Tag Archives: Science

Scientific Inquiry: Arsenic for Phosphorus in Bacteria Cells

As would be expected with significant new scientific claims, scientists are examining the evidence. On her blog, Rosie Redfield, who runs a microbiology research lab in the Life Sciences Centre at the University of British Columbia, disputes NASA’s recent claims. This is how science is suppose to work. Scientists provide evidence. Other scientists review the evidence, try to verify the claims with experiments of their own and the scientific inquiry process moves toward new knowledge.

Arsenic-associated bacteria (NASA’s claims)

NASA’s shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that’s only strengthened by my reading of this paper. Basically, it doesn’t present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).
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The authors then grew some cells with radioactive arsenate (73-As) and no phosphate, washed and dissolved them, and used extraction with phenol and phenol:chloroform to separate the major macromolecules. The protein fraction at the interface between the organic and aqueous phases had about 10% of the arsenic label but, because the interface material is typically contaminated with liquid from the aqueous phase, this is not good evidence that the cells’ protein contained covalently-bound arsenate in place of phosphorus. About 75% of the arsenic label was in the ‘supernatant ‘fraction. The authors describe this fraction as DNA/RNA, but it also contains most of the small water-soluble molecules of the cell, so its high arsenic content is not evidence that the DNA and RNA contain arsenic in place of phosphorus. The authors use very indirect evidence to argue that the distribution of arsenic mirrors that expected for phosphate, but this argument depends on so many assumptions that it should be ignored.
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I don’t know whether the authors are just bad scientists or whether they’re unscrupulously pushing NASA’s ‘There’s life in outer space!’ agenda. I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science’s editors in their eagerness to score such a high-impact publication.

New claims have to provide strong evidence. time will tell if this discovery is actually a discovery. It will be amazing if it is, so I am pulling for it. But the story will need to have much more confirmation before we can be certain.

Arsenate-based DNA: a big idea with big holes

The study published in Science has a number of flaws. In particular, one subtle but critical piece of evidence has been overlooked, and it demonstrates that the DNA in question actually has a phosphate – not an arsenate -backbone.
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Wolfe-Simon et al. used a technique called nanoSIMS to analyze elemental concentrations of the agarose gel at the location of the DNA band. They determined that the part of the gel containing DNA also contained both arsenic and phosphorus. But what did they really analyze?

The answer is that the nanoSIMS determined the concentration of arsenic in the gel – not specifically in the DNA.
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Finally, there’s a simple experiment that could resolve this debate: analyze the nucleotides directly. Show a mass spectrum of DNA sequences demonstrating that nucleotides contain arsenate instead of phosphate. This is a very simple experiment, and would be quite convincing – but it has not been performed.

Changing Life as We Know It

Update: Independent researchers find no evidence for arsenic life in Mono Lake

NASA has made a discovery that changes our understanding of the very makeup of life itself on earth. I think my favorite scientific discipline name is astrobiology. NASA pursues a great deal of this research not just out in space but also looking at earth based life. Their astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

Felisa Wolfe-Simon processing mud from Mono Lake to inoculate media to grow microbes on arsenic.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

Researchers conducting tests in the harsh, but beautiful (see photo), environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.” This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.

In science such huge breakthroughs are not just excepted without debate, however, which is wise.

Thriving on Arsenic:

In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

It is sure a great story if it is true though. Other scientists will examine more data and confirm or disprove the claims.

“We know that some microbes can breathe arsenic, but what we’ve found is a microbe doing something new — building parts of itself out of arsenic,” said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team’s lead scientist. “If something here on Earth can do something so unexpected, what else can life do that we haven’t seen yet?”
Continue reading →

Aerobic Exercise Plus Resistance Training Helps Control Type 2 Diabetes

Exercise Combo Best for Controlling Diabetes

A combination of aerobic exercise and resistance training may offer the biggest benefits for people with type 2 diabetes in helping them control their disease.
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HbA1c is a test that measures blood sugar control for the previous few months. Normal HbA1c is 6% or less. People with diabetes are urged to keep their HbA1c below 7%.

In the study, researchers compared the effects of a nine-month aerobic exercise program, a resistance training program, and combination exercise program vs. not exercising in 262 previously sedentary men and women with type 2 diabetes. The results showed that improvements in HbA1c levels were greatest among those who were in the combination group.
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Thirty-nine percent of non-exercisers had to increase these medications compared with 32% in the resistance training group, 22% in the aerobic exercise group, and 18% in the combination group.

Diabetes is a huge and growing problem. Exercise is a good strategy to remain healthy. It is best to exercise and avoid becoming sick. But if you do get diabetes then it is even more important to take care to exercise properly.

Real Time Hologram Projection Getting Closer

A team led by the University of Arizona professor of Materials Science and Engineering Nasser Peyghambarian has developed a new type of holographic telepresence that allows the projection of a three-dimensional moving image without the need for special eyewear such as 3D glasses or other auxiliary devices.

“Holographic telepresence means we can record a three-dimensional image in one location and show it in another location, in real-time, anywhere in the world,” said Peyghambarian, who led the research effort.

“Holographic stereography has been capable of providing excellent resolution and depth reproduction on large-scale 3D static images,” the authors wrote, “but has been missing dynamic updating capability until now.”

The prototype device uses a 10-inch screen, but Peyghambarian’s group is already successfully testing a much larger version with a 17-inch screen. The image is recorded using an array of regular cameras, each of which views the object from a different perspective. The more cameras that are used, the more refined the final holographic presentation will appear.

The Sahara Wasn’t Always a Desert

Green Sahara

For much of the past 70,000 years, the Sahara has closely resembled the desert it is today. Some 12,000 years ago, however, a wobble in the Earth’s axis and other factors caused Africa’s seasonal monsoons to shift slightly north, bringing new rains to an area nearly the size of the contiguous United States. Lush watersheds stretched across the Sahara, from Egypt to Mauritania, drawing animal life and eventually people.
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by some 3,500 years ago the desert had returned. The people vanished.
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The twilight of the Green Sahara around 4,500 years ago might have been the perfect time to be hunting at Gobero, said Carlo Giraudi, the team’s geologist. As water sources dried up throughout the region, animals would have been drawn to pocket wetlands, making them easier to kill. Four middens found on the dunes and dated to around that time included hundreds of animal remains, as well as fish bones and clamshells—not usually part of a herder’s diet. “The Green Sahara’s climate was rapidly changing,” said Giraudi, “but just before the lake dried up, the people at Gobero would have thought they were living in a golden period.”

There are many values of science: letting our curious minds learn, giving us cool robots and gadgets and letting us learn about the past (and thus about the ever-changing world we live in).

Boa Constrictor Gives Birth to Clones

Snake gives ‘virgin birth’ to extraordinary babies

A female boa constrictor snake has given birth to two litters of extraordinary offspring. Evidence suggests the mother snake has had multiple virgin births, producing 22 baby snakes that have no father. More than that, the genetic make-up of the baby snakes is unlike any previously recorded among vertebrates, the group which includes almost all animals with a backbone.
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“All offspring are female. The offspring share only half the mother’s genetic make-up,” he told the BBC.
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Humans for example have X or Y sex chromosomes; females have two X chromosomes and males have a combination of an X and a Y chromosome. In place of X and Y, snakes and many other reptiles have Z and W chromosomes.

In all snakes, ZZ produces males and ZW produces females. Bizarrely, all the snakes in these litters were WW. This was further proof that the snakes inherited all their genetic material from their mother, as only females carry the W chromosome.

“Essentially they are half clones of their mother,” says Dr Booth. That is because the baby snakes have inherited two copies of one half of their mother’s chromosomes, including one W chromosome.
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More astonishing though, is that no vertebrate animal in which the females carry the odd sex chromosome (in this case the W chromosome) has ever been recorded naturally producing viable WW offspring via a virgin birth.

“For decades WW has been considered non-viable” says Dr Booth. In such species, all known examples of babies that are the product of parthenogenesis are male, carrying a ZZ chromosomal arrangement.

Driver Thanks Engineer Who Hit Him on Purpose

Driver thanks man who hit him on purpose

Driving to a Mariners game, Duane Innes saw a pickup ahead of him drift across lanes of traffic, sideswipe a concrete barrier and continue forward on the inside shoulder at about 40 mph. A manager of Boeing’s F22 fighter-jet program [and engineer by training], Innes dodged the truck, then looked back to see that the driver was slumped over the wheel. He knew a busy intersection was just ahead, and he had to act fast.
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“Basic physics: If I could get in front of him and let him hit me, the delta difference in speed would just be a few miles an hour, and we could slow down together,” Innes explained. So he pulled in front of the pickup, allowed it to rear-end his minivan and brought both vehicles safely to a stop in the pull-off lane.
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Some might say the driver of the truck, 80-year-old Bill Pace, of Bellevue, and anyone Pace’s truck might have slammed into had luck on their side that day. A retiree who volunteers for Special Olympics and organizes food drives, Pace didn’t know it at the time, but he’d had a minor heart attack two days earlier and his circulation was so poor he passed out at the wheel with his foot resting on the accelerator.

Nice story and nice that the article had a tiny bit of science in the story, with another example of good work by an engineer.

Science and Optical Illusions

More illusions by R Beau Lotto, lecturer in neuroscience, University College London

The middle tiles on the cube both have the same color, even though they appear very different to most of us.

The science of optical illusions

the two physically identical tiles do indeed now look very different.
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Why? The information in the image strongly suggests that the dark brown tile on the top now means a poorly reflective surface under bright light, whereas the bright orange one at the side means a highly reflective surface in shadow.
… [from another illusion]
So why do they look so different? Because your brain takes the image on the retina and creates what it sees according to what the information would have meant in the brain’s past experience of interacting with the world.

In this case the angles suggest depth and perspective and the brain believes the green table is longer than it is while the red table appears squarer.

The beautiful thing about illusions is they make us realise things are never what they seem, and that our experiences of the world shape our understanding of it.

Studying illusions can teach us several things. We can learn that it is easy for our senses to be fooled. We can learn about how the brain works. We can also learn how to take into account how our brain works to try and adjust our opinions (to be careful we are not just interpreting things incorrectly). It is amazing to see some of the wild guidance our brains give us. Normally they do a fantastic job of guiding us through our day but they have weaknesses that can lead us to mistaken conclusions.

Monarch Butterflies Use Medicinal Plants

Monarch butterflies eat toxic plants (that they have evolved to tolerate and make the butterflies themselves toxic to predators). They use medicinal plants to treat their offspring for disease, research by Emory biologists shows. When the butterflies are infected by certain parasites the butterflies have a strong preference to lay their eggs on a plant (tropical milkweed) that will help the caterpillar fight the parasite when it eats those leaves (it serves as a drug for them). Their experiments may be the best evidence to date that animals use medication.

The DIY Movement Revives Learning by Doing

School for Hackers

The ideal educational environment for kids, observes Peter Gray, a professor of psychology at Boston College who studies the way children learn, is one that includes “the opportunity to mess around with objects of all sorts, and to try to build things.” Countless experiments have shown that young children are far more interested in objects they can control than in those they cannot control—a behavioral tendency that persists. In her review of research on project-based learning (a hands-on, experience-based approach to education), Diane McGrath, former editor of the Journal of Computer Science Education, reports that project-based students do as well as (and sometimes better than) traditionally educated students on standardized tests, and that they “learn research skills, understand the subject matter at a deeper level than do their traditional counterparts, and are more deeply engaged in their work.” In The Upside of Irrationality, Dan Ariely, a behavioral psychologist at Duke University, recounts his experiments with students about DIY’s effect on well-being and concludes that creating more of the things we use in daily life measurably increases our “feelings of pride and ownership.” In the long run, it also changes for the better our patterns of thinking and learning.

Unfortunately, says Gray, our schools don’t teach kids how to make things, but instead train them to become scholars, “in the narrowest sense of the word, meaning someone who spends their time reading and writing. Of course, most people are not scholars. We survive by doing things.”

I am a big believer in fostering kids natural desire to learn by teaching through tinkering.