaea are amongst the most ancient of surviving lineages, thus supporting the hypothesis that such organisms were amongst the first true living cells.

Identification Of Diamino Acids In The Murchison Meteorite by Uwe J. Meierhenrich, Guillermo M. Muñoz Caro, Jan Hendrik Brederhöft, Elmar K. Jessberger and Wolfram H-P. Thiemann, Proceedings of the National Academy of Sciences of the USA, 101(25):9182-9286 (22nd June 2004) - determination of the existence of a range of interesting amino acid compounds in a meteorite, supporting the hypothesis that some prebiotic organic molecules could have arrived from space, and assisted the formation of life on Earth.

Implications Of A 3.472-3.333?GYr-Old Subaerial Microbal Mat From The Barberton Greenstone Belt, South Africa, For The UV Environmental Conditions Of The Early Earth by Frances Westall, Cornel E.J de Ronde, Gordon Southam, Nathalie Grassineau, Maggy Colas, Charles Cockell and Helmut Lammer, Philosophical Transactions of the Royal Society Part B, 361: 1857-1876 (11th September 2006) - determination of the existence of microbial fossils, possibly dating back 3.4 billion years, suggesting that conditions for the first living organisms were not as hostile as previously thought.

Information Transfer From Peptide Nucleic Acids To RNA By Template-Directed Syntheses by Jürgen G. Schmidt, Peter E. Nielsen and Leslie E. Orgel, Nucleic Acids Research, 25(23): 4794-4802 (1997) - empirical demonstration in the laboratory that information can be transferred from peptide nucleic acids to RNA, as a possible intermediate step in the formation of the genetic basis of life.

Interstellar Glycine by Yi-Jehng Kuan, Steven B. Charnley, Hui-Chun Huang, Wei-Ling Tseng, and Zbigniew Kisiel, The Astrophysical Journal, 593: 848-867 (20th August 2003) - determination that the amino acid glycine is present in detectable levels in deep interstellar space.

Is There A Common Chemical Model For Life In The Universe? by Steven A. Benner, Alonso Ricardo and Matthew A. Carrigan, Current Opinion in Chemical Biology, 8: 672-689 (22nd October 2004) - proposal that a range of alternative chemistries could also produce 'organisms' that canundergo Darwinian evolution.

Kin Selection And Virulence In The Evolution Of Protocells And Parasites by Steven A. Frank, Proceedings of the Royal Society of London Part B, 258: 153-161 (1994) - demonstration that the existence of 'parasitic' systems can drive the evolution of protocells at an accelerated rate.

Ligation Of The Hairpin Ribozyme In cis Induced By Freezing And Dehydration by Sergei A. Kazakov, Svetlana V. Balatskaya and Brian H. Johnston, The RNA Journal, 12: 446-456 (2006) - demonstration that repeated cycles of freezing and dehydration can drive the formation of RNA molecules, thus allowing for their appearance under cold prebiotic conditions.

Lipid Bilayer Fibres From Diastereomeric And Enantiomeric N-Octylaldonamides by Jürgen-Hinrich Fuhrhop, Peter Schneider, Egbert Boekema and Wolfgang Helfrich, Journal of the American Chemical Society, 110: 2861-2867 (1988) - empirical demonstration that relevant lipid compounds are capable of self-assembling spontaneously into hollow fibres.

"Living" Under The Challenge Of Information Decay: The Stochastic Corrector Model Versus Hypercycles by Elias Zintzaras, Mauro Santos and Eörs Szathmáry, Journal of Theoretical Biology, 217: 167-181 (2002) - comparison of the viability of two different protocell models, and their ability to withstand deleterious mutations when subject to evolutionary pressures.

Membrane Self-Assembly Processes: Steps Toward The First Cellular Life by Pierre-Alain Monnard and David W. Deamer, The Anatomical Record, 268: 196-207 (2002) - investigation of the viability of lipid vesicles as the outer integument of the first protocells.

Mineral Catalysis And Prebiotic Synthesis: Montmorillonite-Catalysed Formation Of RNA by James P. Ferris, Elements, 1: 145-149 (June 2005) - empirical demonstration of the viability of the RNA world hypothesis, courtesy of the existence of an effiicient means of producing RNA molecules catalytically on montmorillonite clays.

Mineral Surface Directed Membrane Assembly by Martyn M. Hanczyc, Sheref S. Mansy and Jack W. Szostak, Origins of Life and Evolution of Biospheres, 37(1): 67-82 (February 2007) - Another laboratory demonstration that montmorillonite clays can produce lipid vesicles encapsulating RNA molecules under prebiotic cconditions.

Model Of Self-Replicating Cell Capable Of Self-Maintenance by Naoaki Ono and Takashi Ikegami, in Lecture Notes in Computer Science: Advances in Artificial Life, 1674: 399-406 (25th June 1999) (also available as full paper at arXiv.org: adap-org/9905002v2) - mathematical and computer modelling of a hypothetical protocell, demonstrating that such a system would be capable of dynamic maintenance of its outer integument, and would also be capable of a simplified form of cell division.

Molecular Asymmetry In Extraterrestrial Chemistry: Insights From A Pristine Meteorite by Sandra Pizzarello, Yongsong Huang and Marcelo R. Alexandre, Proceeding of the National Academy of Sciences of the USA, 105(10): 3700-3704 (11th March 2008) - determination that moelcular asymmetry (chiral chemistry) occurs naturally, courtesy of the existence of chiral molecules in a meteorite.

Molecular Dynamics Simulation Of The Formation, Structure, And Dynamics Of Small Phospholipid Vesicles by Siewert J. Marrink and Alan E. Mark, Journal of the American Chemical Society, 125: 15233-15242 (2003) - computer modelling of lipd vesicle formation, and comparison of the model with actual experimental results obtained from real lipid vesicle formation, to ensure the robustness of the model.

Molecular Messages by Jack W. Szostak, Nature, 423: 689 (12th June 2003) - review paper covering the question of defining the information content of organic molecules in a rigorous manner.

Montmorillonite Catalysis Of 30-50 Mer Oligonucleotides: Laboratory Demonstration Of Potential Steps In The Origin Of The RNA World by James P. Ferris, Origins of Life and Evolution of the biosphere, 32: 311-332 (2002) - another paper demosntrating the validity of montmorillonite catalysis for prebiotic RNA formation, demonstrating that RNA molecules up to 50 bases long can be formed via this means.

Montmorillonite Catalysis Of RNA Oligomer Formation In Aqueous Solution: A Model For The Prebiotic Formation Of RNA by James P. Ferris and Gözen Ertem, Journal of the American Chemical Society, 115: 12270-12275 (1993) - another paper on montmorillonite catalysis!

Montmorillonite-Catalysed Formation Of RNA Oligomers: The Possible Role Of Catalysis In The Origins Of Life by James P. Ferris, Philosophical Transactions of the Royal Society Part B, 361: 1777-1786 (7th September 2006) - yet another paper demonstrating the validity of montmorillonite catalysis for RNA formation (!)

Nucelotide Synthetase Ribozymes May Have Emerged First In The RNA World by Wentao Ma, Chunwu Yu, Wentao Zhang and Jiming Hu, The RNA Journal, 13: 2012-2019, 18th September 2007 - paper covering a computer simulation aimed at determining the viability of the self-replicating ribozyme hypothesis.

Nutrient Uptake By Protocells: A Liposome Model System by Pierre-Alain Monnard and David W. Deamer, Origins of Life and Evolution of the Biosphere, 31: 147-155 (2001) - laboratory demonstration of the ability of model protocells to acquire nutrients to fuel their chemical processes.

Organic Compounds In Carbonaceous Meteorites by Mark A. Sephton, Natural Products Reports (Royal Society of Chemistry), 19: 292-311 (2002) - a full assay of organic molecules found in various meteorites, including amino acids, sugar-related compounds, pyrimidines and purines (the latter two essential for RNA and DNA formation).

Peptide Formation Mediated By Hydrogen Cyanide Tetramer: A Possible Prebiotic Process by Sherwood Chang, José Flores and Cyril Ponnamperuma, Proceedings of the National Academy of Sciences of the USA, 64(3) 1011-1015 (1st November 1969) - demonstration in the laboratory of another possible peptide formation process that could have taken place on a prebiotic Earth.

Peptide Nucleic Acids Rather Than RNA May Have Been The First Genetic Molecule by Kevin E. Nelson, Matthew Levy and Stanley L. Miller, Proc. Natl, Acad. Sci. USA., 97(8): 3868-3871, 11th April 2000 - demonstration that electric discharge synthesis produces the precursor molecules required to form peptide nucleic acids, which may have been precursors to RNA.

Peptides By Activation Of Amino Acids With CO On (Ni,Fe)S Surfaces: Implications For The Origin Of Life by Claudia Huber and Günter Wächtershäuser, Science, 281: 670-672 (31st July 1998) - demonstration of another peptide formation mechanism relevant to hydrothermal vents, involving vlcanic carbon monoxide and hydrogen sulphide, in combination with nickel and iron compounds in clays.

Phenotypic Diversity And Chaos In A Minimal Cell Model by Andreea Munteanu and Ricard V. Solé, Journal of Theoretical Biology, 240: 434-442 (2006) - computer simulation work aimed at demonstrating the ability of a protocell model to exhibit emergent complexity.

Prebiotic Amino Acids As Asymmetric Catalysts by Sandra Pizzarello and Arthur L. Weber, Science, 303: 1151 (20 February 2004) - empirical demonstration in the laboratory that amino acids can act as asymmetric (chiral) catalysts.

Prebiotic Chemistry And The Origin Of The RNA World by Leslie E. Orgel, Critical Reviews in Biochemistry and Molecular Biology, 39: 99-123 (2004) - review paper covering relevant research into the RNA world hypothesis.

Prebiotic Materials From On And Off The Early Earth by Max Bernstein, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006) - determination of the viability of the 'chemical seeding from space' hypothesis for a range of organic molecules.

Prebiotic Synthesis On Minerals: Bridging The Prebiotic And RNA Worlds by James P. Ferris, Biological Bulletin, 196: 311-314 (June 1999) - review paper covering relevant empirical findings supporting the RNA world hypothesis.

Preparation Of Large Monodisperse Vesicles by Ting F. Zhu and Jack W. Szostak, PLoS One, 4(4): e5009 (April 2009) - demonstration of a mechanism for producing lipid vesicles of a range of sizes, which may have prebiotic relevance.

Racemic Amino Acids From The Ultraviolet Photolysis Of Interstellar Ice Analogues by Max P. Bernstein, Jason P. Dworkin, Scott A. Sandford, George W. Copoper and Louis J. Allamandola, Nature, 416: 401-403 - empirical demonstration that amino acids can be synthesised in the conditions extant in deep space, by ultraviolet photolysis of relevant precursor molecules within analogues of cometary ices, by replicating the relevant conditions in the laboratory.

Reconstructing The Emergence Of Cellular Life Through The Synthesis Of Model Protocells by Sheref S. Mansy and Jack W. Szostak, [/i]Cold Spring Harbor Symposia on Quantitative Biology[/i], Volume LXXIV (4th September 2009) - summary of current (as of 2009) experimental progress toward building working model protocells in the laboratory.

Replicating Vesicles As Models Of Primitive Cell Growth And Division by Martin M. Hanczyc and Jack W. Szostak, Current Opinion In Chemical Biology, 8: 660-664 (22nd October 2004) - another paper demonstrating that lipid vesicles can perform a range of mechanical and chemical functions relevant to protocell formation and activity.

Ribosomal Synthesis Of Unnatural Peptides by Kristopher Josephson, Matthew C. T. Hartman and Jack W. Szostak, Journal of the American Chemical Society, 127: 11727-11735 (2005) - empirical demonstration of the reassignments of codons in the genetic code of Escherichia coli to code for amino acids not found in nature, thus demonstrating that the genetic code is not a fixed entity.

Ribozymes: Building The RNA World by Gerald F. Joyce, Current Biology, 6(8): 965-967, 1996 - first steps in the synthesis of RNA ribozymes making possible later research.

RNA Catalysis In Model Protocell Vesicles by Irene A Chen, Kourosh Salehi-Ashtiani and Jack W Szostak, Journal of the American Chemical Society, 127: 13213-13219 (2005) - a documented early empirical attempt to construct model protocells in the laboratory.

RNA-Catalysed Nucleotide Synthesis by Peter J. Unrau and David P. Bartel, Nature, 395: 260-263 (17th September 1998) - development of an RNA molecule that catalyses synthesis of nucleotides for more RNA production, this RNA molecule being produced by in vitro evolution.

RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension by Wendy K. Johnston, Peter J. Unrau, Michael S. Lawrence, Margaret E. Glasner and David P. Bartel, Science, 292: 1319-1325, 18th May 2001 - one of the first papers documenting the production of an RNA ribozyme, and demonstration that its replication was high-fidelity, yet imperfect.

RNA-Directed Amino Acid Homochirality by J. Martyn Bailey, FASEB Journal (Federation of American Societies for Experimental Biology), 12: 503-507 (1998) - demonstration of the ability of RNA molecules to perform chiral selection of amino acids.

RNA Evolution And The Origin Of Life by Gerald F. Joyce, Nature, 338: 217-224 (16th March 1989) - review paper covering RNA world hypotheses and extant research.

Selection And Evolution Of Enzymes From A Partially Randomised Non-Catalytic Scaffold by Burckhard Seelig and Jack W. Szostak, Nature, 448: 828-833 (16th August 2007) - demonstration that relevant enyzmatic activity can arise de novo through in vitro evolution of RNA ligases.

Self Replicating Systems by Volker Patzke and Günter von Kiedrowski, ARKIVOC 5: 293-310, 2007 - review paper covering self-replicating chemical systems in general.

Self-Assembling Amphiphilic Molecules Synthesis In Simulated Interstellar/Precometary Ices by Jason P. Dworkin, David W. Deamer, Scott A. Sandford and Louis J. Allamandola, Proceedings of the National Academy of Sciences of the USA, 98(3): 815-819 (30th January 2001) - laboratory demonstration that a range of self-assembling molecules can be synthesised in deep space conditions (cometary ices).

Self-Assembly Of Surfactant-Like Peptides With Variable Glycine Tails To Form Nanotubes And Nanovesicles by Steve Santoso, Wonmuk Hwang, Hyman Hartman and Shuguang Zhang, Nano Letters, 2(7): 687-691 (2002) - laboratory demonstration that certain peptide molecules also self-assemble, this time into tubes and vesicles.

Self-Assembly Processes In The Prebiotic Environment by David Deamer, Sara Singaram, Sudha Rajamani, Vladimir Kompanichenko and Stephen Guggenheim, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006) - demonstration of the sort of chemical processes that can take place on clay substrates resulting in self-assembling molecules.

Self-Organising Biochemical Cycles by Leslie E. Orgel, Proceedings of the National Academy of Sciences of the USA, 97(23): 12503-12507 (7th November 2000) - paper reviewing the plausibility of self-organising chemical processes with or without genetic polymers.

Self-Sustained Replication Of An RNA Enzyme by Tracey A. Lincoln and Gerald F. Joyce, ScienceExpress, DOI: 10.1126/science.1167856 (8th January 2009) - another paper on self-replicating RNA enzymes, this time pairs of cross-replicating enzymes.

Semipermeable Lipid Bilayers Exhibit Diastereoselectivity Favouring Ribose by M. G. Sacerdote and Jack W. Szostak, Proceedings of the National Academy of Sciences of the USA, 102(17): 6004-6008 (26th April 2005) - demonstration that lipid bilayers act as chemical filters, exercising selectivity in the molecules transmitted across the boundary.

Sequence- And Regio-Selectivity In The Montmorillonite-Catalysed Synthesis Of RNA by Gözen Ertem and James P. Ferris, Origins of Life and Evolution of the Biosphere, 30: 411-422 (2000) - yet another paper on RNA synthesis by catalysis on montmorillonite!

Shrink-Wrap Vescicles by Shelley M. Fukijawa, Irene A. Chen and Jack W. Szostak, Langmuir: The ACS Journal of Surfaces and Colloids, 21(26): 12124-12129 (20th December 2005) [Note: published online 10th November 2005] - demonstration that lipid vesicles can undergo major size changes and still retain their contents.

Simulation Of The Spontaneous Aggregation Of Phospholipids Into Bilayers by Siewert J. Marrink, Eric Lindahl, Olle Edholm and Alan E. Mark, Journal of the American Chemical Society, 123: 8638-8639 (2001) - generation of a computer model simulating the formation of lipid bilayers, and verification of the robustness of the model, by comparison of its predictions with experimental results from real bilayer formation.

Single-Molecule Imaging Of An In Vitro Evolved RNA Aptamer Reveals Homogeneous Ligand Binding Kinetics by Mark P. Elenko, jack W. Szostak and Antoine M. van Oijen, Journal of the American Chemical Society, 131: 9866-9867 (2009) - production of an RNA atpamer by in vitro evolution, followed by direct examination of its reaction kinetics at the atomic level using fluorescence labelling.

Structural Insights Into The Evolution Of A Non-Biological Protein: Importance Of Surface Residues In Protein Fold Optimisation by Matthew D. Smith, Matthew A. Rosenow, Meitian Wang, James P. Allen, Jack W Szostak and John C. Chaput, PLoS One, 2(5): e467. DOI :10.1371/journal.pone.0000467 - demonstration that protein folding is optimised by surface residues, thus facilitiating a wide range of evolutionary pathways for new protein formation.

Aggie, at thsi point, I hope you won't mind me skimping on the commentary for the rest of these papers, as I need a break ...

Synchronisation Phenomena In Internal Reaction Models Of Protocells by Roberto Serra, Timoteo Carletti, Alessandro Filisetti and Irene Poli, Artificial life, 13: 123-128 (2007)

Synchronisation Phenomena In Protocell Models by Alessandro Filisetti, Roberto Serra, Timoteo Carletti, Irene Poli and Marco Villani, Biophysical Reviews and Letters, 3(1-2): 325-342 (2008)

Synthesis Of 35-40 Mers Of RNA Oligomers From Unblocked Monomers. A Simple Approach To The RNA World by Wenhua Huang and James P. Ferris, Chemical Communications of the Royal Society of Chemistry, 1458-1459 (2003)

Synthesis Of Activated Pyrimidine Ribonucleotides In Prebiotically Plausible Conditions by Matthew W. Powner, Béatrice Gerland and John D. Sutherland, [i]Nature, 459:239-242 (14th May 2009)

Synthesis Of Long Prebiotic Oligomers On Mineral Surfaces by James P. Ferris, Aubrey R. Hill Jr, Rihe Liu and Leslie E. Orgel, Nature, 381: 59-61 (2nd May 1996)

Synthesising Life by Jack W. Szostak, David P. Bartel and P. Luigi Luisi, Nature, 409: 387-390 (18th January 2001)

Synthetic Protocell Biology: From Reproduction To Computation by Ricard V. Solé, Andreea Munteanu, Carlos Rodriguez-Caso and Javier Macia, Philosophical Transactions of the Royal Society Part B, 362: 1727-1739 (October 2007)

Systems Chemistry On Early Earth by Jack W. Szostak, Nature, 459: 171 (14th May 2009)

Template-Directed Synthesis Of A Genetic Polymer In A Model Protocell by Sheref S. Mansy, Jason P. Schrum, Mathangi Krisnamurthy, Sylvia Tobé, Douglas A. Treco and Jack W. Szostak, Nature, 454: 122-125 (4th June 2008)

The Antiquity Of RNA-Based Evolution by Gerald F. Joyce, Nature, 418: 214-221, 11th July 2002

The Case For An Ancestral Genetic System Involving Simple Analogues Of The Nucleotides by Gerald F. Joyce, Alan W. Schwartz, Stanley L. Miller and Leslie E. Orgel, Proceedings of the National Academy of Sciences of the USA, 84: 4398-4402 (July 1987)

The Descent of Polymerisation by Matthew Levy and Andrew D. Ellington, Nature Structural Biology, 8(7): 580-582, July 2001

The Emergence Of Competition Between Model Protocells by Irene A Chen, Richard W. Roberts and Jack W. Szostak, Science, 305:1474-1476 (3rd September 2004)

The Generality Of DNA-Templated Synthesis As A Basis For Evolving Non-Natural Small Molecules by Zev J. Gartner and David R. Liu, Journal of the American Chemical Society, 123: 6961-6963 (2001)

The Lifetimes Of Nitriles (CN) And Acids (COOH) During Ultraviolet Photolysis And Their Survival In Space by Max P. Bernstein, Samantha F. M. Ashbourne, Scott A. Sandford and Louis J. Allamandola, The Astrophysical Journal, 601: 3650270 (20th January 2004)

The Lipid World by Daniel Segré, Dafna Ben-Eli, David W. Deamer and Doron Lancet, Origins of Life And Evolution of the Biosphere, 31: 119-145, 2001

The Miller Volcanic Spark Discharge Experiment by Adam P. Johnson, H. James Cleaves., Jason D. Dworkin, Daniel P. Glavin, Antonio Lazcano and Jeffrey L. Bada, Science, 322: 404 (17th October 2008)

The Origin And Early Evolution Of Life: Prebiotic Chemistry, The Pre-RNA World, And Time by Antonio Laczano and Stanley R. Miller, Cell, 85: 793-798 (14th June 1996)

The Origin And Emergence Of Life Under Impact Bombardment by Charles S. Cockell, Philosophical Transactions of the Royal Society Part B, 361: 1845-1856 (7th September 2006)

The Origin Of Replicators And Reproducers by Eörs Szathmáry, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)

The Prebiotic Molecules Observed In The Interstellar Gas by P. Thaddeus, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (7th September 2006)

The Roads To And From The RNA World by Jason P. Dworkin, Antonio Lazcano and Stanley L. Miller, Journal of Theoretical Biology, 222: 127-134 (2003)

The Stability Of The RNA Bases: Implications For The Origins Of Life by Matthew Levy and Stanley R. Miller, Proceedings of the National Academy of Sciences of the USA, 95: 7933-7938 (July 1998)

Thermostability Of Model Protocell Membranes by Sheref S. Mansy and Jack W. Szostak, Proceedings of the National Academy of Sciences of the USA, 105(36): 13351-13355 (9th September 2008)

Toward Synthesis Of A Minimal Cell by Anthony C. Forster and George M. Church, Molecular Systems Biology (2006) doi:10.1038/msb4100090

Transcription And Translation In An RNA World by William R. Taylor, Philosophical Transactions of the Royal Society Part B, 361: 1689-1702 (11th September 2006)

Two Step Potentially Prebiotic Synthesis Of α-D-Cystidine-5'-Phosphate From D-Glyceraldehyde-3-Phosphate by Carole Anastasi, Michael A. Crowe and John D. Sutherland, Journal of the American Chemical Society (Communications), 129: 24-24 (2007)

I think that should be enough to be going on with ... I make that 116 scientific papers on abiogenesis. Oh, and if you ask nicely, I can arrange for them all to be mailed to you.

E..gadz Cali, why did you put the list in title order instead of Author-date like normal folks

otherwise, a nice list....

I think I am missing some of those, but will have to check...

Darwinsbulldog wrote:E..gadz Cali, why did you put the list in title order instead of Author-date like normal folks

otherwise, a nice list....

I think I am missing some of those, but will have to check...

All those papers, and not a one of them can claim to have observed the origin of a self-replicating chemical system, that can evolve into a more complex organism.

If someone likes to get a little into the chemistry, this paper is extremely educational, interesting (and free) : http://cshperspectives.cshlp.org/content/2/7/a003467.full.pdf+html

Planetary Organic Chemistry and the Origins of Biomolecules, Steven A. Benner, Hyo-Joong Kim, Myung-Jung Kim, and Alonso Ricardo, Cold Spring Harb Perspect Biol, doi:10.1101/cshperspect.a003467

Abstract
Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as “tar” or “tholin.” These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive “dead ends” under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a “carbohydrate world,” but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.

I think most people who had chemistry at highschool or college level, (who remembers any of it) can read that paper and come out a little smarter It describes many of the challanges in what seems to me an unbiased way, and proposes interesting solutions. If you want to cut straight to the conclusion it's this : We need more research, the potential for finding new chemistry is enormous.

The reaction of carbohydrates under plausibly prebiotic conditions in the presence of these other species has only begun (Weber, 2001). Much more research is needed before a model can capture the entire space of variable contents in a way that suggests what mixtures are productive and what mixtures are nonproductive, for prebiotic synthesis on a complex planet. Ultimately, compatibility issues need to be captured in a table that includes both organic and inorganic species, including cations and anions that are incompatiblewith solubility,redoxpotential, and reactivity.

In other words : People who say the problem is unsolvable and we should just give up(like the JW's) are talking shit and should keep their defeatist, vomit-spraying traps shut. We haven't even begun to scratch the surface of possible combinatorial chemistry under abiotic conditions.

The_Metatron wrote:There is another particle I forgot to mention, that is conveniently outside the discussion in this booklet. That is the prion. A protein that can self replicate.

Fuckin' science and shit. Getting in the way of old time religion like that.

Well, actually, that's not really fair. It's just getting in the way of the creationist claims to be found in this Jehovah's Witnesses brochure.

Prions have a different way of self replication compared to what we normally regard as self replicating, however. Prions are misfolded versions of differently folded proteins that can trigger other normal proteins in their vicinity to fold like themselves.