Alayna Wyland is 7 months old, and she is suffering.

The area started swelling, and the fast-growing mass of blood vessels, known as a hemangioma, eventually caused her eye to swell shut and pushed the eyeball down and outward and started eroding the eye socket bone around the eye.

There are pictures at the link. It's not pretty. I know if my babies had a growth that was almost the size of a tennis ball that was destroying their face, I'd have been camped out at the hospital. But not Alayna's parents! They have a special treatment plan.

The Wylands and their church reject medical care in favor of faith-healing -- anointing with oil, laying on of hands, prayer and fasting. The parents testified at a juvenile court hearing last week that they never considered getting medical attention for Alayna.

According to court documents, Rebecca Wyland anointed Alayna with oil each time she changed the girl's diaper and wiped away the yellow discharge that seeped daily from the baby's left eye.

There they go with the magic anointing oil again! Does that stuff do anything? If we can waste time with homeopathy, maybe it's about time someone did some clinical trials with anointing oil and put that crap to rest (not that it would make a bit of difference…).

The Wylands are rather vile, but at least this is taking place in Oregon, where "it is a crime for parents to intentionally and knowingly withhold necessary and adequate medical attention from their children". Alayna has been placed in state custody for treatment, and both parents have been charged with first degree criminal mistreatment.

But wait, there's more! The father was previously married.

Wyland's first wife, Monique, died of breast cancer in 2006. She had not sought or received medical treatment for the condition, said Dr. Christopher Young, a deputy state medical examiner who signed the death certificate.

She died of untreated breast cancer? That poor woman — that's a hard death, an agonizing death, and often, an unnecessary death — can that entire wretched cult be indicted for torture-murder? They seem to be leaving quite a pile of dead women and children.

The case of the various kinds of blogs hosted on ScienceBlogs has come up on Newsweek, and I get quoted trying to explain how I'm unperturbed by a couple of institutional blogs here.

Not all bloggers feel this way, Myers included. "We've known about those [institutional blogs] for some time--they aren't a problem," he wrote in an e-mail to NEWSWEEK. "Those sites were set up under the same conditions as the blogs of corporate scientist Mark Chu-Carroll, who works at Google, and university scientist PZ Myers, who works at the University of Minnesota. ... [The Pepsi blog blurred] the boundary between advertising and content. I agree that the institutional blogs also blur that boundary, just not quite as much. I can't insist that their blogs be labeled as advertisements, unless I want my blog marked as an ad for the University of Minnesota, or Chu-Carroll's as an ad for Google. It's complicated and messy."

There is some confusion out there, however. I do not claim to represent the University of Minnesota. Mark Chu-Carroll did not claim to speak for Google. My point was that if you take any blogger and look at the chains of affiliations they have (as we all do), we do not try to argue that every possible connection is a direct conflict of interest that demands a prominent disclaimer on the web page.

We ought to reserve the term "ad" for situations where an interest has paid money to be promoted, as PepsiCo did. The Weizmann Institute did not. Google did not pay to have Chu-Carroll peddle the company line, and he didn't. The University of Minnesota did not pay to have me scare away recruit potential students, although I may have done one or the other, accidentally. Weizmann, SETI, and Brookhaven have that in common with me and Chu-Carroll, and none of us cross the ethical barrier in the same way that PepsiCo did.

I actually think it's a good idea for institutions to have blogs at places like Scienceblogs. One thing I mentioned (but was not quoted) in my email to Newsweek is that the real challenge for institutional blogs is for them to be interesting. I rather like this quote from Carl Zimmer that summarizes their problem:

I do not, for example, assume that a piece of research is actually important just because a press release says it is. Imagine a press release with the headline, "Minor study published that is really not all it claims to be." Such things just don't exist.

It's amazing: WikiLeaks has just dumped over 91,000 classified documents from the Afghanistan war on the web. Just like that, we get an actual look at what's been going on over there, unfiltered by the traditional media, and definitely not given a rosy patina by Fox News. Fox New is, of course, treating this as a serious blow to their worldview — which isn't surprising, since reality does great damage to Fox. US Government sources also condemn the release, since it exposes the failures of militarism, and militarism is what the government and its profitable contractors have committed themselves to.

I think it's wonderful. Truth is an essential part of accurately assessing the war.

And the war isn't going well. There are tales of atrocities on both sides, civilians being murdered by both sides, backhanded deals by Pakistan with both the US and the Afghan insurgents, and an increasing number of attacks — we aren't winning at all.

The other shocking bit about this revelation is that it wasn't done by any of the established media organizations — it took a stateless, independent organization to actually break the barriers to information that other media companies respect. Now, of course, Spiegel, the Guardian, and the NY Times are doing a fine job of analyzing the deluge of information…but once upon a time, we might have expected investigative journalists to do that work. I guess it's cheaper to hire a Judith Miller to massage government propaganda than to actually dig into the facts.

This sad fact about the news disappointed me.

Ask yourself: Why didn't Wikileaks just publish the Afghanistan war logs and let journalists 'round the world have at them? Why hand them over to The New York Times, the Guardian and Der Spiegel first? Because as Julien Assange, founder of Wikileaks, explained last October, if a big story is available to everyone equally, journalists will pass on it.

"It's counterintuitive," he said then. "You'd think the bigger and more important the document is, the more likely it will be reported on but that's absolutely not true. It's about supply and demand. Zero supply equals high demand, it has value. As soon as we release the material, the supply goes to infinity, so the perceived value goes to zero."

I have a very low opinion of most journalists — it's a career in disrepute, given the sad state of media affairs, especially with the pathetic state of television news. I glanced at some of the programming going on now, and most of what I saw were mannequins arguing over whether it was right to release these documents, rather than any substantive discussion of the horrors contained within them.

But I will say this: Julien Assange is a hero who is doing a great service to both rescue and revolutionize honest journalism.

There is a site called Christopher Hitchens Watch which, I believe, began with a good cause: it's been around for about 5 years, and initially focused on Hitchens' support of the war in Iraq. That was a good idea: I disagree with him on that colossal waste of lives and money, and his views are fair game. But these kinds of sites that focus on single individuals can fall victim to obsession, too, and demonize everything about their target, and that's unfortunate. It undermines the legitimate complaints when they fuss over the petty, and even worse, when even a little generosity gets characterized as a crime.

The watch site doesn't like this comment from a Hitchens interview, but I think he's actually responding in an entirely appropriate way. He's got cancer; people are wasting their time praying for him. What does Hitchens think of that?

I think that prayer and holy water, and things like that are all fine. They don't do any good, but they don't necessarily do any harm. It's touching to be thought of in that way. It makes up for those who tell me that I've got my just desserts ... I wish it was more consoling. But I have to say there's some extremely nice people, including people known to you, have said that I'm in their prayers, and I can only say that I'm touched by the thought.

Prayer does absolutely nothing, but most of the people doing it mean well and are seriously hoping for the best for him. Strangers who have no part in his treatment aren't doing less because they're on their knees babbling to the sky (although they are promoting such useless nonsense as acceptable), so it neither picks his pocket nor breaks his leg for someone else to believe. It's when belief infiltrates professional practice or public policy that it becomes an evil to be uncompromisingly opposed.

It's a tough line to draw. One doesn't want to be an enabler of stupid expressions of faith, but at the same time, one shouldn't discourage kind intent. Hitchens is in a situation where he's going to have to walk that line a lot.

There are now a few more details on the story of the dog given a communion wafer: the dog's name is Trapper, the majority of the congregation was happy to see him get a cracker, it's just one person who complained, and now dogs have been officially excommunicated from the church. And this is exactly why I despise the so-called "moderate" Christians.

Peggy Needham, the deputy people's warden at the church, said that no further action would be taken.

"The backlash is from just one person," she said.

"Something happened that won't happen again. Something our interim priest did spontaneously.

"This person went to the top and emailed our bishop to make a fuss and change things. But he misjudged our congregation."

No, he didn't. He got exactly what he wanted. Notice that for most people in that church the incident with the dog was heartwarming — it fit well with their charitable vision of Christianity as a welcoming, friendly institution. One person complained, one bitter, dogmatic little man, and you know exactly what arguments he used: it was disrespectful to his imaginary god, it was a departure from church-sanctioned ritual, it gave worth to a mere animal that was reserved for good Anglicans. And the church bought it.

Hundreds of people value the humane, community-centered aspect of their church, and all that gets thrown out for one little pissant who truly believes in the petty, bogus disciplines of his poisonous faith.

I'll believe he misjudged that congregation when at the next communion, every one of them brings up a loved pet to the rail, and the priest serves every one of them. It won't happen, though, because the fear of god now compels them to obey.

Today it's family day with a mob of Myerses hanging about and bickering opinonatedly at a picnic. You aren't invited unless you can show evidence of a recent family relationship; showing evidence that all primates are related is nice, but won't get you in the door.

Tuesday at 6ish I'll be at the Pike Brewing Company waiting upon Ophelia Benson. Come on out! Buy us beer! I'm also thinking I might head up there a little early to visit the Seattle Aquarium, since it's right there in the neighborhood.

Friday at noon I'll be at Room B101, University of the Fraser Valley, Abbotsford BC. This is a free talk, although the group there would gladly accept donations. I don't seem to have a topic for this talk, though…but I do hear that Abbotsford is B.C.'s epicenter of fundamentalism, so I'll probably say inflammatory things about creationism. Whee!

Friday at 7pm I'll be at UBC Westbrook Room 100, 6174 University Boulevard, Vancouver BC to talk about the role of atheism in science. Hmmm. Both of these are inflammatory topics…will British Columbia erupt in riots? Show up and see. Oh, and this talk is not free: $10. There's also a fancy pants reception afterwards that will cost $50.

Saturday at 5:00pm on I'll be attending…my 35th high school reunion with a gang of strange people I haven't seen in decades. You aren't invited unless you were also a graduate of Kent-Meridian High School, Class of 1975.

All times not specified will be spent hunkered over a keyboard. Go away, don't bother me.

We're happier out of a straitjacket than in one.

The participants in the exhausting thread are hereby ordered to explain this impossible phenomenon: rainbows. I don't wanna hear any of your crazy Newton talk and refraction and water droplets, neither.

(via The Skeptic's Field Guide)

(Current totals: 10,691 entries with 1,066,521 comments.)

Most of you don't understand evolution. I mean this in the most charitable way; there's a common conceptual model of how evolution occurs that I find everywhere, and that I particularly find common among bright young students who are just getting enthusiastic about biology. Let me give you the Standard Story, the one that I get all the time from supporters of biology.

Evolution proceeds by mutation and selection. A novel mutation occurs in a gene that gives the individual inheriting it an advantage, and that person passes it on to their children who also gets the advantage and do better than their peers, and leave more offspring. Given time, the advantageous mutation spreads through the population so the entire species has it.

One example is the human brain. An ape man millions of years ago acquired a mutation that made his or her brain slightly larger, and since those individuals were slightly smarter than other ape men, it spread through the population. Then later, other mutations occured and were selected for and so human brains gradually got larger and larger.

You either know what's wrong here or you're feeling a little uneasy—I gave you enough hints that you know I'm going to complain about that story, but if your knowledge is at the Evolutionary Biology 101 level, you may not be sure what it is.

Just to make you even more queasy, the misunderstanding here is one that creationists have, too. If you've ever encountered the cryptic phrase "RM+NS" ("random mutation + natural selection") used as a pejorative on a creationist site, you've found someone with this affliction. They've got it completely wrong.

Here's the problem, and also a brief introduction to Evolutionary Biology 201.

First, it's not exactly wrong — it's more like taking one good explanation of certain kinds of evolution and making it a sweeping claim that that is how all evolution works. By reducing it to this one scheme, though, it makes evolution far too plodding and linear, and reduces it all to a sort of personal narrative. It isn't any of those things. What's left out in the 101 story, and in creationist tales, is that: evolution is about populations, so many changes go on in parallel; selectable traits are usually the product of networks of genes, so there are rarely single alleles that can be categorized as the effector of change; and genes and gene networks are plastic or responsive to the environment. All of these complications make the actual story more complicated and interesting, and also, perhaps to your surprise, make evolutionary change faster and more powerful.

Think populations

Mutations are the root of biological variation, of course, but we often have a naive view of their consequences. Most mutations are neutral. Even advantageous mutations are subject to laws of chance in their propagation, and a positive selection coefficient does not mean there will be an inexorable march to fixation, where every individual has the allele. This is also true of deleterious mutations: chance often dominates, and unless it is a strongly negative allele, like an embryonic lethal mutation, there's also a chance it can spread through the population.

Stop thinking of mutations as unitary events that either get swiftly culled, because they're deleterious, or get swiftly hauled into prominence by the uplifting crane of natural selection. Mutations are usually negligible changes that get tossed into the stewpot of the gene pool, where they simmer mostly unnoticed and invisible to selection. Look at human faces, for instance: they're all different, and unless you're looking at the extremes of beauty or ugliness, the variations simply don't make much difference. Yet all those different faces really are the result of subtly different combinations of mutant forms of genes.

"Combinations" is the magic word. A single mutation rarely has a significant effect on a feature, but the combination of multiple mutations may have a detectable or even novel effect that can be seen by natural selection. And that's what's going on all the time: the population is a huge reservoir of genetic variation, and what we do when we reproduce is sort and mix and generate new combinations that are then tested in the environment.

Compare it to a game of poker. A two of hearts in itself seems to be a pathetic little card, but if it's part of a flush or a straight or three of a kind, it can produce a winning hand. In the game, it's not the card itself that has power, it's its utility in a pattern or combination of other cards. A large population like ours is a great shuffler that is producing millions of new hands every day.

We know that this recombination is essential to the rapid acquisition of new phenotypes. Here are some results from a classic experiment by Waddington. Waddington noted that fruit flies expressed the odd trait of developing four wings (the bithorax phenotype) instead of two if they were exposed to ether early in development. This is not a mutation! This is called a phenocopy, where an environmental factor induces an effect similar to a genetic mutation.

What Waddington did next was to select for individuals that expressed the bithorax phenotype most robustly, or that were better at resisting the ether, and found that he could get a progressive strengthening of the response.

The progress of selection for or against a bithorax-like response to ether treatment in two wild-type populations. Experiments 1 and 2 initially showed about 25 and 48% of the bithorax (He) phenotype.

This occurred over 10s of generations — far, far too fast for this to be a consequence of the generation of new mutations. What Waddington was doing was selecting for more potent combinations of alleles already extant in the gene pool.

This was confirmed in a cool way with a simple experiment: the results in the graph above were obtained from wild-caught populations. Using highly inbred laboratory strains that have greatly reduced genetic variation abolishes the outcome.

Jonathan Bard sees this as a powerful potential factor in evolution.

Waddington's results have excited considerable controversy over the years, for example as to whether they reflect threshold effects or hidden variation. In my view, these arguments are irrelevant to the key point: within a population of organisms, there is enough intrinsic variability that, given strong selection pressures, minor but existing variants in a trait that are not normally noticeable can rapidly become the majority phenotype without new mutations. The implications for evolution are obvious: normally silent mutations in a population can lead to adaptation if selection pressures are high enough. This view provides a sensible explanation of the relatively rapid origins of the different beak morphologies of Darwin's various finches and of species flocks.

Think networks

One question you might have at this point is that the model above suggests that mutations are constantly being thrown into the population's gene pool and are steadily accumulating — it means that there must be a remarkable amount of genetic variation between individuals (and there is! It's been measured), yet we generally don't see most people as weird and obvious mutants. That variation is largely invisible, or represents mere minor variations that we don't regard as at all remarkable. How can that be?

One important reason is that most traits are not the product of single genes, but of combinations of genes working together in complex ways. The unit producing the phenotype is most often a network of genes and gene products, such at this lovely example of the network supporting expression and regulation of the epidermal growth factor (EGF) pathway.

The EGF pathway (from www.sabiosciences.com/pathwaycentral.php)

That is awesomely complex, and yes, if you're a creationist you're probably wrongly thinking there is no way that can evolve. The curious thing is, though, that the more elaborate the network, the more pieces tangled into the pathway, the smaller the effect of any individual component (in general, of course). What we find over and over again is that many mutations to any one component may have a completely indetectable effect on the output. The system is buffered to produce a reliable yield.

This is the way networks often work. Consider the internet, for example: a complex network with many components and many different routes to get a single from Point A to Point B. What happens if you take out a single node, or even a set of nodes? The system routes automatically around any damage, without any intelligent agency required to consciously reroute messages.

But further, consider the nature of most mutations in a biological network. Simple knockouts of a whole component are possible, but often what will happen are smaller effects. These gene products are typically enzymes; what happens is a shift in kinetics that will more subtly modify expression. The challenge is to measure and compute these effects.

Graph analysis is showing how networks can be partitioned and analysed, while work on the kinetics of networks has shown first that it is possible to simplify the mathematics of the differential equation models and, second, that the detailed output of a network is relatively insensitive to changes in most of the reaction parameters. What this latter work means is that most gene mutations will have relatively minor effects on the networks in which their proteins are involved, and some will have none, perhaps because they are part of secondary pathways and so redundant under normal circumstances. Indirect evidence for this comes from the surprising observation that many gene knockouts in mice result in an apparently normal phenotype. Within an evolutionary context, it would thus be expected that, across a population of organisms, most mutations in a network would effectively be silent, in that they would give no selective advantage under normal conditions. It is one of the tasks of systems biologists to understand how and where mutations can lead to sufficient variation in networks properties for selection to have something on which to act.

Combine this with population effects. The population can accumulate many of these sneaky variants that have no significant effect on most individuals, but under conditions of strong selection, combinations of these variants, that together can have detectable effects, can be exposed to selection.

Think flexible genes

Another factor in this process (one that Bard does not touch on) is that the individual genes themselves are not invariant units. Mutations can affect how genes contribute to the network, but in addition, the same allele can have different consequences in different genetic backgrounds — it is affected by the other genes in the network — and also has different consquences in different external environments.

Everything is fluid. Biology isn't about fixed and rigidly invariant processes — it's about squishy, dynamic, and interactive stuff making do.

Now do you see what's wrong with the simplistic caricature of evolution at the top of this article? It's superficial; it ignores the richness of real biology; it limits and constrains the potential of evolution unrealistically. The concept of evolution as a change in allele frequencies over time is one small part of the whole of evolutionary processes. You've got to include network theory and gene and environmental interactions to really understand the phenomena. And the cool thing is that all of these perspectives make evolution an even more powerful force.

Bard J (2010) A systems biology view of evolutionary genetics. Bioessays 32: 559-563.