Tuesday, 4 March 2014

Something Big and Nasty In Russia

Pithovirus sibericum
Biggest-ever virus revived from Stone Age permafrost - life - 03 March 2014 - New Scientist

A couple of scientists have found something big and potentially nasty lurking in the permafrosts of the Siberian tundra, something that could point to a threat to humans and something that raises some fundamental questions about 'life' itself, at least so far as creationists loons and, to be fair, many normal people think of it.

What Chantal Abergel and Jean-Michel Claverie of Aix-Marseille University, Marseille, France found was a previously unknown virus and the largest ever found, so large it is visible under a normal light microscope. It was taken from 30,000 year-old permafrost and proved to be perfectly viable.

The virus, a Pithovirus sibericum, so called because it resembles a Greek pithos or large earthenware jar, complete with a plug keeping its contents in, is 30% larger than the previous largest known virus, pandoravirus, also found by the same team, but has only a fifth of pandoravirus's 2500 genes. Those 500 genes are never-the-less enough for pithovirus to invade amoebae and turn them into machines for making for pithoviruses, and in a unique way, or at least in a way not seen before. The normal virus way of making more viruses is to invade a cell, or even just inject its DNA (or RNA) into the host cell, and then hijack the host genes and convert them into genes for making viruses.

Pithovirus, however, enters an amoeba and migrates to a vacuole (basically a chamber enclosed in a membrane inside the cell) and attach itself to the vacuole membrane, then removes the plug and empties its contents into the vacuole, where they then use their own DNA to make viruses, using the amoeba as a source of raw materials.

There are three competing theories of virus origins, which are not necessarily exclusive in that any could be correct for a given group of viruses.

If on top of this we are now also seeing a possible release of potentially viable pathogenic viruses that are otherwise not living today, this will certainly add a whole further and new dimension to the thawing problem. It may mean that we are confronted not just with indirect climate warming impacts from thawing permafrost, but also direct human-health-related issues.

Torben Christensen, Lund University, Sweden
  • The Progressive Hypothesis, which sees the virus as a gene which has broken free and now exists as an independent entity, able to move between cells and integrate itself into the genome. It seems that a great deal of the human genome may have originated from these 'retroviruses' which have become a permanent fixture.
  • The Virus-First Hypothesis in which the virus is seen as having evolved directly from early replicators, and cells are seen as organised collections of virus-like particles, which viruses can use but have never become fully integrated into.

  • The Regressive Hypothesis where the virus is seen as an extreme form of parasitic reduction, rather like the bacteria which became incorporated into early cells to become organelles like mitochondria and chloroplasts.

Pithoviruses are definite candidates for the third type.

Thirty percent of the world's oil reserves are thought to be hidden under the permafrost, along with gold and other key minerals, so exploration is bound to increase, so we must be careful to take precautions when prospecting – if people become sick with strange symptoms, it might be wise to quarantine and clear them of dangerous new infections before sending them back.

Jean-Michel Claverie
Fortunately, the newly-discovered virus is a specialised parasite of the amoeba and appears to be harmless to human and mouse cells in cell cultures. Fortunate that is because of the ease with which they could be 'revived' after 30,000 years, simply by thawing them out and giving them a supply of amoebae. There is no reason at all why this should not be true of a potentially dangerous pathogen, maybe even ones we have never, as modern humans, encountered before. And this raises the possibility that climate change which is currently thawing out permafrosts and freeing up the viruses held in suspended animation for tens and maybe hundreds of thousands of years may be freeing up dangerous pathogens.

As I mentioned above, not only does this present a problem for us, but the ease with which these viruses can be 'revived' (and I use the term loosely because there was no revival other than thawing needed) presents a problem for people who assume 'life' is some quality or substance which distinguishes 'living' things from inorganic substances; that somehow its presence marks the difference between a rock and a human or between a plank and a tree. We've all seen them come rushing excitedly onto the Internet fully primed by some creationist scam site or fundamentalist religious site, to ask their 'killer' question, "How did the first life arise from non-life?", only to tiptoe quietly away when asked how they are defining life, often after posting some gibberish about souls or breathing.

Successful revival of any kind of ancient virus is always newsworthy. My own group finds bacteria present at all depths in deep ice in the Antarctic and Greenland. The pithovirus is so large that we might be able to see it in ice cores more than 100,000 years old at their bases.

Buford Price, University of California at Berkeley, USA
What these viruses show is that something can exist for at least 30,000 years and probably for very much longer than that, as nothing more than lifeless chemicals and membranes, doing nothing that would be recognised as living because the temperature was too low for the chemical reactions to occur, and can become 'living' again simply by raising the temperature sufficiently for the chemical processes to resume. This is exactly what would happen if a biochemical reaction in a test tube were to be put in a deep freezer for a year and then thawed out. It would simply carry on where it left off yet no one would seriously argue that the test tube and its contents are alive.

So, where was 'life' in these viruses for 30,000 years? Of course, it wasn't there since the viruses did not need to manage entropy and the anatomy and physiology was not doing any chemistry, so there was no life as most people would recognise it.

There is no reason to suppose that the first replicators were anything more than chemical reactions which occurred inevitably because the conditions were right, just as any other chemical reaction occurs. There was no initial 'life' because 'life' doesn't exist either as an entity or a characteristic in its own right and certainly not as some undefined magic ingredient. To ask where life came from is as daft as asking who set fire to the sun.

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