The Evolution of the Evil Scientist. Part 1: The Money

When I was a little girl, the professor from Gillian’s Island was my hero. He was smart, unassuming, and solved a lot of problems. I deduced that scientists were incredible. As clever as physicians, with the power to save lives, but much cooler, as they shunned the limelight. Later in TV history came McGuyer, who fixed an awful lot of problems with duct tape and scientific knowledge.

Nowadays, scientists1 often seem to be on the evil side of the human equation. ‘They’ have conflicts of interest, because their primary activity – research – could be supported by a commercial interest, either a large corporation or their own startup company. Everything is questioned for the agenda. This post considers the impact of a scientists’ source of funding, and a second one will examine public disclosures that scientists now are almost required to make.

A major shift over the past 60 years has occurred in the way scientific research is supported. This page shows the switch in dominance of research paid for by the government versus private industry in the US. Until the late 1970’s, most research was supported by the government. In 2012, only 30% was government funded while more than 60% is industry sponsored. The pressure on academic researchers to commercialize the findings of their research has made for more industry ties – either by licensing to an existing business or encouraging researchers to create their own startup.

While this may cause some to throw up their arms in alarm and shout invectives about the corruption of research and polarized agendas and corporations paying for the results they want, for most of history, private individuals were benefactors of scientists. In other words, someone rich, on whose favour the scientist depended, doled out the money to feed and house the scientist, while they grew hundreds of bean plans, or gazed through a telescope at the stars and then disappeared into a dank library to do endless pages of mathematics. We’ve built our understanding of countless things, like the structure of the galaxy, human anatomy, and the theory of evolution, on the basis of privately funded research. Did any of the individuals who supported the scientists try to influence the conclusions of their research? Probably, but the passage of time, and the work of other scientists differentiate between influence and true findings.

I think part of what keeps science unbiased is that there are people, scientists, that live to investigate, to answer unanswerable questions. They don’t care who makes money out of it. They want to toil in obscurity, reasoning and experimenting things out. Problem is, we all have to eat. So what’s a scientist to do? Most are not in it for the money.

I’ve lived through several rounds of precipitously declining government funding for research, where university administrators warn the faculty (where a good percentage of scientists reside) of declining grants and encourage them to make friends with business people, as a means to survive in the research style to which they have become accustomed. Heck, I’ve even put on events myself to encourage industry sponsors and researchers to chat and form alliances.

To make this discussion more complicated, there is basic scientific research, of the type that asks and answers abstract questions, say about gravitation waves or behaviour of silicon in solid state, and may one day allow better satellite tracking or microelectronics. Then there is applied science, such as new drug testing. Although basic research, or what’s call curious-based research2, is generally of less interest to industry representatives3, a significant portion of development in the pharmaceutical industry has to be done in collaboration with medical researchers. Physicians who do research as well as care for patients, are the ones with the training and opportunity to work with the relevant patients.

As a recent example of how pervasive this sort of support of medical research is, this paper discusses the number of US physicians who report some kind of payment from an industry sources, including research support, consulting fees, or just sandwiches at a conference. The study found that almost half of physicians studied received some kind of payment, with the overall average being a bit over $5000 in a year.

It’s a tricky relationship, between physician researcher and pharmaceutical company. Doctors are the best ones to know which patients need new solutions for their medical conditions. Pharmaceutical companies understand how their new drugs work. They need each other, the doctors and the drug makers, and we need them to need each other, so we can benefit from the new drugs. I can’t imagine a physician that would knowingly harm a patient, particularly to get research money, as the point to research is to discover useful new ways to make people better. It would be like a chef accepting sponsorship to make foul-tasting food. On the other side of the equation, there’s so much potential for conflict of interest, both perceived and real, and some history of abuse of the system.

For both basic and medical scientists, often the choice is to get involved with a big business and accept their backing, or stop doing research. Research on zero dollars a day doesn’t work.

Why has this reality lead many to decide scientists are evil? The scientists I know are noble people who prefer to devote themselves to finding the truth, often the truth of discovering better medicines, over capitalistic gains. Am I naive?

I’m a scientist, and I am defending my colleagues, my tribe. But I have no agenda. Except the agenda I’m suggesting is the one of most scientists: Truth.

——-

1Using a very broad, inclusive definition of scientist here which includes the natural, social and applied scientists.

2This seems like a bit of a cruel joke, because ‘curiosity-based’ research, is far from a frivolous, random or carried out by people skipping through meadows, chasing shiny butterflies, activity.

3A couple of upcoming technologies, artificial intelligence and the Internet of Things, contradict this statement, since we appear to have ideas for implementation of the technology as fast as we can understand it.

 

 

 

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Do I Know What’s Good for my Cat?

Recent moves by various governments have declared dolphins, dogs, cats, chimpanzees, and even animals in general, sentient beings1.

What does this mean – the definition of sentience is consciousness of sensory perceptions, but how does it specify the way animals should be treated? A declaration that animals are sentient, like humans, provokes visions of trying to get dolphins to vote or providing chickens with flying lessons if they want. We’d never force them, of course.

Most of us want to do the right thing by animals. Many scientists study sentience, consciousness, sapience, and/or intelligence in humans and various animals. If a crow recognizes a man who feeds him, is the bird self aware or intelligent or has it learned to associate the smell of the man’s cologne with tasty treats (sentient) or does it contemplate if it is taking advantage of the man as it peaks fruit from his hand (sapience)? I need to read a stack of books and papers at least three feet tall to understand how these terms differ from one another when applied to animal behaviour. I respect the experts, but would like to understand this at a non-expert level.

I did some research on the emerging laws related to animal rights and the answers surprised me. Generally, the idea is to give animals more rights than inanimate objects, and to stop them from being used solely for human entertainment. These new laws and declarations are one part getting the laws out of the dark ages and one part enlightenment.

Why was I surprised? There’s some hype attached to the announcements about the new laws. Somehow2 the concept that animals can sense and are aware of their surroundings, which is a definition of sentience, transmuted into animals having emotions. Certainly animals can feel things. However, it isn’t necessarily the same as a cat feeling sad because it’s raining and there’s no birds to watch or a horse being anxious that its rider has had a few martinis, again, and might need counselling for addiction. If we accept the definition of emotion as an instinctive or intuitive, rather than reasoned, interpretation of a situation, I’d point to the keen instincts animals have. And that the sad cat knows hunting (food) is less effective in the rain and the horse instinctively fears a reckless rider for its own safety.

Do animals love and hate? A dog gets excited when it sees its human, either because of love or the expectation of treats, and a dog growls when a stranger skulks around the yard, but does it hate the intruder or is it defending its territory.

The new laws are to stop animals from being handled in ways that injury them. Previously, animals could be treated in the same way as all types of human possessions (this is the dark ages stuff). No one cares if you hit your table. A lot of people care if you hit your dog. The change in laws make it easier for officials to intervene if someone is doing something harmful to their sentient possessions (animals). Changing the laws so we cause no physical pain to animals seems like the right thing to do.

More interesting are the decisions to stop using animals for our entertainment3 – which I call the enlightened part. In the absence of direct pain and suffering, how do we tell if the animals are being treated well? We associate a cat purring with contentment, but they also purr when they are in pain. So if the cat purrs when stuffed into a silly outfit, is it thrilled or distressed? Is there something wrong with training an elephant to sit on a tiny stool while wearing a flowery hat? Or a walrus to clap it’s flippers and bark for fish? Taking a slightly riskier stance, why shouldn’t we drug tigers into passivity and make them jump through hoops, if the fringe benefits that come with that is a rich diet, medical care, and comfy accommodations? None of these actions are natural but putting on a suit and going to a job interview where we try to say all the right things, regardless of what we really think, is unnatural too.

Wearing a suit is voluntary. The confinement of animals in the circus and other entertainment domains is not. How do we get informed consent from a killer whale? Many people might claim they are trapped in jobs, unable to escape the drudgery or demeaning tasks because they need to make a living.

How do we tell when we’ve gone too far with animals? With sea animals, there are scientists who study the social structures the animals live in and compare it to what we provide. And yes, there is a difference between sea worlds and the wild. One point of evidence that the animals are being treated unfairly is a decreased life expectancy. This seems like a reasonable metric, but when I look at my domestic cats, who are kept indoors because this is verified to increase their life expectancy, I wonder if it’s right. My cat is convinced he should be outside, yet I imprison him in the house, based on the assumption that it’s better for him. I have some guilt, because I reap advantages, with lower vet bills. No worms, fleas, or stitches to repair battle wounds from the neighbouring tom, raccoons, dogs or cars. Domestic cats live longer inside, but are they living a fulfilling life? They don’t breed or do other natural things like hunt nor are they allowed the full range of a territory or their natural habitat.

Questions plague me:

  • How to know what animals really want?
  • What’s best for animals, which may not be what they want?
  • How human-like are they, anyway?

We should only impose our values on the animals when we know they want the same things we do. We could defend all we do as sapience, or wisdom, a quality that presumably sets us apart from other species (hence the name: Homo sapiens). We understand the consequences of our actions, and therefore agree to get vaccinated, even if it is transiently unpleasant.

Humans don’t do whatever we want, we often do what’s good for us, like go to the dentist, eat vegetables and learn mathematical formulas. My cat hates going to the vet and howls like a wild animal when I put him in the car. I don’t think this qualifies as mistreatment, even thought he clearly thinks it does. On the contrary, many decisions to give animals more rights insist on good veterinary care, although the animals dont’ seem to like it.

I haven’t got a witty conclusion to this post. The new laws to treat animals as sentient are to prevent cruelty. We’re striving for enlightenment in our interactions with animals, but I think we have a long way to go to figure out what that means. I’m looking forward to the day when I can communicate with my cat (maybe through artificial intelligence), and let him make the decision to get in the carrier and endure the vet’s prodding, as a alternative to dying prematurely of a preventable disease.

——

1Here’s a few examples:

This blog post http://barkpost.com/good/oregon-court-finds-dogs-are-sentient-beings/ discusses a recent decision by an Oregon court to treat dogs as sentient. It’s a great post for making sense of the law.

A similar story comes from New Zealand http://www.animalequality.net/node/703 , where the law was amended in 2013 and this is interpreted to recognize all animals as sentient, like humans, which provides officials greater power to protect animals in situations of abuse.

And then there was a declaration of by a group of scientists in 2012 http://www.earthintransition.org/2012/07/scientists-declare-nonhuman-animals-are-conscious/ that non-human animals display consciousness.

2 Not too difficult to imagine how if you consider how easily knowledge is perturbed from the truth and circulated as un-facts on the internets.

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The Case of the Mysterious Octopus DNA

Sometimes, exciting scientific things sound lame, so an editor puts a fancy headline on the story to avoid having the average person say ‘MEH’ to a breakthrough. Such could be the case with octopus DNA, and a story titled: ‘Scientific Breakthrough: Octopus DNA is not from this world.’1 Were you skeptical of this headline? Was it because it sounded impossible, preposterous, almost as crazy as someone suggesting the earth is flat or red wine protects against heart disease?

I’m working on a process, a series of five questions, to get an un-hyped understanding of popular media stories on scientific topics. So, let me apply my questions to the octopus situation. By seeing the logic with the octopus DNA story, it may make my method easier to apply to less obvious situations, or situations where your intuition is saying ‘that’s wrong’ but you can’t put your finger on why.

Question 1. What do the numbers really mean?

More numbers might have helped this story. The premise is octopuses are alien and their DNA sequence supports it. How different is their DNA? That wasn’t discussed. But elements in the octopus DNA were found, such as genes, coding sequences, and transposable elements, commonly found in humans and other native earth species. Therefore, octopus DNA can’t be entirely alien.

The story states that Octopuses have 33,000 protein coding genes, far more than humans. Makes them sound more complex, more intelligent, doesn’t it? Until you see this chart2, that ranks number of genes per species and finds grapes ahead of humans. The story could have said that octopuses have more genes than grapes, but that doesn’t sound very special, does it?

2. Is the science in the story from a reliable source and quoted in context?

The original basis of the story was published in the journal Nature, a very reputable source, in Aug. 2015. It does not contain the word ‘alien’. The alien DNA story came along later, quoting a news release titled ‘Landmark sequencing of octopus genome shows basis for intelligence, camouflage’. Neither of these traits are uniquely alien – you can make your own bad pun about how alien intelligence seems in human society sometimes. Camouflage is pretty common in the animal kingdom, ask the spotted leopard lounging in the dappled shade.

How did the story get to be about aliens? A scientist is quoted, who quotes another scientist. The first scientist points out how unusual a the octopus body is. You don’t need a DNA sequence to discover that. All you have to do is observe the octopus and it’s ability to change skin colour with situation, escape predators in a cloud of ink, or unscrew a jar if it’s worth their while. The misrepresented comment is: “The late British zoologist Martin Wells said the octopus is an alien.”1 There have been others who call the octopus alien3, but I believe it’s metaphorical, rather than scientific, even if the quoted individuals were learned professors.

From an evolutionary perspective, octopuses ON EARTH split from the lineage that lead to humans about 500 million years ago. Whatever your definition of alien is, if a creature been somewhere for that long, I think it deserves to be called native.

3. Is the evidence proven or inferred?

The story bounces around through various biological terms, which are connected incorrectly. It states the octopus has ‘incredibly advanced biotechnology’. Biotechnology is not naturally occurring. Biotechnology is technology engineered to make industrial products in a lab based on biologics. No one, to the best of my knowledge, has seen octopuses directing lab operations. There’s mention of transposons, which the story says scientist don’t understand, a spring board to the conclusion that there is something really alien going on in the octopus nerve cells. Why the leap to nerve cells, when DNA specifies what goes on in all cells? Or the conclusion that because scientists don’t understand something, it’s alien. Scientists don’t understand lots of things, like Alzheimer’s disease, selfies, and reality TV, but that doesn’t make them alien.

4. Who has a stake in this?

The folks who posted this story have a long-standing, popular website that deals with spiritual and scientific matters. Perhaps their mission was to demonstrate how science could be taken out of context. Or what the word alien means to different people.

5. Why hasn’t someone done something about this?

Should octopuses be treated differently, now that we know their DNA sequence? I don’t see a reason that the eight-tentacled, water-dwelling creatures are different now that we know more about their biological blueprint.

It’d be easier to declare octopus DNA alien if we had some alien DNA to compare to. It’s not evidence of alienicity that all octopuses have a certain trait, like the ability to change the colour of their tentacles, when no other species on earth can. That means only octopuses can do it, not they are alien. With the same logic, we might conclude that humans are aliens, because we are the only earth species that buys lottery tickets, or wears sunscreen so we can withstand the blistering hot, burning sun, rather than lie in the shade like other sun-sensitive species.

A similar story, with an equally provocative title and equally modest explanation of what’s so exciting is ‘Orangutan DNA is full of surprises’4. Having read the report, I agree, but unless you are a geneticist, I’m not sure the findings will hold the same fascination. Sure, the study told us things we didn’t know before. Orangutans evolve more slowly than humans or chimpanzees (these three are closest evolutionary relatives to each other). This slow rate of change in orangutans could be related to how many transposable DNA elements they have. In the case of orangutans, their DNA contains fewer transposons, and they have evolved slower than humans or chimps. The octopus, on the other hand, has more transposable elements and is more adaptable to changes in its environment.

By the logic of the octopus story, orangutans are less alien that humans. I’ve never seen an orangutan buy a lottery ticket, or apply sunscreen, have you?

3 Such as ‘ “Meeting an octopus,” writes Godfrey-Smith, “is like meeting an intelligent alien.” ‘ from https://orionmagazine.org/article/deep-intellect/

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What if your Doctor was an AI?

This year’s MedEdge Summit. York Region – MedTech conference was affirming. Inspiring in a creative kind of way, rather than the eye-opening, mind-numbing advances in technology that make you think you’ve been hiding in a foxhole with a metal bowl on your head for the past 70 years. We’re on the right track with our crazy, cutting-edge technology to doing something useful. Things are falling into place, in a crooked, bottom of a kaleidoscope pattern.

Ok, there was still some wild stuff discussed, like patients being in charge of their own medical data and sequencing an entire human genome in a few days. Those are the beginning of approaches that I think will turn out well in the long term.

Today, even if we’re presented with our entire genomic sequence on a silver tray, no one knows what most of it means. But we will some day. Until then, we’ll keep doing those studies that give us a bit more evidence what the sequence of 11q21.3 means if you have green eyes and are good at cricket.

Right now, having people control their own medical records is like giving a four year old the keys to the car. Most of us don’t have the training to understand the data we’re presented with. As a small segue, when I was 15, I found my medical file open on a desk. A nurse chided me for reading it. I looked at her in wonder, ‘but, it’s about me.’ She snapped the file shut. In retrospect, we were both right. She took it away because it was written in a language that would confuse or misguide most people, so it wouldn’t be to the patient’s benefit to see it. But, information about me should be my property. That’s seems to be how modern privacy laws are playing out.

Let’s get to the exciting stuff: artificial intelligence. I can see it being useful in medicine because AI could provide the kind of assistance only AI is capable of. An enormous number of researchers are learning new things about human health all the time. Expecting your friendly family doctor to read 100’s of papers a day, while he or she works full time meeting with patients, assessing their conditions and suggesting a growing number of preventative approaches, is just crazy. They are only human.

Enter Artificial Intelligence. It’s particularly good at assimilating vast quantities of information that arrive over long periods of time. It doesn’t need to wrack its brain to put together one study published in South Africa in 2009 with another one from Sweden in 2016 to collect information about a rare disease. That’s easy-peasy for AI and the basis of how we learn about human health. Dozens of separate studies, done in different ways, by different people, come together to lead us to new knowledge. Rarely does one report change medical practice. AI also can provide us with the benefits of analyzing the activities of billions of people. Rumour1 has it that Microsoft was able to find common symptoms that people searched on before they were diagnosed with pancreatic cancer. AI can provide an up-to-the-microsecond summation of all that’s relevant to a patient’s condition.

Great, as far as it goes. But it stops at the sum of all human knowledge and behaviour. Could AI possibly deal with uncertainty and lack of answers better than the current, malpractice-avoidance approaches? AI probably isn’t capable of caring or being sympathetic. In my experiences, this has been all but beat out of the current medical system, with quotas to deliver, expectations to manage, and routinized care. I long for the time when the doctor put the chart down, smiled and said, ‘you’ll be fine. It’s just a bug/growing pains/aging/over exertion/gas/random. Come back and see me in a week if it isn’t better.’

How is AI going to provide us with common sense, perspective, or talk us down from the fear we are dying of an incurable but totally improbably disease? Maybe it can. To my way of thinking, many of the situations where patients need to be told things are ok are based on the natural variability of the human body. Guidelines usually have a range for things like blood pressure, heart rate, levels of cholesterol and more. What does it mean when someone is outside the normal range? More tests can be done for explanations that might be pathological. When those turn up negative, the physician is left with no explanation and the possibility of natural variation. The doctor may have a hard time saying so, just in case there’s something going on. AI could at least quantify the answer with something like ‘there’s only a one in 500 chance of this’, or ‘a one in 248 chance of that’.

How will AI deal with situations when patients need to be consoled? We all die eventually and at some point many of us will need to be told we have a terminal or very serious condition. Will AI develop algorithms to read a person’s expressions and body language so it can tailor its delivery to each patient, or will it defer to its human equivalent? Let the doctor do what may have attracted them to medicine in the first place – care for their patients.

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A Fishy Saga about Science and Knowing what to Eat (Part 2).

Triggered by guilt-induced schisms that I was getting something too good to be true, I dug deeper into the case of a delicious new fish available in grocery stores near you for an astonishingly low, low price.

Part 1 covered the controversy of whether basa was a good thing to consume or not. To find the answer, I needed credible sources of information about fish farming but I had no idea how to identify them so I turned to friends for help, friends who are experts in the area of fish biology.

My inside information lead me to Seachoice.org. They’re on the page two of the google search on basa 1? Who is Seachoice? Their ‘about me’ page suggests an independent organization but I’m not sure of their agenda because the write up is quite generic. The overview about basa, or Pangasius, concludes with a ‘some concerns’ rating. Further down is an avoid rating. So I don’t know who Seachoice is or which rating is the rating. I’m tempted not to spend any more time on their site, but someone I respect told me Seachoice is an authority, so I download Seachoice’s 70 page pdf2 about basa and read.

The first page gets a thumbs up as it reveals an independent person with relevant credentials wrote the report. And I learn more about what Seachoice is all about. The organization’s goal is to empower consumers to make choices about what they purchase. They focus on sustainable practices in fishing, with a sustainable goal of long term fish production not jeopardizing the ecosystem. Their recommendations are based on as much objective evidence as available.

As a food source, basa can be farmed efficiently. The environmental concern is the sludge waste from the ponds which has been found disposed of illegally. The other major concern comes from antibiotics and pesticides found in the fish. A small minority of basa shipments to Europe have been refused due to such contamination.

Basa gets an avoid rating (farmed in ways that harm other marine life or the environment, i.e sludge dumping), EXCEPT if the fish has an ASC, GAA or Naturland certification (whatever that is) and then basa is a good alternative (some concerns about how it is produced). These rating are obtained by an estimated 23% of the basa produced at the time of the report.

Well, at least that’s a goal. I can feast on basa if it has these certifications. I should look into these certifications. But I’m tired. Going to the grocery store shouldn’t be this hard. I’m tempted to do a few things:

  • go with my instincts that tell me if the basa tastes good, my body knows what’s right (but then, we humans do like to eat things that aren’t good for us, like donuts and chips).
  • make my life easy and chose talapia instead (but is talapia ok? – it’s another farmed, recent introduction to the NA market)
  • starve to death while doing research
  • eat fries.

But I devolve. This experience has highlighted to me the challenges of making sense of scientific information even when you try to. It’s hard to identify a credible source, and when you do find it, sometimes it doesn’t answer the question.

As I travelled the path to a truth about basa fish, I wondered what my objective was. I stepped onto the path because my instincts told me that getting something at an extremely good price has its price. It goes deeper than that. What do I value in my food? I know there are animals that die to produce the meat I enjoy. It’s almost impossible that our existence on this planet is without a footprint. There are 7 billion of us, we impact the environment. Sustainability means leaving the environment so future generations can survive; I have no idea what that means. If I look back, my foreparents built cities that I marvel at. They didn’t destroy, they enhanced. But they also changed the earth. We’re facing global climate change and can’t expect the expected.

We can’t solve all problems at once. At least I can’t. I have a much better idea of whether to buy basa at my local grocery store now. If I can find it with certification, I will buy it. But I might still buy it anyway. I could be supporting a local entrepreneur in Vietnam, who will adopt more sustainable farming practice when his or her business prospers.

Meanwhile, I need to get busy developing truth-finding tools for everyone to use when faced with a wall of discord about something that should be based on scientific evidence. Stay tuned.

1Who goes to the second page of a Google search? I’ve heard marketing folks say withering things about having your website turn up as the 11th+ hit on a google search. Are those of us on pages other than page 1 are clearly interested in something other than fiddling with the rules of search engines to get ourselves to the front of the line? Perhaps content, not promotion of content? Marketing is a good thing, most of the time. But I still look at pages two to four, at least, of a google search, because I know there’s gems buried in the glitter.

2http://www.seachoice.org/wp-content/uploads/2011/12/MBA_SeafoodWatch_Catfish_Vietnam_Report.pdf

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A Taste of my own Medicine. (The Beginning of a Fish Saga.)

This doctor needs a dose of her own medicine. A simple query erupted into a full-blown quandary about how to interpret information. About a fish. Me, the doctor of ‘how to understand scientific stories’ is stumped, or at least needs to do a whole lot of reading to figure out the truth.

Here’s how it began. I found a new type of fish in the grocery store: basa. Anything new in the grocery store gets an immediate ‘buy’ from me. Once I have it in my own kitchen, I wonder what it is and how to cook it. Basa is a white fish, frozen as boneless fillets. I steamed some with some garlic and it was delicious. Then I bought more, still at an almost indecently good price. After 6 months, the prices I see are cheaper by a half than frozen sole, haddock and cod.

While delighting in what good fish cakes, chowder and sauté basa makes, a niggle of doubt crept in, and made me uneasy. How could something so good be so cheap? It defies fundamental laws of economics

So I googled. I don’t remember the results of my first search. Perhaps I was relieved to find no glaring resident evil in either the production or nutritional value of Basa so my eyes glanced off the details. If it’s in all the local grocery stores, it has to be ok, doesn’t it?

Shadows of doubt wouldn’t let my mind settle, so I asked my Facebook friends if they knew anything about this wonder-fish. I have a wonderfully eclectic mix of friends, including ichthyologists, those that hunt their own meat, organic food enthusiasts, and zealous vegans. The responses I got to my Facebook question if the fish was appropriate to eat varied from ‘full of toxins’, ‘poor labour conditions on the farm’, ‘Frankenfish’ to ‘tasty, recently introduced to NA, farmed species of catfish’.

Time to read more carefully. There is disagreement. In the top ten Google hits are an informational page from Wikipedia, and two reputable Canadian food suppliers with recipes and a description of the product. Immediately below a headline suggesting consumption of basa causes death1 is a link to more recipes. There’s a video on where the fish are farmed, a Forbes article about how popular the fish is in India2 and an interesting column from The Times.3 I like this last piece. It’s full of opposing views. Apparently, the Australians love this fish, but Americans do not. Two Canadian authorities are cited with conflicting views. The controversy surrounds how the fish are farmed. They are not genetically modified but recently introduced to NA markets from Vietnam. There is disagreement over whether the river where basa is farmed is clean or polluted (you’d think that would be easy to determine, but from 20,000 km away, it’s hard to tell), what the fish are fed, and if are they given too many antibiotics.

At this point, I’d learned a few things, including where the idea basa is full of toxins or poorly farmed came from. But I hadn’t gotten to the truth yet – should I eat it? Or is that the truth I’m seeking? I started probing because of something I call Ann’s Axiom:

If it seems to good to be true

or like it should be illegal,

it probably is

or will be soon.

Delicious fish. Cheap. The free market should push the price up because basa is a desirable commodity. But it hasn’t. What does the free market know that I don’t? Or do I know something the free market doesn’t? That would satisfy my taste for being ‘in the know’.

Ha, but knowledge doesn’t come cheap – it requires work. And reveals there’s another dimension I must add to my self-help approach on how to understand science. Taking a single story and seeing the truth behind it is a good start. But we have to go further. Finding answers to everyday questions that depend on science is also critical.

Stay tuned as this doctor swallows the cod liver oil of humility to continue the quest to understand basa, and more importantly, how to understand how to understand basa and other things, in the next post*.

* The next post may not have the answer to life, the universe and everything. That’ll take at least two** more posts.

** Multiple by two and add 40 (standard approach to estimating jobs).

1http://talk.onevietnam.org/cause-of-death-consumption-of-basa-fish/

2http://www.forbes.com/global/2011/0411/life-vietnam-yogesh-grover-aquaculture-empire-fish-basa.html

3http://www.timescolonist.com/life/ask-eric-is-it-safe-to-eat-imported-basa-fish-1.87907

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Get the Tricorder, Stat!

Remember the gizmo Bones, the doctor on the original Star Trek, held a few centimetres above a patient and it provided all pertinent information including a diagnosis? It’s high time modern medicine got to the same point.

This post is a pure ‘please do better’ to the medical system. We need medical diagnosis to catch up with the 21st century. Many current diagnostic tests seem the equivalent of those creepy cages and metal contraptions of medieval torture.

Here’s what’s set me off:

med test

I saw this poster on a bus in rural Nova Scotia. I understand the motivation. Mammograms, used for screening, are documented to decrease death due to breast cancer¹. Being a responsible medical provider, the NS government is trying to convince people to undergo screening. But the test is demeaning, uncomfortable and with slight risks. They acknowledge the unpleasantness, but still encourage people to do it.

Why support the participation in something uncomfortable? Take a page out of any business marketing book – if you want people to embrace your product, make it appealing to them.

Mammograms are the tip of the medical-testing-draconian-torture iceberg. Another common medical test, supported as a life saver by various medical organizations, is the colonoscopy. Yuk. Begin 24 hours in advance with consumption of a disgusting drink and volumes of water, necessitating that you cling to the outskirts of a bathroom and feel like you ate several tins of browned beans for lunch. To add to the experience, the next day, when you’re feeling at your worse, a perfect stranger shoves a metal tube up your ass, then you feel light-headed and woozy for the next 12 hours. Demeaning, time-consuming and disgusting for the person who cleans the bathroom.

A colonoscopy isn’t that bad and it prevents death due to colon cancer². If you want to undergo a truly harrowing medical test, there’s imagining by MRI. I was prescribed one of these and on my way to the torture, sorry, I mean test, chamber, I looked into the eyes of the woman coming out. I saw fear. When I balked at the test, the technician suggested my doctor prescribe sedating drugs. When I recounted my experience, friends described their coping mechanisms. What else do we willing do that requires sedation, denial and putting ourselves through hell?

I could go on. The worst test I’ve heard of is a screen of lymph node that many cancer patients have. Everyone I know who’s had this test comes out of it in tears.

What are we subjecting ourselves to in the name of medicine?

Consider the basic human reactions that need to be over-ridden for many medical tests:

  • consuming substances that your body wants to vomit
  • enduring ‘discomfort” (either out-and-out pain or something invasive) that your instincts tell you to swat or punch away
  • surrendering all control to a stranger
  • doing things that involve side effects after or before the test including, but not limited to, headache, vomiting, diarrhea, constipation, nausea, dizziness, fatigue, muscle aches and feeling like you’ve been taken advantage of
  • paying for the infliction of discomfort (either directly or through your taxes).

It’s nuts: Enduring degrading, painful, anti-intuitive nonsense, parading around mostly naked, abandoning your worldly possessions (when else do you put down your phone or take off your wedding ring?), spending your time in unpleasant, perhaps grave-like or otherwise confining surroundings. Have I said YUK enough?

Yes most medical tests are beneficial to patients, identifying conditions and facilitating appropriate treatment, reducing pain, suffering and mortality. But more forethought when developing the tests might allow for a more pleasant patient experience. Tech startups do this all time – consider the user experience. All businesses cater to their customers, because happy customers buy more.

The Tricorder, with the nirvana of completely non-invasive testing, isn’t here yet, but it’s a great goal to aim for.

To put a reality-based context to this, there was a contest announced by Qualcomm in 2011³ that invited contestants to develop a real-life Tricorder which detected Anemia, Atrial Fibrillation (AFib), Chronic Obstructive Pulmonary Disease (COPD), Diabetes, Leukocytosis, Pneumonia, Otitis Media, Sleep Apnea, Urinary Tract Infection, and Absence of Condition(4). The device was also expected to give routine physiological measurements of heart rate, oxygen, blood pressure, temperature and respiration rate. I am totally enthusiastic about ‘Absence of condition’. To me, that is the single biggest gap in modern medicine – the ability to say ‘there’s nothing wrong with you’. I know there are liability issues here, but it’s probably what people most need to hear and doctors are most reluctant to say.

Let’s boldly go where no medical diagnosis has been before – to an ideal patient experience.

———————

  1. This is a credible source which attempts to summarize the data: http://www.cancer.gov/types/breast/hp/breast-screening-pdq
  2. http://www.nih.gov/news-events/nih-research-matters/colonoscopies-prevent-colon-cancer-deaths
  3. http://tricorder.xprize.org
  4. http://tricorder.xprize.org/about/overview
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It is really in your DNA?

Corporations might be legal persons but they don’t have DNA.

This expression ‘in our DNA’ is a thorn in the eye of my scientist’s sensibilities when it’s used to describe organizations. I know, it’s just an expression that means something fundamental to behaviour, beliefs or actions. Fair enough as a metaphor.

But, I don’t like it. Because of my propensity to analyze seemingly factual statements to determine if they indeed are factual – a propensity likely influenced by both my genes and my environment.

These are the top hits I found in a google search for ‘in our DNA’:

A company that develops marketing campaigns, has ‘innovation is in our DNA’ as a tagline1

They’re not the only ones who claim innovation is in their DNA. The University of Waterloo says the same.2

Boston University’s claim of what’s in their DNA: “It’s in our DNA: an inherent desire in each of our students, faculty, and staff to vigorously and dauntlessly pursue knowledge—and embrace the unlimited possibilities that come with it.”3

At Princess Margaret Hospital, a cancer-focused treatment and research facility, there’s a ‘why’ gene in their DNA4 while at the Texas A&M University School of Law success is in their DNA5.

Recent news stories suggest that fear of spiders is in human DNA6, while others speculate that space travel is in DNA7, or that our DNA is made of collapsing stars8.

Perhaps the reason ‘in our DNA’ grates on me is that no one completely understands what’s in our DNA.

The genome project has made tremendous inroads into sequencing and mapping human DNA. We have identified all 25,000 odd human genes and given them names and can classify them into functional groups9, but that’s sort of like taking apart a house and being able to classify its parts into nails, pipes, wires and 2’x4’s – useful information but still lacking an explanation of how it all fits together and what it does when it’s assembled.

As far as gene function goes, information is sparse: a few mutant human genes causes diseases such as cystic fibrosis or sudden cardiac death. Another handful are for simple traits, such as eye colour or tongue rolling. Generally, there is no linear map between a complex process, like innovation, and a gene or set of genes.

We are far from understanding how most human behaviours are influenced by genes. Studies on identical twins [genetically identical by definition] investigated the genetic basis to behaviour10 and found about half of any given behavioural response is determined by what’s ‘in our DNA’ and the other half a result of our environment. However, studies to link specific genes to specific behaviours haven’t been as illuminating as hoped, according to Psychology Today11. A thoughtful article on this topic, which considers studies on the propensity of a human populations to explore and migrate to new areas, the so-called restless or explorer genes, is here12. My crude summation is: there’s a tendency, it probably has a genetic component but that doesn’t fully explain the behaviour.

Might innovation be in DNA? Since there’s an on-going controversy in the business literature13 over whether entrepreneurs are born or made, I’m willing to add ‘don’t know’ the behaviour influences of all genes to ‘don’t know’ what makes entrepreneurs and surmise maybe entrepreneurship is in some people’s DNA. But not organizations.

Is it fair for me to object to ‘in our DNA’ when I don’t have an  explanation to offer? We don’t know if innovation or entrepreneurship or the ability to choose killer marketing approaches is in our genes. That’s a joy of human nature – there’s mystery in what people will come up with, given the chance.

Perhaps we should leave the mystery of what’s in our DNA for artificial intelligence to discover, much to its dismay.

——

10for example Wright, W. (1998) Born That Way. Genes. Behavior. Personality. Knopf. New York or Steen, R. G. (1996) DNA & Destiny. Nature and Nurture in Human Behavior Plenum Trade New York.

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The Problem with Processed Meat

Has news of the declaration of processed meat as carcinogenic blown over?

One answer is: I got a really good deal on bacon the other day, validating my first thoughts about the report released Oct 25, 2015 from the World Health Organization that processed meats and maybe red meat are carcinogenic:

Woo-hoo, steak’ll be cheap now.

I do love a good rare hunk of rib steak, flash fried in a bit of butter, with a side of mushrooms and onions. Mmmm. Humans are omnivores and we’ve been eating red meat since, uhm, before we were human. Also, the designation of processed meats – not red meat – as carcinogenic suggested to me that it’s a consequence of processing, not the meat, that’s the greater risk. Finally, lots of things are carcinogenic, but it depends on how much you consume and how often you are exposed. (My first scientist’s segue: the details of the announcement dwelt on the types of cancer and the amount of consumption.¹)

After a bit of data diving, I wondered if this was a good story about the fun you could have with death statistics. Then I settled down and realized only a very small fraction of the population considers statistics fun. (If you are interested, here some details about the relative significance of processed meat in the grand scheme of risk factors for mortality.² )

Adventures in epidemiology aside, I started feeling, instead of thinking. The things that are on the same list as processed meat include asbestos, smoking, sunbathing. Many of us give a healthy respect to avoiding these things, perhaps because we’ve all known someone who has died of a cancer associated with exposure to one of them. The announcement should be taken seriously.

Can we rely on efficient capital markets to take care of us? Only if demand for processed meats fall so low that they are no longer cost effective to produce will the products disappear.

Or should society take a more proactive approach, protecting citizens from hazard and remove processed meat from our grocery shelves?

A fantastic business model would be a new approach to producing savoury, well-preserved meats that avoided the current, toxic processing. Problem is, do we know what that is? I’ve seen some reports³ that suggests it’s nitroamines (carcinogenic in many models 4) generated during high temperature cooking of meats, or maybe other compounds (certain aromatic hydrocarbons), or the fat content, which tends to be higher in processed meats, or maybe the iron in red meat causes excess oxidation and is the culprit?

The biologist in me returns to add: We inherently relish the taste of the things that aren’t good for us. Consider sugar and fat. Donuts. Ice cream. Throw in starch and you’ve got french fries, potato chips. Then add meat. Hamburgers. Pizza. Chicken wings.

Need I go on?

Why do we salivate over fast food gluttonies and not celery, carrots and cod? Because we’re still living with the urges that kept us alive over the past centuries when food was scarce and storing up calories was the best thing we could do for ourselves. If the Neanderthals had had a ready supply of cheese puffs, say at the corner store, they might have out-competed Homo sapiens and we’d be in a very different place today. Perhaps non-existent. Or maybe Homo neanderthals would have been less completive and we’d co-exist. They might let us have cheese puffs if we were very good co-inhabitants of their domain.

I’m side-tracked. Maybe because the topic of processed meat is too complex. Too tied up in what it is to be human. Just as it’s human to get caught up in a sensational announcement about the dangers of a food group we’ve been revelling in for decades.

We learn. We find better ways. We evolve, whatever that means to us.

—–

¹ I made a trip to the WHO website so I could see the data for myself. First a few definitions. Red meat includes beef, pork, lamb and a few other things, like horse. Processed meat seems to be a broad category, including any of the above meats smoked, cured, salted, fermented or other. Already, I’m sceptical. Scientific studies tend to be very specific, not use broad groupings.

Next question, what specifically is the risk? Colorectal cancer, definitely, maybe stomach cancer too.

From the Q&A posted by WHO: “According to the most recent estimates by the Global Burden of Disease Project, an independent academic research organization, about 34 000 cancer deaths per year worldwide are attributable to diets high in processed meat.”

² Considering that there are 7.1 billion people on earth ( retrieved Nov 25, 2015 from here ) and in 2012 about 56 million people died (retrieved Nov 25, 2015 from here  ), processed meats causing 34,000 deaths is a small fraction, at 34,000/57,000,000 or approximately 0.06% of annual global deaths. Of course, if you happen to be one of the people who develop cancer because of processed meats, it is significant to you and your loved ones.

Also from the Q&A posted by WHO: “These numbers contrast with about 1 million cancer deaths per year globally due to tobacco smoking, 600 000 per year due to alcohol consumption, and more than 200 000 per year due to air pollution.”

So, a person’s chance of dying because of eating processed meat is about 1/30th the risk of smoking.

It’s a bit unfair taking a global perspective on this when it really depends where you live what you are likely to die of  (retrieved Nov 25, 2015 from here) . In developing countries, death is much more likely due to cardiovascular and infectious disease, especially in children.

In Canada, it’s estimated that 9,300 people will died of colorectal cancer this year (retrieved Nov 25, 2015 from here). That’s a sizable fraction of the global number of 34,000 (9,300/34,000 or 27%).

If we add the US, where slightly under 50,000 people are expected to die of colorectal cancer in 2015 (retrieved Nov 25, 2015 from here) , we can see that the processed meat number has been overtaken by total deaths from colorectal cancer. Certainly, it’s not the sole cause of such types of cancer. Worldwide, there were 694,000 deaths from bowel cancer in 2012 ( retrieved Nov 25, 2015 from here). So, 34,000/694,000 colorectal cancer deaths due to processed meats. Five percent.

But wait, there’s another dimension to this. How much consumption are we talking?

Q&A on WHO site says: “An analysis of data from 10 studies estimated that every 50 gram portion of processed meat eaten daily increases the risk of colorectal cancer by about 18%.”

Daily? I suppose if you ate a processed meat sandwich every day for lunch, you’d be testing these levels. But occasional consumption, not so much.

³ for example, the abstract to this paper: Cross, A. J. and Sinha, R. (2004), Meat-related mutagens/carcinogens in the etiology of colorectal cancer. Environ. Mol. Mutagen., 44: 44–55. doi: 10.1002/em.20030

4 Retrieved from http://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=658447 Nov 24, 2015

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On Drugs: Emerging Business Models (an update)

Remember the pharmaceutical company(s) that started an avalanche of public outcry for snowballing costs (hundreds of fold increase in months) of certain generic drugs? Well, Imprisis Pharmaceuticals has come up with a solution to get reasonably priced versions of said drugs to patients.

Brilliant,” I thought, on reading how they are going to do it.

Then I chewed my lower lip for a while trying to poke a hole in the concept.

But couldn’t.

Finally, in awe of the simplistic genius, I did a classic face-palm and wondered, Why Didn’t anyone Think of this Before?

Before I get into the logistics of it all, let me say that I’m glad the people who need the drugs, such as the generic pyrimethamine of the branded Daraprim, have better access to them. This report indicates the price will be about $1 per pill, compared to $750 that Turing was reported to be considering at one time (but pulled back from).

The trick, not to imply that Imprisis is doing anything that involves slight of hand or fooling anyone, the clever bit, is that Imprisis will provide generic versions of pyrimethamine by using a method that is, and has been for centuries, a generally accepted practice in pharmacies – called compounding.

Compounding is ancient. Used to be, medicines were all individually made by someone with a mortar and pestle and an apothecary of ingredients. As the pharmaceutical industry became more sophisticated, the creation of medicines was standardized (generally a good thing for safety and cost-effectiveness) and pills were produced under strict manufacturing conditions for the masses. Mass-produced pills contain not only the active ingredient but other things to increase its shelf-life, make it easier to swallow, delay release so once a day dosing is possible, decrease stomach upset and some other side effects, and have become the norm.

Occasionally, a physician will prescribe a specialized formulation, which eliminates an allergen, or allows the drug to be administered in different form, such as flavoured liquid or rub-on gel. Compounding is a wonderful throw-back to physician discretion, allowing the doctor to make a professional decision about what’s best for his or her patient, rather than selecting from a menu of pharmaceutical company offerings. Compounding is also popular with veterinarians, who will suggest using a drug that’s been proven effective in humans but needs to be modified for use in animals.

I’ve used compounded drugs. For my cat – a specially formulated gel that I rubbed on his ear to ease long-term administration. For me – combination drugs for topical administration, antibiotics and anti-inflammatories all in one. What the Doctor ordered for the specific situation.

The differences between branded, mass-produced drugs and compounded ones often includes more extensive testing for the preformed pills because the pharmaceutical giant behind them has funded the studies. Also, the pharmaceutical company has the liability if their medicines do damage. With compounding, the prescribing physician takes on this risk, generally with significant knowledge of the properties of the ingredients in the compounded formulation. Somewhat like buying off the shelf versus DIY. Compounding isn’t practical for all the pills prescribed today – we’d need half the population working as pharmacists to provide the millions of drug doses Canadians take every year.

However, clever Imprisis Pharmaceuticals has come up with a practical approach to providing off-patent, rarely used but badly needed drugs, such as the active ingredient in Daraprim. This is the drug Turing jacked the price on and elicited an impassioned response from the public, often focused on the evils of capitalism, pharmaceutical companies and perhaps hedge funds for good measure.

I’d never heard of Imprisis before this and promptly looked them up. They are a very young company,

whose core business is in compounding of existing drugs for better patient outcomes. Although this year looks like their break-even year for sales, prior to 2015, they’ve lost substantial sums. A not unusual scenario for a biomedical startup.

Am I implying the Imprisis has deduced a brilliant solution, hidden in plain sight before everyones eyes and the company deserves the support to do more good, or am I suggesting that being a pharmaceutical Robin Hood is a brilliant marketing tactic by a small company wavering between financial hard times and glory?

I’m not. I’m just sayin’ there’s many perspectives to every good story.

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