On 29 July, Derek Lowe had a short post about Craig Venter (http://pipeline.corante.com/archives/2010/07/29/craig_venter_venting.php), along with short quote with by Venter describing Francis Collins as a government administrator rather than a scientist, presumably because of Collins’ religious beliefs. It drew some 76 comments as of today. Most of the comments concerned whether religion and science were compatible or not.
Here’s an amusing one
11. bboooooya on July 30, 2010 7:19 AM writes…
“faith or science”
Really? I’ve never seen a discrete electron or neutron myself, but I believe that they exist.
Not able to contain myself any longer, I entered the fray with:
Well, to accept that the complexity of cellular biochemistry arose by chance, just from purely random exploration of protein space, requires a faith that trumps anything in Genesis. For details see http://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/. If you find anything wrong with the purely combinatorial arguments given there, please post a comment there.
Note: When I was posting for “The Skeptical Chymist”, I used the nom de plume Retread. When I started Chemiotics II, the name was taken, so I’m using Luysii presently.
@retread: Interesting how some people are so happy to trot out combinatorial complexity arguments to dismiss the possibility of proteins arising through evolution (especially naive, error-filled ones that ignore the fact that it is not random but directed, that many functional proteins consist of repeated sub-groups, that many proteins share functional domains, and so on, all assumptions which prune the combinatorial tree by dozens of orders of magnitude), and yet do not blink at invoking the existence of an omniscient, omnipotent being of infinitely greater complexity to create these complex proteins …
Something about swallowing camels while straining at gnats springs to mind.
To which I replied
#42 Daen: I am far from happy to trot out combinatorial arguments to dismiss the possibility of the present degree of protein complexity and structure arising by chance. I find many of the uses religion has been and is being put to absolutely horrible. I do not like where my arguments seem to lead. They need to be refuted (but I don’t see how).
You need far more than ‘dozens of orders of magnitude’ to trim down protein space so all aspects of it can be explored. The current champ is titin with 30,000 amino acids, 300 modules of three types (1) immunoglobulinlike, (2) type III fibronectin, and (3) unique PEVK insertions. Even linking them together in any particular order is one in 3^300 possibilities, a number larger than all the baryons in the universe.
Only 1.5% of the genome codes for amino acids, but nearly all of it is transcribed, so proteins are only a small part of the story. Molecular biologists are fixed on proteins (they know lots about them, and the technology to study them has been developing for decades). But there is far more to the story. For just how protein-centric molecular biologists are see the current post about Autism Spectrum Disorder.
Since then we’ve had an example of the good and evil to which religion can be put, an example so perfect that I could never have made it up — the slaughter of 10 medical workers in Afghanistan (in the name of religion of course).
This was followed by
Daen is right. I thought we had already made headway into addressing the combinatorial arguments against protein structure and function. Once we accept the co-operative nature of self-assembly, things begin to look much more reasonable. Even a computer program like Rosetta (which is considered state-of-the-art as far as predicting protein folding is concerned) can pare down the vast space of possible protein folding intermediates to a manageable few by using well-established motifs from known protein structures. If this can be done in a few hours by a computer program for a decent-sized protein, I don’t see why it would require an act of faith to believe that nature could implement such a strategy over billions of years.
To which I replied
#47 Wavefunction: Of course Rosetta can do this. It starts with proteins which already are known to fold into one shape, to find the how another protein (which is known to have one shape) folds into it. Rosetta is basically starting with the answers in hand, and a question which is known to have an answer.
I’ve got to get some stuff I posted on the Skeptical Chymist back when I was writing for them up on my site for you folks to chew on, but I’m going to be visiting family until the middle of next week. In the meantime have a look athttp://luysii.wordpress.com/2009/11/29/time-for-the-glass-eye-test-to-be-inserted-into-casp/.
If mutation is truly random (and it seems to be) I don’t see how nature has the time, space or mass to “do it”.
@retread: You’re missing the elephant in the room, which is so often overlooked by those who invoke a purely combinatorial approach to questions of how functional biological systems arise. The elephant is that all proteins do something useful, which is non-random. A naive combinatorial approach based on pure random chance does not take into account the equally sound physical principles of natural selection, which is anything but random. An organism alive today exists in a state of extreme adaptation, from its gross morphology down to its molecular biology. Working backwards, at every step of the way, its ancestors survived. Mutations conferring an adaptive survival advantage upon those ancestors can be traced backward, generation by generation. Other mutations, which may have been deleterious or which did not confer sufficient advantage, have been lost. Surely you know this; it is at the heart of the modern evolutionary synthesis. So to invoke a pure random chance argument and express surprise at the vast numbers it throws up is incongruous and, worse, plain wrong. Your argument is utterly specious.
56. LeeH on August 1, 2010 10:48 AM writes…
@retread: For a simple concrete example of how good solutions to problems that are seemingly infinite can be generated “randomly” simply Google genetic algorithm solutions to the travelling salesman problem.
Briefly, if a salesman has to travel between multiple cities and you want to know the best (i.e. shortest) way to do it, once you consider a rather trivial number of cities you are considering, if done exhaustively, more possible paths than there are atoms in the universe. Yet, using “random” selective methods (such as GAs) you can have Excel generate good solutions in a matter of minutes.
Perhaps this implies that God is somehow, in a divine, intelligent way, extending his mighty hand into Microsoft’s product. A more likely explanation is that invoking combinatoric arguments, without truly understanding combinatorics, is not the way to refute the conclusions of thousands of man-years of consistent evidence.
@Retread: The point was that Rosetta uses a mix-and-match strategy which makes the conformational space required to be searched much smaller than what would result from random search alone. Nature proceeds in a similar way, non-randomly accumulating pre-existing fragments from known protein structures. It would indeed be miraculous if it were purely random. But it’s really not, and this argument is quite well-trodden.
Using another guy’s blog for the back and forth about this question, didn’t seem quite kosher, so I’ve put up two of the posts I wrote for the Skeptical Chymist (they are the previous two on this blog) which explain my thinking behind my original comment. How life came into being is one of the most profound questions we can ask. Even though presumably scientific, there is no way it can be disentangled from its theological and philosophic implications. Aren’t we fortunate to live when we live, know the chemistry and physics that we know, and possess some of the data needed to address it on a nonintuitive basis.
So start your engines and comment away (either on the previous two posts or this one). I’ll eventually respond to all of them, but it may be a while, as on the 15th I leave for “Band Camp for Adults” for a week.