Category Archives: Commentary

Commentary

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.

Commentary

Is absence of evidence for God evidence of his absence?

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From Christopher Copan Scott. (H/T The Poached Egg)

Excerpt:

There is a central question that must be answered in the philosophy of religion: Is absence of evidence, evidence of absence? The answer is that it all depends on what the thingin question is.

Examine these two scenarios:

Suppose in S1 (scenario one) Bob is invited on a challenge to find one golden ant, the only golden ant, and it happens to be somewhere in the 1.7 billion acres known as the Amazon Rainforest. If you were to find this one golden ant in 24 hours you would be rewarded with a large sum of money. Furthermore, suppose Bob the contestant is unsuccessful in this challenge and as a result complains to the organizers of the event saying that because he could not find the golden ant, it therefore does not exist. The problem with his complaint is that in S1, the absence of evidence for this one golden ant, gives little to no justification for you to conclude the non-existence of it.

Let us go on to S2. Here Bob is confronted with a similar challenge, instead he is not trying to find an ant but an elephant, and the environment is not the Amazon Rainforest, but his small office room. In S2, one’s assertion that the lack of evidence of the elephant in his office is evidence of absence of the elephant would be warranted.

This demonstrates that the absence of evidence is evidence of absence for the existence of a particular entity, if and only if it meets the following two conditions:

1)      If the postulated entity were to exist, we should expect to have some evidence of its existence.

2)      We have thoroughly examined the area which we would expect to find the entity.

Now what does this mean when it comes to the existence of God? This means that those who assert that the lack of evidence for the existence of God provides sufficient grounds to assert that this is evidence of absence must take the burden of proving (1) and (2).

This debate has been taken up in what is called the hiddenness of God. So at the least, in order to assert that the absence of evidence is evidence of absence for God one is required to provide justification for this claim.

For a longer treatment of the question of the hiddenness of God, please see a paper by philosopher Michael Murray, which I discuss in this post. This is an important philosophical problem that rarely comes up in the formal academic debates that we all love to watch with William Lane Craig. On a related note, it’s worth taking a look at the concept of burden of proof as it relates to the problems of evil and suffering. There are lots of links to lectures and essays in that post.

Commentary

What do studies tell us about mainstream media bias?

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Here’s a UCLA study on media bias.

Excerpt:

Of the 20 major media outlets studied, 18 scored left of center, with CBS’ “Evening News,” The New York Times and the Los Angeles Times ranking second, third and fourth most liberal behind the news pages of The Wall Street Journal.

Only Fox News’ “Special Report With Brit Hume” and The Washington Times scored right of the average U.S. voter.

The most centrist outlet proved to be the “NewsHour With Jim Lehrer.” CNN’s “NewsNight With Aaron Brown” and ABC’s “Good Morning America” were a close second and third.

“Our estimates for these outlets, we feel, give particular credibility to our efforts, as three of the four moderators for the 2004 presidential and vice-presidential debates came from these three news outlets — Jim Lehrer, Charlie Gibson and Gwen Ifill,” Groseclose said. “If these newscasters weren’t centrist, staffers for one of the campaign teams would have objected and insisted on other moderators.”

The fourth most centrist outlet was “Special Report With Brit Hume” on Fox News, which often is cited by liberals as an egregious example of a right-wing outlet. While this news program proved to be right of center, the study found ABC’s “World News Tonight” and NBC’s “Nightly News” to be left of center. All three outlets were approximately equidistant from the center, the report found.

“If viewers spent an equal amount of time watching Fox’s ‘Special Report’ as ABC’s ‘World News’ and NBC’s ‘Nightly News,’ then they would receive a nearly perfectly balanced version of the news,” said Milyo, an associate professor of economics and public affairs at the University of Missouri at Columbia.”

Here’s a Harvard University study on media bias.

Excerpt:

The programming studied on Fox News offered a somewhat more positive picture… of Republicans and more negative one of Democrats compared with other media outlets. Fox News stories about a Republican candidate were most likely to be neutral (47%), with the remainder more positive than negative (32% vs. 21% negative). The bulk of that positive coverage went to Giuliani (44% positive), while McCain still suffered from unflattering coverage (20% positive vs. 35% negative).

When it came to Democratic candidates, the picture was more negative. Again, neutral stories had a slight edge (39%), followed by 37% negative and 24% positive. And, in marked contrast from the rest of the media, coverage of Obama was twice as negative as positive: 32% negative vs. 16% positive and 52% neutral.

But any sense here that the news channel was uniformly positive about Republicans or negative about Democrats is not manifest in the data.”

From the Washington Examiner, a study of the political contributions made by the mainstream media.

Excerpt:

Senior executives, on-air personalities, producers, reporters, editors, writers and other self-identifying employees of ABC, CBS and NBC contributed more than $1 million to Democratic candidates and campaign committees in 2008, according to an analysis by The Examiner of data compiled by the Center for Responsive Politics.

The Democratic total of $1,020,816 was given by 1,160 employees of the three major broadcast television networks, with an average contribution of $880.

By contrast, only 193 of the employees contributed to Republican candidates and campaign committees, for a total of $142,863. The average Republican contribution was $744.

[…]The data on contributions by broadcast network employees was compiled by CRP at the request of The Examiner and included all 2008 contributions by individuals who identified their employer as one of the three networks or subsidiaries. The data does not include contributions by employees of the three networks who did not identify their employer.

The CRP is the organization behind OpenSecrets.org, the web site that for more than a decade has put campaign finance data within reach of anybody with an Internet connection.

President Obama received 710 such contributions worth a total of $461,898, for an average contribution of $651 from the network employees. Republican presidential nominee Sen. John McCain received only 39 contributions totaling $26,926, for an average donation of $709.

And more from a study done by the radically leftist MSNBC.

Excerpt:

MSNBC.com identified 143 journalists who made political contributions from 2004 through the start of the 2008 campaign, according to the public records of the Federal Election Commission. Most of the newsroom checkbooks leaned to the left: 125 journalists gave to Democrats and liberal causes. Only 16 gave to Republicans. Two gave to both parties.

The donors include CNN’s Guy Raz, now covering the Pentagon for NPR, who gave to Kerry the same month he was embedded with U.S. troops in Iraq; New Yorker war correspondent George Packer; a producer for Bill O’Reilly at Fox; MSNBC TV host Joe Scarborough; political writers at Vanity Fair; the editor of The Wall Street Journal’s weekend edition; local TV anchors in Washington, Minneapolis, Memphis and Wichita; the ethics columnist at The New York Times; and even MTV’s former presidential campaign correspondent.

And here’s a bit from that same article about The New Yorker:

The last bulwark against bias’s slipping into The New Yorker is the copy department, whose chief editor, Ann Goldstein, gave $500 in October to MoveOn.org, which campaigns for Democrats and against President Bush. “That’s just me as a private citizen,” she said. As for whether donations are allowed, Goldstein said she hadn’t considered it. “I’ve never thought of myself as working for a news organization.”

Those are the facts.

So what?

Now consider this column from Brent Bozell, which explains the difference media bias makes to political intelligence.

Excerpt:

The Republican presidential contest is picking up steam. Obama is consistently polling under 50 percent. This one’s a toss-up, and in the thick of it is the Fox News Channel. It’s not just their role in hosting and vetting the candidates. It’s their role as the chief villain in the eyes of liberal Democrats struggling to push their version of the “truth” about Obama.

Jon Stewart rhetorically asked Chris Wallace about Fox on “Fox News Sunday, because he thought he knew the answer: “Who are the most consistently misinformed media viewers? The most consistently misinformed? Fox, Fox viewers, consistently, every poll.”

In the real world – outside Stewart’s smug bubble – this is garbage. A 2008 survey by the Pew Research Center asked media consumers three questions: which party was in control of Congress (Democrats), who was the secretary of state (Condi Rice) and who was the prime minister of Britain (Gordon Brown).

Let’s document how the viewers of “Hannity &Colmes” were better informed than Stewart’s “Daily Show”  gigglers on basic political facts. Hannity viewers beat Stewart’s on the Democratic majority (84 percent to 65 percent correct answers), Condi Rice (a dramatic 73 percent to 48 percent gap) and Gordon Brown (49 percent to 36). Overall, as a percentage getting all three questions right, Hannity won 42-30.

Just keep that in mind when you are watching the mainstream media news shows. A very good site to bookmark and read is Newsbusters, which documents mainstream media bias daily. I even have an RSS feed of their latest stories on the front page on this blog.

UPDATE: New York Times cites abortion advocates as neutral sources.