Evolutionary biologist Paul Ewald drags us into the sewer to discuss germs. Why are some more harmful than others? How could we make the harmful ones benign? Searching for answers, he examines a disgusting, fascinating case: diarrhoea.

]]> http://badidea.wordpress.com/?p=338 Tue, 13 May 2008 02:58:01 +0000 Bad http://badidea.wordpress.com/?p=338 Last year Steven Pinker wrote a fantastic article on bioethics that somehow had escaped my notice until a commenter recently brought it to my attention: The Stupidity of Dignity.

The point of his essay is not, as one might fear, that human beings lack an inherent dignity or moral importance. It's that the term "dignity" has been so constantly abused that it has become almost worthless in moral debates. It's incoherently defined, capable of having nearly any property, even contradictory ones. And it's all too often used simply as a proxy for the philosopher's or theologian's subjective dislike of some behavior or idea.

Here's the key point of the article:

The problem is that "dignity" is a squishy, subjective notion, hardly up to the heavyweight moral demands assigned to it. The bioethicist Ruth Macklin, who had been fed up with loose talk about dignity intended to squelch research and therapy, threw down the gauntlet in a 2003 editorial, "Dignity Is a Useless Concept." Macklin argued that bioethics has done just fine with the principle of personal autonomy--the idea that, because all humans have the same minimum capacity to suffer, prosper, reason, and choose, no human has the right to impinge on the life, body, or freedom of another. This is why informed consent serves as the bedrock of ethical research and practice, and it clearly rules out the kinds of abuses that led to the birth of bioethics in the first place, such as Mengele's sadistic pseudoexperiments in Nazi Germany and the withholding of treatment to indigent black patients in the infamous Tuskegee syphilis study. Once you recognize the principle of autonomy, Macklin argued, "dignity" adds nothing.

The rest of Pinker's article basically argues that despite an entire volume full of responses to Macklin's challenge, the mostly conservative and religious Presidential Council on Bioethics have failed to answer it. In some cases, as with the notorious Leon Kass, they did worse than fail, exposing bizarre theocratic preoccupations that celebrate death and bemoan liberty in life.

A tour de force. Anyone know of any good responses to, or critiques of, this piece from conservative critics?

What is BioMass? Biomass is biological material derived from living, or recently living organisms. In the context of biomass for energy this is often used to mean plant based material, but biomass can equally apply to both animal and vegetable derived material.  What The Differences BetWeen Biomass aNd Fossil Fuels??

The vital difference between biomass and fossil fuels is one of time scale. Biomass takes carbon out of the atmosphere while it is growing, and returns it as it is burned.  If it is managed on a sustainable basis, biomass is harvested as part of a constantly replenished crop. This is either during woodland or arboricultural management or coppicing or as part of a continuous programme of replanting with the new growth taking up CO₂ from the atmosphere at the same time as it is released by combustion of the previous harvest. 

This maintains a closed carbon cycle with no net increase in atmospheric CO₂ levels.

Categories of Biomass material:

• Virgin wood, from forestry, arboricultural activities or from wood processing
• Energy crops: high yield crops grown specifically for energy applications
• Agricultural residues: residues from agriculture harvesting or processing
• Food waste, from food and drink manufacture, preparation and processing, and post-consumer waste
• Industrial waste and co-products from manufacturing and industrial processes

From the report:

News that scientists have for the first time genetically altered a human embryo is drawing fire from some watchdog groups that say it's a step toward creating "designer babies."

But an author of the study says the work was focused on stem cells. He notes that the researchers used an abnormal embryo that could never have developed into a baby anyway.

Aside from the slippery-slope arguments, this manipulation of human embryos is an affront to the dignity of the human being. See here for more information on stem cells and embryonic development.

"I shall attack Chemistry, like a Shark”. Samuel Taylor Coleridge

‘In January 2001, scientists… produced complex organic molecules under conditions resembling those which exist in interstellar clouds of gas and dust…which, when immersed in water spontaneously created membraneous structures resembling soap bubbles. All life on earth is based on cells, bags of biological material encased in just this kind of membrane. The implication of this work is that space is filled with chemical compounds which can easily give a kick-start to life if they land in a suitable environment, such as on the surface of the Earth.’ John Gribbin, Stardust: the cosmic recycling of stars, planets and people, Penguin, 2001

Who Breathed Chemicals into Life

Who breathed chemicals into life,
made that art of heart and rose -

process greening leaf,
sugaring siren flower.

Who put owl eyes on butterflies,
what for, or how, came eagles -

flying golden from crumbled dust,
hung burning, crucified with light,

dazzling in dusk’s first purple breath -
why came the twitching red-eyed hare,

his russet fur on fire - rocking madly
into nervous twilight, scattering slow

fat rabbits munching grass at sunset,
rusting in the final scene of evening.

Who caused honeysuckle to exhale,
romancing early moths stumbling

into light and perfume, summer evening’s
warm blue mouth - blur-blue - dim-blue -

gold-blue, rose-blue, navy, black; stoning
the still-blue hours - holding its sugared,

signalled breath, until now - time of bat-
flicker, hoots; of stuttering mice moving

grass blades aside with human fingers -
how can all this be, here, accomplished,

asks the man wearing his chemical suit
of miracles, fabulous embroidery of life;

his own experimental design, gorgeous
body and hair, inhabiting these fingers,

this brain; able to pick, read grain
of wheat or sand - feed, calculate -

admire, plant, dream, philosophise.
Why does the kissing of X and Y -

egg and sperm, do anything at all?
What catalyst comes among us -

to that interior dark, savage sex
of lichen, spore, amoebae, dirt -

bumping into moths, moons, bats,
and honeysuckle; night’s speckled

banners hung shining with ignorant planets,
gossiping clusters milky with fogged light -

humming, searching with storm-lamp mind,
these blind fingertips telling dandelion clock

from child’s hair; but just, for a spark
one is able to imagine looks something

like a bright star -
the touch of light.

Interestingly humans aren't the only ones who succumb to peer pressure - rats do too. Rats have a tendency to disregard personal experiences and copy the behaviour of their peers. What's more, the urge to conform appears to be so strong that they will choose to eat food they know to be unpalatable (very yucky) when interacting with other rats that have done the same.

Until now, humans and chimps were the only other animals known to conform in this way. Scientists believe that the discovery emphasises the importance of social learning in the animal kingdom. Read more here.

Planets and life : the emerging science of astrobiology
QH 326 P53 2007

The statistics of gene mapping
QH 438.4 S73 S54 2007

Cytokines in human health : immunotoxicology, pathology, and therapeutic applications
QR 185.8 C95 C992 2007

Bayesian methods for ecology
QH 541.2 M38 2007

HFMD usually affects infants and children, is quite common worldwide and can be caused by a number of different enteroviruses. It is highly contagious and is spread through direct contact with the mucus, saliva, or faeces of an infected person. Like other enterovirus infections (including polio), HFMD typically occurs in small epidemics, usually during the summer and autumn months with an incubation period of 3-7 days.

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Enterovirus infections are common and occur worldwide. Although many infections show no symptoms and often go unnoticed, these viruses are also associated with occasional outbreaks in which a larger than usual number of patients develop clinical disease, sometimes with fatal consequences. The current outbreak is one of these. Initial testing for a variety of respiratory diseases did not reveal any conclusive results, but on April 23, the presence of Enterovirus (EV71) was confirmed. As of May 8th, at least 30 deaths had been reported and the disease had spread to 11 cities and several provinces across China. In all the fatal cases, which represent less than 1% of the thousands of children infected, the victims died with serious complications such as neurogenic pulmonary oedema (breathing difficulties reminiscent to those seen in polio victims).

Enterovirus replication begins in the gastrointestinal or respiratory tract but once the virus is present in the bloodstream may affect various tissues and organs, causing a variety of diseases. Clinically, it is difficult to distinguish the specific cause of most enterovirus infections. Diagnostic testing for non-polio enteroviruses requires specialized laboratory facilities. Diagnosis is made by detecting virus in the throat, in faecal samples or, more convincingly, from specimens collected from the affected part of the body, for example, cerebrospinal fluid (CSF) or biopsy material. A four-fold rise in the level of neutralizing antibody in specimens collected during the acute and convalescent phases of illness provides the best evidence for a recent infection. No specific antiviral agents are currently available for treatment of enterovirus infections, although intravenous administration of immune globulin may have a use in preventing severe disease in immunocompromised individuals or those with life-threatening disease.

EV71 was first isolated in an outbreak of neurological disease in California in 1969. One of the nastier enteroviruses, EV71 has been associated with several epidemics of severe neurological disease in children, mostly in East Asia. An outbreak in Taiwan in 1998 resulted in 129,106 reported cases, 405 children hospitalized and more than 80 deaths. EV71 appears to be emerging as an important virulent neurotropic enterovirus just as poliomyelitis is nearing eradication, but little is known about the molecular mechanisms of host response to EV71 infection.

Transmission of enterovirus infections is increased by poor hygiene and overcrowded living conditions. Improved sanitation and general hygiene are important preventive measures. Measures that can be taken to avoid getting infected with enteroviruses include frequent handwashing, especially after nappy (diaper) changes or going to the toilet, disinfection of contaminated surfaces with bleach, and washing soiled articles of clothing. Enteroviruses are quite resistant to many disinfectants so it is important to use chlorinated (bleach) or iodized disinfectants. During recognised epidemics, it may be advised to close institutions such as schools or child care facilities in order to reduce transmission among young children. Chinese public health experts currently predict that the number of cases will continue to increase and peak around June-July.

Latest News

Related:

• The More Things Change, The More They Stay The Same
• Epidemics to eradication: the modern history of poliomyelitis
• Dynamics of picornavirus RNA replication

‘*The word ‘mechanics’, in this context, is provocative. It stands in opposition to the concept of ‘vitalism’. Vitalists maintain that life is driven by unique processes that are not explicable purely by the standard laws of physics and chemistry, while ‘mechanists’ maintain that life simply required complicated chemistry.’ Note, Ian Wilmut and Keith Campbell, The Second Creation, Headline, 2001

‘Chemist, you breed/ In orient climes each sorcerous weed/ That energises dream – ‘. Herman Melville, 1819-91, The New Zealot to the Sun

‘SURLY: “What else are all your terms,/ Whereon no one of your writers ‘grees with other?/ Of your elixir, your lac virginis,/ Your stone, your med’cine, and your chrysosperme,/ Your sal, your sulphur, and your mercury,/ Your oil of height, your tree of life, your blood,/ Your marchesite, your tutie, your magnesia,/Your toad, your crow, your dragon, and your panther;/ Your sun, your moon, your firmament, your adrop,/ Your lato, azoch, zernich, chibrit, heautarit,/ And then your red man, and your white woman,/ With all your broths, your menstrues, and materials,/ Of piss and egg-shells, women’s terms, man’s blood,/ Hair o’ the head, burnt clouts, chalk, merds, and clay,/ Powder of bones, scalings of iron, glass,/ And worlds of other strange ingredients,/ Would burst a man to name?” SUBTLE: “And all these named,/ Intending but one thing: which art our writers/ Used to obscure their art”.’ Ben Jonson, 1572-1637, The Alchemist

Feeling the Discovered Workings of the Genome

I rub my hands together, feeling frizzy chemical combustion;
skin spawning elastic cell-seal - muffled hinges of articulate
stem-star bone crackling silently under our muscular gloves,

that can stroke notes from gappy piano teeth, but strangle;
comfort, strengthen, punch or pray - the organic red pump,
battery clock and wires, pulsing wrist guages industriously.

I run my fingers through my hair, frazzling the yellow factory,
sparking seed-silk filaments into animal fuzz - ghost remnant
sprouting arty follicles with no imperative for such a display -

kept like a peackock tail, physical halo, scripture of decoration.
My stomach oven growls - independent hunger, acidic machine
processes. Dust launches from me in dirty sun; my own glittering

galaxy of spent particles - each authored with potential me -
my universal signature floating nowhere, nano person-planets
seeded with the means of life, wandering or returning to earth.

I feel the Genome; writing, powering. My own chemicals
dancing - combining, producing, housekeeping, adapting;
such quadrilles, Eightsome Reels, a-waltzing in the heart

and brain. Pagan and religious ecstasy as one, as life.
So much vibration, I burn blue/red/gold as Autumn -
as sparking leaf, touch my small child’s spring hand;

feel silver spiral-fires of reciprocal DNA, sparkling,
chemical crackling of growing hand - practicalities
of bone, blood, skin; presence of art, beauty settling

this pristine home, universal energy flowing around
his head - the mark of a child, child halo; new light
called from old, original - yet still illuminating stars.

There's a new species of spider discovered and the biologist named it after Neil Young. Says the species founder Jason Bond:

"With regards to Neil Young, I really enjoy his music and have had a great appreciation of him as an activist for peace and justice."

As long as the spider isn't poisonous, I guess that name fits.

Neil isn't the first rock musician named after a new species. Roy Orbison got that honor for being named after a species of beetle: the whirligig beetle, or Orectochilus orbisonorum.

It really should have been a Beatle instead.

Until about 1832, when it first seems to have become established as a noun and a concept, the term "scientist" had no really independent meaning. "Science" meant "knowledge" in much the same way as "physic" meant medicine, and those who conducted experiments or organized field expeditions or managed laboratories were known as "natural philosophers." To these gentlemen (for they were mainly gentlemen) the belief in a divine presence or inspiration was often merely assumed to be a part of the natural order, in rather the same way as it was assumed—or actually insisted upon—that a teacher at Cambridge University swear an oath to be an ordained Christian minister. For Sir Isaac Newton—an enthusiastic alchemist, a despiser of the doctrine of the Trinity, and a fanatical anti-Papist—the main clues to the cosmos were to be found in Scripture. Joseph Priestley, discoverer of oxygen, was a devout Unitarian as well as a believer in the phlogiston theory. Alfred Russel Wallace, to whom we owe much of what we know about evolution and natural selection, delighted in nothing more than a session of ectoplasmic or spiritual communion with the departed.

And thus it could be argued—though if I were a believer in god I would not myself attempt to argue it—that a commitment to science by no means contradicts a belief in the supernatural. The best known statement of this opinion in our own time comes from the late Stephen Jay Gould, who tactfully proposed that the worlds of science and religion commanded "non-overlapping magisteria." How true is this on a second look, or even on a first glance? Would we have adopted monotheism in the first place if we had known:

That our species is at most 200,000 years old, and very nearly joined the 98.9 percent of all other species on our planet by becoming extinct, in Africa, 60,000 years ago, when our numbers seemingly fell below 2,000 before we embarked on our true "exodus" from the savannah?

That the universe, originally discovered by Edwin Hubble to be expanding away from itself in a flash of red light, is now known to be expanding away from itself even more rapidly, so that soon even the evidence of the original "big bang" will be unobservable?

That the Andromeda galaxy is on a direct collision course with our own, the ominous but beautiful premonition of which can already be seen with a naked eye in the night sky?

These are very recent examples, post-Darwinian and post-Einsteinian, and they make pathetic nonsense of any idea that our presence on this planet, let alone in this of so many billion galaxies, is part of a plan. Which design, or designer, made so sure that absolutely nothing (see above) will come out of our fragile current "something"? What plan, or planner, determined that millions of humans would die without even a grave marker, for our first 200,000 years of struggling and desperate existence, and that there would only then at last be a "revelation" to save us, about 3,000 years ago, but disclosed only to gaping peasants in remote and violent and illiterate areas of the Middle East?

To say that there is little "scientific" evidence for the last proposition is to invite a laugh. There is no evidence for it, period. And if by some strenuous and improbable revelation there was to be any evidence, it would only argue that the creator or designer of all things was either (a) very laborious, roundabout, tinkering, and incompetent and/or (b) extremely capricious and callous, and even cruel. It will not do to say, in reply to this, that the lord moves in mysterious ways. Those who dare to claim to be his understudies and votaries and interpreters must either accept the cruelty and the chaos or disown it: they cannot pick and choose between the warmly benign and the frigidly indifferent. Nor can the religious claim to be in possession of secret sources of information that are denied to the rest of us. That claim was, once, the prerogative of the Pope and the witch doctor, but now it's gone. This is as much as to say that reason and logic reject god, which (without being conclusive) would be a fairly close approach to a scientific rebuttal. It would also be quite near to saying something that lies just outside the scope of this essay, which is that morality shudders at the idea of god, as well.

Religion, remember, is theism not deism. Faith cannot rest itself on the argument that there might or might not be a prime mover. Faith must believe in answered prayers, divinely ordained morality, heavenly warrant for circumcision, the occurrence of miracles or what you will. Physics and chemistry and biology and paleontology and archeology have, at a minimum, given us explanations for what used to be mysterious, and furnished us with hypotheses that are at least as good as, or very much better than, the ones offered by any believers in other and inexplicable dimensions.

Does this mean that the inexplicable or superstitious has become "obsolete"? I myself would wish to say no, if only because I believe that the human capacity for wonder neither will nor should be destroyed or superseded. But the original problem with religion is that it is our first, and our worst, attempt at explanation. It is how we came up with answers before we had any evidence. It belongs to the terrified childhood of our species, before we knew about germs or could account for earthquakes. It belongs to our childhood, too, in the less charming sense of demanding a tyrannical authority: a protective parent who demands compulsory love even as he exacts a tithe of fear. This unalterable and eternal despot is the origin of totalitarianism, and represents the first cringing human attempt to refer all difficult questions to the smoking and forbidding altar of a Big Brother. This of course is why one desires that science and humanism would make faith obsolete, even as one sadly realizes that as long as we remain insecure primates we shall remain very fearful of breaking the chain.

Despite the fact that I'm an atheist, I recognise that belief offers something that science does not.

Science isn't remotely about a scientist announcing truths or The Truth. It’s about stating things with a certain degree of certainty. A scientist will say, "In this experiment, I observed that A causes B; it didn't happen every single time, and my statistical analyses show that I can be X percent certain that this A/B connection didn't happen by chance." The convention in most scientific papers is that you don't report something until you're more than 95 percent certain. It is impossible with statistics to state something with 100 percent certainty.

Now, I'm not trying to be a postmodernist gibbering about how science is a purely subjective process and there are no objective truths. There are truths, and scientific knowledge produces temporary points of solid ground in pursuit of them. An observation must have predictive power and be capable of independent replication by others. And scientists must be willing to abandon supposed knowledge when a completely different explanation arises—"Hey, this is an orangutan jawbone stained dark, so Piltdown Man really isn't our grandfather." Far more often, scientists are asked to modify their knowledge: "Remember when you said that A doesn't cause B every single time? It turns out that A causes B only when C is happening." This increases the subtlety and nuance of science. As a surprising example, it turns out that the most iconic "fact" in the life sciences is only a temporary foothold: DNA doesn't always form a double helix, and those exceptions are mighty interesting.

So it doesn't even make a whole lot of sense to frame a science/religion fight as who has the truthier truth. But you can state it as, "Which approach gives you more predictive power and ability to change an outcome?" When stated this way, science wins hands down. There's no question that when faced with, say, a sick child, it's better to prescribe antibiotics than to invoke some ceremonial goat innards or to employ a fetish gee-gaw. Even in a country as throttled by religion as our own, the courts have consistently ruled that a parent cannot deny medical care to a sick child and instead substitute attempts at religious cures. That's not why belief resists obsolescence.

The next logical arena in the culture wars is the issue of whether religion or science is better for society. On this front, there's no question which approach has produced more historical (and contemporary) harm. Sure, science has come up with Lysenkoism, eugenics, lobotomies, and the people who methodically tested new uses for Zyklon B. But that doesn't even begin to nudge the scale from its one-sided tilt. And the argument that the likes of Torquemada are aberrations of religiosity is nonsense; they are the only logical consequences of some facets of religiosity. The blood on the hands of religion drips enough to darken the sea.

It might be argued that religious belief remains relevant because of the comfort it can provide. But this one doesn't do much for me. Solace is not benign when reality proves the solace to have been misplaced, nor are beliefs that reduce anxiety when the belief system is so often what generated the anxiety in the first place.

So why is belief still relevant? To this I'd offer a very a-scientific answer. It is for the ecstasy. I'm not talking about glossolalic frothing in the aisles, nor other excesses that most religions neither generate nor value. I mean those instances where you're suffused with gratitude for life and experience and the chance to do good, where every neurone is flooded with the momentness of feeling the breeze on its cellular cheek. A scientist or a consumer of science may feel ecstatic about a finding—that it will cure a disease, save a species, or is just stunningly beautiful—but science, as an explanatory system, is not very good at producing ecstasy. For starters, there are good arguments to be made for why science shouldn't do ecstasy. One reason is that scientific progress so often constitutes minutiae that lurch you two steps back for every three steps forward. It is also because of the content—the gratitude part of ecstasy is particularly hard if you spend your time studying, say, childhood cancer, or the biology of violence, or causes of extinction. By contrast, the potential for ecstasy is deeply intertwined with religiosity, where the mere possibility of belief and faith in the absence of proof is where it can be an ecstatic, moving truth.

This may seem an unfair tilting of the debate against science. After all, you wouldn't write an essay trashing the profession of commodities broker because it doesn't produce ecstasy. But building your life's explanations around science isn't a profession. It is, at its core, an emotional contract, an agreement to only derive comfort from rationality.

Science is the best explanatory system that we have, and religiosity as an alternative has a spectacular potential for harm that permeates and distorts every domain of decision-making and attribution in our world. But just because science can explain so many unknowns doesn't mean that it can explain everything, or that it can vanquish the unknowable. That is why religious belief is not obsolete. The world would not be a better place without ecstasy, but it would be one if there wasn't religion. But don't expect science to fill the hole that would be left behind, or to convince you that there is none.

"Science" we mean the entire enterprise of secular reason and knowledge (including history and philosophy), not just people with test tubes and white lab coats.

Traditionally, a belief in God was attractive because it promised to explain the deepest puzzles about origins. Where did the world come from? What is the basis of life? How can the mind arise from the body? Why should anyone be moral?

Yet over the millennia, there has been an inexorable trend: the deeper we probe these questions, and the more we learn about the world in which we live, the less reason there is to believe in God.

Start with the origin of the world. Today no honest and informed person can maintain that the universe came into being a few thousand years ago and assumed its current form in six days (to say nothing of absurdities like day and night existing before the sun was created). Nor is there a more abstract role for God to play as the ultimate first cause. This trick simply replaces the puzzle of "Where did the universe come from?" with the equivalent puzzle "Where did God come from?"

What about the fantastic diversity of life and its ubiquitous signs of design? At one time it was understandable to appeal to a divine designer to explain it all. No longer. Charles Darwin and Alfred Russel Wallace showed how the complexity of life could arise from the physical process of natural selection among replicators, and then Watson and Crick showed how replication itself could be understood in physical terms. Notwithstanding creationist propaganda, the evidence for evolution is overwhelming, including our DNA, the fossil record, the distribution of life on earth, and our own anatomy and physiology (such as the goose bumps that try to fluff up long-vanished fur).

For many people the human soul feels like a divine spark within us. But neuroscience has shown that our intelligence and emotions consist of intricate patterns of activity in the trillions of connections in our brain. True, scholars disagree on how to explain the existence of inner experience—some say it's a pseudo-problem, others believe it's just an open scientific problem, while still others think that it shows a limitation of human cognition (like our inability to visualize four-dimensional space-time). But even here, relabeling the problem with the word "soul" adds nothing to our understanding.

People used to think that biology could not explain why we have a conscience. But the human moral sense can be studied like any other mental faculty, such as thirst, colour vision, or fear of heights. Evolutionary psychology and cognitive neuroscience are showing how our moral intuitions work, why they evolved, and how they are implemented within the brain.

This leaves morality itself—the benchmarks that allow us to criticize and improve our moral intuitions. It is true that science in the narrow sense cannot show what is right or wrong. But neither can appeals to God. It's not just that the traditional Judeo-Christian God endorsed genocide, slavery, rape, and the death penalty for trivial insults. It's that morality cannot be grounded in divine decree, not even in principle. Why did God deem some acts moral and others immoral? If he had no reason but divine whim, why should we take his commandments seriously? If he did have reasons, then why not appeal to those reasons directly?

Those reasons are not to be found in empirical science, but they are to be found in the nature of rationality as it is exercised by any intelligent social species. The essence of morality is the interchangeability of perspectives: the fact that as soon as I appeal to you to treat me in a certain way (to help me when I am in need, or not to hurt me for no reason), I have to be willing to apply the same standards to how I treat you, if I want you to take me seriously. That is the only policy that is logically consistent and leaves both of us better off. And God plays no role in it.

For all these reasons, it's no coincidence that Western democracies have experienced three sweeping trends during the past few centuries: barbaric practices (such as slavery, sadistic criminal punishment, and the mistreatment of children) have decreased significantly; scientific and scholarly understanding has increased exponentially; and belief in God has waned. Science, in the broadest sense, is making belief in God obsolete, and we are the better for it.

"What was true yesterday remains true even today. The truth expressed in 'Humane vitae' doesn't change; on the contrary, in the light of new scientific discoveries it is ever more up to date," the pope added.

And which scientific discoveries are those? That there is, after all, no "moment" of conception when a magical homunculus pops into being? That even a non-fertilized egg, or potentially any cell in the human body, can be induced to grow into a new human being? That the creation of a human person is a long complex process resulting, eventually, not instantaneously, in specific functional capacities.

The mark of the human search for truth, you see, is that it does change: it updates itself in light of new evidence, apologizes for error. This is doubly true in the case of moral understanding: better knowledge helps us make better decisions, alerts us to moral consequences we may have missed.

Now, I understand that Popes claim to be relying on insights supposedly proscribed by a higher power, and I suppose this is where we must differ. I don't see any evidence of such insight. In fact, the contrary. What I see are doctrines formed in (perfectly understandable!) ignorance of human biology and social experience, now (less understandably) grasping at straws and cherry picking in an attempt to remain relevant, all the while resisting any re-examination.

And while Popes couch their declarations as sincere defenses of moral sense and human dignity, it's hard to take them as seriously as they intend it. Perhaps mainly due to the nature of the institution they find themselves wedded to, there is very little room in which to confront the possibility of error. And when it comes down to admitting doctrinal error or real human dignity, which does history tell us is likely to bend to which?

"No mechanical technique can substitute the act of love that two married people exchange as a sign of a greater mystery," Benedict said in his speech.

I quite agree that sex, as with all human experience, can be part of a greater mystery. But the Pope is sorely abusing the word here: appealing to positive connotations he has earned no right to. Indeed, his entire purpose is to routinize that mystery into the very specific form he believes the universe favors, all in service of a doctrine that is itself no mystery (except in the sense that it's often philosophically unintelligible).

Benedict expressed concern that human life risks losing its value in today's culture, and worried that sex could "transform itself into a drug" that one partner had to have even against the will of the other.

"What must be defended is not only the true concept of life, but above all the dignity of the very person," the pope added.

You know what makes human life lose value and dignity? Cloudy, impenetrably confused moral thinking.

Like the sort that compares a experiencing, feeling human being to a nerveless embryo, and thus mangles any sense whatsoever of what makes human life, in particular, morally important.

Or the sort that stands in opposition to the distribution or even the education of poor people about contraceptive methods to prevent the spread of deadly disease. The one that treats knowledge as a temptation, and ignorance a blessing... if by blessing, you mean infecting your wife with AIDS because your priest declares that condoms are not permitted even within a marriage, even for that grave purpose.

Of course, voice these sorts of criticism within earshot of excitable apologists, and you're bound to hear one or two responses.

The first is to loudly bemoan the supposed scientism-sans-conscience of Catholicism's critics. This response is mere subterfuge. Us "moderns," secular or no, are not nihilists: what we have are different values than the ones promoted by pontiffs, different ideas about where to draw the line on, for instance, stem cells. What we're due in response is debate, not glib dismissals about our supposed moral blindness or vacuity.

The second response is that critics of Catholic doctrine are ultimately just narcissists: heedless pleasure seekers. Oh how they love this endlessly self-aggrandizing accusation! But the character of this sort of argument is both slanderous and baseless. Half the time it doesn't even make sense, as when critics like myself are largely arguing on behalf of the liberty of others (such as homosexual rights that I myself have no need of).

The other half of the time, it's just a backhanded way to justify injustices or restrictions that stand accused of causing harm themselves. It's easy to frame any argument for progress as "selfishly" promoting pleasure and reducing suffering. Easy, but rarely helpful or sensible as a criticism of those ideas or improvements.

And worse, these declarations against demands for human happiness are insincere. For apologists often appeal to the idea that they know, better than everyone else, what best leads to the deepest human happiness. That anything other than their path leads to misery and ruin, not merely in an imagined afterlife, but here on earth. Very well: but others make the same claims about their own contrary paths and philosophies. Thus there is room for legitimate debate.

But, I suppose, such fair debates risk the unacceptable possibility of rational defeat. Simply accusing your critics of hedonistic animality is all the simpler and less dangerous.

The concept of using "God" as an explanation for the unknown is known as The God of the Gaps. The argument continually retreats as long as there is something ultimately unknown in which it can provide an "answer." At the inception of the Abrahamic religions, those gaps were massive. At present day, they're virtually non-existent.

I have thought often for much of my life about such questions that religion however brashly claims to answer. The scientific theory for the beginning of the universe as we know it is the well-known by name, Big Bang theory. There are some things that are not well-known and cause some inane arguments, similar to evolution.

The Big Bang theory states that all the matter in the universe once was part of a singularity (a simplified description being matter compacted very densely), which then rapidly expanded from that point. All observable evidence shows everything moving away from a central location, providing heavy support for the general theory.

What is misrepresented, however, is anything more than that. What is unaccounted for and is speculative at best are the origin of the singularity and time prior to the Big Bang. These are separate cosmogonous questions that do nothing to disprove the Big Bang theory, which is a theory providing the answer to where all stars/galaxies/planets/etc. originated but not when matter was first created.

This and related cosmological study on the progression of matter over time gives a general knowledge of the timeline of the origin of the current state of the universe up to the point of life's existence on Earth. The Miller-Urey experiment has shown that organic material can be generated from inorganic material, even that which is meant to simulate the state of an early Earth.

From the point of life on Earth, Evolutionary biology, again in general terms, has described pretty much the entire timeline of the tree of life on Earth. This includes an extensive fossil record of human evolution as well as arguably even stronger DNA evidence.

What this means is that it's basically known to science the general process from the formation of the universe to the current state of the universe and life on Earth as it is now, over the course of 13.7 billion years. This leaves few options for religion. In fact, I am now at the conclusion that the possibilities left in terms of a creator that are subject to known science are limited to two options:

1. Everything we know and see was created as is at some unknown point in time. That is to say, this falls under the category of our perception of reality itself is subject to the physical confines of our own psyche, or that the only thing we can be sure of is our own mind (solipsism). Basically the argument could be put forth that an all-powerful being hypothetically could have created everything, including our own memories of the past, just 5 minutes ago.

2. Matter provided sometime prior to the Big Bang was put forth divinely. There is very little agreement on the origin of matter itself, if it even has an origin.

Religion was founded on answering the, at the time, unanswerable. Well, we've answered nearly everything in general terms. As long as "moderates" insist of maintaining their religion, they need at least understand what they have no choice if they want to live in reality to believe. There are two options, and clearly the first is crazy (though I guess that would fit right in, then).

Religions should actually take this very well. It should be unifying. Since the holy texts really have no relevance, there may as well be a collaboration. You're all "religions of peace," right?

Современным школьникам жить веселее! Продвинутым учителям также :)

Update: другая визуализация на микробиологическую тему на сайте DNA interactive

And it seems that Foldit players aren't helping to fold proteins in the direct sense either:

Can humans really help computers fold proteins?

We’re collecting data to find out if humans' pattern-recognition and puzzle-solving abilities make them more efficient than existing computer programs at pattern-folding tasks. If this turns out to be true, we can then teach human strategies to computers and fold proteins faster than ever!

So they intend to collect data from the game to help them spot heuristics humans use that can then be implemented in computer programs. They aren't going to take the results of human protein folding as the 'correct' structures.

but, that didn't stop the blogging muse from leading me to a topic. some of you may not like this one:

i went to drop off the pictures to r and a from their "shoot" with the dogs. we got to chatting. 2 topics came up: 1. they're getting married! wonderful news! 2. bees.

and bees let to a bringing out her bug trays!

not too bad. who doesn't love a butterfly, right? and don't most people learn to love moths eventually, as well?

but then...

for the love of all that's holy!

that big ass beetle, the one who looks like a death machine from a milla jovovich movie? that's the palo verde beetle. some of you may remember the story of my cat befriending the one who was trying to assassinate me last summer....only that one was twice the size of this dead guy.

moving on...

yes, that is a hissing cockroach.

let's cleanse our visual pallet with a butterfly...

and here's hoju, howling...

you can catch more of him on my photoblog, dogdailyphoto.wordpress.com.

so, i didn't stay long. and now i'm blogging because i can't sleep since i don't feel well. not to complain. just mentioning why i'm up is all.....

And I’ll start with a favourite of mine, which launched an entire school of thought that touched many corners of biology:

J. Maynard Smith and G. R. Price. The logic of animal conflict. Nature, 246(1):1518, 1973. DOI: 10.1038/246015a0

As a trivial introduction, a few words on game theory: game theory is the study of optimal behaviour in strategic situations, where the optimal choice that one individual makes depends on the choices of the other individuals involved. A brief, concrete example may help. Imagine a foraging situation in which a solitary bird chooses amongst a field of potential food patches. This situation is not best analyzed using game theory, because the bird’s choice is simple: select the patch which maximizes his food intake. However, if we now add in the rest of the flock, the situation changes and game theory is the best way we have of analyzing the new problem. At this point, our focal bird’s choice must necessarily depend not only on the patch that they would prefer, but on the choices of all the other birds simultaneously. If every bird in the flock chooses the same patch, it may now be better for our focal bird to switch to another, less rich patch, because even though their preferred patch is richer they may not actually gain anything from competing to exploit it. (This is a simple example and an even simpler definition, of course, and I refer reader interested in the mechanics of game theory to the references below). An important term to learn is frequency dependence / independent. In the foraging situation above, the bird foraging alone is experiencing frequency independent payoffs, because his payoffs depend only upon his own actions. When the rest of the flock shows up and begins to forage as well, the payoffs become frequency dependent because now the payoff to a strategy depends on the strategy adopted by every other member of the flock present. Strategies which are increasingly common (more frequent) will experience a change in payoff, negative or positive as per the specific payoffs.

Game theory as a field began to acquire a shape and form when Oskar Morgenstern and John von Neumann published a book called Theory of Games and Economic Behaviour (1944), and the applications to economics and other fields like political science were immediate and highly influential. A flood of research followed, with scholars like John Nash, Anatol Rapoport, and Reinhard Selten leading a charge into the new and complex formal mathematics that underlies game theory. However, penetration into my field, biology, was limited until the 1970s, when a small paper in the journal Nature appeared, with John Maynard Smith and George R. Price as the authors (Maynard Smith & Price, 1973) .

The paper was a model of simplicity and clarity. It posed a central question: why aren’t more animal fights fatal? This was a question of some concern, because animals have large repertoires of nasty weapons with which to pursue violent conflicts, but as Maynard Smith and Price pointed out, animals rarely fight to the death. At the time, one of the more popular explanations was a group selection argument, which stated that animals kept fatalities to a minimum to benefit the group or the species. But this didn’t cut it any more, because at the time, group selection in biology was undergoing a violent death of its own. So, for the subject of this paper, the question remained: absent the feel-good explanation afforded by group selection, how could this behaviour be explained? Could it be adaptive on an individual level?

To answer this question, Maynard Smith and Price put forth a novel concept: the Evolutionarily Stable Strategy (ESS). As the authors put it:

Roughly, an ESS is a strategy such that, if most of the members of a population adopt it, there is no ”mutant” strategy that would give higher reproductive fitness (p. 15).

The ESS concept is a difficult one for many to grasp, and I’m not going to go into a full report of the subtleties here. The important points to know are:

• An ESS strategy guarantees that a population which adopts that strategy is uninvadable by a small proportion of mutants using another (single) strategy. If the population is using the ESS strategy A and a small percentage (say 1%) mutates to strategy B, ESS theory guarantees that the B mutants will not be able to invade and will die out.
• For those in the audience who like to see a little math, a slightly more formal definition of an ESS is as such: in an infinite asexually reproducing population of individuals who each adopt a strategy in a frequency-dependent payoff situation and encounter each other in pairs, the expected payoff E to an individual playing strategy I against an individual playing strategy J is E(I , J ). With this (incomplete) notation in place, an ESS is a strategy which satisfies the following conditions:
  • $latex E(I,I) > E(J,I) \forall I \neq J$, or
  • $latex E(I,I) = E(J,I)$ and $latex E(I,J) > E(J,J) \forall I \neq J$.
• In English, this states that for a strategy to be stable, individuals adopting the ESS must receive a higher payoff against other ESS players than mutant individ- uals do against ESS individuals. Failing that, if mutants receive the same payoff against ESS players as ESS players do against themselves, then ESS players must receive a higher payoff against mutants than mutants do against themselves. The first condition states that mutants can’t invade; the second condition says that if they can invade (by drift), that they will still be selected against if they become appreciably common in the population.

To this point, I’ve presented things in a backwards fashion, because the formal definition of an ESS was actually the last thing that Maynard Smith and Price actually did in the paper. To begin, they set the stage by presenting computer simulation results on a set of fictional strategies repeatedly playing a game against each other. The game was a variation of what is now famous as Hawk / Dove, though interestingly Price insisted that Dove be known as ”Mouse” for religious reasons. The game involved repeated interactions between two players who could adopt one of two tactics: ”(D)angerous”, which would be likely to cause serious harm, or ”(C)onventional” , which would be unlikely to cause serious harm. At any point, either player could choose ”(R)etreat”, after which the game would be over. These tactics, D / C / R, along with probabilities for playing each in any round of the game, constituted a strategy. If a player played D, there was a chance that their opponent would be seriously injured, after which the opponent would be obliged to retreat. Payoffs were given for short combats.

In the simulation, five different strategies were tested against each other: a ”total war” strategy known as Hawk, three ”limited war” strategies called Mouse, Retaliator, and Prober-Retaliator, and a final strategy called Bully. Hawk would always play D, until seriously injured or the opponent retreated. Mouse would never play D, and if the opponent played D would retreat immediately. The other three strategies used some combination of C and D in different ways.

The details after that are only of interest to those who would like to read the paper, because the main point to come out of the computer simulations is that t the limited war strategies did better than the total war Hawk. Thus, Maynard Smith and Price were able to demonstrate that under the assumptions of the Hawk / Dove game, it could indeed be adaptive to forego fatal conflict as a result of individual selection. By following this up with a formal investigation of the properties of ESSs, they were able to show that this was not just a fluke but that in the game they used Hawk could not be an ESS.

Maynard Smith was already a well known figure in biology at this point, and he has retained much of the credit for the subsequent explosion of biological game theory and the notion of the ESS. However, he himself freely admitted that Price was a major driver of the initial work on ESS theory. As noted in Ullica Christina’s book Defenders of the Truth: The Sociobiology debate (Christina, 2000), Maynard Smith actually introduced the idea of the ESS first in a book published in 1972, in which he stated in the acknowledgements:

The essay on ’Game Theory and the evolution of fighting’ was especially written for this book. I would probably not have had the idea for this essay if I had not seen an unpublished manuscript on the evolution of fighting by Dr. George Price, now working in the Galton Laboratory at University College London. Unfortunately, Dr. Price is better at having ideas than at publishing them. The best I can do therefore is to acknowledge that if there is anything to the idea, the credit should go to Dr. Price and not to me (Maynard Smith, 1972, p. viii).

(Price’s connection with game theory, his accomplishments in biology, and his tragic character are noted further in Christina’s book.) Further, the ideas developed in this paper and in other work by Maynard Smith were clearly influenced by the work of both Hamilton’s work on ”uninvadable strategies” (Hamilton, 1967) and Fischer’s work on sex ratios in the 1930s (Fisher, 1930). In fact, I remember seeing that Maynard Smith had tried to read Morgenstern and von Neumann’s book, but had failed to get far enough through the dense mathematics to find out that M. & v-N. had effectively beaten him to the punch on ESS theory by several decades (though the source of this escapes me - does anyone know what it is, or know if it’s apocryphal?)

This being the case, though, it was the Nature paper which really brought biological game theory to light, leading to the seminal book on the sub ject by Maynard Smith some nine years later (Maynard Smith, 1982). Those works led to the widespread adoption of a new way of thinking about frequency-dependent problems and optimization in biology, an approach that continues to bear fruit even today. For anyone looking to get a better handle on the intricacies of game theory or to see where its application in biology really started, I recommend that you read this paper. (As a bonus, it’s short - 4 pages - and generally quite readable....)

References:

• Christina, U. (2000). Defenders of the Truth: The sociobiology debate. Oxford: Oxford
  University Press.
• Fisher, R. A. (1930). The Genetic Theory of Natural Selection. Oxford: Clarendon Press.
• Hamilton, W. D. (1967). Extraordinary sex ratios. Science, 156 (3774), 477–488.
• Maynard Smith, J. (1972). Game theory and the evolution of fighting. In J. Maynard Smith (Ed.) On Evolution. Edinburgh University Press.
• Maynard Smith, J. (1982). Evolution and the Theory of Games. New York, NY:Cambridge University Press.
• Maynard Smith, J., & Price, G. R. (1973). The logic of animal conflict. Nature, 246(1), 15–18.
• von Neumann, J., & Morgenstern, O. (1944). Theory of Games and Economic Behaviour. New Jersey: Princeton University Press.

We now know more about the platypus than ever before as it's genome has just been sequenced. That means we know the list of instructions encoded in the animals DNA. Read more here, here or here.

Turkish creationist, bully and general gluteal carbuncle Adnan Oktar got sentenced to three years in prison yesterday, for the crime of creating an illegal organization for personal gain.

You remember Oktar: He's the guy who publishes all those nasty anti-evolution and anti-science books, steals photos for his high-cost, low-information "atlas" of creationism, and successfully sued to shut down this blog's availability in Turkey (Well, this blog and two million others on WordPress).

Reuters has a story on the affair:

A spokeswoman for his Science Research Foundation (BAV) confirmed to Reuters that Oktar had been sentenced but said the judge was influenced by political and religious pressure groups.

Oktar had been tried with 17 other defendants in an Istanbul court. The verdict and sentence came after a previous trial that began in 2000 after Oktar, along with 50 members of his foundation, was arrested in 1999.

In that court case, Oktar had been charged with using threats for personal benefit and creating an organization with the intent to commit a crime. The charges were dropped but another court picked them up resulting in the latest case.

Oktar planned to appeal the sentence, a BAV spokeswoman said. No further details were immediately available.

Oh, yeah -- those political and religious pressure groups. And Oktar's high dollar bullying of government authorities -- what is that?

European, and Turkey, laws against political views may trouble one, justly. In a perfect world, there would be no need for such things, with good and true ideas having a good shot at winning in a fair fight. Oktar specializes in the sort of thuggery that makes a fight for ideas unfair. We might hope this latest action will simply help keep the playing field even, level and fair.

Resources:

• The World (from BBC, PRI and WGBH) audio story on collaboration between Discovery Institute figures and Oktar in Turkey, promoting Islamic creationism
• Oktar gets a ban on Google groups
• National Center for Science Education story
• Adnan Oktar's entry in Wikipedia
• Die Zeit blog story on Oktar's WordPress ban

The news is oddly silent about this otherwise.

Tip of the old scrub brush to The Sensuous Curmudgeon.

The platypus used to be a favorite of creationists: it was a supposed chimera of different animal kingdoms and supposedly a startling mystery for evolution's picture of common descent. These days, however, creationists have mainly given it up as a lost cause: getting exposed as so wrong, so many times, gets humiliating. Instead, it's the modern news media, always awash in its rarely updated panoply of stereotypes and clichés, that still gives us breathlessly confused descriptions of the platypus as a "part bird, part reptile and part lactating mammal."

Understanding what the various "strange" features of the platypus really are and how they fit into the larger history of mammals is essential for anyone who wants to understand how evolutionary biology really works.

‘Life roughly consists of the chemistry of three atoms, hydrogen, carbon and oxygen, which among them make up 98% of all atoms in living beings…life consists of the interplay of two kinds of chemicals – proteins and DNA. Protein represents chemistry, living breathing metabolism and behaviour - what biologists call the phenotype – DNA represents information, replication, breeding, sex – what biologists call the genotype – neither can exist without the other.’ Matt Ridley, Genome: The Autobiography of a Species in 23 Chapters, Fourth Estate, 2000

‘We are made of stardust.’ John Gribbin, Stardust: the cosmic recycling of stars, planets and people, Penguin, 2001

‘At least some life is chemistry,’ Freidrich Wohler, 1828, (following his synthesistation of urea from ammonium chloride and silver cyanide, crossing what had been the sacrosanct divide between the chemical and biological worlds).

‘In short, with the birth of molecular biology, genetics could become an exercise in chemistry: highly refined chemistry, but chemistry nonetheless.’ Ian Wilmut, The Second Creation, Headline, 2001

"Of course, we have a long way to go before the benefits of this work are realised. The unravelled genome is, on its own, simply a list of chemicals. The next stage is to try to understand how those chemicals work together to create the genetic instructions that operate our bodies.” Sir Robert May, Chief Scientific Advisor to UK Government

‘In a sense, human flesh is made of stardust…Every atom in the human body, excluding only the primordial hydrogen atoms, was fashioned in stars that formed, grew old and exploded most violently before the Sun and the Earth came into being. The explosions scattered the heavy elements as a fine dust through space. By the time it made the Sun, the primordial gas of the Milky Way was sufficiently enriched with heavier elements for rocky planets like the Earth to form. And from the rocks atoms escaped for eventual incorporation in living things: carbon, nitrogen, oxygen, phosphorus and sulphur for all living tissue; calcium for bones and teeth; sodium and potassium for the workings of nerves and brains; the iron colouring blood red… and so on. No other conclusion of modern research testifies more clearly to mankind’s intimate connections with the universe at large and with the cosmic forces at work among the stars.’ Nigel Calder, The Key to the Universe, BBC, 1977

‘These stars are the fleshed forebears/ Of these dark hills, bowed like labourers// and of my blood…the tree is caught up in the constellations./ My skull burrows among antennae and fronds.’ Ted Hughes, Lupercal, Faber and Faber, 1960

‘Life begins with the process of star formation. We are made of stardust. Every atom of every element in your body except for hydrogen has been manufactured inside stars, scattered across the Universe in great stellar explosions, and recycled to become part of you. The hydrogen is primordial material, produced in the Big Bang, along with Helium… we are a natural product of the Universe we live in.’ John Gribbin, Stardust: the cosmic recycling of stars, planets and people, Penguin, 2001

‘PROTEIN - The DNA codes for protein. In our cells, proteins are the labourforce. It is proteins that get everything done. Proteins make new cells and destroy old or diseased ones. Proteins break down our food to release energy. Proteins organise the transport of useful chemicals between cells. Often, these useful chemicals are themselves proteins. As well as doing things, proteins are the building blocks for most of your body…The ingredients of a protein are amino acids. To build a protein we need to build a long chain of amino acids. There are 20 different types of amino acids, so there are lots of different protein chains we can build. Biologists give amino acids a code letter, as for DNA’ YourGenome.org
‘Thus, the order of play of four bases in a long molecule does indeed provide an organism with all the information it needs to do all the things an organism does. Astonishing!’ Ian Wilmut, The Second Creation, Headline, 2001

God is a Chemist

God is a chemist.
Chemistry is art,

magic.
Beauty is chemistry.

Earth, life -
poetry

written, spoken
with chemicals.

‘Take Carbon for example then/ What shapely towers it constructs to house the hopes of men!/ What symbols it creates/ For power and beauty in the world/ Of patterned ring and hexagon - / Building ten thousand things/ Of earth and air and water!... Love holds its palms before the flower/ Of anthracite and purrs.’ AM Aullivan, Atomic Architecture

‘THE INGREDIENTS FOR LIFE: 1) Liquid water, 2) Chemical building blocks like carbon, oxygen, hydrogen and nitrogen, 3) An energy source.’ BBC Science, 2006

God the Chemist (1)

God the Chemist,
God the Chemist -

praise his bright materials
prised from unlikely night;

bodies of stars,
blood of light.

Make exultant hymns, symphonies,
to the invented art of First Elements,

cosmic experimentation –
spirit, love and chemicals.

Hail, Holy Alchemist, High Poet,
Philosopher’s Stone of Creativity,

turning nothing
into Earth, Life;

a handful of darkness into green
leaf; transfiguring light into eyes.

Sez myspace.com/stopabortifacients

("Male
34 years old
CHICAGO, Illinois
United States "):

Sez YouTube commenter lilsasami (in response to Mr. "I <3 pre bornz almost as much as I <3 JPII"):

Oh my god! I've been abortin' my four celled babies!

Christ, just when I think the [lifers] can't get any dumber they come out with this shit. Congratulations loons, you just took crazy to a whole new level.

lilsasami = EPIC WIN.

Related: Kathryn Joyce on the overwhelmingly insipid upcoming national anti-contraception action event, Protest the Pill Day ’08: The Pill Kills Babies (h/t Fern Hill).

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