Tuesday, June 19, 2012

Barhaminology: The Bioessentialist Manifesto

Over at his TheBestSchools.org blog, James Barham continues to entertain us with armchair philosophy. In this episode, his view of what biology is really all about.

Barham sets up two views, the Darwinian view, and the bioessentialist view. Guess which one he prefers?

The Darwinian View of Life
  • There is no deep difference between living and nonliving matter; therefore, it is idle to seek “essential” properties or a “definition” of life.
  • In any case, the most fundamental fact about a living thing is its ability to undergo natural selection.
The Bioessentialist View of Life
  • There is a fundamental difference in kind between living and nonliving systems; the main task of biology is to understand the distinctive nature of living matter.
  • The most fundamental fact about a living thing is its ability, by doing work selectively, to maintain itself in existence as the kind of physical system that it is.

Dismiss in passing Barham's purposeful confusion of Darwinism and materialism. Let's go to the videotape! Anyone remember the search for elan vital? It doesn't exist. Living things are made of the same atoms as non-living things. Use the same chemical reactions. Watch the same TV shows. Mr Barham seems to have forgotten that.

Oh, sorry, I didn't notice that the Darwinian was looking at 'matter' and the bioessentialist was looking at 'systems'. For a philosopher, Barham has a tough time setting up his comparisons.

"The main task of biology" - James Barham, armchair philosopher and web technician, has pronounced. It must be so.

"by doing work selectively," - selectively? A bacteria only eats half the available sugar? A virus only makes half the copies of itself that it could? Sperm cells only swim as much as they want? Barham might work selectively but it hardly qualifies as a definition of life.

(My own definition of life, FWIW: Life is a collection of molecules working together to avoid equilibrium for as long as possible.)

The essay is quite long and continues to be silly in the same vein. Genes are contrasted with proteins because metabolism is more important than reproduction. WTF? Since when was living forever an option? Metabolism explains the fossil record, biodiversity, the peacock's feathers and the panda's thumb?

Barham and his dog Marty are not, apparently, made of quarks descended from the Big Bang. Perhaps they were specially created 6,000 years ago. Who knew? Marty ain't made from no quarks! Reductionism is defeated.
For example, they are all explained at a more fundamental level by the Pauli exclusion principle.
Except when it is convenient.

In the case of a true machine, the functional order has nothing whatever to do with the matter out of which the machine is composed. It is imposed upon the matter entirely from without—by us. The material parts out of which a machine is made are supremely indifferent to the purpose the whole is designed by us to serve. Moreover, the stability of a machine resides in the rigidity—not the flexibility, much less the inherent intelligence—of its parts.
In contrast to what happens inside a machine, everything that goes on within a living being possesses an inherent purpose—namely, maintaining the organism in existence. That is the essential difference between living and nonliving things.

So living things are NOT machines. Just don't tell Polanyi and all those folks that want to argue that living things ARE machines, because machines are designed.

Don't quit the web job, James. Armchair philosophy, it ain't for you.

Friday, June 8, 2012

Someone Teach Ann Gauger to Google

Over at the blog of the Biologic Institute (the Discovery Institute's science-y wing), Ann Gauger has been writing regularly about molecules. Her April 30th post, Intricate Coordination, looked at the enzyme carbamoyl phosphate synthetase (CPS). Wow! CPS is complicated! It has two parts, three active sites, and an intramolecular tunnel. And here is Ann's take-away message:

How does a neo-Darwinian process evolve an enzyme like this? Even if enzymes that carried out the various partial reactions could have evolved separately, the coordination and combining of those domains into one huge enzyme is a feat of engineering beyond anything we can do. 

Well, how do we explain this?

First, by understanding that CPS is not a singular 'thing'. Like any biomolecule of any size, it comes in a variety of shapes and sizes throughout the different species of life. In fact, CPS performs an important role in the cell, and is therefore found across Bacteria, Archaea, and Eukarya. We can use CPS to draw a phylogeny, a tree of life. So the first part of an answer to Ann is yes, CPS does evolve. Evolution is the simplest explanation of the many versions of CPS found throughout living species.

Second, we can see that Ann's question is really a sense-of-wonder question. Parts, sites, a tunnel, a  lab under an extinct volcano, sharks with lasers, it is all so amazing. Yes, it is, even if it doesn't have those last two items. But "substrate channeling", as the cool kids call it, isn't unique to CPS. Lots of enzymes do it. Sometimes they use a tunnel of hydrophobic residues, sometimes hydrophillic residues. Sometimes the 'tunnel' is more of a path of favorable charges across the surface of the enzyme, sometimes it is a floppy arm that carries substrates from one place to another as it flops around. Not only has it evolved, it has evolved multiple times for different substrates.

These different functional mechanisms help to keep reactants from floating off into the cytoplasm, thereby increasing the speed and efficiency of an enzyme. AA residues facing into the tunnel can effect the speed with which molecules diffuse down its length, keeping the different parts of the reaction in sync. These qualify as huge selective pressures, so the second part of an answer to Ann is that evolution created these enzymes using the standard preference for higher functioning processes. Natural selection, you've heard of it, right?

Thirdly, we can understand the question to be one of, 'from what functional predecessor did CPS evolve?" If we look at CPS across the various species, it comes in two parts with separate functions, so right there we can see that these parts could have evolved separately, from less specialized or efficient predecessors. The larger of the two subunits, the part with two active sites, seems to have undergone a gene duplication event very early in its history. This subunit seems to have developed from a carbamate-kinase ancestor.

Putting it together, an answer to Ann's question is "Yes, CPS does evolve, by normal functional selection, from clear ancestors via well understood variational events."

"... a feat of engineering beyond anything we can do"? Ummm, no. Looking at the phylogeny, pretty much any branch is a sequence of exaptations, duplications, fusions, mutations, wash, rinse, repeat. Yeah, we can do that. As a matter of fact, we do do that. We've been poking at CPS for a while, pulling the genes apart, putting them back together, mutating it. It is the basic path to understanding how CPS works.

Now I will make a confession. I am not a biochemist or an evolutionary molecular biologist. But I do know how to use Google. Starting from "evolution carbamoyl phosphate synthetase" and ending with "evolution substrate channeling" I learned a lot about CPS very quickly, mostly with the help of papers published in the 1990's. Google is your friend. PubMed is your friend. 

Friends don't let friends blog stupid. Don't follow the path of Cornelius Hunter, he of the "Stuff's Complicated, Must Be Jeeebus" blog tic. Think about it, Ann.

Friday, June 1, 2012

No trend in tornadoes

This is my first post dipping a toe into the churning waters of climate change/global warming.

I saw a pretty visualization over at WUWT of tornado storm tracks, and decided to follow up with looking at the data myself. It is all available from the NOAA Storm Prediction Center site. (I normally go to WUWT for the comedy. The few earnest skeptics are mixed in with a vast number of loons.)

To estimate the energy of a single tornado, I multiplied the track length * the track width * (F+2)^1.5. This gave me a number I felt it was safe to add up across all tornadoes in a year.

Looking at all tornadoes, or at just the severe F4+F5 subset, I did not see any trend in the data when charted in Excel. That is my rough, first pass observation. There certainly are more tornado observations as time passes, but seeing many more small tornadoes isn't changing the big picture much.

Why might that be? Well, one thing that I can think of is that, as spectacular as tornadoes are, they don't actually account for a lot of energy. Or the GW effect might be to shift where and when the occur, not the strength when they do. Actual strength might be limited by some other constraint of atmospheric physics.

As I said above, there are many more tornadoes reported now compared to decades ago. Many commentators put this down to better observational data, the growth of populations in tornado prevalent areas, etc. If there is a GW aspect to number of tornadoes, it will be difficult to untangle from these issues.