I had a wonderful conversation with a friend who is a biology professor south of me specializing in protein evolution. He gave some thoughtful feedback on the discussion of Axe’s work, so I will attempt to accurately convey all of his points along with some of my own thoughts.
One has to be very careful comparing different classes of proteins and generic claims of function. Many have the impression that proteins which function without fully folding into stable 3D configurations are suboptimal precursors to a fully folded, more evolved version. However this perspective is mistaken. The proteins in nature which function without a stable fold have actually “been optimized for multiple competing functional demands.” Their precise “looseness” is essential to their function, so they likely also represent extremely rare sequences of AAs.
Similarly, one must distinguish between any “function” and the specific functions performed by specific proteins which are needed for specific major adaptations. As an analogy, one could ask how likely would a child be able to craft a weapon out of a pile of garbage. The answer depends on what one means by “weapon.” Anyone could craft a sling shot out of a rubber strip and a few sticks. And, it might be useful for hitting a little brother ten feet away. However, the child would never be able to craft a high-precision riffle which Jason Borne could use to hit a target a mile away.
One of the most impressive experiments which started with random sequences was able to generate a chain which bound to ATP and catalyzed hydrolysis. The rarity of sequences for that function is somewhere around 1 in a trillion. I will refer to the chain as miniATPase. Let’s contrast this chain to the enzyme aconitase which changes citrate into cis-aconitate. This protein consists of over 700 amino acids compared to the less than 150 for miniATPase. I will focus on this example since it is part of the citric acid cycle which is a rather common metabolic pathway, and its activity is demonstrated beautifully by a YouTube video, which I encourage everyone to watch.
The enzyme performs several tasks:
- It binds to citrate, so the substrate resides at a precise location in a precise orientation. An neighboring Iron-Sulfur cluster helps stabilize the substrate electrostatically.
- Histone 101 donates proton to remove one OH group from the citrate. The enzyme is now altered.
- Serine 642 acts as a base by accepting a hydrogen from another location in the substrate. The enzyme is further altered.
- The interactions between the enzyme and the altered substrate flip the substrate upside down.
- Histone 101 binds to a proton from a passing water molecule, causing OH to attach to a new location in the substrate.
- Serine 642 returns a hydrogen atom to a new location in the substrate. The enzyme returns to its original state.
- The enzyme releases the substrate, so it can act on another citrate.
The successful conversion of citrate requires the right interactions, both chemical and electrostatic, to take place at the right times. Several amino acids have to be perfectly positioned, and the enzyme needs to have just the right stability, so the positioning is maintained, and the substrate can flip at the right time. Its activity only commences after the chain is perfectly folded. And, every step in the conversion process is essential. Since the enzyme alters during the first few steps, it must return to normal after the last steps, or it could reengineer other molecules. Therefore, it could not have evolved gradually, since the fold had to be highly optimized for all of the steps to proceed properly. The miniATPase example is like the slingshot from the analogy, and aconitase is like a high-precision riffle with a laser scope. Properly challenging Axe’s basic thesis requires one to focus not on the production of simple functions but on the most complex enzymes and other features required for novel adaptations.
Moreover, producing just once enzyme would not typically advantage an organism since most of the products of individual steps in metabolic pathways are useless without other enzymes to further process them. In fact, some intermediates are even toxic to the cell, so they have to be carefully ushered along to other enzymes. One cannot dismiss such challenges simply by referring to such comparatively easy tasks as antibody binding or the generation of other simple functions.
I asked my friend why critics of Axe’s research who specialize in protein evolution have not simply reproduced his experiment with what might be deemed as an improved approach. He responded by commenting that researchers who spend their careers attempting to create new protein folds or carefully study the properties of complex enzymes in nature know from everyday experience that actual enzymes like aconitase (not like miniATPase) are extremely rare. They instead simply believe that some pathway must exist to it from some ancestral protein, but this belief is based purely on faith.
My friend is very interested in this type of research. Would you please provide references and describe the specific examples to which you are referring? What is the most complex enzyme which was studied?
Also, one has be careful in assessing arguments made from comparing proteins in existing species, since they can easily fall into circular reasoning. Specifically, one could assume that undirected processes are responsible for the appearance of de novo genes or the differences between different proteins or other features in different species. And, then one could argue that the fact that those difference came about by natural processes demonstrates their power to create such features. The evidence presented depended on an assumption (the power of natural processes) that the evidence was meant to prove.