(via National Geographic)
Pharyngula
Evolution, development, and random biological ejaculations from a godless liberal
It’s good to know someone is doing clitoris research. The conclusion that we need more studies, though, is only to be expected.
A few years ago, the Discovery Institute set up laboratory to do research, the Biologic Institute, which is in principle a good thing — they do claim to want to take a scientific approach to understanding the origin of life, after all. So far, it’s been less than spectacular. They published one paper on software that models encoding Chinese characters as an analogy to protein folding. It’s mildly interesting, but its connection to intelligent design is tenuous and abstract, and it’s not at all clear how they can use it to expose problems in evolution…and even if they do find a problem in their model, it’s not a given that it will apply to real biology. One has to wonder what the Intelligent Design creationists are actually doing in their lab. Others have wondered and tried to peek into the goings-on, but have been turned away.
Those madcap jokers at antievolution.org have found another way to peek in. The Biologic Institute is a tax-exempt organization, which means they had to file a form with all kinds of interesting information in it — follow the money! You can look at their Form 990, too, just search for “biologic institute” and you’ll get a nice pdf back.
Their income for 2008 was $300,000. That’s a tidy sum of money — compared to what I need to run a small lab at a teaching university, it’s a spectacular sum of money, and is actually about 10 times more than the yearly supply and maintenance budget for our entire biology department (not counting salaries, of course; the Biologic Institute does pay salaries out of that $300K). Oh, what we could do with that much support…
On the other hand, it’s not very much money at all for an outfit with the grand goal “to conduct basic scientific research on topics relating to the origin, organization and operation of living things and their parts, and to the nature of ecosystems and environments conducived to life”. The DI is getting some cheap PR out of this, but nowhere near the amount is being invested that would be needed to address their grandiose goal. By comparison, the National Center for Science Education (you can get their Form 990, too!) had a budget of about $1.3 million in the same period. Here are their goals:
Science Education. The National Center for Science Education (NCSE) is a membership organization providing information and resources for schools, parents and concerned citizens working to keep evolution in public school science education. NCSE educates the press and public about the scientific, educational, and legal aspects of the creation and evolution controversy, and supply needed information and advice to promote and defend good science education at local, state, and national levels.
The NCSE is specific, focused and actually has a good-sized staff that does a lot of work that is visible to the public. We’re getting a bargain there. The Biologic Institute is vague, and while they’re operating on a quarter of the budget, doesn’t seem to do much.
It is a good racket, though. The director, Douglas Axe, receives a salary of $92,000, which is a heck of a lot more than I get paid (not that that means much: college professors in general aren’t exactly rich). Man, if I were in this business for the money, I should have gone into creationism. By comparison, though, you might wonder how much Eugenie Scott gets paid: $77,000. I was surprised — sure, she’s also making more than I am, but she’s a national figure with far more experience than I have. There is also a collection of well-known people like Barbara Forrest and Kevin Padian who serve on the board of the NCSE and get paid nothing. Again, don’t go into science with the expectation of riches.
Forget salaries. They’re the biggest part of most organizations budgets, but the news that people are working there isn’t news — we want to know what kind of nifty science gadgets are whirring away there. That’ll tell us what they’re up to. PCR machines? Sequencers? Lasers? Giant saltwater aquaria and bags and bags of squid chow? Here are there reported assets. Don’t get too excited.
I guess that’s reasonable for an outfit that’s coding up software, and not much else. It’s kind of a let-down if you’re expecting the Biologic Institute were doing biology. (I know, they aren’t; they’re doing biologic, whatever that is).
But let’s not be quick to judge. Maybe they’ve achieved amazing things with a small lab and limited resources. Here’s what they proudly announce as their accomplishments for 2008.
Hang on there…Doug Axe is getting paid $92,000 for getting 4,000 visitors a month to his website? I get more visitors than that in an hour! I’ve got to do some quick calculations here…if I were getting paid an equivalent amount per visit, based on last month’s traffic, I should be getting $67,677,045.43 for a year of Pharyngula! Where’s my money?
Now, unfortunately, I can’t link to the Biologic Institute web site, because if I did, I’d probably increase their productivity 100 fold.
I also believe in dinosaurs, but this video is mainly an opportunity to sight-see a bit of New Zealand. Otherwise, you all know how the ad infinitum thread works — just talk about whatever you feel like.
(Current totals: 10,407 entries with 1,020,544 comments.)
I’m going to my high school reunion later this summer, and I’ve just had a revelation that will color the experience. A Catholic philosopher has exposed the awful truth.
In the column, published last week, the writer argued that one reason the children of gay parents should not be admitted to Catholic schools is the “real danger” that they would bring pornography to school.
I remember high school, and I remember some of the guys who would bring porn to school, or had it in their homes. I remember groups of guys getting together on the football field to snigger over the latest centerfold.
I had no idea they were all gay! Or that their parents were gay!
I’m going to have to bring that up at the party. I’m hoping that all those jocks have melted down into plump balding insurance salesmen, though, so I don’t get beat up too bad.
I’m still baffled by one thing, though. Why were all those hedonistic gay boys drooling over pictures of naked girls? I don’t think I saw a single scrap of gay porn until the internet was discovered and fundamentalist Christians started sending me pictures of men having sex with each other.
Oh, sure, this strategem may have given the LA Dodgers an edge for a few seasons:
Frank and Jamie McCourt, the multi-millionaire owners of the LA Dodgers, have been revealed to have employed a Russian scientist to beam thought waves to boost the team’s chances.
That’s over now, though. I urge all loyal readers to close your eyes, face LA, and beam baseball hatred at them. To really potentiate the effect, you can also wiggle your fingers and go “Nnnn-nna-nna-naaaaa” or speak in tongues while doing it. We’re also going to pray for the New York Yankees*. Dodgers are dooooomed!
Although…
According to Bill Shaikin of the LA Times, the McCourts paid Vladimir Shpunt several hundred thousand dollars over five years to apply his “V energy” and help the Dodgers to victory. Between 2004, the first season under the McCourts’ ownership, and 2009, Shpunt was retained for Dodgers matches, despite the fact that he knew little about baseball.
…you know, “Vladimir Shpunt” is an awesome name for a Russian woo artist.
I might also be persuaded to end my campaign of psychic oppression for a few hundred thousand dollars, myself.
*Don’t worry about it, we’re atheists and already going to hell, so rooting for Satan’s favorite team won’t do you any more harm.
I try to be patient with all the email I get, I really do, and usually the greatest forebearance I can offer is to simply set a piece of email aside and go on. There simply is not enough time to answer everything, especially when my correspondent is better off going to the library, and most especially when the only reply I’m inspired to give is to snarl, “Go away, kid, you bother me.”
So let me introduce you to young Mr Rosenberg. He has written me twice, the first time with a fairly routine set of questions that I politely set aside because I get a few hundred of these every week, and because he was asking the wrong person, and the second time with a pushy rude letter that prompts me to now be impolite and actually answer him. Here’s his first letter, in which he introduces himself, and as is so common in these things, tells me how smart he is. Well, if you’re so clever, Mr Rosenberg, why are you asking me the questions?
Questions on the Universe
Hi Professor Myers,
My name is Andrew Rosenberg, I am 18 years old and I live in Racine Wisconsin. I have been raised in the Lutheran Church since I was born and view myself as a Christian. Recently I have been pondering the universe, especially the existence of God in general. I have the belief that if God exists, then Christianity makes the most sense for me to follow. But that brings up the question…does God exist? I am an intelligent individual, whose thoughts go beyond the typical 2010 senior’s tangents. I graduated valedictorian of my class, and so I thoughtI would like to contact another intelligent individual, such as yourself, who has conflicting viewpoints from me. After all, if you surround yourself with the same types of people all your life, then you will never learn anything or make your own decisions.
My first question for you is this: Christianity aside, what makes you an atheist? I know I could probably find the answer deep in your blog, but to me, atheism is just ignorant of the universe around us. Existence….just the simple existence of a hydrogen atom gives me the thought that something had to, and I hate to say this, create it. With something to create, how could the materials and fabrications that make up the universe–atoms, protons, neautrons, electrons–come to be? What cause the theories such as the big bang? Put the universe’s energy into action. As easy as it is to say that a God does not exist, its just as easy to say that one (multiples?) does.
On the topic of evolution, I have further questions– I fully believe in micro evolution, whether it be by mutation of natural selection…but how can the existence of the world’s first bacterium be? How can proteins and other chemicals come together to make an organism? For if you take that same organism apart and puts its pieces back into a jar of water, it will never come back to life or reassemble itself. So how did such a thing happen in the beggining of time?
The bottom line for me is, yes the existence of some supernatural being who has divine powers seems very far fetched. But the non-existence of such a being seems far less plausible to me. How can we be without a supernatural beggining at some point in the univeral timeline? Something, from nothing. Its a supernatural question in itself that puzzles me, but makes me view atheists as ignorant. No God, yet countless molecules and building blocks that just….appeared? No, it doesn’t make sense.
Please explain any view point or answer that you have to my questions. I am not afraid to be proven wrong.
Andrew Rosenberg
“atheism is just ignorant of the universe around us”…well, la-de-da, says the high school student who hasn’t bothered to look up anything in basic physics, and is demanding that a biologist explain it all to him in an email message.
First strike against him: I am a biologist. It says so right up there at the top left, under my picture. I am not a physicist. As a biologist, I’m even more narrowly specialized than that: ask me about the evolution of multicellular animals, ask me about development, ask me about various bits and pieces of molecular evolution in the last half billion years, and I can probably give you a decent answer, and I might even talk your socks off for an hour. Ask me about physics, the big bang, and cosmology and…I’m a well-informed layman, nothing more. A literate 18-year-old could be just as current on the topic, if not more so, by going down to the library or bookstore and picking up a few texts and, you know, reading them. This isn’t hard.
Go read a book by Brian Greene, Lawrence Krauss, or Sean Carroll; Scientific American has a primer on cosmology, even. If you can work your way through Steven Weinberg’s Cosmology, you’ll be much, much smarter than I am. But pestering random biologists with misspelled missives demanding that they explain particles to them? Dumb.
It’s often part of a cunning ploy, of course, not that I know that this is the case with Mr Rosenberg. I’ve noticed that, after many of my more detailed talks on biology, some clueless creationist will raise their hand and ask me to explain what existed before the Big Bang, completely ignoring the topic I’ve just explained to them. I’ve also compared notes with a few physicists; they’ll give talks on the origin of the universe, and afterwards be asked to explain the evolution of the eye. I think they know better than to ask a question in which they may get a deep and knowledgeable answer, because they don’t want an answer.
I would just have to give a very general answer that we know that heavier atoms are assembled by processes in stellar evolution, that many complex molecules are constructed by natural processes (formaldehyde forms in space, for instance), and that fundamental particles arose in the Big Bang; that physicists I have talked to, like Lawrence Krauss, have pointed out that stuff spontaneously forms all the time, and that there is no such thing as empty space. Try this on for size.
I can say why I’m an atheist, though, and I’ve talked about it numerous times. Here’s a short, succinct image that explains it all.
Mr Rosenberg has not explained why I should believe in his Christian deity at all, and his only explanation for why he believes in his peculiar god is a self-confessed complete lack of knowledge and imagination, which given that he’s the clueless fellow asking a biologist to explain physics to him in 200 words or less, is not at all impressive.
But now, today, I get another message from him. I get these all the time, too, demands from ignorant jerks who are so infused with a sense of entitlement that they think they can demand that I spoonfeed them. “Christian humility” is just an ironic phrase for arrogant insincerity.
A Few Questions for an Atheist.
Hello PZ Myers,
My name is Andrew Rosenberg. Last week I sent you an email talking about why I believe in a creator. You did not respond. I would really like to hear your opinion on what I sent you. I also have another concern about you. I have been following your blog and youtube videos for a little while. I think that it is extremely rude of you to constantly criticize religeous groups on your blog. You do it everyday. I don’t know if lashing out at people gives you confidence because your followers laugh at your witty, little remarks, but I certainly think its rude. Especially when you get in person and you are just a little man with a quiet voice. Yet on the internet you spew forth brash criticisms like a volcano.
But besides those opinions of mine, I would really like to hear your take on my question of existence itself that I sent you.
Andrew
Hey, Andy — GET STUFFED.
You’re a perfect example of why I am rude — I am really tired of pretentious twits who’ve barely got a high school education, which isn’t much to begin with, and who think they’re brilliant because they can answer everything with “goddidit.” Am I rude? You bet. It’s not going to change, either.
But then you exhibit typical inconsistency: I’m a “little man with a quiet voice.” Would I have more authority if I glopped on some pomade and bellowed at you? Do you even listen to what I say in those videos? It’s nothing different from what I write — it’s just that my presentation is different than the howling protestations you get from televangelists.
I will remember what you expect, Andrew Rosenberg of Racine, Wisconsin. If we ever meet, I’ll make a special effort to yell rudely at you and just you, and do my best to send your know-nothing pious butt away crying. And don’t bother writing to me again.
I’ve gotten some email asking for a simplified executive summary of this paper, so here it is.
A large study of almost a thousand autistic individuals for genetic variations that make them different from control individuals has found that Autism Spectrum Disorder has many different genetic causes: there isn’t one single gene responsible for ASD, but a constellation of hundreds, each with the potential to affect the development of the brain and cause the symptoms of autism. They don’t know exactly how each of these genes contributes to the disorder, but they have found that many of them are involved in growth and cell communication and the formation of synapses in the brain.
The bottom line is that there are many different ways to cause the symptoms of autism, and it’s a mistake to try to pin it all on single, simple causes. Any hope for amelioration lies in understanding the general functional processes that are disrupted by mutations in various pathways.
Coming up with simple, one-size-fits-all answers to serious problems is so tempting and so satisfying. Look at autism, for instance: a mysterious disease with a wide range of expression, so wide that it is more properly called Autism Spectrum Disorder (ASD), and the popular press and various celebrities all want it to be pegged to a simple cause: it’s vaccines, or it’s mercury, or it’s the dose of the vaccines, and all we have to do to fix it is not vaccinate, or reduce the number of vaccinations, or use chelation therapy to extract poisons, and presto, a cure! This is magical thinking, pure and simple, and it doesn’t work.
ASD isn’t simple, it’s not one disease, it doesn’t have one cause, and vaccines are definitely not the cause: if there’s one thing the research has done, it’s to thoroughly rule out the idea that giving kids shots at an early age causes autism. What we’re actually discovering more and more is that ASD can be traced to genetic variation.
Again, though, the causes aren’t simple. There is no single mutation to which ASD can be pinned.
For example, one hot spot for an association of genes with autism is the long arm of chromosome 22; cases of developmental delays and autistic behavior have been associated with partial deletions in chromosome 22, and the problems have even been narrowed down to one specific gene, SHANK3, which is expressed in neurons and localized to synapses. We know that if you’ve got a broken copy of this particular gene, you’re likely to have ASD.
How many ASD individuals have this specific genetic change? 0.75%. It is a cause in less than 1% of all affected individuals, but it cannot be the sole cause of ASD in all cases. We have to get out of this mindset that tries to find single causes for complex phenomena; ASD is a case where we have a complex range of disorders with multiple, complex causes.
So how do we get a handle on ASD? This is where the work gets interesting: just because something is multi-causal does not mean that science can’t get a grip on it and that we can’t learn anything interesting about it. We’ve got lots of new tools for analyzing broad properties of genomes now, and one promising line of attack are methods for measuring and identifying copy number variants in individuals and populations.
Copy number variants (CNVs) are surprisingly common. If you’ve had any biology instruction at all, you’re probably familiar with the Mendelian concept that we have two copies of each chromosome, and two copies of each gene. As it turns out, that is an oversimplification: sometimes, a piece of a chromosome is accidentally duplicated, and then you’ll carry two copies of the associated gene on one chromosome, and one copy on another chromosome, for a total of 3 copies. And in some cases, these duplications have occurred often enough that you’ll have many more than 3; the median number of copies of the amylase gene (an enzyme that breaks down starch) in European American populations is 7, with a range of 2 to 15 in different individuals. Get used to it, this kind of variation in copy number seems to happen fairly often.
Now in the case of amylase, the effect of this variation is mild — individuals with more copies of the gene produce more of the enzyme and break down starchy foods faster. It does have evolutionary effects, since cultures with diets rich in starch contain individuals who have, on average, more copies of the gene than individuals where starches are less common in the diet. But what if these chance variations in copy number affect genes involved in the function of the brain? We might see more profound effects on behavior or cognitive ability. The defect in SHANK3 mutations is an example of a reduction in copy number of that gene; what if we could screen populations of ASD individuals not for a specific gene variant, but for the more general occurrence of frequent variations in copy number of any genes…and then we could ask which genes are often affected?
It’s being done. A new paper in Nature describes a screen of control and ASD individuals to identify rare copy number variants associated with autism. It worked! In fact, it worked maybe a little too well, since we now have an embarrassment of riches, a great many genes that may be related to ASD.
The autism spectrum disorders (ASDs) are a group of conditions characterized by impairments in reciprocal social interaction and communication, and the presence of restricted and repetitive behaviours. Individuals with an ASD vary greatly in cognitive development, which can range from above average to intellectual disability. Although ASDs are known to be highly heritable (~90%), the underlying genetic determinants are still largely unknown. Here we analysed the genome-wide characteristics of rare (<1% frequency) copy number variation in ASD using dense genotyping arrays. When comparing 996 ASD individuals of European ancestry to 1,287 matched controls, cases were found to carry a higher global burden of rare, genic copy number variants (CNVs) (1.19 fold, P = 0.012), especially so for loci previously implicated in either ASD and/or intellectual disability (1.69 fold, P = 3.4âÃâ10-4). Among the CNVs there were numerous de novo and inherited events, sometimes in combination in a given family, implicating many novel ASD genes such as SHANK2, SYNGAP1, DLGAP2 and the X-linked DDX53-PTCHD1 locus. We also discovered an enrichment of CNVs disrupting functional gene sets involved in cellular proliferation, projection and motility, and GTPase/Ras signalling. Our results reveal many new genetic and functional targets in ASD that may lead to final connected pathways.
They analyzed both affected individuals and their parents, and found both familial transmission — that is, the child with ASD had received a copy number variant from a parent who was a carrier — and de novo events — that is, the child had a spontaneous, new mutation that was not present in either parent. There is no one single gene that can be tagged as the cause of autism: they identified 226 de novo and 219 inherited copy number variants in affected individuals. No one individual carries all of these variants, of course — the results tell us that there are many different paths to ASD.
Oh, no, you may be tempted to wail, autism is hundreds of diseases, with even more possible combinations of variants, and every individual is unique — this is no way to get a handle on what’s actually happening to autistic kids! Don’t despair, though, this is just the start. Although there are many genes involved, we can try to ask what all of them have in common functionally. There may be common consequences from all of these different genes, so maybe we can identify the common errors in the process of building a brain that lead to ASD.
Here’s a first stab at puzzling out what these genes do. The genes that have been identified as being deficient in ASD individuals are mapped out by known functions, and what jumps out at you is that the hundreds of specific genes fall into a smaller number of functional categories. Many of them cluster in a few functional roles: cell proliferation (genes that affect the number of cells in a tissues) and cell projection (particularly important in neurons, where cells will extend long processes that project into target regions), and a specific class of cell signaling molecules, RAS-GTPases, which are involved in how cells communicate with one another and are particularly important in synapses, or the linkages between neurons.
The second map above ties the various copy number variants to previously known disease genes involved in ASD, and what catches my eye is the dense cloud of variants associated with central nervous system development. That tells me right there that it is inappropriate to treat ASD as something that is switched on or off by simple causal factors: ASD is the product of long-developing, subtle changes in the growth of the nervous system in embryos and infants.
So the conclusion, as expected, is that ASD is a multi-factorial disorder with a strong genetic component — but definitely not single-locus inheritance, as many different genes are involved.
Our findings provide strong support for the involvement of multiple rare genic CNVs, both genome-wide and at specific loci, in ASD. These findings, similar to those recently described in schizophrenia, suggest that at least some of these ASD CNVs (and the genes that they affect) are under purifying selection. Genes previously implicated in ASD by rare variant findings have pointed to functional themes in ASD pathophysiology. Molecules such as NRXN1, NLGN3/4X and SHANK3, localized presynaptically or at the post-synaptic density (PSD), highlight maturation and function of glutamatergic synapses. Our data reveal that SHANK2, SYNGAP1 and DLGAP2 are new ASD loci that also encode proteins in the PSD. We also found intellectual disability genes to be important in ASD. Furthermore, our functional enrichment map identifies new groups such as GTPase/Ras, effectively expanding both the number and connectivity of modules that may be involved in ASD. The next step will be to relate defects or patterns of alterations in these groups to ASD endophenotypes. The combined identification of higher-penetrance rare variants and new biological pathways, including those identified in this study, may broaden the targets amenable to genetic testing and therapeutic intervention.
There aren’t any simple answers. There are some hints of hope for future treatment, though, in the recognition that there are a few functional modules that are being commonly impaired by these many different genes — it at least focuses the direction of future research in to some narrower domains.
One fact is so obvious that it’s unfortunate I have to mention it: no external agent, such as a vaccine, can generate a consistent pattern of duplication and deletions in an affected individual’s cells. These data say it’s an error to chase down transient environmental agents given relatively late in life to people.
Pinto D et al. (2010) Functional impact of global rare copy number variation in autism spectrum disorders Nature doi:10.1038/nature09146.
So, England, how does it feel to have a hereditary moron like Prince Charles fluttering about the country?
The Prince of Wales has blamed a lack of belief in the soul for the world’s environmental problems, and said that the planet cannot sustain a population expected to reach 9 billion in 40 years.
He said he found it “baffling” that so many scientists professed a faith in God yet this had little bearing on the “damaging” way science was used to exploit the natural world.
The Prince pinned part of the blame on Galileo. Criticising the profit imperative behind much scientific research, he said: “This imbalance, where mechanistic thinking is so predominant, goes back at least to Galileo’s assertion that there is nothing in nature but quantity and motion.
“This is the view that continues to frame the general perception of the way the world works, and how we fit within the scheme of things.
“As a result, Nature has been completely objectified — ‘She’ has become an ‘it’ — and we are persuaded to concentrate on the material aspect of reality that fits within Galileo’s scheme.” The Prince said that he believed “green technology” alone could not resolve the world’s environmental problems. Instead, the West must do something about its “deep, inner crisis of the soul”.
Oh, yes — if only we’d return to regarding Nature as feminine, whatever that means, and start believing in souls, we could fix all environmental problems. He’s not very specific, though — could he make some clear suggestions about how pretending the planet is a lady will solve, say, global warming or the oil spill in the Gulf?
Don’t be too embarrassed, UK readers. It could be worse. If Charles were an American, he’d be getting elected to his position as ceremonial woo-meister. At least you can blame it all on the vagaries of the genetic lottery and a royally pampered upbringing.
