Intelligent Design: Context Matters

[This post is part of a series: (Super) Naturalism, ID, and the Book of Mormon.]

If an intelligent designer was involved in the creation of life, how might we know of their involvement? Certainly one way would be for the designer to publicly announce their involvement. But what if we only consider the world around us, how could we tell? Natural theology and its descendant, Intelligent Design, posit that complicated features of life that appear to have purpose bear the hallmark of thoughtful design. Darwin upset the applecart by coming up with a convincing way for apparent design to arise naturally, without recourse to intelligent intervention.

And here we come to a problem: science, which employs methodological naturalism, takes nature as its guide to reveal what nature is capable of. Leading ID proponents have sought to put a cap on the abilities of nature by asserting that certain features are 'irreducibly complex' or contain 'specified complexity.' They have sought to plant these conceptual flags on various biological features, not because any designer has specified direct involvement in the creation of those features, but precisely because such a designation is lacking. Only if the designer does things that cannot be done in the ordinary course of nature can his works be identified. ID proponents assert that nature as we know it cannot produce some of the things that are found--in nature. They justify their position by appealing to archaeology, forensics, and SETI, each of which are accepted scientific disciplines or ventures that seek to uncover the works of intelligent beings. At the same time, they deny that any knowledge about the designer, his methods, or intentions are needed to justify judging something found in nature as intelligently designed.

The problem is that archaeology, forensics, and SETI each operate with a large background knowledge, not only of what kind of things intelligent beings do, but of what kind of things nature does in the absence of organisms with intelligence levels approaching human. They look for the artificial, which is judged against the background of nature [1]. In my opinion, ID proponents have not yet produced sufficient justification for distrusting nature, and without a more thorough knowledge of the universe with which to make comparisons, science can only employ methodological naturalism to probe life's mysteries. Unless the designer decides to speak up in a clear and open manner, nature is all we have.

ID stands in contrast to the Book of Mormon, for which supernatural claims were made from the beginning, and for which scholarly apologetic arguments depend on knowledge of the circumstances of its production.

Notes:
1. For purposes of simplicity, I am not taking up the argument over whether human intelligence is itself a product of nature.

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What Happens When You Grow Bacteria for 20 Years?

I've been pretty busy lately, so I will refer you to Carl Zimmer's post about this. I look forward to learning the molecular genetics involved. Anyway, it would seem to be a clear refutation (among other examples) of the bogus claim that mutations are only harmful or only corrupt genetic information.

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The Book of Mormon and the Supernatural: Context Matters

[This post is part of a series: (Super) Naturalism, ID, and the Book of Mormon.]

Suppose that the Book of Mormon came to light as a single copy discovered in a stack of old books. The book states that it was published in 1830 (assume that you know this to be correct), but there is no information as to who published it--it is an orphaned book. Nevertheless, it attracts the attention of a group of sincere Christians who wonder if it is actually a divine and historical (i.e. miraculous) text. What kind of evidence might they point to?

I don't think there is any. Off the top of my head, I can't think of any semi-scientific/scholarly argument for the historicity of the Book of Mormon that is not fundamentally rooted in the history of Joseph Smith--his claims about the book, what he knew, who his associates were, his timeline, etc [1]. (I would be happy to consider counter-examples if anyone thinks of one.) Remove all knowledge about him, and the miraculous origin and historicity of the Book of Mormon become less plausible by orders of magnitude.

This is implied in the argument by Terryl Givens (among others) that the circumstances surrounding the production of the Book of Mormon eliminate any middle ground regarding its historicity and value as scripture. It is made more explicit in a passage in By the Hand of Mormon (pg. 87).

What distinguishes the Book of Mormon as a religious document...has little to do with its internal claims. In this regard, the Book of Mormon well exemplifies the principle laid down by Wilfred Cantwell Smith and William A. Graham, and endorsed by Shlomo Biderman: 'the element of content is not the major factor in establishing scripture.... Because of the enormous diversity of what is said in scripture, it cannot be defined or characterized by its content.'

Philosopher David Hume wrote that "no testimony is sufficient to establish a miracle, unless the testimony be of such a kind, that its falsehood would be more miraculous than the fact which it endeavors to establish." Hugh Nibley sought to meet such a challenge, and his argument is captured in his parable of the diamond (and it is not hard to find General Authorities that echo it):

A young man once long ago claimed he had found a large diamond in his field as he was ploughing. He put the stone on display to the public free of charge, and everyone took sides. A psychologist showed, by citing some famous case studies, that the young man was suffering from a well-known form of delusion. An historian showed that other men have also claimed to have found diamonds in fields and been deceived. A geologist proved that there were no diamonds in the area but only quartz: the young man had been fooled by a quartz. When asked to inspect the stone itself, the geologist declined with a weary, tolerant smile and a kindly shake of the head. An English professor showed that the young man in describing his stone used the very same language that others had used in describing uncut diamonds: he was, therefore, simply speaking the common language of his time. A sociologist showed that only three out of 177 florists' assistants in four major cities believed the stone was genuine. A clergyman wrote a book to show that it was not the young man but someone else who had found the stone.

Finally an indigent jeweler named Snite pointed out that since the stone was still available for examination the answer to the question of whether it was a diamond or not had absolutely nothing to do with who found it, or whether the finder was honest or sane, or who believed him, or whether he would know a diamond from a brick, or whether diamonds had ever been found in fields, or whether people had even been fooled by quartz or glass, but was to be answered simply and solely by putting the stone to certain well-known tests for diamonds. Experts on diamonds were called in. Some of them declared it genuine. The others made nervous jokes about it and declared that they could not very well jeopardize their dignity and reputations by appearing to take the thing too seriously. To hide the bad impression thus made, someone came out with the theory that the stone was really a synthetic diamond, very skilfully made, but a fake just the same. The objection to this is that the production of a good synthetic diamond 120 years ago would have been an even more remarkable feat than the finding of a real one.

The judgment of whether the making of a synthetic diamond is a remarkable feat depends on knowledge of the context (technology available, etc). Despite Nibley's call for "well-known tests for diamonds," I am not aware of any for the Book of Mormon that can be employed without reference to Joseph and his circumstances.

Notes:
1. Of course, multiple specific references to people and places yet undiscovered at the time of publication would count, although judgment would revolve around how specific, and therefore unlikely, the references were. In the case of the Book of Mormon--taken on its own--Nahom and Alma are suggestive, but not overwhelmingly convincing, in my opinion.

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(Super) Naturalism, ID, and the Book of Mormon

One component of the controversy over ID has to do with the scientific method itself. ID proponents would like to change science to allow supernatural explanations. As one who has followed, published on, and testified in court regarding the ID movement, Barbara Forrest has written,

Science requires testable hypotheses. Because conjectures about the actions of “designers” or other supernatural agents are not testable (at least, no one has yet developed a way to test such conjectures) the methodology of science, sometimes called “methodological naturalism,” limits scientists to the search for natural explanations of natural phenomena. Despite the historical fact that, several centuries ago, scientists abandoned as unworkable the attempt to explain natural phenomena by appeals to the supernatural, ID proponents argue, like earlier creationists, that modern science’s exclusion of the supernatural as a scientific explanation is arbitrary. In Darwin on Trial, Phillip Johnson argues that evolution is accepted by the scientific community only because scientists have made a dogmatic, a priori commitment to naturalism (Johnson, 1991).

It seems obvious to me that invoking acts of God to explain phenomena that we don't understand prevents obtaining deeper scientific understanding. Furthermore, such invocations have failed time and again.

Now a flashback: I remember, as a missionary, reading the preface to Hugh Nibley's Since Cumorah. Regarding the Book of Mormon, he asked,

How could anyone "grounded in naturalism, rejecting the supernatural" be anything but prejudiced in favor of naturalism and against the supernatural?

It seemed obvious to me that if you discount the supernatural from the beginning you will necessarily miss it. If the test is rigged from the beginning, how can it constitute a search for truth?

Given this contradiction, some might argue that either one must accept Intelligent Design along with the Book of Mormon, or reject them both. I disagree and in forthcoming posts I will present some of my thoughts on this issue.

Addendum: In response to comments below, I should clarify that for the purposes of this series, I am using the term 'supernatural' in a straightforward way--i.e. things unknown to science such as God, angels, etc.

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Other posts in this series:
1. The Book of Mormon and the Supernatural: Context Matters
2. Intelligent Design: Context Matters

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Geocentrism Is Alive, If Not Well

This week I received an advertisement in the mail for a free book. The ad asks, "Have scientists been wrong? For 400 years?" The book promotes geocentrism and is published by The Geocentric Bible Foundation, Inc. The associated website contains this statement:

This site is devoted to the historical relationship between the Bible and astronomy. It assumes that whenever the two are at variance, it is always astronomy—that is, our "reading" of the "Book of Nature," not our reading of the Holy Bible—that is wrong. History bears consistent witness to the truth of that stance.

This turns out to be too much even for mainline creationists, who have distanced themselves from geocentrism. (As an aside, the above linked creationist critique of geocentrism contains some nice gems of irony, since mainline creationists are guilty of some of the same sins attributed to the geocentrists. Moral decay due to heliocentrism? Duh, everybody knows it's because of evolution.)

The mailing was addressed to "Resident," so it wasn't specifically targeted to me. I am tempted to request the book, but I think I will pass. First, I would be clogging up my neurons with bogus information that I do not have time to clean out (there's an open mind for you). Second, I don't want to end up on their mailing list--or others like them. Crack-pottery can be entertaining, but I get enough junk mail as is (I'm looking at you, Capital One). Finally, my wife and I are avid readers and we already have lots of books. Unless this book can help offset the law of gravity, or is the kind of novelty item that I can regale guests with, I think it best that I resist the urge. I don't want to make my life that much harder when it comes time to move.

My question is, when is somebody going to do something about the intellectual imperialism of heliocentrism and mainstream astronomy?

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Review of FARMS Review 19:2

I don't know how long it has been available online, but I noticed a few days ago that FARMS Review 19:2 (2007) is on the FARMS website. It seems new to me, but perhaps I just missed it. Anyway, only one review is directly related to science and that is David Grandy's "Ideology in the Guise of Science," a review of The God Delusion by Richard Dawkins. Having recently read the book, I was interested to read this review. FARMS Review is gradually attempting to address secular anti-Mormonism--something I think is important, and this review is part of that effort. [Also of note, don't miss Daniel Peterson's take-down of Christopher Hitchens.]

David Grandy is a professor of philosophy at BYU (my inference). For someone who has taught courses on the history and philosophy of science (Grandy, not me), I have to admit that I was disappointed with his review. I think the whole thing could be summed up with the response, "Oh yeah?!"

A central argument of The God Delusion is that the existence of a supernatural personal God is--in principle--a scientific question, and that although current science cannot disprove his existence, it allows us to say that such a God probably does not exist. In addition, Dawkins makes these additional "consciousness-raising" points (as summarized at Wikipedia):

- Atheists can be happy, balanced, moral, and intellectually fulfilled.

- Natural selection and similar scientific theories are superior to a "God hypothesis" — the illusion of intelligent design — in explaining the living world and the cosmos.

- Children should not be labelled by their parents' religion. Terms like "Catholic child" or "Muslim child" should make people flinch.

- Atheists should be proud, not apologetic, because atheism is evidence of a healthy, independent mind.

None of this is really addressed by Grandy. He demurs at the idea that natural selection has as much explanatory power as Dawkins argues it does, but does not provide a basis for thinking otherwise other than to point to holes in our knowledge and play games with analogies. He charges that the book "is ideology poorly disguised as science." I think it would be more accurate and fair to say that it is ideology informed by science. His introductory story insinuates that Dawkins has attacked a caricature of God, and that the book is not threatening, but he does not elaborate.

Certain passages make me wonder how much attention Grandy paid to what he was reading. For example, he writes,

In the latter part of the book, Dawkins offers an explanation for religion. Believing that only Darwinian evolution can get to the bottom of this matter, he weaves an interesting story. But this is not to say that others, working from different principles, could not weave equally interesting but very different stories.

In fact, Dawkins argued that religion was not directly selected by natural selection, but is a by-product of something else that was. Further, Dawkins wrote,

If, then, religion is a by-product of something else, what is that something else?... I shall offer one suggestion by way of illustration, but I must stress that it is only an example of the kind of thing I mean, and I shall come on to parallel suggestions made by others. I am much more wedded to the general principle that the question should be properly put, and if necessary rewritten, than I am to any particular answer.

In other words, it sounds to me like Dawkins is proposing a hypothesis.

Perhaps I am being too critical. After all, taking on The God Delusion properly would probably require a book of its own; no doubt Professor Grandy has other interests, and this was just a quick summary of his opinion. Further, you ask, "if you're so critical, why don't you write a better review?" My reply would be what I wrote previously: "I do not want to add my voice to those of his critics who obviously miss his point or offer up lame counter-arguments, nor am I equal to the task of taking him on."

I hate to end on a negative note, so I will close with a passage I agreed with.

The goal of harmonizing faith and reason is an old one, but there are pitfalls along the way; and to his credit, Dawkins does a good job of pointing some of them out. If we invest faith in, say, intelligent design, irreducible complexity, or certain versions of the anthropic principle, all of which lean on God to make sense of things, what happens when persuasive naturalistic explanations emerge?

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Why No HIV Vaccine?

This week's Science magazine has a review article titled, "Toward an AIDS Vaccine" (subscription required), by Bruce Walker and Dennis Burton--both of which are prominent in the field of HIV research. Despite 25 years of research and the infamous prediction by a U.S. Health Secretary in 1984 that a vaccine would be available within two years, we still lack a vaccine for HIV. The article summarizes why that is, and I thought that I would summarize the summary here.

Before I continue, I need to provide an extremely quick and painless (I promise) introduction to immunology. The immune system can be broadly divided into 'innate' and 'adaptive'. The innate immune system is quick, but lacks specificity and has no memory. The adaptive immune system is slower to respond--the first time, but it is powerful, specific, and has memory. If the bug shows up again, the adaptive immune system will act swiftly. Vaccines are designed to stimulate the adaptive immune system.

(Not bad eh? Just one more paragraph.) The central players in the adaptive immune system are B cells and T cells. B cells make antibodies, which are Y-shaped proteins that bind specific 3-dimensional protein surfaces. The shape of that surface is determined randomly for each B cell when it is made. Imagine attacking Godzilla with thousands of bear traps; that's sort of like what antibodies do. For our purposes here, there are two kinds of T cells. One kind acts as a surgical strike team to kill cells infected with virus. The other kind acts as central command; these cells give (or deny) B cells and the killer T cells permission to attack. (You can wake up now.)

The basic vaccine problems are summarized in a table that I will adapt for use here as numbered headings.

1. Sequence diversity. HIV mutates a lot--even within an individual. I already knew that, but this sentence caught my attention:

Indeed, the amount of HIV diversity within a single infected individual can exceed the variability generated over the course of a global influenza epidemic, the latter of which results in the need for a new vaccine each year.

Any vaccine worth doing needs to protect across a broad range of strains. Given the diversity found in an individual person, that's a tall order.

2. Infection of critical immune cells. Remember those T cells that act as central command? HIV infects and kills them. In fact, there is a large slaughter of them within days after initial infection. Remember, people don't die from HIV; they die from other infections after HIV has wiped out the immune system. That's why it is called Acquired Immune Deficiency Syndrome (AIDS).

3. Immune Avoidance.

3a. Masking of neutralization epitopes. Remember my Godzilla analogy above? Well Godzilla has lots of scales protecting him, so what you really want to do is to get at his sensitive places--like his Achilles heel, to mix metaphors. The problem with HIV is that its sensitive places--particularly those that are the same among different strains--are covered very well.

3b. MHC down-regulation. Metaphorically, when cells get infected with a virus they have a special flag (the MHC protein) that they can wave around to get the attention of the killer T cells. HIV prevents cells from waving that flag.

3c. Immune escape through viral mutation. This was touched on above; just as the adaptive immune system gets revved up and starts to make some progress, the virus mutates and the adaptive immune system has to start over with the new mutants.

3d. Counter-immunoregulatory mechanisms. This is the same kind of thing as 3b above.

4. Latency. Like other retroviruses, as part of its life-cycle HIV integrates its genome into the host cell's chromosomes. In other words, HIV becomes part of the cell's DNA. Even if you could eliminate every single viral particle from the body, there would still be these cells--sleeper cells, if you will--that would eventually begin making new virus.

Another problem they mention is a good animal model. Since they obviously can't experiment on people, scientists have had to make due with monkeys. Not only is this expensive, but it is not always clear how well the results will translate into humans.

In the wake of a recent trial vaccine failure, HIV experts are calling for the field to get back to basics--basic research. The rest of the article is about future strategies and questions that need to be addressed. I haven't finished reading that part, and it's geek-talk anyway.

Clearly we have major challenges to overcome in order to have a decent HIV vaccine. Given the magnitude of the difficulty, should we just give up and work on something else? I think that would be a mistake for (off the top of my head) two reasons. First, AIDS is a big problem throughout the world and I just can't see giving up on the millions of people who will die. A cheap vaccine is the only hope many poor people will ever have. (Spare me a lecture about lifestyle. Plenty of innocent people get HIV.) Second, HIV research not only teaches us about HIV, it also teaches us about immunology and vaccinology, virology, biochemistry, genetics, etc. These disciplines cannot be walled off from one another. Just to use an example I know something about, research into how HIV gets into cells is successfully being applied to other unrelated viruses. It is not hyperbole to say that HIV research may lead to treatments for other diseases (and vice versa). The benefits of basic research are often unseen at the outset.

So there you go. Now you will have something to talk about during quiet moments at parties.


Science 9 May 2008: Vol. 320. no. 5877, pp. 760 - 764

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Joseph and the Third Option

Over at the FAIR Blog, in a post titled Seer or Pious Fraud,
Keller discusses the issue of how we should view Joseph Smith's pre-plates treasure seeking. I am not going to pass judgment here, but I want to round out his discussion a little bit.

I think the title and the post presents a false dichotomy: that either Joseph genuinely could see treasures, or he was lying. Anybody who spends some time reading or listening to material from the skeptical community (i.e. the community of people who promote science and fight pseudoscience and the paranormal) knows that there is at least one additional option: that people genuinely believe that they have powers, even though they do not.

It is not as simple as someone lying to themselves until they believe it, or even being crazy. Of course, nobody knows what is in a person's heart. However, there are still people who use methods of divination (such as dowsing) to find water or other objects. There are probably some mediums who genuinely think that they can communicate with the dead. There are probably some people that genuinely think Ouija boards can give them messages. And, to use a non-paranormal example, there are people who believe that facilitated communication works.

None of this requires a person to consciously generate falsehoods; they need only fall prey to ordinary human psychology. A few successes--or apparent successes--can go a long way to convince people that some genuine power is at work, even in the face of many failures, which can be explained away. Even if the person does not initially believe that they actually have any powers, others might convince them otherwise. For example, a mentalist who demonstrates the apparent ability to communicate with the dead, and explains that it is a trick based on psychological techniques, may have audience members convinced that there really was something supernatural involved and that the performer does not appreciate their true power. (You don't have to dig too deep into the skeptical literature to find such stories.) Such a performer could become a victim of their own success.

I recently saw a book at my local library that explains how to find things using a pendulum. It is entirely conceivable that an honest and open-minded person might read the book, try it out, and become convinced that it works. Although such methods fail in the face of repeated tests under controlled conditions, those tested usually do not lose belief in their ability--and most practitioners would never be tested under such conditions anyway. As an exercise, consider the video below that I found by doing a simple search. Must I either accept that the man has true powers or decide that he is a liar?

As I said, I am not going to pass judgment on Joseph here, and in my opinion the production of the Book of Mormon does move things into another level of debate with higher stakes, but one need not attribute deceit to Joseph in order to reject the authenticity of his pre-plates (and maybe even some post-plates) activities.

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