The Ongoing Legacy of the Human Genome Sequence

When the first draft sequence of the human genome was announced, I was a research assistant for a lab that was part of the Genome Center of Wisconsin where I created shotgun libraries of bacterial genomes for sequencing. Of course, the local news organizations were all abuzz with the news and sought opinions on what this meant for the future, including that of the lab’s PI and oddly enough, my own. While I do not recall the exact words I offered on camera, I believe they were something along the lines of this is only the first step toward the future of human genetics. Ten years later, we have not fulfilled the potential of the grandiose words used to report the first draft sequence but have gained enough knowledge of what our genome holds to only intrigue scientists even more.

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Mate Selection at Frog Cocktail Parties: Keep it Short, Low, Loud, and Stand Out from the Crowd (Oh, and have a colorful vocal sac, too)

Hyla versicolor (Copes grey treefrog) Photo credit: LA Dawson wikipedia
Hyla versicolor (Copes grey treefrog) Photo credit: LA Dawson wikipedia

When I lived in Sioux City, IA, I had the opportunity of hanging out with a zoologist who studied the Plains Spadefoot Toad (Spea bombifrons). I would go out with her on nighttime listening surveys, and we would slowly drive the gravel farm roads in the middle of nowhere, weaving from one side to the other as we dodged hopping frogs and toads, and I would be amazed as the clamor of these calling anurans rattled my eardrums.

Just last week in Madison, as I took my lunchtime walk, I passed by a roadside wetland, and my ears filled with the calls of Chorus frogs, singing with all their one-inch might in hopes of attracting a mate. And, later that evening, as my daughter and I weeded our garden at home, I heard the crisp bell trill of two American toads carrying over the chorus frogs in the neighborhood.

Congresses of snoring Spadefoot Toads. In-your-face Copes Gray Tree Frogs. Peepers, Chorus Frogs and and Leopard Frogs. The evenings are noisy when the temperatures moderate and these frogs and toads come out to call. The din of the local roadside wetland begins to resemble the din of the local roadside bar, in more ways than one as it turns out.

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An Interview with Ed Himelblau, Scientist and Promega Cartoonist

Self portrait by Ed Himelblau

Many visitors to the Promega Web site enjoy the Cartoon Lab, the repository of the creative illustrations of Ed Himelblau updated several times a year. Recently, I had a chance to gain some insight about the man behind the cartoons.

Sara Klink: Could you give some background information about yourself?
Ed Himelblau: I was born in Chicago but grew up in San Diego. I went to UCSD [University of California at San Diego] and majored in biology and minored in art. I liked molecular biology and working in labs so I decided to go to grad school. I went to the University of Wisconsin at Madison to get a Ph.D. in the Cell and Molecular Biology program. My first academic job was teaching biology at Southampton College in New York. After several years on Long Island, I moved to my current job teaching and doing research in the Biological Sciences Department at Cal Poly [California Polytechnic State University] in San Luis Obispo, CA.

S.K.: Why did you decide to become a scientist?
E.H.: Playing in tidepools as a kid had something to do with it. As an undergraduate I thought working in a lab sounded cool. When I started working in a lab, I thought the work was interesting and the people were a lot of fun to be around. Then I started to appreciate what it really meant to do experiments and learn about how plants grow and develop.

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Use Parallel Structure to Guide the Reader

Getting What You Want from Your Science Writing Part X

computer_keyboardParallel construction signals to the reader that two ideas are of equal importance. If two or more ideas or items are connected by a coordinating conjunction such as “and”, “but” or “or”, then those ideas should be expressed in parallel or equivalent grammatical constructs. Items and ideas of equal importance should be presented using equivalent grammatical structures. Items in a list should be parallel: all verbal phrases, all nouns, etc. Parallel construction guides your reader and helps your reader organize concepts on a first read of your text. Continue reading “Use Parallel Structure to Guide the Reader”

Antibody Art

Double fluorescent staining of CNS cells with Anti-Rat ciliary neurotrophic factor. Nuclei stained with DAPI

There are many levels on which science can be a beautiful thing. Some of these are quite abstract, like the experimental result that exactly proves the theory, the perfect order revealed in a mathematical equation, or the exquisite sensitivity seen in regulation of a signaling pathway. On another level the output of an experiment itself can have a physical beauty of its own. For example, immunofluorescence and immunocytochemistry technologies can generate results that not only reveal information about the subject of the experiment, but also can be quite spectacularly beautiful. Here are a few favorites of mine:

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Degrees of Silence

Listen carefully. Do you hear that?

“What am I trying to hear?” you might ask.

Nothing.

In life, there is constant noise. At home, there is the the hum of the refrigerator, furnace or air conditioner, the faint sounds of traffic outside and a dozen other sources of background noise. At my desk at work, I hear muffled voices of people in the hall, computer printers printing and the clicking of keyboards as people type. Noise is so pervasive that often I don’t notice it anymore. Continue reading “Degrees of Silence”

Analogues

People who know me well have, at some point, heard me hold forth on the subject of Antarctica. It’s a passion of mine, though I’ve never been there. The forgotten continent is like the Sirens, pulling those who dare to trespass upon the ice back to one of the bleakest places on Earth.

I have consumed many accounts of life there, and have configured my internet services to deliver me news reports that deliver little crumbs of information. Anything that mentions Antarctica crosses my screen.

My fascination derives from boyhood dreams of space. Young visions of piloting starships and traversing Martian landscapes – visions of adventure, glory, and alien encounters – shattered in daylight on a January day in 1986 as I sat cross-legged on an elementary school gymnasium floor. It would be years before I saw 2001: A Space Odyssey, but watching the Challenger disintegrate into a fiery end, I immediately understood one of its central lessons: space is not glamorous, glorious, or any more alien than many of the places on our planet. Space is cold, unemotional, and unforgiving. It is intolerant of error, and it is lonely. And despite these things, it is where any future humans can hope to have must lie.

I will never go into orbit, but Antarctica, that’s the next best thing. Cold. Unforgiving. Intolerant of error. Nearly devoid of life except that which we import and resupply, it is where we troubleshoot the logistical problems of sustaining remote and isolated human colonies. Having spread across six other continents, it is our last terrestrial frontier.

No, I will never float among celestial bodies and listen to the low murmur of the universe rippling deep in the dark silence of space. But there is another place where we pursue science, a place closer to home, where I can be cold and alone and maybe catch a stray shard of a broken childhood dream.

Humorous New Types of PCR

Undoubtedly, the polymerase chain reaction (PCR) has revolutionized biological research and has become one of the most common techniques in today’s laboratory. At times, it seems that a new variation of PCR is described in the literature every month. You might think that you are familiar with the dozens of PCR variations, but I am guessing that you haven’t heard of some of these.

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Top Ten Uses for Pumpkin

In honor of Halloween, here is a Top Ten Uses of Pumpkin list for your enjoyment:

10. Means of transportation on the high seas or emergency flotation device (pumpkin boats; see the video).

9. Elementary Math Lessons. Determine circumference and radius. How much does a pumpkin weigh? Estimate the number of seeds. Check out pumpkin math ideas here.

8. Cholesterol-lowering snack. After ruthlessly scooping out the innards of a pumpkin, clean the seeds, bake them in the oven and enjoy your healthy snack. Pumpkin seeds contain phytosterols, compounds that that have been shown to reduce levels of LDL cholesterol, as well as magnesium, a mineral needed in the diet.

7. Physics Laboratory. Pumpkin Chuckin’ Contest (video).

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Following the Unexpected Path: Pipettes, Printers and Beyond

The unexpected path.....
The unexpected path.....

Someone once asked me how I decided to become an editor. My answer was: I didn’t. Sometimes careers just sort of evolve. I graduated from Iowa State University with a degree in genetics and moved to San Diego, the city of sun, sea air and biotech. My plan was simple; I was going to get a job doing lab work, and maybe someday I’d take a year off and write my book (Doesn’t everyone have a book they are going to write “someday”?). I loved research; I once wondered aloud how people who sat at desks all day could stay busy. What did they do all day? Were there really that many papers in the world that need shuffling about? In the lab I got to do something different every day: cloning, plasmid preps, cell culture, transfections, RNA preps, Northerns. It was like following a treasure map and not knowing what was under the big “X”. Continue reading “Following the Unexpected Path: Pipettes, Printers and Beyond”