Quack of the week

The quack of the week winner is Jim Rutz, who is the spokesman for the worldwide house church community, founder of the open church ministries and author of such illustrious books as "The Meaning of Life". He recently earned his quack badge by writing a series of articles against soy and how it is making kids gay. I am not kidding : "Research is now showing that when you feed your baby soy formula, you're giving him or her the equivalent of five birth control pills a day. A baby's endocrine system just can't cope with that kind of massive assault, so some damage is inevitable. At the extreme, the damage can be fatal."

Unfortunately he doesn't quote the source, because I'd like to know where they found that soy can be fatal o infants. In fact the most recent research about soy and post-natal sexual development in the journal of Toxicology Science states that "There were no effects in females dosed with 4 mg/kg genistein, the predicted exposure level for infants drinking soy-based infant formulas. There were no consistent effects on male offspring at either dose level of genistein."

So I have a hard time figuring out how Jim came to the conclusion that: "Homosexuals often argue that their homosexuality is inborn because "I can't remember a time when I wasn't homosexual." No, homosexuality is always deviant. But now many of them can truthfully say that they can't remember a time when excess estrogen wasn't influencing them."

Yes Jim that's what's wrong with America: Tofu. Goddam liberals and their phytoestrogens...

Bayblab podcast Episode8

Episode 8 is now available (rss on the right)! It's a special podcast live from space with Stephen Hawking, as we discuss how you can make sperm cells from bone marrow, how plasma gasification may be useful for waste disposal, we expose a cancer quack and much more...Special thanks to Jaime Corinaldi for his most excellent music. MC Hawking better beware of this new scientist on the block. And a guest star appearance by Leigh Miller!

This may be the best one so far, lets see what the critics have to say: "The bayblab is so much better [than Science Friday]. It even has Stephen Hawking. All Ira Flatow can claim is that he’s interrupted people who are talking about Stephen Hawking." Ben Ferguson

1010 by 2010

That's 10¹⁰ base pairs of DNA sequenced or synthesized by one person in a single day. That's a hell of a lot. More than enough to cover the whole human genome several times. And that's just one person. Imagine how much a factory full of monkey could do. If you think this sounds ridiculous, read the rationale for the prediction in this great article. As shown below, the projection is based on the current exponential growth of biotechnology, mimicking the trend known as Moore's law, where the number of transistors that can be fit on a microchip has been growing exponentially for the last 50-60 years. The article makes some interesting comparisons between the two industries and also features some of the best discussion I've read on the future of biotechnology and its place in society.

License the Technology Before You Play With Your Cat, Travel at Lightspeed

That's right. If you've ever teased your cat with a laser pointer or traveled across galaxies for money, you may just get sued.

Govern yourself accordingly.

Method of exercising a cat

US Patent Issued on August 22, 1995
No. 144473 filed on 1993-11-02

Abstract

A method for inducing cats to exercise consists of directing a beam of invisible light produced by a hand-held laser apparatus onto the floor or wall or other opaque surface in the vicinity of the cat, then moving the laser so as to cause the bright pattern of light to move in an irregular way fascinating to cats, and to any other animal with a chase instinct.

Of course that's not nearly as ridiculous as the anti-gravity spaceship patent:

United States Patent	6,960,975
Volfson	November 1, 2005

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Space vehicle propelled by the pressure of inflationary vacuum state

Abstract

A space vehicle propelled by the pressure of inflationary vacuum state is provided comprising a hollow superconductive shield, an inner shield, a power source, a support structure, upper and lower means for generating an electromagnetic field, and a flux modulation controller. A cooled hollow superconductive shield is energized by an electromagnetic field resulting in the quantized vortices of lattice ions projecting a gravitomagnetic field that forms a spacetime curvature anomaly outside the space vehicle. The spacetime curvature imbalance, the spacetime curvature being the same as gravity, provides for the space vehicle's propulsion. The space vehicle, surrounded by the spacetime anomaly, may move at a speed approaching the light-speed characteristic for the modified locale.

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Inventors:	Volfson; Boris (Huntington, IN)
Appl. No.:	11/079,670
Filed:	March 14, 2005

Two Cool Resources

Doing some surfing, I came across some pretty neat resources. For armchair astronomers, the first is WikiSky, a sort of Google Earth of the heavens. Overlay constellations, find and view photos of celestial objects or just see what stars are overhead right now.

The second is the Encyclopedia of Life. This site aims to be a wikipedia of known species, including photos, maps and including links to journal articles and published genomes. This 'interactive zoo' will have different layers of access from 'novice' to 'expert' featuring more detailed species information. The site isn't up and running yet, but the demo pages (like those linked above) look pretty slick. Read more about it over at Wired magazine.

Placentophagy

Most mammals will eat the placenta after giving birth, in part to hide it from predators that might smell it, and in part to get nourishment. A few mammals do not, including camels and marsupials which simply reabsorb their primitive placenta. Recently it has become almost trendy for women to eat their placenta after giving birth, with some going to great lengths and even suing hospitals in order to bring the meal home with them. Now I understand wanting to have a "natural" birth, but this crosses the line. However if this is your thing, you can find some recipes here, and here, including placenta lasagna, placenta cocktail or roasted placenta. The royal college of obstetrician has already stated that mother do not need to eat their placenta for proper nutrition in our society, so why do people do it? It seems there is a belief that hormones within the placenta such as progesterone, prostaglandins and endogenous opoids might help with post-partum depression and birth pains and production of milk. While there are probably some hormones crossing the intestinal barrier, I doubt one dose will do much for post-partum depression. And preserving it to eat a little everyday will probably deliver doses too small. Wouldn't you get sick of eating the same thing everyday? Dogs eat their placenta after they give birth too. They also eat their own shit. Clearly, "natural" is not always the way to go. And why stop at the placenta, my mice and rats occasionally eat the babies too, if only I could find recipes...

Glow in the dark terrorists

A recent paper in Nature Chemical Biology (arm and leg subscription required) describes a engineered yeast strain engineered to sniff out TNT. First they had to clone many G protein signalling components into a yeast strain such that mammalian olfactory receptor signalling functioned. Then they screened a library of cDNAs from olfactory receptors to obtain a rat olfactory receptor that responds to TNT. This signaling pathway then initiated the expression of green fluorescent protein, thus the yeast glowed green when in the presence of trace amounts of TNT and an awesome biosensor is born. Great work from Dr. Danny Dhanasekaran at Temple University School of Medicine.

I've got kallikreins on the mind

Thanks to some %^&#@ journal editor, I find myself having to update the introduction of a paper on kallikreins. To my surprise, it seems that one of the member of that superfamily (made famous by PSA or kallikrein 3), is neuropsin. Type II Neuropsin seems to have evolved quite recently (5 MY) and is expressed in the frontal lobe of humans and not of other great apes. It may have functions in learning and memory, and it is already speculated that if reintroduced in chimps, they may become indistinguishable from Kamel.

If you are wondering about the artwork above it's anal bum cover : "Nietzsche's Monkey": You haven't heard anything that sounds quite like this. Graduate students in Rhetoric, Critical Theory, and Post-modernist studies will be glad to know someone is finally writing music for them."

Embryonic Stem Cells (tm) by Invitrogen

Caught a great talk today at the OHRI by visiting speaker Mahendra S. Rao, who is probably the world's leading scientist in embryonic/neural stem cell therapies. The talk featured an overwhelmingly impressive wealth of data on neural stem cell biology, particularly pertaining to transplant studies. Most of this work was done in his former capacity as head of the NIH's stem cell program.

What was most interesting about the talk was the work Rao is now leading as VP Stem Cell research at Invitrogen Corp (in the more ES-cell research friendly state of California). He recently took up this post after leaving the NIH as a result of their decision to abandon ES cell research in light of the Bush administration's strong anti ES cell research policies. From what he presented of his new project at Invitrogen, it's obvious they are now about to kick some serious ass in the arena of clinical therapeutic development. They've got GMP-friendly, FDA-approved and production-scalable technologies and ES cell lines ready to go. Couple with that Invitrogen's recent moves that has established the company as the leader in gene expression and cell culture technologies, and what you have is imminent domination of the biological therapies scene. Looks like one of the first applications they will go after is Parkinson's disease, using ES-derived neurons to replenish dopamine producers in the substantia nigra.

Interestingly, while transplanted ES-derived neurons are suitable for applications such as Parkinson's as they can survive long-term in recipient's brain, Rao mentioned that their potential in other regenerative therapies is limited by the fact that we do not yet know how to make the transplanted cells properly integrate into existing neuronal circuitry. Strong impetus for a lot of interesting research in probing neural connectivity...

Roadless

This morning on my bicycle commute I was listening to the Science magazine podcast which is no bayblab podcast but it's good enough for commuting. On the latest episode I was informed that there is no place in the lower 48 states of the United States where you can get more than 35km from a road. Thirty-five kilometers away from civilization is isolated but I still found that stat pretty shocking. The above map shows the 'roadless volume' of areas in the united states. I ganked it from the origonal article in Science magazine (high priced subscription required). 'Roadless volume' meaning area times the distance from a road such that a city block would look like a pyramid with the point being in the center since it is the furthest from the roads. I wonder what this data looks like for a country like canada with large uninhabited areas. There is also a video in the supplymentary material but it's quicktime so I can't get it to work. I have to say that the United States does an excellent job with their parks, (they are large and well managed) and there is actually an effort to preserve roadless area in the US.

Tooth Specialization

A summer student in our lab mentioned that in a course she learned that lemurs have specialized teeth for grooming. I searched for other examples of teeth evolved for something other than gripping and breaking down food, and the most obvious was snake fangs, a great example of evolution. It seems like the hollow syringe like fangs of venomous snakes evolved from grooved fangs that delivered less venomous poisons.

Tiny 10$ PCR machine

This very cool piece of gadgetry made by a grad student at Texas A&M University uses microfluidics, to channel the PCR reaction around tubes which are heated by small metal rods. No pumping required since convection keeps things flowing, and it's all done in 20mins! Truly remarkable for 10$ worth of spare parts. Here is a do it at home version of the project.

Great quotes from Stephen J Gould

I found this great unofficial site for Stephen J Gould which has some great quotes from the evolutionary master:

"Skepticism or debunking often receives the bad rap reserved for activities—like garbage disposal—that absolutely must be done for a safe and sane life, but seem either unglamorous or unworthy of overt celebration. Yet the activity has a noble tradition, from the Greek coinage of ‘skeptic’ (a word meaning ‘thoughtful’) to Carl Sagan's last book, The Demon-Haunted World. […] Skepticism is the agent of reason against organized irrationalism—and is therefore one of the keys to human social and civic decency. […] Skepticism's bad rap arises from the impression that, however necessary the activity, it can only be regarded as a negative removal of false claims. Not so […]. Proper debunking is done in the interest of an alternate model of explanation, not as a nihilistic exercise. The alternate model is rationality itself, tied to moral decency—the most powerful joint instrument for good that our planet has ever known."

It also has the famous passage of Karl Popper's "conjectures and refutations" which deals with science as falsification, which I had been hunting for a while...

Finally, a Digg for Real Scientists

I got a email today inviting me to try out DiscoveR8, a site that is now in beta testing. For those who know Digg, it's basically that but for peer-reviewed scientific papers. For those who have been hiding under a rock for the last year or so and don't know Digg, the concept is that anyone and everyone can submit their own papers or other papers they'd like to share with others who frequent the website. Anyone who comes across your post then clicks the button next to the story to give it the thumbs down or thumbs up and comments for discussion can also be posted. Based on user voting the website keeps track of the most popular papers. How long until your Discover8 ranking is more important than impact factor?

Glycolysis: cancer and heart attacks

Recently Gino talked about an interesting concept at journal club: the Warburg effect. "Because ATP generation through glycolysis is less efficient than through mitochondrial respiration, how cancer cells with this metabolic disadvantage can survive the competition with other cells and eventually develop drug resistance is a long-standing paradox.". This in turn means that hypoxic cells running on glycolysis are more resistant to cytotoxic treatment because of a faulty apoptotic pathway. This effect, surprisingly, may not be limited to cancer cells. Imagine the case of a heart attack. The whole body becomes hypoxic and irreversible damage occurs in the heart and brain tissues. Well it may not be quite so simple. Apparently, researchers were stunned to discover that in fact the cells in the heart shut down and switched to glycolysis but did not die until a few hours had passed. But when we try to resuscitate patients, the sudden influx of oxygen causes a violent switch from glycolysis to the aerobic citric acid cycle, which triggers apoptosis. And so maybe if we could bring oxygen slowly back up we could rescue the heart cells. Alternatively, maybe if we violently brought oxygen to high levels in the tumour we could trigger apoptosis, if their aerobic components are not already defective...

Corkscrew Penis

I was expecting anonymous to post this since the majority of posts in the penis field are from him but since he hasn't I found this interesting summary of evolution of duck mating equipment. It seems as females in a promiscuous species tend to have equipment that gives them some ability to select successful matings. And the males in these promiscuous species have some pretty lengthy equipment.

Sunscreen and Coral Reefs

Recently I snorkeled some coral reefs off the coast of the Yucatan peninsula in Mexico and was surprised to be informed that I should not be using sunblock while doing so. Obviously coral reef preservation is an important concern and I had read that a changing climate is altering the symbiosis in coral reefs and has resulted in coral bleaching, however I was completely unaware that sunscreen (ie blocking my vitamin D production) had an environmental impact. Seriously disappointingly I can't find anything on the internet about sunscreen effects on coral reefs other than claims specifically made by diving/snorkeling sites off the coast of the Yucatan. Also the majority of information on biodegradable sunscreen is from tourist directed websites and forums about Cancun and the Yucatan peninsula. Certainly with something as apparently delicate as coral reefs it is probably best to be cautious but where is the science on this issue? Sounds like a great research project full of sun and snorkeling. Interestingly there is some research on deriving sunscreens from compounds found in coral reefs.
I'm definitely waiting on Melanotan. However because of it's biological activity it might be even more harmful to reef life.

The internets are metaphorically burninating

I don't really like to post about technology here, because our main purpose is science news for grad students, but in case you live under a rock, the internet has officially gone batshit. The encryption key of HD-DVD has been cracked and is on every major news site on the internet, which is a series of tubes in case you didn't know. Digg's front page is littered with that random hexadecimal number. The pages are being pulled down one by one by Digg, google, blogger, you name it, under orders of the MPAA. Can you own a random number? Is it a trademark or a copyrighted creation? Slashdot is making fun of digg, which is hemorrhaging nerd cred by the minute... oh yeah and the key can be found in this genotyping database of age-related eye disease conducted by the National Eye Institute. THINK OF THE BLIND PEOPLE!

Gene therapy in the eye

Finally, after much success in dogs and mice, the use of adenovirus delivery of genes (RPE65) to correct vision problems is becoming a reality in patients. And so far it looks good. I see this as a major step forward in the visionary method of gene therapy, with foresight. There are many advantages to this method of trans-retinal injection, since the eye is immune privileged, and easy to monitor by peering into it.

How will you celebrate your graduation?

At the University of Ottawa, newly minted masters and PhD get to drink a free beer from the mug of knowledge at Nostalgica, the grad pub. In San Francisco they skinny dip in a muddy pond? how do they celebrate in your establishment? Not that we're ever going to graduate and have a real job...