Don McLeroy, a Texas-sized embarrassment

"Somebody's got to stand up to experts that are just--I think--I don't know why they're doing it, they're wonderful people, but the fossil record doesn't do it--why take it out, if evolution is so true and has no weaknesses, I can't see any reason for putting it in there, all it does is give them an extra standard to argue for it. Yes, it's hard to stand up to very brilliant, wonderful people."

Wish we could say the same about Don McLeroy. It's tough to find a worse extemporaneous speaker. (Don't worry, it's not impossible, just tough.)

[via Reed Cartwright]

viruses, the origin of life, and intelligent design

I've blogged many times about the role viruses play in evolution, particularly Endogenous Retroviruses, or ERVs, which insert bits of genes into their hosts. Sometimes beneficially.

This week's NewScientist gives a rundown of some of the latest research into viruses [sub. req.]. The shorthand version: they play a much larger part in evolution than anyone has imagined.

[Patrick] Forterre and others have since built up evidence that early life was a period of wild biochemical experimentation in which molecular systems were constantly being invented and thrown together into new and increasingly complex ensembles (Virus Research, vol 117, p5). Once cells evolved, the experimentation continued, driven by innovation and gene transfer by the first viruses. The result was the creation of numerous alternative living systems, built up from random combinations of the available components. Only three of these systems survive to this day in the form of the three domains of cellular life; much of the rest lives on in the virosphere.

That puts viruses right at the heart of early evolution. "If you consider that viruses have always been more abundant than cells, you should conclude that the flow of genes has always been higher from viruses to cells," says Forterre. "Given this, it should not be surprising that major innovations could have occurred first in the viral world, before being transferred to cells."

Humans aren't immune (couldn't resist):

ERVs have been known of since the 1970s, but the full extent of their infiltration did not become apparent until 2003, when genome sequencing revealed that our DNA is absolutely dripping with them. At least 8 per cent of the human genome consists of clearly-identifiable ERVs. Another 40 to 50 per cent looks suspiciously ERV-like, and much of the rest consists of DNA elements that multiply and spread in virus-like ways. Taken together, virus-like genes represent a staggering 90 per cent of the human genome.

You may be the product of intelligent design. Thing is, the designers were viruses.

Andy Schlafly and his acolytes get eviscerated

PZ Myers holds the camera, and Dr. Richard Lenski wields the scalpel.

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then - as some of your acolytes have suggested - you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren't very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants. In other words, it's not that we claim to have glimpsed "a unicorn in the garden" - we have a whole population of them living in my lab! [http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden] And lest you accuse me further of fraud, I do not literally mean that we have unicorns in the lab. Rather, I am making a literary allusion. [http://en.wikipedia.org/wiki/Allusion]

Oh, there's more.

two decades in the evolving

Ed Brayton points us to a fascinating--and very, very patient--experiment:

If Stephen Jay Gould were alive today, he would be smiling. Maybe even gloating.

New research suggests that the famous evolutionary biologist was right when he argued that, if the evolution of life were “wound back” and played again from the start, it could have turned out very differently.

In experiments on bacteria grown in the lab, scientists found that evolving a new trait sometimes depended on previous, happenstance mutations. Without those earlier random mutations, the window of opportunity for the novel trait would never have opened. History might have been different....

Lenski's team watched 12 colonies of identical E. coli bacteria evolve under carefully controlled lab conditions for 20 years, which equates to more than 40,000 generations of bacteria. After every 500 generations, the researchers froze samples of bacteria. Those bacteria could later be thawed out to "replay" the evolutionary clock from that point in time.

After about 31,500 generations, one colony of bacteria evolved the novel ability to use a nutrient that E. coli normally can't absorb from its environment. Thawed-out samples from after the 20,000-generation mark were much more likely to re-evolve this trait than earlier samples, which suggests that an unnoticed mutation that occurred around the 20,000th generation enabled the microbes to later evolve the nutrient-absorption ability through a second mutation, the researchers report in the Proceedings of the National Academy of Sciences.

Remarkably, in roughly the same amount of time, creationism evolved into Intelligent Design by a similarly subtle mutation--though without much in the way of labwork.

"Science leads to killing people."

Ladies and gentlemen, Ben Stein.

Seriously, all I can keep thinking as I'm watching the interview: this is the guy they wanted as the face for Intelligent Design? The man is a walking catalogue of logical fallacies, scientific ignorance, and smug stupidism.

His own summary of Expelled:

"There's A Neo-Darwinist stranglehold on the academic world. You cannot even mention the possibility that there might have been an intelligent designer who created life, an intelligent designer who created the heavens and the earth, not even the possibility... you can't even ask how the cell got so complicated just by itself, you can't even ask how one day there was just mud and ooze, and the next day there was life, you can't even ask how the planets stay in their orbits, or else you can get fired, lose your grants, lose your tenure. We think that's a very serious issue of academic suppression.

Except that later in the film (and mentioned, without any apparent irony, in the interview), the Charles Simonyi Chair for the Public Understanding of Science at Oxford (and noted critic of Intelligent Design), Richard Dawkins, proves Stein wrong by openly speculating that design by aliens from outer space is at least a possibility. Hmm... still has his job, grants, and tenure. Stein?... Stein?...

Ultimately, Stein presents little more than an argument for ignorance wrapped in a tu quoque, defending ID thusly: "I don't have any scientific proof of that, but the Darwinists don't have any proof either." So, teach 'em both!

The title quote says it all. Though blog neighbor Keith Buhler has labored in vain to deflect five bad reasons to avoid Expelled, there's only one reason needed: Ben Stein.



Sidebar:How do the planets stay in their orbits? Stein encourages students to ask in class, as a challenge to a "Darwinist" teacher. No, really.

PZ Myers: expelled!

He's interviewed in the movie, but the producer wouldn't let him watch the movie.

They singled me out and evicted me, but they didn't notice my guest. They let him go in escorted by my wife and daughter. I guess they didn't recognize him. My guest was...

Richard Dawkins.

He's in the theater right now, watching their movie.

One funny post from PZ Myers. Here's the followup.

wake me when the science happens

I haven't blogged much about Intelligent Design lately, because--and this is going to start sounding like an echo--not much of real interest happens with ID this days. Its pitchmen are a collective embarrassment who do nothing in the way of research and much in the way of antics. Sad.

noodly gingerbread appendages

Flying Spaghetti Monster cookies: coming to a school district near you.

virtual morality, virtual ontology

I've been thinking about theodicy lately--a summer habit--and so I've noticed an intersection between the problem of evil and Nick Bostrom's simulation argument. As I've summarized it:

If we grant that a sufficiently advanced civilization could create a workable simulation of existence, we have every right to suspect we inhabit that simulation.

Brent Silby, in his critique of Bostrom's reasoning, raises the moral issue:

But morality, like all cultural phenomena, evolves. It is a conceit to assume that our current state of moral reasoning will remain unchanged. Highly advanced civilizations may find it morally abhorrent to create a universe and populate it with living beings. Consider life on Earth. We live on a planet full of creatures that have to destroy each other to survive. Humans, who have arguably the highest level of intelligence on Earth, kill animals, pollute the environment, torture children, tell lies, commit crimes, and kill each other for greed. Would an advanced species think it is a good thing to create another universe that could possibly contain this level of pain and suffering? Its possible that a future species would choose not to create a simulated universe because doing so would increase pain and suffering in the world.

The assumption that an advanced species will want to create a simulated universe relies too heavily on the idea that they will share our moral standards. We cannot make such an assumption, so the likelihood that we exist in a simulated universe may be a great deal lower than originally thought. I am not saying that it is impossible. All I am suggesting is that more thought needs to be put into the look of future moral reasoning

I agree that we have to be careful when assigning probabilities to the purported actions of civilizations that could conceivably will us into existence--but I have two in-principle objections to the objection.

First, though morality may evolve, it doesn't prohibit people, ultimately, from acting immorally. Silby's list of human ills is proof enough. A rogue simulation technician might be running our universe as a screensaver, in defiance of The Future's norms.

Second, a simulation is not real. No one at present mourns the death of digital characters, at least not seriously--I hope. We view their suffering as only apparent. Perhaps the simulation engineers of The Future are unaware that their characters have a subjective existence (assuming, of course, that I am not the only character in a solipsist simulation). Since our suffering and pain aren't "real," there is no perceived moral risk in programming us to suffer.

Silby makes an interesting comparison:

Supporters of the Simulated Universe argument may complain here, and state that there is a fundamental difference between their view and the Cosmological argument. They may suggest that their argument is different because it is based on the existence of real creatures that have a biology and use technology, while the Cosmological argument is based on a supernatural God. But I am not sure the there is a difference. From our perspective there is no difference between a supernatural God and a super intelligent species from another universe. Both entities are equally difficult to describe. We can never know the nature of a parent universe. We cannot know about how their biology works because we are unable to visit and have a look. Creatures in the parent universe are unknowable, and from our perspective they are all-powerful.

There is a high epistemic barrier to the Simulation Argument, to be sure. But extrapolating from known technological processes isn't just making stuff up.

I'll admit I had a similarly Clarkesque thought after mulling over Bostrom's argument: the better humans get at creating technology, the less we are "wowed" by omnipotence. In fact, the unintended consequence of the Intelligent Design movement could be that it succeeds--by deflating our view of the divine. Maybe that's the Canny Valley of I.D.

[Shamelessly borrowed from the Uncanny Valley pictured here.]

Behe appears on Colbert, fails to dazzle

Intelligent Design's chairman, Michael Behe, appeared on The Colbert Report tonight to discuss his new book, The Edge of Evolution. Amazingly, though, he stepped into a time warp and came out in 1996, talking about tiny cell factories, Darwin's blob-o-goo, mousetraps, and other discredited arguments for ID.

It was the Black Box all over again--almost as if The Edge of Evolution never happened.

(Which, in a way, is pretty much right.)

Update: Dr. Joan Bushwell has the video, and a rather harsh--and entirely deserved--assessment.

beyond the evidence

Timothy Sandefur, on a creationist's appropriation of "pomobabble:"

Trask argues that magical understandings of the universe are just as acceptable as scientific understandings, but that preferences for science and reason over “revelation,” emotionalism, whimsical impulse, and other “ways of knowing” is just so much prejudice. “Scientific epistemologies,” he writes, “legitimize the exclusion of those who do not understand truth exclusively through empirical verification.” Science is cruelly shoving magical theories away from the table, through its emphasis on such things as testability, or evidence, or replication of results and silly stuff like that....

Moreover, a demand for evidence and experiment is not a religion. A religion is a belief in something in the absence of, or in spite of, the evidence. It is faith—that is, belief in something which is not subject to evidence and cannot be proven.... Science is certainly an epistemology, and, I would argue, part of this complete, nutritious worldview. But it is not a “religion,” and certainly it is not a “religion” in the Constitutional sense of the term. At the time of the Constitution’s writing, “religion” was not understood as referring to secular, scientific worldviews.

My brother, in response, asks,

What problems are there for a political system where the only “evidence” allowed is empirical?

The answer is "not many," at least when the question under discussion is, "What is the proper subject of study in a public school science class?" Matt's error is in broadening the question.

Science doesn't work via "still small voice," "divine light," "burning in the bosom," feelings, visions, trances, or ecstatic revelations. Its purview is observation and experimentation, with a heavy dose of mathematics. It exposes the post hoc and spits out the ad hoc. Its truths are not eternal, but provisional, subject to change with further study. Though sometimes helped along by intuitions and hunches, and hindered by personalities and politics, science ultimately stands or falls on the evidence--no po-mo quote marks needed.

Boston Legal: tried and found wanting

Well, Josh, I tried. I tried to like Boston Legal. I dug the witty banter, especially James Spader's meta "I'm going to cable, that's where the best work is being done" jokes. I had learned to tolerate the bizarre musical interludes--the wailing and womp-wowing every time something "dramatic" happened. Every now and then, what I'd call "TV Law" would run roughshod over real law, but usually in the service of a decent story.

However, one episode destroyed the show's hopes for legal verisimilitude. In "From Whence We Came," the firm defends a school superintendent who has fired science teachers for refusing to teach Intelligent Design. The ID side wins as the judge gives a pap-filled, bromide-bundled speech about babies and "In God We Trust."

Meanwhile, in real life, forcing teachers to give shoutouts to creationism-in-a-slimming-dress is unconstitutional. Something about precedent and logic and evidence--you know, law.

Guess I'm sticking with cable.

nightmares of the deep

Enjoy--if that's the right word--this photo gallery of "Real Life Sea Monsters."


[via Instapundit]

Sal Cordova grabs a pick and a torch and heads down to the quote mines

Ed is on the case.

Sal has completely reversed the meaning of the article and I can't imagine he did so unintentionally. You simply cannot read his description of the article and the article itself without having the utter dishonesty of his misrepresentation of it hit you in the face. Kiss your credibility goodbye, Sal. This is rank, rank deceitfulness. Tell us again about how evolution undermines morality while you tell lies like this.

Of course, if I'm Cordova, I'm paraphrasing: "Sal... unintentionally... lies." 'Cause, y'know, it's an accident. Or maybe I just can't read.

reverse engineering, the design inference, and geology

Despite what Ed Brayton may claim, Michael Egnor is right. The Design Inference--make that the design inference--is all over science. It's simple: you take a something in nature, figure out how it works by imagining and recreating how it's put together, and presto! Reverse engineering, the design inference.

Let's see how geologists use reverse engineering to demonstrate how volcanoes are designed.

This is a real volcano. It has hot, steaming red stuff coming out of the top. That's lava. What's lava made of? Where does it come from? What is it for? To find out, geologists employ reverse engineering.

These are geologists reverse engineering a volcano. As you can see, their work proves that when an intelligent agent, or designer, combines vinegar, red food coloring, and baking soda in a conical papier-mâché structure, lava boils over the top. (This is known as the Timmy-Hortensia theorem, after its original inventors, or discoverers.)

Since it takes a human designer to reverse engineer a volcano, obviously a volcano is designed. Q.E.D.

nature is always weirder than you think

First movement: Peter Wall distinguishes between intuiting design and detecting design.

Nobody has yet come up with a convincing “Field Guide to Discerning Intelligence in the World,” but that did not stop my professor from insisting that I have no basis for failing to see intelligence in “natural” phenomena. Apparently it did not occur to him that since he (via Cicero, or vice versa) was making the proposition that “Intelligence is evident in natural phenomena,” it was up to him to explain why exactly that proposition should be accepted, not up to me to demonstrate why it is incorrect.

Second movement: Kerry Howley notes that twins can come from single human ova chimerically fused with two sperm.

Could our "hook-up culture" have led anywhere else? Blame gay marriage!

what came before RNA? recent origin-of-life research heads in thermodynamic directions

In a recent article in Scientific American, Robert Shapiro explains why ">the prospects for "RNA World" OOL theory are bleak. You can be sure creationist hacks are salivating over this quote:

There is no reason to presume than an indifferent nature would not combine units at random, producing an immense variety of hybrid short, terminated chains, rather than the much longer one of uniform backbone geometry needed to support replicator and catalytic functions. Probability calculations could be made, but I prefer a variation on a much-used analogy. Picture a gorilla (very long arms are needed) at an immense keyboard connected to a word processor. The keyboard contains not only the symbols used in English and European languages but also a huge excess drawn from every other known language and all of the symbol sets stored in a typical computer. The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne. With similar considerations in mind Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth "would have been a near miracle." I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above.

Nobel Laureate Christian de Duve has called for "a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry." DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life....

If that were the conclusion, origin-of-life researchers would have reason to throw down their beakers in despair.

But the end of one hypothesis is just the beginning of another:

Inanimate nature provides us with a variety of mixtures of small molecules, whose behavior is governed by scientific laws, rather than by human intervention.

Fortunately, an alternative group of theories that can employ these materials has existed for decades. The theories employ a thermodynamic rather than a genetic definition of life, under a scheme put forth by Carl Sagan in the Encyclopedia Britannica: A localized region which increases in order (decreases in entropy) through cycles driven by an energy flow would be considered alive. This small-molecule approach is rooted in the ideas of the Soviet biologist Alexander Oparin, and current notable spokesmen include de Duve, Freeman Dyson of the Institute for Advanced Study, Stuart Kauffman of the Santa Fe Institute, Doron Lancet of the Weizmann Institute, Harold Morowitz of George Mason University and the independent researcher Günter Wächtershäuser. I estimate that about a third of the chemists involved in the study of the origin of life subscribe to theories based on this idea....

Systems of the type I have described usually have been classified under the heading "metabolism first," which implies that they do not contain a mechanism for heredity. In other words, they contain no obvious molecule or structure that allows the information stored in them (their heredity) to be duplicated and passed on to their descendants. However a collection of small items holds the same information as a list that describes the items. For example, my wife gives me a shopping list for the supermarket; the collection of grocery items that I return with contains the same information as the list. Doron Lancet has given the name "compositional genome" to heredity stored in small molecules, rather than a list such as DNA or RNA.

The small molecule approach to the origin of life makes several demands upon nature (a compartment, an external energy supply, a driver reaction coupled to that supply, and the existence of a chemical network that contains that reaction). These requirements are general in nature, however, and are immensely more probable than the elaborate multi-step pathways needed to form a molecule that can function as a replicator.

Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle. The greatest amount of new data has perhaps come from Günter Wächtershäuser and his colleagues at the Technische Universität München. They have demonstrated portions of a cycle involving the combination and separation of amino acids, in the presence of metal sulfide catalysts. The energetic driving force for the transformations is supplied by the oxidation of carbon monoxide to carbon dioxide. They have not yet demonstrated the operation of a complete cycle or its ability to sustain itself and undergo further evolution. A "smoking gun" experiment displaying those three features is needed to establish the validity of the small molecule approach.

That's the difference between science and pseudoscience: science requires experimental validity. Creationists have harped for years on the low probability of life's spontaneous emergence in the universe. Meanwhile, scientists have been fashioning, testing, junking, redeveloping, and once again fashioning more and more plausible scenarios, not content to rest in comfortable ignorance.

the dark and twisted imagination of William A. Dembski

(I was going to post something about trends in Intelligent Design, but all it's got going recently is some lame, pathetic tripe. Oh, and warning: some quoted material to follow is graphic.)



William A. Dembski, poster boy for Intelligent Design, has some deep Freudian trauma in his past that bubbles up in his academic writing. The most recent, attempting to justify why Christ's suffering is sufficient [pdf]:

Off the top of my head, there are many forms of death, degradation, and torment that are far worse than the few hours that Christ suffered at the hands of the Romans. Here are three:

(1) Locked in syndrome, in which the body is completely without ability to move or respond but the mind remains fully conscious. Imagine your body being in this state, as a living coffin, for decades.

(2) Being a long-term subject of Josef Mengele’s medical experiments at the Nazi extermination camp of Auschwitz.

(3) Being raped and tortured over a period of months by one of Saddam Hussein’s sons for refusing his advances, and then finally being torn apart by his Doberman Pinschers.

Ask yourself, if you were faced with the horror of such circumstances, what comfort you would find in the Cross if all there were to it was the few hours required for Jesus’ scourging and crucifixion. What comfort would you find in Christ’s words, “Lo, I am with you always, even unto the end of the world,” if for all you can tell, Christ’s suffering was markedly less than yours?

This, part of a speech given at a seminary in October of last year, is obviously another cry for help. Someone with a degree in psychotherapy, please contact this man.

unhitch your wagon from a falling star

Is there anyone with any intellectual credibility in the Intelligent Design camp? 'Cause seriously, whoever that person is, he needs to get the hell out. Nothing but spin, embarrassment, and idiocy from IDers this year. John West Lynch has the whole painful recap.

[Link via Ed Brayton]

Update: Silly typo fixed.

be sure the facts will find you out

Remember the false plagiarism charges that Joe Carter, echoing (but certainly not plagiarizing) the Discovery Institute, leveled against Judge Jones, he of Dover renown?

Ed Brayton reports that fellows of the same Discovery Institute tried to republish part of a book as an original law review article.

Following Irons's revelation of the virtual identity of the Traipsing book and the MLR article, DeWolf, West, and Luskin agreed with the the MLR's insistence that they write a new article, which was finally submitted on September 28, with the new title, "Intelligent Design Will Survive Kitzmiller v. Dover." This "new" article borrowed heavily from the Traipsing book, but Irons and the MLR editors agreed that it was sufficiently revised to meet (barely) the requirement of "original" work. In response, Irons wrote a rejoinder, titled "Disaster in Dover: The Trials (and Tribulations) of Intelligent Design." Both articles will be published in the MLR's next issue, in January or February, 2007.

Professor Irons concluded his study with these comments: "It seems to me the height of hypocrisy for the Discovery Institute to accuse Judge Jones of copying 90 percent of one section of his opinion (just 16 percent of its total length) [emphasis added] from the proposed findings of fact by the plaintiff's lawyers, when the DI itself tried to palm off as 'original' work a law review article that was copied 95 percent from the authors' own book. Concealing this fact from the law review editors, until I discovered and documented this effort, seriously undercuts the credibility of the DI on this or any other issue."

Of course, to undercut credibility, credibility has to exist in the first place.

Update: According to a U of M law prof, the whole issue is one giant confusion. But Ed Brayton isn't quite convinced.

Update update: It's all just a big misunderstanding based on miscommunication and faulty memory, Ed Brayton reports, hearing from the Law Review editor at last.