Once again Egnor proves he's more of a liability than an asset to the cause. Ooblog exchanges some emails with Egnor asking him to define "biological information.

The problem? Egnor can't do it.

No one knows how to measure biological information in a meaningful way. The current ways of measuring information (Shannon, KC, etc) are relevant to sending signals, and are not of much help in biology.

Gene duplication is not a source of significant new information. It obviously changes the way things work in the cell, to some extent, but it can only copy what's there, and we're asking how it got there to begin with.

Even though we can't measure it (and serious investigators like Dembsky are trying to figure this out), we know biological information when we see it. The genetic code, molecular machines, seamless integration of physiology are all obviously the kind of biological information that we are trying to understand. The only source of such information (or functional complexity or whatever) that we know of in human experience is intelligent design. There are no 'natural' codes, aside from biology, which is the topic at issue.

Darwinists have a responsibility to show that undesigned mechanisms can produce sufficient biological information to account for living things. If they don't even know how to measure it, how can they assert that random variation and natural selection can account for it, and why is the design inference ruled out?

Actually, biologists can measure biological information, Evolutionblog has a good post on this aspect, but that's beside the point.

Egnor argues the invalidity of "Darwinism" based on it's inability to measure a metric he can't define better than "he knows it when he sees it".

This is a wonderful new technique. I say that ID creationism shouldn't be given any validity until they adequately explain biologic "godism". I don't know how to define or measure biologic godism, but it's the presence of godliness in biological systems. Until they quantify biologic godism to my satisfaction in a reproducible and systematic way, I don't think we can trust what they say. Biologic godism needs to be measured, mathematically modeled, and fit into a new biological framework before we can trust this new hypothesis of theirs.

Isn't it so much easier to argue with people when you're just allowed to make things up?

Labels: Evolution denialism, Michael Egnor

PZ points out, and the expert agrees, this new paper from PNAS on the evolutionary underpinnings of the bacterial flagellum is a dog.

So, what's the problem? Lots of papers appear in the literature of dubious quality, why should this one be so worrisome?

Well, because it happens to be on the topic of the evolution denialists' favorite example of a "irreducibly complex" biological machine. Now, Matzke, the expert here, has written extensively on why the irreducible complexity argument is absurd, generally and specifically. He also has proposed a model for evolution of the bacterial flagellum.

And it has already occurred with the DI (Behe specifically) quoting Matzke out of context to imply that all understanding of the bacterial flagellum from an evolutionary perspective is somehow flawed.

The PNAS paper reaches conclusions that other workers find very questionable. Nicholas Matzke of the pro-Darwinian National Center for Science Education and Panda's Thumb blog declares the work to be of "canine quality", that is, "a dog." (2) (Although a geographer by training, Matzke has acquired some skills in the area and earlier published his own sequence comparisons of flagellar proteins in Nature Reviews Microbiology.) The bottom line is that Matzke is quite skeptical that the two dozen kinds of proteins in the flagellum core could be derived from a single protein. His point is well taken. Yet neither of the scientists that Science magazine journalist Jennifer Cutraro called for comments expressed any curiosity concerning that startling claim. (3)

Well, Matzke's writings on this are more than adequate to provide an evolutionary explanation for the origin of the flagellum. Notice how Behe also drags out the tired and debunked mousetrap analogy. Not only is argument from analogy an irrelevant contribution to scientific discussion, the analogy isn't even apt. As it has been pointed out again and again, the component parts of a mousetrap are individually useful, and the correct evolutionary analogy (that also applies to the flagellum) is that it could be composed of parts that were already in use in the cell, and simply recombined in a new way. But this is again a distraction. Note how they selectively use Matzke's pre-emptive criticism of a bad paper and the bad paper itself to generate an argument that would seem to cast doubt on an evolutionary mechanism?

This is the problem with science, we are self-correcting our literature, but the literature never goes away, and a denialist selectively quoting Matzke's criticism, this dog of a paper, and ignoring all the other writing on the topic can make it appear we know nothing about the evolution of this mechanism.

So, I give this latest argument a 3/5 on the denialism index. Behe being a bogus expert on anything, the terrible mousetrap analogy serving for our logical fallacy, and the blatant cherry-picking to misrepresent Matzke's writings serves the selectivity category.

By the way, I was sitting in the bar talking to Peter Griesar (who does great work with the One Campaign) about the blog, and he came up with a great suggestion. A visual depiction of each of the criteria of denialism. For instance, for conspiracy theories we would have to have a little gif of a tinfoil hat like this.

For selectivity a cherry would do nicely (for cherry-picking).

For false experts I really want a picture of a chimp in a white coat or maybe a puppet with strings attached. For now this creative commons chimp "thinker" will have to do.


For impossible expectations/moving goalposts, well, goalposts.


And finally for logical fallacy I was thinking a picture of a old-timey robot waving it's arms with sparks flying out of its head (does not compute). This is what I did quickly.


This argument from Behe would therefore garner the following honors.

Labels: Evolution denialism, Michael Behe

Dembski's latest proof that ID is taking the scientific establishment by storm? this paper. Here's the abstract:

The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

Dembski just doesn't get science does he? The authors aren't suggesting that proteins were designed or that evolution is false, they're talking about the relative merit of different protocols for rational protein design. I suppose if you squint really hard and have no idea of what the science involves you could read it that way, but sheesh. What a moron. And what a nice example of selectivity.

**Update - added link to UC**

Labels: Evolution denialism, william dembski

There he goes again.

Darwinists claim that comparative medicine and biology, which is the study of the similarities between non-human organisms and humans, arose from Darwin's theory. That's nonsense. Comparative biology has been the been the basis for biological science for thousands of years, and many of the greatest medical advances, such as Galen's and Vesalius' studies of anatomy and Harvey's discovery of the circulation of the blood, were the fruit of comparative biological research that antedated Darwin by centuries. The father of modern comparative biology was Carolus Linnaeus, who worked a century before Darwin was born.

Hear that? If the science existed in any form before the theory, than that must mean that new theory isn't useful to it. Aside from the straw man that "Darwinists" say that comparative medicine originates from evolutionary theory (such a historical inaccuracy really is a joke), this argument simply doesn't hold water. And when are they going to give up on this "Darwinist" label? Maybe we should take PZ's example and start calling them "Paleyists"

Take physics for an example. Mechanics existed long before Einstein came up with relativistic mechanics. How can you say relativity is indispensible to understanding modern physics? Newton came up with mechanics over a hundred years before Einstein was born!

The answer is simple. The kind of comparative medicine that was done two hundred years ago was helpful, I'm sure, but far less sophisticated than what we do now. As we discussed before the difference between comparative anatomy and the kind of genetic/molecular/physiologic science we do today is, well, huge.

Once again, no data, just bad analogies, bad straw men arguments, and the false statement of natural selection as a tautology. Egnor consistently has proven himself to be the perfect example of a denialist. All I need from him is a nice quote-mining episode or other evidence of selectivity and he's got the 5/5 score.

Now, let's hope for some other denialist examples to emerge, I'm getting bored with the creationists.

Labels: Evolution denialism, Michael Egnor

Marcus Ross has written a review entitled, "Confusion over Intelligent Design and Young-Earth Creationism"(PDF). It's a real publication for the Journal of Geoscience Education, I'm so excited, it has charts and graphs and a table and everything.

It's also a total blast to read, as he creates a taxonomy of bullshit. I'm not being facetious, it's actually quite helpful. However I'll point out one major inaccuracy. He attempts to claim that ID is not creationism because it is based on science and is thus different from Young Earth Creationism (YEC). This has been proven false. When you show up, in Federal court, and say you're not creationists, then someone shows your "textbook" of Pandas and People is just a creationist textbook that you did a find-and-replace of "creationism" for "intelligent design", you're full of shit.

Again this is the deceptive element which Judge Jones pointed out famously in Dover v. Kitzmiller. There is no doubt about it, the objective is the teaching of creationism, and the "Intelligent Design Science" is a farce designed to avoid failing the Lemon test. They operate the same as creationists, they make the same arguments, they use the same textbooks (with some pretty simple editing), they've been called liars by a federal judge for saying they're not creationists, and just like creationists they have no empirical evidence for their beliefs.

Labels: Evolution denialism, Marcus Ross

Jonathan Wells has made the horrible error of trying to deny evolution in PZ Myers' field. The results are pretty catastrophic for Wells. Not only does PZ show that he's wrong, but that the paper he cites selectively actually contradicts his interpretation.

He better go back to harping on Haeckel's embryos and keep his creationists hands out of PZ's territory if he want's to keep all his fingers.

Labels: Evolution denialism, Jonathan Wells

Wow, just...wow.

In response to Orac's challenge to show that the design inference is useful to medical research what is the first example that Egnor chooses? Watson and Crick's discovery of the double-helix structure of DNA.

The reasoning? Well, they reverse-engineered the structure from the X-ray crystallography diffraction patterns (although he forgets to mention that they also used paper models representing the molecules of DNA to help figure out which structures were physically possible), and anything that is engineered is designed (according to Wikipedia), so they were using the design inference.

Am I reading that right? Is this actually what passes for logic these days? What's really sad is that the Discovery Institute thinks they have a winner in Michael Egnor, maybe it's because in the process of advancing denialist arguments they have absolutely no appreciation for what makes a good argument. But really, Watson and Crick, using the design inference? Please.

So, simply put, Egnor is saying because macromolecules follow physical rules and create structures that one can interpret from physical phenomena, that means they are engineered or that one infers design by using the physical laws of the universe to interpret them? Is he suggesting that a macromolecule could not form a regular structure without being engineered? (Oh boy, I hope he does) Or is he suggesting that without inferring design one is no longer allowed to use to laws of physics?

Seriously, this is such a dumb argument I can't even begin to figure out his reasoning. This is another problem with denialists, is that the arguments they make can be so bad, that you get confused since there isn't enough logic present to get an adequate hand-grip. I'm going to have to disagree with Orac and this idea that you can "challenge" IDers to provide evidence for a design inference and that will help prove a point, because they'll just say the design inference is in use already, is used all the time, and everything scientists really do is design inference but they won't admit it because they're part of the evil materialist conspiracy. And then, the sheep that swallow what are just really bad arguments will defend it, to the death, like it's a genius idea.

It's time to stop pretending the Discovery Institute are honest brokers in a debate about the physical nature of the universe, they're just denialists, they have nothing to offer.

Labels: Evolution denialism, Michael Egnor

Again, not to harp too much on the creationists, but the tend to be the more prolific of the WWW denialists. Today alone they have a wonderful example of "poisoning the well"/ad hominem, they're propagating that tiresome Al Gore smear (again poisoning the well/ad hominem), but those logical fallacies are too easy. Instead let's talk about this article, "Who doubts common descent? You’d be surprised" by Denyse O'Leary as a perfect example of selectivity, or in this specific instance, quote-mining.

She selects two quotes in particlar, the first from Malcom Gordon of UCLA in his essay The Concept of Monophyly: A Speculative Essay.

"The phenomenon of a monophyletic origin for the universal Tree of Life probably did not occur ... At the macro-scale life appears to have had many origins."

The second from W. Ford Doolittle's inaugural address to the NAS

"Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true."

Why don't we do these fine scientists a favor and publish the full quotes. Here's the full abstract from Malcom Gordon's paper.

The concept of monophyly is central to much of modern biology. Despite many efforts over many years, important questions remain unanswered that relate both to the concept itself and to its various applications. This essay focuses primarily on four of these: i) Is it possible to define monophyly operationally, specifically with respect to both the structures of genomes and at the levels of the highest phylogenetic categories (kingdoms, phyla, classes)? ii) May the mosaic and chimeric structures of genomes be sufficiently important factors in phylogeny that situations exist in which the concept may not be applicable? iii) In the history of life on earth were there important groups of organisms that probably had polyphyletic, rather than monophyletic, origins? iv) Does the near universal search for monophyletic origins of clades lead, on occasion, to both undesirable narrowing of acceptable options for development of evolutionary scenarios and sometimes actual omission from consideration of less conventional types of both data and modes of thought, possibly at the expense of biological understanding? Three sections in the essay consider possible answers to these questions: i) A reassessment is made of major features of both the concept and some of its applications. Recent research results make it seem improbable that there could have been single basal forms for many of the highest categories of evolutionary differentiation (kingdoms, phyla, classes). The universal tree of life probably had many roots. Facts contributing to this perception include the phylogenetically widespread occurrences of: horizontal transfers of plasmids, viral genomes, and transposons; multiple genomic duplications; the existence and properties of large numbers of gene families and protein families; multiple symbioses; broad-scale hybridizations; and multiple homoplasys. Next, justifications are reassessed for the application of monophyletic frameworks to two major evolutionary developments usually interpreted as having been monophyletic: ii) the origins of life; and iii) the origins of the vertebrate tetrapods. For both cases polyphyletic hypotheses are suggested as more probable than monophyletic hypotheses. Major conclusions are, as answers to the four questions posed above: probably not, yes, yes, and yes.

And, for Dr. Doolittle's sake let's just tack on the next sentence in that paragraph that O'Leary smartly left out.

This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation.

Hmmm. Pretty typical denialist tactic there. Neither of these scientists is really expressing skepticism about evolutionary theory, or evolutionary mechanisms being responsible for things like increasing biological information, bacterial resistance, or speciation, all of which the DI denies. They're criticizing the tree-of-life model as incomplete in describing all the ways new species branch off from their ancestors. The implication being that if there are scientists who feel that the current model of phylogeny or whatever is not fully descriptive, clearly that means that evolution is "controversial" or there is reason to throw out the whole thing.

It also highlights the fundamentally deceptive nature of the denialist. What do you think? Did O'Leary accurately depict these scientists statements? Or does this feel deceptive to you?

Labels: Denyse O'Leary, Discovery Institute, Evolution denialism

Egnor says it was all a joke.

Happy April Fools'! (Or Dawkins' Day, as some of you might know it.)

Over the past month I have engaged in what my friend Bill Dembski ludicly refers to as "street theatre". My posts here have been an outlandish parody of the bona fide Intelligent Design position, liberally injected with many of the more simplistic errors of the Young Earth Creationists. My purpose was to see how far we could go before the gullible Darwinists realized they were being taken for a ride. The Discovery Institute has graciously aided (and abetted!) by allowing me a voice on this weblog and by giving me valuable feedback on my comedic output. Together, we have succeeded in duping the Darwinists (like the foul-mouthed duncecaps at the Panda's Thumb and Scienceblogs).

Our ruse was bound to work for a while; after all, Darwinists eagerly want to believe that Intelligent Design is nothing but "dressed up" Creationism. However, I'm astounded we made it this far, as I truly feared that the Darwinian horde would catch on sooner---but they are even denser than we had expected. Bill Dembski wagered a bottle of Macallan that I would not persevere to this day---but I have, and I will collect. I also owe Casey Luskin a beer; his courageous acting in our podcasts deserves an Oscar.

Thank you, Darwinists, for giving the Discovery Institute plenty of laughs by coining such ad hominem terms as "egnoramus", "egnorance", "Dr. Egnore", and "egnorrants". Not since middle school have I endured such puerile taunts. It was, after all, too easy to exploit the Darwinists' blind bigotry for Intelligent Design theorists. Regardless of how ridiculous my posts were, the Darwinians seriously thought that I was sincere. The doctors in my medical school deal with the realities of microevolution daily (e.g., the evolution of bacterial resistance to antibiotics), yet the Darwinists willingly believed that I could be "egnorant" of these facts.

The Discovery Institute and I hope you have enjoyed our elaborate game. As Bill Dembski has said, we should strive to "be more fun at parties". But on a serious note, and with apologies to Sir Ronald Fisher, Intelligent Design is not Creationism. Intelligent Design theorists embrace evolutionary science and its implications for modern biology and medicine. Common descent is a fine working hypothesis; natural selection can produce some limited forms of information; it would be foolish to deny these. We, as ID theorists, simply recognize one additional fact about our Universe that the Church of Darwin refuses to: when all else fails, laughter is still the best medicine.

Good night and God Bless.

Or did he?

Look closely...

Labels: Evolution denialism, Michael Egnor

Apparently, it's a standard trope.

Preventing the emergence of resistant strains of bacteria is important work, but the insight that Darwinism brings to the problem - the unkilled ones eventually outnumber the killed ones - is of no help. We can figure that out ourselves. The tough work on preventing the emergence of resistant bacteria is done by microbiologists, epidemiologists, molecular geneticists, pharmacologists, and physicians who are infectious disease specialists. Darwinism, understood as the view that "chance and necessity" explains all biological complexity, plays no role.

The Darwinist modus operandi for a century and a half has been to slip a philosophical agenda - scientific materialism - in with the science. They hijack other fields of biology - microbiology, population biology, epidemiology, genetics, etc - then they assert that Darwinism is essential to those fields, then they claim that the hypothesis that random variation and natural selection is the origin of all biological complexity is a "fact" supported by overwhelming evidence. When challenged, they prove the "fact" of scientific materialism by doing a Pub-Med search for thousands of tangential articles from the fields they've hijacked.

Ok, so he thinks that all bacteria have all the resistance genes they will ever have? This guy is a doctor! And he still doesn't get it. You wonder how he would explain how bacteria did not have resistance genes 20 years ago, and now they do. I suppose he'll assert, against all reason, evidence etc., that they've always had those genes, it's just some subpopulations have them and others don't. This defies logic because that would mean that antibiotics would never have worked. If there were always subpopulations with the resistance gene present, bacterial resistance would have been instant from the start. Oy, the stupid. It hurts my brain.

Anyway, he gets 1 point for straw man ("chance and necessity" and the description of bacterial evolution as "the unkilled ones eventually outnumber the killed ones"), he gets 1 point for conspiracy (the materialist agenda hijacking science - whatever), he get's one point for impossible expectations because he describes the act of providing him evidence as some kind of deception and he always gets one point for being a false expert. That's 4/5, but without quoting people or data selectively he's never going to get a 5/5. Keep working on it Egnor.

Labels: Evolution denialism, Michael Egnor

Dumbest denialist video ever. Evolution can't happen because if it did it would contaminate peanut butter.



Wait, what? I think that qualifies as one of the funniest non-sequiturs I've ever heard. 1/5 on the denialism score but, I think they deserve an extra point or two for creativity.

*fixed link*

Labels: Evolution denialism

Well, the creationists at Uncommon Descent have taken notice of us and wear their denialist badge with pride!

I think that there may be some fodder in the current "witch hunt" attitude towards “deniers” for us to use. Consider the following example:

There were a couple of doctors who were "stress deniers" in that they denied that stress caused peptic ulcers. They had the audacity to suggest that ulcers were caused by a bacterial infection. As a result, they were marginalized and scoffed at and (so I understand) heckled and laughed at during presentations. The end result: they won the 2005 Nobel Price in medicine for the bacterium Helicobacter pylori and its role in gastritis and peptic ulcer disease. The take home message that we should shout at every opportunity: today’s "deniers" are tomorrows heros.

Consider also the following:

Copernicus - geocentrism denier

Pasteur - spontaneous generation denier

Darwin - inheritance of acquired traits denier

Einstein - absolute reference frame denier

Gould and Margalis - Darwinian gradualism deniers

Hawking - Steady State Model denier

Conway Morris - purely random evolution denier

Woese - universal common descent denier

etc.
Based on this, being a "denier" is a grand tradition in science, a tradition that science literally cannot do without. Without the bold "deniers" challenging the status quo, there would be no progress in science.

There's a big difference between changing scientific paradigms and being a denialist, although, most denialists like to make egomaniacal claims that they are "paradigm shifters", the HIV denialists are especially this way.

The difference between people like BarryA, Dembski, the other IDers etc., and nobel prize winners (like Marshall who he cites for the H. Pylori discovery - he was here at UVA by the way) is that these real paradigm shifters actually had data rather than conspiracy theories, cherry-picking, fake experts, impossible expectations and fallacious arguments. This also makes the silly assumption that everything that is thought to be true should be challenged, as if this is a univerally healthy behavior. Think about some of our other denialists, like the HIV/AIDS denialists, or the holocaust deniers, does BarryA think they're heroes too to be compared to Einstein Pasteur and Darwin? There are some theories that are ripe for change, some ideas that incompletely describe the natural world, then there are things that are so well documented and supported that to challenge them really means you're just an idiot. In reality the proper comparison is between BarryA, Dembski, O'Leary, Ham, etc., and Peter Duesberg, or David Irving. We do make that comparison, not with the goal of guilt-by-association with holocaust deniers and HIV/AIDS denialists, but because they use the same tactics!

Everybody who upsets scientific consensus is not a denialist. To re-iterate, a denialist is not just someone with a non-mainstream idea (after all evolution is a minority belief in this country so in BarryA's comparison it's the IDers that are the sheep). A denialist is someone who believes that the consensus scientific opinion can be brought down with conspiracy theories, selective data, fake experts, impossible expectations, and fallacious reasoning.

If the IDers actually had data that supported their view maybe they'd have a shot at being paradigm shifters. Instead they're just liars who are determined to distract from real science with their tactics of doubt and confusion for their (barely) hidden agenda of propagating religion, not science.

Labels: Evolution denialism, uncommon descent

This is what denialism.com is all about, the fact that someone like Denyse O'Leary thinks they know how to think, when they really don't. Check out this essay on why ID should be considered by scientists.

When people examine a new idea for the first time, they often approach it from a basis of older, assumed ideas which cause confusion. They can't really evaluate the new idea properly until the source of confusion has been identified.

In discussing the intelligent design controversy with people, I sometimes hear the following comment:

If scientists conclude that something is designed, then they are just taking the easy way out, and they won’t be able to find out anything more about it.

Ok we're starting with a straw man here. Design doesn't make things easier it complicates things with questions like, "who designed the designer?", and "how does this help us make predictions about the natural world?" If God did it, and he's a mysterious guy, that gives us no insight into biology, because who knows why a deity does anything? He's always been so fickle in the past. I guess in a way it's "easy" because it allows you to stop thinking about science, but it certainly doesn't make science any easier. Onward and downward:

On rare occasions, time is permitted for a thoughtful response, so here's one:

Let us look at a real life example: Suppose we say: If the fire marshall's office (FMO) concludes that a fatal fire has been set deliberately, then they are just taking the easy way out, and they won't be able to find out anything more about it.

Wow! An analogy! How about that. Instant dismissal. Give me data or give me death. Anyway, she goes on with this analogy, and on, and on. Finally she's done, and what's next? Another analogy!

Should scientists refuse to consider design a possibility because they are “objective”? Well, how about this: Suppose the FMO gets a call from a leading local politician announcing that he wants the arson investigation called off because the FMO has no business assuming that someone might have wanted that building torched?

If the FMO thinks it has reasonable grounds for pursuing its present line of inquiries, should it meekly accept that argument? Should we assume that the politician obstructing the investigation is “objective”? Or rather that he is trying to defend somebody or something? In the same way, materialists attempting to suppress ID-friendly scientists are hardly “objective” in the matter.

The reason the outburst above is confused is that the speaker assumes that design is not a conclusion that can be arrived at by considering evidence and moving on to identify patterns. Underlying that assumption is a lifetime of steady indoctrination by materialism.

Suppose I took a fish and skinned it, then danced in a circle and sang a song about a daisy, it's still not data, so go away. I guess in a way it is that dastardly materialism they so frequently complain about that causes me to believe in evolutionary theory. But the material in question is data. This materialism canard is just another way of saying conspiracy anyway (Scientists won't listen to those wise IDists because they're just too interested in spreading atheistic/materialistic ideology). Therefore I give Denyse a score of 2/5 for denialism for this argument (one point for analogies and logical fallacies, one point for conspiracy). Not a stunning piece of denialism, but it's getting there.

Labels: Denyse O'Leary, Evolution denialism

Only it again comes from the discovery institute (They really are the most prolific denialists on the Web, sorry to harp on them). See Is Darwinism Indispensable to Comparative Medicine? Meet Galen, Vesalius, Harvey, and Linnaeus." It is essentially a litany of the comparative anatomy that proceeded Darwin's birth followed by this paragraph.

The father of modern comparative biology was Carolus Linnaeus. The 18th century Swedish physician, botanist and zoologist laid the foundation for modern taxonomy. He advanced the binomial ("genus and species") system of classification, and his work is the basis for biological nomenclature used throughout the world today. Linnaeus' system was based on detailed knowledge of the physical similarities and differences between living things. Linnaeus based his classification on his inference that living things were designed.

Was Darwin indispensable to comparative medicine and biology? Consider this. Linnaeus, the father of modern comparitive biology and a devout Lutheran, died during a church service in Uppsala Cathedral on January 10, 1778. That was 31 years and 33 days before Charles Darwin was born.

This sounds like the kind of silly crap that the anti-animal testing people think we do in the lab. We just take apart animals and look at their organs for fun. Ummm, no. In my lab meeting this morning we mentioned/discussed evolution and conserved sequences three times in regards to comparative medicine. What were we discussing? The conservation of promoter sequences in a gene between species as a way of identifying the cis regulatory elements that control gene expression. More simply, the DNA that is upstream of your gene - it's important. It contains little bits of code called cis elements that bind to transcription factors, and when the right transcription factors are bound then transcription starts, mRNA is made, then protein etc. The cis elements that a promoter may contain are varied, and are important in determining the developmental, physiologic and pathologic expression of genes. It's very much like a computer code that controls when a program turns on and off.

The problem is that for a given sequence upstream of the promoter, cis elements may be anywhere from several base pairs away from the gene to hundreds or even tens of thousands of base pairs away, and in the intervening region there will be many sequences that look like they may be important, but really are not. How do you tell what is important and what is not? How is possible to figure out which cis elements are relevant to control of your gene and which you should mutate to figure out what they do?

Well, one clever way to do it (after an initial deletional analysis) is to compare the promoter sequences from multiple species to see what stays the same. It's a pretty simple idea. One would predict that if a sequence is required for the proper control of a gene that it would be preserved throughout evolution as a great deal of the developmental programming and gene expression between animals is conserved (not identical, but similar). So you align the sequences, and the DNA base pairs that have stayed the same from fish, to chickens to mice to rats to humans (or even just mice to humans) are very likely to be the regulatory elements of interest. This is also one of the first things done in analysis of a new protein or cDNA sequence to determine which elements are responsible for the proper structure and function of a protein. Here's an example from my lab of promoter analysis based on conservation between species.



In this case it's a comparison of mouse, rat and rabbit to determine the conservation of the CArG cis elements in the Smooth Muscle Myosin Heavy Chain promoter. The dashes correspond to matches between the promoters, while the letters in the lower strands indicate the differences between species. This level of conservation of cis elements between species is very suggestive of the importance of the element in regulation of the gene. And sure enough, they were.

I suppose though if all biologists did was sit around dissecting animals and doing comparative anatomy, maybe it wouldn't be as relevant to evolutionary biology. After all, they did long before Darwin. But we've progressed beyond comparative anatomy people and yes, in the course of the day, almost every day, we consider the evolutionary implications of the molecular biology we study because it's helpful. This kind of complete and total ignorance of the mechanics of biomedical research is the kind of crap I usually encounter from the anti-testing people, I guess the DI is expanding its frontiers into new areas of idiocy.

Source: Cort S. Madsen, James C. Hershey, Martina B. Hautmann, Sheryl L. White, and Gary K. Owens, Expression of the Smooth Muscle Myosin Heavy Chain Gene Is Regulated by a Negative-acting GC-rich Element Located between Two Positive-acting Serum Response Factor-binding Elements J. Biol. Chem. 272: 6332-6340.

Labels: Evolution denialism

... if we're not nicer to his buddy Michael Egnor. Apparently, when you present arguments that are completely devoid of thought, responding to them with, "your argument is bad and you should feel bad" is proof that your argument is wrong.

We anti-denialists, of course, disagree. Sometimes an argument isn't even an argument. Sometimes the only correct response is to say, that's retarded, go away. But let's go through this real quick.

It's been amusing-and revealing-to observe the recent debates between many in the Darwinist internet community and a professor of neurosurgery, Michael Egnor. A few simple questions have incurred a deluge of ad hominem attacks upon Egnor, mocking his name by calling him an "Egnoramus" who writes "EgnorRants" and using post titles like, "Egnorance: The Egotistical Combination of Ignorance and Arrogance." In fact, Darwinist attacks upon Egnor are nothing new. Last summer a Darwinist wrote that "Michael Egnor is a Crappy Neurosurgeon Who Will Cut out Your Brain and Eat It," and compared Egnor's arguments to taking "a big ol' steaming s*** on a piece of paper and want[ing] that taught as science." More recently, Egnor pointed out the viciousness of Darwinist attacks upon Michael Behe. Egnor was then greeted with telling replies from Darwinist commenters on PZ Myers' blog who wrote things like: "let me say,as [sic] gently and politely as possible, that on this Egnor is full of s***," and "if idiots couldn't weather having their idiocy pointed out to them, they wouldn't BE idiots now, would they." Yet for all their numbers and name-calling, not a single one has answered Egnor's question: How does Darwinian mechanisms produce new biological information?

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In the end, I can cheerfully forgive Kevin Beck, but two questions remain: (1) Why is such name-calling so common among Darwinists? and (2) How do Darwinian mechanisms produce truly novel biological information? I've seen no good answers to question 2, and perhaps their lack of such a good answer is driving the observations behind question (1).

This is an interesting tactic. Apparently we "Darwinists" (along with the "Newtonists" and "Einsteinists") have to tolerate stupid questions that are restated over and over again, answered over and over again, and ultimately ignored only to be asked over and over again. This is the problem with Denialists, and is criteria #4, the impossible expectation. What can we do other than point them at the talk origins page and say again, your question has been answered?

But it is pointless, because the point of being a denialist is that no answer will ever satisfy them. They do not care about data, they do not care about evidence, they do not care about advancing a theory that will improve human understanding. They only want one thing, everyone to believe what they believe.

And this is what irritates me the most about denialists like Egnor and Luskin. The deception. They're just liars. The whole DI is just a front for introducing religion in the name of science. The whole reason they get called names is because everyone knows they're just liars that are trying to create confusion and doubt about real science. Hell, Judge Jones said it best in Dover vs. Kitzmiller (From the Wiki:

"For the reasons that follow, we conclude that the religious nature of ID [intelligent design] would be readily apparent to an objective observer, adult or child" (page 24)

"A significant aspect of the IDM [intelligent design movement] is that despite Defendants’ protestations to the contrary, it describes ID as a religious argument. In that vein, the writings of leading ID proponents reveal that the designer postulated by their argument is the God of Christianity." (page 26)

"The evidence at trial demonstrates that ID is nothing less than the progeny of creationism" (page 31)

"The overwhelming evidence at trial established that ID is a religious view, a mere re-labeling of creationism, and not a scientific theory." (page 43)

"Throughout the trial and in various submissions to the Court, Defendants vigorously argue that the reading of the statement is not “teaching” ID but instead is merely “making students aware of it.” In fact, one consistency among the Dover School Board members’ testimony, which was marked by selective memories and outright lies under oath, as will be discussed in more detail below, is that they did not think they needed to be knowledgeable about ID because it was not being taught to the students. We disagree." (footnote 7 on page 46)

"After a searching review of the record and applicable caselaw, we find that while ID arguments may be true, a proposition on which the Court takes no position, ID is not science. We find that ID fails on three different levels, any one of which is sufficient to preclude a determination that ID is science. They are: (1) ID violates the centuries-old ground rules of science by invoking and permitting supernatural causation; (2) the argument of irreducible complexity, central to ID, employs the same flawed and illogical contrived dualism that doomed creation science in the 1980's; and (3) ID's negative attacks on evolution have been refuted by the scientific community." (page 64)

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"ID’s backers have sought to avoid the scientific scrutiny which we have now determined that it cannot withstand by advocating that the controversy, but not ID itself, should be taught in science class. This tactic is at best disingenuous, and at worst a canard. The goal of the IDM is not to encourage critical thought, but to foment a revolution which would supplant evolutionary theory with ID." (page 89)

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Judge John E. Jones III issued the decision in the case

In his Conclusion on pages 136-138 of 139 of this decision he writes:

The proper application of both the endorsement and Lemon tests to the facts of this case makes it abundantly clear that the Board’s ID Policy violates the Establishment Clause. In making this determination, we have addressed the seminal question of whether ID is science. We have concluded that it is not, and moreover that ID cannot uncouple itself from its creationist, and thus religious, antecedents. […]

The citizens of the Dover area were poorly served by the members of the Board who voted for the ID Policy. It is ironic that several of these individuals, who so staunchly and proudly touted their religious convictions in public, would time and again lie to cover their tracks and disguise the real purpose behind the ID Policy.

There you have it. The real problem we have with the creationists at DI and other proponents of ID is that they are a bunch of lying denialists. They lie and lie and lie, and spew BS all the time, and every effective rebuttal is ignored.

So don't get upset if Casey Luskin cries foul, it's not like they can argue substance over style. He's a denialist, a liar, and there is nothing you can do about it. Just call him a denialist and forget about it, nothing else can reasonably be done. And if denialists don't want to be called denialists, then they need to stop making arguments that are denialist.

Labels: Casey Luskin, Discovery Institute, Evolution denialism

It's amazing how far they'll go to miss the point, these evolution denialists. Take this read of J. Craig Venter's paper in PLoS Biology of the Sorcerer II Global Ocean Sampling Expedition from Jonathan Witt.

"In addition to increasing substantially the size and diversity of these families," the article reports, "the GOS sequences increased the understanding of the evolution and function of these proteins" (emphasis mine). The article offers a repair protein by way of illustration:

One example is those that repair DNA damage due to UV light (photolyases). While sunlight has benefits to the microbes, like with humans, sunlight also has the potential to be harmful to cells exposed to it. The team discovered many new proteins that protect these organisms from UV ray damage and some that are involved in repairing UV damage. These proteins were found in all organisms in the dataset, even in viruses.

So where is the evidence of a gradually evolving UV-Ray-Damage-Repairing protein? How does this increase our understanding of the evolution of these proteins from fundamentally different proteins? It seems to suggest that everywhere we look in the biological world, the UV-ray-damage-repairing proteins are always already up and running at full speed. Perhaps we are learning that the evolutionary process in such proteins is like the singing frog from the Looney Tunes cartoon, the one who would never sing when there was an audience.

Wow. Talk about missing the point. So for those who don't know, Venter is the guy who used to be Pres and CEO of Celera Genomics, the company that developed shotgun sequencing and raced the Human Genome Project towards sequencing the complete human genome (although they ultimately collaborated). Now that that's over, Venter is just ridiculously rich, so he sails around on a yacht collecting samples from oceans around the world, filtering the samples from various depths by size, then shotgun sequencing the genomes that come out of his filters. They can essentially filter viruses, bacteria, and larger multicellular organisms and then shotgun sequence. This allows him to accomplish two main objectives:

1. Create a baseline of the biocontent/biodiversity of different regions of oceans.
   
2. Allow them to discover thousands of new genes.
   

One of the things I learned about the ocean from reading about Venter's little quest is that it is literally teeming with life. It is essentially soup. Every milliliter is chock-full of billions of bacteria, viruses and other tiny little organisms. It's fascinating stuff, and fits with the idea that life began in the sea. But what does the creationist take out of this? That because they didn't explain all of evolution in a sequencing survey of the oceans, they can't talk about evolution at all. This is interesting. Apparently, now, all biologists, in order to be fair to denialists, are no longer allowed to assume evolution created life when discussing their research!

This is fascinating. I don't even know how to characterize this. Is this impossible expectations? Logical fallacy? It's a little mind-boggling. I'm going to go for straw man at the moment, because the argument rests on the assumption that this survey should have shown every transitional protein on the way to the final evolved form as part of a survey of genes. But also, impossible expectations because this is the first time anyone has ever even looked at this stuff and they're supposed to explain the entire evolutionary history, in a single paper?

Labels: Evolution denialism

Oooh, anyone want to go with me to this Answers in Genesis Conference in may? Topics include:

Ken Ham: Dinosaurs, Genesis, and the Gospel
Ken Ham: Genesis: Key to Reclaiming the Culture.
Danny Faulkner: The Origin Of Science And It's Biblical Basis

I will never understand this obsession this guy has with the book of Genesis. Beyond the biblical literalism problem, why this book? If you ask me, the books of the old testament in general aren't the kind of thing anything in their right mind would like to base their culture on. God himself didn't seem to know what he was doing in those books. And the origin of science in the bible? Not, you know, the Greeks? Sounds like fun though.

Labels: Evolution denialism, Ken Ham

Darwin was apparently a racist, eugenicist jerk. Sigh.

I'm not bothering with this one since PZ destroys the argument.

I will just point out the two denialist aspects of these non-arguments.

1. Selectivity: This is quote-mining and using statements out of context as PZ demonstrates. They even have one they like that suggests Darwin beat puppies for fun, I shit you not.
   
2. Logical Fallacy: The Red Herring seems most obvious. Darwin's personal life or beliefs have little to do with scientific fact. This would also easily qualify as poisoning the well.
   

It's pathetic to see what the creationist denialists think should pass for argument.

Labels: Evolution denialism, uncommon descent

Posting at the DI Michael Egnor, their new pet surgeon, ravages the "Darwinists" (who are these "Darwinists" anyway) for their apparent uselessness in understanding the evolution of microbial resistance to antibiotics.

Darwinists claim that Darwin's theory, which is the theory that all biological complexity arose by random variation and natural selection, is essential to our understanding of bacterial resistance to antibiotics. What exactly does Darwinism teach us about antibiotic resistance?

Microbiology tells us that bacterial populations are heterogeneous. Individual bacteria differ from one another. Molecular biology tells us that some bacteria have molecular mechanisms by which they can survive antibiotics. Molecular genetics tells us how these resistance mechanisms are passed to other bacteria and through generations of bacteria. Pharmacology helps us design new antibiotics that circumvent the bacterial defenses.

What does Darwinism add to the sciences of microbiology, molecular biology, molecular genetics, and pharmacology? Darwinism tells us that antibiotic-resistant bacteria survive exposure to antibiotics because of natural selection. That is, bacteria survive antibiotics that they're not sensitive to, so non-killed bacteria will eventually outnumber killed bacteria. That's it.

Microbiology, molecular biology, molecular genetics and pharmacology are indispensable to modern medicine. We've learned much about intricate bacterial defenses against antibiotics, and we've developed hundreds of antibiotics that have saved millions of lives. What has Darwinism added to these miracles? Just this: non-killed bacterial eventually outnumber killed bacteria.

It's funny how they insist on calling biologists Darwinians, it's like calling a physicist a Newtonian, or a Copernican.

Anyway, let's determine the Denialism Score for this particular anti-evolution argument.

1. Conspiracy: None alleged here, other than the subtext of the materialist "darwinist" view being out to subvert religion in all ways.

2. Selectivity: I think ignoring the facts that microbial resistance has taken decades to evolve would be a pretty simple example of the selectivity of this argument. If these bacterial resistance genes have always been present in bacterial populations, why has it only been in the last 20 years that bacterial resistance has become a major problem? Why didn't the beta-lactamase resistance genes appear immediately upon use of penicillin and make the drug rapidly worthless? To believe this requires one to ignore the available evidence and dismiss the natural history of bacterial resistance to antibiotics.

3. False Experts: Well he is one, so that's covered.

4. Impossible Expectations/Moving Goalposts: Perhaps the expectation in the article that "Darwinism" should fly in the window and cure patients if it is to be useful could count as an expectation that's impossible.

5. Logical Fallacies: Well, these are abundant. I'd say he's got red herrings, and straw-men galore.

So I give Egnor about a 4/5 on the Denialism scorecard for this.

Labels: Evolution denialism, Michael Egnor

Let's help Coturnix label the Discovery Institute's latest shill, Dr. Michael Egnor, as he really is, a creationist hack. Want to read about Egnor? The links below should provide a clue to the legitimacy of the DI's latest screwball doctor.


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Labels: Evolution denialism, Michael Egnor