Reconstructing the Ancestral Routes to Nucleobases

A few weeks ago, I linked to a very interesting paper on how life may have evolved. In response to some comments here, the abstract has been revised. Here is the note to me in email:

The abstract was revised to (hopefully) eliminate ambiguity and make it clearer that Sylvain’s proposed chemical steps are not just a partial solution, but rather, go from the first reaction all the way to all the biomolecules necessary to “usher in the RNA world.” The full-picture illustration was also added on the home page to help readers grasp the scope of what is being offered.

To me, one of the compelling aspects of this is that all the relevant biomolecules form in one location through ‘room temperature’ chemical steps that do not require anything exotic.

Topics relevant to the Origin of Life that are addressed in this paper:

  1. Why the relevant amino acids are all left-handed

  2. Why there are 20 standard amino acids, and why those 20
  3. Why the relevant amino acids are all “alpha-amino”
  4. Why the relevant sugars are right-handed
  5. The origin and preservation of homochirality
  6. The origin of nucleobases A, G, C, U
  7. The origin of RNA

  8. The origin of the lipids

To put this into perspective, each one of these topics is a major big deal. That this model shows them as possibly being parts of interrelated cascading chemical steps is stunning. It is interesting to note that these chemical steps take place, not in a “primordial soup,” but in a sheltered microenvironment of a mineral host structure. Since these proposed reactions do not work in water, the concept of life originating in a “primordial soup” may have mislead Origin of Life chemists for many decades.

We’ll see where it goes. If it can actually tackle abiogenesis, it is a big deal.

10 thoughts on “Reconstructing the Ancestral Routes to Nucleobases”

  1. This is one of those areas where after you climb to the summit you find somebody already there.

    Even if this is not the right approach, somewhere out there I am confident the right line of reasoning will be found.

    Why am I so sure? Because the bible states that God is not a god of disorder but a God or order. To me this says that whatever we observe must make rational sense. Even so called miracles, with enough knowledge, will be understood to have rational underpinnings.

    So for me at least, finding those rational underpinnings supports my understanding of God.

    Not to suggest you would, but please don’t confuse me (a believer in a powerful and wise creator) with those idiots that make God out to be Loki the trickster putting rays of light in just the right vectors to fool us into thinking the universe is billions of years old… it is billions of years old and nothing in the bible contradicts that.

    Some people think God guided evolution. I’m not one of those (although I highly respect some that hold that view.) The bible states he formed man (and presumably everything else living as well) from the chemicals of the Earth (dust) which is all this article is suggesting.

    It would be a sad thing to me if anyone takes this article as some kind of proof that God does not exist. To me, the orderliness of things is substantiation of the reality and God that brought it into being.

    The bible says everything came into existence because of the abundance of God’s power. Not until E=mc^2 could that be rationally understood. To me, thinking about the magnitude of that abundance might be considered a religious experience (like looking into the night sky and imagining the distances involved.) For me, a rational understanding confirms God’s existance. A lack would do the opposite for me. In places where that lack exists, the abundance of other evidence suggests those holes will be filled in time. I have absolutely no doubt about that at all.

    Thanks for doing what you do… finding some of the most interesting rational expressions that are out there.

  2. Ken, even Richard Dawkins agrees that there is no proof that God doesn’t exist. That’s actually the whole (scientific) problem with God – he’s non-falsifiable.

    As for the OP, this is really neat. I always have assumed that such a mechanism would eventually be discovered, but the actuality of discovery will of course lead us to even more interesting places.

    I’m really interested in knowing more about the non-water environment of origination. If that’s true then the whole “search for water vapor to search for life” bit in xenobiology might be entirely off. It also allows the possibility of life on worlds, asteroids and comets in this solar system that lack liquid water.

  3. Ken – To put it another way, one argument is that God put together the laws of the universe in such a way that when the universe was created it would inevitably, somewhere among the near-endless deeps of space and time, engender life and eventually mind and soul. And then he “breathed life into the equations” and there was light. And matter, and space, and time. (Note that the word “then” is suspect – we don’t really have words to describe something that happens outside time and space.)

    This to my mind is far more elegant than the messy kludge described in Genesis. Interpreting the phrase “created in His image” to mean that we look like Him is just plain wrong.

    This interpretation also makes it rather difficult to believe that right here is the only place where abiogenesis happened.

  4. Fletcher Christian Says:
    February 18th, 2009 at 8:45 am

    “To put it another way, one argument is that God put together the laws of the universe in such a way that when the universe was created it would inevitably, somewhere among the near-endless deeps of space and time, engender life and eventually mind and soul.”

    ___________

    Why would a deity exert so much effort constructing this elaborate stack of domino’s we call the Universe? Certainly I can see the novelty of being able to just tip the first chip and then sit back and watch the show.

    There are so many irregularities in the Universe that don’t make sense in terms of the effort and energy required to put them together and put them motion. When we look into the Universe we see so many baroque objects that consume massive amounts of mass and energy yet seemingly have little to no purpose otherwise. Even within our own biology we find several mechanisms that are broken or inefficient. Is a human outsmarting God when they can design a reaction or device that performs a better job than what God intended?

    Religious people who believe in God also have no problem describing ‘unholy’ entities and plans. This is a contradiction to a perfect God with a perfect plan. as something ‘unholy’ would be against God’s plan. If he created everything and everything with a purpose then how do unholy entities exist.

    Finally, why is there so much suffering in this life. It certainly seems that a perfect God wouldn’t devise a plan that comprises so much pain and suffering. Doesn’t seem like a very nice God if he intended this enormous level of suffering to exist. I can certainly see that we need lessons in life to show us the difference between good and bad. However, these lessons can be learned with far less suffering than what we’ve experienced.

    No, there are just too many logical problems with the idea of a God who operates in such a way.

  5. Josh says: Why would a deity exert so much effort constructing this elaborate stack of domino’s we call the Universe?

    How much effort is it for a god?

    Josh says: When we look into the Universe we see so many baroque objects that consume massive amounts of mass and energy yet seemingly have little to no purpose otherwise.

    Little or no purpose to YOU, but to Him I’m sure it makes perfect sense.

    Josh says: Even within our own biology we find several mechanisms that are broken or inefficient.

    Again, in YOUR perception it seems that way.

    Josh says: This is a contradiction to a perfect God with a perfect plan. as something ‘unholy’ would be against God’s plan. If he created everything and everything with a purpose then how do unholy entities exist.

    There is no contradiction at all, only one YOU perceive. You have no clue as to what God’s plan is, or if He has one. Unholies exist because He created everything, which includes evil.

    Josh asks: Finally, why is there so much suffering in this life?

    So you can strive, accomplish/fail, and learn.

    Josh says: It certainly seems that a perfect God wouldn’t devise a plan that comprises so much pain and suffering.

    This is why you’re not a god.

    Josh finishes: No, there are just too many logical problems with the idea of a God who operates in such a way.

    There’s the problem Josh. God isn’t about logic, He’s about faith. I’m a firm believer in evolution, but also a firm holder of faith in a higher order. The two are not necessarily mutually exclusive.

  6. The whole “why would God make the world in such an inefficient or inelegant or awkward or whatever fashion” argument is essentially pointless, because the automatic question to these questions is “because that’s how he did it”. If the universe was created, then presumably it was made through the agency of unknown, possibly unknowable laws. If by no other process, God is constrained by whatever laws he imposes upon Himself. Order is inherently a trade-off of opportunity for structure, and any given structure demands in payment whatever inefficiencies dictated by the requirements of that structure.

    Sorry, got side-tracked. Brock, if you check out the paper, the author talks about a process which requires a hydrated mineral micro-environment, especially as how most of the early steps require repeated reactions with water. In other words, double-layer hydroxides or weathered feldspar submerged in an aquatic environment. The minerals provide the matrix, but as I read it, the processes still require liquid water.

  7. This is a contradiction to a perfect God with a perfect plan. as something ‘unholy’ would be against God’s plan. If he created everything and everything with a purpose then how do unholy entities exist.

    This is an old argument, which can be paraphrased like this: “Here’s how I would run things, if I were God. The universe does not run that way. Therefore, God must not exist.”

    The fallacy is that your argument fails to allow for the possibility of a God who does not think like you do.

    For example, a God who is a libertarian. He tells you the consequences of your actions but grants you free will to decide your course of actions.

    Much like a libertarian government might tell people that a certain behavior is immoral and self-destructive but does not outlaw that behavior. The fact that the immoral behavior would continue, at whatever level, would not prove that government does not exist.

  8. Mitch – thanks.

    You other fellas – there’s no point arguing against the God hypothesis. Don’t waste your breath. It’s non-testable. No matter what arguments you come up with the believer can just think of new ones, just as non-testable (like the Master Domino Setter-Upper). You’ll go in circles & circles and never get anywhere. Find a better use for your time. Really.

  9. “Much like a libertarian government might tell people that a certain behavior is immoral and self-destructive but does not outlaw that behavior. The fact that the immoral behavior would continue, at whatever level, would not prove that government does not exist.”

    The continuance of immoral behavior also would not prove that the libertarian government was not just and good. I love this analogy and will probably repeat it.

  10. “Doesn’t seem like a very nice God if he intended this enormous level of suffering to exist.” Maybe he isn’t very nice. Us humans would prefer that he was, of course, and some of us believe that he is despite all the evidence to the contrary.

    Omniscience, omnipotence, omnibenevolence. Pick two.

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