Friday, 12 February 2016

Natural technology: the virus (updated 12 February 2016)

see also Natural technology: the bacterium

http://micro.magnet.fsu.edu/cells/virus.html
a bacteriophage is typically 100 nm long (300 atoms)
one of thousands of highly efficient designs of virus
A few years ago I followed parts of a YouTube course on virology by Professor Vincent Racaniello and was awestruck by one statistic on the first module.


 If you could take all the bacteriophages (a bacteriophage is a particular type of virus which destroys bacteria), and lay them end to end, how far do you think the line would reach? The Moon, the edge of the solar system, the nearest star?  These are orders of magnitude too small. In fact the line would be 200 million light years. This compares with about 2.5 million to the nearest galaxy, Andromeda.  ( I have calculated this independently and get about the same distance. I have also checked the figure of 10exp30 below which was initially regarded with skepticism by biologists. 200 million light years is indeed the right figure. JLS)


There are 10power30 (1 with 30 zeros) bacteriophage viruses in the world’s water supplies. (I am not sure how he defines ‘water supply’ but it doesn’t really matter in this context.)  Elsewhere it has been pointed out that the bacteriophages in soil, water, air and living organisms play a crucial role in maintaining the natural, life-friendly balance of bacteria in the ecosphere. 

 He also points out that there are 10power16 HIV  viruses , of which only a tiny proportion have been discovered and it is almost certain that there will be an HIV virus resistant not only to every anti-viral drug we know about, but to any anti-viral drug  that could conceivably be developed in the future.


More extraordinary than the number of viruses is their biodiversity, reckoned by him to be greater than that of the bacterial, plant and animal kingdoms put together. There were, for example, some 10,000 species of virus found by drilling into a frigid Antarctic lake trapped below a thick layer of ice (Lake Limnopolar, 2009). Many of these were previously unknown to science. No one knows the total number of species in the viral kingdom but they appear to fall into seven classes, each class being divided into orders, families, genus’s and species, as is the case with the other kingdoms. 


 A virion (a single particle of a virus) is only a fraction of the size of a bacterium and has no on board machinery for producing copies of itself. Neither is it able to propel itself – unlike the bacterium, which is much larger in size. It is, however, a complex and ultra efficiently designed molecular machine able to penetrate the membrane of a bacterial cell and use the machinery inside to its own end, to either the detriment or the benefit of the host cell. The internal structure of the cell, with its ribosome, nucleus and proteins, is utilised to make mRNA (messenger ribonucleic acid) which it needs to produce a replica of itself.


Having used the host cell’s machinery to produce a replica of itself the virion then has to have itself ejected from the bacterium. This in itself is a remarkable feat.


Virions also have the capacity to reassemble themselves if broken down into their constituent proteins, which means the proteins have been designed with a unique molecular arrangement out of an astronomically high range of possibilities. Only this one geometry allows the virus to spontaneously assemble itself under the right conditions. It reminds me of the fine tuning of the physical constants of the universe to enable biological life to form.

Since last updating  I have become aware of discoveries made over the last decade or so which affirm giant viruses  many times the size of previously known ones. This is largely because the method of discovering new viruses relied on the assumption that they were too small to be trapped by a filter. It now transpires that there are giant viruses comparable in size and genetic complexity to bacteria. They also  appear to manufacture DNA, not just RNA and there is every reason to suppose they are equally numerous. Some biologists are now proposing that totally new domains of life must have predated the oldest forms of microscopic life discovered to date. The complexity and richness of life 4 billion years ago, only shortly (in geological nuance) after the formation of the earth, is even greater than had been assumed and adds to the depth of the mystery of what lies behind such intelligent systems.

 Because a virus has less goal-oriented complexity than a bacterium could it be that life started off as viruses? This seems logically impossible given that viruses depend on bacteria for their duplication. However, the bacterial, plant and animal kingdoms also depend on viruses. It has been proposed (speculated?), for instance, that speciation - the creation of new species from existing ones - is achieved by the incorporation by viruses of genetically coded beneficial traits from various species into the germ cell of one species to create a new species carrying these traits. The neo-Darwinian 'tree of life' model of evolution still included in text books is no longer given credence by the less dogma-driven evolutionary biologists and it would not surprise me if some mechanism based on what is known as horizontal gene transfer comes to be accepted by the majority, although even this would not explain the extraordinary purposeful irreducible complexity of the first life forms.

Mimivirus (electron microscope image)
A virus has a genome consisting typically of just 15 genes. The newly discovered giant viruses range from the stargate mimivirus
 (1018 genes, 0.4 microns diameter) to the elongated balloon shaped  pithovirus (467 genes, 1.5 microns long).


In describing biomolecular phenomena biologists are forced to use words like


think, decide, employ, ensure, exhibit, store, encode, divide, assemble, manufacture, coordinate, orchestrate....


These all imply that intelligent willful decisions are somehow involved and strike fear into the heart of the neo-Darwinist. Many biologists warns their students to steer clear of such words wherever possible and when forced to use them to hold in mind the (metaphysical) belief that there can be no intelligence because these molecules don’t have brains, as though molecules having brains would be the only way they could purposefully move and that intelligence could be involved in the processes in some way which is beyond present science, at least - if not epistemologically out of the realms of investigation.


He no doubt fears that believers in God will invoke a direct hands-on intervention by the Lord every time an unexplained phenomena or event is encountered. The professor need have no such fear from those who, like me, suspect that intelligence was built into God’s creation at the instant the universe was conceived in the original quantum event, along with space, time, energy and matter. Mind could have been  created as a fifth attribute of the universe. This would explain why there is so much order in the natural world, even where brains are absent. Moreover, since God is greater than the reality we live in I can imagine mind serving as a timeless, spaceless agent by which God pervades the universe.

(The observed progressive evolution, with experimentation built in,  right up to homo sapiens could, in my view, be envisaged as a something analogous to Michelangelo painting a masterpiece, but done by the Creator from outside of space-time. From our perspective this looks like a progress of events in time and space.)

Once one accepts that the universe may have teleological characteristics deliberately designed into it one can look for order in apparently random or unconnected phenomena by constructing experimentally verifiable hypothesis.  To reject faith in the underlying order and interconnectedness of all things is to risk the very future of science as much as would a belief in a god or gods of the gaps. Some scientist put their faith in Chance, the new god of the gaps, and this could plunge us into a new dark age. 

see also

 Intelligence without brains


Natural technology: the bacterium

John
author, 2077 AD
reach me at cosmik.jo@gmail.com