David and Goliath Book Review

David&Goliath

I recently finished listening to an audiobook version of Malcolm Gladwell’s David and Goliath. The nonfiction piece focuses on how being an underdog can occasionally confer advantages that the “overdog” doesn’t expect.

The book uses a wide-range of examples of underdogs overcoming their disadvantages and actually using them as jumping off points to topple bigger and stronger opponents.

This isn’t a new idea to me or the world. Scholars were peddling this theory at least 1,500 years ago when the Roman Empire fell. I first read about it in Frank Herbert’s science fiction masterpiece, Dune, where the fictional race of Freman are hardened by their desert homeland and are able to overcome the forces of the Padishah Emperor. Continue reading

Sacramento Underground Tour

This weekend my wife and I went to Old Sac to take one of Sacramento’s Underground Tours.

Old Sac is a historical neighborhood in Sacramento that has turned into a bit of a tourist trap.

All the old buildings from the Gold Rush in the 1850s and 60s are still there, converted into restaurants and gift shops instead of hotels and supply stores.

(I also feel a personal responsibility to warn you about La Terraza restaurant in Old Sac. Food’s bad! Don’t be tempted by the spectacular view! Stay away!)

Bunch of old buildings, right? What can we learn from the tour?

Tour comes with everything you see here!
Tour comes with everything you see here!

Our tour guide, Schoolmaster Mrs. Appleton, told us the basics of Sacramento history first that every Californian knows. Continue reading

HCl Spill in the Lab

I had an interesting day in the lab. I spilled a large amount of concentrated HCl on the floor!

I would’ve taken a picture of the damage zone, but my first thought was, “Oh shit!” not, “This would look good on my blog.”

HCl is the strongest acid used in most labs. If you’re familiar with the pH scale it goes from 1-14. Water is 7. Orange juice is 3 and stomach acid is 1.

Concentrated HCl is -1. the pH scale is a log scale so that means concentrated HCl is 100 times stronger than stomach acid.

HCl is used all the time in lab work, but often in a more dilute form. I had the concentrated stuff out so I could dilute a small amount of it in a large bottle of water.

I got the amount I needed and then I dropped the large bottle on the floor as I was putting it away. SPLOOSH! CRACK! Glass and acid everywhere!

It started eating away at the floor immediately, BUT WAIT! THERE’S MORE!

HCl is composed of Hydrogen (H) and Chlorine (Cl) in water. In concentrated HCl the acid is so smooshed together that it starts falling apart into its component parts of Hydrogen and Chlorine gas.

Chlorine is a deadly gas! Hurray! -_-

I closed off the room and put a warning sign on it before rushing upstairs to contact my PI (boss).

He came down and we agreed that we needed to call Environmental, Health, and Safety (EH&S). They’re the guys who handle spills in the lab that my labmates and I can’t deal with.

EH&S didn’t come by themselves though!

First five firemen came up. Two cops as well, but they left after I told them I wasn’t injured. Some of the acid got on my shoe but nothing serious.

The firefighters stuck around until EH&S arrived. Three people from EH&S came to assess the situation and after doing so they sent two more people to do the actual cleanup work.

So a small spill of a nasty chemical attracted a dozen emergency response personnel.

Meanwhile I took off my shoe just to be safe and am now wearing a bootie for the rest of the day.

The bike ride of shame awaits me when I go home. EVERYONE WILL KNOW!!!
The bike ride of shame awaits me when I go home. EVERYONE WILL KNOW!!!

The cleanup crew removed all the broken glass and chlorine gas as well as most of the acid that was still on the ground.

Supply cart. The crew is inside cleaning up my mistakes.
Supply cart. The crew is inside cleaning up my mistakes.

After they finished up I came in with Sodium Carbonate (grainy baking soda) to clean up the rest of the acid.

I still managed to work with the dilute acid I made, but what a day!

-GoCorral

The Division: Game Feasibility

I posted a review of The Division earlier. The game plays quite well and if you’re looking for an FPS to play with your friends then The Division should fill that hole nicely.

The plot though!

The plot is barebones, with most of it being shown to the player in hidden conversations between NPCs throughout the game instead of directly telling you what’s going on (a good story device!).

In the game an evil scientist has altered the small pox virus to be extremely lethal and resistant to treatment. Continue reading

Thesis Proposal and Homework

Some of you may be asking, “Where, oh where, has GoCorral gone? Where is the weekly update of his blog? There hasn’t even been a picture of his toenails to tell us he’s still alive!”

Well, I am still alive, I’ve just been rather busy with school these last few days.

Among my many responsibilities I have had:
1. A massive final project on homologous genes to the C. elegans myosin gene, unc-54, that is rapidly approaching 50 pages in length.
2. A final paper on intron retention being the first sign of speciation.
3. Scheduling and preparing my thesis proposal presentation.
4. Grading essays for the basic biology class I am teaching this semester.
5. All the usual stuff I have to do.

I’m keeping a good handle on #1 and #5. #4 is a slow truck that keeps on going.

Due to all the other stuff I’ve been doing #2 did not turn out as good as I would’ve liked. I loved the thesis of that paper, but I wish I’d used more time to find additional supporting evidence and described the supporting evidence in a better fashion.

#3 is the most exciting one! My thesis proposal presentation happened on Friday and was probably the most important moment in my career up to this point.

I got super nervous before giving the presentation and made a few mistakes in the preparation and delivery, but it still went quite well.

Every presentation should have at least one picture of a confused panda.
Every presentation should have at least one picture of a confused panda.

I passed the proposal which means I can continue on with my project! Woohoo! I do have to update my abstract to reflect my definite research goals which were outlined in the meeting.

That’s what I’ve been up to. There’s still more to do! I predict I’ll be done with most of it by the end of next week. After that, regular blog updates will resume.

-GoCorral

NASA is Hiring

I am soooo jealous.
I am soooo jealous.

NASA made an interesting announcement, they’re looking for new astronauts!

This came as a surprise to me as I’d thought NASA had discontinued all manned missions.

As far as I know the halt on manned missions happened for two reasons, funding is tight and NASA is an obvious thing to cut and we already did the man on the moon thing so why go again?

As to the funding, I’m not sure what’s going on there. Regardless, the missions NASA is planning are scheduled ten years out so the funding situation could be entirely different then.

But what are the new missions?

Not going to Mars like Mark Watney in The Martian, but almost as good!

NASA will be landing an astronaut on an asteroid.

There are a group of asteroids called “near-Earth asteroids” that have orbits around the sun pretty similar to Earth’s orbit.

A couple of the near-Earth asteroids are as big two kilometers across (about a mile).

Before landing a person on an asteroid, NASA plans to land a rover like what they did with the Rosetta space probe on a comet. Then a manned mission will commence in 2025.

I don’t know which asteroid NASA will be landing an astronaut on, there are a whole bunch to choose from. Regardless, this appears to be the next step in manned space exploration.

NASA hopes this will be a stepping stone to manned missions on Mars.

In addition to the work on the asteroids, astronauts are spending longer amounts of time on the ISS. They’re doing this so we can see what precautions need to be taken when someone is in space for years at a time.

A mission to Mars would take a year or two, so we need to be prepared for how someone’s mind and body reacts to being in space for that long.

So enough about why NASA is hiring astronauts, how do I get the job?

If you’re like me, upon hearing the news that NASA is hiring you immediately looked up the qualifications they’re looking for.

They want someone with at least a Master’s degree in science or engineering. I’m working on that, so good so far.

The next big qualification is 1,000 hours of logged jet plane fight time.

If you’re paying for lessons and rental time on a plane that amount of logged time would cost upwards of $50,000. So you either have to be really serious about flying jets recreationally, a commercial flyer, or a member of the airforce.

There are a few other qualifications, but nothing as big as those two.

Obviously I don’t meet that requirement, but maybe some kid is reading this and is thinking, “If I get a Master’s in physics and learn to fly a jet then I’d be ready to apply to be an astronaut by the time NASA starts doing missions to Mars.”

That’s the word from the space world!

If you want to read more about the process for hiring astronauts check out these two links: NASA’s Info Site, NASA’s Hiring Site

-GoCorral

Cool Stuff from Last Semester

I did some cool stuff last semester in my science classes that I’d like to show you guys.

The gist of it is… This picture:


This is a picture taken by my lab group in my basic lab technique class last semester of a mouse fibroblast cell moving into a simulated wound on a glass slide.

Fibroblast cells are kind of like the contractors of your body when you get a scratch or wound. There are your first responders to the “disaster,” your immune system, and then fibroblasts go in to start the process of rebuilding your tissue by laying the foundation for other cells to move in.

A lot of scientists are interested in wound healing. How can we make it faster? How can we make it better so people don’t have lingering problems after the superficial injury has healed? How can we prevent infection? How can we prevent scarring?

Those questions are tested with a variety of experiments but one of the msot common is the scratch assay.

A bunch of fibroblasts are grown on a glass slide until they practically cover it. Then the slide is scratched.

The fibroblasts move into the scratch, thinking it is a wound. Their movement into the scratch is measured in a couple different ways and those measurements can tell us a little bit more about how wounds heal.

Which brings me back to the picture my lab group took. Obviously its got a lot of color and is very prety, but what are all those colors? What’s going on in that picture?

My lab group scratched the space above the big cell in teh picture. The cell is now moving into the scratch.

The red lines are called actin. Actin is the support structure of your cells. Cells move by extending actin filaments where they want to go and breaking them down behind them.

The green parts are called vinculin. Vinculin is spread throughout the cell and localizes into spots where the cell is attached to a surface to assist in adhereing to that surface. All those bright green spots are where the vinculin is helping the cell hold onto the glass slide.

The blue parts are cell nuclei. Each cell has one nucleus and I’ll bet you can pick out the one that belongs to all the actin and vinculin in the middle of this picture.

I did a lot more stuff on scratch assays in this class and leaarned a few new techniques, but the best part was definitely getting this picture.

Oh and apologies to any color blind people. I have no idea how to spearatae out the red and green things for you. Enjoy!

-GoCorral

Graduated Student Tour

While letting myself into my lab a woman approached me and said, “Hi!”

She had just graduated UC Davis and was looking around all the buildings she hadn’t been in much.

She was a Landscape Architecture major (didn’t even know you could major in that). My building is for biological sciences, so its understandable that she had probably never set foot in it before.

My lab’s building, Briggs Hall, is interesting from an architecture perspective (but maybe not landscape architecture).

The building was built in 1971 when there were a lot of campus demonstrations (still are! Pepper Spray Cop was at UC Davis).

A method of cutting down on demonstrations was giving students no places to gather indoors. Thus Briggs Hall’s layout is amazing confusing and even I get lost in it after working in the building for several years.

Briggs also doesn’t have any staircases inside. All of the stairs are on the exterior of the building. Don’t ask me what lunatic decided that was a good idea for a four story building.

Anyways, the recently graduated student asked if there was anything interesting in Briggs.

I showed her my lab. She glanced around in it, but not being a biologist she didn’t really understand anything in the lab.

I showed her the -80°C (-112°F) freezer which she did like as summer is starting in Davis.
I also showed her my favorite part of Briggs, the back exit by the police station.
wpid-20150617_140515.jpg
The back exit is where all the old equipment is put that no one wants anymore. These are the pieces that are too big to just throw in the trash.
There’s old computers, old centrifuges, old heating blocks, old incubators. Tons of cool science equipment.
It’s this sort of industrial wasteland and NO ONE EVER GOES THERE.
My lab is super peaceful, but if something ever got too stressful and I needed to go outside, this is where I’d go.
Why does industrial junk calm me down? I had an air filter going in my room constantly when I was a kid. That constant hum while I slept made me associate industrial hums and old appliances with peaceful rest.
So now places like this always calm me down.
Course, the graduated student didn’t get any of that business. Shook her hand and congratulated her on graduating after I showed her the junk pile before going back inside to my lab.
-GoCorral

Fixing the Camera Printer

image
Ancient technology from the long long ago. The printer is the thing on top of the computer tower. The camera is the giant cabinet looking thing to the right of the monitor.

We have something called a “gel doc printer” at my work. It’s purpose is self-evident. It prints documents of our gel pictures.

Gel doc printers are used infrequently and often labs share them. Ours is shared between… probably five different labs? Maybe more.

Taking pictures of gels is important in science. Gels are how we visualize DNA and proteins.

A digital copy is good enough for your own records, but you need a printed copy in case someone claims your digital copy is edited. The gel doc printer provides that physical copy.

Our printer is shared and an issue comes up that when the printer breaks we don’t know whose responsibility it is to fix it.

Usually the breaks are fixed easily. A reboot of the printer or the computer will suffice. Not this time!

This time the printer has refused to print any and all images despite the computer recognizing it as a printer that is plugged in and printing test pages.

Awful looking test pages, but test pages none the less.
Awful looking test pages, but test pages none the less.

I delved into it and realized the printer’s driver’s were outdated. Normally this would be an easy problem to fix. Not so!

You see, the computer the printer is attached to runs Windows XP which is no longer supported by Microsoft.

An unsupported operating system can easily be hacked which means this computer can no longer be connected to the internet. If it was, hackers would have an easy access point to UC Davis’s systems.

What that means is I couldn’t just download an update to the drivers like usual. I had to download the update on my laptop and then move it over to the printer computer with my USB drive.

So I downloaded the drivers and moved them over to the computer. “But wait! You need the driver install program.”

Okay. I get that and move it over. “But wait! You need .Net Framework 4 to use the driver install program!”

Okay… I get that and move it over. “BUT WAIT! You need Windows Service Pack 3 to install .Net Framework 4!”

Okaayyyy… Move that on over. And that one finally installs!

Moving backwards, the .Net Framework 4 installed as well. Along with the patch I got for that.

Then the driver install program laughed at me and said it needed access to the internet after all. I tried installing the drivers on my own, but no luck there.

I researched more on the problem. The printer is able to print out the very first part of all the images. Then it disconnects from the computer, reconnects, and decides the print job is complete.

I found absolutely nothing on how to fix that problem. There were some suggestions that it was a problem with the connection to the computer, but switching the USB port used by the printer changed nothing.

Maybe a new USB cable would do the trick, but I’m unsure if those are available for printers this old or whether it would fix the problem.

For now, all the images are put on USB sticks and printed on different computers.

-GoCorral

Institute of Regenerative Cures

My class got to go on a field trip last week.

150508_002
All the joys of barely being able to see the tour guide when you’re at the back of the group.

I know! Field trips in a Master’s of Science program? How ridiculous!

It was awesome. We went to the Institute of Regenerative Cures in Sacramento.

I arrived early and waited out front with some classmates. Our tour guide arrived and we waited out front a little longer til everyone showed up.

While waiting the tour guide, who had designed the building we were about to go into, told us about his hobby, early television history!

After the primer on early television we entered the building and got a tour of one of the best facilities for practicing biology in existence right now.

The building itself was actually built a long time ago for the California state fair. It was the “women’s building.”

The brick exterior and columnaic entrance have stayed the same since the building was constructed to maintain the historical site. The interior has been heavily modified.

The building had no roof back in the day and was just an enclosure for a bunch of different events that you usually see at state fairs.

The building was sold to the University of California system. They slapped a roof on it, and used it to store records.

Our tour guide said that he was called in to turn it into a biology facility later on. Half the building is used for bio research while the other half is rented out to other companies.

150508_001
The entrance hallway with pictures of the cooler discoveries at the Institute.

The researchers in the Institute are working on a number of things. They researched a treatment for the “bubble boy disease” there. They’re working on using umbilical cords to create bone marrow for transplants, using Tal proteins to treat Huntington’s, creating HIV resistant cells, and helping people who can’t swallow to swallow are just a few of the things they work on there.

Where all the research is done!
Where all the research is done!

The tour guide also showed us the section that he was most proud of as he had designed it. A set of rooms for making the actual drugs and proteins to export to hospitals. Making the drugs requires extremely sterile technique to prevent giving someone who is already sick something that will make them worse. The rooms are designed to be extremely sterile.

To enter the rooms you pass through an airlock where you are required to cover every inch of your body in a disposable gown.

The airlock goes to a hallway with access to three separate clean rooms.

There is “negative pressure” in the rooms. That means that air is constantly entering the room from the top and going out the bottom. This is so that if any cells that are worked with in the rooms get into the air, they will be redirected to teh ground and sucked out through a grate in the wall instead of ending up in someone’s medicine.

The air is cleaned excessively to about 3000 times more clean than average air before entering the facility.

There is a lot of electrical equipment in the rooms that will require replacing eventually. To prevent electricians from having to gown up just to replace a lightbulb, all the eletricals are accessible from panels on the second story of the building.

It was pretty cool for a scientist like me to see the best possible place to do research in. The tour guide mentioned that he does tours of the interior of the super clean rooms for smaller groups. I might take him up on that at a later time!

-GoCorral