Technological Advance

I worked with computers and Moore's Law was the elephant in the room. We would take on projects knowing that they were cutting edge and likely to fail, but during the 2 or 3 years of development we would be saved by newer faster equipment which would mean that our software could in fact meet the tough technical standards required by the project's goals.

But genomics is making Moore's law look like a lazy Sunday stroll compared to the breakneck 100 metre rush being put on by advances in gene sequencing:

Click to Enlarge
I got the above from a fascinating article in Forbes magazine about an Oregon family devastated by a genetic disease that has now been found and decoded by new technologies:

This one family, in Ogden, Utah, has watched as five children in two generations have died from a mysterious disease that science could not explain.. Thanks to huge leaps being made in DNA sequencing and in computer programs to decipher genetic code, researchers were able to find the gene for this disease in just sixteen months. Potentially, this could offer Lundell and her sisters the opportunity to have children via in vitro fertilization, selecting embryos that don’t have the gene.

...

Three new technologies allowed Lyon to find the gene that was causing the boys to die. The cost of sequencing a human genome has been dropping precipitously, from $100 million in 2001 to $10,000 last year, according to Macquarie Securities, an investment advisor. Other new technologies allowed Lyon to focus on just 1% of human genetic material that was likely to provide him answers. And a brand new kind of software allowed him to use information about the family and their genetic material to find the defective gene.

I don't know how the increasing technology advances in biology will shape the future. Just like nobody could really foresee all the applications of computers as they became faster and more diverse. But I have high hopes that 50 years from now people will be living vastly richer and more interesting lives because of this new technology.

There is a lot to get despondent about and become pessimistic on the future. Gloom and doom are popular. Religious zealots want to close off our minds to the future. But human ingenuity and the ability to dream about a better future make me optimistic. Sure some of the new stuff will be abused in the hands of cruel and selfish people. But enough will find its way into the hands of the great majority that overall the future will be better. I look at 10,000 years of civilization where ideas have been cumulative and I see a definite trend despite dark ages and monstrous cruelty. I am optimistic. Since the advent of science just 400 years ago, human society has made giant strides.

Surviving Rabies

This video has an incredible tale of surviving rabies...

Part 1:


Part 2:


Part 3:


This was a disease with a 0% survival rate. But according to Wikipedia, the above protocol for treatment now means:

In 2005, the first patient was treated with the Milwaukee protocol, and Jeanna Giese became the first person ever recorded to survive rabies without receiving successful post-exposure prophylaxis. An intention to treat analysis has since found that this protocol has a survival rate of about 8%.

There is more detail in Wikipedia about the use of this "Milwaukee Protocol":

Giese's treatment regimen has since undergone revision (the second version omits the use of ribavirin). There were 2 survivors out of 25 patients treated under the first protocol. A further 10 patients have been treated under the revised protocol and there have been a further 2 survivors.

In June 2011, yet another young child survived infection with rabies without the benefit of treatment. An eight year old girl named Precious Reynolds, of Willow Creek, Calif., contracted the disease sometime in April 2011, but she did not receive medical care till mid May, after her grandmother took her to the doctor because of flulike symptoms that grew so serious her grandmother said they began to resemble polio. The hospital said doctors followed the protocol first established with Giese. Precious was placed in a drug-induced coma as she received anti-viral medications. She spent two weeks in intensive care undergoing the treatments, and immediately showed that her immune system was strong. She was then moved to the hospital's general pediatric unit.

Only two other people have survived documented rabies in the United States - a Wisconsin teenager in 2004 (Jeanna Giese), and a Texas girl in 2009.

This is an incredible story. It is truly amazing how our great collective wisdom -- aka science -- slowly gives us tools to go where we have never gone before and abilities that were previously inconceivable. I can't understand why everybody is not a fan of science. I do know that not everybody has what it takes to be a scientist, but I don't understand why people would rather believe in superstitions and old wives tales than support the advance of science. We are in a constant battle with "nature" and only science gives us the possibility to improve on the hand of cards we've been dealt from the deck that life makes available.

Doctors are Now Copyrighting Your Thoughts

The horrors of George Orwell's 1984 are arriving a tad late, 2011 instead of 1984, but they are definitely here. Here is a bit from a story on Ars Technica about a dentist demanding that you sign away rights to any opinions about the service he provides -- he is copyrighting your thoughts as "his property"!!! -- before he will agree to treat you:

When I walked into the offices of Dr. Ken Cirka, I was looking for cleaner teeth, not material for an Ars Technica story. I needed a new dentist, and Yelp says Dr. Cirka is one of the best in the Philadelphia area. The receptionist handed me a clipboard with forms to fill out. After the usual patient information form, there was a "mutual privacy agreement" that asked me to transfer ownership of any public commentary I might write in the future to Dr. Cirka. Surprised and a little outraged by this, I got into a lengthy discussion with Dr. Cirka's office manager that ended in me refusing to sign and her showing me the door.

The agreement is based on a template supplied by an organization called Medical Justice, and similar agreements have been popping up in doctors' offices across the country. And although Medical Justice and Dr. Cirka both claim otherwise, it seems pretty obvious that the agreements are designed to help medical professionals censor their patients' reviews.

The legal experts we talked to said that the copyright provisions of these agreements are probably toothless. But the growing use of these agreements is still cause for concern. Patients who sign the agreements may engage in self-censorship in the erroneous belief that the agreements bar them from speaking out. And in any event, the fact that a doctor would try to gag his patients raises serious questions about his judgment.

I love how lawyers bend and twist things into completely cruel and criminal red tape. A person has a right to their own thoughts. A person has a right to express opinion. "Copyright" was never intended as a vehicle to control opinion. It was meant to protect artists from having their works stolen by publishers who refused to pay for the right to profit from another person's work.

Funny... the legal system does nothing to stop torture and abuse of the law. But it enables idiots like the above dentist to tie up court time on frivolous cases where they are trying to suppress the ability of patients to have a free opinion. Nutty!

A Surprising Journey

I enjoy reading Carl Zimmer's articles on science. He has a way with words and ideas and gives the reader a wonderful insight into nooks and crannies of contemporary science. This bit from an article in the NY Times shows how a career in science can be full of surprises:

At the studio Mr. Pell helped Dr. Wainwright and his colleagues build models to test their ideas about biomechanics, creating models of spinal cords, muscles, jaws and dozens of other animal parts. “These models can physically surprise you,” said Mr. Pell. “They can show you things that you didn’t think of before you built them.”

One of Mr. Pell’s biggest surprises came when he tried to make a simple model of a swimming fish. He built a rubber tube with a rounded front and then stuck a rod a quarter of the way down its length. When he put the tube in water and turned the rod back and forth between his fingers, it generated a wave with its tail. While making a new version of that tube, Mr. Pell accidentally nicked the tail end. That new shape, he discovered, caused the water to flow in a different pattern around the tube, creating thrust.

Mr. Pell, Dr. Wainwright and their colleagues got a patent for the design and started a company called Nekton to develop products from it. First, they turned it into a commercially successful bathtub toy. But when the Navy discovered Mr. Pell and his colleagues could get fishlike thrust from something without any moving parts, they encouraged him to get into the business of building underwater robots. Mr. Pell and his colleague at Nekton ended up making a highly maneuverable yardlong robot called the Pilot Fish.

“We started out as a toy company; we ended up as a defense contractor,” said Mr. Pell.

We need a world in which people with the quirky skills and interests needed to create have free rein to create. Innovation makes us all wealthier. Sadly our institutions are set up for rote learning and text book skills and not dreams and innovation. We need to "breed" more eccentrics and dreamers.

Taking Control, Full Control, of Your Life

I found this bit from a post on Dan Ariely's blog very interesting. I've read both his books "Predictably Irrational" and "The Upside of Irrationality". Both are delightful and insightful. I also find his life inspiring: while preparing "fire signs" (a common feature in ceremonies of youth movements in Israel) he suffered third-degree burns over 70 percent of his body from an accidental magnesium flare explosion. He learned many lessons from how he handled himself through this time.

Here is the bit of his post that I found most interesting:

As the American population ages, the debate about the ethics of physician-assisted suicide for terminal patients becomes more important.

...

Outside of philosophical arguments, examination of an interesting finding regarding physician-assisted suicide – know as “The Oregon Paradox” – can add an interesting dimension to the debate. The paradox is the finding that when terminal patients in Oregon receive lethal medication (under Oregon’s Death with Dignity Act), they often feel a sense of greater wellbeing and a desire to live longer. In 2010, of 96 patients requested lethal medication, only 61 actually took it. Even more interesting are the many anecdotal accounts of terminal patients, upon receiving lethal medication, that feel a surge of wellbeing and a desire to persevere through their illness.

Why is this this the case? Looking at this question from an expected-utility perspective suggests that given the option to terminate their own life, terminal patients will decide how long they want to live by comparing the value they expect to gain from the rest of their lives to the expected intensity of their suffering. At the point where future utility is expected to be negative – that is, when the patient’s condition becomes so intolerable that living any longer is not worth the cost – the patient would choose to end life if the option were available.

The critical point from this perspective is that patients choose the amount of time they are willing to continue living with their illness, which will depend how quickly they deteriorate. If the rate of deterioration is slower than expected, then patients should delay terminating their lives; if the rate of deterioration is faster than expected, patients should desire to end their lives quicker.

But now let us say that patients have been prescribed lethal medication and have the option of ending their lives at any point of their choosing. As before, patients don’t want to choose a time too soon or too distant, but with the power to control the end of their lives they no longer have a reason to err on the side of haste! The patients can now wake up every day with the comfort of knowing that they do not have to suffer through pain or stress they might find intolerable.

Being given the option to determine the time of our own death can transform patients from powerless victims of their illness to willing survivors of it. Together, the importance of feeling in control and the ability to reduce (but not eliminate) uncertainty about rate of deterioration adds an interesting new dimension to the underlying ethical debate and seems to provide credence to the benefits of legalized physician-assisted suicide.

It is clear is that we need a greater understanding of the decision-making of patients at the end of their lives, and that with this improved understanding we can construct policy to better protect their wellbeing (for an interesting recent movie on this topic see “How to Die in Oregon”).

I'm a bit of a fanatic. I think people should take responsibility for themselves and have the freedom to make their own choices. On the other hand, I realize that some people really aren't competent to run their own lives (mental deficiencies, moral deficiencies, etc.) So I'm in a bit of a bind. I live under a grand banner about "the nature of man' but realize that there needs to be lots of find print and "lawyerese" to handle the fact that we are not all cookie-cutter the same. In short, I don't really have a simple clear answer to all of life's questions that can be printed on a cereal boxtop. I end up with slogans and qualifications. And I leave it open for debate and clarification. That's the best I think anybody can do.

I do know that even though euthanasia is "illegal" my mother in the 1980s told the doctor's "no heroic measures" for her father which was essentially the code words for "let him die". And with my mother, when she couldn't stand her disabilities from a flubbed brain surgery asked me to "get her out of here!", I did the paperwork to move her to a hospice where she was allowed to die. In effect I signed her death papers.

As Dan Ariely's piece above shows, the issue of euthanasia is not black-and-white as the noisy interest groups would make you think. It is complex. Ultimately it is best left to the family with state intervention only if it is clear that somebody in the family is manipulating things for their own interest and things are not being done in the best interest of the person who is dying. That is a broad rule that requires eternal vigilance and interpretation, but that is the glory of English common law. It is law that is "living" and constantly being reinterpreted as we learn more and as things change. Nothing carved in stone like the religious bigots would have you believe. Instead, a law based on the best judgments of your peers and an honest judge.

Will Food Colouring Help You Live Longer?

Amidst all the ranting about how food additives, especially food colourings, "poison" the food supply, I found this bit from Derek Lowe's blog In the Pipeline interesting:

... treating nematodes (roundworms, C. elegans) with the dye Thioflavin T (also known as ThT or Basic Yellow 1) extends their lives quite significantly - up around a 60% increase in both median and maximal lifespan. Several other related benzazole compounds were also tried, which produced lifespan extension of up to 40%, and at much lower concentrations.

Wouldn't it be hysterically funny given all the hue-and-cry about food dyes being carcinogenic, it ends up that the surprising extension to lives achieved in the 20th century comes down to putting food colouring into the food supply? Or as Lowe puts it:

... as my wife pointed out to me when I told her about this paper, the FDA was just making headlines the other day by recommending that more study be given to any possible links between food dyes and hyperactivity (though stopping short of recommending any warning at this time, due to lack of convincing evidence). On the basis of this latest work, though, I'm starting to wonder if we're not putting enough dyes in our food...

Lowe cites a paper published in the prestigious Nature journal that looks at dyes and their ability to attack and destroy amyloid plaques (the stuff that is believed to cause dementia). This might be a real advance in treating Alzheimer's.

I can't wait for food dyes to become all the rage among health nuts. That will mean we will see people with skin colours of blues, and greens, and yellows, and reds, and oranges, and pinks, etc.

The "Every Life is Precious" Idiocy

First, I care for people and every rational effort should be put into ensuring that people get a fair shot at life and decent treatment.

But I don't buy into this over-the-top, life is "infinitely precious" idiocy. From David Ng at BoingBoing:

Access to life-saving medicines is not a luxury, but a human right.
~Canadian HIV/AIDS Legal Network
To me, the above statement is one of those things that sound like a no-brainer. Put another way, if I were to ask you whether you thought a person's income should determine whether they live or die from something like HIV/AIDS, then I think you would see that the answer is nothing but obvious. But here I am, in Canada, writing this post, because there is a very real danger that members of my government think that this isn't such an easy decision after all - that maybe wealth and business interests do matter when dealing with such ethical choices, and that there is a hierarchy where certain lives are worth more than others.

If you literally believed the above and I told you that I had developed a wonderful cure for a rare genetic disorder that kills 1 person out of the 6.5 billion people on earth each year, and that we could get this precious medicine produced for the modest investment of "only" $45 trillion. Then you, as a believer in the "every life is precious" mantra, would immediately sacrifice the livelihood of the whole planet for a full year -- in other words all 6.5 billion starve to death -- to save this one precious life from this dread genetic disease. Why? Because it would be immoral to use any kind of rational cost-benefit analysis since every single life is absolutely "precious". Nutty!

Having said the above, I actually am close to David Ng in supporting action to make HIV/AIDS drugs available to the world's poor. I would support governments simply seizing drug patents and giving them to factories willing to produce drugs at very modest profits. I have no problem using a "public right" to trump private greed.

But what I don't buy into is the idiotic "every life is precious" credo. If that was so, then if David Ng saw his mother at the hands of a madman killer and he had a gun and could take a clean shot and save his mother. His idiotic "every life is precious" credo would freeze his hand and leave him watching while the madman killed his mother. That's what David Ng is telling you with his patently ridiculous claim of "every life is precious". It is a lie. We do value "all life" but we aren't simpering idiots unable to make rational choices in tough circumstances. Any normal person would coolly kill the madman and free their mother. But David Ng assures us he just couldn't bring himself to do that to save his mother because "every life is precious".

Give me a break!

The first time I seriously considered this matter was nearly 40 years ago when a family living on Vancouver Island had a hydrocephalic child, blind, mentally retarded, with cerebral palsy. The child had undergone several brain operations to relieve pressure on the brain but the condition of the child continued to deteriorate. The parents finally decided "enough is enough!" and told health authorities they wanted no more treatments for their child. But the government of British Columbia took them to court so that taxpayer's money could continue to be flushed down the toilet on a hopeless case where quality of life wasn't going to improve and where the parents wanted needless surgeries to stop. Instead, bleeding heart "every life is precious" types hounded this family through the legal and police systems to try and force them to do what the health authorities wanted done. This while vast sums were being wasted on this hopeless case. I kept thinking: you mean there is no poor child in British Columbia who couldn't benefit from hot meals, warm clothing, better education? Wouldn't the social resources of the taxpayers of BC be better spent on cases where the investment of modest sums will yield outlandish benefits compared to spending outlandish sums where the is little or no benefit to be gained? Sadly, I was in a minority. The government of BC continued to bully this family for years until the afflicted child died of his overwhelming medical problems despite the many, many millions of public funds wasted. David Ng belongs to the camp that would happily throw money at this one hopeless case while turning a cold shoulder to the tens of thousands of young children would have benefited in substantial ways from modest sums spent on them. That's where the blind absolutist logic of "every life is precious" leads you.

Howard Engel's "The Man Who Forgot How to Read"

I recently re-read Oliver Sacks' The Mind's Eye and appreciated the bit about writer Howard Engel, so I decided to follow up by reading Engel's memoir about his experience having a stroke and developing alexia sine agraphia.

This book was a short but very interesting read. You get a feel for his life before and after and you come to understand -- a bit! -- of the struggles that a person with this disability has.

My mother had a brain tumour and had a bit of the parietal and occipital lobes removed and developed "left neglect" and other cognitive deficiencies (particularly the inability to recognize faces). But she had no interest in either relating her sense of the world with these deficiencies or understanding why they had come about. She was an intelligent woman but her horror at her condition left her wishing to ignore reality and spend her time talking about family, friends, and the past. Engel is unusual in being willing to go into fair detail with the symptoms of his condition.

The book alerts the reader to the "little details" that come up with a stroke patient. Things that somebody who doesn't suffer these depravations is slow to recognize. Luckily he had family and close friends who provided a solid support team for him. But despite this you get a feeling for the struggles he underwent.

Another aspect the book brings across is personality. My mother simply gave up on life. Howard Engel fought hard to recover as much of his previous life as possible. In the real world, different people respond to things differently. There is no predicting who will respond how. You can guess, but you are likely to be wrong.

The book is not an unremitting trudge through tragedy. Engel has a light hand and finds humour in his situation. He keeps the tone light so that the book is informative but not depressing.

It is well worth reading.

Robot Ready to be Injected into your Veins

I remember watching Fantastic Voyage and thinking it was pretty cheezy back in the 1960s. But 50 years later, somebody is trying to build a robot that can get in your veins and maneuver do "do stuff" that will be medically useful.

Here's a bit from New Scientist:

... while microbots exist, and they can be made to swim, it's getting them to change direction that has been tricky so far - a bit of an issue if you're even planning on sticking them in a human body, for instance.

Now a system used to propel swimming microbots without the need for on-board fuel has brought this idea one step closer. Researchers at North Carolina State University have coaxed their bots to perform U-turns on command.

The microbot, a mere 1.3 millimetres long, is essentially a diode - an electrical element that only allows current to pass in one direction. The diode is exposed to an alternating electric field, which induces a voltage across it, creating an electric dipole. This dipole pushes on ions in the water, driving them backward and propelling the microbot forward.

...

Miniaturisation will be vital if the robots are ever to navigate human bodies., like in Fantastic Voyage. The group is also investigating "yeast-boats", which use metabolic reactions to motor through glucose or hydrogen peroxide solutions. A similar vehicle may one day carry a molecular doctor on board to make a diagnosis - or dock with diseased tissue to deliver a shipment of drugs.

I won't be first in line for this new medical treatment. I would need to be convinced that it isn't going to cause interesting problems like blocked capillaries or rogue microbots delivering drugs in the wrong locations.

A Medical Emergency

Here is a person, Serene Branson, most likely having a TIA (transient ischemic attack) in the left temporal lobe in Wernicke's area in that leads to a paraphasia (a difficulty speaking correctly):



She was treated by an EMR team who found her "healthy" and told to "go home". From Wikipedia:

On February 14, 2011, CBS Los Angeles reported that Branson had been examined by paramedics and, due to a lack of obvious health concerns, was not admitted to the hospital.

That is the wrong thing to do. With symptoms like this you need to send the person to hospital for observation because they are at high risk of a more serious stroke (or if it isn't a TIA but a tumor or other underlying neurological disorder, it needs to be diagnosed and treated).

My mother had TIAs when she was in her eighties. She was told that when she had the symptoms to go to the emergency room at the hospital. I could never get her to do this. Since the event is "transient" most people think it is "nothing" and that it has passed and they are "back to normal". They feel uncomfortable showing up at the hospital with no evident signs of "illness". Sadly, my mother died of a brain tumour. I think the tumour was in addition to the TIAs and not the cause of them, but since she didn't push the doctors to fully understand her condition she "slipped under the radar" until the tumour made her collapse in the shower and hurt herself to the point that she was rushed to the emergency room. Even then the hospital released her after patching her up. It was only when the family doctor talked to her and heard stories of TIAs and previous falls that he insisted she go back to the hospital for further tests. That is when they discovered the tumour.

If you go the the YouTube sight you will find many, many people making fun of Serene Branson. This is simple ignorance. These people do not understand that they are seeing a serious medical condition. People make fun or and attack things they do not understand. Instead they should recognize their ignorance and use their natural curiosity to dig a little deeper and learn something new. You have a choice: laugh at what you don't understand and be a boor and a fool, or recognize that you are seeing something you don't understand and do the bit of work it takes to understand it so that you are a better person, better equipped to handle medical emergencies and more sympathetic because you understand the world better.

Sadly I see ignorance put on a pedestal in the US. There are religious fundamentalists who tell people that all they need to know is in a book put together over 2000 years ago by poorly educated tribes in the eastern Mediterranean. If you ever look at the early medical books from those times you realize that these people knew next to nothing about physiology. They had no science. When they looked up in the sky they had no clue they lived in a universe with 100 billion galaxies each with 100 billion stars. When they looked around them they had no idea of the teeming microsopic life. They thought disease was "possession". They had no medical understanding. But in the US the fundamentalist churches tell people that the the Bible is "inerrant truth", the evolution is a lie, and that everything you need to know about morality was written down by a barely literate people over 2000 years ago. Tragic.

Unleashing a Modern Plague to Profit by £435 643

Here is a snippet from an article in the British Journal of Medicine documenting the fact that the uproar over "vaccines" started from a greedy doctor who fraudulently altered data to make a case against vaccines in order to collect a consulting fee from a law firm that was suing the vaccine manufacturers:

Unknown to Mr 11, Wakefield was working on a lawsuit, for which he sought a bowel-brain “syndrome” as its centrepiece. Claiming an undisclosed £150 (€180, $230) an hour through a Norfolk solicitor named Richard Barr, he had been confidentially put on the payroll two years before the paper was published, eventually grossing him £435 643, plus expenses.

Curiously, however, Wakefield had already identified such a syndrome before the project which would reputedly discover it. “Children with enteritis/disintegrative disorder [an expression he used for bowel inflammation and regressive autism] form part of a new syndrome,” he and Barr explained in a confidential grant application to the UK government’s Legal Aid Board before any of the children were investigated. “Nonetheless the evidence is undeniably in favour of a specific vaccine induced pathology.”

In short, greed motivated the "researcher" to invent data so that he could satisfy the lawyers and collect his fees. As a result of this fraud, vaccination rates have fallen around the world and children are now getting sick, permanently injured, and dying, all for one man's greed and the credulous public eager to be anti-science and believe any crackpot idea that comes along.

The BMJ article is filled with details and is somewhat difficult to follow for a general audience. Here is a bit from a CNN report that distills the "news worthy" essence:

A now-retracted British study that linked autism to childhood vaccines was an "elaborate fraud" that has done long-lasting damage to public health, a leading medical publication reported Wednesday.

An investigation published by the British medical journal BMJ concludes the study's author, Dr. Andrew Wakefield, misrepresented or altered the medical histories of all 12 of the patients whose cases formed the basis of the 1998 study -- and that there was "no doubt" Wakefield was responsible.
"It's one thing to have a bad study, a study full of error, and for the authors then to admit that they made errors," Fiona Godlee, BMJ's editor-in-chief, told CNN. "But in this case, we have a very different picture of what seems to be a deliberate attempt to create an impression that there was a link by falsifying the data."

Britain stripped Wakefield of his medical license in May. "Meanwhile, the damage to public health continues, fueled by unbalanced media reporting and an ineffective response from government, researchers, journals and the medical profession," BMJ states in an editorial accompanying the work.

CNN invites you to watch the Anderson Cooper report that provides the full story.

It is people like Jenny McCarthy, an actress who has no scientific training, who uses her looks and her public persona to sell the profoundly wrong message that "vaccines cause autism". It just isn't true. But once lies are spread, it is hard to defeat them. McCarthy should be deeply sorry for the deaths and injuries her charlatantism has caused. Sadly, people like Jenny McCarthy are never called to account for the tragedies she has caused. And she is probably so caught up in her self-delusion that she is unwilling to recognize the truth and accept the great harm she has caused.

Update 2010jan10: Here's a bit from Wikipedia where experts validate the fact that uninformed "activists" like Jenny McCarthy have caused the deaths of children:

Following the January 2011 BMJ revelations of fraud by Wakefield, Paul Offit, a pediatrician at Children's Hospital of Philadelphia and a "long-time critic of the dangers of the anti-vaccine movement", said, "that paper killed children", and Michael Smith of the University of Louisville, an "infectious diseases expert who has studied the autism controversy's effect on immunization rates", who said "clearly, the results of this (Wakefield) study have had repercussions."

I believe that Jenny McCarthy, once she realizes the harm she's done, will be horrified and apologetic. But she, like all people who fail to do their homework before getting on a soapbox, needs to realize that words have consequences. We've just seen an example of this with the Gabrielle Giffords assassination. Spouting off a theory without evidence, knowledge, and appropriate theoretical framework is like an unhinged person with a gun: this is trouble just waiting to happen.

Goldacre on "Bad Science"

Here is a talk by Ben Goldacre at a Pop!Tech conference held in Camden, Maine in October. He points out the simple idea of science: pose theories and criticize them. He points out that quacks and fanatics have no problem posing their own theories, but they adamantly refuse to put them to the test of criticism:



Sadly, we live in a "modern" world in which most people are still pre-modern, i.e. they reject science in favour of holding to pet theories which they refuse to question and which they defend viciously.

Oliver Sack's "The Mind's Eye"

This is another delightful read from Oliver Sacks. Yet again he mulls over a subject -- this time vision -- and peppers it with lots of interesting case studies to put flesh on bones. In fact, this time he puts himself front and centre and talks of an eye tumour he developed and how over the course of five years it evolved to take away his stereoscopic vision. If you are an Oliver Sacks fan, as I am, this is yet another "must read" book.

I love the way Sacks peppers his book with unique observations, strange facts, and erudite words. He makes you pay attention. And you learn many wonderful things. It is thanks to Sacks that I was able to come to my mother's bedside and immediately diagnose "left neglect" syndrome. I certainly didn't get any help from the medical staff in understanding her problems. But books like the ones from Oliver Sacks prepare you for the wild affronts that life hands out. And in this book Sacks makes it personal as he walks you through his experience of blindness.

I've been curious about face blindness -- prosopagnosia -- and he has a chapter in this book updating his earlier stories, introducting more cases, and, to my delight, talking about his own condition. He's a wonderfully quirky man and over the years he has let more of himjself into his books. This book is nearly half dedicated to his own conditions. So you get a much greater introduction to Oliver Sacks in this book. At least his conditions. His personal story is better handled in the book Uncle Tungsten.

My first introduction to Oliver Sacks was over twenty years ago when I read his book The Man Who Mistook His Wife for a Hat. All of his books are quirky, insightful, fascinating, and wonderfully educational.

For a Terry Gross's NPR interview with Oliver Sacks about this book, click here. If you read this article and listen to the interview you will get an excellent understanding of Sacks and his latest book.

Everybody "Knows" Government is the Problem, Not the Solution

Here's a bit out of a post by Maxine Udall on her blog Girl Economist that pops that balloon, a favourite mantra of the political right:

My own personal favorite example of the government being an important part of the solution is penicillin, an antibiotic that has saved many lives.

In 1940, Howard Florey and Ernst Chain, at Oxford University, produced enough stable chemical from a mold, penicillium, to test on mice infected with streptococcus. Of eight infected, 4 were treated and recovered rapidly. "Eureka!," you say. "The rest is history, yes?"

Well, no. Not quite.

Florey and a colleague packed up their penicillin and their results and took them to major pharmaceutical companies in the UK, the US, and Canada. None wanted to invest the capital in scaling it for production, mainly because there were signs that bacteria were becoming resistant to the sulfa drugs they were already manufacturing. Even if penicillin were effective for a while, it would eventually become ineffective and demand would dwindle. Where's the profit in that, they rightly asked?

So how did we the people get penicillin (and the many subsequent antibiotics that repeatedly haul us back from the brink of death, bronchitis, and septicemia)? The US government stepped in. The US military pushed a bit on this. After all, who better to sense on the eve of war the potential gains from a new antibiotic? Roughly half of all deaths in at least one previous war had been from infection.

It was a group of government scientists at the US Department of Agriculture who scaled production and increased the drug's efficacy four-fold. And in record time. Imagine. Guvmint scientists produced something quickly, efficiently, and made it (and us) better.

I know what you're thinking. You're thinking that surely now, after the US government and the US taxpayers had volunteered the start up costs, the drugs manufacturers must have agreed to produce it, yes? By the time it had been scaled, it was more apparent than ever that the US might be drawn into a major world war. The military wanted it. Surely an appeal to patriotic duty would move them?

No. I'm afraid not. Not until George Merck, CEO of Merck & Company, agreed to do it and persuaded the heads of several other manufacturers to join him.

I find it amusing that the ideologues of the right think that business can do no wrong. The problem is, these fanatics don't know history, don't know business, don't understand human nature, can't appreciate what a well functioning government bureaucracy can do, and refuse to look at facts. Udall's example is excellent. It isn't unique and it is not rare. Most government activity is hum-drum useful stuff. But if you are an ideologue, "the only good government is a hamstrung, shunk-down, minimalist government". This is just as wrong as the 19th century brain-dead racist maxim "the only good injun is a dead injun".

Who are the 'Good Guys'?

Most Americans will assure you that they are the 'good guys' in the world. That they hold themselves to a higher ethical standard that most other countries of the world. And they certainly didn't stoop to the lows of the Nazi doctors who did unethical "experiments" on unwilling victims.

Well... truth is stranger than fiction.

Many way know about the Tuskeegee experiments. From Wikipedia:

The Tuskegee syphilis experiment (also known as the Tuskegee syphilis study or Public Health Service syphilis study) was a clinical study conducted between 1932 and 1972 in Tuskegee, Alabama, by the U.S. Public Health Service. Investigators recruited 399 impoverished African-American sharecroppers with syphilis for research related to the natural progression of the untreated disease.

The Public Health Service, working with the Tuskegee Institute, began the study in 1932. Nearly 400 poor black men with syphilis from Macon County, Ala., were enrolled in the study. They were never told they had syphilis, nor were they ever treated for it. According to the Centers for Disease Control, the men were told they were being treated for "bad blood," a local term used to describe several illnesses, including syphilis, anemia and fatigue.

For participating in the study, the men were given free medical exams, free meals and free burial insurance.

The 40-year study was controversial for reasons related to ethical standards, primarily because researchers failed to treat patients appropriately after the 1940s validation of penicillin as an effective cure for the disease. Revelation of study failures led to major changes in U.S. law and regulation on the protection of participants in clinical studies. Now studies require informed consent (with exceptions possible for U.S. Federal agencies which can be kept secret by Executive Order), communication of diagnosis, and accurate reporting of test results.

So... that was a once-only, egregious "mistake", right?

Sorry... not so. Here's a bit from Boing Boing about the recent revelation that:

A researcher studying the infamous Tuskegee experiment discovered that American researchers had performed similarly immoral medical studies in Guatemala in the 1940s.

In an attempt to figure out whether penicillin could prevent, as well as cure, STDs, researchers affiliated with the U.S. Public Health Service, the National Institutes of Health, the Pan-American Health Sanitary Bureau (now the Pan American Health Organization) and the Guatemalan government exposed almost 700 Guatemalans to syphilis and gonorrhea without their consent—both through direct inoculation and via hiring of infected hookers.

It's unclear whether any of the subjects ever received treatment to cure the diseases they were unknowingly given.

Secretary of State Hillary Clinton and Health and Human Services Secretary Kathleen Sebelius issued apologies for incident today.

Go read the Boing Boing original to get the embedded links.

Still convinced that Tuskeegee was just a exception to the "high moral standards" of American medicine and US government projects?

I offer the following short list to "jog your memory"...

• The CIA doing drug experiments on unsuspecting individuals, killing some.


• The US Oak Ridge "experiments" on terminally ill cancer patients who were told they were being given treatment for their disease but in fact were being given various levels of lethal radiation dosages so that government "scientists" who record how long it took to die from the new atomic weapons.


• Biological warfare "experiments" carried out secretly over US cities, including New York and San Francisco.

A short Internet search will turn up pages like this that document many, many, many of these "out of character" and "extremely rare" deviations from basic ethical behaviour.

And may I remind you that the US is one of the few countries (other than corrupt dictatorships) that practices torture as public policy (oh sure, it is not "torture" but "enhanced interrogation techniques") and it is the US that brought you the gory details of Abu Ghraib (and many other less well documented horror stories of state-sponsored torture).

The problem is that humans have a built in "blindness". By default we see ourselves as the "good guys" and are always suspicious that the other guys are the "evil ones". It is very, very hard to take an honest look at oneself and see that one is capable of unspeakable horrors, especially when it is your government. But take a walk through US history and you will find ghastly treatment of natives, foreign wars where foreign lives are cheap and "playthings" of bored soldiers, where immigrants are mistreated, where a whole race was subjugated to slavery, where suspected "radicals" and Communists were hounded from their jobs, abused, and imprisoned. The list goes on.

Canada has its own sordid past. It is on a smaller scale because it is a smaller country. I was reminded of this when I taught high school in the mid-1970s in the interior of British Columbia. During WWII Canada, like the US, interned the perfectly innocent Japanese whether they were citizens or not. The property of these internees was seized and never returned. Many were left broken and poor. So I was amazed to discover in my classes many Japanese descendants in a school in the interior, far from the fisheries and farms that the Japanese immigrated to Canada to set up. But these were remnants of a Japanese immigration that was swept up by racism and war hysteria and interned far from their homes penniless after the war and there they remained thirty years later. A historical wrong was never righted.

In short, all countries, and everyone, is capable or vicious deeds. We best keep that in mind to help keep our bad impulses under check for it is when we are convinced that we are the "Good Guys" that most evil is done.

Miracle Cure: Switch Your Microbiome

Medicine knows a heck of a lot less than it pretends to know. My mother spent the last 10 years of her life with a "mysterious" bowel disease that never got diagnosed as she moved from doctor to doctor, each one promising to quickly "solve" the puzzle but soon losing heart after their top 2 or 3 guesses didn't pan out. I wonder if the following is the secret of her problems. From an article in the NY Times by Carl Zimmer:

In 2008, Dr. Khoruts, a gastroenterologist at the University of Minnesota, took on a patient suffering from a vicious gut infection of Clostridium difficile. She was crippled by constant diarrhea, which had left her in a wheelchair wearing diapers. Dr. Khoruts treated her with an assortment of antibiotics, but nothing could stop the bacteria. His patient was wasting away, losing 60 pounds over the course of eight months. “She was just dwindling down the drain, and she probably would have died,” Dr. Khoruts said.

Dr. Khoruts decided his patient needed a transplant. But he didn’t give her a piece of someone else’s intestines, or a stomach, or any other organ. Instead, he gave her some of her husband’s bacteria.

Dr. Khoruts mixed a small sample of her husband’s stool with saline solution and delivered it into her colon. Writing in the Journal of Clinical Gastroenterology last month, Dr. Khoruts and his colleagues reported that her diarrhea vanished in a day. Her Clostridium difficile infection disappeared as well and has not returned since.

The procedure — known as bacteriotherapy or fecal transplantation — had been carried out a few times over the past few decades. But Dr. Khoruts and his colleagues were able to do something previous doctors could not: they took a genetic survey of the bacteria in her intestines before and after the transplant.

Before the transplant, they found, her gut flora was in a desperate state. “The normal bacteria just didn’t exist in her,” said Dr. Khoruts. “She was colonized by all sorts of misfits.”

Two weeks after the transplant, the scientists analyzed the microbes again. Her husband’s microbes had taken over. “That community was able to function and cure her disease in a matter of days,” said Janet Jansson, a microbial ecologist at Lawrence Berkeley National Laboratory and a co-author of the paper. “I didn’t expect it to work. The project blew me away.”

Isn't it odd to realize that over a century after "modern medicine" established itself, a "miracle" cure as simple as re-colonizing a patient with a new set of bacteria, a new microbiome, can be discovered.

On his blog, Carl Zimmer points to a CalTech press release of a new research result:

Biologists at the California Institute of Technology (Caltech) have demonstrated a connection between multiple sclerosis (MS)—an autoimmune disorder that affects the brain and spinal cord-and gut bacteria.

...

Although the cause of MS is unknown, microorganisms seem to play some sort of role. "In the literature from clinical studies, there are papers showing that microbes affect MS," Mazmanian says. "For example, the disease gets worse after viral infections, and bacterial infections cause an increase in MS symptoms."

On the other hand, he concedes, "it seems counterintuitive that a microbe would be involved in a disease of the central nervous system, because these are sterile tissues."

And yet, as Mazmanian found when he began examining the multiple sclerosis literature, the suggestion of a link between bacteria and the disease is more than anecdotal. Notably, back in 1993, Caltech biochemist Leroy Hood—who was then at the University of Washington—published a paper describing a genetically engineered strain of mouse that developed a lab-induced form of multiple sclerosis known as experimental autoimmune encephalomyelitis, or EAE.

When Hood's animals were housed at Caltech, they developed the disease. But, oddly, when the mice were shipped to a cleaner biotech facility—where their resident gut bacterial populations were reduced—they didn't get sick. The question was, why? At the time, Mazmanian says, "the authors speculated that some environmental component was modulating MS in these animals." Just what that environmental component was, however, remained a mystery for almost two decades.

But Mazmanian—whose laboratory examines the relationships between gut microbes, both harmful and helpful, and the immune systems of their mammalian hosts—had a hunch that intestinal bacteria were the key. "As we gained an appreciation for how profoundly the gut microbiota can affect the immune system, we decided to ask if symbiotic bacteria are the missing variable in these mice with MS," he says.

To find out, Mazmanian and his colleagues tried to induce MS in animals that were completely devoid of the microbes that normally inhabit the digestive system. "Lo and behold, these sterile animals did not get sick," he says.

Then the researchers decided to see what would happen if bacteria were reintroduced to the germ-free mice. But not just any bacteria. They inoculated mice with one specific organism, an unculturable bug from a group known as segmented filamentous bacteria. In prior studies, these bacteria had been shown to lead to intestinal inflammation and, more intriguingly, to induce in the gut the appearance of a particular immune-system cell known as Th17. Th17 cells are a type of T helper cell—cells that help activate and direct other immune system cells. Furthermore, Th17 cells induce the inflammatory cascade that leads to multiple sclerosis in animals.

"The question was, if this organism is inducing Th17 cells in the gut, will it be able to do so in the brain and central nervous system?" Mazmanian says. "Furthermore, with that one organism, can we restore to sterile animals the entire inflammatory response normally seen in animals with hundreds of species of gut bacteria?"

The answer? Yes on all counts. Giving the formerly germ-free mice a dose of one species of segmented filamentous bacteria induced Th17 not only in the gut but in the central nervous system and brain—and caused the formerly healthy mice to become ill with MS-like symptoms.

"It definitely shows that gut microbes have a strong role in MS, because the genetics of the animals were the same. In fact, everything was the same except for the presence of those otherwise benign bacteria, which are clearly playing a role in shaping the immune system," Mazmanian says. "This study shows for the first time that specific intestinal bacteria have a significant role in affecting the nervous system during MS—and they do so from the gut, an anatomical location very, very far from the brain."

Mazmanian and his colleagues don't, however, suggest that gut bacteria are the direct cause of multiple sclerosis, which is known to be genetically linked. Rather, the bacteria may be helping to shape the immune system's inflammatory response, thus creating conditions that could allow the disease to develop. Indeed, multiple sclerosis also has a strong environmental component; identical twins, who possess the same genome and share all of their genes, only have a 25 percent chance of sharing the disease. "We would like to suggest that gut bacteria may be the missing environmental component," he says.

Acupuncture

I've had a hard time accepting accupuncture. It's philosophical basis in Chinese medicine is completely unscientific. But, on the other hand, I've seen some incredible surgeries done under the anaesthetic effect of acupuncture. These are hard to believe if there is no efficacy in the treatment. Here are some bits from an article by Ed Young in Discover magazine with the title A biological basis for acupuncture, or more evidence for a placebo effect?:

Nanna Goldman from the University of Rochester Medical Center claims to have found a biological explanation for the pain-relieving effects of acupuncture. She worked with mice that had inflamed paws, and managed to alleviate their pain by using a needle to pierce a traditional acupuncture point near the knee. This painkilling effect only happened when she rotated the needles after insertion.

This effect depended on a chemical called adenosine, which typically surges in concentration after any stress or injury. Adenosine works by docking at a protein called the adenosine A1 receptor, which has well established roles in suppressing pain and is found on neurons that transmit pain signals. Indeed, other chemicals that stimulated this protein had the same pain-relieving effects as acupuncture. Drugs that prevent the body from breaking down adenosine led to even more potent pain relief. And mice that lacked the A1 receptor altogether experienced no pain relief from the needles.

So far so good, but then Ed Young hits you with a sledgehammer:

After reading the paper, you might walk away with that idea that we’re one step closer to understanding how a treatment with real medical benefits really works. It’s littered with statements like “A1 receptor activation is both necessary and sufficient for the clinical benefits of acupuncture” and “medications that interfere with A1 recep tors or adenosine metabolism may improve the clinical benefit of acupuncture”. In the study’s press release, lead scientist Maiken Nedergaard even says, “The new findings add to the scientific heft underlying acupuncture.”

But these results have to be considered in the light of those that came before it. As mentioned above, new scientific discoveries stand on the shoulders of giants and in the case of acupuncture – one of the most well-researched of all “alternative therapies” – those shoulders are particularly large.

Many trials have demonstrated that acupuncture does have some pain-relieving effects – that is not in doubt. And as Steven Novella notes, unlike things like homeopathy or reiki, with acupuncture “something physical is actually happening… so it is therefore not impossible that a physiological response is happening”. But the big questions are whether this effect is genuine of nothing more than a placebo.

Go read the article to find out why you may want to be a bit critical and hesitant to buy into the breathlessly reported discovery of the physiological basis for acupuncture's efficacy.