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Tuesday, September 2, 2014

When You’re Desperate, Anything Is Plausible

Posted by jlwile on November 4, 2011

A commenter left this link on an unrelated post. Since the commenter has, in the past, tried to support several unscientific positions, I assume he or she thought that the experiment demonstrated the plausibility of abiogenesis, the the idea that life might have emerged through a series of incredibly unlikely interactions between nonliving chemicals. Of course, such an idea contradicts everything we know about the study of life, since all life we have ever studied comes from other living things. I have written several articles (here, here, here, here, here, and here) that demonstrate how the data speak against abiogenesis, but those who want to ignore the scientific evidence desperately hope for some special time in the past when all our current evidence doesn’t apply and life could actually spring from nonliving chemicals.

One of the many, many problems associated with any naturalistic origin-of-life scenario is that of stereoisomerism. As I explain here, there are certain biological molecules that can be formed in two different ways. They have the same chemical formula and form mirror images of each other. However, these mirror images are not identical. Think about your hands. When you hold them palms together, they are mirror images of one another. However, no matter how you tilt or turn it, you cannot make your left hand look identical to your right hand. If you put the palm of one hand on the back of the other hand, for example, one hand’s thumb will be where the other hand’s pinky finger is. So while your hands are mirror images, they are not identical. There are many biological molecules that are like that, and we call them chiral molecules. The two mirror images that are formed by a chiral molecule are called enantiomers.

All origin-of-life scenarios start with simple molecules that do not form enantiomers. We call these achiral molecules, since they cannot form two mirror images that are different from one another. This is a problem, because in the lab, when achiral molecules react to form a chiral molecule, an equal amount of each enantiomer is formed. As a result, you end up with a mixture that is 50% one enantiomer and 50% the other enantiomer. We call this a racemic mixture. The problem is that life isn’t like that. In most chiral molecules of life, only one of the enantiomers is used. We call this an enantiopure compound, since it is purely one enantiomer, without any of the other. So any origin-of-life scenario has to figure out a way of producing just one enantiomer, or it has to figure out a way to get rid of the other enantiomer once it has formed.

This is a major problem, of course, and the link that the commenter left claims that a “plausible” solution to this problem has been found. Of course, when you look at the actual paper you find that the process is anything but plausible in an origin-of-life scenario.

The paper1 discusses how researchers were trying to create enantiopure precursors for the production of RNA. Currently, the most fashionable origin-of-life scenarios involve RNA forming first. Thus, to make these scenarios work, we have to first form the molecules that are necessary in order to make RNA, and some of them are chiral. To make RNA, you can use only one enantiomer, so you have to figure out some way of forming these RNA precursors in an enantiopure way.

In the researchers’ experiments, they started with an amino acid mixture that had slightly more (1% to be exact) of one enantiomer than the other. Thus, it wasn’t really a racemic mixture of the two mirror images, but it was close. They suspended it in a solvent (either chloroform or ethanol) and removed any excess solid. They then allowed the solvent to evaporate, so they were left with just the solid that had been suspended in the solvent. To this solid, they added some racemic mixtures of two chiral molecules, dissolved everything in water, and let them react. The reaction produced another chiral molecule that is a precursor to RNA, and it had the correct biological enantiomer in 20-80% excess, depending on the conditions. If they then cooled the mixture to 4 degrees Celsius, the precursor formed a crystal that was enantiopure.

So an amino acid sample that has slightly more of one enantiomer than the other can force a chemical reaction to produce an enantiopure chiral molecule, as long as the right conditions are met. The authors say that this is:

…a concerted sequence of physical and chemical amplification processes that make use of a small initial imbalance in amino-acid enantiomers as the only molecular asymmetry in the system.

In other words, the slight imbalance of enantiomers in the amino acid ends up being amplified in the products of a chemical reaction that occurs in their presence.

Of course, from an origin-of-life perspective, you have to ask a few questions. First, where did the slight imbalance in amino acid enanatiomers come from? Remember, chiral molecules are formed in racemic mixtures, not with 1% excess of one enantiomer. As detailed in a previous post, researchers were able to produce such an excess in amino acid enantiomers, but it required a ridiculously unrealistic scenario. Second, how do we get the nice situation where this sample is then suspended in a solvent that is not water, after which the solvent evaporates? Third, how do we get the racemic molecules to wait until the solvent (that is not water) evaporates to start reacting in the presence of the amino acids? Fourth, how do we suddenly get water into the picture, since the solvent we started with wasn’t water? Fifth, how do we get the lower temperature at just the right time to crystallize out the enantiopure sample? Sixth (and most important), how do these precursors actually react in an uncontrolled environment in order to produce actual RNA, which is just the starting point for the currently fashionable view of abiogenesis? In the experiment outlined in the paper, most of these questions were answered by intelligent intervention – the researchers controlled each step so it happened just right.

Now don’t get me wrong. This is a nice bit of research, and it produces a completely unexpected result. If the experiments are replicated, I expect this technique will be utilized in many synthetic processes. Thus, it is really great research. I just don’t think it is a plausible means by which the chirality problem can be solved in origin-of-life scenarios. It requires a lot of intelligent intervention just to get the precursors of RNA synthesis, while abiogenesis requires no intelligent intervention at all to go significantly further: produce self-replicating RNA that can also catalyze other chemical reactions.

REFERENCE

1. Jason E. Hein, Eric Tse, and Donna G. Blackmond, “A route to enantiopure RNA precursors from nearly racemic starting materials,” Nature Chemistry 3: 704–706, 2011.
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Comments

10 Responses to “When You’re Desperate, Anything Is Plausible”
  1. Josiah says:

    I think the best example of such desperation is when people try to suggest that this RNA could evolve, Darwinian style, and thus explain away the amount of complexity involved in the minimum requirements for cellular life. It apparently doesn’t occur to them that the coding required to make RNA produce RNA is very different from that required to make the DNA, RNA and protein team work together in the cell. It isn’t, to use Behe’s language, a physical precursor to life and therefore even if a RNA world could exist it doesn’t explain where life as we know it comes from at all.

  2. jlwile says:

    I would essentially agree with you, Josiah. The one thing I would add is that it might be possible that the “RNA world” could be a start for life as we know it today, if someone would actually show how the coding in a self-replicating RNA that also has catalytic properties could be transformed into the coding we see in today’s DNA/RNA/proteins system. Of course, no one has come close to doing that yet, which makes the whole “RNA world” hypothesis all the less convincing.

  3. Enoch H. says:

    Dr. Wile,

    Excellent article! Thank you for the information. It is clearly evident that God was directly involved in forming life from non-living things. What I would like to know is how. It certainly could’ve been that everything in the universe simply appeared at His command the way we know it is today, but I kind of doubt that is the way it happened. Do we have any clues into the details of this process, where God formed the universe from nothing, and life from non-life? I would love to hear your thoughts on this, whether in another comment or perhaps a blog post.

    Thanks,
    -Enoch H.

  4. LswaN says:

    Hi Dr. Wile, nice post, I really enjoy reading your blog. One thing has me a little confused, though. Wouldn’t someone who wants to believe in the occurrence of abiogenesis argue that whatever process supposedly started life just ‘chose’ to use only one of the enantiomers in a racemic mixture, and not the other one, resulting in future life using just that one out of the pair? Or is there a specific reason that this would not happen?

  5. Vivielle says:

    This was very interesting, and made me think of the point my organic 1 professor made very strongly- optical activity can’t be spontaneously generated from non-optically active compounds. Which always made me wonder how optically active things originated…

    Anyway, I’m assuming that in the RNA world hypothesis they are assuming that there were no enzymes at that point? Enzymes can, and do, give enantiopure substances, so if they need this slight enantiomeric excess to occur, they must assuming that there were no enzymes, I’m guessing.

  6. jlwile says:

    Enoch, you are most certainly right that God didn’t make things the way we see them now. God delights in His creation, especially in how it develops. There have been some really interesting creationist cosmologies that try to determine how God created the universe. You might be interested in reading what Dr. John Hartnett thinks about how the universe was formed. He has a book entitled Starlight Time and the New Physics that goes into more detail. I think his kind of cosmology shows a lot of promise.

    In terms of the biological creation, I think that God made specific kinds of creatures. These kinds of creatures probably didn’t look exactly like anything we see today, but they would remind you of what you see today. These kinds of creatures had enough information in their genomes to adapt to a wide range of conditions, which allowed them to diversify into what we see today. For example, God probably created one set of creatures that belong to the “cat kind.” These creatures had all the information in their genome to eventually diversify into lions, tigers, panthers, bobcats, domestic cats, etc. The original members of the cat kind probably didn’t look exactly like any of the cats we see today, but if you saw one, it would be instantly recognizable as some form of cat.

  7. jlwile says:

    Good question, LswaN. The problem is that if both enantiomers are present, their chemistry is so similar that it is very hard to separate them. In fact, the most efficient way to select one enantiomer from a racemic mixture is to use the enantiopure form of some other chemical with which it can react. If you don’t have that, it is very hard to separate one enantiomer from other – certainly beyond the reach of an unguided process. So it is plausible that abiogenesis could have “selected” the specific enantiomer it “wanted,” as long as it had at least one enantiopure compound to begin with. There would still be a lot of details to work out, even if you did have one enantiopure compound, but that’s a minimum requirement in order to get the job done.

    This is a typical problem faced in all origin-of-life scenarios. We know how to get things done once we have the first of something (the first self-replicating RNA, the first cell membrane, the first enantiopure compound, etc.). However, getting all those firsts to begin with is what seems insurmountable under any kind of plausible scenario.

  8. jlwile says:

    Vivielle, enzymes can produce enantiopure compounds if they, themselves are enantiopure. That’s what happens in living systems. The genes an organism uses to make the enzymes (and all the complex folding machinery that occurs after the gene is translated) produces one specific enantiomer. That allows the enzyme to select another specific enantiomer. If the enzyme were produced in a racemic mixture, however, it would not be able to select a specific enantiomer.

    You are correct that in the RNA world hypothesis, you don’t start with enzymes. Since specific kinds of RNA (called ribozymes) has been shown to have catalytic abilities (which is the role most enzymes play in living systems), the RNA world hypothesis posits that initially, RNA both carried genetic information AND performed the functions of proteins. Eventually, our current DNA/RNA/protein world evolved from that.

  9. Josh says:

    In an infant Earth, couldn’t non-water liquids be present and have been sublimated during the dramatic changes in climate and temperature of the young planet? (thus making the transition from dissolved in a nonwater solution to dissolved in water more plausible, even likely?)

    Further, couldn’t a large asteroid have struck the planet and caused an immediate large scale change in liquids and temperatures that allowed for some of implausible conditions and rapid changes?

    Very interesting blog, but going through Astronomy the concept that everything formed from gas spewn out into the universe makes perfect sense to me, where as the concept of a god creating everything does not, unless he laid out the ground rules we follow now-but I’m open to challenges to the science.

  10. jlwile says:

    Thanks for your comment, Josh. Certainly non-water liquids could be present in an infant earth, but that’s not enough. Also, liquids don’t sublimate, as sublimation is the process by which a solid turns directly into a gas. For this scenario to be applicable to an origin-of-life scenario, the non-water liquid has to suspend the amino acid solid (without mixing with water) and then evaporate BEFORE any water comes into the area. In a lab, that’s very easy to do. Nature is very messy, however, with solvents mixing instead of patiently waiting on each other to do what they need to do.

    If you want a process to be initiated by an asteroid impact, that makes things even more difficult. Remember, this process works because everything is painstakingly purified, set up, separated, and guided. You throw a huge asteroid impact into the mix, and suddenly everything becomes incredibly messy. The idea isn’t just to make a bunch of changes. That’s easy. The idea is to make specific changes at just the right time. The more chaos you throw into the mix, the harder that is to do.

    As a chemist, I know too much chemistry to think that “everything formed from gas spewn out into the universe.” There are just far too many chemical hurdles to go from something as simple as elemental gases to something as complex as even the simplest protein in life. Right now, the concept of abiogenesis is the challenge to the science, as all scientific observations indicate that life comes from life. There is no observable evidence to support abiogenesis, and there is no remotely plausible mechanism to indicate how it might have happened. I am open to such challenges as well, but they must be scientific challenges. So far, no reasonable scientific challenge to the accepted fact that life only comes from other life has been proposed.

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