Thursday, December 9, 2010

Abiogenesis, Part I

Abiogenesis, Part I

This is more of a brain dump of what I have learned than anything else, so apologies if I ramble a bit.

I do not claim that science has all the answers here (this is an active area of research). But much like the early Church's stance on the Earth being the center of the universe, abiogenesis research has broken claim after claim made by the creationists about how it "must be" and what science has been able to piece together is a compelling series of events. It takes absolutely no faith to see the incredible progress that has been made in this field over the past 55 years (that is, IF the person bothers to actually investigate this field of study).

The original timescale involved was ~0.7B years in a lab the size of the entire Earth (possibly the solar system) so we have a lot of catching up to do in understanding the most likely pathways that the early Earth could have taken in creating the first organic "life" (some chemical structure capable of self-replication, mutation, and natural selection).

If creationists want to prove that abiogenesis is impossible then only need to find some specific STEP that absolutely cannot have happened naturally. Not a fallacious statistical argument saying that it's just too improbable to believe. An actual chemical combination that cannot possibly happen in nature and the specific, scientific reasons why.

So, what evidence do we have in support of a natural abiogenesis?

Here is a good review for starters: How life began on Earth: a status report

Remember that the DNA/RNA genetic system we have today is just what things have evolved into, don't assume they are required to kick start the process. What scientists generally believe happened was that there was a boot strapping process leading up to that first strand of self-replicating material (be it RNA/DNA or something else).

Peptide chains are simply "shorter" chains of amino acids (aka proteins). These naturally formed chains can perform functions, they can "store information", they change over time, and they can reproduce (e.g., see prion research). Those are all the things required for "evolutionary" processes to work over time.

(1) First of all, Jeffrey Bada's experiment showed once again that a wealth of organic chemistry and amino acids are generated naturally in the early Earth environment. There is also the later Miller experiment about organic chemistry in icy conditions (so it could be that an ebbing between warmer and colder conditions are required). The original Miller-Urey experiment was validly criticised for an inaccurate starting mixture, but even later versions of that experiment had corrected those problems.


(2) We are now also aware of a large number of exogenous sources of organic precursors (IDPs, Meteorites, Asteroids, Comets)

Murchison meteorite: 14,000 specific compounds, including 70 amino acids, were identified...tip of the iceberg

(3) This soup can include shorter fatty-acid chains (created in geothermal vents on the clay walls) which under certain Ph conditions naturally form into protective vesicles, these vesicles can also divide under mechanical conditions AND they tend to combine with smaller vesicles into larger ones such that the contents are merged as well -- but tend to only grow so large before undergoing mechanical division.


(4) Unlike modern cell walls, these primitive vesicles are porous which allows building blocks in, which combine with other components and then are too large to escape


(5) Eventually, some of the peptide chains prove beneficial to the fatty-acid vesicle structures.


(6) We know that some peptide chains are self-replicating -- by setting up even a simple peptide chain which can self-replicate we set the stage for evolutionary processes over time to work. And we know that some single RNA strands have been found to be capable of replication as well.


(7) We also know that the Qb virus can reproduce without a cell if the chemical environment is available.

See The Fifth Miracle by Paul Davies (excerpt)

(8) Finally, we're just now at the stage where we can start building complex life from scratch directly in the lab:



There are, of course, many open questions, nobody is denying that -- but they are just questions and there is absolutely no indication that any of these problems are intractable (including ribose and chirality). Try Google Scholar: abiogenesis ribose

There are 100's of more research papers on the subject, this is just barely scratching the surface.

One of the big problems with religious belief structures which claim revelatory knowledge from God is that it blocks people from even attempting to understand what is true. Where in the bible does it explain the mechanism that God supposedly used to create the universe and to create life? If it doesn't speak to the how, then how do you claim to know that organic life could not have happened as part of the natural course of the universal laws which ultimately drive everything?

You should investigate further: Dr M Reza Ghadiri and Dr Jack Szostak

How do you get to RNA without the mechanisms in place today to create it?

That is now at least a half-solved problem, See Dr. Sutherland's research:

the chemicals naturally formed a compound that is half-sugar and half-base. When another half-sugar and half-base are added, the RNA nucleotide called ribocytidine phosphate emerges. A second nucleotide is created if ultraviolet light is shined on the mixture. Dr. Sutherland said he had not yet found natural ways to generate the other two types of nucleotides found in RNA molecules, but synthesis of the first two was thought to be harder to achieve. If all four nucleotides formed naturally, they would zip together easily to form an RNA molecule with a backbone of alternating sugar and phosphate groups.


More resources to read:


and



29 comments:

  1. On the origin of primitive cells: from nutrient intake to elongation of encapsulated nucleotides
    Meierhenrich UJ, Filippi JJ, Meinert C, Vierling P, Dworkin JP.
    Angew Chem Int Ed Engl. 2010 May 17;49(22):3738-50.
    Recent major discoveries in membrane biophysics hold the key to a modern understanding of the origin of life on Earth. Membrane bilayer vesicles have been shown to provide a multifaceted microenvironment in which protometabolic reactions could have developed. Cell-membrane-like aggregates of amphiphilic molecules capable of retaining encapsulated oligonucleotides have been successfully created in the laboratory. Sophisticated laboratory studies on the origin of life now show that elongation of the DNA primer takes place inside fatty acid vesicles when activated nucleotide nutrients are added to the external medium. These studies demonstrate that cell-like vesicles can be sufficiently permeable to allow for the intake of charged molecules such as activated nucleotides, which can then take part in copying templates in the protocell interior. In this Review we summarize recent experiments in this area and describe a possible scenario for the origin of primitive cells, with an emphasis on the elongation of encapsulated nucleotides.

    ReplyDelete
  2. Reconstructing the emergence of cellular life through the synthesis of model protocells.
    Mansy SS, Szostak JW.
    Cold Spring Harb Symp Quant Biol. 2009;74:47-54. Epub 2009 Sep 4.
    The complexity of modern biological life has long made it difficult to understand how life could emerge spontaneously from the chemistry of the early earth. The key to resolving this mystery lies in the simplicity of the earliest living cells, together with the ability of the appropriate molecular building blocks to spontaneously self-assemble into larger structures. In our view, the two key components of a primitive cell are not only self-assembling, but also self-replicating, structures: the nucleic acid genome and the cell membrane. Here, we summarize recent experimental progress toward the synthesis of efficient self-replicating nucleic acid and membrane vesicle systems and discuss some of the issues that arise during efforts to integrate these two subsystems into a coherent whole. We have shown that spontaneous nucleic-acid-copying chemistry can take place within membrane vesicles, using externally supplied activated nucleotides as substrates. Thus, membranes need not be a barrier to the uptake of environmentally supplied nutrients. We examine some of the remaining obstacles that must be overcome to enable the synthesis of a complete self-replicating protocell, and we discuss the implications of these experiments for our understanding of the emergence of Darwinian evolution and the origin and early evolution of cellular life.

    ReplyDelete
  3. Template-directed Synthesis of a Genetic Polymer in a Model Protocell
    Sheref S. Mansy, Jason P. Schrum, Mathangi Krishnamurthy, Slvia Tobé, Douglas A. Treco, and Jack W. Szostak
    Nature. 2008 July 3; 454(7200): 122–125.
    Contemporary phospholipid based cell membranes are formidable barriers to the uptake of polar and charged molecules ranging from metal ions to complex nutrients. Modern cells therefore require sophisticated protein channels and pumps to mediate the exchange of molecules with their environment. The strong barrier function of membranes has made it difficult to understand the origin of cellular life and has been thought to preclude a heterotrophic lifestyle for primitive cells. Although nucleotides can cross DMPC membranes through defects formed at the gel to liquid transition temperature1, 2, phospholipid membranes lack the dynamic properties required for membrane growth. Fatty acids and their corresponding alcohols and glycerol monoesters are attractive candidates for the components of protocell membranes because they are simple amphiphiles that form bilayer membrane vesicles3-5 that retain encapsulated oligonucleotides3, 6 and are capable of growth and division7-9. Here we show that such membranes allow the passage of charged molecules such as nucleotides, so that activated nucleotides added to the outside of a model protocell (Fig. 1) spontaneously cross the membrane and take part in efficient template copying in the protocell interior. The permeability properties of prebiotically plausible membranes suggest that primitive protocells could have acquired complex nutrients from their environment in the absence of any macromolecular transport machinery, i.e. could have been obligate heterotrophs.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743009/

    ReplyDelete
  4. More resources:

    Origins of life on the earth and in the cosmos By Geoffrey L. Zubay, 2000
    http://books.google.com/books?id=8kI1A5538bEC&lpg=PA258&ots=FHaGYFqhko&dq=%22Nucleoside%20phosphorimidazolides%22&pg=PP1#v=onepage&q&f=false

    Complete Course in Astrobiology by By Gerda Horneck, Petra Rettberg, 2007
    http://books.google.com/books?id=PpVdBl2SN4EC&lpg=PA13&dq=%22Nucleoside%20phosphorimidazolides%22&pg=PP1#v=onepage&q&f=false

    The RNA world: the nature of modern RNA suggests a prebiotic RNA world By Raymond F. Gesteland, Thomas Cech, John F. Atkins, 2006
    http://books.google.com/books?id=3mREVdXNzFcC&lpg=PA61&dq=%22Nucleoside%20phosphorimidazolides%22&pg=PP1#v=onepage&q&f=false

    Progress in biological chirality By Gyula Pályi, Claudia Zucchi, Luciano Caglioti, 2004
    http://books.google.com/books?id=MwazbzMkzg8C&lpg=PA299&dq=%22Nucleoside%20phosphorimidazolides%22&pg=PP1#v=onepage&q&f=false

    Symposium on Chemical Evolution and the Origin and Evolution of Life [multiple]

    ReplyDelete
  5. Szostak's publication list:

    http://genetics.mgh.harvard.edu/szostakweb/publications.html

    ReplyDelete
  6. Abiogenesis seminar notes (by Ahmad Kanaan): http://bit.ly/szostakseminar

    ReplyDelete
  7. Exploring the New RNA World: http://nobelprize.org/nobel_prizes/chemistry/articles/cech/index.html (by Thomas R. Cech)

    ReplyDelete
  8. Debunking Christianity's: A Romp Into Theories of the Cradle of Life

    http://bit.ly/g8Priy

    ReplyDelete
  9. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions
    http://nodens.ceab.csic.es/people/afernandez/files/lifeorigin/RNA-synthesis.pdf

    Popular Article:
    http://www.wired.com/wiredscience/2009/05/ribonucleotides/

    ReplyDelete
  10. Meet the primitive plant pathogen "hammerhead viroid"

    Wired: Popular article:
    http://www.wired.com/wiredscience/2009/03/mutationrecord/

    Extremely High Mutation Rate of a Hammerhead Viroid
    http://www.sciencemag.org/content/323/5919/1308.abstract

    See Also:
    Viral Mutation Rates
    Closing the Circle: Replicating RNA with RNA
    Measurements of spontaneous rates of mutations in the recent past and the near future
    Colloquium Paper: The comparative genomics of viral emergence

    A kissing-loop interaction in a hammerhead viroid RNA
    critical for its in vitro folding and in vivo viability
    http://www.uv.es/pena/papers/Gago%20et%20al.,%20RNA%202005.pdf

    Viroid Master List:
    http://nt.ars-grin.gov/subviral/viroids.html

    Google Book: Viroids
    http://books.google.com/books?id=6wVtRfI0V8UC&lpg=PA227&ots=MxO4dmeNLJ&dq=hammerhead%20viroid&pg=PP1#v=onepage&q=hammerhead%20viroid&f=false

    ReplyDelete
  11. Ribozyme-Catalyzed Transcription of an Active Ribozyme, the story of: tC19Z

    http://www.newscientist.com/blogs/shortsharpscience/2011/04/rna-enzyme-makes-another-rna-e.html

    http://www.sciencemag.org/content/332/6026/209.abstract


    Related: Climbing in 190 Dimensions

    http://www.sciencemag.org/content/332/6026/181.full

    ReplyDelete
  12. I did not get through all of what you have written but I am very happy that you have backed up all of your information and I like all that you have to say. I am going into psychology and desiring to link it with physics and nature among other things. I understand the desire to show that what some believe in god could not possibly be true but unfortuantely many people have grown with these beliefs and without their beliefs they may feel naked or vulnerable. I would just like to say that there are many parallels that can be found to help people find the symbolic nature of religion and how it relates to evolution. Through this subtlety people can alow themselves to absorb the information rather than passing it off because they feel threatened. And that is all... I like what you have to say and will be reading more. Thanks for sharing.

    ReplyDelete
  13. Thanks, I really appreciate the feedback. I would be curious to hear more on your ideas about how we can help religious people better understand or accept science. I created an entry to discuss this topic: http://iconoclasm2000.blogspot.com/2011/04/discuss-how-we-can-help-religious.html

    I grew up going to Church so I do feel sympathy for and have some understanding of the difficulties such people face. But, unfortunately, my personal experience doesn't really give me any insight on how to help others.

    For myself, it was based on a hunger for truth and knowledge and INCLUDED a thorough reading of the Bible itself -- and I don't know how to "give" that hunger to others except by showing some of the amazing things that science has revealed to us.

    ReplyDelete
  14. A very good summary! I hadn't thought of prions in the context of this debate; it's pretty compelling stuff when you consider it.

    Quoted for Truth:
    "they are just questions and there is absolutely no indication that any of these problems are intractable"

    This has always been a big thing for me. The religious so often seem to suggest that because we don't have all the answers there must be a god. The fact that we don't know everything yet doesn't mean that we never will, and to argue otherwise is silly and stifles our intellectual growth as a species.

    ReplyDelete
  15. i think it's a great job.

    My recommendation for part 2:
    Since it's addressing creationists' critiques of abiogenesis, perhaps highlight this idea:

    "If creationists want to prove that abiogenesis is impossible then [they] only need to find some specific STEP that absolutely cannot have happened naturally. Not a fallacious statistical argument saying that it's just too improbable to believe. An actual chemical combination that cannot possibly happen in nature and the specific, scientific reasons why."

    and highlight the root of what is req'd of abiogenesis research ==> proteins from "the soup." In much the same way that the DNA evidence is enough to *prove* Evolution, and we don't NEED the fossil record (fossil record is *extra* evidence) likewise, we don't NEED a complete replicating system comparable to DNA to demonstrate the plausibility of an abiogenesis model. Creating the proteins is sufficient (wow, more than sufficient really when you think about how wonderful that really is), the rest is just filling in details.

    You mention it early on, but I'd really hammer that in since these particulars are what the creationists often attack.

    ReplyDelete
  16. More evidence that much of organic chemistry originated in Space and collected here on Earth.

    These are especially important findings due to the DNA nucleobases and analogs that are found along with the chemical processes that yield them.

    "In the lab, an identical suite of nucleobases and nucleobase analogs were generated in non-biological chemical reactions containing hydrogen cyanide, ammonia, and water. This provides a plausible mechanism for their synthesis in the asteroid parent bodies, and supports the notion that they are extraterrestrial," says Callahan.

    If these findings are confirmed by other labs this will be huge.

    http://www.nasa.gov/topics/solarsystem/features/dna-meteorites.html
    http://www.space.com/12578-evidence-space-created-dna.html
    http://richarddawkins.net/articles/642503-building-blocks-of-dna-found-in-meteorites-from-space
    http://www.space.com/12569-meteorites-dna-building-blocks-discovery.html

    ReplyDelete
  17. Another keen bit of research addressing the preponderance of molecules with left-handed chirality.

    Summary:
    http://www.lousycanuck.ca/2011/08/15/abiogenesis-chirality-and-narrowing-down-the-alternatives/

    ScienceDaily:
    'Ancestral Eve' Crystal May Explain Origin of Life's Left-Handedness
    http://www.sciencedaily.com/releases/2010/04/100421121501.htm

    Study Builds On Plausible Scenario for Origin of Life On Earth
    http://www.sciencedaily.com/releases/2011/08/110809144517.htm


    Citations:
    Tu Lee, Yu Kun Lin. The Origin of Life and the Crystallization of Aspartic Acid in Water. Crystal Growth & Design, 2010; 10 (4): 1652 DOI: 10.1021/cg901219f

    Jason E. Hein, Eric Tse, Donna G. Blackmond. A route to enantiopure RNA precursors from nearly racemic starting materials. Nature Chemistry, 2011; DOI: 10.1038/NCHEM.1108

    ReplyDelete
  18. Biologists' Discovery May Force Revision of Biology Textbooks: Novel Chromatin Particle Halfway Between DNA and a Nucleosome

    http://www.sciencedaily.com/releases/2011/08/110818142842.htm

    ReplyDelete
  19. More on complex organic molecules forming in comets: http://www.sciencedaily.com/releases/2013/03/130305131412.htm

    In an ultra-high vacuum chamber chilled to 10 degrees above absolute zero (10 Kelvin), Seol Kim and Ralf Kaiser of the Hawaiian team simulated an icy snowball in space including carbon dioxide, ammonia and various hydrocarbons such as methane, ethane and propane. When zapped with high-energy electrons to simulate the cosmic rays in space, the chemicals reacted to form complex, organic compounds, specifically dipeptides, essential to life.

    ReplyDelete
  20. Possible evidence of a protein-first development, using just 10 amino acids believed to exist on Earth around 4 billion years ago:

    Origins of life? Discovery could help explain how first organisms emerged on Earth

    ReplyDelete