ID, scientifically vacuous and collapsing gaps

| 26 Comments

While researching the nematode work by Azevedo, I ran across the following [url=]website[/url] called ‘Design vs. Descent: A war of predictions”. The original article can be found at the Idea Center

While the article has many problems, one in particular caught my eye

Finally, a study which compared many proteins in humans, nematodes, arthropods, and yeast found that 2 starkly different trees were produced, depending on which genes were used.25 This pattern of different genes yielding very different phylogenetic trees is very common in the scientific literature, and shows that molecular data fail to give a consistent picture of the alleged common descent ancestry of organisms.

25. Mushegian A, Garey J, Martin J, Liu L. Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes. Genome Research 1998;8:590-8.

To my ‘surprise’, the actual article reads as follows

In this study we evaluated the nematode C. elegans and the fruit fly D. melanogaster as model systems for studying human proteins using protein sequence comparison techniques. By applying strict and reproducible criteria for identifying orthologous proteins, we could extract numerous protein-coding genes for phylogenetic analysis. Our simultaneous analysis of multiple orthologous proteins shows that different proteins can generate different apparent phylogenetic tree topologies, strongly suggesting that historical phylogenies should not be inferred based on a single protein-coding gene. Unequal evolutionary rates are an important factor in calculating phylogenetic trees, and indeed it appears that the majority of C. elegans genes are evolving more rapidly than their Drosophila counterparts. The approaches of ortholog extraction used in this work can be used to better define data sets for phylogenetic analysis among a broader range of representative animal phyla. The available portion of the fly proteome appears to be comparatively enriched in conserved protein domains because of abundant representation of phenotypically defined genes, while missing numerous protein families. The ortholog-to-paralog ratio with regard to human proteins is very similar in the two model animals, indicating that the domain architecture in fly and nematode proteins approximates that of their human homologs to the same extent.

In other words, the authors warn that due to differences in evolutionary rates, one has to be careful to use a single gene dataset to infer phylogenetic relationships. In other words, the authors argued WHY these findings were at odds with the vaste amount of fossil and genetic data. While such outliers indeed exist, the overall picture from independent phylogenies shows a coherent picture

“Biologists seem to seek the ‘The One Tree’ and appear not to be satisfied by a range of options. However, there is no logical difficulty in having a range of trees. There are 34,459,425 possible [unrooted] trees for 11 taxa (Penny et al. 1982), and to reduce this to the order of 10-50 trees is analogous to an accuracy of measurement of approximately one part in 10^6.” (Penny and Hendy 1986, p. 414)

This is much better than the accuracy of some physics constants…

To see why common descent is strongly supported by scientific evidence, one need not look further than the excellent 29+ Evidences for Macroevolution by Douglas Theobald.

Okay, let’s add another example from the same page, showing the dangers of gap arguments, when knowledge expands (does this count as a falsification of ID?)

Schwabe and Warr found that proteins such as relaxin, insulins, adrenocorticotropic hormone, somatostatin, histocompatability antigens, neural glycoproteins and microglobulin are distributed in both animal and non-animal groups in ways which differ markedly from predictions of common descent.13

13. Schwabe, C., Warr, G. W., “A polyphyletic View of Evolution: The Genetic Potential Hypothesis.” Perspectives in Biology and Medicine, 27, 3, Spring 1984 pg. 465-484. See also “On the validity of molecular evolution” by Christian Schwabe (TIBS 11 - July 1986 pg. 280-283).

Douglas Theobald on Camp’s usage of Schwabe et al. See also Laurence A. Moran on Schwabe and relaxins. And also Evolution of the relaxin-like peptide family BMC Evolutionary Biology 2005, 5:14

We present here a phylogeny for the relaxin-like peptide family. Relaxin has long been used as an example of a gene that conflicts with the Darwinian theory of evolution [24,32-34]. However, we have shown that these can issues can be resolved when studied in the context of the rest of the relaxin-like peptide family, in particular the new, but likely ancestral relaxin, relaxin-3.

Btw it seems that it was Schwabe who might have been responsible for Denton’s erroneous interpretation of the Cytochrome-C data.

I am not sure why the IDEA center is rejecting common descent, something accepted by most ID proponents such as Dembski or Behe. While YECers may strongly object to common descent, relying on this kind of poor representation of scientific presents a significant risk and liability to Intelligent Design. Not only is Intelligent Design scientifically vacuous in that it does not present any explanation as to how relaxins or other examples can be explained, but the examples show that the gaps for ID’s God to be hiding in are either collapsing or were never really there.

In addition to ID being considered by many to be scientifically vacuous, I see ID as being a threat to education. Is this really what we want to teach our children? That science may not have all the answers? Fine… That ID is based on gaps in our knowledge? Gaps which either collapse with additional knowledge or gaps which have been ‘created’ by ID based on a flawed understanding of the issues involved… Perhaps it is time to teach the controversy and expose ID for what it is and what it isn’t.

26 Comments

Oh, blah. I could go through Casey’s article, but at the outset I see him doing something that echoes previous posts on PT such as “ID apologists as cheating husbands” and Wes Elsberry’s review of Bill Dembski’s arguments “ID is falsifiable and evolution is not. Elsberry pointed out how IDists apparently argue that evolution is not falsifiable while simultaneously claiming to have falsified it–Luskin is now saying this about evolutionist critics of ID. In sum, the notion that some thing is ID is not falsifiable because the “designer” could always have designed it to appear non-designed. But certain assertions by IDists, such as “this biological system was without doubt desgined” can be falsified by demonstrating a non-intelligent pathway for producing that thing. So, he trips up right out of the box.

On to his “predictions of ID.” The first prediction, as Elsberry touched on, is not scientific for the very reasons Luskin (and Elsberry before him) cites above. The second is also flawed for that reason. Evolutionary theory could be stated in a non-scientific manner in this regard, but the science of evolution lies in demonstrating that what organisms we have studied thoroughly do fit into a nested hierarchy predicted by common descent. The third statement is, to my knowledge, unsupported by current scientific data, other than perhaps cases of lateral gene transfer which must be carefully examined. The lack of such phenomena, particularly in features that depend on many genes such as limb arrangements or the specializations of the vertebrate / invertebrate immune systems is a primary piece of evidence for evolution and against design. The fourth peice of evidence doesn’t distinguish evolution from ID because evolution doesn’t necessarily predict that there will be large amounts of nonfunctional DNA. Rather, genes are co-opted to gain new functions, just as organs become vestigial but not entirely uncoupled from the changing characteristics/behaviors of the organism. In sum, contrary to what he says in the next paragraph, he does NOT refute the assertion that ID is a negative argument whose premises are untestable.

And, how nice! He puts a parallel section further down with four predictions of evolution. First, things that appear irreducibly complex can have evolved (options become necessities, loss of ancestral genes that would have made the system non-IC). Second, forms do appear in the fossil record with transitions in between–the amphibian-reptile-mammal/bird transitions are evident both from fossil data and from embryology. Getting nit-picky, hominid fossil data is quite extensive, enough to have thrown out decoys such as Piltdown Man that didn’t fit the emergent picture. The third prediction is well supported by the available genetic data. There are cases of convergent evolution, but in the context of genetic information things can be set straight. The fourth assertion is skewed as I point out above.

Figure 1 is a real hoot. Luskin eloquently carves out a niche for ID–right after you move out of thigns produced by known natural mechanisms and just before you start getting to things that could have been produced by unknown mechanisms. A vast niche indeed.

I’ll let PZ deal with figure 2 if he wishes. It would be nice if Luskin were to put labels on parts a, b, and especially c. It reminds me of how IDists have told me that the PT crowd is “fast with facts.”

Ho hum.

Dave Cerutti Wrote:

But certain assertions by IDists, such as “this biological system was without doubt desgined” can be falsified by demonstrating a non-intelligent pathway for producing that thing.

I’m not sure that that statement is even really falsifiable. It is an opinion, and one can still use the “The designer did it that way” argument to assert that it was still designed, regardless of whether you show a natural pathway for the system to evolve.

It has long been know that you can’t do good phylogeny (family trees) based on single characters (characteristics), or even on several characters until you have some understanding of which characters are more appropriate for the purpose. For instance, take a whale, a dog and a fish. How do you decide which two are the closest relatives?

I forgot to say in the previous comment

“This is a quiz”

Perhaps biologists can hold back for a while to give others a chance.

For instance, take a whale, a dog and a fish. How do you decide which two are the closest relatives?

Show up at the family reunion and find out who’s buying the drinks.

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Father of ID admits it’s really all about saving souls:

Call Them The Evangelical Alpha Males The Discovery Institute, April 17, 2002

That’s why a provocative thinker named PHILLIP E. JOHJSON – patriarch of the “INTELLIGENT DESIGN” movement – has taken a different path. It’s not that he is terribly modest. But Johnson wants to win and he is convinced that aiming the spotlight at others is good strategy. He wants his cause to thrive after he is gone.

“One of things that the CHRISTIAN WORLD is notorious for is a celebrity style of dealing with issues,” Johnson said, speaking at a conference at Palm Beach Atlantic College (which is also where I teach). “That puts a big burden on one person. I never wanted a movement like that.”

..The movement Johnson calls “THE WEDGE” argues that today’s debates over science, creation and morality are, literally, clashes between people who believe there is scientific evidence that God created man and those who believe there is scientific evidence that man created God.

This debate will not be settled overnight, which is why Johnson is convinced he must not fight alone. He believes the stakes are high and getting higher.

“If there is no Creator who has a purpose for your life, then there is no such thing as SIN,” he said. “Sin would mean that you are in a wrong relationship to your Creator. Well, you can’t be in the wrong relationship with the particles. They don’t care. So you don’t need a SAVIOR, to save you from the consequences of your wrong relationship with the particles. …

“When you give away creation, you have given away everything.”

http://www.discovery.org/scripts/vi[…]&id=1245

“The movement Johnson calls “THE WEDGE” argues that today’s debates over science, creation and morality are, literally, clashes between people who believe there is scientific evidence that God created man and those who believe there is scientific evidence that man created God.”

there he goes, doing what all these fundies apparently can’t help themselves of, convincing themselves that this whole thing is about atheism vs religion.

It must be some ingrained shared delusion.

Posted by Sir_Toejam there he goes, doing what all these fundies apparently can’t help themselves of, convincing themselves that this whole thing is about atheism vs religion.

It must be some ingrained shared delusion.

It is THE ingrained shared delusion.

PvM Wrote:

I am not sure why the IDEA center is rejecting common descent, something accepted by most ID proponents such as Dembski or Behe.

To my knowledge only Behe publicly admitted common descent. Dembski undoubtedly accepts it in private, but has yet to commit to it one way or another. But surely you know that, while the official ID position is “don’t ask, don’t tell” (as it is for the age of the earth), most of its spin is specifically geared to lead the average reader to infer doubts about common descent. Most of us who closely follow the ID strategy are in on the scam, and ID strategists know that we are, and that it is a scam. But as long as they can get away with pretending that the weasel word “common design” somehow rules out common descent, they will.

Also, from the link to Douglas Theobald’s critique, it’s beyond fascinating that anti-evolutionist Ashby Camp can’t even get Schwabe’s first name right. And it’s “Christian” no less! The irony is that if ID were anything close to a theory, Schwabe would be their Darwin.

Frank, how do you figure that Dembski accepts common descent in private?

“To my knowledge only Behe publicly admitted common descent. Dembski undoubtedly accepts it in private, but has yet to commit to it one way or another. “

actually, to my own error (I couldn’t believe it myself!), Dembski DID in fact publically espouse his acceptance of common descent (but not natural selection as the mechanism involved) during a televised debate last month. let me see if the video of it is still around.

.. and here it is. IIRC, after being asked about his views, he admits to believing the evidence in support of common descent.

this is about 1:30 into the video clip.

http://telicthoughts.com/?p=65 (click on the dembski and ruse on nightline link)

so not only does he believe it privately, he has publically acknowledged the validity of common descent as well.

He will however, claim that all that “common descent” is by design, and has nothing to do with natural selection.

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If they do get him on the stand, I pledge my undying loyalty to whomever asks him the following question.

“Mainstream scientists say HIV causes AIDS. You say they’re wrong on that too. Do you think we should Teach the Controversy on that? Do you think we should present alternate ‘theories’ to high-schoolers about that too?”

gee steve, you’re a cheap date.

;)

Johnson should watch what he says. There are so many of those damn particles, I’d hate to get on their bad side.

I didn’t catch where Johnson made hints at his AIDS skepticism. Does anyone have the link?

Dave Cerutti Wrote:

I didn’t catch where Johnson made hints at his AIDS skepticism. Does anyone have the link?

I’m not sure which hints you’re referring to, but perhaps this will answer your question.

I didn’t catch where Johnson made hints at his AIDS skepticism. Does anyone have the link?

“Hints”? Hell, he screams it from the rooftops.

That’ll do!

Sorry, I should have googled it first. RIght after I posted I did just that, and found yet more statements to this effect.

www.fuckinggoogleit.com

Rev Dr. Lenny, are you and Reverend and a Doctor of some science? I only ask because of the quotes.

Rev Dr. Lenny, are you and Reverend and a Doctor of some science? I only ask because of the quotes.

As I noted very recently in another thread:

I bought both my ordination and my doctorate in divinity on the Internet. The ordination was 6 bucks, I think. The doctorate was an extra two bucks. That’s why my “titles” are in quotes. But they do give me the legal right to perform marriage ceremonies, baptisms, etc. for whomever I want. Such as, say, gay and lesbian friends.

It’s my way of poking fun at all the creatonuts over the years (like “Dr Dino”) who have tried to impress people with their phony credentials. And it pisses the fundies off no end. :>

But I did study Tantric Buddhism for three and half years and hold the title of Shidoshi, which is the equivilent of an ordained minister in Christianity.

When it comes to creationsit-fighting, my credentials are all in the area of grassroots political organizing, whcih I have done for the past 20-odd years. I know what tactics the creationist/IDers use, I know why they use them, and I know how to counter them.

ID/creationism, despite all its arm-waving, is not about science, it’s about political organizing. And it wont’ be ebaten by science, it will be beaten by political organizing. All the science talk is, in a very real sense, utterly irrelevant.

I’ve had similar conversations with some of the ID people I know here is San Diego. When pressed, they’ll even admit that there’s been a tremendously successful PR campaign, and offer that they wish there was more science, but that’s all they’re going to do. I really think they’re fooling themselves.

I’ve had similar conversations with some of the ID people I know here is San Diego. When pressed, they’ll even admit that there’s been a tremendously successful PR campaign, and offer that they wish there was more science, but that’s all they’re going to do. I really think they’re fooling themselves.

It’s not THEMSELVES they are fooling – it’s EVERYONE ELSE.

ID *is* nothing but a PR campaign. It has no science whatsoever, and it doesn’t give a fying fig about GETTING any science. It is a political attempt to use PR and political force to do exactly what the Supreme Court has already told them they CANNOT do – use public school science classrooms to advance their religious opinions. Nothing more, nothing less, nothing else.

All their “science” talk is a means to the end, not an end in itself. They don’t care about “science” in the slightest and neither do their followers. And that is why all the “science” talk in the world won’t stop them. Or even slow them down.

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This page contains a single entry by PvM published on May 31, 2005 9:06 PM.

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