A Good Challenge to ID

I've been carrying on a conversation with a commenter by the name of John at a post or two over at Biologos. He began by saying that he couldn't see a coherent ID inference for the start and stop codons in the cell.

[A brief explanation: Messenger RNA makes a copy of a strand of DNA that codes for a protein. The first triplet of nucleotides, or the "start" codon, always codes for the amino acid methionine, whereas the last triplet of the strand, or the "stop" codon (of which there are three possible permutations), never codes for any amino acid.]

After much give and take between us, John finally came up with what I consider to be a good challenge for the ID hypothesis. Proteins achieve their function by folding into their specific shapes. In order to do this, it is important to have many or most of the correct amino acids in the correct positions. Because the stop codons do not code for any amino acids, when the ribosomes produce the protein, there is no problem of the stop codons coding for an unwanted amino acid. However, this is not the case with the start codon. Whether or not the protein calls for methionine at the first postion, methionine will be at the first position. Often this could interfere with the correct folding of the protein. So a second process is needed to remove the methionine before the protein can fold and function. From a design perspective this does indeed seem needlessly inefficient. It would seem that a much better process would be for the start codon not to code for an amino acid, also.

So the challenge is for the ID proponents to figure out why an intelligent designer would have used methionine for the start codon, instead of a codon that does not code for an amino acid. And until an explanation is produced, John's challenge weakens, to some extent, most ID hypotheses.

Of course, there may already be a good explanation that I'm not aware of. Any readers who know more about this should feel free to comment.

A very rough first try of a philosophical argument for...

...I'm not sure what:

1. In a rational world (state of affairs?), the future would resemble the past.

2. However, there is nothing contradictory about a world where the future does not resemble the past.

3. The number of ways that the future would not resemble the past far outnumber the ways that it would resemble the past.

4. Therefore, it is very improbable that the future would resemble the past.

5. Therefore, we should not expect the future to resemble the past, unless it had a rational cause.

6. Therefore, our expectation that the future would resemble the past only makes sense if we believe that it has a rational cause.

Telic Thoughts is Alive and Well

I'm glad to see that I wasn't really needed that much at TelicThoughts. They've had some very interesting posts (such as here and here), which I recommend to my readers.

An exercise

At a friend's insistence, I've begun reading Darin Hufford's The Misunderstood God. He quotes the famous love passage from I Corintians 13:

⁴ Love is patient, love is kind. It does not envy, it does not boast, it is not proud. ⁵ It does not dishonor others, it is not self-seeking, it is not easily angered, it keeps no record of wrongs. ⁶ Love does not delight in evil but rejoices with the truth. ⁷ It always protects, always trusts, always hopes, always perseveres.⁸ Love never fails.

Then he suggests substituting the word "God" for "love." So we get:

"⁴ God is patient, God is kind. God does not envy, God does not boast, God is not proud. ⁵ God does not dishonor others, God is not self-seeking, God is not easily angered, God keeps no record of wrongs. ⁶ God does not delight in evil but rejoices with the truth. ⁷ God always protects, always trusts, always hopes, always perseveres.⁸ God never fails."

A helpful exercise for those of us with dim views of God.

More from Feser

Ed Feser really doesn't like ID:

Heads ID wins, Tails you Lose.

So taking my role as a "cultural warrior in the combox" seriously, I'm commenting in the combox there, as well. I'm asking honest questions. Let's hope this leads to clarity.

In Praise of Tinkerers

As an armchair philosopher who is all thumbs, I deeply envy tinkerers. I stand in awe of their ability to conceive, design, create and build things. So when critics of ID attack it on the grounds that it makes God a "mere tinkerer," I have difficulty understand their point. To me, they have just bequeathed one of the highest forms of praise on God that I think is possible, yet they do it with their noses turned up, as if they think calling God a tinkerer is an insult of some kind.

Well, God seems to like tinkerers, too. At least, if the Christian story is true, He liked them so much He decided to be incarnated as one. Or must God take on the form that is closest to His own nature?

Ed Feser's New Post against ID

Aristotelian/Thomist philosopher, Ed Feser, has a new post:

Thomism versus the design argument

The crucial part of his argument:

"Similarly, so long as you insist (for whatever reason) on treating natural substances as if they were a kind of artifact, and on predicating attributes of both the world’s “designer” and of human designers in a univocal way, you will never (from an A-T point of view, anyway) get even one inch closer to the God of classical theism, because you will necessarily be describing the “designer” in a way that not merely falls short of, but is positively inconsistent with, classical theism."

A commenter by the name of Maolsheachlann (how the heck do you pronounce that?) made what I thought was a very good point:

"I don't understand how intelligent design in the ID sense would be different from a miracle. A miracle is a kind of bypassing of the usual operations of nature, and yet it it attests to God-- not to some kind of sorcerer or Urizen. You may not be able to reach the God of classical theism from a miraculous cure of Parkinson's disease, and yet God doesn't disdain to act in this way."

So why must God disdain to directly intervene and create life?

9/11 Truthers and Truth

A movement that describes themselves as a truth movement should be pursuing the truth, even if it seems to weaken their view of what the truth is. I've found a number of instances in the 9/11 Truth movement that seem to be evidence that that it is seeking the truth. A recent example is a recent entry at the blog, ae911truth.org. Architect Richard Gage debated journalist Chris Mohr on the question of what caused the WTC building collapses. Apparently Mr. Mohr did his homework and communicated with NIST, in order to find out their responses to truthers ojbections.

What is admirable is that ae911truth printed the responses that Mr. Mohr received: Answers from NIST.

I haven't listened to the debate, yet. I'll be interested in seeing if there is a written response to NIST's answers.

9/11 Truthers aren't always upfront about weaknesses in their case. Examples that come to mind would be their calling David Chandler a physics professor, when he's only a high school physics teacher, or their not admitting that there might be a problem with the online journal that supposedly peer-reviewed some of their papers. So I'm not claiming they're perfect. But there seems to be some sincere effort to find the truth, regardless of where it leads.

How Important are Gaps?

Are gaps important in design inferences? Most ID proponents seem to think they are. Usually an ID argument tries to show two things:

(1) Natural (non-intelligent) processes (probably) cannot account for x.

(2) x closely resembles designed objects.

And concludes,

(3) Therefore, x is probably designed.

But what if (1) were false? What if

(4) Natural processes not only can but do account for x?

Does that mean that x was not designed?

No. For either

(5) The designer could have either introduced a previous designed object y, knowing that natural processes (probably) would then take y and produce x.

Or

(6) The designer could have produced the natural processes themselves, knowing that they (probably) would in turn produce x.

And if (2) is still true, then the design inference should work.

So really, showing gaps is only one of the ways to construct a design inference.

Mike Gene seems to rely upon (5) in constructing his design inferences.

Thomists seem to rely upon (6) in conducting their design inferences.

Of course, I don't think there's an inherent reason why proving (1) is a bad way to go.

This Should be Interesting

Bradley Monton will be speaking at a Time Travel Conference on April 9th, and telling us on April 8th what happened there. :)

PZ certainly gets this one right.

Somebody Tell Them Dickens London Wasn't a Utopia

"Damn, no. We're in the middle of a storm with 35-50 mph winds howling outside. I guess I'm just going to have to face this universe sober."

Yes, PZ, we're in the middle of a storm. I'll face it with you, but I don't think we'll win this one. I'm hoping Jesus comes soon.

Charlie who?

I hear that Charlie Sheen has been in the news quite a bit, lately. Something about him going completely whacko. In case you didn't know, Charlie is one of those celebrity 9/11 truthers. So what should we conclude from this?

Of course, we 9/11 whackos are already devising our own conspiracy theories about ol' Charlie. Or at least, I am. The powers behind 9/11, in order to discredit 9/11 truth, have been feeding Charlie a regular diet of psychedelic drugs, sure to induce a psychotic state.

So if I start boasting about how my tired blood has turned into tiger blood, somebody check out those vitamin supplements I've been taking.

Objectivity or Subjectivity?

Mike Gene often argues that perceiving design is a subjective exercise and therefore is not science (here for example). But I'm not sure that there is anything that is completely objective. Mike would say that measurement is completely objective, but it isn't. Is the volume in that beaker 50ml or 51ml? I see 50ml. You see 51ml. So we get a third person, who sees 52ml. We keep asking people and eventually get a majority who see 51ml. So now our measurement is what the majority of people see? So if the majority of people see design, then it's designed?

Well, let's fix the problem. We'll have a machine measure the liquid. When it measures out 51ml, it will stop pouring the liquid. The problem is that we first need to calibrate the machine so that it knows what 51ml is. And who gets to do that? Some subjective human being, of course. And we're right back to square one.

But we can argue that whereas most people will agree on whether it is 50ml or 51ml, it is more difficult to get a majority of people to agree of whether something is designed or not. So then the question of objectivity or subjectivity becomes a relativistic one: how easy is it to get a majority of people to agree on something?

So if ID advocates could get a majority of people to agree that something was designed, then it would be objective and science? I doubt that Mike would agree with this. I'm curious what his response would be.

So Many Blogs, So Little Time

I've discovered that I can't visit and read all the blogs on my blog list in a single hour and still have time to contribute to my own blog. I'll have to rotate my reading, visiting half of them per day.
Right now, I'm reading the latest at Mike Gene's blog:

More Thoughts on Scientism

9/11 and Militant Atheism

"9/11 was the last straw!" exclaimed the atheist. I was at a local gathering of atheists, listening to a number of them explain what finally pushed them over the edge and become atheists, or if atheists, become more militant about it.

I had heard this before. Religion was the driving force of the murderous, tragic events of 9/11. Reasonable people of good will should no longer tolerate superstitious nonsense that could have such catastrophic consequences.

I see two problems with this line of reasoning. The first one is that militant atheism could eventually become the driving force of murderous, tragic events: killing off the religious for the sake of society, for example.

Second, as a 9/11 truther, I believe that the real driving force of 9/11 wasn't religion, but probably greed and the lust for power.

Sometimes I wonder what would happen if militant atheists were ever persuaded that the official version of 9/11 was false. And I wonder if their hatred of religion prevents them from seeing what appears to me and over 1,450 architects and engineers to be the obvious truth.

I wonder if Cousin Jerry...

... will respond to Ian Hutchinson's essay.

Who Has the Burden of Proof?

In trying to determine who is "winning" the debate between neo-Darwinists and Michael Behe, we should ask ourselves who has the burden of proof? Is it up to Behe to prove that neo-Darwinism is wrong? Or is it up to the neo-Darwinists to prove that they are right?

One could argue that Behe has the burden of proof. After all, neo-Darwinism is the the consensus view in biology, with few scientists seeing any strong reasons to give it up.

I suggest that recent discoveries have shifted the burden. There is a famous quotation from Bruce Alberts, former president of the National Academy of Sciences:

"We have always underestimated cells. … The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. … Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts."
(Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, 92(February 8, 1998): 291)

When he said that we have always underestimated cells, he was referring to a time after the Modern Synthesis, but before we were able to study the inner workings of the cell.

Behe tells us that "the great majority of proteins in the cell work in complexes of six or more."

Most biologists claim that the origin of these complexes can be explained by neo-Darwinism. Perhaps they are right. But we would like some indication that the great majority of protein complexes, which are composed of six or more proteins, actually evolved from simpler complexes. Which ones? And how? Neo-Darwinism needn't explain the evolution of every protein complex. But I would think at least a half-dozen or so should do, just so we know that it can explain them.

I may be mistaken, but I don't think this has been done, yet. Until it is done, I suggest we withhold assent from neo-Darwinism.