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.


2077 novel: buy & preview options + reviews


see also
 Natural technology: the bacterium

Evolution IS progress

Project GENOME turns junk DNA into treasure

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Tuesday, 10 February 2015

Free will and the limits of science: a reflection

There is a lot of talk among neuroscientists about whether science shows we have free will.

Every sane person knows we have free will and does not consider it to be an illusion. If you were an automaton  without the power to make a decision you would not even be aware of the concept of free will. It is part of what it is to be human. If science ever shows we do not have free will it can only mean that scientific methodology is dealing with a small fragment of a greater multidimensional realm and consequently cannot be right about every aspect and dimension of reality.

Conversely, if science proves we do have free will it will tell us little about its true nature because free will must originate from outside of the deterministic order (within 3 dimensions of space and 1 of time) which can be investigated by logic and experiment. Its true nature lies in a greater multidimensional reality outside of space and time and in some way connected to the self-existential source beyond nothingness from which all reality emanates and originates: God.

The circular arguments of materialism concerning the nature of consciousness and free will arise from an anachronistic mindset, a dualistic mind vs matter thinking that has grown up over the few hundred years since the Renaissance. The latest discoveries in quantum physics, the objective evidence for a soul operating beyond the brain, 

e.g. out of body experiences in which previously unknown objects are reported on by the subject and visual NDEs by people blind from birth

the emergence of the universe  from outside of space-time and the growing awareness that even the universe we have deduced  is over 95% inexplicable, all point clearly to a greater reality than any 19th century materialist could ever have envisaged.

Did mind come from matter or matter from mind? Descartes maintained they are totally unlike each other. So neither does mind cause matter or matter cause mind; they may simply be twin aspects, very different aspects, of one underlying fabric of a realm beyond rational investigation.

So science itself deduces its own severe limitations. Nevertheless it has served us well by revealing at least some of the wonders of the part of creation we know about and allowing us to develop useful technologies beyond the dreams of only a century ago.

Science and technology have been  superb servants of humanity. The danger today is that some want them to be our masters, with the scientists acting almost as priests. In 2077 science and technology are definitely servants in helping defeat violence. At the same time  the SSS cult uses them to achieve evil. Ultimately the battle of good against evil can only be won by human will in a state of humility before our Creator.

John Sears

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Thursday, 5 February 2015

Biomimicry: city design, textile colouring and much else

Water Wall
One approach to keeping the biosphere evolving in a sustainable way is to concentrate on new and existing cities and aim to give them the same ecological footprint as the terrain they cover. It is in cities that over half the world population lives and there seems to be a general consensus that this proportion will continue to increase.

Making a city fit into its ecological niche is much easier for a new city: it can be designed from scratch to store water and emit gases (cabon dioxide, oxygen, water vapour etc.) in similar quantities to, say, a deciduous forest as well as sustain a small amount of local flora and fauna within its boundaries and not cause local soil erosion or pollution.

Some 400 new cities will be needed, for example, to help accomodate the rapidly growing population of India, so it is important to get the design principles right. The methods developed could to some extent be applied retrospectively to existing cities and urban sprawls throughout the world.

A pioneer of biomimicry of cities is Janine Benyus who is working with her colleagues at the Biomimicry Guild and with large corporations such as Walmart, Nike and Interface. Currently she appears to be working with HOK, a large architectural developer, on two major projects: one to build a city from scratch in India and one to retrofit an existing city in China.

What I find encouraging is that after her book Biomimicry: Innovation Inspired by Nature was published in 1997 Benyus was approached more by business leaders than by green activists.

Biomimicry is much broader in scope than city design and involves mimicking nature to achieve more efficient, ecologically sound technology.

 For instance, most butterflies wings only use one pigment, a brown one(?): all the other colours are produced by their microscopic surface structure which reflects and refracts light in a similar way to the droplets of a rainbow. The textile industry is now beginning to colour some of its fabrics this way, so that pigments and dyes don’t have to be used. This should reduce pollution while at the same time providing scope for striking optical effects in the fashion business.

Further examples of how nature offers engineering solutions (these are just a few out of thousands):
  • The abalone, an ear-shaped shell with a pearly interior, generates an inner shell twice as tough as the best ceramics.
  • Diatoms (unicellular algae with silica impregnated cell walls) make glass from seawater and require no furnaces.
  • Spiders manufacture silk as strong as Kevlar (used in bullet-proof vests) and tougher, but without boiling sulphuric acid or high-temperature extruders. Digested crickets and flies are the only raw materials.
  • Trees turn sunlight, water and air into cellulose, which is stiffer and stronger than nylon, and bind this into wood.
  • Snake inspired robots imitating the snake's body shape and movements. E.g. remotely controlled hose for fire fighting.
  • New type of cement based on coral chemistry.
  •  Boat hulls based on shark skin design for hydrodynamic efficiency and reduction in papasite growth.
  • Painless hypodermic needle is being developed which is inspired by the way mosquitos bite
  • Bullet train with a beak inspired by the design of a Kingfisher's bill. This avoids noise pollution when the train emerges from a tunnel.
  • Camouflage researchers are copying the way this is done in nature, e.g. by the octupus.
  • Air conditioning inspired by the air cooling in a termite nest by complex porous surface that generates airflow through the tunnel.

 Certain strains of algae when deprived of sulphur produce hydrogen by photosynthesis instead of oxygen. R&D on this is has been pursued at the Argonne National Laboratory (US Department of Energy) and if successful the hydrogen could be used for fuel cells. Strictly, this is the modification and exploitation of a biological system  rather than mimicry. The economic and sustainability implications would be enormous.
Biomimicry and adaptation of natural systems could do a lot to give us a more sustainable, cleaner and more attractive environment and provide fulfilling employment as the western economies try to escape depression.

 God/nature has provided us with a gift and it would be ungracious/stupid to refuse it.