News flash: genetic engineering may save the American chestnut tree

October 27, 2015 • 8:15 am

The American ChestnutCastanea dentata, was once a proud denizen of eastern U.S. deciduous forests, and prized for its wood. Then, in the early 1900s, the fungus “chestnut blight,” Cryphonectria parasitica, was introduced to the U.S. from Japanese nursery stock. Within a few decades, it wiped out around 4 billion chestnut trees.  Since the fungus is airborne, a few adult trees have survived in the East if they’re several kilometers from the nearest tree, and some trees survive outside the natural range; but the species isn’t coming back. When a tree dies or is cut down within the natural ranges, saplings will sprout from the roots, but before the tree can reproduce it’s invariably killed by the fungus.

Restoring the tree has been a tough problem, as the fungus persists. The American Chestnut Foundation (ACF), a pretty big organization, has done its best by spreading seeds from fungus resistant trees and so on, but now there’s additional hope—thanks to genetic engineering. (Reader Hempenstein is responsible for sending me this brand-new information.) The chestnut is in fact now a Genetically Modified Organism (GMO), with a gene injected into the DNA that makes the tree resistant to blight.

First, check out the photo below, which has just been made public. Left: American chestnuts showing effect of blight. Center: GMO (transgenically engineered) chestnuts infected with blight. Right: Chinese chestnut (Castanea mollissima), showing its susceptibility to blight.

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The following caption and information were provided in an email by Bill Powell, a professor of Environmental Science and Forestry at the State University of New York at Syracuse, Director of the Council on Biotechnology in Forestry, and Co-Director of the American Chestnut Research & Restoration Project. His work is supported by the ACF.
The take-home message:  a single enzyme OxO, whose gene is engineered into the American chestnut genome, confers blight resistance.

This is a small stem blight resistance assay of Ellis 1 wild type American chestnut (left), Darling 54 transgenic American chestnut (center), and Qing Chinese chestnut (right). The Ellis 1 and Darling 54 lines are clonal except that the Darling 54 has the oxalate detoxifying enzyme gene protecting it.  All were infected with a highly virulent strain of the blight fungus, EP155.  After one month, all the Ellis1 were wilted, all the Darling 54 survived (and are still surviving today), and five of the six Qing eventually wilted.  This is demonstrates the high level of blight resistance in the Darling 54 line.

Interestingly, we can still isolate the blight fungus from the Darling 54, showing that the OxO doesn’t hurt the fungus. It just neutralizes its weapon, oxalate.  This is important because by not killing the fungus it greatly reduces the selective pressure to select fungal mutations that may overcome the resistance.  Therefore it should be a very sustainable resistance.

This resistance is heritable as a dominant trait and therefore when outcrossing with surviving wild type trees, half the offspring will be fully resistant.  We also have a easy leaf disk assay that can identify which offspring carry the resistance gene.  This will allow rescuing the genetic diversity of American chestnut that still survives in the forests.

You can see much more information (and a video of the blight-resistance assay) here. If the FDA, EPA, and USDA approves this (and I’m hopeful), the resistant seeds will be distributed for planting, and perhaps these giants will grace our forests again. I wonder if there will be a public outcry against the use of GMO chestnuts.

The fact that the resistance is dominant is a good thing, for any tree with the gene will survive, and those lacking it will not. That means that there’s no barrier to the spread of the resistant trees, even if the added gene gives them reduced fitness compared to the susceptible trees in the absence of the blight.

Here’s Powell talking about the significance of this tree,and describing the restoration project in a nice 15-minute TEDx lecture:

Readers’ wildlife photographs

October 27, 2015 • 7:30 am

Keep those wildlife photos coming in, folks (and an occasional landscape would be fine, too).

We’ll begin with a mammal—a relative of d*gs!—from Stephen Barnard in Idaho:

This coyote [Canis latrans] has been hanging out in the field in front of my house, hunting voles.

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Reader Craig Carpenter sent a photo of a Green Heron (Butorides virescens):

Taken on small lake in North Georgia:
Craig Carpenter
Two photos of a gorgeous bird long stalked unsuccessfully by Australian reader Tony Eales:

After years I finally have a couple of photos of Rainbow Bee-eaters (Merops ornatus) that I’m moderately happy with. His feathers are a bit wet as he’d just gone for a dip and was sitting obligingly enough for me to photograph while waiting for his feathers to dry.

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Wikipedia discusses its diet:

Rainbow bee-eaters mostly eat flying insects, but, as their name implies, they have a real taste for bees. Rainbow bee-eaters are always watching for flying insects, and can spot a potential meal up to 45 metres away. Once it spots an insect a bee-eater will swoop down from its perch and catch it in its long, slender, black bill and fly back to its perch. Bee-eaters will then knock their prey against their perch to subdue it. Even though rainbow bee-eaters are actually immune to the stings of bees and wasps, upon capturing a bee they will rub the insect’s stinger against their perch to remove it, closing their eyes to avoid being squirted with poison from the ruptured poison sac. Bee-eaters can eat several hundred bees a day, so they are obviously resented by beekeepers, but their damage is generally balanced by their role in keeping pest insects such as locusts and hornets under control.

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Tuesday: Hili dialogue (and Leon lagniappe)

October 27, 2015 • 4:35 am

It’s going to be a chilly and rainy Tuesday, with a high of only about 58°F (14°C), as the Killing Season slowly makes its way to Chicago. So far retirement hasn’t changed my schedule, but I have several exciting trips in the offing, which of course will allow for pictures of excellent foreign noms; so stay tuned. Meanwhile in Dobrzyn, Hili is having an adventure on the banks of the Vistula:

Hili: I see new challenges.
A: And what if they are too big
Hili: Then I’ll escape.

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In Polish:
Hili: Widzę nowe wyzwania.
Ja: A jeśli będą za duże?
Hili: To ucieknę.

*******

And in Włocławek, Leon is having rather grandiose fantasies.

Leon: The brave Catman goes to the rescue of downtrodden.

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President Obama talks with Marilynne Robinson

October 26, 2015 • 1:30 pm

As I’ve mentioned recently, novelist Marilynne Robinson has taken to bashing scientism, atheism, and science itself in her latest nonfiction works, for she believes in an immaterial soul and just can’t forgive science for neglecting it. She’s a devout Congregationalist and sometimes preaches at her church in Iowa City.

On September 14, Robinson and President Obama had a long conversation at the Iowa State Library in Des Moines, a discussion that’s now  published in two parts in the New York Review of Books (free; links below).

It’s really more of an interview of Robinson by Obama, but the President gives a lot of his own views on writing, the economy, democracy, and the difficulties of governing. I didn’t find much that was new, but the discussion of religion was mercifully brief and tepid, and perhaps some of you will find some meat.

What I found bracing was the rediscovery of Obama’s intelligence and respect for literature: he’s actually read Robinson’s novels, and the discussion couldn’t have been scripted by Obama’s staff. Have at least a cursory look at the two parts of the interview, and see if you can imagine such a conversation between Robinson and either Donald Trump or Ben Carson. NO WAY.

Part 1

Part 2

WordPress wants information

October 26, 2015 • 12:45 pm

As I’ve mentioned twice, I am getting quite a few comments that post as “Anonymous” because people aren’t filling in (or their device isn’t auto-filling-in) their names and email addresses. If you’re one of these, could you answer the WordPress person’s questions below? (Just put the info in a comment.)

Thanks.

If you’re still having this issue, could you let me know if you’ve noticed any common threads from people who have emailed you to let you know that their names have appeared as anonymous?
For instance, are they using a particular browser, or are they using an autocomplete feature rather than typing their names?

More Republican madness in Iowa

October 26, 2015 • 11:30 am

If you really need more evidence that Republican politics in this country is becoming like the religion of so many of its adherents, driving them to madness and irrationality, read this article from Rachel Maddow’s blog giving the reasons why Iowa Republicans like Ben Carson, who’s now leading Donald Trump by 9 percentage points in a new state poll.

First, a summary of why the Republicans from that state like him. THIS IS NOT FROM THE ONION!:

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Had a good laugh (or facepalm) yet? Here are all the data:

If we combine “very attractive” and “mostly attractive” responses, these are Iowa Republicans’ positive feelings about Ben Carson:
1. “He is not a career politician”: 85%
2. “He has no experience in foreign policy”: 42%
3. “He was highly successful as a neurosurgeon”: 88%
4. “He has said the Affordable Care Act, also known as Obamacare, is the worst thing since slavery”: 81%
5.  ”He has an inspirational personal story”: 85%
6. “He has raised questions about whether a Muslim should ever be president of the United States”: 73%
7. “He has said he would be guided by his faith in God”: 89%
8. “He has said that Hitler might not have been as successful if the people had been armed”: 77%
9. “He approaches issues with common sense”: 96%
10. “He has conducted research on tissue from aborted fetuses”: 31%
The blog notes that we should pay attention to items 4, 6, and 8.
It’s clear that it’s nearly impossible for either Carson or Trump to say something so manifestly stupid or offensive that it would hurt their standings among Republicans. That party is so desperate for a candidate that many adherents have become completely irrational. I wonder what the more liberal Republicans think of this madness.
h/t: Grania

“Concealed carry” of guns doesn’t make us safer

October 26, 2015 • 10:15 am

My loathing of private gun ownership, of the laxity of American gun regulations, and of the NRA is no secret, but when I call for the virtual abolition of private gun ownership in the US (hunting for necessity and target shooting are possible exceptions), I get pushback. “We need to defend ourselves against the bad guys,” say the dissenters. “Given the prevalence of weapons in the U.S.,” they add, “we’re safer if we’re allowed to have our guns.”

Well, we can see how often this kind of justifiable self-defense really occurs, for it’s one of the main justifications for “concealed carry” permits in the US—including a new law allowing concealed carry on Texas college campuses. But, according to several reports, justifiable self defense is extremely rare, whether or not the weapon is concealed. A New York Times op-ed today, “The concealed-carry fantasy,” gives statistics from a new report. The Times summarizes the data:

The more that sensational gun violence afflicts the nation, the more that the myth of the vigilant citizen packing a legally permitted concealed weapon, fully prepared to stop the next mass shooter in his tracks, is promoted.

This foolhardy notion of quick-draw resistance, however, is dramatically contradicted by a research projectshowing that, since 2007, at least 763 people have been killed in 579 shootings that did not involve self-defense. Tellingly, the vast majority of these concealed-carry, licensed shooters killed themselves or others rather than taking down a perpetrator.

The death toll includes 29 masskillings of three or more people by concealed carry shooters who took 139 lives; 17 police officers shot to death, and — in the ultimate contradiction of concealed carry as a personal safety factor — 223 suicides. Compared with the 579 non-self-defense, concealed-carry shootings, there were only 21 cases in which self-defense was determined to be a factor.

And yet:

. . . A Gallup poll this month found 56 percent of Americans said the nation would be safer if more people carried concealed weapons.

In other words, American’s assertion of concealed-carry as an assurance of safety is a fantasy: it’s security theater. The proportion of killings via concealed carry that involve justifiable self-defense is just 3.6%. The other 96.4% of killings were either murders, suicides, or mistakes. That means that over 96% of the time, concealed carry leads not to the aims used to justify it, but to tragedies. And remember, these are not illegal guns, but guns properly licensed for concealed carry. Overall, the policy leads to far more deaths of innocent people than of criminals.

The study cited by the Times is from The Violence Policy Center (free pdf), which includes not just concealed-carry deaths, but all deaths from handguns. Here’s part of its summary:

Guns are rarely used to kill criminals or stop crimes.

In 2012, across the nation there were only 259 justifiable homicides involving a private citizen using a firearm reported to the Federal Bureau of Investigation’s Uniform Crime Reporting (UCR) Program as detailed in its Supplementary Homicide Report (SHR). That same year, there were 8,342 criminal gun homicides tallied in the SHR. In 2012, for every justifiable homicide in the United States involving a gun, guns were used in 32 criminal homicides. 3 And this ratio, of course, does not take into account the tens of thousands of lives ended in gun suicides or unintentional shootings that year.4 This report analyzes, on both the national and state levels, the use of firearms in justifiable homicides. It also details, using the best data available on the national level, the total number of times guns are used for self-defense by the victims of both attempted and completed violent crimes and property crimes whether or not the use of the gun by the victim resulted in a fatality.

. . . The reality of self-defense gun use bears no resemblance to the exaggerated claims of the gun lobby and gun industry. The number of justifiable homicides that occur in our nation each year pale in comparison to criminal homicides, let alone gun suicides and fatal unintentional shootings. And contrary to the common stereotype promulgated by the gun lobby, those killed in justifiable homicide incidents don’t always fit the expected profile of an attack by a stranger: in 35.5 percent of the justifiable homicides that occurred in 2012 the persons shot were known to the shooter.

Now of course gun advocates will argue that guns used in homicides that are not “legally concealed” are stolen or obtained by other illegal means, but many of those guns were stolen from those who acquired them legally. No legal guns, no theft of legal guns for illegal acts. What I argue is that banning all guns will drastically stem the tide of criminal homicides in the U.S., both directly and indirectly. Here are the overall data on criminal homicides versus justifiable homicides between 2008 and 2012. Note the last row that gives their ratio, which is about forty to one:

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Finally, I refer you to this site about concealed carry homicides: Concealed Carry Killers, which tracks deaths due to that policy. You can investigate for yourself; I’ll just present their conclusions:

Concealed Carry Killers is a resource maintained by the Violence Policy Center that includes hundreds of examples of non-self defense killings by private citizens with permits to carry concealed, loaded handguns in public. These incidents include homicides, suicides, mass shootings, murder-suicides, lethal attacks on law enforcement, and unintentional deaths. Only a tiny fraction of these cases are ever ruled to be in self-defense. Any homicide that is legally determined to be in self-defense is documented and removed from the Concealed Carry Killers database and the ongoing tallies.

It saddens and maddens me that we could eliminate so many killings of innocent people, prevent so many suicides, and largely halt mass murders if we’d only get rid of guns in the U.S.  And yet, because we already have so many guns, people tells us that there’s no way to go back, even if we didn’t have a Second Amendment used to justify mass ownership of handguns—an amendment designed to allow states to have militias. I will never own a gun, and I feel safer without one. We’re a civilized society, or so we like to think. There must be a way to stop the madness.