Tag: biology

First step in producing silicon-based life

9:04 am

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.

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Good HDL cholesterol might not be so good

8:55 am

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.

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Antarctic fungi survive Martian conditions on ISS

10:31 am

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.

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

9:34 am

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.

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Mold on ISS plants

9:26 am

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.

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Seeds from archaeological site grow into extinct squash

10:18 am

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!

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Grizzly bear no longer endangered in Yellowstone

4:57 pm

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.

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

4:45 pm

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.

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Real clam digging

6:01 pm

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?

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Yearlong mission on ISS reaches halfway point

9:25 am

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.

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Whiskey tastes strange after being aged in space

12:08 pm

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.

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

9:45 am

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.

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The Earth has a lot of trees!

9:32 am

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.

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Russia to do all-female simulated Moon mission

9:22 am

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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Requiring scientists to document their methods caused positive results in medical trials to plunge

9:35 am

The uncertainty of science: The requirement that medical researchers register in detail the methods they intend to use in their clinical trials, both to record their data as well as document their outcomes, caused a significant drop in trials producing positive results.

A 1997 US law mandated the registry’s creation, requiring researchers from 2000 to record their trial methods and outcome measures before collecting data. The study found that in a sample of 55 large trials testing heart-disease treatments, 57% of those published before 2000 reported positive effects from the treatments. But that figure plunged to just 8% in studies that were conducted after 2000. Study author Veronica Irvin, a health scientist at Oregon State University in Corvallis, says this suggests that registering clinical studies is leading to more rigorous research. Writing on his NeuroLogica Blog, neurologist Steven Novella of Yale University in New Haven, Connecticut, called the study “encouraging” but also “a bit frightening” because it casts doubt on previous positive results.

In other words, before they were required to document their methods, research into new drugs or treatments would prove the success of those drugs or treatment more than half the time. Once they had to document their research methods, however, the drugs or treatments being tested almost never worked.

The article also reveals a failure of the medical research community to confirm their earlier positive results:

Following up on these positive-result studies would be interesting, says Brian Nosek, a psychologist at the University of Virginia in Charlottesville and the executive director of the Center for Open Science, who shared the study results on Twitter in a post that has been retweeted nearly 600 times. He said in an interview: “Have they all held up in subsequent research, or are they showing signs of low reproducibility?”

Well duh! It appears the medical research field has forgotten this basic tenet of science: A result has to be proven by a second independent study before you can take it seriously. Instead, they would do one study, get the results they wanted, and then declare success.

The lack of success once others could see their methods suggests strongly that much of the earlier research was simply junk, not to be taken seriously.

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New Ebola vaccine 100% successful in trial

10:06 am

Using a different experimental approach aimed not only to test a new vaccine but also to stem an Ebola outbreak, scientists have found the new vaccine is 100% successful in providing exposed individuals protection from the virus.

Rather than create a complicated time-consuming trial with a control group getting a placebo — which also allows the epidemic to rage undisturbed — they focused on a different approach:

The Guinea trial — called ‘Ebola, ça suffit’ in French (‘Ebola, that’s enough’) — tested a ring vaccination design, a strategy that was borrowed from successful smallpox eradication efforts in the 1970s. After one patient contracts the disease, their close contacts are vaccinated in the hope of stemming the onward spread of the virus.

The Guinea trial included two arms: one in which adults who had been in contact with someone infected with Ebola and their subsequent contacts were vaccinated shortly after the original patient developed Ebola, and a second in which contacts instead received the vaccine three weeks later. The trial tested a vaccine called rVSV-ZEBOV, which is composed of an attenuated livestock virus engineered to produce an Ebola protein. The vaccine was developed by the Public Health Agency of Canada and then licensed to the drug companies NewLink Genetics and Merck.

Of the 2,014 people who received the vaccine immediately as part of the first arm, none developed Ebola ten days after getting the vaccine. The 10-day window allows the vaccine to summon an immune response and accounts for any pre-existing Ebola infection. (A few people in the immediate vaccination group, however, did develop the disease between 1 and 10 days after vaccination.) That compares with 16 infections among the 2,380 people in the second arm.

The findings mean that the vaccine provided 100% protection from the virus.

The results bring hope that Ebola is now a defeated virus.

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Counting bats on a Saturday evening

8:00 am

While most normal people spend their Saturday evenings going out to dinner followed by either a movie or a show, I spent this past Saturday doing something entirely different: counting bats!

There is a local cave here in the Tucson area that is a maternity colony for one species of bats. During the summer the females gather here to gossip and then give birth to their babies, after which they move on until next year. Because of a desire to help these bats, a few years ago the managers of the cave decided to close it during the summer months. This way humans wouldn’t be there to disturb the mothers during their labor.

The managers also decided to do regular bat counts of the bats leaving the cave each evening to feed, in order to get an estimate of the population size. To everyone’s delight they found the numbers rising year-to-year, following the summer closure. The total population of bats isn’t actually going up, but it appears that bats are finding this cave to be a good place to give birth, so more and more of them are making it their summer residence.

In the end the situation will contribute to an actual rise in population, as providing the maternity colony a safe haven will allow for more successful births and more babies.

In the past three years the bat count numbers over each summer would exhibit a typical bell curve, going up and then declining as the summer progressed, with the largest numbers ranging between 75 to 150 each night. However, last year there was one evening in which no bats left the cave. The bat biologist leading the bat count, Sandy Wolf, has theorized that this might be because the mothers are synchronizing their labor so that everyone gives birth at the same time and, because of that, on that night no one exits for feeding.. She knows that some species do this, but for this particular species such behavior has never been documented.

Anyway, she decided to find out. This has required that someone be at the entrance counting the bats at least every other evening. (In past years the counts were only done about once a week.) This has required more help, and thus Sandy has called for volunteers to do the work.

And that is how I and fellow caver Jerry Isaman ended up hiking up the hill to the cave with digital camera, infrared lights, and monitor this past Saturday.

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Growing and eating lettuce on ISS

8:59 am

Astronauts are about to eat a crop of romaine lettuce that they have grown entirely from seed on ISS.

The story is important as it indicates that the engineering to grow plants in space is continuing to improve. The article however is very wrong when it says that this will be the first salad grown and eaten in space. Russian astronauts have been working on this problem on their space stations since the 1970s, and in at least one case — which was captured on video almost a decade ago — have eaten space-grown lettuce. (I wrote about this event for Air & Space back in 2003.)

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Did some dinosaur soft tissues survive fossilization?

2:36 pm

The uncertainty of science: New research strongly suggests that within dinosaur fossils are found many preserved soft tissues from when the creature was still living.

As early as the 1970s, researchers captured images of what looked like cellular structures inside dinosaur fossils. But did the structures contain actual tissue? Proteins commonly decay hundreds to thousands of years after an organism dies, but in rare cases they have been known to survive up to 3 million years. In a series of studies beginning a decade ago, a team led by North Carolina State University paleontologist Mary Schweitzer reported that they had extracted what appeared to be collagen, the most abundant protein in bone, from a 68-million-year-old T. rex fossil. They sequenced fragments of the protein and concluded that it closely matched that of birds, dinosaurs’ living descendants (see here and here). But other teams haven’t been able to replicate the work, and others suggested that the collagen could be contamination.

The new study, led by materials scientist Sergio Bertazzo and paleontologist Susannah Maidment, both of Imperial College London, has a different strategy for hunting down ancient proteins. Bertazzo, an expert on how living bones incorporate minerals, uses a tool called a focused ion beam to slice through samples, leaving pristine surfaces that are ideal for high-resolution imaging studies. He teamed up with Maidment to apply the technique to eight chunks of dinosaur toe, rib, hip, leg, and claw.

What they found shocked them. Imaging the fresh-cut surfaces with scanning and transmission electron microscopes, “we didn’t see bone crystallites” as expected, Maidment says. “What we saw instead was soft tissue. It was completely unexpected. My initial response was these results are not real.” [emphasis mine]

It must be noted that the new research depends on many uncertainties that still need to be replicated or confirmed.

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$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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