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Author: Brian Krueger, PhD | Views: 18582 | Comments: 2
Last by Brian Krueger, PhD on Mar 17, 2011, 3:25pm
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
Author: Dangerous Experiments | Views: 17684 | Comments: 9
Last by A. H. on Sep 27, 2011, 2:54pm
This week's guest blogger is Joe Hanson. He is currently working on his Ph.D. in Cell and Molecular Biology at the University of Texas at Austin, where he works on things far less interesting than the work you are about to read, specifically mobile genetic elements and ancient introns. He blogs at It's Okay To Be Smart and runs an awesome Tumblr page of the same name (updated ten times as often). Joe can be found on Twitter @jtotheizzoe.

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I was on a little bit of a post-vacation downer this past week. Only, I didn’t actually go anywhere. Instead, the SXSW music (and arts and interactive and style) festival came to me, right at home in Austin, TX. It was a week of uplifting musical and artistic expression emanating from every street corner and bar in town, and much of could even be classified as good! As I look back on the last week, two things jump out at me: 1) Tall cans of cheap, hipster beer and 2) BEARDS.

. . . More
Author: Evie | Views: 17460 | Comments: 13
Last by anonymous on Apr 22, 2012, 3:48pm



Did you hear the news? It would appear our astronomers have found a planet named Gliese 581g, not too far from us, that according to the data, could possibly sustain life as we know it.

Cool!!! This is very exciting! Of course this does not mean they found life on the planet, or that they even have a way to do so, 'cause they don't at the moment. But it does tell us there are other places in this universe that could potentially be not-too-hostile for life as we know it to exist, and possibly for us to explore/relocate to.

The discovery was made by astronomers at the University of California, Santa Cruz, and the Carnegie Institution of Washington. The scientists used data from the HIRES spectrometer at the Keck Observatory in Hawaii, and the HARPS at the European Southern Observatory in La Silla, Chile to come up with this data.

They looked for evidence of 'wobbles' in the movements of stars to locate new planets. If a star were to move unhindered across the night sky, its path or trajectory would be smooth. But if it were to 'wobble' or make a slight off-tra . . . More
Author: Dangerous Experiments | Views: 16974 | Comments: 9
Last by Joseph Bradley on Aug 15, 2012, 5:07pm
Our co-guest blogger of the week is Melissa Hughes. Her scientific interest is one that is quite unique and fairly new compared to other scientific disciplines: food microbiology and food safety. She received her M.S. degree in food science/microbiology back in 2009, and is currently employed at a private food and environmental testing laboratory in the San Francisco Bay Area. On top of being a food microbiologist and overseeing the quality operations in the lab, she also organizes and helps teach various food safety training workshops throughout the year.

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I would bet money that right now you are thinking, “What in the world does a food microbiologist do?” Don’t worry, I get asked that a lot…and then it typically leads to a discussion about a story heard on the news regarding some food-related outbreak or a product recall.

Food microbiology is quite simply the study of those microorganisms (both beneficial and harmful) that impact food and beverage products. It encompasses two major areas: general microbiology and food safety/quality. A proper understanding of microorganisms (especially bacteria, yeasts, molds, and parasites) and those factors that impact growth, survival and pathogenesis provide th . . . More
Author: Brian Krueger, PhD | Views: 17003 | Comments: 136
Last by Isabel on Nov 26, 2010, 3:02pm
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
Author: Brian Krueger, PhD | Views: 15246 | Comments: 9
Last by Michael Schatz on Feb 26, 2013, 12:13am
Aside from the dubstep pumping out of the Roche and Agilent booths, the volume of AGBT has been somewhat muted. There was no grand offering of new hardware or over the top promises of sequencing genomes on what now appear to be vaporware USB thumb drives. This is my first in person experience of AGBT, so as a virgin it seems for the most part to be rooted in the science despite the ridiculous parties and “showgirl” casino nights. The atmosphere here is unlike any other science conference I’ve attended. It’s like the bastard child of a Gordon Conference and a Las Vegas Porn Convention. I really hope that the deep pockets of Sequencing Centers are more influenced by the science than the free dinner parties and alcohol, but I have pretty low confidence in humanity. Regardless, I think everyone in attendance today was overwhelmed by a stunning talk from PacBio and the dramatic advancements of their long read technology.

The PacBio talk came on the heels of what felt like a warm-up opening act from Jeremy Schmutz of the Hudson Alpha Institute. Schmutz has been working with a start-up that was recently acquired by illumina called . . . More
Author: Evie | Views: 14299 | Comments: 9
Last by Silwin Pereira on Jul 22, 2013, 5:41am


You may be asking yourself what is this space junk I speak of, and why am I bothering you with this.. Well, I am glad you asked!

Space Junk is pretty much anything that is left over, discarded, or no longer functioning, that happens to orbit our little globe here.

It can be debris from a space collision, left over parts from rockets, satellites, launch vehicles. Any object that is left adrift, floating in space in our immediate vicinity.

As you may be aware, the growing problem of space junk is becoming more real with every new launch that occurs.

You see, every single satellite system, shuttle mission, or top secret government experiment that is launched into space, requires (at this point) rockets to get there.

As they ascend and maneuver themselves into their target position, they shed large amounts of solid components that have served their purpose, and are no longer required. These can be burned out motor cases, or smaller connecting rings that held the separate stages of the rockets together, or even nuts and bolts that have been ejected.

These shed components, they don’t go anywhere.. they just hang out in orbit for a really really long time, till they eventually come crashing down to Earth. Usually burning up and dis . . . More
Author: Suzy | Views: 14258 | Comments: 18
Last by Suzy on May 17, 2011, 7:04pm
After attending a conference a couple months ago and being forced to sit through some pretty bad presentations, I had in mind to discuss the importance of grad students learning how to put together and deliver a good presentation. This skill is critical and I can't believe how many scientists struggle with presentations. I know it's tough and I know when you're nervous it is easy to forget some things you wanted to say. But there are ways of making your presentation easier for your audience to understand, and make it so it triggers reminders for you, so when the nerves come in, you don't forget what you wanted to say.

My most recent experience really highlighted this problem because as soon as the speaker was done, a man behind me raised his hand to ask a question. He said, "I COULDN'T HEAR A WORD YOU SAID AND I CAN'T READ ANY OF YOUR SLIDES!" He was pissed off. I was too, but I wasn't going to stand up in a room of 100 people and yell at the speaker. But it was true. So many things were wrong in every talk presented.

Honestly, if I pay several hundred dollars to attend a conference and I get up at 7 am to make your 8 am talk (which is waking up at 4 am for me on west coast time), and I get to the room, and now I sit through . . . More
Author: Jeffrey Martz | Views: 13705 | Comments: 3
Last by Mark on Aug 10, 2011, 9:31am
Last time, we introduced the nested classification of Linnaean taxonomy originally created in the mid-18th century by Christian creationist Carl Linnaeus. Using this classification system, we established that human beings are not only animals, but vertebrates…even if we completely avoid saying the word “evolution” and just look at our overall anatomy. Vertebrates, you make recall, are eukaryotes (they have cells with a nucleus), animals (mobile multicellular eukaryotes which eat the cells of other organisms), eumetazoans (animals with organized tissues), bilaterians (eumetazoans with bilateral symmetry), deuterostomes (bilaterians in which the opening for the anus develops before that for the mouth), chordates (deuterostomes which have a notochord, pharyngeal pouches, and a tail), craniates, and vertebrates (chordates with an internal skeleton protecting the brain and spinal chord).

Vertebrates include things that we call "fish," as well as amphibians (like frogs and salamanders), "reptiles" (like lizards, snakes, and crocodiles), mammals, and birds. However, several types of "fish" lack a couple of features possessed by most: notably jaws and a . . . More
Author: Psycasm | Views: 11752 | Comments: 12
Last by Brian Krueger, PhD on Dec 23, 2010, 3:19pm
Last week I dropped the comment that I thought it was normal and healthy for a blogger to check their stats. I was quickly corrected by more experienced bloggers than myself, who made the comment that the discussion generated in their comment boards was a more important metric.

With this, I agree. If I didn't want dialogue I'd write a book. But it seems intuitive that the degree of discussion is necessarily going to be linked views.

So, on my third day of holidays, I've decided to engage in some Recreational Statistical Analysis. There's nothing too fancy here, because there's not much fancy stats could have told me about my blog - with one exception (to my mind), which I will cover at the end.

But first, some descriptives:

Since joining LabSpaces I have made 34 posts, 22 of which were ResearchBlogging posts. I have an average word count of 889.26 (SD=338.78). Across all posts my mean views (as of 21st of December) 394.62 (SD = 253.84), but if you exclude the three outliers (Music Testing Athletes and Psi I, and II) then it drops to 340.97 (SD = 189.60).

Across all posts, on average, I get 8.30 comments (SD = 11.70); but if you exclude the outliers that drop . . . More
Author: Dangerous Experiments | Views: 11895 | Comments: 2
Last by Jeremy Leipzig on Aug 01, 2011, 10:05am
One of the most anticipated events in bioinformatics is the annual Nucleic Acids Research Web Server Issue, an edition that inevitably leads to a cyclic rise in the number of “terminal masters” awarded and gives veterans in the field a chance to type into their browser various exotic foreign top level domains like .sg, .tw, .il, and .org

Web servers, perhaps more commonly understood today as web applications, are a preferred platform for providing analysis and visualization to end-users. The key difference between the web sites featured in this issue and those in NAR’s popular “Database Issue” is that these have to actually do something along the lines of computations with user-uploaded data.



NAR has published a dedicated web server issue every year since 2003 - over 1100 applications have been introduced, though some are repeatedly featured as improvements arise. Perhaps the best way to peruse these sites is through the Bioinformatics Links Directory, a curated index of tools and databases developed by Fra . . . More
Author: Psycasm | Views: 11575 | Comments: 2
Last by JaySeeDub on Jan 09, 2012, 10:51am
I've been thinking about the phenomenon of Earworms lately... If you're not familiar with the term it does not refer to an exotic and horrifying parasite. It's actually a word used to describe the (personally annoying) situation where a song gets stuck in your head.

The most recent example of this, for me, was after listening to a Radiolab episode and hearing a skipping-tune about a stunt pilot who died.



// The tune itself comes on after about one minute of intro... it lasts only 10 seconds and consists of the following:



Lincoln Beachey thought it was a dream

To go up to heaven in a flying machine

The machine broke down

And down he fell

He thought he'd go to heaven, but he went to...

Repeat. Ad Nauseum.



It's short, simple and designed to be repeated. My person experience with Earworms is that the often conform to these characteristics... and in the instances when they do not I tend to extract a simple element from a more complex piece and end up repeating it. For instance I was at the theatre last night (oh yes, how cultured I am) watching Mary Poppins and . . . More
Author: Jordan Gaines | Views: 11321 | Comments: 0
All are very attractive options—particularly for the aging population, and particularly for those looking for a fast, relatively painless solution with little effort on our part.

But did you know that Botox—the quick fix solicited by 6 million Americans each year and 75% of celebrities over the age of 35—is composed of the same deadly toxin responsible for botulism poisoning that can cause paralysis and respiratory failure? Let's examine the mechanism behind this potentially deadly neurotoxin and why, for goodness' sakes, Botox can be used as a therapeutic despite its dangerous potential.

Botox is the trade name for botulinum toxin, a protein produced by the bacteriumClostridium botulinum (below, left). With a relatively low LD50 of 40 nanograms, botulinum toxin (below, right) is one of the most powerful neurotoxins known today. That means that injecting just 40 ng of the toxin is lethal in 50% of the primate population in which it was tested. To put 40 ng in perspective: a gram is roughly the mass of a paperclip. A nanogram is one billionth of a gram.

. . . More
Author: Whitney Krueger | Views: 11715 | Comments: 13
Last by GUEST COMMENT on Jul 10, 2012, 4:25pm
I'm a young researcher. I haven't yet been around the block. I've had one research job for the past 5+ years and that has mostly been spent coordinating influenza epidemiology studies. Only recently have I jumped into the deep end of the laboratory world to tackle the second part of my dissertation.

I know IRBs really well. I've lost count how many I've have to declare war against. I know IACUCs well enough to keep our lab kosher. I know funding agencies and the stress they love to evoke. I know how to convince random people that they should participate in my study - "Help a girl graduate, please!" I know phlebotomy well enough to actually get blood. I know how to coordinate an epi study like nobody's business. I know a random set of laboratory skills, even how to harvest influenza viruses from embryonated chicken eggs.

But why did I choose to do science and public health? Honestly, I chose science because of its cool factor. I thought microbes were fascinating and I wanted to learn as much as I could about them. I can pin point my love for infectious diseases to a specific life event - choosing to do an 8th grade book report on The Hot Zone by Richard Preston. To me, the Ebola virus was fascinating and throughout high . . . More
Author: Jeffrey Martz | Views: 11185 | Comments: 5
Last by Bill Rabara on Nov 13, 2012, 9:35am
In the last blog, I discussed the Law of Superposition. Layers of sedimentary rocks, or strata, are stacked in vertical sequences, with the oldest layers being on the bottom, and getting younger as we go up through the layers. Remember that the study of the sequence of layers of strata is called lithostratigraphy, and the study of the sequence of fossils in these same layers is called biostratigraphy. Both of these studies were pioneered in the early 19th century by a British geologist named William Smith, who was one of the very first to figure out that you could identify the same sequences of rocks and fossils in different parts of England (an excellent book about Smith and his life is The Map That Changed the World by Simon Winchester). Smith was primarily interested in the economic benefits of these observations, and was able to use his knowledge of the sequence of rocks and fossils, and how they were distributed across England, to inform land owners whether or not they could find coal or building stone on their property. What Smith did not fully appreciate during his lifetime was that he had also figured out the primary methods that . . . More
Author: Dangerous Experiments | Views: 39755 | Comments: 6
Last by Logan D on Nov 15, 2012, 3:04pm
This week’s guest blogger is Debbie Knight, a research associate at The Ohio State University. She shares her research thoughts and experiences in her blog (biologyze.com) and tweets about all things science (@acousticgravity). In her spare time, she plays mandolin in a local band and takes journalism classes at OSU.

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When someone asked me what I wanted to be in high school, I would say a “biomedical researcher.” I put those words in quotes here because at that time I had absolutely no idea what it meant (or even what a researcher did), but I knew it sounded like a really cool thing to be.

I also asked my parents for luggage as a graduation gift.

Little did I know these two things would one day merge.

I would like to note that around my junior year of college, I finally did figure out what a researcher does when I volunteered to work in a lab and that research has been my passion for the past two decades.

What I did not know then was that becoming a researcher would lead to travel and adventure.

. . . More
Author: Brian Krueger, PhD | Views: 12671 | Comments: 0

Image courtesy of Shutterstock
If you’re an avid follower of popular science in today’s news media, you might have noticed a recurring theme. Genomics is everywhere. On an almost weekly basis, the New York Times, the New Yorker, Forbes and a myriad of other outlets are publishing stories with overly optimistic ledes about doctors and gene sequencers being replaced by apps and iPhone accessories. You would be forgiven if you thought genomics was “solved” and we’re 5 years out from creating a Star Trek inspired “tricorder” that near instantly sequences your genome and tells you, without equivocation, what malady is afflicting you and how exactly to overcome said disorder. The fact of the matter is that we’re not there yet, not by a long shot.

. . . More
Author: Psycasm | Views: 10920 | Comments: 6
Last by Leighton on Jul 11, 2012, 6:23am
Normally I avoid writing about things I learn in class. I try to use this blog, and the associated podcast, to research topics outside of the boundaries of my normal schooling.

This topic struck me, however.

There's a phenomenon called the False Consensus Effect (FCE) which basically states that we, as individuals, view our own preferences, behaviours and judgements as being typical, normal and common within a broader context; it also suggests we find alternative characteristics as being more deviant and atypical than they actually are.

I asked my tutor, 'Is this a kind of logical fallacy?', being new to the topic and a little surprised I'd never heard of it before...

He responds, 'No, not really. It's basically just a cognitive error. Once you know about it, you really won't ever feel confident in offering an opinion again'. Or something to that effect.

And he's right.

As a self-identified Skeptic, a member of the campus Skeptic's group, and a consumer of the Skeptic media (SGU, Skeptically Speaking, . . . More
Author: Suzy | Views: 9599 | Comments: 6
Last by Suzy on Feb 17, 2011, 10:19am
OK, let’s pick up our discussion where we left off last week, at feasibility. You did it. You successfully convinced a room full of vice presidents and directors, or maybe even the CEO that they should take your fabulous product idea to the next level. You’ve got marketing on board, excited to promote it and now it’s time for the work to begin.

You are the lead scientist so this will be your baby. You most likely are working on other projects too so you have to divide your time wisely. An R&D scientist always has multiple projects as various stages of the development process. You don’t get to spend full time on one thing. You know what your deadlines are and the target dates for giving updates to the committee and you make it a point to meet them.

I think to fully explain how a product is developed it would be helpful to have an example. Let’s use an example of something that no one has ever figured out how to do yet but almost everyone wishes they had a solution for. How about:

A novel method that allows for any protein of any size or sequence or species to fold correctly when recombinantly expressed in E.coli cells.

No inclusion bodies, no toxic . . . More
Author: Dangerous Experiments | Views: 10467 | Comments: 13
Last by Laura Maaske on Jan 08, 2013, 7:58pm
What comes to mind when you think of a medical and scientific illustrator? Is it a kind of art you admire? How do you respond to highly detailed drawings? Do the fleshy human interiors make you squeamish, which is a remark I have sometimes received from clients regarding medical images in general? Does the precision impress you? Does the stiffness offer you stillness or rigidity, something to explore? Do you love the great masters of the field: Leonardo DaVinci, Andreas Vesalius, Max Brödel, Frank H. Netter, John James Audubon?

As a student medical illustrator, I knew what I wanted to learn. I wanted to wrap my mind around the science and the drawing skills I would require in the future. I already had an undergraduate degree in zoology, and our courses in the Division of Biomedical Communications were to be shared with the medical students at the University of Toronto, so science was heavily on my mind. There were . . . More
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