the life of a biochemistry phd graduate student [or what is left of it]

Sticky Tape X-rays

2008-10-23T12:23:00.003-05:00

Something that we all have used is a new source for X-rays. Sticky Tape or Scotch Tape releases X-rays as it is unrolled. Another weird unexplained experiment.

The BBC says:

Peeling sticky tape emits X-rays strong enough to scan a human finger, a remarkable experiment has shown.

US researchers used a motorised peeling machine to unwind a roll of Scotch tape at a rate of 3cm per second.

By placing their apparatus in a vacuum, they measured X-rays strong enough to X-ray a human digit, according to a report in Nature journal.

It is well known that unwinding sticky tape produces sparks of light that can be seen in the dark by the naked eye.

This phenomenon, known as "triboluminescence", is produced by the friction generated when two surfaces rub against each other.

The study, by Carlos Camara and Juan Escobar, of the University of California, Los Angeles, USA, provides evidence for the phenomenon, which was first observed more than 50 years ago.

Here is a quick video:

Here is a link to the full length video, to the news article, and to the full paper all in Nature.

This really is a big problem

2008-10-16T12:34:00.002-05:00

So a while ago I wrote about the Love Mattress and how it would help guys while sleeping as the big spoon. I recently found this video which is helpful if you can't get your hands on a Love Mattress. Enjoy!

Getting Intimate:How To Avoid Trapped Arm Whilst Cuddling In Bed

Breasts or Exercise?

2008-10-03T15:13:00.002-05:00

Best experiment I have seen in a while: What is better, exercising for 30 minutes or looking at breasts for the same amount of time?

Lets find out:

Printer + Water = Awesome Art

2008-10-02T15:07:00.001-05:00

I came across this video and was amazed. It is so entrancing. I just couldn't stop watching it.

Pretty cool, huh?

The LHC Works!

2008-09-10T08:43:00.003-05:00

The Large Hadron Collider had a beam steered all the way around the 27 km tunnel today! Oh man, I hope that the people who believe the LHC is going to cause the end of the world are quaking in their boots!

From the CERN Press Release:

Geneva, 10 September 2008. The first beam in the Large Hadron Collider at CERN1 was successfully steered around the full 27 kilometres of the world’s most powerful particle accelerator at 10h28 this morning. This historic event marks a key moment in the transition from over two decades of preparation to a new era of scientific discovery.

“It’s a fantastic moment,” said LHC project leader Lyn Evans, “we can now look forward to a new era of understanding about the origins and evolution of the universe.”

Starting up a major new particle accelerator takes much more than flipping a switch. Thousands of individual elements have to work in harmony, timings have to be synchronized to under a billionth of a second, and beams finer than a human hair have to be brought into head-on collision. Today’s success puts a tick next to the first of those steps, and over the next few weeks, as the LHC’s operators gain experience and confidence with the new machine, the machine’s acceleration systems will be brought into play, and the beams will be brought into collision to allow the research programme to begin.

Once colliding beams have been established, there will be a period of measurement and calibration for the LHC’s four major experiments, and new results could start to appear in around a year. Experiments at the LHC will allow physicists to complete a journey that started with Newton's description of gravity. Gravity acts on mass, but so far science is unable to explain the mechanism that generates mass. Experiments at the LHC will provide the answer. LHC experiments will also try to probe the mysterious dark matter of the universe – visible matter seems to account for just 5% of what must exist, while about a quarter is believed to be dark matter. They will investigate the reason for nature's preference for matter over antimatter, and they will probe matter as it existed at the very beginning of time.

“The LHC is a discovery machine,” said CERN Director General Robert Aymar, “its research programme has the potential to change our view of the Universe profoundly, continuing a tradition of human curiosity that’s as old as mankind itself.”

Tributes have been coming in from laboratories around the world that have contributed to today’s success.

“The completion of the LHC marks the start of a revolution in particle physics,” said Pier Oddone, Director of the US Fermilab. “We commend CERN and its member countries for creating the foundation for many nations to come together in this magnificent enterprise. We appreciate the support that DOE and NSF have provided throughout the LHC's construction. We in the US are proud to have contributed to the accelerator and detectors at the LHC, together with thousands of colleagues around the world with whom we share this quest.”

“I congratulate you on the start-up of the Large Hadron Collider,” said Atsuto Suzuki, Director of Japan’s KEK laboratory, “This is a historical moment.”

“It has been a fascinating and rewarding experience for us,” said Vinod C. Sahni, Director of India’s Raja Ramanna Centre for Advanced Technology, “I extend our best wishes to CERN for a productive run with the LHC machine in the years to come.”

“As some might say: ‘One short trip for a proton, but one giant leap for mankind!’ TRIUMF, and indeed all of Canada, is delighted to bear witness to this amazing feat,” said Nigel S. Lockyer, Director of Canada’s TRIUMF laboratory. “Everyone has been involved but CERN is to be especially congratulated for bringing the world together to embark on such an incredible adventure.”

In a visit to CERN shortly before the LHC’s start-up United Nations Secretary General, Ban Ki-moon said: “I am very honored to visit CERN, an invaluable scientific institution and a shining example what international community can achieve through joint efforts and contribution. I convey my deepest admiration to all the scientists and wish them all the success for their research for peaceful development of scientific progress.”

1 CERN, the European Organization for Nuclear Research, is the world's leading laboratory for particle physics. It has its headquarters in Geneva. At present, its Member States are Austria, Belgium, Bulgaria, the Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Italy, Netherlands, Norway, Poland, Portugal, Slovakia, Spain, Sweden, Switzerland and the United Kingdom. India, Israel, Japan, the Russian Federation, the United States of America, Turkey, the European Commission and UNESCO have Observer status.

As if you need another reason to vote Democratic...

2008-09-02T08:44:00.004-05:00

McCain's VP pick supports creationism and does not believe in evolution.

From the Boston Globe:

Earlier this year, she [Palin] told the newspaper that schools should not fear teaching creationism alongside evolution. "Teach both. You know, don't be afraid of information. . . . Healthy debate is so important and it's so valuable in our schools. I am a proponent of teaching both. And you know, I say this too as a daughter of a science teacher."

From the Anchorage Daily News:

The volatile issue of teaching creation science in public schools popped up in the Alaska governor's race this week when Republican Sarah Palin said she thinks creationism should be taught alongside evolution in the state's public classrooms.

The Republican Party of Alaska platform says, in its section on education: "We support giving Creation Science equal representation with other theories of the origin of life. If evolution is taught, it should be presented as only a theory."

Seriously? This is just insane. Europe is looking pretty good for a Postdoc if they actually win this election.

On the other hand, Obama says the following in an interview with the York Daily Record (I added the emphasis):

Q: York County was recently in the news for a lawsuit involving the teaching of intelligent design. What’s your attitude regarding the teaching of evolution in public schools?

A: “I’m a Christian, and I believe in parents being able to provide children with religious instruction without interference from the state.

But I also believe our schools are there to teach worldly knowledge and science. I believe in evolution, and I believe there’s a difference between science and faith. That doesn’t make faith any less important than science. It just means they’re two different things. And I think it’s a mistake to try to cloud the teaching of science with theories that frankly don’t hold up to scientific inquiry.“

A candidate after my own heart!

This is something that I feel others need to know about so please pass on this info.

What do you call it?

2008-08-27T15:05:00.002-05:00

Science - Beer = Publications?

2008-08-20T09:13:00.003-05:00

Sciencey beer.

A study has come out from Thomas Grim, an ornithologist at Palacky University, Czech Republic, stating that the more beer a scientist drinks, the less publications they will publish.

I am not a big fan of this study.

The New York Times also published an article about this study and I think that Dr. Mike Webster, an ornithologist from the Washington State University has it right. He says,

“Maybe those with poor publication records are drowning their sorrows.”

I hope this is the case.

There also appears to be a correlation between IQ and drinking wine vs beer. A Danish study shows that wine drinkers have higher IQs than beer drinkers.

I am okay with this since I enjoy wine and beer. I wonder if that just means I have an average IQ?

Paris for Prez?

2008-08-08T13:14:00.003-05:00

I think McCain just got owned.

Paris Hilton Responds to McCain Adfunny videosFunnyOrDie.com

See more funny videos at Funny or Die

Thanks to Noah for sending this one my way!

this slut has 330,000 happy customers!

2008-08-06T19:56:00.001-05:00

what kind of slut services 330,000 people a year?

Seattle's S.L.U.T, that's who! Or what, rather. This might be the dumbest name for a train ever: South Lake Union Trolley. I mean really, who is going to call it that...obviously it is going to be shortened down.

They realized their mistake after a few days and now have changed the name to the "South Lake Union Streetcar." This is not okay. We need to keep the SLUT alive!

A good friend of mine is moving out to Seattle so I need to get on this train and then get the shirt!

Add this to the list of thing to do if you are in the Seattle area!

Lesson Learned: Don't give thesis proposal to someone going camping.

2008-06-30T06:02:00.002-05:00

I have my last major hoop to jump through on Thursday of this week in order to become an honest to goodness PhD. Candidate and therefore have to write my thesis proposal and orally defend it. I have one of the best science writers I know as a best friend and therefore I use her as my personal editor. This usually works fine. She rips me to pieces, I cry, fix my idiotic use of the English language, and move on, but this time she was going camping and took my proposal with her. The results I have yet to see, but the pictures speak for themselves.

Burning Proposal our new yearly tradition.

Apparently, it is not available.

Needless to say, I am scared to get it back.

It's Called epMotion

2008-06-17T10:46:00.003-05:00

I don't know why, but there has been an explosion of viral (yes, yes pun intended) videos from biotech companies promoting their new products. It started with BioRad's Scientists for Better PCR and now it has gone to Eppendorf International's It's Called epMotion.

Enjoy!

When I was your age...

2008-06-05T13:51:00.004-05:00

Stumbled onto this webcomic and thought it would be the kind of story I told as an old crotchety scientist some day. I can't wait to be an old crotchety scientist!

I have been waiting for this!

2008-06-05T10:54:00.002-05:00

I found this one on Geeks are Sexy and have to say I really want to go to Germany now. The Germans have the first upsidedown-looped waterslide in the world! I know lots of water parks have the new slides that propel you up slopes but this is just freaking awesome. If someone can combine the two then I think I will have a new favorite attraction at theme parks!

Check out the video, but be warned it is in German.

The World of Chemistry

2008-05-20T16:56:00.002-05:00

i love chemistry and this video literally got me laughing. yay elements!

See more funny videos at CollegeHumor

too true...

2008-04-25T09:30:00.001-05:00

this is too funny...well played.

See more funny videos at CollegeHumor

shake, rattle, and shoot...

2008-04-19T00:47:00.002-05:00

hello from Chicago,

I am currently at APS (advanced photon source) shooting crystals with the brightest xray source in the US, except that their currently is a problem with the hutch and we can't open the shutter. This explains why I am updating my blog at 2am Saturday morning. The trip has been pretty good so far...save the wandering goniometer and this little vacuum pressure problem. The best part of the trip, however, has to be the fact that I experienced my first earthquake!

I awoke at around 4:30am by the sensation someone was shaking me, but upon opening my eyes noticed that Chris was still asleep and I was still shaking. This utterly confused me since I am not used to moving back and forth on the x, y plane. Being extremely groggy, I decided that I must be dreaming and immediately went back to bed, thinking that this couldn't have just occurred. As soon as I woke up the next morning I thought of the shaking, which meant that I probably wasn't dreaming because I normally don't remember my dreams. I opened my computer and saw on CNN that indeed, there was a 4.5 richer earthquake with an epicenter around 350 miles away.

I love being a Red Sox fan.

2008-04-11T10:59:00.002-05:00

I was reading the daily sports news when I ran across this gem:

Red Sox fan adds high-jinx to Yankees rivalry

The title obviously piqued my interest and I was not disappointed. Apparently a Red Sox fan who is also a construction worker in New York is working on the new Yankee Stadium and without telling anyone put a Red Sox t-shirt in the concrete under the visitor's locker room.

This is pure freaking brilliance. This is going to piss off so many Yankee's fans it isn't even funny, and I am willing to bet, if the floor can be ripped up, it will be.

The Sox/Yankees rivalry is the best in American sports and this is just making it better. I suggest reading the article because it is pretty funny.

insane guitar hero

2008-04-10T14:24:00.002-05:00

this is absolutely ridiculous. Dragonforce, extreme, 100%.

See more funny videos at CollegeHumor

drugs + science = this

2008-03-26T17:58:00.002-05:00

i have to give Dharia (a fellow grad student) props for sending this my way. the following video shows what happens when you combine science and the early 70s. the video shows a dance depicting the process of protein synthesis.

the description on youtube says:

Directed in 1971 by Robert Alan Weiss for the Department of Chemistry of Stanford University and imprinted with the "free love" aura of the period, this short film continues to be shown in biology class today. It has since spawn a series of similar funny attempts at vulgarizing protein synthesis. Narrated by Paul Berg, 1980 Nobel prize for Chemistry.

please listen close to the soundtrack and the narration. it is priceless!

wow!

a scientific explanation for breaking the seal

2008-02-29T14:59:00.004-05:00

urban dictionary defines breaking the seal as

The point at which you first piss after you have been drinking your favorite alcoholic beverage and at this point you will be pissing every ten minutes.

having experienced this phenomenon firsthand I wondered if there was a scientific mechanism behind it.

there is, and interestingly enough, you can train yourself to not urinate so often if you want.

this article is from the ABC of Australia website and deals with "Great Moments in Science." i am not sure why or even how this is great science, but it was interesting none the less.

the article states that

The bladder has a capacity of 500 mL (roughly a small carton of milk). The bladder, like the ureter, has various bands of muscle in its wall – spiral, longitudinal and circular. When the bladder empties, the muscles contract in a specific sequence, starting at the top and working down to the bottom. This wrings virtually all of the urine from the bladder. You get your first urge to pass water with a volume of 150 ml of urine, but usually this can be easily ignored. But it’s harder to ignore the marked sense of fullness that normally happens around 400 mL.

converting the volume into beers means that if you have a completely empty bladder and start drinking, you will start to feel as though you could urinate after one half of a beer (150 mL = ~5 fluid ounces) and you really have to go after finishing that first beer (400 mL = ~13.5 fluid ounces).

this seemed quite early to me to have to go to the bathroom, but it made more sense after reading:

The bladder is a hollow organ that is the reservoir for urine. Urine from the kidneys flows at about 1 ml per minute into the bladder, via the ureters. The ureters have walls of muscle arranged in spiral and longitudinal layers. Every 10-60 seconds, waves of synchronized muscle contraction progress down the ureters, pushing urine into the bladder.

so it would take 15o minutes for your bladder to fill to the 5 fluid ounce point, and 4o0 minutes to get to the "get out of my way" zone. this makes perfect sense because 150 minutes is 2.5 hours and 400 minutes is 6.66 hours, which means at some point around 3 to 4 hours after drinking you are going to break seal. i have found this fits in with my past experiences.

the article also goes on to point out a key fact

Then you have to sit back and literally hold on. Just like five-year-olds physically clutching their groin when they feel they are busting to do a wee, you have to cross your legs, sit down and distract yourself mentally in an effort to ignore the first desire to pass urine. Wait for it to pass, without rushing to the toilet. The idea is to gradually increase the time between each urination, and retrain your bladder back to registering that it is full only when it is actually holding more than 300 ml. This means you get bladder control back, and the bladder stops wrongly sensing fullness at tiny volumes of urine. For most people, this is enough to shift them back to relatively normal bladder habits, full night sleeps and being able to throw away their maps marked with public toilets.

moral of this post...the longer you hold it, the better off the rest of the night will be.

Happy Valentines Day

2008-02-14T14:32:00.001-05:00

nuf said.

Scientists for Better PCR

2008-01-13T15:17:00.000-05:00

All I have to say is WOW! Somebody at BioRad has a little too much time on their hands!

If you want to sing along, here are the words:

The PCR Song

There was a time when to amplify DNA,
You had to grow tons and tons of tiny cells.

Then along came a guy named Dr. Kary Mullis,
Said you can amplify in vitro just as well.

Just mix your template with a buffer and some primers,
Nucleotides and polymerases, too.

Denaturing, annealing, and extending.
Well it’s amazing what heating and cooling and heating will do.

PCR, when you need to detect mutations.
PCR, when you need to recombine.
PCR, when you need to find out who the daddy is.
PCR, when you need to solve a crime.

(repeat chorus)

Wonderful...simply wonderful!

Men, Tired of waking up feeling as though you don't have an arm?

2008-01-03T15:45:00.001-05:00

I love smart designs and this is now one of my all time favorites.

Most guys have had the "fun" experience of waking up with their wife, finance, or girlfriend, only to discover that their arms are wrapped lovingly around her. This is "fun" for two reasons. First, the bottom arm is completely asleep and has been that way for about two hours. Second, you know you are screwed because if you move it and wake her up you get yelled at in that sleepy way knowing full well she will never believe it happened in the morning.

This fun experience sucks. More importantly it can actually cause injury.

Studying the embracing styles of couples in bed showed that placing the arm under your partner's body causes abnormal pressure on the arm muscles, blood vessels and nerves. It occasions weakness and pain in the arms. In some cases (usually in the first months of marriage), tolerating this continuous pressure on the arms causes an affliction called “Radial Neuropathy”. The symptoms are typically weakness in wrist dorsiflexion (i.e. wrist drop) and finger extension.

Enter the Love Mattress.

The Love Mattress is a guys best friend. It has horizontal slats cut into it, allowing the bottom arm to simply rest their. This takes care of both problems because the arm won't fall asleep and it is easy to move if uncomfortable.

(Yes I realize it is ironic that her arm is under him.)

According to the site:

Embracing is a magical human behaviour, and one that distinguishes us from other animals. A loving embrace, especially between partners, is one of the most calming actions. Embracing, and bodily proximity and connection after lovemaking, are very important for strengthening relationships. However, what usually stops this pleasant state is not mental tiredness; it is physical weakness....The Love Mattress offers partners a simple yet effective position for embracing. This mattress allows you to hug your loved one intimately without any wrist or arm weakness. The assembled mattress has the same dimensions as other mattresses, with the added advantage that you can make a gap between joined parts. Your arm and shoulder can occupy the gaps when you are lying on your side. In other lying styles, you can easily find your most comfortable position. For example, if you are lying on your tummy, your foot can project comfortably into the mattress. Anatomical research supports the claim that The Love Mattress provides greater comfort than existing mattresses.

Hear Hear Love Mattress inventor. The bottom arm of men everywhere thank you!

Boston Red Sox: 2007 American League East Division Champions

2007-09-29T10:31:00.000-05:00

so guess where i was last night? i will give you a hint read the title.

as a red sox fan i have no problem saying last night was the highlight of my being a red sox fan. don't get me wrong winning the world series was amazing, but i wasn't there. i didn't get a champagne shower from people such as ortiz and papelbon, but last night i did.

it was the set up that made it amazing. dice k pitched a great game: 8 innings, 2 earned runs, 2 walks, and 8 Ks. papi hit a home run. lowell got two more RBIs. and papelbon closed it out 1, 2, 3.

the win was nice, but the real drama was the scoreboard on the green monster. every time the yanks scored it was boo'd and every time the orioles scored it was cheered. everyone watched the play and then looked directly to the scoreboard. it didn't look good. the yanks were up 8-6 in the 8th and the sox had just won.

it was about 9:45pm.

about half the fans left fenway, but the rest stayed so the orioles/yanks game was put up on the jumbotron in center field. as soon as this happened jeter hit a double and arod hit him in.

9-6 yanks

the bullpen door opened and out walked rivera. all the fans left in fenway left except for about 2000.

it was about 10:05.

rivera went on to allow the bases to become loaded and then of all people jay paton hit a bases clearing triple.

9-9

now there was some drama. the reporters started unpacking there stuff. they started taking pictures of the fans and i felt that normal octoberish sick feeling, only it started early this year.

the yanks came up in the top of the 10th and had the bases loaded with one out. some how they got out of the inning without giving up a hit.

it was about 10:30.

now the orioles are up and the bases are loaded. millar is up and the fans at fenway are cheering for him...he strikes out...we sigh.

bases loaded 2 outs.

melvin mora comes up with the bases loaded...he bunts...

he freaking bunts...

they score...

no outs....

holly crap....

we just won the division for the first time in 12 years...

i am freaking in fenway an hour and a half after the red sox game ended and we just clinched the division.

matt and i ran down towards the dug out and got in second row to the right of the sox dugout.

then the players started coming out and i took these clips...i hope this gets the atmosphere across...

the official red sox video:

and apparently i am on espns photo section for the game:

what a night...it's one i will never forget!