Is There Purpose in Biology?  The Cost of Existence and the God of Love. By Denis Alexander, Chapter 3: Biology’s Molecular Constraints

Is There Purpose in Biology?: The Cost of Existence and the God of Love
By Denis Alexander

Chapter 3: Biology’s Molecular Constraints

We are reviewing the book: Is There Purpose in Biology?  The Cost of Existence and the God of Love. By Denis Alexander.  Chapter 3: Biology’s Molecular Constraints.  Alexander begins the chapter with a quote by Paul Davies, well known physicist, atheist, and author of such books as; God and the New Physics, The Cosmic Blueprint, The Mind of God, The Last Three Minutes, and, How to Build a Time Machine.  The quote is:

“The fact that the universe conforms to an orderly scheme, and is not an arbitrary muddle of events, prompts one to wonder – God or no God – whether there is some sort of meaning or purpose behind it all.”  (Davies, The Goldilocks Enigma, 2007, p.16)

A number of commentators in the last post raised the issue of design (or purpose; if something is designed a purpose is assumed) and the fact we do not have a counter example of a non-designed universe.  Commenter Robert F put it:

“If the universe is designed by a creator, then everything in it is designed. We indeed would have no way of comparing what is designed with what is not, because we have no instances of non-design.”

While strictly true, I suppose, from a strictly empirical viewpoint, I don’t give much weight to the argument for the same reason I don’t give much weight to Solipsism – the idea that only one’s own mind is sure to exist. As an epistemological position, solipsism holds that knowledge of anything outside one’s own mind is unsure; the external world and other minds cannot be known and might not exist outside of the mind. As a metaphysical position, solipsism goes further to the conclusion that the world and other minds do not exist.  While possibly true and impossible to falsify, to me, it’s just no BFD.  We are all going to go on pontificating and commenting regardless.  So check your tired puddle-analogy at the door, after all we are not going to discuss (hat tip to Ken Nahigian):

1. Unintelligent Design (UD)
2. Stupid Design (SD)
3. Clumsy Design (CD)
4. Malicious Design (MD)
5. Design for Some Other Purpose, Causing Accidental Life (DeSOP-CAL)

Since we are all assuming we are intelligent (yes, I know, BIG assumption) we are going to assume God is intelligent as well.  Even if we are atheists, as the Davies quote shows, we still think and act as if our intelligence might just be purposeful.  Otherwise – see Solipsism above. So, can we move on, please?

This chapter is a continuation of the previous one, except instead of dealing with the macro-sized constraint features, Alexander deals with the micro-sized ones; at the molecular level.  This chapter is a difficult read for those without a science background, indeed, it was difficult for me because Alexander is a molecular biologist and he goes deep; so I’m going to lightly summarize.

One of the most amazing and elegant features of the world is the genetic code.  There are four “letters” (U,C,A,G) in the DNA and each “genetic word” is composed of three letters and known as a codon.  Randomly mix up 4 letters to arrange them into 3-letter codons and what you get is the 64 codons shown in the figure. The 64 codons combine to form 20 different amino acids.  The amino acids are the building blocks of proteins, of which we are mostly composed. The genetic code then is the code our body uses to convert the instructions contained in our DNA into the essential materials of life.

The big question for our present context is: how did such an elegant genetic code ever get established?  Are there some chemical and physical underlying principles, associated with systems analysis, which could mean that this particular genetic code might just be the best code that there can be?  There are three main theories of the origin of the genetic code.  Alexander says this:

“… all the ideas summarized in the three main theories very likely play key roles along the way to the genetic code we have today.  What is important to highlight in our present context is that all these ideas depend on orderly, systematic, biochemical ideas and observations.  Were stochastic (chance) events involved in the generation of the genetic code?  Of course – no doubt billions of them.  But there appear to be good reasons why the code we now have appears to function so well in all living things today of planet Earth: physical and chemical constraints ensured that its generation was shaped by the needs of optimum functionality.  If we find life on another planet, as seems very likely (and assuming we don’t contaminate it with Earthly molecules), it also seems a reasonable expectation that information-containing molecules like RNA and DNA will be present in its life-forms, and it would not be at all surprising to find a genetic code if not the same, at least similar, to the one we have on planet Earth.”

Alexander then talks about the physical restraints on RNA molecule selection and protein evolution.  He notes that in the structure of molecules it turns out that basic physical constraints mean that in most situations the full range of possibilities generated by randomizing the options is never achieved, and so natural selection can only act with reference to specific subset of possibilities.  He cites a study by Ard Louis of Oxford that seemed to bear this out.  You can read a summary of the study here.  The study found:

“When you think about evolution, ‘survival of the fittest’ is probably one of the first things that comes into your head. However, new research from Oxford University finds that the ‘fittest’ may never arrive in the first place and so aren’t around to survive.

By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales.”

One reason this occurs is due to the discovery of “hotspot” genes. More than 350 such hotspot genes, meaning genes that are more “evolvable” than others have now been identified.  Alexander cites the example of the 3-spined stickleback fish, which have evolved in the relatively (geologically speaking) short time period since the last retreat of the glaciers trapped ocean sticklebacks in freshwater lakes.

The genes in this case is PITX1 gene that is involved making armor plating (with spikes). The main environment that they live in contains different predator.  One environment, the freshwater lakes, contains dragonfly larvae that can catch the fish by latching on to the spikes. Hence, the environment allows stickleback to evolve with no armor plating.  Alexander says:

“So sticklebacks are predisposed to remarkably rapid changes in their pelvic spines at multiple levels: the relevant regulatory gene is located in a highly changeable area of the genome; the gene in question can act as a master-control body-armor switching apparatus; and variants reduce pelvic spines will be rapidly selected in environments where those spines decrease fitness.  Without such clever “evolvability” living things wouldn’t exist – including us.  It’s yet another example of “Goldilocks biology” – unless the evolutionary systems have these very particular kinds of properties, we certainly wouldn’t be here to discuss the question.  But isn’t that a circular argument – we wouldn’t exist to have the discussion unless precisely these kinds of well-organized systems were in place?  Precisely so, that’s just the point.”

Well, there you have it.  It would be nice to have some extraterrestrial biology to test his speculations.  I will note over 15 amino acids have been identified in the Murchison meteorite by multiple studies, so maybe his speculation is not that far off.  The molecular constraints he points out are a fact, just as the physical constraints are.  The question is; how do you interpret the facts?  Is it mere happenstance? Totally coincidental chance?  Or something more?  And how would we know?  Next week we will delve into Chapter 4 – Biology, Randomness, Chance, and Purpose.  Should at least be interesting, yes?