Optima in Evolution

The belief that fonctionnal proteins able to perform complex functions are rare in sequence space is ground on a sane understanding of biology. But there is worse for you. Indeed, it is not only functional proteins that are rare in sequence space, it is also protein folds, as the article below shows:

The argument for evolution hinges on functional space being almost as large total sequence space for all proteins.

Although this may be true for certain proteins it is almost certainly false for all protein families as gpuccio’s data shows. Natural selection of protein sequence function appears to be restricting exploration due to functional constraint.

I would like to see this evidence. Can you show us that this is true?

@gpuccio’s method can’t tell us the functional space within sequence space, as already discussed. All it can tell us is where the local optimum is from a single starting point.

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Gold is a rare earth mineral, yet tons of it are found all of the time. Winning lottery tickets are rare, yet people win the lottery all of the time.

It isn’t enough to say that they are rare since a random search can find rare solutions.

This is an unsupported claim.

Even if it is true the observation is significant evidence against the claim that functional space is almost equal to total sequence space. Something that evolution needs to establish across all protein types.

What exactly do you mean by a “protein able to perform a complex function”, and how does that differ from functional protein in general?

And what is this supposed “sane understanding of biology” you are referring to? It appears to conflict with the basic principles of organic chemistry they teach in textbooks, in high school, and at universities.

An understanding of the basic principles of biochemistry, such as the electromagnetic forces of attraction and repulsion between charged particles like electrons and protons, which give rise to inter- and intramolecular bonds and are ultimately responsible for determining the physical and chemical attributes of atoms and molecules(such as their degree of polarity, the distribution and magnitude of electromagnetic charges across the structures of molecules), all implies the diametrically opposite.

These are the things that will help you understand why different compounds, for example, have different solubilities in different liquids(why are some things soluble in fats, and others in water? Why do these come in degrees?), how and why these properties depend on physical characteristics of the environment like temperature, pH, and pressure, and that all these properties of proteins(their degree of solubility under different circumstances, their mutual affinities, and their 3dimensional structures) can be manipulated by incremental changes to the amino acid compositions of proteins.

But you haven’t shown that functional proteins in general, are “rare in sequence space”, much less how rare they are. You seem to just have this as an axiom you can’t move beyond. And for which you can’t seem to find any actual evidence.

I don’t see what you think is a problem here. You appear to be mistaking function for fold. But different folds can perform the same functions(and more complex and rare folds can evolve from simpler and more frequent ones), so the probability of a protein sequence adopting some particular fold does not tell you how likely you are to evolve the function of the folding protein(there is even some evidence that de novo proteins evolve from disordered precursors that don’t adopt a stable fold). The article even appears to show that this general property is observed in the history of the evolution of different protein folds.

You keep making this mistake of thinking that the present state of some protein must have sort of sprung into existence fully formed as it appears to day, rather than having evolved incrementally from some other simpler state that performed a simpler, related function.

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What you have failed to establish is that functional space is almost equal to sequence space as exists in a lottery.

What happens if the lottery uses 100 balls instead of 6? The answer is that the chance is overwhelming that no lottery would ever be won during the history of mankind.

Why is anyone still pushing the FI argument when gpuccio’s premise observed FI in extant proteins had to arise by chance alone or by “design” is a false dichotomy and is demonstrably wrong? No one from the ID-Creationist camp has ever addressed or modeled in their calculations the actual iterative feedback process which drives evolution.


It is supported by the phylogenetic signal which clearly shows evolutionary conservation of function. This is extremely strong evidence that we are only looking at a local optima.

Why do they need to be equal?


No. What gave you that idea?

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It seems to be base on a “sane understanding of biology” that no actual sane biologist agrees with.


I second that request.

No one is making that claim.

What we keep pointing out is that you and Gil have neither measured functional space nor total sequence space.

If it’s that important, why not read at least a few of the catalytic antibody papers that describe successful functional searches in only a tiny, tiny fraction of total sequence space?


This statement says the biologists that don’t agree with you are not sane yet you are not a biologist. The evidence for Gil’s case is real.

Then let’s see it.


The abzymes highlight an important point with respect to the claim that functional proteins must be rare in sequence space just because some particular fold is, in that they show that completely different folds can catalyze the same reactions, and can evolve towards recognizing identical substrates from very dissimilar structures.

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Okay. Then bring it!


What is preventing either of you from presenting any, Nigel?

No, the answer would depend entirely on how many people bought tickets. You don’t seem to have even the most basic understanding of probability.