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?

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As Morris goes, so goes the nation

Turn off your TVs. Don’t bother watching the election coverage. I know you’ve all been wondering how little rural Morris, Minnesota, population 5000, would vote in the super Tuesday voting.

Turnout was heavy, with between 400 and 500 people showing up for the caucus, and the results were … (drumroll, please) … about 2:1 in favor of Barack Obama. A landslide victory!

The full, final, official tally for Morris:

Biden 1 0%
Clinton 139 26%
Dodd 0 0%
Edwards 8 1%
Kucinich 2 0%
Lynch 1 0%
Obama 387 72%
Richardson 0 0%
Uncommitted 2 0%

We had a turnout of 540 people, over 10% of the residents of the town. For a caucus. The Democratic base is motivated and ready to get out and change things. Now all we have to do is get the Democratic leadership to go along.

They’ve settled on a name…

…and now they just have to sign the prenup (there is a prenup, right?). Shelley and Steve are merging their two blogs as of early March, and they’ve picked one of the names one of you perspicacious readers suggested.

(I would have just said “This is madness!”, but then Shelley would have kicked me down a well. And they apparently did not like my suggestion of “Food for the Worm. Hmph.”)

Do you like your science snarky?

Sure you do. So you might enjoy this webcast series from Scientific American.

One of the things they mention is the recent “peer-reviewed” “scientific” “journal” from Answers in Genesis (sharply slammed by Larry Moran), and they criticize Nature‘s coverage, which urges scientists to avoid taking “too strong a stance against the journal” because it would “fuel creationist’s claim of scientific bias against religion.”

This is what always happens when you go to appeasers for quotes: you get urged to be a coward in dealing with the opposition.

In which I am criticized

I appreciate sincere criticism, I really do, and despite all the praise for my recent radio debate, I listened to it and mainly heard a lot of things I could have done better. So I like it when I find someone who also offers suggestions for improvement, but at the same time, I have to disagree with one (just one, the others are good) central point he makes.

However, in the future I would warn PZ against calling his opponent ignorant or berating them in a debate like this. Save that kind of stuff when you’re venting to your fellow smart people. Name calling doesn’t convince any of the audience and it gives your opponent a chance to get off the ropes through subversive rhetoric. Using the term “ignorant” allowed Simmons to take the upper hand and make PZ look like a dick even though he was right in pointing out Simmons’ lack of knowledge. Or at least, it would have allowed Simmons to take the upper hand if he didn’t suck so much. In essence, don’t attack the opponent, attack the opponent’s ideas.

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Let us pray

i-694592ab1c79d8dcf9596842757bc6fe-cig_prayer.jpg

Just the title of this book is good for a laugh: The Complete Idiot’s Guide to Prayer. They’ve certainly got their target audience pegged.

As an added bonus, the reviews are amusing.

Have reviewed a number of books on prayer and they usually get too complicated and bogged down.

“Close your eyes and pretend” is too complicated? Are there rules and regulations and rituals that must be performed for this prayer thing that are baroque and beyond my understanding, or is this reviewer the kind of person who finds swallowing to be an act of will that requires concentration and practice?

I just recently returned to my Christain roots and the Complete Idiot’s Guide to Prayer helped answer a question that many of us are afraid to ask; “How do you pray?” I’ve seen it done hundreds of times but it’s all so mysterious. This book explains a variety of options to mix it so that prayer doesn’t become a chore.

I’ve seen it done, too, and no, it isn’t mysterious. People just talk to themselves, silently or aloud. It isn’t hard. It also doesn’t work. But it’s that last line that I found weird.

These people supposedly believe they have a direct, personal relationship with the Supreme Omnipotent Overlord of the Universe, and not only that, but he loves them and is deeply interested in the tawdry minutia of their personal lives. Yet they can consider having a conversation with such a being a “chore”? If such a being existed, and if I were able to talk with him, ask questions, and get answers, I’d be online with the big guy all the time and asking all kinds of questions. He’d be better than Google!

Of course, if he were a colossal tyrannical jerk who refused to answer any of my questions, then I’d consider it a chore. I’d also stop calling him up.

But then, I’m an atheist, and I’m smarter than they are — the Bible says so.