Monday, February 26, 2007

Wait until they get a load of my Scienceball...

From today's NY Times, the story of the gyroball has crossed from the sports page to the science page. Parum-pum.

A quick recap of events. This past off season there was a major pursuit of a hot new pitching star from Japan by the name of Daisuke Matsuzaka, who ultimately went to the Boston Red Sox, who showered him with a cement truck full of money. Of the scrubble to percolate around his arrival was his ability to throw the gyroball, an alleged new kind of pitch that has been thrown in Japan for the last ten years or so.

Last week sports writer Jeff Passan wrote about his encounter with the creator of the gyroball, Kazushi Tezuka, and was...not so convinced. After being told he threw a perfect gyroball without much awareness, he seems to suggest the pitch's real strength is in its mystique, not any (no pun intended) revolutionary innovation.

There's also the suggestion it breaks down a pitcher's arm less, though I imagine the jury's out on that for a while. Maybe Joel Zumaya could continue to play Guitar Hero if he only threw gyroballs instead of flamethower heaters...

Sunday, February 18, 2007

Warming the Rubicon

Global Warming is not a new topic by any stretch of the imagination, but the events of the past 12 months probably give it a new resurgence. Last year Al Gore's seminal work An Inconvenient Truth brought the story back to the forefront with huge cinematic presence. The iconic image of a swirling hurricane storm system rising from an industrial smokestack dredged up sickening memories of the 2005 monster hurricane season. Late January brought ten corporations including big boys like Alcoa, BP America, Caterpillar, DuPont, General Electric, Lehman Brothers and four energy conglomerates to Washington to voice their collective concern. This was promptly followed by a host of top lawmakers, news of G8 members making it a top priority and the real touchstone, President Bush jumping on the global warming issue, this coming from a man who six years ago, through his press secretary said a 'Big No' to the need to change our lifestyles given our consumption needs outstripping every other nation many times over.

But the particle boards of politics are not the boards we saw at the Ripsaw. No, let us only concern ourselves with the science, the data at hand.

Perhaps the biggest problem is the name itself. It's easy to grasp the phrase Global Warming, experience a lack of such relative warmness and dismiss the entire exercise. Let me assure you, here in the gelid depths of Michigan, a little warming would be appreciated here in the thick of February.

Of course, when scientists speak of Global Warming, they don't mean the fun digits the weather man puts on your screen every morning, but rather, the consistent increase in temperature of the world's oceans, our most reliable global thermometer. The data are irrefutable: the oceans have been warming up for most of the past century and show no sign of breaking trends from our production of carbon dioxide.

We here in the States enjoy a second buffer, that is to say our geography. Living in one of the most fertile and buffered lands means our food production rarely suffers, especially coupled with our strong economic ability to purchase surplus from anywhere in the world and seize entire tributaries of product.

If the world were to begin developing conspicuous lesions that would capture the imagination of the press, it would happen in a delicate environment already dangerously balanced; say Australia. A little precipitation redistribution, a bit of advanced deforestation and soil erosion, and we could see famine and civil war collapse into any society within decades. Of course, I'm speaking hypothetically - Australia may have a lot of environmental damage but they're not collapsing. However, this kind of tragedy is already being played out right now in Haiti, in Somalia, in Nepal and in Afghanistan. Why we choose to ignore the very real impact the environmental damage we've done that's causing the severe political turmoil in these areas is likely a product of our lack of understanding of the data. Perhaps that will change soon.

The data is difficult to understand, to devise a plan from it even harder. However, Science is a cumulative effort, a dynamic knowledge body that we constantly modify and shape as new data streams in to shore up certain ideas and demolish others. Nothing is sacred - there is no room for nostalgia or tradition in science, only truth. In that spirit, the data is marching in a specific direction, and it appears for the first time that a true sea change (no pun intended) is occurring with the world at large. Indeed, global warming may be the first thing that unites all peoples together. After all, we haven't quite perfected lunar living, we're all stuck with each other until such an auspicious occasion.

If you're in search of further hard information, enjoy these links.
A fluorescent light bulb here, an efficiency toilet there, a whole mountain of knowledge everywhere, and we all might just have a nice place to live for a lot longer.

Friday, February 16, 2007

Ripsaw Robots #3

Ripsaw Robots will be a new feature that focuses on robotics in a very broad scope. From the useless to the revolutionary to the just plain giant and fantasy, Lish will bring you all the robot fix he can find.

The question I get more often than anything else is "Lish, all these robots are great, but what about my personal needs?" Look no further, because now you can build your own robot slave for just a few dollars. Based on that delicious Roomba techology, you can order parts for your customized mechanical creation right from the convenience of your non-roboticized home.

Often we ask what is so cool about robots, in their silly quest to discover if they have soul. It appears that question is answered. Now that is smooth.

Of course, robots only like to play jazz when they aren't mercilessly disassembling lobsters. "Continuous Flow Stunner" sounds like a wrestler's or Dragonball Z finishing move. On the other hand, 'CrustaStun' has its own creepy appeal.

But if you can't beat them, pretend to be like them, as the adage should say. A NASA historian suggests we will eventually be a cybernetic race. I always loved the Borg when I was growing up; I found the idea of amplifying one's body with technological distinctiveness not a way to lose one's humanity but possibly the only way of reaching forward and claiming it. To be human is to aspire what's in the mind and make it reality, yes?

But at the end of the day, we still have the big questions to answer. Fortunately, it seems we can fix it with robots who drive the Ford Taurus, which should be around at least for a few years. Serve the public trust, protect the innocent, uphold the law or Three things cannot be long hidden: the sun, the moon, and the truth.

Friday, February 09, 2007

It's all relative

A review of the American Museum of Natural History in New York is covering their new Human Origins exhibit. I particularly like the idea of bringing together the fossil and molecular evidence, because doing so is both powerful and essential to really get a clear understanding of both history and mechanism of the process.

I think a trip to NYC is warranted.

Wednesday, February 07, 2007


Following up the recent articles about its role in smoking, the insula is making news again, this time with some interesting commentary.

All mammals have insulas that read their body condition, Dr. Craig said. Information about the status of the body’s tissues and organs is carried from the receptors along distinct spinal pathways, into the brain stem and up to the posterior insula in the higher brain or cortex.

As such, all mammals have emotions, defined as sensations that provoke motivations. If an animal is hot, it seeks shade. If hungry, it looks for food. If hurt, it licks the wound.

Certainly my dogs show a wide variety of emotions, but there's clear limits to more complex emotion behaviors like empathy, revenge or sacrifice. Sounds like there's a wealth of research around that little fatty dingle of brainmeat.

Tuesday, February 06, 2007

(Secret) Viral Agents

In the last two days I've had two people independently ask me about the catching of colds in the Winter months. The Northern part of the States has taken a chill pounding over the past week, and you can expect a rise in sore throats and Kleenex sales.

The battle with the rhinovirus - the virus responsible for most colds - is one of an exponential arms race. With each new defense the body can throw down, the virus adapts, and the process begins anew ad infinitum. A major hurdle we're still dealing with as a species can be attributed to our upright posture
a severe weakness the virus and other bugs have been exploiting ever since we pushed off our knuckles and primarily moved around on two legs. But that's another story..

A virus is little more than a genetic bomb; most of it's components have evolved specifically to disrupt a human host's immune defenses with the core package a bit of RNA and replication protein to borgify and convert a cell into a virus factory.

The human host is no slouch and takes a layered approach to its considerable defense scheme. There are the anatomic barriers. The skin - a thick morass of cornified cells that appear like a gravelly, barren landscape on the microscopic level, sebum secreted from hair follicles give the skin an acidic, unwelcome feeling. The mucous membranes trap and hold invaders so ciliated hairs can ferry them up towards the mouth or nose for expectorations, as well as providing a home for local bacterial flora that soak up as much attachment space as possible in a competitive binding scenario. Should pathogens get all the way down to the gullet, that's usually a danger as well, as the low pH of the stomach will wilt all but the hardiest pathogens.

But should the virus be crafty enough or lucky enough to find a system compromised and get into the body, the host is not without further tricks. Upon detection by fingerprint-like molecules called antigens, the body can recruit dozens of different specialized cells to fight infection. Dendritic cells and other local watchdogs release signaling molecules called cytokines once they detect these antigens. First responder neutrophils arrive and wage a scorched earth warfare, triggering the inflammation response. Inflammation was originally described as having four qualities: rubor, tumor, calor and dolor. That is to say in modern terms, redness, swelling, heat and pain. All the lovely symptoms you'd associate with an upper respiratory infection, or any healing wound. The cytokine storm unleashed by the neutrophils can bring in a host of warriors depending on what the situation calls for. Massive, multi-nuclear macrophages to engulf and destroy necrotic tissues. Cytolytic killer cells designed to identify virally-infected host cells and punch holes in them with an immunologic cannon, faceted B-cells that churn out antibodies to bind up and help perturb and isolate antigens and eosinophils, the firemen of the body who come in to draw down the inflammatory inferno and bring things back towards normal operations.

Of course, these things don't happen instantly, as much as we'd like them to. It normally takes 3-4 days for a first response and 7-10 days for a human immune system to bring its full arsenal to bear and clear out an invading pathogen. The system is, much like the rest of our operations, susceptible to poor maintenance of the body as a whole. Fatigue, dehydration, poor diets, a lack of exercise - or lingering outside without a hat on in subzero temperatures like Mom warned out about - all such things can leave the body ripe for viral colonization.

A couple extra hand washings and a hat go a long way. Stay healthy this season!

Fantastic Voyage

Delicious Cellular Animations!

I always wondered if Coolio was an Asimov fan.

Hat tip to Retrospectacle.

Monday, February 05, 2007

Firefly Science - Luciferase and high throughput screening

Ah, fireflies - or 'Thunderbugs', as I idiomatically referred to them as a child. They are a staple of Summertime nostalgia, and a gateway insect for children to be drawn into the wonderful world of life science. A creature that can eat and create its own light source is something so alien and wonderful to us we are still exploring the science behind it. That said, Luciferase, the principle enzyme responsible for that soft yellow-green glow is a workhorse chemical tool in the high volume screening of compound libraries.

In screening, we often are looking for the activation of genes; that is to say whether the DNA is being transcribed into proteins, where those proteins then go out and perform the various functions of the cell ranging from the germane like cytoskeleton structure to the complex such as the release of a hormone or neurotransmitter. Every time a transcription event occurs, and we can exploit that mechanism for discovery research.

Originally, doing this required the use of radioactive tags - we could label a carbon in a designated molecule that could then be detected as a flash of light. Of course, radioactive work, despite its reliable and reproducible advantages, is not the prime choice of most research labs today.

A gene of interest can be appended downstream with the luciferase DNA and a gene promoter. Doing so allows us to infer that when our gene of interest is activated, our luciferase gene will be activated as well, and the cell will begin to produce luciferase in a ratiometric quantity, dependent on the strength of the promoter.

Now we can assess the amount of our gene of interest by lysing the cell, and adding the substrate luciferin. When this happens, the above reaction can take place, and a product of that reaction is light, which can be detected in the lab by a camera or photomultiplier tube (PMT). The more luciferase present, the more light the lysate will give off to be detected, and from that differential, we can begin to compare different treatments and draw conclusions from those results.

New sources of luciferase are being developed all the time. There's the firefly but there's a lot of different creatures out there with their own ways of giving off light. Mushrooms, sea-pansies and good ol' jellyfish that give us the standby Green Fluorescent Protein (GFP) With a series of enzymes that give off light at different wavelengths, one can create a very involved screen with multiple targets.

Sunday, February 04, 2007

Ripsaw Robots #2

Ripsaw Robots will be a new feature that focuses on robotics in a very broad scope. From the useless to the revolutionary to the just plain giant and fantasy, Lish will bring you all the robot fix he can find.

Alright, I spent far too much time in my chilly, chilly garage keeping my vehicles functioning in the stone cold of Winter. Perhaps I'll find some help amongst my mechanical friends!

The big news I've been scouting this week has to revolve around the developments in the flying car industry. It essentially functions like a helicopter without all the limitations of external rotor blades. Where's your flying car, you ask? Apparently it's just around the corner.

After the embarrassment of the last mission, folks at NASA are taking extra precautions with the landing site choice for the next robot to land on Mars. While robots might not count for life on Mars, it still makes an awesome movie premise.

Perhaps in the future we'll have robots park our cars in the big cities. Such technology already is getting marginal use in space-limited places like Japan. Such garages could easily maximize our ability to cram more and more people into our cities.

Got a robot you want to show off? Maybe you should send it over to the greater Frisco area for the Maker Faire. Perhaps you might get a chance to see these guys and their Star Wars inspired AT-ST lookalike. Let's hope there's no paleolithic society of advanced rodent men. They tend to shun such bold innovations.

But really, as cool as robots are, making them behave like insects is a lot harder than it sounds.

Now if we could only get a robot to change car batteries. Doing so in subzero temperatures is definitely the work for those of the cybernetic persuasion.