Tag Archives: theory

Proton Gradients and the Origin of Life

Mother Jones

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Where did complex life originate? The New York Times reports on new research from a team led by William Martin of Heinrich Heine University in Düsseldorf:

Their starting point was the known protein-coding genes of bacteria and archaea. Some six million such genes have accumulated over the last 20 years in DNA databanks….Of these, only 355 met their criteria for having probably originated in Luca, the joint ancestor of bacteria and archaea.

Genes are adapted to an organism’s environment. So Dr. Martin hoped that by pinpointing the genes likely to have been present in Luca, he would also get a glimpse of where and how Luca lived. “I was flabbergasted at the result, I couldn’t believe it,” he said.

The 355 genes pointed quite precisely to an organism that lived in the conditions found in deep sea vents, the gassy, metal-laden, intensely hot plumes caused by seawater interacting with magma erupting through the ocean floor….The 355 genes ascribable to Luca include some that metabolize hydrogen as a source of energy as well as a gene for an enzyme called reverse gyrase, found only in microbes that live at extremely high temperatures.

About a year ago I read The Vital Question, by British biochemist Nick Lane, which was all about this theory. Roughly speaking, his entire book was about the energy needs of these ancient organisms, which is based on something called a proton gradient. This, it turns out, is a complex and highly unusual way of providing energy, but it’s also nearly universal in modern life, suggesting that it goes back to the very beginnings of life. But if it’s so unusual, how did it get its start?

In the beginning, it could only work in a high-energy environment like a deep-sea vent. In these places, there was a natural gradient between proton-poor water and proton-rich water, and that was the beginning of the proton gradient. It’s not the most efficient way of producing energy, but it was the only thing around 4 billion years ago. So willy nilly, life evolved to take advantage of this, and eventually evolved its own proton gradient inside cells.

Martin has been a longtime proponent of this idea as well, and now he’s produced yet more evidence that it’s likely to be true. The energy producing mitochondria in all of your cells are the result of this. Even 4 billion years later, they still depend on a proton gradient. Protons, it turns out, are the key to life.

POSTSCRIPT: And how is the book? It’s good, though fairly dense at times if you’re not already familiar with some basic chemistry and biology. And toward the end it gets rather speculative, so take it for what it’s worth. But overall? If you’re interested in the origins of complex life, it’s worth a read.

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Proton Gradients and the Origin of Life

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"Gay Conversion Therapy" Group in New Jersey to Permanently Shut Down

Mother Jones

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A so-called “gay conversion therapy” group in New Jersey has agreed to permanently close its doors after losing a landmark court battle this summer.

As Mother Jones reported, a jury determined in June that Jews Offering New Alternatives for Healing, or JONAH, had violated state consumer fraud law by claiming it could help change clients’ sexual orientations from gay to straight. It was the first case in the nation to challenge conversion therapy as consumer fraud.

The plaintiffs—including three of the organization’s former clients—said therapists recommended by JONAH had subjected them to humiliating treatments, including stripping in front of a therapist and reenacting scenes of past sexual abuse during group therapy sessions.

On Friday, Judge Peter F. Bariso Jr. granted a permanent injunction after both sides reached a settlement requiring JONAH to cease operations, permanently dissolve as a corporate entity, and liquidate all its assets.

“The end of JONAH signals that conversion therapy, however packaged, is fraudulent—plain and simple,” David Dinielli, deputy legal director for the Southern Poverty Law Center, said in a statement. The center filed the lawsuit on behalf of the plaintiffs.

Michael Ferguson, one of the plaintiffs, added, “Gay conversion therapy stole years from my life, and nearly stole my life. My hope is that others can be spared the unneeded harm that comes from the lies the defendants and those like them spread.”

Conversion therapy has been rejected by major health organizations, including the American Psychiatric Association, which in 1973 removed homosexuality from the list of disorders in its Diagnostic and Statistical Manual of Mental Disorders. Last year, a transgender teen committed suicide in Ohio after participating in conversion therapy, inspiring a campaign for a federal ban on the practice. New Jersey, California, and Washington, DC, have laws banning licensed conversion therapists from working with minors.

In a pretrial decision in February, Judge Bariso wrote, “The theory that homosexuality is a disorder is not novel—but like the notion that the earth is flat and the sun revolves around it—instead is outdated and refuted.”

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"Gay Conversion Therapy" Group in New Jersey to Permanently Shut Down

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Who Is Ben Carson’s Mystery Physicist?

Mother Jones

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By now, we all know that Ben Carson thinks the pyramids were built by Joseph as grain silos. I’m sort of curious about where this idea came from, and maybe eventually we’ll find out. In the meantime, I’d like to highlight a different part of Carson’s pyramid speech:

“I recently had a discussion with a well-known physicist. He was talking about the Big Bang Theory and how all this obviously culminated into this wonderful, extraordinarily organized solar system that we now have, which you can set your watch by, where scientists can predict 70 years away when a comet is coming. That’s an incredible amount of organization to have originated from just a large explosion.”

Carson then tells the story of how he supposedly stumped the physicist by asking him how he could reconcile such an “organized” universe with the laws of thermodynamics, specifically entropy, which says that systems tend to move towards disorder.

“Well of course he has no answer for that. They never have an answer for any of these things.”

Huh. Not just a physicist, a “well-known” physicist. And Carson says this guy was floored by his question. Apparently he had never given any thought to whether the Big Bang theory was compatible with the second law of thermodynamics.

Conclusion: either this was the stupidest physicist ever, or else Carson was lying. I think you can guess which side I’m on, but Carson can clear this up in a trice by telling us who this hapless physicist was. I sure hope it’s not someone who’s conveniently dead.

POSTSCRIPT: It’s probably worth noting that conservative Christians are just generally a little gaga over the second law of thermodynamics, which they’re convinced disproves the theory of evolution. You can yell “In a closed system!” until you’re blue in the face, and it makes no difference. They’ve stumped you! There are dozens of more sophisticated versions of this argument, too. Carson is just extending this chestnut a little further back in time.

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Who Is Ben Carson’s Mystery Physicist?

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Here’s A Diet That Actually Works, and Has the Science to Prove It

Mother Jones

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Low-fat dietary dogma—and, by extension, the plethora of processed junk the food industry conjured up to indulge it—has passed its sell-by date. But cutting down on sugary foods can trigger rapid health improvements.

Those are the messages of two studies released last week. For the fat one, a team of Harvard researchers scoured databases looking for randomized, controlled trials—the gold standard of dietary research—comparing the weight-loss effects of low-fat diets to other regimens like low-carb. They found 53 studies that met their criteria for rigor.

The result, published in the British journal The Lancet Diabetes & Endocrinology: low-carbohydrate diets “led to significantly greater weight loss” than did low-fat ones. People assigned low-fat diets tended to lose a small amount of weight compared to no-change-in-diet control groups, but cutting carbs delivered better results than reducing dietary fat. “The science does not support low-fat diets as the optimal long-term weight loss strategy,” lead author Deirdre Tobias of Brigham and Women’s Hospital and Harvard Medical School said in a press release.

The study marks the latest indication that your fat-free fro-yo habit is not likely doing you any favors by cutting your fat intake. But its sugary jolt may be doing more harm than you already thought. That’s the suggestion of another new study, published in the journal Obesity, by a team led by longtime sugar critic Robert Lustig, a pediatric endocrinologist in at the University of California at San Francisco.

Lustig is a proponent of the idea that all calories aren’t created equal—specifically, that added sugars (in sodas, processed foods, etc.) do more harm than calorie-equivalent amounts of fats, starches, and complex carbohydrates. To test this theory, Lustig and his colleagues identified 43 kids diagnosed with obesity and metabolic syndrome—defined as a cluster of conditions associated with the risk cardiovascular disease and type 2 diabetes—and tweaked their diets.

For 10 days, the kids ate catered meals with caloric amounts equivalent to their previous diets but with all foods with added sugars removed, replaced with starches. Their overall sugar intake went from 28 percent to 10 percent (representing naturally sweet foods like fruit). Lustig summarized the results in an op-ed:

Diastolic blood pressure decreased by five points. Blood fat levels dropped precipitously. Fasting glucose decreased by five points, glucose tolerance improved markedly, insulin levels fell by 50%. In other words we reversed their metabolic disease in just 10 days, even while eating processed food, by just removing the added sugar and substituting starch, and without changing calories or weight. Can you imagine how much healthier they would have been if we hadn’t given them the starch?

It’s important to note that the results are suggestive, not conclusive. Unlike the studies conglomerated in the low-fat paper, Lustig’s project did not include a control group.

But both the Harvard study and Lustig’s reinforce an emerging consensus that fat is not necessarily a dietary devil, while quaffing sugar at typical US levels might just be.

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Here’s A Diet That Actually Works, and Has the Science to Prove It

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Here’s Why "Arming the Opposition" Usually Doesn’t Work

Mother Jones

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I routinely mock the tiresomely predictable calls from conservative hawks to “arm the opposition.” It never seems to matter who the opposition is. Nor does it matter if we’re already arming them. If we are, then we need to send them even better arms. Does this do any good? Can allied forces always benefit from more American arms and training? That gets tactfully left unsaid.

Today, Phil Carter, who has firsthand experience with this, writes a longer piece explaining just why the theory of indirect military assistance is so wobbly in practice:

The theory briefs well as a way to achieve U.S. goals without great expenditure of U.S. blood and treasure. Unfortunately, decades of experience (including the current messes in Iraq and Syria) suggest that the theory works only in incredibly narrow situations in which states need just a little assistance. In the most unstable places and in the largest conflagrations, where we tend to feel the greatest urge to do something, the strategy crumbles.

It fails first and most basically because it hinges upon an alignment of interests that rarely exists between Washington and its proxies.

….Second, the security-assistance strategy gives too much weight to the efficacy of U.S. war-fighting systems and capabilities….For security assistance to have any chance, it must build on existing institutions, adding something that fits within or atop a partner’s forces….But giving night-vision goggles and F-16 aircraft to a third-rate military like the Iraqi army won’t produce a first-rate force, let alone instill the will to fight.

….The third problem with security assistance is that it risks further destabilizing already unstable situations and actually countering U.S. interests. As in Syria, we may train soldiers who end up fighting for the other side or provide equipment that eventually falls into enemy hands.

There are some things we should have learned over the past couple of decades, and one of them is this: “train-and-equip” missions usually don’t work. Sometimes they do, as in Afghanistan in the 80s. But that’s the rare success. In Iraq, Syria, Libya, and Afghanistan in the aughts, they failed.

So why do we hear cries to arm our allies during practically every conflict? Because it turns out there aren’t very many good choices in between doing nothing and launching a full-scale ground war. One option is aerial support and bombing. Another option is arming someone else’s troops. So if you know the public won’t support an invasion with US troops, but you still want to show that you’re more hawkish than whoever’s in charge now, your only real alternative is to call for one or the other of these things—or both—regardless of whether they’ll work.

And of course, the louder the better. It might not help the war effort any, but it sure will help your next reelection campaign.

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Here’s Why "Arming the Opposition" Usually Doesn’t Work

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Pi Day Health News

Mother Jones

Well, a miracle happened. Last Monday, the 2nd, I fell off a deep cliff. For no apparent reason, I was sleeping very poorly and I spent entire days in a miasma of lethargy so great I was nearly debilitated. Twice things got so bad that I went to the ER.

Then, yesterday, suddenly I climbed back on the cliff. I woke up feeling perfectly normal. A little tired, perhaps, but that’s normal for post-chemo recovery. In all other respects, I’m human again.

So what happened? Theory 1: We’ll never know. Stuff happens for mysterious reasons. Theory 2: It was depression, and it eventually worked its way out of my system. Theory 3: My physician prescribed a different set of sleep meds on Thursday, and I slept better that night.

It’s all very weird, and hopefully it will last. In another week or two the Effexor should kick in, and hopefully that will boost my mood (and improve my sleep) as well. The timing is welcome, since I have a busy few weeks of tests and procedures ahead of me.

So that’s that. I’m still not in tip-top condition or anything, but I’m basically OK for the first time in two weeks. It’s amazing.

POSTSCRIPT/BLEG: My new sleep meds work better than the old ones, but they still aren’t ideal. My doctor mentioned the possibility of trying a med like Lunesta, which I gather is a time-release formulation. Does anyone with moderate-to-severe insomnia have any experience with this? Does it really keep you asleep for a full night? Any personal experiences welcome.

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Pi Day Health News

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Chris Christie: Parents Should Have "Choice" on Vaccines

Mother Jones

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Update, February 2, 2015, 12:20 p.m.: In 2009, Christie wrote a letter in which he appeared to support the theory that autism may be linked to vaccinations. An excerpt from the letter, provided to MSNBC, below:

“I have met with families affected by autism from across the state and have been struck by their incredible grace and courage. Many of these families have expressed their concern over New Jersey’s highest-in-the nation vaccine mandates. I stand with them now, and will stand with them as their governor in their fight for greater parental involvement in vaccination decisions that affect their children.”

Update, February 2, 2015, 10:30 a.m.: Gov. Christie’s office released a statement amending his previous comments to reporters, saying there is “no question kids should be vaccinated.”

New Jersey Gov. Chris Christie called for a “balanced” approach to childhood vaccinations, telling reporters on Monday that it’s important to provide parents a “measure of choice” in their decisions.

“Mary Pat and I have had our children vaccinated and we think that it’s an important part of being sure we protect their health and the public health,” Christie said during a press conference in Cambridge, England, where he is traveling on a trade mission. “I also understand that parents need to have some measure of choice in things as well, so that’s the balance that the government has to decide.”

“Not every vaccine is created equal and not every type of disease is as great a public health threat as others,” he added.

Christie’s comments come a day after President Obama urged parents to vaccinate their children in the midst of a widening measles outbreak that started in Disneyland. The highly contagious disease has since spread to 14 states with at least 102 cases reported, according to the Centers for Disease Control and Prevention.

“I understand that there are families that, in some cases, are concerned about the effect of vaccinations,” Obama said in an interview with NBC Sunday. “The science is, you know, pretty indisputable. We’ve looked at this again and again. There is every reason to get vaccinated, but there aren’t reasons to not.”

The rise in parents who choose not to have their children fully immunized has been cited as one reason for a growing number of vaccine-preventable disease outbreaks in recent years.

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Chris Christie: Parents Should Have "Choice" on Vaccines

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This water lawsuit could be huge and it’s happening in … Iowa?

This water lawsuit could be huge and it’s happening in … Iowa?

By on 12 Jan 2015commentsShare

Ah, Iowa. Frequently confused with heaven, the Hawkeye State is a place of simple yet profound beauty: filled with pink-hued sunsets, rolling hills, golden corn fields, and strapping basketball players. Now, in an effort to preserve the purity of the state’s stunning resources (DON’T give me that look — beauty is in the eye of the freaking beholder, OK?), the state capital’s water utility company is facing off with farmers over fertilizer in an effort to curb water pollution.

Des Moines Water Works sent an intent to sue to three neighboring counties with high nitrate levels in the Raccoon and Des Moines rivers. The utility is fed up with filtering nitrate out of drinking water — it spent $900,000 on the issue in 2013. And the lawsuit just might finally make a difference in a nationwide issue that has been unregulated and out-of-control for years.

Farmers spread nitrogen fertilizer on their corn fields, which becomes nitrate — a colorless, odorless, tasteless compound. Nitrate becomes a problem when it leaks into streams and rivers. In Iowa, underground tile pipes drain the soil beneath farmers’ fields. Those pipes, which are often managed by county governments, bring polluted water to nearby rivers and waterways, and eventually into the unknowing Iowan’s cup of drinking water. Here’s more from NPR’s Dan Charles:

Too much nitrate can be a health risk, especially for infants under the age of 6 months, and it’s difficult to remove from water. …

Bill Stowe, general manager of the Des Moines Water Works, told Iowa Public Radio in an interview last week that “we are seeing the public water supply directly risked by high nitrate concentrations.” …

Des Moines Water Works is now proceeding on the theory that those governments can be held legally responsible for the pollution that their pipes carry.

“When they build these artificial drainage districts that take water, polluted water, quickly into the Raccoon River, they have a responsibility to us and others as downstream users,” he told Iowa Public Radio.

Polluted water is not only a risk to public health — high nitrate levels also wipe out aquatic life from Midwestern lakes all the way down to the Gulf of Mexico.

This isn’t the first attempt to limit run-off. State and federal governments already offer financial assistance to farmers who try to reduce nitrogen leaks. The government-issued dollars can go towards building pollution traps like sediment-trapping ponds and wetlands. (Not only do the wetlands decrease nitrate leaks, they also bolster dwindling waterfowl and bird populations.)

But not every farmer can qualify for the government programs, so Des Moines Water Works is starting to play hard ball. We’ll raise a glass of safe drinking water to that.

Source:
Iowa’s Largest City Sues Over Farm Fertilizer Runoff in Rivers

, NPR.

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This water lawsuit could be huge and it’s happening in … Iowa?

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Former Virginia Gov. Bob McDonnell Convicted on Corruption Charges

Mother Jones

A jury found former Republican Virginia Gov. Bob McDonnell guilty on 11 counts of corruption on Thursday, ending a bizarre trial that featured bad shrimp, a broken marriage, and non-FDA approved dietary supplements. McDonnell’s wife, Maureen, was found guilty on eight charges.

The charges stemmed from the couple’s relationship with Johnnie Williams, the former CEO of Star Scientific, Inc., a pharmaceutical company. Williams, dubbed the “tic-tac man” by the governor’s staff, was pushing two new drugs, Antabloc and CigRx, and needed help getting the pills into doctors’ offices. He lavished gifts on the McDonnells, paying for their daughter’s wedding, taking Maureen on shopping sprees, and letting the couple borrow his “James Bond car”—an Aston Martin—for vacations. At one point, he bid against himself at a charity auction to win a free weekend with Maureen. In turn, the McDonnells became Star Scientific boosters. Maureen went so far as to pitch Antabloc to prospective first lady Ann Romney, telling her it could help her MS.

What’s there to say about the trial? BuzzFeed‘s Katherine Miller has the fullest summation of what happened, but let’s just call it a mess, a soap opera, the world’s worst “Modern Love” column in legalese. It was also a useful corrective to the facade politicians sometimes present when they trot their families in front of the cameras before trying to legislate yours. McDonnell, whose master’s thesis at Pat Robertson’s Regent University made the case for covenant marriage and subservient roles for wives, built his defense on the theory that his own union was too much of a failure for him and his wife to mount a conspiracy. According to the governor, his wife was a paranoid loon who had a crush on the businessman who bought her nice dresses.

At one point, a former aide to Maureen McDonnell—who called the former first lady a “nutbag“—testified that she had received a text message from the governor’s wife alleging that the couple’s chef was attempting to ruin Christmas by serving them bad shrimp. Fed up with the McDonnells (who had accused him of stealing food), the chef, Todd Schneider, handed a trove of documents to federal investigators in 2012 that led to the probe. The lesson, as always, is to be nice to the people who prepare your food.

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Former Virginia Gov. Bob McDonnell Convicted on Corruption Charges

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Your Dog Might Be Jealous

How much is that green-eyed doggy in the window?

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Your Dog Might Be Jealous

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