Tag: biology

$28 billion spent on poor biomedical research?

2:32 pm

The uncertainty of science: A new study suggests that $28 billion is spent on biomedical research that no one can reproduce.

I have no doubt that a vast amount of medical research is so poorly done that no one else will ever be able to replicate the results. However, the article notes that the way the researchers came up with the $28 billion figure is quite questionable, reviewing only about two dozen studies and then extrapolating their numbers across the entire research field. This is highly uncertain and should be taken with a grain of salt.

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Bee die off hasn’t happened

11:39 am

The uncertainty of science: Despite numerous claims by environmentalists and scientists in the past decade that the bee population was dying off, new data from the Agriculture Department suggests that bee populations are now at a 20 year high.

The reason? It appears that beekeepers have been very innovative and creative when faced with disease or other problems that hurt bees. Driven by the profit motive and competition and free to act, they have come up with solutions.

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NSF to help fund the development of implantable antennas

1:47 pm

What could possibly go wrong? The National Science Foundation (NSF) is providing funding for the development of an implantable antenna for health care, including the possibility for “long-term patient monitoring.”

The project is being financed in collaboration with the National Research Foundation of Korea to create a high frequency antenna that can be permanently implanted under a person’s skin. “Antennas operating near or inside the human body are important for a number of applications, including healthcare,” a grant for the project said. “Implantable medical devices such as cardiac pacemakers and retinal implants are a growing feature of modern healthcare, and implantable antennas for these devices are necessary to monitor battery level and device health, to upload and download data used in patient monitoring, and more.”

The grant said that an implantable device could be used for “long-term patient monitoring” and “biometric tracking,” or using technology to verify a person’s identity.

Without any doubt there are many very useful applications for such an implantable device. Monitoring battery life on pacemakers is an obvious one. There will be a problem, however, if anyone but the patient can do the monitoring. I can see too many possible misuses occurring should it be in anyone else’s hands. At a minimum, there are big privacy concerns.

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Chinese scientists do genetic experiments with human embryos

11:22 pm

What could possibly go wrong? A Chinese team of scientists have been experimenting with genetically manipulating the human embryo to see if they can prevent a genetic blood disorder.

The team attempted to modify the gene responsible for β-thalassaemia, a potentially fatal blood disorder, using a gene-editing technique known as CRISPR/Cas9. The researchers say that their results reveal serious obstacles to using the method in medical applications. “I believe this is the first report of CRISPR/Cas9 applied to human pre-implantation embryos and as such the study is a landmark, as well as a cautionary tale,” says George Daley, a stem-cell biologist at Harvard Medical School in Boston. “Their study should be a stern warning to any practitioner who thinks the technology is ready for testing to eradicate disease genes.”

They not only found the technique unreliable in curing the genetic disease, it also produced many more unpredicted mutations.

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Russian hunters find frozen carcass of extinct whoolly rhino

10:38 am

In September Russian hunters accidentally discovered the frozen remains of an adolescent whoolly rhinoceros.

Larger than modern-day rhinos and more suited to extreme cold and harsh environments, the woolly rhino first appeared about 3.6 million years ago. Weighing up to an estimated 4,000 pounds and equipped with 24-inch-long horns, these intimidating creatures co-existed with early humans and were often hunted. Yet for all their strength, the woolly rhino became extinct over 10,000 years ago. Unlike the woolly mammoth, little is known about this species since few specimens have ever been retrieved. Those that have were often mummified to a point where study was impossible, and up until now, no calf has ever been found.

RT reported that experts at the Yakutsk academy will attempt to extract DNA from the calf’s remains and try to come up with a more accurate date on when the creature died. Nicknamed “Sasha,” researchers say the calf died at least 10,000 years ago and may have been 18 months old when it perished.

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Sloppy biosafety procedures found at federal disease center

8:43 am

Does this make you feel safer? An investigation of a federal center for studying dangerous diseases in primates has found serious biosafety procedure violations.

Concerns arose at the center in Covington, Louisiana, after two rhesus macaques became ill in late November with melioidosis, a disease caused by the tropical bacterium Burkholderia pseudomallei. In January, the U.S. Centers for Disease Control and Prevention (CDC) and Department of Agriculture investigators traced the strain infecting the primates to a vaccine research lab working with mice. Last month, as the investigation continued, CDC suspended the primate center’s 10 or so research projects involving B. pseudomallei and other select agents (a list of dangerous bacteria, viruses, and toxins that are tightly regulated). Meanwhile, a report in USA Today suggested the bacterium might have contaminated the center’s soil or water.

…In addition, workers “frequently entered the select agent lab without appropriate protective clothing,” the release says. No center staff has shown signs of illness. On 12 March, however, Tulane announced that blood tests have found that one worker has low levels of antibodies to the bacterium, suggesting possible exposure at the center, according to ABC News.

Is there any area of government expertise that isn’t screwing up royally these days? As far as I can tell, the answer is no. The sooner we as a people can cut back on the government’s resources so that they won’t have the ability to do us harm, the better off we will be.

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Two astronauts gear up for one year in space

5:14 pm

The final preparations are under way for sending two astronauts, one American and one Russian, to ISS for a full year.

Their launch is scheduled for March 27 in a Soyuz capsule.

One other cool aspect of this long mission: The American astronaut, Scott Kelly, has a twin brother, Mark Kelly, who is also an astronaut, though retired. Mark will be duplicating some of Scott’s in-space activities during the mission. Doctors will also compare how Scott’s body changes in weightlessness over time, in comparison to his brother here on Earth.

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Americans demand mandatory food labels for DNA

1:48 pm

We are doomed: A new survey has found that more than 80 percent of Americans support the idea of requiring labels on any foods that contain DNA.

If the government does impose mandatory labeling on foods containing DNA, perhaps the label might look something like this: “WARNING: This product contains deoxyribonucleic acid (DNA). The Surgeon General has determined that DNA is linked to a variety of diseases in both animals and humans. In some configurations, it is a risk factor for cancer and heart disease. Pregnant women are at very high risk of passing on DNA to their children.”

I truly fear for the future, not so much because so many people haven’t the slightest idea what DNA is, but because so many people are so eager to force food labeling (or any other regulation you can think of) on others at the slightest whim.

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Methane does exist in the Martian atmosphere

6:32 pm

The uncertainty of science: Curiosity has confirmed the presence, and fluctuation, of methane in the local Martian atmosphere.

SAM [Sample Analysis at Mars, one of Curiosity’s instruments] has been detecting basal levels of methane concentration of around 0,7 ppbv, and has confirmed an event of episodic increase of up to ten times this value during a period of sixty soles (Martian days), i.e., of about 7 ppvb. The new data are based on observations during almost one Martian year (almost two Earth years), included in the initial prediction for the duration of the mission (nominal mission), during which Curiosity has surveyed about 8 kms in the basin of the Gale crater.

Since methane has a short life expectancy, something must be doing something to generate it.

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New ebola drug appears somewhat effective

10:06 am

Drug trails in Guinea of a new ebola drug suggest that it might have some positive effect on mortality.

A researcher who had seen the data and asked not to be identified told Science that favipiravir did not help all of the patients treated with it at two trial sites in Guinea. In a subset of trial participants who had low levels of Ebola virus in the blood, however, the mortality was just 15%. In similar patients who entered the centers earlier and did not receive favipiravir, mortality was 30%.

The trials with this drug are being conducted without a control group, which makes it harder to pin down the cause of these results. The article also describes several other drugs being readied for testing, some of which are expected to be more effective.

The trials, however, are faced with two issues. First, the easing of the epidemic is making it more difficult to do the studies. And second,

So far, Guinea and Sierra Leone, where Ebola is still infecting dozens of people a week, have refused invitations to join the study. Their main stumbling block is trial design. ZMapp will be the first Ebola treatment that will be tested against a placebo control. “I think that’s the only way to tell whether these drugs are safe and effective,” Lane says. The governments of Guinea and Sierra Leone, as well as Doctors Without Borders, which runs Ebola centers in those countries, have for ethical reasons been reluctant to participate in treatment trials that use a placebo.

The moral dilemma of doing drug tests where some patients get a placebo has always been a problem for medical research. It is therefore not surprising to see it here as well.

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Life found that hasn’t changed in 2 billion years

6:00 pm

Scientists have discovered a micro-organism that has not evolved in more than 2 billion years.

Schopf and his colleagues used a variety of spectroscopic imaging techniques to study sulfur bacteria fossils embedded in deep sea rocks of varying ages. Analysis of the microorganisms from 1.8 billion-year-old rocks from Western Australia and 2.3 billion-year-old rocks collect off the coast of Chile showed that ancient sulfur bacteria looks the exact same now as it has for more than two billion years.

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New data says volcanoes, not asteroids, killed dinosaurs

1:38 pm

The uncertainty of science: A careful updating of the geological timeline has strengthened the link between the dinosaur extinction 66 million years ago and a major volcanic event at that time.

A primeval volcanic range in western India known as the Deccan Traps, which were once three times larger than France, began its main phase of eruptions roughly 250,000 years before the Cretaceous-Paleogene, or K-Pg, extinction event, the researchers report in the journal Science. For the next 750,000 years, the volcanoes unleashed more than 1.1 million cubic kilometers (264,000 cubic miles) of lava. The main phase of eruptions comprised about 80-90 percent of the total volume of the Deccan Traps’ lava flow and followed a substantially weaker first phase that began about 1 million years earlier.

The results support the idea that the Deccan Traps played a role in the K-Pg extinction, and challenge the dominant theory that a meteorite impact near present-day Chicxulub, Mexico, was the sole cause of the extinction. The researchers suggest that the Deccan Traps eruptions and the Chicxulub impact need to be considered together when studying and modeling the K-Pg extinction event.

The general public might not know it, but the only ones in the field of dinosaur research that have said the asteroid was the sole cause of the extinction have been planetary scientists.

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The arrival of two new childhood diseases to America

10:42 am

Link here.

In the span of four months, at least 94 children in 33 U.S. states have developed a devastating form of paralysis with symptoms similar to polio. Some require a ventilator to breathe. And some of the greatest government health minds in the country say they have no idea what’s causing it. At the same time, during the past four months, at least 12 children have died after falling ill with a respiratory virus called Enterovirus D-68 (EV-D68). Again, federal health officials are at a loss to explain the origin of the epidemic.

It appears that the first, now dubbed acute flaccid myelitis (AFM), might be linked to the second.

In a November 7 alert to practitioners, the CDC noted, “the unusual clustering of acute limb weakness occurred against a background of a nationwide outbreak of severe respiratory illness among children due to enterovirus-D68 (EV-D68). Several of the patients in California and nearly half of the 11 cases identified in Colorado had tested positive for EV-D68 from nasopharyngeal (NP) swabs at the time of admission for their neurologic illness. This raised a possible association between these neurologic illnesses and the ongoing outbreak of respiratory disease due to EV-D68.”

Whether both are linked to the flood of illegal immigrant children allowed to enter the U.S. this past summer remains unclear.

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Organic material from Mars?

12:55 pm

The uncertainty of science: Scientists theorize that the carbon material found in a 2011 meteorite could be Martian biological material.

Ejected from Mars after an asteroid crashed on its surface, the meteorite, named Tissint, fell on the Moroccan desert on July 18, 2011, in view of several eyewitnesses. Upon examination, the alien rock was found to have small fissures that were filled with carbon-containing matter. Several research teams have already shown that this component is organic in nature. But they are still debating where the carbon came from.

Chemical, microscopic and isotope analysis of the carbon material led the researchers to several possible explanations of its origin. They established characteristics that unequivocally excluded a terrestrial origin, and showed that the carbon content were deposited in the Tissint’s fissures before it left Mars.

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Ebola’s rate of growth

8:49 am

The journal Science provides a detailed analysis of the infection rate of ebola, as well a reasonable estimate of the present and future number of cases.

The article makes two key points. First, the trends “…clearly show that the number of cases has roughly doubled every 3 to 4 weeks and that this trend is continuing. If underreporting gets worse, however, it may be even more difficult to discern such trends.”

Second, there is some good news in the worst effected countries.

The number of new cases in some areas at the epicenter of the outbreak– Kenema and Kailahun districts in Sierra Leone and Liberia’s Lofa county–has been dropping, and that’s not a result of underreporting, says Dye. “It has happened for a sufficiently large number of weeks now that we are confident that it’s a real reduction in incidence on the ground, probably related to control measures,” he says. “Our colleagues working on the ground believe it is too.”

One important factor has been the increase in safe burials, Dye says. (The bodies of Ebola victims are very infections.) People in the affected areas have resisted abandoning traditional burial practices that carry a high risk of infection, but in these three areas, local leaders, supported by WHO and others, have come to advocate a change. If that happens elsewhere, says Dye, “we expect to be able to cut out a substantial amount of infection in the community.”

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All geckos lost from Foton-M4

8:47 am

Upon the return to Earth today of Russian biology satellite Foton-M4 biologists discovered that all the geckos on board had died sometime during the mission.

The cause of death has not yet been announced. The mission itself had some problems, and returned to Earth about two weeks early. Nonetheless, the Russians also announced that flies on board were still alive upon landing.

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Confirmed: Life in buried Antarctic lake

6:50 pm

American scientists have confirmed that water samples from the buried Antarctic Lake Whillans, first obtained in January 2013, contained almost 4,000 different species of life.

Samples from the lake show that life has survived there without energy from the Sun for the past 120,000 years, and possibly for as long as 1 million years. And they offer the first look at what may be the largest unexplored ecosystem on Earth — making up 9% of the world’s land area. “There’s a thriving ecosystem down there,” says David Pearce, a microbiologist at Northumbria University, UK, who was part of a team that tried, unsuccessfully, to drill into a different subglacial body, Lake Ellsworth, in 2013.

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A blue flask of viruses

9:00 am

The story of the discovery of Ebola.

The next day—September 29—the package arrived: a cheap plastic thermos flask, shiny and blue. I settled down with Guido Van Der Groen—a shy, funny, fellow Belgian aged about thirty, a few years older than I—and René Delgadillo, a Bolivian postdoc student, to open it up on the lab bench. Nowadays it makes me wince just to think of it. Sure, we were wearing latex gloves—our boss insisted on gloves in the lab but we used no other precautions, no suits or masks of any kind.

We didn’t even imagine the risk we were taking. Indeed, shipping those blood samples in a simple thermos, without any kind of precautions, was an incredibly perilous act. Maybe the world was a simpler, more innocent place in those days, or maybe it was just a lot more reckless.

Unscrewing the thermos, we found a soup of half-melted ice: it was clear that subzero temperatures had not been constantly maintained. And the thermos itself had taken a few knocks, too. One of the test tubes was intact, but there were pieces of a broken tube—its lethal content now mixed up with the ice water—as well as a handwritten note, whose ink had partially bled away into the icy wet.

Read it all. The excerpt is from a book length memoir that looks to me to be a very worthwhile read.

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Ebola patient arrives in U.S.

12:11 am

Doctors in charge of the specialized isolation unit for treating dangerous infectious diseases are confident that they will be able to treat the infected patients safely without the disease escaping.

I have complete confidence that a well run facility like this, with modern technology, could keep the disease isolated. The key words, however, are “well run.” I pray that this description still applies to Emory University Hospital.

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Russia loses contact with Photon-M

9:06 am

Russia has lost contact with its Photon-M biology spacecraft, launched last week with a four geckos on board.

The Russians say that the receipt of telemetry from the spacecraft shows it is successfully operating autonomously without help from the ground. And since the Russians have a great deal of experience building spacecraft that can function on their own, I have no reason to disbelieve them in this. What is not clear is whether the spacecraft can come home on its own.

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Newly discovered dinosaur tracks

9:59 am

A cluster of dinosaur tracks discovered recently in Alaska has revealed to paleontologists a wealth of new information about their behavior.

The thousands of impressions, created on a 180-meter-long portion of near-coastal flood plain, today pepper a steep mountainside. Most of the tracks, made somewhere between 69 million and 72 million years ago, were left by hadrosaurs, commonly known as duck-billed dinosaurs (the crested creatures in this artist’s representation).

The consistent and excellent preservation of tracks suggests all the footprints were created within a short time period. Varying in width from 8 to 64 centimeters, the footprints cluster within four distinct size ranges, which researchers suggest represent specific age groups within a multigenerational herd. About 84% of the tracks were made by adult and near-adult hadrosaurs and 13% by young presumed to be less than 1 year old. A mere 3% of the tracks represent juvenile hadrosaurs, a rarity that strongly suggests the young of this species experienced a rapid growth spurt and therefore spent only a short time at this vulnerable size, the researchers report online this week in Geology.

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More fraud in peer-reviewed science

9:36 am

The science journal Nature today announced the retraction of two controversial stem cell papers.

The two papers reporting the stimulus-triggered acquisition of pluripotency (STAP) phenomenon appeared online on 29 January. Questions about the papers arose almost immediately, leading to an investigation by RIKEN, the headquarters of the network of the nationally funded laboratories that is based in Wako near Tokyo. Investigators documented several instances of fabrication and falsification in the papers and concluded that some of these constituted research misconduct on the part of [Haruko] Obokata [the lead author].

Japanese media recently reported that authors had agreed to retract the papers but were discussing the wording of the notice. In the note that appeared today, the authors point to errors previously identified by RIKEN investigations in supplementary documents. They also identify additional errors in both papers, including mix-ups in images, mislabeling, faulty descriptions, and “inexplicable discrepancies in genetic background and transgene insertion sites between the donor mice and the reported” STAP cells. [emphasis mine]

The list of errors now documented sound astonishing. In fact, I can’t see how any serious review by any competent specialist in this field could have missed them all, which suggests that for this research at least the peer-review process is mostly a sham. In fact, in the article Nature admits that its
» Read more

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Hippos in South America?

11:35 am

A wild herd of hippopotamuses that once belonged to a Colombian drug lord are now spreading across the countryside and no one knows what to do with them.

Situated halfway between the city of Medellin and Bogota, the Colombian capital, Hacienda Napoles was the vast ranch owned by the drugs baron Pablo Escobar. In the early 1980s, after Escobar had become rich but before he had started the campaign of assassinations and bombings that was to almost tear Colombia apart, he built himself a zoo.

He smuggled in elephants, giraffes and other exotic animals, among them four hippos – three females and one male. And with a typically grand gesture, he allowed the public to wander freely around the zoo. Buses filled with schoolchildren passed under a replica of the propeller plane that carried Escobar’s first US-bound shipments of cocaine. While Don Pablo masterminded the operations of the Medellin Cartel from his villa on the hill, the locals gazed at the strange animals and even stranger concrete dinosaurs that Escobar built for his son.

When Hacienda Napoles was confiscated in the early 1990s, Escobar’s menagerie was dispersed to zoos around the country. But not the hippos. For about two decades, they have wallowed in their soupy lake, watching the 20sq km (8 sq mile) park around them become neglected and overgrown – and then transformed back into a zoo and theme park, complete with water slides. All the while, the hippos themselves thrived, and multiplied.

The hippos also escaped from the zoo, and because the environmental conditions in Colombia are ideal for these invasive hippos, they are prospering wherever they go.

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