Friday, 27 February 2015

Are some scientists from the planet Vulcan? (In honour of Leonard Nimoy)

I first published this post in 2011 but am republishing it now in honour of the passing of Leonard Nimoy who played Mr Spock in the original Star Trek series. As a keen viewer since the 1980s I have come to feel like an old friend of the missionaries on the Enterprise as they spread western ideals of love, foregiveness, justice and respect throughout the Galaxy - though never daring to mention the ultimate source of these.

 Mr Spock was often teased or rebuked by his crewmates for not understanding aspects of reality that could not be deduced or induced by logic. Love and affection, for instance, are not logical and therefore should not be acted upon. Presumably, being from the planet Vulcan, Mr Spock was not familiar with Goedel’s Incompleteness Theorem, published on Earth in 1931 under the rubric Formally Undecidable Propositions of Principia Mathematica and Related Systems I.

According to the Oxford English Dictionary Goedel’s Incompleteness Theorem states that ‘in any sufficiently powerful, logically consistent formulation of logic or mathematics there must be true formulas which are neither provable or disprovable’.

Separately, the Oxford Dictionary of Philosophy entry on this theorem states the following: The implied moral is that truth in some way outruns provability, at least when that is considered formally.’

This theorem is a landmark in philosophical and mathematical logic. It proves that a scientific theory of everything is inherently impossible and, by implication, we have to go to something transcendental to connect with a greater truth than that reachable by logic alone (important though logic is). What is staggering is that some cosmologists and theoretical physicists of high intelligence persist in ignoring this theorem, often, it seems in a fruitless attempt to pretend there is no creative agency behind the universe. Are they aware of the theorem or is it they don’t understand it or is it just that they don’t want to know?

Unlike scientists, mathematicians on the frontiers of computer technology are forced to adhere to it because it is a powerful tool in gauging the computability of certain mathematical functions.

For an excellent and clear account of Goedel’s world shattering theorem and its implications click here.

Finally, a disclaimer – I am not a mathematical logician or professional philosopher. I am not even intelligent by any conventional measure. However, I am interested in a lot of things and persistent and as one who believes in God I am committed to truth.

Friday, 20 February 2015

Microbiology: our changing perception of nature

Recent developments in the field of microbiology (see below), together with advances in epigenetics, horizontal gene transfer by viruses, fungal networks and quantum biology, contribute towards a perception of the biological world very different from that of a selfish-gene-driven machine. Increasingly it is seen to be an intricately interconnected ecosystem with purposeful evolution of immense complexity. The protein coding gene is only 1% of the human genome: the rest is an unfolding mystery. There is miraculous engineering, organisation, data transfer and decision taking from the macroscopic to the microscopic. Whether it is a tropical rain forest or  biochemical pathways within a cell, the characteristic that stands out is one of systems cooperating to produce new systems of larger functionality.

Results of the Human Microbiome Project

A 5 year study involving 80 research institutions and funded mainly by the US government has sequenced the genes present in the bacteria, fungi and viruses, collectively known as microbes, present in and on the human body. Here are the main results as reported in Focus, August 2012, p.12 and The Economist, August 18, p.62-4.
  • The human digestive system alone has 100 trillion bacterial cells, which is 10x the number of body cells and weighing a total of about 1 kilogramme. NB: bacterial cells are typically only about 1/50th the volume of a human cell, which normally has a diameter in the range 5-40 microns. In all the human microbiome contains 3 million genes compared to the 23,000 of the human genome.

  • There are 10,000 different species of bacteria, viruses and fungi which reside on the skin, on the palms, in the nose, intestines, throat, hair and vagina, behind the ears and in other places.

  • The colony present in a person is unique to that person and the variation between people is very large. Despite this variation there are a core set of functions common to all.

  • Disease lies dormant in almost everyone. Pathogens are present all the time and do no harm until for no apparent reason they go on the attack. E.g.: heart disease, diabetes (both 1 and 2), multiple sclerosis, eczema and asthma. Conversely, they can also protect the body from infection, as with clostridium difficile (severe diarrhoea etc.). This arises when antibiotics kill off the beneficial bacteria.

  • The bacteria in the gut breaks down food that cannot be broken down by the digestive enzymes produced by the body, turning it into vitamins. Surprisingly, the gut bacteria varies substantially from person to person yet the function is the same.

 Expanding on this last point, complex carbohydrates are turned into formic, acetic and butyric acid. These are then  passed through the walls of the gut into the bloodstream where a miraculous biochemical pathway converts them into energy or layers of fat.  10-15% of the energy used by an adult is provided in this way.

See also more recently a post dated 17 February 2015 from the Scientific American
 'Microbes in our gut are essential to our well being.'    

The March 2015 issue of Focus has as its cover story ‘How Bacteria change your mood.’

Antibiotic resistance

 The prevailing dogma has been that bacteria mutate in response to modern antibiotics, until they become resistant. No doubt there is some truth in this, although my understanding is that the actual mutations are far from random. But a much wider picture is emerging. It now appears that bacteria present in the biosphere some 4 million years before modern antibiotics were invented were already resistant to them. In other words when ever a new antibiotic is launched on the market the chances are that somewhere on Earth there is a bacteria which can beat it. This will have big implications for drug research and evolutionary theory.

The evidence for this came to light in the discovery of bacteria present in the Lechuguilla caves in New Mexico. These had been isolated from human influences for 4-7 million years. Of those that could be grown in petri dishes over 70% were found to be resistant to antibiotics.


It may be that antibiotic resistance to any conceivable antibiotic is present in bacteria somewhere in the biosphere and it is only a matter of time before it finds its way to a patient under treatment. If so, the effort should be focused on  more robust ways of treating infections.

Possibly complementing this finding there is recent evidence that resistance to penicillin, sulfonamide and tetracycline is present in soil bacteria. See

I am sure there is much more going on in biology than I can possibly keep track of or comprehend but I hope this gives you a taste of just how much our understanding of the biosphere is evolving.

author, 2077: Knights of Peace
see also
 Natural technology: the bacterium
Evolution IS progress

Project GENOME turns junk DNA into treasure

Reach me

Wednesday, 11 February 2015

The Doctrine of Chance: the New God of the Gaps

Image result for chance diceHear the Doctrine of Chance adhered to by post-Enlightenment unreasonable man,
expressed in Psalm 151  (There are 150 Psalms in the Holy Bible.)

Listen, all ye who are able to hear...

  • The universe of space, time and energy emerged from nothingness as a Big Bang about 13 billion years ago with all its laws of physics and physical constants in place to permit life.
          Why? Chance.
  •   The universe started with precisely the right balance between order and chaos to allow the galaxies, stars, planets and life itself to evolve.
         Why? Chance.
  • The universe was destined to evolve in an ordered, directional way, from a point to the structured expanse we see today.
          Why? Chance
  • The physical constants which govern the cosmological expansion rate, the strength of gravitational, nuclear and electromagnetic forces, and much else, were fixed at the time of the Big Bang and are fine tuned to a hair’s breadth to make biological organisms possible. E.g. the constant governing the strength of weak nuclear forces is fine tuned to 100 decimal places. Had these constants been slightly different there would be no life.
         Why? Chance.
  • The 92 elements of the periodic table were progressively, systematically manufactured over billions of years, mostly in stars, and all these were needed to build the world we know today. The human body alone has 60 of these.
         Why? Chance.

  • The sun is 400x the diameter of the moon and 400x the distance. In the sky they look identical in size. This allowed the sentient beings of Earth to witness solar eclipses not possible anywhere else in the universe we know about, thus stimulating our curiosity and allowing us to discover helium via spectroscopy of the sun’s atmosphere before it was found on the Earth.
          Why? Chance.

  • The moon is just the right mass and distance from earth to spin stabilise its axial rotation and provide smooth, rhythmic tidal movement, both instrumental, if not crucial, to life’s evolution.
         Why? Chance.

  • The information-rich, staggeringly diverse biosphere emerged out of a chaotic and unpleasant environment over some 4 billion years.
           Why? Chance.
  • The sky on Earth is clear enough to allow its sentient beings to see the universe and be inspired by it. As telescopes were invented it became apparent that the universe was vast beyond previous imaginings and that our rare position in the galaxy enables us to see the universe right back to its centre and origin.
          Why? Chance.

  • The Earth has the axial tilt, orbital characteristics, rotational stability,  temperature, plate tectonics, size, mass, oceans, magnetic field and atmosphere which allowed life to get a hold and evolve
          Why? Chance.
  • The Earth is so placed in the solar system as to be shielded from comet bombardment by Jupiter, from frequent asteroid bombardment by Jupiter, Mars and Venus. Other planets are not so protected.
           Why? Chance.

  • Over the 4 billion year history of the Earth mass extinctions due to volcanoes and impacts have allowed evolution to proceed to sentient, cosmos-aware, curious beings.
             Why? Chance

  • If life had not started at this place and this time in the universe it could not have started anywhere else. All the evidence points in that direction (it is rarely mentioned).
             Why? Chance

  • The Earth’s surface is protected from life damaging cosmic rays by its magnetic field (the Van Allen Belts) and from ultraviolet sunlight by the Ozone layer. Other planets are not.
          Why? Chance.

  • Life was miraculously complex and intelligent from its very beginning as bacteria only a few hundred million years after the Earth was created around 4 billion years ago.
         Why? Chance.

  • Humans consisting almost entirely of energy configurations in vacuum, as do all apparently solid entities, have come into being able and thirsting to delve into the manifold secrets of the universe and the nature of their own being.
          Why? Chance.

  •  Water has unique chemical properties essential for life and Earth had enough to host early evolution.
          Why? Chance.

  • Water expands instead of contracts as it is cooled the last 4 deg C above freezing point, while still in liquid form. Without this expansion the oceans would now be solid ice and the planet would be largely, if not wholly, lifeless. No other liquid has this property.
         Why? Chance.

  • Water is transparent at the same wavelength as the yellowish sunlight which illuminates the Earth, thus allowing undersea creatures to see around them and evolve their vision systems. (Any other colour of sunlight would have rendered undersea vision impossible or much reduced.)
         Why? Chance.

  • Sentient beings with eyes perceive the universe and so, in a sense, bring it into existence, with themselves at the centre except by theoretical construct (4D model of space-time).
          Why? Chance

  • Life over billions of years evolved a rich and benevolent biosphere, a Garden of Eden into which Homo sapiens emerged a few tens of thousands of years ago. The intelligence and creative power to make the biosphere were there, presumably, from the first bacteria.
         Why? Chance.

  • Homo sapiens have a highly developed sense of self, a rich imagination, hands able to finely manipulate and write, a vocal system suitable for sophisticated communication, intelligence to make tools, the ability to heal and care for the sick, the desire to do this for both humans and animals, the ability to grow crops and farm livestock, the ability to make computers,  a relentless curiosity about  origins and destiny, the ability to explore other celestial bodies, the desire to do this, an inbuilt conscience, free will and the ability to choose between good and evil, and a sense that there is life after physical death.
         Why? Chance.

The writer of Psalm 151 would like to apologise to the Great Random Event Generator in the Sky lest he hath overlooked in his ignorance any other marvellous examples of Chance.

1984: collective post-modernism

Infinity, eternity and cosmology

Author, 2077: Knights of Peace