The hilarity of this post is hard to ignore. Cordova is actually trying to give the ID creationist movement credit for the discovery that "junk" DNA has lots of functions (as well as suggest that acknowledgement by Sternberg in a review article is some how proof of ID science).

That's an interesting suggestion. I'll have to figure out how to get on this scam, you know, making vague statements then taking credit for others' work. Like, I could say, "we don't know everything about non-coding DNA, there must be something as yet undiscovered" then when they discover something new like miRNA or retrotransposons I can demand my Nobel even if contributed nothing.

Never mind the importance of actually doing benchwork, I can just say my BS theory predicts this or that, and then when other people discover anything I get to claim victory. That's a brilliant idea. It apparently also works when one makes the claim about a decade after the discovery, you see in reverse-vampire conspiracy world, the DI and ID always existed and were always right. Anyway, here's a simple image of what we know about the DNA in a human cell.



As you can see, we've figured out a lot of what that "junk" is, and considering introns were discovered in 1978, promoters were hot stuff as early as the mid-eighties, transposons were discovered in the 50s in corn resulting in Barbara McClintock's 1983 Nobel, and retrotransposons and various other repeat elements that have undergone recent hot study were really discovered as a result of the Human Genome Project which began in the early 1980s it's pretty much insane for the DI to suggest that they had any impact on this science. The sheer arrogance of it is actually pretty extraordinary.

It's also an interesting claim that missing out on the functions of "junk" DNA was the greatest mistake molecular biologists have ever made. And was it ever really a mistake that a majority of us made? I remember back when large portions of DNA were found to be non-coding, not everybody thought that meant they served no purpose. Hell, our lab has been studying that junk for about 20 years looking for things and finding lots of interesting and important pieces of non-coding DNA. To say that it wasn't until the DI or ID showed up that scientists started looking at noncoding DNA is a joke. This has been a hot pursuit for decades. It's almost as funny as when they claim evolution isn't important for molecular biology. In the last 3 days we've had a bunch of talks from visiting researchers, and in every single one they mentioned evolution as a guiding principle in figuring something or another out. I guess I've been more attuned to it lately. For example, in pretty much every talk I saw the researchers used VISTA for conservation analysis of non-coding DNA regions. It's a wonderful program. You enter regions of genomic DNA and it aligns them and shows you areas of conservation. It turns out the areas that are mostly highly conserved across species are usually where the important gene-regulatory cis-elements are. Take for example this little alignment I just did of human, mouse and chicken smooth muscle alpha-actin promoter sequences.



What this shows us is the conservation of sequences between the three species in the sequence immediately preceding the smooth muscle alpha actin coding sequence. The closer the line is to the top - or 100% conservation - the more the sequences have stayed the same over millions of years of evolution. It's helpful because it points to what is important for gene regulation. A promoter might have an element 30 thousand bases away that is critical for regulation of a gene, all the intervening sequence might be completely unimportant, and VISTA will show you essentially what selection has deemed important enough not to change.

Interestingly, when the mouse actin promoter was first put into a transgenic mouse with a reporter gene on it, they only included the first few hundred base pairs (where most the conserved elements and CArG binding sites are), because in tissue culture that was enough to drive expression. However, in the animal, the thing didn't work, the reporter didn't get expressed where smooth muscle actin was. So, our lab looked both forwards and backwards through the promoter and gene and found not only did you see conservation of a elements -2.6kb back (in mice and rats, but not in chicken), but you also had a conserved CArG element in the first intron. We then cloned this sequence that included the -2.6kb and the first intron (out of the rat actually), put the reporter gene on it, and voila, beautiful recapitulation of the expression of smooth muscle alpha actin in the mouse.



The other interesting thing our little Vista plot shows us is that huge portions of sequence still appear to be "junk", that is, they don't appear to do anything, and nature hasn't seen fit to conserve them across species. Often times, researchers create artificially short promoters that take the various conserved regions and cut out thousands of intervening base pairs and they recapitulate endogenous expression perfectly. So to say that "junk" DNA doesn't exist, is well, still unfounded, especially considering papers such as this one in which researchers demonstrated entire megabase regions of DNA could be deleted from the mouse genome, with no ill effect. One day we might figure out a use or reason for so much extraneous DNA, but to say the "junk" hypothesis has been fully disproven is still unfounded, almost as unfounded as suggesting ID had anything to do with discovering additional functions in non-coding DNA (like scientists really sit around reading the output of the DI for anything but laughs).

Also what's this bizarre need for design to mean that everything has a specific function? Aren't we biasing our supposedly non-Christian, or non-deity based "scientific" theory towards a perfect creator? After all, why can't the Raelians be right? Maybe we were designed by imperfect aliens who weren't paying too much attention to the details, or had problems with foresight? And what kind of designer would create our system of cranial nerves? What a complicated inelegant train wreck those are. Why would a competent designer make sure childbirth was so painful and dangerous? What kind of idiot made our urogenital system in general? Reproduction and waste disposal using all the same equipment? Why do men get nipples? What idiot designer would make our terrible system of sinuses. Why does their designer theory need everything to fit into its specific cubby-hole? Why couldn't there be waste, inefficiency, redundancy and mistakes in their designers plan? There's a good explanation for why evolution by natural selection would come up with such inelegant solutions, they just had to work, they didn't have to be pretty. But why would a designer, especially a perfect one, screw these things up?

It's one of the signs of the underlying assumption of ID, and one that the IDers are continuously deceptive about. There is only one possible designer they are interested in pushing, and their assumptions how a designer would operate are the proof. They know which designer they're trying to justify. The fact they won't acknowledge that it's specifically the god of the bible they're pushing as designer is just more proof of the fundamental deceptive nature of the DI.

Labels: Sal Cordova, uncommon descent

Who would say that?why Dave Scot at Uncommon Descent of course.

Well, it started already. Shifting economic priorities from food production to reducing CO2 emission has already started causing significant problems. The environmentalist whackos are at it again. Evidently unsatisfied with derailing nuclear power plant construction in the United States 30 years ago, a whackjob by the whackos that has gotten us into the foreign oil dependency mess we're in today instead of getting most of our electricity from nuclear power like France, their latest stupid panic is going to lead to the starvation of hundreds of millions of people. I don't often laud the French but they at least got their ducks in a row with nuclear power and the U.S. could have too if we'd had the good sense to ignore the environmentalist whackos. Will we never learn?

Yes, what a horrible thing we didn't ignore the environmentalists. Think about how much better we'd be without the clean water act, why, it's been years since we've had a nice beautiful fire on the Cuyahoga river. When was the last time? 1969? And that completely retarded clean air act? I liked leaded gasoline and acid rain, it gave buildings such character, and city air such an wonderful tinge of homey emissions.

Besides being just an appeal to consequences (although not in a direct attack on the science), this is once again an example of the "environmentalists will eat your children" canard. If any other demand had caused a market to create a increase in the cost of food, that would just be capitalism. But when concern from the environment does it? It's a holocaust! Millions will die! Environmentalists will eat your children!

What a load.

Labels: Dave Scot, global warming denialism, uncommon descent

So, who else has heard of the latest conspiracy of the big bad medical research community - DCA?

The thing is some researchers at the University of Alberta published this paper showing that, in rats, DCA could shrink tumors by forcing them to switch their energy metabolism from glycolysis (which tumors tend to rely upon) to glucose oxidation, while largely not affecting normal cells. The result? The tumors proliferated less, underwent greater apoptosis and essentially shrank. A nice promising little result.

The problem was, as frequently occurs with the lay press, they made a huge deal out of a chemical that was essentially only shown to be efficacious against cancer in an animal model of tumor growth. Not that this is a bad thing, but there really needs to be more testing before you start throwing a potential neurotoxin at thousands of cancer patients. But that didn't stop the cranks from coming out of the woodwork, and of course, the quack sites immediately appeared to start selling this with completely inadequate knowledge of the chemical's effect in humans. And the conspiracy-mongers started coming out of the woodworks, sheesh. Orac probably has the best coverage in concert with Abel Pharmboy on the subsequent DCA hysteria and talk of how it will never be researched because evil scientists won't research things unless it makes them money, yada yada yada.

One study of a model of cancer in "nude" athymic rats, animals that have no immune system so that human tumor lines can be studied inside an organism, and people are rushing to take this stuff. And who is egging them on? None other than universal crank Dave Scot at Uncommon Descent.

To date there has still been no start of an FDA-approved clinical trial so it looks like the conspiracy theorists were right - DCA is a common chemical that has no profit potential for big pharma so even though it shrunk several different types of human tumors in immuno-compromised rats 75% in 3 weeks with no adverse side effects, and even though it's been used for decades in humans in treating chronic lactic acidosis so its safety was already well characterized in humans, no one will put up the hundreds of millions of dollars to test its efficacy as a chemotherapeutic for cancer.

This is where denialism and cranks get really ugly - when their disregard for science, careful study of biology, and cautious advance of scientific knowledge leads them to suggest people at their most desperate potentially poison themselves.

DCA may turn out to be a wonder drug. There are signs, however, it is quite dangerous to take, and Dave Scot and other cranks that are pushing this conspiracy theory are essentially encouraging people to take this drug without the proper supervision they would undergo in a clinical trial. No information will be gleaned from this, and the probability people will be killed is quite high. The safety has not been "well characterized" as several studies point to neurotoxicity, one with significant signs of neurotoxicity requiring the drug be stopped, and many of the trials were acute studies in very sick people without long term follow up (go to pubmed and search "dichloroacetic acid" with the clinical trial limit to see whats been done). There is not nearly enough data to suggest widespread use of this drug without extremely careful monitoring and study, and there is quite a bit of data that suggests this drug could be highly toxic.

Irresponsible does not even begin to describe this kind of crankery. This could be deadly, but since Scot is only suggesting people experiment on themselves (and their children, pets etc.) it isn't completely illegal. Anyone else think he and the quacks selling this stuff belong in jail for this though? Where is the damn FTC?

Labels: Dave Scot, DCA, uncommon descent

A good example of why denialists are cranks and not just representing an alternative viewpoint, is when they expand into other fields they use the same methodology to attack. I give you Uncommon Descent arguing against anthropomorphic climate change.

As record breaking cold sweeps the U.S. this Easter weekend, plunging temperatures 20 degrees below average for early April, nary a mention of global warming can be found in the news. Talk about putting a cold damper on Friday's release of the 2007 IPCC report on so-called global warming, the timing couldn’t have been better. Is someone trying to tell us something by making it snow in southern Texas in April just as the IPCC report is released? You can bet your bottom dollar that if the temperature in the U.S. was 20 degrees ABOVE normal we’d be hearing plenty from the global warming alarmists but they are mysteriously silent now. I can’t find a single major news source carried by Google News mentioning the record cold and global warming in the same article. Gee, I wonder why?

Ok. Does anyone else see the salient idiocy? It's pretty obvious to me, and it's a recurring problem with many of the lay global warming deniers. Quite simply, it is the idea these jackasses have that they can stick their hand out the window, feel it's cold, and then pontificate on a global phenomenon. Really, you have to be pretty ill-informed to fall for this kind of ridiculously simplistic attack on global warming, and in all the "off-topic" attacks on global warming from Dave Scott at UC, it's either this drivel, calling Al Gore fat, or suggesting his heating bill has something to do with climate science.

This is why it's denialism folks. There is no real content here. We don't have a real argument, real data, or real facts from the denialist opposition. We just get snide remarks, confusing analogies, and misrepresentation of the debate. Global warming doesn't mean it can't be cold ever. It just means over a given year, globally, temperatures will be on average warmer.

Labels: global warming denialism, uncommon descent

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

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