Crumb Trail
     an impermanent travelogue
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Thursday, March 30, 2006

Habitual acts alter genomes.

The researchers were able to pinpoint and confirm that a single base pair mutation in DNA causing an amino acid change in a protein led to non-shattering rice varieties. This slight change in DNA prevented mature rice grains from easily falling from stalks to allow a more effective field harvest. In essence, humans several thousand years ago unknowingly practiced de facto gene selection by planting varieties with this trait.

Shattering in cereal crops refers to grains easily falling off of plants. The shattering trait of the wild forerunners of rice and cereals prevents effective field harvest and is undesirable for cultivation.

You get what you manage for . . . whether you understand what that will be or not.


Colder and smaller are much the same in at least one way.

"We found that pollen diversity tracks global temperature through time over millions of years. Diversity increases as the planet warms and decreases as it cools. The mystery is that even when global temperatures vary enormously, average temperatures in the tropics don't change much, so why do we see global temperature patterns reflected in tropical plant diversity?" Jaramillo proposes that changes in area drive speciation and extinction in the tropics.

"There is good correlation between area and number of species: more area implies more species. During global warming, tropical areas expand and diversity goes up, the opposite happens during global cooling. If this is the case, fragmentation of modern tropical forest could be equated to a global cooling period, because forested areas are shrinking dramatically, resulting in plummeting diversity in the forests that remain."

I wonder if models of past climate consider this relationship?


Our bafflement increases

"The rapid surface warming of the Antarctic Peninsula and the enhanced global warming signal over the whole continent shows the complexity of climate change. Greenhouses gases could be having a bigger impact in Antarctica than across the rest of the world and we don't understand why. So far we haven't been able to determine the mechanisms behind the warming.
Clearly the air in that region is phlogisticated.


Plant civil defense

A novel enzyme in corn helps the plants defend themselves from voracious caterpillars by disrupting the insects' ability to digest food, and ultimately killing them, according to researchers. The enzyme could be used in tandem with other biological pesticides such as the Bt toxin to prevent the pests from developing resistance and making the toxin more effective.

"The enzyme is found in insect-resistant strains of corn, and it breaks down proteins and peptides in the insects' gut. It is a unique active defense against herbivory," says Dawn Luthe, professor of plant stress biology at Penn State.

Luthe and researchers at Mississippi State University have since developed several lines of corn resistant to multiple pests, using conventional plant breeding and insect-resistant strains of corn from Antigua.

All farmers use pesticides no matter what agronomic system they practice. There has been an evolution of pesticides from more toxic and persistent early compounds based on arsenic, lead and other harsh poisons to more benign and selective ones. That's the story that those reasoning in good faith about pesticides should be telling rather than a false story of a dichotomy between those who use pesticides and those who don't. The issue is only which pesticides are used and over time that becomes an increasingly irrelevant distinction since they are all becoming safe as well as effective.

Sunday, March 26, 2006

Or barding, perhaps.

Researchers report they have created pigs that produce omega-3 fatty acids, which are known to improve heart function and help reduce the risks for heart disease, representing the first cloned transgenic livestock in the world that can make the beneficial compound. The research could be a boost to both farmers and health-conscious consumers seeking an alternative and safer source of omega-3 fatty acids. Currently, the only way for humans to realize the benefits of omega-3 fatty acids is by taking dietary supplements or by eating certain types of fish that may also contain high levels of mercury.
Well, no. Heavy metal fishes are not the only option for those seeking omega-3 fatty acids. Grass eating ruminants supply it too, and concentrates such as cheese made from their milk supply it in abundance.
To stimulate production of omega-3 fatty acids in pigs, a team led by Dr. Dai transferred a gene known as fat-1 to pig primary fetal fibroblasts, the cells that give rise to connective tissue. Dr. Prather's group then created the transgenic pigs from these cells using a method called nuclear transfer cloning. The transgenic pig tissues were then analyzed for omega-3 fatty acids in Dr. Kang's lab at MGH and by Drs. Dai and Evans at Pitt. The fat-1 gene is responsible for creating an enzyme that converts less desirable, but more abundant, omega-6 fatty acids in the animals to omega-3 fatty acids. The results could lead to a better understanding of cardiovascular function not only in pigs, but in humans as well.

"Pigs and humans have a similar physiology," said Dr. Prather, distinguished professor of reproductive biology in MU's College of Agriculture, Food and Natural Resources and a corresponding author with Dr. Dai. "We could use these animals as a model to see what happens to heart health if we increase the omega-3 levels in the body. It could allow us to see how that helps cardiovascular function. If these animals are put into the food chain, there could be other potential benefits. First, the pigs could have better cardiovascular function and therefore live longer, which would limit livestock loss for farmers. Second, they could be healthier animals for human consumption."

hmmm, convert omega-6 to omega-3. That would be a pretty good hack for the human genome too.


Study skew.

Diets rich in omega-6 fatty acids but poor in long-chain omega-3 fatty acids have been connected with heart, autoimmune, and neuropsychiatric disease, but two recent analyses have suggested that high levels of omega-3s may not always improve human health. A meta-analysis published last week in the British Medical Journal found no clear evidence that omega-3 fatty acids protect against cardiovascular disease or cancer. However, the authors acknowledged that their results were skewed by one large study that found no benefits of omega-3 fats. Without that study, their results fit with an earlier meta-analysis that showed that omega-3s can lower risk of death. Another recent review in the Journal of the American Medical Association found no clear anti-cancer benefits from omega-3 fatty acids.

Whether fat-1 pigs could ever offer an alternative to oily fish for consumers is a "difficult question," Van Eenennaam said. "What is going to be potentially problematic is getting through the regulatory process and then, of course, if we were to go all the way, consumer acceptance."

Well, unless something really odd happens the risk of death is 100% for all of us. The issues are when and how, and whether we enjoy the ride.


A new study shows some cancer benefits.

Two new studies by a University of Pittsburgh research team suggest that omega-3 fatty acids . . . significantly inhibit the growth of liver cancer cells. The studies . . . suggest that omega-3 fatty acids may be an effective therapy for both the treatment and prevention of human liver cancers.

Tuesday, March 21, 2006

Not just any old mouse will do.

Interested in getting in on some big cash prizes but don’t have the sequencing capacity or rocketry experience to compete in the more well known X-prize competitions If you’re good with mice, all you might need is time. In putting together the March feature on aging by S. Jay Olshansky and colleagues we came across the Methuselah Mouse Prize or M-prize. Funded by private donors, the M-prize is brainchild of Aubrey de Grey, the Cambridge geneticist who contends that with proper maintenance (yet undiscovered), humans could live for hundreds or even thousands of years. The prize is awarded in two categories that have been variously named over the years but currently go by longevity and rejuvenation. . .

If you can double the current record of 1,819 days, you can capture half the available funds, currently $3.3 million.

It's not quick or sure but it is pretty easy money. . .if you like mouse wrangling.

Tuesday, March 14, 2006

Does your cat's butt glow in the dark?

Apparently the clay in cat litter gives off enough radiation to set off a gamma detector. And its emission signature is very close to that of highly-enriched uranium. The current high-purity germanium (HPG) detectors can’t tell the difference.
The barn cats around here do their business in the rough, so there's no litter around. I'm often glad of that and now more so.


Burn the suckers to death.

Capsaicin, the stuff that turns up the heat in jalapeños, not only causes the tongue to burn, it also drives prostate cancer cells to kill themselves, according to studies published in the March 15 issue of Cancer Research. . .

Lehmann estimated that the dose of pepper extract fed orally to the mice was equivalent to giving 400 milligrams of capsaicin three times a week to a 200 pound man, roughly equivalent to between three and eight fresh habañera peppers – depending on the pepper's capsaicin content.

Hmmm, 400 milligrams of capsaicin, 3 times a week? I probably eat close to that as part of my normal diet, but at a steadier rate over all the days of the week. I could eat more.

Thursday, March 09, 2006

See this muddled beeb article about expected advances in genomics.

Dr Francis Collins, the scientist leading the Human Genome Project, says he expects important new gene sequences governing aspects of personality, such as intelligence and behaviour, to be known very shortly. . .

"We may be able to discover variations that correlate with intelligence, but to actually utilise that, to tinker with the human gene pool, is ethically a very difficult and challenging topic," he said.

"Scientifically, it's not something we know how to do."

And Dr Collins said that even if it were possible to augment intelligence - for example with a pill to raise it - it would potentially create a great divide between "who has access and who does not".

"If this is a particular approach which is very expensive and only available to people with lots of resources, then what have you done? You've created a divide in an already divided world.

"That is a very dangerous and troubling outcome, which I think we should guard against."

Collins is the bureaucrat who was presiding over a multi-decade project to decode the human genome until a maverick entrepreneur in a private company using new technologies ruined his plan to spend his whole career sleeping through the decoding. He's no leader.

And he's not very bright. If we do discover ways to boost intelligence then progress will accelerate. The "divide" he whinges about would move too. There would be those who had more, but those with less would still have an improved material existence, would have more than if the discoveries had not been made. This is not something that any thinking person would want to "guard against". Only a bureaucrat seeking a comfortable place to sit and serve his time would think so.

Monday, March 06, 2006

We tend to think of our star, old Sol, as being a constant in our lives, just as day follows night. But the sun is no more stable than the earth. It has an atmosphere, sort of, and storms so intense that we have nothing comparable to allow analagous understanding. The solar weathermen are predicting heavy weather.

The next sunspot cycle will be 30-50% stronger than the last one and begin as much as a year late, according to a breakthrough forecast using a computer model of solar dynamics developed by scientists at the National Center for Atmospheric Research (NCAR). Predicting the Sun's cycles accurately, years in advance, will help societies plan for active bouts of solar storms, which can slow satellite orbits, disrupt communications, and bring down power systems.

The scientists have confidence in the forecast because, in a series of test runs, the newly developed model simulated the strength of the past eight solar cycles with more than 98% accuracy. The forecasts are generated, in part, by tracking the subsurface movements of the sunspot remnants of the previous two solar cycles. The team is publishing its forecast in the current issue of Geophysical Research Letters. . .

The Sun goes through approximately 11-year cycles, from peak storm activity to quiet and back again. Solar scientists have tracked them for some time without being able to predict their relative intensity or timing.

Forecasting the cycle may help society anticipate solar storms, which can disrupt communications and power systems and affect the orbits of satellites. The storms are linked to twisted magnetic fields in the Sun that suddenly snap and release tremendous amounts of energy. They tend to occur near dark regions of concentrated magnetic fields, known as sunspots.

Solar storms affect earth weather too. They make the sun hotter and over the last 100 years have made a contribution to earth temperatures estimated to be between 4% and 20%. They affect climate in more subtle ways too. Sol also has a magnetosphere which affects the whole planetary system. It shields the system as a whole from cosmic rays and interacts with other magnetospheres, such as that of the earth. Sol's polarity reverses in an eleven year cycle, much faster than Earth, and magnetic storms - sun spots - fluctuate in number and intensity during the cycle. The effectiveness of Sol's field as a shield depends on polarity, a combined effect of polarity and direction of rotation. Sol is both a source and a shield of cosmic rays. There has been recent research on how cosmic rays affect climate. They create high level clouds which alter planetary albedo, reflecting more of Sol's energy and cooling the planet. So, the sun will be hotter but increased cosmic ray bombardment will create high level clouds that reflect more light. The relative intensity of these effects isn't clear.

Other researchers looking at solar cycles for the past 11,000 years have predicted that the the next 100 years will be less stormy than the past 100 years. Good. We could use a little solar dimming while we get our atmosphere spruced up a bit. This comming storm may not repeat again for quite a while.

Saturday, March 04, 2006

Phun things to do with a pressure cooker.

. . . an agriculture engineering professor at the Tokyo University of Agriculture and Technology, said his team has successfully extracted .042 ounces of gasoline from every 3.5 ounces of cow dung by applying high pressure and heat. . .

The team, helped by staff from the National Institute of Advanced Industrial Science and Technology near Tokyo, produced gasoline by adding several unspecified metal catalysts to the dung inside a container and applying a 30-atmosphere pressure and heat of up to 300 degrees Celsius (572 Fahrenheit), Shibusawa said. Details of the catalysts could not be disclosed, he added.

hmmm, I wonder if this has a net yield of energy when all inputs including the energy embodied in the equipment and catalysts is considered? If not there may be better uses for this discovered resource.
In a separate experiment revealing another unusual business potential for cow dung, another group of researchers has successfully extracted an aromatic ingredient of vanilla from cattle dung, said Miki Tsuruta, a Sekisui Chemical spokeswoman. The extracted ingredient, vanillin, can be used as fragrance in shampoo and candles, she said.

Tsuruta said the vanillin was extracted from a dung solution in a pressurized cooker in a project co-organized by a Japanese medical research institute.

Dung shampoo? We'll need some serious marketing brainstorming to find a way to turn the suspicious origins of the product into an asset.

Friday, March 03, 2006

Food moods.

In a study of 106 healthy volunteers, researchers found that participants who had lower blood levels of omega-3 polyunsaturated fatty acids were more likely to report mild or moderate symptoms of depression, a more negative outlook and be more impulsive. Conversely, those with higher blood levels of omega-3s were found to be more agreeable.

"A number of previous studies have linked low levels of omega-3 to clinically significant conditions such as major depressive disorder, bipolar disorder, schizophrenia, substance abuse and attention deficit disorder," said Sarah Conklin, Ph.D., a postdoctoral scholar with the Cardiovascular Behavioral Medicine Program in the department of psychiatry at the University of Pittsburgh School of Medicine. "However, few studies have shown that these relationships also occur in healthy adults. This study opens the door for future research looking at what effect increasing omega-3 intake, whether by eating omega-3 rich foods like salmon, or taking fish-oil supplements, has on people's mood."

Evidence for the benefits of omega-3 fats keeps rolling in, but the naive reserachers always fail to mention the most useful source - grass fed beef and dairy products. While fishes often give you a dose of heavy metals and other pollutants, and are a dwindling resource being hunted to extinction that you have to be a bit selfish to consume given the severity of over fishing, grass fed beef and dairy products have none of these drawbacks.

See this post, Something Fishy, that discusses mercury in fishes, omega-3, beef and dairy.

Drinking just half a pint a day of organic milk as part of a healthy balanced diet gives a useful additional source of this Omega 3 fatty acid, as it could provide approximately 10% of the UK’s Daily Reference Value3 of essential n-3 fatty acid, alpha-linolenic acid.

Organic cheese is an even better source, with a matchbox sized piece of organic cheese providing up to 88% of your RDI of this Omega 3 fatty acid.

Organic isn't the issue since you could have certified organic grain fed animals and thus low omega-3. The issue is grass fed since the omega-3 comes from greens. That's where the little fishes get it and eating the little fishes is where the big oily predator fishes get it. Somebody needs to eat their greens, though some nuts (such as walnuts) have good amounts too.

People can't eat and digest enough greens to get a significant amount, but fishes or ruminants can concentrate it for them. Ruminants do this directly from the foods they eat while most oily fishes are predators that concentrate previously concentrated oils. This is the problem with toxins since each level up the food chain concentrates toxins as well as omega-3. The older a fish is and the higher in the food chain the greater the chance of concentrated toxins.

It seems possible to get non-toxic fish if you are careful. It seems possible to get omega-3 rich meat and dairy if you are selective and specify grass fed. If you do then it's easy to get the RDI of omega-3 while eating a varied diet.

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