Checklist for Quacks

July 13, 2007

Have you ever sat down and wondered, “Am I a scientific quack?” Well, probably not. But I’ve met enough True Believers in pseudoscience to give myself pause. What I really am the person to come up with a scientific breakthrough? How will anyone ever believe me? Doesn’t science trudge along, a la Thomas Kuhn, in the dominant paradigm until the evidence suggesting otherwise is just too overwhelming to ignore? What if I’m part of the new paradigm that will supplant the old, and I want to get the word out?

After all, weren’t many breakthroughs originally derided? Who believed the Earth actually revolved around the Sun? Who knew that Helicobacter pylori bacteria played a role in ulcers? Who knew that RNA interference played such a large role in cell function? Or that cells were programmed to self-destruct as a natural part of development? Or that a thing as wacky as prions actually existed? (After heliocentricity, these ideas won the Nobel Prize for Medicine and Physiology in 2005, 2006, 2002, and 1997, respectively).

Luckily for all of us, Cosmic Variance has compiled an Alternative-Science Respectability Checklist. Excerpts follow:

Believe me, I sympathize. You are in possession of a truly incredible breakthrough that offers the prospect of changing the very face of science as we know it, if not more. The only problem is, you’re coming at things from an unorthodox perspective… Perhaps you have been able to construct a machine that produces more energy than it consumes, using only common household implements; or maybe you’ve discovered a hidden pattern within the Fibonacci sequence that accurately predicts the weight that a top quark would experience on Ganymede, expressed in femtonewtons; or it might be that you’ve elaborated upon an alternative explanation for the evolution of life on Earth that augments natural selection by unspecified interventions from a vaguely-defined higher power. Whatever the specifics, the point is that certain kinds of breakthroughs just aren’t going to come from a hide-bound scholastic establishment; they require the fresh perspective and beginner’s mind that only an outsider genius (such as yourself) can bring to the table.

No sarcasm there. Rule 1:

Acquire basic competency in whatever field of science your discovery belongs to.

But! But! Seems a bit demanding, doesn’t it?

Now, you may object that steering clear of such pre-existing knowledge has played a crucial role in your unique brand of breakthrough research, and you would never have been able to make those dazzling conceptual leaps had you been weighed down by all of that established art. Let me break it down for you: no.

Rule 2:

Understand, and make a good-faith effort to confront, the fundamental objections to your claims within established science.

Continuing:

Scientific claims — whether theoretical insights or experimental breakthroughs — don’t exist all by their lonesome. They are situated within a framework of pre-existing knowledge and expectations. If the claim you are making seems manifestly inconsistent with that framework, it’s your job to explain why anyone should nevertheless take you seriously…. If you claim that the position of Venus within the Zodiac affects your love life, you’re not only positing some spooky correlation between celestial bodies and human affairs; your theory also requires some sort of long-range force that acts between you and Venus, and there aren’t any such forces strong enough to be relevant.

And finally, Rule 3:

Present your discovery in a way that is complete, transparent, and unambiguous.

Not likely. But in case someone still needs convincing, have them submit their theory to the Crackpot Index.


I’m an Addict

June 29, 2007

Admitting you have a problem is the first step to recovery. So, here goes…

I’m addicted to books. When I’m feeling good, I read. When I’m feeling bad, I go book shopping. My town doesn’t have many good bookstores (the really good ones are like an hour away), but one of them has a fair number of used books. Those are my crack cocaine–powerful but cheap and accessible.

I’ve had some really bad trips before. Sometimes I wake up the next morning and think “what the hell was I thinking? I’m never going to read that.” But mostly I keep going back because it feels so good. There’s a certain satisfaction in owning books of my own, sharing them with friends (don’t worry, we use bookmark-exchange programs for safety), and especially the ultimate rush–finishing a book one’s been meaning to snort for a long time.

I get a special kick from nonfiction. And today I got a little more money than I was expecting, and I bought four new books. Like any good addict, I justify my habit with excuses. I did get 4 books for $12.59 (including tax), all by authors I had heard of or on subjects I was interested in before I got the books. They are:

The Mating Mind, by Geoffrey Miller, subtitled “How sexual choice shapes the evolution of human nature.”

A Generous Orthodoxy, by Brian McLaren, some emergent-church theology, subtitled “Why I Am a Missional, Evangelical, Post/Protestant, Liberal/Conservative, Mystical/Poetic, Biblical, Charismatic/Contemplative, Fundamentalist/Calvinist, Anabaptist/Anglican, Methodist, Catholic, Green, Incarnational, Depressed-yet-Hopeful, Emergent, Unfinished CHRISTIAN.” Yeah, so he’s not that concise, but I got to hear him speak last year and thought he’s rather more likable than the majority of ministers/ pastors/ preachers (though I count several of those as friends).

Through a Window, by Jane Goodall, subtitled “My Thirty Years with the Chimpanzees of Gombe.” I know she’s influential/ well-known, and now I’ll get to learn why.

And, Islam: A Short History by Karen Armstrong, author of the A History of God, which I much enjoyed.

So, I’m happy now, high as I am on my fix. I’m shaking a little, and don’t think I’ll be able to get much sleep until I’ve inhaled a little wordage, so I should go back to my alley and read. I promise I’ll stop. But not tonight.


Heteroflexuality

June 28, 2007

Over at Friendly Atheist, Hemant posted this billboard from a Christian group:

asian.jpg

Of course, it’s an “ex-gay ministry”‘s you-can-change-being-gay billboard that’s been Photoshopped to make a rather hilarious point. And the church wasn’t happy with the comparison. That sparked some discussion on Hemant’s blog. Here’s an example of one of the comments:

That’s just not right. What’s worse is, they try to perpetuate that idea that homosexuals can change.

Well, I agree that it’s not right. But I think the discussion of whether people who identify as homosexuals at one point of their lives do so out of pure genetic determinism or pure personal choice is tainted by social norms; the politically-correct views of the accepting left and the it’s-really-hard-to-find-a-hermeneutic-to-get-out-of-this-one views on the Christian right. So, I wrote a rather long comment, and I didn’t want it to just get buried, so I gave it a nice new home here on my friendly blog:

I think it’s important to consider the issue of choosing sexual orientation. It’s very politically incorrect to say these days that (any) people choose their sexual orientation, but let’s talk this through. Hear me out please (no pun intended). First, no one has found a single gene that causes homosexuality in a simple Mendelian way (although many, like Dean Hamer, have tried). Much research needs to be done, but the most you can say is that there is a genetic predisposition. Having a predisposition for something–let’s say liking cheetos–is not synonymous with being “born that way.” However, there can also be a tremendous influence on a developing fetus from its chemical environment during pregnancy, and this is one very likely way in which a predisposition for one sexual orientation develops.

That said, there are most certainly a number of people whose predominant sexual orientation from birth is homosexual, with no desire for the opposite gender. A much larger proportion of a population is predominantly heterosexual, with no desire for the same gender. There does exist a group in the middle though–many of whom choose to identify as bisexuals–whose orientation is more fluid. What exactly influences these people to identify as homosexual, bisexual, or heterosexual? You can bet that their personal developmental psychology plays a role, as well as social norms. Many of these ‘flexible’ people may choose to identify with a group that is not discriminated against (heterosexuals) due to outside pressure. I would bet this is where many of the “conversion” stories come from. A biologically informed opinion would include the factoid that many traits are determined by a complex interaction of genes, developmental environment (pre- and post-natal), social norms, and personal choices.

So, it’s important to recognize that sexuality, for a significant portion of the population, is much more fluid than many people would care to admit. So a Christian ministry can certainly hope to ‘convert’ some people (which is all the more reason to resist such “ministries” that cause people emotional harm). Quoting another comment:

I’m pretty sure he missed the real meaning, it’s not really that Asians don’t choose to be Asian, it’s that there’s nothing wrong with being Asian in the first place.

And that’s exactly what the response should be. It is much easier to respond “I was born this way,” but it’s simply not true for everyone. It’s harder to argue that “because the Bible says so doesn’t make it wrong,” but that seems to really be at the root of all this. Thoughts?


The Tyranny of the Discontinuous Mind (I)

June 19, 2007

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Having recently finished reading Richard Dawkins’ The Ancestor’s Tale (and already posting about it here and here) I feel inclined to offer a brief book review, and then delve into one of the most fascinating recurring themes in the book.

The Ancestor’s Tale tells the history of life. That’s pretty broad. So the questions are how to pick a starting point and what to focus on? The format of the book is unique, beginning with homo sapiens (an understandable bias) and working its way backward in chronological time. This structure constantly reinforces the concept that evolution is not “intentional” or “progressive” in certain specific senses; if the clock was wound back and history was played out with even the slightest variations, any specific species (including humans) probably wouldn’t have evolved, or would be very different. So, viewing evolutionary history frontwards always carries the risk of seeing species evolving “toward” the present, and evolution simply is not directional in that sense. Dawkins calls this misperception “the conceit of hindsight”: We evolved, therefore we were meant to evolve. Not so.

The narrative structure of the book is therefore intentionally counterintuitive, and it’s something that Dawkins handles well. The reader is constantly reminded of this special caveat for evolutionay thinking, as intended by the author. That said, Dawkins also adds narrative wit by paralleling the Ancestor’s Tale to Chaucer’s Canterbury Tales, albeit loosely. Going back in time the narrative slowly picks up more characters. Beginning with humans, then picking up modern species that represent groups that diverged from ‘our line’ at some point in the past; chimpanzees, gorillas, the other apes, Old World monkeys, New World monkeys, more primates, rodents, laurasiatheres, xenarthrans, marsupials, monotremes, sauropsids, amphibians, and so on, back to the dawn of time.

Dawkins also does a good job of discussing various evidences for differing viewpoints and current controversies, clearly demarcating that which is widely agreed upon (chimpanzees are our closest modern relative), often instances in the (evolutionarily) recent past to the uncertain (the order of the rooting of the tree for mixotrichs, archae, and eubacteria), often more distant in evolutionary time.

That said, I liked the book. A recurring point that stood out to me was “the tyranny of the discontinuous mind.” Dawkins often referred to cases where our need to categorize, group, and name things which may in reality fall in a continuum, not discrete categories, gets in the way of the most accurate descriptions.

Names are a menace in evolutionary history. It is no secret that paleontology is a controversial subject in which there are even some personal enmities. At least eight books called Bones of Contention are in print. And if you look at what two paleontologists are quarreling about, as often as not it turns out to be a name. Is this fossil Homo erectus, or is it an archaic Homo sapiens? Is this one an early Homo habilis or a late Australopithecus? People evidently feel strongly about such questions, but they often turn out to be splitting hairs. Indeed, they resemble theological questions, which I suppose gives a clue to why they arouse such passionate disagreements. The obsession with discrete names is an example of what I call the tyranny of the discontinuous mind….

He then offers some excellent examples, which I shall write about soon.


Overwhelming Evidence

June 18, 2007

I came across a fascinating post at an Intelligent Design Creationism blog, called “micro vs. macro evolution – where to draw the line?”

Given the source, and the title, I immediately chuckled. Of course, this is a very difficult question for those whose religious beliefs lead them to reject the overwhelming evidence in support universal common descent. I’m going to offer some excerpts from this post in order to point out a few common themes among conservative Christians and their relationship with Intelligent Design proponents (most of the latter fall into the former category, but many Young Earth Creationist Christians have problems with the ID guys). First sentence:

Like many Christians (and unlike many Intelligent Design purists), I believe that Darwinian evolution cannot possibly account for the diversity of KINDS of animals.

Notice immediately the language of “belief.” There is no appeal here to evidence for a point of view, as this poster isn’t even trying to pose as interested in the science of it all. Also, the concept of “kinds” is highly ambiguous. What makes mammals a different kind from birds? Where’s the line between birds and reptiles (of which they are actually a subset)? Where do you stick a platypus, or an archaeopteryx?

I believe that our designer designed each KIND independently. But, as I mentioned in a previous blog post, it’s clear the designer recycled designs in a pattern roughly parallel to the evolutionists’ discredited “tree of life.” And at this point I have to make an unpleasant conceit to godless evolutionists: the designs of many parts of our body appear to be modified versions of those used in the design of apes. Yes, these smelly, dirty, brutish animals served as a launching point for our design and, though we certainly didn’t descend from them, we have a certain designerly connection to them, much as Windows Vista does to Windows Millennium Edition.

The adjectives are quite fun. Godless evolutionists may certainly describe Dawkins and PZ Myers, but it would be a hard term to fit to Francis Collins. There are probably more religious people who think the theory of evolution is well-proven then there are non-religious people, simply because there are more of the religious, at least in this country.

And of course, animals are “smelly, dirty, brutish” but we could never, ever have descended from them. What evidence is offered as refutation? None. And of course, there is no indication that the writer has considered the overwhelming evidence for universal common descent, be it fossil or genetic. It’s all about what one chooses to believe. In this sense, many believers are much more postmodern than the evolutionists who they think lack a belief in truth. Fascinating.

Then, the poster goes on to say that there is diversity within a population, and that certain traits will be selected for, thereby ceding that evolution occurs on certain scales. So why can’t it account for new “kinds” (whatever those are)?

But it is micro-evolution, and never strays outside the boundary of a KIND. A dog cannot evolve into a cat. In ten million years, I contend, a dog’s descendants will still be recognizable dogs. Indeed, even after a billion years of microevolution, a dog’s descendants will still be something other than cats.

This is silly. If change occurs, then over more time, you have more change. Now of course evolutionary biologists would never claim that a dog would turn into a cat. What they do note is that if at some point in those ten million years you have two populations of dogs that are separated for a period of time, by geography or habits or any other factor that prevents interbreeding, those populations will diverge over time. That’s speciation. And that is considered by many to be the dividing point between micro- and macroevolution. Natural selection does not pretend to predict a dog will become a cat, but to explain that dogs and cats at some point diverged from some common ancestor that had biological similarities to both. The prediction made is that any two other groups separated for a period of time will eventually diverge as well.

But where do we draw the line between kinds, between microevolution and macroevolution? Can a donkey be bred from a horse? Can an alpaca be bred from a camel? Can a tiger be bred from a lion? These all may sound in some way ridiculous, but all of these animal pairs can interbreed, which suggests that they may be of the same kind. Where things can get tricky is when the hybrid born of the mating is itself sterile. Does this mean we’ve crossed a line between kinds, and found the limits of what evolution can change?

These cases of species that are close enough to interbreed but not produce fertile offspring are excellent examples of the fluid nature of biological change. Tigers and lions can produce offspring because they diverged recently enough that they have yet to accumulate the level of genetic difference necessary to prevent all reproduction. However, they have diverged enough to be both noticeably different (unlike species that we humans can’t tell apart with our naked eyes) and noticeably incapable of producing fertile offspring (unlike some species of songbird that while they do not reproduce together in the wild for behavioral reasons, are still physically capable of doing so). Again, an excellent example of speciation and evolution at work, breaking down the idea that each “kind” was created in a perfect, separate form.

I myself have no particular problem with a theory suggesting that all cats are descendant from a common ancestor. I’d even concede that all birds share a common ancestor – from hummingbirds to ostriches. Given enough time, I could see that change happening – it’s just a few orders of magnitude beyond the flexibility humans have brought to the domestic dog. Some quasi-evolutionists even allow for all of Primates (soulless monkeys and apes lumped together with humans) to have descended from a single designed ancestor. I myself could never believe such a thing, since I find it revolting to think my ancestors might have been animals.

Instead of the argument from personal incredulity, you get the argument from personal revulsion. Methinks this blogger has too high a view of humans and too low a view of animals. Biologically speaking, that is.

Some Intelligent Design proponents such as Michael Behe go so far as to say that yes, all species evolved from a common ancestor. They’ve been exposed to the evidence enough to know that arguing against this well-proven fact is simply impossible. However, to maintain some “proof” of an involved God from the physical world (pure faith is the enemy) they take their criticism to the level of evolutionary mechanisms. This critique still fails, but is substantially more subtle than run-of-the-mill Creationism, and has enough pseudoscientific sounding jargon backing it up to fool the scientifically uneducated market they’re aiming at: America’s conservative Christians.

And then you get tension between Christians who believe what they believe because it feels right (and/or it jives with their relatively unscrupulous reading of Scripture) and those Christians who are trying to make a (in their view) scientific argument for believing something. But this blogger talks about the revulsion that rely underlies all of Creationism, including the Intelligent Design movement: many simply reject the proposition that God is not necessary to account for the origin of the human species because it is religiously unpalatable. These rejectionists laud people like Behe (look, he says random mutation doesn’t work!) or Collins (look, a scientist who still believes in God) or Einstein (look, a guy who misleadingly uses the word “God” when talking about nature, thereby confirming our hopes that he’s on our side) to support what they believe by faith, and reject the parts they dislike.


The Edge of Intelligent Design

June 13, 2007

I wrote a little about reviews of Intelligent Design advocate Michael Behe’s new book, The Edge of Evolution, in Behe Does it Again. And then the other day I had the chance to sit down in a bookstore and read a good chunk of the book. The combination of my lack of support for what Behe is doing and my own academic-induced poverty led me not to buy the book.

Behe’s writing’s gone downhill. Gone are the well-worded explanations of biochemical mechanisms. Edge seems to be written in a quicker, outline sort of format with lots of little headlines and even less mass under each heading than with Darwin’s Black Box, his previous book.

Having just finished reading Richard Dawkins’ The Ancestor’s Tale, it’s really interesting to contrast his heavily detailed, frequently-exampled work with Behe’s, which relies on a very few examples to make a point. Jerry Coyne, writing in The New Republic, has an excellent review of The Edge of Evolution (reposted here) which suggests the title of this post and also has a nice introduction to evolutionary biology, if you need it.

Read the rest of this entry »


Dennett: The Reason-Driven Life

June 4, 2007

Daniel Dennett, a philosophy professor at Tufts, plays the friendly grandfather role well. I think it comes off much better than Dawkins’ British accent snipery.

In this video (from TED Talks), Dennett starts off by talking about how humans took an animal (the Aurochs?) and domesticated it over time to improve it, eventually leading to the modern cow. And from there he goes on to religion. His taltk came right after the one by Rick Warren (author of The Purpose-Driven Life), so some of the remarks flow from that. It’s worth watching, and more or less echoes his Breaking the Spell: Religion as a Natural Phenomenon.


Behe Does It Again

June 3, 2007

Be wrong, that is.

Michael Behe (of Darwin’s Black Box fame) has a new book coming out called The Edge of Evolution. While I haven’t read his new book yet, one can ascertain from the title that this will be another “God of the Gaps” argument: Look, here’s a gap that science hasn’t explained (yet), therefore God did it. Behe’s new line will surely be: Look, here’s the ‘edge of evolution,’ the things that haven’t been explained just yet, so therefore God is proven.

If he had just done that in his last book, it would have merely been bad theology or very bad philosophy. But, the whole thing was based on (possibly intentional) factual errors. Behe makes broad, sweeping claims about the dearth of research on molecular evolution. Here’s one:

There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems.

He is very obviously playing to the ignorance of his readership. Unfortunately, this is something one can do when writing books about biology that will have a primarily religious audience (that’s not a slam–it’s a call for religious conservatives to learn more biology). Talk Origins has a nice listing of books and articles on molecular evolution, including those on complex biochemical systems. The present list has 22 books and ~203 peer-reviewed articles on many of the subjects that Behe has claimed he searched for evolutionary explanations for but failed to find: the immune system, blood coagulation, flagella, actin, cell membranes, the citric acid cycle, glycolysis, amino acid biosynthesis, photosynthesis, vision, etc.

To the biologically educated it should be quite apparent that Behe, as a biologist, has found a thrilling new lifestyle as a celebrity within the conservative Christian community, not to mention a profitable book market, by disregarding the amazing amount of research being done by other scientists and publishing popular works making extravagant claims. And because scientists are at the forefront of uncovering the complexity of life, research on the origins of those complex systems is often several years behind the discovery of them. So a biochemist like Behe is well-positioned to write books about the current ‘edge’ of research, point to a (real or imagined) lack of satisfactory explanations, and claim it as evidence for belief. This is bad theology, and very bad science.

ERV, who does some interesting research on drug resistance in HIV, has an article called Good Virus, Bad Creationist that dissects on of Behe’s arguments from The Edge of Evolution, revealing how he takes basic misunderstandings about a field he should (if he were really keeping up with the literature) be familiar with, but is apparently not.

There are really only a few conclusions one can make about Behe. If you think of any other options, let me know:
1) He honestly doesn’t understand the science he’s writing about, or fails to do his research, so the misunderstandings stem from this.
2) Similar to #1, but his ideological/theological leanings blind him from reading the scientific literature objectively (quite possible).
3) He understands that there are scientific explanations for what he’s writing about, and purposefully disregards the facts because he knows (the vast majority of) his readers will never check the facts independently (and on that he’d probably be right).


The Big Bad Reductionist

January 15, 2007

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I picked up a copy of Richard Dawkins’ The Blind Watchmaker used for about $3 the other day. I like to think that the person who sold the book did so because this paperback addition has a horrendously ugly cover, not because of the content.

I’ve been interested in reading The Blind Watchmaker for some time, as it seems to be the most direct reponse to the “argument from design” out there. Of course, my father, who teaches design as it applies to human art and is therefore rather convinced by this apologetic, is the most vocal proponent I know, but I hear jabs about watches found on walking paths and Boeing 747’s found in deserts fairly often from others as well.

Dawkins’ answer is, no surprise, that the watchmaker that designed the complexity of life is a blind one: the “designer” is Darwinian evolution. For now I’ve only gotten to page 13, where he’s currently defending reductionism (or more specifically, the hierarchical variety):

For those that like ‘ism’ sorts of names, the aptest name for my approach to understanding how things work is probably ‘hierarchical reductionism’. If you read trendy intellectual magazines, you may have noticed that ‘reductionism’ is one of those things, like sin, that is only mentioned by people who are against it. To call oneself a reductionist will sound, in some circles, a bit like admitting to eating babies. But, just as nobody actually eats babies, so nobody is really a reductionist in any sense worth being against. The nonexistent reductionist–the sort that everybody against, but who exists only in their imaginations–tries to explain complicated things directly in terms of the smallest parts, even, in some extreme versions of the myth, as the sum of the parts! The hierarchical reductionist, on the other hand, explains a complex entity at any particular level in the hierarchy of organization, in terms of entities only one level down the hierarchy; entities which, themselves, are likely to be complex enough to need further reducing to their own component parts; and so on. It goes without say–though the mythical, baby-eating reductionist is reputed to deny this–that the kinds of explanations which are suitable at high levels in the hierarchy are quite different from the kinds of explanations which are suitable at lower levels… Reductionism, in this sense, is just another name for an honest desire to understand how things work.

On a similar note, here’s an article on PubMed about “Reductionism and Antireductionism,” and another on the “Search for organizing principles: understanding in systems biology.” (The latter seems to advocate principles of holism as opposed to reductionism as a means for understanding complex systems.)

Over at Meta-Library, a writer highlights a quote by Francis Crick (co-discoverer of the structure of DNA), that “The ultimate aim of the modern movement in biology is in fact to explain all biology in terms of physics and chemistry.” The writer (evidently a Christian, a dualist, and not a big fan of reductionism based on his disagreements with Dawkins and Wilson) asks three questions to consider whether Crick’s attempt to reduce biology to physics and chemistry has or ever will succeed. The three questions are as follows:

  1. do the laws of physics and chemistry apply to the atoms and molecules of living things?
  2. are the interactions of atoms and molecules according to physics and chemistry sufficient to account for biological phenomena, or are other kinds of interaction needed?
  3. can biological theories be deduced logically from the theories of physics and chemistry?

The author, a certain Dr. Southgate, answers yes to the first two and no to the last. I think the answer appears to be yes to all three, or at least that yes, these are possible to be deduced– not that we necessarily already have.

Today, during the opening lecture of my physics course, the professor made the statement that electromagnetic forces are what make everything work, at least on the scale that we normally experience–the biological scale (he noted the existence of nuclear forces, which we don’t often experience clearly firsthand). If it weren’t for those electromagnetic forces, gravity would pull a dropped ball straight through the earth because none of the particles would hold together. None of chemistry would work (or at least be the same) if the nature of electromagnetic reactions were different, and biochemistry, biology, ecology, and on and on would each in turn be different.

While all the principles of biology–such as a thorough understanding of human consciousness or religious belief–may not be fully reducible yet, I see no epistemic or ontological limitations that should limit our pursuit of reductionism. So Dr. Southgate would have to justify his answer of “no” to statement number three. Reductionism works; postulating that it will fail in the future because it might explain realms normally coveted by other realms, like psychology or theology- requires an explanation.