Talk:Abiogenesis/Archive 4

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Appropriateness of "Evolution before genes" cite?

Evolution before genes.

This paper came out in 2012 and has only been cited once (per scholar.google.com). Can anyone comment as to whether this has sufficient weight to be listed in the external links section? Garamond Lethe (talk) 21:51, 4 April 2012 (UTC)

I don't see why not, if I understand you correctly. On a hurried scan of the paper, it seems to be a thoughtful and informed discussion of some pertinent points relevant to the subject. It is not cited in the WP article as an authority in establishing a disputed position, but as suggested reading. As for which disputed points it might be expected to support or dispel, I should have to see examples before commenting, but as things stand I have no problem with its presence at the end of the article. JonRichfield (talk) 06:16, 5 April 2012 (UTC)

Ok, that's fair. Thanks! Garamond Lethe (talk) 12:33, 5 April 2012 (UTC)

It is almost a joke that this piece of nonsense has so quickly found its way into the article whilst Marc Tessera's interesting contributions have met so much hostility. Zarcoen (talk) 14:07, 20 April 2012 (UTC)

I actually do have a problem with inclusion of this article. For the record, I haven't read the article, and see no need to. There are literally scores of articles about abiogenesis. Why on earth would we include an article that has only been cited once?? Granted, an article that came out this year is not likely to be cited more than a few times (given that it takes some time to write and publish subsequent papers.) So, I am not at all indicating that this article is faulty, suspect, etc. (As I said, I haven't read it, as reading it would not modify my point one iota.) I would simply argue that virtually any article that has just been released shouldn't be included for further reading, when other articles which have been thoroughly vetted, discussed, etc (above and beyond the standard peer review process, in the sense that its been cited repeatedly, meaning that its really made an impact on the field.) The only possible exception to this rule would be a highly notable article that really turns the field on its head and garners significant coverage.JoelWhy (talk) 14:17, 20 April 2012 (UTC)

I wouldn't mind replacing this with a better-cited paper that handles pre-cellular evolution. Do you have one in mind? Garamond Lethe (talk) 08:06, 22 April 2012 (UTC)

RGA1980 and Trail's Nature Paper

Hi RGA1980,

I'm a little confused about your inclusion of Trail's Nature paper. First, while Nature is certainly a very good publication, this particular paper only tangentially relates to abiogenesis (and has only been cited once). Second, the Miller-Urey experiments are 60 years old now. It looked like you were treating them as though they were the current scientific consensus. Third, your summary of the paper sounds uses far too much jargon: "incorporation of cerium into zircon crystals", "oxygen fugacities", "fayalite–magnetite–quartz buffer", etc. Finally, suggesting that " If this research is correct then the "Soup" Theory would be undermined and alternatives such as Extraterrestrial origins would be necessary for Abiogenesis to have occured." appears to be WP:SYN. Is that the opinion of Trail et al. or your opinion?

Following up: I now have the Trail paper in front of me. The following is the sum of their comments on abiogenesis:

If a highly reduced atmosphere is required for the origin of life, then it may have occurred exceptionally early on our planet. However, pre-4,400-Myr outgassing of H2 coupled with slow escape may have resulted in an atmosphere out of equilibrium with Earth’s interior. Alternatively, a ‘late veneer’ may have served as a source of pre-biotic molecules.

There's nothing about Miller-Urey and nothing about extraterrestrial origins.

I'd like to discuss this before you put your edits back up. Thanks! Garamond Lethe (talk) 07:29, 25 April 2012 (UTC)

Separating facts from faith.

I found it a little odd to read the following statement, "For views on the origins of life outside the natural sciences, see Creation myth" Yet it seems much of what I read in this article is also akin to a naturalistic creation myth, in that much is believed yet not demonstrated and taken on faith. I also think that there is some clever writing, yet the article should be a little more clear for the uninitiated, such the following statement which seems a little ambiguous "Abiogenesis (pronounced /ˌeɪbaɪ.ɵˈdʒɛnɨsɪs/ ay-by-oh-jen-ə-siss) or biopoiesis is the study of how biological life arises from inorganic matter through natural processes. In particular, the term usually refers to the processes by which life on Earth is thought to have arisen" I agree with the second sentence but the first is unnecessary and shows a certain bias. I would also like to see at least a significant part of the article speak of the pre biochemical logistical nightmares involved in the process of creating a living cell through human intel much less through random or unguided forces. — Preceding unsigned comment added by BENNY BALLEJO (talk • contribs) 23:12, 6 February 2012 (UTC)

50 years of research and no artificial life, therefore god did it. And just where is the research on that then? Have we recreated god creating life in the lab; if that was more plausible it would be easier to do than messing about with random processes. SkyMachine ^{( )} 06:30, 7 February 2012 (UTC)

Are you sure we shouldn't beat that dead horse just a little harder? 209.6.28.116 (talk) 20:28, 20 February 2012 (UTC)

Hi Benny and all, you make the error that you propose random or unguided forces are the cause of abiogenesis. This is not so. The forces are tightly constrained and guided by the laws of physics and chemistry. For example the nature of hydrophobic and hydrophilic groups determines the way in which chemical adherence or binding occurs. Spontaneous self-organising structures are found in certain cases but not in others. Chemical and energetic gradients - from hot zones to cold zones create spaces in which certain things can happen at one time but not in others. It is not just chance. Furthermore, differential rates for chemical reactions lead to the appearance of certain species of chemicals but not of others. Abiogenesis requires searching amongst this complexity to trace likely biochemical pathways. Hope this helps, John D. Croft (talk) 17:09, 9 May 2012 (UTC)

Why no mention to Spiegelman's work in the RNA world

Sol Spiegelman's research on RNA evolution was crucial to the establishment of the theory of the RNA world. Why does he get no mention? Also there is no mention either of Gilbert (1986) and Joyce (1991) who coined the term "RNA world". John D. Croft (talk) 19:25, 10 May 2012 (UTC)

That is also perhaps more appropriate for the Rna world article. Garamond Lethe(talk) 22:59, 10 May 2012 (UTC)

Evolutionary biology edit

In response to the change and request, I am not much fussed about the edit, but I do have serious philosophical reservations about the distinction between the emergence of life and the role of Darwinian evolution once independent organisms, cellular or otherwise, with Mendelian reproduction had become established. The entire basis of the emergence of precursors to unambiguous life forms is strongly heuristically selective (though not specifically directive, of course). Stochastic selection would not have worked; it is a popularly misunderstood misconception and irrelevance that creationists keep getting hung up on. Does this affect your views on the heading etc? Cheers JonRichfield (talk) 17:33, 3 March 2012 (UTC)

I am just concerned that laymen will see the template and their misconception that evolution explains the origin of life will be strengthened. While abiogenesis and evolution are closely tied, it may be interpreted differently. Evolution by natural selection is a process distinct from abiogenesis which acts on existing organisms, it doesn't create them. Maybe its best if we just leave out this template, it shouldn't hurt the article. Cadiomals (talk) 18:55, 3 March 2012 (UTC)

Regarding the origins of evolution, the latest theories of abiogenesis all show that evolution was in evidence long before the appearance of the Last Universal Common Ancestor. The time in which a form of Darwinian evolution appears in the process is thus essential. If it appears early on, for example, within the chanmbers of an alkaline thermal vent, for instance, then it is relevant to abiogenesis. Regards John D. Croft (talk) 17:15, 9 May 2012 (UTC)

JDC, the latest theories do not show that evolution was in evidence; that is not their job. They (at most) propose testable hypotheses in a conceptual framework consistent with evolution. Furthermore, be a bit more careful in characterising evolution and "Darwinism". It is not so much that you are wrong to speak of "pre-life" evolution in any form (I am referring to concepts here, not anyone's wording, and I am friendly to the concept myself) but in such a borderline field it is important to keep concepts clear, avoiding the likes of "theories showing" things for example. In Darwinian "natural selection", we have the concept of fairly well-defined populations of discrete organisms. Bears bear bear cubs etc. In the pre-organismal biochemical ecology, natural selection by definition had no organismal populations to select from. The position was too vague for us to be able to say much meaningful about it. It would have been about like trying to define meme evolution in our day. JonRichfield (talk) 10:16, 11 May 2012 (UTC)

Nonsense & nonsensical refs

I have just removed the section on viruses in abiogenesis. It was extremely vague in its content and referred non-specifically to some of the worst nonsense I have seen since von Daeniken Someone or other PhD if you like! That should be pretty conclusive! Furthermore, would some concerned people inspect the article history? Someone seems to be using tactics to hamper inspection of the authorship and creation trails by inserting edits by the dozen. I have had little to do with the article so far, but if this sort of thing isn't cleaned up pretty chopchop, we all will have egg on face. Gotta go. Back later. JonRichfield (talk) 16:02, 9 May 2012 (UTC)

John, I don't know if you are aware, but there is a lot of work being done on Viruses and the RNA world at the moment. For example check out "Origin and Evolution of Viruses" edited by Esteban Domingo, Robert G. Webster, and John F. Holland (Academic Press), has a good introductory article on the evolution of replicons, their connection to Viruses and how viruses give us a window into the RNA world. This was 1999. Since then there has been much work also done within the Cosmology Journal (August 2010) Vol 10, on Viral systems and their role in HGT (Horizontal Gene Transfer) and in the New Scientist on the 21st April this year. The article states "At some point, most of life began storing genetic information in DNA; all the cellular life we know today, and most modern viruses as well, are DNA-based. The switch created a problem familiar to anyone who has upgraded their laptop to a new operating system: how do you port over your old software to the new platform? The genes of RNA life contained solutions to many of the challenges of existence, but because RNA cannot combine with DNA there was no obvious way for the new DNA life to use this information.... Ken Steadman of Portland State University, Oregon... found ...a gene, made of DNA, that looked like the gene for a protein coat from an RNA virus... The find proves that modern viruses can combine information coded in the two normally separate genetic molecules. And it lends support to the idea that it was viruses that performed the upgrade from RNA and effectively gave rise to DNA.... "These are two lineages that we never think of as overlapping," says virologist Luis Villarreal of the University of California at Irvine. The lack of respect for species boundaries echoes what many biologists suspect the original virus world must have been like around the birth of DNA 4 billion years ago, he says.

The parallel with the ancient virus world is not perfect, since the modern viruses' life cycles are very different from those of their ancestors. The primordial virus world was a non-cellular stage in the evolution of life, the details of which are very obscure, says Eugene Koonin, an evolutionary genomicist at the National Center for Biotechnology Information in Bethesda, Maryland." On these grounds I would strongly argue that the notes on Viruses be reinserted. Regards John D. Croft (talk) 18:34, 10 May 2012 (UTC)

That's interesting, but I don't see how it relates to abiogenesis. Garamond Lethe(talk) 18:53, 10 May 2012 (UTC)

One of the problems with the RNA world thesis is that until now there was no way that RNA genetic material could be "uploaded" from RNA to DNA. This was a major weakness of the RNA world hypothesis. This difficulty has been overcome by Steadman's (and the other works cited) discoveries. Uploading from RNA to DNA was essential to abiogenesis as LUCA used a DNA inheritance system, not an RNA one. Hope this helps. John D. Croft (talk) 19:11, 10 May 2012 (UTC)

That sounds like it would be more appropriate for an article on Rna world. Garamond Lethe(talk) 23:28, 10 May 2012 (UTC)

JDC, as a personal favour to my sense of nausea, please avoid refs to anything from Cosmology Journal. If it ever published anything substantial, it did so too discretely for me to detect it. It isn't even fringe stuff. I am not sure that Velikovsky would have swallowed it. I suppose he might. And Fort maybe...? If you took CJ reading material for your sources, you need to do some serious homework. Thanks of course for your information on RNA world and viruses, but a word to the wise: "advances" aren't everything. There is a lot of very loose talk about a lot of very broad assumptions based on some very vague thinking, but making some very bold, but non-explanatory assertions. I have just recently seen in a generally sound popular science magazine, a solemn note on a major advanc in this field; a mechanism by which the RNA-DNA leap could have been made <gasp!> An RNA virus and a DNA virus might have infected the same cell, and their offspring being generated by the nucleic acid machinery of the host, might have landed up in the same offspring! <MEGO!!!> In short, this is a tricky field and there probably are more fringe freaks peddling their wares and fringe suckers swallowing the stuff, than serious workers in related fields. Here is a genuinely helpful and readable ref if you like, a bit old, but conceptually sound: Smith, John Maynard and Szathmary, Eors: The Major Transitions in Evolution. 1997 isbn 9780198502944. Detailed abiotic nucleic acid biochem you need not take too seriously; it is too speculative and has been spouted too assertively (oxidising and reducing atmospheres etc) for us to accept unconditionally every new idea or observation as final. JonRichfield (talk) 10:45, 11 May 2012 (UTC)

"Viral World" problems

John, you need to slow down here.

You've put up four references in your "viral world" section.

1. Ken Stedman isn't a reference; where's the record of the talk that I can consult? And if there was an unpublished workshop report from 2012 is going to pretty much be guaranteed to have WP:Undue problems.
2. Rhawn Joseph is in a fringe publication that's not appropriate to cite in a scientific article. It's also only been cited twice and has to do with the origin of eukaryotes, not the origin of life.
3. Yutin et al. is a perfectly good paper that supports the idea of complex ancestral viruses. I don't see the relevance to an RNA World hypothesis.
4. Holmes is on-topic (but you got the name of the article wrong: it's "First glimpse at the viral birth of DNA"). This is from not quite a month ago. Why is this noteworthy enough for an encyclopedia article?

Please revert this. Garamond Lethe(talk) 23:46, 10 May 2012 (UTC)

Following up: I counted six "Journal of Cosmology" citations in the article right now and I expect they will all need to come out (as well as the text that depends on them). I didn't check to see who added them. If you want to take them out when you're doing your cleanup pass, that would be great. If not, I can take care of it. Garamond Lethe(talk) 00:09, 11 May 2012 (UTC)

That's done. Garamond Lethe(talk) 05:01, 11 May 2012 (UTC)

User:JonRichfield User:John D. Croft edits

Hi John,

Thanks for your several recent edits. I have a few concerns. First, I'm unfamiliar with the "three fundamental principles", and the Science article you cited doesn't mention any such thing. Did you realized that article was from 1966? Perhaps you put in the wrong cite by accident?

I also think the literature is a little more circumspect when it comes to recent experimental results, but those comments will have to wait until I get a few free moments to string together.

Hi Garamond. Thanks for your concerns about my edits. What happened was I did get the citation slightly screwed up. It comes from E. James Milner-White and Michael J. Russell, leading researchers in Abiogenesis in their Article on "Polyphosphate-Peptide Synergy and the OOrganic Takeover at the Emergence of Life", p.67, of the recent 2011 book "Origins, Abiogenesis and the Search for Life" Edited by Michael J. Russell. Russell and Milner White themselves acknowledged the source of the quote as from Eck and Dayhoff's article. I can change the reference if you think it appropriate. The book itself is published by NASA, JPL and Caltech. Its an excellent source. Hope this helps. Regards John D. Croft (talk) 18:54, 10 May 2012 (UTC)

There are several problems here.

1. "Polyphosphate-Peptide Synergy" doesn't say anything about "three fundamental principles" of abiogenesis. Yes, they do quote Eck and Dayhoff to the effect that "One basic evolutionary principle is that every living organism or structure or function had ancestors very similar to itself, but simpler", but that doesn't make it a fundamental principle of abiogenesis, nor does it provide a reliable source to cover what I assume was your contributions of different environments and consistency with science. If these are your own ideas about fundamental principles then the edit needs to be reverted.
2. Current consensus now is that Eck and Dayhoff were wrong (at least with regard to that single quote). Organisms can me more complex or less complex than their ancestors (gut parasites are far simpler, for example). This might not have been appreciate in 1966, but there have been a lot of genomes sequenced since then and the idea of "complexity" has pretty much been abandoned as not very useful. (Looking at Barton's Evolution textbook from 2007 the topic of "complexity" doesn't even rate an entry in the index.)
3. The Journal of Cosmology publishes fringe work, and at this point publishes only fringe work.

It is interesting that the co-editor of this so called "fring work" on Abiogenesis was Nick Lane, the research biochemist and writer. He holds the first Provost's Venture Research Fellowship in the Department of Genetics, Evolution and Environment at University College London. Lane's latest book, Life Ascending, won the Royal Society Prize for Science Books 2010, and his books have been shortlisted for two other literary prizes, named among the books of the year by The Economist, The Independent, The Times and The Sunday Times, and translated into sixteen languages. He is a regular contributor to Nature and New Scientist. Hardly "fringe". Regards John D. Croft (talk) 19:39, 14 May 2012 (UTC)

Hi John,

You're making a very common mistake: it's the work that is fringe, not the researcher. For example, Linus Pauling did fringe work on Vitamin C and Fred Hoyle did fringe work on abiogenesis. So let's take a look at the work.

Lane has two publications in JoC:

#"Chance or necessity? Bioenergetics and the probability of life" (2010), which has been cited four times (once in JoC, once in something called Langmuir that I've never heard of, once in Physics of Life Review and once in a dissertation on Teleological Realism.

#"Intelligent non-design and the origins of life" (2010), which has been cited once, also in the same Physics of Life Review paper.

Contrast that with his "The energetics of genome complexity" paper that he published in Nature the same year. It has 66 citations, starting with Nature Reviews Genetics. That's about as good as it gets for biologists. I would have no problem at all including that paper in a wikipedia article.

So, you're correct in thinking that Nick Lane has done good work. That doesn't mean all of his work is good. We may need to agree to disagree whether or not his bad work is fringe or not, but if the larger community has effectively ignored it I don't see what makes it notable enough to be included in an encyclopedia.

Garamond Lethe(talk) 22:53, 14 May 2012 (UTC)

If you think you've found an article than is an exception you could help demonstrate this by showing mainstream publications that cite it. Absent that, the presumption of people who work is this area is going to be that any paper published there was bad enough that it couldn't be published anywhere else.

Dear Garamond, you wrote that the Journal of Cosmology publishes only Fringe work.

I find that claim unsubstanciated. It is peer reviewed, and it was a special issue on the topic of Abiogenesis. The guest Editor of the specific issue on Abiogenesis was Michael Russell, Ph.D., a researcher on Abiogenesis, Life's Origins at NASA, Planetary Science & Life Detection Section, Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA. His research is central to the topic of modern understandings of Abiogenesis. Russells publications on Abiogenesis include

As to peer review, Creation Ministries International puts out a journal called Journal of Creation that's also peer reviewed. It takes more than peer review to be mainstream.

Here again, you're arguing for the person and not the work. Russell's 2008 article "Hydrothermal vents and the origin of life" in Nature Reviews Microbiology has been cited 116 times and should be perfectly acceptable for use as an encyclopedia reference. His "Why Does Life Start, What Does It Do, Where Will It Be, And How Might We Find It?" in JoC from 2010 has been cited 25 times, which might be considered substantial until you start digging and realize that 15 of those citations are also in JoC (and two others are in arXiv.org, which isn't peer-reviewed).

So if you want a particular article referenced, make an argument for the article, not the author. There may exist an article somewhere in JoC that has been cited heavily in mainstream publications. If you can find that article then I would (after reviewing it closely) probably consider it appropriate for a wikipedia reference.

Finally, I think it's great that you're reading the scientific literature. JoC has figured out that making its articles freely available will mean more people will read them. Science and Nature haven't figured this out yet, and so it's completely understandable why you would end up reading stuff on the fringe. There is good, free stuff out there like PLoS. But if you find a reference that you'd like to read and that is paywalled, drop me a note on my talk page and I'll see if I can track down a copy for you. The lab where I work doesn't have the coverage of a good research university but I can usually find most of the recent stuff without any problem.

Keep reading!

Best,

Garamond Lethe(talk) 22:53, 14 May 2012 (UTC)

1. Russell, M.J. (editor) (2011). Origins, Abiogenesis and the Search for Life. Cosmology Science Publishers, Cambridge, MA, pp. 487.
2. Russell, M.J. (2011). The origin of life. In Encyclopaedia of Geobiology, Reitner, J and Thiel, V. Singer, Dordrecht, The Netherlands, 701-716.
3. Mielke, R.E., Russell, M.J., Wilson, P.R., McGlynn, S., Coleman, M., Kidd, R., and Kanik, I. (2010). Design, Fabrication and Test of a Hydrothermal Reactor for Origin-Of-Life Experiments, Astrobiology, 10, 799-810.
4. Russell, M.J., Hall, A.J. and Martin, W. (2010). Serpentinization and its contribution to the energy for the emergence of life. Geobiology, 8, 355-371.
5. Milner-White, E.J. and Russell, M.J. (2010). Polyphosphate-Peptide Synergy and the Organic Takeover at the Emergence of Life. Journal of Cosmology, 10, 3217-3229
6. Nitschke, W. and Russell, M.J. (2010). Just Like the Universe the Emergence of Life had High Enthalpy and Low Entropy Beginnings. Journal of Cosmology, 10, 3200-3216.<./li>
7. Yung, Y.L., Russell M.J., Parkinson, C.D. (2010). The search for life on Mars. Journal of Cosmology 5, 1121-1130.
8. Russell, M.J., Kanik, I. (2010). Why Does Life Start, What Does It Do, Where Will It Be, And How Might We Find It? Journal of Cosmology, 5, 1008-1039.
9. Russell, M.J. and Hall, A.J. 2009, A hydrothermal source of energy and materials at the origin of life. In "Chemical Evolution II: From Origins of Life to Modern Society". American Chemical Society, pp. 45-62.
10. Nitschke, W. and Russell, M.J. 2009 Hydrothermal focusing of chemical and chemiosmotic energy, supported by delivery of catalytic Fe, Ni, Mo/W, Co, S and Se, forced life to emerge. Journal of Molecular Evolution, 69, 481-96.
11. Ducluzeau, A-L, van Lis R., Duval S., Schoepp-Cothenet B., Russell, M.J., Nitschke W. 2009, Was nitric oxide the first strongly oxidizing terminal electron sink. Trends in Biochemical Sciences 34, 9-15.
12. Martin, W., Baross, J., Kelley, D., Russell M.J. 2008, Hydrothermal vents and the origin of life. Nature Reviews, Microbiology 6, 806-814.
13. Russell, M.J. 2008, On the emergence and early evolution of life. In Life strategies of microorganisms in the environment and in host organisms. Nova Acta Leopoldina, 96, 45-52.
14. Russell, M.J., Allen, J.F., Milner-White, E.J. 2008, Inorganic complexes enabled the onset of life and oxygenic photosynthesis. In Energy from the Sun: 14th International Congress on Photosynthesis, J.F. Allen, E.Gantt, J.H. Golbeck, B. Osmond (editors). Springer. 1193-1198.
15. Milner-White, E.J., Russell, M.J. 2008, Predicting peptide and protein conformations in early evolution. Biology Direct 3, 3: doi:10.1186/1745-6150-3-3.
16. Russell, M.J. 2007, The alkaline solution to the emergence of life: Energy, entropy and early evolution. Acta Biotheoretica, 55, 133-179, Erratum at: DOI 10.1007/s10441-007-9018-5.
17. Martin, W., Russell M.J. 2007, On the origin of biochemistry at an alkaline hydrothermal vent. Philosophical Transactions, Royal Society of London (Ser.B) 362, 1887-1925.
18. Baaske, P., Weinert, F., Duhr, S., Lemke, K., Russell, M.J. & Braun, D. 2007, Extreme accumulation of nucleotides in simulated hydrothermal pore systems. Proceedings of the National Academy of Science, USA, 104, 9346-9351.

That you feel fit to remove him and other the leading researchers on the latest research on the topic of Abiogenesis, greatly weakens the article, I feel. Regards John D. Croft (talk) 19:34, 14 May 2012 (UTC)

Based on the above I don't think those "three fundamental principles" belong in a wikipedia article, and I'd like you to revert those edits.

Garamond Lethe(talk) 22:58, 10 May 2012 (UTC)

Thanks! Garamond Lethe(talk) 20:56, 9 May 2012 (UTC)

Following up: the success of the Miller-Urey experiments was in producing amino acids, which aren't quite "all the chemical components of life" and are certainly only a tiny subset of organic chemistry. Why cite a web page for this when you can cite the original literature?

Yes, you are probably right. What I was trying to find was an easy reference to the recent reopening of Miller's flasks and with more modern techniques, the finding of many more biologically important molecules than the original researchers found (based upon a number of new technological breakthroughs in analysis since Urey and Miller did their work). I'd be happy to have a better reference there should you wish.

The NASA writeup is here. The Science paper is here. Let me know if you'd like a copy of the article.

Would you revert your edits and propose them here in talk one at a time? Thanks! Garamond Lethe(talk) 03:21, 10 May 2012 (UTC) Garamond Lethe(talk) 22:58, 10 May 2012 (UTC)

It has taken me a significant effort to find appropriate places for inserting the edits I have made, as the article was looking decidedly out of date in accordance with more recent research into the field. Trying to increase the readability of the article by linking paragraphs together logically was also a concern. I can give more recent links to the research findings should you wish. Russell's work on alkaline geothermal vents ability to both synthesise methane and the basis of the acetyl-coenzyme A pathway abiogenically, through the proton-motive gradient generated in a carboxylically enriched ocean, has been a major breakthrough in Abiogenesis research. Just check the academic citations index for confirmation. Regards John D. Croft (talk) 18:54, 10 May 2012 (UTC)

I appreciate your efforts trying to make the article more readable, but at the moment there are at least two edits that are factually wrong and that need to be reverted. That could have been prevented if you had vetted them here first. I understand that it's more bother and work up front, but as you don't work in this area it's probably best to do the polishing here rather than in the article proper. Garamond Lethe(talk) 22:58, 10 May 2012 (UTC)

Apologies to Jon Richfield --- I meant John D. Croft. Garamond Lethe(talk) 03:36, 10 May 2012 (UTC)

Abiogenesis is not the study of the LUCA. That's why the word "common" is in there. At this point I think there are enough factual errors that they need to be corrected sooner rather than later. Garamond Lethe(talk) 04:36, 11 May 2012 (UTC)

Proposed Reorganisation of the Article

Hi Folks. I am finding some confusion in the article, and suggest a major reorganisation. Firstly the various theories of a number of researchers get mentioned often twice, sometimes three times. Secondly, it finishes up just producing a list of various theories, without giving any idea of why these theories were proposed, what problems they were intended to remedy, or the interconnections between them. I have been atttempting to insert some of the latest research findings (since 2004) and finding that there is not a logical flow that aids either a historical section, nor a development of the theory. Could we also have an early list of the problems of Abiogenesis and a demonstration of how these problems are being addressed in the latest research. What do others think? Regards John D. Croft (talk) 19:36, 10 May 2012 (UTC)

The article can certainly stand a bit of improvement. Did you have a particular textbook in mind that you were going to use for the history? Perhaps do a mock-up in your sandbox? Garamond Lethe(talk) 23:09, 10 May 2012 (UTC)

Perhaps a good place to start would be to order the various theories a little chronologically. It jumps all over the place. We could use the same content just order them differently. John D. Croft (talk) 20:36, 2 June 2012 (UTC)

That sounds reasonable, although certainly nontrivial in the absence of a textbook that would provide those kind of dates. Still, this is a good excuse to identify the seminal papers associated with each hypothesis, so that's all good. Again, it's probably best to do a mockup in your sandbox as a start and from there we'll be able to tell what needs filling in. As an aside, that arrangement may end up jumping around just as much if alternative hypotheses have been developed contemporaneously, but it's worth taking a look to find out.

One thing you might want to do first is develop a timeline. That would probably be faster and might stand on its own as an independent contribution regardless of the final organization of the article. Garamond Lethe(talk) 23:39, 2 June 2012 (UTC)

Origin of life in hot water

User:Mbreht, a few comments on your edit:

• If you'd like to propose a division specifically for hot-water hypotheses, that needs to be integrated with the rest of the article. As written you edit made it appear that every other hypothesis was did not require hot water, and I don't think that's the case.
• "On the origin of life in the Zinc world". The zinc-world hypothesis has its own section. This citation might best be placed there.
• "Which water is optimal for the origin (generation) of life?" This work is a WP:FRINGE paper that's not appropriate for citing here.
• "Deuterium, heavy water, evolution and life." The only evidence I see of this paper is a cite to it by this paper, which itself is uncited. Does anyone else consider this research to be significant? If not, I think there may be WP:UNDUE issues.
• "First Fossil-Makers in Hot Water." This cite is probably relevant for an article on stromatolites, but those came about long after abiogenesis occurred. I'm not seeing how it's relevant for this artcile.
• "Self-reproduction of supramolecular giant vesicles." Sugawara did not "create a protocell in hot water". From the abstract of that paper: "Our self-reproducing giant vesicle system therefore represents a step forward in the construction of an advanced model protocell."

I appreciate your enthusiasm, but I think you're going to be better served by narrowing your focus quite a bit and working on improving a existing section of the article first. Garamond Lethe(talk) 15:02, 28 June 2012 (UTC)

Dear Garamond Lethe, thank you very much for you comments. I try to improve the quality of poblication. From other side there are a lot of proofs that the life was origin in hot mineral water. Thank you very much for your efforts. — Preceding unsigned comment added by Mbreht (talk • contribs) 09:35, 5 July 2012 (UTC)

Dear Garamond Lethe after your proposals I put me text in Origin of life with more information from the original report of Prof. Sugawara and data of Dr. Ignatov.

Dear Garamond Lethe, in original report Prof. Sugawara explain protocells and this is visible of his research. Some journalists say bubbles, but this is not very correct, because ther is separation of elements of Sugawara cells. For the spectral analysis of water the experiments of Dr. Ignatov show similar spectrum of the part of mineral waters with bicabotates ions, ions etc.

Dear Garamond Lethe, I just published the following text in origin of life. The scientific information is correct and also this is the proof of the topic water in hydrothermal vent. If you have device for infrared spectroscopy is possible to study that. In 2010 with spectral analysis of hot mineral water and cactus juice, Ignat Ignatov demonstrated that hot mineral water has common piques with cactus juice spectrum. After that common piques were observed between the spectrum of cactus juice is sea water spectrum. This is the proof for the type of water for the preservation of living cell. [61]

(Fixed indentation and spacing of above.)

Hi Mbreht. Thanks for dropping by this talk page to help improve your edit. After you've spent a few years interacting with the pseudoscience community you start to pick up general themes. Your description of Ignatov's work is similar to other pseudoscience I've seen. However, there's an easy way around this. Can you find a biology textbook, chemistry textbook or other reliable source that cites Ignatov's work and how it is relevant to abiogenesis? That way you can rely on a disinterested third-party expert, rather than having to take my word for it or evaluate the primary literature yourself. If Ignatov's work is not showing up in textbooks or review articles, then it probably doesn't (yet) belong in an encyclopedia. GaramondLethe 15:29, 5 July 2012 (UTC)

Mbreht, please add your comments beneath what you are replying to, and use ":" to indent. Unfortunately, "scientific correctness" is not sufficient to have work included in wikipedia. If you would like to present reliable sources as to why Ignatov's work is not wp:fringe, please do so. Until that happens I don't hold out a lot of hope that this edit will get in. GaramondLethe 17:58, 5 July 2012 (UTC)

Dear GaramondLethe, thank you very much for your much your answers at the page Talk. Dr. Ignatov estimates that. The measurement of the spectrum of cactus and hot mineral water is real scientific study. The copy right for that is from EUROMEDICA 2010. In Act of copy right there is not level of publications, there are conditions for copy right. Dr. Ignatov will take part in US conference on the Physics, Chemistry and Biology of Water. http://www.watercon.org/participants.html Of course, Dr. Ignatov will do future steps for the research and publications in scientific journals. Was not possible copy right and additional scientific publications. Also in last 10 years there are big changes of the understanding of the life and water. Very interesting new topic is: Water in the Human Body is Informational Bearer about Longevity http://www.medicalbiophysics.dir.bg/en/longevity.html — Preceding unsigned comment added by Mbreht (talk • contribs) 06:47, 18 July 2012 (UTC)

Mehmet quote

Hi User:sadettin. I think you've found an interesting quote there, but I think it's more applicable to the early development of the germ theory of disease. The translation of the quote uses the word "seed", and I think the implication there is that some living thing would have had to generate those seeds. Abiogenesis (and in particular the idea of spontaneous generation) requires that life organize spontaneously without the existence of prior living things. GaramondLethe 17:12, 4 July 2012 (UTC)

"Life Inevitable or just a fluke"

The June 23rd Issue of New Scientist contained a cover story on the issue of Abiogenesis. Nick Lane, the editor has previously pointed to weaknesses in the "organic soup" theories, as not providing an energy flux sufficient to drive the origin of life. He states that the earliest cells seem to have obtained their carbon from a reaction of hydrogen and carbon dioxide, which releases energy. He also mentions that the second clue to the origin of life stems from the discovery made by Peter Mitchell in 1961, on "Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism", published in Nature, July 8. Mitchell suggested that cells are powered not by chemical reactions, but by a positive proton-motive force, between two sides of a membrane of about 150 millivolts. As this operates over only 5 millionths of a metre, its field strength is enormous, equivalent to 30 million volts per metre. Lane further suggests that "inefficient primordial cells must have required more energy not less". He shows how only the 20 year old theory of Michael Russell, now at NASA's JPL Pasedina Lab, provides the best mechanism. The alkaline hydrothermal vents, produced by sea water percolating down into the electron rich iron-magnesium olivine react through serpentisation, producing alkaline, proton poor fluids rich in hydrogen gas, which expands to crack the rock, perpetuating the reaction. Russell's article "On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells" published in the Philosophical Transactions of the Royal Society and widely cited, elaborates on this thesis.

I have tried to present this theory earlier but it has been deleted as I used a publication specialised in Abiogenesis not considered scientifically "pure" enough. The article needs serious updating in the light of current research, and not the recycling of older obsolete theories, which should go into a historical section. John D. Croft (talk) 12:27, 8 August 2012 (UTC)

New Scientist is a primary source (and not a very good one --- it's not peer-reviewed and they tend to prefer novelty over verifiability). Once this theory has made its way into reliable secondary sources then the article can be updated to account for that. GaramondLethe 12:55, 8 August 2012 (UTC)

I was quoting from the Philosophical Proceedings of the Royal Society, not from New Scientist, in the post you deleted. Garamond, you delete articles because they are in a JPL Edited publication on Abiogenesis, from a New Scientist article on the origin of life, and from much cited reviews from Nature in 1961. Nick Lane's book "Life Ascending: the 10 great inventions of Evolution" also seems to be not eligible enough. What would satisfy you. You seem to prefer 81 year old obsolete theories to latest scientific research. I am at a loss to know how to contribute to improving what is a poor article.John D. Croft (talk) 18:32, 8 August 2012 (UTC)

I can certainly understand your frustration. I had to spend a couple of years of research in this area before I was able to make any reliable call as to the quality of articles, and that was with the advantage of having learned to read and write peer-reviewed research in a different domain. So yes, I can see where my disagreements might appear arbitrary if you didn't have a similar background.

If you want to make technical contributions to technical articles then you're going to have to develop a sense for what is considered better and worse; if you're going to want to make technical contributions to controversial technical articles then you're also going to need to learn how to make a persuasive argument for what you consider to be better and worse. That's going to take a significantly larger investment in time and effort and there's still no guarantee that your changes will stick. (I don't mind learning for the sake of learning, but then I'm an academic. YMMV.)

So, I'm willing to listen to an argument as to why a particular paper should be mentioned in this article. If you have a review article or textbook that cites it, that's an excellent reason. Being published in Proc. R. Soc. is certainly good, but Proc. R. Soc. publishes lots of abiogenesis research and I'd be looking for a reason to favor this paper over all the rest. If most of the cites to a paper are coming from fringe and creationist sources, that's a good indication that the paper doesn't belong here.

GaramondLethe 21:34, 8 August 2012 (UTC)

PS: Just to be clear: Martin and Russell's 2003 Proc. R. Soc. paper is perfectly acceptable to cite in this article. Lane's 2010 paper isn't anything special (except that people writing in Journal of Cosmology like to cite it --- seven citations so far) and citing it here would, in my opinion, give it undue weight compared to its actual significance in this area. GaramondLethe 21:48, 8 August 2012 (UTC)

Garamond, I see you ommitted my post about the emergence of a sythetic model including elements of both the Metabolism first and the Self replication molecule theoretical approaches. Can I ask why? John D. Croft (talk) 12:11, 15 August 2012 (UTC)

Sure. Here's the text in question:

More recently, synthetic models involving both self replicating molecules, and a metabolic process have been proposed, for instance that involving deep ocean alkaline [[hydrothermal vents]].<ref>Russell MJ, Martin W (2004) The rocky roots of the acetyl-CoA pathway. Trends Biochem. Sci. 29: 358-363</ref>

1. Synthetic model comes across as a term of art --- so much so that I started googling looking for other "synthetic models" in abiogenesis research. There weren't any, of course. "Synthesized model" would be a little bit better but still awkward, "model that synthesizes" slightly better still, except that....
2. The paper doesn't discus synthesizing two models. This looks like a straightforward metabolism paper to me.
3. Finally, while this is a good piece of work that has received a decent number of citations, you're proposing mentioning it in the lede next to Miller/Urey. The reader will naturally think this article is in the same ballpark. It isn't. (Compare 1707 citations to 117.)

That's why I reverted your edit. GaramondLethe 17:09, 15 August 2012 (UTC)

So where or how would you include information of models that include a synthesis of both metabolism and self replicating molecules? Regards John D. Croft (talk) 11:41, 16 August 2012 (UTC)

It depends on how the paper was written. For example, if the work started with metabolism but explained how metabolism led to a particular kind of self-replication I would file that under "metabolism theories". If there were several such papers from multiple groups it might we worth its own subsection under "metabolism theories". If there were also a significant set of papers that started with self-replication and showed how metabolism fell out that might either get its own subsection under "self-replication" or possibly a new section called "combined theories" (or whatever the authors choose to label their work). GaramondLethe 13:21, 16 August 2012 (UTC)

I would agree to creating a category called "Combined Theories" as Mike Russell's work I feel comes under this category. He shows how ATP and RNA emerge concurrently. What do you think? John D. Croft (talk) 19:17, 16 August 2012 (UTC)

Russell divides the world up into "organic soup and surface metabolism"; neither approach solves the problems of "concentrations and compartmentation" and so Russell suggests a third approach: "life emerged in three-dimensional (3D) compartments consisting of FeS formed at the bottom of the ocean during the Hadean period (before 3.8 £ 109 years [Gyr] ago) through the inflation of FeS precipitates by hydrothermal fluid". Since he has good reason to think that neither "organic soup" nor "surface metabolism" can work, I'm not following how you think he has combined the two. GaramondLethe 19:39, 16 August 2012 (UTC)

Current status

I don't think there is a good reason to exclude the conundrum of life emergence from the lead. The reference in the reverted edit states, verbatim: "The well-known conundrum of this emerging frontier is that we do not yet have a fundamental definition or understanding of life. Similarly, we do not understand life's origins -- how life emerges from chemistry" and this is what the reverted sentence conveyed. There is a plethora of reliable sources expressing the same concern. Harvard University's dedicated Origins of Live Initiative seems quite representative, but many more references could be invoked. Brandmeister^talk 21:12, 24 July 2012 (UTC)

A few comments:

This isn't a very impressive reference. Given the wealth of books and peer-reviewed literature out there, I'd like to see something with a little more heft than a "research directions" page for an academic lab.

This is particularly important because there are reliable sources that state we do have a fundamental definition of life. For example, "a self-sustaining chemical system capable of undergoing Darwinian evolution" has been proposed by NASA in 1994 and has since made its way into textbooks (Gilmour, An Introduction to Astrobiology).

So, do we have dueling experts? I'm not sure that we do. Your citation isn't signed and may have been just a bit of purple prose turned out by an underappreciated graduate student who was tasked with making the website. If I put <site:harvard.edu origins life> into google.scholar.com, I'm seeing plenty of origins work. You might get a bit more traction if you try <site:harvard.edu "definition of life"> where you'll see work that does lament the lack of a widely-accepted definition and several new proposed definitions. At that point, though, you should be probably editing the Life article.

Finally, keep in mind that the lack of a consensus defintion does not preclue study of the phenomenon (e.g., what's the consensus definition of "computer"?). We don't tend to point out this problem in the lede of other articles and I'm not convinced that it needs to be pointed out here. One way of changing my mind would be writing a section in this article with many cites to the peer-reviewed abiogenesis literature where the defintion problem is discussed. Once you've established that the problem exists you'll have a much easier time putting a mention of the problem into the lede.

Let me know if you need any help tracking down articles behind paywalls. My lab doesn't have as good as coverage as I'm used to, but we're pretty good when it comes to astrobiology. I used to work in this area and still have friends in University biology departments, so tracking down the more obscure work shouldn't prove to be too difficult.

GaramondLethe 21:51, 24 July 2012 (UTC)

It is beyond doubt that the question of life's origin is still open, but an ordinary statement for WP:SUMMARY purposes like "Several hypotheses about emergence of life have been proposed" may suffice as well. Brandmeister^talk 22:05, 24 July 2012 (UTC)

I don't see where that sentence would fit in the current lede, but a paragraph that provides an overview of the many hypotheses presented in the rest of the article would be an improvement. Want to take a shot at it? GaramondLethe 22:33, 24 July 2012 (UTC)

Your summary says "require[s] the presence of DNA or RNA". I don't think there has been a theory proposed that requires DNA. Also, "a lot" is a bit too informal. GaramondLethe 16:15, 25 July 2012 (UTC)

Attention Garamond Lethe

You have reverted or deleted several items on the historical aspects, eg: 'Reverted good-faith edit; "authorities" and "traditionalists" need explanation or cites.' There were cites of the authorities of the day. You surely didn't expect 21st century peer-reviewed cites in the 17th century? Browne and Ross are both linked to. Who would you propose as a counter-authority to the likes of Redi and Browne? Oparin? Then you removed the Browne cite, saying: " Reverted good-faith edit; reference not specific enough to be useful." The actual text in question is in the cited material; the material cited is reader-searchable. What difficulty exactly prevented your finding it useful? If you wanted page and verse, what prevented you from locating it and adding it to the citation? It would have been a lot more "useful" than deletion, even if it required more effort. Please explain in time to forestall reversion. JonRichfield (talk) 16:05, 29 August 2012 (UTC)

Hi Jon. Based on my understanding of the history of science, "authorities" is a 20th-century concept (perhaps originating with the politicalization of science). For example, I've never heard of Darwin being contemporaneously called an "authority" on evolution, nor Newton an "authority" on physics. If you know of a cite that states what the contemporary authorities thought (and labels them as such) of course I'll stand aside.

I'm not aware of a modern or historical use of the word "traditionalist" in this context. The word was used as if it were a term of art. If that is indeed the case and you have a cite for it, then I will be happy to admit I've learned something.

As to the Browne citation, you may have better luck than I did in tracking down the correct chapter and verse. If you have succeeded in doing so, please restore the cite with that additional information.

Best,

GaramondLethe 03:36, 30 August 2012 (UTC)

n.b. So I got curious about "authority" and put a few searches into books.google.com. "Authority on evolution" has 42 hits in the 21st century, 52 hits in the 20th century and none in the 19th century. "Authority on physics" has 15, 40 and 0; "Authority on chemistry" has 24, 72 and 0. It's google books, so results should be taken with a sizable grain of salt. A 17th C. use of "authority" in this sense would be really interesting --- here's hoping I'm wrong and you have one! GaramondLethe 03:57, 30 August 2012 (UTC)

Hi Garamond, Ah. I see. Mostly cross purposes. Sorry if I came across too abrasive. Let's see... "Authorities" I used in the 20-21st century sense of "people regarded as being authoritative"; I was not trying to emulate 17th-century modes of expression, nor even current senses along the lines of "people regarded as being entitled to make definitive statements on the basis of their history of personal research and peer-reviewed publications". As such I think that my usage was acceptable and understandable, and I recommend that in similar contexts you hesitate to revert the usage. However, in this connection I think you have a point. Would you prefer it if instead I said something like "influential contemporary writers"? I think that would be less question begging and possibly clearer to the reader in context. Many modern readers certainly would be likely to read unintended significance into "authorities" along the lines that you suggest, and I think that "influential contemporary writers" might entail less risk of such misunderstanding. But I am open to alternative suggestions if you prefer.

Incidentally, following up on this discussion I was interested to discover, and intend including remarks on the point, that apart from Browne's citing of Redi's work, he cited William Harvey with (understandably) great admiration in this very connection. Harvey, among other things, either was the source, or if not, at least quoted the principle of omnia ex ovo. Perhaps unfortunately, he did so in Latin in his book "Exercitationes de generatione animalium. Quibus accedunt quaedam de partu; de membranis ac humoribus uteri; & de conceptione." I suspect that had he written in English, he would be more prominently remembered as a leader in the ranks of early modern opponents of the doctrine of spontaneous generation.

As for using http://books.google.com/ngrams and google books, I use them myself and applaud their cautious use by others. In careful hands such facilities are beyond rubies, and if their sources never did another thing for humanity, they would rank with WP and a few other facilities along with the development of fire, printing, and the wheel. I have no quarrel with your application of them in this connection.

Right. Next. I am a little taken aback by your remark: "...' traditionalist' in this context. The word was used as if it were a term of art." I suspect that you and I are accustomed to using that term in different connections. Again, I am not wedded to its use; if you found it unsatisfactory or confusing, no doubt some other people would as well. I suggest that I/we replace it with something like "writers who adhered to the traditional (or "older", or "established", or something similar) belief (or view, or superstition, or something similar)". Would that address your concerns in this connection? If not, I open to alternative suggestions; I am sure that you get the general intention of what I had in mind.

Mind you, partly as a result of my readings in this matter I have developed a strong suspicion that the traditional (you should excuse the expression!) accepted wisdom in favour of spontaneous generation was not as firmly founded as contemporary writers suggest; it seems to me that at least from the Renaissance on, and perhaps from far earlier, a lot of naturalists had observed that living things generally arose from other living things of similar anatomy and physiology. For my money spontaneous generation was very likely a superstition of the unobservant and an educated, that was largely preserved by the authority of Aristotle. Certainly writers such as Harvey and Browne seem to have held common sense views along these lines and argued very sensibly in those terms. To settle the matter formally however was not so simple and required a great deal of direct observation, something that does not come cheaply. As you know, it took another couple of centuries to settle the matter finally.

Does anyone reading this have any comments on the matter?

As for the chapter and verse in Browne's works, I shall narrow the reference to a single volume, for which I shall give both the download address (editions differ, after all) and the page number. I should have preferred also to give the source, chapter and verse for Ross's blast at Browne, but I have been unable to locate a first-hand source. If you can do better, I should be grateful.

Okay, I think that covers most points for the short-term. Over to you. Cheers and thanks, JonRichfield (talk) 09:29, 30 August 2012 (UTC)

JonR,

Thanks for the detailed reply --- I really appreciate it. Having had some time on the airplane to think about this I think I can give you a more generalized argument against "authorities" and "traditionalists" as well as a potential solution. Here's the text in question:

In the 17th century, such assumptions were being questioned by influential authorities, albeit in the face of traditionalist resistance;

What I was trying (and failing) to communicate earlier is that the above formulation will naturally raise several questions in the minds of more attentive readers: Who are the authorities? Who are the traditionalists? Did they call themselves that, and if not, who did? If labels exist in the literature then certainly we should use them, but deploying labels for the convenience of writing can (occasionally) lead the reader to draw conclusions that we didn't intend.

That said, I think the sentence reads perfectly well as In the 17th century, such assumptions were being questioned; and if you prefer the active voice, In the 17th century, scientists began questioning such assumptions;. Of course, the label scientists runs the same risk as "traditionalists", but I think we'll have an easier time finding a reliable source that labels these natural philosophers as "scientists". Your thoughts?

Nice work on narrowing down the Browne cite. I'm hanging out with several well-read biologists this week so I may be able to make some headway on the Ross cite.

Best,

GaramondLethe 04:53, 31 August 2012 (UTC)

Hi Garamond. You know, it certainly is best to avoid the passive voice when there is a comfortable active alternative, but in our situation it might be the most convenient when, for valid reasons, we are unwilling to characterise the active agents. In the 17th century, such assumptions were being questioned; doesn't hurt my corns too badly and it avoids scientists, a concept that might as validly raise hackles in context as "authorities" could.

Please have look at the following draft of the relevant paragraph. I have been badly distracted so the text my be a bit confused by now. In particular some of the dates of refs that appeared in various editions can be quite hard to follow.:

Belief in the ongoing spontaneous generation of certain forms of life from non-living matter goes back to ancient Greek philosophy and beyond. It continued to have significant support in Western scholarship until the 19th century. It was closely associated with the related belief in heterogenesis, i.e. that one form of life derived from a different form (e.g. bees from flowers). Classical unscientific notions of abiogenesis, now more precisely called spontaneous generation, held that certain complex living organisms are generated by decaying organic substances. According to Aristotle, it was a readily observable truth that aphids arise from the dew which falls on plants, flies from putrid matter, mice from dirty hay, crocodiles from rotting logs at the bottom of bodies of water, and so on. In the 17th century, various writers began to cast doubt on such assumptions. In 1646, Sir Thomas Browne published the first edition of his Pseudodoxia Epidemica (subtitled Enquiries into Very many Received Tenets, and Commonly Presumed Truths), which was an attack on false beliefs and "vulgar errors." His conclusions on spontaneous generation were based partly on the works of William Harvey and were criticised at the time, most notoriously by his contemporary, Alexander Ross, a fervent supporter of the views of Aristotle. In his major polemical work Arcana Microcosmi Ross wrote: "To question this (i.e., spontaneous generation) is to question reason, sense and experience. If he doubts of this let him go to Egypt, and there he will find the fields swarming with mice, begot of the mud of Nylus, to the great calamity of the inhabitants." However, at about that time the works of Francesco Redi presented the first persuasively systematic experimental evidence against spontaneous generation, a trend that gradually led to their comprehensive rejection.

So much for now! JonRichfield (talk) 16:10, 31 August 2012 (UTC)

Perhaps replace "Classical unscientific" with "Classical" and "In his major polemical work" with "In Ross's major polemical work". Also "led to their comprehensive rejection" with "led to its comprehensive rejection". Add the online Ross cite and I think this is good to go. Nice work! GaramondLethe 16:31, 31 August 2012 (UTC)

Cite for Ross Quote

Alexander Ross, an early 17th-century Scottish writer and intellectual, harshly criticized Sir Thomas Browne for questioning the dogma of spontaneous generation. Under the heading "Mice and other vermin bred of puttrefaction, even in men's bodies." he wrote: "He doubts whether mice can be procreated of putrefaction. So he may doubt whether in cheese and timber worms are generated; Or if Betels and wasps in cowes dung; Or if butterflies, locusts, grasshoppers, shel-fish, snails, eeles, and such like, be procreated of putrefied matter, which is apt to receive the form of that creature to which it is by the formative power disposesed. To question this, is to question Reason, Sense, and Experience: If he doubts of this, let him to to Egypt, and there he will finde the fields swarming with mice begot of the mud of [the Nile]." Arcana Microcosmi, (London: Newcomb, 1652), book 2, chapter 10, p. 156.

From the forward written by John MacArthur in Coming to Grips With Genesis: Biblical Authority and the Age of the Earth pg 9-10, Master Books, 2008, Editors: Terry Mortenson and Thane H. Ury.

Now that I've got the Arcana Microcosmi let me see if I can find something a little less creationist.... GaramondLethe 05:12, 31 August 2012 (UTC)

Phew! Thanks for that, but I take your point! It is a bit over the top isn't it?! Still, bless him/them for the ref. You say you have Arcana Microcosmi? I located reference to a site on Google that seems to be the definitive one (http://penelope.uchicago.edu/ross/ross218.html) but cannot get through to it. If anyone has a copy of ross218.html and can make it available, I would be grateful. It would be a salubrious change from that book! ;-) I get the impression that Ross and I would have fallen out immediately and persistently, but he seems to have been pretty spunky, to give him his due. JonRichfield (talk) 12:37, 31 August 2012 (UTC)

Here's the text from the link you provided. Not sure why you can't get in. I'm coming in from a .edu address at the moment, but I would be a little surprised if they're filtering based on that.

V. He doubts whether mice can be procreated of putrifaction. So he may doubt whether in cheese and timber worms are generated; Or if Betels and wasps in cowes dung; Or if butterflies, locusts, grashoppers, shel-fish, snails, eeles, and such like, be procreated of putrified matter, which is apt to receive the form of that creature to which it is by the formative power disposed. To question this, is to question Reason, Sense, and Experience: If he doubts of this, let him go to Ægypt, and there he will finde the fields swarming with mice begot of the mud of Nylus, to the great calamity of the Inhabitants. What will he say to those rats and mice, or little beasts resembing mice, found in the belly of a woman dissected after her death, of which Lemnius is a witness, who thinks this generation might proceed of some sordid excrement or seminal pollution of those animals with which the womans meat or drink had been infected. I have seen one whose belly by drinking of puddle water, was swelled to a vast capacity, being full of small toads, frogs, evets, and such vermin usually bred in putrified water. A toad hath been found in a sound piece of timber.

As you said, he sounds like a very interesting person. If you're restricted to doing science with anecdotes the reasoning really isn't that bad, but of course the rhetoric is what makes it fun. Note that the italic text differs in the two transcriptions. That probably doesn't matter to anyone else, but my undergrad adviser spent some time in the Bodleian Library counting italic semicolons in first editions of Milton and a tiny bit of his rigor rubbed off on me. This text is probably good enough to go in now, but I'm still going to try to track down an original or facsimile edition. GaramondLethe 16:16, 31 August 2012 (UTC)

If you are getting in then it is either personal malice towards yours truly or there is in fact some such filter as you suggest. I have been trying all day and keep getting "connection to the server was reset while the page was loading" etc without any other intimation. All my other stuff is working. As for Milton and semicolons, your advisor must have been compulsive! In those days they used semicolons like we use fullstops, giving "sentences" of many hundreds of words. I first encountered them as a kid reading Swift. It was of course not a wrong, nor even an inferior, convention; in fact I think it had decided merits, adding another dimension of conceptual nesting, but it does read disconcertingly to the modern eye. JonRichfield (talk) 16:34, 31 August 2012 (UTC)

Primordial soup

I admit that the article as it stands could do with a great deal better organisation, particularly concerning the various threads and opinions in its composition. However, I am not comfortable with the splitting off of the primordial soup text into a separate article. It might be a good idea, but I have not noticed its being discussed anywhere, and it is a rather drastic and arbitrary step to take without consultation. Of course, if I have missed any consultation I apologise.

Still, not only do the current articles on this and related subjects still need a good deal of reconstruction and reconciliation, they also need more and cleaner inter-reference. I am not undertaking any of that myself without appropriate prodding, because it is not quite my line, but does anyone else agree that if we do not revert this split, then there is a certain amount of fairly urgent work to be done? JonRichfield (talk) 15:23, 30 August 2012 (UTC)

Jon, I agree with your opinion re the split. I'm on travel today and will take a longer look tonight or tomorrow. GaramondLethe 15:44, 30 August 2012 (UTC)

Jon, I would be in favour of reintegrating the two approaches, or possibly using a Chronological view, say separating the research pre and post 1977. The chemosynthetic ecosystem surrounding submarine hydrothermal vents were discovered along the Galapagos Rift, a spur of the East Pacific Rise, in 1977 by a group of marine geologists led by Jack Corliss of Oregon State University, and I think this led to a spate of new developments in Abiogenesis theory. What do people think? John D. Croft (talk) 19:55, 30 August 2012 (UTC)

I've reverted the change in this article. Biem, I'd be interested to hear your plans for the article. GaramondLethe 04:04, 31 August 2012 (UTC)

I've been cleaning out these past days the french article fr:origine de la vie, which is basically the counterpart of this one ; this is where my interest comes from.

In doing so, I moved some stuff to fr:soupe primordiale, which should have an interwiki link to Primordial soup (being the same subject) but here on en: the theme "Primordial soup" was included in this Abiogenesis, with Primordial soup being a mere "Goto". So I hacked out the Primordial soup article by cutting out the corresponding part from Abiogenesis, just leaving the introduction and a "detailed article" link in the main article, in order to leave a clean overall result (without discussing it, of course).

With the revert, the Primordial soup stuff is now duplicated - I don't mind, really, the only point for me is that fr:soupe primordiale interwikies to a decent content.

As for Abiogenesis, my opinion is that the article is way to long, because of complex developments of side issues ; the cure for that is to transfer side issues in side articles, which I did for "Primordial soup". This theme is a polemical one, and the polemic is not on the "primordial soup" problem any more, so that development has nothing to do in this article. But that's just my opinion, I leave the article to your judgement.

I'm going back to fr:, now, if you want to discuss something with me you can reach me there (and I understand English, fear not the fr: environment ;o) Biem (talk) 06:59, 31 August 2012 (UTC)

Thanks Biem; that lends some clarity to the situation. There is nothing fundamentally absurd about a "primordial soup" split. I have reservations however, concerning the length of an article being in itself sufficient reason to split it. I propose that a more functional approach is to create an outline, a conceptual framework if you like, and derive any splitting and cross-referencing from that. As it seems likely that there might soon be a conceptual restructuring of the article however, with as little polemicism as may be, your split may turn out to have been unfortunately timed. Let's first see how this discussion turns out. JonRichfield (talk) 08:14, 31 August 2012 (UTC)

"Way too long"" is but a symptom, leading to a Wikipedia:Too long; didn't read reaction.

The fundamental criterium (for Wikipedia redaction) is that any article should have but one subject (described by its title). When a subject has enough stuff to make an article of its own, there is no reason to include it as a section in a "main" article. In such a case, a redaction split is the usual solution to the TLDR plague : leave the developments to a side article ; and leave in the main article only a link to the side one, and a short comment to indicate why the side article is important and what conclusion it may bring to the main problematic.

IMHO, the Abiogenesis in its present state has much too long side-developments, and lacks coherency in its progression. A first step to clean it would be to cut out all digression and report them to side articles, and restrict the main article to explain with each side link why that theme is important and what conclusion it can provide to the Abiogenesis problematic (which is the only main subject) - and definitely not expose the whole side-problematic, which is not the main subject. Once you've done that, it's much easier to get the general idea of the problematic involved by the article, and detect what is lacking in the main article for the reader to get a complete and coherent picture of this problematic.

Remember, this is about writing an encyclopaedia, not writing monographies. Macte animo! Generose puer, sic itur ad astra. Biem (talk) 13:24, 1 September 2012 (UTC)

As I said, this is not quite my line and to responsibly and reasonably formulate a structure and perspective for such an article (which is what it fundamentally needs) requires a more professional level of competence in the field than I have to offer. This sounds very glib of course; I am fully aware that to achieve that might well require something like a total rewrite, whether incorporating the current material or not. That may seem very greedy of me, but then I think you will agree that the current unsatisfactory state of the article arose largely from uncoordinated and often partisan efforts from individuals who shared no common perspective. The fact that the field still is largely under development doesn't exactly make matters much easier. Remarks from you folks are very much in line with my feelings and I am perfectly happy to contribute details, references or editing to anything you produce. John's preliminary suggestions sound fine to me so far. Whether they would be a sufficient basis, or whether we need to begin by constructing a more comprehensive outline, I cannot yet say. JonRichfield (talk) 06:44, 31 August 2012 (UTC)

I strongly support making it into 2 articles. I would suggest we have the Conceptual Background to Abiogenesis as a Separate Article with a link at the beginning, and try to keep this article up to date with relevant research. John D. Croft (talk) 19:32, 1 September 2012 (UTC)

I could go with that for a start. I also think that the historical material in this article should be limited to a mention plus a link to the spontaneous generation article. I disagree with Biems's views on article length in general, but not necessarily in particular, and in this particular I think we are on the same side. JonRichfield (talk) 19:50, 1 September 2012 (UTC)

Well, I liked "trenchant"...

Hi, Jon. I do appreciate you making the edit. I do think it warrants a bit of discussion first, so I blew away the entirety of the last sentence.

These surfaces might not only have concentrated these organic compounds in close proximity, but also helped organize them into consistent, non-random three-dimensional configurations, thereby influencing the specificity and consistency of their reactions, both chemically and stereochemically, much as enzymes later did within living cells.

1. I've never heard of chemical reactions being described as "consistent" or "non-random" (and the simulation work I've done with biologists emphasize the inconsistency and randomness of these reactions).
2. I don't know what "specificity" means in this context.
3. Is "chemically and stereochemically" a distinction with a difference?
4. It's my understanding that enzymes operate randomly, inconsistently, and non-specifically.

So I'm confident that you can explain what the above means to you, but that's not what I need. Can you show me where these terms are used this way in the primary or secondary literature? I don't necessary want to add formal citations; I just want some reassurance that you're not inadvertently using these terms idiosyncratically.

I'm on the road for the next three or four days so may not be replying promptly.

Over to you....

GaramondLethe 05:38, 19 September 2012 (UTC)

Hi Garamond,

No problem with the delay; I had to sleep!

It might take me a while to dig out references, and to make matters worse, I doubt that the references would use the identical terms that I did. However, let's explain some of my intentions in replying to your perfectly reasonable questions.

1. I've never heard of chemical reactions being described as "consistent" or "non-random"... Here you take me aback; firstly, I have a personal niggle with the frequently incorrect use of the term "random" to mean little more than varied or unpredictable. In this respect I have sinned somewhat myself in that quoted text. I trust that something like my precise intention will emerge from my circumscription. I am not sure whether your objection is that your various colleagues and contacts disagreed with my intended meaning, or whether they simply would have used different terms. Nor would I argue if someone were to propose different terms. As far as the intended sense is concerned, consider in particular reactions that, in the absence of constraint, incline to inconsistent chirality or branching. I am sure that your colleagues would not expect to get consistent production of L-amino acids, or purely straight-chain fatty acids by passing sparks through a notionally primitive atmosphere, or by the application of charring heat. Conversely, in attempting to produce similar compounds by appropriate application of enzymes and other appropriate catalysts to suitable precursors, I am sure that they would expect thoroughly consistent chirality and straight chains. I am slightly nonplussed by your use of the expression "the inconsistency and randomness" of these reactions. I am certain that you have other concepts in mind than those that I did.
2. Specificity, as I used the term, refers to a reaction that works on a particular combination of precursors, and produces equally definite combinations, or a single product. Very commonly the term and the concept go together with selectivity, meaning that if the reaction is applied to a mix, it will work on only certain compounds in the mix. Here again, such specificity and selectivity are exactly what one expects in large classes of enzymatic reactions, and sees on a large scale in every metabolic chart. It most certainly is not the kind of thing one expects to see in a spark-driven reaction chamber, particularly in the absence of catalysts, right?
3. You say: "It's my understanding that enzymes operate randomly, inconsistently, and non-specifically." Errr...???? Certainly there are necessarily "random" aspects to any reaction in which molecules, ions and even atoms interact unconstrained, but these are not attributes that I would have looked for in enzymatic reactions. I expect enzymes to catalyse reactions and interactions in such a manner as to produce predictable chirality and predictable products (within certain limits; one does not expect quite the same results from applying say chymotrypsin to a protein suspension as when one applies trypsin, but within reasonable context, and ignoring details of which of a number of similar bonds will be cleaved first, one can be pretty confident don't you think?) I think it would help if you could elaborate on your understanding.
4. You ask: "Is "chemically and stereochemically" a distinction with a difference?" In my circles certainly! If I produce tartaric acid by oxidising fumaric acid with permanganate, I expect a racemic mix, whereas a suitably chosen enzyme system will give me a chiral product. Both reactions are reasonably chemically specific (the enzymatic reaction probably more so) but the simpleminded oxidation is not at all stereochemically specific, whereas the enzymatic reaction is highly stereochemically specific in the product it yields. Conversely, given a racemic mix of tartaric acids, I would have great difficulty using inorganic reagents to alter one chirality rather than the other. Most such reagents are not stereochemically selective, even if they are chemically selective. Enzymes on the other hand are commonly highly stereochemically as well as chemically selective. Are we at cross purposes in some way?

It is of course possible that you use other terms in this connection, and if you do so I certainly have no quarrel but I am quite taken aback by our apparent mutual misunderstanding. I had thought that the terms I had used were pretty basic, so I would be grateful if we could continue this discussion until the confusion is sorted out.

Note that in the field of abiogenesis in the sense of this article, a common factor in many of the mineral-mediated proposals involves substances with particular distributions of charges in particular configurations on crystal surfaces and the like. This, you will recognise is no novelty in the field of catalysis, and in recent decades it has grown to greater prominence in industrial chemistry. In particular I remind you that we now use everyday, and very mundane, products that 50 years ago were hardly dreamt of, such as tactic polypropylene. Polymerising polypropylene was easy; getting anything more useful than a messy gum was not! In abiogenesis the attractions of crystals of sulphides, silicates and the like also are analogously important in the production of unbranched carbon chains, unbranched polymers, polymers with their monomers arranged with consistent tacticity, and so on. Living systems have little use for atactic polymers. When molecules grow onto surface-constrained groups, particularly when they are crowded, as on a surface of a crystal, high tacticity is likely to result. Failure to recognise this was an obstacle to early proposals for abiotic mechanisms. That is what I was referring to and I think it is what our friend was trying to refer to, but got hung up on the gene idea, which as you will recognise, is totally inappropriate to the concept.

You also will recognise that many of our most complex and most vital and most constraining biochemical mechanisms are based, not so much on enzymes as such, but on structures of different enzymes that can work together in specific three-dimensional conformations, without which they are essentially useless. Again, this is a difficulty in abiogenic explanations, though it very well explains the uniqueness of certain classes of chemicals and mechanisms in everyday biochemistry and molecular biology. Recourse to such crystal surfaces has been a great relief to certain classes of abiogenic theory.

Okay, let's leave it at that for the moment until you come back.

Cheers for now JonRichfield (talk) 15:57, 19 September 2012 (UTC)

I-5 through Northern California and Oregon is a really nice drive. Ok, let's see what we have here.

1. I am certain that you have other concepts in mind than those that I did. Yep, that's the problem. I think you're trying to say that the clay hypothesis leads to repeatable results, plausible results. That's true, but it's also unremarkable.

2. As to "specificity", again, I'm not sure why this would be considered remarkable either. The model requires some level of specificity and selectivity, but so do all other models, yes? And I don't know that the clay hypothesis has been particularly praised or damned for its want or excess of specificity.

3. As to the randomness of enzymes: If you have an analytical model then there's no randomness at all; just plug in the values and turn the crank. If you're modelling on the molecular level, though, Brownian motion and stranger things are going to be constraining which reactions take place an their timing. The context for this particular sentence was modeling the clay hypothesis on the molecular level. (Again, this is not about your ideas being right or wrong. It's about the domain-specific vocabulary.)

4. I agree there's a distinction and a difference in your circles; is there one in the clay model? And is it important enough to raise in a two-paragraph description?

As an aside, I'm properly impressed with your knowledge of chemistry. It's really strange that we can approach a common field from such different perspectives. To me, chemical models that use calculus or even less math are so simplified as to be uninteresting. They're marvelously effective, of course, but for the problems I'm interested in Monte Carlo simulation is really the only tool in the box. So when I think of, say, enzymes, I'm thinking of blobs of molecules banging around and occasionally doing something interesting.

Or maybe I could just show you a few movies.... this is my mental model of How Chemistry Works. [5]

Ok, so what? Can I send you a few pdfs of the clay hypothesis literature and we both read them? That might go a long way towards giving us a common vocabulary (and frankly you're going to understand the chemistry much better than I will). Let me know if you're interested.

(Bonus philosophy of science tidbit: Randomness is a property of models, not nature.)

Very sincerely,

GaramondLethe 05:26, 20 September 2012 (UTC)

Your complimentary remarks are too kind, but in retaliation, I may say that I find your discussions very rewarding. If you would like to send material for mulling over, feel welcome try [email protected]. Unfortunately tonight I am trying to wrap up more immediate (and less tractable) problems, so I cannot immediately respond properly to your foregoing replies. Tomorrow maybe. But btw, having only passed through the far NW states by Amtrak (son in Washington) I can well envy you your drive! :-) JonRichfield (talk) 19:17, 21 September 2012 (UTC)

Hi again Garamond,

• ...trying to say that the clay hypothesis leads to repeatable results, plausible results. That's true, but it's also unremarkable.

Oh? Why is it unremarkable?

Apologies for replying inline a la usenet, but this is getting a little unwieldy. It's unremarkable because this will also be true for any other published theory that's backed up with any experimental evidence at all (which should be all of them at this point). GaramondLethe 05:43, 23 September 2012 (UTC)

Please note, I hold no brief for any particular proposed catalytic surface or constraint; except that I do believe that at least one of the various proposals, or something much like some of them must surely have played a role; and I suspect that more than one may have — for example it would be easy to believe that different minerals might have played roles in the production of cytoplasm- or membrane-worthy lipids, carbohydrates or peptides. Purely personally you understand, it seems almost mystically beautiful. It is not so much that the proposed mechanisms seemed to promote reactions, as to constrain them. Philosophically (purely my own philosophy of course, don't bother to seek a citation!  ;-) ) this is an enormously powerful concept, along the lines of "form is liberating". I said "almost mystically" but of course that is an emotional reaction, rather like watching a particularly sophisticated gear train do the apparently impossible. It really makes very simple practical sense that any catalyst that imposes some bias towards consistent order should be far more likely to produce something with functional merit, than that simply any old reaction could be facilitated. If you like it is a little like trying to generate text or pronounceable names randomly by computer, a far more demanding exercise than the programming tyro would imagine; simply producing letters at random gets you so little usable material that it is practically impossible to find it among the chaff. One needs to add rules, which essentially means eliminate unpromising candidates. None of this of course gets us much further in the article, but I shall be bearing it in mind while reading the articles you suggest.

• The model requires some level of specificity and selectivity, but so do all other models, yes? And I don't know that the clay hypothesis has been particularly praised or damned for its want or excess of specificity. I wonder whether part of our cross purposes might not have something to do with whether I gave the impression of particularly favouring the clay hypothesis.

I didn't get that impression, no. GaramondLethe 05:43, 23 September 2012 (UTC)

If so it was not specifically my intention; I am simply interested in the principle of catalysis favouring limited classes of reaction and thereby increasing the probability of producing components that are, to coin a term, "co-functional" and that occur often (or consistently) enough to form a basis for natural selection at the molecular biological scale. I am fully aware that many people claim that natural selection could not work before there were heritable units to work on (select from, if you like). I take their point of course, but it seems to me that there was a vaguer form of selection going on during the molecular soup phase of abiogenesis, much as the options for selection during the pre-eukaryotic phases of evolution were more constrained than after the emergence of eukaryota, and similarly, of symbiosis and subsequently of various categories of multicellular functional communities and organisms, as opposed to simple accumulations. I assume that you have read "The Major Transitions in Evolution" by John Maynard Smith and Szathmary?

First I've heard of it. I'm familiar with selection operating at the level of self-reproducing molecules (or systems of molecules), but I've never heard of this being mentioned. Scholar google says it has been cited ~2500 times and I know a lot of the work that's citing it.... strange. Well, thanks for the recommendation --- it's on my list! GaramondLethe 05:43, 23 September 2012 (UTC)

I get the impression that the foregoing was much on their minds when they wrote. Certainly I read the book with a considerable sense of affinity. It seems to me that Darwinism (with all due admiration!) is a specific subclass of a more general principle.

• As it turns out, I did correctly guess that your reference to randomness was indeed of the Brownian, drunkard's-walk type. Yes, I can understand that if you approach chemical interactions and pathways along such statistical lines, it must crystallise one's mind in terms of randomness. Here we do not differ in terms of philosophy as far as I can tell, but rather in terms of emphasis. If we ever get the opportunity to chat about the theory of your work, I think I would enjoy that.

Ping me if you're ever in the San Francisco area. GaramondLethe 05:43, 23 September 2012 (UTC)

• I agree there's a distinction and a difference in your circles; is there one in the clay model? And is it important enough to raise in a two-paragraph description?

Frankly I don't know whether anyone has followed up the clay model to the extent of demonstrating that it specifically works, and if so, that it would be more important or more effective than any of a job lot of other mineral influences on relevant reactions. The editing that I had done in the article was intended to correct a misstatement concerning genes rather than catalysts. It certainly seems that I committed a faux pas by misleading readers into the impression that I was promoting the clay model specifically. As for the question of whether it was important enough, in my personal opinion they principle is more than important; it is vital, even key. Whether it belongs in the position where I made this statement is of course a totally different matter. But I don't think I shall follow that up right now unless you feel that the article is insufficient need of discussion of such points in a suitable place and form.

There's very little in this article that doesn't need to be completely rewritten (or at least reorganized). How does the article dedicated to the clay hypothesis look to you? If it's in good enough shape we can probably just summarize off of that. If it needs work it might make sense to fix that first and then come back here. GaramondLethe 05:43, 23 September 2012 (UTC)

Concerning your aside, I can see some of the charms of the modelling you mention, but of course the evolutionary and biological aspects are at a more abstract level, possibly a more naive level, chemically and mathematically speaking. I have long had an idle conviction that there should be scope for computational modelling of various physical processes, ranging from cosmology to molecular reactions, but even at the entertainment level I hardly ever did anything about it. If that is the sort of thing you are working on I accord you the sort of doubtful respect appropriate to people who go over the Niagara Falls in barrels: admiring, but not emulating...:

One of my coworkers is using 1.2 million processor cores to simulate the human heart. At that scale there's only ~100 heart cells assigned to each processor core, and those only need to solve 17 partial differential equations per timestep. The machine designs I'm working on will have 1,000 million processor cores: at that point you're either not doing heart simulations anymore or you're using molecular dynamics to model biological systems. Good times.... GaramondLethe 05:43, 23 September 2012 (UTC)

...Tidbit: Randomness is a property of models, not nature. I am not so sure about that. There is something paradoxical about randomness; I cannot resist it. It would seem to be such a vacuous, futile concept, and yet it is full of challenges and pitfalls. I am not even certain whether the different concepts of it that I have encountered so far even describe the same thing, or perhaps non-thing. Assuming nature to be causal and deterministic (which I do not see as being the same things) I could see good prospects for arguing that nature excludes scope for randomness from any global point of view (though from points of view involving various degrees of ignorance, it might be hard to tell randomness from simple unexpectedness). But if on the other hand nature is fundamentally nondeterministic than I do not see why there should be no scope for genuine randomness, catastrophe, symmetry breaking, the full nausea. As for the distinction between models and nature, to argue from models is to argue from analogy, but then all knowledge and all argument are from analogy. ("It may be crooked but it's the only game in town!") The validity of the argument depends on the degree of abstraction (how much you have been leaving out) and the cogency of the lines of reasoning along which you have been drawing conclusions. If your model incorporates randomness to accommodate details of processes that are not available to you, and you use the likes of Monte Carlo methods to supplement your ignorance or economise on your processing, that certainly does not prove that nature does the same thing at the other face of the mirror, but equally it does not in all cases prove that there is no randomness in nature. I don't know whether it is possible in principle (ignoring questions of computational feasibility) to deal with Brownian motion as nonrandom (I don't actually believe it is possible, even in principle, but that doesn't prove anything) but an equally interesting question in my opinion concerns the nature of pseudo-randomness in the real world. Analytically speaking, assuming full determinism and causality every single sub-atomic action and interaction would be necessary and necessarily unique, but beyond a certain level it would be impossible, even in principle, to predict simply everything, or alternatively to determine simply everything about anything in the past. Apart from of observer effects, there would be no limit to the amount of information one would need, whereas there are physical limits to how much one can collect and process. And if that applies to a deterministic world, how much more so if we reject determinism.

I'm afraid I'm going to disappoint you here. The koan was meant to communicate that the only way we can perceive the world (beyond raw sensory input) is through models. There are definitely better and worse models, but whether or not those models do a better or worse job at explaining the underlying reality is a philosophical position, not a scientific one. (There's much more to be said about this, but this probably isn't the venue.) GaramondLethe 05:43, 23 September 2012 (UTC)

Talk about treacherous tidbits!  ;-) JonRichfield (talk) 18:25, 22 September 2012 (UTC)

I owe you some papers. Ping me if they haven't arrived by Tuesday. GaramondLethe 05:43, 23 September 2012 (UTC)

Ooopsie! Sorry...

Hi Garamond,

This is very embarrassing. I have just read Clay hypothesis in response to your question and only now do I remember that particular version (no doubt the original) to which I have paid no attention for over 20 years. That part is okay; where the wheels come off is that I now, having read Graham Cairns-Smith, remember having originally read the idea of the crystals conveying info (can't remember where; I already had encountered it before reading the Blind Watchmaker) and dismissed it as not being of practical significance in context. I cannot even remember whether the chemical constraint/catalysis aspect was published in the same document or not. I hope that the documents you email me will discuss any material presenting arguments for how such mineral surfaces might notionally act as templates, or at least as platforms for the preferential formation or concentration of molecules or juxtapositions of molecules particularly suitable for the initiation of abiogenesis. The mere idea of basing the information content of Darwinian selection of organic molecules on Darwinian selection of unrelated inorganic crystal forms, sounds to me about as persuasive as the principle of similarity in magic. For a start, I would need to be persuaded that the different crystals would indeed be subject to practical selection in realistic circumstances, and that those differences would reflect their catalytic merits. There are of course quite a few suggested mineral surfaces and cavities that have been proposed and fervently damned in their turn. That is no excuse of course, but it is easy to get mixed up. I read of mica as one candidate, and thought that I had read of it in the eighties or nineties, but it seems to be a 21st century proposal. Oh well... So far my main interest in them as a category is in the principle rather than their specific individual plausibility. In fact, I suspect that some of them were mainly of importance in generating large quantities of (pre)biologically useful compounds rather than actual proto-cells. JonRichfield (talk) 16:01, 23 September 2012 (UTC)

Hooowww many???

"One of my coworkers is using 1.2 million processor cores to simulate the human heart. At that scale there's only ~100 heart cells assigned to each processor core, and those only need to solve 17 partial differential equations per timestep. The machine designs I'm working on will have 1,000 million processor cores: at that point you're either not doing heart simulations anymore or you're using molecular dynamics to model biological systems. Good times.... "

Good grief Garamond! I thought I had become inured to large numbers in computing, and had lost interest in cellular arrays in the days when 64K processors would have been a lot! If you or your colleague have a ref you can send me to that email address, I know someone not so far from you who should be interested, though I suppose he has kept up with the field better than I have. Are these custom arrays or commercial? JonRichfield (talk) 16:12, 23 September 2012 (UTC)

$DEITY willing and the creek don't rise that work will be an entry for the Gordon Bell Prize to be awarded at the Supercomputing 2012 conference. The machine description is here (see the entry for Sequoia). Basically lots of cheap, low-power embedded processors and a very, very expensive interconnect. Your taxpayer dollars at work (if you're a USAian), for which I am humbly grateful. (This might also be of interest if you want to see what the rest of the world is doing in the area of high-performance computing.) GaramondLethe 02:04, 24 September 2012 (UTC)

Weasel Words

What is the limit on "weasel" words? Is the current 47 "may', 41 "could", 14 "might", and 18 "possib{le/ly/ility/ilities}" the upper limit allowable so that mentioning uncertainties in current knowledge of the early earth's atmospheric content is unacceptable? Dan Watts (talk) 15:52, 19 September 2012 (UTC)

Hmmm... I don't know what the formal limit might be, if any. To my mind the use of the term "weasel words" as if the reasoning were in the words, rather than in the construction of the statement, is barely literate. (This is not an accusation directed at you or anyone else, but a general remark, and not a weaseling one either.) Counting the words may be a convenience, but is not diagnostically reliable. The counts that you mention — did they refer to the entire article or to someone's paragraph in a given section? All those words can be used in highly assertive statements without the slightest hint of weaseling, or even compromise. Furthermore to use them to express uncertainty or understandable lack of information is not as such weaseling. Weaseling is when you copper your bets and hide ignorance or uncertainty by excessive or inappropriate hints at reservations. Would you care to state your point more explicitly? JonRichfield (talk) 16:13, 19 September 2012 (UTC)

I don't think those are weasel words, at least not by the definition provided at WP:WEASEL. "Some," "many," and "most" would be normal examples of weasel words because they obfuscate the source of a statement. Words like those you mentioned are common in scientific articles where multiple theoretical possibilities exist so perhaps that's the case here, but I'm no expert on ancient climate. Sædon^talk 18:51, 19 September 2012 (UTC)

I put

"For example, the Miller–Urey experiment and similar experiments demonstrated that most amino acids, often called "the building blocks of life", were shown to be racemically synthesized in conditions possibly similar to those of the early Earth."

(emphasis added) but "possibly" was stricken with the explanation "Reverted weasel wording..". Dan Watts (talk) 01:43, 20 September 2012 (UTC)

I see what you're saying now. Before I thought that you were trying to say that the article has too many weasel words and that we need to remove some of them. Ok, well I stick by what I said earlier that those words don't quite fit the definition of weasel words. Your particular usage there seems correct to me but if there is a more certain source then we can either omit it or maybe change it to "likely." Although our theoretical models for abiogenesis are incredibly detailed and complex, I do feel a little uncomfortable talking about exact chemical processes and conditions bya with a high degree of certainty (as do most of my bio textbooks). Sædon^talk 02:29, 20 September 2012 (UTC)

What was the purpose of adding "possibly"? Science is always possible, it's not absolute. I think we've got a good idea of what were the conditions of early earth, and the wording, especially with scare quotes was unnecessary to the tone and POV of the article. This article is basically a mess anyways, a target of creationists who have been unable to make headway with evolution, so let's do our best to start cleaning up the writing. Adding in weasel-y modifiers everywhere is unnecessary to good writing. SkepticalRaptor (talk) 06:40, 20 September 2012 (UTC)

The scare quotes were to emphasize what word was the subject of the editing only. If we are certain enough of the early atmospheric constituients that such a modifier is unwarranted, how about a reference? Dan Watts (talk) 16:28, 20 September 2012 (UTC)

Given that you're trying to use the weasel word and scare quotes, how about you provide the citations? Please, no creationist websites as your source, only real peer-reviewed journals. Thanks. SkepticalRaptor (talk) 17:44, 20 September 2012 (UTC)

How about http://www.astro.ulg.ac.be/~mouchet/BIOC0701-1/Cleaves-etal-2008.pdf and http://www.sciencemag.org/content/308/5724/962.short for a pair? Dan Watts (talk) 11:41, 21 September 2012 (UTC)

Well, I'd take these to be two very good references to the fact that our understanding of the earth's primitive atmosphere continues to improve over time. I'm not clear on how they support the change you want to make. GaramondLethe 14:09, 21 September 2012 (UTC)

The title of Miller1953 is "Production of Amino Acids Under Possible Primitive Earth Conditions" (my emphasis). The text reads (in part) "In this apparatus an attempt was made to duplicate a primitive atmosphere of the earth...". Later criticism call the success of the attempt into question and, as a result, we now have much better models.

That said, I don't see a path from the above to the proposed text:

"For example, the Miller–Urey experiment and similar experiments demonstrated that most amino acids, often called "the building blocks of life", were shown to be racemically synthesized in conditions possibly similar to those of the early Earth."

I could see rewriting this as:

An early example, the Miller-Urey experiment, demonstrated that most amino acids, often called "the building blocks of life", were racemically synthesized in an approximation of an atmosphere found on the early Earth.

Comments? GaramondLethe 22:21, 20 September 2012 (UTC)

There is no doubt that you could, but how is "found on the early Earth" accurate in any sense? We don't have access to such an atmosphere. Dan Watts (talk) 13:30, 21 September 2012 (UTC)

Three answers for you.

1. You're asking a good question in the wrong venue. So long as WP:RS, WP:NOTABILITY and WP:UNDUE are satisfied, we're done.
2. A decent definition of science is "the study of what we don't have access to". It's what I do for a living.
3. As to exactly how we're able to reason about something that disappeared several hundreds of millions of years ago, the papers you linked to above cite that work. If you don't have access to it let me know and I'll send you the pdfs. If you would rather have an extended discussion feel free to drop by talk.origins on USENET. I don't post there very often anymore, but there are several scientists who hang out there who will happily answer that question at length. (Being USENET there are several nutters as well; just ignore them.)

GaramondLethe 14:09, 21 September 2012 (UTC)

Well, the first paper in its abstract states "it is now generally held that the early Earth’s atmosphere was likely not reducing" which would at least weaken the current "coditions similar to those of the early Earth".

Science is ususally (as in Wikipedia) described as "a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe", you may note the words knowledge and testable which argue against your definition. Dan Watts (talk) 21:28, 22 September 2012 (UTC)

You can make testable explanations and predictions about things you don't have direct access to. You don't need to open up an unshielded box to determine if there's something radioactive inside. Arc de Ciel (talk) 01:31, 23 September 2012 (UTC)

No doubt on your statement, but his statement contained nothing about direct or indirect, just no access, so your point is good, just not germaine. Dan Watts (talk) 02:55, 23 September 2012 (UTC)

When you said "We don't have access to such an atmosphere" did you mean "no indirect access"? I'm guessing not; someone who is slinging around references to the peer-reviewed literature probably understands that we have multiple indirect methods of characterizing the early atmosphere. Thus, the charitable interpretation was "We don't have direct access", and that is the sense that I used: you don't need science to tell if it's raining now, but since we don't have (direct) access to tomorrow's weather we have to deploy our usual tools of modeling, experimental validation, mathematical techniques and intuition.

If you think that indirect methods of assessing the earth's early atmosphere don't exist, then I guess I should ask if you're basing that idea on your evaluation of the relevant literature or your own personal incredulity. Since you seem to think that the literature can be trusted to inform us that the early atmosphere wasn't as reducing as M&U thought, I'm guessing this isn't the case (but then I don't know why you objected to M&U's paper).

I'm happy to have a conversation on philosophy of science (esp. as I hope to be teaching a grad course in that in a couple of years), but that's probably something that should be done on a user's talk page. If you're curious about how this research is done then that's appropriate to keep here. GaramondLethe 05:15, 23 September 2012 (UTC)

I could agree with:

An early example, the Miller-Urey experiment, demonstrated that most amino acids, often called "the building blocks of life", were racemically synthesized in an (currently debated) approximation of an atmosphere found on the early Earth.

That would fit the situation as I understand it. (But such a sentence would be unwieldy at best.) Dan Watts (talk) 13:12, 23 September 2012 (UTC)

There's not a debate. No one is taking the "side" that M&U have the best approximation of the early atmosphere. That work is important because it showed that amino acids can be created in the absence of biology, not because of their contributions to our understanding of the early atmosphere. GaramondLethe 13:33, 23 September 2012 (UTC)

There is a disagreement as to whether the M&U experiment generated amino acids in some approximation of an early Earth atmosphere, or an atmosphere that was more hospitable to such an endeavor. Dan Watts (talk) 19:53, 23 September 2012 (UTC)

There's no more reason to think that it was more hospitable than to think that it was less hospitable. Arc de Ciel (talk) 20:28, 23 September 2012 (UTC)

Dan, who are the disagreeing parties? Where can I read about this disagreement? To the best of my knowledge, the consensus is that M&U used a reasonable approximation given what was known at the time and we've learned a lot more in the sixty years that have followed. As an example:

But is the “prebiotic soup” theory a reasonable explanation for the emergence of life? Contemporary geoscientists tend to doubt that the primitive atmosphere had the highly reducing composition used by Miller in 1953. Many have suggested that the organic compounds needed for the origin of life may have originated from extraterrestrial sources such as meteorites. However, there is evidence that amino acids and other biochemical monomers found in meteorites were synthesized in parent bodies by reactions similar to those in the Miller experiment. Localized reducing environments may have existed on primitive Earth, especially near volcanic plumes, where electric discharges may have driven prebiotic synthesis. Jeffrey L. Bada and Antonio Lazcano, "Prebiotic Soup: Revisiting the Miller Experiment", Science, 300:2, May 2nd 2003, pp. 745-746.

I honestly don't understand what your objection is. No, M&U isn't the last word, but it's not being cited here as the last word. However, it was (according to Bada and Lazcano) the seminal experiment that began "the modern era in the study of the origin of life". All of this is, to the best of my knowledge, wholly uncontroversial. What am I missing? GaramondLethe 21:10, 23 September 2012 (UTC)

Arc, that's not quite correct. Having a reducing atmosphere was important (see the Science article cited above). GaramondLethe 21:10, 23 September 2012 (UTC)

Dan was trying to say that the actual environment didn't form the compounds as well as the M&U conditions did. I was just pointing out that we don't have reason to think that. Arc de Ciel (talk) 23:03, 23 September 2012 (UTC)

Nature - Letters December 2011 "The oxidation state of Hadean magmas and implications for early Earth’s atmosphere" states:

If our deductions regarding the oxidation state of Hadean magmas are correct, then the speciation of gases emanating from the Earth at this time would have been dominated by CO2, SO2, H2O and N2 (ref. 26).

An atmosphere of this composition is known to yield a lower abundance of sugars and especially amino acids and nucleotides.

Dan Watts (talk) 00:55, 24 September 2012 (UTC)

Cherry picking a primary research study. Letters are also not peer-reviewed. Yawn. Creationist quote mining. SkepticalRaptor (talk) 01:11, 24 September 2012 (UTC)

Which does not equate to "abiogenesis is harder than reported", as you stated in your edit summary. That is YOUR conclusion. Dominus Vobisdu (talk) 01:13, 24 September 2012 (UTC)

We're crossing paths on some really odd articles. Amusing. Isn't it ironic that the same arguments are made no matter the article? SkepticalRaptor (talk) 01:33, 24 September 2012 (UTC)

It's coincidental; our interest areas and watch lists just overlap a bit. And yes, it's always the same old arguments and tactics, whether it's creationism, or quack medicine, or astrology. Keep up the good work, and good luck! Dominus Vobisdu (talk) 01:41, 24 September 2012 (UTC)

SkepticalRaptor, the Letters section in Nature is very much peer-reviewed (criteria for acceptance, difference between articles and letters). I find this particular letter to be well within the current consensus on the topic, particularly in regard to the shortcomings of M&U's work. M&U doesn't belong in this article because they were right. M&U belongs because they came up with a novel way of looking at a hard problem and did sufficient experimental validation to demonstrate their approach had merit. GaramondLethe 02:47, 24 September 2012 (UTC)

Miller-Urey qualification

Based on a productive offline conversation with Dan and after consulting my grad evolution textbook, I'd like the lead to be changed to read, in part (changes in bold):

For example, the Miller–Urey experiment and similar experiments demonstrated that most amino acids, often called "the building blocks of life", were shown to be racemically synthesized in conditions thought to be similar to those of the early Earth.

I prefer not to have citations in the lead unless unavoidable, but I will be adding the cite in the body. As this has been contentious, here is the passage upon which I'm basing this change.

"A question that has been the subject of much research is, where did the molecules come from that were required for life to begin? ....

"In the 1920s and 1930s, A.I. Oparin and J.B.S. Haldane independently suggested that early conditions on Earth might have led to the accumulation of organic molecules that could have been precursors for life. However, these and other theoretical suggestions simply took the results of chemical studies and tried to connect them to the origins of life. They did not try to address specifically what could have been made on the early Earth.

"It was not until the middle of the 20th century that scientists attempted to simulate, in the laboratory, conditions that might have existed on the early Earth. A groundbreaking experiment, performed by Stanley L. Miller, changed how most scientists regarded these prebiotic synthesis experiments. Miller, a student working in Harold C. Urey's lab, created a simulated ocean-atmosphere interface in which methane, ammonia, and hydrogen gas were mixed with boiling water and circulated past an electrical discharge (simulated lightning) (Fig. 4.6). After only a few days under these conditions, reaction products included high yields of amino acids, including many found in modern proteins (Table 4.2). In subsequent experiments using similar conditions, a diverse array of organic molecules were created, including adenine, guanine, cyanoacetylene (a possible precursor of uracil and cytosine), and a variety of sugars. One example is ribose, the key sugar for nucleic acids, which can be produced through a version of the formose reaction(Fig. 4.7) under prebiotic conditions. When additional conditions were added, such as cycles of desiccation and evaporation (which certainly occurred on the prebiotic Earth), the variety of organic productions that were formed increased greatly.

"The Miller-Urey experiment and many of the follow-up studies were performed under reducing conditions, which, in essence, means that no O2 was present, and compounds that were present were oxygen poor and hydrogen rich (e.g., CH4 not CO2 and NH3 not NO2). Miller used strongly reducing conditions because, at that time, a number of scientists believed that the early atmosphere was a highly reducing environment. More recent studeies suggest this may not have been true. Instead, conditions near the Earth's surface appear to have more closely resembled a weakly reducing mix of CO2, N2, water, and other components. Under these conditions, many fewer kinds of organic molecules are created.

"One such location is outer space, which, in general, is a highly reducing environment. ....

"Space is not the only place we might look for the origin of life. Even if the atmosphere of the early Earth was not a reducing environment, there are other places on earth that almost certainly were. Perhaps the best examples are the hydrothermal vents found deep beneath the sea...."

Nicholas H. Barton et al., Evolution, Cold Spring Harbor Laboratory Press, 2007, pp. 93-95.

Comments?

GaramondLethe 20:46, 25 September 2012 (UTC)

It all sounds pretty unobjectionable to me, including the quoted text. JonRichfield (talk) 06:27, 26 September 2012 (UTC)

And I haven't forgotten that I owe you some papers.... GaramondLethe 07:40, 26 September 2012 (UTC)

Nooo problemo! Take your time. Plenty happening at this end. JonRichfield (talk) 12:44, 26 September 2012 (UTC)

That wording is reasonable then. Thanks for the citation. :-) Arc de Ciel (talk) 06:04, 27 September 2012 (UTC)

Glad you got some use out of it. We're kinda in tl;dr territory there, but it's a subtle (and important) point. GaramondLethe 06:37, 27 September 2012 (UTC)

Bret Palmer

Unfortunately, if I understand this correctly, Bret is or was basing his entry, as reverted by Harizotoh9, on a publication of his own. Now, I have a lot of reservations on WP pillars, and in particular with OR, but that really is a bit over the odds. I cannot tell from the text as it stood before reversion, whether I am to support the inclusion of the reference or not, and when I tried to look up the source I could not get further than the abstract, which was not a great deal more informative, but if Bret wishes to make his article text available through suitable channels, I would not mind having a look to see whether to take the matter further. FWIW. JonRichfield (talk) 11:55, 22 October 2012 (UTC)

The hypothetical study reversion

In case the editor whom DrBogdan requested to take it to the talk page, feels like actually doing so, please think again. The reversion was quite correct. You might or might not think that the event or process of abiogenesis itself is hypothetical, and many of us who do not seriously question the concept and reality of abiogenesis would not argue, but the study of potential mechanisms and histories of abiogenesis is as factual and material as any other study. Please be careful about such wording. JonRichfield (talk) 19:43, 6 November 2012 (UTC)

Never mind the theory, mind the lede

Folks, has anyone read the lede lately? I was about to re-state the opening sentence into something incontrovertible <cough>, cogent, coherent, and unobjectionable <hysterical cackling>. Then an insane impulse moved me to read the rest of the lede. It is a mess. Most of it, insofar as the concepts are sound or debatable, belong in the main text and should definitely not be in the lede. It also is badly stated and and badly structured. The only parts that don't belong in the main body of text don't belong anywhere else either. Does anyone envisage making rash offers? JonRichfield (talk) 14:27, 8 December 2012 (UTC)

From "Abiogenesis" to "essentially molten)" the text seems admirably suited to a lead. From "Hypotheses about" to "self-replication" the text seems informative but without a proper home in the article. - Fartherred (talk) 06:52, 10 December 2012 (UTC)

Spontaneous generation called abiogenesis only recently

The article gives the impression that old ideas of spontaneous generation were once called abiogenesis. This cannot be the case because the word "abiogenesis" is first documented to have been used in English since 1870 (Merriam-Webster's Collegiate Dictionary Eleventh Edition) about the time that Darwin wrote Joseph Dalton Hooker about his ideas of abiogenesis. I will correct this false impression. - Fartherred (talk) 07:58, 10 December 2012 (UTC)

Citation needed statements

The following statements have the {{cn}} tag, and were removed and put back. I am not knowledgeable enough on the science to research and find citations for them. I think someone should. If these have no basis in research, then they should be removed.

• The spontaneous formation of complex polymers from abiotically generated monomers under the conditions posited by the "soup" theory is not at all a straightforward process. Besides the necessary basic organic monomers, compounds that would have prohibited the formation of polymers were formed in high concentration during the Miller–Urey and Oró experiments.

• More fundamentally, it can be argued that the most crucial challenge unanswered by this theory is how the relatively simple organic building blocks polymerise and form more complex structures, interacting in consistent ways to form a protocell. For example, in an aqueous environment hydrolysis of oligomers/polymers into their constituent monomers would be favored over the condensation of individual monomers into polymers.

• Waves breaking on the shore create a delicate foam composed of bubbles. Winds sweeping across the ocean have a tendency to drive floating surface particles to shore. Possibly such shoreline sea foam and windblown organic particles could interact on the beach.

--Harizotoh9 (talk) 00:19, 22 December 2012 (UTC)

Very outdated article, needs to mention new experiments

Science has progressed and the useless experiments mentioned on the article have since been replaced.

1) Sydney Fox's proteinoids were proven to be junk in the 1970s

"Sydney Fox and the other researchers managed to unite the amino acids in the shape of "proteinoids" by using very special heating techniques under conditions which in fact did not exist at all in the primordial stages of Earth. Also, they are not at all similar to the very regular proteins present in living things. They are nothing but useless, irregular chemical stains. It was explained that even if such molecules had formed in the early ages, they would definitely be destroyed."

S. W. Fox, K. Harada, G. Kramptiz, G. Mueller, «Chemical Origin of Cells», Chemical Engineering News, June 22, 1970, p. 80.

If the amino acids in his experiments were to be kept at a steady temperature, the amino acids would've disintegrated

Richard B. Bliss & Gary E. Parker, Origin of Life, California: 1979, p. 25.

2) Miller's experiment was based on conditions of the Earth which are now thought to be different (1993)

"Many scientists now suspect that the early atmosphere was different from what Miller first supposed. They think it consisted of carbon dioxide and nitrogen rather than hydrogen, methane, and ammonia. That's bad news for chemists.When they try sparking carbondioxide and nitrogen, they get a paltry amount of organic molecules- the equivalent of dissolving a drop of food colouring in a swimming pool of water. Scientists find it hard to imagine life emerging from such a diluted soup."

Ali Demirsoy, Kalı tı m ve Evrim (Inheritance and Evolution), Ankara: Meteksan Publishing Co., 1984, p. 61.

3) Miller admitted polymerization would not have occurred in his experiments (1998)

"Geologist now think that the primordial atmosphere consisted mainly of carbon dioxide and nitrogen, gases that are less reactive than those used in the 1953 experiment. And even if Miller's atmosphere could have existed, how do you get simple molecules such as amino acids to go through the necessary chemical changes that will convert them into more complicated compounds, or polymers, such as proteins? Miller himself throws up his hands at that part of the puzzle. "It's a problem," he sighs with exasperation. "How do you make polymers? That's not so easy."

Cliff, Conner, «Evolution vs. Creationism: In Defense of Scientific Thinking», International Socialist Review (Monthly Magazine Supplement to the Militant), November 1980. — Preceding unsigned comment added by 166.87.144.212 (talk) 16:24, 26 December 2012 (UTC)

Abiogenesis is not an idea, but a "set of hypothesis" or the "study of life arising from inorganic matter"

Dictionary.com is not a good source of definitions :P It compares spontaneous generation to abiogenesis — Preceding unsigned comment added by 166.87.144.212 (talk) 16:26, 26 December 2012 (UTC)

Definition

The first sentence of a lede should give the definition of the entry. Merriam-Webster is a good source for definitions. That Abiogenesis is often used for the specific case of the origin of life on earth is made perfectly clear in the second sentence of the lede. So, I still prefer my version of the first sentence (the definition of "a-bio-gen-esis" as "not-life-make-process".Northfox (talk) 08:09, 19 January 2013 (UTC)

A dictionary is not a suitable source for an article on a scientific topic (is the definition what scientists mean, or is it an historical meaning once held by some people with no knowledge of the subject?). I won't join the edit war at the moment, but the wording "spontaneous origination of living organisms directly from lifeless matter", is totally inappropriate in an encyclopedic article on the scientific topic. Judging from some of the recent edit summaries, some editors are confused about this topic as abiogenesis involves various hypotheses, all based on the opinion that determining how life probably arose on Earth should be the subject of rational investigation, rather than hocus pocus. Johnuniq (talk) 09:12, 19 January 2013 (UTC)

Agreed. The definition they give for evolution is even funnier. TippyGoomba (talk) 09:25, 19 January 2013 (UTC)

Merriam-Webster is a non-technical source. Low quality and written by non-scientists. --Harizotoh9 (talk) 10:43, 19 January 2013 (UTC)

Truly the lede in this article does need to be changed to move the bias of assuming this to be a fact rather than something that is a theory. There has been no experiments that have shown abiogenesis to be a viable explanation. Particularly Miller/Urey showed that a random creation of these protein molecules produced a result that prohibited amino acid formation. — Preceding unsigned comment added by Lebs27 (talk • contribs) 11:44, 19 January 2013 (UTC)

Lebs27, reliable sources would need to be found before any such material could be included into the article. --Harizotoh9 (talk) 11:48, 19 January 2013 (UTC)

I keep getting censored/talk sections deleted for pointing out the scientific ignorance of whoever edits this article. For the idiot who keeps changing this - hypothesis-observation-theory. Abiogenesis is a hypothesis. Harizotah9- reliable sources for something that has obviously never been demonstrated nor observed? None exist (OBVIOUSLY).Jinx69 (talk) 01:17, 20 January 2013 (UTC)

Define "hypothesis" then? — raekyt 01:30, 20 January 2013 (UTC)

User:Jinx69 has been permabanned. --Harizotoh9 (talk) 09:34, 20 January 2013 (UTC)

Harizotoh9: "Merriam-Webster is a non-technical source. Low quality and written by non-scientists." Please xcuse me when I laugh. I compared the definitions of the following words in Merriam-Webster with the first sentences in the ledes on their English Wikipedia pages. They look pretty much the same to me: osmosis, bird, ship, photon. Other words are described even better in M-W than in wikipedia, e.g. "moon". M-W even covers outdated concepts, such as "Phlogiston theory" pretty good. So, since it cannot be demonstrated that M-W is a low quality source, I suggest to change the abiogenesis definition to the M-W one. Northfox (talk) 13:26, 20 January 2013 (UTC)

addendum about the use of tertiary sources, which shows that it is okay to use an encyclopedia definition : http://en.wikipedia.org/wiki/Wikipedia:Identifying_reliable_sources#Primary.2C_secondary.2C_and_tertiary_sources Northfox (talk) 13:42, 20 January 2013 (UTC)

This is not the place to debate whether or not abiogenesis actually took place. (Another theory is that abiogenesis did not take place on earth. (http://www.nasa.gov/topics/solarsystem/features/dna-meteorites.html) This is an article on a scientific theory, and should state the best current understanding of that theory according to standard scientific sources. Rick Norwood (talk) 14:15, 20 January 2013 (UTC)

It did take place, and this is scientifically uncontroversial - thus the word "hypothesis" is out of place, but your point about the possibility of panspermia is valid and I have edited the text to allow for that.

In the meantime, I have restored the original definition pending discussion (WP:BRD). My main concern (besides the points that have already been made about trying to use a dictionary definition for a technical scientific topic) is that to the best of our understanding, abiogenesis is a process and not a single event. I have made these points in a previous section above. Also, "inorganic" is more correct than "lifeless" as the generation of organic compounds is part of abiogenesis research; this is discussed in the article. Arc de Ciel (talk) 01:37, 21 January 2013 (UTC)

As I have demonstrated with many examples (see my above post with definitions of "osmosis, bird, ship, photon"), wikipedia very often and legitimately uses encyclopedia-style definitions. Arc de Ciel and others have to bring very good arguments against using a similar approach here. Just because this particular encyclopedic entry does not fit your world-view is not enough. A case for arbitration? Northfox (talk) 13:07, 23 January 2013 (UTC)

It's ridiculous to intentionally want to use low quality sources when high quality sources exist. The quality of an article is partly determined by the quality of sources used. Using such a low quality source will decrease the overall quality of an article. I can't see this article surviving GA review while using such a source in the lede. --Harizotoh9 (talk) 13:53, 23 January 2013 (UTC)--Harizotoh9 (talk) 13:50, 23 January 2013 (UTC)

Wikipedia often uses dictionary or encyclopedia definitions when they are uncontroversial. I don't think anyone would object to a dictionary definition of "bird" as a vertebrate with feathers. But, for a complicated scientific concept such as abiogenesis, clearly scientific books and papers are preferred sources. Rick Norwood (talk) 15:37, 23 January 2013 (UTC)

Is it too complicated to put into present tense? Why is arises put back in past tense arose? Its a process. Processes are continuous and usually written in present tense. 'Especially whe in the first sentence of the lede, which gives the difinition. The second sentence gives the more narrow story of abiogenesis on earth, which, in the past tense, describes the once in a 4 b years event. Northfox (talk) 14:17, 24 January 2013 (UTC)

Past tense in the 1st sentence of the lede is pretty anthropocentric. Just because a process is thought to have occured once in the past on earth, we cannot imagine this happening again in some other corner of the universe? Imagine someone finds ongoing abiogenesis on another world. By following the thought processes of the dominating editors of this article, that someone has to coin another word for what he found, because 'abiogenesis' is a thing of the past. By putting the definition in the past tense, abiogenesis is removed from the realm of natural science, since by its very own definition, it is a once in the past process. Never to be repeated, never repeatable. Is that what you want? I don't. Northfox (talk) 13:25, 26 January 2013 (UTC)

Need/Request for Plain English

Abiogenesis is an important subject for anyone interested in how life began on Earth. However, the use of scientific jargon in this article makes it difficult to understand for the non-scientifically trained reader. I have a very good understanding of the concepts in this article, but have absolultely no idea what a Ga is as am measurement of time, and have forgotten how to translate exponential notation eg. 10^9 - I don't know that if that is a billion or a trillion.

To give you a relative example of a well written article, I have a very good understanding of subjects related to quantum mechanics and can fully understand the articles on the famous twin slit experiments as they are written well in plain English without the need for scientific jargon. This article could be greatly improved and appeal to a much broader general audience if simple alternatives to scientific notation were also used e.g writing "2.5 Billion years ago" in addition to the Ga units that I and many people utterly fail to comprehend.

--Savlonn (talk) 15:18, 23 February 2013 (UTC)

Special Creation

The earliest thoughts of the origin of live is Special Creation. The idea still has wide influence and ought to be mentioned. It certainly is not verifiable, as unique events cannot by definition be replicated. It is certainly not scientific either (as it cannot be disproven). But the article does mention other early ideas as to the rise of life, and Special Creation is one of those. It ought to be mentioned, if only briefly. Paul, in Saudi (talk) 04:58, 24 February 2013 (UTC)

Pretty simple, No. Science article, is about science, magic is not science, thus not included in science article. We have articles for those fairy tales, this is not one of those. — raekyt 05:01, 24 February 2013 (UTC)

Excuse me, I ought to have read the whole talk page first. I see you Smart People have hashed this out before. I may not agree with the decision, but I can see you discussed it and I respect both the editors and the process. Paul, in Saudi (talk) 05:03, 24 February 2013 (UTC)

It's actually policy, WP:NPOV, WP:DUE, WP:FRINGE. — raekyt 05:05, 24 February 2013 (UTC)

(Now why am I arguing when I have already surrendered?) As Special Creation is thought to be true by a couple of billion people, it cannot meet the definition of "fringe." But in any case, I retract my question as it has been addressed. I propose we let this drop so I can go back to my obcessive correction of capitalization errors. Paul, in Saudi (talk) 05:19, 24 February 2013 (UTC)

In science it's very very very much fringe, and that's where the policy part comes in why it can't be in this science article. — raekyt 05:35, 24 February 2013 (UTC)

I think that there is room for further discussion here. I agree that Special Creation has no place in a scientific article on abiogenesis. However, the hypothesis of abiogenesis has yet to be emperically proven. The problem therein lies with the dis-ambiguation that directs to this article. "Origin of life redirects here". This is an assumption that is not yet scientific fact in the same way that evolution is.

My point is that although reason points strongly towards abiogenesis as being responsible for the origin of life, the lack of emperical proof would lead a neutral article to allowing for non-scientific alternatives. The disbiguation to this article, with only "abiogenesis" and "creation myth" only provides disambiguation from a scientific article perspective. What is missing is the disambiguation of "origin of life" that allows for other hypothesis without defaulting to the position of an unproven scientific article. Savlonn (talk) 13:28, 2 March 2013 (UTC)

It is as much a scientific fact as gravity. Abiogenesis has more evidence than the theory of gravity does. It's an incorrect assessment to say that it's "not been empirically proven" because thats not really what happens in science. You don't prove anything. Theres a reason why we don't have any competing theory, we know for sure that life can arise from nonlife by some method. The exact methodology and conditions is up for debate, but that it does happen isn't. Noone in the scientific community is seriously entertaining that a magic sky daddy did it, at least not anyone taken seriously and they represent again, the MAJOR fringe point of view. You're confusing that we don't know EXACTLY how with we don't know that it happens. It happens, how is up for debate. — raekyt 14:35, 2 March 2013 (UTC)

Though I don't agree with everything Raeky says, at least not in the way that he says it, he is perfectly correct in general, and in particular he is correct in pointing out that the concept of proof in empirical science (as partly opposed to formal disciplines such as maths or logic) is treacherous at best and in fact might best be dropped altogether. If Savlonn thinks that he could find an example of absolute proof in science, good luck in trying to prove that water is H2O. Or even that there is water. The nearest we come to proof in science is that we have sufficient evidence to render one hypothesis so much more probable than all known alternatives or rivals, that to insist on any other would be unreasonable. Commonly we get by very well with far weaker assumptions. Such as the evidence that Water is H2O and that F=MA and that e=mcc. JonRichfield (talk) 19:35, 2 March 2013 (UTC)

Well said imo - I'm reminded that Bertrand Russell seems to have made an enormous effort in his Principia Mathematica to "prove", greatly simplified, that "1 1 = 2" - apparently, the effort was not entirely successful - at least according to some - seems like one of our very best "facts" may still be a "belief" in some ways? - in any case - Enjoy! :) Drbogdan (talk) 20:35, 2 March 2013 (UTC)

Amino Acids and Proteins

Amino acids when linked by nitrogen bonds form proteins and it is not understood how hundreds of amino acids became spontaneously linked to form the primary structure of a protein.

What is the argument for removing this? KnowledgeIncreases07 08:06, 31 March 2013 (UTC)

Your source can not be used to support the argument you are making, that's why it's being removed, and will be removed. You've also clearly violated WP:3RR and have been reported for doing so. You can't state "it is not understood how hundreds of amino acids became spontaneously linked to form the primary structure of a protein" within the WP:LEAD of Abiogenesis with using a source that doesn't even have anything to do with Abiogenesis from the abstract, and clearly doesn't state what you're stating. Please refrain from making additional edits to this article before discussing them on the talk page. — raekyt 08:18, 31 March 2013 (UTC)

It doesn't have to be a direct quote to be supported from the source! KnowledgeIncreases07 08:28, 31 March 2013 (UTC) From the abstract! Read the fulltext! — Preceding unsigned comment added by KnowledgeIncreases07 (talk • contribs) 08:30, 31 March 2013 (UTC)

What makes you think this article has anything to do with abiogenesis? Plus where EXACTLY does it state that we don't know how proteins form? Even with my BS in Biology this is a difficult to understand article, but I'm quite sure that it's not saying what you think it's saying. — raekyt 08:34, 31 March 2013 (UTC)

Secondly I need to add, WP:SECONDARY is preferred over WP:PRIMARY for sourcing. Discuss here if you think a source is improper before you remove it, it's not clear that you understand your policies when it comes to sourcing just yet. — raekyt 08:21, 31 March 2013 (UTC)

Please address the argument. The fact is is that it is not known how amino acids spontaneously formed the primary structure of proteins. To say otherwise is misleading. The reference I cited discusses protein synthesis including translation, and then goes on to discuss the formation of the tertiary structure of proteins. However, the first and simplest step is the formation of the primary structure of proteins, which the article discusses. So by ignoring the structure of proteins, even the primary structure, you are misleading people to think that it is known how they could spontaneously form. Please don't use circular reasoning in your argument. I list a reference which describes protein synthesis, including translation, which forms the primary structure. I do not elaborate on how we do not understand how the proteins spontaneously formed tertiary structures without chaperones. I simply bring attention to a relevant factor of all living cells, they all have proteins. Each protein has a primary structure or sequence of its amino acids. You might end up removing it from the page, but to do so it to choose ignorance over scholarly discussion. If you have to cite my "presumed" motives as the basis for your reasoning, then perhaps you have little basis for discrediting my scientific discourse. — Preceding unsigned comment added by KnowledgeIncreases07 (talk • contribs) 08:44, 31 March 2013 (UTC)

Heres a source, plus I'm sure from it's citations it would yield more, and many more can probably also be found. — raekyt 17:04, 31 March 2013 (UTC)

Thank you, I am more familiar with wikipedia policy on primary versus secondary sources now. If you would like me to cite Thomas M. Devlin's biochemistry book as a secondary source for my statement about amino acids and proteins, then I will do that. His biochemsitry book and several others support my claim that we do not know how amino acids could spontaneously form a protein, something far different than a proteinoid, is of neutral tone, accurate, supported by the literature, and is not in contrast to any known scientific information. Without fabricating my motives, please address how that is misleading. — Preceding unsigned comment added by KnowledgeIncreases07 (talk • contribs) 08:52, 31 March 2013 (UTC)

Just because you THINK you know that science doesn't have an explanation for it, lack of a source doesn't allow you to insert original research or your personal opinion. If you have a reliable source that states it then that's different. Your source is irrelevant for the article's lead and your statement. — raekyt 09:01, 31 March 2013 (UTC)

Fringe water

I don't like removing articles from external link lists, but I have to support Raeky's removal of Analyticus' items. Those really are right into fringe handwaving. They strongly recall the work of Jacques Benveniste on "water memory". It would be nice simply to say: "Well, who are we to deny them recognition without due discussion and showing conclusively that they are without substance or notability?" However, if they are notable at all, they certainly are not notable for any contribution to abiogenesis, either factual or intellectual, so I don't think that we have to feel too bad about not affording them any attention in this article. JonRichfield (talk) 08:22, 2 April 2013 (UTC)

Life from "Inanimate Matter" or "Simple Organic Compounds"?

FWIW - Is the present definition of Abiogenesis too narrow? - Abiogenesis is being defined as "the natural process by which life arises from simple organic compounds" - do we know, as a fact, that life cannot initially arise from "Complex organic compounds"? or that life cannot arise from "Non-Carbon compounds"? - I don't think we know the answer to either question at the moment - seems a broader, more open-minded, approach to the definition of Abiogenesis may be in order - one suggestion is that Abiogenesis be defined as "the natural process by which life arises from "inanimate matter" - this phrasing would broaden the present definition of Abiogenesis to include the possibility that life could initially arise from "Complex organic compounds" as well as from "Non-Carbon compounds" - of course a clear definition of Life might help with this - but such a definition of Life seems *very* elusive at the moment - another reason, I would think, to maintain as broad a definition of Abiogenesis as possible - if interested, a somewhat related discussion of possible life-forms developing on exoplanets may be found HERE - in any case - Enjoy! :) Drbogdan (talk) 00:52, 11 April 2013 (UTC)

Well, the molecules that we believe that initially sparked life wasn't that complex. Even amino acids are not a very complex molecule individually. We have no examples or even understanding of how it would be possible for non-carbon based life. Silicon based life is the best closest approximation, but Silanes are too reactive, so I don't think there is any serious scientific hypothesis on how it would be plausible. (could be wrong here). I chose to use the additive simple to avoid people thinking that things like DNA would be necessary for life to begin. DO we have any sources that say "complex" is a necessary precursor, or "non-carbon" is possible? — raekyt 02:59, 11 April 2013 (UTC)

Thank you for your comments - there seems to be reliable sources that "complex organics" (possibly in the form of polycyclic aromatic hydrocarbons and fullerenes, at least, are being created in nebulae [and in astronomical amounts?] (see PAH world hypothesis#Polycyclic aromatic hydrocarbons and the related detection in outer space (esp in cosmic dust?) of "amorphous organic solids with a mixed aromatic–aliphatic structure") (and related ApJ reference and Phys.Org reference) and, as well, the theoretical possibility that such "complex organics" may be involved in abiogenesis (see PAH world hypothesis & related) - nonetheless, should "complex organics" or "non-carbon compounds" be ruled out (so-to-speak) in the present definition of abiogenesis as possible avenues to the origin of life when there are no "reliable sources" currently (afaik) that life can actually be created from inanimate matter (or "lifeless" material) of any sort (*including* "simple organic compounds", an overly restrictive (imo) presumption which may, or may not, be true)? - in any case - Enjoy! :) Drbogdan (talk) 16:00, 11 April 2013 (UTC)

There's TONS of sources that say life can arise without some magical sky daddy doing it, so I don't quite get what you mean by "no reliable sources saying it can happen." If you mean, no-one has done in a lab, that's entirely differently. But there's VAST amount of sources saying it can and does happen, the methodologies of exactly how is what's being predicted, debated and tested. There's a reason why the lead stats it does happen, because it did and does. It's not overly restrictive to state that life needs to be carbon based, because that's coming down to simple chemistry, show any reliable source that posits a credible hypotheses for non-carbon based life, and I'll change my mind. Complex vs. simple, is semantics. In biology complex is things like DNA and proteins. The individual building blocks of DNA/RNA and Proteins themselves are not exactly complex. The initial spark of "life" that natural selection would act on and eventually lead to complex life wouldn't of been that complex, again per sources. This article probably really needs brought up to modern speed, and some of the hypotheses probably need axed due to WP:WEIGHT and WP:FRINGE. — raekyt 04:13, 13 April 2013 (UTC)

Thanks for your comment - several points:

• 1) Yes, the process of going from "Inanimate Matter" to life happened in the universe - apparently, at least once - if interested, see My Published Comment in The New York Times about some of this.
• 2) Yes, I agree, a current scientific challenge is determining "exactly how" life came from "Inanimate Matter".
• 3) Yes, I do mean "no one has done it in the lab" - should add that viruses seem to have been created de novo ("from scratch") in the lab (see Virus#Synthetic viruses and "Science (journal)" ref) - a clear definition of life, as noted earlier, might be helpful in understanding if these are, or are not, "life-creating" events of course.
• 4) Yes, it's overly restrictive (imo) to think life needs to be carbon-based (see Carbon chauvinism - apparently, Carl Sagan and physicist Victor J. Stenger also thought being more open-minded about such matters is a better road.)
• 5) Yes, "complex organics", to me, includes polycyclic aromatic hydrocarbons and fullerenes (and not just nucleic acids and proteins) - should note that NIH scientists recently reported studies, based on extrapolating "genetic complexity of organisms to earlier times", suggesting life began "9.7±2.5 billion years ago", billions of years before the Earth was formed - the scientists noted that life may have started "from systems with single heritable elements that are functionally equivalent to a nucleotide".< ref name="arXiv-20130328">Sharov, Alexei A.; Gordon, Richard (28 March 2013). "Life Before Earth". arXiv:1304.3381v1 [physics.gen-ph].</ref>< ref name="NIH-20060612">Sharov, Alexei A. (12 June 2006). "Genome increase as a clock for the origin and evolution of life". Biology Direct. 1: 17. doi:10.1186/1745-6150-1-17. PMC 1526419. PMID 16768805.</ref> (also see Abiogenesis#Coenzyme world and Panspermia#Complexity)
• 6) Yes, I agree, considering WP:WEIGHT and WP:FRINGE in the Abiogenesis article may be indicated.

In any regards - Thanks again - and - Enjoy! :) Drbogdan (talk) 13:23, 13 April 2013 (UTC)

Abiogenesis is a scientific theory

I have no clue why people are trying to remove "theory" from the first sentence of the lead. One editor apparently doesn't understand what a scientific theory is. And another wants to weasel word it for some indecipherable reason. Abiogenesis is a scientific theory based on the evidence and scientific consensus. Like Evolution. Or gravity. Or Cell theory. Or Germ theory. The Big Bang. Etc. etc. etc. SkepticalRaptor (talk) 07:43, 4 December 2012 (UTC)

- Abiogenesis should be considered a law. Despite the failure of every experiment ever to form a self-replicating organism from non-living matter, some hypothesize that abiogenesis should be considered a theory based upon the fact that the building blocks can be formed.

-The current abiogenesis page is more precursor chemistry and not organically related. It is better suited for chemists. As a cellular biologist and biochemist, finding the necessary components of abiogenesis is no where close to finding the sufficient requirements for life. A self-replicating rna molecule or protein is not very relatable to a self-replicating system that maintains homeostasis. Harvard's lab has shown that small liposomes will equally partition very tiny fragments of RNA but has no such evidence of larger proteins or RNA fragments. — Preceding unsigned comment added by 152.79.9.48 (talk) 19:44, 24 April 2013 (UTC)

Actually, there are several theories of how abiogenesis occured, but abiogenesis itself is a phenomenon, like evolution. The difference with evolution is that for evolution, only one theory has significant support, so the "theory of evolution" is shorthand for that particularly theory. Dominus Vobisdu (talk) 07:49, 4 December 2012 (UTC)

If it was anyone else but you DV, whom I trust, I'd probably be rude and snarky. I'm going to strongly disagree with you. There is one theory of evolution that includes several possible mechanisms (genetic drift, natural selection, and something else that I can't remember, but is fairly controversial). The same here. There is a "theory of abiogenesis", that is, life arose from a non-biological chemical reaction (really dumbing that down, but we all know what it is). However, the mechanism of such is under discussion. Scientific theories don't have to describe a mechanism, but is "a well-substantiated explanation of some aspect of the natural world, based on a body of facts that have been repeatedly confirmed through observation and experiment." As you are very aware, creationists misuse the word "theory", but I have found that amateur scientists tend to misuse it too. Here's one article that describes the "theory of abiogenesis" though in context with a particular mechanism. I didn't just cherry pick articles that describe "theory of abiogenesis", I just chose one of the most recent publications (2012). I'll go along with your edit, though I strongly disagree. If you were a creo-bot, I most certainly would revert it. But I would like you to consider my points, however. SkepticalRaptor (talk) 20:32, 4 December 2012 (UTC)

We can speak of "the theory of gravity" or "the theory of evolution" and there would be little scope for confusion. We have many (and counting) candidate ideas of how abiogenesis occurred, and to speak of "the theory of abiogenesis" in the sense of "what a scientific theory is" would lead to some very peculiar looks from anyone who knew the field at all well. The better he knew the theory, the less well he would understand what you meant. OTOH, if you spoke of the "process" or "fact" of abiogenesis, he wouldn't even blink; you don't know the details of how it happened and neither would he, but he (and I hope you) would have a pretty good idea of which ideas might have contributed and which roles some of them might have played. We are confident that abiogenesis occurred. We are not confident of the details. Why speaking of the natural process or event or fact should suggest "weasel words" nonplusses me rather; I thought they were what one might call plain and specific English. Hmmm? JonRichfield (talk) 20:28, 4 December 2012 (UTC)

JR, I would consider that an amateurish description of "theory". That's not a criticism, that's just what counts for good editing on this project. We'd rather use commonplace definitions of words, than really writing as if there's science involved. If you think "facts" are used in science, my case is closed. SkepticalRaptor (talk) 20:35, 4 December 2012 (UTC)

SR, it wasn't a description or definition of a theory, only a discussion of why one would not use the word "theory" in this context. The fundamental concept of a "fact" in science is as you imply, not valid of course, but the informal concept is neither easy nor even profitable to eradicate. We have pretty conclusive reason to suspect that life on Earth (or nearby, if you include panspermia in some form) did not exist say 6 GY BP and pretty conclusive reason to suspect that it does now. Most scientists in most contexts would not squirm too violently if we spoke of the "fact" of abiogenesis at some time in the intervening period. In fact they might speak of weaseling if we avoided the term too religiously. But by all means speak of "assumptions" or the like if you insist. Personally I am not much fussed in this case, but to say "abiogenesis is a theory" grates on my ear, whereas "the body of theory dealing with abiogenesis" does not. (I had been going to write "the theory of abiogenesis" but that could ambiguously suggest the same as meaning as "abiogenesis is a theory".) JonRichfield (talk) 20:57, 4 December 2012 (UTC)

In "plain and specific English" the question of whether abiogenesis was a natural process or an miraculous event is not addressed by writing "We have pretty conclusive reason to suspect that life on Earth (or nearby, if you include panspermia in some form) did not exist say 6 GY BP and pretty conclusive reason to suspect that it does now." One can claim that there is nothing but the universe following the natural laws of physics from the beginning with a singularity until thermodynamic death, but that just pushes the first cause off a way. Who or what caused the laws of physics to favor a big bang? Are the laws of physics a deity sufficient for their own being and worthy of worship? The point of using "natural process" to describe abiogenesis seems to be inferring that not only is abiogenesis an idea but it is a true idea. That sort of thing belongs on philosophy pages not in [[Abiogenesis]]. The panspermia hypothesis is generally contrary to the assumptions of those working to understand a mechanism for abiogenesis, as is the suggestion of Nick Bostrom that the universe could be a sort of computer simulation. Those are published ideas. - Fartherred (talk) 22:50, 5 December 2012 (UTC)

Errr... OK, I guess, but are we talking about the same thing? I certainly wasn't discussing miracles or even miracules, let alone worship, and I didn't think that SR was. I thought he and I understood each other fairly well, but perhaps if you re-read our exchange more carefully...? JonRichfield (talk) 08:25, 6 December 2012 (UTC)

We may not understand each others thinking perfectly as represented by what we wrote on the talk page but I think we are close enough to consensus to move forward with improving the article as time and ability permit. If disagreements show up that way, we can discuss them as they arise. - Fartherred (talk) 04:47, 7 December 2012 (UTC)

I have to strongly object to the lead sentence as written now. The word "idea" can be interpreted as philosophy, and there are many arguments (creationists, etc) that in that direction. It means that if someone with that particular misconception reads that statement, they will stay misinformed. Abiogenesis is a process, and (when referring to the origin of life on Earth) an event. Philosophical articles start out like that; scientific articles should not. Arc de Ciel (talk) 08:41, 8 December 2012 (UTC)

I object to the previous sentence in the lead: "Abiogenesis .... is the natural process by which biological life arose from inorganic matter." because 1) it is not supported by observation or experiment and is therefore not science 2) it is championing the point of view of a clique active on wikipedia, namely the atheist point of view 3) the position that all observable phenomena must arise from natural processes is a philosophical position and as such does not belong in the [[Abiogenesis]] article and 4) it is not referenced. One might call Abiogenesis a theory or a hypothesis, but there should be a reference for it. Even calling it a natural process would be considered if there were a reference from a source comparable to britannica.com supporting such. It would be wrong to have such an unscientific statement in the article, but after all, Wikipedia is not about being right or wrong, it is about having reliable sources well represented.

I grant that respectable scientific theories and whole areas of study have started out as ideas unsupported by experiment or specific observation, and in some cases took a long time to be properly supported and be more than a hypothesis. The idea usually comes before the experiment. Abiogenesis still languishes in the area of hypothesis.

So far "Abiogenesis .... is the idea that life arose from inorganic matter." is the best representation of reliable sources that has been offered, objections by editors, no matter how strong, not withstanding. It suffers from none of the faults I enumerated above. Some atheists might think that it is part of a Christian conspiracy to tweak the noses of any atheistic Wikipedians any time the opportunity arises, but this is not the case. The miraculous occurrence of abiogenesis is not part of the doctrine of any Christian group that I know of. Christians teach that it is proper to love benighted atheists, though not necessarily to associate with them lest some of their errors rub off. The word idea was put in its proper place to enlighten any atheist who considers it established scientific fact that abiogenesis is a natural process and is therefore sadly misinformed. - Fartherred (talk) 06:04, 10 December 2012 (UTC)

Abiogenesis is a hypothesis. A hypothesis is nothing more than a proposed explanation. You don't need a source to call it one.98.209.42.117 (talk) 04:28, 16 December 2012 (UTC)

I agree. However, I do not think that it would improve the article to substitute hypothesis for idea. - Fartherred (talk) 00:02, 17 December 2012 (UTC)

It does suffer from the faults that I enumerated above. The simple statement that abiogenesis occurred is indeed established scientific fact, and is already supported by most of the sources in the article. (Contrary to what you seem to be saying, that statement does not exclude any role for a creator.)

A few explicit statements I found from a few minutes of searching: "the earliest living cells emerged as a result of chemical evolution on our planet billions of years ago in a process called abiogenesis" [6], "the origin of life...was a gradual process" [7],"the origin of life was a process initiated within..." [8], "the appearance of the first living things from nonliving origins, the process sometimes called abiogenesis" [9], and so forth. The word "natural" is superfluous and generally omitted (as in these examples) since this is a scientific article and science only deals with natural processes; but philosophical discussion doesn't belong in this article, as I pointed out and you restated, and I think that including the word helps to clarify what exactly is being discussed. You can also read any number of scientific journal articles that don't make such explicit statements but which simply take it for granted.

Also, your "atheists vs Christians" narrative isn't relevant to the issue. Arc de Ciel (talk) 03:21, 17 December 2012 (UTC)

Your first quote was from Scientific American, to which I do not subscribe and which was unavailable to me. Your second quote left out "...first detailed exposition of the theory that living tissue was preceded upon Earth by a long and gradual evolution... ", a comment in a New York Times review which gives context. Your third quote is from a pdf file which I will wait to access until I use a computer that runs the proper software. The web page that I reached with the address accompanying your fourth quote did not contain the quoted text.

You may be assured that all four sources contain the quotes that I gave you. The fourth quote is at the top of page 47.

I do not see the relevance of your pointing out the "first detailed exposition" quote, which is not even on the same page. The source is one of the foundational books of the field, and your quote helps to illustrate this. (You may also notice that the paragraph refers to abiogenesis as a theory.)

You claim that including the word natural would help to "clarify what exactly is being discussed." However you did include in the article the bald statement that abiogenesis is the natural process by which life arose. This is opposed to abiogenesis being a miraculous event. The only sort of reasoning that I can think of to support such a statement is that there are only natural processes and no miraculous events so the completely unobserved event of abiogenesis must have been a natural process. Is this the reasoning by which you claim that abiogenesis is in a set with "anything confirmed beyond all rational/scientific doubt given our current state of knowledge" from talk even though the event was never observed. Is there some other reason? This is a philosophical position that you put into the article quite in opposition to the statement "...philosophical discussion doesn't belong in this article..." that you wrote above. That is why I reverted the edit that you made and Dominus Vobisdu supported. Nothing you have written so far in any way undermines the propriety of that action.

That abiogenesis occurred is a logical conclusion, following from the observation that life did not always exist, thus at some point it came into existence. The observation is indeed confirmed beyond all rational/scientific doubt.

Like I said, science only deals with natural processes. It is part of the description of science, and whether one thinks that other things than natural processes exist doesn't affect that; this is not a philosophical position except if you are attempting to philosophically redefine science itself. Thus my point that the word "natural" is redundant but using the word increases clarity.

(More specifically, science actually deals with reproducible processes. However, do not misinterpret this as implying that science cannot say anything about single events, which it can.)

If an atheist vs Christian narrative is out of place here, why did you begin it with "there are many arguments (creationists, etc) that [lead] in that direction."? Did I misunderstand you? Were you referring to Hindu creationists?

I was referring to a large group of people who believe demonstrably factually incorrect statements, including ones which might cause them to misinterpret the article.

I am well aware of the scientific process by which scientists make a hypothesis and "simply take it for granted" in their experiments. They hope that way to find supporting evidence or contradicting evidence. However, in the case of abiogenesis those who "simply take it for granted" and publish accounts of abiogenesis being a natural phenomenon without any supporting experiments are not engaging in science but propaganda. - Fartherred (talk) 23:24, 17 December 2012 (UTC)

No. When a statement taken for granted is allowed past peer review, that is generally a sign that it has been established beyond reasonable doubt. The main exception (which I think you're referring to) is where the scope of the paper is solely to argue "if X, then Y," which can happen when X is merely probable.

This is what is supported by experiment: Every living thing had its origin in one or more living cells. Abiogenesis contradicts that and is supported only by reasoning to what is thought to have occurred in the unobservable past. The details of that occurrence are in doubt. Some experimenters hope to provide evidence that abiogenesis is a natural process and illuminate details. - Fartherred (talk) 23:52, 17 December 2012 (UTC)

The past is not unobservable in the sense that you are implying. As I said, there is no experimental doubt about the observation that life did not always exist. Whether or not details are in doubt is irrelevant to whether we know it actually happened - like we know that evolution or the American Civil War happened, despite not knowing all the details. Arc de Ciel (talk) 19:23, 22 December 2012 (UTC)

It seems someone Wikichopped my little contribution to the discussion we see beforehand, even though it differs in no appreciable way in terms of subject-matter from the prior installments. It is very much a shame, but I will repost nonetheless. It seems to bear directly upon the main issue under this heading: which is, should abiogenesis be treated as a fact? Should the language and tenor of the article suggest that it is something scientifically established to have happened?

---"Like I said, science only deals with natural processes. It is part of the description of science, and whether one thinks that other things than natural processes exist doesn't affect that; this is not a philosophical position except if you are attempting to philosophically redefine science itself."--67.84.205.90 (talk) 08:05, 15 February 2013 (UTC)

It is manifestly true that science only deals with what is natural and testable. It can deal with unique events, but only insofar as observable evidence exists *today* that these unique events occurred (e.g. Cosmic Microwaves as evidence for the Big Bang). This evidence must be able to confirm or disconfirm theories of events past, and when overwhelming weight is on confirmation, science can issue a meaningful statement regarding such events.

It is also manifestly true that science does not by nature touch upon the supernatural. In fact, it doesn't even touch upon what is super-measurable, such as epistemology or ethics. So science must remain silent on the subject. For this reason, it is understood that scientists studying abiogenesis would ASSUME only natural processes at work and would not mention the supernatural, because there is nothing they could say about the supernatural. Abiogenesis is the study of life arising from non-life as a natural process, and the addition "natural process" could be considered redundant (as several here have pointed out) though considering the pitfalls surrounding the issue, a little over-clarification wouldn't seem that bad a thing.

From this, one can conclude that however abiogenesis is discussed, it is incorrect (and probably dishonest) to discuss abiogenesis in such a way as to suggest any abiogenic event has ever been demonstrated to have occurred, because there is as of yet no whiff of any understanding of any *natural mechanism* whereby anything that can plausibly be called life can emerge from anything that could plausibly be called non-life. As of now, science has no answer for someone who insists that a celestial pair of spirit hands engaged in deliberately creative acts to create life out of non-life. If you were to say "No! It happened via a natural mechanism!", this person would say "Alright then, what mechanism? Show me which hypothesis has been validated as to exactly how the transition occurred and how it was validated" and the scientist would have no answer, because no mechanism has been discovered; and our friend would not be compelled, scientifically or otherwise, to abandon his belief in spirit hands. Even if the mechanism is to be found, our friend could claim that there must be an intelligence behind the mechanism, and this would be a more purely Theological question. But until this mechanism is found, and until any scientist can provide us with good reason to believe that abiogenic processes exist, and there is thus (by Ockham's Razor) no need to assume spirit hands, it cannot be stated without dishonesty that such a thing as abiogenesis is a real phenomenon, just as it cannot be stated that there is a natural process--Is stupidity a natural process?--determining that I write on this talk page.67.84.205.90 (talk) 08:05, 15 February 2013 (UTC)BiggerDip

What Raeky and TippyGoomba fail to understand is that the discussion in this section is about whether or not the [[Abiogenesis]] article is being used as a soap box by a pro-atheist clique on Wikipedia to promote the idea that abiogenesis is a natural process. In addressing this point the contributions of BiggerDip are germane. The reverting of his/her comments is the misuse and abuse of policy as a weapon and violates the spirit of WP:BITE. BiggerDip does not follow the spirit of WP:STICK in that it continues the discussion after Arc de Ciel acknowledged that 'The word "natural" is superfluous and generally omitted' and on the 22nd of December added the word process without the word natural in defining the topic. Any discussion on such a minor point should not be endlessly protracted, but that can be explained with courtesy rather than deleting comments. - Fartherred (talk) 16:47, 15 February 2013 (UTC)

It is a natural process. Do you have any sources to the contrary? Comments about the religious motivations of other editors are off-topic and unhelpful.   — Jess· Δ♥ 17:23, 15 February 2013 (UTC)

You assume that it is a natural process without any evidence. I looked at the sources presented by Arc de Ciel and in every case their statements supporting that abiogenesis was a natural process were based upon their personal assumption. As far as they are published sources, their baseless assumptions can be represented in the article. That is as much as we need to discuss. - Fartherred (talk) 18:04, 15 February 2013 (UTC)

No. We don't treat sources that way. You are confusing this article with Creation myth (or one of its children), which are about religious ideas concerning the origin of life. This is a science article.   — Jess· Δ♥ 21:49, 15 February 2013 (UTC)

Are you saying no, you do not assume natural process, you have evidence; or no, the published baseless assumptions of scientists can not be sources for this article? - Fartherred (talk) 00:44, 16 February 2013 (UTC)

What are you trying to argue here? This is a science article, therefore due to WP:NPOV, WP:DUE, etc.. we treat it as mainstream science treats it. So what _exactly_ is the goal of this discussion to change? Are you arguing against the innumerable amount of solid reliable sources that can back up the opening sentence? What is the proposed change WITH sources? — raekyt 00:50, 16 February 2013 (UTC) Is there a change being suggested? TippyGoomba (talk) 01:04, 16 February 2013 (UTC)

I believe I was quite clear: "As far as [the sources presented by Arc de Ciel] are published sources, their baseless assumptions can be represented in the article. That is as much as we need to discuss." I think this section should be archived to prevent passers by from beating the dead horse in opposition to our policy. As for sources, what I used with my 5 December 2012 edit of the article is a fine source for Wikipedia, and represents as much research as I intend to do. I have no intention of fighting the majority of editors or deleting arguments that are opposed to my opinions. - Fartherred (talk) 07:05, 16 February 2013 (UTC)

Since this discussion is not yet closed I might add that "Reliably published tertiary sources can be helpful in providing broad summaries of topics that involve many primary and secondary sources, and may be helpful in evaluating due weight,..." as per WP:PRIMARY. Britannica qualifies as a reliably published tertiary source. - Fartherred (talk) 07:44, 16 February 2013 (UTC)

What are you suggesting? Be specific. Eg. "Sentence X should say Y". I have no idea what you're talking about. TippyGoomba (talk) 07:53, 16 February 2013 (UTC)

I am suggesting no change in the article based upon the discussion in this section. I could take sources that Arc de Ciel used for calling abiogenesis a process and convert them to sources supporting the idea that their is no evidence for abiogenesis being a natural process by plainly pointing out the lack of logical connection between the evidence and this conclusion, but it is not my mission in life to correct the failings of the scientific community. It is not Wikipedia's mission to correct the illogical published comments of scientists, but to report them. - Fartherred (talk) 08:08, 16 February 2013 (UTC)

So the sticking points is your arguing that non-scientific sources should be used for a scientific definition, places like Marrian-Webster Dictionary where it's the "supposed" origins of life, or dictionary.com where it's the "discredited theory." Or where you give britannica.com where it's the "idea" that life arose. There's a reason why Britannica is no where NEAR as popular as Wikipedia. In science there is no debate that abiogenesis happened, it's not the "idea", it's not the "theory" (as the colloquial term that people confuse a scientific theory with), it's not discredited. It's a NATURAL process that happened. Exactly how it happened is open for debate, but that it did happen isn't what is being debated. The definition, our first sentence, shouldn't water this down. It should state it's a natural process that happened. Per WP:UNDUE we take the overwhelming scientific sources on this over the non-scientific sources, always. The first sentence should read, "Abiogenesis or biopoiesis is the natural process by which life arose from inorganic matter." because THAT is what is supported by scientific sources. — raekyt 16:31, 16 February 2013 (UTC)

Maybe better, "Abiogenesis or biopoiesis is the natural process by which life arises from inorganic matter." Because it happened once it can and does happen now and in the future across the universe. — raekyt 16:36, 16 February 2013 (UTC)

@Fartherred, "I am suggesting no change in the article based upon the discussion in this section." Ok, then there's nothing to discuss. Raeky, I do like that wording. It seems to be that now, based on the last section of discussion.   — Jess· Δ♥ 17:44, 16 February 2013 (UTC)

The article's first sentence is perhaps incorrect

The first sentence reads, "Abiogenesis or biopoiesis is a natural process by which life arises from simple organic compounds."

This is being stated as a fact; however, is there PROOF that abiogenesis has ever occurred as a "natural" process? Or is it mere speculation and a leap of faith? Unless this is a known fact, and not an assumption, why is this being stated as a fact in a scientific article? Later on, we find this information:

Professor Colin S. Pittendrigh stated in December 1967 that "laboratories will be creating a living cell within ten years,"

That was almost half a century ago when he made that prediction. He was obviously wrong. So exactly what scientific criteria are being used to make the article's opening statement? Dontreader (talk) 19:39, 31 October 2013 (UTC)

It would, perhaps, be a tiny bit more accurate to add "thought to be", "considered to be", "believed to be" or "defined as" after the "is". The last of that list would, I think, be the most neutral. Tamtrible (talk) 22:13, 31 October 2013 (UTC)

Those are excellent suggestions, Tamtrible. Thanks for taking the time to ponder the situation. I agree that a modification (such as one of your suggestions) should be included after the "is", as you indicated. Thanks again. Dontreader (talk) 23:54, 31 October 2013 (UTC)

Already done. Tamtrible (talk) 18:20, 1 November 2013 (UTC)

Thanks, Tamtrible. That looked great to me, but your edit has been changed back to the original form. I have written a message on the talk page of the user who made the subsequent edit, asking him/her to come here. Thanks again. Dontreader (talk) 21:17, 2 November 2013 (UTC)

I put "putative."Mikedelsol (talk) 06:23, 19 August 2014 (UTC)

The problem with "putative" is that the context it creates is the implication that there is an alternative process in addition to abiogenesis being discussed by scientists, which there is not. Thus, it was reverted as being a weasel word.--Mr Fink (talk) 16:13, 19 August 2014 (UTC)

I made that change because in Wikipedia articles, terms are generally defined as their subjects. That is, articles generally don't say "term is defined as...", articles just say "term is...". This is a style convention, not a content convention. A completely fictional subject is still introduced this way. • If your concern is you want the content to reflect the lack of proof, I would suggest treating that directly. For example, like this. That's how most of the dictionaries I spot checked seemed to handle it. —DragonHawk (talk|hist) 20:01, 3 November 2013 (UTC)

Thanks DragonHawk for coming here and for your very clear explanation; I also appreciate your research on the issue and I hope your edit will be kept since it sure looks like a solid scientific solution. The way the sentence was written when I first read the article was philosophically flawed. Thanks again. Dontreader (talk) 21:21, 3 November 2013 (UTC)

Please see the talk page archives for previous discussion on this issue. :-) Briefly, while there are many hypotheses about various stages in the process of abiogenesis, the existence of the process itself is factual. Arc (talk) 08:44, 13 November 2013 (UTC)

I think there is... a legitimate issue here. Entirely aside from any notion of special creation or whatever, there is the possibility that life on Earth was seeded from another planet. Admittedly, this would just mean that abiogenesis happened somewhere else (possibly in deep space or something), but this article is mainly discussing the various theories and hypotheses of how abiogenesis occurred *on Earth*. And, of course, there's always the possibility, however remote, that something wildly different from anything we would recognize as abiogenesis is what actually occurred. Would you be happier with "theory" rather than "hypothesis"? Tamtrible (talk) 20:30, 14 November 2013 (UTC)

The use of "theory" has been discussed as well, actually. For myself, I think a reasonable argument can be made for it, if it's appropriately wikilinked, but the consensus from the last time around was to treat it as a fact instead. I favor this view as well. With respect to panspermia, the definition doesn't speak to that; abiogenesis may have occurred elsewhere, but it still remains the same process.

Further comments (not relevant to any definitional questions): I agree that in some places the article does use prose that assumes an Earth origin when not strictly necessary, and this could be fixed. The current coverage of the topic may not be as bad as you think, though - e.g. see the sections here and here, or run searches for "space," "panspermia," etc. I’m also working on some changes to the article that will probably make these sections more prominent - a mention in the lead might not be out of place either. However, Earth origin is the most commonly discussed by the available high-quality research, so the article's focus still needs to reflect that (WP:DUE). Arc (talk) 10:45, 15 November 2013 (UTC)

It might not be entirely inappropriate, at the *bottom* of the article, to have a short section, saying something like:

Alternatives to abiogenesis

The possibility exists that the first organic life on Earth did not spontaneously arise, or arrive from space by chance, but instead was in some fashion deliberately created and/or placed here. However, this raises the problem of where that deliberate creator came from. If it was an organic life form of some kind, or a product or device originally made by same, that merely pushes the question of abiogenesis back to that life form's place of origin. If it was not an organic life form, directly or indirectly, then it is necessary to explain how something other than organic life, that was not created by organic life, is capable of deliberate action. No such intelligence is presently known to exist. If it was a divine being, then in a meaningful sense the question falls outside the scope of science, though if said being did so in a manner that could also have happened by chance, then it can be treated equivalently.

Or something like that. Someone else can probably phrase it more elegantly. Tamtrible (talk) 19:11, 15 November 2013 (UTC)

In the first part of your suggestion, you're talking about directed panspermia. :-) This isn't about the abiogenic process per se (rather it is a specific hypothesis about how life might spread between planets), but it does have some relevance so it could be mentioned. However, the second part of your suggestion ("If it was not...equivalently") is outside the scope of this article, which is about scientific views (see the hatnote at the top of the page). It may be more appropriate in another article, such as Creation myth, but be aware that you would still need reliable sources to cite your statements. Arc (talk) 21:10, 16 November 2013 (UTC)

Actually, I'm mentioning the remote scientific possibility that organic life was artificially generated by nonorganic life of some sort. For example, crystalline silicon life forms. Something like that would, of necessity, have a different type of origin than organic life, so would not simply move abiogenesis as discussed in the rest of the article to a different origin point. *Then* I mentioned the possibility of divine creation, and essentially said "But that's outside the scope of this article". Tamtrible (talk) 07:52, 18 November 2013 (UTC)

Yes, that specific point (the possibility of generation of organic life by inorganic life) would definitely be within the scope of the article, so it could be included if it were substantiated. Like I said above, you would need reliable sources, and for this example I would also invoke WP:EXCEPTIONAL. I know that speculation about inorganic life can be supported (for example, see Hypothetical types of biochemistry) but the sources would need to specifically make the connection that you're suggesting. Arc (talk) 08:53, 19 November 2013 (UTC)

How would you feel about a header like "Unlikely and/or non-scientific alternatives", with text something like:

Directed panspermia, or life planted on Earth deliberately by some kind of extraterrestrial intelligence, would simply move the process of abiogenesis to an extraterrestrial origin point. If organic life was intentionally created by some sort of intelligent inorganic life form (link here to the hypothetical biochemistry article), this would not require any form of undirected abiogenesis as discussed here, as presumably life forms with wildly different biochemistry would have different origins, but no such life forms are known to exist at present. Discussion of any form of divine creation (link to creation myths page) is outside the scope of this article.

Or something like that. Would that be acceptable without sources? Tamtrible (talk) 17:38, 19 November 2013 (UTC)

You are missing the point. Wikipedia is not the place to publish original thinking on a subject. You need to find a quality source of any such claim you want to add to this article. Wikipedia isn't designed to synthesize new points of view. In other words: No, it wouldn't be acceptable. See my new section on article revision, however.Abitslow (talk) 17:48, 20 November 2013 (UTC)

Hello Arc. You wrote, "while there are many hypotheses about various stages in the process of abiogenesis, the existence of the process itself is factual." Well, by definition, abiogenesis is indeed a process by which life arises from non-living matter; however, the article reads that it's a "natural" process. There is no proof that abiogenesis is a natural process, which is why I prefer "hypothetical natural process". And specifically on Earth, the existence of the process itself being "natural" is not factual. Instead, it's an assumption, a leap of faith, and that's not a scientific approach.

Here's the mistake: we know that there is life on Earth, and we know that there was a time when there was no life on Earth, so we know that at some point life appeared on Earth. But some people have assumed that at some point life arose on Earth "naturally". That's a flawed argument unless you call it a hypothesis. Maybe life arose on Earth naturally, but from a philosophical point of view there are endless possibilities. What if God created the earliest life forms on Earth? The concept of God seems irrational to us but philosophically it's a possibility. Or many gods. Or angels. Or what if advanced extraterrestrials came to Earth and brought primitive life forms with them? Even some scientists believe that perhaps life on Earth originated in outer space. So, life on Earth did not necessarily arise as the consequence of a natural process on Earth. In fact, when you think about it, one could argue that the apparition of life from a lifeless environment is as absurd as the existence of a god. My point is that I believe that if we are to call abiogenesis a "natural" process, it should be called a "hypothetical natural process". Thanks for your time. Dontreader (talk) 09:55, 28 November 2013 (UTC)

I think it's perfectly reasonable to leave off the "hypothetical", *if* we at least briefly discuss, later in the article, possible alternatives--directed panspermia (which either moves the abiogenesis question to another world, or requires life forms sufficiently different from us, such as crystals or cloud-like energy beings, that abiogenesis as discussed in the article would be irrelevant) and special creation (which is a nonscientific approach, so mention of that would just lead to a link to the relevant page and a mention that it's outside the scope of the article). Basically, butt-covering of "If it's not a natural process that happened by some means on Earth, this is what it might have been instead."--at the end of the article, where it won't get in the way. Tamtrible (talk) 06:14, 29 November 2013 (UTC)

Thanks Tamtrible. I'm fine with what you proposed. After all, the assertion that abiogenesis is a "natural" process is merely an assumption, not a proven fact, so that's not the way a scientific article should be written, unless there's a fix somewhere, as you explained. At least there is certainly empirical evidence that evolution has taken place (like the fossil record and DNA analyses), but what I see in the first sentence of this article is a giant leap of faith. Thanks again and have a nice day. Dontreader (talk) 21:58, 29 November 2013 (UTC)

Since we seem to agree that a new section would resolve those concerns, why don't we work on making a proposal for that section? (I know one has been made already, but see the comments on needing reliable sources.) My only additional comment at the moment is that the hatnote at the top of the article is probably sufficient to define the article's scope - it is better style to avoid terms like "this article." Dontreader, you may also want to read my above conversation with Tamtrible. :-) Arc (talk) 00:52, 30 November 2013 (UTC)

Hello again, Arc, and thanks for your thoughts; I had already read your discussion above with Tamtrible, and I addressed you recently there. I understand that you are apparently disappointed that this topic has surfaced once more, but I believe the previous consensus is flawed, and there are multiple problems; for example, at the top of the article we find the following:

"Origin of life" redirects here. For non-scientific views on the origins of life, see Creation myth.

In other words, if a reader searches for "Origin of life", he or she is automatically brought to this article, as if it were a fact that the scientific approach on the origin of life is the true one, even though there is no evidence for this; again, it is a mere assumption, and the inference is that the "Creation myth" article contains purely savage and puerile notions, when in reality it is hypothetically conceivable that (for example) a god created life directly and in a supernatural manner. I don't understand how that note at the top of the article appeared. Wikipedians who are militant atheists? Wikipedians who are proud scientists like Professor Colin S. Pittendrigh, who turned out to be a fool because of his senseless prediction? Look, the creation stories have many ridiculous elements, but there could be some degree of truth in them. We must be cautious. If "Origin of life" redirects here to explain the true origin of life, we must give readers the truth, and the truth is that science is not sure, so indeed a section is needed to address that problem, and I am certainly willing to help.

Also, Arc de Ciel, in the discussion, you stated: "the existence of the process itself is factual." But where is the proof? Every attempt at creating life from a lifeless environment has failed dismally. Even the most primitive conceivable life forms are incredibly complex, so I'm not in the least bit surprised. Am I to understand that you assume that one day a scientific team will finally succeed? As you know, assumptions are not facts, and therefore please explain why the existence of abiogenesis is factual (let alone "natural").

Finally, the first paragraph in the article provides the meaning of "abiogenesis" and then very cleverly implies that it took place on Earth, so that readers will believe that abiogenesis actually took place on Earth; again, it's not stated, only implied, but that should be fixed, I think. The second paragraph does refer to abiogenesis on Earth as an assumption, which is better.

For the record, I was agnostic for some time but then I became a firm believer in God; however, I have a scientific background, and my religious views are regarded as extremely heretical. Thanks for your time. Dontreader (talk) 22:32, 30 November 2013 (UTC)

As someone who has a scientific background, you should realize that the scientific method always assumes that everything has a natural cause, and that this is one of the fundamental aspects of scientific research. After all, if it's not natural, it can't be observed, can't be studied, and can't be disproven. The existence of abiogenesis is absolutely 100% fact, because if it didn't exist, there wouldn't be any life. Wikipedia leans towards science on topics that science studies because science backs itself up with evidence and changes views with new discoveries, something that almost never happens with creation myths. Ego White Tray (talk) 00:16, 1 December 2013 (UTC)

Thanks, Ego White Tray. Indeed, the scientific method always assumes that everything has a natural cause, and that's the way it should be. Wouldn't you agree that the scientific method has been applied to abiogenesis many times? If so, the results have been utterly disastrous. Would you say that scientists are closer now than 50 years ago to creating life from a lifeless environment? If not, how many hundreds of years and experiments must be conducted before the assumption is questioned? Or are you 100% convinced that some day abiogenesis will finally take place in a laboratory if mankind lives on long enough? Because that could only be the stance of an atheist. Even Isaac Newton reached a point when he abandoned the assumption that everything had a natural cause, after careful consideration. Yet Newton challenged very methodically the religious beliefs he was raised with. The main point is this: even though the scientific method always assumes that everything has a natural cause, that does not necessarily mean that everything has a natural cause, and therefore the existence of abiogenesis is not necessarily a fact.

We need philosophers here, in my opinion, because there appears to be a deadlock. For example, if I propose that the concept of God is irrational to human beings because we are but mere close relatives of chimpanzees, and therefore the intelligence of human beings is minuscule, where am I going wrong? What if the concept of God makes sense to an alien civilization that is intellectually a million times superior to us? The scientific community should be more humble. Besides, does ANYONE seriously believe that even the most primitive conceivable life forms - given their enormous complexity - can show up in a laboratory from a lifeless environment? Let some philosophers come here and be given the minimum requirements for the existence of a life form (by consensus) and see what they tell us. Thanks again. Dontreader (talk) 10:01, 2 December 2013 (UTC)

Abiogenesis is a scientific topic, so philosophers are not needed for it, and nature must suffice. If you can't agree with it, you're not really on-board with this whole science thing. The reason that life has not been generated in a lab is simple - it's extremely difficult to do. Modern scientists don't have millions of years for their experiments to work (which was probably the case in nature billions of years ago), and modern scientists need to fight the oxygen that's everywhere, and most importantly, the life that's everywhere that will eat anything they create. Just because scientists haven't succeeded yet, doesn't mean it isn't true - the opposite conclusion is a favorite of creationists and other pseudo-science arguments. Ego White Tray (talk) 15:30, 2 December 2013 (UTC)

Ego White Tray, philosophy and science are not mutually exclusive, but after pondering the situation, I think it might not be viable to include philosophers in this discussion unless they are familiar with this field of science to some degree. I just would like to see more people with different backgrounds here. How can you say that I'm "not really on-board with this whole science thing."? Are you an atheist? Who can deny that Isaac Newton had one of the most brilliant scientific minds in history? Are you not aware of the fact that he approached religion with the same analytical thinking as he did with science, yet he remained a believer in God? He ended up with heretical views on Christianity, yet he remained a believer in God, and he did not believe that everything had a natural cause. Therefore, would you state that Newton was "not really on-board with this whole science thing."?

You also wrote, "The reason that life has not been generated in a lab is simple - it's extremely difficult to do." That is certainly not what Colin Pittendrigh thought, given his regrettable prediction. You have also stated that "The existence of abiogenesis is absolutely 100% fact", which is false. The flawed reasoning you provided for this assertion is not that of rigorous science; instead, it looks more like the reasoning of an atheist. Evolution, for example, has vast empirical evidence, but there is zero evidence or proof that abiogenesis has ever taken place; therefore, to claim that it is absolutely 100% fact is not scientific. Hence, I still believe that abiogenesis should be called a hypothetical process, lest we make leaps of faith not dissimilar to those of religious fundamentalists. Dontreader (talk) 21:17, 2 December 2013 (UTC)

Please stop bringing up religion; it's not relevant to this article. (Especially not speculation on the religion of editors or lack thereof.) Likewise, I don't see the relevance of Pittendrigh or Newton - I don't see any way to relate either of them to this discussion that does not involve a logical fallacy of some sort (appeal to authority, anecdotal fallacy, etc).

Anyways: a failure to completely describe the process (thus far) does not indicate a lack of progress. In fact, a lot of the progress that has been made is described in the article. One of the more important pieces of evidence is the discovery that all the functions of metabolism and heredity can be carried out by a single type of macromolecule (RNA), which shows the plausibility of life forms much simpler than the simplest which exist today. So the simplest answer to your question, "Would you say that scientists are closer now than 50 years ago to creating life from a lifeless environment?" - is yes. But the question is misdirected, because "creating life" is not the proximal goal - rather it is to understand the steps which abiogenesis may have involved. I can cite any number of research papers (or you can look at the ones in the article) that are studying these steps and contributing to our understanding. Arc (talk) 02:45, 3 December 2013 (UTC)

Arc, I brought up Newton and religion again because I perceived that an attempt was made to disqualify me as a contributor to the discussion. If I'm "not really on-board with this whole science thing", then neither was Newton. Anyway, even if the first life forms were much simpler than the simplest which exist today, abiogenesis still has catastrophic problems. Life is an all-or-nothing situation. By definition, the concept of abiogenesis requires a living entity to directly descend from a non-living entity, or at least to be created from a lifeless environment. You said progress has been made; that's good news because the Miller–Urey experiment - although interesting - was a total failure, unless the goal was to merely create amino acids. Wouldn't you agree that even the simplest conceivable living organisms need a protein molecule? If so, how many amino acids found in the Miller–Urey experiment were linked together in a manner that got close to resembling a protein molecule? Or have more successful subsequent experiments properly produced linked amino acids that nearly reached protein molecule status? Let alone the RNA macromolecule which you mentioned, which I assume has a genetic code for vital functions, including viable reproduction. And what about some sort of a cell membrane? Don't you need all of these things, if not more? That's why I question the real progress that has been made. I truly do believe that abiogenesis is hypothetically possible, and it should be called a hypothetical process. Dontreader (talk) 03:45, 4 December 2013 (UTC)

Life is only an "all-or nothing situation" in the definitional sense. The line could have been drawn elsewhere; viruses, viroids and prions are all made of the same type of molecules but are simpler. They exhibit some of the typical characteristics of life but not others - e.g. these groups are all subject to natural selection, meaning that they can increase in complexity given enough generations. "Life descending from non-life" is an oversimplification, because of the very large gray area in between the two categories. The earliest replicator could have been as simple as a polymerase chain reaction (and there is research which suggests this as a possibility).

"Wouldn't you agree that even the simplest conceivable living organisms need a protein molecule?" Nope - see my comment about RNA. A cell membrane is not a prerequisite for life either (and certainly not a prerequisite for a primitive replicator), although it is possible that the first life did have cell membranes. Arc (talk) 05:57, 4 December 2013 (UTC)

Thanks Arc for your observations; however, you are relying merely on hypotheses. For example, has a life form without protein molecules ever been found in nature or produced in a laboratory? I don't think so. Every possibility you wrote is hypothetical (correct me if I'm wrong), and therefore I don't understand why you are so opposed to calling abiogenesis a hypothetical process. Then, whenever it's actually proven to be factual, you could take out "hypothetical" from the article again. Please, what exactly is your problem with that? Dontreader (talk) 10:15, 4 December 2013 (UTC)

What reliable source supports describing abiogenesis as a "hypothetical process"? Is evolution a hypothetical process? A hypothesis is something like "life may have started by process A then B then C" (where A, B and C are described in some detail). A different source may say "no, it was probably X then Y then Z". There would then be two hypotheses waiting for evidence. However, abiogenesis itself is not hypothetical—it is the natural process by which life arose, with many details as yet unknown. If a reliable source says that there is no such natural process, we can add relevant information to the article. Please do not ping other editors unless they have asked. Johnuniq (talk) 10:57, 4 December 2013 (UTC)

So. Anyways. I think at least most of us can agree that abiogenesis should be treated as, in essence, scientific fact about which we do not entirely understand the details, but that at least brief mention of alternatives to abiogenesis happening on Earth or otherwise "naturally" occurring (directed panspermia, creation by nonorganic life forms, possibly essentially unscientific alternatives such as special creation) should be made. At least, that's my read on the above discussion. So, any cogent proposals on how to phrase said brief mention? — Preceding unsigned comment added by Tamtrible (talk • contribs) 16:20, 4 December 2013 (UTC)

Just one caveat. :-) I don't think the article necessarily suffers from lacking such a mention - rather I have said that such a mention would be within the scope of the article (other than special creation, of course) if appropriate sources could be found. A couple of my previous comments: [10] [11]. I think directed panspermia probably has such sources but creation by nonorganic life forms probably does not. But either way it would depend on which sources are brought forward. Arc (talk) 02:55, 5 December 2013 (UTC)

I was pinging other editors just to try to make sure that they noticed my replies. Can someone please explain to me what's wrong with doing so? I would have responded much sooner if someone had pinged me. Anyway, I have read with great interest these newest entries, and whatever you decide to do is fine with me. I'm just sincerely trying to improve the article, but if my arguments are regarded as flawed, at least I have tried my best. This is my final attempt to make my case. Johnuniq was correct until he stated that "abiogenesis itself is not hypothetical—it is the natural process by which life arose, with many details as yet unknown." Unlike evolutionary theory, which has plenty of empirical evidence, there is no scientific evidence for abiogensesis as a natural process. ZERO. Therefore, from a scientific point of view, abiogenesis is NOT a fact; instead, it's a hypothesis or a theory. Johnuniq asked for a reliable source, so how about this one?

http://www.britannica.com/EBchecked/topic/66167/biopoiesis

"biopoiesis, a process by which living organisms are thought to develop from nonliving matter, and the basis of a theory on the origin of life on Earth. According to this theory, conditions were such that, at one time in Earth’s history, life was created from nonliving material, probably in the sea, which contained the necessary chemicals. During this process, molecules slowly grouped, then regrouped, forming ever more efficient means for energy transformation and becoming capable of reproduction."

Isn't that encyclopedia a reliable source?

Interestingly, the Spanish version of Wikipedia calls it a theory, the German version calls it a hypothesis, the French version merely states that abiogenesis is "the study of the generation of life from non-living matter." (and cites astronomer Fred Hoyle), and the Italian version calls it a theory. Yet somehow English-speaking Wikipedians know that abiogenesis is a fact. Dontreader (talk) 01:29, 7 December 2013 (UTC)

Only all sources outside of Wikipedia call it a hypothesis. In fact all the sources Wikipedia uses calls it an hypothesis too. "Yet somehow English-speaking Wikipedians know that abiogenesis is a fact. " no, just the atheists who religiously defend this article. --Suigens (talk) 07:11, 9 January 2014 (UTC)

I think this article needs to be reevaluated somewhat. --200.198.252.200 (talk) 5:58 pm, Today (UTC−5)

I'm going to side with those who want to see the word "hypothesis" or similar wording. Even though it has slowly gotten more and more plausible over the last century, abiogenesis is still very far from proven. I would also oppose using the word "theory" because it generally implies (in science) a much more well-tested explanation. Even a positive demonstration of life forming in vitro would still leave the origin of life on earth question open, as it wouldn't rule out some form of panspermia. Howard Landman (talk) 09:52, 20 January 2014 (UTC)

I wouldn't say current research has shown it to be plausible. Unfortunately it seems anyone disagreeing with the hypothesis is automatically labelled as a creationist by the trolls here (even though creationism, and indeed, the creationism-evolution controversy, is a totally different and unrelated subject). Apparently the bias of some Wikipedians don't want to mention some of the stuff that biologists are saying in regards to abiogenesis. "Nobody understands the origin of life. If they say they do, they are probably trying to fool you." ~ Ken Nealson PhD, 2002 Robert Roy Britt, "The Search for the Scum of the Universe," http://www.panspermia.org/rnaworld.htm# Then there's Andrew Knoll, a respected biology professor who says that he "doesn't know" if the mystery will ever be solved. How Did Life Begin? NOVA and Andrew H. Knoll PhD, Havard University. http://www.pbs.org/wgbh/nova/evolution/how-did-life-begin.html But apparently it's factual to Wikipedia even though it's all speculation and hypothetical to scientists at the moment (and quite possibly forever more) as those sources reveal. --Diskain (talk) 18:11, 12 March 2014 (UTC)

Everything developed from energy and stardust from the Bing Bang, so abiogenesis is a fact. I have no problem calling abiogenesis on Earth a hypothesis, because even if speculation is entertained to give context, abiogenesis concerns itself primarily with hypotheses that fit firmly into existing scientific theories and on the physicochemical laws of the universe. I do however, disagree to insert the word "hypothesis" as an excuse to sneak "goddidit" as an equally valid and rigorous hypothesis. --BatteryIncluded (talk) 01:37, 20 March 2014 (UTC)

The Big Bang concerns the origin of the universe, not the origin of life and is a theory in physics not in biology. I can only deduct from this that you don't understand the theories and hypothesizes that you preach about. Abiogenesis is not a fact then, as The Big Bang theory is something completely different and doesn't even connect to the abiogenesis hypothesis. Indeed, some scientists saw religious implications in the theory which led some (such as Fred Hoyle) to reject it http://en.wikipedia.org/wiki/Big_Bang#Development. The Big Bang is fact. Abiogenesis isn't. --86.21.101.169 (talk) 13:28, 27 March 2014 (UTC)

The only hypothetical aspect of Abiogenesis is how life first arose on Earth. Until Creationists finally cough up any evidence that life was miraculously poofed into existence via direct supernatural intervention, it's a given that life first arose on Earth via natural processes.--Mr Fink (talk) 15:14, 27 March 2014 (UTC)

My fault. I guess I need to pray harder in order to understand science and before I become a "preacher". Cheers, BatteryIncluded (talk) 16:30, 27 March 2014 (UTC)

Most of abiogenesis is hypothetical. Sources are above of scientists calling it speculation and that it may always be unknowable in science, therefore there's no grounding to the idea that "it's a given that life first arose on Earth" via abiogenesis. I'm an deist evolutionist (as well as deist in the general meaning) and I don't accept abiogenesis. Abiogenesis and evolution are two different subjects and an evolutionist needn't accept the former. The fact there's no empirical scientific evidence for abiogenesis (which is a scientific subject) is enough to rule it out entirely at the moment. Since God isn't a scientific matter but a philosophical/religious one then anything citing him would require arguments in those areas, not science. However, there's scientific reason to reject abiogenesis at the moment. To quote Fred Hoyle on abiogenesis, the chance of "obtaining even a single functioning protein by chance combination of amino acids" is as likely as "a solar system full of blind men solving Rubik's Cubes simultaneously." [[12]] Hoyle was also an atheist as I mentioned in my above post, which shows that religion is nothing to do with this and neither is creationism (which is a different topic [[13]]). Whilst I disagree with Hoyle's criticism on the Big Bang, I think his criticism of abiogenesis was mostly spot on. Meanwhile, none of the hypothesized models or processes of abiogenesis adhere to scientific method. You may accept it as "factual" but that's hardly the view of the overall scientific community. In fact, just be skimming through the posts here, there are many educated people here who reject abiogenesis mostly for scientific and not religious reasons. No matter, I'd wager no one in this debate is going to change their mind so I'll close on this. --86.21.101.169 (talk) 00:38, 13 April 2014 (UTC)

When a scientist says "we don't know", it means we don't know yet. It does not mean "you are right and goddidit." But I am very pleased you are closing on this. Cheers, BatteryIncluded (talk) 01:02, 13 April 2014 (UTC)

I propose a simple pre-written answer that should be served to all those bigots out here :

No one is fooled here, we do know what you are actively trying to do.

-FACT- : What you want is -not- proof, but to discredit whatever you disagree with.

-FACT- : Would you be presented with said 'neutral evidence', you would still deny it as assumptions.

You have the right to believe in whatever you want, but please be honest at least with yourself and do not pretend you want proof and neutrality when they clearly do not interest you.

83.145.69.50 (talk) 13:49, 26 June 2014 (UTC)

Collapsing copy of article

Selectivity for a boundary Self-assembled vesicles are essential components of primitive cells. The second law of thermodynamics requires that the universe move in a direction in which disorder (or entropy) increases, yet life is distinguished by its great degree of organization. Therefore, a boundary is needed to separate life processes from non-living matter. The cell membrane is the only cellular structure that is found in all of the cells of all of the organisms on Earth. Reseachers Irene A. Chen and Jack W. Szostak (Nobel Prize in Physiology or Medicine 2009) amongst others, demonstrated that simple physicochemical properties of elementary protocells can give rise to essential cellular behaviors, including primitive forms of Darwinian competition and energy storage. Such cooperative interactions between the membrane and encapsulated contents could greatly simplify the transition from replicating molecules to true cells. Furthermore, competition for membrane molecules would favor stabilized membranes, suggesting a selective advantage for the evolution of cross-linked fatty acids and even the phospholipids of today. This micro-encapsulation allowed for metabolism within the membrane, exchange of small molecules and prevention of passage of large substances across it. The main advantages of encapsulation include increased solubility of the cargo and creating energy in the form of chemical gradient. Energy is thus often said to be stored by cells in the structures of molecules of substances such as carbohydrates (including sugars), lipids, and proteins, which release energy when reacted with oxygen in respiration. Energy gradient A March 2014 study by NASA's Jet Propulsion Laboratory, demonstrated a unique way to study the origins of life: fuel cells. Fuel cells are similar to biological cells in that electrons are also transferred to and from molecules. In both cases, this results in electricity and power. The study states that one important factor was that the Earth provides electrical energy at the seafloor. "This energy could have kick-started life and could have sustained life after it arose. Now, we have a way of testing different materials and environments that could have helped life arise not just on Earth, but possibly on Mars, Europa and other places in the Solar System." Vesicles and micelles Scheme of a micelle spontaneously formed by phospholipids in an aqueous solution When phospholipids are placed in water, the molecules spontaneously arrange such that the tails are shielded from the water, resulting in the formation of membrane structures such as bilayers, vesicles, and micelles. In modern cells, vesicles are involved in metabolism, transport, buoyancy control, and enzyme storage. They can also act as natural chemical reaction chambers. A typical vesicle or micelle in aqueous solution forms an aggregate with the hydrophilic "head" regions in contact with surrounding solvent, sequestering the hydrophobic single-tail regions in the micelle centre. This phase is caused by the packing behavior of single-tail lipids in a bilayer. Although the protocellular self-assembly process that spontaneously form lipid monolayer vesicles and micelles in nature resemble the kinds of primordial vesicles or protocells that might have existed at the beginning of evolution, they are not as sophisticated as the bilayer membranes of today's living organisms. Rather than being made up of phospholipids, however, early membranes may have formed from monolayers or bilayers of fatty acids, which may have formed more readily in a prebiotic environment. Fatty acids have been synthesized in laboratories under a variety of prebiotic conditions and have been found on meteorites, suggesting their natural synthesis in nature. Geothermal ponds and clay This fluid lipid bilayer cross section is made up entirely of phosphatidylcholine. Scientists have come to conclude that life began in hydrothermal vents in the deep sea, but a 2012 study led by Armen Mulkidjanian of Germany's University of Osnabrück, suggests that inland pools of condensed and cooled geothermal vapour have the ideal characteristics for the origin of life. The conclusion is based mainly on the chemistry of modern cells, where the cytoplasm is rich in potassium, zinc, manganese, and phosphate ions, which are not widespread in marine environments. Such conditions, the researchers argue, are found only where hot hydrothermal fluid brings the ions to the surface — places such as geysers, mud pots, fumeroles and other geothermal features. Within these fuming and bubbling basins, water laden with zinc and manganese ions could have collected, cooled and condensed in shallow pools. In the 1990s biochemist James Ferris of Rensselaer Polytechnic Institute showed that montmorillonite clay can help create RNA chains of as many as 50 nucleotides joined together spontaneously into a single RNA molecule. Then in 2002, Hanczyc, Fujikawa and Szostak discovered that by adding montmorillonite to their solution of fatty acid micelles (lipid spheres), the clay sped up the rate of vesicles formation 100-fold. So this one mineral that can get precursors (nucleotides) to spontaneously assemble into RNA and membrane precursors to assemble into membrane. Research has shown that some minerals can catalyze the stepwise formation of hydrocarbon tails of fatty acids from hydrogen and carbon monoxide gases - gases that may have been released from hydrothermal vents or geysers. Fatty acids of various lengths are eventually released into the surrounding water, but vesicle formation requires a higher concentration of fatty acids, so it is suggested that that protocell formation started at land-bound hydrothermal vents such as geysers, mud pots, fumeroles and other geothermal features where water evaporates and concentrates the solute. Montmorillonite bubbles A team of applied physicists at Harvard's School of Engineering and Applied Sciences say that primitive cells might have formed inside inorganic clay microcompartments, which can provide an ideal container for the synthesis and compartmentalization of complex organic molecules. Clay-armored "bubbles" form naturally when particles of montmorillonite clay collect on the outer surface of air bubbles under water. This creates a semipermeable vesicle from materials that are readily available in the environment. The authors remark that montmorillonite is known to serve as a chemical catalyst, encouraging lipids to form membranes and single nucleotides to join into strands of RNA. Primitive reproduction can be envisioned when the clay bubbles burst, releasing the lipid membrane-bound product into the surrounding medium. Membrane transport Schematic showing two possible conformations of the lipids at the edge of a pore. In the top image the lipids have not rearranged, so the pore wall is hydrophobic. In the bottom image some of the lipid heads have bent over, so the pore wall is hydrophilic. Instead of the more popular phospholipids of modern cells, the membrane of protocells in the RNA world would be composed of fatty acids, and that such membranes have relatively high permeability to ions and small molecules, such as nucleoside monophosphate (NMP), nucleoside diphosphate (NDP), and nucleoside triphosphatee (NTP), and may withstand millimolar concentrations of Mg2 . Osmotic pressure also plays a significant role in protocell membrane transport. It has been proposed that electroporation resulting from lightning strikes could be a mechanism of natural horizontal gene transfer. Electroporation is the rapid increase in bilayer permeability induced by the application of a large artificial electric field across the membrane. During electroporation in laboratory procedures, the lipid molecules are not chemically altered but simply shift position, opening up a pore (hole) that acts as the conductive pathway through the bilayer as it is filled with water. The mechanism is the creation of nanometer sized water-filled holes in the membrane. Experimentally, electroporation is used to introduce hydrophilic molecules into cells. It is a particularly useful technique for large highly charged molecules such as DNA and RNA, which would never passively diffuse across the hydrophobic bilayer core. Because of this, electroporation is one of the key methods of transfection as well as bacterial transformation. Fusion Some molecules or particles are too large or too hydrophilic to pass through a lipid bilayer, but can be moved across the cell membrane through fusion or budding of vesicles. This may have eventually led to mechanisms that facilitate movement of molecules to the inside (endocytosis) or to release its contents into the extracellular space (exocytosis). Endosymbiotic theory Main article: Endosymbiotic theory Molecular and biochemical evidence suggest that the mitochondrion developed from proteobacteria The endosymbiotic theory states that several key organelles of eukaryotes originated as symbioses between separate single-celled organisms. According to this theory, mitochondria, chloroplasts, and possibly other organelles, represent formerly free-living bacteria that were taken inside another cell as an endosymbiont. As evidence, the mitochondrion has its own independent mitochondrial DNA genome. Further, its DNA shows substantial similarity to bacterial genomes, particularly, molecular and biochemical evidence suggest that the mitochondrion developed from proteobacteria. The mitochondrion (plural mitochondria) is a membrane-bound organelle found in most eukaryotic cells (the cells that make up plants, animals, fungi, and many other forms of life). A mitochondrion produces adenosine triphosphate (ATP) and it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism. ATP is one of the end products of photophosphorylation, cellular respiration, and fermentation and used by enzymes and structural proteins in many cellular processes, including biosynthetic reactions, motility, and cell division. See also Artificial cell Emergence Endocytosis Endosymbiotic theory Exocytosis Entropy and life Evolutionary developmental biology Lipid bilayer characterization Lipid bilayer phase behavior Model lipid bilayer Planetary habitability Protocell Circus - film. Pseudo-panspermia References