Origins of Life – Darwin’s Little Warm Pond

ResearchBlogging.orgOrigins of life is a tricky business.  We can’t know how it happened.  We weren’t there and chemical reactions and molecules just don’t fossilize well.  The point is not to show how it happened.  Likewise, the point is not (necessarily) to create a new form of life in the lab.  The point is to show that chemistry and physics alone can plausibly create life.

If it can be shown that there are no physical or chemical barriers to the generation of life from non-life, then there is no need for intelligent design.

This is the third installment of my survey of origins of life research. The fourth (future) post is planned to discuss early replication.  The previous posts covered the odds of chemical systems becoming life (for some value of ‘life’) and the ability of nucleobases  spontaneously self assemble

That last bit got to wondering about the actual self assembly and how it works.  First, I have to say that there are many models of how this happened.  Some work in the mid 90s showed how long chain RNAs could self assemble on clay substrates. [1] That was the original article that I was going to write this post about.  One main reason is that creationists can’t complain that long chain RNAs can’t self assemble.  It’s been shown it can be done since around the time that Behe’s Darwin’s Black Box was published. 

However, while researching this post I came across a more recent, and to me, more exciting paper.  Forget all the minerals and catalysts and exotic conditions others have proposed.  According to the authors of this paper, Darwin may well have been correct with life developing in his small, warm pond.

From the authors:

A key step missing in the reconstruction of the origin of living systems is an abiotically plausible synthesis of RNA. To fill this gap, for the robust synthesis and the simultaneous presence of all the necessary nucleic acid precursors (which is possible in principle (22)), an abiotic procedure for their activation and a thermodynamically sound polymerization mechanism are needed.

This paper takes care of the thermodynamically sound polymerization step.  Now, I freely admit that this paper uses cyclic nucleotides, but that is not an insurmountable obstacle [2,3,4,5]. 

So, the authors examined low concentrations (as low as 1 micromol) of cyclic nucleosides in a large variety of conditions to look for evidence of long chain polymerization.  The results are stunning.  Of all the conditions tested (pH differences, presence of minerals, concentrations, etc) the best results came simply from warm water (40°C to 90°C).

Open nucleotides (not cyclic) don’t polymerize in warm water and often degrade under those conditions.  Cyclic nucleotides, on the other hand, formed polymers.  The various nucleotides were tested (A, C, G, U).

The simplest tests resulted in up to a 25 nucleotide chain.  Further (referencing the “What are the Odds post”), the chains formed fast.  An average result was an 11 nucleotide chain forming in less than a minute.  By letting the reactions continue for over 100 hours, molecules larger than 100 nucleotides were formed.  In nothing but warm water.

Further, the authors analyzed the actual chemical bonds to make sure that this was ‘our modern’ RNA being formed.  It was, the normal 3’-5’ phosphodiester bonds were formed.

So, here we have what is effectively modern RNA chains being formed from prebiotic precursor molecules in nothing more than warm water.  It happens quickly and the results are stable.

In my reviews so far, we have the simple fact that very small RNAs can be used as catalysts.  We have the production of RNAs from precursor materials.  And here, we have a completely different method for the production of long chain RNAs.

I think that last bit is very important.  There isn’t just one method that will work, there are at least two, and probably more, chemically feasible methods of getting from base, inorganic precursors all the way to RNA.

And it could have happened, just like Charles Darwin predicted over 150 years ago.

_____________________________________________
Costanzo, G., Pino, S., Ciciriello, F., & Di Mauro, E. (2009). Generation of Long RNA Chains in Water Journal of Biological Chemistry, 284 (48), 33206-33216 DOI: 10.1074/jbc.M109.041905

[1] James P. Ferris, et. al, “Synthesis of long prebiotic oligomers on mineral surfaces”, Nature, Vol. 381, 2 May 1996, pp. 59-61.

[2]  Costanzo, G., Saladino, R., Crestini, C., Ciciriello, F., and Di Mauro, E. (2007) J. Biol. Chem. 282, 16729–16735

[3] Saladino, R., Crestini, C., Ciciriello, F., Costanzo, G., and Di Mauro, E. (2007) Chem. Biodiv. Helv. Chim. Acta, 4, 694–720

[4] Saladino, R., Ciambecchini, U., Crestini, C., Costanzo, G., Negri, R., and Di Mauro, E. (2003) ChemBioChem 4, 514–521

[5] Saladino, R., Crestini, C., Ciciriello, F., Pino, S., Costanzo, G., and Di Mauro, E. (2009) Res. Microbiol., doi:10.1016/j.resmic. 2009.06.001

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22 Responses to Origins of Life – Darwin’s Little Warm Pond

  1. Eugen says:

    Hi Ogre

    interesting post.

    It’s OK to be optimistic re. OOL. Unfortunately I don’t share that enthusiasm. Believe it or not it’s not because religion. I’m not very religious. It’s not because chemistry ,I guess some precursors can be assembled ( with lots of help by the looks of it ).

    I program and troubleshoot automated systems. This is not very scientific but my intuition is telling there is more to it. I get the same feeling when I troubleshoot complex system I’m not familiar with. At first brain is trying to form general logical concepts. After that ,one continues to modularize the system into operational groups. Next, within group you try to find sub group ,sequence and hierarchy of operation. Sub group is broken into tasks,each task is examined in detail and that’s where you usually find the little proverbial devil.
    All along ,at every level you must look for patterns , loops, general stops,redirects etc. It’s quite a process. Fit for Neo :)

    I’m anxiously awaiting your blog on replicators.

  2. ogremkv says:

    Eugen,

    Well, that’s sort of what I’m doing. Reviewing the breakdown of the pieces.

    There’s one problem with your analogy. Life is nothing like a computer program. DNA is not code. There are no if/thens. there are not a lot of things that work in programs. It looks like it should, but the computer/code analogy is way over-rated IMO.

    At this point in the science, analogy is only useful for bridging the gap between experts and non-experts. It’s a teaching tool and not a very good one. We can talk about DNA and organic and pre-biotic chemistry in high levels of detail without invoking analogy.

    Intuition just doesn’t work in science. Heisenberg and the double slit experiments convinced everyone of that.

    Thanks for thinking…

  3. Eugen says:

    Ogre

    10-4 on the warning.

    I was told on one of the forums by frustrated poster “if your only tool is hammer everything looks like a nail”. I agree with that as I look at many issues mechanistically. There is danger of overdoing it so I try to be careful with bio-chemical systems. Similar to what you said ” thank Chutlu I’m not bio chemist” applies here except I would say “thank God”.
    God (for you Chutlu), that stuff was boring.

    OTOH, there is place for analogies. Maxwell, Thomson,Faraday used them heavily to help them explain electro magnetism. Maxwell was encouraging his students by saying how analogies are not about resemblance but about relation.

  4. Pingback: Origin of Life – RNA Self Replicators | Cassandra's Tears

  5. If you liked this Costanzo article, you might also like
    http://cshperspectives.cshlp.org/content/3/4/a003590.full.pdf – a Michael Yarus tour de force looking back past the RNA World to what might have been the first Darwinian ancestor.

    And also
    http://hoffman.cm.utexas.edu/courses/nature_hypothesis_paper.pdf – paper on the evolution of the ribosome. The loop “you need proteins to make DNA and you need DNA to make proteins” is common in creationist literature. It features in Signature in the Cell, for example. However, as this close analysis of the ribosome shows, you need RNA to make proteins, but you don’t need proteins to make RNA. In addition, the rbosome itself is not ‘irreducibly complex’, you can chop pieces off of it until you get down to the core PTC.

    That functional core is a duplicated length of 110 bases. (Do other 110 base lengths have similar function? I don’t know, but I’d bet this is a sloping island, not a stick balanced on the ocean.) This is what most creationist arguments from improbability boil down to, the improbability of this functional sequence.

  6. david salako says:

    Biogenesis refutes abiogenesis. Example of biogenesis is evidently seen during the replication of humans during reproduction. All humans come into this world as a result of being born into it. And this has occured 7billion times on the basis that there are 7billion humans that inhabit this earth. Therefore the evidence is collosal regarding the origin of human life. And yet people are blinded from this simple fact as they seek new alternatives to define their existence. But i say which evidence do you accept, with regards to the origin of your existence,that which has occured 7billion times(being born)? Or that which has not been seen before? The fact is this statement is true:”the more we people are conditioned by their enviroment against the truth they more they fail to see simple facts. The fact is no human has know no other entry into this world, except being born. And the fact is no human will know any exist out of it, except through death. Those who promote any alternatives to these facts are insane.

  7. david salako says:

    The fact is those who promote other alternatives to the origin of life do so because they are trying to eliminate creationism. This is what the age old debate is about. It is about sinful people looking for intellectual ways to protect their favourite sins. GOD is an obstacle to this. Therefore they seek ways to negate the fact that they are accountable to him. Nevertheless the fact is we are all created on the basis of causalty. Causalty is the relationship between cause and effect. Therefore all humans are causes of other humans who are effects who become causes of other humans. However humans are not infinite. Therefore there was a beginning of the first cause. But this cause could not have been born. However this is violates the law of nature. Therefore the cause of this first cause is miracolous because only micracles violate the closed laws of nature. Only God can do that. Therefore God is the origin of life who created the first cause(humans) that began human replication.

  8. OgreMkV says:

    sigh…

    Evidence that God exists?

    If all living things come from living things, where did the first living thing come from?

    There is nothing in your two posts here that is not argument from authority or God of the gaps.

    BTW: Your entire argument is completely and utterly refuted by Ken Miller and Robert Bakker. Both practicing Christians (one of whom is a pastor) and they are both proponents of science and evolution. Ooops.

  9. david salako says:

    The agruement i have presented in relation to causalty is a form of the ontological arguement for the existence of the christian God. Ontology deals with the nature of existence. In relation to God what is normally done is one uses the nature of God as a premise, and then we deduce it objectively from nature. In other words from the things created God’s essential qualities can be deduced and verified. In the example of causalty(above) we can discern signs of God’s power to violate closed biological laws of nature.

  10. OgreMkV says:

    Oh, I see, you’re using a circular argument.

    You assume the existence of God and then define God and how the universe works in such a way that only God could have created it. Then show that only God could have created the universe, life and everything.

    Thanks for explaining that.

    Of course, the problem is that the exact same argument can be made for the Flying Spaghetti Monster, Vishnu, Zeus, Odin, The Hulk, The Fantastic Four, etc, etc, etc.

    That is not how science works.

    Further, you have failed to provide any evidence for the ‘closed biological laws of nature’… whatever that means. For example, in the other thread you posted on, I explained that there are dozens of peer-reviewed papers published each year (I’ve provided links in various places) that would easily show you are correct. All they have to do is show that chemistry, biology, and physics prevents some required aspect of life forming in the natural world. Yet, time and time again, this is not the case. In fact, at this point there are several non-mutually contradictory paths that life could have developed from precursor molecules.

    To show that your claim is correct, you would have to show why every single possible path is wrong. Stating that scientists haven’t created life from scratch yet won’t do it. You have to actually prove that the chemistry or physics would prevent it from happening. In every possible path. Feel free to get started.

  11. david salako says:

    Firstly ogre thanks for the discourse. Now, saying that my arguements have been refuted is not an arguement. For refutations are made by arguements that are consistent with the principles of logic or valid arguements. And using the name of Christians that support your position does not justify that position especially when those christians credibility is very questionable. Moreover there are other Christians who do not support the same views. Therefore which of them is right? Or is it just a matter of pocking sides with the ones who favour the position you like? Moreover Christians cannot be supporters of evolution if they understand our scriptures properly on the basis of the book of Genesis. In that book the bible says man was created whole. Therefore he did not evolve. Moreover there was no blood shed until after the fall of man. But evolution is based on blood shed in order to survive and even-often-on what we may call selfishness. But genesis does not portray such a picture.

  12. david salako says:

    So you see you have stated two christians name whose credibility i have countered. For Christians cannot be evolutionists on the basis i have provided. In fact this issue of trying to reconcile christianity with evolution is impossible because it contradicts the genesis account. However some have tried again by introducing a new concept called thiestic evolution. But again this view is incompatible with the genesis account. Moreover there is what is called the gap theory. Moreover there are 4concepts of evolution that seek to explain the origin of life. However none can be reconciled with christianity. Therefore the christian names you mentioned are definitely faulty. And no i did not assume the existence of God. But rather what i have done is deduced from what is seen in relation to his nature. And i did not say i was using a circular arguement or a chain arguement.

  13. OgreMkV says:

    The gift that keeps on giving. We have the “no true Christian’ argument.

    Which of them is right? That’s exactly the point. Neither of them can be right based on religion. That’s the problem with holy books. Which one is correct? Is the creation myth in the Bible correct? Which one? Genesis 1 or Genesis 2? They are mutually contradictory you know. Why should the Bible be used instead of the the legends of the Vikings? or of the Greeks? or the Hindus?

    Again, since you want to argue about science, then you will have to present your science. You have not refuted any of the established science. You are making the claim that science, 99.95% of practicing scientists, thousands of organizations, and at least a dozen religions are all wrong.

    It is up to you to support your claims. You might find this article interesting: http://ogremk5.wordpress.com/2011/10/05/work-hard-get-the-rewards-you-deserve/

    You, when you make a claim that is contrary to what is established science (established for almost 200 years and with literally tens of thousands of published papers per year and dozens, if not hundreds, of practical applications, processes, and products that result from it), then it is up to you to provide that evidence.

    Why should I defend science? I have in dozens of places in this blog. Read them. There are dozens of books (Luisi’s for example) and thousands of peer-reviewed papers for you to read. Look them up, read them.

    If you agree that science is not compatible with Christianity, then we can easily decide which is which.

    Science, including evolution, simply works. Prayer, doesn’t. It’s not open to interpretation or anecdotal… it’s been shown in double blind studies… Prayer doesn’t work.

    BTW: When you say

    In relation to God what is normally done is one uses the nature of God as a premise,

    and then your conclusion is

    form of the ontological arguement for the existence of the christian God

    Then you are using a circular argument.

    But feel free… you are making a claim that a God exists… provide the evidence. Because, that’s what this is really all about. It has nothing to do with science, except for the fact that science is determining answers to questions that you think are the sole providence of your God. This offends you and if science is right, then your God has no place in your world anymore. What a sad little God, when a simple experiment can refute his existence.

  14. david salako says:

    And you also said that ken miller and another guy who is a practising christians have refuted my position. If they are against such a view then they are against God himself. For to adhere to such views is against orthodox christian doctrines that can be found in the book of genesis. Here is the logic: 1. All existence is finite. 2. Therefore all existence have a beginning and an end. 3. So the first existence was finite. 4. Therefore the first existence had a beginning and an end. 5. Because existence is not infinite it means there was a time when the first existence did not exist because every existence has a beginning. 6. But the beginning of the first existence could not have been via the biology of reproduction and being born on the basis of previous statements. In conclusion it is evident that the existence of the start of reproduction has violated that biological process its-self. This is a violation of the law of nature. Only miracles can do that. Therefore God is the beggining of human existence.

  15. OgreMkV says:

    And you also said that ken miller and another guy who is a practising christians have refuted my position. If they are against such a view then they are against God himself.

    Again, so YOU say. The Catholic church, at least one sect of Muslim, the Hindu community, Methodist, Episcopal, African Methodist Episcopal, Catholic, Southern Baptist, Reform Jewish, and Presbyterian groups + 13,000 signatories from Christian clergy in support of evolution and science.

    Why do you get to judge?

    Let’s take a look shall we?

    For to adhere to such views is against orthodox christian doctrines that can be found in the book of genesis.

    Again, I ask… which version of Genesis? 1 or 2? They are mutually contradictory you know.

    If only one is to be taken literally, then which one and how do you know which is which? Explain in detail.

    Here is the logic: 1. All existence is finite.

    OK, I can buy that.

    2. Therefore all existence have a beginning and an end.

    That’s a bit trickier, you’ll have to explain what you mean here. There is a big difference between cosmology and bacteria. There’s a big difference between bacteria and vertebrates.

    I tend to agree however.

    3. So the first existence was finite.

    Useless statement.

    4. Therefore the first existence had a beginning and an end.

    Another useless statement. The word ‘all’ in the first two propositions takes care of 3 and 4 for you.

    5. Because existence is not infinite it means there was a time when the first existence did not exist because every existence has a beginning.

    OK, we get it…

    6. But the beginning of the first existence could not have been via the biology of reproduction and being born on the basis of previous statements.

    Now, here we have some issues. Are we talking about cosmology? Are we talking about organisms? What are we talking about?

    You also completely fail to take into account the possibility that organic materials can arise from non-organic methods. Which means, you’re logic is no longer valid.

    In conclusion it is evident that the existence of the start of reproduction has violated that biological process its-self.

    No. What is a biological process? Define it. Is the synthesis of urea (an organic compound) biological? Is is biological when it is synthesized from non-biological sources? Where do you draw the line?

    Take humans for example… there had to be a first human right? Well, define human. If we had a complete record (and we have a real good one), then you would find a continuum of homonids beginning with the common ancestor of Chimpanzee and modern humans and ending with modern humans. Where in that sequence do you draw the line and say ‘this is the first human’?

    Even you creationists can’t agree on that: http://www.talkorigins.org/faqs/homs/compare.html

    Now, again, there is not Law of Biology that says all organic things must come from living things. That is another place your argument fails. It is trivial to show that this is not the case.

    This is a violation of the law of nature. Only miracles can do that. Therefore God is the beggining of human existence.

    There is no violation…again… numerous paths are available. This article discusses one such path from non-living to living.

    You claim that miracles can do this too. Provide objective evidence of miracles.

    Provide objective evidence that only God is capable of such miracles. I say that the Flying Spaghetti Monster can do the exact same thing. Prove me wrong.

    You logic is OK, if wordy, but because you have PRESUMED THE EXISTENCE OF GOD, then your conclusions are faulty.

  16. david salako says:

    You see now you are against the christians you were using to support your case by the things you have stated. For you state clearly”neither of them can be right based on religion”. So why use them as an authority? It is clear then you are seeking subjective means to justify your position. But the fact is just because many religions may be wrong, it does not mean that the truth does not exist, just like false currencies in a society does not mean that true currency does not exist. There is a standard of identifying which has been demonstrated to you. If you knew it you would not have used those two christians who are contrary to the scriptures to defend your position. By the way my arguement is not to defend God(that is a by product), but rather, it is to show that the idea or concet of evolution is illogical.

  17. david salako says:

    1. Biogenesis refutes abiogenesis, therefore life could not have originated from non-living things. 2. You only assume that there are numerous pathways for you have no empirical basis for such assumptions that human existence could have begun in alternative ways. 3. But there is clear evidence that human beings have all come from being born. And it is on that basis that my arguement that God is the first cause of human life is based. 4. The genesis problem is not a genesis problem, but rather one of interpretation and understanding. 5. God is not an assumption on the basis of my ontological arguement. 6. In the beginnig of your page you wrote this:” origins of life is a tricky business, we cant know how it happened. We weren’t there……” Therefore how do you know that there are other pathways for life to have begun? 7.To compare God to spaghetti e.t.c is illogical since God is a being and the latter food. Again my ontological arguement demonstrates signs of God’s nature via human life.

  18. david salako says:

    In conclusions there is much contradictions in your view. And i have demonstrated that clearly. But good discourse. Thank you!

  19. Amadan says:

    The problem with David’s ontological argument (actually, Anselm’s) is that it can be used to ‘prove’ the existence of The Perfect Doughnut or The Perfect Anything. On that basis, it proves nothing.

    Another and more important flaw in it is that it assumes that existence is a property. But as Kant pointed out, while we may say that the difference between horses and unicorns is that horses exist, there is no information added to the statement ‘Horses have legs” by changing it to “horses that exist have legs”.

    And can David can give evidence of the existence of, say the square root of -1 or similar ideas? Is the ‘existence’ of that idea qualitatively different from the existence of the god of which he speaks? If so, how? If not, how does he come to ascribe (as he presumably does) that idea with the ability to intervene in the natural world? Can he give us any evidence of such intervention?

    Gods are ideas – human inventions. That much is clearly evidenced by the way way they echo the preferences and prejudices of their apologists.

  20. OgreMkV says:

    You see now you are against the christians you were using to support your case by the things you have stated. For you state clearly”neither of them can be right based on religion”. So why use them as an authority?

    I’m not using them as an authority. I’m using them to refute your comments. There is a difference. You claimed that Christians cannot believe in science. I refuted you with two Christians who still accept science. Whether I agree with them or not, they are scientists and they are well known Christians. Bakker is a pastor.

    Your only response is to claim they are not Christians, but who made you the authority?

    But the fact is just because many religions may be wrong, it does not mean that the truth does not exist, just like false currencies in a society does not mean that true currency does not exist.

    Exactly. How do you know that yours is right and the Flying Spaghetti Monster is not right? Give me some of this objective evidence that you want from me.

    By the way my arguement is not to defend God(that is a by product), but rather, it is to show that the idea or concet of evolution is illogical.

    Then you are wasting everyone’s time. As I have stated and can prove, you cannot get rid of evolution (I’ll note that you seem to conflate evolution, abiogenesis, and cosmology, but I’ll let it go for now). Why not? Because it works. Everything from aerospace aircraft design to combustion mechanics of diesel engines use evolutionary processes to design and improve them. Factories to financial markets use the principles of evolution to increase efficiency. It works. You simply cannot refute that.

    1. Biogenesis refutes abiogenesis, therefore life could not have originated from non-living things.

    You keep saying that as if it makes it right. It doesn’t. Here’s why. Ready?

    When the Earth formed, there was no life on it. Now there is. You are right, the life had to come from somewhere. I say it came from non-organic sources, you say it came from God. I’ve got several thousands research papers supporting my position, you have an old book of myths with so many internal contradictions it’s barely readable.

    You are making a claim. Support it.

    2. You only assume that there are numerous pathways for you have no empirical basis for such assumptions that human existence could have begun in alternative ways.

    How do I know there are numerous pathways? Because the research has been done.

    And now I have a request. Pick one: human life, origin of life or origin of the universe. You are changing goalposts faster than the refs at a World Soccer Championship game. There are NOT numerous pathways to HUMANS. There are numerous pathways to life from non-life. Read up on them.

    3. But there is clear evidence that human beings have all come from being born. And it is on that basis that my arguement that God is the first cause of human life is based.

    This is where you go wrong. There is an excellent fossil record of our ancestors and ancestral species. If you want to use God as an argument, you first have to show that God exists.

    Let me explain this carefully. Even if you disprove evolution, right here, right now… it still doesn’t mean that God did it. This is called the fallacy of false dichotomy. There are other options than God and evolution. You fail to recognize that and thus your arguments will forever be invalid.

    4. The genesis problem is not a genesis problem, but rather one of interpretation and understanding.
    Yes it is. Since the two versions are mutually contradictory, which is correct? How do you know?

    If one of them is to be ‘interpreted’> How is to be interpreted? How do YOU know?

    What else in the Bible is open to interpretation? How do you know?

    Do you see where this is going? As I ALREADY stated. If you declare one part open to interpretation, then you open the entire thing to interpretation and that makes the entire thing totally useless.

    5. God is not an assumption on the basis of my ontological arguement.

    But you said “In relation to God what is normally done is one uses the nature of God as a premise”

    6. In the beginnig of your page you wrote this:” origins of life is a tricky business, we cant know how it happened. We weren’t there……” Therefore how do you know that there are other pathways for life to have begun?

    Because the chemistry and the physics allow for them.

    7.To compare God to spaghetti e.t.c is illogical since God is a being and the latter food. Again my ontological arguement demonstrates signs of God’s nature via human life.

    It is just as illogical to deny Odin, Zeus, the FSM, Vishnu, etc, etc, etc. My ontological argument for the Flying Spaghetti Monster is EXACTLY THE SAME as your argument for God.

    I understand that you can’t see that, but it is. It’s the exact same argument used by Muslims, and Hindus, and Vikings, and American Indians, and every other religion under the stars. Since they can’t all be correct, and none of them actually work, then we are just as good off ignoring all of them.

    See, that’s the thing you keep missing. Science works. Religion, as a basis for doing things in the real word doesn’t work. If you want to think so, then fine. You’re wrong of course. If you want to be right, then provide the evidence that your God exists and is the only God AND that he did the things you claim he did.

    That’s the only thing that will help you.

  21. OgreMkV says:

    “In conclusions there is much contradictions in your view. And i have demonstrated that clearly. But good discourse. Thank you!”

    You have done no such thing.

  22. Cubist says:

    sez davey salako: “To compare God to spaghetti e.t.c is illogical since God is a being and the latter food. ”
    Nonsense; God is food. Millions of practicing Christians munch on His living flesh, and drink His blood, every Sunday (see also: ‘transubstantiation, miracle of”). You are FAIL.

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