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

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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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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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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

Wow! Mrs. Irish has posted pictures of her students using the microscope, slides and workbooks that we helped purchase for her classroom. This is exactly why we work so hard to try to bring in donations through the DonorsChoose program.

There are still 60 or so unfunded projects on our giving page, sp please stop by and help in any way you can.

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Today's featured DonorsChoose project is: Launch a Rocket of Success. Mr. Bradham is looking to buy rocket kits for his science class to teach his students about physics and space exploration. He says that his students are, "eager for knowledge. Unfortunately, they lack the adequate financial means to provide for supplies that could further their understanding of science concepts." Mr. Brandham is looking for a "hook" to get students interested in and excited about science and from past experience with rocketry programs he has found that students are captivated by rocket launches and this provides a stepping stone for him to teach other science concepts in the classroom.

I can't argue with Mr. Bradham's logic. I remember when I was a kid and I got a hold of my first rocketry set. It was a basic ESTES model that I had to glue and assemble myself. I really enjoyed learning about the physics and chemistry of the launches. Launching the rockets in my local park was always a blast, but the hobby was expensive! The engines for my rockets were like $5 and for a grade schooler with a tiny allowance of a couple dollars a month it was hard to fuel my obsession. I think it's very sad that Mr. Bradham can't get the funding from his school for this project because he teaches in a high poverty district. I see enormous value in this type of activity as a teaching tool. The excitement of a rocket launch can quickly translate into student fervor in the class room to try to understand how to make the rockets fly higher and faster.

Mr. Bradham has a long way to go to fund his project though, so we need your help! Every little bit counts, so please donate whatever you can to make this happen.

You can view more projects by visiting our giving page.

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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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Bachmann Says She'd Consider Everglades Drilling by associatedpress

God caused the hurricane and now this shit? It saddens me that these people are top political candidates.

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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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Just messing around with timelapse on my GoPro. This is only about 2 hours before the battery died. Maybe tomorrow I'll set it up for 24hr and plug it into a nearby computer for power.

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A week or so ago someone forgot to close the door on our enzyme freezer tightly. I had just ordered $1,000 worth of NEB enzymes to make high throughput sequencing libraries too... Before the meltdown, I made a couple of test libraries to be sure that the protocol was worked out.

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A quick update on the side project since I'm procrastinating writing a short fellowship grant... About a month ago I realized why my sonications were not working. It turns out that when I moved to Florida from my Graduate work at Iowa, I didn't update my ChIP protocol to reflect a reagent change. At Iowa, we had been using 16% paraformaldehyde as our crosslinking agent. Unfortunately, I was throwing 37% formaldehyde in there instead meaning that I was way over crosslinking my samples which explains why I was having such a hard time shearing the DNA. I practically cemented all of the proteins in the cell together. Anyway, I had some more downtime this week waiting for a new batch of cells to grow for a massive timecourse experiment involving 3 timepoints and 10 different immunoprecipitations for cool proteins. I used this waiting period to optimize sonication conditions with the fancy programmable sonicator.





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In a recent episode of the new TV show, Happy Endings (Episode on HuLu), one of the characters, Dave, gets super excited when he runs into and reconnects with his favorite high school teacher. The only problem is that the teacher turns out to be an alcoholic douche, but Dave spends the entire episode fawning over the guy until he realizes that the teacher is just an underachieving loser who is trying to bed his friend Penny.

The nostalgic undertones of this show got me thinking about my favorite high school teachers. It should be no surprise that my favorite teachers are my science teachers. Many of them helped inspire me to pursue a career in science. I'm not sure if I should thank them or hate them for that.

Regardless, my senior year of high school was exciting because I was taking a bunch of really cool AP science classes. At the time, my favorite teacher award was a dead heat between my AP bio teacher and my AP physics teacher. The physics guy was new to the school. It was either his first or second year there. I really liked his teaching style. He forced us to think about the problems he gave us and always answered our questions with qu . . . More

The University of Iowa will be holding s science writing symposium tomorrow (April 27th). The symposium will be webcast LIVE at this address from 1PM to 5PM CST:

https://webapps1.healthcare.uiowa.edu/webcast/Default.aspx

There's a login screen now, but that will disappear once the talks start.

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I've been working on this project on and off for a few months now. You may remember my previous post about attempting sonication trials. Unfortunately, things in lab have been busy trying to get a new graduate student started and troubleshooting problems with other experiments so I haven't had as much time to devote to this project as I would like. I've spent the past month or so trying to optimize my sonication conditions on a sonicator that's in my building, and I've gotten less than spectacular results (I've tested at least 10 different conditions on this machine ex: buffers, cell densities, sonication intensity, sonication duration). I'm looking to break my DNA up into short 100-300 base pair fragments and previously I was only able to get them down to about 600. I decided it was time to test other sonicators and here are the results.

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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.

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Today I noticed my Tomato Clownfish acting a little friskier than usual. A few days ago I saw a white bump under the female's anal fin and thought it might be a fungal infection because it had a goofy gray tinge to it. I figured I'd just wait and see what developed. Well today I noticed that it was much bigger and longer...It was her ovipositor (egg laying tube)!! She also had a big fat round belly, so that really means only one thing. I watched her and the male clownfish do their dance and the ovipositor grew longer while the male started showing signs of arousal too. I guess a video is worth more than my explanation. I started recording after the first egg went down. It's the little orange sac in the middle of the screen. This patch grows much larger over the course of the 10 minute video. Enjoy!

Mass eggs start going down around the 2 minute mark if you don't want to watch the fish dance.

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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