Biological Strength of Spirit?

I read today that what can only be described as a group of geniuses in Illinois has been quietly making amazing discoveries about the molecular processes involved in DNA, including the fascinating field of epigenetics.

The DNA contains four different nucleic acid bases, called Adenosine, Cytosine, Guanine and Thymine, or ACG and T.  C and G bond together, as do A and T, making the rungs of a long and beautifully coiled ladder of data.

This vast two-dimensional storage system only a few atoms wide (if an atom were a grain of sand, the smallest visible object would need to be at least 4 metres wide) is twisted, coiled and supercoiled repeatedly to such an extent that the collections it forms, the chromosones, become visible through a microscope.

Cytosine

The field of epigenetics deals with a newly discovered layer of meaning superimposed on the DNA itself.  Epigenetic processes seem to be influenced by the experiences and lifestyle of an individual, and leave markers which can survive for many generations – the effects are so long lasting in successive generations of laboratory animals that some researchers believe the markers laid down can’t be turned off.

Methylated cytosine

These processes don’t change the arrangement of the letters, but instead, they can change one of the base molecules – usually cytosine, sometimes adenosine – by swapping one of its hydrogen ions to a more complex methyl group.  It’s as if they swap a capital letter instead of the same letter in lower case.  The 4-character information remains the same, but the changed letter is read differently by the other equipment in the cell.  Therefore while the DNA remains intact, the proteins which it is supposed to make can be switched on or off.  Up until recently, it was thought that this was the main extent of changes caused by “methylation”.

DNA in the grip of methyltransferase (DNMT1)

Above you can see the little molecular machine grabbing the DNA, finding the right sequence and adding a methyl group to the cytosine.   Now, you may well ask, from where do those little machines come from, that is, where are their designs stored and how are they assembled?  How should I know?  I’m only a programmer!

This process is almost always carried out to cytosine bases lying in the sequence:

CG
GC

So as both DNA strands have a cytosine, both strands will be converted with a methyl group. When the DNA is replicated, each of the new DNA double helices will have one old strand, complete with methyl groups, and one new strand, which is not methylated.  But all the machinery has to do is find such a group, and apply the modification to the cystine on the other strand.  Impressive though, for a machine which can’t see and doesn’t seem to have any kind of a memory in which to store its instructions.  What makes it act the way it does?

How to measure the forces need to break apart strands of DNA (http://www.ks.uiuc.edu)

Well, who knows – or to be more precise: it’s a hotly debated topic at present.  But now to the real story: the catchily-named Theoretical and Computational Biophysics Group did a rather clever thing.   By trying to break apart strands of DNA before and after methylation, they proved:

..a role of methylated DNA physical properties needs to be reconsidered as a direct epigenetic control factor. We found through novel and extremely extensive force measurements comparing non-methylated and various methylated DNAs that methylation affects the propensity for mechanical DNA strand separation to a significant degree.

This means that methylation doesn’t just accent the language of DNA, it makes the DNA itself stronger – tougher to break apart – which is important because your DNA, much like your wealth or your beautiful girlfriend, is subject to constant break-ins or attempts to rip it off altogether.

Yes, even on the molecular level there are crooks and predators on the make.  What a neighborhood!  Some attacking machinery from bacteria tries to splice in their own, alien, DNA into ours to mess up the activity of our cells.  So any process which makes the DNA stronger is a boost to our immune systems.

It took some pretty strong DNA to turn this Carrera marble into Moses. I think the horns were a misinterpretation of the Aramaic or Hebrew. But nobody wanted to tell Michelangelo that

It may well be that the resistance some people have to disease is a direct result of epigenetics.  Perhaps the susceptibility to addictions in materialist societies is a result from weakened genetics.  It is striking that in the last days of the Raj, virtually all the male children became alcoholics, something hardly seen before.

Perhaps the races which have had to cope with slavery and oppression by raising their spiritual values in non-violent protests have also increased the resilience of their DNA.  It is true that African Americans led the way in practically all sports, once freed from the chains of slavery.  Perhaps the well researched but otherwise inexplicable tendency of families with strong moral backgrounds to produce men of genius is because of beneficial changes to the DNA by virtue of, well, of virtues – if so, perhaps virtues and vices, far from being arbitrary and meaningless concepts, have biological reflections of their own.

Of course, making statues to preserve myths doesn't suit our advanced civilisation today. Cardiff, the capital of Wales is well known across the UK for its vibrant nightlife

Anyway, it is already known that positive attitudes can defeat the onset of infections or improve the recovery time from illnesses.  From this, and in the light of The TCBG’s work, it’s not much of a leap to suppose the epigenetic system to be closely tied to our emotional state, and an important part of the biology reflecting our strength of spirit.  And to all, a good night.

…………………………………………………………………………………………………………………………

Next week!  How to make this amazing bit of machinery for uncoiling knots:

DNA Gyrase from E.Coli is an enzyme which helps untangle, un-knot and relax supercoils in its DNA. It does so by binding to a strand of DNA, cutting both strands and then, while keeping hold of both cut ends, passing another piece of double stranded DNA through the gap. It then reseals the double stranded break.

Essentially it allows portions of the large circular bacterial genome to pass through itself, to prevent knotting and entanglement. A number of antibiotics (e.g. Simocyclinone D8) target this enzyme, since it is essential to the organism’s survival. Humans also have a form of this enzyme but its construction is different and we are thus not affected by the antibiotics.

(http://beautifulproteins.blogspot.com/)

Posted in biology, Cytosine, Designs in nature, DNA Methylation, Epigenetics, Genetic damage, Human genome, Materialism, Nanotechnology, Natural Intelligence, Proteins | Tagged , , | Leave a comment

Judging the Fabric of Society: the Buddhist Amygdala

“The amygdala pervades the organisation of thought and behaviour at all levels.”

Ralph Adolphs, expert on emotion, memory and social cognition, California Institute of Technology

“By attuning the brain to all manner of threats and pleasures.. the amygdala helps to confer emotional significance on a wide range of experiences. The amygdala helps to give life meaning.”

(David Dobbs, Scientific American)

While trekking in Nepal in the 1970′s, Colorado businessman Adam Engle was so impressed by the warmth and compassion of the Buddhist lamas that, with the late Franciso J Varela, a neuroscientist and Buddhist practitioner, he later co-founded the Mind & Life Institute in Colorado, “to see if we can bridge the gap” between science and spirituality. (Scientific American Mind, Feb/Mar 2006, p40)

Dalai Lama - image from www.mindandlife.org

They have a blog with some very interesting posts, including this one about an 8 week meditation program which shows measurable changes in brain regions associated with memory, sense of self, empathy and stress.

In a study that will appear in the January 30 issue of Psychiatry Research: Neuroimaging, a team led by Massachusetts General Hospital (MGH) researchers report the results of the first study to document meditation-produced changes over time in the brain’s grey matter.

An expert in facial expressions and emotion, Paul Ekman, found that Buddhist lamas were able to correctly interpret facial expressions “much faster and more accurately” than thousands of other people he tested over the years, including lawyers, policemen and judges.  It thus became apparent that meditation strengthened the parts of the brain dealing with the recognition of emotion, and this has a huge implication for the fabric of our society.

How important is the innate ability to discern truth?  Last week a woman who had been a suspect in the murder of her six year old son has been cleared by new evidence – after twenty five years.   On closer inspection we see the evidence was there all along, but was  completely ignored by the legal experts:

Nicholas Loris, 6, was found strangled to death 150 yards from his Davidson County, N.C., home on Feb. 21, 1987.

The Forsyth County Sheriff’s Department credited new technology with helping them to clear Elizabeth Watkins’ name and determine that her son’s cause of death was a dog attack.

“Not only has she been exonerated but the weight from the last 25 years has been lifted from her shoulders,” Watkins’ attorney, David Freedman, told ABCNews.com. “It means everything to her.”

Spending the past 25 years as a suspect cost Watkins a relationship with her older son, who went to live with his father after she became a suspect, as well as the burden of search warrants, DNA tests and always wondering what really happened to Nicholas.

In partnership with the FBI, investigators were able to use new technology to blow up photographs and determine that the claw and scratch marks on the boy’s body came from a number of medium-sized dogs. Nicholas died from strangulation after the dogs pulled his clothing tightly around his neck.

“Once investigators were able to see the wounds up close, they were able to see they were consistent with a dog attack,” Freedman said.

Bill Schatzman, Forsyth County Sheriff, announced at a press conference Thursday that Watkins had been exonerated and the case was officially closed. (ABC World news)

It’s a shame these emotional cripples were unable to recognise a bereaved mother’s emotions.  I can barely imagine the trauma of a mother losing the son she gave birth to, then being accused of his death, and as a result abandoned by her only other son, and then having to live under this shadow of grief and blame for a quarter of a century.  Leaving aside the imbeciles who failed to spot signs of what must have been a ferocious dog attack on a young boy, I cannot accept that any judge should be incapable of distinguishing grief from guilt.

A Texas man declared innocent Tuesday after 30 years in prison had at least two chances to make parole and be set free - if only he would admit he was a sex offender. But Cornelius Dupree Jr refused to do so, doggedly maintaining his innocence in a 1979 rape and robbery, in the process serving more time for a crime he didn't commit than any other Texas inmate exonerated by DNA evidence.

Carrillo, 37, served 20 years but was released from custody on Wednesday afternoon after a judge overturned his 1992 conviction for the drive-by shooting that left one man dead. Witnesses later recanted their testimony, and a dramatic reconstruction of the shooting raised doubts about whether it would have even been possible to identify Carrillo as the shooter.

James Harden, 36, was freed after serving nearly 20 years in the Menard Correctional Center for the 1991 rape and murder of 14-year old Cateresa Matthews, in Dixmoor, Illinois. One of five men, Harden was only 15 years old and suffering with severe learning disabilities and unable to read when he signed a confession that led to his lifetime behind bars.

After eight years on death row, Ryan Matthews was found innocent and freed in 2004.

There are so many cases to choose to show how little interest the legal system has in its clients that it’s hard to know where to start.  The problem seems to be a preconceived notion which infleucnes all subsequent interpretations, no matter the evidence which may refute the original, prejudiced conclusion.

Studies have shown that meditation has both short-term and long-term effects on various perceptual faculties: consider the Poggendorff illusion, in which the black line broken by the vertical shape seems to be continued by the blue line.   The error is caused by the brain translating the shift from left to right without taking into account the amount of vertical movement:

In 2000, Tloczynski et al. studied the perception of visual illusions by zen masters, novice meditators, and non-meditators. There were statistically significant effects found for the Poggendorff illusion (above). The zen masters experienced a statistically significant reduction in initial illusion (measured as error in millimeters) and a lower decrement in illusion for subsequent trials.

“A person who meditates consequently perceives objects more as directly experienced stimuli and less as concepts… With the removal or minimization of cognitive stimuli and generally increasing awareness, meditation can therefore influence both the quality (accuracy) and quantity (detection) of perception.”

In other words, the amygdala, properly trained in meditation, tends to recognise truth rather than reacting along preconceived lines even in emotionally neutral optical illusions, where sheer mechanical judgement is required.  So the skill has nothing to do with enhanced trust or naiivete.  It even increases one’s mechanical accuracy. Nowhere is perception of truth more in demand than in law enforcement and the judiciary.

It has long been known that the large number of coloured people convicted of crimes in America, especially in the South, is largely because of racial prejudice amongst those in the court system.  But even so,  it is hard to believe the sheer neglect of duty and disinterest than in the case of Ryan Matthews:

Ryan’s trial lawyers  had only met Ryan twice during their preparation. They never discussed the facts of his case with him, what he knew about the shooting, or asked him what he was doing that night. They didn’t know that he had a half-brother in a wheelchair who had been shot in the back.

They had never been to the scene of the crime or spoken to the eyewitnesses who couldn’t identify anyone at the time of the shooting but managed to identify Ryan years later, never stressed to the jury the significance of the fact that the DNA in the ski mask worn by the killer was not Ryan’s, never talked to the guy who’d been boasting in prison about killing a white guy in his store, never found out that the boastful guy was in prison for manslaughter, never found out that his DNA matched that inside the ski mask.

In short, they never believed they were representing an innocent boy, though his innocence would later be proven.

(Shauneen Lamb, Guardian)

This shocking disability is bad enough in an ordinary person but inexcusable in brains responsible for discerning truth, yet the legal system seems to thoroughly perpetuate it.  How many cases of innocence are revealed after decades, because of new forensic or DNA tests?   Our professionals concern themselves with legal formalities and lose track of their own senses, just as it has been found that using SatNavs disable the brain’s own spatial mapping abilities.  Could it be that using a crutch weakens one’s legs?  Can such things be?

We have shrugged off the responsibility to discern truth for ourselves and fobbed the job off to experts, and they, in turn, to their machinery.  It’s much easier to absolve ourselves of blame and point to a tedious legal precedent.   Behind this freakish display of stupidity can only be an under-functioning brain, perhaps overloaded by bookish learning but also, damaged by attraction to the financial rewards of the legal system itself.  It seems one can be seriously interested in truth, or in money, but not both.

What kind of mind gravitates to these positions of power to decide on the fate of mortal men?  Cherie Blair is a case in point – an extremely wealthy professional who seems to have given up ethics for the sake of money – a process also known as prostitution:

“The press pounced on an embarrassing episode when she was fined for fare dodging after jumping on a train to Luton, where she was due to sit as a magistrate.” (BBC)

“Most people have difficulty seeing themselves as others see them, but there is something almost psychopathic about Cherie Blair in this respect: she has reached absolute zero when it comes to self-irony or self-knowledge. She tells us that she’s “a good Catholic girl” while detailing her premarital as well as postmarital sex life. She retails offensive tittle-tattle about the queen and other members of the royal family, calling Princess Margaret “a stuck-up old slapper.”

“She goes on at length about her deprived childhood in Liverpool while insisting, “I have no problem with saying I am a socialist.” She then whimpers about the terrible difficulty of repaying a $6 million mortgage on the London house they acquired when Blair was still prime minister—and on top of which they’ve just bought a beautiful country house, formerly Sir John Gielgud’s, for nearly $8 million. (Geoffrey Wheatcroft, Slate)

“Cherie Blair presented the cash-strapped Labour Party with a £7,700 bill for the services of her personal hair stylist during last year’s general election campaign. As Labour struggled with outgoings so large that it had to resort to secret loans from millionaires to stay afloat, Mrs Blair made the party pay £275 a day for a month to keep her hair in shape” (Times)

“On an official trip to Australia, she went shopping at a designer clothes showroom. In what might have been a scene from Supermarket Sweep, she left with 68 items worth £2,000 after being told to take “a few things” as gifts.” (Telegraph)

There is plenty of evidence that materialism damages mirror neurons, the basis of empathy, and it seems also to affect the performance of amygdala.  In fact the whole sensitiv eorgan of the brain seems to come under attack from wealth and privilege, which is why all religions have emphasised an indifference to wealth, and to loss of wealth, focusing instead on the development of the personality, that is, the brain.

The latest statistic show the number of giraffes in the world have nearly halved since 1988 from over 140,000 to less than 80,000. Hunters pay up to a whopping £10,000 for the the chance to slay them - preferring bulls because they are the biggest. The hunts typically last three-to-five days and see tourists using .458 Winchester Magnum rifles to kill the animals. With most hunters flying to Africa from their homes in Europe or America, the costs stretch into five figures (Daily Mail)

From Ekman’s professional evidence we see that meditation’s effect is to make the brain much more sensitive to truth.  In the case of materialism, we can infer that the separation of the personality from the needs and emotions of others results in an inability to detect the truth, and even a complete disinterest in it.   Therefore truth is inextricably linked to sensitivity, which is why sensitivity is so necessary among those who practice any kind of art, as the instrument they are sharpening and enhancing is their own brain.  Fleeting impressions pass equally across all minds, but detecting their significance relies on the sensitivity of the brain.  The qualities of meaning and of truth are not arbitrary as militant atheists would have us believe, and nor are they items of convenience for survival, but as absolute as light and dark are to the eye; the difference perhaps being that we can sharpen the brain to those contrasts, or dim it altogether.

Spiritual practices therefore are not an escape from the world, but a deeper investigation into its reality.  A greater ability to synthesise an otherwise confusing mass of details to form conclusions shows the brain’s potential to be not a greater storage of facts, as commercial education would have us believe, but the greater detection of truth and meaning which those facts represent.

Last weekend my daughter and I went to a small exhibition in Cambridge in which I think the most beautiful painting was a Vermeer called the Lacemaker.  It is known that Vermeer’s model in most of his pictures was his devoted wife Catherine (together they produced eleven children); their love seems as much a part of the portraits as the paint itself, judging by his sensitivity and the patience with which she modelled for him.  Vermeer came from a protestant background, and Catherine from a Catholic one, which seems to have been overcome by the fondness for him of her mother, and perhaps even his conversion to Catholicism.

Amygdala at work?

In contrast to the pretence and deception which people will go to any lengths to avoid, meaning, and its corollary, truth, is what they will go to any lengths to pay homage to – which explains the popular exhibition and the two hour lineup to get in.   In this tiny portrait, Catherine is completely absorbed by her craft, and become one with it; the tiny threads, one vibrating slightly under tension could as well be nerves, so fine are they and so central to the whole activity.  This extraordinarily sensitive picture could only have been rendered by an artist who understood this absorption only too well and with it, pay tribute both to their bond of affection, and to the creative act itself.

It is said that children bring to our mind the nature of their parents; the Vermeer’s children and their works may have long been lost to history but the colourful alchemy between mother and father has survived, carefully preserved for 350 years to pay tribute to the power of the sensitive brain.

The painting’s background is unusual for Vermeer, lacking finely-observed detail of walls, tiles and beaded glass windows.  Instead, perhaps in a burst of inspiration, he abandons realism altogether to leave the weave of canvas practically bare, the fabric sustaining Vermeer’s art in the same way cloth and thread underlie the lacemaker’s.

There are other paintings of the Dutch period which excel Vermeer’s in realism and grandeur, but the many layers of subtle contexts in this tiny work seem to show that people are not attracted by realism and pomp as much as they are by meaning, reflected from a brain sympathetic to their own.  What survives the centuries seems to be that which means most to the human heart: that which has meaning.

Posted in Amygdala, biology, Brain damage, Brain Hygiene, Buddha, Buddhism, Dalai Lama, Detachment from materialism, Genius, Intelligence, Intuition, Jan Vermeer, Materialism, meditation, Meditation, Natural Intelligence, Science and Religion, Spiritual Genius, The Brain | Tagged , , , , , | 6 Comments

The Persistence of Spiritual Vision: the Symbols of Jack Kirby

1. Humanity’s heritage: Symbolic thought

I’m 71 years old.. I used to read the first science fiction books, and I began to learn about the Universe myself and take it seriously.  I know the names of the stars.  I know how near or far the heavenly bodies are from our own planet.

I know our own place in the Universe. I can feel the vastness of it inside myself.  I began to realize with each passing fact what a wonderful and awesome place the Universe is, and that helped me in comics because I was looking for the awesome.  I found it in Thor.  I found it in Galactus.

Jack Kirby, 1988

There are very strong arguments which rely only on logic.  Christopher Hitchens’ claim that we help others not because of the dictates of a God – which might implicate us as incapable of reaching that conclusion on our own – but because we depend on others to make our Earthly experience as positive as possible, indicates that the intellect is capable of putting people before self interest.

In debate with Sam Harris, Hitchens was asked: on what do you base the value of your life, if there is no transcendent God to serve?  His answer was that he had spent his life trying to be free, and trying to help others be free.  There is no argument, whether rational or religious, which can discredit such a view.

Kirby's inspiration for the Hulk came from a news story of a mother who lifted tha back of a car to save her son trapped underneath. "I feel we all have this ability, to transcend our limitations, in times of crisis."

If one abides by the Biblical saying “do unto others as you would have them do unto you” or  “whatsoever ye do unto the least of all thy brethren, that do ye also unto me”, they must see that a human life can be amply justified by service to others, and that such a life embodies a genuine spiritual impulse, no matter the nature of its justification, just as a harmful act such as a punch in the stomach, easily condemned on humanitarian and logical grounds, cannot be justified by using religious ones instead.

Paradoxically, even someone who does not believe in a spirit can create what can only be defined as a spiritual outlook.  Their anti-theism is their private business, and might be understandable if based on characterisations made in ancient religions.  Perhaps denial on those grounds supposes archaic concepts to be the very limit of the field, and if so, one could quite fairly criticise medicine, physics, astronomy, plumbing, marriage, business and table manners on the same basis.   But since ancient symbols must have been limited by the evolutionary capacity of their day, it would be more sensible to construct a platform of protest in the light of modern thought, taking into account recent discoveries in biology, neurochemistry and epigenetics, and their effect on genius and creativity.

To be a complete refutation and not be mistaken for ignorance, idle or mischievous speculation or a quick opportunity for self-puffery, it should also include their own experience with meditation, without which it must be impossible to form any kind of opinion about the subjective experience of concentrated thought acting on the brain.

Jack's lettering from Prize Comics, circa 1949

Each language is a specialised collection of symbols created so intangible thought can be communicated.  As we can imagine, early languages must have given way to more complex ones as the brain evolved.   Religious symbols fulfil much the same function, for an area of thought inexpressible in any other way.  The remarkable thing about languages is not that all are different, or that their forms change over time, but that they evolved independently, and arose not from any external pressure, but to express something internal to the evolving human brain.

It’s surprising to find we humans cannot form an accurate mental picture of greater than about a dozen objects.  So the racial brain working through genius has produced symbols – numbers – which are not objects themselves, but an agreed code enabling us to share these otherwise unmanageable ideas.  We are alone in conceiving such symbolic thought; some primates can be taught a certain amount of it but do not develop it independently, which makes clear the giant leap made by us at some point in the distant past.

Kirby and Simon were the first to bring the romance genre to comics, with Young Romance (1948)

Such symbols began about 8000 BC to represent sheep and other goods, followed around 3000 BC by a further, significant, abstraction: the quantity of these goods represented as symbols in their own right.  Such ideas represented leaps which we take for granted now, but which could only arise from individuals prone to thinking things over and coming up with inspiration: in fact the modern function of humans as teachers to primates might mirror this early, slow process of development between the forward thinking types and the ordinary, slow moving minds of their day.

A very early work from around 1941, in which wisdom is passed from generation to generation and death referred to as "the long sleep"

Spiritual symbols must have predated such elements of trade by a huge distance.  The animism of the Aborigines is supposed to date from 60,000 years ago, the Aurignacian cave paintings (presumed to have more than just decorative purpose, as they are found in inaccessible caves not used for habitation) about 32,000 years and I believe the temple of Gobekli Tepe is reliably dated to about 12,000 years ago.

The ennobling effect on the mind of elegant, overwhelming spiritual symbols was understood by Kirby, and used as a sign of an emotionally sophisticated society. The same conclusion was arrived at by James Watson in his book "DNA", when evaluating the significance of Neandertal funerary rites

We know that 200,000 year old burial sites in Africa show evidence of funerary rites; the Neandertal also developed these rites, and their race dates from 600,000–350,000 years ago, and we know such beliefs existed at least 300,000 years ago.  It would hardly make sense for early man to suddenly develop abstract ideas which changed only slightly over the next 300,000 years, especially when a much more evolved specimen took at least five thousand years to go from symbolic objects to symbolic quantities, so it seems reasonable to believe that religious beliefs and the language to articulate them could easily have emerged as long as half a million years ago.

Therefore if we agree that order in time correlates to order of fundamental importance, the spiritual symbols must have been of huge importance to society, followed only much, much later by a systemised set of symbols encoding objects and their quantity.

Kirby also understood that an image of a God must have an overwhelming, inspiring impact on the mind. "I don't know if there's an ultimate, or where the ultimate lies. Possibly I'm not equipped to answer that question. But the question intrigues me. I feel it intrigues everybody. Like with everybody, it's a question of faith. That whatever the ultimate is, I have to have faith that it exists. And of course, the hero does, too; otherwise he would never lay his life on the line."

The vast gulf needed to be crossed to assimilate these concepts can be appreciated by the five thousand year gap which apparently exists between symbolic representation of objects and the much harder abstraction of their symbolic number.  Bonobo apes have been taught to communicate using symbols but the additional learning required to conceive of organised agriculture for the purposes of trade, the concept of payment values to purchase other goods, as well as the assessment of integrity of character of the trader, are vast, vast leaps into the future.

http://www.ted.com/talks/susan_savage_rumbaugh_on_apes_that_write.html

Symbolic thought is, without doubt, one of humanity’s most precious and hard-earned evolutionary steps, and those who can manipulate symbols with agility are powerful influences on the rest of us.

Kirby's elegant characterisations from the 1950's hit, Boys' Ranch

In well-attended debates where atheistic opinions are based on logic alone, resting a defence of religion on a recollection of ancient events is of dubious worth, and also a little pointless, just as the value of medical science cannot be reckoned by referring to its murky origins or courageous proponents living centuries ago, but by benefits and facts which are to hand today.

If these audiences are polarised into two camps attracted by two completely different things, as if watching the brute force of Hulk Hogan compared to the golden voice of Shirley Bassey, then small wonder that nothing is ever resolved convincingly: each side walks away feeling much the same sympathies as before, and perhaps a little puzzled by the failure of two intelligent minds to somehow communicate the truth of something they both feel so passionately about.

Early Kirby work in partnership with Joe Simon. The fluid lines and dramatic shading were all self-taught under pressure, as were the anatomy and storytelling technique: Kirby's colleagues insist that he never once used an eraser. "Someone told me once that using an eraser just wasted time. I couldn't afford to waste time - I had to make a living." The gangsters and their molls came straight from his childhood

If one can justify humanitarianism by logic, one should also be able to justify spiritual beliefs by present day knowledge.  If not, there is no point in debating.  Convincingly resolving the question of God is perhaps for distant generations.  The biology which is somehow already in motion must be the thing which concerns us the most, along with what we can do to affect it, just as a driver speeding over a collapsed bridge thinks not about its architects or the technical drawings for his car, but where the brakes are!

Kirby borrows a chair from Patrick McGoohan's TV show The Prisoner, to characterise Victor von Doom

2. Misunderstanding the persistence of religious faith

“We all have a kind of feeling that I think we’ve had for thousands of years, that there are higher beings somewhere.  I think all our spiritual feelings stem from that.

The truth is that the Greeks had Hercules, even as the Norsemen had Thor, and through the ages we’ve had heroes similar to them, who’s no more than a superhero.  And today, we have our superheroes: we believe in them because we believe in ourselves.”

But before you wonder why this blog isn’t just called Science and Science.com, the idea behind this post is a much stronger proof of the persistence of spiritual beliefs.  Richard Dawkins once claimed in an interview that religion is perpetuated solely because children are indoctrinated by their parents, who then indoctrinate their own children, and so on.  This idea has become blithely repeated ever since as a criticism of religion, but it shows a complete failure to think, and thereby reversing the accusation altogether, as well as explaining why such minds find this argument entirely credible due to their own failure to think.

The tendency to listen to one’s parents was attributed by Dawkins to a natural selection in which those who did not listen – for example, rebels who disobeyed the urging to avoid snakes or the edges of cliffs – did not tend to survive.  According to Dawkins, it was not religion so much as the tendency to obey authourity figures which was the genetic foundation of religion’s persistence.  This idea supposes that rebels are generally so liable to catastrophe that they die before procreative age and therefore should have been eliminated over the course of tens of thousands of years, producing a docile race of sheep unable to think for themselves.

How does a thinking man propose a theory so completely at odds with observed fact that to refute it, one hardly knows where to start?  The urge to discredit religion seems so great that essentials like simple logic, observed evidence, and even common sense are all desperately jettisoned like hampers of food from a hot air balloon plummeting to the ground.

"I realised I had to find with something new..I couldn't depend on gangsters forever. And so for some reason I went to the Bible, and I came up with Galactus. And there I was, in front of this tremendous figure, who I knew very well, because I always felt him in my life, and I knew I certainly couldn't treat him the same way I would have treated any ordinary mortal character. And I remember in my first story I had to back away from him, in order to resolve that story... of course the Silver Surfer is the fallen angel: when Galactus relegated him to Earth, he stayed on Earth, and that was the beginning of his adventure."

It is only the mentally sturdy rebel able to conceive and energise inventions and advances, corrections to restrictive systems, and resultant changes in society’s direction; therefore, far from being the type found bitten by snakes at the foot of cliffs, he forms the quick-thinking engine of all historical progress.  And since every development is, for a time, a rebellion against the norm, its adoption by the mass mind requires a kind of intuitive faith in the rebel, further accenting the strength of his perceived character – as we can see from the development of symbolic thought.

Whatever symbols, concepts, forms and institutions which have arisen and survive today, are solely down to this class of men.  Without them, man would follow the same direction as the animal world, and our social forms would remain static for millions of years.  Instead, in evolutionary heartbeats, we see a constant drive for change accompanied by colossal jumps in understanding.  In fact it seems as if change is part of man’s mental makeup, and it is the biological urges – eating, sleeping, romance and procreation – which remain constant, and in some cases vary little from the animal world, perhaps as a reminder of our origins.  So while man remains in some way imprisoned by his biology, his mental abilities are his true heritage, and they are free to grow: no one can say where they would lead us as a race.

Metron of the New Gods reaches the end of the Universe, and finds those who tried to broach it came to a sticky end

Another fact so obvious that it should never need pointing out to a champion of evolution is that, apatr from the reforming rebel, it is the willfully disobedient youngsters who account for most – if not all - illegitimate births today, and probably all through history too. These individuals tend to have more partners because the sacrifices and discipline required by pair bonding is not for them, and they must therefore produce the largest number of genetically varied offspring in geographically separate areas, giving their traits by far the most chance to survive.  I know one such free spirit who has a child in England, one in Vancouver, one in Toronto, and one in Egypt; for all I know he may be working on a fifth.

If natural selection were a genuine shaping force – and it clearly isn’t – then common sense tells us the race would be comprised mainly of irresponsible, non pair-bonding individuals by now.

When I created the Silver Surfer and Galactus it came out of a Biblical feeling. I couldn’t get gangsters to compete with all these superheroes, so I had to look for more omnipotent characters.
I came up with what I thought was God in Galactus; a God-like character.

Still thinking about it in the Biblical sense, I began to think of a fallen angel, and the fallen angel was the Silver Surfer. In the story, Galactus confines him to the Earth, just like the fallen angel. So you can get characters from Biblical feelings.

Still another unavoidable fact is that teenagers all go through a stage of rebellion, questioning the dictates of parents, for the simple reason that they must develop the ability to reason for themselves; this mental development and eventual merging with the complexities of wider society is why the childhood of a human being is by far the longest in all the animal kingdom.  As soon as we call a mammal human, even a prototypical human, this period of rebellion is guaranteed.  Not all will go as far as getting a child by the age of 13, but they will question the parents to re-evaluate their ideas, as surely as a toddler entering the “terrible twos” will reflexively answer “no” to everything you suggest.

But why stop at examples of individual behaviour?  A recent experiment which flatly contradicts the idea that religion is propagated by the sheepish took place in Communist Russia – perhaps you heard of it?  The experiment involved hundreds of millions of individuals, in which three or perhaps even four generations were forbidden any exposure to religion by the sternest authority of the state, with ferocious penalties for those who disobeyed.  Without membership of the Communist Party, one could not even own an apartment in a crumbling block.  Dissent was dealt with by imprisonment or the reverse of natural selection ..by a natural Siberian exile.

If religious faith were a simple matter of obedience to parents, these beliefs should have been gladly jettisoned if only to avoid exclusion from society.  In the Soviet Union it would be impossible for any child born after about 1925 to have any idea of religion as an acceptable outlet; still less for one born in the fifties and sixties.  Not only did the country remain separate socially from others, the government’s influence was so all pervasive as to affect every nook and cranny of daily existence. This experiment was as complete and as ruthless in efficiency as it could ever be possible to orchestrate.

By reviving the Norse Gods, as imagined by Kirby, Marvel Comics introduced something new to popular culture. In fact, they were advised that youth would not buy it - yet it became one of their biggest sellers, especially on campus

But no sooner did the Soviet Union fall than the churches in Eastern Europe sprang back into life, lovingly restored to a state exceeding their former beauty. To give you a taste of the Russian mentality: when Stalingrad was surrounded in WWII, the citizens swore no German would set foot in their city.  The Nazi blockade meant starvation set in, alongside constant bombardment.  The city did not fall.

Residents eventually boiled wallpaper to make some thin kind of starch soup, and slept under dozens of layers of cloth and blankets to survive the subzero temperatures.  Death hovered around every doorway. A few gave way to cannibalism, betrayed by their rosy faces and good health.  But these were the exceptions.  The city survived under the harshest and most sadistic pressure.

An imposter posing as Ben realises he must sacrifice his life for another, to atone for a life of jealousy and hatred

These were not latte-sipping, ipad-tapping, cosy armchair scoffers and caviar conoussieurs.  These were a people possessed of an inflexible iron will and indifferent to suffering, to whom all else came second to their patriotic pride.  For this reason, WWII is known in Russia as the Great Patriotic War, a war in which at least 40 millions lost their lives.  When they see programs showing how Britain claims to have won the war, they literally fall silent with astonishment.  So either the religious minds which survived generations of war and repression in secret were the sternest and strongest of all, or, if you prefer, those minds which gravitated to religion only after the fall of the USSR must have been expressing the most hardy, perennial, and captivating sentiments of the soul.

Either way the phenomenon of spirituality, or the mental fabric which dresses it to give form to its ideas, by that I mean religion, has nothing to do with external pressure from family or society, nothing whatever to do with sheepish weakness, and nothing at all to do with escapism.  The urge remains intact because it is generated internally. You could no more remove it from the mass of mankind than you could eliminate the urge to procreate, using banners, leaflets and threats.   Such an idea only seems viable to those who are the spiritual equivalent of eunuchs, and by their own condemnation of a healthy instinct in others, they reveal the startling lack of it within their own selves.  Their childish diatribes against those of simple faith serve to further amplify the warning signs emerging from their own twisted and dissonant personality.

As a matter of fact the sole reason the Communist experiment failed – a reason greater even than the corruption which ate its way throughout the entire structure – was because the ordinary human being was denied a choice of thought.  This state of being is so repugnant to human nature – not surprisingly since, as I have easily shown here, freedom of thought is man’s only true heritage and marker of evolutionary progress – that the amassed resistance was enough to topple a regime so callous that an estimated forty million people were also sent to die in slave labour camps for their crime of free thought.  This staggering statistic is never taken into account by those seeking to criticise religion on the grounds of sheepish continuation because it makes their argument seem puerile and stupid, but there seem to be no other words to describe it.

Kirby's X-Men were based on an extension of the idea of evolution: genetic mutations developing superhuman powers

All these examples show that a propagation of religious faith solely by external pressure is a nonsense, and in any case something which experience of everyday people shows would be an impossibility.  Religious faith seems to be an internal concept limited only by the capacity of that particular mind to which people return, as readily as they do to that source of infinite warmth, the sun.  The variation in forms shows an evolutionary capacity of the mind and the widespread acceptance of each shows the large numbers which simultaneously achieved that particular level.

The widespread and simultaneous resistance to oppressive regimes today in middle east countries, among populations which meekly accepted such dictatorships without protest for ages before, shows the same tendency.  The evolution of mass consciousness is the evolution of the brain, and it is expressed in man’s symbols.  The gifted individuals able to create and manipulate appealing symbols are gifted with an insight into the mind of society at that level of evolution, and they serve an important evolutionary purpose.

3. Spirituality in symbols: the creative life of Jack Kirby

“I don’t know what spiritual beliefs are comprised of.  I only know that I have senses.  And I bring them all into play.  I don’t know what these senses are.. I cant define them.  All my senses are hidden from me.  but they move me…”

But examples of populations in countries we have never visited and can only dimly sense the character of might still be unconvincing.  So the subject of this post is a man who, more than any other single individual, contributed to the visual language of 20th century story telling by the force of his personality, the courage of his convictions, and by sheer genius.  This man is Jack Kirby, one of the true heroes of 20th century America.

It is telling that in the Magic of Reality, Richard Dawkins speaks of his amazement as a child, on being told about the pending arrival of “our train”, at his interpreting this to mean the train actually belonged to his family.   Similarly, Christopher Hitchens’ mother once declared, “if there is going to be an upper class in thic country, Christopher is going to be in it.”  These benevolent conditions were fateful, as they propelled both individuals in to the forefront of academia and social influence from the very beginning.  It is no wonder that their ideas grew from a position of security.

The young Jack Kirby could never have had such delusions: whatever he would have in life, he had to fight everyone else for, from the very beginning.

Kirby gets to grips with microcircuits a decade or so before their use in electronics

At the turn of the 20th century, immigrants flooded into New York from Europe.  Those with family already in America might have followed routes out towards the farmlands of the mid-west or the west coast; those with nothing but the clothes on their backs stayed where they landed, in New York.  They had no other choice: and there were vast numbers of them.

Among the huddled masses yearning to be free who arrived probably around 1913 were an Austrian Jewish couple – Benjamin Kurtzberg and his wife.  Settling in the poorest, cheapest, and most densely crowded slum in all of America’s history, “the couple endured some of the most abject conditions that overpopulation and neglect had ever contrived anywhere.. with 1500-1800 people crammed into a single block” (Mark Alexander, The Wonder Years).  But Benjamin found work in a garment factory, and his family produced two children, the first of whom, Jacob, was born August 28, 1917, later attending elementary and Hebrew school in PS 20.

Kamandi was Kirby's vision of a post-apocalyptic Earth arising from man's inability to manage his technological powers. The animals, meantime, had developed larger brains and complex societies, while man had degenerated back to prehistoric mental levels

My father was Conservative. We were never Orthodox, but we were Conservative. I went to Hebrew school. It was above a livery stable, the Hebrew school.

Until the day I die I’ll never forget that wonderful table we used to sit at. Hebrew school was a rough place. An airplane flew over one day and I ran over to the window and everyone was pushing and shoving each other, and some guy really shoved me out of the way — I knocked him clean out.

I was about 12. Because I wasn’t bar mitzvahed yet. They had to pick him up. But I was so eager. That was such an innovation to hear the sound of the motor of an airplane flying overhead. I just had to get there in front. I was attracted by everything that seemed to be new and advanced.  I saw the Time Machine.

(Interviewed by Gary Groth)

Jacob showed early promise in art, sometimes angering the landlord by sketching over the corridor walls in their slum tenement.  Hardened by constant gang fights and anti-semitism in the densely packed quarter, his character mirrored the resilience of the spiritual beliefs growing inside of him, and forced him to rely on instinct to better himself.  Of the crowded, hostile slum, he said:

I hated the place because I… well, it was the atmosphere itself.  It was the way people behaved.  I knew that there was something better, and instinct told me that it was uptown, and I’d walk every day from my block to 42nd Street where the Daily News was, where I could be near the Journal, the Hearst newspapers.

I’d run errands for the reporters.  My boss was playing golf in the office, and he was shooting golf balls through an upturned telephone book, see?  That’s the kind of job I wanted!

By age 18 ni 1936 the entirely self-taught Kurtzberg was already working with the Lincoln Newspaper Syndicate, drawing newspaper strips and editorial cartoons.

I was drawing editorial cartoons for the syndicate, and I drew a thing called “Your Health Comes First.” I was called in once for drawing an editorial cartoon when Chamberlain made that pact with Hitler.

By using different styles and aliases for each (such as Jack Curtiss, above) Kirby's output gave the impression of a large stable of artists

“Where does a young squirt like you,” he says, “get the nerve to do an editorial cartoon on Chamberlain and Hitler?” And I told him I know a gangster when I see one, see?  Hitler was gobbling up all of Europe.

Jacob Kurtzberg eventually changed his name to Jack Kirby not to disown his Conservative Jewish roots – but because he wanted to be an American.  This ambition took a huge amount of personal confidence – after all, he might still have been a failure, except now, one disowned by his family.

On each comic strip I put a different name: I was Jack Curtiss, Jack Cortez… I didn’t want to be in any particular environment, I wanted to be an all-around American.  I kept Kirby.  My mother gave me hell.  My father gave me hell.  My family disowned me.

This act shows Kirby was not the kind to give in to the dictates of others, even though the mother in those days was sacrosanct.  In one childhood incident Kirby was beaten unconscious by a rival gang, then carefully left at his parents’ door.  The other kids took the time to make his clothes presentable and straighten out his hair, only to reduce the shock to his mother.  Even against this all-powerful maternal influence, Kirby was ready to rebel if it meant he could closer approximate his vision of himself.

This beautifully rendered sequence revealed why Black Bolt, the leader of Kirby's genetically altered raced of "Inhumans" remained silent his whole life

How could such an individual maintain that most intangible belief in the spirit – without it arising internally and continually renewing itself?

Galactus was God, and I was looking for God. When I first came up with Galactus, I was very awed by him. I didn’t know what to do with the character.

Everybody talks about God, but what the heck does he look like? Well, he’s supposed to be awesome, and Galactus is awesome to me. I drew him large and awesome. No one ever knew the extent of his powers or anything, and I think symbolically that’s our relationship with God.

Distribution ad showing rapid saleability of Kirby's ideas in the early 1960's (Lee & Kirby: The Wonder Years, Mark Alexander). After Kirby left Marvel in 1970, the company failed to produce any further ideas of note

Using Kirby as an example, we can see that far from being a sign of meek obedience spiritual ideas are a source of strength and of inspiration, growing from an internal discussion, and feeling.  Though in the light of history there can be no religious or historical group under more pressure to abandon their beliefs altogether than Judaism, spirituality can never be judged by those who are indifferent to the very idea of the spirit.  Spirituality, like creativity and genius, hunger and thirst, instinct and reaction, is a property of each individual, and is dealt with afresh by each generation.

Ragnarok, the "Twilight of the Gods" (Götterdämmerung in German) was intended by Kirby to bring the series of Thor to an end, and to introduce a new language comprised of godly concepts more in keeping with scientific thinking

In fact, if we believe in evolution, this has to be the case.  The question remains, from where did all these spiritual ideas emerge?  Myths, certainly, arose from genius of ancient times – minds which were more advanced than the average.  But men such as Kirby were not men of compromise or shifting allegiance.  The Austrian Jewry who arrived penniless in America’s new world may have been refugees but they were also bold adventurers, bringing only one thing of value – their spiritual faith.  Simon Baron-Cohen in his Zero Degrees of Empathy calls the confidence given by a positive and loving family “the internal pot of gold” whose currency is equally life-saving in any adverse situation.

"The Silver Surfer is the way I feel when I read the Bible," Kirby admitted in a 1989 conference. Part of the surfer's appeal was his serenity in the face of opposition; ancient myth held that the soul of man was tied to the flesh by a silver cord, broken only in death

A similar claim can be made for an active spirituality, that the resilience it lends to the individual is a connection with natural intelligence.  Nowhere is this dynamic more present than in men of genius such as Kirby.  By their raw power, inspiration and appeal they become not the pernicious infection of lazy, unthinking intellectual capitulation, but the driving force behind mental expansion.

Bored of the repetetive nature of the plots, Kirby intended to herald the end of one series, and the beginning of a new one. On discovering this, the publishers forbade it and quickly rewrote the climax

Spiritual ideas are formless until combined with a given medium – whether music, art, literature, poetry or the spoken word – just as a fabric draped over an invisible object reveals its form.  This is the secret of all talent and genius, and perhaps of life itself: the intangible combining with a mysterious, undefined energy, impresses its complexity and beauty in a form bearing witness to the nature of that intangible spirit itself.

Spiritual ideals meet the lackadaisical drop-out mentality of the Hippes (1966)

Ordinary ideas, too, remain formless until they emerge in the communicative symbols of an alphabet – necessarily restricted and limited by this defining act – and rise to higher levels, by words, by grammar and syntax, and even rhythm and abstraction.

In a completely different alphabet, the mouse protein Cyp2el contains exactly 493 amino acids. True!

Compare the different ways a mere 493 characters can be used.  Firstly, this enchanting pre-nuptial sentiment expressed by a highly educated and proficient lawyer, representing a desire for a harmonious betrothal immune from base material concerns.  To all thinking people, this, my friends, must be the purest poetry:

The parties enter into this agreement to provide for the status, ownership and division of property including future property owned or acquired by either or both and wish to affix respective rights and liabilities that may result from this relationship.

The parties recognize the possibility of unhappy differences and accordingly desire that the distribution of any property that either or both may own will be governed by the terms of this Agreement

..and insofar as the statutory law permits intend that any statutes that may apply to them by virtue of legislation will not apply to them.

I could read that all day for inspiration.  But now, try to wade through this incomprehensible rant by an unhinged mind which neither knows nor cares for the wonderful precision of language:

How do I love thee? Let me count the ways.
I love thee to the depth and breadth and height
My soul can reach, when feeling out of sight
For the ends of Being and ideal Grace.

I love thee to the level of everyday’s
Most quiet need, by sun and candlelight.
I love thee freely, as men strive for Right;
I love thee purely, as they turn from Praise.

I love thee with the passion put to use
In my old griefs, and with my childhood’s faith.
I love thee with a love I seemed to lose
With my lost saints, I love thee with the breath,
Smiles, tears, of all my life! and, if God choose,
I shall but love thee better after death.

With which writer should you build a secure matrimonial ladder to the stars?  I am sure the conclusion is obvious!

This variety of emotion can never belong to lifeless marks on paper but only to the mind bent on manipulating them, to communicate its otherwise intangible thought.  The thought and the language must arrive together, as does the spider’s web and his ability to create and manipulate it.   This synchronicity is all around us in nature, so that every living form can also be seen in the surroundings it creates, always organised and designed in a specific and creative manner.  The mythical vampire who cannot be seen in a mirror reverses the intuitively understood fact that the normal mind reflects itself in every medium it touches.  This tendency is so automatic and immune to fakery, that its opposite is not a misleading impression, but no impression at all.

Kirby often recycled classic film ideas and wrapped his own plots around them: note changes in layout and character size, to make the design more dramatic and easier to read on the newsstand

Take formless patriotism, requiring a symbol designed by creative intelligence – from an individual who feels patriotism in themself.  Divinity likewise requires expression in a symbol of some kind – the variance in forms is to be expected: the consistency being in the tendencies they symbolise.  Emotions in the viewer are thus generated or stimulated by the more powerful original ones within the creator.

"I tried to make my characters relate to the human condition. The Hulk, I feel, is someone who is inside all of us... the ability to transcend our own limitations when the need arises. I made Captain America very patriotic... patriotism is a feeling that runs very deep. I feel that the deeper the appeal of a character, the larger the audience it will gather."

A persuasive sense of reality – not a scientific sense, but a symbolic one – arises in the mythical symbols of beings possessed of some definite aim creating energetic forms and thereby imbuing meaning within an otherwise formless and meaningless material.  The nature of the creating energy is encoded within the form itself.  Thus the concept of symbolism is both explained, and put to use.

This is certainly the active principle in the life of Jack Kirby: armed with nothing more than a pencil and paper he created his own symbolic language.  When we compare these to the first crude carvings made tens of thousands of years ago, we are seeing evolution, and its form and direction has always been dictated by men of genius.

After being forced to abandon his own idea for the purposes of sales, Kirby quit Marvel and went to rival DC, where he began by illustrating the death of his previous pantheon of Gods including Thor, who is seen at mid left

“You’re born with a soul–God wants you to do something with it, not give it away.  Nobody has the right to tell you what you should do with it.”

“What I try to say is that you’ve been given a life, and you have to live that life. I couldn’t live it for you.. and I can’t die for you either.. when it’s time for you to die, you’re the one that has to go, not me.“  (1989 discussion with a fan at conference).

“They were the first gods in comics, and so I began thinking along those lines. I began to ask: everybody else, other societies, all had their gods, but what were ours? What was the state of our society, and where were our mythic figures?  I’m a guy who lives with many questions.. because I was never able to resolve them.”

“I try to ask what’s out there, and I can’t resolve that.. I don’t know if anybody can. I sure would like to hear the answers.. to know the ultimate answer, and I find that search entertaining.  You know, if my life was to end tomorrow, I would be satisfied.. I’d have to say the questions have been teriffic.”

Kirby eventually developed his idea of New Gods who each had their own character, purpose, and tragedy. Izaya (perhaps a mutation of Israel) was forced to exchange his newborn son, to keep peace between planets.  His inheritance became The Source, a place where the wisdom of the old gods was expressed in revelations, which men were free to follow or discard, forming the principle of life.

Kirby's symbol for the nature of revelation.

He cheerfully worked at fever pitch and never missed a single deadline in more than forty years.  Always pushed for time and money, he once tried to cut back by using cheap pulp paper after which Mike Royer, his inker at the time, despaired of being able to keep up with him, as he had to actually iron the pages to stop them from curling during inking.  He rang Kirby in a panic.  “This new paper you’re using is terrible – it’s curling up as soon as I put ink on it,” he complained.  Kirby just laughed, “well, I didn’t have any problem drawing on it!”

While his imagination searched for the possibilities in our universe, his intellect tried to define man’s relation to it.  He reasoned that Earth was a tiny speck of matter in an infinitely large creation, and that forces far beyond our control would not concern themselves with our fate.  Despite this, he emphasised the mind of man as the key to all questions, perhaps even the question of immortality itself.

The gods in his work seemed to emerge from somewhere beyond his conscious thought, and the strangeness puzzled him at times; when asked about it at various conferences he would try to rationalise it as best as he could.  “I must have a hangup of some kind.  I’m prone to my own environment and express it in terms of gods.  Maybe I was oriented to some sort ofm ythology.  I speak in terms of mythology.  I’m communicating in my own way.”  This paradoxical state in which created ideas seem to have bypassed the intellect altogether has been experienced by many artists, including Neil Diamond, who sought to understand why his output would lean towards a mysticism not arrived at step by step but already fully formed in words and music.

A terrified pilot trying to evade capture behind enemy lines fails to realise he has already died, but finds relief at the warm and understanding nature of the next world, in this moving story story from 1970

Gopi Krishna’s poetry, the content of which often took him by surprise, would appear in his mind in rhyming couplets, he said, multiplying like snowflakes which grew bigger and bigger, written down as fast as was humanly possible, but many of which would necessarily be lost as the brain struggled to keep up.  The end result was a kind of revelation with messages he could never have arrived at consciously.  This same idea appears in religious literature throughout history, meaning that the creative mind shares attributes attributed to one ni touch with a higher form of intelligence.

The experiences of Ayrton Senna in which he felt an overwhelming and greater intelligence than his controlling his car at dangerous speeds, or the despair of Russian painter Isaak Levitan felt at his inability to completely capture on canvas the depth of mystical feelings within, and the puzzling appearance of creatively perfect ideas in dreams, such as the complete melody for Paul McCartney’s “Yesterday” have all been well documented.  These observations indicate the creative brain is liable to influences beyond its normal capacity, giving birth to ideas which arrive already surrounded by mystery.

In one memorable Kirby story, Thor supervises the release of warlike Trolls captured in Asgard.  The goddess Sif protests they should all be slain for the evil they had planned.  He replies, “Thou hast no inkling how precious is all life, even such as theirs.”   Jack believed in life because he believed in himself, and people believed in his work because he, in turn, believed in them.  He once claimed that you could take any four-issue story from his comics and turn them into a film, as he had already worked out the best pace at which the arcs of plot and elements should be interwoven, and the angles which would make each scene the most interesting.

Although he hardly profited from them in his lifetime, and his family still maintains a legal battle to gain some share of their continuing turnover, his ideas have become a billion dollar film and entertainment industry, and his own life was a testament to the redeeming power of faith creativity: that a boy from the slums could raise himself to a world famous name through his talent alone.

Farewell, Jack Kirby!

God, by Jack Kirby. And Jack Kirby.. by God

Posted in Evolution, Genius, God, Intelligence, Intuition, Jack Kirby, Natural Intelligence, Richard Dawkins, Science and Religion, Spiritual Genius, The Brain | Tagged , , , , | 2 Comments

Genome Sequencing

According to the Independent newspaper, Life Technologies of San Francisco have developed a small machine called the Ion Proton Sequencer – which costs £149,000 – and are offering to  sequence an entire human genome in a single day, for $1,000 (£650).

All you need is one of these - and they'll probably be able to get your DNA off it too

This sounded very interesting so I just rang their offices in San Francisco to find out if, once the genome is sequenced, you could resequence it again in a few weeks or months, after perhaps a change in lifestyle, and compare the result to see if changes had occurred.

After a few false starts on their phone system (someone over there can really play the piano) I found the very helpful Redela Fullaton who explained that though their machines can perform the sequencing, or their resellers could, and align the genome to compare with established markers, they didn’t handle the tertiary software to perform  comparisons; this might be available from other suppliers such as Soft Genetics.

But interestingly she said by the end of 2012 they would offer cloud storage so you could keep all your sequences online, in order to apply software to them.  She also encouraged me to create a login to the Ion Community which I shall do this evening.. a wonderful conversation, very friendly.   This all seems to anticipate a mass market.  I’m still interested in showing that meditation and various spiritual practices, no matter how imperfectly realised while sliding down the razor blade of life, must have some effect on the genes; if not, you wouldn’t have the consistent kind of family profile producing genius, and the degrading results of greed.  And now the technology seems to be appearing like in the early days of computers.

For all I know, someone has already set all this in motion – but what fun to try and figure it out for ourselves!  I remember last year someone got some online gamers to work out the 3-d structure of a folded protein by collaborating and pooling their results, and someone else created a “folding at home” network which enabled unused CPUs around the world to be tapped into to work out the animation steps, which they made into a short film.

http://gadgets.boingboing.net/2009/02/02/vital-statistics-fla.html

The prices are bound to drop; at £650, a gene sequence resembles the price of fairly small PC flatscreens from around 1998, 14 years ago – I recall those fell to nearer £450 by about 2000, as I bought four for a training room – and annoyingly, within another year or two were down to less than £200.  They soon became mass produced as people scrambled to save desk space and cut the heat output and radiation scare from those massive CRT boxes; China got involved and the prices fell to next to nothing.

If so, this means you could in theory sequence your genes every month and keep track online of the changes made.  This in itself would be a fantastic technical service to offer someone, if it doesn’t exist already.  I built my own database to handle genome storage last year, just out of curiosity – it’s a set of 26 tables, each with 100 columns of 240 characters each.  All you would need for the storage of the base pairs themselves would be maybe 550 records per table, with 3 tables left over for ID and various changeable parameters which I haven’t figured out yet.  Something else you could develop would be a graphical tool to compare the changes.

http://www.genome.gov/images/content/cost_per_megabase.jpg

So by comparison, the raw data of an individual genome of base pairs isn’t such a large database – and you could use checksums or some other gimmick to compare large chunks in one go.  So you could feasibly store and compare a reasonable number of versions and show the differences in real time.  In my rough genome system I thought I would probably need a reference table which had the offsets of each known codon, protein coding area and so on, and I’d built all the translation tables for RNA and amino acids, and downloaded the codons for a few proteins from a protein data bank. So I could make the thing even tighter in places by not keeping the codons but the amino acid letter instead, saving 2/3 the space.

Anyway, whatever has been developed by Life Technologies or Soft Genetics is bound to be fully developed and far more sophisticated, but the process of making it gave me an idea about how much data is involved.  It’s a lot, but not unmanageable – certainly less than 300 Mb per genome.  And as computing power is increasing so quickly, you can get ever more sophisticated software to graph the differences and do all kinds of things.  I think I saw a 1 Tb backup drive at PC World the other day for less than £100.  That’s 1,000 Gb or 3,300 genomes even with my crude little system.

The Ion Proton Sequencer - one day everyone will have one next to their PC, their iPad and their copy of the Dhammapada

So perhaps soon, the idea of monitoring your genes to see how your lifestyle is affecting it is something you could plug into your PC just like you might go on a diet and chart your progress.

You could perhaps one day work out what the best time is to have a child, and people would share information online as to what kind of lifestyle had the best effect.  Of course, people love to try things for themselves, so they’d be keen to join in.  You’d have a database of genes, and people could feed in data about their children’s genetics – anonymously of course – but with a view to helping other people see how things progress from generation to generation, and what lifestyle promotes the healthiest biology.  Having worked with computers since I was 14, I have great confidence in the ingenuity of the human race.

It’s gonna be fabulous!

"I think there is a world market for maybe five computers".. Thomas J Watson of IBM, 1943 (alleged quote!)

Posted in Designs in nature, Evolution, Human genome, meditation, Proteins, Religious disciplines, Ribosome, Science and Religion, Telomerase, Telomeres | Tagged , , , , | 1 Comment

Thanks for Another Day!

This morning I saw a hearse making its sombre way along to the local church.  The sun is shining today and I felt so grateful that my time wasn’t up yet.  Although after today’s post, it might not be long!

I was thinking, they have all these checks to make sure people don’t take 100ml of fluid or a pair of nail clippers onto an aircraft, with perhaps good reason.  At least, since Larry and George took down the World Trade Centre to launch invasions and tighten the grip on Middle Eastern oilfields – and collect $6bn in hastily arranged insurance money – all of which I can understand and appreciate.  But how is it that people are allowed to walk into the highest positions of government without a single check being done on their brains?

Here they are, voted in on a tide of equal parts hysteria and cash, to make decisions about prisons, nuclear weapons, medical research, healthcare, drug addiction, euthanasia, abortions, mental illness, overseas slaughters and a hundred other things which affect possibly millions of people, not just the hundred or so flying to the Isle of Wight, but there is never any kind of checkup by qualified people to give an indication whether they have any mirror neuron activity, oxytocin production, capacity for empathy, or liability to childish tantrums.  Links to weapons companies?  Shush now, child – we’re busy chanting slogans!

"Drill, baby, drill!" They went a little quiet after the Gulf spill

They could have a scanner on the way into the White House like the ones in airports, to quickly check the MRI activity.. run a few checks on empathic reactions, look for sociopathic tendencies and so on.  It wouldn’t take long – and think of the lives it would save.

“I’m so sorry sir, scanners show zero empathy.  Would you come with me for a moment..?  I’m afraid you’ll have to give me those nuclear codes – yes, just for now if you wouldn’t mind.  Of course, you’re quite right, it’s probably all a mistake – these machines, eh?  They can send a man to the moon, but – well, never mind, we’ll do our best to clear it up in a jiffy.  There might be a teensy delay – I’ve just seen Mr Mugabe and Mr Blair go through.  May I get you a coffee?”

The most that actually happens is the New York Post finds they lit up a spliff in college, but even this is soon turned into a public relations success as they come clean.  And who really cares?  The real problem is once they walk into that office, they can do years of damage, bring the world to its knees, incarcerate all their enemies, tear up the constitution, build black hole prisons, kidnap innocents, launch wars, allow Glaxo to experiment on orphans, torch World Trade Centres, decimate the rainforest – the planet’s lungs – wreck the ozone layer and steal money from hundreds of millions of taxpayers, funnelling it to their weapons-happy friends. 

“Ah, hold on – 100ml of Evian?  I’m ever so sorry, ma’am, you’ll have to leave it here with us.  We can’t take any chances you know!”

Understandably, everyone wants to stop the criminal mind from entering their shops or living in their neighborhoods, or getting on one of our airplanes.  But running an entire country and changing the destiny of a planet?  “Oh, right this way, sir – we’ve got you a seat at the UN and your limosine is being cleaned now.  And may I say, oh, what a splendid suit you’re wearing!

Mass killer montage: they all seem very good with their hands. I put their total tally at about 150 million dead, but that could be on the low side. Thank heavens they never tried to take tweezers on an airplane though

These zero-empathic sociopaths are wily critters - they get everywhere (Bush Sr with Eisenhower, Nixon and Kissinger)

Posted in 911, 911 scam, Dick Cheney, Dictators, Genetic damage, George Bush, Hitler, Kim Jong Il, Larry Silverstein, Mental Illness, Mugabe, Tony Blair | Tagged , , , , , , , , | 5 Comments

Synthesis and Understanding – the Spirit of Art: Tom Thomson

Yesterday an exhibition of paintings at the Dulwich Picture Gallery came to an end after nearly twelve weeks; it was called “Painting Canada: Tom Thomson and the Group of Seven”.  It was a really stunning display of 52 large canvases and around 70 smaller sketches, in a cosy and accessible South London gallery in which even a Rembrandt could be examined up close.

The casual atmosphere was worth experiencing in itself.  Many Canadian accents could be heard, which was telling: the purpose-built Kleinberg Gallery in Ontario is the normal repository for Group of Seven works, and is impressive, if a little contrived (and annoyingly, occasionally closed off to the public: pirated by the wealthy for their various political and social climbing functions – things which would have dismayed the artists themselves) but it was really something to see these masterpieces holding their own, so far from home.

That said, it seems all the more remarkable that it took so long for these paintings to return to a global audience: there are many in the art world who know only two things about Canada’s Group of Seven – that all were from Canada, and, that there seems to have been seven of them.

In Toronto’s Distillery District in December a very avante-garde gallery owner advised me that admiration for Thomson had mired the Canadian art movement in passé sentimentality while the rest of the art world surged ahead.  Sharks!  Unmade beds!  Formaldehyde!  Piles of deckchairs!  But looking at the bulbous optical illusions on display, some with fibreglass human limbs jutting out at alarming angles (two years each in the making) Thomson’s deft colour studies made in perhaps an hour or two seemed all the more charming.

One of the few surviving photos of Thomson, a keen fisherman and entirely self-taught painter

In fact Thomson’s contribution was made well before the informal group of seven painters actually gave themselves a name.  Thomson lived from 1877 – 1917, working as a commercial artist and attempting occasionally to incorporate the Art Deco style into his livelihood, but developing a love for painting at the age of 33 – once again showing the importance in a creative individual of this point at which the nervous system and brain become mature.

Sample of Thomson's commercial output, and perhaps also his sensitivity to the poetry of like-minded men such as Scotland's Robbie Burns

Thomson’s life story remains controversial in part because of his death in a strange accident on a lake in Northern Ontario.  The circumstances were mysterious because he was a highly capable and experienced woodsman and canoeist, though he seems to have drowned after suffering a head injury and falling from his canoe.  The body was only found more than a week later, and confusion reigned as it was buried and then disinterred; some dispute has even arisen as to where the body actually now lies.

But be that as it may, and though his painting career, which had begun in 1911, lasted merely six years, his work was a major influence on the others in the group and many of his images remain the most instantly recognisable, and proudly identified as Canadian, a century later.

Six of the Group of Seven, plus their friend Barker Fairley, in 1920. From left to right: Frederick Varley, A. Y. Jackson, Lawren Harris, Fairley, Frank Johnston, Arthur Lismer, and J. E. H. MacDonald. It was taken at The Arts and Letters Club of Toronto.

The first time these paintings were shown to the British public was in London on the 8th January 1925 – exactly 87 years ago today – and they received enthusiastic reviews:

“A school of landscape painters who are strongly racy of the soil” .. London Times

“The foundation of what may become one of the greatest schools of landscape painting” Morning Post, London

which was a contrast to much of the reception afforded them in their native Canada:

“They are garish, affected, freakish”  .. Toronto Star

“A single narrow and rigid formula of ugliness”.. Saturday Night, Toronto

In fact there had been some enthusiasm in Canada, which was remarkable for a country at that time more interested in selling off its wildnerness to the highest bidders and thereby climb the capitalist ladder, than indulging a group of Toronto’s commerical artists fooling about with paints.  Perhaps the group made much of whatever skepticism there was, to enhance their status as rebels, but in any case, they certainly had their work cut out not just to make their mark, but to even earn a living from a town more interested in wealth than trivial art.  Thomson’s own opinion of Toronto was “it is a great town – great to get out of.”

Although capitalism had yet to reveal its widely destructive side, Thomson was already sensitive to the damage done by logging and burning, and the deaths of lumberjacks caught in the vicious tumble of tons of wood, suddenly unjammed by their own skill in the fast flowing rivers of northern Ontario.  His Crib and Rapids (1915) shows the tumbling logs emerging from a chute, two of which form a precise cross, reminiscent of the many wooden markers along the shore where lumbermen were lost, “dying horribly by drowning or the vicious battering of the logs”  (Andrew Hunter, Mapping Tom).

Path Behind Mowat Lodge (1917)

By nature, Thomson seemed a spiritual cousin of Henry David Thoreau, the American philosopher whose life seems well summed up by his own maxim, “simplify, simplify, simplify.”   Thoreau was no doubt more politically sensitive and outspoken – once refusing to pay his poll tax on a point of principle, and being sent to jail for it; he declared the prison to be a great waste of stone, unable as it was to change his mind in the least.  At one point, according to Emerson, he was refused permission to borrow some valuable documents from the esteemed Harvard library, whereupon his forceful tirade to the astonished trustees convinced them that it was he, Thoreau, not they, who was the rightful guardian of this knowledge, and that their rules now appeared so foolish that thereafter he was granted an open pass to borrow whatever he liked.

Sketch for The West Wind (1916), often read as a cipher for the struggles of the soldier in WWI

Thompson was no such firebrand, but shared Thoreau’s need for privacy, and ability to derive ideas direct from a rapport with nature.  It was said that he enjoyed the company of the loggers, and the other artists, but once the drinking and singing became too boisterous, he would quietly slip away to be alone in the wilderness to commune with nature.

“I cannot help but wonder if Thomson’s radiating contour outlines are less spiritual auras than responses to the spectral signatures of elements radiating their excess energy.  His powers of observation were not only acute, but scientific.  By 1917 Thomson was calling his sketches “records”, given that they functioned as data-filled documentation of nature.  His uncle, Dr William Brodie, was a well-known naturalist, with “the eye of the scientist and of the artist”, whose extensive collection of specimens was internationally recognised.

He encouraged expansive scientific thinking about the dynamism of life, drawing on Western and Eastern philosophical traditions, and rethinking Charles Darwin’s theory of natural selection within a universal, even mystical context… Thomsons’s canvas [The West Wind] can thus be read as a compelling reworking of a nineteenth-century botanical study into a kind of visualised periodic table.”

..Anna Hudson, A Revelation of Tom Thomson

In art, as in life, we admire that which is characteristic, unmistakeable, and not weakly defined or easily lost to trivial reality or contending, extraneous forces.  As  William Blake said “the great and golden rule of art, as well as of life, is this: that the more distinct, sharp and wiry the bounding line, the more perfect the work of art, and the less keen and sharp, the greater is the evidence of weak imagination, plagiarising, and bungling..”

Autumn's Garland

What set the Group of Seven’s work apart was that it defined itself boldly; projecting this boldness on to the Canadian landscape – formerly considered entirely unsuitable for painting due to its raucous and uncouth state, compared to the flowing and cultured hills and valleys so sought after by the European painters at that time – it found a hitherto unsuspected majesty in the landscape, which gradually transformed itself into what could even now be called a Canadian national identity.

Above all else, art requires that the confusing detail be stripped away, but not altogether lost – it must be be synthesised through the painter’s own understanding so that each element stands as a cipher for reality, and the unity of these self-made parts is a process happening not on the canvas, but in the mind of the artist.  It is this mental contribution which makes art a worthwhile endeavour, enabling the rapport between the mind of the creator and the observer.

The Jack Pine (1917), probably Canada's mostfamous painting. Interestingly, when seen in greyscale, the entire sky is seen as one shade of grey, meaning that every colour has been carefully weighted to have an identical "value", the relative darkness of lightness, taken apart from the variation in colour. This kind of accuracy is difficult to achieve, when dealing with the different characteristics of each pigment

This is why it is pointless to try to paint anything with which you are not capable of becoming emotionally involved.  The late Lucien Freud, suerly one the the most devoted, active and able painters of the 20th century, was alert to this essential need; he once attempted a portrait of a distinguished gentleman but gave it up as hopeless after a few sittings.  When asked why, he exploded, “but how on Earth could I paint with that man in the room?!”

Autumn Birches, 1916. "Never before had such knowledge and the feeling for such things been given expression in paint. Thomson's canvases are unique in the annals of all art especially when it is remembered thathe was untrained as a painter. His master was Nature." ..FB Housser, A Canadian Art Movement: The Story of the Group of Seven, 1926

As a result, the most powerful art is that which expresses the emotional state of the artist himself, which cannot be achieved without some mastery of the mechanical processes, but also requires an intuitive understanding of the subject.  A portrait painter must have some connection with his subject, even if this only gradually forms during the process.  Freud’s own sessions were known to extend for months: small wonder his paintings capture every physical nuance of his subjects and evoke such a thorough knowledge of their form.

Constable painted portraits to earn a living, often stunned at the sheer incomprehension of the painting process on the part of his sitters, one of whom once declared herself far too busy for a sitting as her husband had requested, but offered instead a lock of her hair for Constable to use instead.  Of course his most remarkable ones are not of the families who simply wanted a portrait to impress their friends, but of the girl he was later to marry, and the people with whom he felt a solid kinship.  Vermeer’s most frequent subject was his own wife, and his pictures resound with concentration and absorption.  One cannot paint anything one is not interested in, and to do so seems tantamount to a certain kind of dishonesty, a prostitution, even an act of self-destruction.

First Snow in Autum, 1912-13

The resulting process of simplification arising from emotion  is the mark of genius, in which the fractal complexity so beloved of the technician can be resolved into a shape dictated by the mind and consciousness.  The artist is no longer a menial observer and timid taker of notes but a genuine creator, and bonds with his subject in a way which can only be described as mystical.  The movements of the large and small motor muscles, recorded in the movement of paint on the surface, are no longer embarrassments of technique but become things of pride, evidence of thought, proof of certainty.  The light that gives them this impact emerges from the mind itself.  His vision becomes surprising and even startling, being entirely unique, and not seen before that moment – reflecting as it does the individual character of his most prized possession – his own self.

Among some learned minds, one may well consider this internal light worthless:

“Is there life on other planets? Nobody knows.  If you forced me to give an opinion one way or the other, I’d say yes, and probably on millions of planets.  But who cares about an opinion? There is no direct evidence.”

.. Richard Dawkins, the Magic of Reality, p188

No evidence – other than our own strong and distinct and convincing impression, of course, which we must immediately discard as worthless!

“Thoughtless people contradict as readily the statement of perceptions as of opinions, or rather much more readily; for, they do not distinguish between perception and notion. They fancy that I choose to see this or that thing.

But perception is not whimsical, but fatal. If I see a trait, my children will see it after me, and in course of time, all mankind, — although it may chance that no one has seen it before me. For my perception of it is as much a fact as the sun.”

..Emerson, Self-Reliance

To the natural mind, an opinion carries its own weight by the fact of its very existence.  Music is an opinion, and likewise all art and philosophy, all original thinking, all intuition, all common sense, all natural intelligence and genius; every man who calls himself a thinker is in the business not of slavishly borrowing the thoughts of other men, or timidly accepting his own only on condition they have the support of others’ experiments and the cheering of the mob, but in honouring his own opinion and nourishing his ability to generate it.  What else is relevant to his existence?

Autumn Scene

This fully explains the attraction which the work of such sensitive men as Thomson generates even a hundred years on – that there are chords we never tire of, showing as they do that the human mind is not the storage bin which modern education mistakes it for, but possessed of an inbuilt, active and enthusiastic energy which can expand to take in any number of subjects, lending to them its own natural beauty.   If you ever get a chance to see Thomson’s work, take it – such things are good for the soul.

Posted in Genius, Intuition, Natural Intelligence, Richard Dawkins, The Magic of Reality, Tom Thomson, Uncategorized | Tagged , , , , | Leave a comment

Beyond Intellect: Natural Intelligence

I saw a very interesting discussion this afternoon between TV show host Bill Maher and Richard Dawkins from 2010 in which the topic of religion arose, and specifically Christianity, which Dawkins described as emerging from:

 “..a wandering tribe of Middle Eastern persons.  Why would they have any more wisdom about the origin of the world, or the origin of anything else?  ..that particular myth is the myth that just by sheer chance [the Judeo-Christian myth] happens to have come to our civilisation.

There are thousands of myths in the world and none of them are any better than any of the others..some of them are a lot more poetic than that one, but that’s all you can say.”

This central premise is what creates the gulf between the spiritual-minded or those of faith, and the scientifically-minded: that useful knowledge can only come from the intellectual accumulation of facts as a harvest of experimentation, and that other sources of knowledge are all equal – in being pretty well worthless.  But on the evidence of Dawkins’ own well-researched – and admittedly, thoroughly readable – the Magic of Reality, we can completely discount this idea.

Original plate featuring Dave McKean's artwork, presented to James Randi

Infallibility of logical thought might be an understandable viewpoint for one who built all their knowledge incrementally, enlarging on conclusions presented by those who came before him.  Such a process is also seductive and rewarding, as all new discoveries remain tantalisingly out of reach until they become intellectual possessions.  By and large the world of science is based on such knowledge, since if it were not, it would have to be called a creative art or perhaps a faith of some kind; of course, the human mind also plays its part, and its tendency to immediately dismiss anything beyond the intellect’s grasp as being worthless leads to problems:

“For the genome is littered with dead genes. Huge wastes of DNA territory comprise a graveyard of discarded, superseded old genes (plus meaningless sequences of nonsense DNA that never functioned) with occasional islands of current, extant genes that are actually read by the translating machinery and turned into action. Dead, untranslated genes are called pseudogenes.”

..Richard Dawkins, “Dawkins on Darwin,” published in The Times UK, February 11, 2009

Babbage's most ardent supporter, Ada Lovelace (after whom a programming language is named) along with the London Science Museum's working model of his calculation engine. A second one was assembled for a museum in America, and I had the good fortune to have a lengthy chat to the engineer building it - who seemed quite enthused to have someone to talk to about his work

As time moves on, science is finding that there seem to be very good reasons for the DNA’s habits of preserving certain components, as you might expect from a mechanism able to maintain a consistency of data duplication – terabytes of information – over a 400 million year period in the case of some ancient species which survive to this day.  DNA has now been classed as a branch of information science, although this delayed conclusion must have been intuitively obvious from the start.   As long ago as 1820, Charles Babbage proposed that there should be a medium in which organic life could be coded very much in the way computer software was.

Babbage conceived of God as a man of science and a programmer, who uses natural laws to create the cosmos. Instead of ‘perpetually interfering, to alter for a time the laws he had previously ordained; thus denying to himself the highest attribute of omnipotence’, a celestial program had been devised at the time of the creation.

Babbage speculated that God had created ‘one general and comprehensive law, from which every visible form, both in the organic and inorganic world flows, as the necessary consequence of the first impression of that law upon matter’, this law being responsible for ‘all the combinations and modifications of matter’.

http://bedejournal.blogspot.com/2009/03/charles-babbage-and-divine-programmer.html

This was all quite prescient, as Babbage invented not only the computer but the software to go with it.  Babbage’s habit of projecting idealised and perfected forms of his own personality traits onto a universal dimension is consistent with a similar trait in every society which expressed its knowledge and hopes via myths and spiritual literature.

“For me, the most important outcome of the human genome project has been to expose the fallacy that most genetic information is expressed as proteins … In contrast to protein-coding genes, the extent of noncoding intronic and intergenic sequences increases markedly with complexity; only 1.5% of the human genome encodes proteins ... These observations suggest that we need to reassess the genetic orthodoxy, deeply ingrained and given superficial reprieve by uncritically accepted assumptions.” John Mattick, University of Queensland, “The genomic Foundation Is Shifting,” February 18, 2011, Science Magazine Vol. 331 no. 6019 p. 874. Image: electron density map of the quinolone binding sites of a topoisomerase IV - DNA complex. First published in Nature Structural & Molecular Biology

This serves to show that (certainly in complex systems) value is assigned in proportion to our understanding.  Whatever yields insight is of the highest value: we cannot afford to jettison the leaps of understanding characteristic of genius.  How exactly do these leaps come about – often repeatedly – in a single individual surrounded by hundreds, if not thousands, of similar individuals (often with an even greater intellectual or analytical capacity) all labouring towards the same goal?

Srinivasa Aiyangar Ramanujan was one of India's greatest mathematical geniuses, making substantial contributions to the theory of numbers, elliptic functions, continued fractions, and infinite series. In 1914, he was invited in to Cambridge University by the English mathematician GH Hardy. He worked there for five years producing startling results, and proved over 3,000 theorems in his lifetime. According to Ramanujan, inspiration for his work came many times in his dreams. A Hindu goddess, Sri Namagiri Lakshmi of Namakkal, would appear and present mathematical formulae which he would verify after waking. "While asleep I had an unusual experience. There was a red screen formed by flowing blood as it were. Suddenly a hand began to write on the screen. I became all attention. That hand wrote a number of results in elliptic integrals. They stuck to my mind. As soon as I woke up, I committed them to writing."

Natural intelligence gives an insight of a different form than analytical thought.  It can simplify a knotty, complex problem into a concept – a difficult task – allowing the intellect to fathom the details for itself.  At other times, it presents fully finished solutions to a mind which has already tried to attune itself to the nature of the problem.  While the intellect often complicates a problem by adding detail to it, and then elaborating still further in a fractal-like pattern that feeds on its own curiosity, yet never changes the initial direction of research, natural intelligence can go to the root of an issue and lay the foundation for the long avenue of implications which follows.

The birth of societies can even be attributed to these flashes of inspiration, and its characteristic giant leaps which the intellect unaided seems incapable of.  It is as if a pitch black room is suddenly illuminated by lightning searing the form, mass, and colour of every object contained within it onto the mind in one unforgettable flash, after which it becomes a matter of unravelling the details, something the intelect is exceptionally good at.  This flash of insight – a eureka moment, or brilliant inspiration which can shape an entire career, followed by schools of thought – is, by far, the most valuable tool in the brain’s arsenal, and the true engine behind man’s evolution.  To dismiss it as unscientific is a serious error.

According to Benjamin Farrington, former Professor of Classics at Swansea University:

“Men were weighing for thousands of years before Archimedes worked out the laws of equilibrium; they must have had practical and intuitional knowledge of the principles involved.

What Archimedes did was to sort out the theoretical implications of this practical knowledge and present the resulting body of knowledge as a logically coherent system.”

To emphasise its importance I have decided to try to write a book this year, called something like “Natural Intelligence: the Bridge between Science and Religion.”  A superbly talented photographer in America has offered to help out, and through dint of several days of intense hard work we have between us managed to amass a large and thoroughly useful store of enthusiasm.

Natural intelligence from ancient times was the foundation of myth, and, in a highly extrapolated and defined way, combined with the experiences of real people from a particular point in history – such as Guru Nanak, Shankaracharya, Buddha, Jesus, Mohammed, and so on – the source of more modern religion, and certainly of spirituality, since none of these ideas can arise from intellectual efforts alone.  In fact, the intellect is liable to discount them altogether, as we can easily see from Dawkins’ interview with Maher.

No great school ever existed which had not for primal aim the representation of some natural fact as truly as possible.

..John Ruskin, The Two Paths, 1878   (I have an original copy!)

Natural intelligence is also the force behind great art and music, poetry and literature – because in all these fields, no such height can be reached through intellectual efforts alone.  Otherwise the faculty of genius would be a pointless redundancy, something nature is not in the habit of creating.  The names of those who became genuinely connected to natural intelligence – even those with personality flaws – invariably resound through history, and are fondly remembered long after their passing.

Gauguin's final resting place - Calvary Cemetery, Atuona Hiva Oa, Marquesas Islands, French Polynesia

The remarkable thing is that natural intelligence is also behind the march of science.   Of course, the first generation of scientists were born to devout families, or families of a strong moral nature,and the extremely sudden – evolutionarily speaking – appearance of minds which thought in a different way than even their own parents, is a strong indication of how evolution works en masse, and does not wait for the much-belaboured “natural selection” to gradually increase the desired components, while vastly more numerous redundant components explode at the same or greater rate.

Since natural intelligence can only emerge from a brain at least partly remaining in a natural, undisturbed state, it is no surprise that many modern thinkers felt disinclined to tamper with it in the battery farm of state education, earning poor grades for their resistance.   Many later achieved their greatest successes after a period in which through various circumstances they were relieved from inordinate pressures and stress, leaving the brain free to follow its own natural trend.  Einstein’s breakthroughs came not while studying in University – an environment for which he seemed totally unsuited – but while his mind was free to build its connections undisturbed, in his humdrum and relatively undemanding job as a junior patents clerk.

The problem is not simply that those of faith prefer the scriptures as a source of scientific knowledge, a recurring complaint made by Dawkins, especially as regards Islamic Faith Schools or Young Earth Creationists.  The problem is also that prominent men of science fail to see past the colorful imagery – which made the best technology of their day – the true nature of myth and scriptures, and the huge advance they represented to primitive tribes.  Both positions are equivalent errors in blotting out an entire arm of human thought, creating a lopsided personality with a distorted view of themselves, of their world – and of everyone in it.

Atlas carrying the ball of Heaven (inscribed with the constellations) ..not the Earth. Greek mythology was intended to openly project the human personality onto a universal dimension. Our habit today of creating larger than life fictional superheroes with a human alter ego, arises from the same tendency. Harpies, for example, were a series of winds with a troublesome, disruptive aspect, and no purpose other than causing discord. They were very different than other winds which might bring warmth or rain, and were an effective cipher for persons of similar character; the name is used in the same context to this day.

“The immense distance between a [primitive African] statue and a statue by Praxiteles is the immense distance between animistic religion and the intellectual insight of a Greek at the higest point of their civilisation.

The Greeks attained a religious equilibrium which can only be called felicity: they lost all fear of the external world – they actually turned sympathetically towards this world, and their art became an expression of what they saw with friendly eyes – an idealisation of Nature.

Man now saw beauty everywhere in living things, and the organic rhythm of life was the quality he tried to express in his art.

Even where great artists have created their masterpieces in apparent isolation from any religious faith, the more closely we look into their lives the more likely we are to discover the presence of what we can only call a religious sensibility.  The life of Van Gogh is a case in point.

The sense of glory, which is the offspring of spiritual courage, is entirely absent in the art of primitive man.  It is this sense, followed in different directions, which leads to the highest attainments both of classical art and of the Christian art of the Middle Ages.”

..Herbert Read, The Meaning of Art, 1935

In Dawkins’ most recent book, The Magic of Reality, many chapters begin with examples of myths that have attempted to explain various natural manifestations, such as sunrises, earthquakes and even the beginning of the world.  He then goes onto explain the scientific reasons behind these events; his stance towards myths has definitely softened – in one place he even refers to “beautiful myths”.

There are some which are quite remarkable in their accuracy as to describing the spirit of certain natural events – which he points out, could not be understood by people at the time.  But since these myths came from somone at the same evolutionary level, the irresisitable conclusion is that they emerged from individuals who were somehow more in tune with natural intelligence: we would call them geniuses.

Otto Loewi (1873-1961), a German born physiologist, won the Nobel Prize for medicine in 1936 for his work on the chemical transmission of nerve impulses. In 1903, Loewi had the idea that there might be a chemical transmission of the nervous impulse rather than an electrical one, but was at a loss on how to prove it. He let the idea slip to the back of his mind until 17 years later he had the following dream. "The night before Easter Sunday of that year I awoke, and jotted down a few notes on a tiny slip of paper. Then I fell asleep again. It occurred to me at 6 o'clock that during the night I had written down something most important, but I was unable to decipher the scrawl. The next night, at 3 o'clock, the idea returned. It was the design of an experiment to determine whether or not the hypothesis of chemical transmission that I had uttered 17 years ago was correct. I got up immediately, went to the laboratory, and performed a single experiment on a frog's heart according to the nocturnal design."

This is an important point, as it shows the existence and influence of such minds from the very earliest times.  As Dawkins says in his interview with Maher, primitive simply means behaviour more towards the ancestor.  Inversely, therefore, genius must be behaviour more characteristic of future descendants.  Since the average future descendant will of course not be a genius, it means the genius is an early arrival at a later evolutionary state.

Therefore the genius is the vital expression of evolutionary truth, since they alone provide the target towards which the rest of the race gravitates, partly by example, and partly again by natural intelligence: the awareness that a truth or idea does indeed represent a genuine advance.  And fittingly, the Latin root of the word religion, according to Max Mueller, means a reverence for the Gods or a study of divine things, while the word genius means guardian spirit.

One morning in a dream McCartney heard a classical string ensemble playing: "I woke up with a lovely tune in my head. I thought, 'That's great, I wonder what that is?' There was an upright piano next to me. I got out of bed, sat at the piano, found G, found F sharp minor 7th -- and that leads you through then to B to E minor, and finally back to E. It all leads forward logically. I liked the melody a lot, but because I'd dreamed it, I couldn't believe I'd written it. I thought, 'No, I've never written anything like this before.' But I had the tune, which was the most magic thing!"

Richard Dawkins has certainly done his homework regarding myths.  Take as an example, the ancient Japanese myth that earthquakes resulted from Japan riding on the back of a gigantic fish called Namazu: whenever Namazu flipped his tail, the Earth would shake (p.210).  Or the ancient Maori myth that Mother Earth was pregnant with her child, the god Ru: whenever baby Ru kicked or stretched inside his mother’s womb, there was an earthquake (p.211).  Or the West African legend that two giants hugging caused the earthquake, and yet another from a West African tribe who believed they lived on top of a giant’s head: the forest was his hair, and the people and animals were like fleas wandering around on his head: earthquakes were what happened when the giant sneezed (p.213).

"...I was sitting writing on my textbook, but the work did not progress; my thoughts were elsewhere. I turned my chair to the fire and dozed. Again the atoms were gamboling before my eyes. This time the smaller groups kept modestly in the background. My mental eye, rendered more acute by the repeated visions of the kind, could now distinguish larger structures of manifold conformation; long rows sometimes more closely fitted together all twining and twisting in snake-like motion. But look! What was that? One of the snakes had seized hold of its own tail, and the form whirled mockingly before my eyes. As if by a flash of lightning I awoke; and this time also I spent the rest of the night in working out the consequences of the hypothesis." Said an excited Kekulé to his colleagues, “Let us learn to dream!”

What Dawkins notices is that all these myths are different.  To his scientific thinking, this means – inaccuracy.  But what do all these myths have in common?  The very important idea that earthquakes are not a result of any Godly malevolence or human sin, events designed to force a reformation of character on the part of the tribespeople.  The earthquakes are correctly attributed to forces over which they have no control and which arise from natural activity on a much grander plane of existence from theirs.

The West African myth of the giant is very effective, as it portrays humanity being practically insignifcant in the real scheme of things, in which more universal elements went about their business without intending to benefit or harm humanity in any way.  The idea that man is a small and insignificant element when taken in a global context is an advanced one.  They also promote the idea of the Earth as a living entity, which is significant in allowing for the planet’s sometimes unfathomable rhythms and motions, and a very important concept for other reasons which I shall return to in a moment.

Here's another silly old fable which we can ridicule! It was a primitive tribe's attempt to show what they thought of a molecule - a bunch of coloured bouncy balls joined with tubes. Well, how are molecules really? Can atoms have colours when they're smaller than light wavelengths? How about those tubes and letters floating about? Of course, it's absurd. How silly they were in those days! Well, we can laugh at it now, but in ancient times - oh wait, hang on, no no, this is our current way of explaining an unimaginable idea. Sorry!

In other words, elements in all these myths – fantastic as the imagery may seem when looking for precise diagrams and formulas today – correctly mirror the purely incidental nature of upheavals in the solidity of the very ground on which people lived, no matter how disruptive or damaging they may be, and they embody the highly advanced idea of man’s relative insignificance in the universal scheme of things – a theme one of humanity’s most advanced intellects – Stephen Hawking – often returns to, to hammer his point home.

So the language and imagery might be primitive, but this is normal human communication and doesn’t seem to have been superceded at all.  Just ask Stephen Hawking about “human bacteria” on a tiny planet, or Richard Dawkins about the “currant bun” atomic model.   My three year old daughter once rushed in from the garden, wailing, “I’ve scratched two of my legs!”  It might have seemed funny, but I hardly needed to correct her: the message – even if her vocabulary lacked the word both – was still heartfelt, and clearly understood.

Dawkins’ habit of leaving the observer out of the reckoning might explain why the brain and consciousness are not covered in his book but also leads to simple errors.  He declares that his love of a Jules Verne story in which the hero flies to the moon and sees colours undreamed of on Earth, is sadly a fantasy, as we will only ever see all the colours that exist now.  “There are no colours outside the range that we are used to.” (p170)  He forgets that colour is a projection of five special molecules of the opsin family, which (incredibly) yield electrical impulses in response to photons.  But there are some tetrachromatic retinas – in many animals, and seemingly in more than 2% of women – able to perceive not just the three primary colours but an additional one yielding another part of the electro magnetic spectrum altogether which I can neither know or describe.

Bearing that in mind, it is quite possible that the man of the future may be blessed with additional colour vision, just as our ancestors in the distant past – according to Pictet’s study of languages, and as we would expect after evolving from the animal world – saw perhaps only two colours – red and black.  How the universe would look to even a slightly altered visual system, it is hard to imagine.  How it would look to a massively altered one – whose components might already be encoded in the genes – it is impossible to say.

It has been established that the Himba people perceive colors differently from most Euro-Americans – they easily distinguish close shades of green, barely discernable for most people.

The leading explanation is that the Himba created a very different color scheme which divides the spectrum to dark shades (Zuzu in Himba), very light (Vapa), Vivid blue and green (Buru) and dry colors – probably due to their specific way of life. However other explanations exist that have not been ruled out yet.

[Wikipedia]

Pp 210-211, illustrations by Dave McKean, Magic of Reality

The Japanese myth of the giant fish is especially accurate in showing the apparently solid land mass being not fixed but floating on a movable layer of some sort, a seemingly impossible concept at the time but which of course proved to be the case.  The Maoris take the idea a stage further by proposing that quakes arise from a process of birth, which has a truth of a different sort, as the tectonic plate movements do give rise to new land formations – on which people can live – over tens of thousands of years – a fact that the Maoris could not possibly be expected to have known intellectually.

The habit of describing concepts visually to express understanding is common even among the scientific.  Rutherford describes his concept of the atom in terms of what all could imagine: a solar system, and JJ Thomson’s earlier version was referred to as the “currant bun” model.  Both prove to be wildly inaccurate, but neither comes in for criticism!  On page 92 Dawkins himself describes carbon as being like a Tinker Toy building set, or a school of fishes, or soldiers marching in formation, in three dimensions.

Sherlock made his move:  “Watson, come here – I need you.  Arrest this man!  Yes, you rascal, this is the myth police!”  Spring Heel’d Richard was unrepentant: “It’s a fair cop, you rozzers – but Catholicism is to blame.”

The “Tree of Life” of myth and fable is a good example of persistent imagery.  These days, of course it has been replaced by a far grander, more detailed, more technically accurate and impressive analogy – wait until you see it!  Can you guess what it is..?  Well, it’s sort of – sort of a tree actually.  But it has branches and we’ve added names and everything.

That Eukarya moment: science's Tree of Life. Is this an advance of concept, or only of detail? "..the Pueblo and Navajo peoples have a myth of life that is a tiny bit like the idea of evolution: life emerges from the Earth like a sprouting plant growing up through a sequence of stages." (p.56, magic of Reality) A lot like the theory of evolution, I would say, from looking at this very scientific tree!

All of these cases show that natural intelligence has had a hand in man’s mental upbringing from the very earliest times, with the inference that if advanced concepts beyond the reach of the average man were available to those with a gift for natural intelligence, it must also be the case that the modern state of knowledge could benefit likewise.  To say otherwise would imply that advanced conclusions are only possible at rudimentary stages, which belies evidence of modern inspiration in modern times, and the associated desire to seek it out, to further one’s aims.  Inspiration is as much a part of reality as incremental scientific discovery, as the progress of science is filled with leaps of genius.  Strangely:

..The ancient civilisations of Greece, China and India all seem to have arrived at the same idea that everything is made from four “elements”: air, water, fire and earth. (p.77)

Nor can natural intelligence be criticised as crudely lacking in precise, factual detail:

In the 1920′s a now famous German scientist called Ernst Mayr did a pioneering study of the birds of the New Guinea highlands.  He compiled a list of 137 species, then discovered, to his amazement, that the local Papuan tribesmen had separate names for 136 of them. (p.55)

..Richard Dawkins, the Magic of Reality

Natural intelligence presents itself in surprising ways.  I have been studying amino acids, with the hope of building a working hemoglobin molecule, and was a little daunted by the complexity of the structures, and the difficulty in understanding all their functions.  One night after studying my sketched images of the molecules intently for about an hour, I had a dream in which three rabbits, one a dirty charcoal gray, were hopping about, followed by a mouse darting from place to place.

New engineering problem, new amino acid at the ready: "a big surprise was the discovery of a 22nd amino acid in methane-producing archaea of the family Methanosarcinaceae in 2002: pyrrolysine. The archaea use it in proteins that they need for energy conversion. Pyrrolysine is located in the catalytic center of the proteins and is essential for their function. The energy generation process of the archaebacteria would not work without pyrrolysine." (http://www.sciencenewsline.com/biology/2011111900320007.html)

I’d hoped for some blinding flash of revelation about amino acids and was disappointed to see such mundane use of dream imagery.  Then I realised that the three most common components of the amino acids – carbon, nitrogen and oxygen – arranged themselves in hops from one fixed arrangement to another, whereas the hydrogen ion could move among many more points and had much more flexibility in its arrangement, darting from one place to another in many smaller, though still discrete, steps.

To further bolster this interpretation I realised that the gray rabbit must represent carbon, since carbon in one state can be as soft as charcoal!  I admit there is also the old saying, “you can’t catch two rabbits” which perhaps is also near the mark.. I try to do too many things sometimes.   My other ambitions this year are to put together a Christmas rock concert with the school band to trump even our last one, write a book, have an exhibition of paintings, and build a working molecule.. and  I suppose I had better earn a living and write some software too.

Hydrogen ion and carbon molecule considering a union

Myths have something else in common which perhaps understandably – as it undermines the purely scientific aim of the book – has nevertheless passed beneath Richard Dawkins’ attention – they propose a personality or intelligence (albeit motivated by concerns and worldviews completely beyond our own narrow existence) behind surprising Earthly phenomena.  And wherever you have a personality, you can draw two conclusions: one is that a predictability of some sort must exist, and therefore the possibility of analysis.  For example, the kickings of a baby in the womb might not be predictable, but the constant nature of birth is, and is related in some way to the normal human concept of birth, and its importance to the overall progression of the universe can be appreciated.

But the other conclusion is that natural forces are represented as having a personality to which humanity must be related if only by virtue of having one of our own.  In the myths, this is by virtue of a shared life – ours brief and narrow in scope, compared to beings portrayed on a universal level with vastly greater aims and vision.

Suppose then that we have two groups of people, one of whom believing the Earth to be a living, intelligent, and sentient life form – albeit with a lifespan of billions of years – which has given birth, somehow, to all life upon it, including us, and granted us the air, water, nutrients, warmth, food and shelter with which to thrive and follow our destiny.  Foolish, and primitive?  Well, take the second group then, which believes the Earth is a lifeless resource fit only to be consumed and devoured, or manipulated, flattened and trashed in accordance with our wishes.

Of these two worldviews, which do you suppose is fit to live in harmony with a planet?  And after a millenium of one or the other, on which would you prefer to be born?  The modern era was bequeathed an unspoilt paradise, largely by those who abided by the spirit of the ancient myths treated as absurd in the Magic of Reality.   very well, then – what kind of shape have we left it in?

Food for thought – and Happy New Year to all readers!

"When you look at it from up here, you get an appreciation that our world is a beautiful place, and we really do need to take care of it".. Sally Ride, first American woman to enter space, with a concept no different than that of the ancient myths: that our planet is to be considered as we would any living being. This simple idea carries far more weight than treating every aspect of the world separately, complicating the answer to what is a very simple question: one of respect

Mitcha Anderson from Amazon Watch: explaining that Chevron built thousands of pits in the Ecuadorean rainforest, in which they dumped toxic waste: each had overflow pipes guaranteeing that rain would carry the pollutants into nearby streams, poisoning both the people and the ecosystem - 50% more oil was spilled in the "Amazon Chernobyl" than in the Transocean/Halliburton/BP Gulf spill. Ecuador is seeking $18bn in damages: this was upheld in a New York court, after which a roomfull of lawyers over at Chevron changed tack and requested to be tried in Ecuador instead - perhaps hoping a quick bribe might get them out of a sticky black mess. Instead, unsurprisingly, the court upheld the ruling

A tendency to leave the human element out of the equation altogether results in lengthy discussions and promotion of technology while never mentioning its careless use or even deliberate abuse. The problem is of human nature - the element often left out of the equation altogether - with the difference now that technology magnifying human disdain has the power to disrupt the balance of a 4.5 billion year old planet, something no tribe of former times could do - or would ever want to

Posted in Chevron's Amazon Chernobyl, Dreams, Education, Genius, Intelligence, Junk DNA, Myths, Richard Dawkins, Science Watch, Sixth sense, Spiritual Genius, The Brain, The Magic of Reality | Tagged , , , , , , , , | 2 Comments

Wise Wittgenstein

This is part of an illustration – altered to feature different text – by Dave Mckean on p102 of Richard Dawkins’ The Magic of Reality:

McKean's illustrations - which are on virtually every one of Magic of Reality's 265 pages - are very impressive in their diversity and fluency, all the more so considering they must have been assembled in somewhat less than 16 months.

McKean proves to be an imaginative illustrator, caricaturist, draughtsman, digital manipulator, portrait artist, cartographer, graphic designer, comic strip creator and storyboarder – and intriguingly, though undoubtedly under pressure of time he never resorts to duplication of even seemingly insignificant details, instead rotating their perspective and shadowing or otherwise varying them to fit a slightly different sequential context.

For example, in the picture above you can see the chairs are not mirror images of each other in any aspect.  The book itself is very readable, though surprisingly has no introduction to the brain or the nature of consciousness, understandable perhaps if Dawkins considers their natural offshoot – the phenomenon of spirituality – as merely an erroneous extrapolation of ancient myth.

The original text details Ludwig Wittgenstein’s discussion with a pupil of his about the justification for man’s persistent error in thinking that the Sun revolved around the Earth being simply because it looked that way.

But I find the argument surprisingly portable – perhaps because although Earth-centric thinking has long since been corrected, the way in which even highly educated people think has not changed at all!

Posted in Great thinkers, Intelligence, Ludwig Wittgenstein, Natural Intelligence | Tagged , , , | Leave a comment

More Non-Random DNA Wonders

Links to the following five research articles are given for those who wish to delve more deeply into their reasoning, but the gist of each is as follows:

(1)  The codon bases have a non-random correlation with the kind of amino acids which they code for.  In other words, the first out of the three letters of a codon actually relates to the kind of amino acid chosen, which gives the language a deeper meaning that might have relevance to the efficiency of the error checking machinery

"Now class, what does this circular chart represent..? Yes - Mr Dawkins? Tsk tsk! It is most certainly not a dartboard. Ah yes.. you there at the back - Dennett, is it..? Good God, no, it is not a roulette wheel either! Has even a single one of you done your homework?!"

(2) The greater or lesser effect of errors (mistranslations) of duplication within the DNA code is called the “load on the code” and is minimised by its current arrangement to such an extent that only 3 in 100,000 other possible codon mappings would have a marginally safer error rate.

To further add to the unlikelihood of randomness the 100,000 subset was already made on the assumption that all 100,000 would already be given the advantage of the type-signifant first letter of the codon (detailed in (1) above) known to have an error-reduction benefit.  [The number of completely random alternative arrangements which would be less effective at error-reduction - by virtue of a random first letter - would be 64*63*62*61*60..*45 which if we forget about start and stop codons I work out as 47,732,870,256, 486,900,000,000, 000,000,000,000.  Then take away 36,267,774,588,438,900,000 which is the 3 results per 100,000 estimated as being more fault-tolerant than the current design - giving a "bad set" of 47 * 10 to the power 33 - which means if you had a trillion planets around every known star in the Universe, you could try a different arrangement on every planet and still only get a highly fault tolerant system once.]

But none of these arrangements, assumed to be more fault tolerant (which they may well be) have been evaluated as to the effect they would have on other processes such as speed of protein assembly within the ribosome, or the combined molecular effect of the billions of changes throughout the length of the entire chromosones.  Suffice to say that it can only be a non-random safety level which adequately explains why life forms can remain perfectly functioning and unchanged for 200 million years (sharks).. 160 million years (Isopods).. or certain insects presumed to have formed during the Silurian period (400m years ago), during all of which time the codon mapping must have remained constant – unless it is suggested that an intelligent mechanism substituted the codons and the duplication equipment while keeping the protein synthesis identical.

Anticodon-amino acid enrichment observed in ribosomal structures is correlated with the canonical genetic code. The distributions of the average enrichment value of codon (Left) or anticodon (Right) for 1,000,000 random codes are shown with the arrow pointing to where the canonical code stands. The correlation analyses were performed using (A) a specific subset of amino acids that is optimal for the canonical code; (B) all amino acids except cysteine; and (C) a subset of amino acids optimal for each code. A significant proportion of randomized codes have a lower average enrichment than the canonical genetic code in ribosomal anticodon-amino acid enrichment. (www.pnas.org)

But, as Richard Dawkins says in his analysis of the laryngeal nerve (specifically of the giraffe but in general, also in the human design) and its evolution from the fish model, the DNA can’t go back and start again.  Since the embarrassing “backwards retina is bad design” argument has long been discredited, let’s at least agree to rule that out.

160 million year old genetics -- yes, still working fine!

(3) the present coding system is given further weight by finding that within the ribosome, anticodons are enriched near the areas relative to their function within the ribosome, to a level such that the probability of this effect being random is extremely low.  In other words, the ribosome behaves as if it’s already geared up and ready to work with the existing code – and yet the ribosome seems to be one of the most ancient parts of the whole DNA engine.

..beautiful graphic from http://ionsource.com/virtit/VirtualIT/aainfo.htm

(4) and speaking of ribosomes, they are so well structured that even when the component parts are broken down by chemical catalyst into long molecular fragments and more than fifty different proteins – they reform into a functioning ribosome as soon as the divisive chemical forces have been removed, independent of any enzymes or assembly machinery – and carries on working.  Design some machinery which behaves like this and I personally will build a temple to your name!

Maybe he simply threw the dice 10,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000,000 times. But who swept up all the rubbish? Image: http://faithforthinkers.blogspot.com/

(5) and last but not least, evidence that the DNA is a toolkit: non-random correlations between similar structures – unsurprising in itself – but occurring in completely unrelated proteins.  This is evidence that the same kind of engineering underlies separate biological components when similar functionality is needed.  With a smallish toolkit of 20 amino acids, you would expect random constructs to be full of illogical or redundant features that other components somehow had to compensate for.

What you actually find is that protein structures are so perfectly aligned that they  immediately spring from a two dimensional pattern into a three dimensional shape (complete with cross-member welds, sprung sections, and fully integrated behaviour such as expansion and contraction completely reliant on a perfectly balanced three dimensional design) via the laws of physics, chemistry and electrical engineering, and further, in their actions fulfilling laws of biology.

They are so hard to understand because understanding requires mastery of all these schools of thought as well as the ability to think in terms of three dimensional electrical forces.  The speed at which they snap into shape and later carry out their functions is frightening – as many as ten million actions in a second, in the case of some enzymes.  This ingenuity and success does not lie in the three dimensional state – at this stage it is already too late to modify the strip of amino acids to correct for errors – but in the original two dimensional strip of DNA.   This is a staggering achievement by any standards.

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1. Non Random Codon – Amino Acid Mapping

For the first time it is shown that each of the three codon bases has a general correlation with a different, predictable amino acid property, depending on position within the codon. In addition to the previously recognized link between the mid-base and the hydrophobic-hydrophilic spectrum, we show that, with the exception of G, the first base is generally invariant within a synthetic pathway. G– coded amino acids show a different order, being found only at the head of the synthetic pathways.

The redundancy of the nature of the third base has a previously unrecognised relationship with molecular weight. The bases U and A (transversions) are associated with the most sharply defined or opposite states in both the first and second position, C somewhat less so or intermediate, and G neutral. The apparently systematic nature of these relationships has profound implications for the origin of the genetic code. It appears to be the remains of the first language of the cell, predating the tRNA/ribosome system, persisting with remarkably little change at a deeper level of organisation than the codon language

http://www.sciencedirect.com/science/article/pii/0303264789900592

Molecular representation of a ribosome: 250,000 atoms. The idea that a superhuman intelligence can understand it actually gives a target for human intelligence to aim for, since if it was a completely random design, there would be no point in studying its particular arrangement with the hopes of understanding its logical function, since any other random arrangement might be equally effective

2. Non Random Fault Tolerance in Codon Mapping

The average effect of errors acting on a genetic code (the change in amino-acid meaning resulting from point mutation and mistranslation) may be quantified as its ‘load’. The natural genetic code shows a clear property of minimizing this load when compared against randomly generated variant codes.

Here then, we ask whether this ‘historical’ force alone can explain the efficiency of the natural code in minimizing the effects of error. We therefore compare the error-minimizing ability of the natural code with that of alternative codes which, rather than being a random selection, are restricted such that amino acids from the same biochemical pathway all share the same first base.

We find that although on average the restricted set of codes show a slightly higher efficiency than random ones, the real code remains extremely efficient relative to this subset P = 0.0003. This indicates that for the most part historical features do not explain the load- minimization property of the natural code. Once mistranslational biases have been considered, fewer than four per 100,000 alternative codes are better than the natural code.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1689495/

3. Non Random Anticodon Toolkit in Ribosome

The establishment of the genetic code remains elusive nearly five decades after the code was elucidated. The stereochemical hypothesis postulates that the code developed from interactions between nucleotides and amino acids, yet supporting evidence in a biological context is lacking. We show here that anticodons are selectively enriched near their respective amino acids in the ribosome, and that such enrichment is significantly correlated with the canonical code over random codes. Ribosomal anticodon-amino acid enrichment further reveals that specific codons were reassigned during code evolution, and that the code evolved through a two-stage transition from ancient amino acids without anticodon interaction to newer additions with anticodon interaction. The ribosome thus serves as a molecular fossil, preserving biological evidence that anticodon-amino acid interactions shaped the evolution of the genetic code.

http://www.pnas.org/content/107/18/8298.full

Analysis of ribosome structures, shown on the left, from four different species revealed a non-random affinity between anticodon-containing RNA triplets and their respective amino acids, shown on the right). Credit: David Johnson, Salk Institute for Biological Studies

4. Self-Assembling Ribosome

Ribosomes are complex cell organelles consisting of ribosomal RNA (rRNA) and a number of different protein molecules. One of the major questions one can ask about the ribosome is how these component molecules are assembled into the final organized structure. As described in the preceding article, we have recently succeeded in developing a reconstitution system that, under well-defined conditions, produces physically and functionally intact 30 S ribosomes from free 16 S RNA and free 30 S ribosomal proteins from E. coli (Traub and Nomura, 1968). Reconstituted 30 S particles synthesized under optimal conditions were found to be indistinguishable from the original 30 S ribosomes with respect to their sedimentation coefficient, their protein composition, and their capacity to bind aminoacyl-tRNA and to synthesize protein in response to messenger RNA (mRNA). Furthermore, this total reconstitution system proved to be independent of the presence of additional macromolecular structures…

http://symposium.cshlp.org/content/34/63.extract

5. Toolkit Structures in Protein Amino Acid Sequences

Unrelated proteins with high percentage identity. Hemoglobin β-chain (pdb code 1hds chain b, ref. 38, Left) and cellulase E2 (pdb code 1tml, ref. 39, Right) have 39% identity over 64 residues, a level which is often believed to be indicative of homology. Despite this high degree of identity, their structures strongly suggest that these proteins are not related. Appropriately, neither the raw alignment score of 85 nor the E-value of 1.3 is significant. Proteins rendered by rasmol (40).

http://www.pnas.org/content/95/11/6073/F2.expansion.html

Why reinvent the wheel? ..Exactly

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Posted in Amino Acids, biology, Designs in nature, Evolution, God, Nanotechnology, Ribosome, Science and Religion | Tagged , , , | Leave a comment

Dreams Do Come True!

A few months ago I had an intriguing dream.  In it, my mother and my late father were sitting beside each other behind a white desk, leaning forward expectantly towards me, and looking very bright eyed and happy.  Above the desk was a fancy light, a complex of various twisted and folded rounded tubes, suspended from the ceiling.

A week or so later, my mother told me that in memory of my dad, she had been organising a donation to the Toronto General and Western Hospital with the idea of creating something of use to technologists and hematologists there, and thanks to the imagination and active participation of dad’s colleague and good friend Dr Dominic Pantalony, it was now just a question of organising the opening ceremony.  When I heard that, I saw that the dream signified my mother and father creating something together, and I also took it to mean that my father was very enthused about it.  She was nonplussed by my dream, but my family is used to these eccentricities of mine.

My father’s brother, the late Lindsay Steven Carstairs, at age 20 had been the youngest doctor to quality in the UK in 1939, when my father was only ten years old.   Both were accomplished musicians and artists but their father had insisted they both become doctors: Steve became a radiologist – there’s a library named after him in Faro – while dad became a hematologist:

Notably, Dr. Carstairs was the first person to identify drug induced autoimmune hemolytic anemia and his seminal paper published in Lancet (Incidence of a positive Coombs’ test in patients on alpha-methyldopa, Carstairs KC et al, Lancet 1966; 2: 133-135) is still referenced in the latest editions of major text books.  Throughout his career he was published in prestigious journals such as the American Journal of Respiratory Cell and Molecular Biology, The Journal of Pathology and Bacteriology and Cancer Genetics and Cytogenetics.

Dr. Carstairs retired from the University Health Network in 1994.  In tribute to his life’s work his family, together with the Department of Laboratory Hematology, established the Kelvin Carstairs Fund for Education in Laboratory Hematology in 2008. The purpose of the fund is to advance the education of laboratory hematology technologists through educational events, seminars and conferences held within UHN as well as externally.

[Biography prepared by Robert Windrum]

Later, on reflection, and after seeing similar curved shapes in my incursions within the fascinating field of proteins, I realised the tubular light must have represented hemoglobin, or a comparably complex protein, onto which light might well be shed by this research facility.  The dream therefore was an elegant cipher of many ideas in one very easy to remember image, imbued with a very positive feeling, although I remember feeling a little embarrassed, seeing as I’d had nothing to do with the organisation of any of it.

Some of the remarkable equipment available, for shared analysis and digital transfer of diagnostic information

Some of the money went towards a research room which was opened four days ago, and I was invited to give a small talk for ten minutes on behalf of the family, which I was delighted to accept, despite my usual fear of public speaking.  We just returned from yesterday – which explains the lack of posts on this blog.  The reception afforded us at the hospital was wonderful.  Some of the technologists and administrators had worked with dad for many years, and were unfailingly enthusiastic in their memories of him.

Opening the ceremony, a Dr Sheridan who, like us, emigrated to Canada from the UK, opened the event by recalling Dad’s welcoming advice: “Canadian wine is so poor you can’t drink it.  Don’t delude yourself – you can’t even use it for cooking.”  Another memory expressed was his insistence that quality is truth: the greater quality produced in their lab analyses, the nearer to the truth they approached with the diagnostic information yielded.

I’d worked out a few things to say and the moment I pushed through the nerves and stood up it seemed that people connected.  This is not always the case in the software world, where once-bitten types are understandably looking for some weakness or exploitative aspect in your approach, sometimes just to make their authority felt.  But this meeting felt more like that of an extended family.

Frinton on Sea, 2004

I felt privileged to be part of such an event, seeing as I contributed nothing other than turning up.  I also saw the dedicated, generous, enthusiastic nature of these unsung heroes of the medical world, and it seems to me that with such personalities at the sharp end of research and education, the future of medical progress must be in very good hands.   Well done, Mum and Dad.

..his favourite comic strip: the cerebral Pogo, by Walt Kelly

Posted in biology, Education, Hemoglobin, Uncategorized | Tagged , , | 2 Comments