the scientist's best friend

so as a scientist in training i have had my fair share of literature wrestling, with the literature usually kicking the crap out of me, spitting in my face, and mocking me while i cry, bloodied and battered.

the fight usually begins with a pubmed search, at which time pubmed decides that there is no paper, in the 17million papers it has indexed, that fit my criteria, even though i know it was just published in biochemistry, nature, or science. once i find the paper of interest i have to follow a link to another site, which, if it is nice, recognizes i am a Brandeis university grad student and allows me to download the pdf.

at this point i have already taken a right hook followed by an uppercut to the jaw, but at least i am still standing.

so now i must figure out what pdf i just downloaded since the different places from which you are allowed to download all use a different, nonsensical naming pattern. some of my favorites are the random numbers, the name of the website from which you are downloading, or the random sequence of letters and numbers.

so now the literature is just baiting me for the "finish him" move when it rips my head off and throws it at my body causing both to explode.

finally i determine which pdf i want open and print it...my head is flying towards my body in slow motion.

there must be a better way...

i was just wandering around the web when i found this website: http://mekentosj.com/. i already had some of their software (enzymeX and 4peaks), but i noticed that they also had a new program up.

PAPERS!!!

this software is amazing! here is the blurb on the site:

Do you have dozens of PDF files from your favorite scientific articles scattered on your harddrive? Do you also try to desperately organize them by renaming and archiving them in folders? But like the piles of printed articles on your desk, you can't keep up with all the new papers you download, and despite all your efforts it has become impossible to find that one article.

Finally that all belongs to the past. We've been there, trust us, we know. That's why we wrote Papers, our latest application exclusively for the Mac. Papers will revolutionize the way you deal with scientific papers. Search for papers using PubMed, directly retrieve and archive PDFs, and read and study them all from within Papers, your personal library of Science.

so here are my favorite features:

1. creates an organized folder in my documents with all of the papers organized into folders by year, then into folders of first author, then renames the pdf via journal name_first author_year.pdf
2. did i mention it does this automatically
3. look up papers already downloaded and fixes their information and then does the aforementioned
4. has a built in pubmed search
5. built in web-browser
6. full screen pdf mode which i might be able to read a pdf on my computer rather than killing thousands of trees
7. one place to go for all my paper needs

i really suggest you check this program out...you get a 30 day trial, after which it costs $40, but after using it for 2 days i have already decided to purchase a license!

for all you windows people out there sorry...not for you...mac only!

so now that i have the power of papers you might be wondering what happend in my fight! well lets just be thankful that my head is coming at me in slow motion, otherwise i might not have had time to download, install, and learn to use papers, but since i did; i caught my head, sutured it on, and punched the literature in the face.

this did not bode so well for me since it just called its friends magazines and newspapers and proceeded to beat me into next year.

Hear this literature...i will be ready for you!!!

in about 4.5 years!

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it's been said before and much better than i ever could say it

i love quotes.

as anyone who has spoken to me already knows, i am not the most eloquent speaker, but i can carry a conversation quite well on almost any topic. for this reason i use quotes in order to say things that i know others have already said, better than i ever could...for example:

I quote others only in order the better to express myself.
~Michel de Montaigne

see, that nicely sums up the entire last paragraph in eleven words, whereas i needed fifty-three words...five fold more, i think you get my point.

since i found a new quote that i really like, i decided to list some of my favorite quotes and explain what they mean to me:

my newest addition:

Life's journey is not to arrive safely at the grave, in a well preserved body; but rather to skid in sideways, totally worn out, shouting...holy shit...what a ride!
~Unknown

i just stumbled upon this on two days ago and have been letting it sink in. i think the reason i like this quote so much is because i have a new found appreciation for life [yes i know, corny, but true]. i think i really like the idea of living life to the fullest and this quote sums that feeling up.

The advantage of the emotions is that they lead us astray, and the advantage of science is that it is not emotional.
~Oscar Wilde

the fine line that one must walk in the sciences; for one part your science must be calculated, unemotional, and rational, but at the same time it must bring out emotions in you and others...that is what makes some science good science and some scientists good scientists.

Wake up naked drinking coffee
Making plans to change the world
While the world is changing us
~Dave Matthews

i like this quote so much because it is true; while you are changing the world, it indeed is changing you, changing your opinions, changing your plans...it shows how everything we experience shapes us and our ideas.

In three words I can sum up everything I've learned about life. It goes on.
~Robert Frost

so life goes on...don't get too stressed, don't get too worried, life continues no matter how bad of a day day you have, while at the same time remember that the good times can end, and life will continue too. the pragmatic life quote.

If you want to tell people the truth, make them laugh, otherwise they'll kill you.
~Oscar Wilde

i consider myself an honest person...if you want to know the truth then ask and i will tell you, but i try to do so with humor otherwise no one would come back for more [of the truth or of me].

I wasn't kissing her, I was whispering in her mouth.
~Chico Maroc

such a nice way to say you were making out and got caught. someday i want to have the balls to say this to someone and keep a straight face while doing so.

A photograph is usually looked at - seldom looked into.
~Ansel Adams

photographs are an attempt by the photographer to show you some insight that he/she had. next time you look at a picture, try to find it. this sums up why i love photography; do people feel what i felt when i took the photo?

I am not young enough to know everything.
~Oscar Wilde

graduate school has been a shock since i have found that i really know absolutely nothing about biochemistry. this quote explains why. as i progress i realize that i know very little, but am learning a lot.

there is a quote for everything...now all you have to do is find it...i leave you with this quote to make myself feel better about always using other people's words:

Misquotation is, in fact, the pride and privilege of the learned. A widely-read man never quotes accurately, for the rather obvious reason that he has read too widely.
~Hesketh Pearson

good i feel better now.

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google i am your bitch

i am an admitted google whore...i use the google search engine, gmail, gtalk, google calender, blogger, google docs, google analytics, google webmaster tool kit, google toolbar for firefox, google browser sync, google page creator, google glossary, and google scholar!

in case you weren't counting that is 13 different google applications! yes, i am a WHORE!

so when i am online i am using a google related application constantly. so when i found this picture online by Randy Siegal i felt that most of the new applications would be very useful! For the full effect check this out!



Your Brain: for those times you you can't remember something, but you know you know
Your Home: where are my keys...thanks google!
Family: birthdays, anniversaries, gift ideas, must i say more?
Friends: find out where they are and what they are doing so you can choose whom to grace with your presence
Ex-friends: find out where they are and what they are doing so you can make their life a living hell
Relatives: when are they coming to visit and how long...what annoys them so that they will leave
Co-workers: who will do your work for you and what your bosses really really like
Ex-spouse(s): i also assume this means ex-girl/boyfriend(s) so do i really need to explain this one?
Enemies: keep those suckers close
Satellite Photos of People You Want to Spy On: you know, that girl you are interested in, or i guess your kids or something
Satellite Photos of People Spying on You: keep those suckers close
Medical Records: i love how this is vague about who's records...find out when to make a move on that great apartment the old man lives in
Credit Reports: identity fraud?
Tax Records: what years did i forget [not] pay my taxes?
Phone Records: who called me and who did i call last night?
Court Documents: what happened last night?
Other People's Conversations: what did you say last night?
Books: just read that last page!
Movies: what was that line in office space?
TV Shows: what was that line in family guy?
Music: what was that 50 cent lyric?
Pornography: nuh said
Your Past: who am i?
Your Present: what am i doing?
Your Future: where am i going?

oh man i cannot wait until google takes my entire life over...google i am your bitch!

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step on a crack, break your mother's back

so do you remember when you were little and someone said "step on a crack and break your mother's back?

i do...and no matter how mad i was at my mother, i never could seem to step on enough cracks to do any damage (just kidding mom...no but seriously, i tried so hard and never could do it...i think once she put her back out, but i didn't count that)!

so you might be wondering what brought on this little bit of reminiscing...well it was this comic:


i have totally done that...for example, no stepping on the cracks between sidewalk pieces, or when i was a kid playing in the woods, when i couldn't step on the ground because it was lava or water...(yes i had fun when i was little).

it made me start thinking about how i walk...which of course led me to start thinking about how other people walk, and i came to the conclusion that walking is like your dna or fingerprints, only better!

look around some time, everyone's walk is different...everyone has that one little part that makes their walk theirs.

i for example have a stride of 16.8 inches, for a complete cycle of 33.6 inches. i slowly swing my arms as i walk, but do not bounce. once i got over my depression about how i just measured my step size, i started looking at other peoples walks.

here are some of my favorites i observed:



the bounce - this walk is one that everyone would recognize...the person looks like they are taking a little jump each time the take a step, kind of looks like they are trying to work out the calfs, but failing miserably

the waddle - this person looks like a duck...nough said

the power stride - this person usually is wearing a power tie if male, or a pant suit if female and is walking with a purpose even though they just graduated business school and hold no power

the strut - the over confident walk usually performed by those who have no reason to do it

the model - think tyra banks only not on a runway or dressed up

the oh my god don't come near me - the people who have a personal bubble and thus keep everything 2 feet away from them...kind of the gas molecule model

the limp - not people who are really hurt, but those who have that slight limp and usually heavy gold metal chains and 6XL shirts with jeans that would fit four of me



so hopefully next time you are out you will look at how others are walking and add some more categories to my list...and if you get up after reading this and analyze your walk don't feel bad...i used a yard stick to figure out mine!

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"I'm really sorry you have to die."

so my PI [principle investigator aka boss] is gone giving a talk today so i am procastiniating doing work...

so what did i decide to do, why take the myers-briggs personality test! if you have never heard of the myers-briggs personality test here is the blurb about it on wikipedia:

The indicator differs from standardized tests and others measuring traits, such as intelligence, instead classifying people's preferred types. According to Myers-Briggs Theory, while types and traits are both inborn, traits can be improved akin to skills, whereas types, if supported by a healthy environment, naturally differentiate over time. The indicator attempts to tell the order in which this occurs in each person, and it is that information, combined with interviews done with others who have indicated having the same preferences, that the complete descriptions are based on. The indicator then, is akin to an arrow which attempts to point in the direction of the proper description. The facet of the theory which posits that the features being sorted for are in fact types, and not traits which can be improved with practice, is hotly debated.

However, proponents of the indicator will explain that to learn about one's inborn traits is to create the opportunity to improve how one applies them in different contexts. In that sense, the MBTI can yield much personal change and growth.

The types the MBTI sorts for, known as dichotomies, are extraversion / introversion, sensing / intuition, thinking / feeling and judging / perceiving. Participants are given one of 16 four-letter abbreviations, such as ESTJ or INFP, indicating what their preferences are. The term best-fit types refers to the ethical code that facilitators are required to follow. It states that the person taking the indicator is always the best judge of what their preferences are and that the indicator alone should never be used to make this decision.

since the key words in the description do not mean what you would expect here are the official descriptions of what each means:

The terms Introvert and Extravert (sometimes spelled 'extrovert') are referred to as attitudes and show how a person orients and receives their energy. In the extraverted attitude the energy flow is outward, and the preferred focus is on other people and things, whereas in the introverted attitude the energy flow is inward, and the preferred focus is on one's own thoughts, ideas and impressions.

Sensing and Intuition are the perceiving functions. These are the nonrational functions, as a person does not necessarily have control over receiving data, but only how to process it once they have it. Sensing people tend to focus on the present and on concrete information gained from their senses. Sensing prefers to receive data primarily from the five senses. Intuitives tend to focus on the future, with a view toward patterns and possibilities. These people prefer to receive data from the subconscious, or seeing relationships via insights.

Thinking and Feeling are the decision making (judging) calculus functions. They both strive to make rational choices, using the data received from their perceiving functions, above. Thinking people tend to base their decisions on logic "true or false, if-then" connections and on objective analysis of cause and effect. Feeling people tend to base their decisions primarily on values and on subjective evaluation of person centered concerns. Feelings use "more or less, better-worse" evaluations. It could be said that thinkers decide with their heads, while feelers decide with their hearts. When Thinking or Feeling is extraverted, decisions tend to rely on external sources and the generally accepted rules and procedures. When introverted, Thinking and Feeling decisions tend to be subjective, relying on internally generated ideas for logical organization and evaluation.

Judging and Perceiving reveals the specific attitudes of the functions. J or P records which of the strongest of the judging functions or perceiving functions is outwardly displayed. People who prefer judging tend to like a planned and organized approach to life and prefer to have things settled. People who prefer Perceiving tend to like a flexible and spontaneous approach to life and prefer to keep their options open. (The terminology may be misleading for some—the term "Judging" does not imply "judgmental", and "Perceiving" does not imply "perceptive").

so are you probably wondering what my type is...

drum roll please...

that wasn't enough drumming...

ENTJ

so that means Extraverted iNtuitive Thinking, and Judging...so here is the description from Joe Butt regarding ENTJs:

ENTJs have a natural tendency to marshall and direct. This may be expressed with the charm and finesse of a world leader or with the insensitivity of a cult leader. The ENTJ requires little encouragement to make a plan. One ENTJ put it this way... "I make these little plans that really don't have any importance to anyone else, and then feel compelled to carry them out." While "compelled" may not describe ENTJs as a group, nevertheless the bent to plan creatively and to make those plans reality is a common theme for NJ types.

ENTJs are often "larger than life" in describing their projects or proposals. This ability may be expressed as salesmanship, story-telling facility or stand-up comedy. In combination with the natural propensity for filibuster, our hero can make it very difficult for the customer to decline.

TRADEMARK: -- "I'm really sorry you have to die." (I realize this is an overstatement. However, most Fs and other gentle souls usually chuckle knowingly at this description.)

ENTJs are decisive. They see what needs to be done, and frequently assign roles to their fellows. Few other types can equal their ability to remain resolute in conflict, sending the valiant (and often leading the charge) into the mouth of hell. When challenged, the ENTJ may by reflex become argumentative. Alternatively (s)he may unleash an icy gaze that serves notice: the ENTJ is not one to be trifled with.

so when i read this the two things that really stuck out were the fact that i would be good at running a cult and i'm really sorry you have to die. so if you are in my future cult and you are going to die i will pretty much just laugh at you!

after reading my description, at first i started to worry that i am a dick, but after talking to some of my friends, we decided i am only a dick sometimes...what a relief! i also immediately begin to make a plan about how this would be a great blog post and made sure i brought this plan to fruition! finally i want to make sure that you know your role in reading this post...you are the reader and i am the writer! do NOT forget the role i assigned to you because it will not change unless i assign you a new one.

i suggest you take the test too [click on the title of this post to go the the test i used]...its about 72 questions, takes about 15 minutes, and is just fun to think about...comment with your results!!



P.S.

PLEASE JOIN MY CULT!!

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aprils fools

april first, aka april fools day, a day to find out how much people really like you. my feeling is that if you trick them and they continue speaking to you, they probably are your friend.

so did you get tricked today?



I didn't, well not really, well maybe a little...but it didn't count!



one of my good friends had this as his away message:

TIME SENSITIVE:

FREE SOX BLEACHER SEATS. CALL 617-247-1835 AND SAY "MATSUZAKA" WHEN THEY PICK UP BUT BEFORE THEY GREET YOU.

ONE PER PERSON, ONLY VALID UNTIL 5.

so as a die-hard redsox fan, i sat in front of my computer knowing damn well that this is a joke, but wanting to call the number just in case...so what did i do?

i sent brett and IM and told him that his joke wasn't funny hoping that his reply would be "its not a joke!" unfortunately his reply was "hahahaha." my heart sank, my voice got an octave deeper, so i replied in the saddest typing i have ever been part of "i wonder how many people had called," without revealing that i had already put the number in my phone just in case...brett explained that the number was for nan ling, a restaurant in boston.

this exchange got me thinking...what are some of the best april fools day jokes of all time...conveniently i found this list via google. here are some of my favorites:

In its April 1985 edition, Sports Illustrated published a story about a new rookie pitcher who planned to play for the Mets. His name was Sidd Finch and he could reportedly throw a baseball with startling, pinpoint accuracy at 168 mph (65 mph faster than anyone else has ever been able to throw a ball). Surprisingly, Sidd Finch had never even played the game before. Instead, he had mastered the "art of the pitch" in a Tibetan monastery under the guidance of the "great poet-saint Lama Milaraspa." Mets fans everywhere celebrated at their teams's amazing luck at having found such a gifted player, and Sports Illustrated was flooded with requests for more information. But in reality this legendary player only existed in the imagination of the writer of the article, George Plimpton.

In 1977 the British newspaper The Guardian published a special seven-page supplement in honor of the tenth anniversary of San Serriffe, a small republic located in the Indian Ocean consisting of several semi-colon-shaped islands. A series of articles affectionately described the geography and culture of this obscure nation. Its two main islands were named Upper Caisse and Lower Caisse. Its capital was Bodoni, and its leader was General Pica. The Guardian's phones rang all day as readers sought more information about the idyllic holiday spot. Few noticed that everything about the island was named after printer's terminology. The success of this hoax is widely credited with launching the enthusiasm for April Foolery that then gripped the British tabloids in the following decades.

The April 1998 issue of the New Mexicans for Science and Reason newsletter contained an article claiming that the Alabama state legislature had voted to change the value of the mathematical constant pi from 3.14159 to the 'Biblical value' of 3.0. Before long the article had made its way onto the internet, and then it rapidly made its way around the world, forwarded by people in their email. It only became apparent how far the article had spread when the Alabama legislature began receiving hundreds of calls from people protesting the legislation. The original article, which was intended as a parody of legislative attempts to circumscribe the teaching of evolution, was written by a physicist named Mark Boslough.

In 2000 a news release was sent to the media stating that the 15th annual New York City April Fool's Day Parade was scheduled to begin at noon on 59th Street and would proceed down to Fifth Avenue. According to the release, floats in the parade would include a "Beat 'em, Bust 'em, Book 'em" float created by the New York, Los Angeles, and Seattle police departments. This float would portray "themes of brutality, corruption and incompetence." A "Where's Mars?" float, reportedly built at a cost of $10 billion, would portray missed Mars missions. Finally, the "Atlanta Braves Baseball Tribute to Racism" float would feature John Rocker who would be "spewing racial epithets at the crowd." CNN and the Fox affiliate WNYW sent television news crews to cover the parade. They arrived at 59th Street at noon only to discover that there was no sign of a parade, at which point the reporters realized they had been hoaxed. The prank was the handiwork of Joey Skaggs, an experienced hoaxer. Skaggs had been issuing press releases advertising the nonexistent parade every April Fool's Day since 1986.

In 1998 Guinness issued a press release announcing that it had reached an agreement with the Old Royal Observatory in Greenwich, England to be the official beer sponsor of the Observatory's millennium celebration. According to this agreement, Greenwich Mean Time would be renamed Guinness Mean Time until the end of 1999. In addition, where the Observatory traditionally counted seconds in "pips," it would now count them in "pint drips." The Financial Times, not realizing that the release was a joke, declared that Guinness was setting a "brash tone for the millennium." When the Financial Times learned that it had fallen for a joke, it printed a curt retraction, stating that the news it had disclosed "was apparently intended as part of an April 1 spoof."

so there have been some really, really good april fools day jokes over the years, but none i have ever experienced caused such a swing in my emotions as brett's little joke did. for that reason i commend you brett for being the only person to trick me in a long long time [even though i didn't call the damn number].



p.s.

does anyone want some of this food that magically got delivered to my place from nan ling??

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