Horizontal Gene Transfer and Intelligent Design Theory


AUTHOR: Graham Lawton

SOURCE: "Why Darwin was Wrong About the Tree of Life"

COMMENTARY: Allen MacNeill

A recent article in the New Scientist trumpeted the news that "Darwin was wrong", at least insofar as his "tree of life" was concerned. To be specific, the author stated that new discoveries in the field of horizontal gene transfer had invalidated Darwin's "tree of life", as illustrated by his diagram in the Origin of Species.

Horizontal gene transfer (especially as the result of viral transduction) has been known to occur for almost half a century. In my undergraduate genetics course at Cornell (which I took in the spring of 1972) we did a lab in which we used lambda bacteriophage to transfer genetic material from one bacterial colony to another. Ergo, none of the mechanisms of HGT described in the article in New Scientist are all that new.

Indeed, I have listed at least six mechanisms of HGT in my blogpost on the “engines of variation” located here. In that list, they are numbers 28, 29, 33, 36, 40, and 41. Most of these HGT mechanisms have been known for decades and are among the best understood mechanisms of increasing both genetic and phenotypic variation.

What is relatively new is the application of the information gained about HGT to phylogenetic reconstruction. HGT is the rule among bacteria, and apparently occurs fairly frequently among eukaryotes as well. Evolutionary biologists, and especially phylogeneticists and systematists have been using HGT data for phylogenetic reconstruction for over a decade, even among eukaryotes. So, once again this is not new.

However, there is currently a tread at Uncommon Descent to the effect that
(1) the New Scientist article is pointing out that "Darwinism" is a bankrupt theory, and

(2) that HGT is more easily explained as part of "intelligent design theory" (ID).

Does the increasing recognition of HGT and its use in phylogenetic reconstruction mean that the current theory of evolution is invalid, or that ID can explain these phenomena better? On the contrary, the more we learn about HGT the more it seems to be even more random and undirected than vertical gene transfer (i.e. genetic recombination and heredity via reproduction). To be specific, the overwhelming majority of identified HGTs are of non-coding DNA sequences that have no detectable effect on the phenotypes of the organisms in which it has occurred.

That is, almost all of the DNA sequences that have been unambiguously shown to be the result of HGT are sequences that do not code for proteins nor participate in the regulation of coding sequences. Rather, they are sequences that have “gone along for the ride”, especially as the result of RNA retroviral HGT. Such sequences are so common that they are routinely used to construct and modify genetic phylogenies, as well as to determine genetic homologies.

The vast majority of HGTs are essentially neutral genetic mutations, as first described by Motoo Kimura in his neutral theory of molecular evolution. As such, they produce an immense amount of genetic variation without producing a corresponding amount of phenotypic variation. Furthermore, when such phenotypic variation does occur, it is more often deleterious than beneficial (usually mildly deleterious, as pointed out by Tomoko Ohta in her nearly neutral theory of molecular evolution). Only very rarely are such HGTs beneficial, and then only in relatively restricted ecological and evolutionary settings.

But neutral or slightly deleterious genetic changes (such as those produced by the vast majority of HGTs) are exactly the opposite of what one would expect to see as the work of an “intelligent designer”. Such an entity would (as several of the commentators in this thread have suggested) tailor HGTs to produce adaptive (i.e. beneficial) changes in the phenotypes of the recipients of its HGTs. Either that, or the “intelligent designer” doesn’t “tailor” its HGTs at all, but rather produces them randomly, rather like a dealer in a card game. But in that case, the actions of a soi dissant “intelligent designer” would be indistinguishable from Darwinian evolution, and including any reference to its actions (and/or inferring its existence) would be unnecessary (and would therefore violate Occam’s razor).

One last point: although the vast majority of HGTs produce either no phenotypic effect or slightly deleterious phenotypic effects, a relatively small number produce phenotypic effects that are correlated with increased survival and/or reproductive success. Unlike the vast majority of HGTs, these beneficial HGTs rapidly proliferate in the populations in which they arise, in exactly the way Darwin proposed in 1859. That is, they are preserved and passed on (while deleterious HGTs are eliminated), and thereby become more common over time among the populations in which they occur.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Martian Rocks and Intelligent Design


AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

Take a good, long look at the photograph at the top of this post (it's from NASA). Does anything about it strike you as odd? Go ahead, I'll wait...

For example, do the rocks in the photograph appear to be simply "randomly" scattered about? How about size; are there patterns in the distribution of the different sizes of rocks in the photo? And how about placement - are any of the rocks in lines, or do they show similar orientation of edges, do any of them have a coating of dust or sand on them, and are any of them stacked on top of each other (or even overlapping)?

Hmm...the more you look at this picture, the less it looks like a random and unrelated collection of objects (that is, rocks). Indeed, it looks as if someone (perhaps Someone "intelligent" with a lot of time on His hands) spent no small amount of time arranging them (after all, such arrangements apparently cover a significant fraction of the surface of the planet Mars).

It's observations like these that lead some "intelligent design theorists" (IDTs) to infer the existence and active interference in natural processes of an "intelligent designer". A significant subset of IDTs go on to infer that this "intelligent designer" is the God of the Judeo-Christian-Muslim-Mormon faith(s). In so doing, they are following the lead of the founder of the neo-Palean "intelligent design and natural theology" movement, the Anglican minister Rev. William Paley. True, what we see in the photograph is rocks, not Rev. Paley's pocketwatch, and that's the windswept plains of Mars, not a windswept heath on Earth, but "design is design" and all design points to the existence of a "designer", right?

Furthermore, many IDTs use a very familiar mode of argument in asserting the existence of "intelligent design". We could call this mode of argument the "duck" argument, as in the old saw "if it looks like a duck, flies like a duck, and quacks like a duck, it's a duck".

What's the operative word here? The word like, of course, which is the tipoff that what is being marshaled is an "argument by analogy".

I have already written about the weaknesses of arguments by analogy (see here, here, and here). Most recently, I pointed out in a critique of a recent blogpost by Dr. Steven Fuller, that arguments by analogy are extremely weak: they lack almost all logical force. Dr. Fuller replied that what IDTs (including himself) use are not, in fact, arguments by analogy. Instead, he argued that what they (and he) were pointing out were "partial identities". That is, a pattern of rocks like the one in the photograph is "partially identical" to, say, a flagstone patio set in place by a "designer" having access to large amounts of dust and sand, but only a few, small rocks.

What, precisely, does the phrase "partial identity" mean? Is it something like being "partially pregnant" or "partially dead"? Or does it mean "only partly identical"? I thought that "identical" meant "identical". That is:
Two things that are identical are the very same in each and every possible way.

Isn't a thing that is "partially identical" to some other thing also "like" that thing? Seems so to me. Indeed, the phrases "partially identical"and "partial identity" seem to me to be oxymorons, plain and simple.

To be as precise as possible:
"Partial identity" is identical to "analogy"

Ergo, Dr. Fuller apparently agrees with me that ID arguments are essentially "arguments by analogy" and therefore have virtually no logical force.

But, to get back to the curious behavior of the rocks on Mars...what's that, you say? The "behavior" of the rocks? Can it be that the rocks are "behaving"?

Indeed, they are. After long and patient analysis, it has become clear that the rocks on Mars (at least the ones in the size range shown in the photograph) "behave". To be specific, they move around on the dusty/sandy surface of the Martian plains.

Furthermore, their movement is not random. On the contrary, there is a very precise pattern to it. The rocks shown in the photograph actually move against the wind, and away from each other. The latter pattern of movement is why they appear to be non-randomly placed on the surface of the Martian plain. Furthermore, they move apart at a rate that is apparently related to their size. Small rocks move apart further and faster than large rocks (very large rocks apparently don't move much at all).

In the parlance of "intelligent design theory", something that acts non-randomly in such a way as to produce non-random patterns of activity is an "agent". Furthermore, according to IDTs, agents are "intelligent" by definition. If it moves like an agent, arranges itself like an agent, and produces patterns that are "partially identical"/analogous to patterns produced by an agent, it's an agent.

Ergo, the rocks in the photograph are either agents, or have been arranged by agents.

Or not.

Here's another explanation for the arrangement of the rocks on Mars:

Wind removes loose sand in front of the rocks, creating pits there and depositing that sand behind the rocks, creating mounds. The rocks then roll forward into the pits, moving into the wind. As long as the wind continues to blow, the process is repeated and the rocks move forward.

The rocks protect the tiny sand mounds from wind erosion. Those piles of sand, in turn, keep the rocks from being pushed downwind and from bunching up with one another....

The process is nearly the same with a cluster of rocks. However, with a cluster of rocks, those in the front of the group shield their counterparts in the middle or on the edges from the wind...

Because the middle and outer rocks are not directly hit by the wind, the wind creates pits to the sides of those rocks. And so, instead of rolling forward, the rocks roll to the side, not directly into the wind, and the cluster begins to spread out.


In other words, the pattern of rocks shown in the photograph is the result of purely natural forces and the explanation presented above is a "naturalistic" explanation.

There is, of course, an essentially infinite number of imaginable explanations for the arrangement of the rocks in the photo. They could have been arranged by an invisible "agent" who prefers rocks to be "organized". They could have been arranged during the creation of Mars (which, of course, happened on 23 October 4004 BC, along with the creation of all of the other planets, asteroids, comets, planetismals, bolides, etc.). They could have been placed by little green men or hexapedal strongly-thewed Barsoomians, taking a break between sword fights. The list of possibilities is quite literally endless.

However, the scientific consensus is that the "naturalistic" explanation in the block quote above is most consistent with observations and with an assumption that natural processes alone are sufficient to explain them. "Agents" may be involved, and so may Barsoomians, but neither are necessary to explain the arrangement and behavior of the Martian rocks, and so they are not included in a scientific explanation of such arrangement and behavior.

The same is the case for biological organisms and the explanation for their existence: the theory of evolution by natural selection. All of the explanations listed above, including not only wind erosion and "intelligent rock placement", but also tiddly-winking six-armed green warriors (and obsessive-compulsive demiurges), are consistent with the pattern shown in the photograph. However, only the scientific explanation contained in the block quote is also consistent with the universal assumption underlying all of the natural sciences: that only natural forces by invoked to explain observed patterns in natural objects and processes, until such forces are shown to be insufficient to explain such things.

It should also go without saying that, if one is in favor of explaining the arrangement and behavior of Martian rocks in the incredibly limited environment of science classes in the public schools, rather than going into all of the imaginable explanations (including Tars Tarkas and Jaweh Elohim), one should stick to the explanation(s) worked out by practicing professional scientists, and confine the other explanations to classes intended for the non-empirical speculations of amateur philosophers and theologians (or am I being redundantly redundant?)

P.S. To Dr. Fuller: contrary to your aspersion, I am not a "closet theistic evolutionist" — like Newton, "I make no hypotheses!" Unlike Newton, I am an anarchist Heinlein-libertarian Zen Quaker evolutionary psychologist who prefers not to be labeled.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

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As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

Natural Theology, Theodicy, and The Name of the Rose


AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...
"Before, we used to look to heaven, deigning only a frowning glance at the mire of matter; now we look at the earth, and we believe in the heavens because of earthly testimony."
- Jorgé of Burgos, The Name of the Rose, by Umberto Eco (William Weaver, translator)

It's a new year and a new administration (in more ways than one), and over at Uncommon Descent (the former weblog of mathematician and theologian William Dembski), social epistemologist and "intelligent design" apologist Steve Fuller has begun a series of posts on the subject of theodicy.

I read his first post on the subject with some interest, as I have just finished re-reading (for the fifth time) Umberto Eco's novel, The Name of the Rose. When I was a kid, it was inconceivable to me that a person could re-read a book. That was like seeing a movie over again; it just never happened. But now I often re-read books, and any movie or television show can be viewed as many times as one can possibly stand it.

One of the reasons I re-read books is that I've found that I often discover new things in the book on re-reading. What I had never noticed before about The Name of the Rose is that one of its main themes is the relationship between empirical evidence (that is, evidence that we can observe, either directly or indirectly) and faith, as exemplified by the epigram for this blogpost.

What Jorgé of Burgos (a thinly veiled portrait of Jorgé Luis Borges) is speaking about is the relationship between empirical evidence and faith. He laments that in past times one's belief was entirely justified by faith, but now (in the 14th century) one's belief was grounded in empirical observation; that is, evidence derived from the observation of "base matter". Jorgé's theology, which could be called revealed theology, was based on scripture and religious experiences of various kinds (especially as portrayed in the Holy Bible and the biographies of the Christian saints).

The "new" way of thinking that Jorgé laments is natural theology, a branch of theology based on reason and ordinary experience, according to which the existence and intentions of God are investigated rationally, based on evidence from the observable physical world. Natural theology has a long history, reaching back to the Antiquitates rerum humanarum et divinarum of Marcus Terentius Varro (116-27 BC). However, for almost two millennia natural theology was a minority tradition in Christian theology.

The replacement of revelation theology by natural theology represents a fundamental shift in the the theological basis of belief in the existence of God, which began in the 1st century BCE, but which reached the tipping point in the early 19th century. In 1802 the Reverend William Paley published Natural Theology: or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature. Charles Darwin himself praised Paley's work, and it had a profound effect on the direction of Christian theology, especially in England and America.

Paley's argument in Natural Theology is that one can logically infer the existence and attributes of God by the empirical study of the natural world (hence the name "natural" theology). Paley's famous argument of the "watch on the heath" was based on the idea that complex entities (such as a pocketwatch) cannot come about by accident, the way simple "natural" objects such as boulders do. Rather, Paley observes that a pocketwatch clearly has a purpose (i.e. to indicate the time) and is composed of a set of designed, complex, interactive parts (the gears, springs, hands, face, case, and crystal of the watch) which we know for a fact are designed. He then argues by means of analogy that living organisms are even more clearly purposeful entities that must have a designer.

I have already pointed out the weaknesses of arguments of analogy. I have also criticized Steve Fuller's arguments vis-a-vis "intelligent design theory" (see here as well).

What I want to do in this blogpost is to analyze Fuller's first blogpost at Uncommon Descent on "ID and the Science of God". Fuller begins with a recapitulation of the definition of "intelligent design" contained in the mission statement of Uncommon Descent:
ID is the the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose [emphasis added]

Fuller takes this definition quite seriously, arguing that the "intelligence" that does the designing in ID exists "outside of matter" (i.e. outside of the natural, physical universe). He then points out that this "intelligence" is "...a deity who exists in at least a semi-transcendent state. But then he poses the crucial question: "[H]ow can you get any scientific mileage from that?"

I would extend Fuller's question by turning it around: How can one get any theological mileage out of the idea that the existence and attributes of the deity can be inferred from observations of the natural, physical universe? This is precisely the program of natural theology, and it is the reason that I believe that natural theology is both intellectually bankrupt and ultimately destructive of belief in God. And, I am apparently not alone in this second belief; several of the comments on Fuller's post express essentially the same misgivings.

The problem here is the problem of theodicy. Fuller asserts that theodicy was originally a much broader topic than it is today. According to him,
Theodicy exists today as a boutique topic in philosophy and theology, where it’s limited to asking how God could allow so much evil and suffering in the world.

However, according to Fuller, theodicy once encompassed
"...issues that are nowadays more naturally taken up by economics, engineering and systems science – and the areas of biology influenced by them: How does the deity optimise, given what it’s trying to achieve (i.e. ideas) and what it’s got to work with (i.e. matter)? This broader version moves into ID territory, a point that has not escaped the notice of theologians who nowadays talk about theodicy. [emphasis in original]

Setting aside Fuller's historical analysis of the meaning(s) of theodicy (which I believe is both incorrect and the reverse of the actual historical evolution of the idea), I believe that Fuller gives Christians who still believe in the primacy of revelation over reason good reason to be concerned about the theological implications of ID:
"[Some theists are] uneasy about concepts like ‘irreducible complexity’ for being a little too clear about how God operates in nature. The problem with such clarity, of course, is that the more we think we know the divine modus operandi, the more God’s allowance of suffering and evil looks deliberate, which seems to put divine action at odds with our moral scruples. One way out – which was the way taken by the original theodicists – is to say that to think like God is to see evil and suffering as serving a higher good, as the deity’s primary concern is with the large scale and the long term.

I have pointed out in an earlier blogpost that this line of reasoning necessarily leads to the conclusion that God (i.e. the "intelligent designer" of ID theory) is a utilitarian Whose means are justified by His ends. As I have pointed out, this conclusion is both morally abhorrent and contrary to Christian doctrine. Fuller agrees, pointing out that "...religious thinkers complained about theodicy from day one":
"...a devout person might complain that this whole way of thinking about God is blasphemous, since it presumes that we can get into the mind of God – and once we do, we find a deity who is not especially loveable, since God seems quite willing to sacrifice His creatures for some higher design principle."

This was precisely my point in my earlier post, and it parallels Darwin's feeling about the more negative attributes of the deity.

However, Fuller takes a different tack in his analysis of theodicy:
"...it’s blasphemous to suppose that God operates in what humans recognise as a ‘rational’ fashion. So how, then, could theodicy have acquired such significance among self-avowed Christians in the first place...and...how could its mode of argumentation have such long-lasting secular effects...in any field [such as evolutionary theory] concerned with optimisation?

He then goes on to make essentially the same argument as that put forth by almost all ID supporters, an argument by analogy:
We tend to presume that any evidence of design is, at best, indirect evidence for a designer. But this is not how the original theodicists thought about the matter. They thought we could have direct (albeit perhaps inconclusive) evidence of the designer, too. Why? Well, because the Bible says so. In particular, it says that we humans are created in the image and likeness of God. At the very least, this means that our own and God’s beings overlap in some sense. (For Christians, this is most vividly illustrated in the person of Jesus.)

And how, precisely, is this an argument by analogy? Here it is:
The interesting question, then, is to figure out how much of our own being is divine overlap and how much is simply the regrettable consequence of God’s having to work through material reality to embody the divine ideas ‘in’ – or, put more controversially, ‘as’ — us. Theodicy in its original full-blooded sense took this question as its starting point. [emphasis added]

By "overlap" Fuller clearly means "analogy"; that is, how analogous is the "design" of nature (presumably brought about by the "intelligent designer", i.e. God) to human (and therefore divine) "design"? This inquiry, therefore, is based on the assumption that finding such analogies is prima facie proof that "design" in nature is the result of "intelligence" (and therefore, by extension, "divine intelligence").

But, as any undergraduate in elementary logic has learned, arguments by analogy alone are not valid evidence for anything. This is because there is nothing intrinsic to analogies that can allow us to determine their validity. As I have pointed out in an earlier blogpost, all analogies are false to some degree: the only "true" analogy to a thing is the thing itself.

Fuller lists four reasons why theodicy became important at about the same time as natural theology. These are:
• that the widespread publication of the Holy Bible not only facilitated the rise of Protestantism, it also made possible "individual confirmation" of one's "overlap" (i.e. analogy) with the deity;

• that "...theodicists...read the Bible as the literal yet fallible word of God. There is scope within Christianity for this middle position because of known problems in crafting the Bible, whose human authorship is never denied...."

• that "...theodicists...claimed legitimacy from Descartes, whose ‘cogito ergo sum’ proposed an example of human-divine overlap, namely, humanity’s repetition of how the deity establishes its own existence. After all, creation is necessary only because God originally exists apart from matter, and so needs to make its presence felt in the world through matter...."; and

• that the Scientific Revolution shifted the focus of theology from revelation to empirical investigation, grounding belief in God and His intentions in observable reality via arguments by analogy.

Let's summarize all of this before going on. According to Fuller, theodicy entails that:
1) the Holy Bible illustrates the analogies between humans and God;

2) the Holy Bible is an imperfect document, written by imperfect humans (and, by extension, should not necessarily be taken literally);

3) the Cartesian cogito ergo sum provides a paradigm of the analogy between human and divine "intelligence" by pointing to the connections between "supernatural" ideas and "natural" phenomena, and

4) the scientific method, fundamentally grounded in empirical verification, provides the most valid paradigm for understanding reality.

Here is where I find the connection to The Name of the Rose. Umberto Eco has pointed out that the title of his novel has several allusions, including Dante's mystic rose, "go lovely rose", the War of the Roses, "rose thou art sick", too many rings around Rosie, "a rose by any other name", "a rose is a rose is a rose", the Rosicrucians...there are probably as many meanings as there are readers, and more. Eco asserts that the concluding Latin hexameter,
stat rosa pristina nomine, nomina nuda tenemus ("and what is left of the rose is only its name")

points to a nominalist interpretation of his novel (see "Accuracy, Precision, Nominalism, and Occam's Razor".

And I agree with his assessment; the name of the rose is not the rose. Or, as Korbzybski put it, the map is not the territory. However, this conclusion can be taken in one of two ways. According to the first (which is based on Platonic idealism), the idea of the rose is what "matters". That is, the idea of the rose pre-exists the rose, and therefore brings the rose into existence. The idea of the rose, therefore, is what is real (hence "Platonic realism"). This is the approach taken by revelation theologists, natural theologists, and ID supporters: that the "design" of the rose (i.e. the "idea" in the "mind" of the "intelligent designer") comes first, and is made manifest in the actual, physical rose.

However, an alternative interpretation is that the rose comes first; our name for the entities which exhibit "roseness" is based on our perception of the analogies between those observed entities we come to call "roses". This is the approach taken by virtually all natural scientists, especially evolutionary biologists. As I have pointed out elsewhere, the "designer" in this case is nature itself; the environment (both external and internal) of the phylogenetic lineage of the entities we call "roses". The "design" produced by this "designer" is encoded within the genome of the rose, and expressed within its phenotype, which is made manifest by an interaction between the rose's genome and its environment.

This view is perhaps most succinctly expressed by Darwin himself, in the concluding paragraph of the Origin of Species:
It is interesting to contemplate an entangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner, have all been produced by laws acting around us. [emphasis added]

Darwin saw the physical world as being entirely regulated by a set of natural laws, including laws which had the effect of producing the "origin of species" and evolutionary adaptations. In his published writings, he declined to attribute the authorship of such laws to a deity, and in his private correspondence he generally refused to speculate on it as well.

This is precisely the same position taken by almost all evolutionary biologists, and is echoed in the words of William of Baskerville, Umberto Eco's protagonist in The Name of the Rose, who at the conclusion of the book says:
"It's hard to accept the idea that there cannot be an order in the universe because it would offend the free will of God and His omnipotence."
- William of Baskerville, The Name of the Rose, by Umberto Eco (William Weaver, translator)


REFERENCES CITED:

Eco, U. (Weaver, W., translator) (1983) A Postscript to The Name of the Rose. Harcourt, Brace, Jovanovitch Publishers, New York, NY, ISBN #015173156X, 84 pages.

For those who are interested, I will be keeping up with Steve Fuller's later posts on this subject at Uncommon Descent. For now, have a happy new year!

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

On Weird Theories



AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

"... say what you like about the tenets of National Socialism, Dude, at least it's an ethos."
- Walter Sobchak, The Big Lebowski (1998)

I had a next-door neighbor who worked for an aerospace company. One summer afternoon we were sitting beside his barbeque in his back yard, having one of those stream-of-consciousness conversations that often accompanies the guzzling of a six pack or two (his brand was Pabst Blue Ribbon™). I don't remember how the subject came up, but somewhere along the line I must have done what my wife calls "hitting the core-dump button." And he did; for the next couple of hours I listened in semi-horrified fascination as he expounded on his "theory" of reality. Basically, it was a weird variant on the "eagle and snake" mythology of the Aztecs, except that in his own weird theory the snake was the major icon. He went on and on about how the world (and time and everything else) was, at some much deeper level of reality, a snake. Ouroboros and the Midgard Serpent and Satan in the Garden of Eden and Freud's phallic symbols and the Caduceus and on and on and on...it was all tied together in a huge, complicated, and ultimately deranged web of relationships. It clearly was very meaningful to him; at times he seemed on the verge of tears. He showed me a medal of the Aztec eagle-and-snake image, which he wore around his neck at all times (even to bed and in the shower). He told me how it got him through some bad times in Vietnam, and later when he almost broke up with his wife. The emotional connections were so intense that he was shaking at times, and there was a catch in his voice.

This wasn't the first (or the last) time something like this has happened to me. Several times – on the bus or in the bus terminal, on a long car trip with a friend, at the airport, over lunch, at a picnic for work or a fraternal organization – someone hears or thinks of the word or phrase that "hits the core-dump button" and out it all comes. You sit there, in awe and trepidation, while the core-dumper gives you their entire "weird theory" of reality, all in one huge, steaming, highly charged, stream-of-consciousness pile. Sometimes it's clear that they have never articulated this before to anyone. Other times it's clear that they've been working on this particular monolog, maybe for years, and have already "gifted" others with a very similar version. Every time it's always intensely emotional for them, as the whole weird mess unspools and they search your face for some sign of recognition, of empathy, of understanding.

And, with me at least, they don't get that. I listen politely, trying not to look perplexed or horrified, waiting for the whole thing to come tumbling out, and hoping for something to then divert us – the burgers starting to burn or the bus arriving or the teller asking for my driver's license. I nod sometimes, and grunt in what I hope is a non-judgmental way, and quietly wish for someone or something to intervene before the core-dumper realizes that, not only to I not empathize, I think they're nuts.

Because they are, at some very deep level. Almost all of us are; completely whacked. What we almost all have, buried deep in our psyche, is what I call a "weird theory of reality," in which we believe passionately, and into which we shoehorn almost every perception we have about reality. Furthermore, it's clear to me that people have always had such "weird theories" about reality. Today it's alien abductions or UFOs, astral projections, mental telepathy, ESP, clairvoyance, spirit photography, telekinetic movement, full trance mediums, the Loch Ness monster and the theory of Atlantis. Yesterday it was angels and demons, fairies, gnomes, trolls, heaven and Hell, transubstantiation, faith healing, walking on water, flying, and speaking in tongues. Tomorrow...well, I can't say for sure, but I am sure it will be something weird.

What makes modern "weird theories" different from those of the past is that today everyone has their own "weird theory". When people lived in small agricultural villages or even smaller hunter-gatherer groups, people had weird theories, but these were pretty similar within those groups. Heresy was difficult, if not virtually unthinkable, because everyone in a particular group was in constant verbal and emotional contact with virtually everyone else, and there was a strong incentive to conform to group norms of belief.

This pattern persisted into historic times with the establishment and enforcement of "state religions" - that is, weird theories of reality that had the force of political coercion behind them. People may have had personally idiosyncratic versions of the group's weird theory, but they generally kept these to themselves. These "group weird theories" (GWT) were the mythologies that held such groups together, that gave them a sense of shared experience and shared purpose, and that facilitated group coordination. This was often a good thing, but sometimes a bad thing: it made possible group coordination in agriculture and response to natural disasters, but also facilitated warfare and small-scale genocide.

What characterizes us now is that our weird theories are almost entirely idiosyncratic, especially in the First World. We have largely given up the large-scale group mythologies and religions of the past, and replaced them with what could be called "personal mythologies and religions". That Protestantism is the most influential religion in America today is precisely because it isn't a single religion: it's thousands, even millions of little idiosyncratic religions, with some shared similarities. Schism, right down to the individual level (and even within individuals at different times in our lives) is the norm, and so our weird theories are not only weird, they're mutually incomprehensible.

So, are the various sciences also "weird theories"? Anyone acquainted with the current state of quantum physics would almost certainly agree, as would most evolutionary biologists. But, it's not really the same, because although there are many weird theories in science, there is also an underlying agreement that is deeply "unweird" – the idea that empirical verification and logical inference is the basis for all of our weird theories.

Ultimately, the difference between non-scientific and scientific "weird theories" is that eventually the latter become generally accepted by the scientific community in the same way that the grand overarching religious weird theories of past centuries were. Yes, there are still schisms in science (think of the controversies surrounding punctuated equilibrium versus phyletic gradualism), but in the long run these schisms tend to heal themselves. Thomas Kuhn described this process well, but he also asserted (and most scientists would agree) that eventually the various scientific communities agree on their dominant paradigms. Science, in other words, tends to become more unified over time, as deep connections between the various weird theories stitch them together into "grand unified theories".

By contrast, the non-scientific "weird theories" schism and schism and schism, until they become the incomprehensible idiosyncratic messes that one taps into when one hits the "core-dump button". Indeed, one of my personal weird theories is that this is a good way to distinguish between useful (i.e. "true") and pointless (i.e. "false") weird theories: the former tend to unify your ideas with those of the other members of your community, whereas the latter tend to separate us to the point of mutual incomprehensibility.

Hence, the quote from The Big Lebowski: say what you say what you like about the tenets of (insert scientific discipline here), Dude, at least it's an ethos.

RECOMMENDED READING:

Shermer, M. (2002) Why People Believe Weird Things: Pseudoscience, Superstition, and Other Confusions of Our Time. Holt, New York, NY, ISBN #0805070893 ($17.00, paperback), 384 pages. Available here.

Sowin, J. (2008) 25 reasons people believe weird things. Pseudoscience, Life, Science, Religion, 28 April 2008. Available online here.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

The "Intelligent Design" Movement on College and University Campuses is Dead


AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

On 22 December 2005, I posted a critical analysis of a press release on the Kitzmiller v. Dover decision, written by Dr. William Dembski, one of the founders of the "intelligent design" movement (Dr. Dembski's press release is apparently no longer available online). My analysis of Dembski's press release was hosted by Ed Brayton at his blog, Dispatches from the Culture Wars (you can find it here). In my analysis, I noted that Dr. Dembski had made a series of statements that were so divergent from the actual facts that they could be interpreted as symptoms of delusional thinking on the part of Dr. Dembski, if not deliberate falsehoods.

Here's the claim by Dr. Dembski that I would like to re-examine in this post:
Three years ago, there was one Intelligent Design and Evolution Awareness (IDEA) Center at the University of California-San Diego. Now there are thirty such centers at American colleges and universities, including UC Berkeley and Cornell. These centers are fiercely pro-ID. [emphasis added]

Dr. Dembski strongly implied in his press release that these IDEA Centers were essentially research centers, such as those commonly found at college and university campuses.

Well, they aren't...or, rather, weren't. They weren't "research centers" or anything like it. They were clubs, similar to the kinds of student-centered special interest clubs that abound on most college and university campuses. Such clubs have several characteristics in common:
1) they are founded, supported, and run by students (sometimes with support from affiliated national organizations),

2) they often have to have permission from the administration to use classrooms or other facilities for meetings, and

3) they sometimes receive funding from students, derived from student activities fees.

To do these things, campus organizations typically have to show that they have no political or religious requirements or ties, as this could jeopardize the academic institution's not-for-profit educational status. This was a problem for IDEA Clubs, for several reasons:
1) they were usually founded, supported, and run by students who received encouragement and training to do so from the national IDEA Center, a spinoff of the Discovery Institute in Seattle, Washington, the political "nerve center" of the "intelligent design movement";

2) the IDEA Clubs often met in campus classrooms or other facilities; and

3) some IDEA clubs did in fact receive funding derived from student activities fees.

This was problematic for two simple reasons:

1) the Discovery Institute receives much of its funding from religious organizations, especially those supported by Christian "reconstructionist" Howard Ahmanson (that this is the case can be easily verified by reading the so-called "wedge document", formulated by the Discovery Institute as a fund-raising tool);

2) the IDEA Center required that the founders and officers of the IDEA Clubs they helped organize and support be Christians.

This was the case for the IDEA Club chapter founded at Cornell University, with whom I had several debates and public meetings. The requirement that the Cornell IDEA Club's officers be Christians was withheld from its membership by its founders until it was made public by their opponents. This caused dissension within the club and eventually led to the modification of this policy by the national IDEA Center administration.

And so, to the purpose for this post: it appears from all indications that the IDEA Club "movement" (and, by extension, the "intelligent design movement" as a whole) is dead. You can verify this by going to the website of the national IDEA Center and clicking through the various links located there. I did that this morning, and found it very enlightening. To save you time, here is what I found (the links are listed first, followed by what they lead to):

Upcoming Events
: empty (no events listed)

Press Releases:
: except for a press release on "Expelled: No Intelligence Allowed" (the movie) and the online publication of the Spring, 2008 Light Bulb Newsletter (see below), the most recent press release is dated 11/11/06

Classes & Seminars: last updated spring 2004

IDEA Conferences: none

ORIGINS News Updates: last updated 2005

The Light Bulb Newsletter: started publication online (.pdf format) in 2002; listed as quarterly, but only eight out of twenty-six issues have been posted; most recent issue (Summer 2008) consisted almost entirely of a review of the movie "Expelled" (see link, above)

Listserves & Discussion Boards: none

Events Archive: last updated 05/24/07, previously updated on 07/26/03

Student Training Conferences: (for students interested in forming an IDEA Club) last conference held on 09/27-28/02

Ah, but this only indicates that the national IDEA Center is now moribund. Surely something is happening in the 35 international chapters, located at high schools, community colleges, colleges, and universities around the world? Well, here's the list, followed by what you find when you click on the link:
Armstrong Atlantic State University (GA): last updated 01/09/06; virtually no content

Baraboo IDEA Club (academic affiliation not listed) (WI): 404:File Not Found

Braeside High School, Nairobi, Kenya: IDEA Center press release, dated 09/15/03; when link to actual site clicked, received 404:File Not Found

California State University, Sacramento (CA): no events, no content, last updated 11/14/02

Cornell University (NY): when link to actual site clicked, received 404:File Not Found; blog last updated on 03/11/07

Fork Union Military Academy (VA): IDEA Center press release, dated 08/14/04; no actual website or content linked or listed at associated institution

Franciscan University of Steubenville (OH): IDEA Center press release, dated 03/12/04; no actual website or content linked or listed at associated institution

George Mason University (VA): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Hillsdale College (MI): IDEA Center press release, dated 09/20/03; no actual website or content linked or listed at associated institution

James Madison University (VA): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Midwestern State University (TX): IDEA Center press release, dated 04/13/04; no actual website or content linked or listed at associated institution

Myers Park High School (NC): when link to actual site clicked, received 404:File Not Found

Poway High School (CA): no content or events listed (no date listed for last update)

Pulaski Academy (AR): IDEA Center press release, dated 09/15/03; no actual website or content linked or listed at associated institution

Scripps Ranch High School (CA): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

Seattle Central Community College (WA): when link to actual site clicked, received 404:File Not Found

South Mecklenburg High School (NC): IDEA Center press release, dated 08/14/04; no actual website or content linked or listed at associated institution

Stanford University (CA): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

Tri-Cities IDEA Club (WA): no events listed; last updated on 05/08/08

University of California, Berkeley (CA): 403:Access Forbidden

University of California, San Diego (CA): when link to actual site clicked, received 404:File Not Found

University of Illinois, Urbana-Champaign (IL): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

University of Mississippi ("Ole' Miss") (MS): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

University of Missouri (MO): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

University of Nebraska, Lincoln (NE): when link to actual site clicked, received 404:File Not Found

University of Oklahoma (OK): when link to actual site clicked, received 404:File Not Found

University of the Phillipines: IDEA Center press release, dated 07/11/04; no actual website or content linked or listed at associated institution

University of Texas, Dallas (TX): no events listed; last updated on 06/14/05

University of Victoria (BC): no events listed; last updated May, 1999

University of Virginia (VA): IDEA Center press release, dated 08/14/04; no actual website or content linked or listed at associated institution

Vanderbilt University (TN): IDEA Center main website homepage; no actual website or content linked or listed at associated institution

Wake Forest University (NC): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Western Baptist College (OR): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution

Westminster College (MO): IDEA Center press release, dated 04/06/05; no actual website or content linked or listed at associated institution


And there you have it: not one of the IDEA Clubs affiliated with an academic institution is still functioning. Indeed, only one of the clubs listed has even updated its website during the past year (the Tri-Cities IDEA Club).

UPDATE (01/04/09): The Tri-Cities IDEA Club website has now descended into "Under Construction/Placeholder" Hell, and so all of the current links to IDEA Clubs at the national IDEA Club website are currently non-functional.

Furthermore, a quick statistical analysis is also illuminating:
1) there are 39 IDEA Clubs listed, not 35 (as stated at the IDEA Club main website);

2) of the 39 listed IDEA Clubs, eight (21%) are located at high schools or community colleges;

3) four (17%) are located at religious institutions;

4) nine (23%) simply do not exist (i.e. have 404: File Not Found at their link); and

5) 18 (46%) have links that simply redirect to either a national IDEA Center press release or main website homepage.

These are the "intelligent design research centers" about which Dr. Dembski spoke so glowingly in his analysis of the effects of the Kitzmiller v. Dover Area School Board decision.

What can one conclude from this analysis? I conclude five things:
1) that the national IDEA Club website is essentially what is known online as a "shell site" (that is, a place-holder with no real content);

2) that the "movement" represented by the IDEA Club organization peaked in late 2005 or early 2006 (around the time of the Kitzmiller v. Dover trial);

3) since then (i.e. since Judge Jones issued his now-famous decision) it has died almost everywhere;

4) the majority of the output of the "intelligent design movement" consisted of press releases (and produced no empirical science of any kind); and

5) my conclusion in my critical review of Dr. Dembski's analysis of the Kitzmiller v. Dover Area School Board decision was essentially correct: he was (and probably still is) either delusional or a bald-faced liar.

So, why did I illustrate this post with a picture of a dodo? Because, like the "intelligent design" movement, the dodo was notorious for its stupidity and that fact that it is extinct.

UPDATE (09/01/09): All of the current links to IDEA Clubs at the national IDEA Club website are currently non-functional; if this keeps up, they may fossilize.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen

It's Darwin-Malthus Day!


AUTHOR: Allen MacNeill

SOURCE: Original essay

COMMENTARY: That's up to you...

Most readers of this blog are aware that next year is the Darwin Bicentennial. It's the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of the Origin of Species. Regular readers also know that this celebration really started this past July 1st, which marked the 150th anniversary of the joint presentation of Darwin and Wallace's theory of evolution by natural selection at the summer meeting of the Linnean Society in London.

However, what many people don't know is that today is also a very significant anniversary of a crucial development in Darwin's theory of evolution by natural selection. On this day in 1838, Darwin
"...happened to read for amusement 'Malthus on Population,' and being well prepared to appreciate the struggle for existence which everywhere goes on from long-continued observation of the habits of animals and plants, it at once struck [him] that under these circumstances favourable variations would tend to be preserved, and unfavourable ones to be destroyed. The result of this would be the formation of new species." [Darwin's Autobiography, page 83]

According to his autobiography, Darwin read Malthus' famous essay in the evening, and the idea of natural selection sprang fully formed into his mind: "Here then I had at last got a theory by which to work...", and indeed he had. But Darwin was an extraordinarily cautious man, always seeking to avoid controversy and notoriety. In his autobiography he says,
"...I was so anxious to avoid prejudice, that I determined not for some time to write even the briefest sketch of it."

And indeed, he did not. It wasn't until 1842 that he felt confident enough about his theory to set it down on paper, and it wasn't until two years later that he had this original "pencil sketch of 1842" copied out and put into a form that he felt confidant enough about to share with his closest friends. It was this "Essay of 1844", along with a letter to the American botanist, Asa Gray, that were read at the July, 1858 meeting of the Linnean Society along with Alfred Russell Wallace's unpublished manuscript "On the Tendency of Varieties to Depart Indefinitely from the Original Type", which marks the beginning of evolutionary theory's annus mirabilis.

So, the "evolution revolution" really began on a rainy evening in late September in 1838, when Charles Darwin read Malthus "for amusement"...

...and it's also my birthday.

As always, comments, criticisms, and suggestions are warmly welcomed!

--Allen