Decision making in biosystems

Decision making is one of the distinguishing properties of biosystems. Decision making of course does not necessarily mean conscious decision making, which is exclusively human. On the contrary, the ability to make decisions can be observed in every living organism even in unicellular species as a type of molecular logic, in the form of chemotaxis). Chemotaxis is chemistry-driven motility: towards areas of increasing concentrations of friendly chemicals (positive chemotaxis) and away from increasing concentrations of hostile chemicals (negative chmotaxis).

Macroevolution = Machines Creating Other Substantially Different Machines

By definition, biological macroevolution is the hypothetical emergence of higher taxa (new classes, phyla, kingdoms) from the ones that exist at any given point in time, by itself, i.e. without recourse to intelligent agency. Many authors maintain that combinations of law-like necessary factors (such as natural selection) and stochastic factors (mutations, genetic drift and recombination in the case of sexual reproduction) are causally sufficient to explain hypothetical macroevolution.

Creepy-Crawlies Use Cogs

The cogs used in hind legs of Issus coleoptratus.

To synchronise mechanical motion of their legs when jumping, chrysalises of small insects Issus coleoptratus use cogs. Thanks to such a simple mechanical device the insects reduce asynchrony of their hind leg movements down to about 30 microseconds.

What is code and does DNA have one?

A coding function maps a set of objects to a set of symbols: O → S , where S is a set of symbols (tokens); O is a set of objects. A decoding function is the inverse and maps the set of symbols back to the set of objects: S → O. Without loss of generality S can be thought of as a set of configurations of a material system. The set of coding function values is determined by the semantic cargo voluntarily attached by the decision making agent to specific configurations. 

Why I think biological macroevolution is a practical impossibility

Notwithstanding the correctness of using statistical reasoning [Abel 2009, Durston et. al. 2007] when dealing with the organisation and functioning of biological systems, the strength of statistical statements falls short of what is needed in order to demonstrate the practical impossibility of spontaneous/necessary emergence and subsequent evolutionary development of life. There will always be individuals wishing to believe in a slimmest chance of something happening. You can't do anything about it because such is human psychology. The missing persuasive power can be found in considering the cybernetic foundations of biology. Here I will use ideas from personal communications and from [Abel 2011]. These ideas are not mine. I am just mulling them over here.

Biological evolution is (а) differential survival and (b) reproduction of already existing biological forms. In the modern synthesis both (а) and (b) which boil down to stochastics (random variation) and deterministic law (selection) are considered sufficient for the emergence of new functionality and, consequently, of all observed biodiversity.

A challenge for evolutionists

Dear Colleagues,

Can anyone of you who believe in the power of undirected evolution (excuse my tautology) experimentally demonstrate the emergence of working code from a blank sheet only by chance and/or necessity? In your experiments you can use stochastic processes and deterministic law. You are not allowed to use any guidance/choices stemming from agency.

A little quiz: guess what it is

What is it?

Two more references to Kirk Durston

Here are two very interesting references I encountered very recently:

1. A video-clip of Kirk Durston's presentation:

http://www.metacafe.com/watch/10335610/the_origin_of_life_requires_intelligence_kirk_durston_phd/

2. A paper again by K.Durston, which is a summary of his and his colleagues' 2007 paper on measuring functional complexity of proteins where they published remarkable results showing statistically significant amounts of functional complexity across a sample of 35 protein families. The interesting bit here is that to date, no one has been able to demonstrate convincingly that causation other than rational agency is capable of producing large amounts of functional sequence complexity. This newer summary is free from technical details and is easier to read for a non-biologist:

http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf

On the importance of Christian tradition in a programmer's speak

Christ is Risen!

Imagine you want to create a complex software product composed of a number of modules. You delegate the development of those units to your team, having worked out in detail a common interface which determines the interaction between the modules. Every member of your team develops their own unit. However, if during development the integrity of the common interface is compromised, there will be no product even if every module functions correctly in isolation. This can happen e.g. as a result of removal of some key API in either of those modules.

ID: The snow is melting

I encountered a very interesting paper by Prof. Michael Sherman [1], Director of the genetics lab at Boston University Medical School.

I can only comment that the publication of scientific papers like this one demonstrates that ID is science. Not only does the author propose a new theory which easily explains observations that cannot be explained by Darwinism (or at least as elegantly and as easily), but he also formulates new hypotheses and discusses scientific experiments to validate them.

Reference

1. Michael Sherman (2007). Universal genome in the origin of metazoa: thoughts about evolution. In Cell Cycle. 2007 Aug 1;6(15):1873-7.

Design detection is a variant of the Turing test

It can be shown that purposive design detection in configurations of matter is a variation of the Turing test.

Fig.1. The Turing Test (courtesy Wikipedia). Receiver С is to detect the actual sender, a computer A or a human В, given that С has no knowledge of which of the other parties generates particular messages.

BioTRIZ and ID

I attended a very interesting workshop at Bath on BioTRIZ yesterday. BioTRIZ is an amalgamation of TRIZ (the acronym originating from Russian meaning "the theory of inventive problem solving") and biomimetics. TRIZ is an empirical theory of invention. Its main contribution is in formulating a set of basic principles of innovation. These principles — there are forty of them — are, figuratively speaking, symbols of the alphabet of a language for cross-domain interpretation of innovation ideas.

ID is an abductive theory

Charles Sanders Peirce (1839-1914)

In intelligent design detection (ID) the notion of plausibility is important. This is because ID has an abductive core.

Free will as a consequence of the third type of causation

The interest of various scientists in the philosophical notion of free will, i.e. the ability of cognitive agents to make choices unconstrained by factors external to decision making, has consistently been growing lately. The philosophical implications of quantum mechanics as well as recent advances in psychology and health care, esp. concerning near death experiences of patients returned to active life, demand a definitive answer to the question of whether our free will is genuine at all.

Is our world based on chance?

Let nothing lead you to disbelief. Do not say: this or that happened by chance or for no reason. In everything that exists, there is nothing disorderly, uncertain, purposeless or random. Do not say: misfortune or evil hour, for only unreasonable people say so. "Are not two sparrows sold for a farthing? Аnd one of them shall not fall on the ground without your Father" (Matt. 10:29)? How many hairs are there on one head? And not a single one is neglected. So can you see God's supervision, from which not a thing, even a tiniest one, can escape.

St Basil the Great, Homilies on the Book of Psalms, Psalm 32. 
Translation from Russian is mine — E.S.

I would like to discuss my recent debate on the Internet with an incognito Creationist. Despite the fact that we share the same philosophical views, my colleague disagreed vehemently with some things that I say here in my blog. His concerns can be summarised as two questions:

• Is our world based on chance?
• What is chance?

According to my opponent, the Holy Fathers of the Church did not accept chance contingency or randomness as a scientific category. This does not seem right to me. Yes, they argued against chance but metaphysically. Let us discuss this apparent contradiction in a bit more detail.

Professor Larry Moran is Wrong

I recently encountered another discussion between proponents and opponents of ID (Dr Douglas Axe vs Dr Larry Moran). And guess what, this discussion was again around  protein functionalty and the plausibility of Darwinian paths in the configuration space from one functional protein to another. 

Dr Moran's argument as laid out in his blog Sandwalk is, basically, this. We, stupid IDers, do not understand how it all works. Dr Moran asserts that we cannot say that protein evolution is statistically implausible based on two existing functional proteins A and B whose functions are extremely far apart in the configuration space (in fact, so far apart that a Darwinian path is implausible on the gamut of the whole universe). By the way, there are no provably demonstrable Darwinian paths between any pair in a majority of existing proteins.