Friday, March 15, 2013

Long-Term Thinking of Cockatoos

The concept of self-control has always been one we humans tend to pride on being uniquely ours. We lump most animals into the category of being subject to instinctual desires, with little in the way of preventing themselves from acting on impulse. The truth, however, is far different and far more interesting.

An experiment was done recently wherein a group of Goffin cockatoos were given a sample of food, with the promise of a greater amount of food later on provided they did not eat the food currently in front of them. Nearly all of the tested bird resisted the food they had currently, even when it was placed directly in their mouths, in favor of the future reward. Such long-term thinking was thought to only have been exhibited in humans, and in fact the data from the cockatoos might suggest performance on par with the average human child.

While it is definitely interesting simply to look at a very intelligent animal, it also brings up much of the anthropocentrism present in the scientific world at large. If we know now that a trait we thought distinctly human turns out not to be, what other potential "human" characteristics are actually some of those shared with numerous other organisms on this planet.

The Eagleman Stag

I was saving this post for the end of the quarter because of what it deals with.Our ever shortening time is only made apparent to us at the very end of things. And as we approach the end of this quarter, and for most of you, your first year here, the idea of starting over is at least interesting. I guess it's not biology, but it's a biologists approach to some sort of theology.

Thursday, March 14, 2013


Call me TED obsessed, but some of these videos are super cool. Stewart Brand, formerly an internet developer, is now backing the biotech industry push for the use of cloning to reintroduce extinct species. While many think that this research is unethical due to the nature of human intervention, Brand argues that human intervention is what caused these species to go extinct in the first place (giving the example of the American Passenger Pigeon). Furthermore, he focuses on reintroducing key species to environments devastated by their loss.

Pulling together many examples of recently extinct animals (whose tissues and DNA have been frozen or preserved), Brand forms a pretty comprehensive study of the entire field. He quotes research being done by several members of a team that he and his wife assembled, all working towards the common goal of de-extinction through biotechnology and cloning.

If you're still not convinced, then check out the footage of the Thylacine (Tasmanian Tiger) at about 3:08. How awesome is that? (I want one)

Stewart Brand: The dawn of de-extinction. Are you ready?

Mutant Frogs

Researchers from Tufts university have found that tadpoles that have eyes grafted to their tails can actually use them and in some cases retain them into adulthood despite the disappearance of their tails.  This finding goes to show the extraordinary degree of brain and nerve plasticity present in vertebrates which could have implications in our understanding of evolution (namely the degree to which animals are prepared to deal with mutation).

The article is here.

The World's Strangest Ecosystem

If you could think of the largest and most diverse ecosystem on the planet, what is the first thought that comes to mind? Tropical environments, such as rainforests or reefs, might be the most prevalent answer, but new research indicates that it might not be the right one. Scientists discovered, after analyzing buried continental crust off the coast of Washington, that the sea floor is home to a diverse array of microbes all responsible for chemosynthesis (i.e., the production of energy from inorganic substances), specifically with carbon dioxide. Additionally, given how much of buried crust is in the ocean, this could be one of the largest ecosystems in the world.

While this definitely has implications as a potential carbon sink for the anthropogenic emissions of carbon, it also raises some other key questions. Namely, the fact that these wide hose of organisms can survive in a habitat that is relatively deprived of both oxygen and light, which could hold astounding implications for potential life both on Earth and across the cosmos. It seems that the (somewhat) old adage is true that "life finds a way."

Growing Back Adult Teeth!

Hey everyone! Play any hockey lately? Crash on your bike? Well, if you've done any of those things and lost some teeth in the process, all hope is not lost! Check out this article on scientists growing new adult teeth: Teasing Out New Teeth

The researchers have been able to take the cells taken from the gums of an adult human and combine them with cells taken from the molars of fetal mice and grow new teeth. However, they're still not ready to use this method clinically, so keep your teeth safe! (at least for a few more years)

To the Bat-Cave...or not

I thought I'd make me last post about White-Nose Syndrome; even though I mentioned it in an earlier post, I think it's a really important issue and everyone should know about it because it's going to start affecting all of us in the near future. A lot of this text is from a presentation I did a few years ago in Maine, so feel free to skim if it's too long.
There are 45 species of bat in North America, and more than 1,000 in the world. Bats live on every continent except Antarctica. White-Nose Syndrome is caused by the fungal pathogen Geomyces destructans, and is identifiable in hibernating bats by a white, fuzzy fungal growth on the bat's nose, ears, and wing membranes. The fungus can also cause skin ulcers or lesions, and thrives in darkness, high humidity, and low temperature (below 20 degrees Celsius), the conditions found in bat hibernaculums. 

When bats hibernate, they slow their metabolism and lower their body temperature to within a few degrees of ambient cave temperature; in this state, their immune system is weakened, and their inability to fight off infection makes them ideal hosts. Rather than causing the collapse of internal organ systems like most pathogens, Geomyces manifests as a skin infection that becomes a chronic disturbance during hibernation. A bat's wings make up about 85% of the surface area of its body and are used in important procedures like body temperature regulation, blood pressure and gas exchange, as well as flying and feeding. The fungus leeches water out of an infected bat's wing tissue, causing it to wake up early due to thirst. Although bats periodically wake up from hibernation to drink, this process burns up to 90% of a bat's fat reserves. If they have to wake up with greater frequency, they can become emaciated. An infected bat burns all of its fat reserves trying to fight off the fungus, and must either leave the cave to hunt for food before there are enough insects out to sustain it, or starve to death inside.

White-Nose Syndrome was discovered in Howe's Cave in Albany, NY in 2008; within the year it had spread to other caves in New York State, Connecticut, Massachusetts and Vermont with an infection rate of 90%. By 2009 it had reached New Hampshire, Pennsylvania, New Jersey, Virginia and West Virginia, and by March of 2010, it had been found in Tennessee and Oklahoma, all the way up into Ontario, Quebec and New Brunswick. As of this year the disease has killed over one million bats, spread to 19 states and 4 Canadian provinces, and continues to move westward. Howe's Cave is visited by tens of thousands of tourists each year and the disease has grown outwards in a way that suggests Geomyces might be an exotic species recently introduced to the U.S., but researchers don’t know if this is the case or if it was already present and began infecting bats for some other reason. WNS cannot spread to humans, but we are active transmitters of it: the fungus can hitch a ride on caving equipment or visitors’ clothes, but can also be spread by bat species that don’t return to the same cave every winter. The fungus can survive in dead bats on the floor of the cave, and doesn't die with its host like most parasites. Similar fungal growth on bats has been documented in Europe, but without the subsequent mortality levels. WNS could potentially have come from Europe, where Old-World bats had developed an immunity to it over thousands of years and infected New-World bats, who had no resistance to the disease, or the fungus could have been present in North America all along, but only recently mutated to infect bats in this way. 

Some of the species affected include big and little brown bats, eastern pipistrelles, northern long-eared bats, Virginia big-eared bats, Indiana bats, and gray bats. The latter three are federally listed endangered species, but all North American bat populations are vulnerable. Most species have an average lifespan of 10-20 years, with only a single offspring per year; infant mortality rate is very high and around 50% of baby bats die during their first winter. A majority of the hundreds of thousands of hibernating bats in New York state inhabit just five caves, and half of the 52,000 Indiana bats that winter in New York return to just one abandoned mine that is now infected with WNS. In addition to their low rate of reproduction, bats migrate hundreds of miles to their summer ranges and can easily spread the infection to other populations along the way. Bat populations don't fluctuate over long periods of times, and it is unlikely that they will recover from such a drastic decline. 

Why should we care about bats? For starters, insectivorous bats have a huge economic value, saving farmers an average of 74 dollars per acre of cropland in the U.S. that would otherwise be sprayed with expensive and toxic insecticides. A single bat eats its own weight in insects every night - about 3,000 mosquitoes that might otherwise spread diseases like West Nile. Bats suppress insect populations, pollinate flowers and disperse seeds, and are overall crucial to maintaining a healthy ecosystem in both agricultural and forestry sectors. Recently, a study was done on the effect of bats on agriculture in Ohio; if WNS continues to kill bats throughout the U.S., farmers in Ohio could suffer losses of anywhere from $740 million to $1.7 billion, depending on how many bats the state loses. In parts of Texas, the estimated value of bats in controlling cotton pests is $1.7 million per year. The estimated total economic value of bats to U.S. agriculture (and potential losses due to WNS) ranges from a low of $3.7 billion to a high of $53 billion.

In an effort to reduce human transmission of the disease, there has been a voluntary moratorium on caving activities in the infected areas; some unaffected states have closed caves in known bat habitat as a preventative measure. Government funding for research of the disease is quite modest, but scientists are trying to find a cure. Captive breeding might become the only option to preserve species severely affected by WNS. Unless we take action, most of our native cave-hibernating bat species could go extinct within a decade. 

Small Fish and Coastal Carbon Cycles

You may not think that small fish such as anchovies- and their poop- can have a big impact on coastal ecology and food webs. A major characteristic of temperate coastal ecosystems is upwelling, where cold water from the open ocean moves to shallower water along the coast, bringing important nutrients with it. One of the transported molecules is carbon dioxide: algae at the ocean’s surface live in nutrient rich waters from upwelling (they need a combination of light and nutrients). They are consumed by copepods and other zooplankton, which are in turn consumed by “small forage fish” such as anchovies. Their fecal matter, which is rich in carbon, sinks into the deep sea, where it doesn’t work as a greenhouse gas to warm the planet. Scientists from Rutgers University and the Virginia Institute of Marine Science examined the sinking rates and contents of fecal matter of small forage fish in the Santa Barbara Channel. They found that pellets sink at a rate of about 2500 feet/day and that they contain up to 22 micrograms of carbon per pellet. When high numbers of forage fish gather in areas like the SB channel to feed, the rate of carbon fixation increases dramatically, up to as much as 251 mg per square meter per day.

The results of their study have important implications for many coastal areas with lots of upwelling, including the western coasts of North South America. The implications of changing ecosystems through fishing (especially the large-scale Anchovy fisheries of the west coast of Peru, which have suffered large declines and population “crashes” over the last 30 years) may be both larger than expected and have implications beyond the imagining of most scientists. Perhaps a fish-free diet may be one of the most effective ways to “go green” as our understanding of coastal and fishery ecology continues to change.

Procrastination... for science!

Just in time for finals, here are some really cool examples of the interface between cloud computing and biological research (they’re addictive!)

Zooniverse is a grouping of projects that require massive data analysis. From space rocks to the seafloor, you can record data in pieces of images by marking features and locations. There are several projects analyzing space data, such as measuring explosions on the sun, one looking at most of the Western North Atlantic coastal seafloor, and another measuring recorded bat and whale calls. Check out the different projects: they’re hosted by a wide range of universities but they all have taken an innovative approach to data analysis (instead of having undergrads do it!).

There’s also eteRNA, a project designed by researchers looking to create a “large-scale library of synthetic RNA designs.” EteRNA takes the form of a puzzle game, but uses real experimental results to give the player feedback on the functionality of their puzzle. According to the site, many of the “puzzle” processes for determining RNA structures could be done with a computer, but cloud sourcing is faster and more efficient. The eventual goal of eteRNA is to use large groups of people to independently design, test, and make (digitally) their own projects. The site envisions nanotechnology projects such as “the first RNA random-access memory” for computing and nanomotors and LED displays.

Black Bat Flower


While researching the genus Tacca, which contains many fascinating examples of flower diversity and evolution, I found an interesting article about the biomedical applications of the plant. This is the Black Bat Flower, Tacca chantrieri. There are 30 other species in the genus. T. chantrieri is found primarily in Asia, specifically China, Indochina, and Malaysia. I was originally looking at this species as an interesting example of pollination specialization: it’s pollinated by flies.
However, it also contains very potent toxins that may have biomedical applications as cancer-fighting drugs. An important chemotherapy drug, Taxol, is derived from the Yew family. It’s a microtubule stabilizer, meaning that it freezes intercellular microtubules that are vital to cellular processes. This kills both healthy and cancerous cells. Also, the body can eventually build up cellular resistance to Taxol, and it is potentially toxic at high doses. Scientists from the University of Texas have been isolating substances from the Bat Flower in hopes of finding a better, plant-derived alternative. Now, a substance has been found with the same properties as Taxol that can specifically target cancerous cells. This property has been observed in other plant-derived cancer drugs, but this is the first drug with the same potency- and fewer harmful effects- as Taxol. The team also discovered exactly how the taccalonolides interact with microtubules and target cancer cells specifically. In terms of the plant’s biology, these toxins may be partly responsible for the low rates of cancer (and mutation) in plants.

Pulling bacteria apart: antibacterial nanopillars

The first natural surface to kill bacteria solely through structure was recently found.

How does one kill bacteria through structure you might ask. Well, the clanger cicada (a locust-like insect) has wings covered in an array of "nanopillars" which serve to stretch the bacteria's membrane and cause ruptures in the bacteria's membrane.

One of the lead researchers said the rupturing effect is more like "the stretching of an elastic sheet of some kind, such as a latex glove"

Kinda cool eyh?

Check out the article and the corresponding videos here: Insect wings shred bacteria to pieces

For added effect couple the video on the article with the Jaw's theme song

But seriously. Do it.

Retiring Chimpanzees

This January, a group of chimpanzees previously used for medical research retired in their new home, Chimp Haven, located in Louisiana. For many of these chimpanzees, it was the first time stepping outdoors and walking around in a natural setting. Some of them had been in labs for more than 5o years, so they were awed and confounded when they were released. Watch the footage of this heart-touching moment below.

For now a total of 110 chimpanzees will retire to Chimp Haven, while the NIH continues to review 450 other chimpanzees. According a recent article, 400 will be sent to various sanctuaries, but 50 may be kept for future medical research. As one would expect, this a controversial topic among researchers as well as the public. Some believe that the chimpanzees should no longer be used for research, while others think they are crucial for medical trials since they are so closely related to humans. The NIH is expecting to make a decision by the end of March, and are willing to accept comments on the chimp plans here until the 23rd.
Sorry I didn't want to give away my presentation so I held off on making my blog post. But here is the link to the paper I read. It's really interesting to look specifically into the differences they found within the UV patterns and the diets of the caterpillars; I just discussed it very briefly in my presentation. It also talks about some of the photographic techniques used to take these pictures which is also sort of intriguing.

Also here's a kind of strange video that talks a little bit more about the UV butterfly patterns and has some really nice pictures of them.


Wednesday, March 13, 2013

Bug BioEngineering: a defense against other "bugs"

Recently it has been discovered that cicadas wings aren't bacteria free due too chemicals, but instead use a clever piece of engineering to prevent the pesky pests from living on their wings.  The cicadas have nano-pillars on their wings that are the same size as the bacteria and as the bacteria settle the nano-pillars stretch the bacteria causing it to rupture.

Breath Test for Stomach Cancer

 An Israeli and Chinese team has developed new test to detect stomach cancer by analyzing patient's breath.  This test, which is still in its early stages, could make the diagnosis of gastric cancer much easier.  The ease of diagnosis is critical because as of now,  80% of people treated for stomach cancer receive their diagnosis too late for surgery.  The simplicity of this device also makes it ideal for use in developing countries where doctors and endoscopic devices are scarce.
We should probably rethink the way we judge things now that even breathalyzers can be used to further the good of humankind.  To quote Bill Watterson "there's treasure everywhere."
For the full paper click here.

Female Butterflies can Smell if a Male Butterfly is Inbred!

When animals breed with a relative, their offspring are more likely to have genetic disorders.  The disorders cause inbred males to be weaker, and less able to defend himself and others.  Natural selection tells us that in order for the female to ensure the highest chance of survival for her offspring, she is expected to avoid mating with a weak male, provided the fact that she is able to distinguish between a male who is inbred or not.
Previous studies have shown that the mating success of a male butterfly is lower if they are inbred.  But this leaves the question of how the females can distinguish which males to avoid.  New research has revealed that inbred male butterflies produce much less sex pheromones than "normal" ones, making them less attractive to females.

One of the researchers, Erik van Bergen, explained that traits used by males to attract females are often strongly affected by inbreeding.  "For example, inbred male zebra finches produce a lower number of different individual songs and inbred male guppies have less conspicuous colour patterns.  Additionally, in one cricket species, the inbred males are known to produce less acoustic signals while trying to attract females."

For the butterfly pictured above, Bicyclus anynana, it is crucial that the female avoids breeding with an inbred male, due to the fact that approximately 50 percent of inbred males are sterile.  Should the female mate with a sterile male, none of her eggs will hatch and she will not produce offspring.
Butterflies were put in the same area in order to ensure inbreeding.  The scientists marked the genitals of the males with fluorescent dust of different colors to indicate inbred and outbred males.  During mating, the dust is transferred to the female, which can be detected using UV light.  The antennae of several females were then painted over with nail polish in order to prevent them from detecting the amount of sex pheromones produced by the males.

The researchers found that the females with covered antennae, had no preference for males and therefore mated with inbred and normal males equally.  The females with uncovered antennae, however, mated significantly more often with normal males.

Van Bergen added, "We know that inbreeding contributes to the decline and eventual extinction of small and isolated populations, so it is valuable to have more knowledge about the processes involved in general."

Foolish Seedling Disease

This is purely for the sake of humor, but Foolish Seedling Disease in rice, caused by a surplus of gibberellic acid from the metabolism of the fungus Gibberella fujikuroi, is known as "bakanae" in Japanese. This phrase also translates to "thin noodle seedling" or "stupid rice crop", both apt descriptions of the disease.


New York City has its own bee! Lasioglossum gotham, pictured above, was discovered in 2011 by Jason Gibbs, along with 10 other new species of bee first identified in the New York and Brooklyn Botanical Gardens. 

While a drastic decline in hive populations of North American honey bees due to Colony Collapse Disorder has received a lot of attention in the past few years, many people don't realize that new species of bee are still being discovered at an astounding rate, even in one of the country's most urban areas. New York City alone is home to more than 250 species of bee; “natural areas like urban parks and rooftop and botanical gardens," said Gibbs in an interview with AMNH, "provide the nesting sites and floral diversity that bees need.”

Many of the new species were described by comparison with museum catalogs; if you're interested in learning more about them, you can visit this database on known bee species of the world, or this New York Times article, with comments from Rev. Jeremiah Lott Zabriskie, the famous Brooklyn entomologist who originally called Gibbs' attention to these new species by sending him a specimen of L. katherinae.

Robot Bees!

"Autonomous robot bugs sound like creatures from a sci-fi flick, but they could be a reality very soon."

Both troubling and exciting, it looks like scientists want to solve the problem of the declining bee population by introducing robotic bees to act as pollinators. There's no telling what effect this would have on an ecosystem, and it would be scary and interesting to find out how this would impact natural selection in an environment with these man-made pollinators.

Let there be sight!

Last quarter, several of us attended the keynote lecture for the grand-opening of UCSB's Center for Stem Cell Biology and Engineering (there were some good refreshments afterwards). For those of you who missed it, Professor Mark Humayun from USC discussed two promising areas of research for restoring sight in patients suffering from macular degeneration: retinal prosthetic implants and stem cell therapy.
In addition to Humayun's research, this article discusses the work done by UCSB's Dennis Clegg and lots of other scientists in the field. Very cool stuff!

Vision Quest: Futuristic Fixes That Could Help the Blind See Again

Closer to us than we may think

Chimpanzees have long been considered one of the closest species to our own and recent insight into chimp society has further pushed the association.  A gang of chimpanzees were captured on video overtaking their alpha male.  This was spurred after the second-ranking male fled a fight with the alpha male and "four others charged and beat" the alpha male.

Wilson says "male chimps compete for access to small numbers of females, so they have an incentive to kill each other. But rival groups sometimes attack them, so they also have a reason to keep their fellow males around for support. It is a trade-off. Kaburu says Pimu's group did not have close neighbours, so the other males may have been less worried about outside threats."

Watch the interview of the event here:
Read the whole article here: Gang of chimanzees kill their alpha male

How To Save a Life... Or Not

It's the microbial invasion!!!
For some time, there has been talk about how antibiotics could no longer be a viable method of preventing infection. In the article, Analysis: Antibiotic Apocalype, the author, James Gallaghar, starts off by stating:

"A terrible future could be on the horizon, a future which rips one of the greatest tools of medicine out of the hands of doctors."

Can't you imagine Morgan Freeman saying that in the beginning of a sci-fi film? But in all seriousness, it's really hard to imagine a world in which a common cold could kill you. Not that it can't already. If the cold is left untreated, your immune system is weak and the environmental conditions are less than ideal, then yes, a cold could really kill you. But in many parts of the world, aside from third-world countries, it is rather easy to obtain antibiotics to cure the cold. And to boot, if the common cold could kill you, then what about other things like surgeries or births or anything that exposes the insides to the outsides? The bacteria could really have a hayday.

So, why didn't we do anything about it? Sir Alexander Fleming, the discoverer of penicillin, already warned us about microbial resistance ages ago, during his Noble Prize speech:

"It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body. The time may come when penicillin can be bought by anyone in the shops. Then there is a danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug, make them resistant."

Clearly, this is a difficult task to take on. If we increase the amount of antibiotics that are used, we could easily kill not only ourselves, but empower the bacteria to be immune to even higher doses of the antibiotic.

So, what to do? Well, the article doesn't provide much insight into what research is being conducted to trying and overcome this problem. So much for preventative measures.

I know that this post just made you feel all warm and fuzzy inside, but on a brighter note, this could be a really interesting research topic if there is not a lot of work being done on it. And I'm sure that a lot of drug companies could pay boatloads of money for this research to be done, if it isn't already going on.

How's This for Intimidation?

This frog creates one of the most adorable squeaking sounds. Although this noise tends to make people smile or laugh, it's real function is to deter predators from eating this tiny two inch Namaqua Rain Frog.  In addition to the sounds it makes this frog is also able to inflate its body as another form of intimidation to predators. Hopefully viewing an adorable little frog can help alleviate some of that dead week stress!

The Woman Behind HeLa

Henrietta Lacks was diagnosed with cervical cancer in the 1950s. During the course of her treatments at John Hopkins a sample of her tumor was taken and grown in culture. At the time Dr. Gey was doing research at John Hopkins with the hopes of creating the first immortal cell line. Most cultured cells would die out after a short period of time, limiting their usefulness. Henrietta's did not. Her cancer cells gave birth to the first immortal cell line known as HeLa.

HeLa cells are currently used in research labs across the globe and their use has allowed for many significant scientific discoveries. Many companies got started producing HeLa cells, and vials of cells continue to be sold today.  However Henrietta received nothing, not even basic acknowledgement. Her family lived on unable to afford even basic health care and completely unaware the HeLa existed, or was in fact Henrietta's cells. Henrietta finally received full acknowledgment when her story was told in The Immortal Life of Henrietta Lacks by Rebecca Skloot. The creation of HeLa and it's use in the scientific community raised many questions about issues such as consent, biological ownership, and many others. Her story functions as a reminder that, especially as scientists and researchers, we have a responsibility to understand and take into account the ethical implications of our actions. If you have a chance I highly recommend reading the book, it is very well written and thought provoking.

Skloot, Rebecca. The Immortal Life of Henrietta Lacks. New York: Crown, 2010. Print.

Telomeres and Life Expectancy

(Credit: NHGRI)

Did you ever want to know how much life you have left to live?

I certainly don't, its a threatening thing to know and it takes all the excitement out of death. Nevertheless, scientists have discovered a link between the length of your telomeres and life expectancy. Telomeres protect the coding sections of DNA by providing a buffer zone to be cut slightly shorter each time a cell divides. When the whole telomere is used, the cell stops dividing and just gets older, eventually degrading whatever body system it is a part of.

A 20 year long study by a team from the University of East Anglia is looking at a population of Warblers on an isolated island with no predators. They are measuring the lengths of the birds telomeres as well as their life expectancy. While findings display a correlation, it isn't strong enough to predict the life of any one individual with accuracy.

Why can't we give the life expectancy of just one warbler? To give an analogy, think of two hourglasses. While looking at the amount of sand in the top of the two hourglasses we can approximate how much is left for them; yet the size of the opening in one hourglass may differ from the other, and will take a different amount of time to drain its sand. In other words, individuals may vary in the amount of oxidative stress they are subjected to during life, and these oxidants can accelerate the degradation of telomeres.

In November, the East Angia researchers stated that "It would be virtually impossible to do such a study in humans. For one thing it would take a very long time to study a human lifespan. Also in humans we would normally, quite rightly, intervene in cases of disease, so it wouldn't be a natural study" (Dr. Richardson).

But unfortunately, they were completely wrong, as a study published last week from Salt Lake City proved that in heart disease and stroke patients, telomere length is indeed a strong predictor of survival time for the patients. The researchers also stated smoking, pollution, and lack of exercise as ways to hasten telomere shortening. 


Conditions Once Suited for Ancient Life on Mars

What everyone has thought for years has now been confirmed!

Mars once had conditions that, at one time or another, may have been a home for... (wait for it).. Life!

On Tuesday NASA scientist confirmed the NASA rover Curiosity found key chemicals necessary for life near an ancient stream bed. The findings also included evidence of multiple periods of wet conditions on mars since we assume life on Mars would need water.

Whether or not life (probably microbes) exist[ed] on Mars is still a popular and heated debate but alas we know it could have existed.


Read the full article here: "NASA Rover Finds Conditions Once Suited for Ancient Life on Mars"

Clogged Arteries Still Prevalent in Ancient World

"Mummies Reveal That Clogged Arteries Plagued Ancient World"

"Scans suggest there's more to heart disease than a modern diet."

Interesting article about clogged arteries being as prevalent of a problem in Ancient Egypt as they are today. Turns out, being on a hunter-gatherer diet doesn't help out your arteries as much as we thought it might.

You may ask, "Aren't the mummies they're inspecting the royal families who must be exercising less and eating fattier foods?" Well, recent findings have shown that even the common men and women had the same problems. The data does, however, point out that the clogged arteries were caused by different factors than they are today, so it's still probably not a great idea to pay too many visits to McDonald's.

Tuesday, March 12, 2013

Drink a little bit, and live a little bit... longer

What if i told you that consuming your favorite pinot is the same as drinking from the fountain of youth?  You would probably think I was a little crazy, but don't tell that to Harvard's David Sinclair.  Sinclair recently discovered that resveratrol which is present in wine, directly leads to the activation of protien, SIRT1 which will help  you live a more healthy and long life.  Of course Sinclair also notes that there soon will be more practical and powerful compounds which act in a similar way to resveratrol, but in the mean time enjoy your fruity beverage(responsibly) and live a longer and healthier life!

Article can be found here

The Man in the Cave

During our discussion of circadian rhythms, an experiment involving the determination of the natural human circadian rhythm was mentioned. The scientist behind this experiment was Michel Siffre, who spent two months completely isolated in an underground cave. Following his personal isolation he performed similar experiments to try and determine the natural circadian rhythm of humans.
       His personal experience illustrated a rhythm a  little longer than 24 hours, between 24.5 and 25. However, his further experiments and those of others demonstrated people falling into a 48 hour cycle.

In an interview with Cabinet magazine, Siffre pointed out

"The forty-eight-hour cycle is a fact. I observed this phenomenon, and I’m sure of this finding, but nobody understands what could be responsible for such a large desynchronization of the sleep-wake cycle"

Further studies of this type have been ceased due to the ethical issues involved with isolating a person in a cave for extended periods of time with limited contact.

The interview with Siffre can be found here.

No Skull? No Problem!

We have compiled an interesting record of things that people have been able to make using 3-D printers and there seems to be something else added to that list every day.  The newest addition: prosthetic skulls.  While replacing pieces of a damaged skull is not really new (think Master and Commander), a recent surgery performed last Monday used a 3-d printed implant to replace seventy-five percent of a man’s skull. While details (including the kind of events that make it necessary to replace three-fourths of one’s skull) are not abundant yet, the article can be found here.

Smell the Roses While You Can

One of the several mechanisms that plants use to attract pollinators is scent. Petals can produce volatile compounds, essential oils that evaporate in warm temperatures, such as methylbenzoate. However, according to Natalia Dudareva at Purdue University floral scents are slowing disappearing. Increased fragrances tend to reduce life span, and as humans have selected for a longer shelf life flowers have started to lose their scent.  Dudareva is looking at the genes that are involved with producing scents, which is important for florists as well as to help crops get pollinated. 

The way it was(n't)

They don't make movies like this anymore. This was pretty much state of the art for special effects prior to computer graphics. I think my favorite parts are the regular creatures that are made to look huge with a variety of camera tricks. I'm going to take a break from posting daily for a couple of weeks whilst I try to write lectures for my new EEMB class next quarter. I will return in April.


As we mentioned in class, sometimes scientists make big mistakes, like in 1964 when Donald R. Currey cut down the oldest tree alive to study its rings. The bristlecone pine, which he labeled WPN-114, turned out to be approximately 4,900 years old. There was a lot of controversy after it was cut down, and I found an article which takes into account five different points of view, from Curry himself to natural park advocates and other scientists.

"In fact, this short tale of an old tree dispatched—which is now an old story—has many versions. I cross-date five predominant chronologies, joined at their source like five needles bound in a fascicle, but diverging toward their ends"

Read the full story about Prometheus here!

Monday, March 11, 2013

Your daily dose of parasites

I found a very lovely AMNH-curated blog with all the parasites your heart could desire. You can sort by host animal or type of parasite, check out the recommended reading, and there's also a long list of contributors who've done interesting work in the field of parasitology. Choice entries include the cochineal (Dactylopius coccus), a cactus parasite used to make carmine red dye, in honor of New York City's Fashion week, as well as that for the common Vampire bat (Desmodus rotundus), which is known to display reciprocal altruism - a bat that eats particularly well one night may regurgitate some of its meal to feed hungry neighbors, trusting them to repay the favor when it doesn't feed successfully. Plus, each entry comes with lively little pictures of our bloodthirsty friends.

On the subject of bats, if you're not aware of WNS (White-Nose Syndrome), a cold-loving parasitic fungus that's decimated North American bat populations in recent years and has now spread to populations in 20 states, you should definitely read up on it:

Or ask me, I've been following this issue since 2010 and love talking about it.


Bloody massive

A little something for the marine biologists. I enjoyed this video, Worlds Largest Blue Whale colony - Discovered in Sri Lanka, and thought some of you might too. It's amazing that a large group of the largest organisms ever to have existed could have gone relatively unnoticed until lately. There's another, similar, video at the New York Times site that features the same researcher Asha de Vos

Sunday, March 10, 2013

Impact of a Genetic Bottleneck on Cheetahs

Today it is well known that, like many other species, Cheetahs are current residents of the endangered species list. As the number of surviving individuals in a species begins to drop, a  decline also occurs in the genetic variation of the species. This is one of the significant challenges faced by breeding programs as they try and maintain genetic variation with a limited number of available individuals.

It is estimated that Cheetahs experienced a genetic bottleneck around 10,000-12,000 years ago. This occurrence,  in addition to their current decline in numbers, has had significant impact upon the species genetic variation.

In the paper, Genetic Basis for Species Vulnerability in the Cheetah, the genetic similarity between Cheetahs is investigated. Multiple studies were performed to test for similiarity including examining the high occurrence of malformed sperm in both captive and wild Cheetahs. Another test involved small skin grafts being performed in order to determine the histocompatibility between unrelated Cheetahs. How long it takes for a rejection to occur indicates how similar two individuals immune systems are. Many of the Cheetahs failed to have rapid rejections, and only a couple showed signs of long term rejection. This indicated a level of similarity between immune markers that caused the immune system to fail at recognizing the Cheetah's own cells versus those of another Cheetah.

This level of genetic similarity presents reproductive challenges for the Cheetah, as well as increased susceptibility to disease. Many Cheetahs face high infant mortality rates, in addition to other issues. However, behavioral factors also play a role in the success of Cheetah reproduction, so it is possible to raise breeding success rates. Many breeding programs underway are working to preserve the remaining genetic variation of the Cheetah, as well as increase the species number. After all, who could resist wanting to protect those adorable fuzzy babies!

In addition to the article, more information about Cheetahs may be found at:

Extremophile algae?

Extremophilia - not just for prokaryotes:

How to Thrive in Battery Acid and Among Toxic Metals

In the movie Alien, the title character is an extraterrestrial creature that can survive brutal heat and resist the effects of toxins.

In real life, organisms with similar traits exist, such as the "extremophile" red alga Galdieria sulphuraria.

In hot springs in Yellowstone National Park, Galdieria uses energy from the sun to produce sugars through photosynthesis.

In the darkness of old mineshafts in drainage as caustic as battery acid, it feeds on bacteria and survives high concentrations of arsenic and heavy metals.

How has a one-celled alga acquired such flexibility and resilience?

To answer this question, an international research team led by Gerald Schoenknecht of Oklahoma State University and Andreas Weber and Martin Lercher of Heinrich-Heine-Universitat (Heinrich-Heine University) in Dusseldorf, Germany, decoded genetic information in Galdieria.

They are three of 18 co-authors of a paper on the findings published in this week's issue of the journal Science.

The scientists made an unexpected discovery: Galdieria's genome shows clear signs of borrowing genes from its neighbors.

Many genes that contribute to Galdieria's adaptations were not inherited from its ancestor red algae, but were acquired from bacteria or archaebacteria.

This "horizontal gene transfer" is typical for the evolution of bacteria, researchers say.

However, Galdieria is the first known organism with a nucleus (called a eukaryote) that has adapted to extreme environments based on horizontal gene transfer.

Prairie Dogs Disperse When All Close Kin Have Disappeared

Unlike most species, that tend to leave a territory in order to avoid competition from relatives, prairie dogs will leave their home territory after all of their relatives have disappeared.  Three species of prairie dogs contain individuals that are more likely to disperse in the absence of nearby relatives.  Behavioral ecologist John Hoogland recently published an article in Science regarding this new study.  He has been studying the ecology and social behavior of prairie dogs in the national parks of Arizona, South Dakota, and Utah for the past 40 years.  According to his study, females are 12.5 times more likely to disperse when close kin are absent for one species, and 5.5 time more likely for another species.
Hoogland stated, "Prairie dogs are excellent models for a study of dispersal because they are easy to live-trap, mark, and observe.  And they usually move only short distances to nearby territories."
He also stated that prairie dogs do compete with nearby kin for resources, such as burrows and mates.  However, they also cooperate with each other in the digging burrows, defense of the home territory,giving alarm calls when large predators are nearby or have attacked, and helping to chase away small predators.  Prairie dogs also participate in communal nursing (the suckling of non-offspring), which can be life-saving for the offspring of close kin when the biological mother has died.
Hoogland hypothesizes that the benefits of cooperation with close kin exceed the costs of competition with them.  He believes that when all close kin disappear, individuals disperse because they have nobody with whom to cooperate.  When possible, prairie dogs often disperse to a territory that contains close kin who dispersed there beforehand, allowing cooperation amongst kin.

Saturday, March 9, 2013

DeExtinction Event

This looks interesting.

Revive & Restore, with the support of TED and in partnership with National Geographic Society, is convening a day-long conference to showcase the prospects of bringing extinct species back to life, along with a discussion of the ethical issues that will raise.
TEDxDeExtinction is a TEDx event that explores a bold topic: reviving extinct species and re-introducing them to the wild. Can it be done responsibly? Should it be done at all? The full-day conference brings together a range of speakers to dive into the emerging idea of de-extinction.
The program is here and the whole thing will be webcast at this link this coming Friday - March 15th.

Friday, March 8, 2013

Marine biology job seminar

There's an ongoing job search for a faculty position in marine biology. I haven't posted most of the job seminars because they've been during our class time (doh!). But on Monday we have:


Monday March 11, Noon, MSB Auditorium

Dr. Craig Osenberg (UF)
From here to there: spatial patterns, marine reserves, and habitat restoration

Dr. Osenberg is a Professor in the Department of Biology at the University of Florida, Gainesville.  He is a population and community ecologist who uses a combination of field experiments and observations, mathematical modeling, and quantitative synthesis to address fundamental questions in ecology such as the coupled dynamics of spatially segregated systems.

Thursday, March 7, 2013

Nobody is perfect

Bruce sent me this and points out that it is noteworthy for (a) science not being perfect, (b)
brevity and (c) Cesare Emiliani was a REALLY big name in Paleooceanography.

It is also worth noting that the mistake (in the calculated values in a table) did not alter the main conclusion of the original paper.

Wednesday, March 6, 2013


When I talked about the Bristlecone Pines being the oldest known single organisms I mentioned that some clonal organisms were much older.

Here's a nice little slideshow about Pando, an 80,000 year old (give or take a few) grove of Quaking Aspen trees in Utah.

The grove which  has about 47,000 stems connected by a single root system  has spread over about 106 acres. The average age of the individual stems is about 130 years.

There's a link to an older article in Discover magazine which has more details on the clone, aging techniques used and some amusing stories:

Since my colleagues and I nominated Pando as the world’s largest organism, he has captured the attention of dozens of newspapers and radio stations across North America, and some of the reactions have been quite funny. Some see Pando as a threat: I received a call from someone asking, Does this giant clone, spreading vegetatively, pose a threat to the people living in southern Utah? 

Tuesday, March 5, 2013

To Accept or Not To Accept?

The Thinker
I saw this article on my twitter feed amidst about 10 tweets about the baby girl who was cured of HIV this past Sunday. So, since I'm pretty sure that most of you have already heard of the news about the baby girl, my congratulations to the doctors, the baby and her family, by the way, I decided to choose this particular article.

The title of this article is Monkeys Stay Away from Meanies. The article is about a study done on Capuchin monkeys where they showed the Capuchin monkeys different scenarios of people helping other people open a jar. Later, these people offered food to the monkeys. It turns out that the monkeys showed no preference to the people who helped open jars or were trying to open their own jars. The monkeys accepted food from either person. However, if person A refused to help person B open their jar, then the monkey tended to take food from person B when they offered food.

"The animals showed no bias against people who
 failed to help because they were busy opening their own jar. But they tended to avoid people who were available to help but did not do so.

The reason for this is that:

" “Explicit refusal to help is a signal that you’re dangerous, that you’re negative,” says Kiley Hamlin, a developmental psychologist at the University of British Columbia in Vancouver, Canada."

Listen to your mom, and don't accept things from strangers. :-)

How Bats Find Flowers

Being a bat-pollinated flower must be hard. While all the other flowers have pollinators with numerous unique traits that allow for no mix-ups between pollinators, moth and bat-pollinated flowers seem to lack much in the way of variety. Other than size, their scent and color are pretty much identical, so what is a bat-based flower to do? Apparently, use acoustics. A relatively recent study found that certain flowers use shapes which provide a unique acoustic vibration that allows for bats to pick up on its trait via echolocation, allowing them to find flowers that no other organism could.

Plant physiology

One of the leading plant physiology textbooks, called, not surprisingly, Plant Pysiology, by Taiz and Zeiger, has quite a bit of material online including supplementary essays that are perfect for this class. Take a moment to read one, or more...

Essay 4.1, A Brief History of the Study of Water Movement in the Xylem - Hanno Richter, University of Agricultural Sciences, Vienna, and Pierre Cruiziat, PIAF-INRA-UBP, France
(August 2002)

Essay 4.2, The Cohesion–Tension Theory at Work - Pierre Cruiziat, PIAF-INRA-UBP, France, and Hanno Richter, University of Agricultural Sciences, Vienna
(May 2006)

Essay 4.3, How Water Climbs to the Top of a 112 Meter-Tall Tree - George Koch, Northern Arizona University; Stephen Sillett and Gregg Jennings, Humboldt State University; Stephen Davis, Pepperdine University
(May 2006)

Essay 4.4, Cavitation and Refilling - James K. Wheeler and N. Michele Holbrook, Department of Organismic and Evolutionary Biology, Harvard University
(March 2007)