To Seq, or Not to Seq

Seq—shorthand for “sequence”— has become a more recognizable term thanks to a novel and provocative genomics initiative called the BabySeq Project. The project, officially launched in May 2015, was designed to explore the impact of whole-exome sequencing (WES) on newborn infants and their families. A randomized, controlled trial to sequence healthy and sick infants and then provide sequencing information, it is the first of its kind. Those infants randomized to receive WES undergo genetic sequencing of all protein-coding genes and analysis of about 1,700 genes implicated in childhood health, along with 18 years of follow up genetic counseling.29813751-nov-2-blog-post-nicole-600x470-web

The project is directed by Robert C. Green, geneticist and physician at Brigham and Women’s Hospital, Harvard Medical School and the Broad Institute, and Alan H. Beggs of Boston Children’s Hospital and Harvard Medical School. Funding, totaling $25 million, comes from the National Institute of Child Health and Development and the National Human Genome Research Institute. Continue reading “To Seq, or Not to Seq”

Back to Basics: Organizing Your Writing like It’s a Hamburger

The "hamburger" scheme for organizing a paragraph.
The “hamburger” scheme for organizing a paragraph.

Last night I was helping my daughter, who is in fourth grade, with her homework. We had completed a math worksheet, a geography worksheet and had moved onto writing. For her paragraph assignment, she was supposed to write about a special place. So I began drawing the concept map that we typically use to help her organize her thoughts. She stopped me before I could get started.

“No Mom, wait,” she grabbed the pencil and paper from my hands, “I have a better idea.”

She drew five shapes on the paper.

“We should write the paragraph like it’s a hamburger. The first sentence is the topic—it’s the top of the burger, tells you what is inside—it makes you hungry to read more. Next comes the juicy, meaty part. Three details—three sentences. Then the bottom bun, the summary that supports the whole paragraph. It’s the hardest to write.” She proudly sat down with her drawing and pencil.

“I LOVE that,” I exclaimed. “That’s a great way to organize a paragraph.”

“Yeah,” my husband looked up from his Suduko that he had been working on, “and the cheese goes right here.” He pointed to one of the three boxes my daughter had drawn underneath the bun.

“And the lettuce over here,” my daughter giggled.

“Well, I like mine with lettuce and tomato,” I chanted with no apologies to Jimmy Buffett, “Heinz 57 and French-fried potato..,”

“A big kosher pickle,” my daughter joined in, and the evening’s homework activities degenerated from there. (Sometimes it’s the parents who are easily distracted.)

My daughter’s hamburger graphic was new to me, but the concept wasn’t. It is a solid method for organizing a piece of writing, and it can be applied all kinds of writing—from a paragraph, to an essay, to a speech and even to a scientific article. Continue reading “Back to Basics: Organizing Your Writing like It’s a Hamburger”

Science Is Not a Wet Blanket: A Marketing Plan for Antibacterial Soap

The relationship between science and marketing usually has great chemistry: effective marketing evokes an emotional response that compels people to buy something, which enables companies to research and develop new products. Let’s call this the honeymoon phase: things seem pretty great on the surface, yet they really need to sort out some uncomfortable truths. For example, don’t these two advertisements make you feel shocked that you aren’t sanitizing your hands before you eat? While cleverly executed, they are a little misleading because they paint a very stark picture of hygiene.

protex-ad-rock-paper-scissors
Ad text: “Rock, Paper, Scissors.” Protex worked with the agency Y&R in Brazil to create this ad in 2012.
Lifebuoy worked with the agency Lowe in Indonesia to create this ad in 2009.
Ad text: “You eat what you touch.” Lifebuoy worked with the agency Lowe in Indonesia to create this ad in 2009.

These ads were created before scientific consensus was reached on the safety of 19 antibacterials. An earlier review of 27 relevant studies found that antibacterial soap was no more effective than regular soap and increases the risk of antibacterial resistance. Has science effectively put an end to antibacterial soap? What should a company that makes both regular and antibiotic soap do to comply with the new FDA ruling without losing revenue?

Identifying Marketing Opportunities

Adhering to good science doesn’t mean stomping out the creativity of your marketing team. Instead, marketers can gain inspiration from the diverse impact bacteria have on human health and present their products in the right context. Continue reading “Science Is Not a Wet Blanket: A Marketing Plan for Antibacterial Soap”

Common Misconceptions About Scientific Terms: Volume 2

Misconceptions About Scientific Terms Volume 2Media coverage of the Zika virus and colistin-resistant E. coli have introduced new terms for some people. What do they all really mean? Even people with technical backgrounds may benefit from a refresher. This set of eight terms covers topics related to diseases and nutrition. This article is a continuation of my previous blog post about scientific words that are frequently misunderstood.

Epidemic

Common misconception: A disease that is going to kill all of humanity or turn us into zombies.

What it means for scientists: According to the Centers for Disease Control, an epidemic is “an increase, often sudden, in the number of cases of a disease above what is normally expected in that population in that area.” This could happen with a new strain of the flu or with something more devastating like Ebola. There is an endemic level, or baseline, for the number of people affected by the flu at any given time, and an epidemic would be a significant increase from this level. The endemic level for diseases like Ebola would be zero. Epidemic diseases that spread across multiple continents are considered pandemic. Continue reading “Common Misconceptions About Scientific Terms: Volume 2”

Common Misconceptions About Scientific Terms

science-lecture-DNAScience touches our lives every day, yet far too often, scientific concepts become misrepresented in the media. This problem is not an innocent one; swaying public opinion on policies about climate change and vaccination has a large impact on public health. It is the responsibility of every person to achieve a basic level of scientific literacy. More important than being able to recall a library of scientific facts is the decision making process we go through; a mindset that is asking questions and addressing uncertainty can serve as a barrier against deception. Understanding the words common among scientific studies should help non scientists navigate through the sea of information they encounter online.

This article covers nine common misconceptions about scientific terms. We recognize that there are hundreds of words that are misused, so we encourage your contributions below.

Continue reading “Common Misconceptions About Scientific Terms”

Can’t Go to A Conference? Try Following the #Hashtag

Members of an audience at a scientific conference may tweet what they hear or see, and because these messages are free and open, it has the potential to reach anyone, anywhere in the world. This has profound implications for the communication of science, enabling discovery, discussion, teaching, and learning outside of the confines of the conference itself. Image credit for globe: NASA Goddard Space Flight Center on Flickr. doi:10.1371/journal.pcbi.1003789.g001
Members of an audience at a scientific conference may tweet what they hear or see, and because these messages are free and open, it has the potential to reach anyone, anywhere in the world.
This has profound implications for the communication of science, enabling discovery, discussion, teaching, and learning outside of the confines of the conference itself. Image credit for globe: NASA Goddard Space Flight Center on Flickr.
doi:10.1371/journal.pcbi.1003789.g001

AAAS included a session on social media at the 2015 annual meeting. This year the #AACR15 stream was so busy, by the time I finished reading a tweet that piqued my interest, it had almost scrolled off the bottom of my feed–a bit like an agarose gel that was running too fast. Scientists are connecting with other scientists on forums like reddit to discuss cloning strategies and transfection issues, and the Global Biological Standards Institute (GBSI) is running a huge campaign to educate life scientists about cell line authentication (#authenticate) through social media.

Social media have decidedly entered the science mainstream with attendees at meetings posting to twitter and Facebook from their Instagram accounts, societies setting up multiple hastags for meetings and popular sessions, and journals tracking not  just the “old-fashioned” Impact Factor, but rather social media shares, comments, retweets and likes of articles. Increasingly social media are the impact factors in science communication.

Live tweeting at meetings is rapidly becoming a way that hot topics are being disseminated far beyond the limited reach of the presentation room at the conference center, and PLOS One recently published an article by Ekins and Perlstein that provides guidance to meeting organizers and attendees for live tweeting events. The article talks about what a hashtag is and how it is used. It is great for novices or experienced social media users who might have missed that one particular twitter abbreviation, but the authors go beyond the technical aspects of tweeting to discuss the promise and potential of reaching a global audience with the leading edge science that is presented at scientific conferences and the richness that can be gained by bringing more people into the discussion.

Have you ever “live tweeted” a talk or event or followed a live tweet stream? Do you have a favorite  scientist “live tweeter” that you follow? Let us know in the comment section below. How are you, as a scientist, using social media?

 

 

 

Compelling Science Communication

An archive of 35mm slides. There's probably one in a dark corner of your lab.
An archive of 35mm slides. There’s probably one in a dark corner of your lab.

Back in the dark ages, when I was in graduate school, if we were traveling to a conference to give a presentation, we always made sure that our slide carousels (yes, scientific talks used to be given from 35 mm slides) were in our carry-on baggage. That carousel was more important than our underwear or our toothbrush, no trusting it to baggage claim.

Things have improved markedly, I’m happy to say. Now everything has to go in the carry-on baggage, because most PIs don’t have the financial room in their grants to pay for checked bag fees. Fortunately, we can store copies of our presentations on several different clouds and bring a thumb drive or two on board the plane, tucked safely away in the underwear in the duffle bag that doesn’t quite fit in the overhead compartment. No need to choose between unwieldy slide carousels and clothes.

But are PowerPoint® and Prezi® presentations the best way to communicate your science? When you hit your audience with slide after slide of bullets are you killing their interest? When you show that slide of three years worth of work and say “Don’t worry about trying to read this…” are you killing your presentation?

Is there a better more compelling way to communicate science? Accurately. So that people care. So that people understand.

FameLab International certainly thinks so. Begun in 2005 by the Cheltenham Science Festival in the UK, FameLab seeks to promote better science communication through sponsorship of a competition in which scientists and engineers have three short minutes to communicate their science with enthusiasm and accuracy–armed “with only their wits and a few props that they can carry on stage.”

It is truly a global competition with over 5,000 young scientists and engineers from 25 countries around the world competing for the grand prize each year. The Grand Final Competition is held in June each year, but you can take a sneak peak at some of the entrants on the FameLab Facebook page now.

Here’s a winning taste from the 2014 competition. There is more on the FameLab YouTube channel.

Why Not Go Swim in the Lakes

The results of wading only, but this guy still needs a rinse to be safe.
The results of wading only, but this guy still needs a rinse to be safe.

We are moving into the third week of May here in southern Wisconsin and have finally had a day or two near 80 degrees. Yesterday was a warm humid, day, the kind that makes a person think about taking a swim. I live in a city with four lakes, so a fresh water swim is never far away.

We humans have many options for keeping cool in warm weather; short and short-sleeved clothing, for instance. Dogs, on the other hand, have fewer options for cooling off.  Whether dogs shed or is trimmed, they still sport a lot of fur/hair and suffer when temperatures rise. Again, thoughts turn to swimming.

In our city of lakes, when the dogs and I are walking, water is never far away. However, we generally stay out of the lakes, no matter how warm it is. We know that these lakes sometimes contain blue-green algae.

About Blue-Green Algae
Blue-green algae, also known as Cyanobacteria spp. exist around the world and are found in the fossil record, according to the Centers for Disease Control on an informational page about this organism. Fresh water, brackish water and salt water all can host cyanobacteria.

There are a number of these photosynthetic bacterial species. Several of the species found in Wisconsin include Anabaena sp., Aphanizomenon sp., Microcystis sp., and Planktothrix sp., according to the Wisconsin Department of Natural Resources (DNR). And there are others. Continue reading “Why Not Go Swim in the Lakes”

Big Data Takes Education By Storm

weather blog

Gone are the days when the phrase “educational TV” would inevitably send shudders of dread through kids and teens. Quite the contrary, many of today’s educational programs are fast-paced, expertly narrated and full of surprising, fun, and visually engaging facts and science trivia. But while no doubt entertaining, are these programs still any good at their core function, namely teaching the kids actual concepts useful for understanding modern science?

The long-running PBS educational series, NOVA, aims to satisfy this goal by providing not only standard teachers’ notes and lesson plans to accompany its shows, but also by investing in extensive and realistic online laboratories in which students can explore actual scientific datasets. A good example of this approach is provided by the NOVA Cloud Lab, which is actually far more exciting than it sounds, as one of its main sections concerns the formation and study of storms. Continue reading “Big Data Takes Education By Storm”

Bird vs. Window: Windows 900-Some Million; Birds 0

Cedar Waxwing at rest.
Cedar Waxwing at rest.

In the battle of bird vs. window, the birds are getting “skunked”.

Perhaps something like this has happened to you? You are in your east-facing kitchen making coffee early on a nice spring morning. The sun is just coming up, birds are at the feeder, just off the patio, 12-15 feet from your kitchen window, enjoying their equivalent of breakfast.

There’s a sudden flurry of activity outside, you see a streak as something flies past, followed by several “thuds” on the window. A Cooper’s hawk, also ready for breakfast, spotted easy prey at the bird feeder and zoomed in for a meal. While the hawk was unsuccessful– didn’t catch a single bird—the bad news is that in fleeing, the birds at the feeder mistook the reflection of your window for open space, and flew directly into the glass.

You rush outdoors to find three birds lying on your patio, stunned but alive. You gently move them off the patio into the grass where you hope they’ll be able to shake it off and return to feeding. And when you get home after a day at the office, the birds are gone. But there is a neighborhood cat that’s always lurking, plus raccoons and a dog in the unfenced yard next door. You don’t know if the birds made it or not. Continue reading “Bird vs. Window: Windows 900-Some Million; Birds 0”