Tag Archives: biology

Polio returns to Nigeria

Two years after the last previous case and only one year from declaring Nigeria polio-free, two children have been diagnosed with the crippling virus.

They are going to immediately begin immunizing 5 million children in the affected region.

Coincidentally, that area has been the epicenter of an insurgency waged by Boko Haram, an Islamist militant group that has killed tens of thousands of people and displaced more than 2 million since their fight began in 2009. During Boko Haram’s time in Borno, the group has been responsible for destroying hundreds of health centers, and has caused so much damage in some areas that it has become hard for vaccinators to do their jobs effectively.

One can’t help wondering if these new cases occurred because of this Islamic insurgency.

Posted on the road from Tucson to the Grand Canyon.

July 12, 2016 Zimmerman/Batchelor podcast

Embedded below the fold. I spent a large portion of the podcast talking about the medical problems caused by long-term weightlessness, and how it might limit our ability to send humans to other planets. We also touched on the possible consequences to space policy should Donald Trump pick Newt Gingrich as his VP.
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Vision problems from weightlessness

This article provides an excellent review of the vision problems caused by long term exposure to weightlessness, including the efforts to study the problem on Earth.

Bottom line:

Before a human trip to Mars — a journey of six-to-nine months that NASA says it wants to achieve by the 2030s — researchers agree that VIIP [the name given to this problem] must be understood much better. VIIP could be the first sign of greater dangers to the human body from microgravity. “We’re seeing the visual and neural, ophthalmic manifestations of it,” Barratt said. “I’m fairly certain this is a bit more global than that.”

Richard Williams, the chief health and medical officer at NASA, agrees that what we do not know about VIIP still poses the biggest threat. Ironically, one of the only ways to get more knowledge is spend more time in microgravity. “The longer we stay in space, the more we’re going to learn,” Williams said.

Kelly describes medical issues from weightlessness

In prepared remarks to a congressional subcommittee today, astronaut Scott Kelly described the medical problems he has experienced since returning from his 340 day mission on ISS.

Kelly claimed in these remarks that weightlessness caused permanent effects (which this news article decides to emphasize), but I think that might be an overstatement. None of the specific problems he experienced appear to be permanent ones, and in my interviews with Russian astronauts who stayed even longer on Mir they noted no permanent effects. One did say however that the recovery time tended to match the mission time, so that if you spent a year in space it took a year to completely recover. Kelly has only been back about three months, so his recovery is certainly not over yet.

Update: Kelly’s remarks were part of a hearing promoting legislation that would give astronauts lifetime medical coverage from the government. Thus, there is a bit of lobbying going on here.

New jellyfish spotted at 2 miles depth

A NOAA mapping robot working two miles beneath the ocean surface recently captured video of a species of jellyfish previously unknown.

The newly discovered jellyfish has two sets of tentacles, short and long. When the the long tentacles are even and extended outward, and the bell is motionless, this could mean it’s readying to ambush its prey, scientists speculate. Inside the bell, red radial canals connect what scientists say looks like the bright yellow gonads.

I have posted the video below the fold.
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Fake images in biology research papers

The uncertainty of peer review: A new study has found that since 1995 as many as 5.5% of all biomedical research papers per year contain duplicate or faked images.

Bik, who is at Stanford University in California, spent two years looking at articles published from 1995 to 2014 in 40 different journals, hunting for instances in which identical images were used to represent different experiments within the same paper. She cross-checked the duplications that she found with her two co-authors, both microbiologists.

Overall, 4% of the inspected papers contained such images, the researchers found. But rates ranged from over 12% in the International Journal of Oncology, to 0.3% in the Journal of Cell Biology, which has since 2002 systematically scanned images in its accepted papers before publication. Journals with higher impact factors generally had lower rates of duplicated images.

…Many of the problems were probably sloppy mistakes where people selected the wrong photograph, says Bik. But half or more look deliberate — because images are flipped or rotated or the same features occur twice in the same photograph. [emphasis mine]

Essentially, a significant number of scientists in medical research are purposely faking data.

Avoiding the period in space

New research has outlined the techniques available to female astronauts to prevent menstruation in space.

Rather than researching the consequences of women having a period in space, the researchers are recommending that women avoid them completely, something that appears to have been the policy of NASA on ISS. This is a big mistake. The whole point of having a space station is to find out the consequences to the human body imposed by weightlessness. Future space explorers will need to reproduce. We need to know now if that will be possible.

China grows mouse embryos in space

During a two week unmanned biology satellite mission, Chinese scientists successfully demonstrated that mouse embryos can develop in weightlessness.

The team developed an embryo culture system and placed it within a small enclosed chamber [on the spacecraft] that provides the ideal conditions for the embryos to develop in space. While the chamber was in orbit, a camera attached to the experiment took photographs of the embryos as they developed in microgravity, and sent these images back to Earth. With the aid of their imaging technology, the researchers were able to observe how the mammalian two-cell stage embryos developed into blastocysts under microgravity after four days. Blastocysts are structures formed in the very early development of mammals. In humans blastocysts begin to form five days after fertilization.

The researchers will now compare their space-developed embryos to those cultured in normal laboratory environments on Earth to see what differences there are between the two at both a cellular and molecular level.

None of this proves that life can be conceived and grow in weightlessness. It does however suggest that it might be possible.

Liver damage from weightlessness?

The uncertainty of science: Mice flown for almost two weeks on the last space shuttle mission in 2011 have shown evidence of the early symptoms of liver disease.

The mice spent time orbiting the Earth on the final space shuttle flight in 2011. Once they returned home, teams of scientists were allowed to share and study their internal organs.

Jonscher’s team found that spaceflight resulted in increased fat storage in the liver, comparing pair-fed mice on Earth to those on the shuttle. This was accompanied by a loss of retinol, an animal form of Vitamin A, and changes to levels of genes responsible for breaking down fats. As a result, mice showed signs of nonalcoholic fatty liver disease (NAFLD) and potential early indicators for the beginnings of fibrosis, which can be one of the more progressive consequences of NAFLD. “It generally takes a long time, months to years, to induce fibrosis in mice, even when eating an unhealthy diet,” Jonscher said. “If a mouse is showing nascent signs of fibrosis without a change in diet after 13 ½ days, what is happening to the humans?”

This result doesn’t prove that weightlessness causes liver damage. It only suggests that more research is needed, though the data from six month to year long missions suggest that the liver harm to humans is either non-existent or temporary.

Tetanus boosters can work for almost thirty years

The uncertainty of science: A new study has found that tetanus vaccine booster shots might last three times longer than previously believed.

The study looked for tetanus antibodies in 546 adults who had received the tetanus vaccine at some point in the past. Of those 546 adults, the researchers found that 97 percent still had sufficient antibodies to fight off tetanus. Since tetanus boosters are also designed to fight diphtheria, the same percentage also had antibodies to fight off that disease.

The researchers then looked at the amount of antibodies present in each individual compared to the amount of time that had passed since they received their vaccines. The result was that the study determined the half-life of a tetanus booster to be about 14 years, which means that the average person should be able to go about 28 years between boosters, or almost three times as long as the current CDC recommendation.

The half-life for diphtheria immunity was found to be even longer, at about 27 years, or roughly 54 years between boosters.

White nose syndrome found on Washington state bat

Bad news for bats: Scientists have confirmed a bat with white nose syndrome in the state of Washington, 1,300 miles further west than the previous detection.

On March 11, hikers found the sick bat about 30 miles east of Seattle near North Bend, and took it to Progressive Animal Welfare Society (PAWS) for care. The bat died two days later, and had visible symptoms of a skin infection common in bats with WNS. PAWS then submitted the bat for testing to the USGS National Wildlife Health Center, which confirmed through fungal culture, molecular and pathology analyses that it had WNS.

I hate to express such a thought, but I can’t help wonder about the legitimacy of this detection. It is so far west and so far from the nearest other bat with white nose syndrome I cannot understand how this bat came to be infected, naturally. In order for this discovery to be confirmed they are going to have to detect it again, and more than once, on a number of bats. Otherwise, it will remain suspect and a possible false positive.

The worst part of this is that the government is surely going to begin instituting draconian measures to protect the bats in Washington, as well as across the entire western United States, even before this detection is confirmed. Having this single detection will make it much easier for government officials to ban humans from many more places, even though white nose syndrome is nowhere close.

Does captivity hurt or help killer whales? Scientists disagree

The uncertainty of science: Two different science research teams strongly disagree about the positive or negative effects of living in captivity for killer whales.

In a decision hailed by animal-rights groups, the US marine-park company SeaWorld Entertainment announced last week that it will no longer breed killer whales. But whether captivity harms the planet’s biggest predator is an area of active scientific debate.

The latest arguments centre on two 2015 studies that drew dramatically different conclusions about the lifespans of captive killer whales (Orcinus orca), relative to those of wild populations. Although many factors affect well-being, an apparent discrepancy between the survival of captive and wild animals has long been cited by activists as evidence of the poor welfare of captive killer whales.

One of the studies is authored by a team largely made up of researchers at SeaWorld, which is headquartered in Orlando, Florida, and owns several animal parks that keep killer whales; the other is by two former killer-whale trainers at the company who feature in the 2013 documentary film Blackfish, which is critical of SeaWorld. In letters published last week, authors from each paper accuse the others of cherry-picking data to support positions on whether the animals should be captive — charges that each team in turn rejects.

Obviously, each science team has its own agendas. The result unfortunately is that the science is cloudy and unclear.

Injected stem cells cure osteoporosis in mice

Scientists have discovered that an injection of stem cells into mice with osteoporosis was able to completely cure them of the bone disease.

Researchers at the University of Toronto and The Ottawa Hospital had previously found a causal effect between mice developing age-related osteoporosis and a deficiency in mesenchymal stem cells (MSCs). One of the promising attributes of MSCs is that, while they can grow into different cells in the body just like other stem cells, they can be transplanted without the need for a match. “We reasoned that if defective MSCs are responsible for osteoporosis, transplantation of healthy MSCs should be able to prevent or treat osteoporosis,” says William Stanford, senior scientist at The Ottawa Hospital and Professor at the University of Ottawa.

To put this reasoning to the test, the scientists injected MSCs into mice with the condition. Six months later, which is one quarter of the life span of the animal, they observed a healthy functional bone in place of the damaged one. “We had hoped for a general increase in bone health,” says John E. Davies, co-author of the study. “But the huge surprise was to find that the exquisite inner ‘coral-like’ architecture of the bone structure of the injected animals – which is severely compromised in osteoporosis – was restored to normal.”

The importance of this discovery for space travel is that it might eventually allow scientists to use it to somehow prevent the loss of bone density during weightlessness.

First step in producing silicon-based life

The Horta live! Scientists have succeeded in creating a bacteria that can produce hydrocarbon compounds that incorporate silicon into their make-up.

To get biology to adopt silicon, Frances Arnold, a chemist at the California Institute of Technology (Caltech) in Pasadena, along with postdoctoral assistant Jennifer Kan and graduate student Rusty Lewis, started by isolating a so-called thermophilic bacterium, which grows in hot springs. Like many organisms, the bacterium contains an enzyme called cytochrome c, which shuttles electrons to other proteins, making it widely useful in biochemistry. In some cases, however, enzymes in thermophilic bacteria expand their roles to carry out other reactions on the side. So the Caltech researchers tested their microbe and found that in rare cases its cytochrome c also added silicon to hydrocarbons.

In nature, Arnold notes, cytochrome c’s silicon-adding ability is so feeble that it’s probably just a byproduct of the enzyme’s function—not even close to its primary role. To try to beef it up, the team incubated the bacteria with silicon and carbon compounds and selected the organisms that produced the most hydrocarbons that incorporated silicon. After only three rounds of this artificial selection, the enzymes had evolved to churn out silicon-containing hydrocarbons 2000 times as readily as natural cytochrome c. “The power of evolution really shows up when a new function appears and then is forced to adapt via directed evolution,” Arnold says.

For now, the silicon-spiked hydrocarbon compounds, called organosilanes, probably aren’t useful either to the bacteria or to industry. They’re short and stubby, unlike the long chainlike versions that chemical companies make for uses such as adhesives, caulks, and sealants.

As the article notes, they really are very far from creating a silicon-based life. Still, to get silicon incorporated into carbon-based organic chemistry is a significant first step, as it demonstrates that the theory of silicon-based life might very well have merit.

Good HDL cholesterol might not be so good

The uncertainty of science: New research now suggests an explanation for why in some cases having a high level of the supposedly good HDL cholesterol is not a good thing.

They think it is genetic, and that some people are missing the genes that help the HDL work to clean cholesterol out of the body. It is important however to recognize the uncertainties here. They still do not understand very well how this all works.

Exploding nanobubbles destroy cancer cells

Scientists have found a way to use tiny nanoparticles of gold to destroy 100% of the cancer cells in mice.

The engineering is complex, but the nanoparticles tend to cluster around cancer cells, and when heated cause water around them to vaporize, destroying the cells. Human trials expected within two years.

Antarctic fungi survive Martian conditions on ISS

A European experiment on ISS has found that fungi from Antarctica can survive in a Mars-like environment.

For 18 months half of the Antarctic fungi were exposed to Mars-like conditions. More specifically, this is an atmosphere with 95% CO2, 1.6% argon, 0.15% oxygen, 2.7% nitrogen and 370 parts per million of H2O; and a pressure of 1,000 pascals. Through optical filters, samples were subjected to ultra-violet radiation as if on Mars (higher than 200 nanometres) and others to lower radiation, including separate control samples. “The most relevant outcome was that more than 60% of the cells of the endolithic communities studied remained intact after ‘exposure to Mars’, or rather, the stability of their cellular DNA was still high,” highlights Rosa de la Torre Noetzel from Spain’s National Institute of Aerospace Technology (INTA), co-researcher on the project.

Does this prove that life exists on Mars? Not at all (though I wouldn’t be surprised if we see news articles in the mainstream press over the next week suggesting exactly that). It does show us once again that life is resilient and could develop in many very extreme environments.

Fraud detected in science research that suggested genetically modified crops were harmful

The uncertainty of peer review: Three science papers that had suggested that genetically modified crops were harmful to animals and have been used by activist groups to argue for their ban have been found to contain manipulated and possibly falsified data

Papers that describe harmful effects to animals fed genetically modified (GM) crops are under scrutiny for alleged data manipulation. The leaked findings of an ongoing investigation at the University of Naples in Italy suggest that images in the papers may have been intentionally altered. The leader of the lab that carried out the work there says that there is no substance to this claim.

The papers’ findings run counter to those of numerous safety tests carried out by food and drug agencies around the world, which indicate that there are no dangers associated with eating GM food. But the work has been widely cited on anti-GM websites — and results of the experiments that the papers describe were referenced in an Italian Senate hearing last July on whether the country should allow cultivation of safety-approved GM crops. “The case is very important also because these papers have been used politically in the debate on GM crops,” says Italian senator Elena Cattaneo, a neuroscientist at the University of Milan whose concerns about the work triggered the investigation.

I know I am generalizing here and have not actually researched this, but I would bet that many of those same anti-GM websites and the people who support them are also firm believers in human-caused global warming. Similarly, I would guess that if you asked these scientists above who wrote the anti-GM papers they also would be firm believers in human-caused global warming. I know this is a guess, but based on years of watching these political battles I think a very safe guess.

Mold on ISS plants

In December four of seven zinnia plants in a greenhouse on ISS became sickly or died because they were receiving too much water and developed mold.

The story doesn’t really tell us much, but this paragraph reveals I think some fundamental management problems in the way NASA is running the station:

ISS commander and NASA astronaut Scott Kelly reported the mold to Mission Control Dec. 22 just as Veggie principal investigator Trent Smith was trying to manage the water problem. In pictures, Smith saw water on the plants a few days before. He told Discovery News he was trying to relay a command from NASA’s station operations team to increase fan speed in Veggie, but the mold developed before the command could be put through. One solution was, on Christmas Eve, to designate Kelly “commander” of Veggie. Kelly now has more autonomy to make changes to Veggie’s conditions if he feels the plants need it.

The scientist noticed a problem but was unable to cut through the communications bureaucracy to talk to the astronauts so that changes could be made quickly. Meanwhile, the astronauts on board ISS had not been given the freedom to make common sense changes themselves. The result is that some of the plants died.

The solution, to give an astronaut more “autonomy”, is one that the Russians learned a long time ago on their Mir space station. It was also a lesson NASA learned even longer ago on Skylab. Moreover, when astronauts are finally flying interplanetary spaceships to the planets with greenhouses just like this, they will have to have that autonomy, no matter what rules NASA establishes. It seems amazing to me that NASA is still learning this lesson now.

One more thought: It is not really a problem that the scientist had trouble reaching the astronauts quickly. In fact, it probably indicates an area of management that NASA is handling well. Communications from the ground up to ISS can be a major problem, as everyone wants to talk to the astronauts and if NASA didn’t control that communications the astronauts would never have time to do anything. Thus, placing limits on that communications makes sense, though once again it also requires that the astronauts be given a great deal of freedom to make their own decisions, as they might not be able to talk to the right experts whenever necessary.

Seeds from archaeological site grow into extinct squash

Update: It appears the story below is bogus. (Hat tip Pzatchok.) It appears to be a combination of two different stories, one in which gardeners from the Miami Nation in Indiana donated old seeds to a research group, and the second where that same research group attempted to grow seeds found in a Kentucky cave, with poor results.

Original post:
Students who discovered some ancient seeds in a clay pot at an archaeological site in Canada successfully planted them to grow a previously extinct species of squash.

Not all the seeds grew, but enough did. Moreover, the new squash produced new seeds. This once extinct squash is no longer extinct. And according to the article is also tastes delicious!

Grizzly bear no longer endangered in Yellowstone

Good news! Federal wildlife officials have determined that the grizzly bear population in and around Yellowstone has recovered so well that they have the option of removing the species from the endangered species list.

The latest count of grizzlies in the Yellowstone region puts the estimated population of the hump-shouldered bruins at just over 750, well exceeding the government’s recovery goal of 500 animals, according to the U.S. Fish and Wildlife Service. That compares with just 136 believed left in the Yellowstone ecosystem – encompassing parts of Wyoming, Montana and Idaho – when grizzlies were formally listed as threatened throughout the Lower 48 states in 1975, after they were hunted, trapped and poisoned to near extinction.

Not surprisingly, the article notes how environmental and American Indian groups oppose changing the bear’s status. Want to bet that they win the day and the bear remains endangered? Science really has very little to do with the endangered species act these days. It is all politics.

A hybrid coyote/wolf prospers in the eastern U.S.

A new hybrid species, two-thirds coyote and one-third wolf with a little bit of dog, has spread throughout the eastern United States in the past century.

The animal’s range has encompassed America’s entire north-east, urban areas included, for at least a decade, and is continuing to expand in the south-east following coywolves’ arrival there half a century ago. This is astonishing. Purebred coyotes never managed to establish themselves east of the prairies. Wolves were killed off in eastern forests long ago. But by combining their DNA, the two have given rise to an animal that is able to spread into a vast and otherwise uninhabitable territory.

Called either the eastern coyote or the coywolf, it is estimated that their population could now be as high as a million.

Posted from Mexico City.

Real clam digging

An evening pause: Rocco had suggested this short video about the joys of going out and digging clams. I prefer the video below, of a real clam doing its own digging, because it shows us something we normally don’t see and that is really amazing. Who would have thought that a clam could bury itself so quickly, with a single digging foot?

Yearlong mission on ISS reaches halfway point

The yearlong manned mission on ISS is now halfway over.

If they complete their planned 341-day mission through March, Mark Kelly and Mikhail Kornienko will have logged the fifth and sixth longest human flights in space. They will not complete a full year in space, (as has been advertised by NASA), something that four Russians did in their Mir space station, including one flight of fourteen and a half months.

I had not realized that this mission was not actually a complete year until I read the story above. In reality, they are actually only spending just over eleven months in space. I find this very disappointing. The whole reason to have ISS is to do these long missions. To cut this short of a year seems silly. If anything, they should take advantage of the situation and try to push to break the longevity mission of 14.5 months.

Whiskey tastes strange after being aged in space

Whiskey that was aged for three years on ISS was taste-tested this past week in Scotland, and the testers all found the taste “completely unlike anything they have ever tasted before.”

The space whiskey had a much smokier quality, with flavors akin to cherries, prunes, raisins, and cinnamon, he said. He also noted that the whiskey’s aftertaste was “pungent, intense, and long, with hints of wood, antiseptic lozenges, and rubbery smoke.” This was in contrast to the Earth-aged whiskey, which had richer flavors more characteristic of whiskey drinks. The space whiskey still had strong flavor, but they were strange, Lumsden said — and not particularly good. He still has yet to figure out why. “That I haven’t been able to work out yet,” he said.

This is not the same Japanese whiskey that was recently sent up to ISS. That is a second experiment, along the same lines.

New engineering gives a man paralyzed from the waist down the ability to walk again.

Using a new exoskeleton design combined with non-invasive spinal simulation engineers have made it possible for a man paralyzed from the waist down to walk again.

Leveraging on research where the UCLA team recently used the same non-invasive technique to enable five completely paralyzed men to move their legs, the new work has allowed the latest subject, Mark Pollock, to regain some voluntary movement – even up to two weeks after training with the external electrical stimulation had ended.

Pollock, who had been totally paralyzed from the waist down for four years prior to this study, was given five days of training in the robot exoskeleton, and a further two weeks muscle training with the external stimulation unit. The stimulated and voluntary leg movements have not only shown that regaining mobility through this technique is possible, but that the training itself provides a range of health benefits in itself, especially in enhanced cardiovascular function and improved muscle tone.

The new system has been created as an amalgam of a battery-driven bionic exoskeleton that allows users’ leg movements to propel the unit in a step-by-step way, and a non-invasive external stimulator to trigger nerve signals to create the leg movements. In this way, Pollock made significant progress after being given just a few weeks physical training without spinal stimulation and then five days of spinal stimulation exercise an hour a day over a week-long period. “In the last few weeks of the trial, my heart rate hit 138 beats per minute,” said Pollock. “This is an aerobic training zone, a rate I haven’t even come close to since being paralyzed while walking in the robot alone, without these interventions. That was a very exciting, emotional moment for me, having spent my whole adult life before breaking my back as an athlete.”

His ability to walk is not achieved easily, and without extensive help and preparation fades. However, the results here are very hopeful that future developments will make it possible for paraplegics to once again walk.

The Earth has a lot of trees!

The uncertainty of science: A new estimate of the number of trees on Earth has increased that estimate seven-fold, from about 400 billion to 3 trillion.

The previously accepted estimate of the world’s tree population, about 400 billion, was based mostly on satellite imagery. Although remote imaging reveals a lot about where forests are, it does not provide the same level of resolution that a person counting trunks would achieve.

Crowther and his colleagues merged these approaches by first gathering data for every continent except Antarctica from various existing ground-based counts covering about 430,000 hectares. These counts allowed them to improve tree-density estimates from satellite imagery. Then the researchers applied those density estimates to areas that lack good ground inventories. For example, survey data from forests in Canada and northern Europe were used to revise estimates from satellite imagery for similar forests in remote parts of Russia.

That these same scientists can, in this same story, also claim with almost certainty that the number of trees on Earth has declined precisely 46% since homo sapiens appeared 12,000 years ago illustrates the difficulty humans have to remain skeptical. How do they get this precise number for the tree count 12,000 years ago? It appears to me that they have allowed the modern environmental agenda of blaming the evil destruction of the environment on humanity to cloud their thinking.

If scientists have discovered a seven-fold error in their count today, I am sure the margin of error for an estimate for 12,000 years ago will be much higher.

Russia to do all-female simulated Moon mission

The competition heats up: The Institute of Biomedical Problems in Moscow has announced plans to do an all-female eight day simulated mission to the Moon.

Currently scheduled for October-November 2015, the experiment will differ from the Mars-500 venture not just in duration but most notably in crew composition. For Moon-2015, all the participants will be women, drawn from the staff at IBMP itself.

In their July announcement, IBMP named the ten volunteers from whom the actual crew will be chosen. All have strong scientific, medical or research backgrounds and many have worked in the space or aviation medicine sphere, working closely with cosmonauts before or after visits to the International Space Station (ISS).

The Institute’s focus is medical, so the goal is not to develop engineering to get to the Moon but to study the human body and how it reacts to living in a spacecraft environment. In this case, they can’t simulate weightlessness so the only thing they can study is how the crew interacts with each other in a confined space for a period of time.

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