Category Archives: Origin of life

Speculative Naturalism

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The standard design-theorist argument hinges on the assumption that there are three logically distinct kinds of explanation: chance, necessity, and design.  (I say “explanation” rather than “cause” in order to avoid certain kinds of ambiguities we’ve seen worked out here in the past two weeks).

This basic idea — that there are these three logically distinct kinds of explanation — was first worked on by Plato, and from Plato it was transmitted to the Stoics (one can see the Stoics use this argument in their criticism of the Epicureans) and then it gets re-activated in the 18th-centuries following, such as in the Christian Stoicism of the Scottish and English Enlightenment, of which William Paley is a late representative.   Henceforth I’ll call this distinction “the Platonic Trichotomy”

There are at least two different ways of criticizing the Platonic Trichotomy.  One approach, much-favored by ultra-Darwinists, is to argue that unplanned heritable variation (“chance”) and natural selection (“necessity,” if natural selection is a “law” in the first place) together can produce the appearance of design.  (Jacques Monod is a proponent of this view, and perhaps Dawkins is today.) The other approach, which I prefer, is to reject the entire Trichotomy.

To reject the Trichotomy is not to reject the idea that speciation is largely explained in terms of the feedback between variation and selection, but rather to reject the idea that this process is best conceptualized in terms of “chance” and “necessity.”

So what’s the alternative?   What we would need here is a new concept of nature that is not beholden to any of the positions made possible with respect to the conceptual straitjacket imposed by the Trichotomy.

Reification of the tree metaphor

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A brief note to a regular reader.

The Darwinian “tree of life” is not an actual tree. It is a diagram of relationships. Therefore it can survive without having established its “roots”.

It could be granted that the origin of life was artificial, or even supernatural, and the theory of evolution would still be applicable within its domain.

This is not the first time the error in the essay challenge has been pointed out, but it costs us little to hope that a sincere individual, in no way guilty of peddling a religiopolitical agenda, would acknowledge the mistake.

The Programmer and N.E.C.R.O.

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A computer programmer noticed that he was not able to type very much in a single day.  But he mused that if there were a large number of software bots working on his code, then they might be able to proceed via totally blind trial and error.  So he decided to try an experiment.

In the initial version of his experiment, he established the following process.

1. The software was reproduced by an imperfect method of replication, such that it was possible for random copying errors to sometimes occur.  This was used to create new generations of the software with variations.

2. The new instances of the software were subjected to a rigorous test suite to determine which copies of the software performed the best.  The worst performers were weeded out, and the process was repeated by replicating the best performers.

The initial results were dismal.  The programmer noticed that changes to a working module tended to quickly impair function, since the software lost the existing function long before it gained any new function.  So, the programmer added another aspect to his system — duplication.

3. Rather than have the code’s only copy of a function be jeopardized by the random changes, he made copies of the content from functional modules and added these duplicated copies to other parts of the code.  In order to not immediately impair function due to the inserted new code, the programmer decided to try placing the duplicates within comments in the software.  (Perhaps later, the transformed duplicates with changes might be applied to serve new purposes.)

Since the software was not depending on the duplicates for its current functioning, this made the duplicates completely free to mutate due to the random copying errors without causing the program to fail the selection process.  Changes to the duplicated code could not harm the functionality of the software and thereby cause that version to be eliminated.  Thus, in this revised approach with duplicates, the mutations to the duplicated code were neutral with regard to the selection process.

The programmer dubbed this version of his system N.E.C.R.O. (Neutral Errors in Copying, Randomly Occurring).  He realized that even with these changes, his system would not yet fulfill his hopes.  Nevertheless, he looked upon it as another step of exploration.  In that respect it was worthwhile and more revealing than he had anticipated, leading the programmer to several observations as he reflected on the nature of its behavior.

Under these conditions of freedom to change without being selected out for loss or impairment of current function, what should we expect to happen to the duplicated code sequences over time and over many generations of copying?

And why?

[p.s. Sincere thanks to real computer programmer OMagain for providing the original seed of the idea for this tale, which serves as a context for the questions about Neutral Errors in Copying, Randomly Occurring.]