Dinosaur proteins from T. rex and hadrosaurs

The controversy over the finding of Tyrannosaurus rex proteins in a fossilized bone
continues, with a long article in Wired magazine this week exploring the issue. The Wired reporter, Evan Ratliff, takes a refreshingly skeptical view through much of the article. It's a good read, and I recommend it.

But first, an update on the science: Mary Schweitzer, John Asara and colleagues published a new report in Science on May 1 describing their analysis of an 80-million-year-old fossil from the dinosaur Brachylophosaurus canadensis, a hadrosaur that is 12 million years older than T. rex. Once again, they found fragments from collagen, the protein that is a major component of bone, and as with their original T. rex study, they claim that these represent original dinosaur proteins. And as before, they found that the dinosaur proteins most closely resemble modern birds – in particular, ostrich.

The new study spends a significant amount of effort addressing the question of contamination. This question has been raised in at least two ways. Tom Kaye and colleagues reported in PLoS ONE that the soft tissue found by Schweitzer could be explained as a bacterial biofilm, rather than as preserved dinosaur tissue. I still like the biofilm explanation, and I don’t see how the new study refutes it. The study contains many microscope photos showing how the fine structure of the fossilized bone resembles modern ostrich bone, but preserved physical structure is not in question. The real question is, did dinosaur proteins survive for 80 million years in these bones?

The second contamination question emerges from this: Marty McIntosh discovered – after Asara released his mass spec data to the public – that the original T. rex sample contained hemoglobin. This finding has been discussed in the mass spec community, and privately among a group of scientists (including me) following this story, but it has not been published (as far as I know) until the Wired article.

Hemoglobin! Now, from what I know, we don’t expect to find much hemoglobin in bone tissue, and we sure don’t expect to find it in 68-million-year-old fossils. Could this be another big discovery? Or could it, perhaps, be that the sample is contaminated with modern proteins, perhaps from ostrich?

Upon further inquiry, a number of scientists learned that John Asara’s lab had indeed used its mass spec equipment to analyze samples of ostrich bone. Asara reports (in the Wired article) that the ostrich sample had been analyzed long before either of the dinosaurs:
“Asara conducted his ostrich and T. rex experiments a year and a half apart, separated by roughly 1,500 mass spectrometry runs. According to Asara, none of those spectra, nor samples of the soil surrounding the fossils, nor his daily control runs—in which he sequences known solutions to check for contaminants—turned up any ostrich hemoglobin.”
The new Science paper on the hadrosaur proteins doesn’t mention the (unpublished) hemoglobin fragments in the T. rex data, so this important question was not addressed. Well, if Asara’s lab handled ostrich material, then I remain skeptical of their assurances that ostrich couldn’t have possibly contaminated the original T. rex samples. And Marty McIntosh explained to the Wired reporter that “a chemical modification on the hemoglobin makes it more likely to be contamination.” McIntosh submitted a paper on his results to Science, but they rejected it – perhaps because it called into a question a finding that Science’s editors have obviously endorsed. That’s too bad.

If the T. rex sample was contaminated, that throws all the results into question. It also throws into question the new hadrosaur results – if contamination was a problem before, it might be still. The best way to resolve this is for an independent group to take the original fossils and repeat the study. I know that there are groups trying to do exactly this, but the fossils are controlled by paleontologist Jack Horner, who thus far has refused to share them with anyone but Schweitzer.

Extraordinary claims require extraordinary evidence, as any good skeptic knows. The finding of intact collagen protein in dinosaur fossils is certainly an extraordinary claim, and the finding of hemoglobin is even more stunning. Alas, the alternative explanations (statistical artifacts - see my earlier blogs and Pavel Pevzner's article in Science - and contamination by bacteria and/or ostrich tissue) are much more likely. I'd love for these results to be true - intact dinosaur proteins! Think of all the evolutionary comparisons we could do if we can reconstruct the past 80 million years directly from the molecular record! But I'm afraid I remain skeptical.

Alt meds for pets? Really?

The Washington Post has had two articles this week on "alternative" treatments, both of them very poorly researched, both written by reporters who just couldn't gush enough over the possibilities for cures promised by promoters of treatments such as Reiki, homeopathy, acupuncture, and Chinese herbs. It's too painful for me to repeat the claims of the first article - which was little more than marketing hype, focusing on a physician who was offering these treatments to her human patients - so I'll just mention today's article, which is titled "Going Beyond the Usual Rx for Rover: Alternative Treatments Gaining Acceptance."

According to the article, veterinarians who believe (despite the complete lack of evidence) "that such alternative therapies as acupuncture and Chinese herbs can help animals struggling with arthritis and allergies are finding growing acceptance from some peers and an eager reception from pet owners." The article quotes several veterinarians (is it really accurate to call them vets? I wonder) in northern Virginia who now specialize in acupuncture and homeopathy for pets.

The evidence for these therapies, when they've been studied properly, is that they offer no benefit other than the placebo effect. For treatment of pain, patients who think they're getting almost any treatment (including acupuncture) tend to report that they are feeling somewhat less pain - even if the treatment is a "sham" treatment such as a sugar pill or sham acupuncture. That's fine for people, but what about pets? You can't explain to Fido why the good doctor is sticking needles into him. Ouch!

These treatments aren't cheap - "alt vets" charge about $100 for an acupuncture session, according to the article. One doctor in Bethesda, Maryland offers ozone therapy to treat cancer and kidney failure. I wonder what that costs? Do these vets know that the American Cancer Foundation strongly advises cancer patients against ozone therapy (yes, it is heavily marketed for people too), noting that "there is no evidence that ozone is effective for the treatment of cancer"?

From the Post article, it's pretty clear that the placebo effect is once again operating, but it's affecting the pet owners, not the pets. Several owners are quoted saying how they saw their pets improve after homeopathy or acupuncture. One dog owner brings her border collie in for an "acupuncture tuneup" (no, I'm not making this up! if only I were so clever) every three months. The owner, who obviously believes this works, reports that "after a session here, she [the collie] runs like a puppy." I would too, after escaping those sharp needles for another three-month reprieve!

Frightening quack autism treatment

One of the most bizarre and frightening "treatments" being promoted for autism is a drug, Lupron, which suppresses testosterone. Treatment with Lupron is also known as "chemical castration," and as you can imagine, it's a very serious and potentially harmful drug. But Mark and David Geier have decided - despite the complete lack of evidence for this - that excess testosterone causes autism, and that (therefore) Lupron will cure it.

The Geiers have been promoting this for years, but a recent article in the Chicago Tribune caught my attention. The title of the article is ' "Miracle drug" called junk science', and the Tribune deserves some credit for producing a reasonably skeptical article. "Lupron is the miracle drug," says Mark Geier, who doesn't hesitate to make outrageous claims. Mark Geier has an M.D., although he is not qualified in the specialties (such as pediatic neurology) that he would need to understand autism. His son, David Geier, has only an undergraduate degree in biology. Despite this, they are marketing their "Lupron protocol" around the country, happy to profit from this outrageous, harmful treatment. The Geiers have filed for a patent on their Lupron treatment, and they charge $12,000 to autistic patients for initial diagnostic tests, plus $5000-$6000 per month for the Lupron therapy.

The Tribute article was prompted by an appearance made by the Geiers in the Chicago area, where they were speaking at the Autism One conference. Here is a quote from the Geiers' abstract of their presentation:
"Finally, attendees will be presented newly published peer-reviewed clinical studies on over 200 patients diagnosed with autism showing that interventions designed to lower or significantly reduce the functionality of testosterone (and other androgens) were observed to significant improve clinical outcomes. The new information presented may provide an important alternate treatment course for many patients diagnosed with autism that are presently administered psychiatric medications. "
It sounds reasonable - but only if you don't know anything about the Geiers' history, or the profits they are making from their supposed "cure."

As evidence for their Lupron treatment, the Geiers often cite a study they published themselves several years ago, which experts have pointed out is deeply flawed. (Somehow I doubt that they ever point out that some of their published research was subsequently retracted by the journal Autoimmunity Reviews.) The Tribune reporter interviewed Dr. Paul Kaplowitz, chief of endocrinology at Children's National Medical Center in Washington, who pointed out that the Geiers don't seem to understand that the blood tests they used in their study did not show elevated testosterone. Kaplowitz asked, "Is Dr. Geier just misinformed and he hasn't studied endocrinology, or is he trying to mislead?" Admittedly, it's hard to know in cases like these whether the quacks are truly ignorant, or whether they know they're peddling nonsense and just don't care.

Local Chicago-area doctor Mayer Eisenstein, who is making the Lupron protocol available and who supports the Geiers, was also interviewed by the Tribune. Eisenstein has his own pseudoscientific claims, and he too is a featured speaker at the Autism One conference. His speaker abstract states:
"if children do not get polio because of the polio vaccine but later die of a cancer caused by the SV40 virus received as a contaminant in the vaccine, the risk may outweigh the benefits."
Ouch. There's no evidence that the polio vaccine causes cancer - none whatsoever. That doesn't seem to be a concern for Eisenstein, whose bio on the Autism One site proudly claims that "he has formulated natural pharmaceuticals which can be used to treat many chronic medical conditions." These are modern snake-oil salesmen. Maybe Eisenstein is really so ignorant that he thinks the polio vaccine was a bad idea, but I think he just doesn't care.

By the way, if you want a guide to autism quackery, take a look at the Autism One conference site. But be warned: if you care about science, you might be in for a painful experience. I couldn't take it for long myself.

Also quoted in the Tribune was Dr. Simon Baron-Cohen, a professor of developmental psychopathology director of the Autism Research Center at Cambridge University, who said "The idea of using it [Lupron] with vulnerable children with autism, who do not have a life-threatening disease and pose no danger to anyone, without a careful trial to determine the unwanted side effects or indeed any benefits, fills me with horror." Well said.

What's hard for me to understand is how the medical profession can allow someone like Mark Geier to continue to practice medicine. One of the principals that all medical students are taught, supposedly, is "first, do no harm." Apparently, Mark Geier didn't learn that one.