Ah, Portland…

It’s a very Oregonian thing, you see. It’s the World Naked Bike Ride, in which 5,000+ residents show up downtown, take off all their clothes, and pedal about. They also visit museums. I’ve been to a surprising number of Oregon events where people just shuck off everything, completely unselfconsciously. Damned hippies. Gotta love ’em.

There are photos at the link, but mostly tasteful — at most you’ll be flashed with a few bare butts.

The Supreme Court decision on patentable genomes

I’m shocked. Just totally surprised. And it was unanimous — the Supreme Court determined that human genes cannot be patented. This is excellent news.

Why is it a good decision? Because medical DNA analysis was turning into a patchwork of competing landgrabs. Sequencing technology is coming along so nicely that more and more diagnostic tools are available, that can analyze big chunks of the genome for, for instance, known dangerous mutations. But at the same time, many stretches of DNA were ‘owned’, or patented by various companies. A company called Myriad had the patents on the genes BRCA1 and BRCA2 which, when defective, are associated with a higher frequency of breast cancer. Another company which might have a tool for analyzing a piece of chromosome 17, where BRCA1 was located, would have to intentionally mask their analysis, hiding the sequence of the BRCA1 gene, or they’d have to pay royalties to Myriad.

This is an increasingly ridiculous situation. Imagine if 50 competing meteorological forecasting companies each had rights to the weather above a different state, and a weather service in Louisiana had to pay the weather service in Florida for the right to examine clouds and wind and pressure to the east, and you couldn’t have a national or worldwide weather analysis without paying a thousand petty weather barons. That’s where we’ve been in genetics, with an increasingly balkanized genome and a welter of companies expecting payment if you looked at the DNA sequence in an individual patient.

Francis Collins, director of the National Institutes of Health, who has long argued for limiting private control of DNA data, said today that he was pleased with the ruling. “Our position all along has been that patenting DNA in its natural state does not provide any benefit to the public. There have been concerns that you might have a $1000 genome sequence, but a $500,000 royalty fee to use it. We can breathe a big sigh of relief that this will no longer threaten to inhibit the progress of DNA research.”

So, smart move, Supremes. For once they made a decision that didn’t simply back corporate interests.

One complication, though. They made this decision based on the logic that the genetic sequence wasn’t an invention of the company — it was just what they found there — making that unpatentable. But they also made a decision that cDNA was patentable, which is a little weird.

cDNA isn’t exactly an invention by the company. Here’s what it is: the genomic sequence of a messy human gene is a cluttered mess. There are regions called exons which code for the proteins of the gene product, but they’re broken up by intervening sequences called introns. What the cell will do is copy the whole messy DNA sequence into RNA, and then enzymes come along and snip out the introns and splice together the exons into one continuous sequence. It’s like finding an interesting magazine article in which every other paragraph is interrupted by an ad, so you cut it up, throw away the ads, and tape the story together into one complete, uninterrupted flow of text. It’s a tedious exercise, but your cells do it all the time.

So this processed RNA is simply the coding part of the sequence, with all the useless bits cut out. Most of our genes are more intron than exon, so this is a fairly significant task; the BRCA1 gene, for instance is made of 24 exons, so those 24 chunks are splice together to make the final RNA molecule.

Your cells do not naturally produce cDNA, so the judges are sort of right to recognize it as an artificial process. To make cDNA, that spliced-together RNA is processed by a reverse transcriptase in the lab, making a complementary sequence of DNA. It gives you a new chunk of DNA without all the introns cluttering it up, which you can then insert into a bacterium, for instance, and put it to work making the full RNA/protein for you.

I guess it’s a reasonable compromise to say cDNAs are patentable. There is some specificity to it: you might be selecting a particular splicing variant (there are 38 different kinds of RNA produced from different patterns of cutting and splicing BRCA1 RNA, for instance) with a specific mutation, producing a particular molecular construct that is useful for diagnostics or for experiments. In that case, you have used the sequence to build a useful probe or tool — it seems fair to say your tool is a patentable creation, especially since the underlying genetic sequence is not patented, so someone else could come along and build their own tool from scratch.

There’s still one troubling thing about the decision, and it was Scalia who pointed it out.

Although the court’s opinion was unanimous, Justice Antonin Scalia added a divergent view. While he agreed with the decision, he could not personally stand behind the “fine details of molecular technology” cited by his colleagues, he wrote, because “I am unable to affirm those details on my own knowledge or even my own belief.”

So the judges came to an acceptable decision in this case, but truth be told, none of them are trained in molecular biology and genetics, so they weren’t actually competent to make that decision. This is a problem that’s only going to grow worse and worse as biology becomes more powerful and more esoteric. It’s also a little worrying that Scalia thinks mere belief might have been a useful barometer in making a decision — but the case was so far beyond the bounds of what he understands that I suspect he and the other judges based their decision entirely on the recommendations of the lawyers presenting briefs for their scientist clients.

Hey, Ken Ham: don’t run away!

The Houston Atheists have a challenge for you. Aron Ra and I are willing to lower ourselves to engage you in debate. This is a very rare exception to my policy of refusing to debate clowns — you should take advantage of it.

Houston. 1 August. You’re going to be there anyway. We’ll meet you to discuss your belief that the earth is only roughly 6000 years old, and that common descent is false. Imagine the prestige you’ll acquire when you rout the scientists with your logic and evidence! Imagine real hard!

If you don’t show up, Houston Atheists will be putting on a series of talks that directly refute the nonsense Answers in Genesis peddles, without you there to challenge it.

Television “science”

Are you a film crew person looking for work in the UK? Multiple opportunities have opened up for the crew for a documentary!

A new Covent Garden-based film company seeks a producer of marketing and distribution, a researcher/presenter, a camera operator, a sound person, a runner, and an editor, for its first documentary, called Laughing with Women. Why are women, on average, slightly less funny than men? Does gold-digging in particular impair women’s joke-making ability? If women publicly reject gold-digging, do they become as funny, or funnier than men?

If the radical and revealing street-based social experiment at the centre of our documentary proves gold-digging does make women less funny (as pre-production research suggests) then our findings will make headlines around the world, our film’s two minute teaser trailer attached to all those news and blog articles. The full documentary will be shot to a broadcast-quality standard and format, giving mainstream television companies worldwide the opportunity to purchase broadcasting rights (if they’re feeling brave enough) whilst we maintain a virtually guaranteed revenue stream from our already established hardcore of supporters and fans around the world, who, along with everyone else we intrigue, will be able to enjoy Laughing with Women on newly launched pay-per-view channel, Vimeo on Demand (VoD) – where VoD itself takes a very modest 10% cut. The documentary has the potential to be translated into several languages – gold-digging a familiar if hidden story in every country, until now.

Positions available…

Producer of marketing and distribution

Researcher/presenter

Camera person

Sound person

Editor

All positions paid at the minimum national wage or above, to be negotiated.

Shooting dates…

The main shoot, testing the documentary’s key hypothesis, and the kind of fireworks it will generate, will take place from August 1st, for 10 days, in central London. Eight to ten other shooting days will be organized for soon after. If interested in getting involved, please email your show-reel and/or CV, along with a paragraph or two saying hello, explaining in a little detail why you are specifically interested in working on Laughing with Women – and what your individual take on it all might be – also outlining your availability. Interesting respondents will be contacted for a Covent Garden meeting soon, where the whole plan, and a closely linked follow-up project can be discussed.

That isn’t a documentary. They’re not building a story around an established science fact, they’re inventing a premise that they simply assume is true, and are then designing an “experiment” (more likely a contrived set of sight gags) to “prove” their claims on video. I can roughly predict what they’re going to do: they’re going to approach women, insult them by suggesting that they’re venal gold-diggers, and then demonstrate that angry women don’t have much of a sense of humor about sexist assmonkeys harassing them. Hypothesis proven! Of course, if women were actually funnier than the men in their sample, you know that wouldn’t get aired — they have a prejudice, and by god, they’re going to make it appear true.

And then they hope that people will be “brave enough” to make their video go viral when it confirms conventional bigotry. If their little dog-and-pony show doesn’t get picked up any broadcasters, it isn’t because they’re afraid to pander to stereotypes — turn on your TV and look, that’s never a problem — but because this “documentary” will be so patently slanted and dishonest that it is a slap in the face to real documentaries everywhere.

Wait a minute…they’re looking for a people to do camera and sound, a produce, a presenter, and an editor, for a show that is going to be a series of confrontations and requires almost no writing. So there is basically no crew at all right now, just a no-talent hack sitting on his ass in his office dreaming of putting together a show to prove to the world that women lack a sense of humor and are all gold-digging bitches. He sounds like every MRA in the world.


I called it. This is the dream of no-talent hack Tom Martin, who brings nothing to the project other than a resentment of women.

Goddamnit Bill Maher

Anyone else remember when Rush Limbaugh called President Clinton’s daughter Chelsea a dog? It wasn’t just petty and cruel, but it was an attack on a child, and it was disgusting. It was symptomatic of the derangement of the right wing that people actually laughed and defended it.

Now Bill Maher is laughing at Sarah Palin’s Down syndrome child. It’s the same thing.

Futrell didn’t think he’d hear the HBO personality mock former Gov. Sarah Palin’s special needs child or hear the crowd laugh right along.

Futrell, a former Las Vegas sports broadcaster and Breitbart News contributor, says on his blog that Maher used the term "retarded" to describe young Trig Palin during the comedy performance.

The one thing I can respect about Palin, that she seems to treat all of her children equally, is a joke to Maher. Thanks, guy, for being such an awful, ghastly, horrible liberal, and for lowering yourself to mocking the children of your political opponents.

(via Joe.My.God)

These cancers aren’t curing themselves! Nurse, more radioactive lead atoms on whirling rays of light!

This guy, Ramachandran Lyer, has been spamming my email pretty much nonstop today. He’s very excited, I guess — he thinks he has discovered a cure for cancer. Let’s take a look, shall we?

Radioactive lead can cure Cancer- Mechanism: My view

The human body is made of atoms. Every cell, in Skin, bone, nerves, veins is the compound of various atoms. The deficiency of a particular mineral will result in diseases. For example iron deficiency results in thrombasthenia, hemophilia and anemic.

Not so fast! This is an amazing preface. So the justification for your treatment begins with the fact that we’re made of atoms? Oh my god, that’s true! I can’t argue with that at all!

And yes, mineral deficiencies can cause health problems! Ramachandran is like an oracle speaking nothing but truth — sweet incontestable truth. This has been established in his very first paragraph.

For curing this we are injecting blood and platelet. The blood transfusion, if often carried out will weaken the walls of veins and lungs. If the same iron/ Hb is eaten by cancer cell, the iron cannot be replaced by more blood as the mound will suck the Hb and cancer cell grow and block the way.

Wait, curing “this”? What is the referent here? Cancer, I presume, from the title?

But we don’t cure cancer with blood transfusions. We don’t even try. Well, I suppose we try to address leukemias that way, but isn’t it more to keep the patient alive than to actually treat the cancer? I’m getting confused, Ramachandran. Your aura of infallibility is fading.

So, cancer is a mound that sucks iron away from healthy hemoglobin. OK, that’s novel. Do you know anything about cancer biology, Ramachandran? Because it’s a little bit more complicated than that.

To prevent this cancer cell from sucking the iron, we are to coat/ laminate the iron with lead, and lead cannot be sucked by the cancer mound. This lamination on Hb will stay for 2 to 3 days and comes out through motion.

Whuzza…laminate the iron with lead? Just like that? But the iron ions in hemoglobin are all bound up in this lovely heterocyclic ring — how do these lead molecules fit? How do you “laminate” the iron without disrupting its respiratory function? And what does this have to do with cancer?

The physical atom of lead or any metal cannot be broken as astral atoms.

I do not know of these astral atoms.

But if the same atom is sent in to the body as whirls of light rays, in the form of vibrations (here is a theory the air / aether carry the light rays) created by lighting herbal oil which produce/ let out lead, on heat, penetrate in to the body through skin, as ascorbic acid, forms amino acid in bile, mix with blood and laminates the haemoglobin and prevents cancer cells from sucking the iron as it’s nourishment.

I knew vibrations would have to come into play somewhere in here, but Ramachandran also tosses in aether and herbal oils! Bravo!

I guess I see how Ramachandran’s planning to laminate the iron with lead, with a kind of photonic airbrush, with whirling light rays swooshing out of burning herbal oils. That could be dramatic, but I’m not convinced that Ramachandran actually has any evidence that he can do that.

The blood that produced heat due to friction of cells will create vacuum in the blood compound/ components. This vacuum should be filled with aether immediately which has the attraction power to pull the light rays created by the oil lamp lit with herbal oils that is filled with other minerals along with lead and resins in the same herbal. This heat created by vacuum, if not filled will shrink and to adjust itself, will suck hydrogen from the blood for neutralizing and oxygen is eaten by Cancer mound, and patient needs more oxygen and water. The heat shows the blood is acidic, and we feel the increase in pH with salt water may give some relief to the patient.

OK, now that’s just crazy talk.

My dear friend Ramachandran is a graduate of the Utkal University of Culture, which does not have a medical or scientific program of any kind. I haven’t quite been able to figure out what they teach or do there, but they do have a kind of mission statement.

Culture in its essence is viewed here as ways of loving together.

Odisha has a unique distinction of acting as a confluence of diverse faiths by striking harmony amongst religious faiths from animism, fetishism, shamanism, ancestore worship to highly evolved froms of religions like Brahminism, Jainism, Buddhism, Islam, Chiristianity and Mahima Dharma.

Vaishnavism, Saivism, Saivism, Sakta , Ganapatya, Sour-all forms of Brahminic worship are conceived in the wonderful matrix of the great and grand cult of jagannath that embraces in its grandeur quintessences of different religions signifying world-view. The Oriya literature contained this world-view in its essence;

“Let my lie rot in hell”
But be the world saved’’ –(Bhima Bhoi)

These lines of the saint poet Bhima Bhoi express sentiments of self-sacrifice and selflessness for the well-being of the world at large. Through centuries, the state retained its cultural identity within the mainstream of pan-India culture. Odisha is a land of rich and diverse artistic achievements. Its ageless art and flourishing cultural are the products of a long historical process.Spiritual, philosophical, professional and human dimensions are merged into the process to yield finest efforts of cultural life. Against this background, Odisha Justifiable pioneered the establishment of the first ever University of culture of the country.

Well, alrighty then! They teach word salad and oogley-boogley piety. Ramachandran certainly is a fine product of his education.

Is it a Godwin if it’s accurate?

Yet another Republican has once again argued that the trauma of rape makes women infertile: Trent Franks of Arizona claimed “the incidence of rape resulting in pregnancy are [sic] very low.” He’s just one more in a long line of thugs spouting pseudoscientific lies.

“In the aftermath of Akin’s statement, the St. Louis Post-Dispatch reported on a 1972 essay by an obstetrician named Fred Mecklenburg, who cited a Nazi experiment in which women were told they were on their way to die in the gas chambers—and then were allowed to live, so that doctors could check whether they would still ovulate. Since few did, Mecklenburg claimed that women exposed to the emotional trauma of rape wouldn’t be able to become pregnant, either. (He also argued that rapists are infertile because they masturbate a lot.) The essay was published in a book financed by A.U.L.”

A.U.L. is Americans United for Life, a pro-life advocacy group with increasing clout because of its success in drafting model state laws to restrict abortion. The line from the Nazis to Mecklenberg to Akin and Frank runs through Jack Wilke, a doctor who is the former head of the National Right to Life Committee. He said, "What is certainly one of the most important reasons why a rape victim rarely gets pregnant, and that’s physical trauma." And he stuck with this when the Los Angeles Times called to ask him about Akin last year. When I asked A.U.L. head Charmaine Yoest about the claim that rape rarely results in pregnancy, she was smarter and called it “a distraction.” Abortion opponents sure do keep bringing it up, though.

Right, the “argument from hideously unethical evil Nazi experiment” is just what I’d expect Republicans to do.

They always surprise you

Creationists most powerful weapon is their ability to catch you off guard with their unbelievably stupid answers to questions, and here’s a beautiful example. Someone tries to get creationists to explain how they reconcile deep space with a young earth.

I would like to discuss what appears to be a major body of evidence against young earth creationism – astrophysics.

The distances to a large number of astronomical objects have been measured by a variety of methods. Astrophysicists consider the distances to galaxies to be of the order of millions of light years, and the majority of stars within the Milky Way to be up to 100,000 light years away. If this were true, and given the invariance of the speed of light, clearly YEC is false (irrespective of the status of evolution).

Just as one example, a cepheid variable star in the galaxy M81 was observed by the Hubble telescope and measured at about 11 million light years away. See here: http://outreach.atnf…e_cepheids.html

So what is the YEC position in regard to this. Is it:

a ) The speed of light is not invariant, or

b ) All of the objects observed by astronomers, from stars to galaxies to quasars, do in fact exist within 6000 light years of Earth?

I read that, and thought, I know! I know! It’s c) they’re distant, but the light was created en route! I’m so smart.

And so wrong. Surprise! Here’s the answer one creationist gave.

If it takes 11 million years to travel to earth, how can i see it now? I’m only 20.

If it takes 11 million years to travel to earth then the viewer would need to be 11 million years old.

Aaaaaand…we’re done here. I’m gonna go close my eyes and rest a bit.