Cutting-edge science and long-pondered questions explained in plain English. Bad science gutted. Great science extolled.

Monday, March 31, 2008

Race-Specific Cancer Gene (Sort Of)

Using population genetics methods, scientists have found an allele (a form of a gene, due to mutation) that increases the odds for colon cancer by 10% if a person is of European ancestry (specifically Scottish ancestry) but not Japanese ancestry.

Interestingly, this allelic variation is not in the coding region of the gene but in the non-coding region, suggesting that it is a regulatory sequence that can increase or decrease the expression of a protein.

The increase is seen only for colon cancer and not for rectal cancer.

The scientists did not rule out diet or lifestyle factors as the reason for the difference in the effect of the gene.
For example, it is possible that Gene + haggis + scotch = colon cancer, while Gene + sushi + fugu does not.

Sunday, March 30, 2008

Quotable Scientists: Henry Fairfield Osborn

"Evolution is the most firmly established truth in the natural universe."
--Henry Fairfiel Osborn, American paleontologist, (1857-1935)

Ring My Bell: Solar Flares Produce Oscillations

Solar flares cause recoil in the sun (like the recoil from shooting a gun,) that cause oscillations within the sun. Like a bell, the whole sun "rings" at various frequencies.
This finding could help us understand the physics of our sun and other stars.

Saturday, March 29, 2008

Science and Religion: The Missing Link

Science education is not designed to destroy religious faith. Science is a different subject than religion. Science is concerned with the natural world and universe, not the supernatural or theological. Most scientists will deny that science destroys faith in a Deity or Deities.

However, the study of science introduces people to ideas that are at odds with what religious organizations promulgate as true. This occurs most often when religion intrudes into the domain of science and not vice versa. When religion states that it has the answers to scientific questions, such as when the Bible states that the Earth is flat (All quotes, KJV: Daniel 4:10-11, Matthew 4:8) and immobile (Examples: I Chronicles 16:30, Psalm 93:1,) science disproves these hypotheses by definitively showing that the Earth is neither flat nor immobile.

Thus, science contradicts many edicts of religion when religion ventures out of its territory.
Science truly undermines religious faith, however, because it teaches people to think. Science teaches people to search for testable, real-world answers to problems and questions rather than rely on superstition, magical thinking, or laziness.

When asked, "Why is the sky blue?" a person of faith can only answer that God decrees it or formulate an inaccurate scientific answer. A person with some science background understands water vapor in the air refracts incoming sunlight toward the blue end of the visible light spectrum. Scientific endeavors, such as rockets and telescopes, have shown that there is no solid firmament above the Earth, as the Bible states.

When asked, "Why did I get sick?" a person of faith can only answer that God willed it, while a microbiologist could isolate the bacteria or virus that caused the infection and provide antibiotics or antivirals to eliminate the infection.

At a magic show, a person who relies on faith to explain the world can only marvel at the wonders. A person with a scientific background notes the smoke and mirrors and the rabbit under the podium, noting that the hat must have a removable panel.

When confronted with horrors in the world, a person of faith can only say that God willed it, perhaps to give Christians something to do. They might pray for God to provide food for the starving. A scientist, however, creates fertilizers, dams, or new strains of drought-resistant crops.

Science teaches people to think of logical, physical causes for events. This makes people less gullible.

By making people less gullible and intellectually lazy, yes indeed, science undermines religious faith.

TK Kenyon, Author of RABID and CALLOUS: Two novels about science and religion, with some sex and murder.

Friday, March 28, 2008

A Psychopharmamusical!

And you thought Hair had a lot of drug references.

Genetic Link to Autoimmune Diseases Type 1 Diabetes and Sjogren's: Hox11 gene

This fascinating paper from the Faustman lab at Harvard links a developmental gene, Hox11, to the later development of the autoimmune diseases Type 1 Diabetes and Sjogren's syndrome.

Also important, it links the hearing loss often seen in Type 1 diabetes directly to the Hox11 gene malfunction, not the later autoimmune attack.

This paper suggests that treatment of Hox11 deficiency in people with mutations could prevent Type 1 diabetes, Sjorgren's syndrome, and hearing loss.

Figure from the paper showing deterioration of the ear in Hox11 genetically modified mice:

Comparison of NOD and C57BL/6 cochlear structures. (a) A schematic area of interest in the cochlea. (b–g) Histological cross-sections of the mouse cochlea were processed and cochlear structures were compared between NOD and C57BL/6 animals at 5–8 weeks of age. Structural abnormalities were found in the spiral ganglion, spiral ligament and organ of Corti in the NOD mice. (b and c) The spiral ganglion cells of the NOD mouse were greatly deteriorated (arrow, b), relative to the C57BL/6 control (arrow, c), with only the Schwann cell nuclei remaining. (d and e) There was also atrophy of the spiral ligament, as seen by the loss of cells in the NOD specimen (arrow, d), which is in sharp contrast to the fully populated spiral ligament in the control (arrow, e). (f and g) The organ of Corti of the NOD specimen appeared to be deteriorated and to have many fewer cells (arrow, f), including hair cells, compared to the control (arrow, g). Defects similar to those observed in the NOD cochlea were present in the NOD-SCID cochlea as well.

Thursday, March 27, 2008

Instant Nanotech Test for Mad Cow Prions

Researchers at Cornell University have developed a nanatechnology platform to detect prions at low concentrations that, hopefully and soon, will be used to detect Mad Cow Disease prions in blood -- instantly.

That's right. Instantly.

Mad Cow disease prions are responsible for the transmission of bovine spongiform enchelalopathy to humans, causing new variant Creutzfeld-Jakob disease (nvCJD,) an incurable neurodegenerative disease, much like Alzheimer's plus Parkinson's, but kills people in just a couple years.

Right now, the "gold standard" of prion detection is to remove brain matter from an animal that is suspected to be infected (and is dead), inject that into another animal, wait for a long time, then kill the other animal and necropsy its brain. This can take years and (get this) only detects the prion infection 31% of the time.

That's a terrible assay.

The new nanotech assay technique developed by Harold Craighead and company use a "tuning fork" technique. A nano-sized tuning folk is coated with antibodies against the abnormal conformation of the prion protein.

For many other assays, the added weight of the antigen (in this case, the prion) would be enough to change the pitch of the nano-tuning fork when a vibration in the assay liquid sets the fork vibrating. However, because prions are so light, this doesn't work. The researchers used secondary antibodies and metal conjugates to increase the weight of the prions, thus the added weight changed the pitch of the vibrating fork by a detectable amount.

This assay would be invaluable to eliminate prion-infected cows from getting into our food chain, which caused the outbreak of new variant Creuzfeld-Jakob Disease in England a decade ago.

This assay could also test biomedical stocks, such as human growth hormone obtained from human cadavers (yep! that's where it comes from.) for nvCJD prions. Several doctors in France were just indicted for involuntary homicide for not being vigilant enough concerning cadaver HGH and thus infecting over 100 French children with nvCJD.

It's especially a concern when slaughterhouses are unscrupulous about slaughtering and processing "downer" cows, which are sick and possibly infected with mad cow prions.


Tuesday, March 25, 2008

Best Scientific Images of the Year II

Wellcome has awarded their prizes for best scientific images of the year, and they are pretty.

This micrograph, taken with a laser scanning confocal microscope (see post below,) is a picture of colon cancer cells. The fluors used are not labelled, but I shall make some educated guesses.

Blue here is a nuclear stain, meaning that it stains DNA in the nucleus of the cell, such as DAPI or BOBO.

The green fluor is a cytoskeleton stain. The cytoskeleton component stained here appears to be filamentous actin, because I see some stress fibers through the cells. The stain is probably phalloidin (a toxin from death cap mushrooms) conjugated to a fluor.

The red color is more ambiguous. It seems to colocalize with the cytoskeleton in some cells (red + green = yellow) but is more diffused and cytoplasmic in others. Could be an actin binding-protein or another component of the cytoskeleton.


Best Science Photos of the Year

Wellcome has named its best scientific images of the year, and several are from my own favorite microscope, a laser scanning confocal. Personally, I like Zeiss. Zeiss is nice.

This is a micrograph of an HIV virus. (This image is not from a laser scanning confocal microscope. Viruses are too small to be seen with a LSM. You need an electron microscope to see viruses, let alone viral structures.)

The core in the middle is the RNA chromosome and associated core proteins. The blue half-shell is the viral capsid. The yellow proteins are the ride-along gooey things called the tegument.


Monday, March 24, 2008

White Whale (Shark): Not Quite Moby Dick, But Big and White and Fishy

This albino whale shark was spotted off the Galapagoes. Nifty video.
Expelled! Again!: "Framing Science" People Pandering to Opiated Masses


First, PZ Myers, noted and eminent science blogger and professor, was not admitted to a pre-screening of the film Expelled!, an ID drive-by documentary on evolution, and blogged about how he was thrown out at the whim of the producers. (Previous post: here.)

Myers's guest, Richard Dawkins, was admitted without fuss (as the producers probably did not recognize him, and when asked to show identification, he produced his British passport under his legal name, "Clinton Richard Dawkins.")

It must be noted that both Myers and Dawkins appear in the film Expelled!, for which they were interviewed under false pretenses, and the piecemeal editing of their interviews was journalistically unethical.


After some brouhaha, Matthew Nesbit, a professor of communications, blogged:
"As long as Dawkins and PZ continue to be the representative voices from the pro-science side in this debate, it is really bad for those of us who care about promoting public trust in science and science education. Dawkins and PZ need to lay low as Expelled hits theaters. Let others play the role of communicator, most importantly the National Center for Science Education, AAAS, the National Academies or scientists such as Francis Ayala or Ken Miller. When called up by reporters or asked to comment, Dawkins and PZ should refer journalists to these organizations and individuals."
At the risk here of being arch, isn't "communications" what people who flunk out of business major in?

More to the point, Nesbit is utterly wrong. He compares the evolution vs. ID debate to politics, comparing Myers and Dawkins to, "Samantha Power, Geraldine Ferraro and so many other political operatives who through misstatements and polarizing rhetoric have ended up being liabilities to the causes and campaigns that they support."

This comparison is a fallacy.

Science is not politics, which is convincing a majority of the people that your political theory is the correct one to vote for on the day of elections in the majority of the voting districts. Politics seeks to create consensus.

Science is the truth. Myers and Dawkins should not be compared to Power and Ferraro, but to Galileo, Darwin, and Copernicus. No matter what the ID guys believe, they're wrong. Convincing more people that creationism is valid will not make it less wrong. Religionists' balking at evolution is just another example of irrational, superstitious flailing.

Nesbit's whole philosophy, "Framing Science," in which mostly non-scientists try to reconcile science with religion, which are several systems of contradictory and unsubstantiated beliefs, is a waste of time.

Yes, we should try to break it gently to religionists that they've been utterly wrong all these years, but eventually, the obvious truth of science will prevail. It's only a matter of time, another scientific concept.

I admit, when I saw Nesbit's blog and its title, "Framing Science," I thought it was a provocative anti-science blog, like when the cops "frame" someone for a crime. Perhaps that wasn't the best moniker for their movement. You would think that a communications major might have thought of that.

Another non-scientist "framing" guy, Chris Mooney, blogged that the PZ Myers controversy is giving the film loads of free publicty, is thus counter-productive, and also suggested that Myers should refrain from more discussion.


Nesbit's post led PZ Myers to this sputtering reply, which is perhaps less eloquent than his usual posts but heartfelt, in which he said in part, "Fuck you very much, Matt. You know where you can stick your advice."

Again, scientists are not politicians, who strive to form consensus or convince voters, or religionists, who seek to silence the opposing viewpoint.

People should go see that film and laugh at it for the dreck it is. The public should understand that Dawkins and Myers were interviewed under false presenses (the film makers told them it was a documentary about science and education, not a religion drive-by of evolution,) and with shoddy journalistic ethics (including the old trick of setting the camera and the interviewer at 90 degrees to each other, and thus the subject looks back and forth between the camera and the interviewer, producing a "shify-eyed" effect that is associated with lying or unreliability.)

Scientists seek the truth, and when we find it, we tell other people the truth. If there are contrary opinions, we debate the evidence and logically decide whose model is more accurate.

That's the problem with non-scientists like Mooney and Nesbit. They're operating in the rhelm of opinion, not truth. They're seeking to sway people with propaganda, not evidence and logic. They're using the enemy's faulty weapons against the enemy, who designed them, have the blueprints, and know where the weak points are.

Evolution is model with huge amounts of scientific evidence backing it up.

Sure, all models are wrong, but some models are useful.

Evolution is a useful model. It explains the past and, contrary to what ID guys will tell you, it accurately predicts future results.

ID and creationism in general do not accurately predict future results, except perhaps that creationists lie to themselves and others and will continue to do so.

Mooney and Nesbit are in the wrong on this issue.

Myers and Dawkins should not shut up.

Scientists tell the truth. Politicians and religionists seek create consensus or to silence the opposition. Pandering to their illogical and ignorant views will only endow them with a false sense of superiority, to go along with their false view of the universe and their false beliefs.

To PZ Myers and Richard Dawkins: Once more into the breach!

TK Kenyon

Friday, March 21, 2008

Your genes might be selfish, but your brain isn't.

Social psychologist Elizabeth Dunn of the University of British Columbia (UBC) in Vancouver, Canada, performed a series of studies on, admittedly, small groups to determine what contributes more to happiness: giving money away or spending it on yourself. She gave people money, told them to either donate it or splurge with it, and then quantified happiness levels.

In the spirit of Christmas cheer (even though this is Easter weekend,) either donating the money to charity or buying a gift for others produced more happiness than keeping it or spending it on oneself.

This empirically tested and quantified altruism is a lovely addition to the study of ethics. The studies should be replicated with larger sample sizes, but they are worth reading.

TK Kenyon

Thursday, March 20, 2008

Creationist Movie Doesn't Have A Clue

At the new creationist movie called Expelled, eminent science blogger PZ Myers was waiting to get in for a screening.

A cop pulled him out of line and told him that he couldn't go in and that he had to leave the premises immediately, or he would be arrested.

But wait! There's more. There's so much more. I laughed so hard that I had an asthma attack. A bad one. And then I read it again.

Read THE REST OF THE STORY at Pharyngula.

Oh, man, I wish I had been there.

TK Kenyon

Wednesday, March 19, 2008

If we have learned one thing from the history of invention and discovery, it is that, in the long run - and often in the short one - the most daring prophecies seem laughably conservative.

--Arthur C. Clarke (1917-2008), The Exploration of Space, 1951

Tuesday, March 18, 2008

Neuroethics: Not as rational as you think.

Marvelous new online, free, open-access journal that everyone should read: Neuroethics. The first issue includes an unflinching look at the field of neuroethics (as distinct from Bioethics,) and the way that the brain determines ethics and morality.

In the first issue, editor Dr. Neil Levy has written an elegent overview of the field, including a neuroethicist's view of the notorious Trolley Problem, namely, if a trolley is hurtling toward five people on a track, and you hold a lever that will change the track so that the trolley is shuttled onto a track where it kills only one person, should you pull the lever. Most ethicists and ordinary folks say "yes," for the greater welfare is at stake.

However, if the problem is changed subtly so that your choice is between allowing the trolley to crush the five people or pushing a large, beefy man onto the track to obstruct and stop the trolley, most ethicists and ordinary people will say no, that this violates the man's rights, and you should allow the trolley to slaughter the five people.

Neuroethicists have identified where the real problem is: the difference between these two scenarios is not merely “action,” as the Kantian folks dissemble, but emotion. We do not want to be actively responsible for the death of a human being, and a particular human being (the large, beefy man) at that.

The real problem is: since it is emotion that informs our ethical choices, ethical choices are not rational.

The journal also has a
lovely article on “The Popular New Genre of Neurosexism” by Dr. Cordelia Fine, comparing recent mommy-brain books to the painfully terrible science of the 1800’s, in which eminent scientists actually promulgated that women’s education should not be too rigorous because it would divert energy to their brains and away from their ovaries, rendering them sterile. (Testicles, apparently, had an independent energy source.)

This excellent new journal deserves bookmarking. Do it now to avoid the rush.

TK Kenyon

Author of RABID: A Novel and CALLOUS: A Novel, where neuroscience, morality, and murder intersect.

Monday, March 17, 2008

It's News To Me: We're Scientifically Illiterate

Despite the fact that science affects us each and every day, cable news channels spend almost no time examining and reporting science. On average, five hours of cable news coverage contains 71 minutes of politics, 26 minutes of crime, 12 minutes of disasters and 10 minutes of celebrities.

Science, technology, health and the environment received just six minutes of coverage (with health and health care accounting for half of that.)

IMHO, there are three reasons why science gets little coverage.

(1) "If it bleeds, it leads." Bad news is news. Science is rarely bad news. Most of the time, science leads to good news, like cures for diseases or an expansion of our knowledge of the universe. Science rarely leads to murder or mayhem (except at the International Herpesvirus Workshop, because we're wild folks, but I digress.)

(2) A lot of people don't understand science. You can blame this on the pitiful state of science education, but part of the problem is the "Two Cultures" mentality fostered by CP Snow, et al, (, and the fact that science itself is compartmentalized, fractionated, and vernacular.

I have a PhD in microbiology (virology,) and I like physics and a lot of other science, but I can't read an issue of Nature or Science cover-to-cover because most of the papers in there are too far out of my field for me to understand. Sometimes, I can get the jist, but I couldn't talk about it with any alacrity. ( .

(3) Lack of celebrities. I'm not going to merely bemoan our celebrity-driven culture, but people with influence drive the memes.

Yeah, lots of people worry about the environment and global warming, but Al Gore, already a big-timer, got the best-selling book.

Admiral Richard Hawkins noted in 1662 that oranges and lemons cured scurvy, but he wasn't a celebrity. Captain Cook, who was a celebrity explorer, was credited with discovering that limes prevented scurvy in 1775, over a hundred years later, and only then was the practice of taking citrus on voyages adopted by the British navy.

Maybe if we recruited better looking scientists....

TK Kenyon
Author of RABID and CALLOUS, two novels with good-looking scientists.
New Gluten-Free Blog -- Celiac Maniac!

For those of you who are gluten-free enough to care, I've started a new blog, because what the world needs is yet one more celiac blog. Celiac disease is an autoimmune condition associated with genetic factors, specific HLA alleles, and caused by an immune reaction to a peptide in the wheat (and wheat-like) protein gluten. The antibodies to gluten then cross-react with several proteins found in the digestive tract, causing damage to the jejunum section of the small intestine. Symptoms are many, varied, and non-specific.

It is, however, important to me to share the word of health.

TK Kenyon
Author of RABID: A Novel and CALLOUS: A Novel