Blobologist-approved reads: Privilege, pigeons, polyester, paleontology & pythons

My ScienceSeeker editor’s picks: The between conferences edition

A field guide to privilege in marine science: some reasons why we lack diversity by Miriam Goldstein at Deep Sea News

A much-needed list of the barriers that can prevent people from making it in science. If you’re a scientist, I insist that you read this.

A Dream Deferred: How access to STEM is denied to many students before they get in the door good by Danielle Lee at The Urban Scientist

Miriam Goldstein’s field guide prompted an important post from Danielle Lee, in which she shares her stories from the trenches of high school science fairs. Even if you’re not a scientist, I insist that you read this.

Pigeons: Darwin’s Unappreciated Avian Assistant by Michael Wheelock at The Incubator

Why pigeons and not finches should be remembered as Darwin’s best feathered friends.

My Sweaty Valentine by Rebecca Guenard at Scientific American Guest Blog

Why is it that polyester always make you smell so bad? Rebecca turned her sweaty synthetic experience at ScienceOnline2013 into a wise-cracking journey into the science of B.O.

Why Paleontology Is Relevant by Sarah Werning at The Integrative Paleontologists

Turns out it’s not just because paleontologists often teach anatomy to med students.

Calories aren’t right on labels and maybe that’s OK by David Despain at Evolving Health

Does a doughnut = an apple? Does a calorie = a calorie? Does a whole rat = a blended rat? The answers to these questions and more in David’s fascinating write up of a AAAS meeting session on counting calories.

 

 

 

 

Two books that made me a biologist and the common ancestry of me and my not-especially-adorable study organism

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Last year on Darwin day I had the time to write a personal reflection on my Darwin fangirldom. This year, I have no experiments to tend to, but I still have six impossible deadlines to make before breakfast (seriously, I do). So, with no time for reflection, I’ll just recycle my thoughts from a year ago, warts and over-earnestness and all:

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203 years ago today, Charles Darwin was born. Darwin’s most wonderful idea, evolution by natural selection, eventually became the organising principle around which the field of biology is built. But from a more self-absorbed perspective, that idea is also what first attracted me to biology.

I’m wearing my ScienceOnline2012 temporary Darwin tatoo for the occasion.

In high school, I wanted to grow up to become either a filmmaker or an English professor. But I was also a giant nerd, and in Year 11 I won an award for biology, the prize for which was a book voucher. For the sake of the award ceremony I decided I should choose a book about biology–The Panda’s Thumb by Stephen Jay Gould. The cover featured a panda intensely inspecting its thumb, which resembled another intensely focused panda displaying another thumb, which was yet another panda, and inside were 35 essays on topics close to the paleontologist-writer’s heart: evolutionary theory, Darwin, the history of science, and the politics of human difference. Frankly, to my teenaged eyes it looked boring, but I read it anyway. I had long known the principles of natural selection, but in school the ideas seemed dry and cramped. My dinosaur phase had come and gone without me ever thinking too hard about the processes that turned the descendants of walking reptiles into flying birds. Gould’s reflections, on the other hand, gripped me with an intensity that I think is best encapsulated by the expression of the panda from the front cover. He (Gould, not the panda) made me think about adaptation and change in new ways. He used unforgettable stories from nature, like bacteria that sense magnetic fields, the pseudogenitalia of female hyenas, the mites that die before they are born, and of course, the panda’s ‘thumb’ that is really a modified wrist bone. He turned the bearded anonymity of Darwin into a tangible person, one that grappled with real data and put together his ideas as best he could. He picked apart those ideas with fire and grace. He drew me in to a world of scientific debate and I couldn’t get enough.

I quickly read every Gould essay I could get my hands on, and because I was spending so much time browsing the biology shelves of the public library, I started picking up other books on biology.  One day, I came home with The Making of Memory: From Molecules to Mind by Steven Rose (fully illustrated). The book was not only about the neurobiology of memory, it was about what it meant to be a scientist. It opened with a kind of ‘day in the life’ of a neuroscientist and an extremely memorable description of a two-scientist production line, in which one person was responsible for cutting the heads off baby chicks, and the other scooped out the brains for analysis. As a vegetarian, and a snuggler of all things adorably fluffy, that book made me squeamish, but it also gave me the strange idea that I too could be a scientist, chipping away at our understanding of the world.

Factoid that connects the two books that made me a biologist: Rose was a Marxist. Gould was not, but was often accused of being a secret Marxist by his detractors.

But the book also made me sad. I thought science was out of reach for a book geek like myself. One night, at a gathering of restless teens, I told a friend about my new idea.

“I want to be a neurologist. But I can’t be, because I don’t think I could cut the heads off chicks all day.” My friend looked like she wanted to shake me.

“You could totally be a neurologist,” she insisted. “I want you to be one. You could employ me to deal with the chickens for you.”

Although that didn’t sound like a practical solution, the more I talked about my idea, the more confident I became. I asked my school’s vice principal if it was too late to drop my humanities electives and pick up chemistry. It was. He talked about how many months I’d missed, and how I would have to catch up by myself with the textbook. Then he told me that he knew I could do it.

So, fifteen years later, here I am, a soon-to-be-unemployed biologist. I lost interest in neurology at some point, but I never lost my love of Gould, and of Darwin, and their beautiful ideas. I tried, briefly, to become an evolutionary ecologist, before I realized I didn’t have enough maths training. Instead I find myself a specialist in the ways of the bakers’ yeast (brewers’ yeast, to its friends). Yeast are fungi, like mushrooms, but single-celled and not especially adorable. However, they do have their benefits as a study organism. The most important of those benefits, for my line of work, is that like every other living thing on earth, yeast are my relatives.

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OK, I guess giant yeast can be cuddly. Photo from flickr by piefairy.

About a billion years ago, there was a free-living, single-celled organism not too dissimilar from a yeast, or a cell from my body, or one of the rat cancer cells in petri dishes that I will feed  as soon as I have finished this post.  That ancient organism had a nucleus, which is to say that a membrane separated its DNA from everything else inside the cell.  That cell also carried a vital, energy-generating, pet bacterium (the mitochondrion). It also had a system for transporting things in and out of the cell in bubbles of membrane (the endomembrane system). At some point in its life cycle, it must have had a single, whip-like flagellum that flapped from its posterior end. This busy cell was the last common ancestor of  both me and of the yeast I have just arranged onto a nutritious bed of jelly to be ready for an experiment next week.

Because we are related by heredity, many of the things I learn about those yeast cells will also be true of my own cells. I take advantage of this fact to study a human disease called antitrypsin deficiency using quickly dividing, cheap-to-grow, non-adorable yeast cells. When I make a discovery in yeast, I test whether it might also hold for mammalian cells by repeating the experiments in those rat cancer cells I should be tending. If my ideas are borne out by those experiments, then I turn them over to the medical scientists that study antitrypsin deficiency in the millions of humans that are afflicted by the disease worldwide.

Without an evolutionary framework, the way that I study antitrypsin deficiency wouldn’t make sense. It’s thanks to Darwin’s ideas that I became a biologist, but it’s also thanks to Darwin’s ideas that my work has value. So, please raise a glass of whatever you like to drink on a Sunday and wish a Happy Darwin Day to biologists, to all of humanity, and to our Opisthokont* cousins.

*Opisthokonta is a class of organisms that includes fungi and animals. Yeast and I are both opisthokonts because we are eukaryotes, but are more closely related to each other than to plants and our other, weirder, eukaryotic cousins.

Curiosity killed the parrot? My guest post at Scientific American blogs

There’s too much to say about kea, those playful, destructive and slightly obsessive-compulsive snow parrots from New Zealand. I wrote a guest post at Scientific American Blogs this week on the problem of lead poisoning in wild kea populations, but there were a million things I had to leave out for fear of boring people with kea overload. If I ever finish my homework, maybe I’ll  write more about them, in the meantime please enjoy:

Wheelie bin raids

The Kea Conservation Trust

The 1993 documentary Kea: Mountain Parrot

Kea - Mountain Parrot

Update (24th Jan):

Just plain ol’ footage of kea flying around:

Blobologist-approved reads: poos, penguins & professors

My ScienceSeeker editor’s picks: The dying January edition

This Penguin: An Unexpected Journey by Elizabeth Preston at Inkfish

This is the story of a disoriented penguin in a hood and ear muffs. This is a story about science.

Fecal Transplants: A Clinical Trial Confirms How Well They Work by Maryn McKenna at Superbug

The ether has been awash with poo stories recently, but none have been more block-busting than the first clinical trial of fecal transplants. Also, it’s nice to hear good news reported by McKenna, since good news tends to be scarce on the “terrifying emerging disease” beat.

Back to Work! Autonomy and the Stress of Being a Professor by Kate Clancy at Context and Variation

Many people wrote excellent responses to that silly Forbes column about how professors have the least stressful job, but the one that got me the most riled up was this one. If you’re in academia, it might kick you in the guts, and it might make you feel empowered, and it might do both.

 

 

No, squeezing breasts does not cure cancer

You may have seen reports that squeezing breasts cures cancer.

You may have seen these reports a few days ago, at such esteemed British purveyors of science news as the Daily Mail and Huffington Post UK (no, I haven’t linked to the articles). If you looked today, you may have seen similar reports, along with similarly tacky stock images of boobs being squeezed, at news sites and blogs all over the world.

You are probably not surprised to learn that squeezing breasts, pleasant as it might be, will have absolutely no effect on anybody’s cancer.

This is yet another case of the UK media finding a jokey angle on a small science story that sends it viral overseas. I’ve seen it happen many times (which is why I enjoyed this slightly bewildered article about the phenomenon), but this time it really bothered me. That’s because usually this cycle starts with research that was already a joke (or publicity stunt) to begin with, but in this case the story was about some real science.

I suppose I also took it a bit personally because I was involved in publicising the particular nugget of research at the center of the boob squeezing madness. I’m an associate of the Public Information Committee of the American Society for Cell Biology, which means I help pick out which research from the society’s annual meeting we will promote to the press. This story, presented at the ASCB meeting by Berkeley grad student Gautham Venugopalan, was an easy choice because the science is new, interesting and medically relevant.

And no, he did not squeeze breasts and then measure cancer regression rates – that would be pointless and weird. What he actually did was compress breast cancer cells that were growing in the lab. Remarkably, a brief squeeze prompted the cancer cells to arrange themselves into highly organized spherical structures that are usually only formed by non-cancerous breast cells. The finding is intriguing because these well-behaved cells presumably still had the same cancer-causing genetic mutations that they started with. Venugopalan and his colleagues had somehow blocked the effects of those mutations.

This is precisely the kind of effect that Mina Bissell’s group, who collaborated in the research, searches for. Bissell argues that an important reason why cancer mutations do not always lead to cancer is that a cell’s behavior is strongly regulated by its “microenvironment” – its immediate surroundings, including neighboring cells and a gel-like goo called the extracellular matrix. You can see her discussing this idea in a TED talk in which she describes the experimental system that Venugopalan used. This system simulates the breast cell microenvironment using a gel enriched with extracellular matrix proteins and signaling factors. Bissell’s lab has previously shown that they can force cancerous cells to behave like normal cells by manipulating the signals that come from this simulated microenvironment.

Venugopalan took the system in a different direction, however. He is a member of Daniel Fletcher’s group, who study (among other things) the tiny mechanical forces that cells experience within their microenvironment. Neighboring cells push and pull each other in many ways as they do their various jobs; some cells are compressed as they slide between others, some cells are tugged around because they are stuck together into networks of interlocking cells. But cells are not just passively buffeted, they treat mechanical forces as sources of information, signals about what is going on around them, and in turn manipulate those signals to change their microenvironment. Such mechanical signals can influence the development and spread of cancers in a variety of ways that are still being unravelled.

The Berkeley experiments have contributed to this growing field by demonstrating that signals generated by compression can override certain cancer mutations. Understanding those signals might one day lead to drugs that could control cancers in people, not just in dishes. We even have a clue for where to look for the signals – the effects of compression disappeared when the researchers blocked the function of E-cadherin, a protein that helps glue neighboring cells together.

This work is preliminary. It hasn’t been peer reviewed yet and there’s no guarantee that the findings will translate from the dish to the clinic, but the results were still newsworthy enough for some publications that ignored the boob squeezing angle (like NatureScienceNews, Medical Daily and ironically, the Huffington Post US). You might wonder what is so bad about research being mentioned by publications that would normally not bother to cover it. You might argue that it’s a good thing for people who are hooked in by the pictures of breasts to end up reading about some science, given that most of the earlier articles described the science relatively accurately (ignoring the headlines and leads).

My response would be this travesty from MsnNOW (a tip of the hat to Ankur Chakravarthy, who found this first):

Squeezing breasts could prevent cancer, best study ever says

Getting to second base, the holy grail for hormonal boys, is now science: New research has shown that squeezing breasts could prevent malignant breast cells from causing cancer. This doesn’t give pervy dudes license to grope you on the subway, ladies, but it does mean boob-grabbing should be a regular part of your self-care routine (yes, absolutely try it DIY-style). Experiments found that physical pressure led cells back to normal growth patterns, and that even after compression was no longer applied, the malignant cells stopped growing. Spread the word, boob-lovers of the world.

This is the Chinese whisper effect of viral news, with each new aggregator leaving out more and more context until you’re left with only an echo of the original science.

Counting fish

Update: December 10 – I won a travel award! I’m going to ScienceOnline! A hearty thanks to NESCent, and you should all go read the other awesome winning posts – on bed bug ground zero, bee housekeeping, and evolutionary escapes from environmental toxins.

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I’m entering this post in the 2012 NESCent evolution blog contest. The winners get a travel award to attend ScienceOnline 2013!

Pink salmon, Bear Creek by K.Yasui/2011 USFWS Alaska Fish Photo Contest. Shared under this Creative Commons license.

Pink salmon spend two salty years in the ocean before they return to their birthplace to spawn and to die. If that birthplace was Auke Lake, near Juneau, Alaska, then a returning salmon can only reach its final destination by passing through a narrow opening in the weir at Auke Creek, which drains the lake into Auke Bay. Every year, thousands of pink salmon pass through the weir’s trap, both adults fighting upstream and juveniles coasting the other way. Each one of those fish is counted by researchers who stand thigh deep in the cold water, monitoring the trap every day between March and October. This marathon fish count stretches back to the 1970s, and has provided one of the most detailed records of a salmon population anywhere in the world. Combined with a fortuitous little genetic experiment performed at the weir in 1979, the Auke Creek data have also given us some long-sought evidence that the annual rhythms of the natural world are evolving in response to climate change.

Auke Lake is the body of water on the left  and Auke Bay is on the right. Migratory fish that need to move between the two must travel the short creek in between. Photo by Gillfoto, used under this Creative Commons license.

Many things have changed in the decades since the fish counting started. Average stream temperatures are higher by more than one degree celcius, the salmon are returning to the lake nearly two weeks earlier, and the entire migration season falls within a narrower window of time. Although we can’t say for sure that the migration shifts are caused by the temperature change, it falls into a pattern that has been observed for many other organisms all over the world. Birdsbutterflies, frogs, flowers, plankton – to name just a few – are slightly shifting the timing of their big, seasonal life events, all consistent with a response to a warming climate.

But do these timing shifts count as evolution? Without evidence of genetic change in a population, such shifts might be just the result of individuals adjusting within their normal range of behaviors. Genetic evidence to the contrary is extremely hard to come by – so even though biologists have long believed that the many examples of shifting seasonal traits must include some examples of rapid evolution, they haven’t had the hard genetic data to show it.

Luckily, some three decades ago, fisheries biologist Anthony J Garrett started an obscure little experiment at Auke Creek. Recently, that experiment was extended and repurposed by Ryan P Kovach, a graduate student from University of Alaska, Fairbanks, and David A Tallmon of University of Alaska, Southeast, to confirm that the Auke Creek salmon have indeed evolved.

In the 1979 experiment, Garrett tinkered with the genetics of late-migrating salmon just enough to let him trace their fortunes. Historically, the fish counters could distinguish between two relatively distinct populations that migrated about twenty days apart – the “early run” and the “late run.” Interested in these sub-populations, Garrett looked for a gene variant to use as a genetic “marker” for the late-run fish. The genetic marker he chose was naturally present at low levels in the population, but seemed likely to be selectively neutral – neither harming nor helping the fish that bore it. He captured all of the very last migrating pink salmon of the season and only spawned those that carried the genetic marker. The offspring of those fish rejoined the naturally spawned population, and by the time the next generation returned, late-run salmon had a five-fold increased frequency of the genetic marker compared to the early run.

Because all those diligent Auke Creek fish counters in waders were also taking DNA samples throughout the spawning seasons, we know that the frequency of the late-run marker stayed constant for about a decade, confirming that the marker was indeed selectively neutral. The “marked” fish and their descendants kept turning up reliably late until 1989, when stream temperatures during the spawning season reached the second highest on record.

By 1991, the late-run marker had faded back to the low natural levels found in the early-run fish, and in parallel, the fish counters saw a dramatic decrease in the number of salmon turning up late. In a single generation, the distinct late-migrating subpopulation had practically disappeared, making the average migration time of the entire population significantly earlier. In 2011, twenty years later, the data looked much the same as in 1991 – which means the Auke Creek salmon population is probably still dominated by descendants of the 1989 early run.

So this is interesting news for biologists looking for evidence of climate change-driven evolution. But what does it mean for salmon? Today, Auke Creek pink salmon are as abundant as ever, and thanks to that hot 1989 summer, the population is now adapted to a slightly warmer climate. But because of that adaptation process, they are also less genetically diverse and less behaviourally diverse, which means they might not be so lucky when up against other natural selection events in the future. There is also a limit to how early a salmon can spawn. If temperatures continue to rise, at some point Auke Lake could cease to be a viable salmon spawning ground, with effects that would ripple through the region, both ecologically and economically. It would also bring an end to the salmon counting.

Auke Creek Salmon Research. Photo by Alaska Fisheries Science Center, NOAA Fisheries Service (Public domain).

Genetic change for earlier migration timing in a pink salmon population

Ryan P. Kovach, Anthony J. Gharrett and David A. Tallmon

Proc Biol Sci. 2012 Sep 22; 279 (1743):3870-8

Blobologist-approved reads: Sexy slime molds and sleep cravings

My ScienceSeeker editor’s picks for this week: The dying semester edition

Starving to be Social: The Odd Life of Dictyostelium Slime Molds by Alex Wild at Compound Eye

Slime molds sound gross. But they are not gross, they are AWESOME. And here is proof they can be beautiful as well.

Re-Awakenings by Virginia Hughes at Last Word About Nothing

Fascinating story about hypersomniacs, who just can’t get enough sleep, and the scientists who think it might be caused by imbalance of a mysterious “sleep molecule.”

Blobologist-approved reads: Zombies and a flash of light

My ScienceSeeker editor’s picks for this week: The dying turkey edition

What this week’s list lacks in quantity, it makes up for in awesomeness and excellent writing:

 

Animal vision evolved 700 million years ago by Lucas Brouwers at Thoughtomics

On blind light-detectors and the humble beginnings of the animal eye.

Mycoplasma “Ghosts” Can Rise From the Dead by Jennifer Frazer at Artful Amoeba

You know what would be weird? If you could kill an organism until it was dead, empty out its guts until it’s just a hollow shell and then bring it back to ‘life’ again by adding ATP. Yeah, that would be weird.

 

Blobologist-approved reads: Time for some navel gazing, DNA testing, natural selecting and group decision making

My ScienceSeeker editor’s picks for this week: The dying swan edition

Thanks to the chaos of becoming a full-time student again, it’s been mostly impossible to blog my ScienceSeeker picks for the last few months. But today I’m stuck at home with pleurisy and a mandate to take it easy, so here goes:

Weaving together the DNA of parenthood by Nathalia Holt at Backstory

Backstory is an interesting new blog at SciLogs, and last week’s post was the moving story of a mother who responded to her son’s rare genetic disorder by starting a direct-to-consumer genetic testing company. It’s easy for me to get cynical about DTC genetic testing, but I had never thought about it from exactly this perspective before.

The Death of Natural Selection by Laura Jane Martin (a guest post at Scientific American Blogs)

This post is a reflective response to recent chit-chat about nature’s “right to evolve,” a proposal that to me sounds deeply confused and misguided. Martin poses a seemingly simple question: “…is there a species, anywhere, with an evolutionary trajectory that has not been affected by humans?”

Political animals by Miss Behavior at The Scorpion and The Frog

Given its obvious relevance to politics this week, Miss Behavior asks a pertinent question about how social animals make group decisions, given that the individual members are neither terribly bright, nor terribly well informed. This is awesome.

After 2 Years Scientists Still Can’t Solve Belly Button Mystery, Continue Navel-Gazing by Rob Dunn (another guest post at SciAm blogs)

So you’ve probably heard of Rob Dunn’s belly button biodiversity  project. If you haven’t, you are missing out big time and you should read his post, and possibly all of his other guest posts at SciAm. If you have heard about it, you should read this anyway, not so much because it describes the interesting results that they just published in PLoS One, but because it does a great job of describing what it’s like to fall down the rabbit-hole of a new research problem. One question leads to another, and another, and the more work you do, the richer and more interesting and more confusing it gets. And then you meet the guy who hasn’t washed in years.