Criticism. Essay. Fiction. Science. Weather.
is located at the unassuming corner of two wide, western streets in Boulder, Colorado. The product it caries may be full of taste, but is neither tasteful, nor toasted. This shop serves deep fried donuts, vulgarly smothered in a bevy of glazes and toppings; perhaps the most unique and amazing donuts I have ever tasted. Each donut is made to order, from batter to box right in front of your eyes. You can have a maple glazed graham cracker donut and a apricot glazed snickers donut and any other combination you can imagine. As I watched the creation of my donuts, I couldn't help but salivate at the scientific analogies, in this case, to the secretory pathway of a cell. The express purpose of the cellular secretory pathway is to synthesize and package proteins for release from a cell. Some familiar secretory proteins include hormones and neurotransmitters.
The Tastefully Toasted donut is born when batter is squeezed through a nozzle and drops into a vat of frying oil. In the secretory pathway, ribosomes translate an mRNA template into a chain of amino acids and push the growing protein through small pores into the Endoplasmic Reticulum (ER). Just as the oil cooks the batter into a crispy donut, the specialized pH environment and accompanying chaperones within the ER provide the perfect atmosphere for our young protein to fold, allowing it to establish the 3D structure which will define its function. An uncooked donut is just a blob of batter, and an unfolded protein is just a string of amino acids, characterless, bland, inedible.
After the donut reaches the perfect tinge of golden brown, it is transported slowly out of the oil on a conveyor belt, and the donuts make there way to the topping station. After a protein passes through the folds of the ER, it is packaged into small vesicle membranes and transported to the Golgi Apparatus, another membrane bound compartment and the location for most post-translational modifications--in other words, the glazes and toppings. Here the donut is met by the donut chef, who individually dips each donut into its own glaze flavor and then coats the top half of the donut with the prescribed topping.
In the secretory pathway, special enzymes use specific hallmarks of the amino acid sequence to modify the protein. Even the seemingly small addition of a few Nitrogen atoms can be vital to establishing the flavor of a protein. In fact, sugars are added to both protein and donuts in their modifications. Scissor enzymes can also cleave the protein to remove pieces unnecessary to the final product or create two smaller proteins from an initially longer sequence. Although I didn't see it happen to my donuts, the donut chef would certainly have removed any burned sections, and probably cut my donut in half if I wanted him to.
After each donut is finished, it is placed in a special box, impervious to any and all sugary dripping, and sealed tight once all ordered donuts are present. After modification in the Golgi, the proteins are packaged into secretory granules, dense vesicles that travel to the edge of the cell membrane, where they wait for an external signal to trigger the release of their contents. My donuts sat in their box for some time before I ate them. It was morning when they were made, but they looked more like desert to me. When the urge called though, I popped open the box to find my array of detectible donuts. Even two days later, the last donut was still quite good, just as peptides in secretory granules can stay cued before their release is signaled. Retracing to the start of the process, each TT donut is made to order. In a similar way, although the release of secretory proteins is at the level of the secretory granules, up-regulation of DNA transcription into mRNA can call in an order for more of a specific protein.
To be fair, there are many differences between these two processes, one of the largest being that the secretory pathway is a factory sized operation as opposed to the individualized nature of the TT experience. Tastefully Toasted is also a truly one-of-a-kind shop, potentially the only place on earth that you can buy a hazelnut glazed granola donut. This stands in contrast to the millions of cells in each and every one of our bodies that enact the secretory pathway each day of our lives.
The God of the Gaps
has His eye on Dover, PA. The Dover Area school board now requires that science teachers include intelligent design theory -- ID
-- in their lessons as a counterpoint to evolutionary theory. That requirement has caused a group of parents to take the board to court arguing that ID is not serious science, but a Trojan Horse for sneaking God and religion into public schools. The continuing debate about separation of church and state is important, but the thing about ID is that it's not a scientific theory in the first place.
Delimiting the bounds of science is a matter of philosophy and by no account a done deal. But the US Supreme Court has turned out a handy working definition which is consistent with mainstream scientific thinking. The unanimous 1993 decision in Daubert v. Merrell Dow Pharmaceuticals
set five guidelines for expert scientific testimony and, by extension, good science:
1. Theories and techniques need not have been proven, but they should have been tested and not falsified. Thus, for a start, theories must be testable and falsifiable.
2. Theories and techniques should be subjected to peer review and publication -- communication and criticism are vital to modern science.
3. Experimental techniques should have a known error rate
. Any test of a theory should have an attached confidence level. What good is a test result if you don't know how reliable the test itself is?
4. Theories should be subject to standards governing their application. Thus, independent groups in a field should be able to share experimental results in a meaningful way. Everyone should play by the same rules.
5. Theories and techniques should enjoy acceptance by at least a significant minority of the scientific community.
On all five points, the frontrunner concept of ID, irreducible complexity, strikes out.
On Monday, ID advocate Michael Behe
testified for the defense of the Dover Area school board. Behe's rallying cry is the concept of irreducible complexity, which is based on the notion that the intricate workings of organisms, especially on the molecular level, rely on separate but interdependent parts. Irreducible complexity supposes that each part would have been useless without the others, and so none of the parts should have evolved out of a passive process like natural selection. Thus, collections of special, coordinated parts may be the signature of an Intelligent Designer. Bombardier beetles, which produce and store separately the chemical ingredients for a dramatic, explosive spray, are poster children
for irreducible complexity.
For this concept, the problem with testing and falsification is that the 'experiments' have already taken place that gave rise to the irreducibly complex features that Behe observes today. Nobody knows just how those experiments were conducted and whether there was a Designer guiding the process or not. Asking scientists to re-evolve by natural selection beetles equipped with explosive sprayers might falsify the concept by showing that natural selection is indeed powerful enough to yield complex interdependencies. But who's to say that the Designer wouldn't be tinkering behind the scenes the second time around? And anyway, the beetles' evolution took billions of years the first time around. With testing out of the question, a test error rate becomes meaningless. Strike two.
While Behe has been published
for his work on protein evolution, there is no peer-review discourse on ID experimentation. Without journal literature, there has been no establishment of regular practice for work on irreducible complexity. Not surprisingly, then, the biology community has been generally unimpressed with the notion of irreducible complexity. For example, Ken Miller, coauthor of a widely used biology textbook, wrote in his book Finding Darwin's God
, "Behe is wrong." Strike five.
Since its modern inception, in Ferdinand Canning Scott Schiller's 1903 book, Humanism
, ID has been doomed to fail as good science. Schiller writes, "It will not be possible to rule out the supposition that the process of evolution may be guided by an intelligent design." Thus it will not be possible to give science a fair go at ID and the concept will not fuel constructive discourse. In a way, the case of the Dover Area school board is, well, academic. Even if the board is allowed to require ID in science class, the subject will never be science and it will never make a good counterpoint to evolutionary theory. ID won't even make a good lie to children