Archive for: July, 2011

Paying thanks to John Dalton....

Jul 27 2011 Published by under Lab, Uncategorized

who passed away on this day way way back in 1844, you know before we had iPhones or debt ceiling squabbles.

Any of us that do protein know what a Dalton is and today is the day for us and anyone else who uses atomic mass to pay homage to the deceased English chemist and physicist.  Dalton was also an accomplished meteorologist and even did a little work on colour blindness.  But a big knock on the Brit was that he was not such so meticulous at measurements and played a little fast and loose, but otherwise he was a decent bloke.

Thanks J-Dog!  I'm going to pour out some marker ladder for my homie and celebrate with a little Zeppelin..

You gotta love the old Gospel song that was popularized by Blind Willie Johnson and masterfully played by Zep. Page playing in the open A-chord slide guitar, JPJ rocking a fretless base, and John Bonham's rapid machine gun firing of the drums, and plant ain't so bad either.

 

 

One response so far

Oh crap, I think I'm collaborating...

Jul 26 2011 Published by under Lab

Damnit I've really gone and done it this time.  This all started when the bossman came to me with a neighboring PI and said unto me:

"Genomic love thy neighbor scientifically."

And I said unto him, "Yes, Lord."

So now I'm stuck providing technical expertise to a project that I have no experience in but am well versed in the methods to be used.  Originally I thought I would just be helping with experimental design, giving them my protocols, troubleshooting, and analyzing data.  My hope was that I give them the tools to do what they need in their lab and we just see how it all shakes out.

Well that was the plan.  The PI and trainee both want to learn to do the work and the PI has asked to do it in my lab, AT MY BENCH, and under my supervision.  Shit.  Not really what I'm looking for right now as I'm already up to the gills in work as it is.  But if they don't mind a little bit of hurry up and wait to accommodate my workload then we should be able to knock this out.

So just lean on me yo, I got this!

 

5 responses so far

So sad...

Jul 22 2011 Published by under Uncategorized

This was a letter to the editor in my local paper.  The writer of the letter was responding to an editorial article that talked about New York legalizing gay marriage and that this was just a matter of time for the rest of the country to come on board.

""Same-sex marriage" is an oxymoron. I look forward to the REDACTED providing equal coverage of an opinion regarding the importance of preserving marriage between a man and a woman and the fact that science cannot provide irrefutable evidence of a gay gene or gay DNA. If people of the same sex choose to commit to a civil union, that is their business, but it does not justify government involvement of an institution that it did not create and should not redefine.
Hopefully, our society will continue to embrace and preserve the traditional marriage between a man and a woman as the cornerstone of our society intended for procreation and the education of offspring.
Susan"

This initially just made me mad but then I shift back to sadness because they are proponents of individual freedom, yet don't want to let a subset of people be who they want to be.

5 responses so far

How comic books got me into DNA...

Jul 20 2011 Published by under Uncategorized

So earlier this week I posted how my love of sports accidentally got me interested in science but what got me interested in DNA? Easy, comic books. No I'm not joking either. Growing up I loved sports but I was also a bit of a comic book nerd. My two dreams going up were to hit a home run in little league baseball (mission accomplished) and to become a comic book writer (mission not so accomplished as of yet). Why a comic book writer? Easy, I can't draw for shit but I was drawn to the way the authors could use a sparse amount of words, panels, and the visual effect to somehow richly develop characters and convey a powerful story of the human condition.

Yeah yeah, fan boy, we get it you love comic books, but how does this relate to you giving a rat's doodoo maker about DNA. Once again, easy, the X-Men. Now coming up I read most of the great comic book cannons: Alan Moore's Watchmen and From Hell, Neil Gaiman's The Sandman, and Frank Miller's Sin City. But X-Men was the first comic book that I ever laid eyes and hands upon in the old drugstore in town when my dad took me to the counter to get a sandwich and a soda. Now this may sound archaic to many but yes in fact many drugstores and stores had lunch counters in them and they could make a jam out Lime Rickey.

So the premise of the X-Men were a group of initially humans that were "mutants" who had special powers. Initially I was enamored by their special powers and how they coped with being different from everyone else. This is what struck a chord with me as I was really the only brown kid amongst a see of white and black. I was short, skinny, had a funny last name, and looking for a place to fit. Due to my early onset of myopia and constant requirement of glasses during my primary education years, I was initially drawn to the character of Cyclops.

He was bound to wear glasses forever but he had a cool power where he could in a less than polite manner fuck some stuff up with energy beams that were emitted from his eyes. I was fascinated with his mutant powers and was jealous how come I couldn't do that. Why didn't laser beams shoot out of my eyes when I took off my glasses?

Simple dummy: its fiction and you aren't a mutant. But I didn't know that, so I had to figure out what a mutant was so I consulted my all knowing oracle of knowledge, my grandmother's Funk & Wagnall's encyclopedia set. Now I couldn't find mutant in that volume but I found the term mutation, spawning further searches for genetics, DNA, Mendel, and reproduction. But this wasn't enough for me, I made my dad take me to the local library where I was able to get my grubby little hands on a dogeared copy of James Watson's The Double Helix, which piqued my interest in DNA.

From their I would go on to grab a biology textbook and learn about Avery, MacLeod, and McCarty providing evidence for DNA as the hereditary material in the cell, Meselson and Stahl showing semi-conservative replication, and how this young upstart Kary Mullis's PCR process would revolutionize biology.

So while I may never become a comic book writer, I'm eternally grateful for my childhood indulgence that lead me down the path that would eventually make me a scientist.

11 responses so far

Thanks iTunes Shuffle...

Jul 20 2011 Published by under Uncategorized

Usually my iTunes shuffle puts together a Dimaggio-like streak of crappy tunes, but not this morning during cell culture.  The stars must have aligned, Eric Cantor woke up on the right side of the bed, and someone sacrificed a chicken in their backyard to give me this solid 10 hit string of music while splitting cells.

Who are you?  -- The Who

Start me up -- Rolling Stones

Sympathy for the devil --  Rolling Stones (not really shuffling but I love this tune)

Rapper's Delight -- Sugar Hill Gang

Don't Cry -- Guns N' Roses

A boy named Sue -- Johnny Cash

Grinnin' in your face -- Son House

Part time lover -- Stevie Wonder

All along the watchtower -- Jimi Hendrix

Tightrope -- Stevie Ray Vaughn

You were solid today iTunes, now I have high expectations for you... so stop playing shit like...

4 responses so far

How my lack of a fastball got me interested in science

Jul 17 2011 Published by under Uncategorized

As a kid growing up I never had much interest in science. I mean I used to watch Mr. Wizard and Bill Nye the Science Guy, but I was way more interested in baseball. In fact that was pretty much all my friends and I could think about as kids coming up in the south. My best friend growing up was a kid named Gerry who lived down the street from us. Like most of the people who lived by us, we were of the lower class ilk but unlike us they were black.

My mother, who was brought up as a Southern Democrat, met Gerry's father and the rest of his family as a kid when she was shifted from her lilly white school to "negro" school during the enforced and albeit slow desegregation of the Johnson Administration. My grandmother had the option to keep her in white school but allowed her to go to the black school because in her opinion, "colored people are no different then white people like you and me, they deserve the same treatment and opportunities that we are afforded." My family always had a progressive stance on race and would get strange looks and hear the soft whispers of racism when a black boy was invited to sleepovers with my uncle when he was a young boy.

I gravitated to Gerry because I looked nothing like the white kids and my skin tone was only a few shades lighter than that of Gerry. So I preferred to spend my days hanging out with Gerry and his friends, playing sandlot baseball. I didn't have far to go, the sandlot was just across the street from my house. On this huge tract of property was a large seedy motel that faced out to the road and behind it lay an empty lot that had WWII cinderblock duplexes lining the perimeter. Our deal with the motel owner was that we would pick up trash around the property and maintain the sandlot and in exchange we got to play as much baseball as we wanted. The owner was a decent guy, he put a picnic table out back by the field for us to use. This came in handy when on Fridays we would make our weekly pilgrimage to the local Piggy Wiggly and buy up a bucket of fried chicken and come back with watermelon. Since my bike didn't have a basket and I was adept at riding with one or no hands, I was usually tasked with transporting the watermelon. As soon as we made it back to the sandlot, I'd run home and grab a bucket of water and a knife to cut up the watermelon. Napkins were dispensable, we had t-shirts with which to wipe our hands with. Those soccer weenies could use napkins, we were men who played baseball damnit.

Gerry idolized Bob Gibson growing up as a kid, having heard the stories of his pitching from his father and grandfather. And I can say Gerry had the same ferocity on the mound that Gibson did, except that this was tempered by the fact that his faded St. Louis Cardinals hat sat about 8 inches higher than placement of Gibson because of Gerry's big afro. But this kid could pitch. Like Gibson he was all about the speed but unlike Gerry had a bigger plate to work with. Growing up poor, we couldn't afford bases, so we used brick pavers for all the bases but home plate. Home plate was a municipal manhole cover, its large size gave Gerry ample space to "paint the black" as it were.

But lets be honest we weren't going to lay off pitches, we were a bunch of hackers. Occasionally when Gerry wanted to hit, I'd trot out to mound (regulation 10", thanks for the fill dirt dad). Now I was the antithesis of Gerry: he was tall, I was short; he had a well-muscled physique, my skinny ass couldn't even intimidate a neighborhood cat; Gerry had some zip on his fastball, my fastball might get there next week if you were lucky.

What I lacked for velocity I made up for in movement, I threw a curveball that pissed Gerry off to no end. And I threw it and threw it, and continued to throw it through high school (to the detriment of my rotator cuff and elbow). Gerry had to know the secret to my curveball and in exchange he would teach me his change up. While Gerry picked up my curveball over a full summer I could never replicate his change up. Mainly because it wasn't a change up at all! A change up should have less velocity than a fastball but the crazy thing was, Gerry's got faster. Same arm slot, same release point, just a modified grip that should have made it go faster. But it didn't.

And no one could touch it. You might get lucky and foul off of it, but none of us get better than a lucky single off that damn pitch.

My first interest in science came when Gerry's dad took us to the local minor league baseball game, who back then were an affiliate of the Kansas City Royals. Before the game started we walked past the cotton candy vendors straight to the boiled peanuts and grabbed a bag. Next to the boiled peanut man was kids mound and radar gun.

I held the peanuts and Gerry lit up the gun with a 70 mile per hour pitch. Not bad for a kid just starting middle school. Next it was my turn, and I reared back to find my inner Koufax and try and blow one past the gun. Nothing. My fastball was so slow it failed to even register on the gun. And it wasn't a gun malfunction because I made about six more tries to get something to come up on the gun. And never could.

We were fascinated with how the radar gun worked that night after we got back home we walked down the street to my grandmother's house. So this was in the pre-interwebs days, so I got all my knowledge from her Funk & Wagnalls's encyclopedia set. We spent that night reading about radar, projectile motion, and basic physics.

The genesis of our scientific interest was in how something knew how fast we were throwing and how we generated speed on our pitches and how we could get more.

Sadly, a year or two after this, Gerry moved away when his dad got transferred to another military posting and we never kept in touch. I still hope he is wearing that faded Cardinals hat and hopefully teaching his kid to throw my curveball. I somehow imagine that his fastball is an autosomal dominant trait that his kid would already have inherited.

7 responses so far

The fun stuff...congratulations to a reader

Jul 14 2011 Published by under Uncategorized

Sometimes you write to incite, sometimes you write to inspire, and sometimes write to release. But once in a while, its not a bad thing to write to give thanks. I think one of the fun things about writing and having people actually come here and maybe read what I have to say is when I get a question or a comment. The human aspect of helping people is really the most fun part of doing this. So to all the people have emailed me, thanks for actually giving a damn about what I have to say and to all those who have read anything I've written (all 7 of you), I'm grateful for your patronage.

Now moving on...

A reader recently asked me about meetings to attend in our field and I suggested one that I have been to before and will be attending in the future. Well low and behold they applied and got a travel to defray the cost of their attendance. So dear reader who shall remain nameless, way to kick some ass. I'm proud for you and can't wait to meet you at the meeting.

Oh and you do owe me a beer for recommending the meeting to you. And don't think you are getting off cheap with a Bud Lite. Big Daddy Kane has a taste premium draughts.

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NCATS Update from His Majesty Collins

Jul 12 2011 Published by under NIH

Francis Collins, the current NIH director who I affectionately call BoHonkeyPmpStick, put out a piece in Science Translational Medicine about the newly proposed NIH IC, the National Center for Advancing Translational Science (NCATS).  According to Collins, the mission of NCATS is to

“catalyze the generation of innovative methods and technologies that will enhance the development, testing, and implementation of diagnostics, therapeutics, and devices across a wide range of human diseases and conditions.“

To my knowledge, NCATS sphere of influence will include the CTSA program, Offices of Rare Diseases Research, Cures Acceleration Network, Therapeutics for Rare and Neglected Diseases, and the FDA-NIH regulatory science collaboration.  To my knowledge NCATS will absorb programs mainly from National Center for Research Resources (NCRR) and some from the National Human Genome Research Institute (NHGRI), probably with respect to GWAS is my guess.

Interesting article that boils down to BoHonkeyPimpStick trying to prime the scientific community for NCATS and to stoke the fire in the translational sciences folks, who are almost as whiney as all these neuroscience or deep-sequencing assholes.

 

2 responses so far

Weekend Wrapup

Jul 10 2011 Published by under Uncategorized

-Go see the Beginners.  Its a wonderful film about seeing how a widower father deals with being gay and how his own son deals with his relationships.

-Netflix has turned me into a documentary-watching asshole.

-As political discord is at an all time high, watch Boogie Man:  The Lee Atwater Story and Bush's Brain to see genesis of modern mudslinging politics.

-There is nothing better than a cold beer and some good Jazz music.

-Congrats to the US women's World Cup team for surviving the match against Brazil.

-Congrats to the new Mr. 3000, Derek Jeter.

And to send you off into the work week, here is some good tunes...

 

 

No responses yet

Flood

Jul 05 2011 Published by under Uncategorized, Vendor

Vendors usually fall into two different classes:  the tick who is easily removed from the skin and the four foot tapeworm that is so far up my ass that I don't think I will ever get rid of them.  Well I guess now it's time to add in a new class of vendor, The Flood.  No I don't mean the parasitic species that almost ruined the entire Halo video game franchise or that shitty Jars of Clay song, I mean the vendors that are constantly flooding my inbox.

Listen I know we all get the random emails offering this new product or that fantastic service, but this is different.  A few months back I talked to a vendor rep who represents a smaller biotech company because I was looking for a chemical inhibitor to an enzyme of interest to test for sensitivity using a particular assay.  The rep said they would email me back with what her company had and damn if she didn't.

Now I really only wanted the chemical inhibitor to test on my specific genetic background but she tried to sell me the following:
-a cell line knocked down for the protein I wanted to inhibit
-purified recombinant protein
-a cell line over expressing the protein
-a completely different assay even though I stated upfront that I already had an assay

Guess what was the one product she didn't email me about?  The damn chemical inhibitor!  What makes it worse is that she had a back and forth discussion over products and what I might be able to use with a product scientist at the company.  And she carbon copied myself AND my PI on all of them.

Now I love to know the inner workings of places but seriously in just an hour my inbox had over 25 email exchanges between the rep and the product scientist.  I listed the emails as spam, they kept coming.  Listed them as junk and they kept coming.  I was thinking of sliding our IT folks some money on the sneak tip to block them at the mail server level if possible.

Then I just broke down and emailed them to stop emailing me and I'll find what I need in their catalog.

Four hours later I got an email saying maybe this assay might be good to try.

I think I'm going to have a rage induced stroke.

5 responses so far

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