Thursday, October 16, 2008

The New Scientist: Origin of life found from 50-year-old samples

In 1953 Stanley Miller used an apparatus like this one to simulate the chemical conditions on Earth before life evolved.

Miller's experiments produced amino acids, complex oily hydrocarbons, and other organic molecules - the building blocks of life. A graduate student at the time, Miller went down in history for
being the first to show that these essential molecules could have been generated on a lifeless Earth.

Stanley Miller passed away in 2007, leaving the contents of his office and lab to a former student.

Here, vials containing samples from the 50-year-old experiments were found and later reassessed using modern techniques.

It turns out that Miller's experiments were even more successful than anyone had imagined. Vials from his volcanic experiments contained a rich mixture of amino acids, including some that have never been found in simulated early Earth experiments before. The New Scientist has the details.

Link to the article: Volcanic lightning may have sparked life on Earth at The New Scientist

Also see:
The Miller Urey Experiment

Tuesday, October 14, 2008

The Universe on E8

"Whoa, duuuude, I'm a surfer! I surf! Watch me surfing! And I'll talk about some physics too! Whoa!!!"

In a really intriguing TED talk, Garrett Lisi talks about his theory of everything, describing all particles and interactions of said particles as manifestations of mathematics' 'most beautiful structure.' Can't say I'm completely sold on the idea, but it sure is pretty. And it fits in quite nicely with my habit of seeing patterns within patterns within patterns, always thinking there's probably some structure to it. The biggest difference, of course, is that I'm just dreaming and this guy's actually creating maths and theories with it.

And you might not be seeing a video, instead seeing two buttons asking which version of flash you're using. Apparently TED's player is ancient, and a piece of garbage. Just click on 8 and you should be able to see it.

Tuesday, September 16, 2008

Brian Cox > Old People

The debate here is whether or not the LHC was worth the cost, and Brian Cox dominates.

Via Bad Astronomy.

Tuesday, September 9, 2008

Big Bang Day

Tomorrow's the big day! The LHC gets switched on for the first time! The TED Blog has a little writeup on it, which most importantly links to the CERN live webcast of the whole ordeal. So make sure to check that out tomorrow morning!

Saturday, August 23, 2008

All about ATLAS

What with the LHC preparing to open up and kill us all with its supermassive micro black holes of doom and destruction, finding the ATLAS channel on YouTube is a blessing. Aside from letting me enjoy some Holst, they've got plenty of extremely informative videos about how the ATLAS detector will work, and I highly recommend watching. Here, I'll make it easy to get started:

And as an added bonus, I couldn't help but notice some PROOF that ATLAS is evil and will destroy the planet. Here's a screenshot taken from their Episode 2 video. It's a slice of the detector:

Look familiar? I believe it does, and I believe it's so unmistakable that this can be considered official proof that dark forces are at work here, consciously plotting thee destruction of this entire planet.

Monday, August 18, 2008

More Visual Goodness

While I'm on the subject of great advancements in visual technologies, here's another project (also out of the University of Washington!) that's quite amazing, although this one can potentially lead to much more dire consequences.

The idea behind this paper and accompanying video is that by combining video with a few photographs of the filmed area, you can enhance or change the video in very convincing ways. Enhancement can include increasing film resolution, HDR, and outright film manipulation on the order of removing objects or completely replacing pieces with alternate content. Watch the video for a good idea of what this is all about.

Using Photographs to Enhance Videos of a Static Scene from pro on Vimeo.

Saturday, August 16, 2008

Remember Photosynth?

That might be a strange question, but I'm just going to assume that everyone else has also been drooling over this Microsoft research/University of Washington project. And in case you haven't, it's basically a tool that takes in a large volume of photographs of any given environment, figures out how they are stitched together, and thereby creates a three dimensional environment in which you can walk around. All from flat, 2D images! Well it would appear that the technology has made it into a future product called Photo Tourism. My guess is that they intentionally chose the most boring name possible to increase the surprise and awe that will be experienced upon using the product. Success is when such extreme surprise causes at least one fatal heart attack.

Anyway, what in the world am I talking about? Here, watch the video.

Aside from the terribly unattractive UI (which is temporary, no doubt), the video shows off a bundle of features that are new to me and make the virtual 3D world much more friendly to navigate. I can't wait to play with this, and I really can't wait to see how useful it might be.

Thursday, August 14, 2008

Weight Loss Miracle Tea

Loose oolong tea leaves. By Minato.

Surely you've heard of this tea, a "celebrity secret" and magical fat melter. Extremely aggressive advertising has made it difficult to ignore.

Bombarded with nine tea ads for every ten on facebook, I eventually started to wonder - just what are these guys actually selling people?

Turns out that this miracle draught is oolong tea. The same oolong tea you can buy at your grocer for 2-3$ a box.

Loose leaf oolong tea has a gentle flavour and contains polyphenols (the magical ingredient). Polyphenols are a group of plant molecules that may or may not have health benefits. (The science is inconclusive.) Polyphenols can be found in a large variety of food sources, including fruits, vegetables, beer, chocolate and other teas. [Wikipedia]

Despite the claims of fat melting properties, the only way anyone is going to loose weight drinking oolong tea is if they drink so much of it that it becomes a replacement for high calorie drinks, like pop and coffee with cream.

Not that my readers are likely tea-dieters, I'm just annoyed by the scamming.

Monday, August 11, 2008

Neat Lightning

I've been watching this thing all day long. Might as well put it in a nice easy-to-find location so I can view it from anywhere.

Lightning! In slow motion! It turns out that the dancing sparks are called leaders, discharges originating in the negatively charged thundercloud and following ionized air, eventually drilling down to a positive charge (the ground) and creates a discharge path that we see as the big bright blinding and really really awesome bolt of lightning. I must harness this power.

For all the beautiful thunderstorms I've seen growing up in Texas, I've apparently never seen the mechanics of lightning before. Fascinating stuff.

From Today's Big Thing.

Thursday, August 7, 2008

Tachikomas are Real?

The Hexapod Robot is is the closest thing I've seen to a real life Tachikoma. Not just because of its insect-like limbs, every aspect of its movement comes off as inquisitive, which gives a really impressive effect. It reacts to humans in a number of interesting ways. He follows your movement. Get too close and he'll lean back, looking a bit frightened or cautious. Apparently if you stay staring at him for a while, he'll take your picture and upload it somewhere. Neat project!

Via Technovelgy by way of io9.

Leno's Steam Power

I've known that Jay Leno has an impressive garage, but I had no idea he had steam-powered cars! I'm developing a minor obsession with steam power (but where to build my own in the city?), so seeing this video just makes me salivate.

Leno takes us through a typical day in the life of a turn of the century car owner, including the half-hour start-up process, getting yourself nearly blown up, and enjoying the one-gear wonder that is your steam-powered auto-mobile. Enjoy!

Via The Steampunk Workshop.

Update! Here's another Leno video showing off a later, much more refined, steam car.

Wednesday, August 6, 2008

Dinoflagellate Bloom in Halifax

red_tide, originally uploaded by Laura Urquhart.
Been to the Halifax waterfront recently? You may have seen something like this.

From Red water a puzzler, NS Chronicle Herald:

It looks like weeks of dry weather followed by heavy rains may have brought a phenomenon known as red tide to Halifax Harbour.

The water behind the Maritime Museum of the Atlantic had a rosy hue on Monday. Mayor Peter Kelly said the federal Fisheries Department had taken samples but wasn’t able to process them because of the Natal Day holiday.

He said the department’s guess is the discoloration was caused by red algae.

Marlon Lewis, a professor of oceanography at Dalhousie University, said algae levels in the area around the harbour are the highest he’s seen in two years.

"It’s not a very big (red tide), I wouldn’t say," Mr. Lewis said over the phone Monday. "Not compared to the others I’ve seen where the water turns a kind of brick red."

Mr. Lewis said the algae levels are high, but nothing abnormal for Halifax. He said it probably won’t hurt anything.

When algae die, their decomposition eats up oxygen. Mr. Lewis said in years past the algae levels in the Bedford Basin have been so high that the lack of oxygen has actually killed fish. He said he’s seen lobsters crawl out onto the beach to get away from the choking water.

The recent weather has been great for algae growth, he said.

"We had a big amount of rain a couple weeks ago after a very, very long dry spell," explained Mr. Lewis.

"It was like a big pulse of nutrients coming in."

Tuesday, August 5, 2008

Cynara cardunculus - The Globe Artichoke

Blooming Artichoke, originally uploaded by RemyOmar.

Favourite foods can take us by surprise when viewed in an unfamiliar context.

Artichokes - a favourite of mine - are actually the heads of a large (1.5-2 m tall), immature thistle. If left unharvested, they will bloom.

A Mediterranean native, Cynara cardunculus is considered invasive in the southern United States. Efforts are being made to eradicate the alien and replace it with native species.

Alien Invasion, originally uploaded by acastellano.

Monday, August 4, 2008

Swirling Tail: SEM of a Dinoflagellate

The "Montauk Monster" is a little nasty looking. This SEM photograph is much nicer.

dinoflagellate, originally uploaded by sconartist.

I showed this image to introductory biology students, and some were able to identify the single-celled algae right away. The give away is the spiral-like flagellum resting in the central groove. (If you don't know what a flagellum is you can think of it as a tail that propels a single cell.)

The spiral-like tail causes the cell to spin as it moves through the water - thus it's name. "Dino" means spinning, and "flagellate" refers to the cell's tail.

The "Montauk Monster" - Identified!

I first caught news of the "Montauk Monster" via Gawker last Tuesday.

Along with many others, I've been biting my lips in anticipation - just what the hell is this thing? (And why do we want to know so badly?)

Finding out is a matter of patience, and counting on the omniscience of the internet. I told my partner, "It's probably not a hoax, and eventually a savvy biologist will surface and tell us exactly what this thing is and what happened to it."

That biologist is Darren Naish of Tetrapod Zoology.

He's written an excellent article with new photographs, skull comparisons and decayed details photoshopped in.

Check him out to discover the true identify of the Montauk Monster!

Friday, August 1, 2008

The Big Picture: Large Hadron Collider nearly ready

I know that you all added The Big Picture to your RSS feeds when Daniel linked them back in June pointing out the Cassini and Chaiten Volcano collections. That's why you've already seen these amazing images of the LHC - right?

Image Caption:
View of the CMS (Compact Muon Solenoid) experiment Tracker Outer Barrel(TOB) in the cleaning room. The CMS is one of two general-purpose LHCexperiments designed to explore the physics of the Terascale, theenergy region where physicists believe they will find answers to thecentral questions at the heart of 21st-century particle physics. (Maximilien Brice, © CERN)

Or - if you're like me, you neglected to add TBP, have been missing out, and needed a friend to remind you of what you've been missing out on!

Wednesday, July 30, 2008

Going To Space

Found a great post on the Flickr Blog this morning. Some guys in Oklahoma sent a Pentax camera into space on a balloon. Over 104,000 feet straight up, photographing all the way up and back down. They wrote software to model balloon flight dynamics and used weather data to predict where the balloon would travel; the camera and related gear landed about twelve miles from its launch point.

This is seriously cool stuff. There are some really detailed descriptions of their process on the Pentax Forums here, here, and here. Also, make sure to check out the entire Flickr set.

Tuesday, July 29, 2008

LHC & Neurochip Rap

Physicists rap to you from CERN and... somewhere with lots of statues to inform you about the awesomeness of the LHC, the Higgs Boson, extra dimensions, and imprinting rudimentary memories onto networks of living brain cells. Woah! I actually learned something.

These videos are simultaneously so awesome and so campy that it hurts. You've been warned.

Large Haldron Rap


Daniel discovered these gems, but he didn't post them (?). He has totally been scooped!

Monday, July 28, 2008

The Smiling Parasite: Giardia lamblia

When I first showed my brother this picture of an axolotl he said, "Go away. That doesn't exist." (Too cute.)

What a great reaction! So when I received a similar reaction to Giardia lamblia this evening I knew it was time to blog.

See more images of giardia. (The scientific diagrams are especially cute looking.)

Giardia lamblia is a single celled organism. What we perceive as eyes are actually twin nuclei (spherical compartments that contain DNA) and the "mouth" is a parabasal body (don't ask).

This notably cute protozoan is responsible for giardiasis (better known as beaver fever and backpacker's diarrhea) and symptoms include "loss of appetite, lethargy, fever, explosive diarrhea, hematuria (blood in urine), loose or watery stool, stomach cramps, upset stomach, projectile vomiting (uncommon), bloating, flatulence, and burping (often sulphurous)." [Wikipedia] Giardia lamblia lives in the small intestine and spreads when infected fecal particles are able to contact food or water that will be ingested.


I saw this a while back, but it wasn't nearly this refined. Amazing.

levelHead v1.0, 3 cube speed-run (spoiler!) from Julian Oliver on Vimeo.

Via 3 Quarks Daily

Friday, July 25, 2008

My Very First Brain

, originally uploaded by rachaeldawn.

Tonight I began work on my very first brain. This photograph is proof that I obviously know what I'm doing. Never mind the excessive protective gear... it's totally not because I'm terrified of the soldering iron.

Tuesday, July 22, 2008

Do you need 8 glasses of water a day?

Everyone's heard this bit of conventional wisdom and some folks struggle awfully hard to maintain it - but do you actually need 8 glasses of water a day? The answer is a simple "NO".

Nobody seems to know where this health myth originates, but it is not based on scientific evidence. For most people, having a drink when thirsty is enough to meet daily liquid requirements. Pushing oneself to drink additional water is not only unecessary, but can be damaging to your health. Water intoxication occurs in extreme cases and can result in altered mental states and death.

Monday, July 21, 2008

Science in Art: The Illustrations of Carl Buell

Therapsid Morph

This is another of the illustrations I did for Don Prothero's book,"Evolution, What the Fossils Say and Why It Matters". The caption in the book reads... "The transformation from primitive synapsids like Ophiacodon and the fin-backed Dimetrodon to the predatory gorgonopsians to the weasel-like Thrinaxodon and finally to true mammals is one of the best transitional series in the entire fossil record."

The fossils of these animals were found and this transition took place from the early Permian period through the Paleozoic/Mesozoic extinctions to the Triassic.

Thylacine Dingo Comparison

Although we talk all the time of the incredible diversity of life on our planet, that diversity is really an amazing amount of variation on a relatively very few themes.

Here we have a recently extinct, marsupial Thylacine (3.) and its ecological equivalent (and replacement in Australia), the Dingo, a placental canine carnivore. These mammals have had separate evolutionary histories since at least the early Cretaceous. Both are the descendants of little insectivorous creatures that lived in the shadow of the dinosaurs. So are aardvarks and elephants, but in this case both these creatures evolved to do the same ecological task. And apparently the best functional form for a cursorial mammalian predator is “doggish”.

Seems that Carl doesn't have a change to update much, but he keeps a fabulous blog called "Dealing with the Beasts" under the pen name Olduvai George. Don't miss his flickr photostream.

Sunday, July 20, 2008

Dragon Fruit (Hylocereus undatus)

Maybe you have eaten one of these? Every now and then you can find them at the supermarket for 8$ a piece. The skin is bright fuchsia and the inside is pure white with black seeds. They are very striking.

The fruit (also called pitaya) grow on long slender branches of the cactus around a woody trunk.

Exotic Plant, originally uploaded by Lazy Soup.

I have been growing this plant from seeds taken from the last dragon fruit that I ate. Most (if not all) of the seeds planted germinated, and this happened very fast. Keeping them moist, they continue to grow surprisingly quick.

What amuses me about these seedlings are their two cotyledons (seed leaves). Being a cactus of it's particular sort, these are the only leaves this plant will ever have - a nod to it's heritage as a dicot (one of the two major groups of flowering plants) much like our embryonic gill slits are a nod to ours.

It will be several years before these cacti are ready to produce large night-blooming flowers, and bear fruit.

Monday, July 14, 2008

Science in Art: Myosin 2,000,000X

Myosin 2,000,000X, originally uploaded by David Goodsell.

Dr. David Goodsell makes exquisitely detailed to-scale watercolour and digital paintings of cells and the molecules of life.

The molecule featured in the image above is myosin, which was discussed a few posts back in "How Rigor Mortis Works".

His webpage is a little difficult to navigate, but worth your time for all the fantastic and colourful illustrations viewable there.

Saturday, July 12, 2008

Giant Golden Book of Biology

This beautiful little book from 1961 was designed to introduce children to biology. I just love the cute and stylish illustrations, which touch on the major concepts of a first year biology class.

In this image you can see a cnidarian, a pterophyte, a dinoflagellate and a member of hemiptera... to name a few!

Click to view more images of these great illustrations by Charley Harper.

Wouldn't it be grand to own a copy?

Friday, July 11, 2008

The Biology of Sexual Preference and Behaviour: Perspective from Drosophila

Mating Fruit Flies, originally uploaded by arbil.

Drosophila mating. (Above.)

Smell plays an important role in who a fruit fly chooses for a mate. That's because fruit flies rely on smell to tell them the sex (male or female) of the other Drosophila they encounter.

Typically, when a male fly smells a female he will engage in sexual behaviour and approach her. She will reciprocate by engaging in correspondent female sexual behaviours. Why do they do this? Let's explore the genetic basis of sexual behaviour in Drosophila.

Fruit flies have a gene called the fruitless gene. The fruitless gene produces a protein called Fru. The Fru protein is expressed (that means that it's working in and on) areas of the antennal lobe, in particular - Fru works on brain cells (mAL neurons) located there. The fruitless gene is only expressed in male fruit flies. A fruit fly smells through it's antennal lobe.

Catch all that? The fruitless gene in fruit flies affects cells that process smell in Drosophila, but only in males. Smell is very important in mate selection and sexual behaviour.

So what exactly does fruitless do?

Early in development both males and females have the same number of mAL neurons in their antennal lobe. As both sexes develop, mAL neurons die. Mature females typically have 5 mAL neurons remaining and these have a female-specific shape. Mature males on the other hand, have 30 mAL neurons remaining and these have a male-specific-shape. Only male mAL neurons grow extensions that connect to the subesophageal ganglion, an area of Drosophila's brain that processes smell and initiates male sexual behaviour. These male differences are all due to the work of Fru.

In other words, the fruitless gene causes brain cells that process smell to connect to more brain cells that initiate male sexual behaviour in a fly.

So, what do you think will happen if the fruitless gene is turned on in a female fly? What do you think will happen if the fruitless gene mutates so that fru is not expressed in male flies?

  • In the first case, the expression of fru will cause the female to develop mAL neurons like a typical male, and she will exhibit male sexual behaviour when she smells another female.
  • In the second case, the lack of fru expression will cause the male to develop mAL neurons like a typical female, and he will exhibit female sexual behaviour when he meets up with another male.

I hope you guessed the correct answer! Fru may be expressed atypically in nature, as well as in the lab.

At this point you may be wondering what happens to the male sexual area of the subesophageal ganglion in female flies. It becomes a vestigial area. You may be surprised to learn that many female animals have vestigial brain areas that control male sexual behaviour, including most mammals. Hmmn!

So, we've learned that a single gene can control what sort of sexual behaviour a fruit fly exhibits - male typical or female typical. Isn't that neat?

Of course, human sexuality is far more complicated than Drosophila's! (And even Drosophila's is more complicated than described here. Other genes and mechanisms have important roles to play, as do environmental factors.) Experts agree (based on quite a lot of good evidence) that when it comes to humans, both biological and environmental factors play an important role in sexual preference. And the role these factors play in sexual orientation varies considerably between individuals.

All the same, it's not unlikely that similar mechanisms are at work in creating human sexual behaviour and researchers are on the hunt for our own copy of the Fruitless gene.


Fruitless gene - A gene studied in fruit flies that produces the protein Fru.
Fru - A protein that alters the development of mAL neurons in the antennal lobes of Drosophila.
Antennal lobe - For Drosophila, this is the first stop in processing smells. It is the rough equivalent of the olfactory bulb in humans.
Neuron - Cells of the nervous system are called neurons. When people talk about brain cells they usually mean neurons.
Subesophageal ganglion - An area of the fruit fly brain, part of which controls male sexual behaviour.

Recommended reading:
- Seattle Times: Born gay? How biology may drive sexual orientation.
- Wikipedia
- Nelson's "An Introduction to Behavioral Endocrinology" 3rd ed. p.209-213

Also see:
Fruitless specifies sexually dimorphic neural circuitry in the Drosophila brain

Written for Homosecular Gaytheist in response to some comments on Reed's post on homosexuality in penguins. Unfortunately, some folks hope homosexuality is simply a product of lonliness, while others think that it's about aggression (and irresponsibly enough, feel quite confident asserting that scientists do too). Questions are welcome.

Wednesday, July 9, 2008

Wanna hear a story about attempted MURDER, BOMB THREATS and more ... ?

If you've spoken to me at all within the last week, then you know that I've been pretty fascinated with the Church of Scientology.

There's an incredible story to hear here, and the more you learn the weirder, scarier and more incredible it gets.

You may already know that this religion was founded by a science fiction writer, and that high ranked members believe that the insane souls of aliens cause all human suffering.

You may have already seen Tom Cruise in a cape.

But you may not know that this story includes:
  • an internal secret service agency and a secret navy
  • high suicide rates and high pressure abortions
  • attempts to destroy critics through harassment, litigations and framing
  • destroyed families and abandoned children
  • 100,000,000 year labour contracts
  • salvation that costs 350,000$
And a whole lot more...

... rolled in with a historically unique fight with Anonymous - a group of unorganized geeks who read the same websites and who are raising awareness about Scientology, originally provoked by attacks from the church designed to shut down popular websites and destroy the lives of contributing critics.


The Church's Official Website

Scientology's Religious Freedom Watch Web Site (Warning: Intense, litigious and very bizarre.)


A former Scientologist Tory Christman's YouTube channel.
Xenu TV on YouTube
CNN interview with Scientologist Tommy Davis
Annonymous: Call to Action
Footage from a meeting of Scientologists, including Miscavige and Cruise

Anti-Terrorism LOL

Picture from today's Big Picture post, Anti-Terrorism Exercises in China. Loltype through Splow's AirLolCatGenerator

Tuesday, July 8, 2008

Crocuta Crocuta - The Spotted Hyena

Fighting, originally uploaded by laurentrouas.

Spotted hyenas have a reputation for gross behaviour. No surprise since:
  • They have a bone crushing bite which helps them to break up the skeletons of their prey, which they eat.
  • They are an aggressive species. It is not unusual for new cubs to kill their siblings within hours of birth.

Spotted Hyaena (01129), originally uploaded by giamplume.

However, this isn't quite fair. For one, spotted hyenas are highly intelligent and exhibit a wide array of sophisticated social behaviours including:
  • deception
  • recognizing trustworthiness
Their intelligence and social ability makes them comparable to certain primate groups.

Combat, originally uploaded by laurentrouas.

But Corcuta crocuta is most famous for it's unusual sex role and appearance reversals.
  • Women rule. Females are larger and more aggressive. Even the lowest ranked female in the dominance hierarchy comes before the highest ranked male.
  • Females have masculinized external genitalia that closely resembles the male genitalia and is capable of producing erections. This structure allows them to choose absolutely who they will and will not mate with. Amazingly, they even deliver young through this pseudopenis.

About that:
  • Males are less aggressive and more submissive, but in adulthood have higher levels of circulating androgens than female hyenas. Androgens are male hormones that are associated with aggression and dominance behaviour in mammals, including humans.

  • We don't understand why females develop masculinized genitalia.

    Some background: In most mammals (again, including humans) a fetus exposed to high androgen concentrations will develop male reproductive structures. Human women with congenital adrenal hyperplasia may have moderately to severely masculinized genetalia. Alternately, genetic males with faulty androgen receptors (AIS) can develop completely as females.

    With this in mind, you might expect that female spotted hyenas are exposed to unusually high concentrations of androgens while in the womb and you would be correct. However, steps taken to block the effects of androgens on the developing fetus have no effect on the development of masculinized genitalia. For scientists, this is quite surprising and weird!

  • Just sayin' ...

    More Please:
    The Paradoxical Predator
    Who's Laughing Now?
    Spotted Hyena @ Wikipedia

    Science in Art: Animal Form and Function

    The artwork below isn't too accurate, but it encourages viewers to think about the relationship between form and function.

    Xray for air travel, originally uploaded by danjrule.

    "All wings are airfoils, including those of planes." - Biology: Concepts & Connections

    via Street Anatomy

    ps. This guy's other art isn't sciencey, but it is pretty cool and view-worthy.

    Monday, July 7, 2008

    Crinoids / Feather Stars

    Crinoid art (SDV_5886)
    Originally uploaded by Sven De Vos
    Image caption: Crinoids, or Feather Stars, are not only spectacular by themselves, they also host spectacular commensal animals like small shrimps, cling gobies and tiny lobsters, most perfectly disguised within the Crinoid. I will post some pictures of those later.

    As Echinoderms, they are family of Starfish and Urchins. However they have their mouth on the upside, unlike their family members.

    Crinoids are suspension feeders. With tiny tube feet on their arms they catch plankton and detritus, to be directed trough a central channel towards the mouth.

    Over 500 distinct species are described. The earliest traces of those animals go back almost 500 million years!

    How Rigor Mortis Works

    Rigor Mortis
    Originally uploaded by M.H - Ghosts_&_Spring

    Very generally, a muscle consists of bundles of muscle fibers and the nerves that excite them. Muscle fibers are very long cells that contain bundles of myofibrils. And myofibrils consist of repeating units called sarcomeres. Sarcomeres can contract, and when many sarcomeres contract simultaneously their muscle does too.

    So, our nested units from largest to smallest are:
    muscle > muscle fiber > myofibril > sarcomere

    The contracile mechanism of a sarcomere consists of thin filaments and thick filaments. Thin filaments are made of a protein called actin and extend lengthwise into the sarcomere from either end. Thick filaments are made of a second protein, called myosin which also extends lengthwise in the space between the thin filaments.

    This diagram will help you visualize the arrangement of the thin and thick filaments within a sarcomere. Thick filaments also have regions called "heads" depicted as circles in the diagram.

    ATP is a high energy mollecule and is the molecular currency of energy transfer within a cell. When ATP interacts with a thick filament head it loses a phosphate group and energy is transferred from the ATP mollecule to the head, causing the head to extend into what is called it's "high energy position". The head will stay in it's "high energy position" until a message is send to the sarcomere telling it to contract. The message comes in the form of calcium ions.

    When a nerve excites a muscle fiber a cascade sequence of events occur that lead to the release of calcium from compartments made of fatty membrane that surround myofibrils. Released calcium ions enter sacromeres and attach to the thin filaments causing them to change shape so that docking sites for the for the thick filament heads appear. The cascade continues as thick filament heads bind to these docking sites and undergo a change in shape that pulls on the thin filament bringing it closer to the center of the sarcomere. This act effectively shortens or contracts the muscle on a molecular level, and (as stated earlier) when many sarcomeres contract simultaneously their muscle does too.

    The thick filament head is now in it's "low energy position" and will stay attached to the thin filament docking site until another ATP mollecule interacts with it, releasing it back into it's "high energy position". ATP also powers pumps that remove calcium ions from the sarcomere and place it back inside it's membrane bound compartment.

    Two more pieces of background. 1. ATP is produced within a cell for use by that cell. 2. When a person dies ATP production comes to a halt, and cellular supplies are rapidly depleted.

    From "Biology: Concepts and Connections"

  • "A whole muscle can shorten about 35% of its resting length when all its sarcomeres contract."

  • "A typical thick filament has about 350 heads, each of which can bind and unbind to a thin filament about 5 times per second."

  • Rigor Mortis

    If you haven't been bamboozled by all the new science jargon then you may have already guessed how this anatomical set-up results in the post-mortem condition known as rigor mortis (from Latin, meaning "stiff death").

    Remember that in a relaxed muscle, thick filament heads are in their "high energy position" and are not bound to the thin filament. Unlike other molecules that expend the energy gained from ATP right away, the heads are waiting for calcium to arrive and unlock their docking sites.

    Have you guessed now?

    The membrane compartment that surrounds the myofibril decomposes before the sarcomeres that make up the myofibril do. No longer contained in it's membrane compartment, calcium ions may enter sarcomeres and unveil the docking sites for thick filament heads. The heads expend the energy that they acquired prior to death by binding to the thin filaments and sliding them towards the center of the sarcomere, contracting the sarcomere...

    ... and when many sarcomeres contract simultaneously their muscle does too, resulting in the disturbing twitches and gruesome postures of rigor mortis. Eventually the sarcomeres decompose too, muscles relax and rigor mortis comes to an end.


    Muscle fiber - A muscle is a bundle of muscle fibers which are long, multinucleate cells that contains bundles of myofibrils.
    Myofibril - Myofibrils are strands of repeating sarcomere units surrounded by a modified endoplasmic retriculum called the sarcoplasmic retriculum which acts as a calcium sequestering compartment.
    Sarcomere - Are the fundamental contractile units of muscles consisting of thin and thick filaments. The thick filaments have heads that pull the thin filament to the center of the sarcomere, contracting it.
    ATP - Adenosine triphosphate, the molecular energy currency of cells. When it loses a phosphate group and becomes ADP (adenosine diphosphate) energy is transferred.
    Protein - Proteins are long chains of amino acids which form a diverse group of mollecules. Proteins carry out a wide array of functions and can be thought of as the mollecular machinery of cells.
    Thick filament - Made of myosin, the thick filament has portions called "heads" which can attach to the thin filament and pull it towards the center of a sarcomere.
    Thin filament - Made of actin, the thin filament protrudes from either end of the sarcomere. When calcium binds to the thin filament docking sites for the thick filament heads are revelealed which they may bind to causing contraction.

    Friday, July 4, 2008

    Microscopic view of Utricularia, a carnivorous plant.

    Utricularia_2006-09-30, originally uploaded by Penet.

    The carnivorous aquatic plant Utricularia produces those curious organs which are bags it uses to trap small animals and digest them...

    Ultricularia (aka bladderwort) on Wikipedia

    Sunday, June 29, 2008

    Sunday Science Finds

    Zombic cateripillars are slaves to developing Glyptapanteles wasps:
    The Voodoo Wasp
    (Also see A Fluke of Nature @ Damn Interesting.)

    Photosynthetic Marine Microorganisms do it for less oxygen:
    Startling Discovery About Photosynthesis: Many Marine Microorganism Skip Carbon Dioxide And Oxygen Step @Science Daily

    Cute & clever taxonomy:
    Curiosities of Biological Nomenclature

    From the main page:
    "Scientific names of organisms are not usually known for their entertainment value. They are indispensable for clarity in communication, but most people skip over them with barely a glance. Here I collect those names that are worth a second look.

    Some names are interesting for what they are named after (for example, Arthurdactylus conandoylensis, Godzillius), some are puns (La cucaracha, Phthiria relativitae), and some show other kinds of wordplay (such as the palindromic Orizabus subaziro). Some have achieved notability through accident of history, and many show the sense of humor of taxonomists.

    Thursday, June 26, 2008

    Dynamic Architecture

    While we're on this whole skyscraper kick, how about a wind-powered tower? David Fisher, a French architect, is in the approval stage for two towers—one in Moscow and one in Dubai—where each floor rotates independently of one another, driven by wind turbines fitted in between each floor (which also creates the electricity to power the building, and possibly other nearby buildings as well). And Fisher's buildings will be less expensive to build because the core is all that's built on-site. The rotating pieces will be built elsewhere in a modular fashion, attached to the core and sent up. They'll be built from the top down!

    Fisher's company, the Rotating Tower Technology Company, has these two projects on display at its website, and the videos are really quite stunning.

    Via The Guardian by way of io9.

    Wednesday, June 25, 2008

    Taipei 101 on flickr

    Just because I'm taken...

    by Fishtail@Taipei

    See more of flickr's most interesting images of th Taipei 101 building here. Many are very striking. For New Years the whole building produces fireworks.

    Taipei 101 Damper movement on 12 May 08

    Video caption:
    Happened to be visiting Taipei 101 when the tremors from the earthquake in Sichuan was felt in Taipei..The damper is 660 ton in weight suspended on the 92 floor to 87 floor..

    YouTube video of the Long Now technology display at Maker Faire 2008

    Massively Gigantic Pendulum

    So the Long Now Foundation, a group established to think about culture in the framework of 10,000 years as opposed to our current norm of thinking about this year, this moment, fast/faster/fastest, has been working on what they call the 10,000 Year Clock. It will be an entirely mechanical device that will tick once every year and last as long as the name says. From what I've seen so far, it's a beautiful piece of machinery, and it's been quite a bit of work for these guys.

    In a new post on their blog today, they mention something they found while researching pendulums for their clock. In one of the tallest skyscrapers in the world, the Taipei 101 building, right up near the top, is a 728 ton tuned mass damper to help prevent the building from swaying during harsh conditions such as storms and quakes. The thing sways, and it offsets the sway of an entire skyscraper!

    Look at that thing! It's humongous!

    Also, while I'm writing about the Long Now Foundation, I should also mention that they have regular seminars which have become available as a podcast that I highly recommend. If that link doesn't work, you should be able to search the iTunes store for Long Now or SALT.

    Tuesday, June 24, 2008

    Tiny endemic, on flickr

    Image by Nuysia@Tas.

    Endemic species are found in one area, and no where else in the world. As such, they are extremely sensitive to habitat degredation and easily threatened.

    From the caption:
    The Tasmanian viviparous seastar, Patiriella vivipara. Adults achieve a full size of 13mm across. This tiny species is endemic to Tasmania, is known from a handful of locations and is considered threatened. Rather than going through the usual planktonic larval stage that most seastars go through, this species hold the larvae in it's gonad until they are fully formed. These minute baby seastars emerge from the backof the parent. This reproduction method limits the spread of this species to suitable habitat elsewhere along the coast.

    View distribution map.

    Patriella vivipara at Parks & Wildlife Service Tasmania web site.

    Open Letter to Ministers re: Bill C-61 from LibriVox founder

    An excellent open letter to our Minister of Industry from LibriVox founder Huge McGuire.

    I am the founder of LibriVox, an all-volunteer, web-based project to make audio recordings of public domain texts and give them away for free. Since our inception in 2005, we’ve run on a yearly budget of $0; yet we’ve become one of the most prolific makers of audio books in the world, with a production rate recently topping 100 books per month. We’ve got a catalog of some 1,500 audio books, including authors such as Dickens, Cervantes, Austen, Dante, Darwin, Sun Tzu, Hobbes, Einstein, and Plato. We also have a number of Canadian classics from Leacock, Lucy Maude Montgomery, and others. We have thousands of volunteers around the world, who make audio versions of texts and give them away because they believe access to knowledge and great literature is one of the most precious gifts we can give to each other. We’ve gained some fame over the years, with articles in the NY Times, radio spots on the BBC, as well as many more mainstream and web media mentions and profiles. The Vice President of Creative Commons recently called us “perhaps the most interesting collaborative culture project this side of Wikipedia.”

    LibriVox is the sort of project that is on the outer edge of copyright case law, because what we do was not possible even a few years ago. At our core, we are about reading old books, but we use digital recording software, distributed production models, mass online collaboration, bit torrents, blogging and podcasting, online forums and wikis, bandwidth, mp3s and zip files, all to make recordings of old texts and give them away online for free.

    I have some personal objections to Bill C-61 as it has been tabled, objections you’ve heard no doubt from thousands of concerned and angry Canadian citizens. But I wanted to outline two concrete examples of how Bill C-61 would criminalize legitimate activities of Canadian LibriVox volunteers.

    Read whole letter here.

    * I tried to contribute to LibriVox a year or two ago, but found that I'm no good at reading at a slow, good-for-listening pace. I also have several audio books from their site on my iPod including The Origin of Species and the autobiography of Olaudah Equino.

    Monday, June 23, 2008

    Charlie Angus on Bill C-61, Canadian DMCA

    So, not science - but definitely technology and ethics. I promise to get on with some fun science posts once I've finished this terrible summer class.

    "But C-61 is about greed, not just rewards, about stifling the age-old enjoyment of sharing music with friends. It imposes a rigid black-and-white legal framework on a multihued, free-flowing landscape. It's about insisting on horse-and-buggy etiquette in an automotive age." - From The beat will go on despite the federal Conservatives @ The Vancouver Sun

    Wednesday, June 18, 2008

    The Big Picture

    This isn't necessarily science-y, but this is probably my favorite new blog of all time.

    The Big Picture is a daily photoblog full of very hi-res pictures focusing on a theme a day. It's a very young blog, and already there are too many good choices to link to here. But I'll try to exercise some restraint and link to the Cassini collection and the Chaiten Volcano collection.

    So amazing!

    Thursday, June 12, 2008

    Heads Up!

    Canadian DMCA is worse than the American one!

    Also: Michael Geist Blog.

    Any suggestions on who to write besides the usual MPs and PM?

    Edit: I received a mass email from Ministers Prentice and Verner and have already sent a reply cc: everyone I could find without spending too much time since I have a big exam tomorrow. I suggested that these two debate Doctorow and Geist live and air it on YouTube.

    Wouldn't it be phenomenal if they actually did . . .

    Monday, June 2, 2008

    Can Life Evolve in Simulated Worlds?

    Many cute little characters like this "Norn" are the stars of a computer game called "Creatures". In the game, the little characters hatch from eggs, then proceed to learn, forget, eat, get old, get bored, become curious, etc, etc, all seemingly without the player's interference. Could these little creatures really be called alive? Steve Grand, the head programmer of the game believed the answer to be "Yes", and he wrote a whole book to explain why.
    The book is called "Creation: Life and How to Make it". On the whole I recommend it, though the cockiness of the title rears its head in the writing as well. My opinion is that the author's philosophies about what life is, and his critiques of other such philosophies are a little hasty, however there are one or two very valuable ideas I came away with.
    The first is the idea that while simulations (of life) never become the real thing (actual life), a simulated world or substrate is able to give rise to things that have every right to be called real. For example, one could write a computer program to simulate the behaviour of atoms in some physical space. Under no interpretation would those atoms ever be called real atoms. However, should they begin to cluster into molecules, then perhaps those molecules could be called "real". I think the argument gets more compelling if one takes it up to an even higher level, to proteins, cells, etc. How would a cell "know" that it's constituent atoms were simulated? Does it make a difference?
    Regulars to the blog take note: this argument made me think of my objection to things like the "Big Dog" robot displaying real intelligence. Its behaviour is directly programmed, rather than arising naturally from some lower level ideas of gravity, orientation, etc (and perhaps essentially, a desire not to fall!).
    Of course, Grand claims in his book that his game provides detailed rules for a virtual world, and for both neural and "digestive" systems for his creatures, and from this substrate springs what he claims is bona-fide life. This leads me to the second thing I liked about the book; the details about the extremely clever design required to program learning (and forgetting!) creatures using very finite computer memory. I admit, after scoffing at his philosophy, his programming ideas about how to simulate lifelike neurons and chemistry in his creatures were nearly inspiring.
    For two disappointing final notes, Grand admits he doesn't believe his creatures are conscious; just alive (he says consciousness is tied up with models of the world which his creatures do not have). Secondly, I downloaded a free mini-version of the game called Docking Station, and found that despite all the intelligent simulating I knew was going on, the game was gaudy and somewhat boring. However, you may be interested to know that at the printing of Grand's book, the population of both Creatures, and Creatures players worldwide numbered several million each.

    Saturday, May 31, 2008

    Artificial selection produces an impressive array of wild mustard varieties.

    - "Artificial selection is the selective breeding of domesticated plants and animals."
    - "For example, broccoli, cauliflower, cabbages, Brussels sprouts and kale are all varieties of a single species of wild mustard."

    Wikipedia entry on Brassica oleracea, Brassica.

    Textbook cited: Biology: Concepts & Connections. 5ed. Campbell, Reece, Taylor & Simon.

    Vegetarianism is about human rights; an argument from biology.

    This week (of June 2) my biology students will be reading a chapter on communities and ecosystems.

    Here are a few selected facts from their readings, for your consideration:

    - "Each day, planet Earth receives about 10^19 kcal of solar energy." The textbook compares this amount of energy to the energy of 100 million atomic bombs. For your reference, one kcal is equal to 4184 joules.
    - "Most of this energy is absorbed, scattered, or reflected by the atmosphere or by Earth's surface."
    - " . . . only 1% is converted to chemical energy by photosynthesis."
    - " . . . on a global scale this is enough to produce about 170 billion tons of organic material per year"
    - "When energy flows as organic matter . . . much of it is lost at each link in (the) food chain."
    - "The efficiencies of energy transfer (from one level of the food chain to the next) usually range from 5 to 20%. In other words, 80 to 95% of the energy . . . never transfers from (one level) to the next."
    - "An important implication of this stepwise decline of energy in a trophic tructure is that the amount of energy available to top-level consumers (carnivores) is small compared with that available to lower-level consumers (herbivores)."
    - This explains why "food chains are limited to three to five levels; there is simply not enough energy . . . to support another (level in the food chain)."

    For example:
    1,000,000 kcal of sunlight > 10,000 kcal of plant vegetation > 1,000 kcal of primary consumers > 100 kcal of secondary consumers > 10 kcal of tertiary consumers

    - "Eating meat of any kind is an expensive luxury, both economically and environmentally."
    - "Based on the rough estimate that 10% of the energy available in a trophic level (level of the food chain) is available at the next higher level up ... the human population has about ten times more energy available to it when people eat corn than when they process the same amount of energy of corn through another tropic level and eat corn-fed beef."
    - "It is likely that as the human population expands, meat consumption will become even more of a luxury than it is today."
    - Demand for meat drives up the prices of grains, fruits and vegetables because "potential supply of plants for direct consumption as food for humans is diminished by the use of agricultural land to grow feed for cattle, chickens and other meat sources."

    And the pièce de résistance: Boss Hog: America's top pork producer churns out a sea of waste that has destroyed rivers, killed millions of fish and generated one of the largest fines in EPA history.

    What do you think of this post format? It makes it much easier for me to share interesting facts & ideas that I'm thinking about on a short time budget, but it's no good if you guys find it unpleasant to read. If it's a hit, then let me know if there are any topics in biology you'd like me to cover.

    Textbook cited: Biology: Concepts & Connections. 5ed. Campbell, Reece, Taylor & Simon.

    Wednesday, May 21, 2008


    From One Laptop per Child, this is the design for the XOXO, planned for a 2010 release. The current iteration looks very much like a toy, but this thing is just sleek. Oh, to be a child in 2010!

    They showed off the current design at the Design and the Elastic Mind exhibit, and before that I wasn't terribly interested in the project, but getting close certainly piqued my interest. They're creating a new interface designed to be natural for children to use, which indeed means natural to anyone not entrenched in the current (am I really about to say this?) desktop/window paradigm. Which plays a part in a larger move towards natural interfaces that I'm very much thrilled to be in the midst of. What will a generation of children raised on this mean for computing? For communication? I can't wait to see!

    Via TED.

    Tuesday, May 20, 2008

    ‘At least 12% of US biology teachers are creationist’

    So says research reported on in The Great Beyond. What in the world is wrong with us?

    Saturday, May 17, 2008

    Bioluminescent Tides

    "Bioluminescent dinoflagellates (Lingulodinium polyedrum) lighting abreaking wave at midnight. The blue light is a result of a luciferase enzyme (like firefly luciferase, but the enzyme in L. polyedrum shares no similarity with that of the firefly enzyme). Under the right conditions, the dinoflagellates become so numerous that the water takes on a muddy reddish color (hence the name "Red Tide"). The bioluminescence is only visible at night. The photo was taken 6/26/2005with a Canon Rebel XT - 6s, f5.6, ISO 1600, 85mm (135mm equiv)."(Images and text from Flickr's msauder. Click to view the rest of his photostream.)

    Apparently, "the last sinking of a German U-boat in WWI occurred in 1918, when dinoflagellate bioluminescence revealed its location (Tarasov 1956)."
    (Live Marine and Freshwater Phytoplankton)

    Fractal Furniture


    Wednesday, May 14, 2008

    Shrimp Eyes

    Apparently the most enviable species on the planet is not the ant eater. Far from it, in fact. It's the mantis shrimp.

    Look at that guy. He can do so many things that you can't. Specifically, he's got 11 or 12 primary colors ranging from infrared to ultraviolet and can apparently, as researchers have recently discovered, also see six forms of polarization. You see something like one form. An interesting fact from the linked press release is that "the physics we used to understand what was going on [in the mantis shrimp's eye] is the same physics that we use in quantum computing for optimal storage of information."

    Via The Great Beyond.

    Bird Brain!

    For a couple weeks I've had a tab open in my browser with the sole intent of writing a quick post about it. I came across an old Neurophilosophy article talking about avian intelligence, crows in particular. It cast birds in a completely new light for me, which is always a welcome event. They went from being creatures that lived in a completely foreign way to being more familiar thinking beings, problem solvers. There are videos included in that article that demonstrate the ability of these crows to learn and adapt to our environment in what I think are remarkable ways. They craft tools with whatever they have lying around; they use traffic to crack nuts!

    A perfect followup to that article is this video of Joshua Klein talking at this year's TED conference in which he discusses the intelligence of crows and explores the possibility of humans working symbiotically with them. Definitely worth ten minutes of your time.

    Thursday, May 1, 2008

    Blue Brain

    Somewhere in Switzerland, a team of researchers has spent a great deal of time learning exactly how a neocortical column works and they've built a supercomputer to simulate it perfectly.

    It didn't take long before the model reacted. After only a few electrical jolts, the artificial neural circuit began to act just like a real neural circuit. Clusters of connected neurons began to fire in close synchrony: the cells were wiring themselves together. Different cell types obeyed their genetic instructions. The scientists could see the cellular looms flash and then fade as the cells wove themselves into meaningful patterns. Dendrites reached out to each other, like branches looking for light. "This all happened on its own," Markram says. "It was entirely spontaneous." For the Blue Brain team, it was a thrilling breakthrough. After years of hard work, they were finally able to watch their make-believe brain develop, synapse by synapse. The microchips were turning themselves into a mind. #

    Henry Markram, the director of the Blue Brain project, takes issue with the strictly-empirical nature of neuroscience and favors a more model-based approach akin to physics. It's in that spirit that he and his team have come up with Blue Brain, where its "virtual neurons are more real than reality."

    After scaling up the current iteration of Blue Brain, he plans to give his virtual brain a body in the form of a robotic rat (all his work is being modeled around the likeness of a two-week old rat) and watch it grow into a real mind, learning through its body just as any 'real' animal.

    This is one of the most exciting articles I've read in ages, and I urge you to take the time to read it yourself. I always sort of wondered how we'd get from our current state of technology to Kurzweil's Singularity, and this has the distinct feel of being the direct course to that end.

    Wednesday, April 30, 2008

    Resistors, Inductors, Capacitors... Memristors?

    It seems HP Labs has brought to fruition the physical realisation of an additional, theoretically predicted, fundamental circuit element: the memristor. Originally described in Chua, 1971, numerous sources are claiming that HP has produced a 'practical' (for some value of practical) physical incarnation of the predicted device. ("The Missing Memristor Found" abstract)

    My understanding is that the memristor functions as a time-varying resistor whose resistance varies depending on the history of its voltage. What will the consequences be? So far there is a lot of talk about practical applications including persistent memory and faster pattern recognition... I want to hear about the (presently) impractical applications.

    "Building an analog computer in which you don't use 1s and 0s and instead use essentially all shades of gray in between is one of the things we're already working on," says Williams. -- Wired, Scientists Create First Memristor, April 30th, 2008
    Next thing... a neural interface?

    Richard Dawkins this Saturday

    I may just be the only reader of this blog in the NY area, but I believe this is worth mentioning anyhow. Richard Dawkins will be giving a talk bright and early this saturday morning, and you can apparently RSVP in the comments section of this post to get put on the list to attend.

    There's probably a catch, but I'd say it's worth a shot.

    Update: Full! My new plan is to crowd around the entrance and scream like a teenage KISS fan the second I see someone I've seen a picture of before. They'll be forced to let me in.

    Tuesday, April 29, 2008

    Beautiful Robots



    Those are via Engadget.

    Also there's the AirRay:

    I got to see the AirRay as well as a couple pneumatic water-dwelling robots on display at the Design and the Elastic Mind exhibit at the MoMa on Sunday. I'll be posting some details of all I saw there here or on the other blog before too long. So neat!

    OH! And this is a natural place to link Theo Jansen's Strandbeasts, kinetic sculptures that Jansen speaks of as living beings that will roam the beaches.