#3 is false too. It is possible (or even likely) that the first proteins were composed of amino acids that had a preference for forming bonds with those of the same chirality.
The only reference I have ever seen related to this claim is based on the Salt-induced Peptide Formation (SIPF) reaction. The authors of a primary study start by stating that no chiral bias exists with AAs under normal conditions.
Because this energy difference is very small (for amino acids in the order of 10^−38 to 10^−35 J; proportional to Z5, Z being the atomic number) it cannot lead to a significant stereoselective differentiation by itself, but still requires amplification mechanisms to yield a stereoselective preference for one chiral form in the prebiotic reaction pathways leading towards the origin of life.
They then describe the exploitation of a parity violation in Cu(II) based on the weak nuclear force to bias, in some AAs, L-L binding over D-D binding. Under certain circumstances Cu(II) can form a complex which generates this bias, but the conditions include starting with unrealistically high concentrations of Cu(II). Moreover, the bias was only highly significant for Valine, and some AAs actual showed dominance for D-D binding. Most significantly, the reported experiment only used pure L-L or D-D amino acids. The researchers did not demonstrate bias of chiral binding over non-chiral binding (L-D). I suspected they tested this possibility, but the results were too disappointing to report. As a consequence, the mechanism has only been used as a possible explanation for dominance of L-proteins over D-proteins today, not the selection of L-AAs in protein formation.
Moreover, it is not clear that the amino acids for a functional protein need to be all L-AA. All that is important is that they eventually they all become L-AA, not that they start out this way.
#4 is false too. It is not clear that the amino acids for a functional protein need to be exclusively peptide bonds. I’m not sure exactly what you mean by “alternative bonds.” Perhaps the ester bond? However, read the paper I just linked to. That is less stable than the peptide bond, and the peptide bond is favored thermodynamically (right?).
The current opinion seems to be that homochirality was a prerequisite for functional enzymes due to the need for chains to form stereoregular structures.
Homochirality is now believed to be not just a consequence of life, but also prerequisite of life. Because stereoregular structures such as a protein beta sheets, for example, do not form with mixtures of monomers of both candidness, as described below.
Herdewijn and Kisakurek (Eds.), Origin of Life, p. 218
For the same reason, AAs need to form solely alpha-peptide bonds. Examples of other bonds include the beta-carboxyl group of aspartic acid, the gamma-carboxyl group of glutamic acid, and the epsilon-amino group of lysine. Studies conducted several years back indicated that the non-alpha bonds formed as often as the alpha bonds. (For more detailed discussion, see Mystery of Life’s Origins, p. 157)
However, the situation is actually far worse that I described. All OLL experiments which yielded multiple amino acids also produced several other byproducts in greater total abundance than nearly all of the AAs. As a result, the possible number of bond types formed in any realistic scenario would be quite large. Therefore, my estimate of 80% for forming the alpha-peptide bond is very likely over an order of magnitude too high.
The key question is now, however, more pointed. How can we trust the mathematical arguments being offered here if they lead to a solid conclusion that something is impossible, and then a simple experiment demonstrates them possible? I do not think we can trust them.
One has to be careful distinguishing between what is possible in highly controlled experiments and what is plausible in realistic environments. For instance, the Ester-Mediated Amide Bond experiment you referenced started with 100mM concentrations of amino acids and lactic acid, and the solution was then dehydrated and rehydrated under very controlled conditions. In the end, it did not produce pure peptide chains but chains with ester bonds, even after numerous dry-wet cycles. The ester bonds would have prevented proper chain folding.
In addition, the chances are quite remote for a pond on the early earth to meet all of the corresponding conditions:
- It must have contained very high concentrations of lactic acid (or the equivalent) and amino acids in the right proportions.
- Some heat source must have evaporated the entire pond with the right amount of energy for the right amount of time to remove the water, yet not damage building chains.
- After each evaporation, the pond must have filled with water with additional alpha-hydroxy acids without removing the contents.
- The AAs and chains must have been shielded from reacting with surrounding molecules.
Equally problematic, the maximum chain length achieved was 14, and that length was only for the smaller AAs. The ones with longer side chains created products which were “more complex.”
http://www.pnas.org/content/114/36/E7460.full
A recent article reviewed experiments attempting to generate polypeptides, and it described how the proportion of chains in all circumstances drops off exponentially with length as described by the Flory–Schulz distribution. Based on this equation, the authors estimated that the proportion of chains 40 units in length would have been 1 part in 10 trillion. They responded to this discouraging result by proposing a model for smaller chains combining into larger ones, but they acknowledged that it was founded purely on speculation. In reality, even this meager estimate results from experiments which used ideal (even miraculous) conditions. In realistic settings, the proportion would drop with length far faster. As a result, my estimate of 80% for the addition of an AA to a chain was again extremely generous.
Let me repeat my calculation with more realistic numbers. I will assume a chain of 40 AA in length, so I will us the 1 in 10 trillion figure. And, I will assume a solution of molecules matching the output of the most successful OOL experiment based on the most likely conditions. I will also combine the probabilities of the right bond forming for any given AA with another AA, as opposed to another molecule, and that associated with the homochirality condition. As a result, I will drop my estimate of an L-AA bonding to another L-AA with an alpha-peptide bond to 10%. My calculation for a candidate chain then becomes the following:
P = (.10)^40 * 10^-13 = 10^-53 (i.e. clearly implausible)
I have not shown Jim Tour my calculations, but I will be sure to do so after more analysis.
The remarkable nature of enzyme chemistry is that the active site consists of key side chains in close proximity which work together for some function such as ligand binding or driving specific chemical reactions. They also create the right local environment which is crucial. However, those AAs are not often close together in the unfolded AA sequence. Their coordinated activity only begins after the protein properly folds to form the active site. Even a small difference in the final folded structure can completely eliminate one of the key functions. The positioning and orientation of ligands need to be accurate to within the width of an atom, and the same holds true for the positions of side chains which drive the reactions. Therefore, any observed catalytic activity before folding is not typically associated with the driven reactions after folding. In other words, the chemistry at the active site is not the sum of chemical activities induced along the unfolded chain which can gradually improve through mutations and then combine together after the folding is complete.
My focus is on the point where a protocell creates an internal environment which is held away from equilibrium. At that point, enzymes must be present which interconnect two reactions, so the enzyme must be highly specified. I would be interested in anyone’s knowledge of the smallest enzyme which interconnects two reactions, where one goes uphill. I am very confident that the size would be well above 40 AAs.
The challenge with the OOL is that along the path to a minimally functional cell numerous metabolic pathways would have to form and interconnect. And, as the system moves away from equilibrium, they would have to become increasingly efficient and complex. However, the idea that selection can drive this process forward is implausible until the proteins are encoded into DNA and then the corresponding decoding process originates. RNA is too unstable for the job. Until that time, improved enzymes could not be the result of random changes to the sequences since proteins do not self-replicate. New proteins would have to originate outside the cell through some miraculous process and then find their way into the cell. In fact, even after the encoding-decoding initiated, selection would still not operate until the entire cellular system developed high-fidelity self-replication.
You contend that the drive towards racemic mixtures and dilution would have acted on time scales of seconds or less. Do OOL researchers in the field agree with that assessment? I’m just curious: if they do, then the attention given to Sutherland’s OOL scenarios in science news reports makes no sense at all.
I was careful to state that many of the processes would have been very fast, not all. Fast reactions would include dilution and many of the cross-reactions. The breakup of proteins would have taken years to decades. This timeframe might seem long compared to waiting for a coffee at Starbucks, but it is minuscule compared to the time required for some new enzyme to find its way inside the membrane of a protocell which could reside hundreds of miles away. The racemization would have been much slower, but not likely slower than any process which could have pushed towards homochirality.
Sutherland’s research is not taken very seriously by many is the OOL community since the reactions required so numerous highly orchestrated steps. Even he has become more sober-minded as of late about their relevance.
That I agree with. I imagine everyone does. But the key question is how small of an infinitesimal fraction are we talking about? That requires dividing one large number by another much larger number (both of which are uncomputable), with enough confidence to make a statement absent evidence. I’m not sure that is within the bonds of science.
Nearly all OOL scientists would fully acknowledge that the proportion of configurations of molecules forming life to non-life is too small for nature to stumble upon life by chance. For instance, Eugene Koonin estimated that the likelihood for the simplest translation mechanism from RNA to proteins based on ribozymes forming was 1 in 10^1000. The actual process of translating from AA sequences in a protein to RNA and then back to a protein using the same code would have been much more difficult. Researchers instead argue that natural driving tendencies helped beat the odds. However, nearly every known natural tendency would have made the odds far worse than pure chance.
Every attempt to explain the OOL falls into three categories. Those experiments based on highly realistic conditions produce negative results. Those which use a modest degree of investigator control produce meager to very modest results. And, those experiments which produce seemingly encouraging results use high levels of investigator control – numerous highly specified steps are used to force desired outcomes. In short, the constant message is that intelligent design is an essential component of the origin of life.