So You Want to Be a Molecular Biologist?

Short on time tonight, but this was too cool a thing to pass up.

So You Want to Be a Molecular Biologist?
I saw this link over at Credit Bubble Stocks and you know I had to click over:
DNA is now DIY: OpenPCR ships worldwide

The eagerly awaited OpenPCR kit is now shipping! UPS picked up the first batch of kits and OpenPCRs are on their way to users in 5 continents and 13 countries around the world. For $512, every OpenPCR kit includes all the parts, tools, and beautiful printed instructions – you ONLY need a set of screwdrivers.

A PCR machine is basically a copy machine for DNA. It is essential for most work with DNA, things like exposing fraud at a sushi restaurant, diagnosing diseases including HIV and H1N1, or exploring your own genome. The guy who discovered the PCR process earned a Nobel Prize in 1993, and OpenPCR is now the first open source PCR machine.

WOW!

Now first I want to congratulate the OpenPCR team. It looks like they made a true performance PCR machine using basic parts and have it at an attractive price point. $512 is amazing for a good PCR machine that is reliable. The model is a 16 well (16 samples at once) which is not too bad, I would have thought maybe a 4 sample machine at most.

Garage Labs, or Home Labs have been getting more and more popular as the price points for technology have come down and the science behind the techniques is easily gobbled up in the information age. The New York Times ran an item on this which included the OpenPCR work:
Home Labs on the Rise for the Fun of Science

So is this the time to become a mad scientist yourself? Well, maybe and no.

I have to admit I am an inch away from buying an OpenPCR machine tonight. I would love to see how it works and all the effort in the project seems like it should be rewarded. Still, garage days for new era science? A few stumbling blocks come to mind.

Regulations
I can only speak for Massachusetts, but there is no way you can manage biological samples (not your own) at a residence without risking huge problems.

Reagents
Some biology reagents can be had from basic household items, while others really cannot. Things like alcohol and deionized water should be easy, but PCR enzymes are going to have to be ordered. PFU and Fusion are not going to get shipped to a residential address anytime soon. Consumables like DNA-free PCR tubes and other items also are not easy to get at a non-academic or business location. Pipet tips, the list goes on and on.

Waste
A PCR reaction must be seen on an agarose gel to make sense, unless you have a cool real-time system that can read DNA bands in a tube (big bucks!). To visualize DNA you can stain with ethidium bromide (potent carcinogen) or move to newer products which are non toxic but require special equipment to visualize. SYBER Green and Gold come to mind. In any case all this stuff and all the plastic stuff needs to be disposed of and once it shows up in your garbage, you are going to get a visit from the town at a minimum, and maybe a SWAT team at worse as they track down your amateur laboratory.

Clean Start Hard to Come By
For real basic things, careful handling of samples would be acceptable, but say you wanted to type ribosomal DNA from some crazy bacteria you found in the garage? How can you be sure your work space, equipment, and tools are not covered in other bacteria? DNA is everywhere, it can be a real hassle to limit contamination. DNAase and UV crosslinking are steps taken to make sure an area is clean. You want to do that to your garage?

I don't want this to come away as a nasty "I am a scientist defending my field" sort of thing. Trust me, I would LOVE to do all my lab work at home and save the commute! Please make this happen! Maybe robots in the future can be commanded form my smart phone to do the lab work?? Now there is an idea.

I have huge respect for the work by OpenPCR, and maybe for some simplified experiments using things one can get legally and easily would be excellent fun for an at home project. This stuff is not hard to learn, but can be really fun to do when you see the results. The "A-Ha!" moment is always a winner. An OpenPCR machine along with some sets of experiments enclosed? Now we are cooking. To be fair they may already be on this.

Years ago I had this idea for a company that would take a cheek cell sample from Mom, Dad, and the kids. A RFLP analysis or other fingerprinting could be done and then a high resolution picture could me sent back as a family diagram sort of thing. Of course I never got around to it. Last check, somebody did! Just like my idea way back when for a curvy radiator for cars for more surface area cooling, too late.

Have a good night.

Just the Good Stuff

Who needs deep thought on a Friday night? Not I!

What about "Personalized Medicine"?
Reader Watchtower asked a question about how having genomic information may play a role in possible treatments for people. This is an area that I have tons of experience and knowledge about so you can imagine I wanted to go all out! For the sake of brevity and simplicity I will just use a few links and offer some commentary.

I was at a company when I first started working that was at the forefront of thinking about "personalized medicine". Today it even has it's own Wiki entry!:

Personalized MedicinePersonalized medicine is a medical model emphasizing the systematic use of information about an individual patient to select or optimize that patient's preventative and therapeutic care. Personalized medicine can broadly be defined as products and services that leverage the science of genomics and proteomics (directly or indirectly) and capitalize on the trends toward wellness and consumerism to enable tailored approaches to prevention and care.

This sounds complex but it is not too bad. Every person has a unique genome. While maybe 99.9% of it is just like anyone else's there may be differences (as small as single nucleotide polymorphisms, SNP's or as large as gene fusions or re-arrangements) which can be used to predict how various treatments may impact that person. This is especially true in the case of cancer cell genomics. Some treatments may target a certain pathway to kill the cancer, but if that patient's cancer can side step that pathway or has a mutation in that gene then the treatment may not work at all and would be a waste of both time an resources.

Pharmacogenetics is a large area of interest right now as companies are looking to find their target markets ever more tightly. Clinical trials will often screen a patient group for markers that have been shown to be important for a drug's activity. One can focus on patients that will see a benefit this way.

I think the question was more in a broad sense and in that way having the genomes of various types of people (Norther European, Asian, African, etc) can help the choosing of treatments. We are still a ways away from being able to sequence a person's genome quickly, but luckily most time just small sections need to be looked at to determine the best treatment options. This goes on right now, no waiting for the future! Looking ahead I think the focus will result in better treatment on a patient to patient basis and cut down on dead end treatments. Still, there is a long way to go. Hope this helps!

Writing Sample
I have often teased that I sort of work on a possible long short story (novella?) that has been in my head for some time. I do try and think about it from time to time, but it never seems to come out right. I wanted to put what I had written down for the prologue section on here and see if it grabs anyone. No title, that's in flux, but here is how it would be set up:

Prologue
Look, I never set out to make "the device".

I was a kid in second grade with a new set of colored pencils. One day I sat down and started drawing. This led to the first schematics of the machine I imagined. It all made sense at the time, very useful, and I even thought it was possible. I was in second grade!

Don't ask me if I had a vision. I was not visited by aliens. No God whispered in my ear. I was just doodling and something appeared from no where. If I had it to do over, I would have drawn a fucking rainbow or a pony.

But I didn't.

Let me know what you think!

Good Joke
Caught this over at the Big Steel Keg cooking board. Men, do we need to enroll?:
CLASSES FOR MEN
Southwest Tech is offering a new 2 year associates degree: Becoming a Real Man. That's right, in just six mini-mesters, you, too, can be a real man as well as earn an associates degree in MA (Male Arts).
Please take a moment to look over the program outline.
FIRST YEAR
Autumn Schedule:
MEN 101 - Combating Stupidity
MEN 102 - You, Too, Can Do Housework
MEN 103 - PMS: Learn When to Keep Your Mouth Shut
MEN 104 - We Do Not Want Sleazy Under things for Christmas
Winter Schedule:
MEN 110 - Wonderful Laundry Techniques
MEN 111 - Understanding the Female Response to getting in at 2AM
MEN 112 - Pa renting: It Doesn't End with Conception
EAT 100 - Get a Life, Learn to Cook
EAT 101 - Get a Life, Learn to Cook II
ECON 001A - What's Hers is Hers
Spring Schedule:
MEN 120 - How NOT to Act Like a Buttface When You're Wrong
MEN 121 - Understanding Your Incompetence
MEN 122 - YOU, the Weaker Sex
MEN 123 - Reasons to Give Flowers
ECON 001C - What Was Yours is Hers
SECOND YEAR
Autumn Schedule:
SEX 101 - You CAN Fall Asleep without It
SEX 102 - Morning Dilemma: If It's Awake, Take a Shower
SEX 103 - How to Stay Awake After Sex
MEN 201 - How to Put the Toilet Seat Down
Elective (See Electives Below)
Winter Schedule:
MEN 210 - The Remote Control: Overcoming Your Dependency
MEN 211 - How to Not Act Younger than Your Children
MEN 212 - You, Too, Can Be a Designated Driver
MEN 213 - Honest, You Don't Look Like Tom Cruise
MEN 230A - Her Birthdays and Anniversaries Are Important
Spring Schedule:
MEN 220 - Omit! ting %&*! from Your Vocabulary (Pass/Fail Only)
MEN 221 - Fluffing the Blanket After Passing Gas Is Not Necessary
MEN 222 - Real Men Ask for Directions
MEN 223 - Thirty Minutes of Begging is NOT Considered Foreplay
MEN 230B - Her Birthdays and Anniversaries Are Important 2
Course Electives:
EAT 101 - Cooking with Tofu
EAT 102 - Utilization of Dining Utensils
EAT 103 - Burping and Belching Discreetly
MEN 231 - Mothers-in-law
MEN 232 - Appear to Be Listening
MEN 233 - Just Say "Yes, Dear"
ECON 001C - Cheaper to Keep Her

I pass many but not all of these!

Fascinating
Some nifty finds today.

Maybe a Native American went back to Iceland with the Vikings?:
Native Americans Visited Europe 1000 Years Ago
Very interesting and found via genomic sequencing!

Money tends to stay in certain geographic areas. Check out how closed up New England is with the cash!:

Very interesting.

Video Killed the Radio Star
Some items of possible interest.

Here is how all that genomic sequencing gets done in an easy to see sort of way:

There are newer ways that this is done as well, but this covers the basic idea. Here is a PCR reaction.

I think the film "The Fountain" could have been an all time great, but they missed the mark a little. Still, it is well worth a look and I can recommend it:


Just picked this classic up and will probably watch it tonight, "American Werewolf in London":

Awesome!

Rock Blogging
A few tunes to send you off for the weekend.

Gawains provided quite a list to choose from, so let's take a trip with KISS and "Room Service":

Never heard that one. My favorite KISS clip here.

Get your lighters up for Saigon Kick's ballad "Love is on the Way":

You know you like that one!

This maybe a repeat, but who cares! "Signs" by Tesla is a good tune:


I am past the no 1 year repeat zone with Soul Asylum and "Runaway Train":

'And everything seems cut and dry, day and night, earth and sky'

I like Garbage, not that kind, the band! Here is "The World is Not Enough":

Nice!

Two left. Two and out.

A little Pat Benatar goes a long way! Here is "All Fired Up":

Love that lady!

Last call! Get up, get up and get down, 911 is a joke in your town!

Close the show with a live clip of Metallica's "Ride the Lightning":


Have a good night.