Facts, not Fantasy

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Saturday, May 29, 2010

We all love Dr. nancy Snyderman

I didn't know about this post over at the JREF Forums for a while, but it recently got bumped up so I got a chance to read it.  Seems Dr. Snyderman has some great things to say, and some good ole fashioned smack down on idiots.

Dr. Nancy Snyderman is NBC's chief medical editor. This morning she did a profile of Dr. Paul Offit, author of the new book Autism's False Prophets.

The profile was pretty good, not great, it missed a few points. But check out what happened during the "outro" after the report. Dr. Snyderman had mentioned that she personally had been "physically ambushed" by anti-vaccine people, and then she totally got into Matt Lauer's face about referring to the vacccines/autism thing as "controversial."

It was a sight to behold:


Dr. Nancy Snyderman: Its time for everyone to redirect the questions toward finding the cause of autism. It is NOT, however, vaccinations.

Matt Lauer: Controversial subject, Nancy.

Snyderman: NOT controversial subject!

Lauer: Well but controversial for parents who still believe.

Snyderman: It is not controversial, Matt! It's time for kids to get their vaccines.

Lauer: If it weren't controversial you wouldn't be ambushed.

Snyderman: No! It's not controversial. I really mean that. The science is the science. We are going to start to see outbreaks of polio and measles in this country if we don't start talking about the real problem. It's NOT controversial.

Lauer: We will talk about it more here, Nancy, thanks.

Snyderman: You bet, Matt.

Lauer: We're back right after this.
Kudos, Dr. Snyderman, kudos.

There is a complete video online as well.  The good part where she smacks down Lauer at the end starts around 5:00  http://today.msnbc.msn.com/id/26184891/vp/27453507#27453507  (Flash & Javascript required, of course, as for most web videos.)

If you click on the title of this blog, then you can go to the thread where this discussion is going on at the JREF.  There are a few more posts about Dr. Snyderman as well as a few more NBC spots and the Nightline show.  There is also the cranks that still think that vaccines are poison and such.  Their posts are almost funny if it wasn't for the public danger they represent.

Skeptics PWN Anti-Vax Scumbag Wakefield at His Own Rally

There is really nothing much I can add to this, so I will just paste it, and leave it be:

Skeptics PWN Anti-Vax Scumbag Wakefield at His Own Rally

Posted by mattusmaximus on May 27, 2010
**Update: Check out my follow-up post for more news, photos, and video of this event.
============
Well, congratulate me folks – I’m now officially part of a squad of skeptical ninjas :)
Today, there was an anti-vaccination rally in Chicago, and the king of anti-vax woo & nonsenseAndrew Wakefield himself – showed up. I suppose he decided to hang with his anti-vax homies here in the U.S. seeing as how he’s essentially lost his license to practice medicine in the United Kingdom because of his fraudulent work there.
Anyway, the new skeptical group I’m part of, the Women Thinking Free Foundation (WTFF), caught wind of this wave of woo headed our way (we’re based in Chicago) and we decided, with two days notice, to mobilize and counter protest… and we did! I did not personally attend the counter protest, as I had to teach today, but I and many others were working behind the scenes to help organize it.
The word went out like wildfire across the Internet – via email, Facebook, Twitter, blogs, and message boards – and we were able to gather a group of about 10 people there. In addition, our WTFF ninjas were able to hand out plenty of pro-vaccine literature to passers-by who might have otherwise thought that Wakefield and his ilk weren’t batcrap crazy. Here are some examples of our handouts we whipped up as part of WTFF’s new “Hug Me, I’m Vaccinated!” campaign…
It went really well. Apparently, a whopping 50-100 anti-vaxxers showed up; ironically, with just a couple of more days of prep & organization, we might have been able to have almost as many pro-science people there. In addition to handing out literature, our skeptical ninjas also took some photos & video, which I will share with you after it is all processed. Until then, I leave you with this little gem…

That’s Wakefield in the middle, unwittingly posing with two of our skeptical ninjas who infiltrated his rally. In fact, the girl is wearing a Surlyramics necklace that says “Hug Me, I’m Vaccinated!” and moments before this snapshot was taken she handed him a note. It said how much of a horrible person he is for spreading anti-vax nonsense and scaring people out of vaccinating their children. She told me that he didn’t look at it & just put it in his pocket, thinking that he got the phone number from some hot young lady. Here is the text of what she wrote:
Dear Andrew Wakefield,
I know that you truly believe that what you are doing is helping people and that the ends justify the means, but I just want you to know that the things you are doing – the actions you have taken in the past have hurt people – killed people. Your work has scared and manipulated parents into not vaccinating their children, putting them and their entire community at risk, all in the name of safety. Children have died because of you. I just want to make sure that you fully understand that.
Sincerely,
**********
Message to Wakefield and the anti-vax woosters:
I’m reasonably sure there will be more photos & video to follow. Watch this space for updates.
This whole affair was, in my humble opinion, an outstanding success. In this “Hug Me!” event, we have officially put Wakefield and his ilk on notice that anywhere they go, they’re likely to be confronted by skeptics who are willing to stand up to their nonsense & fear-mongering woo. We at WTFF hope that this event will serve as a template for other skeptical & pro-science groups to follow in monitoring & holding pseudoscientific folk like Wakefield accountable in the court of public opinion.

A bit of Wakefield Research

So over at the James Randi Educational Foundation, one of the users did a bit of research and dug up this interesting bit of information:

I just realized Brian Deer has posted page images of the entirety of Wakefield's original 1997 patent application for the so-called "measles vaccine" he was planning on making his fortune from, once he's discredited MMR. The final 1998 version is also there.

http://briandeer.com/wakefield/vaccine-patent.htm
http://briandeer.com/mmr/1998-vaccine-patent.pdf

It will make hilarious reading for all the biomedical scientists here. It's the whole goat colostrum transfer factor thing, which is utter woo from start to finish. It's dressed up as science, but he's really just dreamed up the whole thing on the back of the theorizing of a quack called Fudenberg.

This makes it quite clear that the project to market his product was well advanced before the controversial paper was even published. The money he was getting for investigating these children and supporting their legal actions was only the start of it, and frankly small beer to what he seems to have been expecting to make if the MMR had been withdrawn and his goat colostrum nostrum adopted instead.

So far as I know, no safety or efficacy testing was ever done on this snake-oil.

I also sort of wonder how many mice he envisaged using in the first stage of the manufacture, and then how many pregnant goats would have been needed to provide enough of this product for widespread use? What about the kids they produced, which would be surplus to requirements once born, and also vulnerable liabilities when deprived of their mothers' colostrum which the kids need to provide their own passive immunity. I presume they'd just be killed when they were born?

The mind boggles, frankly. I wonder what the animal rights people would make of it? Gadzillions of mice injected with measles and then killed, with their tissues then injected into huge herds of pregnant goats spread out all over the countryside, with their kids being killed at birth so that the mothers' colostrum can be harvested.

Wow.

And as I said, if anyone thinks that even taking colostrum by mouth is "safe and natural", google "bovine neonatal pancytopenia". Oh, but Wakefield wanted to inject the colostrum-derived product right into the children's bodies, just like a vaccine.

You know, maybe more details of what he was planning (and is actually doing on a small scale, I understand) need to be highlighted.

Rolfe.


If anyone had any doubt as to how much of a slimeball this Wakefield ass is, they really can't... And reading the rest of the thread is interesting as well (just click on the title of this post).

Friday, May 28, 2010

Vaccine preventable death – Matthew Meyers

And two more frightening and heart-wrenching stories from Vaccine Central blog... I really think that I need to figure out a direct feed from that blog to here since what we care about are the same things. Not only is this another murder by negligence induced by the paranoia and lies of the anti-vax pro-disease nutters, but there is also yet more outbreaks of preventable diseases... And if you have a baby, I hope you don't live anywhere near Rockford, Ill. Otherwise your baby may end up dead like Callie Grace Van Tornhout or Dana McCaffery (and possibly many more like them).

Add one more child to the list that these despicable liars need to explain why they approve of their death...

Vaccine preventable death – Matthew Meyers

Age at death – 14 years

Cause of death – Meningococcal meningitis

Vaccination status – Unknown, possibly unvaccinated. “She didn’t know he was at-risk,” said a family member referring to Matthews mother.

Synopsis - Meyers came home from a track and field meet complaining his ribs hurt. His mom, Renee Gardner, of Lake George, thought it might be the flu, and the 14-year-old went to bed and slept through most of the day Saturday.

“On Sunday morning, she heard him moaning and groaning and called her son, Bill Meyers, who lives on the other side of the lake, to come and help,” Dufore said.

Matthew Meyers fell out of bed and was unresponsive. The family called 911, and he was taken to Clare Medical Center, where tests determined he had meningococcal meningitis. Meyers was airlifted to Covenant HealthCare in Saginaw.

After a week-long battle, Mathew succumbed to the disease shortly after 5 AM on Friday, 05/28/2010. Our heartfelt condolences go out to his family. We are very sorry for your loss.

A fundraiser bake sale will be held Sunday at the Swiss Inn located at 105 W. Park St.

A benefit dinner will be held June 5 at 2 p.m. at the Clare Eagle’s Club, where some of the local donations collected will be presented to Matthew’s mother.

Cash support may be sent to the Matthew R. Meyers Fund, c/o Community Alliance Credit Union, 37401 Plymouth Road, Livonia, MI 48150.

Sources

Facebook Page

Mlive.com

Morning Sun

WNEM.com

The Clare County Review

ABC Local Report


Winnebago County reports a whooping cough outbreak

READ THE FULL ARTICLE AT THE CHICAGO TRIBUNE
ROCKFORD, Ill.

Winnebago County health authorities are investigating an outbreak of whooping cough.

So far 33 cases have been reported this month. That compares with only one case on average earlier this year.

Half are in 11- and 12-year-olds. Children that age should get booster shots because immunity from early childhood pertussis vaccines can wane. Sue Fuller of the county health department says adults should be sure to have booster shots too.

READ THE FULL ARTICLE AT THE CHICAGO TRIBUNE

Thursday, May 27, 2010

Vaccine Preventalbe Death – Callie Grace Van Tornhout

This blog entry makes me sad and disgusted at the anti-vax pro-disease nutters! I guess you can now add Callie Grace Van Tornout to Dana McCaffery's as children who should have their names seared into your memory. Every single anit-vax pro-disease nutter should also be forced to carry pictures of these children with them, and have to explain to everyone that they helped cause the death of these babies. Yes, I am angry!


Age at death – 5 weeks

Cause of death – Pertussis (whooping cough)

Vaccination status – Had not received first pertussis shot, because she was too young

Synopsis - Callie Grace was born on Christmas Eve 2009. By the last week of of January 2010 she developed a dry cough which got worse as time went by. When she stopped breathing at the pediatrician’s office she was taken to the hospital. While under observation at the pediatrics ICU, at 1:12am on January 30, 2010 she perished due to respiratory failure. When the tests came back, they were positive for pertussis, or more commonly known as whooping cough. Unfortunately, Callie was too young to receive the vaccine, the first dose of which is given at 2 months. She lacked immunity and was unable to fight off the disease. Our hearts go out to Callie’s parents. We are very sorry for your loss.

CNN iReport

CNN Article



And if that wasn't bad enough, I predict there will be more. As this article shows:

Cases of whooping cough more than double in California

THE FULL ARTICLE AT THE LATIMES
To protect babies too young for vaccination, health officials suggest vaccinating anyone who will come into contact with newborns.

California health authorities say that cases of whooping cough reported to the state have more than doubled so far this year — 346 cases from Jan. 1 to April 30, up from 129 cases during the same period last year.

Four newborns have died from the disease — two in Los Angeles County and two in the Central Valley. Amid concern that this may be the worst year for whooping cough since a 2005 outbreak killed eight infants in California, health officials are recommending a new strategy to protect babies too young for vaccination.

The strategy is called “cocooning” — vaccinating mothers, fathers, grandparents, siblings and anyone else who will be in contact with newborns. It’s a relatively new concept because a vaccine for whooping cough, also known as pertussis, first became available for adults and adolescents in 2005.

“If you can’t vaccinate the baby, you vaccinate everyone who comes into contact with them,” said John Talarico, chief of the immunization branch at the California Department of Public Health.

Babies are vulnerable in their first year of life because they cannot get their first pertussis vaccination until they are at least 6 weeks old. Even then, infants are still at risk because they need several more boosters, said Dr. C. Mary Healy, an expert on pediatric infectious diseases at Texas Children’s Hospital in Houston.

Studies show it is family members, particularly mothers, who infect infants with whooping cough, which was a significant killer of infants in the United States until widespread inoculations began in the 1940s.

Though many people were inoculated as children, immunity begins to fade after five years.

One problem in managing this extremely infectious disease is that the telltale “whooping” sound made after a coughing fit does not occur initially. Sometimes, infants with pertussis never make the “whooping” sound.

In infants, “diagnosis of pertussis is often delayed or missed because of a deceivingly mild onset of runny nose,” with an undetectable or mild cough, the state said in a recent bulletin to physicians.

Even worse, infants infected with pertussis usually do not have fever, which could leave parents and doctors with a false sense of security that the illness is not severe, said Dr. James D. Cherry, a UCLA pediatrics professor and an expert on pertussis.

The illness in newborns younger than 3 months old can quickly escalate.

“The babies will cough all their air out, the oxygen in the blood will decrease, then they may pass out and they may have seizures, convulsions,” Cherry said.

The bacteria can also cause pneumonia and death.

READ THE FULL ARTICLE AT THE LATIMES

Saturday, May 22, 2010

The Facts In The Case Of Dr. Andrew Wakefield

I have been seeing this "comic" around the internet lately, and wanted to reproduce it here as well. It pretty much sums it up very well. As others have said, this needs to be printed out and placed in every pediatrician's waiting room throughout the world.

The Facts In The Case Of Dr. Andrew Wakefield

A fifteen page story about the MMR vaccination controversy. As ever, I'm sure a few spelling errors have slipped past me. Feel free to point any out so I can correct them.

The reference links for the strip are in the next blog entry.

Now! Let's have a heated debate!

1 MMR Vaccination Scandal Story



2 MMR Vaccination Scandal Story

3 MMR Vaccination Scandal Story

4 MMR Vaccination Scandal Story

5 MMR Vaccination Scandal Story

6 MMR Vaccination Scandal Story

MMR 7 Vaccination Scandal Story

MMR 8 Vaccination Scandal Story

MMR 9 Vaccination Scandal Story

MMR 10 Vaccination Scandal Story

mmr 11 Vaccination Scandal Story

MMR 12 Vaccination Scandal Story

MMR 13 Vaccination Scandal Story

MMR 14 Vaccination Scandal Story

MMR 15 Vaccination Scandal Story

Monday, May 17, 2010

Web Page Migration (Part 2)

For those that may have noticed a formating problem with the web pages this past week, I have managed to solve the problem. Sadly, it means that if you had links or bookmarks for the page, they all end in PHP instead of HTML now. Please update your links and bookmarks. Thank you.

Today in the News (17 May 10)

And a few more news articles for today. And snarky comments because I am in a snarky mood.

(Can't be stopping 500,000 deaths with an evil vaccine, can we?)

Rotavirus Vaccine Greatly Reduces Hospitalizations for Acute Gastroenteritis in Children. Study Finds

ScienceDaily (May 14, 2010) — Vaccinating infants against rotavirus, a leading cause of severe diarrhea and dehydration among babies and young children, was associated with a dramatic decline in U.S. hospitalization rates for acute gastroenteritis. The findings appear in a study, now available online, published in the June 1 issue of The Journal of Infectious Diseases.

Worldwide, rotavirus infection is estimated to cause more than 500,000 deaths each year. Before a vaccine was introduced, the virus led to an estimated 55,000 to 70,000 hospitalizations in the U.S. annually. A vaccine, RotaTeq, was licensed for use in the U.S. and recommended for routine use in infants in 2006.

In this study, Aaron T. Curns, MPH, and colleagues at the Centers for Disease Control and Prevention (CDC) and the Agency for Healthcare Research and Quality examined hospitalization rates for acute gastroenteritis during the typical rotavirus season among U.S. children under 5 years of age. They compared these rates over two periods: from 2000 to 2006, before the rotavirus vaccine was introduced; and after, from 2007 to 2008.

Using hospital discharge data from 18 states accounting for almost 50 percent of the U.S. population, researchers compared the median hospitalization rate for gastroenteritis from all causes during the two time periods. Researchers considered the months January through June to be the rotavirus season.

Hospitalization rates for gastroenteritis were 16 percent lower in 2007 and 45 percent lower in 2008 compared with rates before the vaccine was introduced. During 2008, infants aged 0-2 months had a 28 percent reduction, while those 6-23 months of age had a 50 percent reduction. Rates among children aged 3-5 months and 24-59 months declined between 42 percent and 45 percent. The researchers estimated that approximately 55,000 acute gastroenteritis hospitalizations were prevented during the 2008 rotavirus season because of vaccination. Hospitalization rates during this season were substantially diminished with rates one-half to two-thirds lower at peak activity compared to previous seasons.

The researchers noted that the observed declines in hospitalizations exceeded their estimates and also occurred among age groups that were too young or too old to receive the vaccine, suggesting that these children may have been protected by the "herd immunity" caused by their peers being vaccinated.

In an accompanying editorial, Geoffrey A. Weinberg, MD, and Peter G. Szilagyi, MD, MPH, of the University of Rochester School of Medicine & Dentistry in New York, highlighted the importance of such vaccine effectiveness studies, which provide a real-world view that can improve the planning of public health initiatives. An advantage of the study design is its analysis of how well vaccination works within a population, they wrote.

"These encouraging findings are important for emphasizing the benefits and increasing the acceptance of rotavirus vaccination in the United States and will also help other countries assess the value of rotavirus vaccines for their children," the researchers said. In light of the study's results, "it remains essential to continue monitoring acute gastroenteritis hospitalization rates during subsequent rotavirus seasons to fully understand and document the impact of vaccination as the program matures in this country."

Fast Facts:

  1. Rotavirus infection leads to more than 500,000 deaths worldwide each year. Before a vaccine was introduced in 2006, rotavirus resulted in an estimated 55,000 to 75,000 hospitalizations in the U.S. annually.
  2. Hospitalization rates for acute gastroenteritis among children were 16 percent lower during the 2007 rotavirus season and 45 percent lower in 2008, compared with rates before rotavirus vaccine was introduced.
  3. An estimated 55,000 acute gastroenteritis hospitalizations were prevented during the 2008 rotavirus season in the U.S. Reductions also occurred in other age groups that did not receive the vaccine, probably due to "herd immunity."

(Oh, but we all know the Amish don't have these diseases, right?)

Rare Disease in Amish Children Sheds Light on Common Neurological Disorders

ScienceDaily (May 12, 2010) — So often the rare informs the common. Penn researchers investigating a regulatory protein involved in a rare genetic disease have shown that it may be related to epileptic and autistic symptoms in other more common neurological disorders.

A team of researchers from the University of Pennsylvania School of Medicine, led by Peter B. Crino, MD, PhD, associate professor of Neurology and director of the Penn Epilepsy Center, demonstrate how mutations in the STRAD-alpha gene can cause a disease called PMSE (polyhydramnios, megalencephaly, and symptomatic epilepsy) syndrome, found in a handful of Amish children. PMSE is characterized by an abnormally large brain, cognitive disability, and severe, treatment-resistant epilepsy.

Specifically, in an animal model, they found that the lack of the STRAD-alpha protein due to genetic mutations causes activation of the signaling pathway involving another protein called mTOR. In humans, this in turn may promote abnormal cell growth and cognitive problems in the developing brains of children. STRAD-alpha and mTOR proteins are part of a complex molecular network implicated in other, more common neurological disorders, many of which have autism-like symptoms as a component.

"The identification of a new gene that regulates mTOR provides fascinating insights into how mTOR pathway dysfunction may be associated with neurological disorders," says Crino. "Each new mTOR regulatory protein that is identified provides a new possible therapeutic target for drug development and treatment."

The research on PMSE -- published in the Journal of Clinical Investigation -- reveals clues about more common neurological disorders characterized by benign tumors and malformations of the brain, the most common of which is tuberous sclerosis complex (TSC). The root cause of TSC also lies in mutations in proteins along the mTOR pathway, however a different protein is affected compared to PMSE.

"It is quite compelling that TSC, a relatively common disorder, and PMSE, a rare disorder, are linked by a common cellular pathway, and exhibit similar severe neurological features," notes Crino. "In our study, we found that we could reverse some of the cellular features that result from STRAD-alpha deficiency in cell culture models of PMSE. This provides important conceptual support for more widespread treatment approaches that modify mTOR signaling in neurological disorders associated with epilepsy, autism, and cognitive disability."

Current estimates place tuberous sclerosis complex-affected births at one in 6,000. Nearly 1 million people worldwide are known to have TSC, with approximately 50,000 in the United States.

PMSE, on the other had, has only been described in 25 people in Lancaster County, PA. It's incidence among other Amish populations, let alone the rest of the country, is unknown. PMSE is also known as pretzel syndrome in the Amish community, because the lax joints of patients fold over easily. PMSE was identified in an Amish, or Old Order Mennonite pediatric population in 2007 by researchers from Penn and the Clinic for Special Children in Lancaster, PA, a genetic clinic devoted to the needs of the Amish.

The mTOR pathway normally controls cell growth, but in PMSE uncontrolled mTOR signaling leads to increases in brain size and areas in which the cerebral cortex is malformed. To prove this, the researchers knocked down the activity of the STRAD-alpha protein in a mouse model and caused malformations of the developing brain. The structure of these malformations was similar to what is seen in human PMSE and TSC and supports the conclusion that normal brain development in part depends on normal STRAD-alpha function. Localized brain malformations are among the most common causes of epilepsy and neurological disability in children.

This research was funded by the National Institute of Neurological Diseases and Stroke.

Ksenia Orlova, PhD, a graduate student in the Crino lab and Kevin Strauss, MD, Medical Director at the Clinic for Special Children, were also co-authors on the JCI paper.

(That pesky science, always refining our understanding!)

New Insights Into Genomics of Speciation

ScienceDaily (May 12, 2010) — A new study by a team of researchers led by University of Notre Dame biologist Jeffrey Feder could herald an important shift in thinking about the genomics of speciation.

The paper appears in the Proceedings of the National Academy of Sciences.

The prevailing assumption among scientists about how the genomes of newly forming species should differ during the earliest stages of divergence with gene flow speciation is that it will be characterized by a few regions of strong differentiation, amidst a remainder of the genome that remains unaffected by natural selection and thus relatively undifferentiated. This analogy of "genomic islands of speciation" has come to dominate the evolutionary genetics community.

"The island concept has crystallized around an attractive hypothesis termed 'divergence hitchhiking,' in which selection on one or a few genomic regions drives speciation," Feder said.

In the new paper, Feder and his colleagues report experimental and genomic evidence that contrary to the prevailing assumption, speciation in the classic apple maggot fly system Rhagoletis pomonella involves genome-wide differentiation driven by natural selection.

"Our result in Rhagoletis conflicts with the current thinking about how the genomes of newly forming species could differ during the earliest stages of divergence-with-gene-flow speciation," Feder said. "Rather than finding just isolated 'genomic islands' of genetic divergence, we instead discovered 'continents' of divergence encompassing large swaths of the genome."

He points out that past work on the genomics of speciation lacked experimental data and thus may have been unable to detect genomic regions under weaker natural selection, establishing a view of speciation involving genetic divergence in just a few, isolated genomic islands.

Rhagoeitis pomonella fruit flies originally attacked the fruit of hawthorn trees. But about 150 years ago, a portion of the hawthorn fly population shifted and began to feed on apples. In ecologically adapting to apples as a new host plant, apple flies are becoming genetically distinct and reproductively isolated from hawthorn flies. Apple and hawthorn flies are therefore considered to represent "host races" in the early stages of actively diverging into species. As such, the apple and hawthorn races of Rhagoeitis pomonella provided Feder and his fellow researchers a unique opportunity to conduct a direct experimental test of the island versus continents hypotheses.

"This type of comprehensive data, particularly the experimental results, are missing from the bevy of genome scan studies performed in the last few years lending support to the island hypothesis," Feder said. "Without experimental data on responses to selection, these genome scan studies alone can be biased toward identifying isolated outer loci, supporting the island hypothesis.

"We foresee that as mass genotyping techniques continue to advance, it will be these types of inquires and questions that come to dominate the emerging field of population genomics and speciation. We hope our study offers a glimpse of what the future may look like."

The research was funded by the National Science Foundation and the United States Department of Agriculture.

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.

Wednesday, May 12, 2010

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!

Sunday, May 02, 2010

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 lunacyEntertainment/cultureMedicinePopular cultureQuackeryTelevision
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.