Archive for October, 2012

Bioengineering is coming fast.

Tuesday, October 30th, 2012

An interesting article from bbc explains how concrete treated with a species of bacillus can “heal concrete” cracks by making more limestone.

Experimental concrete that patches up cracks by itself is to undergo outdoor testing.

The concrete contains limestone-producing bacteria, which are activated by corrosive rainwater working its way into the structure.

The new material could potentially increase the service life of the concrete – with considerable cost savings as a result.

The work is taking place at Delft Technical University, the Netherlands.

It is the brainchild of microbiologist Henk Jonkers and concrete technologist Eric Schlangen.

If all goes well, Dr Jonkers says they could start the process of commercialising the system in 2-3 years.

From the article, it sounds like these are not engineered bacteria but engineering may increase yield.

“Micro-cracks” are an expected part of the hardening process and do not directly cause strength loss. Fractures with a width of about 0.2mm are allowed under norms used by the concrete industry.

But over time, water – along with aggressive chemicals in it – gets into these cracks and corrodes the concrete.

“For durability reasons – in order to improve the service life of the construction – it is important to get these micro-cracks healed,” Dr Jonkers told BBC News.

Bacterial spores and the nutrients they will need to feed on are added as granules into the concrete mix. But water is the missing ingredient required for the microbes to grow. Concrete is the world’s most popular building material, but cracking is a problem

So the spores remain dormant until rainwater works its way into the cracks and activates them. The harmless bacteria – belonging to the Bacillus genus – then feed on the nutrients to produce limestone.

The bacterial food incorporated into the healing agent is calcium lactate – a component of milk. The microbes used in the granules are able to tolerate the highly alkaline environment of the concrete.

The cost will be high per unit but in the overall scheme of things, reduction in maintenance and longer functional life will dwarf cost issues.

Far out there.

Saturday, October 20th, 2012

Once again, Craig Venter is looking for new challenges. The latest may be Martian DNA.

I have thought for some time that life on Mars is going to consist of microorganisms and be buried several feet below the surface of the planet soil. I have even blogged about it before.

Now, there is a possibility of a nucleotide sequencer that could go to Mars on the next probe in 2018.

In what could become a race for the first extraterrestrial genome, researcher J. Craig Venter said Tuesday that his Maryland academic institute and his company, Synthetic Genomics, would develop a machine capable of sequencing and beaming back DNA data from the planet.

Separately, Jonathan Rothberg, founder of Ion Torrent, a DNA sequencing company, is collaborating on an effort to equip his company’s “Personal Genome Machine” for a similar task.

“We want to make sure an Ion Torrent goes to Mars,” Rothberg told Technology Review.

Although neither team yet has a berth on a Mars rocket, their plans reflect the belief that the simplest way to prove there is life on Mars is to send a DNA sequencing machine.

“There will be DNA life forms there,” Venter predicted Tuesday in New York, where he was speaking at the Wired Health Conference.

Venter said researchers working with him have already begun tests at a Mars-like site in the Mojave Desert. Their goal, he said, is to demonstrate a machine capable of autonomously isolating microbes from soil, sequencing their DNA, and then transmitting the information to a remote computer, as would be required on an unmanned Mars mission. Heather Kowalski, a spokeswoman for Venter, confirmed the existence of the project but said the prototype system was “not yet 100 percent robotic.”

Doing this on Mars would avoid the problem of contamination by earth organisms. New life forms that don’t use DNA might be a problem but most people who have thought about this believe that DNA is the genetic material of all life forms. Of course, protein, which may have been the original genetic material on earth could also be the Martian equivalent.

We are starting to see commercial spacecraft develop and one was used to reach the international space station recently. A Mars mission is another order of complexity but by 2018, it may be an option.

UPDATE: A new report describes obtaining natural gas (methane) from coal using bacteria or archea.

Many coal beds contain large amounts of methane that can be harvested by drilling wells. In recent decades, researchers have demonstrated that a large fraction of the natural gas found in the coal beds is produced by naturally occurring microörganisms that feed on coal, and they have found ways to stimulate the microbes to produce more methane. Luca Technologies, based in Golden, Colorado, is using this approach to increase production from coal beds with existing methane wells. Another company, Next Fuel, based in Sheridan, Wyoming, recently showed that it could use similar technology to produce methane from coal beds that didn’t already have methane in them, raising the possibility that vast amounts of coal that’s currently too expensive to mine could be converted into natural gas.

What will we find on Mars that might be an analogous system ?

First impressions of the second debate

Tuesday, October 16th, 2012

Obama was much more animated and his supporters will be happier tonight.

I think Romney was more impressive but I am a partisan. What surprised me was a focus group collected by Frank Luntz that decided that Romney won overwhelmingly. These were Obama voters in 2008. Their comments were very interesting. One woman supported Obama because of his comments about contraception. She was pretty much alone.

Obama said some things that will be in RNC ads next week.

1. He said that oil and gas leases were increased on public land during his administration. That is not true and Romney called him on it. Chris Wallace checked the facts and Romney was correct.

2. He said that Romney would raise taxes on the middle class and he had cut them. I don’t think anyone believed him. Romney did a good job, better than the first debate, in explaining his proposals.

3. The was only one question on Libya and Obama lied about what he said the day after the attack. That was foolish and we will see the Rose Garden statement many times before the election. He mentioned terrorism but the connection with Benghazi was not made. For weeks after, Obama and his underlings, especially Susan Rice the first black UN ambassador, kept offering the styory of the anti-Muslim video.

4. The concerns about Candy Crowley as moderator were well based. She cut off Romney multiple times and Obama talked right past the clock. He ended with 7 more minutes of time. In addition, contrary to the agreement, Candy Crowley inserted herself into the questioning and supported Obama in his assertion that he had described the attack on the Benghazi consulate as terrorism. She later, after the debate was over admitted her mistake. That will be a topic untii, the election.

5. There was a dumb question about an “assault weapons ban.” Romney did well to note that automatic weapons are already illegal, a detail that escapes most Democrats, like Diane Feinstein

All in all, I thought Romney did well and Obama improved his performance from last time, although at the cost of a number of falsehoods that will provide fodder for the large Romney ad budget in the next two weeks.

Craig Venter and biofuels

Monday, October 15th, 2012

Biofuels have gotten somewhat of a bad rep with conservatives because they are linked to Obama’s green energy boondoggles. Steve Hayward, at Powerline, thinks that success will be enough to turn the greenies against them. First they will be genetically engineered and will be developed by “Big Oil” partnering with entrepreneurs like Craig Venter who deciphered the human genome with private resources. He was in competition with the government funded “Human Genome Project.” My book review of Venter’s autobiography is here.

Venter does well in explaining his research and the article follows it well.

Venter said in an interview, “It’s pretty obvious that there’s nothing in the natural world to make the levels that are needed,” and he pointed to algae oil yield volumes needing approximately 20,000 gallons per acre equivalent of algae.

Venter and his research team, of course, in spring 2010, successfully created the first synthetic bacterial cell, which was controlled completely by a synthetic genome. Or as Venter explained it in his recent interview, as the first cell “to have a computer for a parent,” or “designed DNA on a living system.” Venter now says he has increasingly realized that a fully synthetic cell is the way to go to create competitive algae fuel. When it comes to tweaking naturally occurring algae cells, he says, “you’ll never get there with that. We need a fundamental change to how we approach all this.”

This will be enough to antagonize the Luddite Greenies who are ideologically hostile to genetic engineering. Some writers are already predicting problems.

Venter, the first mapper of the human genome and creator of the first synthetic cell (pictured above), said his scientific team and ExxonMobil have failed to find naturally occurring algae strains that can be converted into a commercial-scale biofuel. ExxonMobil and Venter’s La Jolla, Ca.-based Synthetic Genomics Inc., or SGI, continue to attempt to manipulate natural algae, but he said he already sees the answer elsewhere — in the creation of a man-made strain. “I believe that a fully synthetic cell approach will be the best way to get to a truly disruptive change,” Venter told me in an email exchange.

Venter made his remarks before a conference this week on the future of energy at the New America Foundation in Washington, D.C., and in subsequent emailed replies to questions.

When announced in July 2009, the Venter-ExxonMobil alliance of colossals attracted wide publicity. It called for ExxonMobil to spend up to $600 million if publicly undisclosed milestones were reached in the lab. The Wall Street Journal said the partnership might signal “a coming of age” for algae biofuel. Greenbang fretted that the alliance might actually prove “unholy,” but not Gigaom, which said it could be “algae’s big break.”

The terms of the alliance omit the fully synthetic approach that Venter is now advocating, so he is conducting “an ongoing dialog” with Exxon about a new agreement, he said. He appeared to suggest that such a new compact would require more Exxon investment.

If I were in charge of investing in alternate energy research, I would take what Venter says very seriously.

I assume that our skill set in this area has been one of the attractions for Exxon to work with us. Our success at building the first synthetic cell is only from last year and had not been achieved when we formed the agreement between SGI and Exxon. So I would say it is an ongoing dialog.

The future lies with algae and modifications of coal. Ethanol is a dead end. Venter is not the only one interested.

One of the dangers of using the synthetic algae cells is the fear that the cells could somehow be let loose on the outside world, which Venter admits could wreak havoc like turning the oceans into a sea of lipids. But Venter says that designing an organism that has self-destructive properties (it can’t live outside a lab, or it dies with a certain time period) could contain such an organism.

Algae oil company Solazyme, went public this year, and plans to commercialize its algae fuel in the coming years. Solazyme tweaks existing efficient algal strains and grows its designer algae in fermentation tanks without sunlight by feeding it sugar and then using existing industrial equipment extracts the oil. Solazyme’s stock is trading a bit under $10, way down from its IPO price of $18.

I would bet on Venter, first of all because he thinks in terms of private, profit making business. His record is pretty impressive and he has hired a lot of the world’s experienced scientists. I have previously written a number of blog posts on related topics, here, and here, and here, and here.

It’s interesting that the Titanic is being eaten by “Rusticles” that that are eating the iron in the hull. Bacteria that eat iron in an oxygen-free environment are only one of the marvels that are being discovered in the depths of the ocean and in hot vents in volcanic pools.

The Tea Party will win in the end.

Monday, October 15th, 2012

Frank Rich, a furious and frantic left wing writer for the NY Times, has concluded that liberalism will not be successful in transforming American society because the American public “loathes government and always has.” His essay in New York magazine is interesting although it drifts into his usual hostile rhetoric in the end.

Were the 2012 campaign a Hitchcock movie, Mitt Romney would be the MacGuffin—a device that drives a lot of plot gyrations but proves inconsequential in itself. Then again, Barack Obama could be, too. Our down-to-the-wire presidential contest is arguably just a narrative speed bump in the scenario that has been gathering steam throughout the Obama presidency: the resurgence of the American right, the most determined and coherent political force in America. No matter who is elected president, what Romney calls severe conservatism will continue to consolidate its hold over one of our two major parties. And that party is hardly destined for oblivion. There’s a case to be made that a tea-party-infused GOP will have a serious shot at winning future national elections despite the widespread liberal belief (which I have shared) that any party as white, old, and male as the Republicans is doomed to near or complete extinction by the emerging demographics of 21st-­century America.

Here, Rich cannot resist dismissing Romney as an “inconsequential plot device” but he does recognize that conservatism is more in tune with American values than the political left, of which he is an enthusiastic member.

(more…)

Joe Biden vs Joe Biden

Saturday, October 13th, 2012

I just can’t improve on this. It was done by a reader of Powerline.

Joe Biden and the debate

Friday, October 12th, 2012

A clownish Joe Biden mugged, groaned and interrupted Paul Ryan for 90 minutes last night. It was an odd spectacle but, apparently, just what the Democrats wanted. He lied about the Libya story and now Bill and Hillary Clinton may be thinking rebellion. Biden strongly suggested that the State Department was to blame for the murders because they did not ask for more security, in spite of the testimony before Congress the day before. If Hillary thinks she sees the bus coming, she may jump ship and it won’t be pretty.

With tensions between President Obama and the Clintons at a new high, former President Bill Clinton is moving fast to develop a contingency plan for how his wife, Secretary of State Hillary Clinton, should react if Obama attempts to tie the Benghazi fiasco around her neck, according to author Ed Klein.

Biden also lied about Iran and their nuclear ambitions. He dismissed the danger of doing nothing. He said they do not have a “delivery system.” They have a delivery system named Hezbollah. Iran may not have an intercontinental ballistic missile that can reach the US, yet. If Iran were to choose to attack the US, a container ship and a US port are much more likely to be involved than a new missile. Certainly, Israel is within reach as are the countries of Europe. Saudi Arabia is within reach. The Sunni-Shia rivalry is sufficient motive but the other reasons should not be ignored. Iran is ruled by a sect of suicidal maniacs.

Ryan capably described the Romney-Ryan tax proposals and his Medicare plan. I expected the abortion question and I thought it was well handled. Biden, of course, lied about the administration’s rules for health insurance coverage of contraception and abortion. That is not a big issue for me as I am pro-choice but the dishonesty is annoying. The “47% issue” and Ryan’s mention of a “30% who are takers” will not bother many people who agree and the offended are likely Obama voters no matter what happens.

It will be interesting to see what the result will be. The left, of course, is excited by the nasty tone Biden adopted.

On their $5 trillion tax cut, Romney/Ryan really need to either start naming the loopholes they’d close to pay for it or just admit they can’t make it revenue neutral without whacking the middle class. The VP was appropriately relentless on this point. Even I’m starting to feel sorry for them every time someone brings up this little flaw in their plan. I suspect I’m not alone in realizing that this country simply can’t afford to elect people promising a tax cut of this magnitude who, when it comes to paying for it, essentially say “trust us, we’ll find a bipartisan solution.”

The “$Five trillion tax cut” has been thoroughly debunked, including Stephanie Cutter’s retreat from the claim.

But, as I pointed out, Gov. Romney has already taken capital gains and dividends-for example-off the table. Now, here’s the revealing part: Larry said, and I know many in the investment community, including Mitt, feel exactly the same way, “I don’t consider those loopholes.”

So, here is a lefty who wants to raise taxes on investment income and capital gains. I don’t see enough responses pointing out that this income has already been taxed as ordinary income. Mitt Romney and most investors had salary income, taxed at the rates of the time, which they saved and invested. The capital gains and dividend income is income that was already taxed once. The left simply does not understand this.

Ryan kept his cool and Biden played the fool. An Althouse was impressed as I believe many women were impressed.

As I said, I’m tired of the yelling. I found the debate really hard to watch, but I kept watching because I was committed to live-blogging. Even still, I got catatonic. There was a point when I didn’t write anything for 20 minutes and then I said:
Biden has been yelling at Martha Raddatz for the last 15 minutes (as the subject is war). It’s so inappropriate!

The previous post had been:
The stress level is rising. Biden is so angry. Why is he yelling? Ryan needs nerves of steel not to lose his cool. I’m impressed that Ryan, when he gets his turn, is able to speak in an even, natural voice. It’s hard to concentrate on the policy itself, because the emotional static is so strong.

That shows how I felt: pain. So here’s my question. Ratings were down, I see, but when were the ratings taken? In the beginning? How did the ratings drop off over the course of the 90 minutes?

I have seen many comments about people, especially women, turning off the debate because of Biden’s rudeness and blustering. The ratings were down and the question is when were the ratings surveyed ? Of course, last night was also a big sports night. I think Ryan did better than the initial impressions suggest.

If Obama uses the Biden debate tactic as a model for next Tuesday, the election may well be over.

Reflections on the debate

Saturday, October 6th, 2012

The reverberations are still going on after the Wednesday debate. The theme coming from the Obama campaign is that Romney did not tell the truth about his policies. Most of the discussion on the non-campaign left is like Bill Mahers’ who said “It looks like he took my million and spent it all on weed.”

One of the most peculiar reactions was at the U of Wisconsin the next day. Hundreds of UW students were filing into an Obama on-campus campaign rally and were asked by a Breitbart writer if it was unfair that Obama couldn’t use his Teleprompter in the debate. Amazingly, most of the students agreed. What would a Teleprompter do ? Would they stop the debate for a few minutes while Obama’s handlers thought of a good response?

The polls will take a few more days to show the response but already something is going on. A poll of Illinois’ 10th Congressional district last August was ignored but another poll now suggests that Illinois might be in play in this election.

There is a new poll out of Cook county that should make President Obama, Robert Gibbs, David Axelrod, and the rest of the Obama reelection team nervous. In Illinois’ most populous and most Democratic county things are not looking so good for team Obama. In Cook county, home of Chicago, Obama only leads Mitt Romney 49 to 37. This is bad for Obama because he needs as big of a lead as he can get from Chicago Democrats in order to hold off the fact that he will lose the rest of the state, and in some areas of Illinois by a lot. Things are so bad for President Obama in Cook county that the suburban areas are breaking for Romney 45-38(the City of Chicago still goes to Obama 60-29).

The next debate is supposed to be on foreign policy and it is interesting to speculate on what Obama will do to recoup his loss this week. First debates have been weak for previous presidents. Reagan was criticized for looking old and a bit out of touch in his first debate with Mondale.

Still, there have been a long line of incumbent presidents who bombed their first debate.

Reagan, H.W. Bush, Clinton and Bush all had middling to bad receptions after the first debate as an incumbent seeking re-election.

Advice for Obama will be plentiful next time.

If Obama wants to seal this election win from behind a podium, the ball is in his court alone. He’s got to recover and rebound in the next debate.

Still, Obama needs to get a Red Bull into his system for next time, because former incumbents with a bad second debate — Ford, H.W. Bush, and Carter come to mind — don’t tend to get their second term.

I expect him to try to be more aggressive. Foreign policy is not a good area for him but, no doubt, we will hear about Osama bin Laden and Romney’s inexperience. He runs a risk of further weakening the traditional Democrat support from Jewish voters (See above about Illinois) if they get into the Israel and Iran situations. Romney has to avoid looking as though he wants war with Iran and I expect Obama to bring this up. Still, Romney has good points about the failure of Obama to support the people of Iran when they were demonstrating against their own government, and the disclosures about intelligence that came from the White House.

The second debate is Romney’s chance to close the deal and how he conducts himself will be critical. So far he and his campaign have done a very good job. I was not one who complained that he was not aggressive enough. Charles Krauthammer thinks he should have given a foreign policy speech sooner, after Benghazi, and maybe that is right but he plans one Monday and the tide seems to be turning right now.

I’ll bet the audience for the VP debate this week will be larger than usual as Paul Ryan makes his national appearance for those who haven’t been following the election closely until now. I expect he will do very well. Biden is an old school politician but he lied his way through the debate with Sarah Palin and she did not point them out. Ryan is another numbers gut, like Romney, and won’t let him get away with it.

The debate

Wednesday, October 3rd, 2012

I watched the debate tonight and agree with the MSNBC folks that Romney was a big winner. Chris Matthews was beside himself. Most of the MSNBC folks agreed that Romney won. I watched with a couple of items in mind.

I was certain that Obama’s handlers were worried about him seeming irritable and thin skinned. When he was irritated, ha gave this big insincere grin. Romney probably took the advice of someone who told him to look at Obama and smile slightly. He did not do a Gore and roll his eyes or sigh.

His answers were very good and he got Solyndra in and the Medicare rebuttal of the $716 billion deduction. That seemed to shut up Obama on Medicare.

He did a good job getting the deficit into the discussion.

No mention of Bain Capital.

Romney did very well in explaining the Massachusetts “Romneycare.”

Obama missed his TelePrompTer.

Great job, I think.