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Interesting Insights Along the Way


The following entry was originally posted by Paul Draper on his facebook site. I think the thought, while perhaps a bit simplified, is a starting point for an excursus into the understanding of the interface of science and religion.

The Marvelous Tale of Chaperonin, the Patron Saint of Useless Proteins
Paul Draper

September 9, 2009 at 1:08pm

I know next to nothing about biology, and I yesterday I heard the most amazing thing, mentioned almost in passing. I was struck dumb by it, but I get the feeling that if I said, "Wait a sec, that's extraordinary!" a biologist would say, "Oh, yeah, crazy s&$# like that happens all over the place in biology." And I'm going to try to explain this in the way I understand it, not the way a biologist would understand it, because... well, I'm not a biologist.

Proteins are made of long chains of amino acids, which are little T-shaped molecules, and where the left tip of the cross-bar of the T of one molecule connects with the right tip of the cross-bar of the T in the next molecule, leaving all those vertical legs sticking out of the side of the chain. There are 20 different kinds of those vertical legs, and they all have different chemical widgets at the ends. Some have the chemical equivalent of velcro side A, some velcro side B, some hooks, some eyes, some magnetic north poles, some magnetic south poles, some little oily bits that recoil from water, and so on.

And what happens is that this long chain tends to kink and twist and fold up, controlled completely by the velcro side A on one amino acid finding the velcro side B on another, the hook on one finding the eye on another, and so on. You get phone-cord spirals and bobby-pin bends and loom-shuttle sheets first, and then it tangles up some more. The thing is, how it tangles up, and the final shape of the tangled up mess is EVERYTHING to how the protein works. It's got to have that pocket lined with strips of velcro, or that knob with magnet poles, to be the enzyme it's supposed to be or the cell membrane ion channel it's supposed to be. If it doesn't fold up to that shape, then it's useless, and the key is that what shape it will tangle into is completely controlled by that sequence of T's with different widgets.

Now, you can imagine how evolution plays here. Sequences that fold up into a shape that isn't useful will be eventually culled, and sequences that fold into a shape that do something useful will be kept. So there's a natural mechanism for sorting out what in the end gets made and doesn't get made. Evolution is a heartless taskmaster, and proteins that don't do anything worthwhile get the pink slip.

But wait! There's a very complex protein called chaperonin, and it is another thing that folds up to serve a specific purpose. It looks like a snake-charmer's basket, complete with a lid. And what it does is this: It opens its lid and accepts an amino acid chain AND HELPS THAT CHAIN FOLD ITSELF CORRECTLY TO BE USEFUL. That is, it takes a protein that, on its own, would fold itself into something that is useless, and it helps it instead fold itself into something that is useful.

The question at the heart of this is: who ordered the chaperonin?

How does evolution, the heartless taskmaster, look at a useless protein and figure out that maybe there's inner value to that protein, if only there were a guardian angel that could help it do what it can't do on its own? What evolutionary happenstance created the patron saint protein whose sole purpose is to elevate more humble proteins to useful purpose?

This is the kind of thing that, the more you look at it, the more you marvel at how beautiful it is. There is soul in even the coldest machine, if you walk slowly enough to notice it. That's the way I see it, anyway.

Below is my original response to Paul:

Beautifully said, nicely explained. And only one of many things that argues against strict exaptation or even strict empiricism. When we come to a point like this, we enter into the realm of the philosophical subtext of science and we are no longer on the ground of what can be proven--merely what can be observed. Thank you for the note.

I would add to it that while some of the details may not be exactly on target, I think the overall discussion accurate for a layperson and insightful.

I don't think the conclusion is ultimately "intelligent design." But rather that God is imprinted on all of creation--without exception. In this way, I am far closer to Francis S. Collins than Michael Behe. But now we've gotten to the unstated philosophy that underlies any given theory. And philosophy, of itself is not subject to the rigors of the scientific method--such a method is incompatible with the means and ends of most philosophical investigation and most objects that philosophy purposes to examine. That is to say, the observations and explanations of the natural world are certainly subject to the rigors that science brings---however, the underlying whys may not always be amenable to the methods of science.

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But the real point is . . . Whitman


from Proust Was a Neuroscientist
Jonah Lehrer

But Whitman also knew that his poems were not simply odes to the material body. This was the mistake that his Victorian critics made; by taking his references to orgasms and organs literally, they missed his true poetic epiphany. The moral of Whitman's verse was that the body wasn't merely a body. Just as leaves of grass grow out of the dirt, feelings grow out of the flesh. What Whitman wanted to show was how these two different substances--the grass and the dirt, the body and the mind--were actually inseparable. You couldn't write poems about one without acknowledging the presence of the other. As Whitman declared, "I will make the poems of materials, for I think they are to be the most spiritual poems."

Sometime back on the Disputations blog, there was a lengthy interchange about the resurrection of the body, in which Tom repeatedly stated (and, I've come to acknowledge, correctly) that the resurrection of the body dealt with the real body that we experience and in some mysterious way ARE right now. That is to say that what we have now will be the real body we have at the resurrection. And this makes perfect sense if the body is more than a container, but is in some way the vehicle and the reality of much of what we are.

I know, that doesn't make any real sense, and I'll have to think it through further to say something more like what I mean. The bottom line is that the body helps to define the mind and the mind the body and moving our present intellect, and perhaps even spirit to some new conveyance would in a very deep way violate who we are. God would not do that because He loves us as we are and loves who we are--without our bodies we are not that same person.

Or so it would seem that Whitman says--and there is much to agree with in the hypothesis.

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For the Hyperrationalists


One of the things that most disturbs me about some of the arguments and statements I have read regarding reason and the Church is that were one to take them at face value, they would seem to imply no place whatsoever for the emotional life. As a result, I found the following interesting:

from Proust Was a Neuroscientists
Jonah Lehrer

One of Damasio's most surprising discoveries is that the feeling generated by the body are an essential element of rational thought. Although we typically assume that our emotions interfere with reason, Damasio's emotionless patients proved incapable of making reasonable decisions. After suffering their brain injuries, all began displaying disturbing changes in behavior. Some made terrible investments and ended up bankrupt; others became dishonest and antisocial; most just spent hours deliberating over irrelevant details. According to Damasio, their frustrating lives are vivid proof that rationality requires feeling, and feeling requires the body. (As Nietzshce put it, "There is more reason in your body than in your best wisdom.)

Now, pro forma for me, I must go and look up this Damasio and see on what evidence he bases these conclusions. They are interesting and make a certain sort of intuitive sense--but that is insufficient when making these arguments a matter of the scientific record. So, if I find anything of interest, I'll try to post.

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Chaitin's Number--Omega

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Oh, no, don't ask why. Just go and explore the complexities of a non-computable, nearly undefinable number in support of Gödel's theorem.

No, no, just go.

Okay, just a hint--it is related to the stink beetle yesterday.

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BPM 37093


Check it out with google--

pulsating white dwarf has a heart of diamond, estimated to be a diamond of blue-green tint. Boy--make that available and South Africa would be in for a hard time of it!

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Supercool Human Assist Devices

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An exoskeleton to help in military operations, but what might it mean for people with debilitating disaeas such as ALS or MG?

As one correspondent noted to me: "The takeover has begun." We are Borg. But in this case borg may mean significant improvements in the lives of those stricken with horrible illnesses. Not today, not tomorrow, but in the near future. What a wonderful, terrible thing the human imagination can be.

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Stem Cell Breaktrhough


I have long contended that there would be ways to get the benefits of stem cell research without the ethical implications of taking them from embryos. I have not yet read the referenced papers, so this could just be media hype. However AP reports that such a breakthrough has been accomplished. If so, it may be the source of great benefit to humanity. Just as possible is that it will return nothing or even negative effects. Let us hope and pray that scientists doing this research proceed with all due caution.

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The Linnaean Flower-Clock


This link, sent by a fried (thanks FPJ) is really fascinating. When flowers bloom or close. Practical--not really--but interesting? Absolutely.

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