Stories tagged Life Science


One way to determine the health of an estuary is to test some of its “vital signs”. Important vital signs in rivers and estuaries include things that affect the quality of the water for the health of the various living organisms that call that water home. If there are toxic materials, or even too much of a good thing, like oxygen, organism throughout the food chain can suffer.

One such vital sign can be the development in rivers and estuaries of “red tides”. This term is used to describe large “blooms” of phytoplankton in coastal waters. Phytoplankton are tiny floating plants. They obtain energy through the process of photosynthesis and must therefore live in the well-lit surface layer, where they account for half the photosynthetic activity on our planet. “Red tides” don’t have to be either red or associated with tides, but they concern scientists, because they can produce toxins that can overwhelm other organisms in the water.

Plankton bloom: Plankton bloom flows under Astoria bridge.
Plankton bloom: Plankton bloom flows under Astoria bridge.Courtesy Alex Derr, CMOP

CMOP is studying a plankton bloom that is dominated by one type of organism called Myrionecta rubra. The organism is technically a eukaryotic protist, a single-celled organism that floats in the water column. Under certain environmental conditions, the cells grow exponentially to millions of cells per liter of water within a few days. The cells are red and the shear numbers of them reflect the sun’s light and enhance their red color in the water.

Myrionecta rubra
Myrionecta rubraCourtesy CMOP

CMOP researchers Herfort and Peterson traveled to Astoria to collect samples of the plankton bloom. They gathered samples in both the dense red water and in clear patches of water. These samples helped them compare the conditions in the water and the influences the red tide organism might have on its environment.
CMOP scientists have already analyzed several samples collected during previous year’s blooms. Herfort and Zuber use molecular biology techniques to look at the genetic fingerprints of these organisms and others associated with the bloom. This molecular work is carried out in collaboration with Lee Ann McCue Ph.D., a scientist from Pacific Northwest National Laboratory, who performs genetic sequence analysis. Herfort said, “Our data will improve our understanding of the ecological impact of Myrionecta rubra bloom on the Columbia River estuary.”
Red tide, close-up
Red tide, close-upCourtesy CMOP

Eventually whatever caused the Myrionecta rubra to grow rapidly will change and they will no longer have a source of nutrients. Peterson stated, “When they die, they decompose and bacteria can feed on the decomposed material. This growth of bacteria then draws down the oxygen in the water around them while they are respiring”. So while the bloom itself is not toxic in this case, here’s where another vital sign comes in: the bacteria’s respiration may have a harmful effect to other species, by depleting oxygen available to them. (Due to a great deal of water flow and flushing in the Columbia River, this is currently not a danger.)

What's next?

Unanswered questions that CMOP researchers are exploring include:

  • Is the Myrionecta rubra an important “vital sign” for the estuary?
  • What controls the timing and behavior of the bloom?

The CMOP research team wants to start answering these and other questions by using a combination of physiological studies, molecular work, and observations and simulations from their end-to-end coastal margin observatory (SATURN). They hope this will provide clues about the factors that lead to plankton blooms, and ultimately improve the ability to predict these events.


Pssst!: I think you would look just wonderful in a tiny hat! Also, watch out for ferrrets.
Pssst!: I think you would look just wonderful in a tiny hat! Also, watch out for ferrrets.Courtesy USFWS
According to a scientist at Northern Arizona University, prairie dogs may have the most complex non-human language. That means that this prairie dog (specifically, the Gunnison’s Prairie Dog) may linguistically exceed even dolphins, whales, non-human primates, and box turtles.

But I’ve watched prairie dogs before, and it doesn’t seem like they’ve got a lot going on. What do they even have to talk about?

My assumption would be that they mostly focus on how other prairie dogs would look dressed up in tiny clothes, and what sort of clothes they might wear, and if male prairie dogs would have to wear suits and female prairie dogs would have to wear dresses, or if any prairie dog would be allowed to wear a suit or a dress.

Apparently not.

The scientist, who has been studying prairie dogs for thirty years, says that the rodents have developed their sophisticated “bark” to warn the other members of their colonies about the specific details of approaching predators. The tiny sonic variations of each bark can contain information about what sort of animal is approaching, what color it is, and from which direction it’s coming.

Prairie dogs react to different predator species in different ways. For something like a coyote, they will retreat to the mouth of their burrows and stand up to watch the approaching animal. For a badger, on the other hand, they will “lie low to avoid detection.”

To test his hypothesis about the complexity of prairie dog barks, the scientist recorded barks associated with different predators in a variety of situations, and then observed the behavior of all the members of the colony after the bark was heard. He then replayed those recordings to other prairie dogs when there were no actual predators nearby, and found that they reacted in precisely the same way as the threatened animals.

It’s like if an axe murderer burst into a crowded gymnasium. Someone might shout, “Run! There’s an axe murderer at the door!” and everyone would run away from the door and try to get behind something axe-proof. If, then, you were to shout, “Run! There’s an axe murderer at the door!” into a crowded (but murderer-less) gymnasium, people might still run away from the door to get behind something axe-proof because of the specific information in the warning. It would be a different reaction than if you were to just scream, or if you shouted that acid was raining from the ceiling, or that the world’s biggest clown had was digging up through the floor.

It’s sort of the same with prairie dogs, really.


Yes, of course I'm in a tobacco field: You guys figured out what?! But how? Of course... with a virus! I'll meet you at the tobaccoratory!
Yes, of course I'm in a tobacco field: You guys figured out what?! But how? Of course... with a virus! I'll meet you at the tobaccoratory!Courtesy Lauras512
Yeah, I’ll tell you what it can’t do: it can’t get that stink out of my freakin’ mittens.

But, besides that, tobacco is an interesting plant, and useful for a lot more than giving us cancer and temporary good feelings. Currently, some scientists are thinking that tobacco might be able to give us electricity-producing solar panels too.

It all started one sunny afternoon, when two scientists were lying in an open patch in a tobacco field, holding hands and watching the occasional cloud drift by.

“Isn’t tobacco great?” asked the first scientist.

“Yes,” sighed the second. She had just woven a bracelet from tobacco leaves, and was feeling like there couldn’t be a better plant in the world.

“But, really,” the first continued. “It’s really great.”

“Yes…” said the second, wondering where her colleague was going with the thought.

“Like, it sits here all day, just being tobacco…” started the first scientist.

“Which is great,” interrupted the second scientist.

“Which is great,” agreed the first scientist. Then she went on. “And it’s so good at sitting here, absorbing the sun… I wonder… I wonder…”

“Wonder what?” asked the second scientist, propping herself up on one elbow to look at the other scientist.

“Well, I wonder if we couldn’t use tobacco’s sunlight-gathering abilities to make, you know, solar cells. For electricity.”

The first scientist let herself sink back on to the ground, brushing dirt from the arm of her white lab coat. “You’re drunk,” she said.

“No! Well… maybe a little,” admitted the first scientist. “But I think it could work. Tobacco has evolved to have its chromophores—its sunlight-gathering molecules…”

“I know what a chromophore is,” said the second scientist.

“To have its chromophores very efficiently spaced out in its cells,” the first scientist went on. “If we could just figure out a way to make tobacco produce more chromophores, we could extract them from the plant, and coat solar cells with them. It could be a cheap, environmentally friendly way to make solar panels!”

“But how are we going to entice tobacco to produce more chromophores? By asking politely?” pointed out the second scientist.

“Yeah…” The first scientist frowned. “Yeah, I suppose you’re right. Never mind.”

In the warm air of the sunny tobacco patch, the suggestion was soon forgotten, and the first scientist drifted off to sleep. The second scientist played with the new tobacco bracelet on her wrist, and wrinkled her nose as a gentle gust of wind blew dust through the surrounding plants. She sneezed.

“Wait a second!” The second scientist shook the first scientist awake, looking excited. “What if we infected the tobacco with a virus?”

“What?” asked the first scientist sleepily, having all but forgotten about the idea.

“We could engineer a tobacco virus that would cause the plants to make more chromophores!” She gestured at the field around them. “We could just spray it on the field, like… like… like a giant sneeze!”

The first scientist jerked upright and gripped the second scientist’s shoulders tightly, her expression so intense it was frightening. The green of the tobacco all around them reflected in her eyes, giving her a Bruce Banner-ish, pre-hulk out look. The second scientist shivered.

“You,” whispered the first scientist, “are… a… genius!”

And that’s pretty much how it all went down.

This sort of thing takes time, though, so we shouldn’t expect the big tobacco/solar power juggernaut to get off the couch any time soon. Tobacco’s natural chromophore arrangement makes chains of molecules that could be ideal for absorbing light on solar panels, but they haven’t been made to produce electric current just yet. Once that gets figured out, however, it could lead to cheaper solar cells, with some biodegradable components. (On the other hand, they would likely have a shorter lifespan than other types of solar panels, but, hey, who doesn’t like throwing stuff away now and again?)


hamburger: what is it really made from?
hamburger: what is it really made from?Courtesy PixelAndInk
No fries. I’m watching my diet.

Yeah, I said ammonia burger. Haven’t you heard that your favorite fast food beef gut –bomb was most likely treated with ammonia? It’s not like the teenage fry cook at the burger joint reaches under the counter and grabs the bottle of floor cleaner to splash on a sizzling grill. However, there is still extra ammonia used to treat a ‘portion’ of your burger. Just a little extra ammonia injected during a specially patented process that makes up a percentage of the meat to form a patty. That ‘portion’ is where I think the real story lies.

Over the last few months, the news wires have been releasing stories about this specially patented process, including leading breaks by the New York Times. The stories center on the company, Beef Products Inc. (BPI) located in South Dakota. BPI developed the procedure of treating beef trimmings with ammonia to reduce the presence of harmful bacteria such as salmonella and E. Coli. Some of their main customers include McDonald’s, Burger King, and local food conglomerate Cargill. BPI had performed so well during USDA inspections that by 2007 they were exempted from testing. Its customers have stood firmly by its side. Last summer, things changed when school outbreaks of salmonella resulted in a banning of BPI meat products in some states. The pressure is on the U.S. Department of Agriculture now to investigate any issues.

No one wants to eat meat products contaminated with E. Coli or salmonella. But the whole idea of eating something treated with ammonia just doesn’t sound safe. Was it too many years of Mr. Yuck stickers as a child? I realize ammonia is a naturally occurring substance and can be already present in meats. When I really began to search my inner self about this angst, I found that what truly bothered me was the product being treated. This ammonia process wasn’t used on all beef. Slaughterhouses don’t give the fated bovines an ammonia bath before packaging. This process only is used on beef trimmings. Just say those two words to yourself slowly… pause and contemplate. Beef Trimmings.

raw ground meat?: i'd guess that the pink slime is what holds it together.
raw ground meat?: i'd guess that the pink slime is what holds it together.Courtesy cobalt123
Described by one source as a “pink slime”, trimmings are the last vestiges of muscle tissue left from a good butchering. It has been separated from the ‘majority’ of bone, cartilage and connective tissue. It is then spun by centrifugal force to remove fat, pressed, screened for metal, frozen, chipped, and pressed into 60 pound blocks. In the end, it only need be 12% visible lean tissue to classify as trimmings. The USDA has standards on what constitutes both meat and trimmings. This scrap used to be regulated to pet food and cooking oil. Do we really need to be mixing some into each of our double cheeseburgers? I’d be curious to know what percentage of trimmings makes up that quarter pound patty. Take out the trimmings and we can skip the whole ammonia question.

Recent questions are being plumbed by many parties about these food safety issues. Requests for documents have been met with some resistance by BPI. They seek to block any release of the research done by the Iowa State professor who published supportive findings. Now the courtroom waltzes begin and the delay of answers drags on. I’m certain this won’t be the last we’ve heard of those tasty ammonia treated trimmings.

I think i'll change that order to a chicken sandwich. That's 'free-range' correct?


Alien, immigrant, visitor...: Whatever you want to call them, jaguars are not native to the US.
Alien, immigrant, visitor...: Whatever you want to call them, jaguars are not native to the US.Courtesy Joachim S. Mueller

I’m not sure where to put this one. On the one hand, we’ve had a long discussion on the dangers of introducing non-native species into America’s wild habitats. That was about cheetahs; this is about jaguars; but the idea (a bad one) remains the same.

OTOH, Bryan wants us to keep track of scientific decisions made by the administration, to make sure they hold to the pledge made in Obama’s inaugural address to base scientific decisions on scientific observation and data. This story could certainly go there as well.

Since I can’t make up my mind, I may as well start a new thread:

US Fish and Wildlife Service ignores scientists, takes initial steps toward introducing non-native jaguars into US.


Elysia chlorotica: You think you're so special, don't you?
Elysia chlorotica: You think you're so special, don't you?Courtesy lauredhel
Some of you may already know my feelings on mollusks. In short, I’m against them.

It’s not that I necessarily want them all exterminated, or anything. It’s just that mollusks, with their tentacles and beaks and pseudopodia and large brains, freak my Schmidt out. And I tend to live under a “you’re either with us or against us” credo, and mollusks obviously aren’t “with us.” (They aren’t with me, anyway. Frankly, most things aren’t.)

But I get by. I know that there are mollusks out there, doing… I don’t know what. Probably something utterly horrible. But we leave each other alone, and more or less leave it at that. It’s a workable arrangement.

Now and again, however, a mollusk stretches its squishy neck out and, by its very existence, makes cracks in the already fragile JGordon/Mollusca peace. It’s like the cold war, really—if one side does something strange, or develops a fantastic new piece of technology, the other side gets a little nervous. So, naturally, I’m a little cagey about this news:

There’s a marine slug (a mollusk, of course, that feeds itself through photosynthesis.

Are you kidding me? I’m all, “I think I’ve got chronic anxiety!” and this lousy slug is like, “That’s too bad. Also, I feed myself with sunlight.” I can’t even get groceries because my car battery died (there’s a very scary tree near my bus stop, so that’s out), and this little jerk is a phototroph. If I had laser eyes, or something, the situation would be a little more balanced, but last time I checked I didn’t have laser eyes.

I have to give it to the slug, though—it’s a pretty neat trick. Early in its approximately one-year-long lifecycle, the slug eats some photosynthetic algae. From that point on, the slug is photosynthetic; it feeds itself by using sunlight to convert CO2 and water into sugar, just like plants do. What’s more, the photosynthesis isn’t being performed by algae inside the slug (some organisms, like lichen contain algae, which feeds them). The slug itself has genes for photosynthesis, and the photosynthesizing genes from the algae are just required to kick-start the slug’s own abilities. And then, BAM, a photosynthetic animal.

The leaf-shaped slug, which lives in salty swamps in Eastern Canada and grows to be about an inch long, is remarkable not only for its photosynthetic abilities, but also for something unique in the process written above. Getting those kick-starting genes from the algae requires gene transfer. Passing genes from one species to another is a rare and complicated thing, but some microscopic, single-celled organisms have been known to do it. This is the first time gene transfer has been observed between two multi-cellular organisms (the slug and the algae, of course).

Aside from being, well, just sort of weird, the slug’s gene transferring abilities might turn out to be useful in the future of gene therapy, where new genes are inserted into cells to combat diseases. A practical application whatever transferring mechanism the slug and algae use is a long way off, though. And, anyway, I’ll be damned if I ever use anything that came from a mollusk.


How does food matter to human evolution? We could ask this guy?
How does food matter to human evolution? We could ask this guy?Courtesy Lord Jim
What makes human beings so special? How did we evolve into an agriculture-developing, city-building, history-making, world-changing species that can live on every continent and even in outer space?

Scientists have been asking questions about our evolutionary trajectory and human "uniqueness" for as long as there's been science - and guess what? We still don't know the answer! Some of our best theories are explored by anthropologists in the PBS television series The Human Spark, airing throughout the month and also online at the PBS website. If you're curious, you might want to watch, but don't do it on an empty stomach! Many of the theories that anthropologists have developed to explain how we became human involve food.

That food and evolution would go hand in hand is not really surprising, since food is necessary to survival and an important and dynamic part of our environment. Did a search for nutritious plants and animals lead our ancestors to new environments, causing our species to adapt and change? Did hunting and eating meat mean the evolution of new physical characteristics? How has agriculture changed our environment and species over time? How will present and future foods change what it means to be human in the future?

Some evolutionary theories involving food look not just at what we ate, but how we ate it - namely the invention of fire and the use of heat to cook food. Think about it: our Hominid ancestors needed calories in order to develop into the big-brained humans we all know and love. How did they do it? And what did this mean for human evolution?

Sure, eating meat was an important dietary step, but cooking root vegetables can transform hard-to-chew or even poisonous plant parts into nutritious food that can be consumed out of season. With cooking, environments that would otherwise provide few nutritious options suddenly become bountiful. This change in diet may also have led to changes in body size and shape - even social structures! Large teeth and jaws were less desirable once food could be more easily chewed, and delaying the gratification of food until it could be cooked may also have meant that our species had to develop new social skills.

Those social skills - the same ones that mean you and I can now share a burger or beer without fighting each other for scraps - may be one of many "sparks" that makes us human.

If you live in the Twin Cities, you can meet an anthropologist and here how he thinks food impacted human evolution by attending tonight's Cafe Scientifique program in Minneapolis.


Retina as indicator of disease: This is not exactly what the optician will see when s/he examines your eye...that would be too easy.
Retina as indicator of disease: This is not exactly what the optician will see when s/he examines your eye...that would be too easy.Courtesy Cayusa
Alzheimer’s disease, that is. A technique developed by researchers at University College London (UCL), located on Repetitious Redundant Lane, allows your optician to not only find the proper lens prescription, but also screen you for early stages of Alzheimer’s disease. Their method takes advantage of the fact that the cells in the retina (the light-sensitive lining in the back of the eye) are direct extensions of the brain. As shown in the picture below, the retina is continuous with the optic nerve (also known as cranial nerve II), which then leads straight into the brain. The UCL researchers have found that the amount of retinal cell damage corresponds directly to the amount brain cell deterioration. They have also identified a particular pattern of retinal damage that is characteristic of Alzheimer’s patients.

Relation of the eyes to the optic nerve: Here you can see how closely connected the retinas (the back of the purple blobs) are to the optic nerve, and to the brain.
Relation of the eyes to the optic nerve: Here you can see how closely connected the retinas (the back of the purple blobs) are to the optic nerve, and to the brain.Courtesy William Vroman
The way to measure this damage simply involves using special eye drops that highlight dying retinal cells. Your optician can then observe the extent and configuration of the deterioration. Research shows that cells start to die ten to 20 years before Alzheimer’s symptoms start to surface, so this procedure could be used to diagnose the disease in its early stages. This test would be quick, easy, and inexpensive, and being able to detect the disease early would allow doctors to treat, and possibly reverse the symptoms of this disease.

So far, the researchers have only tested this technique on mice, but they will start to test human subjects in the near future. According to UCL, you might be able to receive this test within the next five years. However, there are some reasons that people might not want to screen themselves. There is fear that insurance companies could increase the premiums of middle aged people who test positive. There are also people who would just rather not know they may have this devastating disease in their future. How about you? Would you want to know?


WaveLengths, the award-winning public television program from Arizona Public Media updates viewers on what was once the most talked-about experiment in the world--the Biosphere 2 in Oracle, Arizona.

Biosphere 2: New TV program takes you inside Biosphere 2.
Biosphere 2: New TV program takes you inside Biosphere 2.Courtesy Biosphere 2

"WaveLengths: Planet in a Bottle" revisits the famous life sciences laboratory to learn about the research currently being conducted inside, and exactly how it can help find answers to environmental questions arising in the new millennium. This new episode of WaveLengths includes research and work televised for the very first time.

(See a preview here.)

"WaveLengths: Planet in a Bottle" premieres Monday, January 18 at 6:30pm on PBS-HD Channel 6.

Segments include:
  • Two years and 20 minutes: Jayne Poynter is one of eight "Biospherians" who were sealed inside the artificial environment for a little over two years. Poynter talks about the challenges the team faced as they grew their own food and recycled their air and water within the immense greenhouse. The problems with living extensively in a sealed environment, says Poynter, were not all environment-related.
  • Biosphere 2's future: The management of this unique structure and its surrounding campus was assumed by The University of Arizona in 2007 now scientists from Arizona and around the world use this remarkable facility to find solutions for understanding climate change and other global problems that threaten the planet. WaveLengths Host Dr. Vicki Chandler takes a walk with Biosphere 2 Director Travis Huxman to talk about the relevancy of the new research going on in the largest sealed facility on Earth.
  • High tech rainforest: How are plants and forests responding to the changing environmental conditions on Earth? Dr. Kolbe Jardine is one researcher using a hi-tech chemistry lab in conjunction with Biosphere 2's rainforest biome to learn more about plant interactions.
  • Critical ocean viruses: The invisible life of the ocean--its microbes--is as critical to other ocean life as plants and trees are to the land. The artificial ocean of Biosphere 2 is now helping scientists discover what kind of impact climate change can have on the ocean's microbial life. Researcher Matt Sullivan is focusing on this invisible life to help us better understand the crucial role it plays in ocean productivity, and the overall health of our planet.
  • Climate change and vegetation shifts: Some regions in North America are seeing rapid vegetation transformations because of invasive species. Here in the Southwest, the invasion of the non-native bufflegrass could change our desert landscape forever, and a better understanding of why these changes are taking place in relation to climate change is happening inside Biosphere 2.