The NYTimes has recently implemented a paywall system where users will be charged for access after a certain number of page views. Whatever your opinions of this system are, there is an easy way around it. I heard rumors on twitter that following a link from twitter or facebook to an article would not count against your "free" pageview limit. Someone has started a twitter feed that links to every new NYTimes article. This seemed a little excessive to me so I tried changing the web referrer in firefox instead. Essentially, whenever you visit a website, your web browser tells the webserver where you last visited. It's really easy to lie about where you've been using the FireFox plugin RefControl. All you need to do is:

1. Install the plugin.

2. Go to -> Tools -> Add-ons

3. Scroll down to RefControl and click on it

4. An Options button will appear. Click it.

5. In the new window click Add Site.

Fill out . . . More

With the launch of this year’s “Rock Stars of Science” campaign, there’s been a lot of talk about how to best promote science. I’m no marketing guru, but I am a scientist. This latest campaign is better than last years', only because it’s more diverse, but I think it really misses the boat. Is the public really going to be inspired by a couple of pictures in GQ of scientists looking uncomfortable and over dressed in the presence of Rock Stars? The most appalling aspect of this campaign is that there is no highlight of the researchers or their science. There truly are some science all stars in this group, many of which are well spoken.

However, the Rock Stars of science pages in GQ only list the scientist’s name and title, while the “Rock stars” get a one or two sentence summary of how awesome they are for standing in on these pictures. What’s the real focus of this campaign? To promote Bret Michaels’ latest reality TV dreck? If a reader wants to actually understand why these scientists were chosen and what they’re doing to cure disease, they have to visit the website. I find it hard to believ . . . More

I’m totally late to this party. I spent the morning writing my rebuttal to DrugMonkey and Co, doing the news, and cranking out a few pesky experiments. Ah, to live the life, right? Anyway, I’ve noticed that all of the good topics are now taken so I have to scrub the bottom of the bucket. I think one of the most important decisions I made in my scientific career was when I decided where I wanted to go to graduate school. The factors that play ball in this game are numerous and obviously not the same for everyone, but here’s my rundown of all of the things I wish I knew before heading off to graduate school.

Not to be too bitter about my undergraduate experience or anything, but the graduate school preparation was horrendous. No one told me from the beginning, “If you want to go to graduate school, here’s the X, the Y and the Z.” This may all sound like common sense, but some of it is not and having someone tell me all about X, Y, and Z my freshman year would have been helpful.

Do grades matter?

YES. They matter as much as they do for your annoying pre-med classmates, especially if you want to go to a . . . More

"This is the one thing you never want to mess around with. You'll wake up in the middle of the night crying like a baby and you'll have no idea why." These were the sage words of my undergraduate advisor, it's too bad they got discarded with everything else that I learned in undergrad.

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My scientific career has been filled with plenty of misadventures and screw ups. Most of them are really boring mistakes that didn't involve bodily harm, and only resulted in weeks of repeated work or extended nights in the lab re-preparing samples. Though, every good scientist has an epic fail story locked away in their skeleton closet. I think many of us go into science in the beginning thinking that we're unstoppable know it alls. That is until some event punches us in the gut to tell us, "Open your eyes and pay attention or else next time I'm going to aim a little lower and negatively affect your chances of reproduction."

When I was in undergrad, I worked on a bunch of projects ranging from ecology field studies to molecular biology projects in plants and fish. One of the last projects I worked on was one where we were trying to determine if fish bacterial infections could be transferred from mother to egg. This project involved c . . . More

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In the current political climate it has become clear that science is a major target of Republican directed budget cuts. However, the soundbytes of politics do not represent the importance of science in our lives. Because of this, I think it's extremely important that we explain why some of our model systems are so important for understanding how viruses and ultimately human disease work.

In the lab that I run, we currently work on mutating two different herpesviruses. One of these is Kaposi's Sarcoma Herpesvirus (KSHV) and the other is Murid Herpesvirus 68 (MHV68). Both of these viruses are gammaherpesviruses. In humans, KSHV only really ever becomes a problem in individuals who have a compromised immune system such as those infected with human immunodeficiency virus (HIV). KSHV is an interesting virus because its default program is latency, meaning that once it gets into your cells, it turns itself off and waits for conditions which allow it to grow and take over. This is akin to a bear hibernating in the winter. We do not understand how or w . . . More

Open science is a wonderful concept, but what happens when reporters start writing stories on data that has not been properly reviewed and vetted by the scientific establishment? Before this week, I had never really considered this question. Open science at its core is a wonderful utopian idea where scientists do their work in the open and publish their notebooks in real time on the web for everyone to see. The idea is that with this kind of transparency, better science will be done and scientists can collaborate more easily. Because all of the data will be on the internet and searchable, more scientists will be able to benefit from the open resource. Of course, there are numerous criticisms of open science. One being that it will be extremely easy for researchers in highly competitive fields to be scooped by competitors who have bigger labs or more resources at their disposal. However, it didn't occur to me until I saw stories popping up that open science could be abused by the media.

Almost a year ago, NASA held a press conference touting that it had found "alien" life. A group of researchers reported that they had found a bacteria (GFAJ-1) in Mono Lake that incorporated arsenic in place of phosphate in its DNA backbone. This press conference and the sub . . . More

I know, know, paper is so 1990 but I just wanted to pull a paper over at Nature to read during seminar later. Unfortunately I used the big fat "Print" button on the manuscript page. This is what I got:

I guess next time I'll just download the PDF and print it that way. However, even I know that if you stick blocks of text and figures in DIV or P code blocks, they won't get hacked off by the browser print renderer. I think some web developer was sleeping at the keyboard. A good example of this on LabSpaces can be seen if your try printing this page. You'll notice that in the browser rendered view, all 3 images butt up on one another, however in the print preview, the third image is moved to the bottom of the second page. This is because the image is in a DIV and the browser knows to not cut images in DIVs in half.

I can't be the only person that's ever tried using that button, right?

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I recently posted a picture of the congressional vote count for the Lilly Ledbetter Fair Pay Act showing the absolutely disgusting bi-partisan divide over this vote in 2009. Republicans should be ashamed.

However, someone added a link to an Examiner article posted a few days ago that said the Obama White House paid women 15% less in 2011. The article essentially says that Obama is a massive hypocrite and Democrats are truly the ones waging the war against women. If you read not very far into this story, they say the numbers are based on median salary, not the mean, and it's not classified by job title OR GS class (which would really get at equal pay for equal work - the whole point of the Ledbetter act!). Unfortunately, when I went to grab the data from the White House page, it didn't list GS class or gender. It'd be a lot more accurate to use GS class for this type of analysis because that takes into account the amount of experience a person has in each position, but doing the averages by job titles is still MUCH better than taking the median of the salaries. In a profession such as US politics whic . . . More

Here are the slides from the presentation I gave on Monday. We recorded a video, but I'm not sure how it turned out. I have a feeling the audio is going to be bad so I might just sit down and do it over again this weekend on my laptop.

Two of the slides are movies. The first is a clip from "Flock of DoDos" where some lady says scientists are horrible communicators and the other is the AARP shrimp on treadmills commercial.

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Every once in a while I find myself having a "grass is greener" moment in science. I sit at the computer thinking about all of the annoying things in lab that aren't working and wonder, "If I could answer any question, given unlimited resources, what would I choose to study?" This, my friends, is where I prove my unhealthy obsession with fish.

If money, fame, and science groupies weren't a priority, I'd spend my time and resources trying to find a cure for Cryptocaryon irritans, which is better known in the tropical fish industry as white spot disease, Ich, or Crypto. Crypto is a nasty little bug. It's a protozoan ectoparasite that lodges itself in the epidermis of fish where it grows until it drops off to mature into an Aliens inspired cyst that spits out 300 new little bastard parasites that go on to infect more host fish. In the open ocean, this guy isn't so terrible because its chances of infecting a host are minimal considering the massive amount of water a parasite has to travel through to find a new host. This is a completely different story at an aquaculture facility or in the home aquarium where fish are typically stocked to capacity in relatively small volumes of water. A single cyst can quickly turn into a fish killing epidemic. . . . More

AARP put out a commercial a few months ago deriding wasteful spending in Washington. Unfortunately, the soundbytes don't accurately represent the full story behind the spending. Have a watch before continuing.

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Yesterday there was some buzz over at Huffington Post about a stem cell cure for HIV. I first ran across the article via a link a friend of mine had posted on Facebook. The HuffPo piece is scant on details, so I’ll provide a quick run down on what’s going on here. But first, a lesson in HIV virology…

Human immunodeficiency virus (HIV) was first discovered in the 1980’s when gay men and IV drug users started turning up in hospitals with very odd opportunistic infections like Kaposi’s Sarcoma Herpes virus. These individuals had severely compromised immune systems and the original name given to the condition was gay related immunodeficiency disorder (GRID). The discovery of a viral cause of the disease came in 1983 from the labs of Luc Montagnier (recently won the Nobel Prize for this work) and Robert Gallo (recently didn’t win the Nobel Prize and is kind of pissed about it).

Genetic tests have shown that HIV originated in African monkeys and is related to a similar condition in monkeys called Simian Immunodeficiency Virus (SIV). It is thought that the virus was passed on to humans through the consumption of “bush meat” in sub-saharan . . . More

I'm going to preface this by saying that I am not a medical expert. I don't even begin to pretend I know anything about medicine or how to cure diseases. I do watch those cheesy "Untold stories of the ER" shows on Discovery and TLC though, and sometimes I partially remember things they say about diagnoses.

This story begins back when I was finishing up my PhD at Iowa. I had successfully defended my thesis (thank god) and was out on a drinking excursion with "the boys" the weekend before I was moving down to Florida to start my new job. The evening started out just like any other, we pregamed at my buddy's apartment drinking cheap beer, cooking up some quick dinner and bullshitting about how much being a graduate student sucks. You know, the typical poor graduate student routine.

We finally got a cab and made it down to "downtown" which in Iowa City consists of 3 businesses and 75 bars filled with helplessly drunken co-eds. I swear it wasn't more than 15 minutes into the night when my buddy, who shall be referred to as "Dr. Millner" from here on out, started hiccuping. These weren't your normal "Hiccup for 10 minutes and be done with it" type of hiccups, these things were going to last for hours. Of course, being a medical student an . . . More

One of the biggest problems facing the eradication of hard to kill viruses such as HIV is that viruses mutate readily. A standard technique for creating lasting immunity against viruses is the creation of vaccines. These have been used for years to eradicate a multitude of viruses. There are three standard types of vaccines that have been used in the past. There are attenuated viral vaccines which use a weakened form of the virus to challenge the immune system, killed virus vaccines which use dead viral particles to trigger the immune system, and finally there are peptide vaccines which use the expression of a specific viral protein to trigger the immune system. Although these approaches work readily for many viruses, in the case of a small subset of human pathogens, such as for HIV, these techniques cannot be used to create lasting immunity. In these cases, the virus mutates so readily that any immunity gained is quickly lost because the immune system can no longer recognize the virus.

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I'm beginning a new project in lab. It's a series of ChIP-seq experiments and the first step to doing ChIP-seq properly is optimizing sonication conditions. Here's a trial run with the sonicator I plan on using. The DNA shown in the gel is from cells containing latent herpes virus. We're looking to shear the DNA so that the bulk of it is between 100 and 600bp. For ChIP-seq we extract and purify the DNA in the 100-300 range in the gel. Looks like about 13 cycles of sonication should do (sonication past this point doesn't result in smaller fragments, don't want to risk over sonicating)! Actually, I think I'm going to do this again on Monday. I looked back at some old data and I should be able to get the fragment sizes a bit smaller by increasing the pulse time. I'll post an update soon!



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When I started graduate school at Iowa, I went in there with a chip on my shoulder.  They didn’t choose me, I chose them.  They weren’t a highly ranked “elite” institution, so to make my mark I had to work for the biggest and the best that Iowa had to offer, or so I thought.  I sought out the highest profile researchers at Iowa and picked the one that best aligned with my interests.  No matter what school you look at, there’s always, “That Professor.”  You know who I’m talking about.  The professor who publishes the most papers, who has the most respect.

I did my homework on my mentor.  I read a bunch of old papers, I understood the direction and the goals of the lab.  I remember our first lab meeting vividly, well, I remember how I felt after the lab meeting.  I was exhausted.  My brain physically hurt.  I thought I knew it all going into that meeting and I realized I didn’t know anything.  It was a wake up call, but I think I liked that feeling.  It was fresh and challenging.

During my rotation, I put in ungodly long hours, not because I thought it was expected of me, but because I wanted to.  At this point in time I was enamored with the science.  It’s funny how this changed for me as I look back on my four and a half years in t . . . More

Here's a true timelapse video of a day in lab. Pictures were taken every minute for 24 hrs. The video goes from about 4am to 4am the next day.

And because someone asked...The images were taken with a GoProHD Hero camera and then compiled in Windows Live MovieMaker. Images are displayed for 0.1 seconds.

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In a previous post I mentioned that I spent the first year of graduate school working on a dead end project that was going nowhere. I’m going to present and discuss the findings of the paper that changed the direction of my thesis project and ultimately lead to the completion of my PhD.

In the fall of 2006, I was finishing up the last few experiments on a project trying to link P53 (a very important protein in cells that helps to prevent cancer) to one of the most important transcriptional activators, P-TEFb. I should probably pause for a second here to give a little bit of background on P-TEFb so that what follows is somewhat understandable. Positive transcription elongation factor b (P-TEFb: Pee Tef bee) is a protein kinase (read as on/off switch) that regulates RNA polymerase II transcription of most genes. RNA polymerase II is the protein responsible for messenger RNA (mRNA) transcription or the process of turning DNA into mRNA. Without mRNA, the transfer form of DNA, proteins cannot be made by the cell, and life does not exist. Essentially, P-TEFb tells RNA polymerase when it’s ok to start making RNA. You can think of P-TEFb as the starter at a track meet, you know, the guy th . . . More