October 09, 2005

The Next Big Thing?

Hyperstitional fanatics might argue that taking the spread of H5N1 strain avian influenza as a topic was irresponsible in the extreme, but it seems to cross various lines of interest and it's beginning to blot out chunks of the future.

Bird Flu arrives in Europe.

CDC Bird Flu page.

Nature's Bird Flu archive.

(Should be enough here to give us something to panic about until reaching agreement on the next discussion topic)

Posted by CCRU-Shanghai at October 9, 2005 08:20 AM | TrackBack




Perhaps the most alarming recent discovery is that the 1918 'Spanish flu' was a pure bird flu:

"A LAB reconstruction of the 1918 flu virus, cause of the deadliest global pandemic ever recorded, is showing frightening similarities with H5N1, the bird flu that killed dozens of people across east Asia last year.

The genetic sequences of the reconstructed 1918 virus show that it was a pure bird flu that adapted to humans, not a hybrid between a bird and a human flu like the relatively mild flu pandemics of 1957 and 1968. That is particularly worrying because H5N1 bird flu is steadily evolving to become more lethal in mammals without combining with a human flu.

First Jeffery Taubenberger at the US Armed Forces Institute of Pathology in Rockville, Maryland, and colleagues isolated and sequenced the virus's genes from the preserved tissues of people who died after contracting the 1918 flu. They announced this week that in three previously unsequenced genes coding for the three-protein RNA polymerase complex, which replicates the virus, there are 10 mutations that do not occur in bird viruses but do occur in nearly every human virus (Nature, DOI: 10.1038/nature04230). Taubenberger thinks these may be crucial mutations that allowed the 1918 virus to adapt to humans.

Ominously, the same mutations have also been turning up in the polymerase genes of H5N1 - and in H7 and H9 flu viruses that have killed people. So far H5N1 has not picked up more than one of the mutations in any of the three proteins at the same time, not several as in the 1918 virus. "This is good news," says Taubenberger. "But that they share any of these changes suggests the possibility of parallel evolution."

[needs a subscription, but maybe this link works?]
[no subscription]

[A rather crass, callous point: If/when H5N1 adapts to humans through mutation, it will be unwelcome, real-time counter evidence to any claim that natural selection and adaptation cannot be observed in progress. Evolution live on TV.]

Posted by: sd at October 9, 2005 11:08 AM



'Spanish flu' was partly so devastating because it led to pneumonia and formed alliances with 'secondary bacterial pneumonias'.

The 25/18 ratio and the 'W' curve are also peculiar.

"The strain was unusual in commonly killing many young and healthy victims, as opposed to more common influenzas which caused the bulk of their mortality among newborns and the old and infirm. People without symptoms could be struck suddenly and be rendered too feeble to walk within hours; many would die the next day. Symptoms included a blue tint to the face and coughing up blood caused by severe obstruction of the lungs.

Mortality in the fast-progressing cases was primarily from pneumonia, by virus-induced consolidation. Slower progressing cases featured secondary bacterial pneumonias while some suspect neural involvement led to psychiatric disorders in a minority of cases. Some deaths resulted from malnourishment and even animal attacks in overwhelmed communities

The social effects were intense due to the speed of the epidemic. AIDS killed 25 million in its first 25 years, but the Spanish flu may have killed as many in only 25 weeks beginning in September 1918. The Spanish Flu vanished within eighteen months, and the actual cause was not determined at the time.

In September 2000, Noymer and Garenne published a study that poses an ætiological theory explaining the unusual W-shaped mortality age profile of the virus. This profile is characterized by a mode in the 25–34-year age group. Usually, influenza has a U-shaped profile, being most deadly to the young and the old."


Posted by: sd at October 9, 2005 11:18 AM



More on Spanish flu:

A first had account of the Spanish Flu:

Posted by: sd at October 9, 2005 11:21 AM



The theory that The Black Death and The Bubonic Plague are two different diseases, the former caused by a virus, the latter caused by bacteria:

Spread by stealth

One of the most striking aspects of the Black Death was its success. Arriving in southern Europe in 1347, it spread 2200 miles in three years – right up to the Arctic Circle, barely hindered by the cold, killing ~50% of the population of many towns in its path. How was this possible?

After plotting a bell curve for a range of infectious diseases, Chris and Stephen Duncan wrote an equation to describe it and then constructed a computer programme to model it. This allowed them to feed in variables like incubation period, transmission rate and size of the target population, and generate graphs of the predicted time course of epidemics of different diseases. These graphs confirmed that the longer the incubation period, the longer the duration of an epidemic – and vice versa.

“It seems that the plague’s latent period was 10-12 days”, says Chris Duncan, “while the infectious period prior to the appearance of symptoms lasted 20-22 days, giving a total incubation period of about 32 days. This is exceptionally long and it explains why the plague could jump very long distances even in the days of primitive transport: for three weeks, people didn’t realise they had been infected. People generally died five days after the first symptoms appeared, so the average time from infection to death was about 37 days. This is an interesting finding, because European health authorities had quickly determined on 40 days as a safe quarantine period for the plague.”

Two different diseases

This finding raises more questions than it answers. For the past century, historians have assumed that the Black Death was synonymous with bubonic plague, since many people afflicted by the Black Death developed the swollen glands known as ‘buboes’. Alexandre Yersin had shown that the infectious agent in bubonic plague is a bacterium, now known as Yersinia pestis, which afflicts rodents and can be transmitted by their fleas – so historians also assumed that rats and/or their fleas were responsible for transmitting the Black Death.

“Many historians continue to argue along these lines”, comments Sue Scott, “and that’s probably because they find the science inaccessible. The key facts are as follows. The incubation period for bubonic plague is just 2-6 days, not 32 days – and the disease spreads quite slowly, at around 8-12 miles per year, whereas the Black Death could cover this distance in a single day.

“Once people exhibited symptoms of the Black Death, death was sure to follow, whereas human mortality from bubonic plague is lower, and the disease is not particularly infectious: today people with bubonic plague are nursed in open wards.

“Then there’s the issue of transmission … bubonic plague is transmitted by rat fleas but, as Graham Twigg pointed out in 1984, rats were unknown in Britain’s rural areas until the 1720s when the brown rat first arrived in Britain – 50 years after the Black Death vanished; Britain’s only other rat species, the black rat, never strays far from ports. At the time, people assumed transmission was person to person – and this would explain why the Black Death was able to reach Iceland in the 15th century – yet there were no indigenous rats at the time and rats were not introduced to the island until hundreds of years later.”

“The Black Death was quite simply a different disease”, asserts Chris Duncan, “and the main questions to consider are – what was it, and could it come back? Our best guess at the moment is that it was some kind of emergent haemhorrhagic fever, rather like Marburg and Ebola, and the infectious agent was probably a virus. Could it come back? Possibly, but we’re more likely to encounter a completely new disease – like SARS.”


Posted by: sd at October 9, 2005 11:30 AM



For a classic literary account of the effects of plague on society and morals, see Boccaccio's Introduction to 'The Decameron'


Posted by: sd at October 9, 2005 11:34 AM



sd - before getting to the black death ...

this looks like being an interesting test of the bio-social profundity of 'progress' - my guess (for what it's worth (which isn't much)) is that this will turn out to be much more containable than the more dramatic speculations would suggest. The Chinese (and global) management of SARS surprised people with its effectiveness.

Of course, the curve-ball is whether WWIV dynamics upset the equation - could plague-suicide deliberate vector intensification become a factor upsetting epidemiological control strategies?

Posted by: Nick at October 9, 2005 12:49 PM



Unfortunately, The Black Death is highly relevant:

"On the basis of a 14th-century account by the Genoese Gabriele de’ Mussi, the Black Death is widely believed to have reached Europe from the Crimea as the result of a biological warfare attack"

from Gabriele de’ Mussi's account:

“Oh God! See how the heathen Tartar races, pouring together from all sides, suddenly invested the city of Caffa and besieged the trapped Christians there for almost three years. There, hemmed in by an immense army, they could hardly draw breath, although food could be shipped in, which offered them some hope. But behold, the whole army was affected by a disease which overran the Tartars and killed thousands upon thousands every day. It was as though arrows were raining down from heaven to strike and crush the Tartars’ arrogance. All medical advice and attention was useless; the Tartars died as soon as the signs of disease appeared on their bodies: swellings in the armpit or groin caused by coagulating humours, followed by a putrid fever.

“The dying Tartars, stunned and stupefied by the immensity of the disaster brought about by the disease, and realizing that they had no hope of escape, lost interest in the siege. But they ordered corpses to be placed in catapults [1] and lobbed into the city in the hope that the intolerable stench would kill everyone inside. [2] What seemed like mountains of dead were thrown into the city, and the Christians could not hide or flee or escape from them, although they dumped as many of the bodies as they could in the sea. And soon the rotting corpses tainted the air and poisoned the water supply, and the stench was so overwhelming that hardly one in several thousand was in a position to flee the remains of the Tartar army. Moreover one infected man could carry the poison to others, and infect people and places with the disease by look alone. No one knew, or could discover, a means of defense."


Posted by: sd at October 9, 2005 03:11 PM



The author of the text in the link above disagrees with the thesis that the events at Caffa led to the European pandemic, but does not doubt that biological warfare involving plague took place.

The fact that the Tartars who lobbed the cadavers into the city were themselves dying from the plague also gives the scene a 'suicide' flavour.

Posted by: sd at October 9, 2005 03:17 PM



> this will turn out to be much more containable than the more dramatic speculations would suggest

if the current avian virus mutates so that it can travel from human to human then it will be very difficult to contain.

one way the avian virus could mutate is by getting code from human flu viruses.

Bird Flu Similar to Deadly 1918 Flu, Gene Study Finds - National Geographic News, October 5, 2005

"The sequence evidence from 1918 suggests that the virus is from completely avian origins," said Adolfo Garcia-Sastre, a microbiologist at Mount Sinai School of Medicine in New York City.

Human immune systems would likely be caught off guard by a purely avian virus to which they have no acquired immunity.

The century's other great pandemics, of 1957 and 1968, were sparked by hybrid flu viruses—human flus that acquired some genes from an avian source.


Posted by: sd at October 9, 2005 03:47 PM



new acronyms:

LPAI - Low pathogenic avian influenza
HPAI - Highly pathogenic avian influenza

This document from the Avian Influenza Technical Task Force focuses on the spread through the migratory bird population:

"It has been long known that wild birds represent a reservoir for avian influenza viruses worldwide. This is a concern because many of these birds are migratory and travel over long distances and across international borders. Wild birds have been known to introduce novel influenza genes into a population that, when re-assoted with existing viruses, can generate a dissimilar virus with different antigenic and other biological differences. The influenza viruses are easily spread by fomites and survive and spread well in water. Furthermore, certain species of ducks are able to carry influenza viruses without exhibiting any clinical signs of disease.

The AI virus has adapted to the environment in ways such as 1) the use of water for survival and to spread ii) has evolved in a reservoir (ducks) strictly tied to water. The water in turn influences movement, social behavior and migration patterns of water bird species. It is therefore of great importance to know the ecological strategy of the influenza virus as well, in order to fully understand this disease and to control outbreaks when they occur.

The control of avian influenza infection in wild bird populations at this stage is not feasible - from a logistical, environmental and biodiversity point of view. Indiscriminate culling of wild migratory birds would be ineffective in preventing further spread of avian influenza and their hunting would likely cause disperion of the birds."


Hitchcockian horror?: H5N1 has an 'environmental strategy'.

Posted by: sd at October 9, 2005 07:11 PM



sd - it would be ridiculous to downplay the problem complacently, of course, but given the (comparatively) limited impact of the 1957 and 1968 pandemics, perhaps the 1918 example counts as something of an extreme case.
The level of preparedness, while far from adequate, must be orders of magnitude superior to that anticipating any previous major flu outbreak.

Posted by: nick at October 10, 2005 02:24 AM



US flu preparation (from Wired mag via Glenn Reynolds):

Posted by: nick at October 10, 2005 02:43 AM





Posted by: northanger at October 10, 2005 06:00 AM



Italian, from Medieval Latin īnfluentia, influence (so called apparently from the belief that epidemics were due to the influence of the stars). See influence.

Posted by: northanger at October 10, 2005 06:08 AM



northanger - 'nice' resonances, and anyone with 360-connections should be especially concerned about all that - dontcha think?

Posted by: nick at October 10, 2005 07:01 AM



"perhaps the 1918 example counts as something of an extreme case."

Let's hope so.

National Geopgraphic has a rather terrifying feature on Bird Flu in its Polish print edition - now National Geographic isn't generally known for panic, sensationalism or scaremongering (as far as I know, though someone can correct me if I'm wrong). Based on interviews conducted in Hong Kong, China and Thailand, it certainly seems as if the mix of unregulated poultry farms and wild birds could be a recipe for pandemic disaster. The article also mentions that Laos and Cambodia are unknown quantities here - again poverty is a key factor.

Posted by: sd at October 10, 2005 07:57 AM



sd - that's all undeniable, but weren't those factors also in play in the last two (relatively limited) pandemics? I'm pushing this line for partly devil's advocate reasons: 'testing' the highly questionable thesis that, despite all the alarming evidence, there seems to be a systematic bias in the direction of hyperbolic overestimation of threats. Put another way, the resilient threat-management capabilities of modern societies tend to be underestimated, perhaps because these capabilities - especially techno-scientific (e.g. medical) advances - are always unprecedented at the margin and their potential contribution thus escapes accurate calculation. In any case, without foolishly dogmatizing on the subject, it's the 1918 outbreak that looks like the outlier to me.
This is all about the scale of the catastrophe though - which could easily reach millions of fatalities even on relatively optimistic assumptions - not the probability of the pandemic occurring in the first place, which must surely be just a matter of time (for the reasons you and National Geographic give - this part of the world is one enormous informal virus laboratory).

Posted by: nick at October 10, 2005 08:55 AM



Maybe it's a question of strategy. The 1918 virus 'chose' it's victims and its allies very wisely - the healthy, mobile 25-34 year-old folk, bacteria associated with pneumonia. It also was far ahead in terms of strategy. In 1918 scientists were looking for bacteria and didn't suspect that it was viral infection. 57 & 68 failed to reach pandemic proportions because humans had the strategic upper hand.

With the current threat of avian flu (accrding to National Geographic) one of the dangers seems to be that while scientists focus on H5N1, another virus might be the one to make the human to human mutation. It wouldn't be too far fetched to label this strategy 'a decoy'.


1. how metaphorical is the use of the word 'strategy' when describing viruses?

2. just how much intelligence and cunning are we willing to credit viruses with?

Posted by: sd at October 10, 2005 10:56 AM



for example, if The Black Death was indeed a virus, then it's long incubation period seems to have been the key to its strategic success.

Posted by: sd at October 10, 2005 11:01 AM



intelligent viruses - love this topic!
With retroviruses its not difficult to assemble a broad sketch of intelligence machinery, although it requires interlock with a (DNA) target. Turing machine potential is now an accepted characteristic of this assemblage. Ordinary viruses require something far more exotic ...
Any virus completes its replication cycle by capturing a cell and its molecular machinery - if it can find what is necessary to build cognitive apparatus then it can start thinking. With the right cascade effects it might not even require a huge complement of viral genes to accomplish this. Everything depends on the target providing the right sort of resources.

There's probably a broader sense of 'strategy' (encompassing 'decoys' etc) that would inhere at the level of the evolving viral population with the ultimate 'subject' being natural selection itself.
But is there an intermediate position between:
(a) molecular viro-genomic computerized intelligence, and
(b) diffuse evolutionary 'intelligence' ??

Posted by: Nick at October 10, 2005 11:50 AM



A strong and fully functional immune system is impervious to viruses; the medical work of Julius Hensel, the reports of www.acresusa.com and all the other stuff you guys are in complete denial about but I go for big time have born that out for me.

Nick: " .. .bias in the direction of hyperbolic overestimation of threats."
neglect and moronic practice transfered into a threat is a bigger problem. Both converge to bring about, spontaneously generate problems, confining flocks for instance, to evade contact with infected and migrating siblings exposes them to (stressful) conditions that conjure epidemics in its own bio-industrial rites.
-------- v

Posted by: Chris's content page hypered at October 10, 2005 12:08 PM



"A strong and fully functional immune system is impervious to viruses" - this seems a tad overstated

Posted by: Nick at October 10, 2005 12:33 PM



Nick: threat-management capabilities [. ..] especially techno-scientific (e.g. medical) advances - are always unprecedented at the margin and their potential contribution thus escapes accurate calculation.

piet: in light of what I said before and with the same laws of reversal applied this reads: t-s advances dig in and entrench, even amidst growing wreckage, denying, prosecuting and imprisoning accurate calculation.

Posted by: Chris's content page hypered at October 10, 2005 12:41 PM



"A strong and fully functional immune system is impervious to viruses" - this seems a tad overstated

Especially when you consider the Aztec/Inca encounter with the smallpox viruses. Did they die in swathes because their immune systems were not strong and fully functional?

Posted by: sd at October 10, 2005 01:01 PM



look fellas, how many times more often do ethnicities invade each other as compared to migration patterns of birds changing in similarly 'radical' ways? Hmmm?

Posted by: Chris's content page hypered at October 10, 2005 01:35 PM



Immunity being a matter of habit (elimination, embeddiment, bonsai whatever else can be taken to mean LOCAL or CYCLICAL) I don't think the smallpox related wipe-outs are relevant here (no matter how much I have myself read up on the Mandan case, thanks to the accusations directed toward Ward Churchill for twisting the ((scarce)) facts and no matter how much discussion about whether epidemics are byproducts or leading accomplices of imperialisms interest me).

Posted by: parapetpiet at October 10, 2005 01:42 PM



sd's example was strongly influencing my thoughts on this too - any chance of decrypting what looks like a truly interesting series of suggestions here - or is that just naive?

e.g. CCPH last - is there an obvious answer to this question? seems to me there's a lot of variability and cross-current disturbance in both cases (with domestication of poultry, environmental disruption, etc)

Posted by: Nick at October 10, 2005 02:28 PM



"A strong and fully functional immune system is impervious to viruses"

somewhat contraticted by the 1918 Spanish flu too.

Posted by: sd at October 10, 2005 06:22 PM



oops. contradicted. though 'contraticted' sounds quite nice.

Posted by: sd at October 10, 2005 06:24 PM



Nick - on the question of intelligent viruses...

On many levels, viruses display intelligence without cognition. If intelligence is defined as the ability to solve problems quickly and economically, then viral replication is more 'intelligent' than the solutions that complex cellular life has come up with.

Genes that build complex survival machines with brains take great risks by spreading their replication process over many years, as offspring are incubated, carried, nurtured and guarded on their path from helplessness to maturity. This necessitates vast investment in security which in turn necessitates investment in locating and absorbing nutrition: claws, teeth, sensory surveillance and cognition an immune system - all of these require constant feeding and energy spent on feeding. Not to mention the farcical amount of energy and time spent on sex.

Yet a complex, big-brained survival machine which took months to build and years to grow can be reduced to a hemorrhaging wreck within a matter of days if it meets a virion.

Viruses are a nightmare of efficiency, with their genomes coding for the minimal amount of protein needed to form a capsid envelope, they have refined gene transportation to its bare minimum. Relying entirely on vectors and hosts for transport, energy and replication machinery, viruses have come up with what is definitely the swiftest and most cost efficient 'solution' to the replication 'problem' - the most fundamental problem for any chemicals which have plunged into Darwinian time and built DNA trees from the eternal exchange of the RNA world.

Whether ancient viruses escaped from the RNA world (tooled up,with transcription enzymes intact) without submitting to the reign of the cells, or whether current RNA retroviruses are of recent origin, renegade genetic material which broke away from multicellular life forms, the acellular line of flight viruses are on is a more 'intelligent' option than the laborious production of lumbering big-brained survival machines.

While animals have been wasting their time eating rutting and nurturing, viruses have defined themselves biologically by what they do: they cut and paste code, and copy. Nothing more, nothing less.

Posted by: sd at October 10, 2005 10:46 PM



some thoughts inspired by:

Evolution of Retroviruses: Fossils in our DNA

Retroviruses have the most ‘intelligent strategy’: they 1) put a selection pressure on the host for resistance to the virus and 2) write themselves into the host’s germ line so that a) members of the host’s species which cannot resist and live with the virus are killed off, and b) the virus is passed on as part of the host’s genome in all the surviving members of the species.

By integrating themselves “into the permanent genetic information of the host cell,” exogenous viruses become endogenous proviruses. A host which manages to ‘fix’ an exogenous virus as an endogenous provirus is also conferred an advantage: the integrated provirus can block infection by the exogenous virus (and related viruses) that gave rise to it. The virus trades resistance for fixation. The virus calls all the shots – the host is lucky that the best (evolutionarily stable) strategy for the virus is to enter into ‘a benign relationship’

“A well-evolved host-virus relationship, in general, allows efficient infection and spread of the virus without causing sufficient morbidity or mortality to significantly impair the function of the host in this process. In some cases, the relationship may be completely without pathogenic consequences; in others, there may be relatively limited disease(such as common cold, warts, gastrointestinal symptoms) from which the host recovers fully; in still others there might be severe disease(such as rabies or influenza) that might lead to the death of the host but, at the same time, promote the spread of the virus. Genetic factors that affect this process tend to be highly species-specific, so that transmission of a virus into a new species is often associated with considerable morbidity and mortality. Indeed, most of the time this morbidity and mortality will lead to extinction of the virus in the new species, so that most emerging viruses (Ebola is a good example) rapidly disappear from the new host. In the rare case, the virus will be able to spread in the host at a rate sufficient to ensure its survival. In this instance, pathogenic effects unrelated to transmission efficiency will put considerable selective pressure on both host and virus in the direction of a more benign relationship, and genetic changes in both host and virus that contribute to reduced pathogenicity will be selected. Following transmission to a third species, however, the process will, most likely, begin again. HIV and related retroviruses are an example of this kind of evolution, since these viruses do not, in general, cause significant disease in the large numbers of African monkey species that they infect, but are quite virulent when they infect other species, such as humans or Asian monkeys. No doubt, the end point of the coevolution of HIV and humans will be a more host-friendly interaction, but no one should want to participate in the process of evolution that will take us there.”


Viruses have so successfully integrated into our genome that it is somewhat foolish to use the ‘us and them’ framework when thinking about ‘them’: “In humans, there are about 80,000 proviruses or their remnants, comprising about 6–8% of the genome, or about twice as many as genes. In other words, there are more proviruses in us than there is us in us.”

While all primates have been assailed by retroviruses for millions of years, and have adapted to life with them, over the last 11,000 years humans have been exposing their genetic material to viruses which had formed benign relationships with genomes on distant branches of the evolutionary tree. As food production and animal domestication began after humans spread over the globe, this meant that sedentary humans who were in close contact with domesticated animals and integrated their viruses unwittingly waged biological war on humans they came across who had not had the luck to be infected by the same viruses.

One of the most uncomfortable facts of human history is that viral infection and resistance have contributed to processes which conferred an evolutionary advantage on some groups of humans over others. Fitness is determined by the extent to which the species can integrate disease.

This is Jared Diamond’s story and, perhaps not surprisingly, he has been branded a ‘crypto-fascist’ by left wing anthropologists who accuse him of absolving colonialism of its guilt. Marxist anthropologists insist on condemning the colonial ‘ideology’, while Diamond is more interested in describing the geographical, technological and biological factors and forces which enabled colonialism. Marxist anthropologists could run their moral indignation program on top of Diamond’s platform, but they seem reluctant to face basic facts. Ironically, on some levels Diamond’s thesis is more Marxist than Marxism: modes of production not only determine cultural and mental representations, but, with the viruses unleashed through farming, they also determine the genome.

[For excellent Diamond stuff:

particularly here:


For the bemusing Diamond anthropology blog debate:

savageminds.org/2005/07/24/anthropology%e2%80%99s-guns-germs-and-steel-problem/ delong.typepad.com/sdj/2005/07/a_better_class_.html ]

Posted by: sd at October 11, 2005 01:18 AM



sd - how to judge the 'problems' that intelligence is supposed to solve? Why replication, for instance, and not more fundamentally, plain survival, even if this means transformation? Nothing replicates without risk of being transformed by its 'embeddiment', as Piet would say, in a dynamic environment. If survival is the most fundamental problem then replication would amount to propagation, either as adaptation to/on a certain set of conditions (human genome adapting to viruses) or evolution. Perhaps I am comparing two very different things - one is adaptation on the genome, and another the evolution of the species, but I am curious as to how life - however characterised - can be considered 'intelligent': if it is a matter of mere replication, and replication can amount to propagation, shouldn't we distinguish in some way between the intelligence of organisms that have evolved to maintain an edge on their ability to replicate, and those that haven't? And would this difference be a real difference or a matter of lookiing at the same thing from difference angles?

Posted by: Tachi at October 11, 2005 01:46 AM



sd - great stuff ... [processing]

Posted by: nick at October 11, 2005 03:39 AM



Tachi - good, stimulating questions. I haven't got time to do them justice at the moment, but here are a couple of initial reactions.

"adaptation on the genome, and another the evolution of the species"

Evolutionary theory which treats the species as the unit of selection has obvious difficulties when dealing with viruses. The definition of a species is a lineage which has mutated and inbred to such an extent that it can no longer reproduce with other lineages. Virus strains mutate at such a rate and exchange code other strains with such fluidity that it is very difficult, if not impossible, to track their Darwinian tree lines. Viruses are too efficient and open to the potential that comes from direct code-swapping to get trapped in the ponderous line of retreat that building a species amounts to.

With viruses, life is reduced to its bare minimum, where sections of code recombine and replicate without even bothering to build their own cells or the other machinery of meat security.

Evolutionary theory which treats the species as the unit of selection also runs into problems when it comes to explaining how complex, big-brained organisms evolved from single cell eukaryotes. Our genes have lived in a variety of species which are now extinct (e.g. the common ancestor from which chimps and hominids evolved). All the species which roam the planet today are merely the ends of lines driven by gene alliances and adaptive mutations - so it is the individual genes (or maybe sections of code within genes) which ally to form a genome that are really the unit of selection.

Genetic Selection pressure on the level of genes means that genes have to be strategic - those with the best strategies get (themselves) replicated. Of course strategy does not imply cognition. The point is that building complex multicellular machines with big brains is just one strategy, and the parasite strategy of viruses is another.

The fact that it is viruses that dictate the terms to multicellular organisms - backed up by a very real threat of extinction - would seem to indicate that the viral strategy is more 'intelligent', in terms of game strategy, than that of getting locked in a species.

Viruses, like Octavia E. Butler's ooloi, are defined by their strategies and what they do: their form is as close as can be to their function. Multicellular organisms, stratified and exposed to tragedy as a result of their colossal investments, are remote from their function.

"would this difference be a real difference or a matter of looking at the same thing from difference angles?"

Dawkins would say it's a matter of looking at the same thing from different angles. D&G pragmatics relevant here - the question is not which way of looking is true, but rather which way of looking works best. The gene as unit of selection has more explanatory power than the species as the unit of selection, and probably has more practical utility too. Nick's point about narratives also ties in here.

Posted by: sd at October 11, 2005 10:02 AM



sd, tachi - both 'populations' and 'intelligence' need some intense thrashing out somewhere down the line. Distributed molecular machinery complicates these (already challenging) concepts - with viruses operating so radically in a medium of 'external relations' that they bring the issue to a crisis.
Agree form/function intimacy is crucial, as is the connected body/behaviour relation - viruses assemble a 'body' (set of adequate organelles) through the entire circuit of their replication, making their (an)organic completion essentially technological: dependent on extrinsic components.
[... interrupt ...]

Posted by: Nick at October 11, 2005 12:00 PM



SD - fascinating response to my naive questions, and wish to process more, though some other questions immediately come to mind.

It would seem that even though genes may be the most basic unit of heredity and therefore allowing species to be the basic unit of evolution, the fact that genes can propagate virally without a heredity mechanism shows that it is not genetically-facilitated heredity - and thus heredity-facilitated evolution of species - that is the exclusive or most intelligent modus operandi for genetic (and hence material?) replication.

So are genes the most fundamental unit of intelligence, if we take 'intelligence' to be loosely 'problem-solving matter'? Perhaps this would imply that units of intelligence (better than units of 'evolution' as commonly extended to culture etc) co-exist only on the biological strata.

But surely there are other units of intelligence - on cultural, social, techno-capital stratum - that have some interface with the biological? But then what kind of unit could facilitate cross-strata traffic, and what would this look like?

I guess what I am trying to approach is something that connects genetic propagation (with its viral and evoluationary dual strategies) to material problem-solving on other strata.

Posted by: tachi at October 11, 2005 12:08 PM



Obviously cognition, language and technology can provide a massive boost to an organism's problem solving capabilities (though they can also cause problems by opening up the organism to infection by fact-evading memes). However, this problem solving capacity runs on, and serves the interests of, the basic problem-solving platform of multicellular life until the problem of freeing cognition, language and technology from hardwired genetic programming is completely solved. When humans deliberately tamper with their own genetic material, they have taken the long way round.

Viruses have been taking the short cut to their genetic material for (probably) billions of years and have evolved complex strategies involving direct manipulation of genetic material and 'cunning' manipulation of vectors (e.g. triggering sneezing).

Posted by: sd at October 11, 2005 01:27 PM



sd - basically, viruses ARE their genetic material. Other than an elementary coat they are pure biological information. Their role is informational-catalytic, with intelligence emerging at a higher level in the assemblages they operationalize for the 'purpose' of replication (don't really have a problem with purposive language, as long as strict neodarwinian teleonomy maintained, as 'settled' in conversation with Binky).

To get at intelligence, the first step is to rigorously grasp this informational characteristic, and proceed (perhaps in stages) to the modality of information processing that can be usefully identified with versatile problem-solving capabilities.

tachi - heredity is in fact subverted from the beginning by (retroviral) lateral transfers and information grafting - perhaps best conceived as a persistence of the RNA world (see sd above) - the notion of closed heredity might well be no more than a simplified model, pedagogically useful for the exposition of certain genetic processes, but without true phylogenetic instantiation.

Posted by: Nick at October 11, 2005 02:37 PM



'viruses ARE their genetic material' - well, yes.

For me the feedback component is always baffling - is there a genetic element responsible purely for assessment and strategy development? Or is it pure swarm experimentation and merciless natural selection?

Posted by: sd at October 11, 2005 04:37 PM



a very on topic article from this week's New Scientist - here in its entirety because it's premium content...

The Word: Pathosphere

08 October 2005

NEW biological weapons are being created right this minute - though not in any secret laboratory or military base. Out of reach of international legislation, there is a genetic lending library of evil in action, and while you may not realise it, you are intimately involved. It's been going on for millions of years, but we have only just begun to explore this sinister new territory. Welcome to the pathosphere.

What is the pathosphere? It is the surprisingly vast and growing gene pool in which pathogens, the microbes that cause disease, meet and mingle. Scientists have long known that the so-called plastic genome of many pathogens allows them to readily swap genes, transferring genetic material in information packages called plasmids. Now it seems they have access to a much broader supply of genes than previously believed. Frederick Blattner, a geneticist at the University of Wisconsin, Madison, named this genetic lending library the pathosphere - the realm that blurs the lines between pathogen species.

The pathosphere was unveiled in 2001 when researchers mapped the genome of the microbe Escherichia coli. They found a shocking number of differences between benign and vicious E. coli strains, suggesting that the strains can quickly acquire large amounts of new genetic material, not only from relatives within their species but from an alarmingly large range of bacteria. On the family level, a huge bank of genes is being shared among bacteria including salmonella (food poisoning), shigella (more food poisoning), yersinia (plague) and even plant bacteria.

What's so sinister about the pathosphere? Its existence means that pathogens are more closely connected than we thought. They are able to trade genes in bulk, and conspire to enhance one another's survival skills. A relatively benign bacterium can survive an antibiotic attack, then hand over the genetic secrets of its success to more vicious pathogens.
“There is a genetic lending library of evil in action, and you are intimately involved”

Right now, Hong Kong is battling a plague of antibiotic-resistant bugs, the result of heavy antibiotic use during the SARS epidemic. And just two weeks ago the UK's Health Protection Agency reported a new variant of E. coli that is resistant to all but a few antibiotics.

Even worse, the pathosphere's embrace is perpetually widening. Research discussed at last month's meeting of the Society for Invertebrate Pathology in Alaska shows that some human pathogens acquire dangerous survival skills while hosted by invertebrate species. A spider's saliva houses bacteria that can rot human flesh. With gene swapping occurring between vertebrates and invertebrates, the pathosphere ascends another rung of the ladder from family to order.

Should we be frightened? Definitely. As drug-resistant genes circulate in the pathosphere, new bioweapons are continuously produced. But on the bright side, the fact that pathogens once believed to be disparate are actually connected means that we could develop one knock-out solution and apply it to the central gene bank as a cure-all for a whole host of ills.

From issue 2520 of New Scientist magazine, 08 October 2005, page 58

Posted by: sd at October 11, 2005 06:29 PM



sd - pathosphere piece absolutely fascinating, but it seems almost incompatible with the continued existence of organic life! What puts a ceiling on pathosphere malignancy?

Posted by: Nick at October 12, 2005 01:42 AM



sd - "this problem solving capacity runs on, and serves the interests of, the basic problem-solving platform of multicellular life until the problem of freeing cognition, language and technology from hardwired genetic programming is completely solved."

> does this imply that the problem of organic life is subordinate to the problem of something inclusive of but beyond it?

The 'problem' of freeing cognition etc is for what, since it seems difficult to conceive of problem without some form of agency. Surely it cannot be related to the organic/biological strata, but then what constitutes 'information' that could possibly traverse this strata and others?

... are humans, the product of genes' 'evolutionary' strategy to replicate (as opposed the the 'viral' strategy), the bridge from pure biological information to non-biological (artificial/inorganic/machinic) information? if so, ironic that the least 'efficient' strategy turns out to be the most consequential for the planet.

will read the pathosphere piece soon, though in need of some basic microbiology/genetics lessons ... any recommended sites online?

Posted by: tachi at October 12, 2005 02:35 AM



tachi - am seriously rushed off my feet, but here are a few links:

from northanger - you can test yourself (tricky!)

for some Dawkins - here's his classic account of memes:


for Carl Woese:
(if you click on the abstracts you can get to the complete texts online)

and some relevant wikipedia pages:


Posted by: sd at October 12, 2005 11:29 AM



tachi- some stuff here too

Posted by: sd at October 12, 2005 02:43 PM



tachi - as biotechnology advances the biology/artifice distinction breaks down, and perhaps more interestingly the artificiality of this distinction emerges ever more clearly (bacteria already engage in 'biotechnological' operations involving viruses and plasmids to cut-and-paste genetic material (if 'genetic' is even ultimately applicable to bacteria)). Lynn Margulis is excellent on all of this. A distinction between open/closed lineages is probably more realistic, although this cuts through the various 'strata' you refer to.

Part of this discussion awaits a 'missing link' zig-zag on the topic of intelligence, more specifically, whether there is an abstract problem-solving schema more efficient than trial-and-error searches, allowing for a notion of discontinuous 'evolution' beyond neodarwinian processes in the widest sense (which includes 'genetic algorithms' and probably Popperian scientific method). If not, then there really are no radical distinctions to be drawn, but merely gradients, accumulations and thresholds, differentiating a continuous variation-selection experimentalism that stretches from the beginning of replicator chemistry into market-dynamized human societies and the technosphere.

Posted by: Nick at October 12, 2005 03:22 PM



recreation of Spanish Flu in the lab surely hugely germane to this topic - because viruses are essentially equivalent to their genetic material they cannot become extinct in the same way organisms can, their lineages are purely communicative, rather than substantial

The implications of this event are quite wide-ranging. Krauthammer
(www.washingtonpost.com/wp-dyn/content/article/2005/10/13/AR2005101301783.html) says:
"This is big. Very big.
First, it is a scientific achievement of staggering proportions. The Spanish flu has not been seen on this blue planet for 85 years ..."

Posted by: Nick at October 15, 2005 12:02 PM



The first comment I posted on this thread refers to this - reconstructing the 1918 virus led to the discovery that the 1918 strain was originally a bird flu.

New Scientist are rather less enthusiastic than the Washington Post however:

Scientists have rebuilt the 1918 virus and are studying it to see what made it so deadly ("Bird flu warning from replica virus ints at"). Without a doubt, this is a triumph for virology - and for scientific curiosity. We want to know what made 1918 flu so different from other flu viruses, especially since we know that sooner or later its relatives will launch another pandemic.

Yet somewhere a voice is screaming: they've reconstructed one of the most deadly viruses of all time! They are studying it in live mice, and at only the second-highest level of biological containment. The people handling it are not wearing full protective suits, but merely taking antiviral drugs that may not be totally effective. If someone catches the infection, it could prove impossible to contain.

Is the work worth the risk, given that our immediate problem is not the 1918 virus but knowing what form the next flu pandemic might take? The latest work has found that H5N1 bird flu, the leading candidate for the next pandemic, is evolving in similar ways to its 1918 relative. So there may be real dividends from finding out what made that monster tick. But is it being handled with the respect it deserves? Why is the work not at the highest level of biosecurity?

We are solemnly informed in a press release that the editor of the journal Science, and a few top US science and health officials, say it's OK. That's nice, but it smacks of a self-regulating industry saying "trust us". Science is not supposed to be done by imprimatur. What reasoning led to this decision?

As it happens, we all have some immunity to the 1918 family of viruses because the Soviet Union accidentally released a milder one in the 1970s. Would that counter the 1918 virus? Has anyone done the tests? The level of biosecurity adopted for this virus potentially affects us all and the choice should be made in a transparent manner. Congratulations on recreating 1918 flu. Now tell us why we shouldn't be scared."


The benefits of reconstructing 1918 flu are obvious, but not having high levels of biosecurity...? Duh. (if this is true).

Posted by: sd at October 15, 2005 07:18 PM



If the 40 day incubation period for the Black Death is viewed as an intrinsic part of viral strategy, then maybe we can think of reconstruction as kind of incubation period - reconstruction as part of the viral game plan. Even if the virus 'never took this eventuality into consideration', it is now a component of the strategy for both players. From the point of view of the virus, 'taking something into consideration' is merely equivalent to having an algorithm ready to apply to a particular eventuality.

A crude question could go something like this: reconstruction is in whose interest? Who will ultimately benefit from H5N1 being transported around the world and analysed in labs? Especially if the virus is subjected to controlled mutation (as seems to be happening). The outcome is that the viruses are preserved as a pure potential. Their codes are valuable to humans for the development of vaccines - again they have the upper hand. The human genome integrates exogenous viruses, making them proviruses with a permanent place in the genome. Laboratories reconstruct exogenous viruses, making them permanent residents of scientific infotech. The mechanism is the same: viruses trade their value (to genome security) for preservation and replication after years of 'death'. Viruses seem to be jumping on the life extension bandwagon.

Posted by: sd at October 15, 2005 08:11 PM



Science needs to be more paranoid?

Posted by: sd at October 15, 2005 08:12 PM



sd - scientific ignorance (especially in a competitive strategic environment) is probably more hazardous than the most reckless scientific activity - there's an arms race dynamic that might be seen as pushing everybody into higher zones of catastrophic risk, but then - "Panic is creation" (D&G) ;)

Posted by: Nick at October 16, 2005 02:01 AM



things disappearing from this thread!

Posted by: sd at October 17, 2005 07:05 AM



I've managed to save up roughly $75058 in my bank account, but I'm not sure if I should buy a house or not. Do you think the market is stable or do you think that home prices will decrease by a lot?

Posted by: Courtney Gidts at March 8, 2006 06:00 PM



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