CRISPR-Cas9 for an RNA world

CRISPR has the revolutionary potential to alter gene expression by cutting DNA.

Now NmeCas9 is a protein that cuts not just DNA, but RNA.

This has scary potential for viruses (made from RNA), but having read very little (and I don’t think very much is known yet), but I am interested to see how this progresses.

Read about it here, and keep checking on NiB. I see myself writing more about this in the future.

 

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The promiscuous process driving antibiotic resistance

“While overuse of antibiotics has been fingered as the driver of resistance to these drugs, the contribution of bacterial sex plays an underappreciated role, one that could bedevil efforts to fight antimicrobial resistance.”

Want to hear more about this sexy and interesting outcome of bacteria doing it*?

Read more here!

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*I’m pretty sure that’s how the song goes:

Birds do it.

Bees do it.

Bacteria do it and it drives the evolution of resistance.

Pretty sure.

 

Conservation stories from the front lines

The stories of science are told many ways, in many places. Scientists share the ups and downs of the research process over raucous conference cocktails and long hours on the road, across lab benches and conference call lines, and around campfires after long days in the field. These stories underlie every scientific paper yet rarely appear alongside the tables and graphs. To read the often dull, sometimes tedious reports that fill the scientific record, you’d never know that science is a human endeavor, like any other, shaped by tragedy, comedy, and (mis)adventures.

So over at PLoS Biology there is an entire issue dedicated to this. To the knee scrapes, the mosquito bites, the drudge and the euphoric moments of discovery. So get over there and read about them!

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Huddled against the wind, picking through weeds to find snails. Cold, wet and a little tired.

“Fits neatly inside a lizard’s cloaca”: scientists review products on Amazon

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Ziploc bags can be used as snail carriers. Food containers make good little bee homes. A salad spinner makes a good PCR centrifuge. Any scientist who’s ever done field work knows that everyday household projects can be game changers.

And now, scientists are reviewing these products on Amazon.

Read about them here!

 

No regrets

Dr. Wesley Loftie-Eaton is one of my favorite microbiologists. He has a flair for adventure, an impeccable sense of style and an entire outfit for “action adventure” purposes. In a former life he studied plasmids, and road his bike across various countries in Africa to raise awareness about antibiotic resistance. This his post as part of the “Academia to Industry” series. 

It has now been one year, almost to the day, since I made the switch from academia to industry. Do I regret it? Hell no!

I am South African and it is in my home country that I earned my PhD in Molecular Microbiology. It is also where I first started working as a postdoctoral scientist. But my desire to work abroad was huge. I soon moved to the USA to work as a postdoc and with the idea of landing a position faculty position in academia. Eyes on the prize, keep moving forwards.

However, science is not my only passion.  I have an insatiable wanderlust, am an avid outdoors person, incredibly social, and love making cinemagraphs (animated still photos). But all these were put on the back burner while I was in the US, and the latter completely fell away. I rarely did any of my other activities because I was spending all my time in the lab – until I heard a comment from our director; “If you are not in the lab working at 10 o’clock on a Friday night, then you’ll not get anywhere because somebody else is and that person will get the grant”. It’s then that I realized what it would cost me, personally, to stay in academia and I started thinking about my career differently. I am a scientist, but that’s not all that I am.

So when the time came I left academia (and the US) in pursuit of a work-life balance where I did not have to feel guilty about taking weekends for myself. I found this balance working as a Senior Scientist in the Research and Early Development Department of Roche Sequencing Solutions, Cape Town.  Now, when I go home at the end of my day, work stays at the office and my weekends belong to me again. In fact, work-life balance, stress management and other “soft skills” are regarded as important for the overall health and success of the employees and company. For that reason all our employees are presented with personal development courses on a regular basis. Unheard of in academia, right?

The best part is I still get to do exciting science. Sadly, I cannot discuss our research here for confidentiality reasons. That’s the worst part of the job. Not being able to share your discoveries goes against the principle of science. But I can tell you that we are working on developing a new single molecule DNA sequencing technology and I spend about 80 to 90% of my time in the lab working on my contribution to this effort. We also have weekly lab meetings specific to our research group, I get to attend international conferences and our department has regular journal clubs and seminars. Sounds pretty familiar, right? However, one of the biggest differences is that our directives come from the top, and your research is not your own, as it is in academia. But the scientific creativity with which we achieve those goals, remains our own. Creativity is encouraged and overall the research faces a much less constrained by budget.

In hindsight, when I was intent on a career in academia, I was blind to the possibilities in industry. I always felt that industry was a betrayal to science.  As a result, I only allowed myself to look at what possibilities existed once I realized that academia, in its current format, may not be the perfect fit for me anymore. I was very wrong. Science in industry can be equally as fun, stimulating and rewarding as in academia.

And, at the end of the day you have to ask yourself what you want, what you expect, and what you are willing to give up to enjoy what is important to you. Neither academia nor industry are perfect. I traded the scientific freedom to work on projects of my own interest, and to discuss my research openly for more freedom in my personal life. It has honestly been a worthy trade. But I don’t regret my time in academia. Had I not had the research experience and publication record, I probably would not have stepped into this research-intensive position as a Senior Scientist and probably then would have enjoyed industry much less.

So, looking back at how I got to where I am now, industry via academia, did I make the right choices? Hell yes!  

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Let’s move beyond the rhetoric: it’s time to change how we judge research

Impact factors were never meant to be a metric for individual papers, let alone individual people. They’re an average of the skewed distribution of citations accumulated by papers in a given journal over two years. Not only do these averages hide huge variations between papers in the same journal, but citations are imperfect measures of quality and influence. High-impact-factor journals may publish a lot of top-notch science, but we should not outsource evaluation of individual researchers and their outputs to seductive journal metrics.

So what can we do to combat this? What’s the solution? Read about it here!

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Trying to Fix the Gender Imbalance in Science Press

Women in science face a gauntlet of well-documented systemic biases. They face long-standing stereotypes about their intelligence and scientific acumen. They need better college grades to get the same prestige as equally skilled men, they receive less mentoring, they’re rated as less competent and less employable than equally qualified men, they’re less likely to be invited to give talks, they earn less than their male peers, and they have to deal with significant levels of harassment and abuse.

Additionally, women are literally being written out of science stories.

Read about Ed Yong’s desire to combat this pattern, and what he learned in the process, here.

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Science’s Pirate Queen

Over half of all research, according to one study, is now published by the big five of academic publishing: Reed-Elsevier, Wiley-Blackwell, Springer, Taylor & Francis, and, depending on the metric, either the American Chemical Society or Sage Publishing. Elsevier, for example, boasts a nearly $35 billion market cap. It has reported a nearly 39 percent profit margin for its scientific publishing arm — which dwarfs, by comparison, the margins of tech titans such as Apple, Google, and Amazon.

And Alexandra Elbakyan and SciHub are trying to do something to combat that. And similar to research gate they are being crazy sued because of it.

Read about it here!

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A new series! Scientist in Industry

Last year, NiB ran a series called “When I Grow Up”, providing insight on various stages of the academic career ladder (undergrad, MS, PhD, Postdoc, finding a faculty job, having kids, the early years).

This year, to compliment that, I’m running a series about leaving the academic ladder and going into industry. I’ve been pretty openly talking about the research showing that there are very few jobs in academia, and more importantly, that those jobs may not be the jobs we want.

So in this space every Tuesday, we’re going to hear about other professional possibilities, what it’s like out there, how researchers decided to leave the ivory tower, and what the other side looks like.

Stay tuned.

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Happy Birthday, Darwin! And Please Enjoy a Slice of Phylogenetic Fruit Cake.

Today is Charles Darwin’s 209th birthday.

In an earlier post, I explained how to prepare a special list of music to honor the occasion. In this playlist—a “phylogenetic playlist”—songs are named for organisms and are arranged in order to reflect the evolutionary relationships among these organisms. The Beatles’ “Blackbird,” for example, might be paired with Prince’s “When Doves Cry,” consistent with the fact that Old World blackbirds and doves diverged approximately 80 million years ago.

Music is a great way to start a celebration. But no birthday party is really complete without cake and ice cream, and I’d like to address that need today.

Let’s start with the cake.

Over the years, people have prepared many clever and beautiful cakes, framed as tributes to Darwin. One cake charts the 1831-1836 journey of the HMS Beagle, on which Darwin served as a naturalist, gathering specimens from around the world. Other cakes capture stages of human evolution, or recreate famous portraits of Darwin, or laud Darwin as a personal friend.

Any one of these cakes would make a fitting birthday centerpiece. However, in this post, I’d like to argue in favor of another possibility—something I call a “phylogenetic fruit cake.”

Cake

In a classic fruit cake—or fruitcake—fruits are mixed together randomly. In a phylogenetic fruit cake, in contrast, the arrangement of the fruits is decidedly non-random.

Much like the songs in a phylogenetic playlist, the fruits in a phylogenetic fruit cake are arranged to illustrate evolutionary relationships. Both are constructed using the same rules as a phylogenetic tree—a diagrammatic tool long favored by evolutionary biologists.

In any phylogenetic creation, species are arranged at the tips of branches. Points at which branches intersect represent common ancestors. Relative degrees of relationship—whether species A is more closely related to species B or to species C, or is equally closely related to both—can be inferred by comparing the number of shared ancestors.

Fruits are produced by flowering plants. Many species can be assigned to one of two divisions: monocots or eudicots. Within the eudicots, many fruits belong to one of two large categories: either the asterids or the rosids. Within the rosids, in turn, many fruits belong to the family Rosaceae; these include blackberries, strawberries, apples, and cherries.

These divisions reflect the species’ evolutionary histories, and can therefore be directly applied to the design of a phylogenetic fruit cake.

To build my fruit cake, I started with ten different species of fruit. (In some cases, I used slices, in other cases whole specimens.) I positioned these pieces on the upper surface of a frosted cake, with an eye to diagramming the fruits’ evolutionary histories. Write-on frosting served as my “branches.”

For example, bananas and pineapples are monocots. So, I paired the banana slice and the pineapple slice, using write-on frosting to delineate the connection. Kiwis and blueberries are asterids. So, I paired the kiwi slice and the blueberry in just the same way.

The remaining six fruits are rosids. They include grapes and oranges, in addition to the four Rosaceae species that I outlined above. In order to sort out these relationships more finely, I took advantage of divergence time estimates available at Time Tree.org.

Fruit Phylogeny

To tease out these relationships, I was especially reliant on Time Tree’s “Load a List of Species” option, which can be found at the bottom of the page. Here, you can upload a list of species in .txt format, and Time Tree will propose a tree.

As I positioned the fruits, I used Time Tree’s proposed tree as a model. According to Time Tree’s estimates, for example, oranges are more closely related to Rosaceae species than the grapes are, and so I positioned both accordingly. Time Tree’s estimates also led me to pair the blackberry with the strawberry slice, and the apple slice with the cherry.

My cake constitutes just one example of the form. If and when you make your own phylogenetic fruit cake, I’d encourage you to incorporate your own favorite fruits.

Whatever design you settle on, however, try to space out your fruits as evenly as possible on the cake surface. Remember: at the end of your Darwin celebration, you’ll want to cut up this cake, and distribute a slice to each of your party guests. To make this division as slick as possible, you’d ideally like to have one—and only one—piece of fruit per slice.

Here’s another pro tip: without special preservation techniques, exposed pieces of fruit will rot quickly. So you should either makes plans to finish this cake in short order (and if your party is big enough, this shouldn’t be a problem) or else be careful to refrigerate the leftovers.

Almost as essential as a birthday cake is birthday ice cream. And you can build a Darwin-worthy sundae using the very same skill set we’ve already discussed.

The example that I am presenting here contains the three basic flavors: strawberry, chocolate, and vanilla.

Ice Cream

Strawberries come from the genus Fragaria. Chocolate is produced from seeds of the plant Theobroma cacao. Both plants are eudicots. Even more specifically, both are rosids. So these two flavors are linked, using a pair of branches made of chocolate syrup.

Vanilla, however, is a derived from an orchid—a monocot. In this sundae, therefore, vanilla serves as the outgroup, and is positioned on an earlier-diverging branch.

What I’ve just described is a minimalist sundae. When you make your own sundae, I’d challenge you to incorporate some additional ice cream flavors, like pistachio, peanut butter, or peppermint.

You might also experiment with new ways to represent the branches. In my sundae, I’ve used chocolate syrup. But in your own sundae, you might try building your branches out of whipped cream or trails of sprinkles—just as you prefer.

Once the desserts are ready, it’s time to light the candles. If you’re feeling sparkly, you might position all 209 candles along the branches of your cake. (Imagine it: many lines of descent, lit up in 209 points of flame! What a gorgeous, gleaming, flickering tribute to make to the story of plant evolution! And to Darwin!) But if 209 candles feels too ambitious, you might settle for a simple “2018” candle. Or take clever advantage, somehow, of the fact that 209 can be factored into 11 and 19.

Either way, though: with the candles set, it is traditional to sing “Happy Birthday.”

To be clear: I am using the word “traditional” very loosely. Because, of course, “Happy Birthday” is anachronistic. It didn’t actually become a song until well after Darwin’s death.

Still, I think that, by now, any “true to Darwin’s time” principle has been thrown out the window.  In the playlist that I suggested previously, the oldest song was the 1967 “White Rabbit” by Jefferson Airplane. Let’s remember, too: all of the molecular data, available at Time Tree.org, which was so essential in constructing these birthday creations, came well after Darwin’s time.

So, I am not personally inclined to sweat these things. I’d say: go ahead and sing, “Happy Birthday.”

On top of that: I think that the appropriation of modern birthday trappings is in many ways concordant with concepts at the heart of evolutionary biology.

The past has shaped us; the past defines us. But we live—we must—in our present environment, not in the long ago. Change happens. And the here-and-now is the only place in which we can make our way.

So, really? As long as our hearts are in the right place, I can’t imagine that Darwin would begrudge us a few modern conventions.

Ultimately, though: these are quibbles. Because at the end of everything: after all of the careful preparation, and all of the talk—and once the candles have been blown out—we come to what is arguably the very most important part.

That’s right: You get to eat it.

So, anyway: sing, or not—just as you care to. But, above all, dig in.

Because it’s going to be delicious.

Bio: Rachel Rodman has a Ph.D. in Arabidopsis genetics, and presently aspires to recontextualize all of art, literature, and popular culture in the form of a phylogenetic tree. Won’t you help her?