Culturing Science – biology as relevant to us earthly beings

Archive for January 2010

The Science of Moscow’s Stray Dogs [Link]

You may have heard about the stray dogs of Moscow — tens of thousands of them roaming the streets in their own packs, begging, and even riding the subway.  In this Financial Times article from January 16, Susanne Sterthal interviews a biologist, Andrei Poyarkov from the A. N. Severtsov Institute of Ecology and Evolution, who studies the ecology of these dogs on his spare time.

Poykarov’s unofficial conclusion: the dogs are becoming more wild.  He places the dogs into 4 different niches, each of the niches occupying a different location, method of food acquisition, and, most importantly, relationship to humans.  The homeless dogs don’t live with people, but hang out with them outside in public spaces.  The beggars can not only smell who has food on them, but can tell who is most likely to give it to them.  The scavengers’ relation to people is mainly trash-based, by digging through our dumps for food.  The last niche is the real wild dogs: dogs that only interact with one another, view people as dangerous, and hunt for food.  And this is in the 7th largest city in the world!

In the 1940s, before his exile from the Soviet Union, a biologist named Dmitri Belyaev had similar interests to Poyarkov.

Under the guise of studying animal physiology, Belyaev set up a Russian silver fox research centre in Novosibirsk, setting out to test his theory that the most important selected characteristic for the domestication of dogs was a lack of aggression. He began to select foxes that showed the least fear of humans and bred them. After 10-15 years, the foxes he bred showed affection to their keepers, even licking them. They barked, had floppy ears and wagged their tails. They also developed spotted coats – a surprising development that was connected with a decrease in their levels of adrenaline, which shares a biochemical pathway with melanin and controls ­pigment production.

“With stray dogs, we’re witnessing a move backwards,” explains Poyarkov. “That is, to a wilder and less domesticated state, to a more ‘natural’ state.” As if to prove his point, strays do not have spotted coats, they rarely wag their tails and are wary of humans, showing no signs of ­affection towards them.

Most people in the city are not convinced that these dogs are dangerous — although they probably should be.  Poyarkov estimates that out of all the tame dogs released into the streets, only 3% survive the wild dogs.  (I don’t blame the wild dogs — a lot of pets these days look deceivingly like rats.)

So here’s the lesson: don’t let your babies out on the street at night, and dream of a post-apocalpytic Moscow landscape where dogs rule.

Written by Hanner

January 21, 2010 at 8:11 am

Photosynthetic Evolution: how 2 organisms gained or lost the ability to eat sunshine

9/13/2010 Update

New research has come out that changes the story told below. Wägele et al. sequenced cDNA transcripts from RNA produced by slugs dependent on their plastids alone, and did not find the RNA to produce the proteins for plastid use in any meaningful quantity. But the slugs aren’t just using the proteins they got upon original ingestion; we simply do not know what is happening.  For a thorough write-up, I highly recommend this post from The Spandrel Shop entitled “Solar Sea Slugs: part plant, part animal… or not?”

Original post (01/20/2010):

The variety of protist life -- from Finlay, B.J. & Esteban, G.F. Protist, 149, 155-165 (via the British Society of Protist Biology).

Biologists and taxonomists love to put organisms into categories to help us organize the complicated living world.  I grew up on the 5 kingdom system of classification: plants, animals, fungi, bacteria and protists. The first four categories seemed simple enough, but the term “protists” always confused me.  This kingdom seemed to be a dumping ground for all the single-celled organisms that we didn’t know what to do with, ones that had evolved so far from their ancestors that their origins were unknown.

I’ve stumbled upon two fascinating articles about such animals that are out of place.  The first is about microorganisms that were once photosynthetic — and thus evolved with the cyanobacteria and plants — but no longer go through photosynthesis.  The second is about a sea slug that has developed the ability to photosynthesize, or harvest energy from the sun.  Imagine stumbling upon these animals for the first time.  The former would be placed in the animal kingdom due to its heterotrophy, or tendency to get its nutrients from food.  The latter would be baffling: is it some freak highly-organized plant, or an anomalous, energy-producing animal?  Thanks to our increasingly understanding of evolution, scientists have been able to figure out where these strange creatures came from.

The first story is about evolution driven by competition for food between many species of microorganisms.  In terms of energy acquisition, I usually think about two categories of organisms: the heterotrophs, which get their energy from eating, and the autotrophs, which create their own energy from outside inputs such as the sun.  But there are also the mixotrophs, which are able to do both.  To be a mixotroph!  How wonderful would it be to get energy from standing under the sun if you wanted, but you could also be able to eat a hearty meal for the same gain!  On first thought, this appears to be the best life strategy, allowing an organism to get energy whatever way is easiest at the time.

Scientists from the University of Potsdam in Germany and the Austrian Academy of Scientists propose that, in some circumstances, having both strategies may be too much (open access paper here).  In order to be a mixotroph, the organism needs to fit all the machinery required for both processes inside its single cell, increasing its size.  A bigger mixotrophic cell not only loses access to smaller food items, such as ultramicobacteria, but also has to compete with larger heterotrophic organisms, which are solely dedicated to eating and thus can do so more efficiently.  These scientists created a model showing how, under low-light conditions, it would be energenically beneficial for mixotrophs to be rid of their chloroplasts and other organelles needed for photosynthesis so that they could become physically smaller and have access to the smaller foods out of the range of other heterotrophs.  Thus, we have animal-like organisms that evolved from plants.

The second story is about a sea slug, Elysia chlorotica, which has gained the ability to photosynthesize.  It did not evolve this trait in the traditional sense, but rather picked it up from another organism.  The slug’s green color is not self-made, but is present due to its collection of chloroplasts, the photosynthetic center of a cell, from its prey.  Due to an unknown mechanism, the slug is able to hoard only the chloroplasts of its algal food source Vaucheria litoria.  Not only that, but it uses these chloroplasts to go through photosynthesis itself, which it can continue to do 5 months after it last ate V. litoria.  (And this is a slug that only lives for 10 months total.)

This is not as simple as it sounds, however.  You need more than chloroplasts to photosynthesize; you also need genes to encode all the specialized proteins needed to make sunlight into energy!  The big question regarding these slugs was: where did they get these genes?  Scientists working together from Maine, Korea, Iowa and Texas (paper here) compared sections of the nuclear DNA between the slug and its algal food and found identical segments, suggesting that the slug had not evolved these genes on their own, but had acquired them through horizontal gene transfer, or a transfer of DNA from an origin other than one’s own parent.  In this case, they suggest, a segment of the algae’s DNA broke off and joined the slug’s own DNA, an incredibly rare event.  This gene acquisition was so beneficial that it spread through the population, causing E. chlorotica all over the oceans to hoard the chloroplasts of their prey.  And there ya have it, folks: a photosynthetic animal.

Ain’t this a wonderful world we live in?

Learning about the histories of these organisms makes me drool, thinking about the uncategorized protists out there.  What kind of stories do they have to tell?

de Castro, F., Gaedke, U., & Boenigk, J. (2009). Reverse Evolution: Driving Forces Behind the Loss of Acquired Photosynthetic Traits PLoS ONE, 4 (12) DOI: 10.1371/journal.pone.0008465

Rumpho, M., Worful, J., Lee, J., Kannan, K., Tyler, M., Bhattacharya, D., Moustafa, A., & Manhart, J. (2008). Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica Proceedings of the National Academy of Sciences, 105 (46), 17867-17871 DOI: 10.1073/pnas.0804968105

Written by Hanner

January 20, 2010 at 10:43 pm

Why research articles should be publicly accessible (Shulenburger 2009, PLoS Biology)

I cannot even count the number of times when I have been denied access to a journal article I needed.  Oftentimes, it was while I was working on a paper in college and couldn’t read the paper that all the other scholars cited, or the paper that supported an argument I was trying to make.  And this was despite the fact that I was at an academic institution that subscribed to many journals to allow its students access to research.  Maybe, being a small college, the specific journal wasn’t chosen for subscription, or the particular year was unavailable.  There are few things more frustrating!

And it only got worse over the summer when I was no longer in academia.  Although unemployed, I wanted to try and keep up with the scientific world, but was often thwarted due to the fact that I had no money and couldn’t afford to subscribe to journals or buy individual papers.

I do understand why journals charge for access to their articles.  To maintain rigorous review processes to keep a high standard for legitimate research, journals need to hire staff to organize reviewers and select papers for publication.

But it often seems contrary to scientific goals.  We scientists like to believe that we’re in a community where we share information with one another, building off of one another’s discoveries, combining our minuscule projects together to create a larger picture of progress.  But how can we do that if we cannot read each other’s papers and keep up to date on the onslaught of information coming out daily?

It’s a difficult balance — to keep scientific standards high but also make research publicly available.

David Shulenburger wrote an interesting piece in the open-access journal, PLoS (Public Library of Science), available here, addressing this subject.  He suggests two different approaches.

The first follows the lead of Harvard, MIT and University of Kansas: research mandates.  When a researcher from any of these institutions submits a paper for publication, they require that the copyright belong to the university, and that its immediate publication on the university website is permitted.  This allows the universities to create databases with publicly-available articles from the school to help researchers locate collaborates within their own institutions, as well as provide a public list of the results and successes of these institutions.

Of course, this could create a disadvantage to researchers at these institutions.  Unless most or all universities submit these research mandates, the journals could simply choose to accept non-mandated papers so that they themselves will hold the rights.

Shulenburger’s more inclusive suggestion recommends a general public access policy for all journals.  This would mean that the journal could continue to charge for papers up to a year after their publication.  While this would keep some scientists from up-to-the-minute details in their field, it would create an environment where a high-quality review process is supported so that scientific rigor is upheld, while allowing the public access to older papers, which arguably should be available for a true scientific community to exist.

As a careful observer of scholarly communications, I’m convinced that the public goods aspect of faculty research will ultimately compel public access to it. Public goods have the characteristic that use of them by one individual does not diminish their value to others. In fact, the knowledge presented through scholarship generally becomes more valuable as it is shared more widely and becomes a building block upon which further scientific advances may occur.

Shulenburger, D. (2009). University Public-Access Mandates Are Good for Science PLoS Biology, 7 (11) DOI: 10.1371/journal.pbio.1000237


Written by Hanner

January 11, 2010 at 11:58 pm

Posted in Journal Article

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Endangered species awareness: 2 cool projects

Endangered species were the first type of conservation I remember learning about.  I did a panorama of the black-footed ferret in 3rd grade.  A project on the manatee in 4th grade led to a sirenian-obsessed pre-adolescence.  These are cute animals, and we are destroying their habitats!  WE MUST SAVE THEM!

Endangered species are a great way to connect a public, which may not be interested otherwise, to conservation efforts.  It’s a near-tangible way to pinpoint a specific problem, a specific animal even, and get people involved.  Some conservationists argue that this isn’t a good method, that the focus on CMF, or charismatic megafauna (such as the endangered whales, tigers, lions, manatees, etc.), ignores the smaller and uglier microbes and insects, which are going extinct at a much higher rate.  But, hey, you’ve gotta start somewhere!

Seychelles Sheath-Tailed Bat by Molly Schafer

The Endangered Species Print Project was started by the artists Molly Schafer and Jenny Kendler, who met at the Art Institute of Chicago and bonded over “nature-geekery.”  After years of art shows filled with works based on natural imagery, they decided to start a project to help save some of the animals that inspired their work.

The ESPP releases prints, the sales of which go towards specific conservation organizations.  Each print stars an endangered species and the number of prints of each work corresponds with the number of animals left remaining in the wild.  For example, there are only 37 prints available of the seychelles sheath-tailed bat, and 222 of the madagascar fish eagle.

By limiting the print-editions, there is a reaction in the buyer to want the rarest print (as is an art-buyer’s instinct), accompanied by the creeping realization of what the rarity of that print means, and of how distant our lives are from these animals’.  Sure, we can buy a piece of art that is a symbol for a single animal that exists in the wild; this art can donate money to help save this specific animal; but in the end, these species are nearly gone from the planet, and far more needs to be done than buying a piece of art.

That being said, this is a wonderful project to support, as it spreads conservation awareness while donating money to good causes.  Buy prints here for $50 a pop (no matter the print/wild quantity).

Extinked, which took place in November, involved the tattooing of the endangered species of the British Isles on chosen human “ambassadors.”  Detailed scientific drawings were made of the species, and common citizens applied to the artists for the honor of being blessed with the drawing of the specific animal for life in the form of a tattoo.  Even if the species does go extinct, it’s form will live on in the skin of at least one Brit for another 100 or so years.

And isn’t that one purpose of art?  To commemorate a certain event or person or time?  I like to imagine the effects of this project much like the living books in Ray Bradbury’s Fahrenheit 451, where people would memorize the text of books and teach it to one more person before they died to keep the book alive through the book burnings.  Pass on your extinct animal to the next person, so that at least a glimmer of prior biodiversity can be remembered by a small group of people.

Written by Hanner

January 11, 2010 at 12:32 pm

Posted in Art, Link

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