Pharyngula

The Discovery Institute doesn’t understand the protein folding problem. I mean that literally: they don’t understand the problem. Scientists don’t know the answer, but they have a clear understanding of the problem.

PNAS published a “Perspective” article, “The Nature of Protein Folding Pathways,” by S. Walter Englander and Leland Mayne. Unsurprisingly, they try to approach the problem from purely materialistic presuppositions. There is no mention of specificity, amino acid sequence, or digital information.

You see, there really is an interesting problem here: given a specific amino acid sequence in a protein, what 3-dimensional shape will the protein take? It turns out that’s really hard to calculate. We also can’t do it in reverse very well: given a certain desirable shape for a protein, what sequence will fold into that shape? There are so many interactions with the environment as the protein is assembled, that we can’t calculate them all. The paper takes a simplifying approach to estimate the shape by breaking it down into little modules called foldons. It’s still hard and only an approximation.

But here’s the thing: you can take any amino acid sequence — you can design your own, or you can assemble random amino acids — and it will fold. It will often even fold relatively reliably in certain ways, although proteins also demonstrate a misfolding rate. Why? Because it is the nature of proteins to be floppy and twist and bend until their energy is minimized. It is not surprising or unexpected that proteins fold. The challenge is to calculate in advance how it will spontaneously fold.

Let’s talk about the weather. It’s a similar problem; we know that moisture and temperature and air movements and topography will necessarily interact to produce a pattern of weather. We know that some generalities are reliable: Minnesota will be cold in January, Florida will be hot in July. That the weather is hard to predict does not imply that a god must be an imponderable variable in the equation — the complexity of the problem is sufficient to account for our difficulties.

The Discovery Institute does not understand any of this. Reading their summary is a bit like listening to Dark Age Scandinavians talk about the weather. Have you taken Thor into account?

While it is true that sophisticated techniques can see the protein fold as a series of stages, this ignores the main problem: How does DNA know in advance what sequence will build the first foldon, and the second, and the third, and so on, till a functional protein results?

But…but…how do the clouds know to make rain? How did the lightning know that Arnfrøðr had stolen Bjálfi’s goat, in order to strike him righteously?

DNA does not know anything. The protein will fold, following the rules of physics and chemistry. The DNA did not “know” in advance; protein sequences were selected after the fact for their functional effects, not built to spec.

We would like to ask these authors how DNA knew to code for chaperones that can help other proteins fold correctly. Those chaperones had to be coded in DNA such that they would fold correctly themselves first. And add another question: how were all the other molecular machines in the cell built that repair or dispatch misfolded proteins? What created the Golgi apparatus where proteins are finished, packaged, and delivered to their work sites?

How did Thor know to make Dyggvi’s shield arm strong, so he could defend Erik in the battle line?

It’s a kind of molecular retrospective coronation to decree that because X exists, X had to have been made present for a specific purpose. The whole collection of proteins and chaperones co-evolved; it’s a constraint on protein evolution that an amino acid change that leads to a non-functional folding would be as deleterious as a null mutation. And the pattern of that folding is a product of multiple components in the cell, so it’s not at all surprising that there are contingencies between multiple proteins.

I look at their questions, and I see a bunch of people who really have no grasp at all on the basic principles of evolutionary biology…who think that invoking Thor somehow simplifies the whole problem.

The information in DNA cuts through the vast conformational search space, and finds the route to the functional fold rapidly, sometimes within microseconds. ID is the only way to navigate a vast search space and arrive at a destination on time. Intelligent design can build self-organizing systems that obey the laws of thermodynamics, just as in the analogy of magnets on a string spontaneously folding into a wrench. Even if entropy increases as the protein folds, guiding the polypeptide through the funnel-shaped energy landscape to the final product, this does not negate the design that went into the system. It amplifies it.

The whole thing has this nonsensical attitude behind it, confusing cause and effect. It’s like assuming that since all the phenomena going on inside a tornado are beyond our ability to calculate precisely, somewhere there must a super-computer that is calculating exactly, moment by moment, the movement of every particle of dust, every broken bit of lumber, every flying cow in the vortex.

I hate to break the news to you, but tornadoes happened before the weather service had the capability to predict where they would appear. Knowledge isn’t causal in these cases.

Also, Yngvi is a louse!

Comments

  1. #1 doombot
    October 24, 2014

    One of the most persistent failures of imagination I associate with Creationism is the inability to conceive of a universe, or any complex system, without an endpoint. This belief that everything has some kind of endpoint, and probably a purpose, makes it nearly impossible to develop an objective understanding of real* systems. Which is too bad, because real systems, and especially self-organizing ones, are totally cool.

    *Ones that can be demonstrated to exist 😉

  2. […] Source: Protein folding probably requires the assistance of Frigg [Pharyngula] […]

  3. #3 proximity1
    October 27, 2014

    For others like myself who find the paywall a barrier to access to the cited article, I suggest a free-access paper Proteinfolding andmisfolding :mechanism
    and principles
    (2008) by S. Walter Englander[1*], Leland Mayne [1] and Mallela M. G. Krishna [1,2 ] published by Quarterly Reviews of Biophysics [ Page 1 of 40. f 2008 Cambridge University Press 1
    doi:10.1017/S0033583508004654 ]

New comments have been temporarily disabled. Please check back soon.