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

SEE ALSO   FACEBOOK PAGE



reach me at
cosmik.jo@gmail.com

Monday, 19 January 2015

Hold on to the Truth, not the Theory of Everything

While there is life there is hope...
The film Theory of Everything sounds as though it will be moving to watch, probably inspirational. It ought to be since Hawking is admirable for his will power in overcoming the limitations of his illness and using his powerful, creative mind to explore the limits of human knowledge. However, one has to bear in mind that a human being can only go so far. Recent science and philosophy shows that a real theory of everything is untenable - mainly because the 'everything' that such a theory would need to describe would include itself - a logical impossibility.  

I understand that Hawking himself has come to accept this since writing A Brief History of Time. Having abandoned this quest he seems to have become less than rational in his understanding of reality, as I hope to demonstrate below. He is not alone and I contend that the approaches of some theoreticians to the limits we are now coming across in trying to explain properties of the cosmos like fine tuning for life and the emergence of space-time (Big Bang) from existential nothingness are bizarre and unscientific, and arise from an understandable but needless fear of resorting to a god of the gaps.


Science is precious not only as a voyage of discovery but as the source of the prosperity of western civilisation through engineering, agriculture, transport, hygiene, and medicine, and more recently of other parts of the world which have followed its methods. But it needs guarding.

Recently I read a timely criticism of the way science is reported in the popular press and interpreted by society at large (Bad Science, by Ben Goldacre). The cover blurb lists scaremongering journalists, pill pushing nutritionists, flaky statistics and evil pharmaceutical corporations.  Most of these distortions of objective truth come from outside the scientific establishment, threatening it with commercial or grant-related pressures.

Yet there is another enemy of academic research, in my view more insidious. It comes from the academics themselves.

In the 14th century the priest William of Occam proposed a concept which has been religiously followed by scientists to this day and is a cornerstone on which the exponential ascent of Western science has been built: Occam’s razor : a new scientific theory should explain the greatest number of phenomena for the least number of assumptions.  A theory which satisfies this criterion and which can be experimentally verified is deemed one step closer to an objective truth for which scientists strive, knowing that they will never reach it, but that what counts is the constant search for it.

There has also been a belief in the sacredness of truth. Professor James Lovelock, who professes not to be a religious man, recently referred to it as the ‘Holy Ghost’ of truth. In a BBC Beautiful Minds documentary Lovelock related how a prominent neo-Darwinist (Richard Dawkins) had bullied the editor of Nature into suppressing his now widely acclaimed ideas on earth systems science, later known as Gaia. In March 1995 Dawkin also purportedly pressurised the editor of the Times Higher Education Supplement into not publishing a commissioned article, already trailored to appear in the next edition, since it attacked neo-Darwinism. See the Open Society and its Enemies. Such practices risk turning the foundation of science into sand and undermining the  power of peer reviewed academic publishing.

At the time the Big Bang theory of cosmology was first proposed Fred Hoyle (a leading astrophysicist and cosmologist at the time) opposed it in the face of mounting evidence, simply because he thought it implied the existence of a Creator. Instead he proposed a steady state model in which the universe was eternal and atoms just spontaneously appeared in the vacuum. A definite case of letting one's beliefs get in the way of truth.

The Grand Design by Stephen Hawking and Leonard Mlodinow (2010) is a well written guided tour of modern elementary particle physics and cosmology which I found absorbing, if taxing in parts. I can certainly recommend this as a way of updating one’s understanding.

However, it resorts to post modern metaphysics, namely the abandonment of objective reality, the basis on which physics, chemistry, biology and engineering is built:


'Though realism may be a tempting viewpoint, as we'll see later, what we know about modern physics makes it a difficult one to defend.'

[22% through the book on my  old iPhone Kindle app]

Even special relativity theory acknowledges an objective reality and works out by mathematics (the Lorentz transformations)  how time, space and mass will seem to observers moving at different relative speeds. All its equations are verified by experiment. Quantum phenomena are difficult to pin down and very odd; e.g. in the famous double-slit experiment a pattern appears on a screen hit by particles according to whether one determines or does not determine the paths by which they arrive (NB: the experiment is so designed that measuring the path does not physically disturb the particle). This is no basis for abandoning belief in an objective reality: the challenge is to modify our models of reality, i.e. get a bit closer to the ultimate reality,  until we get some powerful model which incorporates those happenings which at present do not appear to make sense. Lightning did not make sense before the concept of electricity was devised and if you have ever had an electric shock you will know that the concept of electricity corresponds to something real.

Instead, Hawking (who other physicists disagree with)   throws out objective reality, adopts unsound mathematics (e.g. subtracting infinities from infinities) and makes non sequitur extrapolations from bizarre pictorial interpretations of a mathematical tool (Feynman’s ‘sum over histories’ method) for calculating the probability of a quantum event and links this to cosmology on the grounds that our universe probably started as a quantum phenomenon. The authors give up on trying to explain rigorously what they call our ‘apparently’ miraculous universe, which they admit is fine tuned for life to an inexplicable degree, and avoid the need to do so by postulating an unimaginably large number of other universes (10 with 500 zeros after it; there are 'only' 10 to the power 80 atoms in the whole universe) with laws loosely defined by a network of string theories collectively called M-Theory, and an arbitrary number of dimensions (11 instead of the 4 we know: 3 of space and 1 of time; why not 10, or 99, or 100, or 1000 or any number you can think of?) ), all as much beyond scientific testing as Santa Claus. How such a monster assembly ever came into being is not mentioned.

This approach explains nothing and everything. If we observe a new unexplained phenomenon there is no need to delve into it, invent a radical new approach and laboriously come up with a rigorously peer reviewed theory. Just say it is there by chance and was bound to happen in some universe somewhere. Suppose someone found that viruses on earth were spontaneously assembling in synchronization with fluctuations from a black hole. No need to explain. It just happens to occur in our universe. No surprise! If it had not started we would not be here to see it.

William of Occam must be turning in his grave, as must Newton and Einstein.

Science has reached an  impasse. Quantum phenomena like the double slit experiment, quantum erasure and entanglement have been modelled in several different ways, none of them sufficiently established to serve as a consensus theory. Attempts to unify the 4 forces of nature (electromagnetic, gravity, weak nuclear and strong nuclear) are in disarray, as appears to be indicated by the Large Hadron  Collider results. Even if a Unified Theory is achieved it will only be a theory of certain aspects of reality, not a Theory of Everything.

Cosmology is also confronting questions over inflation, the holographic principle (by which  our 4D space-time world would be the encodement of a 2D world), dark energy, dark matter, vacuum energy and much else. Over 70% of the stuff of the universe is a complete mystery, as is the way both ordinary and dark matter is orchestrated. All we know is that something is there and that some phenomena occur which can be predicted and modelled.

 Neo-Darwinism, though still having something to offer in terms of micro-evolution, struggles to come to terms with increasingly sophisticated mechanisms of macro-evolution, e.g. epigenetics, horizontal gene transfer, emergent complexity, sudden leaps forward in speciation and evolutionary convergence, which do not fit well with  blind adherence to evolution by descent with random incremental modifications. For some reason these increasingly compelling new findings in evolutionary biology are not getting into BBC science shows such as Horizon yet they should be embraced, not brushed aside. I have not yet come across a major science programme which stresses the importance of the recent discovery that the 98% of DNA referred to as junk only a decade ago is now accepted as being crucially functional. Recent discoveries showing that evolutionary pathways repeat themselves indicate that the mechanism of evolution is not random. Again, barely a mention in the popular science media.

When confronted with the inexplicable it is surely the job of the scientist to find new more powerful models, not retreat in denial or in order to satisfy some favoured view or ethos or ideology or metaphysical view or theology, or just to get career advancement or funding or the approval of the press or one’s friends.

 It is of course impossible to eliminate these worldly influences but, whether one is a scientist, an interested layman (like me) or just one who wants the world to go on advancing in a benevolent way, one can at least try to hold on to scientific truth as an ideal.  Science is not, I maintain, the only answer to human fulfillment; but it is a God-given gift without which human progress stops. We descend into chaos with no prospect of a peaceful, prosperous life in the material world.

 John


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
To contact me email
cosmik.jo@gmail.com