A pinch of salt in the lab

Ever see those amazing deaf-defying (thank you, Grant!) death-defying feats and the announcer at the end says: “Do not attempt to do this at home?”

Well, do not attempt to do this in your lab.

I don’t know why I recalled the following little anecdotal story from my student days. Perhaps watching and enjoying the way people in my own lab interact and help one another stirred some dormant memories. Perhaps my upcoming jury duty scheduled for next (more on this at a later date).

I was the first student to graduate with a Ph.D. from my mentor/supervisor’s laboratory. But I was not the first to start a Ph.D. in the lab, and there were several additional candidates who didn’t make it through.

Now this is not a reflection on my former mentor; she is an excellent scientist, great mentor and motivator, and a very good friend to this day. But she had her standards for performance and behavior, and many a student didn’t make the cut.

One such new student was attached to me to shadow me and learn the tricks of the trade when I was roughly halfway through my stint in the lab. She apparently smoked, had a moderate case of halitosis, and had an irritating habit of continually touching my arm when talking to me. But I was polite (for awhile), grinding my teeth and soldiering on.

My mentor frequently checked in with me to see how our new student was doing. In the beginning, wanting to give her a chance, I was non-committal, but my adviser’s sensors were perceptive enough to see that I wasn’t pleased.

It wasn’t just the irritating touching or smoky lab coat (although that didn’t help)–I began to sense an underlying laziness–a trait for which I have little patience.

It started when I realized that after showing her the same procedures 3 or 4 times, she still hadn’t bothered to write out the protocol in anticipation of doing it on her own the next time. There was little attempt to write down where the key reagents were in the refrigerator or freezer, so I would inevitably be called 10 times a day to show her again and again where to look.

This was only the beginning. When she was unable to get her immunoblots working on her own, my mentor asked me to give her my own stocks of reagents to help troubleshoot. Those reagents included the “homemade” Enhanced Chemiluminescence reagents that I had carefully spent a few weeks calibrating so that our lab could save hundreds of dollars and not have to pay for the commercial kit.

Of course I obliged, and was happy that my own reagents solved the problem. But our new student, let’s call her N, seemed to think that this was the perfect permanent solution–to have Steve as her personal solution maker.

I asked once, twice and thrice. Finally I told her to make her own reagents. She agreed (thoughtful, wasn’t she?). But over the next few weeks I noticed that my reagents were dwindling at a very rapid rate. I asked her if she was still using my reagents–still politely–and “No” was the answer. But again and again, I seemed to notice that my stocks were being rapidly depleted.

One evening, when I left the lab, she was the only one still working. I slid out to the hallway fridge and made a very small dot to mark on the bottle of one of my buffers exactly what volume remained. I knew that she would need that buffer (hers or mine) for her experiment. The next morning I had incontrovertible evidence that someone was pinching my buffer. I had no doubt who it was, but I had no proof.

What to do? My adviser by now knew that I did not have a very high opinion of this student, and she usually took my advice on such matters. But I did not have conclusive-beyond-a-shadow-of-a-doubt proof.

Then I had one of those brilliant ideas (*claps self on back)–one that if converted to chess, would be equivalent to a back-rank mate. Or in European football, a goal scored by the keeper. I decided-to——-replace the key buffer that I suspected her of pinching with that remarkable clear liquid known as H2O. Can you see it coming? Yes–if she were to steal my buffer (pH 8.5) with plain old agua (pH 6.5), there was no way that her enhanced chemiluminescence would work. The ultimate result would be a perfectly blank film coming out of the developer.

The outcome? 24 hours later, N was packing her belongings and looking for another lab.

Now, my adviser–despite taking very fast action to depose a student caught lying numerous times at a very early stage of her career–was not thrilled with my brilliance. She was upset that I had ruined a potentially important experiment (which I offered to do to compensate). But when I asked her “How else could I prove that she had been taking my reagents again and again,” she had no answer. And when I continued and said, “Imagine if she lied about little things like salt buffers what kind of data she might have fabricated later on,” she began to appreciate my strategy.

But you have been warned: Don’t attempt this in your own labs…

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Chile-ing out

This post comes on the heels of the heat wave that we’ve been suffering through (and my dreams of glaciers and mountains), here in the American Middle-West, which in itself comes in the wake of the flood. It also comes in envy of some of the fantastic photos that Steffi has posted over the past months in this post and others.

But the real inspiration came from the laboratory. We’ve recently had several new people join the lab, something which I usually find rejuvenating. We also have a student scheduled to graduate in two days time, and she has already arranged a big party at my house. To pour salt on the wounds, she complains to me that some of her friends are scared of me and might not want to come! I was tempted to tell her—oh never mind–back to the point.

Where was I? Oh yes, so I was recently asked what my policy is about vacations. I think that newer recruits are often surprised to hear that I am all in favor, and not just for a long weekend.

One cannot do bench science by remote control, but for hard working determined researchers, there’s nothing like a real vacation to spur some creativity as well as keep the motivation high. I know this, because I myself took a 6-week break in the course of my Ph.D. for a trip to Patagonia in S. Chile and to the beautiful Lake District north of there.

We started out flying from Santiago to Puerto Natales, several thousand miles south of the capital.

a youthful me, in 1996 in Puerto Natales

By the way, this photo is of course in mid-summer. This was a very colorful town, with locals happily wearing shorts and t-shirts when the weather topped 6 or 7 deg celcius. Brrr.

Puerto Natales from the hotel

We did not stay there long, as our goal was to get to the magical Torres del Paine National Park: our plan was to hike the famous circuit route, generally a 7-day hike + 2-3 additional days to climb to the base camp of the “towers.”

The famous circuit route around the park- carry in and carry out

While the skies poured rain on us the first days on route to the base camp (before beginning the circuit), we did get clear views of the towers:

Blood, sweat and tears to get to this photo, Torres del Paine, 1996

A strange and barren windswept landscape greeted us on the circuit.

Feeling freedom and clean air

This one felt big enough to make me his supper:

El condor pasa. Indeed.

There were times when I wondered if we were going in the right direction, if this wasn’t a prelude to the famous Alaskan “Bridge to Nowhere”.

Bridge to Nowhere? Where have I heard that before?

Perhaps this had to be the most amazing site. After getting stuck in our tents in a snowstorm and being unable to climb to the highest pass on our route, we finally made it the next day (at the time, I was thinking–I’m too old for this!). To arrive at the high point and look down on this–the Grey Glacier. Spectacular!

The masked marvel--me reaching the pass and shocked to see the frozen river a thousand meters below me.

Having finally descended to the glacier level, we were astonished to see that it’s height above the water was 80-100 meters.

Grey Glacier--the blue color at the bottom is from the condensed/packed ice

While I could go on and on with many more photos from this park, and later climbing the Villarica volcano (and peering into its depths!), I will leave that for the next heat wave, if I sense any interest…

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It is what it is

As a scientist who spends a lot of time looking at data, I sometimes feel that we venture into an area where we are in danger of over-interpreting our results. On the one hand, it is a perfectly natural and human characteristic; to speculate and even use imagination to try and gain a deeper understanding of the complex world around us.

Frequently, however–in my realm of science–such over-interpretation can often be premature, and even detrimental if one gets locked into a specific mindset–an “idee fixe”–at too early a stage. Especially since our initial ideas so frequently turn out to be wrong.

Consider a simple hypothesis posed as one sets out to dispel prove test one’s idea. In my field, we usually need to gather a fair bit of data from casting a wide net of experiments before we can actually see a cohesive picture emerging. So initially, this requires some patience and the ability to suspend–at least temporarily–one’s speculations and over-interpretations until enough information is out there on the table to propose a model.

Sometimes, it is necessary to stop and say: “It is what it is”–otherwise, over-interpretation can lead us to the following type of scenario as this brilliant sketch by Eric Idle and John Cleese illustrates.

Idle: “Jarrow United came of age in a European sense with an almost Proustian display of modern existentialist football, virtually annihilating, by midfield argument, the surely obsolescent defensive philosophy of Signor Alberto Franfrino.”

Cleese: “Well, I hit the ball first time and it went in the back of the net.”

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Where have all the good times gone?

I recently spent a wonderful vacation in Washington, DC–replacing a planned driving trip to Mesa Verde in southwestern Colorado and some of the nearby parks in Colorado, Utah and New Mexico. All because of a pain in the neck, that I am again happy to report–is now gone. We’ll get there eventually.

I lived for 4+ years in the DC area, from 1999-2003, and visiting the Smithsonian museums on weekends was one of our favorite past-times. This time, we had an opportunity to go with children now at an age where they could fully appreciate the magnificence of the Washington Mall.

One of the days we visited the museum of American History. There were many exhibits, and we had to pick and choose. One of them was about science labs and research in the US. A must see, and extremely well presented.

What struck me in particular was the evolving way in which science and scientists are viewed. We know today that “Geeks and Freaks” seems to be a common conception, along with evil and/or obtuse researchers lacking in any human emotions. But was it always like this?

Apparently not. It seems that scientists and science were once accorded the highest respect of the American public. For example, look at this comment, photographed at one of the exhibits:

Respect for Science! Today homeopaths and creative design proponents seem to have eroded the respect for scientists

And how about this? Laboratories as cultural symbols of truth! Oh those were the days…

Laboratories as cultural symbols of truth--*sigh*

Where have we gone wrong? Is there any way to turn back the clock?

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Mr. President, can you save science, please?

Scientists love to complain. That is not to say that they enjoy the situation that they are complaining about, but to me it seems as though in the US there is a level of fatalism that translates into inertia. And of course, being busy surviving has always been a valid excuse.

This weekend I decided to take another small step to do something for science; to write a letter to the President of the United States. I sent it to the White House. I do not expect much, but at least it gives me the impression that I am trying.
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Dear President Obama,

This is an appeal to you from a basic biomedical research scientist and citizen of this country to help save science before it is too late.

Allow me to introduce myself: my name is Steve Caplan, and I am an associate professor in the Department of Biochemistry and Molecular Biology, at the University of Nebraska Medical Center (UNMC). I have been here for eight years; I run an active basic research program and teach graduate and medical students.

Although my family originally hails from Canada, I was born in the US during my father’s medical residency in the mid-1960s. After my childhood in Canada, I moved to Israel where I eventually obtained my Ph.D. and finally arrived back here in the US for post-doctoral studies at the National Institutes of Health (NIH) in 1998. In 2003, realizing that the US was still the most opportune place for thriving scientific work, I accepted a faculty position here in Omaha at (UNMC). While I still believe the US maintains the best infrastructure for science in the world, if things do not change within a few short years this will no longer be the case.

Before continuing, I would like to note that the scientific community is tremendously appreciative of the funding that NIH received as a result of the American Recovery and Reinvestment Act (ARRA) and your support for science. However, as helpful as the ARRA awards were, the mood among scientists in the US today is grim, and the United States is on the verge of losing an entire generation of trained biomedical scientists.

Let me start by first describing the situation as I see it. New investigators are finding it incredibly difficult to obtain funding right now. In this system, after spending about 15 years of undergraduate, graduate, and post-doctoral training, the lucky and talented few who are able to obtain independent research positions are being weeded out of the system. A researcher who is unable to attract grant funding will not get tenure and his or her door to other scientific positions will be closed. True, not all new faculty members deserve to stay on as independent researchers. However, in today’s almost hostile atmosphere, I am familiar with a good number of very talented and successful people who are in the process of being lost to the system.

Adding to this, I can relate to you that many institutions have completely stopped hiring new faculty that have just completed their post-doctoral work; instead they elect to head-hunt and hire experienced faculty from other institutions who already have funding. As you can imagine, in the long and even intermediate run, this will have a terribly detrimental effect on the future of science.

Unfortunately, the issue of funding is not just problematic for newer faculty members. It is extremely depressing to see so many senior faculty members looking tired and haggard, and speaking out about retirement. Please understand that this vocation is one of love, and there have always been a great number of “retired” professors who would go on forever working just for the advancement of science. This reflects a deep frustration that will undoubtedly trickle down to the next generation of scientists.

Since I’ve been a faculty member these past eight years, I’ve seen the budget for my grants decrease steadily. On the other hand, the cost of equipment, reagents, and of course the salaries for my personnel has been increasing with the cost of living. As a consequence, it is becoming harder and harder for researchers to survive—not to mention thrive.

The NIH has done its best to try and address these issues. It has made a number of changes in the grant system, from the way grants are submitted to the way they are reviewed. However, the bottom line is that these are cosmetic changes that will not improve the situation. Without a significant commitment to support science from the US government, this country will soon be overtaken as the global science leader by European and Asian nations.

I suppose that in times when the national debt is a major issue that some skeptics might ask “what has science ever done for us?” The answer is that science—including very basic and fundamental science—has had an enormous impact on the US and the world. There is a tendency to think that science that isn’t designed or targeted towards specific diseases is dispensable. After all, the public wants and deserves better medical treatments and advances against such terrible maladies as cancer, heart disease and other ailments. Historically, however, it turns out that the greatest advances have often come serendipitously from the basic sciences.

US Nobel Prize laureate Arthur Kornberg discussed some of the greatest biomedical research findings, including penicillin, x-rays, the polio vaccine and genetic engineering, noting, “No matter how counter-intuitive it may seem, basic research has proven over and over to be the lifeline of practical advances in medicine. Without advances, medicine regresses and reverts to witchcraft.”

Other skeptics may say that this is fine, but the US can’t afford to spend so much money on science. The truth is, that the US can’t afford NOT to spend more money on science. These skeptics are probably altogether unaware of the economics of science. Each invention spurs new patents and industry, creates companies, jobs, and of course revenue for the US government. Consider even a single laboratory. We won’t even deal with the construction of the building and all the work needed to bring a new laboratory into existence—we’ll start with a new position being created.

When a new faculty member is hired, and allocated a certain amount of “start-up” money for his/her lab, this immediately leads to the purchase of large and small equipment. In addition, the new faculty member will likely hire a technician, take on a couple students and perhaps a post-doctoral fellow. More jobs are created, more taxes are paid, and American companies benefit. The continued success of such a laboratory enhances both the local and federal economies.

So what could possibly be a better investment?

As a scientist and concerned citizen of this country, I beg you to reevaluate the priorities and needs of this country. I hope very much that you will come to the conclusion that support for science needs to be made an immediate national priority.

I thank you for your time and wonderful service to this country and the world.

Respectfully yours,

Steve Caplan, Ph.D.

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Any bets on a reply?

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Nicosia, there I went…

A short time ago Larnaca, Cyprus made the news for holding a large civilian wedding for multiple couples from Israel.

I have already blogged about the discriminatory policy that a successful start-up country and high-tech power such as Israel has against women. The advance of the theocratic powers in Israel are, in my view, the country’s number one threat.

I may have been ahead of the curve, but for this very reason–an unwillingless to bend and bow before Israel’s orthodox religious establishment, my spouse and I married in Nicosia, Cyprus. Been there, done that.

How can such a country, despite producing a female Nobel prize winner for chemistry last year, hope to ever achieve meaningful equality for women when the religious establishment blockades the most basic of human rights.

Below is an editorial from the Israeli newspaper Haaretz that sums it all up.

Israel must grant all citizens the right to civil marriage
The radicalization of the rabbinical establishment have led to a situation where the status of women – on issues of marriage, property rights, child custody and divorce – is swiftly deteriorating.
–Haaretz Editorial–

The dozens of Israeli couples who married about two weeks ago in a mass ceremony in the city square of Larnaca, Cyprus, didn’t do so in order to break the Guinness record for mass weddings. They were forced to take part in this expensive procedure, far from home and family, because in Israel, there was no way they could have a civil wedding.

The United Nations has issued a report on implementation of the Convention on the Elimination of All Forms of Discrimination Against Women, which Gili Cohen (Haaretz, July 5 ) noted was handed to the government authorities here in February of this year. The UN is not interested in the coalition arrangements of successive Israeli governments. Like an earlier report that examined trafficking in human beings, this report deals particularly with the blatant undermining of women and their status.

Although Israel likes to boast that it is “the only democracy in the Middle East,” and signed the convention requiring it to ensure equal rights for women in marriage and family relationships, it is ranked, according to Prof. Ruth Halperin-Kaddari, who heads Bar-Ilan University’s Rackman Center for the Advancement of Women’s Status, “in a bad place in the middle,” and Israel, in effect, stands “among the countries of the developing world and the Muslim world.”

The continuing abandonment of the areas of marital relationships and family to the control of the Orthodox establishment is not the legacy of the government of Prime Minister Benjamin Netanyahu alone, but during his tenure there has been a worrisome worsening of the situation: The Haredization and radicalization of the rabbinical establishment have led to a situation where the status of women – on issues of marriage, property rights, child custody and, above all, divorce – is swiftly deteriorating. The thundering silence of Justice Minister Yaakov Neeman in light of the reactionary norms that have taken over in the rabbinical courts and the ease with which the government has been expanding the powers of the rabbis have only exacerbated the situation.

Although the government has made several attempts to promote limited legislation for civil marriage for those “ineligible for marriage,” this initiative is the product of a political effort to conciliate a small group among immigrants from the Commonwealth of Independent States, and has nothing to do with the principle of equality. The right to marry and to start a family is a basic civil right, as is a woman’s right to equality in all areas of life. If Israel is still interested in being considered an open society and a progressive country, it must implement the recommendations of the UN commission, and enable all of its citizens to marry, divorce and live equally.

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The horrible F-word

A week ago I returned from Washington DC from an NIH grant review session. At NIH, the forbidden F–word, is of course “funded.”

However, as bad as the funding is right now, sometimes we scientists need to put things in perspective. A real F-word that is out there in many states in many areas of the US right now is: FLOODING

On my flight back from DC, despite having seen and heard the news for weeks and weeks, I was nonetheless shocked as the plane began to descend into the Omaha area. Flying low over Western Iowa, Missouri River looked like the sea. I could see roads submerged entirely underwater, telephone poles barely poking above the surface, barns and homes almost completely invisible, and of course miles and miles of farmland turned into swamps.

The flood, as seen from above

The flood, as seen from above-2

There were bridges sitting above the rising water, with no visible road, reminding us of the infamous Alaskan “bridge-to-nowhere”.

I did not try to take photos, but here is a link to an Omaha news station showing aerial video of Nebraska, Iowa, and, farther north upstream, Gavin’s Point Dam close to the border of the 3 states.

Today, we ventured from our high point well west of the river to the downtown region where the Missouri River separates eastern Nebraska from Western Iowa, and crossed the pedestrian bridge to the Iowa side. Although nothing like some of the aerial photos, the power of the river and its rushing currents was something to behold.

Benches underwater at the Omaha promenade-Missouri River

A parking lot under water, downtown Omaha

On the pedestrian bridge- where is the Iowa side river bank?

where is the promenade?

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Bathroom breaks and other news of the day

I’ve come to the realization that a little chronic pain can be good for the soul. That is, if the chronic is not too chronic. Readers of this blog may remember my whining and complaining about neck pain—a recovery and more pain.

I am now delighted to report the absence of pain—so palpable that I can acutely feel it. This is mostly due to my highly dedicated and knowledgeable physical therapist, along with heat, electrical stimulation, proper ergonomics, better posture and a series of exercises designed to strengthen unused muscles while at the same time preventing activation of overused muscles. Thank you physical therapy!

I’m celebrating, but I’m going to be doing my best to avoid going through this process again.

One of the first things I’ve learned is that meetings can be bad for the body. At all cost, I find it crucial to get up and stretch as many times as necessary, no matter how shocked the other people in the room appear to be by my eccentric behavior. I’ve been standing and bending and stretching at national meetings for grant review, as well as at local meetings in my own institute.

At a recent curriculum meeting, I found myself sitting right back down in my chair when the topic of bathroom breaks during exams came up for discussion. It turns out that at a certain institute, in certain courses, graduate students have been requesting bathroom breaks at an alarming rate during the course of three-hour exams. Well, when you gotta go, you gotta go.

However, intelligence reports have been leaked (no not through Wikileaks) maintaining the students have been pulling notes or cell phones out of their pockets in the restroom/bathroom/w.c.—which of course is cheating.

Years ago, the response to cheats often used to be that those who cheat are really cheating themselves, because they haven’t learned properly. But this doesn’t do the trick—especially since the students are graded on a curve, and there is fierce competition for fellowships and other rewards.

This makes it incumbent upon course coordinators to ensure that justice is served.

Easier said than done.

In fact, how does one accomplish this? Multiple ideas were put forth:

1) Restrict students to one restroom break during the course of the exam.

Does this help? Once can be enough for cheating, yet might not be enough for a student with a weak bladder or stomach upset.

2) Chaperone students into the restroom.

This would require, in addition to the instructor proctoring the exam, a female and male teaching assistant to sit there for three hours solely for the purpose of escorting students to the restroom. How productive! And then what? Do they venture into the stalls with the students? Or frisk them before going in? Or should we purchase a body-scan machine that “sees through the clothing of an individual”—like the TSA (Transportation Security Authority) at US airports?

So what can course coordinators do?

Another idea was to split the exam into several sections. A student leaving for the restroom would have to finish and turn in his or her test section before going to the restroom. Each test section could be designed to take about 45 min. or an hour, with a five-minute restroom break before the next section starts.

Does this solve the problem? I don’t know. For one, what happens if the student genuinely or disingenuously asks for the restroom after 15 min.? Does he or she need to forfeit that entire test section? Would that be fair? An additional issue is that some students are stronger in some sections and others are better at different sections. Traditionally, the three-hour exam has allowed students were good at one section to whiz through it quickly and spend a lot of time on the sections that they find difficult. With this new proposal, students would lose this advantage.

I don’t have an answer, but would be curious to hear how these issues are dealt with “over the pond” or at any other institutions. Also, if anyone has any creative ideas to deal with these messy issues, I’d love to hear from you.

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Best Protein Names–the winners!

Recently, we announced a competition for the best/funniest protein names. Now, after great debate among the professional judges, I am proud to report the winning protein names for this year’s contest.

Drumroll, please…

First Place: INDYI’m not dead yet
from Cath Ennis

Second Place: CHEAPDATE
from Cath Ennis

Third Place: SPAM1
from… Cath Ennis

Looks like a clean sweep for Dr. Ennis!

Honorable Mentions:

1) Merlin
from Richard P. Grant

2) Batman
from MGG

Thank you for your contributions, and we look forward to another contest in 2012.

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Put your money where your snack is!

One of the nice things of living in Omaha is the variety of great summer camps available for kids. In the course of the last eight years here, our kids have been attending a huge number of really exciting and worthwhile camps.

One of the best of these camps is the University of Nebraska at Omaha (UNO) series called “Aim for the Stars“. Run by the physics department, it has a natural bias towards the sciences, and over the years we have found the kids participating in such weekly camps as: adventures in chemistry, advanced zoology, advanced geology, art in science, amusement park robotics, go green, get your game on: strategies of the mind, mathemagic, engineering, patterns and percussions, physics with toys, science fiction, totally cool math and science combo, and the list goes on.

I wish I could take a sabbatical and participate in a lot of these camps!

Having done many of these camps, this year my daughter decided to add a new one to her repertoire: Fitness.

In fitness camp, the idea was not simply to run the kids around a track until they fall off their feet–instead, to combine a reasonable amount of exercise with some academic understanding of nutrition, anatomy and physiology and fun. For example, they spent a good deal of time discussing the “food plate”–a term that has now replaced within my day was known as the food pyramid. Here is a great example of a little project but she did with her friend showing what a dietitian’s work might be like graphically.

At the end of the week, my daughter can now join Henry in calling herself a “Celebrity Nutritionist.”

Having said all of these good things about the camp, where the counselors explained calories, fats, complex carbohydrates and so on, I found it extremely amusing–if not actually sad–when my daughter explained to us the first evening after camp how her first day went.

She told us about what she learned, what the counselors had imparted about health and diet and food–and so on–and that she was upset to find that when it came to snack-time, they handed out a packaged snack known here in the US as “Little Debbies“. Information on the nutritional value is found at this link.

If 13-year-old kids see the irony of this type of “do as I say, not as I do” education, then I think it’s time for the camp to reevaluate its nutritional policy and put their money where their snack is.

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