The Universe Within

Close your eyes. All around is darkness.

Now imagine that you within yourself, An electron in a lower rib.

Look up, your inner space is the heavens, Your molecules seem as far apart as the stars. Vast spaces exist between each part of you. Your organs are galaxies.

And yet you know what your electron sees has order, symmetry and function, Spiralling energy fields unite and govern. Intelligence invisibly pervades.

Stay quiet for a moment and look at yourself. All you see is true. For this is what you really are, From the viewpoint of an electron.

And you ask yourself, is the world without, like this world within?

Come Closer

Imagine, you have grown vastly and are now a molecule within, floating by an underwater city; by the side of a cell.

You see other cells looming in the distance In the sea that surrounds. Colours flicker on their surfaces. They seen like vast ocean liners, floating factories, power stations.

Bright pulses flash as messages race from one cell to another, photon to photon, across vast oceans, fingertip to fingertip, co-ordinating movements.

From the cell you can see cargo ships being launched - as retroviuses bud out carying precious genetic information encoded. Others arrive, dock at your cell and pass in their codes. Within the precious cargo is being woven into the tabestry of your ever evolving DNA.

The sea is teeming with activity. Wrecking crews take away the now empty ships From horizon to horizon the cell cities pass by. Between them, a thousand fleets of virus boats pass, Liquid crystals carrying information

Some cells are rich red with oxygen to fuel all. Others, paler, watch for intruders .

Only the odd ship or city is weeded out.

In general harmony Harmony, co-operation, seems to be the spirit of this world.

YOU GROW

To cell size and become aware that around you

vast numbers of cells are grazing, the buffalo bacteria of your inner plains.

And the more you look, the more you see that there is a multitude of species, herds of bacterial giraffes, deer and rabbits, forests of fungi, shoals of viral fish, all seemingly living in harmony.

, . And you become aware of something else. An ether, watchfulness Above all cells, above the herds, forests and shoals, An over-riding intelligence

A consciousness reaching beyond your vast universe.

It rules your world.. Is it Gaia? Is it God?

No - it is you. The cellular cities, the virus fleets, the myriad herds, are ruled by you. You are responsible for their welfare. You govern their atmosphere, their oceans.

You are Gaia, you are God of your inner universe,

Yet they are part of you

and In their harmony rests your health and well-being.

\ For your divinitydoes not exist unless in conjunction with them

for this God and Creation canot be separated.

But before you go, reflect, meditate again. For big as you are, You are also the smallest.

Look out of the window at the universes beyond.

Is our inner world an image of the whole?

Comments on the above meditation

It pictures an inner world that is normally and healthily ruled by harmony but if one listens to many virologists a very contrary impression is given of the same world. They speak of a world ruled by selfishness in which constant warfare rules. Retroviruses are said to hijack, invade, subvert - as if they are essentially non-terrorists rather than something that every healthy cell produces in order to transport codes - which is 101 biology. They thus encourage the public to fear this inner world - and to massacre it with antibiotics.

All viruses, all bacteria, are primarily seen in this view as potential enemies, outsiders, strangers, invaders. If we could, we would put up passport controls to prevent their entry.

Their view reflects St Augustine of Hippo's highly influential teaching, who in his work 'The Two Cities' depicted our world as fallen into disharmony and ruled by Satan. In this lower world we are constantly at warfare with the forces of evil. Harmony exists elsewhere, in a separate supernatuatural 'City of God' or Heaven. In his teaching the souls of non-human beings, called 'daemons' by the Greeks, became our 'demons' - evil creatures that we have to fight.

In this world-view our survival is through being selfish. We hunt out and kill all possible rivals in an endless war of survival. Thus the theory of the selfish gene. It is todaybut an application of the worse of the capitalistic ethic to the inner world, and a very militaristic and masculine view of our world.

The contrasting perhaps more female-view is that survival is through cooperation and learning to live together - and this is precisely what we see our microbes doing. It is well known in biology that we live best together through serving each other's needs. This seems to be true of the vast numbers of microbe and fungi species that live within us.

Lets look at some examples. This is what the BBC website currently reports about a major family of viruses in us, the retroviruses, that carry double strands of genetic code in the form of RNA. "HIV is a particular kind of virus - a retrovirus. While simpler than ordinary viruses, retroviruses tend to be harder to defeat. They embed their genes into the DNA of the cells they target, so that any new cells that the host cell produces also contain the virus genes ... Furthermore, the "envelope" the HIV virus particle is contained inside is made of the same material as some human cells, making it difficult for the immune system to distinguish between virus particles and healthy cells."

Let's look on this from the viewpoint more common in biology. It has been known since the 1980s that every cell, no matter if in a human, a bird or a vegetable, produces its own retroviruses - perfectly healthily. This is part of the natural process of life. We have in each of our cells tiny engineers, "transposons", that constantly rework our DNA in an apparent effort to find new combinations that work better. It is how evolution happens.

Sometimes our cellsdecide to share pieces of this code with other cells - when they do, they bud them out of the side of the cell, wrapping them as they go with a protective coat of protein. They are then 'retroviruses' travelling with their cargo between cells.

But from the viewpoint reflected in this BBC report, which is only reflecting in this the dominant ideology, retroviruse by being made of parts of us, are not of us, but deceptively 'harder to defeat' enemies infiltrating our fortress. What about coming to the obvious and opposite conclusion? They are simply parts of us - and this is why our immune system does not attack them.

The BBC report then goes on to say "It hijacks the cell, inserts its own genes into the cell's DNA and uses it to manufacture more virus particles. These go on to infect other cells. The CD4+ host cells eventually die, although scientists do not know exactly how."

What about trying for size a different interpretation of the same facts? The retrovirus arrives at a cell and passes into this its cargo of genetic code. This is welcomed by the cell and incorporated into its DNA. Thus genetic information is shared. The container that brought the cargo is thrown away, and becomes debris in the blood - it does not continue to exist as a retrovirus.This is what actually happens.

Later on the cell produces more retroviruses - for this is what cells do. They bud harmlessly out of the side of the cell. When these arrive at other cells, they are not fought off as invaders - but their cargo is accepted. This is why each cell has receptors to bring this on board - to serve its needs, rather than to serve an invading 'infector'. It would be ridiculous for it to have evolved receptors otherwise .

The BBC goes on to report that the cells 'eventually die' (as all cells do) although scientists do not know exactly how." Yes, exactly. Despite over 20 years of monitoring and the spending of over $190 billion on HIV research, a retrovirus has never been seen to kill a cell.

And to give another example: this is a description of retroviruses given in a BBC report about Israeli virologists. "REHOVOT, ISRAEL -- April 13, 2005 -- Retroviruses are among the trickier and more malicious disease agents, causing AIDS and cancers such as leukaemia. The viruses manage to sneak into cells with the help of special protein assemblies scattered all over their surfaces. These retrovirus surface proteins cause the membrane envelope of the virus to fuse with the membrane of the cell, spilling virus RNA into the cell to wreak damage."

There is little need to comment. They 'sneak' in - by using the receptor proteins that our cells provide for them! The BBC here describes all retroviruses, not just HIV, as malicious disease agents - no hint here of them being any value to us - or being naturally made by our cells - as taught in all biology courses.

When I came to look at the original research claimed to link retroviruses to leukaemia and to AIDS - I was shocked to find that this was primarily because an enzyme RT (reverse transcriptase) was found in the cancer - and also in lab samples taken from AIDS patients. The researchers in their published papers expressly claimed RT was unique to HIV, thus its presence proved the virus present. But today it is widely known, and taught in our secondary school biology courses, that RT is naturally present in every cell of the human body and not unique to any retrovirus. This was well known in science at the time of these experiments. RT is used by all cells to move DNA about by shifting it into a more mobile form, RNA. But this is a whole different story of scientific errors that I will tell in other articles posted here.

The Function of Viruses

I write above of retroviruses, as these are the viruses our cells produce - but what of viruses as a whole. How different are they as a family?

It seems they tend to move more from one person to another, or from species to species. They carry their genetic code in the form of DNA or RNA - while retroviruses only carry it as RNA. They are of a wide variety of shapes and sizes - while retroviruses are defined as of a particular size. They carry their codes to cells, just as retroviruses do, but then they are not always harmless in their effects. This could be because their codes have originated outside us - and may not be in harmony.

But this is something humans have lived with since the first. Could it be that their general beneficial effects outweigh the harmful?

In biology their role in the first cell, our most distant relative, is now in open discussion. The vital energy centre of our cells, the power station of our mitochondria, is widely thought to be an inclusion in our cells that once lived outside us. The transposons within our cells that give our DNA adaptability - could they have once have been retroviruses? In other words, did our cells evolve out of a group of virus and bacteria that came to live together as a cooperative whole?

Could it also be that the microbial kingdom is still contributing to our welfare and genomic adaptability by providing us with useful new genetic codes? Is this why our cells have evolved receptors to allow these codes to enter? Is there a symbiotic relationship between viruses and us?

Dr Luis P. Villarreal, the Director of the Centre for Virus Research, University of California at Irvine wrote in an article entitled 'Can Viruses make us Human?' 'This question will seem preposterous to most ...their effect on host evolution has long been thought to be like that of a predator on its prey, eliminating the host with weakened defences. How can we propose any constructive role for viruses?' He goes on to argue that 'stable persisting viruses represent a major creative force in the evolution of the host.'

He notes that genes cannot explain the differences between the apes and humans, as they are practically identical in both, but he finds something else that can. A much larger part of our DNA has been assembled with the help of retroviruses. This was once described as 'junk or selfish DNA,' simply because scientists did not understand its function. But this retroviral inheritance is very different in humans and in apes. He notes that most of this is clearly from 'endogenous retrovirus' (ERV) made by human cells and that this might well have 'endowed the host with major creative acquisitions in the evolution of life', even the ability to talk.

Nevertheless he still refers to retroviruses as 'parasitic'. This language I feel comes from seeing these viruses as separate entities that use humans rather than as part of humans. He speaks of their codes in our DNA as 'products of past colonisation events by persisting genetic parasites'. This suggests they came solely from outside us.

The word 'parasite' describes independent creatures out to survive by drawing energy from other organisms. Human retroviruses are no such thing. This interpretation belongs to the selfish theory of evolution where every particle is out for itself. But what if there is cooperation - would they then be parasites?

Many scientists also say viruses are not living creatures. They say this is confirmed by drying them, for they turn into crystals - that later can be restored to live by hydration. But why should this mean they are not alive? It all depends on how life is defined. Others say organs of reproduction are needed to be alive - but why? Retroviruses are born as part of us. Surely they share our life?

What then of the other viruses that our cells may also birth, such as measle viruss, flu and more? We too produce them - but with imported codes that are more foreign. They may be distant ancestors perhaps, may be dangerously dissimular, but are still alive.

When working out our 'theories of everything' we have long left ourselves out of the equation. We known we are sentient beings, self-aware, conscious and intelligent - all properties we then leave out of our general theory of everything as if we are not part of nature. In the meditation above it would be an error if an electron similarly declared no sign of intelligence and consciousness in the world around it.

We cannot so easily separate ourselves. We now know the basic amino acids of life pervade space, but what we are not so aware of is that we ourselves live in oceans of genetic codes, Lengths of code are present by the million in the water we drink and bath in, in the very air we breath. They swirl around us. They are the codes of life, the detailed information that life uses to build the bodies it inhabits. Yet today many scientists see many such codes as pathogenic - and thus declare us in danger.

Many such codes float without protection. They can be from dead cells. When lengths of code are protected by a coat of protein molecules, then we call them viruses. When much longer lengths of code are enthroned in water within a protective protein shell, then we call this a living cell.

Some biologists today are challenging Darwin; they say the way our cells manipulate DNA indicates that random events do not govern evolution, that he got his theory at least partly wrong, that our cells are living information systems, constantly monitoring their environment and making appropriate decisions.

When a survival crisis looms, then our cells are equipped to make dramatic decisions, involving large movements of DNA and, substantial genomic changes - and perhaps large shifts of genetic codes from cell to cell through the use of retroviruses. This is what we now observe in our laboratories.

However Darwin admitted he might have got evolution partly wrong in the later editions of his work. He said 'spontaneous' changes in cells perhaps are not so spontaneous, that he may have made mistakes 'in our ignorance' of how they work. He wrote: 'It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure, independent of natural selection.' (Origin of Species, 6th edition, Chapter XV, p395)

This is how hospital 'super-bugs' evolved. We know that threatened by antibiotics they evolved immunity from these drugs. But they did not do this by using tools unique to them. We have the same tools in every cell of our bodies. We are constantly engaged in the same process, protecting ourselves from toxins. Why else do we mostly live to 80, when our environment is full of new toxins?

We also now know that these 'super bugs" did not acquire immunity by making antibodies, but by massive inner genomic changes, in which they made the genetic codes required to produce the chemicals needed to neutralise antibiotics.

The production of antibodies is also achieved through genetic changes. Certain white blood cells have the ability to rapidly cut and paste and reshape genetic codes on the massive scale required to produce millions of antibodies tailored to mark for destruction specific molecules.

How long have we known our DNA can repair and change itself? For quite some time. In 1984 Dr Barbara McClintock won a Nobel Prize for her discovery that the genome of every organism has systems for repairing and restructuring itself.

Before her time, the newly discovered DNA was seen as an encoded 'bible' containing instructions for building every part of us, a bible that rarely changed - and if so only through chance events. This was part of a mechanistic theory of life. What she found was that our DNA was instead a part of a dynamic system - not just a reference work but a book that is constantly rewritten as new information is assembled. This she said raised the question of if we had vastly underestimated the abilities of cells? In her Nobel Prize address she talked of 'how the cell senses danger and instigates responses to it that are often truly remarkable."

Evolutionary biologist Dr. James A. Shapiro of Chicago University is fascinated by the information systems within all organisms - and how experimental work shows cells seem to direct their own evolution and to make decisions - for this was totally unexpected. In the past biologists did not believe such higher functions of life existed in cells. He wrote 'The expectation of its [biology's) pioneers was that molecular biology would confirm the reductionist, mechanical view of life.1?3 However, the actual result of molecular studies of heredity, cell biology and multicellular development has been to reveal a realm of sensitivity, communication, computation and indescribable complexity.4?6

Accidental events cannot drive evolution, he argues, because 'the accidents are efficiently removed by cellular proofreading and repair systems' and 'a species that depended exclusively on independent random changes ...would not be very competitive in the evolutionary sweepstakes.

He then spoke of retroviruses, saying the codes they transport into our DNA 'carry with them a defined set of regulatory signals that can affect the reading of nearby DNA sequences in very particular ways. This is an example of non-randomness.' He adds, 'In addition to proof reading systems, cells have a wide variety of repair systems to prevent or correct DNA damage from agents that include superoxides, alkylating chemicals and irradiation. '22

He notes that the human genome contains in all some 2,8 million retrotransposons, making up some 42% of our whole genome. Our retroviruses are made by these. So what is a retrovirus? They serve us by networking our cells together, providing a way of sharing codes. Otherwise every cell would have to reinvent the wheel for itself.

So what then of HIV? Isn't that a retrovirus? The blaming of AIDS on a retrovirus is what has given them a bad name. But Dr Robert Gallo, who was the first to claim HIV was a retrovirus, already thought retroviruses highly dangerous. From the late 1970s he wrongly suspected them of being the cause of cancer since they were associated with genetic changes in our cells. We now know that cancer is mostly caused by toxins. The same year that Gallo announced he had found HIV, Dr Barbara McClintock was preferred to him by the committee that awards Nobel Prizes. But Gallo stuck to his more hostile theory of retroviruses, and so too has AIDS science . No other retrovirus is known to kill. To maintain his theory, AIDS science has had to award abilities to HIV unlike those possessed by any other retrovirus.

So what then of antiretroviral drugs used to attack HIV? If I am right in my more positive view of retroviruses, if the scientists quoted above are right, then we are attacking a virus that helped make us human, that plays a vital role in protecting us, that helps to form and to protect our DNA. Such an attack cannot but eventually make us very ill. Smithklienbeecham, a maker off these drugs, says they will cause body wasting identical to that seen in AIDS cases.

But in general, this issue is vastly larger than that of AIDS. The warfare model of microbial and cellula health affects our view of illness and of life - and dominates much of Western medicine.

I want finally to leave you with one thought - as this is my working hypothesis page. If intelligence and consiousness prevades our universe, just as it prevades our inner world, is this an alternative answer to the current debate over intelligent evolution and Creationism?

 

 

Some Online Reading and References.

Thinking about bacteria as multicellular organisms (1998)

James A. Shapiro. 1996. "Darwin's Black Box: The Biochemical Challenge to Evolution."   (book review) National Review, Sep 16, 1996 v48 n17 p62(4)

Shapiro, J.A. 1997. A third way [alternative to Darwinism & Creationism]. Boston Review 22 (1), 32-33. (at

Shapiro, J.A. 1999. Transposable elements as the key to a 21st Century view of evolution. Genetica 107 (1/3):171-179. (reprinted in Georgia Genetics Review I: Transposable Elements & Genome Evolution , edited by John F. McDonald, Kluwer, 2000)

Shapiro, J.A. 2002. A 21st Century View of Evolution . J. Biol. Phys. 28: 1-20. (PROCEEDINGS of the 4th International Conference on Biological Physics, Kyoto, Japan, July 30 ? August 3, 2001) 

Shapiro, J.A. 2002. Genome Organization and Reorganization in Evolution: Formatting for Computation and Function. In From Epigenesis to Epigenetics: The Genome in Context, L.Van Speybroack, G. Van de Vijver, and D. de Waele (eds.), Ann. NY Acad Sci 981, 111-134.

Lectures at the Institute for Theoretical Physics, UC Santa Barbara, March, 2001

Thinking about Genome System Architecture

Natural Genetic Engineering -- the Toolbox for Evolution: Prokaryotes

Natural Genetic Engineering -- The Toolbox for Evolution - Eukaryotes

Natural Genetic Engineering and Adaptive Mutation (1997)

http://www.iscid.org/james-shapiro-chat.php

Reverse transcription in genome evolution T. Mourier Department of Evolutionary Biology, Biological Institute, University of Copenhagen, Copenhagen (Denmark)

Cytogenetic and Genome Research   Vol. 110, No. 1-4, 2005 

Transposable Elements May Have Had A Major Role In The Evolution Of Higher Organisms