Sunday, January 31, 2016

Zika, baby--is not your friend.

There’s Zika in our future. Count on it.

You’ve read lots about the Zika virus, another in the toxic deck of playing cards dealt by the Aedes aegypti mosquito, the yellow fever mosquito. Others include Dengue, Yellow Fever and Chikungunya. 

Zika can also be carried by the Aedes albopictus mosquito, the Asian tiger mosquito.

We’ve got them in Hawai`i. Lucky Hawai`i, we are one of the first places on the planet to be invaded by both. They are both alien invaders. In pre-human Hawai`i, there were no native mosquitoes.

So far, only one person is known to have arrived in the islands with Zika, and it appears not to have spread from that case. The most likely source of the virus is in travelers returning from areas where the virus is rampant.

It’s in Samoa, and almost anywhere in the tropical and subtropical Americas. How widespread is it in the Americas? Check this list: Barbados, Bolivia, Brazil, Colombia, Dominican Republic, Ecuador, El Salvador, French Guiana, Guadeloupe, Guatemala, Guyana, Haiti, Honduras, Martinique, Mexico, Panama, Paraguay, Puerto Rico, Saint Martin, Suriname, U.S. Virgin Islands, Venezuela.
Oh, it just got reported this week in Jamaica.

There’s a lot of information about Zika at this Centers for Disease Control (CDC) site

Zika is in a class of disease-causing organisms called flaviviruses. They include West Nile virus, dengue fever, tick-borne encephalitis and others.

The upshot is that the disease is not that big a deal for adults—certainly nowhere near as painful and symptom-filled as the dengue fever that’s now running through the Big Island. Primary symptoms are fever, rash, joint pain, or conjunctivitis (red eyes), muscle pain and headache. And most infected people—four out of five—have no obvious symptoms at all (although presumably they can still spread the disease.)

However, there are concerns that in some people an infection with Zika could lead to Guillain-Barré Syndrome, an immune system disorder. CDC notes that there are increased cases of Guillain-Barré in Zika infections, but they haven’t confirmed the relationship.

Same thing with birth defects. Pregnant women who get Zika in Brazil seem to have an increased rate of children born with microcephaly, or abnormally small heads, “and other poor pregnancy outcomes,” CDC says. There’s still far more to learn, but women are encouraged to avoid Zika infested areas if pregnant, or if likely to become pregnant, and to use precautions if they must be there. 

Here are the precautions, but the basic rule is to do everything you can to avoid being bitten by a mosquito, including chemical mosquito repellants and protective clothing. 

World Health Organization Director-general Margaret Chan last week convened an emergency panel, to meet Feb. 1, 2016, to look into the association between Zika and birth defects and Guillain-Barré. Here is her statement.

And there are all sorts of conspiracy theories running around already, as there were about AIDS and Ebola. One of them is that genetically modified mosquitoes are somehow involved in transmission.

The opposite is true. A number of initiatives are being used to determine whether genetically modified mosquitoes can be used to stop the virus, but they are happening after Zika already burgeoned. And a test of a genetically modified mosquito in one Brazilian city, Piracicaba, appears to have protected many residents there.

Zika appears to have changed its character and become more of an epidemic and less of a rare and isolated disease as much as 10 years ago, long before genetic modification techniques on mosquitoes were being attempted in Brazil. 

To be clear, Zika was first identified in 1947 in the forests of Uganda in monkeys. It was found in 1952 in humans in Uganda and Tanzania. It popped up occasionally here and there as people moved it around the globe. It got to Southeast Asia in 1966, and by 1970 was in India, Pakistan, Indonesia and Malaysia.

It first appeared in the Pacific in Yap with a couple of hundred cases in 2007. 

Zika had been rare and isolated before Yap. The Yap case was the first to be described as an outbreak.
The New England Journal of Medicine described the Yap cases in a paper in 2009. 

“The virus could have been imported by a person with undetected infection. Serologic evidence of Zika virus infection in humans has been reported in the Philippines, and travel between Yap and the Philippines is common,” the journal article said.

In an ominous bit of prediction, the 2009 paper warned that this disease, the way it was behaving on Yap, was a threat throughout the Pacific as well as the Americas. 

“The accessibility of air travel and the abundance of mosquito vectors of flavivirus in the Pacific region raise concern for the spread of Zika virus to other islands in Oceania and even to the Americas,” the paper said.

The outbreak in Tahiti/French Polynesia four years later was the largest known Zika flare-up in history.

One suggestion is that Tahitian canoe paddlers competing in the Va`a World Sprint Championship in Rio brought it to Brazil in August 2014. Here is a report on that. 

It seems to be spreading in Brazil with the same ferocity as it did in Tahiti. It was reported as a full-fledged outbreak by mid-2015. 

Here is a World Health Organization fact sheet on Zika

Here is a fact sheet for health professionals on Zika from the European Centre for Disease Prevention and Control. 

How bad could it be?  In Tahiti in 2013, 35,000 suspected cases were reported, although far fewer were confirmed. There are fewer than 300,000 people in all of French Polynesia--so more than 10 percent of the population was possibly impacted.

Brazil alone has more than 200 million people, and the rest of South America has nearly that number. The World Health Organization reported Zika is spreading explosively through the Americas. 
© Jan TenBruggencate 2016

Wednesday, January 6, 2016

Not all vegetarian diets the same, and full vegan's not the best for long life

Eat vegetarian and you’ll live longer. No brainer, right? 

Actually, it’s complicated.

Most studies suggest that a vegetarian lifestyle gives you longer life. But some vegetarians do better on some measures than meat eaters—but there are also some vegetarians who do far better than other vegetarians. 

Spoiler alert: based on our review of the biggest studies, you should eat mostly vegetarian, but eat some dairy and fish, too. You’ll live longer than by eating a pure vegan diet.

Certainly not what we expected. So, what’s going on?

Heart disease is a major killer. It seems clear from most studies that a vegetarian or largely vegetarian diet is associated with lower heart disease, especially in men. A famous series of British studies found that 1 in 20 vegetarian men have hypertension, while 3 in 20 meat eaters do. The numbers are less stark for women, but they still hold. American studies have similar results.

But ultimately, one way of looking at the data with respect to heart disease is that this particular study did not find that the vegetarian diet made all the difference—rather that body weight did. “Non-meat eaters, especially vegans, have a lower prevalence of hypertension and lower systolic and diastolic blood pressures than meat eaters, largely because of differences in body mass index.”

So, what’s going on there?

This related study found that if you’re eating a high-fiber diet that’s low in protein, you’re less likely to be fat. And the previous study says if you’re less likely to be fat, you’re less likely to have high blood pressure. 

But here is perhaps the more interesting and perplexing study result: Despite a higher death rate for people with high blood pressure, the British studies on more than 50,000 individuals showed that the overall death rate of vegetarians studied wasn’t much different than that of meat eaters. 

That’s weird, right? Because it flies in the face of accepted logic.

Well, there are a couple of things going on. One is that even the British non-vegetarians in these studies may have been eating better than the average Brit, since meat-eaters in this study have better health outcomes than the national average. (One clue: part of the study involved meat-eaters who shop at health food stores.)

When the massive British study is paired with an even bigger study of American Seventh-Day Adventists, the picture gains some clarity, but some more complexit.

It seems that British vegetarians eat a different vegetarian diet than American Seventh-Day Adventist  vegetarians do. Maybe not as good a vegetarian diet, in terms of promoting long life.

The British results, from what’s known as the EPIC-Oxford studies, are very different in overall mortality from American ones in the American Seventh-Day Adventist study by Loma Linda University School of Public Health researchers. This one was on more than 96,000 American Seventh-Day Adventists, half of whom follow some version of a vegetarian diet, but about half of whom don’t.

The American study found death rates among vegetarians was significantly lower than among meat-eaters, but that the rates differed between different kinds of vegetarians.

The American Loma Linda researchers knew about the British study, and looked into the differences. Their finding: “It appears that British vegetarians and US Adventist vegetarians eat somewhat differently.”

And that matters. “Although vegetarian diets are healthful and are associated with lower risk of several chronic diseases, different types of vegetarians may not experience the same effects on health.” So says this study.

A big difference: American Seventh-Day Adventist vegetarians  ate far more fiber, and far more vitamin C. Close to 70 percent more fiber and Vitamin C in the Americans. Maybe there are other differences, too. But those stood out.

“… the vegetarians in our study consume more fiber and vitamin C than those of the EPIC-Oxford cohort: mean dietary fiber in EPIC-Oxford vegans was 27.7 g/d in men and 26.4 g/d in women compared with 45.6 g/d in men and 47.3 g/d in women in AHS-2 vegans; mean vitamin C in EPIC-Oxford vegans was 125 mg/d in men and 143 mg/d in women compared with 224 mg/d in men and 250 mg/d in women in AHS-2 vegans,” the Loma Linda study says. 

Loma Linda researchers also noted that there are a lot of different kinds of vegetarian eaters. Here’s the list Loma Linda used to describe their sample: vegan (No red meat, fish, poultry, dairy or eggs); lacto-ovo vegetarian (Consume milk and/or eggs, but no red meat, fish or poultry); pesco-vegetarian (Eat fish, milk and eggs but no red meat or poultry); semi-vegetarian (Eat red meat, poultry and fish less than once per week); non-vegetarian (Eat red meat, poultry, fish, milk and eggs more than once a week). 

In general, the more meat you eat, the poorer your outcome in these studies—with one major caveat. People who ate fish with their vegetarian fare, even when they included milk and eggs, were even less likely to die early than vegans.

© Jan TenBruggencate 2016

Tuesday, December 29, 2015

CRISPR-Cas9: understanding gene editing, for the rest of us

Everybody’s talking about this new gene-editing technology borrowed from bacteria—but is there any way to make it understandable to normal folks?

Let’s try.

This is new stuff. It matured to usefulness only in the past three or four years—the original paper was just published in 2012 It lays out the technology folks casually call CRISPR-Cas9.
The system lets laboratories essentially cut-and-paste genetic material, with accuracy previously unattainable. Sometimes it just lets you go in and flick a switch, turning something off. It is based on the immune system used by some bacteria, as well as most of the life forms called archaea.

The technique lets researchers select a very specific spot in DNA, and snip it open to remove or insert something. The cell then naturally repairs itself.

The difference from the old genetic engineering techniques, is essentially like the difference between doing archaeology with a backhoe or with tweezers. It's like using a word processor to cut-and-paste instead of paper, glue and scissors.


It’s useful to know a tiny bit about DNA and RNA—the genetic components of anything that is alive. 

DNA is the basic blueprint. In life, it is what dictates whether something will be a temperate fruit tree, or an edible mushroom, or an ocelot or a human.

RNA carries out the instructions of the DNA. 

If it were a football game, DNA would be the rulebook and RNA would be the players.

Is that too strange an analogy? How about this: DNA is the plan; RNA carries out the plan.


So, researchers in the 1980s noticed that in some bacterial DNA, they were occasionally seeing a repeating pattern. There were sections where a certain bit of DNA would repeat between random other sections, like the apples in this example: Apple, orange, apple, pear, apple, grapefruit, apple, banana …

They called it CRISPR, for Clustered Regularly-Interspaced Short Palindromic Repeats. It was an interesting pattern, but what did it mean?

A couple of researchers figured out that the repeating apples were actually pieces of DNA of a virus that was attacking the bacteria. Those apple pieces would make RNA that would launch and attach itself onto the attacking virus.

Meanwhile, the intervening DNA bits—the orange, pear, grapefruit, banana—would follow up and work with a protein (called Cas9) to go and split apart the virus DNA. 

Thus, the virus was inactivated. And the bacterium was cured from viral disease. Cool stuff.

The immune system of a bacterium acted like a genetic pair of scissors with its own GPS. The GPS gets it to a specific location, and then the scissors snip the DNA open.

Another way to think about it: the bacterium has the ability to recognize a new enemy, and can send out its genetic ninja teams to attack the enemy.


As they studied it, scientists realized this was a potential tool kit for adjusting genetics--that they could adapt this system to pluck a piece out of DNA changing how the organism works. And they also figured out how to insert a new piece of DNA if necessary, before the cell healed the cut ends.

A genetic Swiss army knife.
A pretty clear explanation of all this is here 

Here’s a video with some interesting graphics that discusses the system. 

And here is a video of one of the discoverers, Jennifer Doudna, which is a little tougher to understand, but she’s a key player. There are plenty of YouTube videos of her describing the process.

And how important is it? Well, Doudna and Charpentier are getting really famous. They have been named among Time Magazine’s 100 most influential people in the world. They’ve picked up the $500,000 Gruber Genetics Prize and the $3-million Breakthrough Prize in Life Sciences. They just missed this year's Nobel Prize, but they might get it next year.


The world moves forward on the CRISPR front with amazing speed. 

The technology is being used to amend tobacco DNA to produce anti-cancer drugs. There’s work to use CRISPR to turn off genes in cancer cells, effectively killing the cancer. In crops, changes can be so precise that they essentially add nothing to the genome, but still have a favorable effect.

In this paper, from last month, co-author Wendy Harwood of England’s John Innes Centre, said you can make just the tiniest change to turn off a particular feature. 

“Stopping particular genes from working is one way to develop disease resistant crops, for example with resistance to mildew or to produce crops without unwanted compounds including toxins.

“The final plants produced in this way have no additional DNA inserted so they are essentially the same as plants with naturally occurring changes to genes or plants that have been bred using conventional mutation breeding methods,” Harwood said.


Doudna, of the University of California, who worked with Emmanuelle Charpentier of the Max Planck Institute for Infection Biology, in making the discovery, talks here about some of the ethical implications of their finding.

Well, yes. You might be able to cure cancer and cystic fibrosis and sickle-cell anemia and maybe HIV. And you might be able to make new medicines to cure other diseases. And you might be able to engineer crops to fight disease without pesticides. And maybe make mosquitoes that can’t transmit dengue and malaria. 

But you might also bioengineer humans. You want a baby boy who will grow to 6-foot-2, with an IQ of 145, curly black hair and green eyes, and can run a 40-yard dash faster than Usain Bolt? We might be able to engineer that.

Maybe that’s good, but, um, maybe not. Remember the Nazis and eugenics?

Doudna and her team are thrilled about the possibilities of their technology, but wary about some of the implications.

She has called for a “global pause” in redesigning human embryos while we think about those implications.

John Travis, of the journal Science, wrote earlier this month about the National Academy of Science’s International Summit on Human Gene Editing. 

He quotes a mother who lost a child to genetic disease: “"If you have the skills and the knowledge to eliminate these diseases, then freakin' do it.”

But genetic changes are permanent, and “before we make permanent changes to the human gene pool, we should exercise considerable caution,” said another participant at the summit.

Most of the concern expressed to date about CRISPR involves its use in engineering human genetics, not so much other life forms. The Center for Genetics and Society and Friends of the Earth have issued a position statement opposing the use of the technology in humans.

© Jan TenBruggencate 2015

Saturday, December 26, 2015

The Top Ten Energy Stories in Hawai`i, 2015

Whew, it’s been a big year for energy in the Islands—big enough that it’s risky to pick just 10 of the biggest Hawai`i energy
stories of 2015.

But we’re not shrinking violets at RaisingIslands, so with the caveat that folks can disagree, here we go.

Number One: The top energy story of the year is certainly the controversial proposal by the Florida electric behemoth NextEra Energy to merge with Hawaiian Electric Industries, the corporation that includes Hawaiian Electric, Maui Electric and Hawaii Electric Light. The merger was announced in December 2014 and the PUC docket seeking approval on January 14, 2015. 

It seems like every community group in the state asks to intervene in the HECO/NextEra. The PUC approves 28 intervenors, among them the Renewable Energy Action Coalition of Hawaii, Hawaii Island Energy Cooperative, Kauai Island Utility Cooperative, Hawaii Water Service Co., Ka Lei Maile Alii Hawaiian Civic Club, Maui County, Sun Edison, Hawaii Solar Energy Association, Friends of Lanai, Puna Pono Alliance, Hawaii County, Ulupono Initiative, AES Hawaii, Blue Planet Foundation, SunPower Corp., Tawhiri Power, Hawaii PV Coalition, Paniolo Power, The Gas Co., Hawaii Renewable Energy Alliance, the state Office of Planning, Sierra Club, Hina Power Corp. and the Honolulu Board of Water Supply. Those, and a few others. Some have since dropped out, but still… 

2. The state announces that its goal is for Hawai`i to be100 percent powered by renewable energy by 2045, although it is something of a theoretical standard. Under the language of the commitment, the state could meet the 100 percent standard and still burn some oil. 

3. Gov. David Ige announces in August that he’s against Hawaiian utilities using liquefied natural gas (LNG) to replace oil and coal for energy production, arguing that it would detract from the state’s movement toward renewable energy solutions. 

4. The Kaua`i Island Utility Cooperative dedicates the state’s largest to date solar array, at Anahola, Kaua`i, which replaces the previous largest array at Koloa, also on Kaua`i, which in turn replaced the next previous largest array, also on Kaua`i. KIUC has more solar power per customer on its grid than any other utility in the country. On sunny days, most of the island’s electricity is generated by solar. 

5. It’s not purely a Hawai`i story, but the federal government’s extension of renewable energy tax credits means Hawai`i’s solar and wind industries get a big boost—federal tax credits stay at 30 percent through 2019. 

6. NextEra/HECO merger announcement prompts neighbor island utility self-determination proposals:  Hawai`i Island Energy Cooperative is formed in hopes of capturing Hawaii Electric Light if it becomes available ; and Maui Mayor Alan Arakawa studies a municipal power utility for Maui County. 

7. The Department of Hawaiian Home Lands announced a contract with NextEra affiliate Boulevard Associates LLC for a 60-megawatt wind farm at Kahikinui on Maui, which is a little smaller than the state;s biggest,  the 69 megawatt Kawailoa wind farm on O`ahu. But if built, the Kahikinui windfarm would make Maui the wind capitol of the Islands, adding to the 51 megs of wind power at Kaheawa and 21 megs at Auwahi.

8. KIUC announced plans with Solar City to build the biggest dispatchable solar/battery plant in the nation: a 13-megawatt solar array with a 52-megawatt-hour battery. 

9. Continuing on the battery front, Tetris owner Henk Rogers, through his company Blue Planet Energy, starts selling Sony’s lithium ion phosphate battery technology along with Blue Planet’s own software suite, under the name Blue Ion. And several other vendors are also marketing battery systems for solar arrays.

10. Finally, solar development rolls on. The PUC approved nearly140 megawatts of new solar for O`ahu. Three projects are by Sun Edison and one by Eurus Energy. These, if built, will finally knock Kaua`i out of first place in the biggest-solar-farm category, since each of these plants is bigger than the biggest one on Kaua`i. 

(Full disclosure: This blog’s author, Jan TenBruggencate, serves on the elected board of directors of the Kaua`i Island Utility Cooperative.)

© Jan TenBruggencate 2015