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!





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 acumenThey 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.



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 AppleGoogle, 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!


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, Postdocfinding a faculty job, having kidsthe 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.


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.”


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?

The US Postal Service make Bioluminescent Stamps!

The photographs of Dr. Edith Widder, founder, CEO and senior scientist at ORCA, will appear on US Postage forever stamps!

Bioluminescence, the ability of living things to generate their own light, is demonstrated by the 10 examples on the stamp: a transparent deep-sea comb jelly,  the firefly squid, deep-ocean octopus, midwater jellyfish, deep-sea comb jelly, mushroom, firefly, bamboo coral, marine worm, crown jellyfish, a second type of marine worm, and sea pen.

Read about it here.