February 17, 2020

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.

The Genetic Code

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.”

A fully armored stickleback from the ocean near Loberg Lake (top), and a low-armored stickleback taken from Loberg Lake in 1994 (bottom). The fish have been stained with a dye called Alizarin Red S, which stains bones, in order to highlight their differences. Photos courtesy Michael A. Bell, Professor of Ecology and Evolution, Stony Brook University.

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?

Comments

  1. John barry says

    Mike the G Man, Another good series that challenges my 10th grade understanding of science. I know a little about DNA from watching the Forensic Files and Investigative Discovery channel on TV. Based on my recent trajectory of life I believe I am de evolving as my brain and muscles in my body are disappearing due to lack of use. Luckily I have passed on my genes prior to the de evolution. Seriously , I do appreciate the article as you have made it understandable and I can at least follow the chain of thought.

    I notice that Mr. Alexander is using the un evolved spelling of Dennis which just underscores the multi pathways that all things in life evolved. Natural selection and intelligence decided that the second n was not needed .

  2. Robert F says

    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.

    But this is a philosophical argument, not a scientific one, nor is it scientific evidence. I agree with the philosophical argument you are making, and think it is true, but that doesn’t allow one to adduce design versus non-design instances in the universe as scientific evidence for design, when by your admission there would be no instances of non-design if the universe is created. We are dealing with philosophy here, not scientific evidence.

    • Robert F says

      I.e., the existence of design cannot be detected or measured scientifically, and so its existence cannot be used as a scientific argument in support of the existence of a creator.

      • Mike the Geologist says

        Alexander is not making such an argument, as I summarized in the Introduction and Chapter 1. His points are much more modest: the biological descriptions in Chapter 2 and Chapter 3 counteract the assumption that evolution is NECESSARILY purposeless. This doesn’t force the inference that biological processes must be part of God’s Trinitarian order, merely that biological evolution can be consistent with a theological matrix. Alexander has written criticism of ID of the type promoted by the Discovery Institute so he is not arguing for it in this book. Perhaps my summaries don’t stress this enough and I’m giving a misleading impression of where he is going. If so, I apologize. I’ll try to be clearer.

    • Adam Tauno Williams says

      > that doesn’t allow one to adduce design

      I’m with you, it cannot be deduced. But that is not the only form of Logic/thought. The question is if it is in any way reasonable to infer Design. It is not as is inference is unheard of in Science.

      > We are dealing with philosophy here

      Descartes or Hume? I am open to setting their arguments aside on utilitarian grounds: they aren’t useful. I cannot object to that setting aside as I set aside their arguments every day – – – going to the grocery store is an act of setting aside their arguments.

      Still, I don’t know that I am on the track to get to Design from here.
      I’m still waiting for the Mike drop moment [pun, intended! 🙂 ]

  3. Stephen says

    Ah…”meaning”.

    I don’t think the universe has any meaning but NOT because it is meaningless, but because it is transcendent of meaning altogether. What does chloryphyll “mean”? Plate tectonics? The erosion of the Himalayas into a flat plain a million years from now?

    What IS available to us is the experience of being alive. Which is what I suspect most people “mean” when they talk about meaning.

    • Christiane says

      Brilliant comment, Stephen

      it reminds me of this:

      “After one moment when I bowed my head
      And the whole world turned over and came upright,
      And I came out where the old road shone white.
      I walked the ways and heard what all men said,
      Forests of tongues, like autumn leaves un-shed,
      Being not unlovable but strange and light;
      Old riddles and new creeds, not in despite
      But softly, as men smile about the dead

      The sages have a hundred maps to give
      That trace their crawling cosmos like a tree,
      They rattle reason out through many a sieve
      That stores the sand and lets the gold go free:
      And all these things are less than dust to me
      Because my name is Lazarus and I live.”

      The Convert
      BY G. K. CHESTERTON

      https://cdn.i-scmp.com/sites/default/files/styles/1200×800/public/d8/images/methode/2019/05/02/293d314a-6c58-11e9-994e-1d1e521ccbf6_image_hires_053852.jpg?itok=PRSYTGX_
      Speaking of ‘life’,
      may we give thanks for the life of Riley Howell, an American hero, who gave his own life to save many students and UNC/Charlotte
      . . . Riley charged at the shooter and knocked him over, and took a fatal bullet in the process of saving others, may his memory be blessed in our land that needs its heroes NOW more than ever; and may he live forevermore in the Kingdom of Our Lord

  4. An interesting post, Mike G. One of the great puzzles, at least to me, regarding evolution is the wide range of stability shown by species over deep time.

    Whereas the featured spiky fish above has evolved rapidly, other species such as the living dinosaurs that are alligators and crocodiles apparently haven’t changed much in tens of millions of years. And horseshoe crabs and many primitive fish seem to have been cool as is for hundreds of millions of years. Whence the difference? Are they uber fit, or do they just have trouble even generating new variations?

    There must be something to the survival of the fittest vs. actually available variability that is discussed here today. When I write a genetic algorithm to solve a machine learning problem, I can play God and control, and generally maximize, the available search space that the population’s genes can explore. Nature instead apparently operates more restrictively than I generally appreciate.

    Good stuff, Mike.