Casey Luskin’s “Junk” Arguments

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In a classic ‘bait and switch’, Casey Luskin, ‘argues’ that the “classic “Junk DNA” icon of neo-Darwinism needs updating” because a Yale University news release shows how differences in the regulatory elements between humans and chimps explain the human thumb and foot development.

In a classic misdirect, Luskin, a lawyer by training, includes regulatory elements as “junk DNA” even though the original definition of “Junk DNA” only included pseudo-genes, and even though regulatory elements were since long known not to be ‘junk DNA’, in fact the conservation of said regulatory elements was something that rendered it anything but ‘junk’.

Casey’s “junk” argument continues to conflate and confuse as to what neo-Darwinian theory says about it, and includes the customary quote-mining while avoiding actual understanding.

An example

Casey Luskin Wrote:

In 2006, Michael Shermer asserted, “Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.” [2]

[2.] Michael Shermer, Why Darwin Matters: The Case Against Intelligent Design, pg. 75 (Times Books 2006).

Now what is the actual argument by Shermer?

DNA is information, and if the Law of Conservation of Information requires the input of an Intelligent Designer in order to increase specified complexity of the genome, we have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, tandem repeats, and pseudogenes, none of which are involved directly in the making of a human being.

Why does Luskin fail to inform us of the context of the argument? Well, the answer is really simple: The facts do not support his vacuous claims about neo-Darwinism and “Junk DNA”. To argue that people did not know that there are countless regulatory elements ‘hidden’ in the “Junk DNA” ignores the history.

For those interested in the real science behind these findings, please read John Timmer’s Genomic study finds enhancer of human hands (or feet) or Did a gene enhancer humanise our thumbs? at Not Rocket Science.

The Yale news release may help explain Luskin’s “confusion” but he should know that rather than accepting news releases, one should look at the actual papers to arrive at one’s conclusions.

In the journal science Science, Wray and Babbitt provide their perspectives on the study.

Abstract: Nearly half a century has passed since François Jacob and Jacques Monod demonstrated that specific noncoding sequences are required to activate genes that metabolize lactose in the bacterium Escherichia coli (1). In a prescient observation, they noted that mutations in these regulatory sequences might play a role in the evolution of organismal traits. They further argued that gene function is not only based on the biochemical activity of its product but also on how the gene’s expression is regulated. This idea was expanded in 1975 in an influential paper by Mary-Claire King and Alan Wilson (2), who proposed that trait differences between humans and chimpanzees are primarily due to regulatory changes in gene expression. Decades elapsed, however, before it was feasible to begin testing these ideas in detail. Two papers in this issue, by Prabhakar et al. on page 1346 (3), and by Hong et al. on page 1314 (4), demonstrate the power of combining bioinformatic approaches with experimental tests to characterize such regulatory regions.

A major impediment to studying the evolutionary importance of mutations in regulatory regions is simply knowing where to look. DNA sequences that regulate the transcription of genes occupy no fixed position relative to coding DNA regions and are often diffuse and widely dispersed. Even when the position of a regulatory element is known, there is the added challenge of identifying which mutations have functional consequences. Within coding sequences, the genetic code imposes familiar regularities: Mutations that change protein structure can be identified exhaustively and unambiguously. By contrast, identifying functional mutations within regulatory regions requires experimental tests of putative regulatory elements from different species or individuals–a costly and time-consuming process. Bioinformatic methods offer a way to identify promising functional noncoding regions and to narrow the focus for experimental tests.

The study in question was also published in science as Human-Specific Gain of Function in a Developmental Enhancer Science 5 September 2008: Vol. 321. no. 5894, pp. 1346 - 1350

Abstract: §

Changes in gene regulation are thought to have contributed to the evolution of human development. However, in vivo evidence for uniquely human developmental regulatory function has remained elusive. In transgenic mice, a conserved noncoding sequence (HACNS1) that evolved extremely rapidly in humans acted as an enhancer of gene expression that has gained a strong limb expression domain relative to the orthologous elements from chimpanzee and rhesus macaque. This gain of function was consistent across two developmental stages in the mouse and included the presumptive anterior wrist and proximal thumb. In vivo analyses with synthetic enhancers, in which human-specific substitutions were introduced into the chimpanzee enhancer sequence or reverted in the human enhancer to the ancestral state, indicated that 13 substitutions clustered in an 81-base pair module otherwise highly constrained among terrestrial vertebrates were sufficient to confer the human-specific limb expression domain.

As to the scientific vacuity of Intelligent Design, ask yourself the following simple question: How does Intelligent Design explain these findings? Is it anywhere similar to how Dembski ‘argued’?

Dembski Wrote:

As for your example, I’m not going to take the bait. You’re asking me to play a game: “Provide as much detail in terms of possible causal mechanisms for your ID position as I do for my Darwinian position.” ID is not a mechanistic theory, and it’s not ID’s task to match your pathetic level of detail in telling mechanistic stories. If ID is correct and an intelligence is responsible and indispensable for certain structures, then it makes no sense to try to ape your method of connecting the dots. True, there may be dots to be connected. But there may also be fundamental discontinuities, and with IC systems that is what ID is discovering.

William A. Dembski Organisms using GAs vs. Organisms being built by GAs thread at ISCID 18. September 2002

Michael Eisen describes his views on the Scientists cynical use of “Junk DNA”, if only ID proponents could show a similar skepticism.

Finding regulatory elements is quite a bit more complex than finding genes, and only recently the computational power has allowed science to more accurately study regulatory elements. In this case

John Timmer Wrote:

The recent paper focuses on a sequence, called HACNS1, which is about 550 bases long. If it were picking up mutations at random, the human version would be expected to have four; instead, it has 13 differences with the chimp sequence.

In other words, science found how a sequence had more than the expected number of differences between humans and chimps. Such an observation requires an explanation.

This lead to the conclusion

John Timmer Wrote:

HACNS1 lies outside of any known genes, suggesting it is regulatory DNA. The researchers hooked it up to a gene that couldn’t otherwise be expressed and injected the DNA into mice. As expected, the regulatory function caused the gene to be expressed in a very specific pattern in the head and limbs. The key result came when the chimp version was hooked up to the same gene and injected into mice–the limb expression was severely reduced or absent.

The obvious inference here is that the sequence drives human-specific gene expression, specifically in the areas that form the hands and feet, which are obviously quite distinct in humans. The researchers also made two constructs that had only six of the 13 changes from chip to humans and found that these drove expression was somewhere in between the humans and the chimp sequences, which is exactly what you’d expect from a gradual, evolutionary change.

There’s still work to be done, as HACNS1 lies about halfway between two different genes, and the researchers don’t know which of the two it regulates. Still, it’s a pretty exciting result, and worthy of the attention it received.

And that is how real science works.

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ERV alerted me to Luskins latest attempt to, well, um, I'm not sure what because all he succeeds in doing is undermining several ID talking points. ERV tackles Luskin's post in her own inimitable style (linked to above) but I... Read More

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But, but, but how could 13 SIMULTANEOUS changes all occur? You can’t actually expect anyone to believe that this is evidence for evolution.

Well, someone was going to say this eventually. I just thought I would beat them to it.

A good Behe impersonation. How do you feel now?

David Stanton said:

But, but, but how could 13 SIMULTANEOUS changes all occur? You can’t actually expect anyone to believe that this is evidence for evolution.

Well, someone was going to say this eventually. I just thought I would beat them to it.

Is the Discovery Institute still trying to use the “Junk DNA has purposes that evolutionists can not find” argument?

And how come they haven’t attempted to explain why pufferfish of the family Tetraodontidae have almost no Junk DNA or introns?

Oh, wait, they’re not in the business of looking at “pathetic levels of detail,” or even explaining anything.

He needs a very cold shower, followed immediately by a very hot shower.

And lots of thorough scrubbing.

PvM said:

A good Behe impersonation. How do you feel now?

David Stanton said:

But, but, but how could 13 SIMULTANEOUS changes all occur? You can’t actually expect anyone to believe that this is evidence for evolution.

Well, someone was going to say this eventually. I just thought I would beat them to it.

Stanton Wrote:

Oh, wait, they’re not in the business of looking at “pathetic levels of detail,” or even explaining anything.

Even a researcher from an entirely different field can appreciate the progress and the amount of time and effort that goes into this research.

And Dembski’s classical blurted out comment captures the behaviors I have personally witnessed in the fundamentalists I have had to work around (literally). In any group effort, they manage to sit around gaping like little children in a high chair waiting for mommy to put food in their mouths. It’s disgustingly pathetic in the true sense of that word.

Mike Elzinga said:

Even a researcher from an entirely different field can appreciate the progress and the amount of time and effort that goes into this research.

And Dembski’s classical blurted out comment captures the behaviors I have personally witnessed in the fundamentalists I have had to work around (literally). In any group effort, they manage to sit around gaping like little children in a high chair waiting for mommy to put food in their mouths. It’s disgustingly pathetic in the true sense of that word.

And yet, they have the nerve to mock us because we prefer to feed ourselves, intellectually speaking.

I’ve never really understood how IDists can claim that the absence of junk DNA in a designed organism is a prediction of ID.

Who’s to say that their putative designer didn’t use a design that either used junk DNA in an essential process or perhaps generated junk DNA as a necessary byproduct?

For example, if I were to analyze a memory dump from a computer that’s been running for a few hours, there are going to be regions of memory that have nothing but junk/garbage left in them from old programs that are no longer running. That’s just the way computers are designed to operate.

They tell us we have no way to infer what the designer would or could have done, yet in the very next breath they try to claim that ID can predict that a designer just “wouldn’t have done it that way” when it comes to junk DNA.

When I have made this point to ID sympathizers in the past, they just say that I don’t understand ID. When I then quote Dembski’s own words about the inability of ID to predict anything about the designer, and ask them to help me understand why that doesn’t prevent them from making predictions about specific design decisions made by said designer, they won’t or can’t give give me a straight answer.

Of course, it’s fairly obvious what’s happening. Since God is the only designer they would consider possible, and since God is perfect and his designs are perfect, then there is no place for imperfect stuff like so-called junk DNA in his designs. That would be tantamount to heresy.

Because this would be counter to the religious expectations that said designer (wink wink) was able to create a perfect creation.

tacitus said:

I’ve never really understood how IDists can claim that the absence of junk DNA in a designed organism is a prediction of ID.

Didja see Luskin’s gripes about an article discussing engineering design that took its inspiration from biostructures? The article said the inspirational biostructures were the products of eons of evolution. “Yeah, and your point is?”

“THE MEDIA TRIES TO QUASH INTELLIGENT DESIGN OVERTONES!”

“Well … actually, I think it was more of a case that they didn’t expend any cycles on it.” I’m not even going to bother to complain about this.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Tacitus Wrote:

When I then quote Dembski’s own words about the inability of ID to predict anything about the designer, and ask them to help me understand why that doesn’t prevent them from making predictions about specific design decisions made by said designer, they won’t or can’t give give me a straight answer.

Where did Dembski make such claims?

PvM said:

Tacitus Wrote:

When I then quote Dembski’s own words about the inability of ID to predict anything about the designer, and ask them to help me understand why that doesn’t prevent them from making predictions about specific design decisions made by said designer, they won’t or can’t give give me a straight answer.

Where did Dembski make such claims?

I found it

Dembski Wrote:

But what about the predictive power of intelligent design? To require prediction fundamentally misconstrues design. To require prediction of design is to put design in the same boat as natural laws, locating their explanatory power in an extrapolation from past experience. This is to commit a category mistake. To be sure, designers, like natural laws, can behave predictably (designers often institute policies that end up being rigidly obeyed). Yet unlike natural laws, which are universal and uniform, designers are also innovators. Innovation, the emergence to true novelty, eschews predictability. Designers are inventors. We cannot predict what an inventor would do short of becoming that inventor. Intelligent design offers a radically different problematic for science than a mechanistic science wedded solely to undirected natural causes. Yes, intelligent design concedes predictability. But this represents no concession to Darwinism, for which the minimal predictive power that it has can readily be assimilated to a design-theoretic framework.

I was interested since our resident troll B/Jobby, who is not welcome on my threads except when explicitly invited, stated that Dembski did not say this.

It helps putting claims in context.

Dembski Wrote:

Yet unlike natural laws, which are universal and uniform, designers are also innovators. Innovation, the emergence to true novelty, eschews predictability. Designers are inventors. We cannot predict what an inventor would do short of becoming that inventor. Intelligent design offers a radically different problematic for science than a mechanistic science wedded solely to undirected natural causes.

Who would have predicted quantum mechanics? When one of the mesons was discovered, it was a surprise (I. Rabi asked, “Who ordered that?”)

There are many points in scientific history where the scientific community was genuinely puzzled about how things worked. There was nothing in the minds of scientists that would suggest some novel design lay just around the corner. The expectation was that some new natural laws were operating and needed to be elucidated. In every case to date this expectation has been exactly what happened.

Nature appears to invent only because humans haven’t thought of what nature can do without the full experience of nature from the full range of perspectives of all living creatures and the data provided by instrumentation that can detect phenomena far beyond the sensory ranges of any living organism. Nuclear energy would not have been even conceivable in the Middle Ages. Radio waves, radar, lasers, sonic navigation by bats, whales, and dolphins were also inconceivable.

We have no idea how most animals on this planet perceive their universe.

The idea that designers invent unpredictable designs which betray the existence of these designers is simply hubris by humans who think somehow they are the pinnacle of existence and nothing else can do anything that is unthinkable by humans.

So Dembski’s criterion of “unpredictable inventiveness” as a signature of a designer is completely bogus. It simply shows that Dembski is completely out of touch with reality and what goes on in science. People with no imagination or foresight are always surprised by the most mundane things. That’s why they fall on their faces so often.

Mike Elzinga said:

So Dembski’s criterion of “unpredictable inventiveness” as a signature of a designer is completely bogus.

Well … it MIGHT be the signature of a Designer … but how could anyone tell?

Dembski wants to have it both ways: “There are events which are forever beyond the explanation of science.” Possibly – but what, then, would the sciences have to say about them? We can admit we may not have an explanation now, but can we prove we won’t have one tomorrow, or ten thousand years from now?

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Casey Luskin reminds me of Muhammad Saeed al-Sahhaf

http://en.wikipedia.org/wiki/Muhamm[…]eed_al-Sahaf

better known as Baghdad Bob.

pvm: I found it

Yep, that was it.

Carl Zimmer pwns junk DNA reports

A helpful reminder for Casey

Those who do not know their science history are doomed to repeat bad news hooks.

Hint: Regulatory elements were first reported in the 50’s enhancers in the early 80’s…

Wow…

and

Those who complain about a supposed unilateral neglect of potential functions for non-coding DNA simply have been reading the wrong literature. In fact, quite a lengthy list of proposed functions for non-coding DNA could be compiled (for an early version, see Bostock 1971). Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

genomicron: Word about junk dna

Anyone familiar with the facts would be hard pressed to make arguments like the one Casey continues to make.

iml8 Wrote:

Well … it MIGHT be the signature of a Designer … but how could anyone tell?

That is the concise argument that ID/Creationists use to trump all other arguments. The fact that it might be a signature of a designer means it is the signature of the Designer. Slippery conflation works with the rubes because it is one of the standard shticks used by their leadership.

PvM said: Anyone familiar with the facts would be hard pressed to make arguments like the one Casey continues to make.

Casey is a lawyer first and a scientist (a distant) second. A lawyer has to be able to argue either side of a question. Casey’s client, the Dishonesty Institute, has no actual scientific facts on its side. Whether or not Casey is familiar with the facts (or even able to understand them, as has been proposed here) is not the question - he is constrained to make the arguments he makes (as weak and ignorant as they are) because that’s all his side has to work with.

To use another contemporary metaphor, Casey is a lipstick applicator, and has a pig for a client. Don’t blame him because his lipstick doesn’t work.

Does anyone know of a humanities-grad friendly overview article about non-coding DNA? I’d like to read up a bit before opining on Luskin’s argument.

PvM Wrote:

John Timmer Wrote:

The recent paper focuses on a sequence, called HACNS1, which is about 550 bases long. If it were picking up mutations at random, the human version would be expected to have four; instead, it has 13 differences with the chimp sequence.

In other words, science found how a sequence had more than the expected number of differences between humans and chimps. Such an observation requires an explanation.

Would “Such an observation deserved investigation ” be better here. Is it not an example that might enlighten jobby about the scientific method to assist in his search for the elusive missing information in the human genome, discussed at considerable length in the “Immune to evidence” thread? The original observation could be due to a statistical fluke, but it opened up an area where meaningful research could be done to establish whether these changes had significance or not.

Dembski Wrote:

.…Yes, intelligent design concedes predictability. But this represents no concession to Darwinism, for which the minimal predictive power that it has can readily be assimilated to a design-theoretic framework.

Perhaps I’m confused, but isn’t Dr Dr D contradicting himself here? First he says that there is no predictive power in ID. Then he says that the predictive power of “Darwinism” can be assimilated into ID. Wouldn’t that give ID some predictive power?

What am I missing here?

Mike Elzinga said:

That is the concise argument that ID/Creationists use to trump all other arguments. The fact that it might be a signature of a designer means it is the signature of the Designer.

To which the answer of course is: “Well, we can accept that it’s evidence of a Designer – if you rule out all natural causes first – INCLUDING ALL POSSIBLE CAUSES WE DON’T KNOW ABOUT.”

That’s what the Dembski EF was supposed to do, but one would search in vain for how it even touches this uncomfortable obstacle. The very first time I ran into Conservapedia, they took a somewhat more direct approach to this problem, simply stating: “That’s an unreasonable demand for proof.”

I think just stared DUMBFOUNDED at that: you MUST be putting me on! You MUST be! “This had to have been a miracle because all possible natural explanations have been ruled out.” Ah: “So, exactly how have all natural explanations, even the ones currently unknown, been ruled out?”

And of course no comment really needed on the intriguing way absolute proof is required for The Other Guy but, conveniently, not such an issue for Our Gang. That is not news.

I think it is a good thing for science to always acknowledge the possibility that miracles could occur – as part of the principle of keeping an open mind to all possibilities, even those that we wouldn’t bet on to save our lives. It might have the handy virtue of providing a snappy response to the Phil Johnson insistence that science rise above materialism: “But we admit miracles could occur – we just have no cause to accept that they have so far.”

But again, of course that will not make them happy. Will anything? Their goals are so foggy and self contradictory that they are unachievable. And even acknowledging the possibility of miracles is a mere formality, for we can hold the concept and look it over for as long as we like – and still never figure out what good it does us.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

tacitus said:

I’ve never really understood how IDists can claim that the absence of junk DNA in a designed organism is a prediction of ID.

Different IDers argue different things. Some claim junk DNA & maladaptations are the result of original sin or entropic decay (and thus are predicted by ID). Others, like Casey, argue that ID predicts there is no junk DNA.

They don’t seem to have a problem with this and rarely argue directly against each other; consider Behe’s circumspection at Dover regarding the definition of ID (“they could have phrased it better” instead of “they’re wrong.”). I guess its a mighty big tent. :)

JPD,

A good overview of “junk DNA” can be found at the link that PvM provided above. However, you don’t have to read about junk DNA to know that Luskin’s argument is nonsense. He isn’t even talking about “junk DNA”, he’s just too ignorant to know it and he hopes you are as well.

Here’s what I blogged regarding it:

ID has problems with keeping its dogma straight

But in fact, DNA isn’t exactly like a blueprint. Only a fraction of its sections are directly involved in creating proteins and building life. Most of it seems to be excess DNA, where mutations can occur harmlessly. Edge of Evolution, p. 66

The above is a rather unexceptional statement by Behe, a reasonable inference from past data, if possibly it is being superseded by later research results.

But one of the more persistent, if typically bizarre (particularly in light of how IDists typically deny that “design” has any expectations, other than irreducible complexity and the like), claims of IDists is that ID predicts that most “junk DNA” has uses. Somehow, one of their “leading lights” failed to recognize this “prediction,” quite possibly because it cannot be derived from the vague claims of “ID theory.”

Of course evolution doesn’t really make predictions either way about “junk DNA,” other than that nothing in evolution precludes junk DNA from existing in genomes (very little apparent junk DNA exists in most prokaryotic organisms, while tandem repeats, duplications, and transposons almost certainly produce some true junk DNA in eukaryotes). This hasn’t prevented IDists from claiming that “neo-Darwinism” insists that much of our genomes has to be junk. Here’s a recent example from the ignorant Casey Luskin:

Study Challenges Two Icons of Evolution: Functional Junk DNA Shows “Surprising” Genetic Differences Between Humans and Apes … These sources promoting the classic “junk DNA” icon of neo-Darwinism need updating, as a Yale University news release from earlier this month recalls the fact that “[i]n the last several years, scientists have discovered that non-coding regions of the genome, far from being junk, contain thousands of regulatory elements that act as genetic ‘switches’ to turn genes on or off.” In this case, the junk triggered genes that control human thumb and foot development.

Most studies that have claimed that humans and apes have nearly identical genomes have primarily looked at the gene-coding portions of the genome, not the non-coding DNA (formerly claimed to be “junk”). Perhaps as biologists study the non-coding regions of our genome, they will find evidence that challenges two icons of evolution: Not only does “junk” DNA have function, but humans aren’t as genetically similar to apes as was once thought. [bolding added] Casey Luskin lying for the DI

I guess if you have nothing honest to say, just pick your favorite lie and call it an “icon of evolution,” never bothering to consider why it is that Behe repeats “the classic “junk DNA” icon of neo-Darwinism,” being oblivious both to its “neo-Darwinian” status and to any “prediction” of ID that “most junk DNA” will be found to have a purpose.

The only apparent reason for the constant drumbeat about how “junk DNA” really does have function, and that ID is supposed to predict that it does while “neo-Darwinism” is supposed to predict otherwise, is that IDists are desperate to come up with any kind of evidence for their claims. That they have none is adequately shown by the fact that one of ID’s “leading theorists,” Behe, fails to recognize either assertion in his most recent book, in spite of his own eagerness to fault “neo-Darwinism” at every turn.

You’d think that people who just make up things as they go along would have the sense to get together to get their stories straight. ID fails even to design its own propaganda intelligently.

ID has problems with keeping its dogma straight

Glen D

Mike Elzinga said: When one of the mesons was discovered, it was a surprise (I. Rabi asked, “Who ordered that?”)

The Rabi quotation is in regards to the muon, which is a lepton, not a meson.

The point of Rabi’s question was that the muon was the first elementary particle that was discovered that did not seem to have a purpose. That is, the previously discovered particles, while puzzling in many ways, had clear roles in explaining ordinary matter and energy.

The first models where things like muons must exist have come from string theory. Obviously, Rabi’s question is far from resolved

We have no idea how most animals on this planet perceive their universe.

Some of the recent discoveries in this regard are beyond astonishing. It’s only been discovered in the past couple of years that star-nosed moles use their heavily tentacled noses to create a “visual” image, much like the way bats use sound. There’s a starfish whose entire body is an eye, operating on entirely different principles than retinas. There’s a crustacean with a bobbing eye that is actually scanning like a TV camera. There are the 24 slightly out of focus eyelets on a box jellyfish, but no central nervous system. There are shrimp that communicate with polarized light and have 10 different color receptors. Cats lack sweetness tasting. Humans are virtually smell-blind compared to chimpanzees–that’s actually half of our genetic difference right there.

The list goes on and on. And this is what we know.

iml8 said:

To which the answer of course is: “Well, we can accept that it’s evidence of a Designer – if you rule out all natural causes first – INCLUDING ALL POSSIBLE CAUSES WE DON’T KNOW ABOUT.”

That’s what the Dembski EF was supposed to do, but one would search in vain for how it even touches this uncomfortable obstacle. The very first time I ran into Conservapedia, they took a somewhat more direct approach to this problem, simply stating: “That’s an unreasonable demand for proof.”

I think just stared DUMBFOUNDED at that: you MUST be putting me on! You MUST be! “This had to have been a miracle because all possible natural explanations have been ruled out.” Ah: “So, exactly how have all natural explanations, even the ones currently unknown, been ruled out?”

And of course no comment really needed on the intriguing way absolute proof is required for The Other Guy but, conveniently, not such an issue for Our Gang. That is not news.

Howard van Till wrote a nice rebuttal to this Dembskian version of the bait-and-switch of known versus total natural causes a few years back. Since I lack the math background to criticize Dembski’s argument from that angle (but there are so many other angles), it’s good to see an astrophysicist’s demolition of the premises.

http://0-web.ebscohost.com.uncclc.c[…]0sessionmgr2

That link may or may not work. I’m new at this.

iml8 Wrote:

I think it is a good thing for science to always acknowledge the possibility that miracles could occur – as part of the principle of keeping an open mind to all possibilities, even those that we wouldn’t bet on to save our lives.

Headline: SCIENTIST ADMITS MIRACLES OCCUR EVERY DAY!

I suppose it depends on how the direction the discussion is heading. My more common experience has been that simply acknowledging that miracles (of supernatural origin) can occur is taken as an admission of defeat for science and a win for sectarian dogma; at which point the discussion ends with victory declared by the fundamentalist.

It’s extremely childish, and I don’t enter into these conversations with fundamentalists any more (I was once young and stupid and had lots of energy; now I am old and stupid with nowhere near as much energy).

JPS said:

That link may or may not work. I’m new at this.

It requires a login – unfortunately, sounds interesting, repost possibly? BTW, you can check links when you do a “Preview”.

There’s another amusing angle to Dembski in his insistence on the unpredictability of the Designer. This is very much the same as the classic response to the question of why the Designer would have done something silly like run our windpipe through our throat: “Well, we don’t know what a Designer would have done.”

“Ahhh … so this is different from saying WE DON’T KNOW?” We already knew that.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

Mike Elzinga said:

… at which point the discussion ends with victory declared by the fundamentalist.

But they ALWAYS do! So what else is new? Dembski’s “connect the dots” pitch was basically admitting defeat and then declaring victory. Indeed, that seems to be Dembski’s normal mode of operation.

I don’t have any problem admitting the possibility of miracles, but I quickly add that they wouldn’t be my first option (rather the last), and that I haven’t seen any evidence to accept that they have occurred.

I was thinking a bit more along this line. Humans seem to have a natural inclination to believe in the supernatural, and among tribal cultures the line between the natural and supernatural is not just thin but nonexistent. Over the past few thousand years the sciences emerged and gradually sorted the natural out from the supernatural. Die-hard fundamentalists haven’t sorted them out. They believe that miracles occur and that they are a reasonable explanation for things, as good or possibly even better than natural explanations. They simply do not understand why others would consider miracles to be the explanation of last (by infinite regression or something that resembles it) resort.

It could be argued that the inclination towards the supernatural explanation versus the inclination towards the natural explanation is a matter of taste, but alas for the supernatural option, if it comes down to evidence that might persuade a skeptic, an explanation that actually can be put to use, or for that matter the historical record – the natural option wins hands down.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

william e emba said:

Mike Elzinga said: When one of the mesons was discovered, it was a surprise (I. Rabi asked, “Who ordered that?”)

The Rabi quotation is in regards to the muon, which is a lepton, not a meson.

The muon was originally named the mesotron and later renamed the mu meson when the pi meson was discovered. Mesotron and meson meant a particle intermediate in mass between electron and proton. When physicists realized it was more like an electron than a pi meson, the meaning of meson became “integral spin stronly interacting particle” and the mu meson renamed to muon. see Wikipedia.

william e emba Wrote:

The Rabi quotation is in regards to the muon, which is a lepton, not a meson.

Yeah; thanks William. I was remembering incorrectly the specific particle.

Some of the recent discoveries in this regard are beyond astonishing. It’s only been discovered in the past couple of years that star-nosed moles use their heavily tentacled noses to create a “visual” image, much like the way bats use sound. There’s a starfish whose entire body is an eye, operating on entirely different principles than retinas. There’s a crustacean with a bobbing eye that is actually scanning like a TV camera. There are the 24 slightly out of focus eyelets on a box jellyfish, but no central nervous system. There are shrimp that communicate with polarized light and have 10 different color receptors. Cats lack sweetness tasting. Humans are virtually smell-blind compared to chimpanzees–that’s actually half of our genetic difference right there.

Indeed! These are just some of the most fascinating discoveries. And having had some experience with the physics and technology underlying these methods of “perception”, I have sometimes tried to imagine what it must be like to process information in these ways.

One of my earlier areas of applied research involved the concepts that go into Fourier optics, auto correlation, holography, side-looking radar and sonar, chirped radar and sonar, ultrasonic imaging, and the various techniques for extracting information from sound waves or electromagnetic waves.

But we also knew back in the 1960s and 70s that many of these techniques had much broader applications to other forms of “imaging” with other phenomena. At some point in the sensory systems of animals (and perhaps plants) the “transducers” that detect sound, light, chemicals, and other stimuli from the environment convert these stimuli to electrical impulses in the nervous systems of these organisms. How those nervous systems are organized and behave and process the data can pull tremendous amounts of information out of those stimuli. And some of our research was aimed in that direction. Since then there have been many more developments. Some of these are still highly classified.

iml8 Wrote:

Humans seem to have a natural inclination to believe in the supernatural, and among tribal cultures the line between the natural and supernatural is not just thin but nonexistent. Over the past few thousand years the sciences emerged and gradually sorted the natural out from the supernatural. Die-hard fundamentalists haven’t sorted them out.

That seems to capture the process pretty well. It certainly would not be surprising that early humans would project themselves onto the natural world in order to interpret it and, in the process, perceive beings larger than themselves. And somewhere around the time they started burying their dead along with tools and trinkets, there must have evolved some concept of an “afterlife” and the “supernatural”.

The fact that die-hard fundamentalists haven’t sorted this stuff out yet might be a reflection of the fact that the human brain has not changed all that much in interval of time between us and early tool-making humans. There has been only an accumulation of experience, some of which doesn’t stick very easily.

Mike Elzinga said:

The fact that die-hard fundamentalists haven’t sorted this stuff out yet might be a reflection of the fact that the human brain has not changed all that much in interval of time between us and early tool-making humans.

John Derbyshire, who has views on religion that I closely identify with – not a believer but with no problems IN GENERAL with those who are – wrote something in his articulate way that hit the nail right on the head:

[The] experience of raising two kids … was one I found de-spiritualizing. For one thing, it pushes genetics right in your face. (I recently heard quite-new parent Jonah Goldberg, in conversation, wonder aloud how anyone ever came to believe in the “blank slate” theory of human nature. I share Jonah’s bafflement.) … Again, it made me realize how perfectly natural religion is. We have a religious module in our brains, and with little kids you can actually watch it waking up and developing, like their speech or social habits. The paradox is, that to the degree that you see religion as natural, to the same degree it becomes harder to see it … as supernatural.

I might add – re your comment about the inclination of Darwin-bashers to declare victory – that, as I think you observed yourself, it is not really an issue in evo science to worry about how they will misinterpret statements. They will always find something to misquote or misinterpret; that is the focus of their energies. No, the concern is that the statements are accurate, intelligent, and clear. To the extent the Darwin-bashers apply pressure to do so, they are doing a favor.

White Rabbit (Greg Goebel) http://www.vectorsite.net/gblog.html

william e emba said: There’s a crustacean with a bobbing eye that is actually scanning like a TV camera.

I used to know a guy who rode a motorcycle hundreds of miles each week - in spite of having one eyeball poked out with a stick when he was a toddler. When I asked how he could do that, he explained that he subconsciously scanned his head back and forth, continuously putting his one eye alternately in the positions that two eyes would occupy, and his brain somehow synthesized a good 3D image. Bobbing works.

Paul Burnett Wrote:

When I asked how he could do that, he explained that he subconsciously scanned his head back and forth, continuously putting his one eye alternately in the positions that two eyes would occupy, and his brain somehow synthesized a good 3D image. Bobbing works.

This looks like a case of image alternation which enhances slight differences between images because of persistence of the images for a short period of time in the nervous system or the brain. If depth can be pulled out of this by the brain, then it can work.

There are other well-understood processes taking place with our vision. In the jargon of image processing it is called “dithering.”

Dithering pops up frequently. Our eyes quiver almost imperceptibly to us, but it is an important part of the proper functioning of the eye. It helps bring out the overall pattern in the image on the retina. In the signal and imaging processing areas it is sometimes called “poor man’s low pass filtering.”

It works by randomly and slightly scrambling the higher spatial frequencies in the image. This slightly “softens” the image as it appears in its electrical form in the optic nerve. It reduces “noise” and allows the built-in gains in adjacent sensors in the eye to adjust properly relative to those receiving the brightest light.

Further processing comes from persistence of vision. Sensors that respond too quickly and sensitively are also a source of noise in the electrical impulses emerging from the sensor and going to the CPU (brain). So all sensors have a time window in which they respond to changes in signal. Again, in the jargon of image or signal processing, the signal coming out of the sensor is a “convolution” of the time aperture of the sensor and the time variation of the stimulus. This has a slight smoothing effect that dampens noise.

Once these signal and imaging processing ideas are understood, one can begin to make some inferences about what is taking place in the image and signal processing systems of other organisms.

However, to further infer what a creature “perceives”, one has to know how the entire nervous system is involved in the processing. For example, extended arrays of sensors can feed into a nervous system that puts in suitable delays that would “synthesize and aperture” (much like a lens gathering light and focusing it) that improves the spatial resolution of the stimuli being sensed.

Bats are probably using the phase relationship between their own echoes and a persistent ‘echo” of the transmitted signal in their nervous systems. That would keep bats from being confused by the echoes of thousands of other bats blasting out their chirps at the same time. Whales and dolphins use “chirped” sonars that are much more accurate in determining distances and directions and are less prone to interference by other sounds. They work primarily on autocorrelation.

And so it goes. Nature has sorted out signal and image processing systems that humans only learn about in advanced courses in physics and engineering. But none of it is designed.

iml8 Wrote:

No, the concern is that the statements are accurate, intelligent, and clear. To the extent the Darwin-bashers apply pressure to do so, they are doing a favor.

Indeed; and I think this has actually happened with the clarifying of science to the general public.

I remember when it was simply taken for granted that the public kept up and read people like George Gamow and other authors who were fairly good at explaining science to the layperson. Working scientists are too busy, and most are not very good at producing an engaging (while still accurate) popular work.

As it turned out, science was advancing too quickly for even popularizers to keep up. And, much to my own dismay, some of the popularizations unwittingly propagated misconceptions which were picked up and exploited by pseudo-scientists.

Unfortunately, well-financed propaganda organizations such as the Institute for Creation “Research”, the “Discovery” Institute, Answers in Genesis, and others have sprung up and are offsetting many of the efforts of scientists and popularizers of science.

But didn’t we learn all about that from the “arms races” in evolution? Just knowing about it apparently doesn’t remove us from it. Oh the irony.

Paul Burnett said:

Casey is a lawyer first and a scientist (a distant) second. A lawyer has to be able to argue either side of a question. Casey’s client, the Dishonesty Institute, has no actual scientific facts on its side. Whether or not Casey is familiar with the facts (or even able to understand them, as has been proposed here) is not the question - he is constrained to make the arguments he makes (as weak and ignorant as they are) because that’s all his side has to work with.

Paul, much as we all have a little fun sticking the knife into lawyers, this isn’t quite right. While it is indeed a lawyer’s job to represent his client, the lawyer is still supposed to follow the rules of the court such as keeping testimony relevant, not giving misleading information to the court, complying with discovery, and so on and so on. Luskin is clearly not interested in this. If he were representing his clients in a court case, his current behaviour could very well see him reprimanded by the judge, and even in some of the more egregious behaviours, charged with contempt of court or disbarred. Fortunately for Luskin, the DI is very careful never to take on these cases themselves and only to present their fellows as witnesses. That way the DI never gets lumbered with the costs and political repercussions when the case is inevitably lost.

And, just by the by, it is worth remembering that the great outcome in the Dover trial was the result of a lot of hard work by lawyers who wouldn’t accept Luskin’s behaviour as just what lawyers do, and was decided upon by a judge (who was of course a lawyer). Lawyers are not the enemy; in the case of teaching creationism/ID in school, it is in fact the legal system that has turned out to be the only damn “estate” of public life that has had the integrity to stand up and consistently do the right thing.

Chris Lawson said: While it is indeed a lawyer’s job to represent his client, the lawyer is still supposed to follow the rules of the court such as keeping testimony relevant, not giving misleading information to the court, complying with discovery, and so on and so on.

You’re right, and I know that. Luskin wouldn’t dare pull any of this in an actual court setting. (Does anybody know if he has actually argued a case in court?) But, being a lawyer, he knows how to play to the court of public opinion, and how to game the system for maximum effect for his client. (And being an apostate scientist helps.)

I have the greatest respect for the lawyers on the winning side at Dover - and particularly Judge Jones. But for the life of me, I can’t imagine what the Thomas More lawyers were thinking…they didn’t seem to have a clue.

Paul Burnett said:

But for the life of me, I can’t imagine what the Thomas More lawyers were thinking…they didn’t seem to have a clue.

Ditto. Nobody expects lunatic-fringers to have a clue. But the lawyers were clearly professionals. I think they just had such a poor grasp of science – not just in the technical sense, but in how science operated – that they never understood just how lost at sea they were.

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

Luskin seems to think that Dembski’s contrived “Law of COnservation of Information” has validity and it relevant and applicable.

What an imbecile.

iml8 said:

Ditto. Nobody expects lunatic-fringers to have a clue. But the lawyers were clearly professionals. I think they just had such a poor grasp of science – not just in the technical sense, but in how science operated – that they never understood just how lost at sea they were.

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

The Thomas More Law Center seemed to rely very heavily on the Discovery Institute, and actually believed that ID was scientific. They weren’t in on the Toot’s scam; rather, they swallowed it hook, line, and sinker. They honestly thought they had a shot at winning the case, and when Dembski pulled out (because he, at least, is aware enough of the fragility of the scam to know that it would never survive a court challenge; hence the move to “teach the controversy”), it devastated them.

The DI’s plan was doomed to collapse from the start because while the ground troops heard the religious dog-whistle loud and clear, as intended, their authoritarian nature meant that they took the claims to scientific validity at face value and ran with them, to the detriment of the scam.

I suspect that (on the principle that if all you have is a hammer all you see is nails) the TMLC approached the Dover trial as a legal issue, without understanding that the case was going to be decided on a scientific basis. The odd thing is that there are plenty of lawyers with engineering degrees who work on patent cases and plenty of lawyers with MDs or the like who work on product liability cases – and I would place a very large bet that both those categories of cases make Establishment Clause cases very small beer in comparison. I’m a bit surprised that they didn’t have anybody with a technical background on board.

White Rabbit (Greg Goebel) http://www.vectorsite.net/tadarwin.html

It makes sense if the TMLC is really all about the Jesus, and makes its bread and butter through wingnut welfare. What with Liberty University and its ilk establishing law schools and grad schools that completely insulate the students from reality, we may soon be up to our ears in people with ‘professional’ degrees whose educations have been thoroughly focused on The Jesus, with no practical concerns like patent law or product liability.

I really should try to find out what people know about the TMLC; are these actual experienced lawyers or recent graduates of the fundie-school Bubble Universe? We’ll be seeing more people like them in the future, no doubt, and it will be worthwhile to be forearmed…

minimalist said: It makes sense if the TMLC is really all about the Jesus, and makes its bread and butter through wingnut welfare. … I really should try to find out what people know about the TMLC; are these actual experienced lawyers or recent graduates of the fundie-school Bubble Universe?

Their Wikipedia article ( http://en.wikipedia.org/wiki/Thomas[…]e_Law_Center ) makes them sound pretty naive / ignorant (take your pick).

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This page contains a single entry by PvM published on September 28, 2008 11:56 AM.

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