Field of Science

Ayala way up on his religious pedestal

Yeah so, Francisco Ayala got the Templeton Prize for conflating science and religion, but that's already old news.

But seriously, it is now awarded to someone who "has made an exceptional contribution to affirming life's spiritual dimension, whether through insight, discovery, or practical works". (Wikipedia.)

From 2001 to 2008 it read "Templeton Prize for Progress Toward Research or Discoveries about Spiritual Realities".

Before 2001: "Templeton Prize for Progress in Religion".

Ayala is an evolutionary biologist and also a former Dominican priest. So what insight does he have? What discoveries has he made? What practical works has he carried out?
Ayala unequivocally finds no contradiction between science and religion because “if properly understood, they cannot be in contradiction because science and religion concern different matters and each is essential to human understanding.”
So, by his own words his work in science cannot have informed him about anything spiritual.
Religion or faith determines the purpose, values and meaning of life.
That would mean that those without religion (or of the wrong one?) cannot understand the purpose of life, what the right values (morals) are, or what the meaning of life is, I suppose. Personally, being without religion and only spirits in the form of alcohol, I can say that even without religion I can determine the purpose, values and meaning of life just fine, thank you. And I know many like me can, too. Not a problem, Frrancisco. Ergo, religion is , at least, not the only determinant of those notions.
Professor Ayala was born in Madrid, Spain in 1934 and raised during the repressive Franco era. He was uniquely aware of the horrific slaughter of the innocents during the Spanish Civil War as depicted by Picasso in his monumental mural Guernica. Ayala refers to this masterpiece to explain the difference between science and religion. Science can assess the massive dimensions and pigment of the painting, but it takes religion (faith) to impart the horror bestowed on the peaceful village of Guernica in Basque country.
Whaaaaat? It takes religion to communicate how terrible bombing a village full of women and children is, now? Festivus for the rest of us?

Is it only me who finds it inconsistent when Ayala says that science and religion are sort of NOMA like, but TF practically says the opposite?

Lastly, let me chime in the those who have already objected to the NAS being part of this prize: The NAS is a scientific institution, and should not get involved with a foundation with seeks to conflate science and religion. Jerry Coyne, PZ Myers, Larry Moran.

Thirteen year-old sues university to enroll in course

Here's a news story about Colin Carlson, a sophomore at the University of Connecticut: he is suing the university because they won't let him enroll in a course that would take place in South Africa. Why on Earth not?, you may ask. The reason is that he is too young, and herein of course lies the really interesting thing about Colin. He is only 13. And the extra weird quirk to the story is that his major isn't the usual math or physics, like savants are supposed to study. He studies ecology and evolutionary biology.
He said that once he's completed his undergraduate studies, he wants a Ph.D. in ecology and evolutionary biology and a degree in environmental law for a career in conservation science. He intends to earn the two degrees by age 22.
Good choice!

Homophobia as state policy

It's a funny damned thing that when a nation finally drags itself out of the stone-age, it's always too much to hope that the people who do it aren't somehow cavemen after all.

Prime minister of Zimbabwe, Morgan Tsvangirai is the main man running against President Mugabe, who runs one of the most ridiculous countries on Earth. Tchangisvai might have gotten Nobel's peace prize last year (Obama caused .093% more peace). Great man, in other words.

Except that he is in complete agreement with hatter Mugabe on writing the new constitution: The both will not consider adding gay rights to the new constitution they're drafting, because homosexuals are "worse than dogs and pigs”.

But, perhaps in another few decades things will have changed for the better... even dogs or pigs or gays might be treated with decency. All three would be too much to hope for.
ZANU-PF’s [Mugabe's party] thematic talking points on the constitution say “. . . we should not allow same-sex marriages as this is taboo in African culture and traditions. The Bible also forbids same-sex marriages. The constitution should specifically outlaw homosexuality, lesbianism, sodomy, etc.”
African tradition (any tradition) my ass! But, if it says so in the Bible, then who are we to argue?

Time to stop eating Nestlé products

Join Greenpeace's protest against Nestlé's use of palm oil.

"Nestlé, the world's largest food and drink company, is making some of your favourite chocolate bars using palm oil from destroyed Indonesian rainforests. As a result, threatened species like orang-utans are being pushed into extinction and huge quantities of greenhouse gas are being released, accelerating climate change." -- Greenpeace

Time to stop eating anything made by Nestlé, including HÄAGEN-DAZS® Ice Cream and more. Jebus, they make a lot of food products!!!*

Thanks to Margaret for bringing this to my attention.

* Note that in the United States KitKat is not made by Nestlé.


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I'm busy with deadlines - a paper submission, a class assignment, a talk preparation, job applications, spam sushi, etc. etc.

In the meantime, since you have nothing better to do, enjoy this:

Bush shakes Haitian's hand and...


The damned field of biology and the cursed theory of evolution

As an evolutionary biologist working on theory, I feel trapped from both above and below.

From one direction we have everyone but biologists thinking that they understand evolutionary theory. Natural selection is such an easy thing to grasp, right? Offspring vary in size, speed, eyesight, and those that are better help the organism to have more offspring. Heritability ensures that evolution can take place. Creationists think they understand it, and while they are clearly off their rockers (i.e. they have a foregone conclusion, and that's not a way to do science, among other problems), at least scientists from other fields understand the premise of evidence. Except for philosophers (motto: "I think therefore I have something to contribute").

Jerry Fodor is a case in point. Listen to this conversation only if you have absolutely nothing better to do for an hour.

Rubbish. Very briefly, Fodor think pleiotropy (not that he knows that term) invalidates the theory of natural selection. Yeah, I know! Even ignoring that NS is presented as a theory, rather than just the mechanism of evolution that it is, saying that because two phenotypic traits can be linked (the example given is hearts pumping blood and making thump-thump noises) makes it impossible to talk about selection for.
We should stress that every such case (and we argue in our book that free-riding is ubiquitous) is a counter-example to natural selection. Free-riding shows that the general claim that phenotypic traits are selected for their effects on fitness isn’t true.
You can read more reviews of Fodors book here and here. Suffice to say that I find it hugely annoying that philosophers who clearly have not understood the theory suddenly barge in with non peer-reviewed tripe to claim what evolutionary biologists are doing wrong. Call it arrogance, and see if I care. Call it arrogance when the plumber tells the mechanic to buzz off when the mechanic meddles with plumbing, or when the linguist calls the economist a fool for interfering in linguistics.

The point is just that if you want to switch field of work, please learn what there is to learn before you attempt to dismantle it. Otherwise, you wasting my fucking time! And I really think Sober thought so, too.

So that was the curse. Here is the damnation.

The field of biology is damned because it's hard, and because biologists aren't too clever.

Whoa, let me rephrase that.

The scope of what is to be explained is vast, and the complexity of it is vast. Physics (a field mostly considered harder than biology, because it uses mathematics) is mostly about natural processes that are very simple, and that makes it much easier to use complicated math to describe them, which is the triumph of physics, but also what makes it so hard to be good at.

Biology, on the completely other hand, is largely about counting frogs. Dissect the toad and describe what you see. Data collection, in other words. If we did physics that way, we'd go around observing apples falling from various heights of apple trees growing in different parts of the globe with slightly varying little g. And when we'd be done, we'd move on to pears.

The world of living things is so much more complex than the world of elementary particles, and that is what makes theory so hard, and why so little has been done so far. one way to advance theory in biology is by simulations (much used in physics, too), and it is here that I have met a fair amount of hostility in biology. The usual objection is that when you do simulations (and this could equally well apply to mathematical analysis) you construct a simpler model of the real world, by simulating, for example, only point mutations and natural selection in a static fitness landscape, and that's not realistic. And that is true. It's not realistic because it doesn't include every process we know of. Genetic drift, insertions and deletions, recombination and cross-over, gene duplication, transposable elements, other species, a changing environment, natural disasters, etc. etc. etc. But suppose we made a simulation like that, to the best of our ability, what would be gain? We could see that the output would be consistent with the real world, as far as we can observe it, and that would be good. But, like in physics, you have to keep some things constant in order to see what the effect of each component is. If you want to know the effect of point mutations, do make sure not to include indels and TEs, or you won't know which mechanism is responsible for you results.

Don't forget that understanding of nature ends with theory, and that if we aren't allowed to theorize, then we're missing out. If everything we say about biology has to be backed up with data at every turn (and here I am mainly talking about getting papers published in peer-reviewed journals), then this enterprise of understanding nature might never get there.

P.S. I am not talking about trying to advance theory that is inconsistent with data, nor I am trying to dis backing simulations with data.


Single-celled life for the win

Equal rights for fertilized human eggs. Save the blastula!

Another attempt at outlawing abortion - because we can pick and choose which parts of the Bible should influence modern society (at least stoning of cursing children is out).

The always odious AFA is pushing for redefining what it means to be a person.
In the Roe vs. Wade decision, Justice Blackmun declared: "If this suggestion of personhood is established, the appellant's case [the case for abortion], of course, collapses, for the fetus' right to life would then be guaranteed specifically by the [14th] Amendment."

The California Human Rights Amendment will amend the California Constitution to define human rights beginning at biological development (e.g. conception), and it will ensure that a preborn baby of any age has the same equal rights and full protection under law as adults. This important initiative will defend and protect the most vulnerable members of our society - our preborn children.
Except that 128 cells inside a woman's womb can hardly be considered a member of society.

Does equal rights for blastulas mean that we cannot imprison pregnant women? Do we have to inform blastulas of their rights? Can a blastula have its own attorney?

And why stop at the "preborn"? Is the fertilized oocyte really the first home of the soul? How about punishment for spilling sperm?

Should we now have funerals for all the "preborn" who are spontaneously aborted?

And should this ridiculous idea - that a collection of cells growing in a human female's uterus is a person and member of society - be passed into law, then it will be a great advance for God, and a sad day the the rest of us.

Poetry on evolution

Yesterday, at a local farmer's market, a young guy was sitting with a typewriter and a sign saying "Free poems". I asked him to write a poem about evolution, and this is what I got:

I asked him if he was religious, and he answered that he was.

Three points:
  1. True, a single cell contains a machinery that is incredibly complex. The components and the way they interact are high in number, and we don't know them all. It is indeed hard to imagine how such a thing could evolve, but this is mission impossible; difficult should be a walk in the park.
  2. No evolutionary biologists (in their right mind) are saying that it happened by accident. However, we can understand what is meant when creationists phrase it like that. Random chance does have a lot to do with evolution, and that can be construed to mean 'accident' (even though that word carries a negative connotation, which, in the case of life, I find hard to accept). However, and of course, natural selection is anything but chance - more like the exact opposite, in fact - and no evolutionary biologists (in their right mind) contests that natural selection is an important evolutionary mechanism (though it is discussed how important relative to other mechanisms, like genetic drift or developmental bias). What creationists might mean is that the component of chance, with or without natural selection to weed out the negative, un(re)productive results, they do not accept.
  3. Thus, it takes a huger amount of faith, the creationists think, to accept evolution rather than creationism. Creationism is in a sense not complex. If one refrains from asking questions about the nature of the creator, then it is pretty simple to say "God did it". The irony here is that accepting evolutionary hypotheses does not require faith at all, but is based on evidence (which is largely the antithesis of faith). Religious faith is in spite of the evidence, while science always follows the evidence. The evidence may not be complete, and so we must withhold judgment until more evidence is in. And that is the status on the question of the origin of the cell. It is not the status of so many other questions about the origin of organic life, where we have so much evidence for evolution that it takes faith only the religious can muster to deny it.

CoE featured on Discovery Channel

Yes, it's true. Carnival of Evolution has made its way into the (more) popular media of television. Sort of.

On TV, Larry Moran, Professor of Biochemistry at the University of Toronto and author of the blog Sandwalk, very deliberately chooses to show his blog post with the CoE logo on it, clearly to build his credibility as an expert on evolution. And nipples.

All you professors out there who are will be giving interviews, take a hint! Have The Origin on your bookshelf and the CoE logo on your screen. That way no one will doubt your expertise on evolution.

See TV-clip here, and Larry's post about it here.

P.S. This post is not an endorsement of Larry's statements about why men have nipples.


Consider slapmyfaceism, the belief that a good hard (or soft) slap on your face is a good thing. So, are you a slapmyfaceist? Would you like one right now?

I am an aslapmyfaceist. You could also say I'm a non-slapmyfaceist, but I prefer to say aslapmyfaceist.

Some people who are slapmyfaceist don't like it much when I criticize their slapmyfaceism. What's wrong with a solid smack on the cheek once in while? Perhaps one before dinner, or at least one at bedtime, eh? No thanks, I just don't want one. Why not? It hurts! So what? I don't like hurting. Et cetera, et cetera.

Often the slapmyfaceist will then proceed to ask what I am if not a slapmyfaceist. Well, I say, I just an aslapmyfaceist. But, that's just a negative. You gotta believe in something!? In terms of slaps on the face, I don't believe in it, I say. But then what? Then nothing. But a belief must be for something, rather than just against, they tend to say. Or shout.

Look, I believe in all sorts of things. For example, I'm a drinkabeerist, and an havealaughist, to mention a few cherished beliefs. But so am I! the slapmyfaceist will say. Those are all together different (and not mutually exclusive) categories Are you a pokeintheeyeist, or a punchinthestomachist (all varities of slapmyfaceism), then? No, I say, none of those. I'm just aslapmyfaceist. I simply think your belief in slapmyfaceism is nonsense. The point in being an aslapmyfaceist is only that. I argue against slapmyfaceism, and that is worthwhile in itself.

Then there are the accommodationists who think that slapmyfaceists and aslapmyfaceists can get along fine, as long as they don't talk negatively about each other. Focus on the things you have in common, like havealaughism. These new aslapmyfaceists just needs to be respectful of the slapmyfaceists and their (otherwise misguided) belief that inflicting some sort of bodily pain is a good thing, for consenting adults as well as little children.

In my opinion the slapmyfaceists are more than welcome to go around slapping themselves and each other on their faces at home, but not in public. Why not in public? Because I believe it is a bad thing, especially when they hit really hard, like the fundamentalists, who believe everyone should get a heavy whack on the mouth whenever they talk to someone - the moderates who just think a weak slap on the cheek once in a while will suffice are more benign, but I still don't see the point (or any evidence that doing so is a good thing). Crucially, keeping this practice out of official institutions, like the government, is important, and the fact that it is unthinkable to be elected president of the US without be some kind of slapmyfaceist is unacceptable. Other nations laugh America in the face because of this ridiculous belief.

And as for children, please keep your slapmyfaceism away from them until they are old enough to decide for themselves. Teach them that there are many different beliefs, such as kickinthebuttism, wedgieism, and pullmyfingerism. That way they will perhaps come to question these beliefs as a whole, and that whether you are a slapmyfaceist or not is mostly dependent on where you were born and the belief of you parents and peers, rather than some spiritual insight that being slapped on the face is better than getting kicked in the butt.

Weekend accommodationism

Turkey takes another step back toward the middle ages

Turkey is such a fucked up country in many ways, and now they can add another.

It is now illegal for women to go abroad and get artificially inseminated. Doing so could get them up to three years in Turkish prison.
Insulting "Turkishness", taking part in demonstrations, or showing the slightest sympathy for the banned Kurdish Workers' Party, for example.

Now you can add to that long list the crime of using a foreign sperm donor.
It is also a crime to hide the father's identity:
A spokesman at the Department of Health, Irfan Sencan, said the regulation was covered by article 231 of the criminal code, which makes it a crime to conceal the paternity of a child.
The moral conundrum of this boggles my mind.

While they present the new law as having to do with the right of the child to know their father and grandfather, it is horribly in line with the general oppression of women. just like Prime Minister Erdogan's call for women to have at least three children each. Keep them breeding, but make sure the father are decent Turkish men.
It is hard to imagine pregnant women being put on trial just for the way they conceived, but not impossible in Turkey, where last month a 15-year-old Kurdish girl was jailed for nearly eight years just for taking part in a demonstration.
Wow! Eight years? For demonstrating? For a 15-year old? Honestly, fuck that shit. And Turkey is even thinking about the possibility of joining the EU?! This way it just ain't gonna happen, dude. The rest of the members won't tolerate new members with laws that belong in the middle ages.

Oh boy! Liberty students evaluates evolution

Students from Liberty "University" visit the Natural History Museum in Washington. They are creationists, but purport to want to learn about evolution (of course, in order to understand its flaws, but still...)
The young "creationists" examined a model of the Morganucodon rat, believed to be the first and common ancestor of mammals that appeared some 210 million years ago.

Lauren Dunn, 19, a second-year biology student, was unimpressed.

"210 million years, that's arbitrary. They put that time to make up for what they don't know," she said.
Arbitrary? It's based on radiometric dating. Time to learn some geology and physics, Lauren. You can't falsify evolution by hearsay.
Nathan Hubbard, a 20-year-old from Michigan and a first-year biology major who plans to become a doctor, regarded the model with suspicion.

"There is no scientific, biological genetic way that this, this rat, could become you," he said, seemingly scandalized by the proposition.
No scientific mechanism that you know of. Score another one for not learning anything at Liberty.
"In order to be the best creationist, you have to be the best evolutionist you can be," said Marcus Ross, who teaches paleontology and says of Adam and Eve: "I feel they were real people, they were the first people."
Okay, so while trying to be the best evolutionist (ignoring that the term should be "evolutionary biologists" - evolutionists are more precisely anyone who believes in evolution) you can be, feeling that Adam and Eve were real people is acceptable as a way of knowing to this teacher of paleontology. Stunning!
David DeWitt, a Liberty University biology professor, opens his classes with a prayer, asking God to help him teach his students.

"I pray that you help me to teach effectively and help the students to learn and defend their faith," he says.
Wait, I thought he was teaching biology. Learning to defend faith (the antithesis of science) really isn't part of a normal, academic, biology curriculum. It reeks of nitpicking the evidence to suit your needs.
At the Smithsonian Institute, among crowds of weekend visitors, the Liberty University students visited the evolution exhibition,.
But Darwin's explanation for why giraffes have long necks -- that they evolved over time so they could reach higher foliage -- and displays of fossil evidence failed to sway them.
Not that I think it makes any difference to creationists, but I don't buy that explanation either. I believe long necks and legs evolved through sexual selection - male giraffes fight for territory with their necks and legs (this previous post includes great footage of two necking males - it's a must-see).
Though Ross acknowledges that the United States is among the most welcoming environments in the world for creationists, he said it can be difficult to convince people to take him and his beliefs seriously.

"The attitude is when you are a creationist you are ignorant of the facts," he said.
That's because you're ignorant of the facts!

Alternatively, some creationists do appreciate the facts, and yet somehow manage to reconcile that with their faith, like Todd C. Wood, who is a truly remarkle mental gymnast. Yet others lie through their teeth.

Evolution highlights XVII

The age of the Earth (4,613,542 and eighteen days) is taught in high school physics classes, and not in biology classes. But, more students are willing to accept human evolution (taught in biology, if at all) if they accept that the Earth is billions of years old.
Using that information, they created a model that shows, for example, when a student's religious and political views are liberal, they are more likely to believe that the Earth is billions, rather than thousands, of years old and to know more about evolution. Conversely, students with conservative religious and political views are more inclined to think the Earth is much younger (20,000 years or less) and to know less about evolution.
The question is what the causal factor is. If it's knowing the age of the Earth before learning about evolution, then we have an answer. If it's something else, such as religious and political views, that cause belief in a young Earth and also in creationism, then making sure that students know the real age of the Earth will make no difference.

My old lab at UCSB has identified the gene involved in light sensivity in Hydra, which shares a last common ancestor with humans about 600 million years ago. Whatever the gene was used for that long ago (perhaps sensitivity to light), it is fair to say that the origins of vision dates that far back.
Oakley explained that there are many genes involved in vision, and that there is an ion channel gene responsible for starting the neural impulse of vision. This gene controls the entrance and exit of ions; i.e., it acts as a gateway.

The gene, called opsin, is present in vision among vertebrate animals, and is responsible for a different way of seeing than that of animals like flies. The vision of insects emerged later than the visual machinery found in hydra and vertebrate animals.
A new amphibian fossil skull has been described. It is dated at 300 million years ago (not quite as old as the famous 375 mllion year old Tiktaalik).
Fedexia striegeli was described on the basis of a remarkably well-preserved fossil skull. Unlike many other fossil finds, the fossil skull remained three-dimensional and did not suffer post-mortem crushing over time by the compaction of rock formations above it. The preservation of the skull is so precise that even the middle-ear bone, known as the stapes, remains perfectly intact and in its correct position, a very rare discovery in fossils.

Also noteworthy:

Flowering Plants May Be Considerably Older Than Previously Thought

ASU scientists narrow down origins of malaria

Phylogenetic Analysis of Mexican Cave Scorpions Suggests Adaptation to Caves Is Reversible

Small Dogs Originated in the Middle East, Genetic Study Finds

Scientists Discover 600 Million-Year-Old Origins of Vision

Drastic Musk Ox Population Decline 12,000 Years Ago Due to Climate, Not to Humans

Unselfish Molecules May Have Helped Give Birth to the Genetic Material of Life

Scientia Pro Publica 23: Beginning

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

Welcome to the twenty-third edition of Scientia Pro Publica, where some of the best science-blogging is featured with much fanfare.

It has been a pleasure reading all the submitted posts. It always is. I have increased both my factual knowledge about nature - and thus my horizon - in ways that I think would not be nearly as easy if it wasn't for the science bloggers. Thank you all.

This time there was a fair number of submissions (I've used a couple of statistical methods to estimate the number, which gave a value of 263.29 ± 41 SD), so I've separated them into eight different posts to make it easier to navigate them. Use the links above to find the other pages.

Scientia Pro Public 24 will be hosted by Andrew at 360 Degree Skeptic on April 5th. Go ahead and submit your posts for that edition already using the online form at Blog Carnival.

Contributing blogs:

A DC Birding Blog Agricultural Biodiversity Weblog Bioblog: Biology in the News Code for Life Deep Sea News Deep Thoughts and Silliness EcoTone EnviroBuzz Genetic Future Lab Rat Living the Scientific Life making owls cool since 1986 Maniraptora: Tastes Like Chicken mental indigestion PhD to be Rangle Reconciliation Ecology rENNISance woman Reportergene Save Your Breath For Running Ponies Savvy Saplings Theoretically Speaking The Phytophactor This View of Earth Thoughtomics time travelling The Primate Diaries xenobiotica 360 Degree Skeptic

Scientia Pro Publica 23: Biology

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

The oldest living tree (and organism?) might be Pando, an aspen root that's be shooting trees" for perhaps 80,000 years. It's also the heaviest living organism at over 6 million kilograms. Eric has more on The Earth's Oldest Trees:
The world's oldest trees are not necessarily trees as we think of them. They're not one trunk with branches and leaves that has stood for a million years. The oldest trees are actually clonal colonies, a series of genetically identical individuals deriving from one ancestor. With trees, that means a really old root colony that has continually produced shoots over millennia.

Gynandromorph. The hell? birds that are male on one side and female on the other? This is not fiction - they really exist. Grrl Scientist takes them on in Gender-Bending Chickens: Mixed, Not Scrambled. Journal article
Like northern cardinals, domestic chickens are sexually dimorphic. So when Dr Clinton first saw these oddly lopsided chickens, he was immediately impressed by the birds' striking appearance: the larger male side had white feathers, spurs, large wattles and breast muscles, whereas the smaller female side showed the characteristic dark coloring, small wattles, and the lack of spurs (Figure 1).

Eric Michael Johnson presents the history of the different roles played by Darwin and Spencer in the Middle East. Journal article
If Darwin's work was already "social" and could be applied to politics with the ease that some authors have suggested, why did the editors of al-muqtataf need to emphasize the sociology of Spencer to pursue their political goals? The discussion of Darwin in this Arabic journal, at least as Elshakry presents it, emphasized his biological ideas and never made a connection between Darwin and the ideas of social Darwinism. While ideologues such as Weikart or Harun Yahya are unlikely to give up in their attempt to tar and feather Darwin with Spencer's philosophy, it's comforting to know that science enthusiasts in the Middle East knew the difference.

What Popeye the sailer man and fish at the bottom of the ocean have in common? Dr. M explains that they both eat spinach. For, the interesting observation here is that these fish are resource generalists, which implies something about evolutionary dynamics. Spinach, Popeye, and Fishy Pigeons. Journal article
Ahh, but what about spinach, you ask? Recent work by Jeffreys and colleagues indicates that macrouirds do indeed eat spinach. Baited traps with spinach placed on the deep-sea floor, quickly attracted fish and then spiraled into feeding frenzies (video at the BBC). But wait! You are asking yourself how often does a rattail actually encounter spinach or for that matter other leafy greens? Here in lies the genius. Spinach is just an easily obtainable surrogate for any land plant and the question is whether deep-sea fish are even equipped to detect a plant food fall. Apparently they can. This study indicates these dominating organisms of the deep can quickly utilize a variety of food sources in the deep; they are opportunistic.

Mike Fowler makes an argument that is I feel very strongly about. He has done population modeling, and his simulations are invariably quite simple compared to the real world. Some reviewers will argue that the simulations aren't close enough to reality, and therefore useless. However, throwing everything into the model makes it impossible to say which components are responsible for the observed effects, and therefore it is not just easier, but at times also imperative to keep the models simple, as Mike explains in Why I do what I do (and don't what I don't) Journal article
So why do I use the simple models? With competition models, you only have to worry about the distribution of competitive strengths (a single kind of interaction) among species. With natural enemy models, you will have to think about how interactions work across trophic levels, and might have to consider how competition works within trophic levels on top of that. There are more things to think about controlling and varying, making any results harder to investigate, think about and ultimately communicate. It's a bit reductionist, but I think it's worth understanding what happens in simpler models, to allow us clearer insight before we start dealing with the more complex models.

It is easy to make the assumption that bigger brains - meaning higher intelligence across species - implies high fitness, but big brains is not an advantage in all species, as Katie Kline explains in The phrenologist’s guide to ecological competence Journal article
They found that the migratory birds tended to have smaller brains than their resident relatives. While there likely are other contributing factors, the scientists propose that the longer migration routes led to the development of smaller brains—an ecological selection that possibly balances the costs of an energy-intensive flight.

Kelsey Abbott has a thing for critters with remarkable genitalia, so she couldn't possible not dissect this story about a beetle with a penis twice the length of it's body: Shouldering: Penis Extraction in Rove Beetles. Journal article
This unassuming poop-populating beetle has what scientists call “exaggerated genitalia.” When fully extended, the male’s flagellum (essentially a guiding rod for the sperm delivery system known as a spermatophore tube) is more than twice the length of the male beetle’s body. While impressive (and disturbing), living with such a long schlong isn’t nearly as glorious as it may sound.


He begins by slowly separating himself from his mate, exposing just a bit of the flagellum, keeping it under tension. He tucks the flagellum between his mesothorax and prothorax (parts of his shoulder) and then backs farther away from the female so that half of the flagellum is free. With the flagellum held taut in his shoulder, the male turns away from the female to extract the rest of the flagellum and then carefully coils it into the aedeagus (the holster for the flagellum and spermatophore tube). If he extracts and stores his equipment properly, he can mate up to five times in one hour. [Emphasis added.]

Ancient DNA is the coolest, and extracting it from fossils is a big deal. NOt easy, and so far n oone had been able to do it from fossil eggshells. But now they've done it, from the shells of the heaviest bird ever, Aepyornis maximus. GrrlScientist says that Ancient DNA Isolated from Fossil Eggshells May Provide Clues to Eggstinction of Giant Birds Journal article
Using their new method, most eggshell samples from both ratites and from other Holocene birds yielded aDNA, indicating that avian eggshell can potentially preserve DNA for very long periods of time, even in hostile environments that have not traditionally been conducive to long-term DNA survival.

Microbial resistance to novel drugs is both an extremely important area of medical science, and one of the best examples of evolution caught in the act. As if dealing with microbes that can evolve resistance to one drug wasn't enough (it is), now bacteria can apparently also evolve resistance to other drugs. Jim Caryl describes A radical source of antibiotic resistance… Journal article
The aim was to determine whether treatment with one antibiotic could confer cross-resistance resistance to other antibiotics.


The researchers found that true enough, growth in one of the antibiotics – most notably ampicillin – resulted in cross-resistance to a number of the other antibiotics.

Science writer Ferris Jabr explains How Does a Venus Flytrap Work?
On the inside of each lobe are three or more tiny sensitive hairs. If an insect, spider or human finger touches more than one of these hairs—or the same hair more than once—in fewer than 30 seconds, the trap will snap. Interestingly, rain rarely triggers the traps because the likelihood of a raindrop falling in exactly the same place twice in under 30 seconds is negligible—a good thing for the Venus flytrap, who would otherwise starve every time it rained.

What could be more phascinating than a natural loo made of a plant? Phytophactor presents the (somewhat misnamed) giant pitcher plant and Real Crappy Plant Research
By positioning a nectar reward on its lid, small mammals like tree shrews are positioned such that when they defecate, the “results” end up in the pitcher. And when you think about it, this particular pitcher does sort of look like a toilet.

Matt explains how the assassin bug (Stenolemus bituberus) has two fascinating ways of catching spiders in OMG, Assassin Bug. What Do You Mean You've Never Seen The Jackal?
When stalking, the assassin bugs will rely on stealth to reach their prey undetected, severing and stretching the silk threads of the web between itself and the spider, and approaching it with an irregular, bouncing locomotion. Exploiting periods of environmental disturbance (caused by wind, for example), together with the vibrations created by its cryptic stepping movements, the assassin bug creates a kind of “smokescreen” effect to mask its approach.

When luring, however, the assassin bug will manipulate the silk vibrations to deliberately reveal its location on the web and draw the spider to it, plucking the threads to emulate the twitching, panicked movements of ensnared prey for up to twenty minutes. “The spider thinks it’s getting a meal, but instead gets eaten itself,” says Wignall.

Puerto Rican stray dogs, aka sato, aren't prized as much as pedigree dogs, but Bonn Aure thinks their bad reputation is undeserved; the distinction is artificial and based on aesthetics. Dog Days: The Sato in Punta. Journal article
A recent study by Gray et al (open access) also said that the small dog haplotype is derived from Middle Eastern gray wolves. They revealed that “all small dogs possess these diagnostic mutations, the mutations likely arose early in the history of domestic dogs.”

Ravens and crows are my favorite birds (unless velociraptor counts as one). I've seen crows chase off hummingbirds, stealing "their" nectar from coral tree flowers. But apparently they aren't as clever as I thought wished for. John describes a test that's too hard for some of them: Meat on a String: A Possible Limit to Corvid Intelligence? Journal article
It seems that researchers have found a limit to corvid intelligence. Even if they do not have the benefit of causal reasoning, crows and ravens still best other bird species at the string pulling problem. Some finches can complete a simple string-pulling task but have a much higher error rate, and many finches never figure out the solution. Even naïve crows, however, can solve the simple string problem almost immediately. Their larger forebrains may allow corvids to process and act on visual feedback more quickly than birds in other families.

Scientia Pro Publica 23: Conservation

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

For reasons that need to be obvious to everyone, most stories about conservation are pretty grim, and this one presented by John is no exception. The Interior Department, Audubon, and a coalition of other conservation-minded organizations announced the 2010 State of the Birds report, an attempt at Predicting the State of the Birds.
Mitigation is going to become increasingly important as the climate continues to warm. At this point it seems unlikely that we will see effective action from the U.S. Congress on climate change. Even if the EPA is successful in imposing greenhouse gas restrictions, its restrictions may not reduce emissions quickly enough. So we are likely looking at some pretty dramatic changes over the next few decades, and long-term conservation plans will need to account for that.

Millions of pills are thrown away or flushed out every year, and this poses a problem for the environment. Joseph Lents discusses proper ways of Drug Disposal:
In conclusion, we need to minimize waste in health care and that requires the proper use and disposal or recycling of medications. To prescribers, ensure the necessity and quantity of the prescriptions you write, and to patients, be adherent to the drug regimen that you've been prescribed. If after this there are still unused drugs that need disposal look for a recycling program in your area and if none exist follow the recommendations for proper disposal.

Humans are trashy creatures. We produce inordinate amounts of stuff that we just want to get rid of, but Denis DuBay reminds us that You Can't Throw It Away.
So food scraps and grease that go down your drain add to the most important water pollution problem facing America today. But put them in the trash and they go to a landfill, which has an array of problems all its own. What can you do?

This is the part an ecologist loves.

Start a compost bin in your backyard!

Do you eat exotic foods? You might be harming the ecosystem you live in if what you eat are really invasive species. M.L. Henneman considers that The food on your table might create more invasive species. Journal article
Our current policies are clearly not working to prevent new invasives, because the species importers (pet stores, commercial nurseries) currently get all the financial benefit of importing new species, without any of the societal cost for those that become invasive. Some argue sometimes that even if a species becomes a pest, the local ecosystem will just eventually adapt to its presence. It’s not really a great argument given that multiple native species affected by the invasive could go extinct over a much shorter time scale than evolution would normally act to curb it, but a recent paper could (unfortunately) give this idea some legs.

The Greater Sage Grouse of North America is deemed fit to be on the endangered species list, but, according to Obama's Interior Department, the need of another species takes precedence, as Madhu explains in a post In which energy development is more endangered than the Greater Sage Grouse:
"based on accumulated scientific data and new peer-reviewed information and analysis, the greater sage-grouse warrants the protection of the Endangered Species Act..."!


"... but that listing the species at this time is precluded by the need to address higher priority species first."


"we must find common-sense ways of protecting, restoring, and reconnecting the Western lands that are most important to the species’ survival while responsibly developing much-needed energy resources."

Scientia Pro Publica 23: Ethics

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

Is it ethical to subject animals to experiments for the benefit of human health? Eric Michael Johnson has written two related posts on using animals for experiments, in which he discusses the politics of animal testing and voices his own opinion on the matter: Animal Rights and Human Rights and Animal Testing Statistics and Perspectives.
But animals already are less than human. This is where an understanding of evolution is important. When viewed along the continuum of evolutionary time we know that our species shares a close kinship with other primates and mammals. If it is universally accepted that humans should not be experimented upon, what about an individual that is 98.6% human (or rather, shares 98.6% of our DNA) such as chimpanzees? What about 93% in the case of macaques, the most used primate in invasive experiments today? This is a complicated issue and is something that requires a great deal of public discussion.


My own view is that we should eliminate all testing on Great Apes as soon as possible as proposed under the bipartisan House Bill HR 1326 The Great Ape Protection Act that is currently before the House Committee on Energy and Commerce. We should also conduct a review on the use of primates in general, the same way that the European Union has been engaged in for the last couple of years.

What are the ethical implications of lab workers testing testing their own DNA in the lab? Cath Ennis discusses such problems with Personal genethics:
My undergrad department used to get students to extract and stain their own chromosomes in a second year cytogenetics lab, but stopped a couple of years before I started the course when one student was found to have a balanced translocation that suddenly shed light on her sister's recent miscarriage. The university department ended up paying for her entire family's genetic counselling costs.

Jeremy Cherfas explains how agricultural policies has increased yields but made it difficult for smaller farmers to compete in The Green Evolution that preceded the Green Revolution. Journal article
The standard litany against the Green Revolution is that it failed to banish hunger because the technologies it ushered in were no use to small peasant farmers. Farmers with access to cash and good land did well, but poorer farmers on marginal land got nothing out of the revolution, and if they did somehow buy into it (subsidies, handouts) they were worse off afterwards. That’s not to deny that the Green Revolution increased yields, especially of wheat and rice. Just to say that it did nothing for most smallholders.

Scientia Pro Publica 23: Medicine

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

Joseph Lents is a student of pharmacology, and here he presents acetazolamide, an drug that can cure Altitude Sickness
Surprisingly when acetazolamide is used to treat altitude sickness, especially when used in prevention (before ascent), it slows the over-secretion of fluid in the corpus callosum assisting in the mitigation of the headache, nausea, loss of appetite, shortness of breath, dizziness, drowsiness, fatigue and changes in consciousness or gait. Additionally, studies have shown that those who take acetazolamide to treat altitude sickness had improved lung function and less difficulty sleeping after rapid ascent to altitude.

S. E. Gould has given up bacteria for viruses, and here tell us both about the Norovirus and Clinical Research. Journal article
The virus enters the body through the mouth, and invades the small intestine, resulting in lesions in the small intestine tissue and an increase in mucus production. This affects the absorption of nutrients, and leads to build-up of food in the stomach (which can't move down into the intestine) which in turn leads to vomiting and diarrhoea and generally feeling unwell.

One Elsevier journal, Medical Hypotheses, is apparently neither peer-reviewed, nor requiring that the medical hypotheses presented in published papers is correct, but just that they are crazy radical. Bob O'Hara objects to Elsevier's move to change these things (though he thinks peer-review would be a good idea) in Medical Hypotheses to be Falsified?
These questions have been brought into sharp relief by the journal Medical Hypotheses.This journal has, well, a reputation. The editor in chief, Bruce Charlton, has taken a deliberately different approach to the journal. Its aim is set out in its guidelines to authors:

The purpose of Medical Hypotheses is to publish interesting theoretical papers. The journal will consider radical, speculative and non-mainstream scientific ideas provided they are coherently expressed.

The journal has a reputation for publishing some weird stuff, including AIDS denialism. Charlton has a deliberate policy of selecting articles because they raise radical ideas, rather than because they look correct. Obviously, he's asking for some controversy, and now he's got it. The Scientist reports: Journal editor facing axe.

Two studies use whole-genome sequencing for disease discovery. Daniel MacArthur writes about the promises and the problems of that in Disease hunting with whole genome sequences: the good news, and the bad news. Journal article
The basic problem here is that we're still extremely bad at differentiating between mutations causing serious disease and perfectly benign polymorphisms - each of us have genomes littered with genetic variants that look like nasty mutations but have little or no effect on health. In fact, Lupski's genome illustrates this nicely: one of the mutations causing his disease is a premature stop codon that disrupts the function of a gene - but his genome also contains an additional 120 stop codons disrupting other genes, presumably without severe health effects.

For an individual, being a cheater can be highly advantageous, if you can get away with it, but for the population, it limits growth. This has important consequences for fighting bacterial infections, as Lucas Brouwers explains in Wolves, Bacteria and Cheaters Journal article
By using different grades of cheating, Jiricny and colleagues have shown the inherent vulnerability of cooperative systems. This work also might have clinical implications, since the Pseudomonas that infect patients suffering from cystic fibrosis seem to lose social functions over time, possibly because social cheaters emerge and overtake the cooperators. Non-conventional antibiotics that target the slower growing cheaters might be more effective in treating Pseudomonas infections.

Scientia Pro Publica 23: Physics

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

I really didn't know that nuclear power plants are just fancy steam engines. Arun Sinha explains How Nuclear Power Works:
The U-235 is placed in a container in a nuclear reactor, where it absorbs neutrons. On being hit by a free neutron, the uranium atom splits into two smaller atoms (typically krypton and barium) and releases two to three neutrons and a huge amount of energy as heat. This event is known as fission.

Peppe Liberti presents two cool experiments you can do at home. The Science Education with makeshift equipment
· a transparent plastic lid of a container for CD or DVD
· a torch
· a screen (a piece of rigid paper, a wall, …)
· water
· a thick brown sheet of paper
1. Construct, with thick brown paper, a cone with a small hole in the top 2 mm high and with the base slightly larger than the opening of the torch.
2. Place the paper cone on the torch.
3. Fill the lids of water (you can also add a little white tempera).
4. Point the torch on the outer edge of the lid.

Scientia Pro Publica 23: Psychology

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

Prosopagnosia is the condition of not being able to recognize faces. Grant Jacobs presents a paper on The inheritance of face recognition (should you blame your parents if you can’t recognise faces?) Journal article
Jeremy Wilmer and his colleagues estimated the heritability of face recognition to be 0.7, quite strongly genetic. This indicates that genetics would explain 70% of the effects that determine a person’s ability to recognise faces.


There appears to be some debate if face recognition is a distributed process, involving different parts of the brain, or one involving a centre within the brain devoted to face recognition. This study supports the latter view.

Andrew Bernardin espouses the view that reporting on scientific experiments that did not show interesting, positive results is also important. When the (often less intriguing) null hypothesis cannot be ruled out, that, too, is worthy of being shared. He gives examples of Two Noteworthy Null Results in Psychology and Gender Differences:
IU study finds no consensus in definitions of ‘had sex’

A new study from the Kinsey Institute at Indiana University found that no uniform consensus existed when a representative sample of 18- to 96-year-olds was asked what the term meant to them.

People who have deep conversations with others are happier, research has shown. It may be that the conversations are the causal factor, but there are other alternative explanation, as Andrew Bernardin recounts in Talk and Well-Being: A Correlation to Question. Journal article
The research findings include two noteworthy results.

1) Greater well-being was related to spending less time alone and more time talking to others: The happiest participants spent 25% less time alone and 70% more time talking than the unhappiest participants. [bold mine]

“Related to” = there was a correlation. Causal?

2) The happiest participants had twice as many substantive conversations and one third as much small talk as the unhappiest participants.

Elizabeth Moritz categorizes lab-workers into types based on what kind of golves their wear in the lab: What your gloves say about you. I don't wear any, but there's no such type!

Scientia Pro Publica 23: Conclusion

Beginning | Biology | Conservation | Ethics | Medicine | Physics | Psychology | Conclusion

Research Blogging has nominated a lot of its contributing blogs for various awards, some of them in multiple categories, and many more not at all. 96well looks at the statistics and argues that nominations apparently had nothing to do with popularity nor productivity. As a result, This blog is for sale.
I'm sure to be a very-bad writer, and I'm not pretending to write common interesting things in this niche-blog, but I don't consider serious of researchblogging to include in its best of the best, blogs with only 8, 3 or even 0 (zero!) icon-posts. The researchblogging icon was designed to:

distinguish your serious posts from news, politics, family, bagpipes

and serious icon-posting means to accomplish strict mandatory guidelines in the communication of the scientific research and to influence official citation metrics. Researchblogging, being irrespectful of its own icon, was irrespectful of its origins and of most of its productive and popular bloggers**.

Lastly, our Scientia Pro Publica administrator, GrrlScientist, has come up with the idea of advertiszing all the sciencey blog carnivals on Twitter. I'm the admin of Carnival of Evolution, and I wholeheartedly concur - we need to raise awareness of our carnivals, because we need people to read our blogs to expose more people to science. Introducing the Science, Medicine, Environment and Nature Blog Carnival Twitter Feed.
I am interested to read your thoughts about the most effective use of this twitter feed as we develop it to promote communication with the public about science, the environment, nature and medicine. If you are the host or manager of a blog carnival and you think it fits the spirit of this twitter feed, please either leave a message here or contact us at this email address so the URL of the most recent edition can be tweeted.

★ ★ ★ ★ ★

And with that we have at last come to our only friend, the end, of this huge-ish edition of your favorite general science blog carnival, Scientia Pro Publica. For those of you who've made it this far (and for those who skipped), here is a special treat that I want to share with you all: a few videos by an animal-loving band called The Beetles. I just discovered them last week, and they're really great. Lovely tunes, though they could work a bit on their instrumental skills. Unfortunately, as far as I can see they might have broken up already. Here are a few songs about the stone gardens that some octopussies make, wanting to be a walrus, and one of several songs about birds. The last of these three is a poetic one about research on Turdus merula:

Ask a priest about evolution...

Interesting questions:
Are we evolving away from belief in God? Why did thousands of intelligent people let themselves be deceived by investment fraud king Bernie Madoff? Is morality really in decline in the West and can it be reconstructed?
Yes, interesting questions asked of the wrong people:
Michael Reiss, Professor of Science at the Institute of Education University of London, a specialist in evolutionary biology (and an ordained Anglican priest) walked us through the history of theories on altruism as an evolutionary phenomenon (like vampire bats who support each other by offering up blood if a mate didn't succeed in his own hunting) and the advantages of being good at deception (think Bernie Madoff).

Even so, just knowing something has an evolutionary origin "tells you nothing about whether it is valid or useful," Reiss says.
Wut? Valid? WTF does that mean? What does it mean that some product of evolution is invalid? I really have no idea. And neither does science, because validity is a judgment, and nature doesn't judge. Only creatures do, such as humans imaginary gods. That a scientists speaks like this is embarrassing, and this is a good example of the muddled thinking that rsults when science is mixed with religion.
"Is God actually dying?" mused Barbara Bradley Hagerty of National Public Radio.

"I'm not a prophet," quipped Reiss. "I have absolutely no idea." Still, he observed, human conceptions of the divine are very different today than in the past, different often than their own parents, and that it would not be surprising if they continued to change.
The notion that God is dead is amusing (ignoring for a moment that he is also imaginary). That Yahweh is omniscient and omnipotent is at best only hinted at in the Bible [Correction: no it isn't. It says so somewhere - see Arend's comment below.], and is up for a different interpretation. As recall it says somewhere that he is eternal, but not that he is immortal. Either way, it could be that the story of Yahweh was written down long after the events took place, and therefore badly remembered by the authors. Suppose Yahweh, like Odin and Zeus, actually could die, then maybe he did. That would explain a lot, like the amount of miracles in the past, but absence of them now.

Anyway, that was a slight aside. Sorry. I don't do theology, because I think it is an empty exercise in philosophy about the nonexistent.

Homescooled children excels at critical thinking?

The perils of homeschooling is hotly debated in the blogoshphere at the moment (and all the time), and here is a good article to get a feel for what the problems is: the billion dollar homeschool textbook industry is dominated by books with a Christian slant, which most notably do not present evolutionary theory correctly.
Christian-based materials dominate a growing home-school education market that encompasses more than 1.5 million students in the U.S. And for most home-school parents, a Bible-based version of the Earth's creation is exactly what they want. Federal statistics from 2007 show 83 percent of home-schooling parents want to give their children "religious or moral instruction."
One issue is whether homeschooled children are being "brainwashed" (I put that in quotes because I do feel it is a very strong term for what happens, though not wholly inappropriate), or if they actually learn to think critically. The two seem to be opposites, I think. If anyone wants to try to make the argument that they're not, I'd be willing to listen.

But, if five out of six (or, 555 out of 666) homeschooled children are homeschooled by evangelical Christians, then it seems unlikely that homeschooled children as one group will be free from religious indoctrination (is that better than "brainwashing"?).
The textbook delivers a religious ultimatum to young readers and parents, warning in its "History of Life" chapter that a "Christian worldview ... is the only correct view of reality; anyone who rejects it will not only fail to reach heaven but also fail to see the world as it truly is."

When the AP asked about that passage, university spokesman Brian Scoles said the sentence made it into the book because of an editing error and will be removed from future editions.
Editing error? That must be publisher speak for "changing our minds when we're found out".

A few links to find more blogging about homeschooling:

Creationism, education, and the state
In the comments here you'll find an egregious example of a homechooled adult who thinks he and other homeschooled are critical thinkers extraordinaire.

Evolution and home-schooling redux
Jerry Coyne's blog - Jerry is in the middle of the debate.

Christian Mother Blog Button
Christian blogger on homeschooling.

Update 3/17:
Jerry Coyne has a post on a revealing discussion with Michael McHugh who sells homeschooling materials.
McHugh’s suggestion for how to educate your kids involves choosing which worldview suits them best, and then selecting the “facts” that fit this worldview. I am not making this up: he says it explicitly.