My Clone Armies May Soon Be Manifest…..

Published last week in Nature, scientists have created mice solely from iPS cells. In normal person speak, this means that cells taken from adult tissue (skin cells), treated to become stem cells, were then coaxed into becoming embryos, and then grew into entire mice. Entire fraking mice. Meet Tiny.

The scientific implications are huge. This shows that an entire organism can be grown from adult cells, which means that mature tissue could give rise to an entire new organism.

This method doesn’t require the egg cell which was needed for Dolly to be successfully cloned. If an entire organism can be grown from iPS (induced pluripotent stem) cells, then the tedious manipulation involved in the cloning process might be avoided, with the same results.

Like Dolly, the new organism, genetically identical to its source, carries no threat of transplant rejection should one be required from the new organism. On an unrelated note, have you seen the film The Island?

The ethical implications of this research are also pretty big. I’ll leave it as an exercise to the reader to look into all the different dystopias that could result. My favourite goes something like this:

My dreams of world domination may become reality in the foreseeable future. However, if the whole human cloning thing never pans out (i.e. the “bioethicists” get their say) then maybe just I’ll make do with legions of mouse-clone warriors. I mean, look just how terrifying they are:

 Fear Me!
 

See:

Wired Science: Living, Breeding Mice Grown From Skin Cells
Scientific American: Meet "Tiny," a mouse grown from induced stem cells
And the actual article at Nature: iPS cells produce viable mice through tetraploid complementation

We knew it was only a matter of time before they turned on their masters

The robot apocalypse may soon be upon us.

The robots, they have rendered their opinion on humans, and they say that we’re delicious.

Robot Identifies Human Flesh as Bacon

A prototype robot, used to analyze foods  and drink using light-based (spectrographic) methods, said that the hand of a subject tasted just like bacon. It doesn’t take a brain surgeon to recognize that this is grim news for the entire human race. Once the masters, we soon shall be prey.

So keep your head up, or this may be the last thing you see.

Image credit: Paul Burnett - www.paulburnettphotography.com

Blue Rats and Gatorade Shenanigans

A cool bit of research published Monday in PNAS showed that rats injected intravenously with a blue dye shortly after spinal cord injury appear to fully recover function after healing, while without it, they remain paralyzed. The photogenic side effect is, one might imagine, becoming a Smurf.

Cool, interesting research. Hopefully it pans out.

From Wired Science, Blue Food Dye Treats Spine Injury in Rats:

“We just had proof of principle,” Nedergaard [the researcher]said. “We didn’t have anything we could give to patients.” Then, while searching for chemicals with structures similar to the P2X7 receptor, the scientists came across FD&C blue dye No. 1, completely non-toxic and approved by the FDA in 1928.

Cool, but hold on. From the telegraph, under the vastly overstating headline Blue M&Ms 'mend spinal injuries':

The compound Brilliant Blue G blocks a chemical that kills healthy spinal cord cells around the damaged area - an event that often causes more irreversible damage than the original injury.

There’s one slight problem here. FD&C blue dye No. 1 and Brilliant Blue G are not the same chemical. They’re similar, to be sure, but a simple Wikipedia search shows that Blue No. 1 and BBG are not the same. Maybe I’m nitpicking. Maybe I’m not.

I know the desire to say that Gatorade and M&Ms cure disease is tempting. I know that saying that sort of thing is bound to draw in readers, and a slight omission seems prudent, but when CNN writes (title: Same blue dye in M&Ms linked to reducing spine injury):

The same blue food dye found in M&Ms and Gatorade could be used to reduce damage caused by spine injuries, offering a better chance of recovery, according to new research.

I call foul. Lazy, lazy journalism. F minus. See me after class.

But perhaps “Compound that manages to ruin every biochemist’s favourite shirt has potential therapeutic application” just doesn’t sound as nice to the public.

 

See the article at PNAS: Systemic administration of an antagonist of the ATP-sensitive receptor P2X7 improves recovery after spinal cord injury
And previous work establishing the use of Coomassie Brilliant Blue G on the relevant receptor: Brilliant Blue G Selectively Blocks ATP-Gated Rat P2X7 Receptors

Here We Lament the Chemistry Sets of Olde…

An interesting take on the changing face of science education, Wired Science looks at the metamorphosis of toy chemistry sets of the past and compares to those found today. Check it out – Dangerous Science.

I had one of the more modern ones myself, and unfortunately it still sits, hardly used, in a closet. There certainly wasn’t anything that exploded (or indeed, very interesting) in that one. I sort of wish now that I could have been able to play with some old-fashioned sodium metal or nitric acid as a kid.

Read about it here: Endangered Species – The Chemistry Set
And here, with quotes by Nobel Laureates on their chemistry set experiences: The Chemistry Set Generation

Scientific Literature in Undergraduate Education

Larry Moran at Sandwalk asked a a few weeks back about how undergraduate education exposes students to scientific literature:

Exposing Undergraduates to the Scientific Literature

As a rough analogy, I liken the initial experience of learning of the scientific literature to landing in a foreign country and learning the language without guidance. One flounders around a lot, having difficulty with the simplest of tasks, and there’s a lot of exaggerated waving of hands involved. The process is tedious, frustrating, and difficult because there is not much help provided with regards to how to navigate the complex webwork of publications to find the information you need. And next thing you know you’re stuck in an Slovakian jail for reasons unknown. And your cellmate is starting to get just a little too friendly…

Anyway.

I’d say my own problems getting used to research in the literature stems from several places:

1. Newly published papers require a background of knowledge to understand that the initiate doesn’t have.

2. Old papers use obsolete methods, have hypotheses that may have been proven wrong, and use terminology that has been changed or discontinued. This is rarely ever corrected in the literature, one needs a background to know what to trust.

3. Licensing on papers makes finding information difficult as one can spend 10 minutes obtaining a paper just to discover it does not have the information needed.

4. Research takes time, and when deadlines loom, it becomes less and less reasonable to take the time and read through 10 papers to get the understanding needed. The focus often shifts to picking through and skimming for details, which doesn’t teach anything about proper research, and you’re left no better off.

When I consider the time I spent learning how to research (if you’re generous and assume that I actually can now), there aren’t many good memories. Much of my exposure comes from looking for specific facts in an obscure paper published in the 1960s. This sometimes comes as a result of being required to look up references that are obscure, just for the sake of reporting a technique that is widely accepted in practice today. I don’t know how many times I’ve referenced A rapid and sensitive method for the quantitation of microgram quantities of protein or Cleavage of structural proteins during the assembly of the head of bacteriophage T4.

It wasn’t until late in my undergrad when I really came to appreciate that the list of references on a paper are not just there to give credit, but more often to lead the readers to where previous information has been published, if desired. This basic idea of how the scientific publishing system works was never really introduced to me, and I went a long time before learning to properly follow the breadcrumbs to find the information I wanted.

So how might the process move more smoothly for undergrads in a course?

I’d say for beginners, a list of “classic” articles would go a long way to making things easier when looking for a reference on a technique or system. For a given project, a handout of some relevant papers could be provided. This would be pampering upper-year students, but certainly would help ease in new initiates.

To help get them familiar with the infrastructure and process of physically or digitally finding a paper, provide the information for the paper, but see that the students obtain the papers themselves (by, say, requiring method information from the paper). This would help ensure that students could learn to use respective web and library resources, hopefully before any real crunch time came down and the actual science had to be done.

In later classes, this list could be scaled back or removed, but in introductory science classes, this sort of help could be a useful way of easing into learning the system.

The problems with learning the literature are not just with learning to be a scientist and review papers, but largely just overcoming the technical, time-limited, and copyright-related drawbacks that come with the current system of publication. It is definitely not an easy system to jump into blindfolded, flailing around. Some basic guidance early on would go a long way.

Europe photo leftovers 2: Leipzig Völkerschlachtdenkmal

On my way across Germany last summer, I stopped for a night in Leipzig. On recommendation from coworkers I made a point of seeing the Leipzig Völkerschlachtdenkmal (roughly: memorial to the peoples’ battle). This monument (seen above, partially under restoration) is the largest monument in Europe, marking the place of Napoleon’s critical defeat at Leipzig. The monument was built to mark the 100th anniversary of the 1813 battle, which was a decisive turning point in European history.

 

Inside the memorial, immense statues line the walls  - see the people standing by the statue’s knee. I was primed (by a 6’8” guy, no less) that one truly feels tiny beside the immense titans seated in the memorial, but still found myself somewhat shocked by just how goddamn huge the statues were. Seriously - their sandaled big toes were fatter than my leg.

The monument, constructed in the German Empire under Kaiser Wilhelm II, garners mixed feelings in Germany. It stands as an emblem of German nationalism, and I think it’s an understatement to say that German nationalism was a pretty bad thing. Hitler was known to deliver speeches in front of the monument, hijacking the powerful imagery conveyed by the 91m concrete and granite monument. While it was erected to commemorate the liberation of German peoples from invading forces, and celebrate national unity, it was used as part of the Nazi propaganda machine. One might imagine, then, why the monument is a little controversial.

Off the radar on many tours of Europe, this made for an interesting stop in my trip. If there’s a take-home message to be had, it would be to definitely consult with any locals and find out what exists where you otherwise might just stay a night or pass right through. I can guarantee you’ll always find something interesting.

Copernicium

 
Picture snapped at Deutsches Museum in Munich

A few weeks back it was announced that one of the periodic table elements, Ununbium, (Uub in the table above)  is getting a name. Several heavy elements that are stable in theory remain placeholders with generic names until they can be shown to exist, i.e.. can be created in laboratory. In 1996, The Helmholtz Institute Centre for Heavy Ion Research produced the element, and now that results have been replicated by independent researchers, Ununbium has been christened Copernicium.

The group has decided to name the element in the tradition of naming new elements after famous scientists (see Einsteinium, Curium, Bohrium, Fermium). So once again it’s time to go out and buy a new periodic table to hang on the wall. You have one hanging over your bed too, right?

See: BBC News

Side note: I’m going to plug the trivia site Sporcle, which subtitles itself “mentally stimulating diversions”. Their periodic table quiz (already updated) is unequalled and has actually improved my knowledge of the elements. Extremely useful for times when I really need to know my Hafnium from my Iridium.

Moon Lander Spotted From Space

In the news I missed – then discovered two days later category, an image from the Lunar Reconnaissance Orbiter (LRO) showing the location of the Apollo 11 lander on the moon.

 Image from NASA/Goddard Space Flight Center/Arizona State University

The lander can be seen in the centre of the image, casting a shadow to the right. The sites of Apollo 14, 15, 16, and 17 have also been photographed, and 12 is planned in the next few weeks.

Will this convince those who think NASA faked it? Ha. If only.

On Scientific American: Apollo 11 Lander spotted by Lunar Satellite
And also see SciAm’s Apollo 11 40th anniversary report

The Illusion of Sex: Contrast and Gender Perception

Image courtesy Dr. Richard Russell, Harvard University

Interesting research in press for the journal Perception shows that a contributing factor to perceived gender of a face is merely contrast. The above image is of the same androgynous face, digitally treated to both increase (left) and decrease (right) the contrast, and the result is a change in perceived gender. Without any anatomical differences, the relative darkness of lips and eyes compared to skin change our perception, and changes our fundamental idea of what we are seeing.

This image took third prize at the visual illusion of the year contest, though the phenomenon is more than just a trick of visual perception. Recognition of things like faces (and voices) is a far more complicated process than it seems from everyday experience. Computers have a hard time with them because we use numerous shortcuts (heuristics) in our processing, which often aren’t logical to a machine (or we don’t know them yet). This image illustrates well how we take visual cues and build heuristics from the world around us, and how these shortcuts can lead us to make gross changes in perception from small changes in input. Usually this works well – imagine finding a friend in a crowded room if you had to concentrate on the face of every single person?

There is a cautionary note here. This work highlights the fallibility of our senses, and that we need to be careful to stay objective in cases where we can be fooled by what we see or hear (taste, touch, or smell?). This is especially true in cases, like advertising,  where editors may use information like this to skew our understanding or opinions. Stay vigilant. Stay skeptical. Stay classy.

Random internet find for the day: Car-Baked Cookies

Car-Baked Chocolate Chip Cookies

Rationally, I know there’s really nothing wrong with it, but it just seems weird. I’m sure they’re fine to eat, but it seems that you would only do this once, to say your car gets hot enough to literally bake in.

Amusing? Yes.

Tasty? Very possibly.

Practical? Maybe if you don’t own an oven. And it’s the summer. And you have a potluck to go to that evening. And you have lots of spare cookie dough lying around…

F#@king Unsurprising New Study

In at least 5 sources yesterday, including the evening news (i.e. it broke out into mainstream media) I heard about a study that claims that swearing reduces pain. The study, to be published by researchers at Keele University in the journal NeuroReport August 5, asked students to place their hand in ice water and repeat either neutral words or explicatives. The swearing group both lasted longer and reported less pain.

I don’t find the results that novel. Anyone who has stubbed their toe in polite company can attest to the fact that having to grin and bear it is much worse than being able to run around, curse for a while, and be done with it. Of course such an anecdote doesn’t count as science and so a real study shows us that there is a definite effect, but not one I find to be deserving of the press it seems to be getting.

There seems to be two reasons people find this interesting:

1. “People get to drop the F bomb for science!?!?!?!?”
2. “Can I use this to swear and get away with it?”

Neither of these have to do with the science, or the interesting questions raised about the role swearing actually plays in psychology and culture. While the researchers get attention, it is for the wrong reasons. They are looking for why swearing exists. The media wants to know how the knowledge can be used.

Compare article titles from two science news outlets:

"%&#$!" Makes You Feel Better – ScienceNews.org
Why the #$%! Do We Swear? For Pain Relief – Scientific American

One does it right, reports the science and results of the study. The other takes those results out of context, suggesting (in step with the evening news I caught) that one should change their habits in order to lessen pain, which has little to do with the actual study results.

I’m always disappointed to see that the only science stories to make the popular press so often just miss the point all together. There are even interesting stories to be told, but the press takes the low road and almost says “Stave off cancer by cussing everyday!”

Argh. I need some amusement, so I’ll end off with a classic internet meme, which couldn’t be more appropriate. To all the kids out there, earmuffs! This is time for grown-up talk.

Bonus irony: Note the spelling of “incompetence” at 1:55. Yes, I notice because I’m anal about stuff like that.

Ben Harper’s Drummer is Insane

The Montreal Jazz Festival ended last night, and the final act was Ben Harper and Relentless7. The show, in keeping with the rest of the Jazz Fest, was incredible. Rather than give an overview of the concert as I did for Patrick Watson, I just want to make one comment.

Ben Harper’s drummer (nee Jordan Richardson) is crazy. At one point he drummed by slapping the snare and cymbals with bare hands, and early in the show he used maracas as drumsticks.

In absence of any video online for the concert yet, this appearance on Jimmy Kimmel highlights the insanity pretty well.

Glyco-wha?

Once upon a time, I was taught about a magical process called glycolysis. I learned how this amazing process can, through a series of reactions, generate energy for life, and all of the fascinating steps along the way. I then wrote an exam on the subject, and promptly erased it from my memory.

A year later, once again I was taught about glycolysis, but this time alongside her slightly backward fraternal twin sister gluconeogenesis. Again, fascinating. Again, quickly forgotten. (image from Lehninger Principles of Biochemistry)

Still another year later came the fantastic experience that was BIOC 4230, Metabolic Processes. And guess who was there. That’s right, old friend glycolysis, with a few more tricks to show off. Learned. Exammed. Vigorously scrubbed from recollection.

One might have guessed she would come back into my life once again, and she has. I thought it was over. I thought I could move on.

But alas, the problem with a pathway being one of the first biochemical processes worked on is not just that it was the first one studied, but that in being so, it paved the way for many new studies to follow, and in many cases, techniques that are used in labs even today. This is similarly the case with the pioneering gene-regulation system lac operon, and bacterial/phage genetics prototype lambda phage system (I’m sure there are lots of other examples), both of which have become intimately integrated into routine techniques of molecular biology.

Glycolysis, the workhorse of biochemistry and dread of all intro biochem students, seems to have a pretty bad reputation. What I’ve come to appreciate is that not only does it provide an understanding of a central energy pathway in life; not only does it provide multiple examples for the study of biochemistry conveniently in one place, but remains useful to new applications to this day. It’s relative age, while making it seem like stuffy, boring science, means that most if not all kinks have been ironed out; essentially everything about the enzymes of glycolysis is known, at least from a technical standpoint.

This flies in the face of the oh-so-common undergraduate lament (that I, of course, never uttered) of:

“Why should I have to learn this if I am never going to use it? It is old science that no one needs to know anymore. I want a degree without having to learn anything!”

…or some less cynically distorted variation thereof. Well, case in point, readers. One student has found himself actually needing to know his basic biochemistry for his biochemistry work. This calls for a celebration!

But it will need to wait for a while. The fact that glycolysis and its enzymes are so well established means that if I’ve spent two weeks getting a reaction to work that continues to sit in a cuvette like so:

then I can’t blame glycolysis for stupid pyruvate kinase stupidly not carrying out the stupid reaction to give me a stupid signal and get some stupid data to get my stupid project off the ground. Stupid.

Important Medical Breakthrough via The Onion

From the Onion:

Scientists Discover Gene Responsible for Eating Whole Goddamn Bag of Chips

This makes me feel a little bit better. I need not be ashamed anymore. Thank you, genetic determinism, for making me feel better about my low self-control.

As a biochemist, I’m interested in the mechanism by which this gene might exert it’s effect:

"People with this gene have up to four times the amount of fritoceptors normally found in a human," Alvaro said. "This increases their pleasure response to snaxamine-2, the human body's principal chip-eating hormone, which is released in response to giant handfuls of chips being shoveled into the mouth. This tends to promote entire-goddamn-bag-eating behavior in those individuals who possess the series."

Makes sense.

Patrick Watson Rocks

Patrick Watson played the Montreal Jazz Festival this evening, and I have to say I was blown away. Shadow puppetry, a parting of the crowd to march through while performing (crazy megaphone-backpacks involved), and a bicycle mounted atop a skyjack all were used as part of this incredible show. While I’m not really one for dissonance and falsetto wailing à la Coldplay, the showmanship more than made  up for it, making for a thoroughly enjoyable show. The Montreal Jazz Festival needs to be commended for bringing the band to the main stage of the festival and working together to put together all of the logistics for what must have been an incredibly difficult show to organize. The concert, a free outdoor concert featured for the 30th anniversary of the Jazz Festival, illustrated that creativity in musical performance doesn’t stop with the music.

I’m sorry to say I have no pictures to present as my camera batteries died. I’ll see what pops up on teh netz in the next few days and report back. Check out the band for yourself though, they’re brilliant.

Check here for music videos, the show was supposedly broadcast live there, though either the window has passed or I’m to stupid to find out how to see it. There were definitely serious filming going on, so the video is out there somewhere.

As for the show, it opened up with crew flapping 5-foot sheets of metal on all sides around the crowd to build to a thunderous roar, at which the curtain was drawn and the band began. Images were projected onto adjacent buildings, creating stunning visual imagery to accompany the music. The song Beijing included a bicycle running in place, far above the crowd atop a 50-foot platform. Perhaps escaping the notice of some listeners, the musicians kept perfect time with the ticking of the bicycle wheels. That sort of thing takes incredible talent.

Some time later, following a duet with Lhasa de Sela, the band strapped on insane-looking backpacks with audio equipment and megaphones to broadcast as they slowly wended their way through the crowd to a small stage set up in the middle of the audience. There they handed out kazoos and encouraged us in the crowd to play along. A drum solo by Montreal drummer Guy Nadon let the band get back to the stage, where they joined him in performing the next song, punctuated by a particularly memorable tin can drum solo.

A song written inspired by the book Where the Wild Things Are was accompanied by a world-class shadow puppeteer, who produced a remarkable shadow-likeness of Patrick as he opened and closed the song. Also notable was the image of a fox (wolf?) running, the pace of which followed the music, and monsters of various sorts, to go along with the song’s theme. The last piece of the main set, written for Patrick’s son, featured silhouettes of boys jumping on trampolines projected on the walls and ended with a bundle of huge white balloons rising above the stage. All came together for stunning imagery to enhance the music.

The show finished with the obligatory encore, which Patrick specifically commented was a little silly, as we’ve all come to expect them at any show of this scale. After the big finish, including fireworks along the length of the crowd, and everyone was about to leave, they came out again for not one, but two more encores before the lights finally died and they sent us home. The trickster - his comment about encores wasn’t really expressing cynicism, but setting us up to be actually surprised by the real encores. Fantastic showmanship.

All through, I couldn’t help thinking that while the crowd was in the high thousands, it seemed as if the performance were just for a few people. With all of the expensive effects, security, and the like, he maintained a personal setting with the crowd through casual banter, being unafraid to laugh at himself or technical issues, and a general attitude of earnestness. Perhaps this was best highlighted when the shadow puppet projector died. Patrick stopped the show, restarted the band, and continued the song with the projector working again. This comfort and casual attitude on stage makes Patrick Watson the person and the entire band fantastic performers and as (in my mind, at least) performing ability tends to dictate longevity in music, I have the feeling they’ll keep amazing, innovative shows coming for years in the future.

Update 12.07.09: As promised, here’s some of what has hit the webz over the last week since the show:

The Montreal Gazette: Patrick Watson in his Elemental

Montreal Jazz Festival: Day Five at Nyani Quarmyne Photography
and Photos of the Show

Patrick with his speaker-backpack on Flickr via Kipourax

Photos from the Jazz Fest site itself

And here at urb.com

Oh, and the live stream of the concert is up now where I mentioned it above.

The Science Scouts: Awesome

If you do, or ever have, worked in a lab, you need to check out the Science Scouts. Do it now.

Badges are presented in recognition of scientific accomplishments like setting things on fire, successfully dodging monkey feces, and making fruit flies get it on. Particularly memorable badges include:

The emergency evacuation due to science badge

The I’m a marine biologist and, to be honest, I kind of f**ing hate dolphins badge

The have violated the posterior of an animal in the name of science badge

and the science deprives me of my bed badge (three levels, corresponding to the degree of red-eye suffered as a result of experiments)

I’m waiting on a sustained frost burns while “working” with dry ice badge, or inadvertent acid and base spills keep my hands soft and smooth badge.

Montreal Photojournal 3: Jazz Festival Opening/Stevie Wonder

The world-famous Montreal International Jazz festival kicked off the other night, with opening act Stevie Wonder. Literally ducking and weaving through the crowds of umbrella-wielding concertgoers got us to about 100m from the stage before we had to stop, not close enough to see the stage all that well, but in good view of one of the large projection screens placed along the length of the venue. While I’m not all that familiar with Stevie’s music, I found out that, as one might imagine, I knew more of his music than I thought I did. And as usually happens in this instance, it has prompted me to now (perhaps too late?) seek out and get to know his music better.

Wet concertgoers

Waiting for the show to start

The crowd of 200,000 people filled the Place-des-Arts concert area and stretched backwards far up the street. Even in intermittent rain, the downtown was filled with people out to see the show.

Projections onto the adjacent buildings

The organizers, veterans now at the 30th annual Jazz festival, know how to put on a good free show. They made use of the adjacent buildings including the somewhat more distant Complex Desjardins tower, to project images on. It made for an event that expanded outward from the site of the concert and into the rest of the city.

  The concert in full swing (full Motown?)

The recent death of Michael Jackson prompted Stevie to address the crowd and to celebrate the art of a gifted musician and performer.  At several points he paused his act to play some of MJ’s songs to the audience. He was visibly distressed at times but nevertheless continued the show, and towards the end played many of his best-known songs, which myself and the crowd really got into. Dampness and constantly getting bumped in the crowd made the experience not the most pleasant, but the opportunity to see a legend of music at his craft certainly made it worth the discomfort.

Now, if you’ll excuse me, I must go listen to “Superstition” again.