Pet-Peeve Vigilante

Posted on June 19, 2011 by Steve Caplan

I have a feeling that this blog may not be particularly popular with animal lovers, but I have a “pet-peeve”. Now I have nothing against pets–in fact I had a dog for 13 years who even traveled with me from Israel to the US and spent his last couple years here with me. Right now we have Vanilla the guinea pig–her partner Mocha (an Abyssinian guinea pig succumbed to illness a couple years back).

But I am angry, and my confidence is shaken. Two days in a row I’ve been chased by dogs when out on my daily walks. Now this is not generally a common occurrence–in fact the vast majority of canine owners keep their pets on a leash outdoors, or at least have them close enough or well enough trained not to bother passersby.

But I have a history of being chased by dogs. As a youth, I ran marathons and at that time dog owners did not have a high level of awareness about keeping the dogs under control. Since I lived in a city (although I am somewhat leery of calling Winnipeg a city), inevitably I ended up interacting with the canine world. I was bitten, chased, harassed, barked at, and scratched. One time, when a particularly large canine individual came at me in attack mode, I actually climbed up on the hood and roof of a parked car–much to the chagrin of the angry owner. But I was able to outrun him as well.

In my neighborhood, we did have a dog owner on our street whose dog would wander around and sometimes act threateningly towards our children. The same dog, often loose in his own front yard, tried to bite me once en route to my path and got a mouthful of keys. That was enough for me, and since the owner showed neither remorse nor attempted to display greater responsibility, I called the “pound” and was told that someone would have a talk with the owner. This, along with the inherent threat of having the dog impounded seemed to work, as the dog has never been observed on the loose since.

On Friday afternoon, returning through my neighborhood and climbing uphill after a 10 km walk, as I minded my own business on the sidewalk and listened to the calming tunes of Simon and Garfunkel on my iPod, I looked up to see two dogs racing towards me. One was coming right at me, while the other one–clever in his evilness–was seeking to outflank me from the side. I could feel the immediate adrenaline–the flight or fight response as I quickly realized there was nowhere to go, and that I would be unable to outrun this pair at near exhaustion after my walk in the heat. There were no rocks nearby, no sticks or tree branches–I was in a defenseless desert.

With no choice, I steeled myself for impact and readied myself to try and kick my way out. Suddenly, a couple appeared at the entrance of one of the houses down the street and must’ve shouted to the dogs. I could hear nothing except “The Boxer” directly in my ears. Of course I hadn’t even had time to take the speakers off. As abruptly as it started, the dogs veered around and raced back to their masters who quickly ushered them into the house and closed the door, without uttering an apology.

So I thought this was a completely isolated and highly unusual incident when I set out for another walk down a different part of the trail yesterday. On my way back down the linear trail the path took me on an underpass along the Creek. Suddenly, on the trail itself I saw two lone dogs trotting in my direction. Now while they weren’t running at me as I experienced the previous day, I did notice that the lead dog appeared to be a pit bull. Indeed, as the dogs approached, I saw that he had some kind of muzzle apparatus over his mouth–that I wouldn’t have trusted for a second. My strategy this time was to keep moving slowly and not make any sudden movements that might startle these dogs. There were a few nervous seconds, but they passed me and although the second dog made a bit of a wide arc and seemed to show some interest in following me, they eventually turned towards the creek and disappeared.

It could’ve been worse, much worse.

So what do I do now? Do I ignore it and chalk it up to statistics? To rotten luck? Or do I go out and purchase some kind of pepper spray–which hopefully, I would never have to use?

I thought that when I was discharged from the military that I would never have to hold any kind of weapon again. So do I now become some kind of “pet-peeve vigilante?”

Suggestions and recommendations are most welcome; truthfully, I really don’t know what to do.

Posted in Uncategorized | Tagged , , , , , , , , , , , , , , , | 15 Comments

What’s in a name?

Posted on June 16, 2011 by Steve Caplan

What a great way to begin a blog–scooped before I’ve even started!

I started with this great–and not so original idea, apparently–of having a little contest: everyone is invited to send in their all time favorite names of proteins.

In my own career, I once had the opportunity to name a protein. It was back in 2001, and I was racing to do “RACE-PCR” and clone the human homolog of the gene that coded for protein involved in lysosome fusion. I was not only racing against potential competitors, but also against the Human Genome Project.

In any case, one day I will perhaps be able to tell my grandchildren that I cloned one of the last genes before the human genome was published, and that I ended up giving it a very uninspiring name–based on its homology to the yeast protein Vam6p/Vps39 (Vam=Vacuole Morphology; Vps=Vacuole Protein Sorting), we called it: hVam6p/Vps39. The distinguishing part here, is the “h” for human.

In my view, this was a missed opportunity for giving the protein a really “cool” name, like “superglue”, or “family reunion”, or “sardine maker” based on the function of this protein in inducing fusion of lysosomes with one another.

So now I turn to you all and give you the opportunity to send in your favorite protein names. Please limit to no more than three names per person. I have already assembled an expert panel of local judges from Nebraska (nothing rigged here!)–my own 2 kids–who will announce the winning name and submitter by July 1, 2011.

Although I myself am disqualified, here are a few of my favorites:

JNKKK (Jun N-terminal kinase kinase kinase—how ridiculous can you get?!)
NUMB
nuclear fallout (NuF)
spaghetti squash

LET THE CONTEST BEGIN!

Posted in humor, research, science | Tagged , , , , , , , , | 11 Comments

Out of context!

Posted on June 14, 2011 by Steve Caplan

It’s time for some self promotion coupled with the release of frustration. Back in December, at the Annual American Society for Cell Biology meeting in Philadelphia I met Jenny (Rohn) and suggested an idea for something that might be of interest to the readers of LabLit.com.

For many years now–in fact since my Masters degree when I published my first paper–I have been continuously barraged with an array of applications for postdoctoral positions. Until eight years ago, when I received the reins of my own laboratory, these applications were nothing but a futile footnote for me. Recently however, the styles, content and general lackadaisical appearance of these applications by so-called professionals had begun to irritate me.

Out of this primordial soup the idea to write an instructional/comical blog: “How NOT to get a lab job” was born.

Jenny, of course, did a great job editing and arranging the piece, which consisted of nine letters (applications) that I received verbatim (without names or institutions, of course), along with a translation of how a PI would view such a letter. A few of the letters were graced by cartoons drawn by my daughter.

I was thrilled when Jenny wrote to me that the piece appeared to be quite popular and was receiving a lot of traffic.

I was less than thrilled when I began to receive e-mails accusing me of being disrespectful to other cultures, insensitive, not at all funny, and even–yes even chauvinistic.

I know from experience that every time one takes a stand–one way or another someone will find a reason to be insulted. However, I also know that by not taking a stand and keeping my mouth shut I will also not be immune to criticism.

I went back and read all of the letters and my “translations”. I read the introduction and the summary (that Jenny had me write) again and again. In summary, I had written the following statement:

“There is an old story about the mother who takes her child to kindergarten on his very first day, and says to the teacher, ‘My child is extremely sensitive. If he ever misbehaves, please reprimand the child next to him – that will be enough to make sure he gets the message.’ So, I hope that those of you planning to go out on the job market will take this into consideration and learn from the examples of how not to get a lab job.”

I answered a few of the angry e-mails, doing my best to convince the authors that a cartoon of a woman holding onto her husband’s tail as he peers through a microscope does not mean that I think the male component of a couple is necessarily a better scientist. This cartoon merely accompanied a very poor letter written by the female component of couple who made no attempt whatsoever to explain why she deserved or wanted a job in my lab, except for the fact that her husband received a position in my Institute.

It’s easy to take an isolated letter–or in fact just the cartoon and the situation– completely OUT OF CONTEXT and turn this into a vendetta against a male chauvinist. After all, politicians are experts at this type of manipulation.

But I sincerely hope that those of you who know me and have had a chance to look at the context will realize that these letters and my portrayal of the authors has nothing to do with chauvinism or disrespect–but merely an opportunity to explain and teach others the importance of carefully crafting proper job application letters.

Posted in Education, humor, research, science | Tagged , , , , , , , , , , | 24 Comments

In need of a distraction-part two, the unconscious bias

Posted on June 4, 2011 by Steve Caplan

I have blogged recently about trying to distract myself from neck pain. One of the suggestions was that I drop a 7 pound hammer on my toe, but I declined to take this advice not just because it was given by Henry, but because I like to walk. That seems to be one of the few things that doesn’t hurt and sometimes even loosens up my neck a bit.

Fortunately, although Omaha is a city with huge urban sprawl, there are wonderful bike trails that move along creeks and streams in between various lakes throughout the city. As I mentioned, the city itself is very spread out with the Eastern border being the Missouri River (which is in danger of flooding right now) and separates downtown Omaha from the town of Council Bluffs, Iowa.

We happen to live at the western end of the city and there are a wide variety of walks that I enjoy not far from where I live. One of my favorite haunts is/was Lake Zorinsky, named after the first Jewish Mayor of Omaha, Edward Zorinsky and a member of my “tribe”, as Henry would say.

This is a beautiful place to walk or bike with the lake narrowing at one area and being crossed by a bridge on 168th St. and making a figure 8 trail around the lake. The west side, in particular is very wild and aside from the birdlife, deer and wild turkeys can frequently be seen.

The lake is stocked with fish and draws many fishermen from the area. Some fish from quiet spots by the side of the lake or in small boats or canoes, while others launch motorized boats from a special dock. Unfortunately, a colonizing form of mussel probably from the Great Lakes, was recently identified in Lake Zorinsky, causing the engineering corps to make an executive decision and drain the lake. The rationale was that before the winter, it was calculated that if the water was drained or very low, the mussels would freeze and die and the lake would later be refilled. Unfortunately, right now it’s quite an eyesore.

Having been an Omaha for almost 8 years and being an avid walker I am pretty familiar with most of the nice trails. Since on weekends I can usually manage to find a couple hours to walk (about 4-5 miles in one direction and 4-5 miles back), I get an opportunity to see quite a few areas of the city. Now that my favorite lake has become Lake non grata, I find myself enjoying a particular walk down the very long West Papio trail. I can walk for about 5 min. through my neighborhood until I come to a small and little-known Park trail called Woodhaven Park.

This leads to the main trail, where I can turn and walk along the stream either south or north. There are numerous bridges to cross the stream and this trail probably goes 15 or 20 miles, not including its connection with the lake.

A week ago, I even saw a garden-variety snake by the side of the trail.

Today, in need for my distraction, I took the south route and decided to take a new fork in the path. It was not the prettiest route, as after three or 4 miles it moved into semi-industrial area. But I was curious to see where the trail would lead and I went on walking forward for close to an hour. Finally, I arrived at an underpass going right under a street. The area looked vaguely familiar, but I could not quite place it-I knew I had gone south and knew approximately where I was, but this was not one of the main roads I had expected to see.

With mounting curiosity I climbed up from the underpass and could see a small plaza with a sandwich/coffee shop, a parking lot for a 24-hour gym, and the medical imaging company. The name was familiar, something I knew that I had seen, but could not quite place. I moved along down the sidewalk to try and get my bearings and suddenly I could see it: the words were printed clearly on the side of the building for all to see. Right in front of me, less than 50 yards away stood “Community Rehab“–the very place that I have been doing physical therapy three times a week this past month.

Now how is that for an unconscious bias when looking for a distraction?

Posted in humor, Uncategorized | Tagged , , , , , , , , , | 3 Comments

“Rigged”- a complex educational experience

Posted on June 1, 2011 by Steve Caplan

A few years back when I was trying to teach my children how to play chess, I came across a really great teaching aid. It was called: “Fritz and Chesster“. I am reminded of this program now because when the child or adult would try and move the Bishop in an illegal fashion, a New York accented voice would pipe up and say, “diagonally, not any which way, diagonally.”

This blog is not–I promise–about chess. I brought up that point because this is the type of blog where I am not really sure where to start, what to focus on, or in which direction to move first. There are a series of complex education-related issues that I would like to touch upon, so forgive me if this comes out somewhat rambling.

For the past five years, I have been witness to an absolutely astounding educational program for elementary and middle school children (ages 8-14) designed to teach them the art of public speaking and raise their confidence by participating in the Modern Woodmen of America Speech Competition. This annual speech contest is an event that I have come to really appreciate.

Each year, the contest has a theme that allows the children to choose a suitable topic with care, research that topic, and write a 3-5 minute speech that they present at their own school. This gives them a wonderful opportunity to do research and put together a logical speech that should be convincing to the audience. The younger grade children receive some editorial help from teachers, but the ideas and content have to come from the children. Then, through much practice and hard work, the participants become “desensitized” to the pressures of oral presentations, and finally deliver their speech in a school competition with an audience of other students, teachers, family members, and of course, judges.

My daughter has been an avid participant in this competition over the past 5 years, and I have had the opportunity of attending many competitions–school competitions, school district competitions (where the winners from different schools compete with each other) and up to the Nebraska State championships–where a couple years ago my daughter was the runner up (2nd place) and narrowly missed going on to the US National championship. That year, the competition theme was “someone who has touched many lives.” My daughter chose J.K. Rowling, making a compelling case for how the Harry Potter series has enticed many young people to become readers, and the positive influence that reading has on humanity. Notable speeches dealt with the Holocaust (1st place that year), Gandhi, Mother Theresa, Martin Luther King, and the list goes on. It was an outstanding educational experience to listen to these young people make their cases. I can’t say enough about how much confidence such competitions instill in young people–knowing first hand how difficult graduate students find it to present seminars. For more on how to deliver the very best seminars, I refer you to Stephen Curry’s recent blog.

In particular, since my daughter previously attended a very small private school, I had the pleasure of witnessing children who appeared to have little aptitude for delivering speeches improve consistently year after year until their speeches were exceptionally well done. Similar to languages and chess (and many other academic endeavors), it appears that oration is a largely learnable skill, especially at a young age. Sure, some children will always excel more than others, will be able to put together a logical argument for any speech (or parental wish–try getting them to go to bed at a decent hour when they are better than you at debating!) and have that extra charisma–but from my experience, with a little coaching and patience, it seems that almost every child is able to put together a coherent and worthy speech that he/she can take pride in.

By the way, just as a rambling aside–unlike experiences at chess, these competitions are heavily skewed towards girls, who tend to constitute about 75% of the participants, and an even higher percentage of the winners at each stage.

Where am I going with this blog? Well, after generally praising the competition and everything related to it–including the good sportsmanship and support for all participants, whether their speeches were excellent or not–I hope that this next bit does not come across as “sour grapes.” I have always been against parents who become overly involved in their children’s sports, becoming upset if their child does not play well enough or succeed. They are out there to learn and have fun–in my humble view–not to become professionals. But I see that other parents have differing views. Nonetheless, I would like to share with you all the bizarre experience that my family encountered recently at the Nebraska State Championship.

For those of you on the other side of the pond, Nebraska is an east-heavy state. Omaha, at the south eastern end, has a greater metropolitan population of about 1 million people, and the capital and next largest city (Lincoln) is only 45 miles west. Yet the state extends about 500 miles west, and is extremely sparsely populated west of Lincoln. In any case, this year for the first time since our daughter began to participate in this competition, it was decided that the contest would be held in Hebron, Nebraska, population under 2000.

We had no qualms about taking a half day off work to drive out 150 miles–after all, our Prius gets good gas mileage–and we were curious to see a small Nebraska town. This year, the speech contest theme was “The Greatest American Invention” (see details below):

School Speech Contest Details

Instructions for participants*

“An American Invention” is the topic for the 2011 School Speech Contest.

The United States of America is the birthplace of many great inventions. Students are asked to select one invention and discuss it in their speech.

In organizing their speeches, students can consider these questions:

What is the greatest invention in United States history and why?
Who is the American citizen(s) who created this great invention?
How did the invention positively impact American life? And how does it continue to improve the quality of life for people?

Students can use the questions above to help formulate ideas, but they should not be limited by the list.

Speeches must be at least three minutes and no longer than five minutes long. Speeches must be in the students’ own words. Complete rules are outlined in the contest organizer’s booklet.

Judging criteria
Contestants will be judged using the following 100-point system

40 points for material organization
This accounts for theme and subject adherence, structure, content, logic and color.

40 points for delivery and presentation
This includes voice, pronunciation, enunciation, gestures and poise.

20 points for overall effectiveness
This scores impression and effect.

We had already witnessed some so-so choices by children at the school competition level–“The Doughnut”, for example being weeded out (although the delivery was poor anyway). By the district competition, we were already exposed to some excellent themes and excellent content combined with sparkling deliveries. “The Teddy Bear” was a very polished speech that probably lost points for not being significant enough. Among the best speeches (that received 2nd and 3rd places and also went on to the State Championship) was a speech about “Smoke Detectors”, and a speech that I thought was outstanding: “The Atomic Bomb.” The latter, delivered by a 12 year old boy, was extremely compelling as he presented his case in an unusually mature and measured manner, not at all daunted by the enormous complexities of his chosen topic. His point, that “greatest” doesn’t necessarily mean “most wonderful,” was well taken.

Now to the absurd. The host school had 3 competing children. The school principal, who hosted the competition, introduced the judges–all three were local (teachers, etc.), and one was his sister-in-law of the principal. That seemed odd, but well, small town, small pool to choose from.

The speeches were mixed. There was a beautifully orated speech about “The Washing Machine”–well researched, excellent flow, and flawlessly presented. I assumed that although it was very strong, it might lose points for its ability to convince the judges of the “greatness” of the invention. There was a speech on “The Telephone,” but I thought is was weak in presentation, with the inital opening gimmick of starting the speech while pretending to be on the phone with a friend being far too long (over a minute of the 3-5 minutes allotted). There was “Facebook”, which I found weak compared to what I thought the speech would be about in the first place–the computer. “Cool Aid,” a local western Nebraska invention was ridiculous, in my view. There was a well delivered speech with fairly weak content (made a poor case) for “High Speed Stroboscopic Photography.” The young lady spoke very well, but I found it irrelevant to hear that she had spent a school field trip at a local museum devoted to this type of photography–it turns out that it was developed by a local Nebraskan from the town. The final speech, which was weakly delivered by a 14 year old boy, was about “Duct Tape.” Neither theme, content nor delivery were compelling, and my wife whispered to me (ah, the advantage of speaking Hebrew!) “That was the worst speech,” when it was done.

In the end (biased though I am), I could not help feeling that the 3 children from my daughter’s district were heads and shoulders above the rest. Imagine our astonishment when the principal announced the judges choices: First place: “Duct Tape,” and two other local children from the school in 2nd (“High Speed Stroboscopic Photography”) and 3rd place (“The Telephone”). As good sports, we clapped and applauded the winners. As we were leaving, a parent of the boy who discussed “The Atomic Bomb” said: “Duct Tape? How could the judges possibly send someone to represent Nebraska giving a mediocre speech on Duct Tape?”

Our daughter took it very well. She understands that in speech contests, statistics apply. There is a lot of subjectivity among the judges. Over the years, several times she has come in 2nd place in her school, but 1st place later in the district–proving subjectivity in these types of competitions. I fear, however, that she learned a more complex educational experience this time–sometimes no matter how hard one tries, things can be “rigged” against you. The only thing to do is to shrug it off, pick up the pieces, and go on fighting the next battle. And that, too–unfortunately–is a valuable lesson.

***For those of you who are interested, Mika has kindly agreed to make the audio (but not video) of her speech “The Blood Bank” available for Occam’s Typewriter readers (below)***

The Blood Bank- Nebraska State Speech Competition 2011



Posted in Education, science | Tagged , , , , , , , , , , , , , , , , | 5 Comments

In need of a distraction

Posted on May 29, 2011 by Steve Caplan

I am in desperate need of some light and cheery distraction (where’s Cath when I need her?!). For the second time in the past four months I am suffering from some kind of ergonomic misery that I seem to have inflicted on myself by over-indulging in computer-based work. The “phenotype” is severe neck pain that radiates down my right arm.

When this first began to bother me some time ago, I did what any busy scientist would do and ignored it, hoping of course that it would just go away. It did go, but not away–instead it went and migrated right down from my neck to my arm. At this point, the pain compelled me to finally see a doctor.

I happen to have a really great physician–one I arrived at through a rather difficult process of trial and error. My previous physician had scared the bejesus out of me by a number of rather “insensitive statements”, and I dropped him like a hot potato. My current physician, recognizing my complaint for what it is–personal abuse–sent me for physical therapy. Through an intense eight meetings, the wonderful and dedicated physical therapist was able to relieve my pain and get me back to the state where I could continue to abuse myself. And of course I did, which is why I am suffering a relapse far more painful than the original aggravation. This is despite the intense amount of strengthening exercises that I do daily–including the closing of a strong elastic strap in my office door frame in order to do rowing exercises in between bouts of writing on the computer. The former, by the way, has become an event of much merriment for my students, who come to watch and photograph me doing my exercises on their cell phones.

So by now, those of you who have reached this point without logging off your computers forever or tossing them out the window, you are probably wondering “is it worth reading on?” What kind of a “nudnik” is this guy? If your Yiddish is not up to par, a nudnik is a kind of irritating, tiresome type of person. Anyone come to mind? No, don’t answer–that was rhetorical.

There is a joke about how do you define a nudnik? The answer is: it’s a person who you ask “how are you?”–and he actually answers, in great detail.

After this rather long-winded beginning, I thought that I might finally focus on what I hope might be an amusing little anecdote. I was reminded of this as I suffered from some rather uncomfortable side effects from some of the pain medications that I’ve been taking.

This is a story about allergies and cats. Hopefully I won’t be offending anyone–as I know there are a lot of cat-lovers out there–but I’m a dog person and never really “got on” with cats. Anyway this goes back to my student days, when I shared a two-bedroom apartment with a mathematics student. He was a really nice guy–but well, a stereotypic mathematician. He often forgot to tie his own shoes, and he had some funny eating habits. For example, I guess no one ever taught him not to slurp his coffee. In the beginning I thought he was doing it as a joke, until I realized that “what you hear is what you get.” I thought it might have been more effective for him to put the powdered instant coffee on his tongue, and just pour boiling water down his throat directly from the kettle. But I digress.

One day I was asked to cat-sit for a few weeks, and I made the mistake of agreeing. This was a vengeful and unrepentant feline species, who being upset for being abandoned with a non-cat-lover, took out her revenge by crapping in every conceivable place in the apartment–except her litter box. To make things worse, she would sit on me when I was working, and when I need to get up to answer the phone or for any other reason, she would get angry and scratch me.

Soon after her arrival, I noticed that my flatmate began frequent bouts of sneezing and coughing. Immediately I suspected that he might have allergies to cats, but was afraid to make that suggestion because I had no solution if the problem was indeed the cat. After a week or so, he went to his doctor and the good doctor assured him that it was unlikely that he had any allergies to the cat.

The next afternoon when I returned home from classes, I noticed that my flatmate had forgotten to close his bedroom door. I walked over and saw the cat snuggled comfortably on his pillow. That night, I couldn’t sleep because of the incessant sneezing and coughing coming from my flatmate’s room. In this case, I knew that his physician was wrong.

Although in this case, my flatmate was not the cat owner and had no reason to overcome his allergies (once the friggin cat was gone), I have noticed that cat lovers will go to unusual extremes to maintain contact with these animals–delegating essential parts of their homes as “cat zones” and “cat free” zones, undergoing long-term desensitization torture and exposure to cat dander, and so forth. Now why would any sane person do that?

But then I recalled that my father, a pediatrician, told me once about a former pediatric partner who loved chocolate, but was seriously allergic (poor guy). It turns out that he would occasionally give himself a shot of anti-histamine and then go binge on the chocolate.

And then there was this other unfortunate loser who would take pain medication and do physical therapy/torture for his neck so that he could continue to write silly blogs… I guess it’s not so different after all.

Posted in humor | Tagged , , , , , , | 20 Comments

Use it or lose it?

Posted on May 24, 2011 by Steve Caplan

Ever wonder what the effect of technology is on our developing brains? This is something that I’ve been thinking about for some time now. I recently put some of these thoughts into words in my blog entitled: “PhD survival: is a jack of all trades a master of none?” in which I discuss how the advent of technology in the form of scientific kits impacts the average PhD student.

I would like to expand upon this idea a little bit and move beyond the laboratory. But first, going back to my recent blog it seems that there was a consensus (with which I agree) that we cannot and should not hold back technology, but rather we need to know where to draw the line so that we scientists don’t become numbed zombies. Pretty much everyone who responded noted that researchers need to maintain some basic level of knowledge of how the various magical kits work, and certainly to have the skills to go to the literature to figure it out when necessary.

Up until the last decade or so, I think this was a consensus in day-to-day life as well. For example, in most elementary school educational systems, teachers still felt it necessary for their students to master the multiplication tables, to do long division, etc., even though calculators can readily do that for us. However, calculators (for the most part) cannot solve polynomials or quadratic equations, and children don’t learn how to factor in their heads will be at a serious disadvantage in algebra and higher math.

With the advent of so many new technological advances in our day-to-day life, I think that the distinctions of which skills need to be upheld are becoming more difficult to make. One might easily make the argument that in the pre-cell phone age, people had to be far more organized and to schedule and plan things much more carefully. Obviously, I am not maintaining that we go back to the old and less spontaneous days, but there are some skills that really may become a thing of the past–for better or for worse.

One of these skills, is the art of navigation. Having spent many long hours–particularly nights–navigating with topographical maps, I felt a little bit uncomfortable when we finally caved in and bought a GPS–global positioning–system for our travels. For me, an integral part of every journey was successfully finding the way. I taught my kids how to use a compass, how to read topographical maps and how to do basic triangulation to elucidate our position on a map. In the car, I taught them to look carefully at the topography–at the little gullies and streams and low points, and to listen as the engine straining as it gradually moves up an incline that might not be so easy to spot.

It’s been well documented that navigation skills are linked with reasoning in the brain. Most of you on the other side of the pond are probably more familiar with the studies done on London cabbies than I am, but it’s pretty clear that the hippocampus and other areas of the brain become highly developed in those with excellent navigation skills.

So aside from pilots–who obviously need to know the basics of manual navigation–is this a skill that will soon disappear from the face of the earth? I, for one, find that I no longer prepare well in advance for journeys having seen the map and memorized my route–I too have become dependent on the new technology. But not to this extent.

Posted in Education, research, science | Tagged , , , , , , | 2 Comments

A shocking business

Posted on May 19, 2011 by Steve Caplan

Some recent repairs that we had done on our home, coupled with Henry’s recent post “Build” led me to recall an odd event that occurred in my home some years ago.

We were new in the city of Omaha, and owned a home for the very first time (more accurately, held a mortgage). In the course of having the house inspected prior to purchasing it, the inspector had recommended adding GFCI (ground fault circuit interrupter) electric receptacles in our kitchen, which are supposed to reduce the risk of fire hazards.

Being Mr. Dr. Safety, I decided that this was a prudent thing to do. So, not knowing anyone in Omaha who could recommend a reputable electrician, and not wanting to fry myself in the process of do-it-yourself, I opened the Yellow Pages and plucked out a name and number. I soon had an appointment scheduled for an electrician to come and do the job.

Being a male feminist who shares the duties of staying home from work for such events (and shuns “beauty pageants”), I packed off my spouse and kids to school and work, and awaited the arrival of the electrician. He soon arrived, with a rather dilipidated white truck that had obviously seen better years–perhaps better decades.

The electrician came into the kitchen, and was quick to spot the problem as soon as I pointed it out. He moved to the left of the existing socket, and then to the right. He nodded his head slowly. I thought that he would go down on his knees, like a golfer lining up that perfect putt, but he spared me that image. Instead he went back to his truck and brought his tools along with the GFCI receptacle.

Now, normally when I am entertaining workpersons in my home, I bring my laptop down from my second floor home office to the kitchen table where I can keep an eye on what’s happening. However, in this case I had some ill feeling that I had better keep an even closer eye on the events in my kitchen.

The electrician busied himself undoing the screws from the receptacle to be replaced, and then began to unscrew the attached wires. I asked, rather politely–not wanting to offend the electrician’s expertise– “Don’t you want me to close the circuit on the breaker board?”

He looked at me the way a teacher looks at a failing-but-trying student: “I’m an electrician–don’t worry, I’ve done this hundreds of times.” Based on the appearance of his vehicle, I tried not to doubt him.

I was still watching as he began to attach the new GFCI receptacle, when suddenly there was a tremendous popping/crackling noise, and the electrician was flung clear across our kitchen where he became briefly intimate with our refrigerator. I was shaken, and rather shaky as I helped him up, asking him if he was okay. He brushed off his pants, looked at me and said, “Yeah, I’m fine. It’s no big deal. Happens to me all the time.”

Needless to say, I later made a big “X” on his Yellow Page advertisement, noting: “Don’t call him–don’t want him killed-in-action.”

From then on, through recommendations only–research is important in everyday life too!

Posted in humor, research | Tagged , , , , , | 4 Comments

Don’t underestimate the enemy

Posted on May 11, 2011 by Steve Caplan

Don’t mistake me–I am all for promoting the wonders of science and scientific research–you will be hard pressed to find a better advocate than me. And after all, there is a growing awareness among scientists that research should be translated into layman’s terms, so that the general public can have some rudimentary understanding of what we scientists are up to, day and night.

However (and this is the key “however” that comes immediately prior to the rejection of a manuscript or grant proposal), we must take special care not to over-simplify and patronize (to “dumb-down”, as the new expression says). Worse yet, we must never–and I mean never–fall prey to the danger of hubris and gloating, especially to “The Emperor of all Maladies“.

Accordingly, I was rather shocked and extremely disappointed recently to see a campaign advertisement in a highly visible and public place flaunting the “Emperor of all Maladies“.

researcher and institute intentionally obscured

CANCER DOESN’T STAND A CHANCE? WHO THE HELL ARE WE KIDDING?!

Who among us does not have friends and family who suffer or have suffered and died from cancer? Can those responsible for this campaign–“Cancer Doesn’t Stand a Chance”–stand in front of the beaved families of millions of cancer victims and look them in the eye?

In my humble view, such bombastic statements are very dangerous to scientists and research, as they are simply untrue and ultimately harm the integrity and credibility of science and scientists.

Anybody care to weigh in on this one?

Posted in research, science | Tagged , , , , , , , , | 4 Comments

Ph.D. survival: is a jack of all trades a master of none?

Posted on May 5, 2011 by Steve Caplan

Over the years science has changed a great deal. In just the last 50 years or so we’ve seen a major revolution in scientific research, due primarily to our understanding of DNA and ultimately how it codes for protein. But there have been quite a few changes even in the 12 or 13 years since I received my Ph.D. One of these changes, which I would like to address in this blog, relates to the way that science is done. More specifically, the way in which science is done by today’s Ph.D. students.

I hope, dear reader, that you will not already have tired of my reminiscences of what it was like when I was a Ph.D. student. If you have, I suggest you either logout now, or take a deep breath and read on.

If you got this far, then either curiosity got the better of you, or you haven’t read too many of my blogs. In any event, as a Ph.D. student in the 1990s, I was expected to master various techniques in the course of my studies. In my case, it was a combination of some work with mice, a lot of protein biochemistry, and some very standard and basic sub-cloning techniques. I spent an awful lot of time working on different types of two dimensional gel electrophoresis; in other words separating proteins both by size (molecular weight) and by charge, or alternatively by size and whether or not the proteins were linked by disulfide bonds.

As a principal investigator now, and a mentor of graduate students, I see that things have changed considerably. The students of today need to utilize many more techniques than I did in order to progress. It is not uncommon for a student who is versed in biochemical techniques to also have to learn various physiological/cell biological assays that might be outside his/her “comfort zone”. A lot of this has to do with the ‘globalization of science’, and the arrival of the kits on the scene.

These kits are both a blessing and a curse. On the one hand, they really do allow students to rapidly employ a huge arsenal of techniques that simply would not be possible without a simplified ready-to-use system available. On the other hand, it appears that many students–perhaps anxious to take advantage of these kits as quickly as possible–do not really make an attempt to understand the science behind them.

Unfortunately, this has led in some cases to students who are basically “buying science”. What I mean by this is that some of the most fundamental and important elements in the students’ scientific education are being lost. For example, I’ve come across students who have performed one of the most basic cell biology/biochemistry experiments–the immunoprecipitation of proteins with antibodies–with such kits. For those who are not familiar, this is a very basic technique where one uses a specific antibody to pull down and precipitate a specific protein from a cell lysate.

For those lacking experience with this basic technique, these kits are perceived as an easy way out. They contain pre-prepared lysis buffer to break up the cells and make a lysate from which the immunoprecipitation can be done. Instructions are given, but the rationale for each step is lacking. The problem is that there really isn’t a “one-size-fits-all” lysis buffer and system for immunoprecipitation. The concentration of salt can be critical, as can the choice of detergent used to make micelles from the membranes, as well as a host of other factors that can also be of importance. I find that some of the students have absolutely no clue what’s contained within these magic buffers, and of course this precludes any possibility of troubleshooting, should the experiment not succeed. So the rapid progress that can be attained with pre-prepared kits and solutions comes with a price–students who are no longer masters of their own research.

But is it all really bad? Not necessarily. If students and researchers are aware of these potential pitfalls, and at least stay technically conversant with some of the most fundamental techniques used, then the age of the kits can actually propel research forward quite rapidly.

A PI and his students become almost like a child in a candy store; all the techniques are available–one only needs money to pay for them. In fact, this has become the age of outsourcing in science. When I began my Ph.D., researchers were still carrying out cumbersome DNA sequencing reactions in their own laboratories. Today, no scientist worth his/her salt (sorry, another awful pun) would waste time doing this. It’s all sent out to companies or sequencing facilities at the university itself.

So, one possibility is that laboratories will decline in size over time. The researchers; PI, postdocs and Ph.D. students will all need to spend more time thinking, more time reading, more time figuring out which new assays will be applicable to the research; how to best spend the money to get “the most research for the buck.” There will be less work at the bench, and more thought given to which kits to order and what work to outsource and to whom.

Is this a scary scenario? I don’t necessarily see it that way; I think that as long as researchers maintain a firm grasp key number of scientific techniques, it’s probably a good development for science. The better students adapt and learn, and the better mentors ensure that their students understand the technical concepts of the science that they carry out. After all, many of us scientists firmly believe that critical thinking is the key component of graduate education. And there’s no reason that this element should be lessened in the new age of science.

How about some “Yays and nays” from the other side of the pond?

Posted in Education, research, science, Uncategorized | Tagged , , , , , , , , , , , , , , , , | 13 Comments