Archive for the 'Biology & Environment' category

The Christmas Bird Count

Dec 07 2010 Published by under Biology & Environment

For over a century the Audubon Society has organized a massive citizen science undertaking: The Christmas Bird Count. Tens of thousands of volunteers help take a census of the bird populations of Canada, the United States, Mexico and Central and South America.

Data from the annual surveys has provided biologists and conservationists a picture of long term changes in the distribution of North American bird populations.

For example, analysis of data collected over the past 40 years shows that the the winter range of many bird populations - 177 of the 305 species examined -  has shifted north, in some cases hundreds of miles. The shift correlates with an increase in mean January temperatures of almost 5 degrees during that period, and it's likely that climate change is at least partially responsible. Based on that data, the Audubon Society's report on birds and climate change (pdf) concludes that "ecological disruptions that threaten birds, other wildlife and human communities [due to climate change] are likely already in motion".

The Christmas Bird Count has also helped identify common bird species - from  meadowlarks to hummingbirds -  that "have taken a nosedive" over the past 40 years.

On the other hand, doves and pigeons have expanded their ranges along with growing urban and suburban development.

It's data that would be difficult to collect without an army of volunteers.

If you'd like to participate, this year's Christmas Bird Count begins on December 14th and runs through January 5th.  You'll need to register for a count:

There is a specific methodology to the CBC, but everyone can participate. The count takes place within "Count Circles," which focus on specific geographical areas. Each circle is led by a Count Compiler. Therefore, if you are a beginning birder, you will be able to join a group that includes at least one experienced birdwatcher. In addition, if your home is within the boundaries of a Count Circle, then you can stay home and report the birds that visit your feeder once you have arranged to do so with the Count Compiler. There is a $5 fee to participate in the CBC for all field participants aged 19 or older.

Find a count circle near you (unfortunately only searchable by state or province).

Even if you can't participate in the Christmas Count, you might be interested in similar bird observation projects:

Images from  from Our Winter Birds: How to Know and How to Attract Them by Frank M. Chapman (1918).  Chapman, an ornithologist with the American museum of Natural History and officer in the Audubon Society, proposed the first Christmas Bird Count in 1900. Top image: Tree Sparrow. Bottom Image: Northern Shrike.

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Sudoku-solving bacteria

Dec 01 2010 Published by under Biology & Environment

One of the goals of synthetic biology is to engineer bacteria into biological "machines" that can be used to produce energy, deliver drugs, or synthesize materials. If the engineered bacteria could selectively communicate with each other, would expand their possible uses.

A team of students from the University of Tokyo decided to create E. coli bacteria that could selectively communicate with each other for this year's Internationally Genetically Engineered Machine (iGEM) competition, held last November 6-8 at MIT.

Sudoku Puzzle

Sudoku Puzzle

As a proof-of-principal for their bacterial communication system, the Japanese team created microbes that could solve a Sudoku puzzle.

Sudoku puzzles are usually made from a 9x9 grid made up of nine 3x3 squares. The numerals 1 through 9 can only be used once in each row, once in each column, and once in each 3x3 square. The puzzles start out with some of the numbers already filled in, and the goal is to fill in the blanks. You can see an example of a starting grid over on the right -->

Even though a Sudoku puzzle uses numbers, it's not a math puzzle - no adding, subtracting or other number manipulation is required. It's a logic puzzle. It could work just as well with nine different pictures or nine different letters or nine different colors.

The simple logic rules of the game were an ideal way to demonstrate the ability of the modified bacteria to communicate.

The Japanese team's modified bacteria were designed to solve a 4x4 Sudoku grid.  They engineered 16 genetically different bacteria, one for each spot on the grid. Each of those strains of bacteria has the ability differentiate into one of 4 types. Each of those types can then direct "detection bacteria" to produce a corresponding fluorescent color.

Just like any Sudoku puzzle, the grid begins with some of the squares already solved, like this:

E.Coli Sudoku Puzzle

The differentiated bacteria produce signals that tell the other bacteria their type. The undifferentiated bacteria are able to detect which of the 4 types are already present in the same "row",  "column" and "block", while ignoring information from irrelevant "squares". For example, undifferentiated bacteria representing square 4 would need to detect which differentiated types were already present in squares 1-3 (the same row), squares 8, 12, and 16 (the same column), and squares 3, 7 and 8 (the same block).  They would have to ignore the bacteria in irrelevant squares 11 and 13.

Here is their video of how the system works, which is a bit clearer than my explanation:

The students already have figured out - at least theoretically - how to modify their system so that bacteria would be able to solve a 9 x 9 Sudoku grid.

But that isn't the only use of such engineered microbes. Bacteria that can differentiate between relevant and irrelevant communications could ultimately be used to design bacterial logic circuits for parallel calculation devices. Maybe someday we'll be able to use bacteria to plug away at difficult computing problems.

You  can read the technical details to learn more about the biochemistry of the system.

And if you want to test your own Sudoku skills, I recommend the daily puzzle here.

(Project via New Scientist)


Top image: A Sudoku layout generated by the GNU programSu Doku Solver and contributed in the public domain by Lawrence Leonard Gilbert. From Wikipedia.
Bottom Image: "16 kinds of E. coli corresponding to each cell" by the UT Tokyo iGEM team, shared under a Creative Commons Attribution-ShareAlike license.

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Fall Color, SoCal Style

Nov 01 2010 Published by under Biology & Environment

It's fall here in the Northern Hemisphere. The nights are getting longer and temperatures are getting cooler.

Trees in cool climates are preparing themselves for winter by breaking down the chlorophyll in their leaves so that the nutrients can be used  in their roots and trunks. As the green-colored  chlorophyll disappears, yellow pigments in the leaves are revealed.  Some also start producing red pigments, likely to help the trees store up nitrogen.  The result can be spectacular, with whole forests clad in fiery yellow and orange and red.

That said, as a California native, I never fully understood the New England fall color frenzy when I was living in Boston. Along with the weather forecasts the local news stations would have fall color reports., apparently so you would know where to join the zillion other leaf peepers who jam the back roads of Maine and New Hampshire in late September and early October. I'd just as soon see the forest past it's peak if it means fewer people.

Here in the southwest, the foliage has apparently just hit it's color peak. That's not really noticeable, at least where I live.  Few of the native trees and shrubs here change color in the fall. Many don't even lose their leaves for the winter.  Not surprising, considering that winters here are pretty mild. At higher elevations where snow is common, the forests are pine, not leafy trees.

That's not to say that there aren't plenty of colorful reminders that fall is here and winter is approaching.

Non-native trees like liquidambar (sweetgum) provide color to residential neighborhoods and parks.

Colorful apples are ripe and ready to pick - and delicious to eat.

Pyracantha berries are plentiful, much to the delight of the local birds.

The lakes are stocked with colorful fish.

Lantana and other flowers are in bloom.

Pumpkins - both real and artificial - add orange to the landscape.

And of course there are the colorful political signs, which will vanish (hopefully) after tomorrow.

Of course this coloration is due to human intervention - non-native plants and animals, man-made signs and decorations.

You have to look to the hills and skies for the true natural colors of autumn: hillsides sprouting green from the first rains of the season, blue skies, and orange sunsets.

Fall is my favorite season.


(If you are interested in my nerdy take on seasonal change, check out my post about Night and Day at Science in My Fiction)

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Mad Science! Human-animal hybrids

Oct 30 2010 Published by under Biology & Environment


I noticed then the abnormal shortness of their legs, and their lank, clumsy feet. All three began slowly to circle round, raising and stamping their feet and waving their arms; a kind of tune crept into their rhythmic recitation, and a refrain,—“Aloola,” or “Balloola,” it sounded like. Their eyes began to sparkle, and their ugly faces to brighten, with an expression of strange pleasure. Saliva dripped from their lipless mouths.

Suddenly, as I watched their grotesque and unaccountable gestures, I perceived clearly for the first time what it was that had offended me, what had given me the two inconsistent and conflicting impressions of utter strangeness and yet of the strangest familiarity. The three creatures engaged in this mysterious rite were human in shape, and yet human beings with the strangest air about them of some familiar animal. Each of these creatures, despite its human form, its rag of clothing, and the rough humanity of its bodily form, had woven into it—into its movements, into the expression of its countenance, into its whole presence—some now irresistible suggestion of a hog, a swinish taint, the unmistakable mark of the beast.

~ The Island of Doctor Moreau, H.G. Wells (1896)

Creatures that are neither human nor animal, but rather something in between, have probably been part scary stories since people began telling them around the campfire.  However, what sets The Island of Doctor Moreau apart from traditional tales of werewolves and sphinxes, is that the humanized beasts are not the offspring of the gods or suffering from a curse. In H.G. Wells tale, his monstrocities were the product of science, rather than the supernatural.

Of course the Beast People of The Island of Doctor Moreau are not human at all. Instead they  leopards and apes and hyenas and pigs surgically modified into human shape – "triumphs of vivisection".  The Doctor even made some of his Beast People by combining parts from different animals:

You begin to see that it is a possible thing to transplant tissue from one part of an animal to another, or from one animal to another; to alter its chemical reactions and methods of growth; to modify the articulations of its limbs; and, indeed, to change it in its most intimate structure.

I don't doubt the Doctor would have eventually used human parts in his experiments, given the opportunity.

And I think it's partially that fear, that scientists will create monsters of dubious humanity in the blind pursuit of science,  that had caused several US states (and countries like Canada) to pass laws banning creation of human-animal hybrids.

But when scientists create chimeras or hybrids of different species, they aren't interested in creating humanoids with animal characteristics like you see in science fiction-horror movies such as Splice. At least the scientists I know aren't trying to do that.

Instead, human and non-human genes and organs are combined to further biomedical research and treatments.

Organ transplantation

Organ transplantation has become a fairly routine part of medicine. The problem is that there are far more patients who need replacement organs - more than 72,000 on the active waiting list in the US - than there are healthy organs to transplant.

The Young Family

One potential solution is xenotransplantation - the transplant of organs from baboons, pigs or other animals into humans.  While non-human animals seem to be a promising source of tissue for biological joint replacements, transplants of hearts, kidneys and other organs from animals to humans have had limited success.  A major part of the problem is the rejection of the non-human tissue by the human immune system.

The solution? Engineer non-human animals to grow human organs. Sounds like mad science, right?

Here's a science fiction version:

Jimmy's father worked for OrganInc Farms. He was a genographer, one of the best in the field. He'd done some of the key studies on mapping the proteonome when he was still a post-grad, and then he'd helped engineer the Methuselah Mouse as part of Operation Immortality. After that, at OrganInc Farms, he'd been one of the foremost architects of the pigoon project, along with a team of transplant experts and the microbiologists who were splicing against infections. Pigoon was only a nickname: the official name was sus multiorganifer. But pigoon was what everyone said.
[... snip ...]
The goal of the pigoon project was to grown an assortment of foolproof human-tissue organs in a transgenic knockout pig host - organs that would transplant smoothly and avoid rejection, but would also be able to fend off attacks by opportunistic microbes and viruses, of which there were more strains every year. A rapid-maturity gene was spliced in so the pigoon kidneys and livers and hearts would be ready sooner, and now they were perfecting a pigoon that could grow five or six kidneys at a time.
~ Oryx and Crake
, Margaret Atwood (2003)

Nothing like Atwood's pigoons currently exists.  However, pigs are being genetically engineered to express human anticoagulants and human proteins that modulate the immune system.  The resulting organs are not completely human, but they hopefully will be humanized enough to prevent the hyperacute rejection of the transplants.

Scientists in Japan have taken a slightly different approach. They used monkey stem cells to grow monkey organs in sheep. Presumably similar techniques could be used to grow human organs from human stem cells.

And  it's not just big animals that are being engineered with human genes.  Transgenic mice with functional human-like immune systems have been used to produce human antibodies for therapeutic purposes. A bit more oddly, tilapia have been engineered to produce human insulin as a potential source of transplanted islet cells to treat Type 1 diabetes.

Animal Models of Human Disease

For both ethical and practical reasons, it is often not possible to study the causes and potential treatments for disease directly in humans. Instead, animal models of human disease are used.  A potential stumbling block to such research is that mice and other non-human animals aren't necessarily infected by the same microbes or afflicted with the same disorders as humans.

One way around that is to make the research animals more biologically similar to humans. For example, mice with humanized immune systems are being developed to  allow screening of vaccine candidates for HIV and other viruses.

More controversially, mice were injected with human stem cells that ended up as functional components of the mouse brains. The hope is that the stem cell therapy research for brain diseases like Alzheimer's and Parkinson's.

There are many other examples: transgenic pigs used to study human retinitis pigmentosa, mice with humanized livers to study drug metabolism, and zebrafish engineered with human oncogenes to study cancer and so on.

Stem Cell Research

The Minotaur

The biggest controversy over human-animal hybrids is not the creation of disease models or organ donors.  It's research that touches on human reproduction.

While it may be possible for humans and chimpanzees to mate and have offspring,  there is no evidence that this has ever happened. Instead, the great concern lies in the use of human-animal hybrid cells for cloning and stem cell creation.  For example, the author of the recently passed Arizona law that bars the creation of a human-animal hybrid cited recent research in the UK that did just that:

Rep. Nancy Barto, R-Phoenix, who wrote the measure, said there's no evidence such research is going on in Arizona or any other state. But she noted that scientists in the United Kingdom reported putting human DNA into empty cow eggs.

So why create human-cow hybrids? The scientists' intention was not to create real-life minotaurs.  Instead, cow egg cells had most of their DNA content removed, then replaced with nucleus and DNA from human skin cells. The idea is that such "cytoplasmic hybrid" cells can be stimulated to start dividing, then, after a few days, harvested for stem cells.  The resulting stem cells would be for the most part human, since all of the nuclear DNA is derived from human cells.

Why use cow egg cells? For practical and ethical reasons. Human eggs are in short supply. I strongly doubt that people who oppose the development of the creation of human-cow stem cells would be any happier if they were entirely human.


Apparently human-animal hybridization has been used in the development of indy rockers:

A major advance in musical evolution? or a crime against nature and good taste?

More information:

Free science-fiction with human-animal hybrids (because who doesn't like some creepy SF?):

Top: ManBearPig from the South Park episode ManBearPig
Middle: Swine Flu by Chuck “Caveman” Coker, on Flickr, showing Patricia Piccinini's sculpture "The Young Family"
Bottom: Tondo Minotaur © Marie-Lan Nguyen / Wikimedia Commons

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The Golden Age of Skin Science

Oct 22 2010 Published by under Biology & Environment

Sarah Haskins takes a look at the sciency-sounding advertising for skin care products:

For the record I am pretty much face Amish.

(Also, to be fair, your skin does have more than 2 layers, if you count the 5 sub-layers of the epidermis)

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Beauty in Miniature

Oct 19 2010 Published by under Biology & Environment

Mosquito heart by Jonas King

Nikon announced the winners of their "Small World" photomicrograph competition, and the results are stunning. Many showcase the beauty of biology.

The first prize photo, taken by Vanderbilt University graduate student Jonas King,  shows a close up of a mosquito's heart with different structures labeled with fluorescent dye:

The green dye binds with muscle cells and shows the underlying musculature. The blue dye binds with cellular DNA and shows the presence of all the mosquito’s cells. The point of view of the image is top down. The mosquito’s body lies horizontally with its head to the left. The heart is the narrow tube that runs horizontally across the middle of the picture. The muscles that wind around the heart show up clearly in green. The triangular-shaped bundles perpendicular to the heart are called alary muscles and they hold the heart up against the mosquito’s back. Each of these bundles is centered on one of the heart valves, which do not show up clearly. The mosquito’s body consists of a series of segments and the broad strips of muscle that run parallel to the heart are intersegmental muscles that hold the segments together. The vertical muscles at the top and bottom of the image wrap around the mosquito’s body and are called intrasegmental muscles.

The resulting photo turns that complicated bit of anatomy into a lovely piece of abstract art.   Click on the thumbnail to see the full size photo.

5-day-old Zebrafish Head by Hideo Otsuna

Second prize went to University of Utah scientist Hideo Otsuna, for his photo of a 5-day-old zebrafish head. It uses fluorescent dyes to label different parts of the fish's nervous system. The image appears to look down on the top of the head, with the front of the head at the top of the photo. The prominent blue bulges on each side are the eyes.  Zebrafish are often used to study how the development of the brain and nervous system because they grow rapidly and are mostly transparent, which means internal structures can be relatively easily observed in intact animals.   You can see in this photo what a 60-hour-old zebrafish looks like under normal light.

Living Red Seaweed by John Huisman

I also quite like the 6th place photo, which shows a 40x magnified view of living red seaweed, taken by John Huisman of Murdoch University. It reminds me of the sort crackling pattern you might see on the floor of a dry lake bed in the desert. Just beautiful.

Be sure to check out all top 20 photos, as well as the images that won the popular vote.

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Recent Reading – 10/12/10

Oct 12 2010 Published by under Biology & Environment, Recent Reading

Some interesting recent posts elsewhere:

Blog Carnivals

Scientists of All Sorts

Nature & Science

Medicine & Health

Science Writing

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Big cats hunting pumpkins

Oct 09 2010 Published by under Biology & Environment

Big Cat Rescue is an organization that rescues big wild cats - tigers, lions, leopards - that have been abused or abandoned. Their sanctuary in Florida houses more than 100 big cats.

After Halloween, they get the left-over pumpkins from markets for the cats to play with. It looks like they really enjoy it.

They note on the YouTube page that the cats aren't eating the pumpkins, they are just playing with them. Watching tigers easily sink their jaws into a pumpkin that's as big as a human head makes me wonder how anyone could think keeping one as a pet is a good idea.

(Thanks to mom for sending me the video!)

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She mates and she kills

Oct 07 2010 Published by under Biology & Environment

Redback Spider

Miss her, kiss her, love her, wrong move you’re dead

If yesterday's post about black and brown widows made you want to learn more about venomous spiders, you should check out DN Lee's latest post at SouthernPlayalisticEvolutionMusic. Her look at sexual cannibalism in Latrodectus spiders (like black widows) is set to Poison by Bell Biv DeVoe.

Alternatively, if you prefer your cannibalistic spider-like creatures in science fictional form, you should read James Tiptree Jr.'s "Love is the Plan, the Plan is Death".  If you don't have a copy of Tiptree's stories,  you can read the Nebula-winning tale at the old SciFiction site (dead, but still accessible through the Internet Archive).

When I see your littlest hunting claws upraised my whole gut melts, it floods me. I am all tender jelly. Tender! Oh, tender-fierce like a Mother, I think! Isn't that how a Mother feels? My jaws are sluicing juice that isn't hunger-juice—I am choking with fear of frighting you or bruising your tininess—I ache to grip and knead you, to eat you in one gulp, in a thousand nibbles—

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Good news, everyone! Brown widow spiders have arrived

Oct 06 2010 Published by under Biology & Environment

Black widow hanging out on my planter

I don't like spiders. I know, deep down, that they are unlikely to hurt me, and that they eat flies and other pesty insects.  Even so, I have a visceral reaction when a  spider crawls into my vicinity. I'm pretty much OK with spiders that stay outside (although stumbling on a big one, like the one Zuska found on her rain barrel might cause me pause1).

But black widow spiders (Latrodectus hesperus) are another  story. They are indeed venomous and their bite is supposed to be quite painful. Just reading about the symptoms makes me cringe:

Severe muscle pain and cramps may develop in the first two hours. Severe cramps are usually first felt in the back, shoulders, abdomen and thighs. Other symptoms include weakness, sweating, headache, anxiety, itching, nausea, vomiting, difficult breathing and increased blood pressure.

But no one in the U.S. has died from a black widow bite in over a decade, so it's not that bad, right?

Fortunately, black widows rarely end up inside the house. Instead they make their webs in dark nooks and crannies, usually only coming out after dark or if they are disturbed.  Their amorphous webs - straight from a haunted house - are pretty easy to spot and sweep away.  They leave me alone and I pretty much leave them alone.

Brown is apparently the "New Black"

But then one of the local newspapers had to run an article ensured to freak me out a bit: "Brown Widows Now in Inland Area"

Brown widows (Latrodectus geometricus) are cousins to the  black widow. They are more drably colored than the black widow, with brown bodies and an orange or yellow hourglass on the abdomen.  Brown widows are originally from  South Africa, and have been working their way west from Florida for the past 10 years or so. Only recently have they appeared in Inland Southern California.

How do brown widow spiders compare to black widows? According to the article:

  • Brown widows are more abundant than black widows. According to Rick Vetter, who studies spiders at UC Riverside, "Where you might find six or seven black widows in a backyard, now you find 100 brown widows."
  • Brown widow venom is twice as toxic as black widow venom.
  • Brown widows live in more open locations - such as under patio chairs and in chain link fences - than black widows

They sound pretty nasty, right?  I'll admit I went out to my patio and made sure there weren't any webs on my plastic patio chairs shortly after reading the article.

But the real story - easy to overlook among all the scary-sounding description2 - is that brown widows are much less likely to bite than black widows, and when they do, they don't inject as much venom. That means that they aren't actually considered to be dangerous.

As the UCR Spider Research site explains:

A South African medical journal reports on the bites of 15 brown widows in humans (Muller 1993) . Only two symptoms of brown widow envenomation were reported in the majority of bite victims: 1) pain while being bitten and 2) a mark where the bite occurred. That's it. Not much more. The bite of the brown widow is about the same as any non-poisonous spider. It hurts and leaves a little mark on the skin. It is no big deal. There are none of the serious, protracted symptoms that one would exhibit when bitten by a black widow.

So the appearance of the brown widow really is good news, at least from the public safety perspective, because they may be displacing the black widow, which is dangerous.

I'll still be happier if I never run in to one.

If you want to help track the spread of the brown widow spider in California, you can mail any brown widows you find outside of San Diego, Orange, or Los Angeles County to Rick Vetter at UC Riverside.

If you are in Los Angeles County, you can also participate in the Los Angeles Spider Survey, sponsored by the Natural History Museum of Los Angeles.


1. Where "pause" means that I get my husband to move it away from any outdoor equipment I want to use.

2. Especially when the article concludes with advice from an entomologist with the National Pest Management Association who advises (not surprisingly) dusting with pesticides or calling an exterminator. "Kill them all" seems a bit over-the-top advice for non-dangerous spiders.

Top image: By me.

Bottom image: thumbnail of graphic from the Press-Enterprise article "Brown Widows Now in Inland Area". Click the thumbnail to see the full-sized image.

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