DNA

Another post that I wrote some time ago.  With my studies in biochemistry now under way, I am ready to publish it.

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Ever since Watson and Crick described the structure of deoxyribonucleic acid we have been fascinated with the chemistry of life.  Their description of the spiral molecule. the sugars of its backbone, and the structure of the bases that make up the ladder holding the spiral together has fired the imagination of physicists, chemists, biologists, mathematicians and philosophers for the last half-century and will continue for centuries to come.

And I should add programmers.  For the DNA code is just that -- a program for how to duplicate itself and the body whose cells it inhabits.  All done with 4 bases, Adenine, Cytosine, Guanine and Thymine, the pairings they make across the double helix of the DNA molecule, and the triplets of such pairings that encode, with the help of RNA, for the production of amino-acids.

Recently is was announced that a Shakespeare sonnet had been encoded in DNA!  Now this is not to say that the sonnet could be reproduced from the DNA in a normal biological process.  But using a suitable interpreter, the sequence of base pairings could be interpreted as an alphabetic sequence, as the alphabetic sequence of a particular sonnet.

All of this is miraculous enough -- rather since the hand of god has no involvement in the process, wondrous enough, but what intrigues me today is the energy involved in the process.  Everything in the replication of DNA conforms to chemical and physical rules.  These rules are well understood, in terms of the conservation of energy, in terms of the energy of chemical bonds, in terms of exo- and endothermic reactions.  Adenosine Tri-Phosphate for instance is created in an endothermic process, with a catalytic enzyme (tautologic, all enzymes are catalysts) - ATP synthase, inside the organelle mitochondrion.  Each ATP molecule is then transported across our animal cells to a location where its energy can be released, in an exo-thermic reaction further modulated by another enzyme, resulting in the production of ADP, Adenosine Di-phosphate.  ADP then migrates back across the cell to a waiting mitochondria where it is recycled back into ATP.

None of this is orchestrated.  None of it is planned or designed.  But it happens.  And it happens in such a way that the cell lives, respires, transpires, and reproduces.

And it happens in such a way that the exchange of energy in each step of the process, conforms to the rules of the first and second laws of thermodynamics: energy is conserved and entropy increases.

Yet in that simplicity, lies the success and multiplicity of life.  Life exists because it survives.  There is no other reason.  If cells did not (and indeed do not) survive, then there are no more cells, and there is no life.  Life is basic survival, at a microscopic cellular level.

This fact of survival, argues for a remarkable energy transport system within the cell, a transport system that in many life forms exists through several stages of development, and in some species through several generations.

In the case of insects, their DNA defines development through egg and larval stages before the adult creature completes a reproductive cycle.  In the case of some butterflies, such as the Monarch, many generations are involved in a complex life cycle covering continents.  In the case of Homo Sapiens, our DNA describes our embryonic development as well as much of our adult behaviour.

All described by DNA.  All requiring the simple physical processes of energy transfer through enzymatic chemical reactions deep within the cells of all living creatures.

I find it hard to believe that DNA accomplishes this alone.  Certainly, DNA codes for the production of amino-acids.  But there is more than amino acids involved in our metabolism.  DNA only succeeds in a cooperative sense with the rest of the mechanisms inside a cell.  Without mitochondria there would be no ATP.  Mitochondria we know are transmitted through the female egg -- there are no mitochondria in a sperm cell.  What of the other organelles, the Golgi body, ribosomes, centrioles and so on.  Are they inherited or produced as a result of the fusion of egg and sperm, from the DNA?  What is the role of so-called junk DNA?  Is it really junk, or are there other translation processes that we have yet to identify?

My projection is that there is much more to be discovered about the mechanics of life, that will continue to astound us in the years ahead.

On submission

I wrote this some time ago following another loss of life.  It seems to me that the message of tolerance towards all people and religions, but of intolerance of intolerance, is lost in our grief.  My decision to publish this now follows the murders in the Quebec City mosque.
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The word Islam, means submission, submission to the will of God.  Therein lies the greatest threat that Islam poses.

It is not that submission itself is a problem.  We submit all the time to forces beyond our control.  Recruits into any army are trained to submit to the orders of their superiors.  Employees in any corporation are expected to submit to the instructions of their bosses.  When we fall in love we submit to the demands of another.   But always within some norm of reason.

In all these situations, free will is involved.  And at any time, that free will can interfere and lead us to resign from an army or an employment, or to fall out of love.  The submission is tempered by known contractual terms

The contract with Islam does not permit a withdrawal from its terms.  Submission is absolute and permanent.  Anyone who subsequently resigns from the faith, is labelled a heretic.  Other religions have labelled once believers as heretics and tortured them to "encourage" them to return.  None have claimed the right to kill such unbelievers in quite the way that Islam does.

Similarly the apostates are treated as less then worthy, treated with extreme contempt for which the extreme unction of termination is considered the only justifiable resolution.

I dont care what your faith is, and I will defend your right to believe whatever you want.  But don't let it interfere with my right to do so similarly, whether it pleases you or horrifies you.  Most likely, if you are threatened by my beliefs, or in my case, my non-beliefs, then it seems to me that you lack confidence in your faith yourself.  If your beliefs are solid, then no other person or faith should be able to shake them.  A reaction to condemn heretics, is evidence of your lack of confidence in what you believe yourself.

Again, I dont care what your faith is.  But, if your faith is in a non-existent god, then you are wrong to have that faith.  And if that is an insult to your God, then your faith is singularly weak.  If you have submitted to a non-existent entity, then you are fooling yourself and all to whom you promote the idea.  Unless and until the faithful can provide the incontrovertible evidence of such an entity -- and I doubt they ever will, I will continue to be a sceptic in all matters of religion.

On why I'm taking a biochemistry course

I am fascinated by the fact that DNA works.  I am fascinated by the idea that chemistry and physics are intimately involved in how it works.  I want to know more about why and how the apparently most important chemical in our bodies works.

When I was at school, my best subject was Chemistry.  Yet I specialised in physics.

Physics teaches that there is an immutable set of laws that govern the behaviour of all matter.  These laws govern the miniscule, the infinitesimal and the macro scale of our universe.  One of those laws, talks about all things being local.  Nothing exists on the grand scale, except through the local interactions of matter, the electrical and atomic forces that exist on different atoms and molecules, the spins of molecules, and the multidimensional folding of chains of atoms.  The local interactions extend upwards through the emergent systems of larger scales.  But those emergent systems only exist because of the underlying chemical and physical properties of matter.

A chemical law that emerges from the underlying physics is that all inter-matter dependencies rely on the exchange of energy.  Chemical reactions can be exothermic or they can be endothermic.  Often, reactions exist in some kind of equilibrium, where a continuous exchange of energy (thermal and chemical?) results in a stasis, an apparently static arrangement.  Maybe there is energy in the environment that varies and changes the nature of the stasis.  As the environmental energy levels change so does the equilibrium point of a chemical reactions.

Lastly there is the fundamental law of physics, that of Entropy.  Everything is going to slow down, and lead to the ultimate energy death of the universe.

How does DNA operate in such a way not to violate these laws?  What are the basic mechanisms of cell biology that enable the cell to function?  When scientists talk about DNA generating enzymes that influence behaviour on an organism level, what is the basic energy equation that enables this to occur and then to continue to occur?  When a mitochondrion delivers a molecule of ATP how can it do that?  What “benefit” does the mitochondrion receive in return?  What is the energy gradient through a cell, that enables transport through a cell and then beyond its membrane?

How does DNA function over distance?  What is the driving force that leads to its replication?  Why and how?

Everything else flows from that.  Evolution, human society.  It all depends on the mechanisms, physical and chemical, of DNA.

Whether a study of biochemistry will reveal answers to these questions remains to be seen.  Maybe the study will show that I am asking the wrong questions.  Whatever the answers, I am taking an undergraduate course in biochemistry.  There may be other ways of doing this, but the idea of getting a degree in the subject is appealing, now in my retirement.