Tuesday, 27 January 2015

Natural technology: the bacterium

image credit: https://ufhealth.org/anaerobic-bacteria

The simplest form of life – a single-celled organism such as a bacterium – is made up of 10 million million atoms. Cells within the human body are at least comparable in structure. They form a system immeasurably more complex than anything artificial, comprising a hierarchy of integrated subsystems and architectures using thousands of different proteins, their actions orchestrated in some inexplicable manner.

In his book The Way of the Cell (Oxford University Press, 2001,  p.329) Franklin M. Harold compares it to a high tech factory comprising

  • Control mechanisms regulating the automated assembly of parts and components

  • Software languages and their decoding systems

  • Memory banks for  information storage and retrieval

  • Quality control systems with error fail-safe and proof-reading

  • Assembly processes involving prefabrication and modular construction

Each one of these functions requires intelligence, decision-making and information exchange to an extraordinary degree and the whole organism responds and adapts to the external environment in a purposeful way. Moreover, the entire mobile factory has the ability to self-replicate in a few hours.

A bacterium is an example of a single-celled organism. To get a better idea of the scale of the engineering task solved by nature consider just one part of a bacterium: the propulsion unit. This is a microscopic propeller for driving the bacterium through a fluid. The propeller takes the form of a whip made of a protein called flagellin, which is why the whole propulsion unit is called a flagellum.  

The flagellum is about 2 microns in length and is powered by a motor only 1/5th this size. It can spin at 10,000 r.p.m. and stop the spin in only one quarter of a revolution and instantly start spinning in the opposite direction. Connecting the flagellum to the drive shaft is a hook protein which acts as a universal joint which allows the propeller and drive shaft to rotate freely. The drive shaft penetrates the wall of the bacterium with the aid of a bushing material comprising several types of protein and connects with a rotary engine which gets its energy from the flow of acid through a membrane, itself a complex process yet to be understood. Altogether, the flagellum comprises over thirty different proteins. (This is based on an interview with M.J.Behe reported in a book called The Case for a Creator by Lee Strobel.)

If any one part were missing the whole power unit would not work and each subunit would be useless unless connected into the whole system. A bacterium or any single cell is packed full of complex subsystems like this and they all have to be integrated and choreographed for the bacterium to work.

 Bacteria are incomprehensibly numerous (not surprisingly, given that most of the natural world is incomprehensible in the way it is organised and interrelated). Each person has 10 times as many  bacterium cells as cells in the body-brain system, i.e. 100 trillion vs a mere 10 trillion. They reside mainly in the gut and skin. On the planet as a whole their biomass exceeds that of all the plants and animals put together. The total number is estimated at 5 x 10power30 (5 followed by 30 zeros). Placed end to end they would stretch thousands of millions of light years into space. This may seem difficult to believe - but check with a mathematically inclined friend  or do the calculation yourself.  Let me know if he or she gets a different answer!

What I had not realised until recently is the extraordinary efficiency of the DNA base-pair coding to achieve such a complexity of functions. It does not seem to have much to do with the amount of the coding. The simplest forms of life sometimes have more DNA than a  human being. Evolution  is about creativity and efficient problem solving using minimum resources. Competition between life forms for resources is a factor, but only a factor. In order to compete a biological entity must first be viable.

 Bacteria were around very early on in the history of our planet –  some  5% of the the way through its 4.3 billion years. So the facile answer that it was evolution 'what did it' won’t wash (i.e. the 'evolution of the gaps' argument, by analogy with the 'god of the gaps'). I believe there is evolution and has been since the universe began – but that’s a description, not a causative mechanism. I picture it as the Creator, who is outside space-time, painting a work of art, experimenting creatively, intelligently, as the cosmic masterpiece unfolds, with each atom, star and organism falling into a tapestry. To us it looks like a progressive sequence of events.

Regardless of their recognition of the existence of a Creator I believe that some biophysicists are already looking into the possibility of intelligence entering our universe through quantum phenomena. If it proves to be the case it will be revolutionary indeed.

See also

Natural technology: the virus

The passive gene


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Wednesday, 14 January 2015

ET life: what are we looking for?

To search for extra terrestrial life we need to understand what life is. Until we know what it is we cannot expect to know how it started and if we don’t know how it started we can’t define the conditions needed for it and so do not even know what conditions to search for beyond our own planet, let alone recognise life if and when it is encountered unless it happens to be life as we know it....

What is life? The mystery remains. Biologists, chemists and physicists can never answer this question. All they can do is describe observable phenomena which accompany it. The reason becomes apparent when you consider the nature of any known organism from a virus to a blue whale.

At any one instant it is a wonder of finely balanced stasis or equilibrium, a mind bogglingly complex hierarchy of structures, substructures and superstructures, from those observable with the unaided eye down to the tiniest, detectable only by electron microscopy. All of them functional and crucial to the whole. Occasionally we come across a structure which appears to be unnecessary but is later found to be highly functional (e.g. ‘junk’ DNA segments have recently been found to be at least as functional as genes).

All these structures comprise atoms and each atom is all space. Even the elementary particles which make up electrons, protons and neutrons are probably vibrating configurations of concentrated energy (follows from string theory, apparently). But let’s assume such particles to be purely solid matter. It nevertheless remains true that if the entire universe, filled with trillions upon trillions of stars, were crushed down until all such particles coalesced into one continuous solid, the result would be equal in size to a sugar cube.

So an organism at a particular point in time and space is a snapshot of a seething, vibrating configuration of energy in empty space – ghostly and ethereal rather than solid. Even if you stub your toe on a rock the pain you feel is a sign of reconfiguring and interacting energy fields.

All forms of life (e.g. you or me or a rhino or a frog or a bacterium or a virus) are observed to be reproducing, growing or dying. Yet the atoms which make up an organism are being shuffled and  moved and reconfigured in space-time continuously, even when the organism does not show visible signs of change (e.g. all the skin on your body is renewed completely every 28 days, including spots and blemishes). And this marathon of organisation and re-organisation continuously adjusts to the changing world of whatever the organism is a part, which is not only the surrounding environment but, in the last analysis, the whole universe. It is comparable in one sense to the way a candle flame maintains its shape and thermal properties despite the fact that its constituent atoms and molecules are continuously being changed.

What is death? This could be the result of the sustaining creative agent of life ‘deciding’ that the organism has completed its role. Once this happens the daily plethora of mutations are no longer repaired and illness follows but the sustaining creative agent …. This is the essence of life, the source of free will and order, the eternal life which continues after biological death. It is not disease which causes death. It is the cessation of the life principle which allows disease to develop unchecked that results in death. In a sense, the onset of death causes terminal illness.

(An illustration of our ignorance on the life question is that of speciation. How does a new species form? There are over 16 different  definitions of speciation in the scientific literature, or so I understand. Forgive me if I don't count them!)

It requires a massively unimaginably super-intelligent directing agent to create and recreate and repair and control and organise and dispose of and pass on these energy systems which comprise every creature or plant in the biosphere, whether or not this is confined to earth or not. One cannot begin to conceive of the nature of this orchestral conductor. Whatever it is, this agent, it also ensures that each organism is coordinated with all the other organisms that make up the biosphere.

That is the nearest we can get to defining life. So far we have encountered biological life as carbon-based systems and it is not possible within the boundaries of logic and proven physical principles to have any other form of biological life. There are only 90 stable naturally occurring elements in the periodic table (and 2 more which occur naturally but are not stable as well as a few which don’t occur except fleetingly in particle accelerators like the large hadron collider). No other elements could exist anywhere, except for a fraction of  second, because they don't have a stable atomic structure and observations of stellar and interstellar spectra confirm this. Carbon is the only element having an electron shell structure (which determines valency) permitting it to combine with other atoms in a  sufficiently versatile way to permit the life principle to bring about biological organisms.

In fact even restricting ourselves to carbon-based life we have no idea how it started or what drives it so we can’t define the conditions needed for it to begin or flourish. All we can do is look at Earth and say that certain conditions accompany life. But this is complicated by the fact that life depends on life and the environment, the Earth’s ecosystem and even its geology. (E.g. it has recently been shown that plate tectonics is lubricated by clay layers formed by living organisms, yet plate tectonics, unique to Earth,  is necessary for the maintenance of life because it is needed to cycle carbon around the biosphere. So plate tectonics affects life and life affects plate tectonics.)

But how would we detect anything else but carbon-based biological life? The invisible and undetectable organising agent which is the essence of biological, and perhaps spiritual, life, is here on earth amongst us but beyond detection and analysis. 'It' could be universal. It may be love, sustaining and directing and building and destroying the galaxies, black holes, dark matter, stars, planets, meteors, comets, asteroids, interstellar gas and every conceivable manifestation of life. Ot it only shows itself in some form recognisable to us when it chooses. It could even be from outside of our 4D reality, i.e extra dimensional.

Biological life appears on our planet accompanied by extraordinarily unique panoply of conditions. Even the solar system and Milky Way Galaxy seem precision engineered to permit a stable, life-friendly environment on Earth. Every new exoplanet discovery makes it seem increasingly unlikely that any of the billions of planets in the universe harbour advanced, sentient beings. 0% of an infinite number is zero. If there is other life to be discovered it may require mystics and priests rather than teams of SETI (Search for Extraterrestrial Intelligence) scientists to sense its existence and allow us to relate to it, while science restricts itself to what can be learned about how the natural world operates at a level detectable by scientific investigation within our 4 dimensional reality.

A challenging and noble task in itself.

John Sears
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Sunday, 11 January 2015

The story of a canned drink

It is customary to drink beer, Coke, lemonade etc. from an aluminium can. Given the convenience of storing and transporting the drink around this is not surprising (although personally I have a tendency to snap off the ring pull, leaving the can sealed). However, there is a price to pay for this convenience when one considers the enormous amount of energy and environmental destruction that goes into the production of a pop-top alumimium can.

Womak and Jones in their book Lean Thinking tracked down the manufacture of a can of English cola (presumably fairly typical of most canned drinks. The data is from the 1993 book but the overall picture is still essentially the same.)

  1. Bauxite ore is mined in Australia and trucked to a chemical reduction mill.
  2. At the mill each ton of bauxite is purified to half a ton of aluminium oxide in half an hour.
  3. The Al oxide is loaded onto an ore carrier bound for roller mills in Scandinavia.
  4. In Sweden or Norway the Al oxide is taken to a smelting plant. Each half ton is smelted down to one quarter ton of aluminium, which is converted into 10 metre ingots.
  5. Each ingot is heated to 480 deg C and rolled down to a sheet 30 mm thick. The sheets are wrapped in 10 ton coils and transported to a warehouse.
  6. The coils are transported to another country for rolling down to 3 mm sheets.
  7. The Al sheets are sent to England for punching and forming into cans.
  8. The cans are washed, dried, and base painted. Product information is then painted on.
  9. The cans are lacquered, flanged, sprayed inside with protective coating, loaded onto pallets, forklifted and warehoused.
  10. They are then shipped to a bottler where they are washed and cleaned again.
  11. After filling with cola pop-top lids are added at the rate of 1500 cans per minute.
  12. The cans are inserted into cardboard cartons made of forest pulp originating in some other part of the world (e.g. Siberia or British Columbia).
  13. The cartons are shipped to a distribution warehouse and finally to the supermarket.
This leaves out the production and transport of the drink itself. In the case of the English cola drink this involves mining phosphates from deep open pit mines in Idaho, USA; refining this to food grade; and shipping caffeine from chemical plants abroad to a syrup manufacturer in England.

All these production and transportation steps use up energy, sometimes huge amounts – e.g. the conversion of the mined phosphate to food grade uses electricity at the same rate as a town of 100,00 people. The metal used also defies belief. Even after allowing for recycling the USA ‘throws away enough aluminium to replace its entire commercial aircraft fleet every three months.’ Natural capitalism by Hawken et al, 1999.

Other examples from Hawken et al :
  • Semiconductor chips generate 100,000 x their weight in waste.
  • A laptop computer produces nearly 4000 x its weight in waste.
  • 1 quart of Florida orange juice requires 2 quarts of gasoline and 1000 quarts of water to produce it.
Should we feel guilty when our lifestyle is so dependent on these things?  Partly, but we are trapped in a greed-driven multinational system which is kept afloat by crazy accounting which ignores the real world. To change that system, one which ultimately must lead to war, is our only option. Either from top down or bottom up, or both at the same time, it has to change; and that means people themselves have to change both individually and collectively, and at all levels of society.

As one who believes in our Creator I think this can only only happen by getting closer to the one who created us.  Reason is of paramount importance; but reason alone is not enough, as was learned at the cost of millions of lives and decades of misery by the disciples of Marx, Engels, Lenin and Mao Zedong.
Feedback welcome.