The Proof Is in the Proteins

This bit of news and science has been making the rounds for a bit, and I just wanted to post the entire article here. I know that the general population will misunderstand many fine points on this article, so I hope that if there are questions, people will ask them as opposed to just going off with an unsupportable idea in their head.

For instance, one comment I see is that all life shows that it only arose once on earth. That may or may not be entirely true. it just means that all the life we currently have came from a common ancestor that survived. Life may have arisen several times, but none of the other life forms survived. Our type of life was so much more successful and drove the other life out (to extinction even). You know, evolution!

The Proof Is in the Proteins: Test Supports Universal Common Ancestor for All Life

One researcher put the basic biological assumption of a single common ancestor to the test--and found that advanced genetic analysis and sophisticated statistics back up Darwin's age-old proposition

By Katherine Harmon

ALL IN THE FAMILY: The common assumption that all life on Earth emerged from a single common ancestor has been a difficult hypothesis to prove. New analysis sorts out some of the competing theories.

Earth's first life-form, floating in the proverbial froth of the primordial seas that eventually gave rise to trees, bees and humans, is not just a popular Darwinian conceit but also an essential biological premise that many researchers rely on as part of the foundation of their work.

In the 19th century, Charles Darwin went beyond others, who had proposed that there might be a common ancestor for all mammals or animals, and suggested that there was likely a common ancestor for all life on the planet—plant, animal and bacterial.

A new statistical analysis takes this assumption to the bench and finds that it not only holds water but indeed is overwhelmingly sound.

Was it not already obvious, from the discovery and deciphering of DNA, that all life forms are descended from a single common organism—or at least a basal species? No, says Douglas Theobald, an assistant professor of biochemistry of Brandeis University and author of the new study, detailed in the May 13 issue of Nature. (Scientific American is part of Nature Publishing Group.) In fact, he says, "When I went into it, I really didn't know what the answer would be."

Despite the difficulties of formally testing evolution—especially back across the eons to the emergence of life itself—Theobald was able to run rigorous statistical analyses on the amino acid sequences in 23 universally conserved proteins across the three major divisions of life (eukaryotes, bacteria and archaea). By plugging these sequences into various relational and evolutionary models, he found that a universal common ancestor is at least 10^2,860 more likely to have produced the modern-day protein sequence variances than even the next most probable scenario (involving multiple separate ancestors).*

"Evolution does well where it can be tested," says David Penny, a professor of theoretical biology at the Institute of Molecular BioSciences at Massey University in New Zealand and co-author of an accompanying editorial. Yet, he notes that evolution can make "testable predictions about the past (especially quantitative ones)" tricky at best. "That Theobald could devise a formal test," he says, "was excellent…. It will probably lead to a jump in what is expected of the formal evaluation of hypotheses, and that would help everybody."

Common ancestor acrimony
The mid-20th-century discoveries about the universality of DNA "really nailed it for people" in terms of establishing in popular—and academic—culture that there was a single universal common ancestor for all known life on Earth, Theobald says. And since then, "it's been widely assumed as true," he notes.

But in the past couple decades, new doubt has emerged in some circles. Microbiologists have gained a better understanding of genetic behavior of simple life forms, which can be much more amorphous than the typical, vertical transfer of genes from one generation to the next. The ability of microbes such as bacteria and viruses to exchange genes laterally among individuals—and even among species—changes some of the basic structural understanding of the map of evolution. With horizontal gene transfers, genetic signatures can move swiftly between branches, quickly turning a traditional tree into a tangled web. This dynamic "throws doubt on this tree of life model," Theobald says. And "once you throw doubt on that, it kind of throws doubt on common ancestry as well."

With the discovery of archaea as the third major domain of life—in addition to bacteria and eukaryotes—many microbiologists became more dubious of a single common ancestor across the board.

A test for evolution
Other researchers had put certain sections of life to the test, including a similar 1982 statistical analysis by Penny testing the relation of several vertebrate species. Theobald describes the paper as "cool, but the problem there is that they aren't testing universal ancestry." With advances in genetic analysis and statistical power, however, Theobald saw a way to create a more comprehensive test for all life.

In the course of his research, Theobald had been bumping against a common but "almost intractable evolutionary problem" in molecular biology. Many macromolecules, such as proteins, have similar three-dimensional structures but vastly different genetic sequences. The question that plagued him was: Were these similar structures examples of convergent evolution or evidence of common ancestry?

"All the classic evidence for common ancestry is qualitative and is based on shared similarities," Theobald says. He wanted to figure out whether focusing on those similarities was leading scientists astray.

Abandoned assumptions
Most people and even scientists operate under the premise that genetic similarities imply a common relation or ancestor. But as with similarities in physical appearance or structure, these assumptions "can be criticized," Theobald notes. Natural selection has provided numerous examples of convergent physical evolution, such as the prehensile tales of possums and spider monkeys or the long sticky insect-eating tongues of anteaters and armadillos. And with horizontal gene transfer on top of that, similar arguments could be made for genetic sequences.

"I really took a step back and tried to assume as little as possible in doing this analysis," Theobald says. He ran various statistical evolutionary models, including ones that took horizontal gene transfer into consideration and others that did not. And the models that accounted for horizontal gene transfer ended up providing the most statistical support for a universal common ancestor.

Murky origins
Theobald says his most surprising results were "how strongly they support common ancestry." Rather than being disappointed about simply backing up a long-held assumption, he says that at least, "it's always nice to know that we're on the right track."

These findings do not mean that a universal common ancestor establishes the "tree of life" pattern for early evolutionary dynamics. Nor, however, do they infer a "web of life" structure. The tree versus web debate remains "very controversial right now in evolutionary biology," Theobald says, reluctant to pick a side himself.

One of the other big unknowns remaining is just when this universal common ancestor lived and what it might have looked like—a question that will take more than Theobald's statistical models to answer. Theobald also notes that the support for a universal common ancestor does not rule out the idea that life emerged independently more than once. If other, fully distinct lineages did emerge, however, they either went extinct or remain as yet undiscovered.

Research will likely push on into these dusky corners of early evolution, Penny notes, as "scientists are never satisfied." He expects that researchers will try to sort back even earlier, before DNA took over, and assess the early stages of evolution during the RNA days.

On a more foundational level, Penny says, the paper should not put an end to the assessment of ancestral assumptions. Instead it should be a reminder that "we have never thought of all possible hypotheses," he says. "So we should never stop considering some new approach we haven't thought of yet."

*Erratum (5/13/10): This sentence was changed after publication. It originally stated that a universal common ancestor is more than 10 times more likely.

Web Page Migration

Folks,

Just a quick note to let you know I am aware of the problems with the web page. Heck, I even know what the problem is (my top and bottom php directories are messed up). My host migrated to a better server, but in the process borked up the path pointing to those PHP files. As soon as I figure out what the new path is, I will get it pointing to the right one! My apologies!

Fronline Reports on Anti-Vax Manufactuversy

I just wanted to repost a couple of other stories/blogs that I saw as a result of the Frontline episode that was on PBS.

The Vaccine War: Telling it (mostly) like it is about the anti-vaccine movement

Category: Antivaccination lunacy • Entertainment/culture • Medicine • Popular culture • Quackery • Television
Posted on: April 28, 2010 3:00 AM, by Orac

Yesterday, I expressed concern about a FRONTLINE episode that was scheduled to air tonight entitled The Vaccine War (which, by the time you read this, should be available for online viewing in case you missed it). My concern was that there was going to be a heapin' helpin' of false balance, based on the promotional materials. My concerns were later somewhat assuaged based on the pre-airing reaction of the anti-vaccine movement, which was fairly wary, if not hostile even. Of course, any television show that doesn't conclude that their view that vaccines cause autism is at plausible or even likely is virtually guaranteed to have an infiltration of anti-vaccine loons in the comments attacking relentlessly, but I was heartened to see a review like this proclaiming the documentary to be very much science-based and intolerant of the misinformation, pseudoscience, quackery, and lies of the anti-vaccine movement. I could only hope.

Another indication that The Vaccine War might be OK from a science-based perspective was that the antivaccine crank blog Age of Autism (AoA) preemptively set up a post in which the merry band of antivaccinationists proclaimed that they would be live blogging and live Tweeting the special. Conveniently enough, they included links to the PBS Ombudsman, links to FRONTLINE, its Facebook page, and its Twitter stream, presumably to facilitate said influx of anti-vaccine loons to those locations to protest most piteously being mistreated by a television show pointing out that there is no evidence that vaccines cause autism and, even worse, pointing out that anti-vaccinationists are endangering children. Then there's a convenient post full of links to AoA misinformation, cherry picking, and distortions, presumably to provide said anti-vaccine loons with links to use when they protest most piteously their treatment on FRONTLINE.

So I decided to wait until the show aired, watch it, and report back to you, my readers, in the meantime savoring a couple of characteristic reactions, first from the grand macher of the anti-vaccine movement, reclaiming his place now that Jim Carrey has apparently dumped Generation Rescue's spokescelebrity Jenny McCarthy, your bud and mine J.B. Handley:

I personally spent 2 hours with Jon Palferman and Kate McMahaon, the producers of the piece. The whole point of my meeting was to explain that this was not Parents vs. The Science and that our community takes its cues from doctors and scientists. I encouraged them to interview Jon Poling, Bernadine Healy, Boyd Haley, and many others.

When Jenny was interviewed, Jay Gordon sat next to her the entire time and was also part of her interview - let's see if they show him.

I told Frontline, "Get all the people from the other side you want, just be fair in telling the totality of our story, and don't turn this into a Parents vs. the science" like the NY Times did."

My response back from Kate McMahon:

"FRONTLINE will carry out a detailed and even-handed investigation including voices from all sides of the controversy including parents, activists, physicians, scientists, lawyers, politicians and vaccine manufacturers. We will examine the evidence relating to an association between increases in the prevalence of autism and hypothesized causes such as MMR vaccine, thimerosol and other toxins associated with vaccines."

Here's hoping they live up to what they said they would do.

Here's hoping they don't, I thought. But clearly J.B. wasn't too happy, which gave me hope that The Vaccine War would be science-based. Then I saw these Tweets from everybody's favorite pediatrician to the stars, apologist for the anti-vaccine movement, and pediatrician to Jenny McCarthy's son Evan Dr. Jay Gordon:

PBS show about vaccines. Don't bother to watch it.

And:

A number of scary articles in newspapers today to augment PBS' scary vaccine show tonight. They interviewed me for 2 hrs and cut it all.

Gee, sounds like sour grapes, doesn't it? It's also interesting that Jenny McCarthy had Dr. Gordon sitting next to her the whole interview, probably because she's so prone to saying incredibly stupid things. Of course, Dr. Jay is also fairly prone to saying pretty stupid things, too; so I don't know if he's much of a safeguard to the message. I guess we won't get to find out.

So how did the show turn out? Here follows my impressions and semi-live blogging. Feel free to watch the show (embedded at the top of this post) and check it out for yourself.

The Vaccine War (viewable online)

The opening montage did a bit too much of the whole "balance" thing in that it included J.B. Handley blathering and Jenny McCarthy spewing her same brain-dead false dilemma of measles versus autism. (She'd choose the measles, of course.) I was able to forgive that, because it's very much setting up the story. The show then launched straight into a birth and a list of the vaccines that children get, with Melinda Wharton of the CDC and Paul Offit pointing out how much good vaccines do, how we no longer see diseases that once killed thousands or even milions.

Then it's straight to Ashland, OR and the woo and a mother named Jennifer Margulis, who is a writer for that "natural" repository of woo Mothering Magazine and spewing nonsense about "natural immunity" versus vaccines, claiming that it is better than vaccine-induced immunity. Dr. Donna Bradshaw-Walters was then introduced, and she describes how 28% of Ashland's children are missing some or all of their vaccines, pointing out that it is only a matter of time before there is an outbreak there. It was refreshing to note that there are pro-vaccine parents, one of whom predicted that it would get ugly if there were an outbreak in which vaccinated children started to get sick because of unvaccinated children forming a repository for disease that can spread to vaccinated children whose vaccines didn't "take," for whatever reason. The show then described the SSan Diego measles outbreak and how unvaccinated children are a vector for infection, even to the vaccinated, who are less likely to be infected but not immune, as no vaccine is 100% effective.

There was then a segment at Pfizer. This may not have been the best idea strategically, given how it feeds into the distrust of big pharma, although the scientist interviewed, Dr. Emilio Emini, did a good job of pointing out how vaccines prevent disease. Still, right there, I could envision doubting parents becoming suspicous. Then, of course, there is Dr. Paul Offit, who, although he is the Dark Lord of Vaccination to the antivaccine movement, who is nonetheless the one of the most effective provaccine voices. Happily, Offit makes no apologies for having gotten rich from a vaccine. He is enormously proud of it, as he should be.

One thing this show revealed that I didn't know was that bioethicist Arthur Caplan had actually contracted polio in his youth. No wonder he is so effective when he argues for vaccines. Equally effective is a scene in which paramedics are being trained, part of their training being to watch videos of children with pertussis and rotavirus. The video of the child with pertussis is horrifying; the suffering of such children is incredible. This class even pointed out that chickenpox can actually be fatal, showing a child with staph sepsis in the pox lesions.

Unfortunately, Margulis demonstrates the burning stupid by asking why we are still vaccinating for polio as polio has become more rare. This woman was truly irritating and moronic. Worse, she kept popping up throughout the show, sadly enough. But that wasn't enough. There had to be Barbara Loe Fisher, too, spewing her usual anti-vaccine line. Unfortunately, here's where FRONTLINE falls down. The show seriously represents BLF as a "vaccine watchdog," rather than what she is, an anti-vaccine propagandist. Bad FRONTLINE!

Similarly, the interview with Jenny McCarthy is infuriating, as usual, but there was a rather interesting tidbit in the complete online interview:

How long after the MMR was that first seizure?

You know, a lot of people think, and probably from me saying in some interviews, that it was after the MMR I noticed changes.

I don't think it was just the MMR shot that caused any kind of trigger with autism. I think it was a compilation of so many shots to a kid that obviously had some autoimmune disorders. So I would say maybe a couple of months, a month or so after the MMR, I started to notice some physical ailments such as constipation, rashes, eczema. That was like the first little sign. And then the train just kind of descended from there.

This is very different from the stories she was telling around the time she released her first book, and she even seems to be acknowledging it as she dances around a very simple question. Indeed, I remember McCarthy saying in interview after interview how she saw the "light go out of Evan's eyes" right after the shot. For example, anti-vaccination activist Ginger Taylor cites what Jenny McCarthy said in her 2007 interview with Oprah:

Jenny says even before Evan received his vaccines, she tried to talk to her pediatrician about it. "Right before his MMR shot, I said to the doctor, "I have a very bad feeling about this shot. This is the autism shot, isn't it?' And he said, 'No, that is ridiculous. It is a mother's desperate attempt to blame something,' and he swore at me, and then the nurse gave [Evan] the shot," she says. "And I remember going, 'Oh, God, I hope he's right.' And soon thereafter-boom-the soul's gone from his eyes."

Notice how Jenny appears to have changed her story from its being the MMR to its being a gradual process due to too many vaccines. Truly, her story shifts more than the sands of the Sahara.

This segment ran right into an interview with J.B. Handley. There was really nothing new there in that J.B. claims that "tens of thousands" of parents tell him that their children were "never the same" after vaccines, combined with his simplistic mantra: Vaccines cause brain damage and autism is brain injury. Ergo, to him, vaccines cause autism. Of course, it is not really true that autism is "brain injury." It is a difference in the brain, but there's no good evidence that autism is primarily due to "brain injury," although there's all sorts of quackery out there that purports to treat "vaccine injury" to the brain.

Here's another point where the FRONTLINE special drops the ball a bit. The show immediately goes into the MMR fear mongering provoked by Andre Wakefield. The problem is that J.B. Handley wasn't about MMR. Generation Rescue until recently said that autism is a "misdiagnosis for mercury poisoning." But the MMR has never had mercury in it, ever. In conflating these issues, FRONTLINE confuses two related issues that are not really the same thing, particularly when it starts showing a speech by Robert F. Kennedy, Jr. at the Green Our Vaccine rally from two years ago. As someone who knows about the anti-vaccine movement and its history, this was irritating, and it is more than just a nit to pick.

That being said, I do like how, right after a segment in which Jenny McCarthy claims that scientists won't study whether vaccines cause autism, the show immediately goes on to show that that she is either mistaken or lying, take your pick. (Personally, I think she's too stupid to realize how wrong she is about this.) The issue has been studied extensively in multiple countries, and no link between vaccines and autism has been found. Moreover, FRONTLINE did a good job of explaining how correlation does not necessarily mean causation. Just because a diagnosis of autism is made soon after a vaccine does not necessarily mean the vaccine caused autism. It finished this middle part of the documentary by documenting the fall of Andrew Wakefield, in particular pointing out how some of the children in his studies had been referred through lawyers suing vaccine manufacturers.

The beauty of this segment is how FRONTLINE showed that, no matter how much evidence, with J.B. Handley saying, "I don't give a fuck about the MMR in isolation in one study." (Yes, he did use the F-word, although it was bleeped out and turned to "crap" in the online transcript.) This was rapidly followed by a demonstration of Barbara Loe Fisher shifting the goalposts asking for more epidemiological studies and basic science studies. It is, as Dr. Offit put it, a classic shifting of goalposts, with Jenny McCarthy blathering about her "mommy warriors" and how "Evan is her science."

Unfortunately, this segment depressed me, because it shows just how much science doesn't matter in trying to persuade these parents and how the web perpetuates not just the old vaccine myths, but facilitate the spread of new ones. It demonstrates just how much the Internet's "democratization" of knowledge devalues knowledge, expertise, and science. The forces of pseudoscience proliferate and infiltrate, and, quite frankly, those of us who promote science-based medicine are way behind the eight ball in trying to counter these messages. One thing I had no idea about was just how effective the Desiree Jennings story had influenced high school students not to vaccinate. Roughly half of one class who hadn't taken the H1N1 vaccine said that the reason they didn't take the vaccine was because they saw Desiree Jennings on YouTube. This makes me think, more than ever, that blogs such as this one and others are essential in tearing apart such bad information. The result of this information is people like the mothers in Ashland that I discussed last time who ask, "If vaccines work, who am I hurting by not vaccinating?"

The result was shown in the story of a baby who came down with pertussis and almost died. Her situtation was so bad that a chaplain was brought in for possible last rites.

Near the end of the show, there was presented a focus group of people who discuss vaccination. What was interesting is how much vaccination is viewed as a parental choice rather than a societal duty. This in and of itself is not necessarily a bad thing. The problem is that this choice is being increasingly undermined by misinformation on the Internet and out there. The message of the anti-vaccine movement that the days of "paternalism" are over echoes very strongly with the whole "health freedom" movement. It's very difficult for anyone to make a well-informed choice when most of the information that pops up when you search the Internet is from the anti-vaccine side.

In the end, I was mostly relieved by The Vaccine War. It was science-based, and it pulled no punches in asserting that there is no good scientific evidence that vaccines cause autism. True, it did confuse the issue of the MMR vaccine and thimerosal-containing vaccines, and that's more than a minor mistake. It also was far too kind in its treatment of Barbara Loe Fisher, calling her organization, the National Vaccine Information Center a "vaccine safety" advocacy organization, when it is an anti-vaccine organization, plain and simple. It did a little better with Generation Rescue, showing a bit of the sheer insanity behind the organization and how, no matter how much evidence there is against its position, it never looses sight of its founding principle, namely that it's absolutely, positively always the vaccines. Always. Those complaints aside, FRONTLINE did a far better job than I expected in deconstructing the anti-vaccine movement. It didn't compromise on the science, although it may have compromised a bit in how it describes, for example, the NVIC and Generation Rescue.

Will The Vaccine War change minds? Maybe. There's no way it's going to change the minds of hard core antivaccinationists of J.B. Handley's ilk. Almost nothing I can think of can. But it might--just might--reassure parents on the fence that all that horrible stuff they're hearing on the radio, seeing on TV, and, above all, reading on the Internet about the evils of vaccines are not based in science. That's actually quite an achievement.

Frontline - Jenny McCarthy Changes her Story Again

I watched PBS’s Frontline on vaccines last week, and thought it overall pretty good. Not perfect (what is?) but the numerous howls of protest from the crank Age of Autism blog (I lost count of the number of their posts) and on the Huff Post, should be enough to tell you it hit the right marks. Orac has a detailed review, The Vaccine War: Telling it (mostly) like it is about the anti-vaccine movement, so I really don’t need to review it in detail.

There is just one thing I want to highlight, though. It wasn’t on the actual TV program, but on PBS’s full online Jenny McCarthy interview. It was this:

[Questioner:] How long after the MMR was that first seizure?

[Jenny McCarthy:] You know, a lot of people think, and probably from me saying in some interviews, that it was after the MMR I noticed changes.

I don't think it was just the MMR shot that caused any kind of trigger with autism. I think it was a compilation of so many shots to a kid that obviously had some autoimmune disorders. So I would say maybe a couple of months, a month or so after the MMR, I started to notice some physical ailments such as constipation, rashes, eczema. That was like the first little sign. And then the train just kind of descended from there. [My bold.]

Jenny is saying that her son’s autism didn’t start immediately after just one shot (the MMR), but that “some physical ailments” of autism appeared over “a couple of months.” This was just “the first little sign.” (Note, just a “little” sign at that point.) But, here’s the thing, as I wrote in The Two J.B. Handleys, Jenny had, only three years ago, stated quite clearly and unambiguously something very different:

"Right before his MMR shot, I said to the doctor, 'I have a very bad feeling about this shot. This is the autism shot, isn't it?' And he said, 'No, that is ridiculous. It is a mother's desperate attempt to blame something,' and he swore at me, and then the nurse gave [Evan] the shot," she says. "And I remember going, 'Oh, God, I hope he's right.' And soon thereafter -- boom -- the soul's gone from his eyes. [My bold.]

Note, not “some physical ailments” or just a “little sign” – back then it was “the soul's gone from his eyes” which, I think you’ll agree, is completely different. Also not over “a couple of months,” but “boom.” Different story.

Why does this matter? Well, Jenny, Handley and the rest have been telling us for years that the reason they know vaccines cause autism is that their kids got autism “boom” right after the vaccine was given. (With Handley it was after a shot containing Thimerosal, while with Jenny it was MMR which never had Thimerosal, but we’ll gloss over that for now.) Now that Wakefield’s MMR hypothesis has been discredited, and numerous epidemiological studies have failed to find a link with Thimerosal, the only way to keep their vaccines-cause-autism claims alive is to move the goalposts. And you see that in the Frontline program – Jenny says it’s not MMR, or Thimerosal, or too many vaccines at once – it’s “all of the above.” She actually says she doesn’t know what it is that’s causing autism, but she knows it’s the vaccines, somehow. But the thing is, if they’re now saying the signs of autism appeared gradually over several months, on what basis are they saying vaccines cause autism? If autism appeared gradually, and not “boom” after one shot, then they don’t even have the correlation (vaccine immediately followed by autism) to rely on.

And what’s more, they know they’ve changed their story and they know they’ve moved the goalposts. Why do I say that? Well, when I wrote The Two J.B. Handleys less than ten weeks ago, I included a link to the interview with the Jenny “boom” quote on Jenny’s own Generation Rescue site, Jenny: Evan's Story. Check that link now. Search Generation Rescue for any part of that interview. It’s gone. Disappeared. Never happened. Not part of the official anti-vaccine history any more. (And I know Handley read that post and saw the link because he appeared in the comments four days after I wrote it in an attempt to defend himself.) If you needed any more proof of the dishonesty and intellectual bankruptcy of Generation Rescue and the anti-vaccine kooks, there it is. Fortunately for us, there is one thing that George Orwell didn’t imagine when he wrote his famous 1984 novel, and that’s the Wayback Machine – the cache that never lets anyone completely disappear inconvenient facts they want you to forget. Courtesy of the internet, here again is what Jenny said in 2007, Jenny: Evan's Story – “and soon thereafter -- boom -- the soul's gone from his eyes.”

The hallmark of the pseudo-scientist and the kook, is they they won’t change their beliefs no matter what the evidence, instead they devise ad hoc explanations and move goalposts to accommodate contradictory evidence. Jenny and Handley have been caught, again, doing just that. Rather than re-evaluate their beliefs, they just change their previous story so that it fits the currently known facts. And they try to cover their tracks by deleting the now embarrassing things they said before. Rather strangely, they fail to notice that, with their new story, there is no longer any reason to link vaccines to autism. Either autism occurred “boom” just after the shot (and so they can point to correlation), or it didn’t. Which is it? They want it both ways.

Funnily enough, there was one thing in that PBS interview with Jenny, that I though she got right. It was this:

…that night went on Google and typed in "autism." And on the corner of the screen, in the sponsored links, it said, "Generation Rescue." And I decided to click on it, because right underneath it, it said, "Autism is reversible." And I thought to myself, well, this must be a load of crap, because if it was true, why didn't the best neurologist in the world tell me there's something I could do to reverse autism?

Precisely. And if she’s only stopped right there she could have avoided making a complete fool of herself.

Today in the News - 2 May 10

Just wanted to start up an old tradition that I had going here that I sort of let fall by the wayside. I won't be doing this daily due to schedule constraints (unless someone else decides to follow my format).

Mathematicians Offer Elegant Solution to Evolutionary Conundrum

ScienceDaily (Apr. 25, 2010) — UBC researchers have proffered a new mathematical model that seeks to unravel a key evolutionary riddle--namely what factors underlie the generation of biological diversity both within and between species.

Evolutionary biologists have long recognized that the emergence of rare traits within a population can spur diversity. For example, being one of a few under-sized predators in a population dominated by larger-sized predators can offer advantages--access to an abundance of small prey--and increase the likelihood of that trait prospering in the population.

"But existing mathematical models that incorporate these 'rare type' advantages tend to have some serious shortcomings," says Michael Doebeli, a researcher at UBC's Biodiversity Research Centre and professor with the departments of Mathematics and Zoology. "They rely on single traits--like body size--and predict that the advantage offered by that trait has to be very significant in order to maintain large amounts of diversity."

So Doebeli and research associate Iaroslav Ispolatov applied a new model to the riddle, which they outline in the journal Science.

Building on classical competition models for single traits, they designed their mathematical theory to gauge the evolutionary impact of multiple traits in concert, and found that adding this layer of complexity significantly lowered the threshold for the maintenance of diversity and the evolution of new species.

"When you model one trait at a time--in isolation--you often find that ecological interactions aren't strong enough to drive divergence. But with many traits acting in concert, even very weak interactions can generate diversity. Our approach mirrors the complexity of reality more closely--if you think about it, all living organisms have at least dozens, if not hundreds, of ecologically relevant traits," says Doebeli.

Mathematically, the biological phenomenon is reflected in fundamental properties of eigenvalues of quadratic forms. The theory would help explain the extraordinary amount of diversity found in many ecosystems, for example in the microbial world of oceans. In fact, the initial proving ground for the model might well be microbial populations.

"It would be interesting to to test whether at the genetic level, pathways controlling different traits are regulated in concert to enable the inheritability of diversifying traits along multiple phenotypic axes."

Pre-History of Life: Elegantly Simple Organizing Principles Seen in Ribosomes

ScienceDaily (Apr. 13, 2010) — With few exceptions, all known forms of life on our planet rely on the same genetic code to specify the amino acid composition of proteins. Although different hypotheses abound, just how individual amino acids were assigned to specific three-letter combinations or codons during the evolution of the genetic code is still subject to speculation.

Taking their hints from relics of this evolution left behind in modern cells, researchers at the Salk Institute for Biological Studies concluded that after only two waves of "matching" and some last minute fiddling, all 20 commonly used amino acids were firmly linked with their respective codons, setting the stage for the emergence of proteins with unique, defined sequences and properties.

Their findings, which will be published in next week's online edition of the Proceedings of the National Academy of Sciences, provide the first in vivo data shedding light on the origin and evolution of the genetic code.

"Although different algorithms, or codes, were likely tested during a long period of chemical evolution, the modern code proved so robust that, once it was established, it gave birth to the entire tree of life," says the study's lead author Lei Wang, Ph.D., an assistant professor in the Chemical Biology and Proteomics Laboratory.

"But the universality of the code makes it very hard for researchers to study its formation since there are no organisms using a primitive or intermediate genetic code that we could analyze for comparison," he explains.

Cells provide a dazzling variety of functions that cover all of our body's needs, yet they make do with a very limited number of molecular building blocks. With few exceptions, all known forms of life use the same common 20 amino acids -- and only those 20 -- to keep alive organisms as diverse as humans, earthworms, tiny daisies, and giant sequoias.

Each of the 20 amino acids is matched to its own carrier molecule known as transfer RNA (tRNA). During protein synthesis, which is coordinated by so-called ribosomes, amino acids are brought out one by one by their respective tRNAs and inserted in the growing protein chain according to the instructions spelled out in the universal language of life -- the genetic code. The code is "read" with the help of anticodons embedded in each tRNA, which pair up with their codon-counterparts.

Several hypotheses have been put forward to explain why codons are selectively assigned to specific amino acids. "One of the theories, the stereochemical hypothesis, gained some traction when researchers could show that short codon- or anticodon-containing polynucleotide molecules like to interact with their respective amino acids," says graduate student and first author David B. F. Johnson.

If chemical or physical interactions between amino acids and nucleotide indeed drove the formation of the genetic code, Johnson reasoned, then he should be able to find relics of this mutual affinity in modern cells. He zoomed in on ribosomes, large complexes consisting of some 50 proteins interacting closely with ribosomal RNAs.

"Also, the ribosome emerged from an early evolutionary stage of life to help with the translation of the genetic code before the last universal common ancestor," explains Wang, "and therefore is more likely to serve as a molecular fossil that preserved biological evidence."

When Wang and Johnson probed bacterial ribosomes for imprints of the genetic code, they found evidence that direct interactions between amino acids and nucleotide triplet anticodons helped establish matching pairs. "We now believe that the genetic code was established in two different stages," says Johnson.

Their data does not shed much light on the early code, consisting of prebiotically available amino acids -- the kind generated in Stanley Miller's famous "zap"-experiment. But once some primitive translational mechanism had been established, new amino acids were added to the mix and started infiltrating the genetic code based on specific amino acid/anticodon interactions.

"We found evidence that a few amino acids were reassigned to a different codon but once the code was in place it took over," says Johnson. "It might not have been the best possible solution but the only one that was viable at the time."

The work was supported in part by the Searle Scholar Program, the Beckman Young Investigator Program and the National Institutes of Health Director's New Innovator Award.

Rewiring of Gene Regulation Across 300 Million Years of Evolution

ScienceDaily (Apr. 12, 2010) — Researchers from Cambridge, Glasgow and Greece have discovered a remarkable amount of plasticity in how transcription factors, the proteins that bind to DNA to control the activation of genes, maintain their function over large evolutionary distances.

The text books tell us that transcription factors recognise the genes that they regulate by binding to short, sequence-specific lengths of DNA upstream or downstream of their target genes. It was widely assumed that, like the sequences of the genes themselves, these transcription factor binding sites would be highly conserved throughout evolution. However, this turns out not to be the case in mammals.

Reporting in the journal Science, the authors traced the evolution of gene regulation by comparing the binding of evolutionarily conserved transcription factors in the genomes of five vertebrate species -- human, dog, mouse, short-tailed opossum and chicken -- spanning 300 million years.

In all tested species, the transcription factors CEBPA and HNF4A are master regulators of liver-specific genes. By mapping the binding of CEBPA and HNF4A in the genomes of each species and comparing those maps, they found that in most cases neither the site nor the sequence of the transcription factor binding sites is conserved, yet despite this, these transcription factors still manage to regulate the largely conserved gene expression and function of liver tissue.

Paul Flicek, leader of the Vertebrate Genomics Team at EMBL-EBI, an outstation of the European Molecular Biology Laboratory, and coauthor on the paper said "The evolutionary changes in transcription factor binding in the five species have left clues that we can use to explain how function is preserved but not necessarily sequence. What we have learnt is that although the transcription factors regulate similar target genes in all five species, the binding events underpinning this regulation have not been conserved as the species diverged."

"By studying changes in transcription factor binding, we can understand the evolution of gene regulation," said Duncan Odom from Cancer Research UK Cambridge Research Institute and coauthor on the paper. He continued: "Differences in gene regulation are central to explaining differences between species, and gene misregulation is a key causative factor in diseases like cancer."

The results reveal that sequence conservation is not the whole story when it comes to maintaining tissue-specific gene regulation.

New Insights Into the Implications of Autism Onset Patterns

ScienceDaily (Apr. 24, 2010) — Kennedy Krieger Institute has announced new study results showing that when and how autism symptoms appear in the first three years of life has vital implications to a child's developmental, diagnostic, and educational outcomes. Published this month in the Journal of Autism and Developmental Disorders, this study found children with early developmental warning signs may actually be at lower risk for poor outcomes than children with less delayed early development who experience a loss or plateau in skills.

Researchers collected data from 2,720 parents through the Interactive Autism Network, the nation's largest online autism research project. Through custom questionnaires and standardized rating scales, researchers examined differences in early milestone achievement (e.g., first words, walking, phrase speech, etc.), autism symptom severity and diagnosis, and educational supports between children with three different patterns of autism symptom onset:

• Regression (n=44%): A loss of previously acquired social, communication or cognitive skills prior to 36 months
• Plateau (n=17%): Display of only mild developmental delays until the child experiences a gradual to abrupt developmental halt that restricts further advancement of skills
• No Loss and No Plateau (n=39%): Display of early warning signs of autism spectrum disorders without loss or plateau

Results from the study, currently the largest to have examined regression in autism spectrum disorders, provides strong evidence for poorer developmental outcomes in children who experienced regression, a controversial topic among autism researchers. More specifically, children with regression had a significant increase in severity of autism symptoms, the greatest risk for not attaining conversational speech, and were more likely than any other group to require increased educational supports. These findings were markedly worse for the children whose parents reported the regression as severe.

This study was also one of the first to examine the implications of developmental plateau, which tended to occur around the child's second birthday. When compared to children with No Loss and No Plateau, these children were more likely to need educational supports and receive an autistic disorder diagnosis, which is typically more severe than other diagnoses on the autism spectrum (i.e., Asperger's syndrome or Pervasive Developmental Disorder -- Not Otherwise Specified). Children with No Loss and No Plateau were at the least risk for poor outcomes.

"Children who plateau or regress have a later manifestation of autism, but when it manifests it devastates their development," said Dr. Paul Law, corresponding study author and Director of the Interactive Autism Network at Kennedy Krieger. "Children with developmental plateau are an especially under-researched group, and these findings have important implications for those designing and prioritizing clinical evaluations."

Previous studies have reached a variety of different conclusions concerning outcomes for children with regression. Some research has found these children fared worse in the long-term, while other studies found no differences in outcome between these children and those without regression. In examining these discrepancies, the current study suggests researchers who require children to have near typical development prior to regression may be missing the most severely impaired children in their findings. In fact, 35 percent of parents in this study had concerns about their child's general development before they noticed the more obvious signs of skill loss.

"Parents have good instincts when it comes to their children," said Dr. Rebecca Landa, co-author and director of Kennedy Krieger's Center for Autism and Related Disorders. "If they're concerned, they shouldn't wait to see a professional for immediate in-depth screening and developmental surveillance. We know from other research that the sooner you can diagnose autism and start intervention, the better the child's outcomes."

In addition to Landa and Law, authors of this paper are Luther Kalb and J. Kiely Law, both of Kennedy Krieger Institute. Lead author, Luther Kalb, will present these findings in May 2010 at the International Meeting for Autism Research in Philadelphia, PA.

This research study was supported by grants from Autism Speaks.

About Autism

Autism spectrum disorders (ASD) is the nation's fastest growing developmental disorder, with current incidence rates estimated at 1 in 100 children. This year more children will be diagnosed with autism than AIDS, diabetes and cancer combined, yet profound gaps remain in our understanding of both the causes and cures of the disorder. Continued research and education about developmental disruptions in individuals with ASD is crucial, as early detection and intervention can lead to improved outcomes in individuals with ASD.

Dual Approach Gives a More Accurate Picture of the Autistic Brain

ScienceDaily (Apr. 22, 2010) — A new study, the first of its kind, combines two complementary analytical brain imaging techniques, to provide a more comprehensive and accurate picture of the neuroanatomy of the autistic brain. The study, published in the April issue of neuroimaging journal Human Brain Mapping, was conducted by researchers at The Montreal Neurological Institute and Hospital -- The Neuro, McGill University and the Université de Montréal. The findings provide critical insight into autism and possible markers for the disease for use in early therapy and therapeutic strategies.

Autism is a complex spectrum disorder thought to affect 1 in 166 people. Autistic individuals have difficulties with social interaction, communication and repetitive behaviours, which can lead to isolation and emotional problems. They may also have enhanced abilities particularly in auditory and visual perception.

Although structural brain differences have been reported in autism, the reports are inconsistent. The Neuro research team's objective therefore was to investigate neuroanatomical differences using a dual-analytic approach, combining cortical thickness analysis (CT) and voxel-based morphometry (VBM) together for the first time in the same participants. The team studied a group of young adults with autism of average intelligence and similar language ability relative to closely matched typically developing controls.

"The findings are significant from a functional perspective because the anatomical differences are found in brain regions known to play a functional role in the core features of autism such as social communication and repetitive behaviours, says Dr. Krista Hyde, research fellow with Dr. Alan Evans at The Neuro, and lead investigator in the study. "This is the first step to looking for clues or markers that would help us correlate structural differences with functional and behavioural characteristics."

The advantage in analyzing brain anatomy using CT and VBM is the complementary nature of the two methods, which in combination provide a direct measure of cortical grey matter, regions of the brain that consist primarily of nerve cell bodies. The combined method also provides a measure of subcortical grey matter as well as white matter, regions of the brain composed mainly of nerve cell fibres which have myelin sheaths, the protective covering that insulates and supports nerve cells. "The converging results found from CT and VBM analysis, allows us to make more confident interpretations about the structural brain differences found in autism," adds Dr. Hyde.

Regional differences in grey matter were found in socially-relevant and communication-related brain areas, as well as in areas implicated in repetitive behaviours and those found to play a role in empathic behavior. The study also identifies grey matter increases in autism in the visual cortex and for the first time, in the primary auditory cortex. "We believe that the visual and auditory cortical thickness increases may be related to enhanced visual and auditory perception in autism."

"These new results are extremely important because they offer a more accurate picture of the autistic brain, helping researchers improve early autism treatment strategies," says Dr. Anthony Phillips, Scientific Director of the Canadian Institutes of Health Research (CIHR) Institute of Neurosciences, Mental Health and Addiction. "Autism rates have been rising steadily in Canada, so CIHR is proud to support researchers who devote their time to look into this neurological condition."

The study's findings provide vital insight into autism by identifying structural differences in functionally relevant areas of the brain in a group of individuals with autism using a dual analytic approach for the first time.

The study was funded by The Canadian Institutes of Health Research.

Guillain-Barré Syndrome Cases Low After 2009 H1N1 Vaccine

ScienceDaily (Apr. 21, 2010) — A new study finds that reports of a neurologic disease called Guillain-Barré syndrome (GBS) have been low after 2009 H1N1 vaccination, according to a research study that will be presented as part of the late-breaking science program at the American Academy of Neurology's 62nd Annual Meeting in Toronto, April 10 -- 17, 2010. The study is one of the first national reports of the occurrence of GBS after 2009 H1N1 vaccination.

GBS is a rare disorder in which the body's immune system attacks part of the peripheral nervous system, causing tingling and weakness of the arms and legs. While it is not fully known what causes GBS, it is known that about two-thirds of people who get GBS do so several days or weeks after they have been sick with diarrhea or a respiratory illness. Except for the swine flu vaccine used in 1976, no other influenza vaccines have been clearly linked to GBS. It was not anticipated that the 2009 H1N1 vaccine would be associated with an increased risk of GBS.

Scientists analyzed information obtained from the Centers for Disease Control and Prevention and US Food and Drug Administration Vaccine Adverse Event Reporting System (VAERS) and found that there were 35 reports of GBS following 2009 H1N1 vaccination around the country by the end of the year 2009. This amounts to 3.5 reports of GBS per 10 million people vaccinated. All cases of GBS except one were reported within six weeks of vaccination, with 23 cases reported within the first two weeks after vaccine administration. One report of death and one of disability were reported in the 33 patients who were hospitalized.

The number of GBS cases reported by the same researcher was only slightly higher after seasonal flu vaccination in 2009: 57 reports of GBS were received by VAERS , an estimated rate of 7.3 reports of GBS per 10 million vaccinations. The rate of GBS in the general population is estimated to be between one to four cases per 100,000 persons per year.

"Although preliminary, these reported cases of GBS do not appear to show an increased risk of GBS following vaccination with either the 2009 H1N1 or the seasonal flu strain and the safety record for these vaccines is excellent," said study author Nizar Souayah, MD, with New Jersey Medical School in Newark. "CDC, FDA and neurologists around the world are continuing to closely monitor people after vaccination for this disease."

Since VAERS receives voluntary reports of adverse events from manufacturers, providers, vaccines, and caregivers, cases of illness may be either over or underreported, and calculation of actual rates is not possible. VAERS cannot determine cause-and-effect, and an adverse event report only indicates that the event occurred sometime after vaccination. The American Academy of Neurology, along with the Centers for Disease Control and Prevention reached out to neurologists in the fall of 2009, requesting that they report to VAERS any possible new cases of GBS following receipt of vaccination.

More vaccination news, some good, some not so good

I have a couple of news items from Dr. Plait's blog today. One is a collection of vaccine news, but another is a story that should hit home to people.

More vaccination news, some good, some not so good

Some vaccine news I missed in the past few days…

1) A pertussis outbreak in California has already killed two infants. This event resonates with what happened in Australia a year ago; vaccination rates are low, and the victims are too young to be vaccinated themselves. With herd immunities compromised, the littlest and most defenseless reap the effects. This is not necessarily caused by the antivaxxers, but it’s worth noting.

2) There is apparently a small outbreak of polio in Tajikistan. Vaccinations are critical, but so is sanitation.

3) PBS airs a documentary called "The Vaccine Wars" tonight. It’s about what you think it’s about. Check your local listings.

4) H1N1 is still out there, and still hurting and killing kids.

5) A bunch of kids got pretty sick after vaccinations in Australia. It’s unclear what happened, and officials are investigating it.

6) The good news? At least for Finland, it’s good: 97% of kids there are vaccinated. For everything. Amazing.

Tip o’ the needle to Antti Säämänen, Doug Troy, William Mount, and Greg Stitz.

Help a kid with leukemia… and help many, many more

Heather Steingruebl is a BABloggee. She contacted me and told me some chilling news: her daughter Elise was recently diagnosed with leukemia. She’s being treated, and I know we all hope things go well for her.

But in the meantime, this makes Elise susceptible to many preventable diseases. We need people to get vaccinated! As Heather says,

Vaccinate. Elise and thousands of kids like her are counting on not dying from things like measles and whooping cough while they fight cancer. Unless it’s a specific health risk to you or your child, just vaccinate. Please.

She also implores people to get on the bone marrow donation registry. Search around online for information on how to do this. I plan on doing this myself.

My heart goes out to her and her family, as it does to anyone affected by this awful illness. I’m going to find out what booster shots I need, because I take this issue very seriously. I hope you do too.

I just found a blog called Photon In The Darkness, and plan to add it to my feed. The author has some great articles up, and I think that there will be plenty more. I would like to highlight one of them as an inaugural article from there. This is one of those cases where, as repeatedly stated, humans are very poor at assessing risk.

Let’s run the vaccine risk/benefit numbers!

March 12th, 2010

While reading another ‘blog, I found - in the comments - one of the worst examples of “bad epidemiology” I have ever seen. I won’t embarrass the commenter by name or by quoting, but the gist of their “argument” was that (in the US) the risk of vaccination exceeds the risk of the vaccine-preventable disease.

I think we’ve all heard that before.

There were many problems with their math, not the least of which was being too lazy to look up the actual numbers, but I realized that this was the tip of a much larger iceberg of innumeracy, especially as it pertains to understanding prevalence and risk.

So, to begin at the beginning, let us start with fractions.

Most of the time, risk or prevalence is expressed as a fraction, although it may not always look like a fraction (e.g. 1 in 100 is the same as the fraction 1/100). And - harkening back to our elementary school days - the two components of a fraction are the numerator (the top number) and the denominator (bottom number).

I bring up these apparently irrelevant mathematical issues because, in the world of risk and prevalence, there are two major types of errors: numerator errors and denominator errors (although, sometimes, there are errors of both).

In the example I mentioned above (the ‘blog comment), the risk of contracting a certain vaccine-preventable disease was calculated (wrongly, I must add) by dividing the number of people in the US who contracted that disease in a year by the population of the US. This was then stated - indirectly - to be the risk of an unvaccinated person contracting the disease.

Perhaps you’ve already noticed the error - it’s a denominator error. Since most people in the US are already immune to this disease (mostly by vaccination), the proper denominator would have been the number of unvaccinated people in the US. Let’s see how this changes the numbers:

If we use measles as an example, there were 140 cases of measles reported in 2008 (still compiling and verifying 2009 reports). At the end of 2008, according to the US Census Bureau, there were 300,459,786 people in the US. If we use the incorrect method from the example, that would give a “risk” of contracting measles of 0.47 per million per year (1 in 2,146,141 per year).

That seems a pretty low risk, doesn’t it? It’s a bit higher than your “risk” of winning the Powerball lottery, but still quite low.

But is it accurate? [Hint: No]

The correct way to calculate your risk of contracting measles is to divide the number of reported cases in the US by the number of vulnerable people in the US. By “vulnerable”, I mean those people who haven’t been vaccinated and haven’t had measles. That is a bit harder number to find.

The CDC’s NIS shows that, in 2008, 92.1% of children ages 19-35 months had received at least one MMR vaccination. Going back as far as 1994, that number seems fairly steady - about 90 - 92%. By the age of school entry, that percentage (in the 2007 - 2008 school year) was up to 94.9%. Even if we assume that this percentage doesn’t change, it would mean that - at most - 5% of the population is vulnerable to measles.

But even that isn’t an accurate number, because people born before the measles vaccine was available (1963) - and even the years immediately after the vaccine was introduced - would have gotten the disease if they weren’t vaccinated (it is highly contagious).

By 1968, the incidence of measles had dropped low enough to assume that anyone born after 1968 who was not vaccinated is not immune. So, that means that 5% of the US population age 41 or less is vulnerable to measles. This estimate compares with the value found by Hutchins et al (2004) for measles immunity in 1999, which supports the estimate.

According to the US Census Bureau, there are about 172 million people in the US age 41 years or less, so that gives us - at most - 8.6 million vulnerable people. Now the risk of contracting measles is 140 divided by 8.6 million or 16.3 per million per year (1 in 61,428).

After calculating the risk of contracting measles, we need to calculate the risk of death or serious complications. Measles has a case-fatality rate of 2 per thousand, so the risk of contracting measles and dying of it is about 0.03 per million per year - in the current situation, where 95% of the population is immune.

Other serious complications of measles include pneumonia (about 6% of cases) and encephalitis (1 per 1000 cases). Adding these to the risk of dying brings the total risk of serious complications to 0.8 per million per year. If we exclude pneumonia as a “serious” complication, the combined risk of contracting measles and having a permanent, life-altering (or life-ending) complication is 0.05 per million per year.

The risk of serious complications (i.e. death or permanent disability) from the MMR vaccine (discounting the as-yet-undemonstrated “autism connection”) is less than 1 per ten million doses (1 per million allergic reaction, less than 10% of which are “life threatening” = less than 1 per ten million), which (because the recommendation is two doses) works out to less than 0.2 per million per lifetime. With an average lifespan of 75 years, that works out to less than 0.003 per million per year, so the risk from the disease is over ten times greater than the risk of the vaccine even with 95% of the population immune.

Oh, and by the way - the MMR vaccine protects against three diseases, not just measles. We’ll just ignore that for right now.

And even this approximation doesn’t show the true risk of forgoing just the measles vaccine (let alone the MMR) because we haven’t considered how having a large immune population prevents spreading and how that has limited the number of measles cases reported.

Measles is transmitted from person-to-person, a single infection provides life-long immunity and it has no non-human reservoir and no known long-term carrier or dormant state. In this respect, it is similar to smallpox, polio, mumps, rubella, and many other vaccine-preventable diseases. If it is not transmitted, the measles virus “dies out”. It doesn’t “hang out” in the environment. That is why measles could be eradicated, just as smallpox was.

Currently (since 2000), measles is not endemic in the US, largely because there aren’t enough susceptible (non-immune) people in close enough contact to keep the virus going. Measles in the US is an imported disease that, until 2008, was rarely transmitted beyond the person importing it and any under-age (i.e. less than 2 years old) or immune-compromised people they came in contact with.

Starting in about 2008, the percentage of immune people in the US had slipped far enough that imported cases were able to spread locally in pockets of non-immune people. The August 22, 2008 edition of Morbidity and Mortality Weekly Report (MMWR) details two outbreaks of measles that occured in the US that year. In both cases, the outbreaks occured within groups that did not vaccinate for religious or philosophical reasons and were home-schooled.

This latter point is worth noting - even though these children did not attend a public or private school, they still contracted measles from one another.

Here is a telling statement from the MMWR report:

The number of measles cases reported during January 1–July 31, 2008, is the highest year-to-date since 1996. This increase was not the result of a greater number of imported cases, but was the result of greater viral transmission after importation into the United States, leading to a greater number of importation-associated cases. These importation-associated cases have occurred largely among school-aged children who were eligible for vaccination but whose parents chose not to have them vaccinated. [emphasis added]

As the percentage of non-immune people in the country rises, imported measles cases will spread to more people, further raising the risk of infection to non-immune people and increasing the already large benefit to risk ratio of vaccines.

What this shows is that those people who choose to not vaccinate should - at the least - take precautions against associating with other people who don’t vaccinate. This would help reduce their risk of infection to the levels I calculated above.

Perhaps they should wear some sort of lapel pin, similar to what many fraternal organisations (e.g. Masons, Rotarians, etc.) have. Except, of course, that instead of stepping forward and embracing when they see a fellow member (with or without secret handshake), they should immediately turn about and walk briskly in opposite directions, to avoid transmitting vaccine-preventable diseases.

As the events of 2008 showed us, there will not be a gradual increase in measles spread as vaccine coverage declines - there will most likely be an abrupt increase as the percentage of non-immune people (and their proximity to one another) crosses a critical threshold.

And it is important to note that non-immune people are not just the children of parents who choose not to have them vaccinated. They include children too young to be vaccinated and people who are immune-suppressed due to disease, cancer or genetic disorders. They include the elderly, whose immune systems are weaker, and those people who - for one reason or another - did not develop an adequate immune response to vaccination.

Those who choose to not vaccinate and think they are letting others take the risks for them are fooling themselves; they are taking the greater risk - even now.

Prometheus

Non-hyperlinked References:

Hutchins SS, Bellini WJ, Coronado V, et al. Population immunity to measles in the United States, 1999. J. Infec. Dis.. 2004; 189(Suppl 1):S91–7

Measels outbreak because anti-vax is dangerous

Measles Resurgence Tied To Parents' Vaccine Fears

A generation ago, up to 4 million U.S. children got measles every year. Hundreds died, and thousands were left with permanent brain damage. Thanks to vaccination, those days are over, at least in this hemisphere. But health officials worry about the growing number of children who are vulnerable when somebody brings measles from another part of the world.

It happens regularly. Vancouver is trying to contain a measles outbreak sparked when foreign travelers visited for the Olympics, carrying two different measles viruses from Asia.

The first recognized infections — in two Canadians and a visiting American — occurred around the Olympic closing ceremonies. "Downtown Vancouver was shoulder-to-shoulder on many days of that period," notes Dr. Monika Naus of the British Columbia Centre for Disease Control.

So far, measles has spread to 16 people in Vancouver, Naus says. Half of them are in one large unvaccinated household. The parents reject vaccination.

"It's not a religious issue," Naus says. "A friend of the family who had anti-vaccination sentiments was influential in convincing them not to get vaccinated."

Many parents who refuse to get their children vaccinated worry that vaccines — and the one for measles, mumps and rubella in particular — cause autism. It's a belief that persists despite years of studies and expert panels that find no scientific link.

Health officials say there are growing pockets of vaccine refusers in communities across the land. The numbers are not great. But these pockets of "intentionally unvaccinated" children give the virus more opportunities to spread when it does arrive.

And even if the number of measles cases in each outbreak is kept small, the arrival of measles disrupts lives and forces public health officials into high gear to contain the damage.

Ask Karen Waters-Montijo, chief of immunization at the San Diego County health agency. She and her colleagues, including officials at the U.S. Centers for Disease Control and Prevention in Atlanta, write about the impact of a 2008 measles outbreak in the April issue of the journal Pediatrics.

Waters remembers the February day when a public health nurse called to report a confirmed case of measles: a 7-year-old boy who had picked up the virus during a family trip to Switzerland.

As unlikely as it seems, Switzerland is one of those European countries where measles vaccination rates have fallen considerably below 95 percent — the level public health officials say is necessary to prevent measles from circulating in the community.

When Waters heard about the case, she says, "I just about fell off my chair. The child had two siblings, attended public school. The family wasn't vaccinated. And in fact, there were a lot of unvaccinated children at the school, as well."

They were "intentionally unvaccinated," meaning their parents had filed Personal Beliefs Exemption forms to opt out of the vaccinations that are required for schoolchildren. Parents of almost 10 percent of the students at Patient Zero's school had signed PBE forms.

That may not sound like much. But no virus is more contagious than measles. "If a measles-infected person walks into a room with 10 uninfected people," says Dr. David Sugerman of the CDC, "nine of them will get infected."

Moreover, anyone who goes into that room within the next two hours after the infected person has left is likely to get measles, too.

So Waters and her colleagues were alarmed when they learned that it had taken a week before the measles infection of Patient Zero was diagnosed. In the meantime, he had exposed many people in doctors offices and clinic waiting rooms, as well as in school. He had also infected his siblings, and they had exposed many others.

"It was slow to be recognized, and there's a good reason for that," Waters says. "We hardly ever see any measles cases. Most doctors have never seen a case." Once the first patient was diagnosed, moreover, health authorities were slow to be notified.

Once they found out, health authorities kicked into gear, tracing everybody who came into contact with the first cases — and everybody who was in contact with them. That net captured people who got exposed (and, in some instances, infected) at supermarkets, circus performances, fairgrounds and a Hawaii-bound airplane.

It added up to 839 people. Of those, 73 were unvaccinated children — 25 whose parents chose not to get them vaccinated, and 48 children under 12 months who were too young to be vaccinated.

To limit the spread of the virus, San Diego County officials asked parents of those 73 children to keep them at home. Many of them were pretty unhappy about that.

"Imagine, you start off on a normal day," Waters says, "and you're getting ready to drop your child off at their child care place, and you're greeted by a public health nurse who says your child has been exposed to measles, and we'd like you to go home and be there for the next three weeks while we monitor you for symptoms."

Parents of exposed children who believed in vaccination were incredulous and angry, she says: "They said, 'What do you mean, people don't get vaccinated? Why is this happening?' "

In the end, the San Diego outbreak was confined to a dozen children. No big deal, you might think — except that it upended a lot of lives, and the county spent $10,000 for each of those cases in order to keep the virus from spreading more widely. That, and the fact that more than 95 percent of the general population was immune, kept the outbreak far more limited than the previous San Diego measles outbreak in 1991, when there were 1,000 cases and three deaths.

Afterward, Waters and her colleagues looked into who the vaccine refusers were and what their attitudes toward vaccination were.

They're college educated, higher-income and believers in the power of a "natural" lifestyle — things like organic food and prolonged breast-feeding — to keep their children's immunity strong enough to ward off vaccine-preventable diseases.

And they just don't believe it when government officials like Karen Waters say vaccines don't cause autism.

"It is wrapped up in their attitudes about government," Waters says. "I don't think they think I'm the enemy. I think they think I'm well-intended but misinformed."

Many communities have pockets of vaccine refusers. So the United States and other countries with growing numbers of "intentionally unvaccinated" people are likely to see more outbreaks.

There's bound to be occasional importation of measles from countries with circulating virus. These aren't only developing nations; they include Ireland, Germany, Israel, Japan and the United Kingdom, where measles had been eliminated until large numbers of parents started opting out of vaccination programs.

CDC officials are watching the Vancouver outbreak closely, as neighboring Washington state has sizable populations of vaccine refusers.

"If measles crossed the border into those populations, there's a potential for a sizable outbreak," says Dr. Jane Seward of the CDC.

Back in San Diego, Karen Waters is still trying to persuade skeptical parents to get their children vaccinated. She says refusers are not bad guys in this drama.

"You know, these are very nice people," she says. "They care a lot about children, as I do. We all want safe vaccines. We all want healthy children, and we all want answers about autism. It's unfortunate there's a group of people who are off on this track, that believe vaccines are at the root of this problem."

So far Waters hasn't changed many minds. She knows of a thousand families who have refused to get their kindergartners vaccinated. That's 100 more since that last San Diego measles outbreak.

Why I HATE the term "Missing Link"

The popular press will readily describe ANY kind of newly discovered hominid fossil as a missing link, which for 99% of the time is just BS as there wasn’t any missing link before the find. Additionally, it is almost always claimed that it will “rewrite our understanding of the history of the human species” or some such tripe.

The press blows a lot of science out of proportion and helps to mess up the general public’s understanding of what’s going on. This will certainly not, “rewrite the history of human evolution by filling in crucial gaps in the scientific knowledge.” It certainly will give us more knowledge and fill in details that were previously fuzzy. Wording like this keeps people unreasonably skeptical of science, making them think that scientists have no idea what they are talking about because every new thing “rewrites” our understanding. If everything says everything else is false, why should we trust science? And then the media turns around and makes fun of people for being “ignorant”…

This looks like an interesting find that will add to our existing knowledge of human evolution – all fine and good, but it’s not revolutionary in any way since its discovery really was to be expected from what we already knew.

New Hominid Shares Traits With Homo Species: Fossil Find Sheds Light on the Transition to Homo Genus from Earlier Hominids

Two partial skeletons unearthed from a cave in South Africa belong to a previously unclassified species of hominid that is now shedding new light on the evolution of our own species, Homo sapiens, researchers say. The newly documented species, called Australopithecus sediba, was an upright walker that shared many physical traits with the earliest known Homo species -- and its introduction into the fossil record might answer some key questions about what it means to be human.

The fossils are between 1.95 and 1.78 million years old, and in this week's issue of Science, the peer-reviewed journal published by AAAS, the nonprofit science society, two reports describe both the physical characteristics of this new Australopithecus species as well as the ancient environment in which it lived and died. The emerging picture is one of a hominid with a bone structure similar to the earliest Homo species, but who employed it more as an Australopithecus, like the famed "Lucy," would have.

These new fossils, however, represent a hominid that appeared approximately one million years later than Lucy, and their features imply that the transition from earlier hominids to the Homo genus occurred in very slow stages, with various Homo-like species emerging first.

"It is not possible to establish the precise phylogenetic position of Australopithecus sediba in relation to various species assigned to early Homo," wrote Lee Berger, a lead author of one of the Science reports. "We can conclude that… this new species shares more derived features with early Homo than any other known australopith species, and thus represents a candidate ancestor for the genus, or a sister group to a close ancestor that persisted for some time after the first appearance of Homo."

Many scientists believe that the human genus Homo evolved from Australopithecus a little more than two million years ago -- but the origin has been widely debated, with other experts proposing an evolution from the Kenyanthropus genus. This new Australopithecus sediba species might eventually clear up that debate, and help to reveal our direct human ancestors.

"Before this discovery, you could pretty much fit the entire record of fossils that are candidates for the origin of the genus Homo from this time period onto a small table. But, with the discovery of Australopithecus sediba and the wealth of fossils we've recovered -- and are recovering -- that has changed dramatically," Berger said.

The name itself, "sediba," means "fountain" or "wellspring" in the seSotho language, spoken in South Africa, and indeed, researchers do believe that the new fossils will provide a wealth of information about our human origins.

For now, these new hominid fossils make it clear that the evolutionary transition from small-bodied, and perhaps more tree-dwelling, ancestors to larger-bodied, full-striding bipeds occurred in gradual steps.

Berger, from the University of Witwatersrand in South Africa, along with Paul Dirks from James Cook University in Australia began a study on the distribution of cave deposits in the Cradle of Humankind -- a World Heritage Site, set aside for its physical and cultural significance -- in January 2008. Months later, Berger discovered the two partial skeletons in cave deposits at Malapa, South Africa, and analyzed the remains, including most of a skull, pelvis, and ankle of the new species with colleagues from the U.S., Switzerland, and Australia.

The two Australopithecus sediba -- an adult female and a juvenile male -- were found close together in a portion of the cave system that had been protected from scavengers, so the fossils are very well-preserved. The researchers describe the hominid's physical traits, highlighting the unique pelvic features and small teeth that it shared with early Homo species. Based on its physique, they suggest that the new species descended from Australopithecus africanus, and that the hominid's appearance signified the dawn of more energy-efficient walking and running.

"These fossils give us an extraordinarily detailed look into a new chapter of human evolution, and provide a window into a critical period when hominids made the committed change from dependency on life in the trees to life on the ground," said Berger. "Australopithecus sediba appears to present a mosaic of features demonstrating an animal comfortable in both worlds."

In a separate report published in Science, Paul Dirks and colleagues from around the world analyze the Malapa cave system, date the fossil deposits, and describe the geological and ecological environment that Australopithecus sediba would have dwelled in long ago.

"We think the environment sediba lived in was, in many ways, similar to the environment today," Dirks said. "For example, one with predominantly grassy plains, transected by more vegetated, wooded valleys. However, the rivers flowed in different directions and the landscape was not static, but changed all the time."

The caves at Malapa are not randomly distributed, but occur along fracture zones that criss-cross the landscape. They consist of mostly quartz, chert, dolomite, and peloids -- though there are also iron-oxide coated grains, ooids, shale, and feldspar in the rocks.

"The fossils occur together in a near-articulated state in the sedimentary remains of a deeply eroded cave system," Dirks continued. "They were laid down by a single debris flow, indicating the timing of their deaths were closely related and occurred shortly before the debris flow carried them to their place of burial."

The researchers identified the fossils of at least 25 other species of animals, including saber-toothed cats, a wildcat, a brown hyena, a wild dog, antelopes, and a horse in the cave as well. They suggest that the Malapa caves were tens of meters deep when the Australopithecus sediba fossils were deposited -- and also propose that the cave dwelling could have acted as a death trap for animals seeking water.

"One possible explanation for their entry into the cave could have been that they needed water," said Dirks. "To explain the fossil assemblage and their well-preserved state, we would speculate that perhaps at the time of their death, the area in which sediba lived experienced a severe drought… Animals may have smelled the water, ventured in too deep, fallen down hidden shafts in the pitch dark, or got lost and died."

Science writer Simon Singh wins libel appeal

More good news for the forces of reality.

A science writer has won the right to rely on the defence of fair comment in a libel action, in a landmark ruling at the Court of Appeal.

Simon Singh was accused of libel by the British Chiropractic Association over an article in the Guardian in 2008.

Dr Singh questioned the claims of some chiropractors over the treatment of certain childhood conditions.

The High Court had said the words were fact not opinion - meaning Dr Singh could not use the fair comment defence.

However, the Lord Chief Justice Lord Judge, Master of the Rolls Lord Neuberger and Lord Justice Sedley ruled High Court judge Mr Justice Eady had "erred in his approach" last May, and allowed Dr Singh's appeal.

BBC News science correspondent Pallab Ghosh says that, had Justice Eady's ruling stood, it would have made it difficult for any scientist or science journalist to question claims made by companies or organisations without opening themselves up to a libel action that would be hard to win.

Dr Singh described the ruling as "brilliant", but added that the action had cost £200,000 "just to define the meaning of a few words".

"After two years of battling in this libel case, at last we've got a good decision. So instead of battling uphill we're fighting with the wind behind us," he said.

"The Court of Appeal's made a very wise decision, but it just shouldn't be so horrendously expensive for a journalist or an academic journal or a scientist to defend what they mean.

"That's why people back off from saying what they really mean."

The British Chiropractic Association said it was disappointed to lose the appeal but it was "not the end of the road".

BCA president Richard Brown said: "We are considering whether to seek permission to appeal to the Supreme Court and subsequently proceed to trial.

"Our original argument remains that our reputation has been damaged. The BCA brought this claim only to uphold its good name and protect its reputation, honesty and integrity".

In the article in April 2008, Dr Singh suggested there was a lack of evidence for the claims some chiropractors made on treating certain childhood conditions such as colic and asthma.

The BCA alleged that Dr Singh had effectively accused its leaders of knowingly supporting bogus treatments.

The case has become a cause celebre for the science community and led to calls for defamation law to be rewritten so it does not interfere with scientific debates.

His high-profile supporters include Stephen Fry, Ricky Gervais and Harry Hill, all from the world of entertainment.

Dr Singh said: "The judges are clearly unhappy on how libel laws can impact on discussion, on how this libel suit has quashed debate about chiropractics to a large extent.

"They're particularly unhappy about the way scientific discussion can be silenced by libel laws. That's a real boost to the libel reform campaign."

Coalition for Libel Reform spokeswoman Tracey Brown said: "This case has brought out of the woodwork the fact that so many other discussions are being killed, from discussions of cardiology to human rights to medicines.

"We're now pushing ahead for bigger changes to the law so that we have the kind of public interest defence that means it wouldn't have taken two years and £200,000 to find out whether Simon can defend himself."

British scientific organisation the Royal Institution welcomed the judgement.

Director of programmes Gail Cardew said: "It will encourage scientists and the public to discuss evidence freely without fear of legal threat."

Quick Post from Dr. Plait

I have been swamped with numerous other duties, and my team of collaborators have not had a chance to take up the slack. Thus, i just wanted to copy/paste a couple of real quick posts from Dr. Plait that may be of interest to you:

More truth-based weapons against the antivaxxers

A few antivax links for your amusement:

1) When challenged about their bizarre and provably false beliefs, a lot of antivaxxers claim that they have personal experience with their kid. That’s anecdotal and uses a small sample size, and so is prone to all sorts of logical failings. But what if the sample size is much larger and uses scientific reasoning? Then you get something like this good spanking of antivax nonsense by an actual pediatrician.

Tip o’ the syringe to David Whalley.

2) The Australian Vaccination Network is one of the most pernicious and awful of the antivax groups, as regular readers know. They may be on their way out — science, apparently, can inoculate us against such infections — but it’s still worth keeping up with the sort of offal they spew, since other groups do it as well. This article by The Australian Skeptics is an excellent exposé of AVN mendacity.

3) Healthday has an alarming article about the San Diego 2008 measles outbreak which exposed over 800 people because one family decided not to vaccinate their kid. Yes, one family started an minor epidemic that cost over $170,000 to contain and nearly killed one infant. I hope antivaxxers are proud of that one.

4) Orac once again leaps into the fray with a magnificent exposure of some bold antivax lies. It’s amazing to me just how low some antivaxxers are wiling to go — cheating, twisting, distorting, and out-and-out lying — to promote their agenda of bringing back preventable diseases.

They say they care about kids. Maybe they do. But making sure children get measles, rubella, pertussis, and other life-and-limb-threatening diseases is sure a funny way of showing it.

Taking the Plunge

Dylan Otto Krider wrote a nice piece about antivaxxers in the Denver magazine recently. He interviewed me for it, and I’m pleased with how it came out. Otto is one of the good guys, and one of the few in the MSM willing to take this topic on without pandering to nonsense to provide false "balance":

One of [Plait's] latest causes has been debunking the antivax movement that he sees as dangerous. “They don’t have anything to stand on except emotions,” he says. “They play on the heartstrings, and unfortunately, people tend to listen to their emotions.”

He says the antivax movement is having an effect. “You can see it,” he says. “The number of people getting vaccines is going down.” What he finds particularly annoying is that when things change — for example, thimerosal has been largely, although not entirely, eliminated as a preservative in vaccines — antivax groups just “move the goalposts” and claim vaccines do something else.

I’m glad to see this getting more press, and I’m very glad to see the antivaxxers getting hit harder and harder. Every time their garbage is aired out, a few more kids get a chance to live a life with a lower risk for preventable diseases.