When is a Flaw not a Flaw?

As you know, I have often pointed to the proteins as an incredible design material, raising the question as to just how much the blind watchmaker is dependent and indebted to protein biochemistry.  A recent study highlights yet another way in which protein biochemistry may be an essential prerequisite for the evolution of complex life.

First, you can read the summary of this research by Ariel Fernández and Michael Lynch here.  Then, come back and I will help you detect the teleological echo of this work.

The first thing you need to do is recognize the non-teleological framing of these findings.  You’ll note the title of the news article – Errors in Protein Structure Sparked Evolution of Biological Complexity.  This theme of error is stressed again and again:

The study, published in Nature, suggests that the random introduction of ERRORS into proteins, rather than traditional natural selection, may have boosted the evolution of biological complexity. FLAWS in the “packing” of proteins that make them more unstable in water could have promoted protein interactions and intracellular teamwork, expanding the possibilities of life….. Fernández and Lynch focused on DESIGN FLAWS called “dehydrons,”…..The result suggests that structural ERRORS accumulate in large organisms such as humans due to random genetic drift…..To confirm that the accumulation of structural FLAWS in proteins….. proteins from the smaller populations were more FLAWED…. Despite these ACCIDENTAL benefits, the accumulation of too many structural FLAWS…. The implication that complexity initially arose BY ACCIDENT may be provocative… The discovery that FLAWED proteins….

Yet there is no powerful and objective reason to think we’re dealing with flaws, errors, and accidents from the context of evolution.  Instead, we could just as easily view this as part of the protein’s intrinsic activity – in inbuilt propensity to form multi-protein complexes in the correct context.

Look at it this way.  In his 2003 paper, Ariel Fernández describes the dehydron as follows:

This work identifies a factor for protein association and supramolecular organization by determining a structurally encoded marker, the dehydron, which signals a packing defect in the monomeric structure.

And

Thus, a systematic study of known structures of individual proteins, protein complexes, and virus coats leads us to establish that the structural defects related to dehydrons play a significant role in determining protein associations and the organization of supramolecular assemblies.

Okay, the dehydron is a defect when it comes to packing monomeric proteins.  But it is a facilitator when it comes to forming supramolecular assemblies.  So is this really a design flaw?  No.

Recall what Bruce Alberts noted over a decade ago:

We have always underestimated cells. Undoubtedly we still do today. But at least we are no longer as naive as we were when I was a graduate student in the 1960s. Then, most of us viewed cells as containing a giant set of second-order reactions: molecules A and B were thought to diffuse freely, randomly colliding with each other to produce molecule AB—and likewise for the many other molecules that interact with each other inside a cell. This seemed reasonable because, as we had learned from studying physical chemistry, motions at the scale of molecules are incredibly rapid. … But, as it turns out, we can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.

If the old view of cells was correct, where the cytoplasm of the cell was “dominated by randomly colliding individual protein molecules” and “cells as containing a giant set of second-order reactions,” then we would have a real design flaw.  But instead it turns out the packing “flaw” is what enables the formation of molecular machines and more.  What appears as a defect from the perspective of packing individual proteins looks like an ingenious solution to getting proteins to form complexes capable of coordinated activity.

In fact, Fernández himself emphasizes the dual meaning:

“We hate to hear that our structures are actually lousier,” Fernández said. “But that has a good side to it. Because they are lousier, they are more likely to participate in complexes, and we have a much better chance of achieving more sophisticated function through teamwork. Instead of being a loner, the protein is a team player.”

If you want proteins to remain in a monomeric state and function as efficiently from this state, then yes, it’s lousy.  But if you want proteins to escape the monomeric state and achieve greater things by working as a team, then there is nothing lousy about it.

Fernández also notes:

“Natural designs are often one notch more sophisticated than the best engineering,” Fernández said. “This is another example: Nature doesn’t change the molecular machinery, but somehow it tinkers with it in subtle ways through the wrapping.”

Exactly.  The core principles of protein biochemistry front-loads the appearance of complexity.  All ya gotta do is tweak the system.  And that’s where Michael Lynch’s work comes in:

Everybody wants to say that evolution is equivalent to natural selection and that things that are sophisticated and complex have been absolutely selected for,” said study co-author Ariel Fernández, PhD, a visiting scholar at the University of Chicago and senior researcher at the Mathematics Institute of Argentina (IAM) in Buenos Aires. “What we are claiming here is that inefficient selection creates a niche or an opportunity to evolve complexity.”

And

“It’s not an argument against selection, it’s an argument for non-adaptive mechanisms opening up new evolutionary pathways that wouldn’t have been there before,” Lynch said. “It’s those first little nicks getting into the protein armor that essentially open up a new selective environment.”

Take in the implication.  The road to greater complexity is opened up by pushing the blind watchmaker, the only non-teleological “designer,” off to the side.  In other words, by minimizing or suspending the oversight of natural selection, the intrinsic aspects of life’s chemistry are better able to express themselves and build upon themselves.  We have another glimpse into the intrinsic aspect of evolution.

Recall this sentence from the ScienceNews article:

The implication that complexity initially arose by accident may be provocative within the field of evolutionary biology, the authors said.

There is no accident here.  There is a built in predisposition among proteins to form multi-component complexes and this predisposition is released whenever the populations become small.  In other words, this type of thing is bound to happen again and again across the globe and over deep time.

This research can show us what proteins can do without natural selection – they can nudge life toward a more complex state.  Now, what can natural selection do without proteins?

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