The Entangled Bank

This summer I have been reading Darwin's Dangerous Idea by Daniel Dennett. The dangerous idea according to Dennett is Darwin's notion of natural selection which Dennett views as an idea not just tied to biology but also extends to other areas of study as well including religion and morality. Dennett's basic view point is that natural selection amounts to an algorithm, a mindless procedure that when followed the same way from the exact same starting point yields the same result. Dennett compares natural selection to a universal acid which can eat through anything by which he means that natural selection attacks all of our preconceptions about how various aspects of the universe and human nature came about and are developing today.

Dennett's ideas are controversial because they violate the notion of a truce between science and religion which according to Steven J. Gould can be viewed as being two separate, I believe this is his term, Magisteria. So in a sense maybe Dennett is playing into the hands of those Intelligent design proponents who argue that Darwin's ideas are atheistic because the universal acid of natural selection eats away completely at the concept of God except as a hands off sort of entity in the Deistic sense. Dennett doesn't have much use for that sort of God and I must admit I agree here.

Dennett views natural selection as providing a construction crane which takes a population to very localized fitness optima along with the other agents of evolution, provides a sort of bootstrapping leading to the generation of more mindless cranes taking a population other sorts of localized optima in what he calls design space. Though his design space is effectively infinite in size. In contrast the believers in intelligent design and even many evolutionary biologists are looking for skyhooks- basically ways of explaining design not from the bottom up as Dennett does but dropped down above, hence the skyhook metaphor.

Of course, Dennett's ideas have been roundly criticized, and I think his book suffers from a bit of a side speculation about the motives of Gould and some other biologists, but especially Gould, but Dennett's ideas should be better known by biologists. He does a good job of explaining why certain ideas such as panspermia and intelligent design are not taken seriously by biologists. One of his points is very much where I come from. He notes that biologists love constraints and difficult exacting conditions that need to be specified for their hypotheses to be tested. Even though panspermia can in principle be tested, it leads to nothing in terms of its predictions because it renders lots of things possible. The same thing is true of Intelligent Design except here there is not even a mechanism (not even a spaceship!) and the designer can do anything it wants.

Sometimes evolutionists are accused of postulating pathways to particular adaptations in terms of just so stories and Dennett admits this but notes that there are criteria for developing and testing evolutionary explanation. Not everything really goes. For those in different disciplines who doubt the power of Darwin's dangerous idea Dennett offers the hope that the spread of the natural selection viewpoint ultimately leaves our understanding of ourselves stronger than before, presumably because the traditional skyhook ideas that cover they way we often without even thinking about it, understand ourselves and our nature, are etched away leaving the cranes upon which we have developed. The human mind then becomes the ultimate crane opening up new realms of design space which we can never exhaust!

Darwin's Dangerous Idea: Evolution and the Meanings of Life, 1995, New York: Simon & Schuster, London: Penguin.

Dennett's homepage.

http://ase.tufts.edu/cogstud/~ddennett.htm

May 25, 2005

The Lord God Bird

It is said that we make our own reality.

Well then, mine is full of wasps and wolves

And the Lord God Bird and the darning needle

That knits all things seen and felt

Such as old man's beard pallid in the White Mountains in August,

Or things that I have maybe seen

Like that legless lizard glimpsed well beyond its range when turning over rocks,

Or things that I have neither seen nor heard such as the Lord God bird

From the realm of the mourning dove cooing her lost cousin.

All knitted into a seamless whole by the darning needle

So that things come flapping from one realm into another

Until they come into the realm of what is now sure

Where they dissolve into the universal acid

Of the here except for those things that are really here

All along like the Lord God Bird

In the bright realm of its Pileated cousin.

So the Ivory Bill Woodpecker has been rediscovered.

So what is the significance of this. The significance is really quite simple. This bird represents a piece of the 3.5 billion year old biosphere, or what one philosopher has called the results of the R & D process that has led to the modern biosphere, an R & D process carried out by natural selection and the other processes of biological evolution. Finding this bird not extinct is like find a folio of Shakesphere plays only better, like finding the remains of an ancient Greek machine only better because it as we are is the result of the impersonal intelligence of the universe, another shall we say, sacred branch on life's tree, a distant cousin thought lost, returned.

February 5, 2005

Viewpoint discrimination and Naturalism

According to intelligent design advocates, scientists today are largely guilty of something they call viewpoint discrimination because we practice a kind of science that to their mind does not allow for discussion of alternatives to evolution. http://www.intelligentdesignnetwork.org/sci_standards.htm

Further this viewpoint discrimination arises by espousing something the ID proponents call naturalism or at other times "methodological naturalism". It is conveniently forgotten that science IS viewpoint discrimination because scientific explanations generally must meet certain common sense criteria. Scientists routinely reject certain hypotheses from immediate consideration if they have not been framed in a way that allows them to be empirically tested. For example, the notion of continental drift was generally rejected until data suggested a testable explanation of how the continents might move.

Supposedly methodological naturalism "irrefutably assumes that cause and effect laws.... are adequate to account for all phenomena". This is not what methodological naturalism really is about. As a religious person I certainly don't accept that. The ID proponents confuse methodological naturalism with metaphysical naturalism. See Pennock(2004). In science, our explanations are couched in terms of cause and effect because it is precisely these types of explanations that are testable and useful. The science and technology upon which the material fruits of our civilization are based demonstrates the power of this approach.

Some philosophers, such as Alvin Plantinga http://id-www.ucsb.edu/fscf/library/plantinga/mn/MN3.html , argue that methodological materialism excludes certain legitimate questions. For example, he sees no reason to exclude the following line of reasoning from science.

"God has created the world, and of course has created everything in it directly or indirectly. After a great deal of study, we can't see how he created some phenomenon P (life, for example) indirectly; thus probably he has created it directly."

This is reasonable on the surface, but it misses a key aspect of scientific reasoning. His conclusion "thus probably he has created it directly" is actually a hypothesis and it ought to be amenable to the hypothetical deductive line of reasoning used in science. If God created life directly then we ought to observe such and such pattern when we look to the natural world. Pointing back to the the observation that we can not see how he created some phenomenon is not permissible as it is the sort of circular logic that evolutionists sometimes are accused of.

Statements about the action of God based on the absence of evidence are legitimate statements and may even be correct, but to be scientifically valid they must be able to generate testable predictions beyond the observations that led to the formulation of the statement.

Pennock(2004) notes the following:

"Unlike the Darwinian mechanism, which explains how biological complexity can arise from simple processes, the design hypothesis simply pushes the problem of complexity back a step and exacerbates it. It is certainly not simpler to explain biological complexity by reference to a mysterious agent who is infinitely greater in complexity. The hypothesis fares no better with regard to other explanatory virtues (Pennock 1999, 2003)."

For a balanced and humorous discussion of naturalism see:

http://preterhuman.net/texts/science_and_technology/Darwinism-Chapter%2011.pdf

Dr. Pennock's home page:

http://www.msu.edu/~pennock5/

Pennock's 2004 paper in pdf format is currently on his web site at

http://www.msu.edu/~pennock5/research/papers/Pennock*DNADesign.pdf

January 14 2005

The Watch. Intelligent Design. Here we go again.

In Kansas we are having to deal with controversy about the teaching of evolution, this time from the intelligent design approach. The scientific community is being accused of dogmatism and not wanting discussion of alternatives to evolutionary theory. We have been even accused of "view point discrimination". Nothing could be farther from the truth. Scientists are by nature skeptical. The problem in teaching science is that in science we want to teach important scientific ideas, and not every idea qualifies in terms of the empirical support available for the idea. The Intelligent Design hypothesis is not scientific.

Consider finding a watch on a beach, one of intelligent design favorite icons. According to an intelligent design advocate, even a person unfamiliar with watches would understand the watch as being the product of some sort of intelligence. Therefore, since even the simplest living thing has many parts working together as does a watch, living things must also be designed by some sort of intelligence. Let's assume this argument is correct and that you are a scientist.

As a scientist you would have a few questions of the advocate. For instance, what is the nature of the designer? Is the designer the same thing as what we call God or is the designer some sort of space alien, Does the designer have any limitations? What is the motivation of the designer? Using the watch analogy, what is the function of the watch? How did the watch come to be? If there is a designer how does the designer affect the universe to bring about a design? Can I explain how the watch works? The intelligent design advocate is silent on all these questions, but thinks that it is enough to say that the intelligent designer exists. The advocate professes not to care what the designer is or how the designer operates to bring about living things. There can be no scientific examination of these questions.

The intelligent design advocate need say no more than that the designer exists. But you are scientist. Scientists ask questions about the universe. So you develop a set of testable hypotheses. You and other scientists working over several hundred years develop a set of repeatedly tested hypotheses based on reasonable assumptions, come up with a theory about how the apparent design of living things came to be. It's not a complete theory and it too raises lots of questions. Scientists LOVE questions by the way. These questions can be examined both in and outside the laboratory unlike the major questions one might want to know about the Intelligent Designer. Such a scientific theory exists today. It is called evolution.

Now which would you rather see taught in a science class? A scientific theory, namely evolution or a hocus-pocus hypotheses (Intelligent Design) about which even basic questions are off limits. It's your choice. In fact, why even bring up the Intelligent Design hypothesis in a science class except perhaps to point out that it is not science. ã Paul G. Decelles 1/14/05

November 19, 2003.

Does the future need us? Our new technologies have great promise, but in our rush to embrace them are we making humans superfluous and endangered?

Why the Future Doesn't Need Us. You have heard of utopia. In this article Bill Joy, one of the pioneers of modern computer technology asks us to consider the possibility that our new technologies could lead to the opposite of a utopia- namely a dystopia. Heavy reading both worth it.

I don't agree with his pessimism but I also don't buy into blind acceptance of new technologies. Remember the first law of ecology- We can not do just one thing. Everything we do is likely to have unintended consequences.

November 10, 2003

Invasion of the Killer Earthworms?

We tend to think of Earthworms of a natural part of our environment. But a little known fact is that North America does not have many native species of earthworm. This appears to be a result of a loss of our original earthworm fauna in the last ice age. Europe on the other hand has a rich fauna of earthworm species much of which was accidentally introduced by the European colonists. While we tend to think of earthworms as beneficial to soils a view popularized by Charles Darwin and perhaps legitimate for the horrible soils we have in our lawns, the truth is more complex as noted in this article http://news.nationalgeographic.com/news/2003/01/0102_030102_earthworms.html. Earthworms not only may be harmful to many forest soils in North America but also may be responsible for unintended changes in the abundance of native plants and perhaps the replacement of some native plants with introduced species.

August 23 2003. Cell Intelligence. Are cells intelligent? Sometimes it's fun to consider really offbeat ideas. It keeps the juices going and provide new insights into various phenomena, even if the ideas are wrong. A friend recently sent me Guenter Albrecht-Buehler's site at http://www.basic.northwestern.edu/g-buehler/cellint0.htm. Dr. Buehler asks us to consider the possibility that individual cells are in some sense of the word intelligent. We already know that cells can sense and respond to their environment, sometimes in fairly sophisticated ways. Buehler argues that cells can actually collect and interpret information from the environment and in a sense are capable of some sort of abstract thought.

Buehler sum's his ideas up in two statements:

A. If cells can measure space and time, they must be able to derive abstract data from physical signals.

B. If cells have eyes, they must be able to order and integrate countless signals.

Buehler then seems to equate the basics of intelligence with the ability to integrate signals and produce abstract representations of the world. Buehler presents the results of experiments that to him suggest that the cell is able to use centrioles to detect infrared light and he presents a functional analysis of the centriole to support his contention. Personally I suspect he is pushing the claim that cells are really intelligent and I am also suspicious of what seems to me to be a post hoc analysis of centriole design. But hey, take a look for yourself.

I don't have any problem with the second part of his thesis. It is pretty clear that cells do integrate information. It is even clear that some cells do have ability to detect light and even move toward or away from light. For instance, Euglena has an eyespot with a shade that enables the organism to orient toward visible light. But whether or not this sort of ability really implies integration of visual information let alone intelligence is not at all clear to me.

Buehler's site does bring into focus a basic question namely what is intelligence and how would we recognize non human intelligence? Might intelligence be found in some unexpected places? Personally I define intelligence in part as the ability to respond to identify and solve problems that have not been encountered before. Humans do this..at least we are supposed to be able to do this though sometimes I wonder and at least some other animals can do this. Possibly computers can do this but that is still not clear. But can cells do this? That is not clear and I am not sure how one would set up a novel situation in which cells could do this.

I suspect that there are not sharp boundaries between stereotyped and intelligent behavior. For example colonies of social insects constantly receive information and integrate it and while each worker in the colony is relatively limited, the whole colony seems able to behave as if it is doing fairly complex problems of information integration and resource allocation. Not so far different perhaps from our own nervous system where in each neuron is quite limited in ability and yet intelligence emerges from the collective activity of these neurons.

July 9 2003. Chimeras and medicine Scientists have for a number of years been able to take embryonic cells from unrelated species to produce organisms which have cells from both individuals. For example mouse human chimeras are important in medical research because after all you can't do many types of experiments on humans and chimeras are used
in drug production. Chimera technology is itself controversial, especially among anti genetic engineering activists such as Jeremy Rifkin. See for instance Scott Anderson's discussion of chimeras at:

http://www.spiked-online.com/Printable/00000006D9BF.htm

from Spiked Science, a wonderful publication that deals with the study of risk in science.

Also see Rifkin at http://www.foet.org/chimerapatent.htm.

Recently the boundary of what chimeras might be useful for has been expanded by some researchers in the United States. The researchers showed that it is possible to take cells from a 3 day human embryo, implant them in an unrelated human embryo and end up with an embryo that is a mosaic of both sets of cells. The researchers did not allow this embryo to develop beyond the few days needed to verify that the transplanted cells indeed would spread.

See: http://news.bbc.co.uk/2/hi/health/3036458.stm

The medical rationale for doing this sort of procedure would be to provide way way to correct certain types of genetic disorders by providing cells with a functional copy of the gene. This particular study probably made the news because the researchers transplanted cells from a male embryo into a female embryo. They did this because the presence of the Y chromosome in the cells derived from the male embryo makes those cells easy to track.

Aside from the long term medical issues, this sort of research is bound to be controversial. After all, we typically view a human being as being the union of one sperm with one egg leading to a single zygote. Here we have the potential of an offspring literally from two zygotes or from four parents. Thus, this research is bound to be seen in many quarters as tampering with the natural order of things. Since such a chimera does not match our preconception of what is normal human reproduction, are they human? Certainly the ethics of this sort of research and medical intervention needs to be carefully thought out.

But as noted by Anderson, human chimeras are not entirely unknown. For example mothers appear to contain viable cells from their offspring for many years, the significance of this finding is not clear. In transplants, the patient in a sense also ends up as being a chimera of sorts, say with the liver of an unrelated individual.

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July 2 2003 A busy summer at the Entangled Bank.....Been since April since I updated this? Wow. Well was sick for a couple weeks...you might say I got hacked by a virus. Was not SARS but did mean I missed a few days of teaching and that doesn't normally happen. Speaking of viruses, SARS seems to be on the wane but it may crop up again. Also there are other virus threats. See for example: Newsday.com - Deadly Ebola, Avian Influenza Reemerging which discusses the threat from Ebola virus and also an resurgent and deadly influenza. Get your flu shoots folks!

Viruses are constantly evolving and jumping from species to species so be alert.

This summer I am not teaching, getting ready to buy a house and took a trip to the North West to visit my sister in Boise ID and a friend who lives near Seattle. Had a choice between seeing Seattle or hiking in the old growth forest. Now that is a no brainer for a biologist - hiking in the old growth forest it was. The new picture on the Bank's opening page is from this trip. Unfortunately I did not have a good camera with me so had to be content with one of those disposable cameras.

I see that there have been some interesting discoveries about the Y chromosome:

Y chromosome sequence completed: DNA readout reveals genetic palindromes safeguard male-defining chromosome.

Abundant gene conversion between arms of palindromes in human and ape Y chromosomes

Often times we think of the Y chromosome as not being very interesting because it is relatively small compared to the X chromosome, but the Y chromosome does have important genes related to testis formation and a switch gene that turns on the developmental pathway towards maleness. These genes do not have homologs with genes on the X chromosome and one mystery has been how is this genetic information maintained in the face of mutation.

It turns out that the Y chromosome has large palindromic regions. A palindrome is a sequence that reads the same in both directions. For example, ABCCBA is a simple palindrome and Amanaplanpanama is a more complex English palindrome Small pallindromic regions are known from DNA sequences but the Y chromosome shows wide scale pallindromic organization. Apparently, though this is still controversial, the pallindromic sequences are used to compare copies of genes and screen out certain important types of mutations. In the chromosomes not involved in sex determination, an important proof reading step takes place during prophase i of meiosis. And in a sense, the Y chromosome is able to do this recombination with itself. I suspect that this works best for what are called frame shift mutations. Check out mutations here.

Biology affects all areas of biology so for you business types check out this link:

Yahoo! News - Economists Walk on Behavior's Wild Side

which attempts to explain the gyrations of the stock market in terms of basic findings in animal behavior.

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April 12 2003. Evolution is messy: The Case of the Cape Bee. .

One of the things I try to impress upon my students is that evolution is messy and often times leads to unexpected results. This is the case because evolution is opportunistic. Take the case of the Cape honeybee. The Cape honey is normally considered a subspecies of the domestic honey bee Apis mellifera.

In most honeybee societies the colony contains a single queen who lays all the eggs or at least the eggs that will develop into females while the workers are sterile. Recently Cape Honeybees were accidentally introduced by bee keepers into regions of South Africa where the "African" honeybee is used extensively for honey production. Unfortunately for the African Honeybee the Cape honeybee has an interesting adaptation that enables it to take over the African Honeybee colonies.

Unlike other honeybees, the worker bees of the Cape honeybee can reproduce asexually. That in itself is not all that unusual in that worker bees can lay male eggs in the absence of control by the queen, and in some strains of honeybees worker egg laying is quite common. Male eggs are produced from unfertilized haploid eggs either by queens or by worker bees, But only the queen bee produces new females and does this from diploid zygotes by fertilizing an egg with sperm from a drone. In the Cape bee, the workers have evolved a neat trick.

First they produce haploid gametes via meiosis, just as the queen does. Then two gametes combine to form a diploid zygote which can develop into a diploid female bee, a process called automictic thelytoky.

See: 10 January 2002 Nature 415, 163 - 165 (2002) Parasitic Cape honeybee workers, APIs mellifera capensis, evade policing.Stephen J. Martin, Madeleine Beekman,Theresa C. Woesler & Francis L.W. Ratnieks.

also, http://www.biologie.uni-halle.de/zool/mol_ecol/social%20parasitism.html .

In a sense then the Cape honeybee can be considered a social parasite because it takes over the African bee nest entirely after a while. The resulting colony is a poor honey producer, hence the concern of African bee keepers about the spread of this bee. The resulting workers produced by the Cape bee can and do lay eggs in the comb of the same colony and can take over other colonies as well. One of these social parasites can lead to the destruction of the original colony in a single season since the Cape bee workers do not work in the host colony of other strains of bees.

One wrinkle is that while this is asexual reproduction the resulting workers produced by one of these bees are not genetically identical to the laying worker. This is because crossing over still happens. So these asexually produced workers are more properly considered pseudoclones See, http://www.americanscientist.org/Issues/Sciobs02/02-09sciobsclones.html.

The Cape bee is not always a social parasite of other strains of honeybee, but it has a number of preadaptations that allow it to take advantage of this opportunity. First not only does it have workers capable of laying female eggs but these bees also drift from colony to colony and have a pheromone system that evades the normal controls on worker reproduction and causes host workers to preferentially feed young Cape workers.

There are other species of social parasites that are so specialized that they cannot survive on their own but are entirely dependent on the host colonies. Such parasites are fond in ants for instance. What has happened with the Cape bee is analogous to what happens with cancer where certain cells in the body break the rules by which cells regulate their reproductive cycle in the body. As noted by American Scientist the Cape honeybee has infected African bee colonies before but the infections have not taken. Perhaps the current invasion is more successful to the detriment of the bee keepers because the current invading strain has just the right combination of traits for successful invasion.

In a sense though this story is a bit similar to the Killer bee story in the New World where the so called Killer bee had just the right set of adaptations to spread through the domestic honeybee populations in North and South America. In a sense perhaps the Cape Honeybee invasion is a type of poetic justice as the Killer Bee's ancestor is the African bee which was accidentally released by a bee keeper in Brazil during the 1950's.

Both these examples should remind us of the quirkiness and opportunistic nature of evolution. These bees- African bees introduced into the New World and the Cape Bee introduced into the African bee's African stronghold- had a certain set of predaptations which enabled then to exploit an opportunity. What will happen next with the Cape Bee is not clear, but some scientists believe that this situation provides a good chance to study the evolution of social parasites. But we shall see. Evolution after all is messy.

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April 4 2003. Protesters as Terrorists? A proposed law in Oregon would treat demonstrators who block streets and disrupt commerce as terrorists, http://story.news.yahoo.com/news?tmpl=story&u=/nm/20030403/ts_nm/life_protests_dc_1.

Persons found guilty of violating this law would face 25 years in jail. This is one of those 'I don't believe someone would propose this' ideas. Granted people who demonstrate should expect to be punished if they violate reasonable laws- but branding them as terrorists is going way too far. First of all the punishment does not fit the 'crime' and probably would be branded as cruel and unusual punishment.

But there are a couple of deeper issues. First, passive civil disobedience is a time honored tradition in dealing with oppression or a government that just flat out refuses to listen to its citizens and laws should not be made that unreasonably singles out people who choose passive civil disobedience as an option. Perhaps the proponents of this law have forgotten the role of civil disobedience in the the struggle for justice in places such as India, Pakistan, Russia and oh yes the civil rights movement in the United States.

The second issue is that this law trivializes terrorism. People who do civil disobedience are not terrorists, yes they cause disruption, but to equate them with the terrorists who destroyed the world trade center, or the Oklahoma City bomber is an Orwellian twist of language that does an injustice to true victims of terrorism. Who after all is terrorized by dissent, even civil disobedience? Oh I get it! Those whose interests are threatened by dissent whether they be American politicians, Communist party bosses, oh and of course the real terrorists whereever they may be.

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April 1 2003 . What with the threat of SARS growing, now a potential problem related to global warming has surfaced, shall we say. Scientists at the Wood's Hole Oceanographic Institute have found clear evidence that global warming has triggered release of methane from undersea deposits. This is significant because methane is itself a major greenhouse gas. The study's authors note that there are 10,000 billion tons of methane in ocean sediments, largely in the form of methane hydrate. The study is significant because it suggests that we really do need to be concerned about global warming and our effects on the Earth's atmosphere because even small initial changes in the Earth's temperature could bring about a rapid and catastrophic release of methane and lead to unexpectedly large warming effects. http://www.whoi.edu/media/Hinrichs.html

On the SARS front the current information coming out suggesting that SARS is spreading in Asia and I believe we need to be concerned that this could become a major epidemic. The best information is at http://www.cdc.gov/ncidod/sars/

This disease is starting to cause widespread panic as evidenced by recent news reports. SARS doesn't appear to be more deadly than certain strains of influenza but it is still not clear how easily the virus is spread. Right now infections are pretty spotty which suggests maybe it is not air borne. The jury is still out on that issue. People are right to be concerned about this virus but it is too early to panic. We have identified the virus, there is evidence that it can be treated with antibodies from previously infected people and we can apparently test for the virus in people. So we are making progress.

That said, where this virus could really cause a problem would seem to be in areas of the world such as Africa where people are in poor physical condition due to famine and war and HIV as well as in areas with aging populations such as Europe and America.

According to the World Heath Organization there have been 1804 cases of SARS reported world wide as of today with 62 deaths. Hong Kong has taken the step of quarantining residents in an apartment complex with a cluster of SARS cases: http://www.who.int/csr/don/2003_03_31/en/. It makes sense to do this given the uncertainty of how easily this virus spreads and the population density of the Hong Kong area which puts people in very close contact. This particular apartment complex has 15,000 residents.

What' s the best advice for stopping this disease and other viruses? Nothing hi -tech or draconian: just wash your hands, http://www.cnn.com/2003/HEALTH/03/30/health.pneumonia.infection.reut/index.html.

The World Heath Organization is also monitoring conditions in Iraq as the war there proceeds the WHO site, http://www.who.int/en/, is worth checking out from time to time for a different sort of war information than what we get on American media.

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March 25 2003. Apparently corona viruses, http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2003/03/25/MN86517.DTL , are now being considered as the likely cause of the pneumonia. Corona viruses commonly cause respiratory illnesses and scientists now suspect that perhaps a new strain of the virus has arisen. Again like the paramyxoviruses, corona viruses are common in other animals as well. Indeed I am familiar with these viruses from my dog show days since epidemics of these viruses would spread through dog populations.

Corona viruses get their name because the viruses protein coat looks like a crown in electron micrographs.

Why is it taking so long to identify the cause of this disorder? Several reasons, first of all the number of alleged cases is relatively small and its possible that cases caused by several different viruses are lumped together. Secondly, viruses are everywhere and its possible that researches are cuing in on viruses that just happen to be there but are not the cause of the pneumonia. Thirdly we cannot do controlled experiments on humans to test the ability of different viruses to cause SARS; the conclusions are reached by careful inference and that takes a large patient base and time.

More on Corona viruses:

CDC press release: http://www.cdc.gov/od/oc/media/pressrel/r030324.htm

About corona viruses: http://www-micro.msb.le.ac.uk/3035/Coronaviruses.html

SARS Update!

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March 21 2003.
Bug updates.The virus has apparently been identified as a paramyxovirus,according to
the BBC http://news.bbc.co.uk/2/hi/health/2862991.stm

"John Oxford, professor of Virology at Queen Mary's School of Medicine,
said a similar virus had been discovered in Holland last year.

"It is rather slow-moving, rather restricted to families and hospitals,
not a rip-roaring affair, but still very nasty. "

Appearently this class of visures is quite capable of jumping between species. Here
http://www.cdc.gov/ncidod/eid/vol4no2/philbey.htm , is another report of one of these viruses, this one tentatively called Menangle virus jumping from fruit bats to humans. Indeed Menangle virus is the third documented virus jump from fruit bats to humans.

These viruses cause some familiar human dieseases such as measles and
mumps: http://www.bio.psu.edu/People/Faculty/Whittam/apdbase/v11.html.
These are also widespread bird and mammal viruses, causing for instance
Newcastle disease in chickens and pigeons,
http://www.cvm.umn.edu/avian/SFPC/PigeonParamyxovirus.html.

Of course it seems that humans manage to complicate things by thinking about using these viruses for other purposes, warfare for example.

Lam(2003) writing in antiviral research
http://dx.doi.org/10.1016/S0166-3542(02)00204-8
Antiviral Res 2003 Jan;57(1-2):113-9

argues that we should be on the alert to the potential of one of these paramyxoviruses as a terrorist weapon. Lam notes:

"Nipah virus, a newly emerging deadly paramyxovirus isolated during a
large outbreak of viral encephalitis in Malaysia, has many of the
physical attributes to serve as a potential agent of bioterrorism. The
outbreak caused widespread panic and fear because of its high mortality
and the inability to control the disease initially. There were
considerable social disruptions and tremendous economic loss to an
important pig-rearing industry. This highly virulent virus, believed to
be introduced into pig farms by fruit bats, spread easily among pigs and
was transmitted to humans who came into close contact with infected
animals. From pigs, the virus was also transmitted to other animals such
as dogs, cats, and horses. The Nipah virus has the potential to be
considered an agent of bioterrorism."

Other paramyxovirus links:

A picture of a typical paramyxovirus:
http://web.uct.ac.za/depts/mmi/stannard/paramyx.html

virology and relication:
http://www.tulane.edu/~dmsander/WWW/335/Paramyxoviruses.html

Good general link.
http://www.stanford.edu/group/virus/1999/leanna/paramyxovirus.html

Meanwhile the pneumonia continues to spread. As of last report about 300 cases woldwide not counting the original Chinese cases. Mortaility looks to be about 5%. And in a testament to the power of travel to spread new diseases, the virus may have reached Kansas as a Kansas man is one of 13 suspected cases in the United States,
http://www.ljworld.com/section/citynews/story/125687.

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March 17 2003
New Bugs. Again there are a series of reports of mysterious viruses and antibiotic resistant strains. A newly observed infectious pneumonia has begun spreading after first being observed from China. This is just the latest of a number of diseases to catch the public attention.

See the World Health Organization, http://www.who.int/csr/don/en/ ,and the Centers for Disease Control, http://www.cdc.gov/, for the latest information. The diesease, more properly a syndrom called SARS for sudden acute respiratory syndrome, http://www.cdc.gov/ncidod/sars/ , first was noted in China and has spread through South East Asia, mainly to health workers.

It is interesting, and a bit scary, that scientists have not as of today been able to identify the cause of the syndrome, though most scientists suspect a virus. We have had a number of disease scares and it seems likely that new viruses and newly evolved versions of current viruses and bacteria will become greater and greater threats inspite of our improved technology.

Some of the threats:

Antibiotic resistant bacteria: For instance see this story concerning Streptococcus pneumoniae from the National Institutes of Health, http://www.nlm.nih.gov/medlineplus/news/fullstory_11935.html. Antibiotic resistance has been known since the 1950's and is a natural result of evolution brought about by humans inadvertantly acting as an agent of natural selection.

Viruses jumping from other host species to humans. This has been known for a long time. For example influenza viruses are known from a wide range of animals and many of the new influenza strains that infect people are known to arize first from other species such as pigs and then spread to humans. See the CDC influenza site, http://www.cdc.gov/ncidod/diseases/flu/viruses.htm.

Other recent examples include:

West Nile virus, a virus transmitted to people from birds by mosquitoes, http://www.cdc.gov/ncidod/dvbid/westnile/.
Hanta virus from certain rodents http://www.bact.wisc.edu:81/ScienceEd/discuss/msgReader$28
Ebola virus possibly from other primates http://www.cdc.gov/ncidod/diseases/virlfvr/virlfvr.htm
HIV possibly from other primates http://www.cdc.gov/ncidod/diseases/submenus/sub_aids.htm

The non human source for Ebola virus is still not known but this virus has recently decimated populations of endangered lowland gorillas. It is believed that when people eat meat from primates, the virus gets a foothold in local human populations.

These viruses are part of a larger problem, CDC journal at http://www.cdc.gov/ncidod/eid/ ; general article, http://news.bbc.co.uk/1/hi/sci/tech/979523.stm .

The emergence of new diseases doesn't just threaten us but threatens the other species that we depend on: For example http://www.apsnet.org/online/feature/NewViruses/abstracts.htm from the American Phytopathological Society, chronicles some of the recent new diseases in crop plants and the reasons for the spread of new plant diseases:

Overuse of pesticides and herbicides
Over confidence in our ability to control disase causing organisms and viruses
Increased transportation of plant materials and travel
Increased contact with wild relatives of domestic plants as we explore new areas and exploit the wild relatives of domestic plants for their germ plasm.

New diseases are evolving all the time for instance plague may have developed when the non pathogenic ansestor of the plague bacterium aquired a gene for an enzyme from another organism. See http://www.niaid.nih.gov/newsroom/releases/geneleap.htm , The plague organism somehow aquired the gene for an enzyme called PLD. This enzyme improves the plague bacterium's ability to colonize the gut of fleas and so these 'enhanced' organisms had an evolutionary advantage. Bad news for us since now the plague was more easily transmissbale to humans.

The original article for this study is at:

BJ Hinnebusch, AE Rudolph, P Cherepanov, JE Dixon, TG Schwan, and A Forsberg. Role of Yersinia murine toxin in survival of Yersinia pestis in the midgut of the flea vector. Science 296:733-35 (2002).

The big lesson is that disease causing organisms are constantly reshuffling, transferring and mutating genetic material in new and unexpected ways that often humble even the most advanced human technology. As I sit here, one ear listening to CNN about the threat to the world from Iraq, I wonder to the degree we are as a species ignoring greater threats posed by disease causing organisms constantly evolving new strategies in response to our technological advances.
Update!

Entangled Bank , Green Fuse Poetry, Previous Page, Next Page ,Top of Page

March 13 2003

Why am I doing this? Several reasons. First to serve as an incubator for new ideas and new ways looking at the universe(whatever that is). Second to log interesting web sites and my explorations of the web in an informal way that might be of interest to my students and other visitors. Finally as a focused journal to keep the juices going. Green fuse is a reference to the Dylan Thomas poem that begins something like:

"The force that through the green fuse drives the flower..."

The complete poem is here:

http://www.bigeye.com/theforce.htm

or here:

http://www.poets.org/poems/poems.cfm?prmID=1161

Dylan Thomas has been an important force in my life since I first heard a recording of him reading his poetry and I constantly turn to him for inspiration and insight. I am amused to see that he has become a sort of cottage industry. Some Thomas sites include:

http://www.dylanthomas.com/

Dylan Thomas.com??? Where you can order all sorts of stuff. Wonder if that is approved by his estate and as general overview:

http://www.poets.org/poets/poets.cfm?prmID=151

Feedback? Write me if you have comments you would like to see here. If your comments are thoughtful and might be of interest to others I will add them. This is not an autmated BLOG so I do this manually. I have thought about doing a BLOG format and may switch to that eventually. See http://www.blogger.com/ for more about BLOGS.

Entangled Bank , Green Fuse Poetry, Previous Page, Next Page ,Top of Page

Short Fuses:

05/20/05 Intelligent Design as JUNK Science.

http://www.newyorker.com/fact/content/articles/050530fa_fact

Wonderfully clear discussion of the problems with intelligent design by W. Allem Orr in the New Yorker magazine. The upshot, which I agree with, is that scientists aren't concerned about Intelligent Design because they are being dogmatic but because it is junk science.

02/06/05 Irreducible complexity: Intelligent design's key idea on trial.

http://www.stephenjaygould.org/ctrl/ruse_irredcomplex.html

A short expose of Intelligent Design's key idea: irreducible complexity by Michael Ruse. Ruse's comment that evolution functions at times as a secular religion is often cited as a justification to include Intelligent design in the science curriculum. I can't imagine antievolutionists will be citing these Ruse comments.

02/05/05 Testing Darwin. A very nice article about how computer simulations using 'artificial organisms' are helping scientists test and refine hypotheses about evolution. This article draws on the work of Robert Pennock and his web site

http://www.msu.edu/~pennock5/

contains further details.

07/09/03 Spiked Science. About our obsession with risk and junk science from a conservative/libertarian pespective. Of course one person's junk science is another person's established science.

07/02/03 Some very nice micrographs and movies can be found at:

Nikon MicroscopyU: Digital Movie Gallery

A site devoted to the study of monarch butterflies!
Monarch Watch : Dedicated to Education, Conservation and Research

04/12/03 Complexity Digest, http://www.comdig.org/, an online resource for the study of complex phenomona in a wide range of fields from biology to economics to politics. Contains links to articles from all over.

03/13/03 Haiku and Chemistry? Of course! Visit The Periodic Table of Haiku. Thanks to Doug Patterson.