Archives for the month of: October, 2012

Most viruses you probably know of our transmitted person to person (or from another biological source) in a process called horizontal transmission. However, another transmission pathway exists: vertical transmission. Retroviruses are one example of a virus that can be vertically transmitted.

Retroviruses, as the name implies, work backwards. The traditional pattern of genetic expression is to proceed from DNA, through RNA, and finally into proteins. Retroviruses on the other hand start with their own viral RNA, convert it into DNA, and insert that information into the genome of their host cell. The most familiar retrovirus in modern times is the HIV virus. Occasionally a retrovirus will infect an animal’s germ line, those cells that lead to sperm and eggs. If those reproductive cells are used in fertilization, then the viral DNA becomes a part of the genome of the next generation: it is vertically transmitted.

Retroviral DNA in the genome is referred to as a provirus, and it accounts for four to ten percent of vertebrate genomes (eight percent in humans). According to Jack Lenz, a professor at Albert Einstein College of Medicine, the original functions of proviruses in the human genome are open to speculation. While HIV is harmful to the host, other retroviruses can have positive effects or simply be replicating selfishly but neutrally. While the proviral DNA in the modern human genome is typically categorized under “junk DNA,” Lenz says some sections appear to reactivate every ten to 100 thousand years, reinserting a new copy of themselves into the host DNA. These copies can serve as “genetic fossils” for mapping our evolutionary past.

Jonathan P. Stoye, Head of the Division of Virology at the Medical Research Council’s National Institute for Medical Research in London, authored an article published this June in Nature Reviews Microbiology laying out an overview of the complex relationship between retroviral and vertebrate DNA. Stoye describes an evolutionary arms race on a genetic scale between the regulatory structures in vertebrate DNA and the nimble efforts of the retroviral RNA to reverse transcribe itself. The same genetic fossils studied by Lenz are found in other vertebrate genomes, detailing a history of viral/host interactions dating back many millions of years.

Some retroviruses can be transmitted vertically and horizontally. The subject of several papers since 2006, the koala retrovirus has been devastating zoo and wild populations of the marsupial. The origins of the retrovirus remain unknown; while it resembles a virus found in gibbons, it is unclear how the pathogen might have jumped species. In koalas the virus can produce cancers and an AIDS-like immune disorder.

A paper published this July in the Australian Veterinary Journal, took blood and tissue samples from 708 koalas across the continent. The areas with the highest percentage of pro-virus positive koalas were four regions of Queensland and New South Wales at 100% and mainland Victoria at 72.2%. This suggests a northern location for ground zero of the virus. However the numbers of viral copies per cell differ between these northern regions, from a mean of 165 copies per cell in Queensland koalas to far below one copy per cell in Victorian koalas. According to the authors, this confirms that we are seeing a virus that is transitioning from a horizontal to a vertical means of transmission.


Provirus in humans are called junk DNA, but active retroviruses on their way to becoming proviruses can have devastating effects. The retrovirus plaguing koalas today is still poorly understood and HIV in humans, while treatable, still has no cure. In his paper Stoye describes what we might learn by better understanding human proviruses. We know human cells have found ways to neutralize or perhaps even utilize the viral DNA in their genome. If these cellular and genetic defenses can be harnessed, it may lead to a treatment for active retroviruses like HIV or koala retrovirus.




Phone interview with Jack Lenz 10/12/12

Simmons et al. “Prevalence of koala retrovirus in geographically diverse populations in Australia.” Australian Veterinary Journal. Volume 90, Issue 10

Stoye. “Studies of endogenous retroviruses reveal a continuing evolutionary saga.” Nature Reviews Microbiology. 10, 395-406 (June 2012) doi:10.1038/nrmicro2783




Does the mysterious Bigfoot live among us? Those in search of him may have to look no further than their mirrors.

Discoveries of new archaic humans prove Homo sapiens shared the planet with our evolutionary cousins more recently than previously imagined. There were the Neadertals in Europe and the Denisovans of Asia; the tiny “Hobbit” of Flores lived alongside humans as recently as 18,000 years ago. This certainly is sufficient explanation for the origin of the wild man stories found in nearly every culture, but are there any more recent legends?

This is the thrust of an article by David Robson published earlier this year in New Scientist. He writes that most Bigfoot sightings have alternative explanations. Indeed, sighting hotspots have been mapped almost exactly to the home ranges of known large mammals like bears and buffalo. Nevertheless, it is possible to entertain the notion as a possibility in light of the recent existence of our evolutionary cousins.

Now new genetic evidence suggests truth may be stranger than fiction: Bigfoot may not be lurking in the woods but in our own DNA. Advances in genetic analysis and new fossil remains seem to suggest that Europeans and Melanesians share between one and five percent of their genomes with Neandertals and Denisovans, respectively.

Matthew Jobin is an anthropologist who has mapped human and Denisovan DNA, specifically looking at immune system genes. His statistical models support a scenario where human populations in Asia acquired certain genes by interbreeding with Denisovans. Combined with research on Neandertal genes, this suggests that some modern day humans are hybrids.

The Clan of the Cave Bear, written in 1980 by Jean M. Auel, fictionalized historical interactions with Neandertal and early Europeans. Previously consider more fiction than science, Jobin says the author may now be vindicated. The ways in which humans and archaic population would have interacted are open to speculation. Did we form peaceful alliances or did we take their women as spoils of war? The only thing the interbreeding hypothesis says for sure is that we got it on.

Jobin says this new evidence may lead us to “broaden the lines around what is human.” We have gotten used to thinking of the human species as one group, alone on this planet in our uniqueness, but we now know that has not always been the case. We know little about the cultures of archaic groups. Neandertals possessed a cruder tool culture than contemporary humans and their larynxes would have produced less sophisticated sounds, yet their average brain size exceeded that of modern humans. Even less is known of the Denisovans, who are physically represented by only a couple finger bones, a toe, and a tooth. Despite any cultural differences and their distinct genetic distance from humans, Jobin says, when our ancestors met these groups “we saw them as people.”


Robson, David. “Are there any other hominins left?” New Scientist. 3/24/2012, Vol. 213 Issue 2857, p42-42, 2/3p

Phone interview with Dr. Matthew Jobin 10/19/12

The spread of ecological pests around the world is an unfortunate side effect of the modern era of global travel. Dubbed invasive species, these pests can wreak havoc when introduced to new habitats. While international trade is the primary culprit in introducing non-native species, domestic recreational travel is often responsible for spreading invasions into a country’s interior. A major example in recent U.S. history is the spread of insects as stowaways in untreated firewood.

Firewood first drew the concern of conservationists in 1996, when it was implicated in the spread of Asian longhorned beetle (Anoplophora glabripennis). The invasion of this tree pest was first documented in Brooklyn, probably introduced as an accidental passenger inside  the wood of crates used in international trade. Within a month, the beetle was found 50 km east in Amityville, N.Y. This distance is far outside the normal dispersal rate of the beetle, so ecologists pointed to infested wood transported from Brooklyn and being sold as firewood as the vector of spread.

A species of concern today and known to travel in firewood is the emerald ash borer (Agrilus planipennis) another Asian beetle. As the name implies, the emerald ash borer is a pest to all North American ash species (Fraxinus spp.) and the economic costs alone (to say nothing of ecological impacts) has been projected to cost more than $10 billion over a ten year period. Let’s look at three articles published this year that detail the prevalence of firewood transport, the risk of infestation, and the effectiveness of laws aimed at untreated firewood.

Dispersal of Invasive Forest Insects via Recreational Firewood: A

Quantitative Analysis

Published in the Jounral of Economic Entomology, this paper attempts to put some hard numbers on the prevalence of untreated firewood transport. Previous surveys at U.S. campgrounds  indicate the percentage of campers transporting their own firewood is between eight and 57 percent. However, the authors of this study wanted to develop a clearer picture of the potential for long distance transport of firewood.

Since data on actual firewood was lacking, the authors decided to model the distances traveled by American campers as a surrogate. Compiling data from the National Recreation Reservation Service over a five year period, the authors mapped the home ZIP codes of campers and connected them to the ZIP code of their destination park. While this model involves many simplifications of actual behavior, they found that the majority of campers traveled less than 250 km, with most of those trips being less than 100 km. Some connections with moderate volume of travel did measure greater than 1,000 km, and the longest connections were associated with very few reservations.

So while most campers make trips within two hours of home a portion do travel long distances, and some of those are likely to bring their own firewood. But how dangerous is untreated firewood?

Retail Firewood Can Transport Live Tree Pests

Published in Forest Entomology, this paper aimed at determining the likelihood of infestation for untreated firewood. A survey of retail firewood in 18 states found that 52 percent of the wood came from out of state and 50 percent of the wood showed signs of infestation. To produce a more quantitative picture, the authors of this paper purchased 419 firewood bundles from retailers in Colorado, New Mexico, Utah, and Wyoming. They put the bundles in a controlled setting and waited to see what crawled out.

The authors observed the firewood for a period of 18 months. Live insects emerged from 47 percent of the bundles. An average of 11 insects emerged from each bundle, with a range of one insect to a staggering 520. The long term risk is also great, with insects emerging up to 558 days after purchase date.

The authors of this paper recommend a simple heat treating, but the most commonly legislated precaution is simply to forbid the transport of all untreated firewood across state borders or into parks. But what makes for the most effective regulations?

Motivation for compliance with environmental regulations related to forest health

The authors of this study, published in the Journal of Environmental Management, conducted a mail survey with 495 usable returns. The survey was aimed at identifying the strongest influences governing compliance with environmental regulations. In the context of the survey, firewood users had irregular,  short-term interests in compliance, the cost of complying is reasonable, and the costs of non-complying are low (such as having to surrender firewood at the park gate).

The authors consider a number of factors influencing compliance and found that normative motivations (such as sense of civic duty) have a mild influence while calculated motivations have the strongest influence. Calculated motivations include the price of locally-sold firewood and the convenience of purchasing it. The authors see this survey as a guide for designing effective environmental regulations.


To  observe the consequences of removing a top predator, ecologists have traditionally relied on small scale experiments. Recently humans have caused a number of accidental mass extinctions, which have produced “natural experiments” across entire ecosystems. One such natural experiment in the forests of Guam has found results that far exceed the expectations of small-scale experiments; in the decades since the island’s birds were wiped out by invading snakes, spider populations have reached levels no one could have predicted: Guam has 40 times the number of spiders as neighboring islands!

Dr. Haldre Rogers, a Huxley Faculty Fellow at Rice University, has long been fascinated with the eerily silent forests of Guam. Almost three decades ago, the brown tree snake was first introduced to Guam as a stow-away aboard American military planes. This arboreal reptile was the first snake species on the island and birds were naive to the threat. Now almost all native species of birds are extinct on the island. Strict regulations have so far allowed the neighboring islands of Rota, Tinian, and Saipan to remain snake-free, but otherwise essentially similar to the ecosystem of Guam. This region of the Philippine Sea provided a perfect natural experiment for Rogers to study the absence of insectivorous birds. Her findings were published on PLOS ONE.

As Rogers explains, past small scale experiments using bird nets to create a bird-free branch or tree have shown consistent increases in spider populations. Her team decided to examine this trend on a larger scale by counting the spiders in several similar tracts of forest on Guam and nearby islands in both the dry and rainy seasons. The results showed an average forty-fold increase in total spider populations on Guam compared to nearby islands. Rogers describes having to carry a stick  with her to knock down spider webs when trekking through the forest of Guam — a precaution not needed on neighboring islands.

Previous small scale experiments predicted at most a 25-fold increase in spider populations, a far cry from the results of Roger’s natural experiment. However she stresses the importance of both study types. Natural experiments have a timeframe of decades compared to weeks or months and can demonstrate larger impacts, but the results are only correlative. Smaller scale experiments, on the other hand, can control more variables and isolate specific mechanisms. Together, “manipulative and comparative experiments give the strongest predictive power.”

“Past  studies have primarily focused on the loss of species from direct predation,” says Dr. Betsy Von Holle, Assistant Professor at the University of Central Florida. Few studies have “focused on trophic level effects and ecosystem responses.” Von Holle sees a great untapped potential for future studies of invasive species to shift their attention toward secondary effects down the food chain. She says the increased number of spiders on Guam will likely alter the populations of herbivorous insects on which the spiders prey, which in turn could mean long term changes in the communities of plant species which comprise the silent forests.



Phone interview with Dr. Haldre Rogers (9-14-12)

Phone interview with Dr. Betsy Von Halle (9-17-12)

Rogers H, Hille Ris Lambers J, Miller R, Tewksbury JJ (2012) “‘Natural experiment’ Demonstrates Top-Down Control of Spiders by Birds on a Landscape Level.” PLoS ONE 7(9): e43446. doi:10.1371/journal.pone.0043446

In 1964, biologist George G. Simpson criticized exobiology, the study of life outside of Earth, as a science without a subject. Even after exobiology was reincarnated by NASA at the turn of the millennium as astrobiology, Simpson’s accusation still holds some truth: to date there is no direct, unambiguous evidence for extraterrestrial life. Yet the NASA Astrobiology Institute holds yearly seminars and the Journal of Astrobiology has been publishing papers on the subject for a decade. NASA’s Curiosity rover is currently on a mission which includes searching for Martian life. In a paper published this August in Nature and provocatively titled “Astrobiology: Frontier or Fiction,” a physicist and a biologist lay down a hard critique of the state of Astrobiology in 2012.

While Astrobiologists may not have any aliens to dissect, they make due with theory and correlation. The authors of the paper say it is akin to the study of theoretical particles. One example is the study of extremophiles, microorganisms that live in extreme environments like boiling hot geysers, brine pools at the bottom of the ocean, or highly toxic lakes. The reasoning goes that if life on Earth can thrive in such extreme conditions, it may be able to survive in the harsh environments of alien worlds.

Astrobiologists also look at various heavenly bodies and compare the conditions there to life-sustaining environments on Earth. The article cites the evidence for water in the Martian past and the liquid water oceans on moons like Jupiter’s Ganymede and Europa and Saturn’s Titan and Enceladus.

The authors do write that astrobiology is a worthy pursuit of science. As they say, it would have been foolish for chemists to stop with the first periodic table when the gaps in the elements clearly showed where undiscovered ones might exist. In the same way, the tree of life here on Earth allows us to imagine that other and different kinds of trees might exist.

However, they write, the danger lies in researchers using “astrobiology” as a buzzword to reel in grant money. An example is the so-called “arsenic-based DNA” of a microbe discovered in a saline Californian lake that captured the attention of science news earlier this year. Some astrobiologists jumped on this as evidence of a “shadow biome,” or groups of alternate life forms living side-by-side our own. However, subsequent analysis found nothing special about the DNA of these microbes.

The authors say biology is the last branch of science yet to prove its worth outside of Earth. Yet they believe that if NASA and other space agencies obtain funding on a scale with the construction of the Large Hadron Collider, we will be able to answer the question of whether extraterrestrial life exists in our solar system within a couple of decades. The most likely target for such a mission is the aqueous ocean beneath the icy surface of Europa, which is kept warm and liquid by the gravitational forces of Jupiter.


Lazcano, Antonio; Hand, Kevin p. “Astrobiology: Frontier or Fiction.” Nature. 2012, Vol. 488(7419), pp. 160-1

Image credit NASA

Exquisite Beast

I’ve been following an ongoing art project on tumblr called The Exquisite Beast. The premise is two artists alternate drawing the successive stages in the evolution of an imaginary creature. The thing is more art than biology; it jumped the shark for me what the Beast went from two limbs to six limbs to no limbs back to six limbs. But if you don’t take it so seriously they do play on some interesting anatomical motifs. This by now quite ancient lineage has lived on land, flown through the air, floated through the air, lived underwater, lived underground, and glided through the trees. The concept has also prompted other tumblr users to create similar projects.

[This is not to be confused with “An Exquisite Beast,” a different internet art project.]

To the untrained eye, one crow may look the same as any other. However, a new study published in the Proceedings of the National Academy of Sciences demonstrates that crows can remember human faces and past interactions.

Dr. John Marzluff, an avian ecologist and professor at the University of Washington, led a team of researchers to study the ability of crows to recognize human faces. It was the first study to use brain imaging on wild animals behaving normally.

Marzluff’s team members captured wild American crows (Corvus brachyrhynchos) while wearing a “threatening” mask. The mask was a latex copy of an actual face (one of Marzluff’s graduate students) with a neutral expression, but the stressful act of capture represented threatening behavior. Crows were then kept in a lab setting and fed and cared for by a researcher in a “caring” mask, molded from a different face.

Captive birds were then shown images of either a researcher wearing one of the masks or an empty room. Immediately after viewing the stimulus, crows were anesthetized and placed in a PET scan.

Analysis of brain activity collaborated with observed behavior. Crows presented with threatening masks had brain activity in regions associated with fear and blinked less while observing the stimulus. Among the areas elicited by the caring mask were those associated with hunger, suggesting the crows had connected their caregivers with feeding.

As for the ability of crows to recognize individuals of other species, Marzluff says “there is anecdotal evidence for cats and dogs,” whereas the uniformly predatory red-tailed hawk always produces the same response: flight.
Web Bonus: During my interview, Marzluff discussed an earlier experiment conducted in the wild. This experiment involved mostly negative stimuli; the researchers captured and released crows while wearing masks. Marzluff returned to the same site over a period of seven years and the crows continued to recognize and attack anyone wearing the masks. Even crows who had never been captured learned socially to attack the masked scientists. This cruder version of the experiment simply used store bought masks: one a cave man and one of former Vice President Dick Cheney.


Phone interview with Dr. John Marzluff (9/19/12).

Marzluff J et al. (2012) Brain imaging reveals neuronal circuitry underlying the crow’s perception of human face. PNAS. doi: 10.1073/pnas.1206109109