Saturday, February 25, 2012

Fun with Proteins and how Proteins Really Fold...

Today, I spotted a post on Facebook with a photo of some of my cousin's kids playing Twister. I was knee deep into making figures with Ramachandran Plots, and structures for a paper I am working on. I thought it might make a good analogy for protein folding. So I did some artwork. See what you you can spot in the details...

Sunday, February 12, 2012

The History Delusion: Intelligent Design Gerrymanders Tesla

Last month Vincent Torley, via the Uncommon Descent website, (link) posted a pre-emptive attack against my blog series. His tactics included rolling out anonymous faux-experts doubting my credibility, rants on probability, the Cambrian explosion and even some inspirational poetry. I must thank him for writing exactly what I anticipated. That is, he took a position that the process of human design is solitary, mysterious, and magical, based on the solipsistic autobiography of Nikolai Tesla.

Gerrymandering Tesla

In addition to defending science and evolution, my argument is this. Intelligent Design gerrymanders historical evidence to support its claims against science and evolution. I use the term gerrymander as it aptly describes how ID shifts and rearranges the borders of reason to exclude both historical and scientific evidence. Exposing the bad history within ID propaganda is important because history is easier for laypersons to understand. It does not require an advanced degree to fact-check. Readers can decide for themselves.

In the post about Tesla, Torley spent more time attributing his magical inspiration to God than uncovering the history of inventions made by Tesla’s predecessors. Gerrymandering in this case applies to the sole-sourcing of Tesla’s autobiography and his entertaining eureka story. This is as expected. Torley puts forward a misleading caricature of a Tesla that appears magical, mysterious and not coincidentally, one who attributes his inspiration to God.

How is the ID viewpoint on Tesla historically misleading? Tesla’s AC motor and radio inventions were incremental improvements and insights completely dependent on his experience with the designs and efforts of his predecessors. Changes Tesla made to existing designs of DC generators, which he did while under the employ of Thomas Edison, were incremental changes to an accumulated complex design.

These designs began with Michael Faraday and were incrementally improved by at least seven others over the span of decades. Conceptualizing the changes to make a motor run on AC was solving a small problem of mechanical and electrical redesign. There were already AC generators, as well as DC motors and generators, and the latter two were well known to be reversible systems. A non-incremental complex design by Tesla would have been the design of an AC motor without any prior motor or generator designs, or theory as precedent. That would have been magical and mysterious, but that is not what happened.

Tesla’s contributions to radio were also incremental and replaced by better ideas soon after. The critical thinker can find all the relevant information on Wikipedia and Google Patents to see that a body of precedent designs and training led Tesla’s mind in the direction of invention. Precedent and existing information, far more than divine inspiration, was the key to his success.

Prior trial and error led to electromagnetic theory and physical laws. These, in turn, allow men like Tesla to make predictions and not repeat the trial and error process. The application of ideas is incremental and requires nothing more than disciplined study and practice. If you apply some academic rigor to account for the design history of the first AC motor, or the first voice radio, you get a list of contributors. But the list is even longer than you might think.

Why the Factory Matters

Replication matters because it is the entire process that must be compared. To bring the human design process in parallel to biology, the two must be laid bare, side by side and compared at every stage. One cannot limit the design discussion to only include the invention or idea formation itself. That is not sufficient. One must trace the generations back in history in both realms, from concept to complexity, without the convenient exclusion of evidence.

How do we account for the contribution of human minds to the design of the AC motors or radios you see and use today? The mass production of serial copies of these products is based not only on the mind of Tesla, but the minds of all the engineers and contributors that made the factories to produce these devices. The factories are far more complex. An enormous number of patents describe machines inside factories – ones that we never see. These unseen machines manufacture parts and assemble them into the finished product. So Tesla is not alone. If all who contributed ideas to manufacture AC motors were alive today and assembled in one place, Tesla would be lost in a crowd.

To compare human design to biological complexity, the factory must be considered as the ribosome, transcription, and DNA replication complexes are themselves factories that manufacture biological polymers like proteins, RNA and DNA. Without exception, mass-production and factory design requires the contribution of many individual human minds, each one contributing incremental improvements. Complexity in factory design grows by generational iterations. The best examples of which are from the early glass factories of Owens-Illinois Corning. History shows these factories started from simple ideas like the bicycle pump and the Gatling gun, and grew in complexity. These are examples you won't find in Wikipedia, but are ones I have researched for a book I am writing on the topic.

Touting the solo Tesla story to support the ID analogy gerrymanders away the necessary factory analogy and has an ugly side effect. It misinforms students that that only the chosen few can invent.  Intelligent Design is religion, disguised as science, and identified as such by excluding both research practice and the accumulation of evidence. It is harmful to students and does not belong in science or history class.

Finally, it may be useful for the Uncommon Descent readers to note that Vincent Torley's Ph.D. thesis in Philosophy is extensively based on evolution, complete with sample phylogenetic tress and information from the fossil record. His thesis mentions neither Intelligent Design or Creationism. A few quotes from his thesis:
Prescott considers the appearance of the platyhelminthes in the fossil record (565 to 544 million years ago) to be the next major breakthrough in the evolution of action selection, after the evolution of cnidaria. He cites research by Raup and Seilacher (1969, cited in Prescott, 2007, pp. 9 - 12) showing that trace fossils of meandering foraging trails left by the earliest animals possessing bilateral symmetry can be generated by combining four simple behaviour mechanisms, one of which functions as a centralised conflict-preventing mechanism, of vital importance to an organism with a primitive brain and bilateral symmetry.

Nerve cells are only found in animals. In fact, they are unique to so-called "true" animals (the subkingdom Eumetazoa awhich excludes sponges). The simplest of these "true" animals are the Cnidaria - commonly known as coelenterates, including animals such as jellyfish, sea anemones, corals and freshwater hydra, which possess the most rudimentary nervous systems found in nature. Fossil evidence indicates that cnidaria were present in the Ediacaran period, 635 to 542 million years ago (Prescott, 2007, pp. 3 - 4).

Conclusion 6.2: The appearance of multicellular organisms, a primitive nervous system and a centralised nervous system represent important milestones in the history of action selection. However, none of these milestones entails a capacity for internally generated flexible behaviour, which seems to have arisen later in evolutionary history.

So as regards Torley's question to me regarding the Cambrian explosion, I leave the exercise to him to refer to his own Ph.D. thesis for the answer.