Proton Gradients and the Origin of Life

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.

So how has the country been doing during President Obama's term in office? Here's a scattering of indicators and how they've changed from 2008 (the last year of the Bush presidency) to now:

  1. Unemployment rate (U3): DOWN from 5.8 percent to 4.7 percent.
  2. Underemployment rate (U6): DOWN from 10.6 percent to 9.6 percent.
  3. Violent crime rate (per 100,000 residents): DOWN from 459 to 366.
  4. Fear of crime: DOWN from 37 percent to 35 percent.
  5. Uninsured rate: DOWN from 19.7 percent to 10.3 percent.
  6. Number of illegal immigrants: DOWN from 11.8 million to 11.3 million.
  7. Illegal immigrants from Mexico: DOWN from 6.6 million to 5.6 million.
  8. Teen pregnancy rate (per thousand females): DOWN from 40 to 25.
  9. Current account balance (trade deficit): DOWN from 4.6 percent of GDP to 2.3 percent of GDP.
  10. American war deaths: DOWN from 469 to 28.
  11. Inflation rate: DOWN from 3.8 percent to 1.1 percent.
  12. Shootings of police officers: DOWN from 149 to 120.
  13. Abortion rate (per thousand women): DOWN from 19 to 16.9 (through 2011).
  14. Federal deficit: DOWN from 3.1 percent of GDP to 2.5 percent of GDP.
  15. Drug abuse: DOWN from 22.4 million to 21.6 million (through 2013).
  16. Drug abuse among teenagers: DOWN from 7.7 million to 5.2 million (through 2013).
  17. Household debt (as percent of disposable income): DOWN from 12.8 percent to 10 percent.
  18. Public high school graduation rate: UP from 74 percent to 82 percent (through 2013).

I'm not presenting this stuff because I think it will change anyone's mind. Nor because Obama necessarily deserves credit for all of them. You can decide that for yourself. It's mostly just to get it on the record. And it's worth noting that none of this may matter in the face of two other statistics that might be more important than all the rest put together:

  1. Median household income: DOWN from $55,313 to $53,657 (through (2014).
  2. Americans killed in terror attacks: UP from 14 to 50+ (so far in 2016).

If you measure household income more broadly, it looks better than the raw Census figures. And household income has finally started increasing over the past couple of years. On the terror front, the absolute number of American fatalities from terrorist attacks is obviously very small. Still, the number of brutal attacks in the US and Europe (the only ones Americans care about) has obviously spiked considerably over the past year.

Are these two things enough to outweigh everything else? Maybe. Come back in November and I'll tell you.

We now have four polls out that were taken after the Republican convention: CNN, CBS, Morning Consult, and Gravis Marketing. They show an average post-convention bounce for Trump of 6.3 points. That's higher than the normal GOP bounce of about 4 points. They also show Trump leading Clinton by an average of 2.5 points.

This is not, by itself, anything for Democrats to be worried about. They'll get their own bounce this week, and it won't be until mid-August that everything settles down and we have a good idea of where everything really stands. But we can say two things. First, Donald Trump is suddenly going to start talking about polls again. Second, although liberals might have thought the Republican convention was a dumpster fire, it's obvious that Trump's message—even delivered in angry, apocalyptic tones—resonates with a lot of people. Democrats better hope that Team Hillary has an effective answer to that.

John Schindler on the DNC email leak:

The important part of this story is that Russian intelligence, using its Wikileaks cut-out, has intervened directly in an American presidential election....The most damaging aspect to the DNC leak is the certainty that Moscow has placed disinformation—that is, false information hidden among facts—to harm the Democrats and the Clinton campaign.

....It’s obvious that Moscow prefers Trump over Clinton in this election, which ought not surprise given the important role of Putin-friendly advisors in the Trump campaign, and what better way to help is there than to discredit Team Clinton?

This is mostly interesting for where it appeared: the New York Observer, which is owned by Jared Kushner, Ivanka Trump's husband. Sometimes you can't even count on family to protect you.

Today brings one of the weirdest stories of any recent presidential campaign: Hillary Clinton's campaign has essentially accused Donald Trump of being a pawn of the Russians. Not in hints; not from an unaffiliated Super PAC; not in a deniable statement from an arms-length surrogate; and not in vague "doesn't put America first" terms. Friday's release of hacked emails from the Democratic National Committee, says Clinton's campaign manager, "was done by the Russians for the purpose of helping Donald Trump." And Trump intervened to change the Republican platform last week in a way that "some experts would regard as pro-Russian."

Believe it or not, though, that's not the weirdest part of this story. The weirdest part is (a) Clinton's campaign might be right, and (b) this is not really getting an awful lot of attention from the media.

Let that sink in: the Clinton campaign has explicitly accused the Russians of being on Team Trump and suggested that Trump might be on Team Russia. And although the media is covering it, it's not the top story anywhere. Seriously. WTF does it take these days to lead the news?

In a nutshell, here's the evidence. A few months ago, when the DNC's email was hacked, outside experts immediately said it looked like it had been done by the Russians. Here's the New York Times:

Researchers have concluded that the national committee was breached by two Russian intelligence agencies, which were the same attackers behind previous Russian cyberoperations at the White House, the State Department and the Joint Chiefs of Staff last year....Evidence so far suggests that the attack was the work of at least two separate agencies, each apparently working without the knowledge that the other was inside the Democrats’ computers.

....The experts cited by Mr. Mook include CrowdStrike, a cybersecurity firm that was brought into the Democratic National Committee when officials there suspected they had been hacked....Officials at several other firms that have examined the code for the malware used against the Democratic National Committee and the metadata of the stolen documents found evidence that the documents had been accessed by multiple computers, some with Russian language settings.

Eventually the email cache ended up in the hands of Wikileaks, which published it on Friday. "The release to WikiLeaks adds another strange element," says the Times, "because it suggests that the intelligence findings are being 'weaponized' — used to influence the election in some way." Other similar stories include this one from the Washington Post and this one from Defense One. Beyond that, Russian media has become conspicuously pro Trump over the past year.

So that's the evidence that Russia is backing Team Trump. But what about the evidence that Trump is on Team Russia? This is a little trickier, but it turns out Trump has an impressive number of pro-Russian views:

  • The Washington Post: Trump didn't bother much with the Republican platform, but on one topic he pulled out the heavy artillery: against the advice of virtually all conservative foreign policy analysts, he insisted on gutting a plank that said the US should provide weapons to Ukraine. Also: for many years, Trump's campaign chair, Paul Manafort, was a lobbyist for Viktor Yanukovych, the pro-Putin former president of Ukraine.
  • The New York Times: A few days ago, Trump told David Sanger and Maggie Haberman that he might not defend the Baltics if Russia invaded them. He also suggested that the US had little moral authority to condemn human rights abuses in other countries—a decidedly unusual view for someone running on an extreme nationalist platform.
  • The Wall Street Journal: Trump has also suggested that NATO should reorient itself from defending Europe against Russian aggression and instead place more emphasis on Middle Eastern terrorism.
  • Josh Marshall: "Trump's foreign policy advisor on Russia and Europe is Carter Page, a man whose entire professional career has revolved around investments in Russia and who has deep and continuing financial and employment ties to Gazprom."
  • Slate: Trump has teamed up with Russian investors frequently on projects, and for years has lavished a surprising amount of praise on Vladimir Putin.
  • The Washington Times: Trump has been unusually sanguine about Russia's intervention in Syria. "Let Russia fight ISIS, if they want to fight ‘em," Trump said last year. "Why do we care?"

Needless to say, there could be innocent explanations for all these things. Still, they add up to a suspiciously large number of positions that are not just pro-Russia, but unusually pro-Russia. Item #1 has no support among other conservatives, and items #2-6 have no real equal in either political party.

So what's going on? The evidence that Putin would like to install Donald Trump in the White House is pretty strong. The evidence that Trump would pursue Russia-friendly policies in return is much more circumstantial, but still pretty substantial. Manchurian candidate jokes aside, this is something that deserves a lot more coverage than whatever Trump happened to tweet last night.

Friday Cat Blogging - 22 July 2016

Somebody pointed out last week that we haven't seen Hopper for a while. Is that true? Maybe! So here she is, in all her green-eyed glory.

Have a nice weekend, everyone. We deserve one after four days of the Republican convention.

I work for a 501(c)(3) nonprofit, so I'm keenly aware that I'm not allowed to endorse candidates. That means y'all will just have to guess who I'm voting for in November. I apologize for having to keep you in such suspense.

Until recently, though, I had no idea why non-profits weren't allowed to endorse candidates. Then I began hearing about the "Johnson Amendment" from Donald Trump. Obviously someone put a bug in his ear, and he's been repeating it like a mantra for weeks now. So what's this all about?

The “Johnson Amendment,” as the 1954 law is often called, is a U.S. tax code rule preventing tax-exempt organizations, such as churches and educational institutions, from endorsing political candidates. At the time, then-Senator Lyndon B. Johnson was running for re-election, and he and other members of Congress pushed the amendment to stop support for their political opponents’ campaigns, George Washington University law professor Robert Tuttle has explained. Many have also argued the amendment served to stop black churches from organizing to support the civil rights movement.

“All section 501(c)(3) organizations are absolutely prohibited from directly or indirectly participating in, or intervening in, any political campaign on behalf of (or in opposition to) any candidate for elective public office,” the IRS explains of the rule on its website. “Violating this prohibition may result in denial or revocation of tax-exempt status and the imposition of certain excise taxes.”

There you go. So why has Trump suddenly decided this is a threat to democracy? You can probably guess: because conservative churches want to endorse Republican candidates and give them lots of money without losing their tax-exempt status. Jerry Falwell Jr. explains:

In recent years, religious liberty group the Alliance Defending Freedom has advocated for its repeal, arguing that the law is unconstitutional and lets the IRS “tell pastors what they can and cannot preach,” and “aims to censor your sermon.”...“This is something that could make a difference with Christian voters in the fall,” Falwell says. “It is almost as important for Christians as the appointment of Supreme Court justices.”

My first thought about this is that it would provide yet another avenue for big money in politics. I can imagine rich donors setting up, say, the Church of the Divine Supply Siders and then funneling millions of dollars in dark money through it. Fun!

On the other hand, in a world of Super PACs and Citizens United, why bother? They can already do this easily enough, just as churches can set up "action committees" that are legally separate and can endorse away.

I'd genuinely like to hear more about this. Within whatever framework of campaign finance law we happen to have, is there any special reason that nonprofits shouldn't be able to endorse, organize, and spend money on behalf of a candidate? I have to admit that no really good reason comes to mind. Am I missing something?

Did you miss Donald Trump's post-convention press conference? No worries! Twitter has you covered:

The latest survey of purchasing managers suggests bad news for Britain:

The U.K. economy likely contracted in July as businesses responded to the uncertainty created by a vote to leave the European Union by cutting output and payrolls, according to a survey of purchasing managers at manufacturers and service providers....The U.K. PMI is a measure of activity based on monthly questioning of 600 manufacturing companies and 650 service providers since 1998. It has a close correlation with official measures of economic growth.

....Markit said the measure fell to 47.7 in July from 52.4 in June, the sharpest one-month drop on record. A reading below 50.0 signals a decline in activity, and a reading above that level indicates an expansion.

Is this a temporary dip, or a sign of things to come? Obviously we don't know yet. But that's a helluva big drop for a single month.

Republican Presidential Candidate Donald Trump, speaks during the final day of the Republican National Convention in Cleveland, Thursday, July 21, 2016.

It's over. Finally. Here are today's five best moments:

  • Trump says blandly that he might not come to the aid of our NATO partners in the Baltics if Russia invades them. Mitch McConnell chalks this up to a "rookie mistake." Newt Gringrich won't even go that far: "Estonia is in the suburbs of St. Petersburg," he says. "I'm not sure I would risk nuclear war." How confidence inspiring.
  • Trump's speech leaks hours early, upstaging the evening speakers. It is a stunningly dystopian description of a country in terminal decline, possibly the gloomiest speech ever given by a presidential contender.
  • Jerry Falwell Jr. passes along a strained joke his father told him. Dad was musing about being interviewed by Chelsea Clinton, who asked him what the biggest threats to the country are. He answered "Osama, Obama, and yo mama." This went over well on the convention floor.
  • Trump pal Tom Barrack highlights one of the worst deals Trump ever made: overpaying for the Plaza Hotel and then being forced to sell it at a loss a few years later. This is supposedly an example of what a great dealmaker Trump is.
  • Trump tells America: "I am your voice." And: "Nobody knows the system better than me, which is why I alone can fix it." If this reminds you of the kind of thing a cult leader might say, you're not alone. And the whole speech was spat out with a delivery that was scarily reminiscent of Mussolini or Fidel Castro.

By the end of Trump's speech, his campaign slogan for the next three months was clear: "Make America Fear Again." Buckle up.