Can your respect for Geoffrey Simmons plummet a little lower?

Fresh from his recent reappearance on KKMS, where he debated me with a new strategy which gave him a slight chance of winning (i.e., one in which I was not present), Geoffrey Simmons is now crowing victory. It’s very strange. Why would anyone with any sense think that demanding a ‘debate’ in which one is unopposed and has a sympathetic moderator and which suppresses audience input is in any way anything but an act of cowardice and intellectual bankruptcy?

This is posted on Evolution News and Views, the Discovery Institute’s version of Pravda, but since they don’t bother to link to any of my articles to which they specifically refer, and since they don’t take comments themselves, I see no point in linking to them. Here is the complete text of Simmons’ vainglorious howl of triumph.

Against Stupidity, God Himself Is Helpless – Old Jewish Proverb

Before the recent KKMS (MN radio) debate, Dr. P.Z. Myers blogged on Pharyngula that he would decimate me. Within minutes of the show’s conclusion, he blogged that he accomplished his goal, never conceding a single point from an hour long show. It is worth one’s while to read his blogs and those that follow as they readily speak to the character of these folks, much moreso than I could ever do. Richard Dawkins was also quick to compliment the professor and add to the feeding frenzy. Again, no concessions. They had their hearing aids turned off before the show even started.

Other than winning points for outright rudeness and making up fiction, what part of the debate did this tax-paid professor win? Could it be the five or so fossil pieces from dog-size animals that represent intermediate species between land animals and the quadrillion-cell whale with unexplained tons of blubber, communication skills that span thousands of miles, a windpipe separate from the esophagus (unheard of in land animals), segmental decompression, a heart the size of a Volkswagon, ability to dive thousands of meters deep or eat a krill diet? Or, was it the fact that a sperm and egg cell can unite to form a 10-75 trillion cell human being without going through 10-75 trillion trial and errors? Perhaps it was my misunderstanding of their ways of critiquing the theory of evolution? To me, it’s like having your brother correct your homework. Lastly, where is the rule that says one has to have an alternative and provable explanation for the origin of life before one can criticise Darwinian thought? Cannot a child point to the leaks in a dam and warn people of an impending flood without any knowledge about dam construction? Their rule, this requirement, doesn’t exist.

– Geoffrey Simmons, M.D.
Author of What Darwin Didn’t Know and Billions of Missing Links

So much, so wrong.

We all had our hearing aids turned up, I assure you. How else could we laugh at Dr Simmons’ remarks?

For a perfect example, look at his claims here: he claims the whale fossil series consists of “five or so fossil pieces from dog-size animals”. Go ahead, look at any summary of the fossil evidence for whales; there are far more than 5 pieces, and the size of the animals ranged from a 100 pound deer-like beast to, well, whale-sized. You can also find nice diagrams of nasal drift — remember, Simmons claimed there was no evidence of blowholes in the fossils. There were no concessions to Simmons because Simmons was wrong on every point.

I’ve read his books, and as usual, he resorts to the litany of complexity to make his case. He doesn’t stop to consider how all that complexity arose, just its existence is all he uses to claim justification for his claim of Intelligent Design creationism. That doesn’t fly, Dr Simmons. We have mechanisms that generate such complexity and refine noise into functionality that do not require intelligent intervention. Sure, single-celled zygotes develop into organisms with many trillions of cells. We can study that and find lovely developmental mechanisms behind it; we can watch mitoses occur; we can find the molecular interactions that lead to differentiation. Telling me that there are lots of cells there does not support your apparent contention that they all poofed into existence with the assistance of a meddling cosmic superbeing, either phylogenetically or ontogenetically.

Oh, and little children who call up the National Guard and demand that we evacuate the town because the dam is leaking when they’ve never seen the dam, know nothing about how the dam is constructed, and have no evidence that it is leaking other than that the crotch of their pants are suddenly wet, are not brave heroes. They’re petty liars seeking attention.

The controversy expands

Our little grievance with a certain paper in Proteomics has made it to the attention of the Chronicle of Higher Ed. Some of the new info (there isn’t a lot) is right here:

Michael J. Dunn, the editor of Proteomics and a professor at University College Dublin’s Conway Institute of Biomolecular and Biomedical Research, told The Chronicle that “it’s not our policy to promote creationism” and added that the journal might retract the article.

As was the case with a less-well-known journal that inadvertently published a creationist paper (The Chronicle, September 24, 2004), the paper in Proteomics had passed peer review. In fact, one of the reviewers for the mitochondria paper, said Mr. Dunn, “does a lot of reviewing for our journal.”

Maybe they ought to lighten that reviewer’s workload, because something slipped by him or her. Or maybe, as some have speculated, something got inserted after the review.

Gonzalez goes down

Guillermo Gonzalez’s appeal of his tenure denial went before the Iowa State University board of regents this morning.

To no one’s surprise, his appeal was denied. Seriously, this was a no-brainer; it would have been grounds for suspicion if the board of regents had overruled the opinion of his peers to force Gonzalez on the physics and astronomy department.

Now Dr Gonzalez needs to quit trusting the blandishments of the Discovery Institute and get to work on reconstructing his career. Peter Irons wrote me this morning and asked what odds I’d give on Gonzalez getting tenure; I’d have said they were incredibly long. Now the next question for the betting people out there: what are the odds that he’ll revise his tenure strategy to land a job with academic credibility vs. taking the easy way out and going to some joke of a Bible college and trying to get rich off his ‘martyrdom’?

A sloppy simulacrum of science

Go read this first rate summary of an ID meeting by one of its unsympathetic attendees. It’s genuinely bizarre. The talks by the ID proponents are frankly, complete garbage (not that the account is that blunt), which explains the message everyone got afterwards.

A few days after the meeting ended, we all received an email stating that the ID people considered the conference a private meeting, and did not want any of us to discuss it, blog it, or publish anything about it. They said they had no intention of posting anything from the conference on the Discovery Institute’s web site (the entire proceedings were recorded). They claimed they would have some announcement at the time of the publication of the edited volume of presentations, in about a year, and wanted all of us to wait until then to say anything. These actions made me aware of the extent to which the ID movement was willing to bear false witness in order to achieve its goals, and that kept me from falling prey to my empathy for the underdog.

A stealth science meeting? I’ve heard of requests to embargo discussion outside of a meeting until publication — which is reasonable, since many journals are jealous entities who demand that their submissions be virginal and unpublished anywhere else — but that’s not the case here. After reading the account, it’s clear that they’ve got no science and bad science, and really just want to control the release of information, so they can massage their PR and generate false impressions of scholarly work.

[Read more…]

Is that David Horowitz I smell?

The beautiful state of Washington, my native home and still home to many of my family members, has some people ready to enact some major legislative stupidity. David Horowitz was a right-wing nut who was making noise a few years ago with his witch hunt for evil leftists (Hi, Michael!) and his promotion of an Academic Bill of Rights, which was basically a ham-handed attempt to force academia to grant special privileges to intellectually bankrupt ideas, all under the guise of “fairness”. The Washington bill reeks of that familiar stench.

This bill aims to impose the ideological biases of ignorant politicians on the curricula of the state’s universities. It claims to be about “intellectual diversity,” but it’s really about stripping intellectual responsibility from the hands of professors. You can read the whole thing, but as an example of the kind of superficial promises the bill wants to make, but which do little more than corrupt the integrity of the classroom, look at this clause:

Develop a procedure in which a student may present his or her objection to a classroom assignment due to its opposition with the student’s conscience.

What, exactly, is a student’s conscience here? Well, if a UW biology professor tries to demand her students understand the mechanisms of evolution, a creationist student could formally demand accommodation for his beliefs. A chauvinist in a feminist history class could demand a better grade for his paper claiming that women have been oppressing him because they keep turning down his demands for dates. Basically, it throws the doors wide open and allows students to turn their subjective, poorly formulated, or even falsified “objections” into legitimate excuses to subvert the classroom…which is exactly the intent of deranged ideologues like Horowitz.

I know some Washington state residents read this blog. Get on the phone or email to your representatives and tell them that SB 6893 is a disaster in the making and that they better not support it. In particular, if your rep is on the Committee on Higher Education (which contains two of the sponsoring senators, unfortunately — Shin and Delvin) make sure to voice your displeasure and let them know that anyone who supports this abomination of a bill is no friend to higher ed.

I am amused

Poor Geoffrey Simmons, so painfully pathetic. He’s back on KKMS right now, given an hour where there isn’t one of those wretched evolutionists to point out the absurdity of his comments. So far, all he’s doing is giving a litany of complexity — the eye is so complex, and the eyes are at the top of your head to give you the best visibility, and they’re exactly the right distance apart to give you binocular vision. It’s painfully panglossian and naive.

Oh, and he snipes at the ‘experts’ and claims that the ‘Darwinists’ don’t understand the complexity of childbirth, unlike him, the MD. Good grief, I’m a developmental biologist!

You can tell that without me there he’s feeling free to make up even more lies, not that he was significantly inhibited the last time he was on.

Hmmm…should I suggest that maybe they should give me a solo hour on air too, to discuss what evolution and biology are actually about? I doubt that they’d take me up on it; they’re clearly desperate to make up for their embarrassment last week by giving Simmons a little uncritical bootlicking, and they would feel no such obligation to me.

Go ahead, call in at 651-289-4499 and let them know how tiny and frightened this makes Simmons look.

Now I know how Jesse James felt

Suddenly, lots of people want to debate me. I’m really not that much into the debate business, and I think most of the people who want to battle me don’t need a high-level argument about biology — they need a remedial course in elementary science. Especially since most of the challenges are rather like this one:

http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=47a2cb894dc2340b;act=ST;f=14;t=1274;st=24870

Note that the drooling animals are clamoring for P.Z. Myers and Dembski to have a “debate.” What is to debate? Myers is a rabid mad man, completely out of control. His condition is progressive, irreversible, incurable and hopefully terminal.

Besides, Myers is an intellectual coward and won’t “debate” anyone of substance. Neither will Dawkins nor Hitchens. The word “debate” doesn’t even exist in the lexicon of science. It is reserved for lawyers, politicians and evangelists.

Myers immediately retired from the contest at “One Blog A Day” after arrogantly introducing his “Pharyngula” thread with much fanfare, leaving Martin and I with the wonderful opportunity (which we thoroughly exploited) to reduce the Darwinian hoax to a shambles. I sure hope someone preserved it because it is gone now.

I would love to confront him anywhere, with or without his equally deranged cronies – Dawkins and Hitchens. It would be a rout! I can’t even goad them into recognizing my existence. Myers is a cowardly victim, a “prescribed” vendor of hate, the epitome of cultural, moral and ethical evil. There is nothing that can be done for him or for his colleagues and followers. They are “born that way” losers in the lottery of life. Until they are gone they will remain a menace to Western Civilization. Hopefully that won’t take too much longer.

It is hard to believe isn’t it?

“A past evolution is undeniable, a present evolution undemonstrable.”
John A, Davison

Sorry, John, I do have standards, and I don’t debate the mentally ill and logically incoherent (really, read what you write. You sneer that “debate” isn’t in the lexicon of science while you challenge me to a debate. Think about it.) (Oh, wait, never mind. The irony of your challenge is so bold that it is clear that you don’t read your own words, and you definitely don’t think.)

And I’m currently scheduled to debate Angus Menuge of the DI this spring. I’ve already agreed to talk with one droning bore of a theologian, why should I also meet with Dembski?

P.S. Any of you drooling animals who wants to comment on this faces a challenge: Davison is banned here, as are his numerous pseudonyms, so you’re going to have to be circumspect lest you invoke his name and your comment ends up awaiting moderation.

A baffling failure of peer review

A dismaying update: the paper in question contains a significant amount of outright plagiarism, and large chunks of text are taken literally from Butterfield et al. 2006, “Oxidative stress in
Alzheimer’s disease brain: New insights from
redox proteomics,” European Journal of
Pharmacology 545: 39-50. I hope we hear from Han and Warda sometime; they’ve got a lot of ‘splaining to do.

Mitochondria are fascinating organelles. They are the “powerhouses of the cell” (that phrase is required to be used in any discussion of their function) that generate small, energy rich molecules like ATP that are used in many cellular chemical reactions, but they also have important roles in cell signaling and cell death. They also have a peculiar evolutionary history, arising as endosymbionts; their ancestors were independent organisms that took up residence inside eukaryotic cells in a mutually happy and long-lasting relationship. They exhibit some interesting relics of that prior history, as mitochondria have their own private strand of DNA which encodes some of the genes needed for the chemical processes they execute. Other genes for those functions have migrated over evolutionary time into the nuclear genome, which means the mix of gene products operating in the organelle are from two sources, the mitochondrial and nuclear genome. It’s a good subject for studies in proteomics.

Right now, there is a paper that is available as an Epub ahead of print in the journal Proteomics. It is not promising. In fact, all you have to do is read the title to make you wonder what the authors, Warda and Han, were smoking: “Mitochondria, the missing link between body and soul: Proteomic prospective evidence.”

Attila Csordas asks, “Can you tell a good article from a bad based on the abstract and the title alone?”, and I’m inclined to say yes. Sometimes you get pleasant surprises in the full paper that were not well described in the abstract, but when the abstract and title contain hints that the bridge is out and that somebody has switched the train to the wrong tracks, you can predict that there will be a train wreck if you read further. Here’s the abstract. I’ve highlighted one provocative statement.

Mitochondria are the gatekeepers of the life and death of most cells that regulate signaling, metabolism, and energy production needed for cellular function. Therefore, unraveling of the genuine mitochondrial proteome, as the dynamic determinant of structural-functional integrity to the cellular framework, affords a better understanding of many still-hidden secrets of life behind the already known static genome. Given the critical mitochondrial role under different stress conditions, the aim of the current review is to merge the available scientific data related to mitochondrial proteomes and frame them into a reliable new agreement extending beyond the limited already accepted endosymbiotic hypothesis into broader fundamental mechanisms orchestrating cellular outcome on behalf of cell survival. The focus of this work is to cover first the mitochondrial proteome/genome interplay that is currently believed to be implicated in a range of human diseases. The mechanochemical coupling between mitochondria and different cytoskeleton proteins and the impact of the mitoskeleton on mitochondrial structure and function are then addressed. Further crosstalk between mitochondria and other cellular organelles, e.g., the ER and the nucleus is then discussed. Additionally, the role of mitochondria in apoptosis and the mitochondrial contribution in intercellular communication mediated by gap junctions are also described. These data are presented with other novel proteomics evidence to disprove the endosymbiotic hypothesis of mitochondrial evolution that is replaced in this work by a more realistic alternative. Furthermore, the role of mitochondria in development of oxidative stress-based diseases, e.g., neurodegenerative and cardiovascular diseases is pointed out together with the prospective proteomics view as an alternative prognostic and diagnostic tool for interpreting many mitochondria-related anomalies. The insights generated by recent proteomic research that provide a rational impact on possible mitochondrial-targeted therapeutic interventions are also discussed.

My blog makes a career out of describing train wrecks, so how could I not continue on and read the paper?

[Read more…]