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Protein binding: by chance or intelligent design?

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Dr. Fazale Rana has this interesting post up on protein binding at Reasons to Believe.

Excerpt:

Nobody likes getting the flu. In fact, the influenza virus represents a serious health challenge. For most people it causes a few days of misery, but tragically for others, it takes their lives.

Biomedical researchers are looking for ways to develop therapies against the strains of the influenza virus that avoid destruction by the immune system or fail to respond to antiviral drugs. Recently scientists from the University of Washington and The Scripps Institute made progress toward this end. They designed novel proteins from scratch that bind to the stem region of hemagglutinin, a viral protein that plays a central role in the infection process.1 The hope is that the new proteins will have therapeutic use and also help with diagnosis.

This advance has obvious biomedical importance. It also contributes toward understanding the fundamental nature of protein-protein interactions (PPIs), and with this insight comes powerful new evidence that life stems from a Creator.

Often, in order to carry out their function, proteins must interact and bind in a highly specific manner with other proteins. These PPIs are selective. If the wrong proteins bind to each other, the interaction is of no use to the cell.

A large and varied population of proteins crowds the cell’s interior. Even the simplest bacterium harbors several thousand different types of proteins, along with numerous copies of the other biomolecules inside it. The jam-packed environment complicates things. Proteins are more likely to encounter the “wrong” partners than the ones they are designed to interact with.

Biochemists are currently working to understand the specificity of PPIs and how proteins avoid unintended interactions. As it turns out, protein surfaces are carefully structured to allow strong interactions between protein pairs while minimizing the strength of the unwanted interactions. Recent work by Harvard scientists indicates that the concentration of PPI-participating proteins in the cell is also designed carefully.

In other words, protein structure and concentrations have to be precisely regulated to promote the PPIs critical for life.

The rest of the article talks about all the intricate and cutting-edge engineering and computation done by the scientists to create a situation where the proteins could bind, and then ends with this:

When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:

…cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.2

If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?

If you have to involve human intelligence to this degree, then I think that the best explanation is intelligent design.

News

Operation Fast and Furious: The ATF gunrunning scandal

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From the Heritage Foundation think tank, the latest on the Obama administration’s facilitation of assault weapon sales to Mexican drug cartels. (I.e. – “gun control”)

Excerpt:

The U.S. government intentionally sells assault weapons to Mexican drug cartels. Those cartels use those weapons to kill, among others, a U.S. law enforcement officer. The White House deflects questions on the subject. The director of the Bureau of Alcohol, Tobacco, Firearms, and Explosives (ATF), who watched the gun sales on video in his office, stonewalls Congress. So does the Justice Department. The whistleblower that exposed it all is fired.

Paperback novel or real-life Obama Administration scandal? Time’s up.

Just last week, Vince Cefalu, a special agent in the ATF for 24 years, was dismissed from his job after helping expose an operation code named “Operation Fast and Furious,” which was designed to purposefully put assault weapons into the hands of Mexican drug cartels so they could then be tracked to collect intelligence.

The operation itself is an exhausting series of unbelievable mistakes and lapses of judgment, but the Administration’s response is even more disturbing, as is the subdued media reaction.

According to the written testimony of Supervisory Special Agent Peter Forcelli: “ATF agents assigned to the Phoenix Field Division, with the concurrence of their local chain of command, ‘walked’ guns. ATF agents allowed weapons to be provided to individuals whom they knew would traffic them to members of Mexican drug trafficking organizations.”

The goal was to uncover larger criminal conspiracies across the border. Without informing Mexican authorities, the ATF facilitated over 2,500 assault weapons entering Mexico illegally. The only modern “tracking” method was a rigged-up GPS from Radio Shack that Forcelli took it upon himself to install, since the only other tracking method would be serial numbers on the guns. That device failed.

ATF agent John Dodson, who feared that this operation would cost lives, was told to stand down and “fall in line” by supervisors. Dodson testified to Congress: “Although my instincts made me want to intervene and interdict these weapons, my supervisors directed me and my colleagues not to make any stop or arrest.”

ATF agent Olindo James Casa agreed. Casa testified:

On several occasions I personally requested to interdict or seize firearms, but I was always ordered to stand down and not to seize the firearms.

Later, guns sold in this operation were discovered at the scene of a shootout in Arizona in December 2010 in which Customs and Border Protection agent Brian Terry was killed. As Forcelli testified: “To allow a gun to walk is idiotic.… This was a catastrophic disaster.”

Since then, we have learned that this operation had support in Washington and that its tactics were not a secret. Forcelli testified that Assistant U.S. Attorney Emory Hurley helped orchestrate the operation and that U.S. Attorney Dennis Burk “agreed with the direction of the case.” E-mails show that Deputy Assistant Director for ATF Field Operations William McMahon was “so excited about Fast and Furious that he received a special briefing on the program in Phoenix.”

Acting ATF director Kenneth Melson actually watched—yes, watched—live video surveillance of the operations from his office in Washington. He and his deputy were briefed weekly on the operation.

[…]As of today, the only person punished for Operation Fast and Furious has been someone who helped expose the details. Accountability for this massive operational failure is essential, and it will come only with more media attention.

It’s a mighty peculiar kind of gun control, isn’t it? But I could see how it would help the Obama administration to lobby the public to support increased gun control laws. All it cost was the lives of a few law enforcement agents. I’m sure that their families will understand.

Obama had the reputation for being soft on crime and criminals going as far back as his days as a state senator.

Excerpt:

As a state senator, Obama has been no defender of the unalienable right to life. He twice voted against bills prohibiting tax funding of abortions. In April 2002, he voted against a bill to protect babies born alive after a failed abortion procedure. A similar federal law passed later that year. In 1997, Obama twice voted “present” on an Illinois partial-birth abortion ban. He absented himself from a third vote on the measure. In 2001, he voted “present” on a bill to notify parents when their minor children seek an abortion. He also voted against a cloning ban in 2000, although he voted for it in 2001. In 1999, Obama voted against requiring school boards to put Internet pornography filters on school computers meant for students’ use. In 2001, he voted “present” on a bill to keep pornographic book and video stores and strip clubs from setting up within 1,000 feet of schools and churches. In 2003, he voted in the Health and Human Services Committee for a bill requiring “age appropriate” sex-education for students in kindergarten through fifth grade.

Despite his talk of promoting reading among inner-city youth, Obama has repeatedly opposed bills designed to promote discipline in public schools. In 2001, he twice voted “no” on a bill to let school districts require unruly students to complete suspensions before they can be shuffled into a new school district. He voted “present” on an almost unanimously passed bill requiring adult prosecution for students who fire guns on school grounds. Obama has been markedly soft on crime. In 2001, he voted against a bill that added extra penalties for crimes committed in furtherance of gang activities. He also voted against a bill making it a criminal offense for accused gang members, free on bond or on probation, to associate with known gang members. In 1999, he was the only state senator to vote against a bill prohibiting early prison release for criminal sexual abusers.

That article was written in 2004. If only we had looked at Obama’s record before we elected him.

News

Obama blasts private jet tax breaks created by his own stimulus

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From the Heritage Foundation, my favorite think tank.

Excerpt:

The chief economic culprit of President Obama’s Wednesday press conference was undoubtedly “corporate jets.” He mentioned them on at least six occasions, each time offering their owners as an example of a group that should be paying more in taxes.

“I think it’s only fair to ask an oil company or a corporate jet owner that has done so well,” the president stated at one point, “to give up that tax break that no other business enjoys.”

But the corporate jet tax break to which Obama was referring – called “accelerated depreciation,” and a popular Democratic foil of late – was created by his own stimulus package.

Proponents of the tax break lauded it as a means to spur economic activity by encouraging purchases of large manufactured goods (planes). So the president’s statement today – and his call to repeal that tax break generally – is either a tacit admission that the stimulus included projects that did not, in fact, stimulate the economy, or an attempt to “soak the rich” without regard for the policy’s effects on the economy.

For many Americans, those effects could be dramatic. Cessna and Gulfstream have facilities in a combined 15 cities nationwide (and another four abroad). A significant decline in consumption of private jets would undoubtedly have adverse effects on at least some of those local economies. Given the sizable bump in consumption that the initial tax break yielded, its repeal would likely have that economic domino effect.

Rightly or wrongly, any increase in the taxes paid by any US-based business is going to result in higher prices for consumers, or layoffs, or both. Even talking badly about businesses causes them to feel uncertain about the future. And when businesses are uncertain, they don’t hire people and they don’t expand. Obama’s solution to the recession created by the Democrat housing policies was to take money from the private sector and blow it on the public sector. Private companies realize that the bill is going to come due soon, and they are sitting on their money in case Obama succeeds in his plan to raise taxes on businesses.