Radio Freethinker

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Posts Tagged ‘DNA’

RFT Ep 255 – Dirty Dozen Edition

Posted by Don McLenaghen on June 13, 2014

Download the episode here! 

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The dirty dozen and misreporting toxic food

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A loyal listener told me that they regretfully were switching to organic apples. “Why?” I asked. They said they read on the CBC website about the Dirty Dozen…the 12 most toxic laden fruits and veggies in our supermarkets.

I discovered the Dirty Dozen is published by the Environmental Working Group (EWG)…I investigated their claims, evaluated their data (not really theirs but the USDA) and after a little more research proclaimed the story rubbish.

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It got worse though, first because it was such a poor example of “journalism” by the CBC…it took be a few minutes to raise some red-flags about the story and an hour or 3 to complete debunk it…and yet the CBC not only reported uncritically but expanded by include and even worse study.

Secondly, i seem to have my loyal listeners that they did not seem to know how to evaluate this story. So listen to see both why the dirty in the Dirty Dozen applies to the EWG more than the flora and how you too can debunk a story like this.

Further Reading:

Blinded by Science

Our semi-regular segment about cool science stories…this week:

Blinded by Science – Mice gotta run

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Ever wonder why a mouse will run in those little wheels? Do they like it, are they bored or is it a sign of psychosis? Well, someone did some finally set out to answer that question…list to find out why and how snails came in second place in the wheelly marathon.

Further Reading:

Blinded by Science –  The Beast asteroid

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This past weekend a continent-killing asteroid whizzed by the earth, what makes this one so scaring is we did not know it was coming until April this year. We talk about the asteroid and the need to increase spending in locating near-earth object…especially those that might want to hit the planet .

Further Reading:

Blinded by Science – DNA expands

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DNA is the foundation of all life on earth…as far as we know the universe. Well, scientist have improved on the (at least) billions year old formula. No longer are we limited to the traditional two base pairs…they have added another. Why? How? Listen and find out.

Further Reading:

Prairie Correspondent – Reflections on the phrase “thank god”

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This week, our correspondent reflect on “thank god” how we use it, abuse it and well, just sometimes get it wrong.
Web Wisdom – How to choose your news

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There is a lot of  “news” on the internet…most of crap. Listen in on a Ted-Ed talk that help show you how to separate the chaff from the wheat.

D-Day…meaning to Canada and the context of controversy

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D-Day is 70 years old. One of the most pivotal moments in western history. It is also a story of coming of age for Canada as one of the three nations (along side the US and UK) to be given the task of taking a beach (Juno)…we, not only succeeded but was perhaps the most successful under some of the hardest resistance of any of the landing forces.
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I also talk about how heartless and stinging the Harper Government has been in only providing about 40% of the funds need for our dwindling number of vets (most 90 and up) participate in this 70th anniversary. Or it started out that way, but i go where the evidence leads me, and as it turns out (from my research, please correct me if i have it wrong)…Canada seems to be the only nation subsidizing our vets at all.
Tuesday, February 4, 2014
I started out being negative because of the large amount of bad press this issue has received, which now seems unwarranted. This lead to more important question…why the anger?
As it turns out, context is everything. Listen and find out why people are so angry over what seems to be a generous government.
Further Reading:

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Good Big Data and you

Posted by Don McLenaghen on July 9, 2013

This is Part 1 of a 2 Part Series on the good side of big data. Following will be another series on the bad side of Big Data.

Part 1: You are a fountain of data…

We have all heard about Big Pharma, Big Oil, Big Sugar…Big John. However, the new kid on the big block, Big Data, is coming of agmobile-spew-590x310e.

So what is data? Simply put, it is a fact or figure that has been recorded. Be it your age on an application form, or the type of browser you are using stored in an electronic cookie.

In the modern age, not only are we creating more data…partly because there a lot more of us, there is also computer technology which has allowed us to not only measure more of the world in more ways but as well store data longer, access it easier and ‘interpret’ it faster.

In the past, the only way to record data was to write it down. That required a person, pencil, paper and time.

Computers can do this alone and in milliseconds…and our storage capacity moves from a dozen data points on a piece a paper to billions on a memory stick.

How big is Big Data?

All the data created by humanity from the dawn of awareness to 2003…equals about 5 Exabytes, we now produce that every 2 days.

The amount of information generated in a day is seventy times more than found at the library of Congress.

The amount of information each one of us faces in a single day, is more than someone in the 15th century would face in a lifetime.

global-mobile-data-traffic-forecast-by-region_x582So, how is Big Data better than old data?

Let me give you a practical example.

In the old movies where you had a cop ‘tail’ a suspect. The cop would make notes every hour or so, about were the suspect was, what they were doing…This will give you an idea of what the suspect is doing, but minor details may be missed.

Now, you put a GPS tracker, wireless camera and record his electronic shadow…and you have a complete record of what the suspect is doing.

Not only that but this data is easy to access. So, in the past, if you had a hunch, you could go back “into the files” which may necessitated a trip to a warehouse, search a card catalogue, then finding the box where the report was, then reading all the reports with the hope of solving a cold case.

Big Data, not only makes it simple to search old records as in a Google search, but you can set up flags…that is if a crime had three elements in common with a cold case, you would be notified…automatically.

ibm_watson_x220In another more uplifting angle, a nurse will take a patients vitals 3 or 4 times a day. It’s not practical to have a nurse constantly monitoring a pulse…but a function digital recorders can accomplish easily.

It is able to record your vitals every second and store it indefinitely.

In a recent discovery in Toronto, this constant data awareness is now being used to help save the lives of premature babies.

Well, first let me give you a quick medical primer…every day we cycle through the fight-or-flight (FoF) response and the rest-and-digest (RaD) response.

This is normal, however, doctors noticed that in premature babies, this cycling leveled off two days prior to a detectable infection. That is, an infected baby will spend more time in each state (FoF and RaD) before ‘cycling’ to the next state…thus having fewer switches between F0F and RaD per hour.

So Big Data was able to see an infection two days before the doctor could. This will likely result in saving thousands of lives.

It is now possible for us to monitor everything every day and store it forever.

toon409It will make it possible for us to keep track of our exercise, spending…every aspect of our lives. For instance spending too much time in front of the monitor…well there are apps that detect your inertia, correlate that with the days travel pattern and remind you to go out for a walk.

It is a growing part of how we manage our days. In fact we may look back and wonder how we lived with the ‘fog & grog’ of old data.

I heard an interesting analogy.

If we got our Visa bill and all it said was how much we owed them…if there was no itemization, no one would blindly pay it!

But we do that every month when we pay the hydro bill without knowing the ‘detailed’ particulars of what we are paying for…i.e. what is the ‘charge’ or cost of toasting my bread…the load of laundry I did…how can you be a ‘green’ if you don’t know this data!

Well, there is now available a monitor that plugs into an electrical system that can ‘read’ the digital signature of all your electrical devices and discern how much electricity is being used.

bildeKeeping with hydro, another thing that new Wi-Fi meters might help us do is to determine when we use our electricity.  You see, the cost of electricity is based on the overall current usage, so during a hot afternoon…AC running….doing your laundry may cost twice as much as if you left it for the night. There are dryers that have this auto-timing ability built in.

Of course you would need to restructure more than the meters and your dryer.

Big Data allows for better greening of our world by allowing us to see in detail not only energy usage but in helping us adapt renewable energy sources to our grid. As mentioned, one of the obstacles to solar power, for example, is that it’s only available during the day…and more energy is produced in the afternoon than other times.

If we knew in detail what appliances were the biggest users of electricity, we could use them during peak solar output…and minimize our nighttime power. The opposite of my Wi-Fi example because now we rely upon largely fossil fuel plants that produce the same amount 24/7…so cost is not based on supply, like renewables…but on demand.

One of the good things Big Data brings is the ability to do this…something impossible a generation ago.

genome-project-cartoonAnother area of Big Data is genomics. It is now possible for a few grand, to get our DNA sequenced. This makes it possible for us to tailor medical treatment.

There are drugs developed that are effective treatments for diseases but for 10% of the population…well, they are fatal, so the drug is shelved.

But with big data…we will have our DNA profile on record; so for those at risk, the drug will not be prescribed, while the rest will be able to access the treatment.

DNA data also has it’s controversies as well.

First, we don’t yet really understand how to interpret it. I was listening to a debate about whether doctors should tell patients who have had sequencing, the total results or should they withhold some.

The argument to withhold was based on the idea that for most ‘genetically’ linked conditions, there are a lot of false positives…as much as two thirds. Also, for conditions that are incurable, are we not subjecting the patient to unnecessary torment?

The other side, is of course it’s our data, we should know what we can…as long as the appropriate caveats are given.

One item in the news lately is the US Supreme Court decision to allow security forces to take DNA samples from suspects. Many have likened this to finger printing, and have no problem with it.

cartoonBut in the Big Data world, this is a poor analogy. A fingerprint is a single point of data uniquely tied to one person. Your DNA is billions of points of data that not only are linked to you, but all of your relatives. Not only is the suspect, and at this point they are only a suspect, having their privacy breached…I mean what can be more personal than our life essence in the form of DNA…but one’s whole family’s  as well for generations.

And DNA is not only an identifier, it is a complete medical record of sorts.

In one way this is a frustrating time, because as our ability to collect data is expanding exponentially….our ability to process this information has lagged behind. But it is exciting as well because as computing power increases and the sheer number of computers increases…data processing is catching up to data collection.

We are fountains of data…with the devices we use…the data about us they can provide. Think about your location apps, and motion sensors, and the like.

mbcn1609lDid you know that modern pacemakers record every heartbeat, every ‘assist’ you need….and it will then upload that to the manufacturer, who can use the data to tweak the software on a pacemaker…potentially inform the doctor of health issues…oddly enough though, the ones I know of, the manufacturer will not let you see the data. Although your heart generated the information, the data itself is somehow proprietary…?

Another example of where personal big data has surprising results is a sensor carpet that can predict when you will fall. It is designed for the aged and infirm.

magic-carpetBasically what happens is it learns the walking pattern of a person, if that pattern alters in a curtain way, it then will signal an alarm warning that the person is likely to fall soon or a fall has occurred. It can do that by detecting slight variation in you stance, gate, muscle usage…lots of pieces of data that can be mined to make predictions.

There is an app developed for diabetics. One problem patients face is that during bouts of depression, they often skip medication leading to obvious health complications. Well, this app tracks their activities and can predict two days prior the subject will be suffering from depression. A warning can then be sent to friends, family and/or caregivers or just an alert to the person themselves.

It does this by noticing the number of calls you make, your tweeting frequency, how far from home you go…correlated variations in your daily pattern…again lots of little pieces of data that is can used to predict the onset of depression.

Another way the world is being datafied is the sources and types of new information generated. IF we think about the web…we know of things called cookies and trackers and even bots…maybe.

If you are on your phone or tablet or PC…when you click on a web site not only is the root data point…the page you are going to…created but also where you are when you clicked, the time of day, the type of devise, where you came from, what page you are going to next…

The dimensions of data have increased. One expert likened it a cyclopes gaining a second or third eye. Not only are you getting more data, but new dimensions of seeing that data and how all this information is related.

BizarroIn the arena of commerce…Big Data comes from big corporations. IF you think about your corner store…no I don’t mean the 7/11 but the old time mom and pop corner store. In a day they would have tens of sales…if business was good a few hundred a week…and several thousand over their life time.

Wal-Mart alone generates over a million sales transactions an hour. THAT is Big Data and they are using it.

Do you know what product becomes a big seller when a hurricane is looming?

Pop tarts…the data doesn’t say why but whenever a hurricane warning comes out, Wal-Mart brings out the pop tarts.

5651.stripAnother great advancement…well, depending on your perspective, is the ability for marketers and companies to target ads and promotions specifically to you that you genuinely might want (not all data mining gets this right). They will track your purchase history, cross-reference that with other purchases and can predict what you are interested in.

And this marketing has shown weird connections, like people who buy hair dye are also looking for kitty litter…insert crazy old cat lady joke now…

I offer the following funny interaction and perhaps to foreshadow of our next show about the dark side of Big Data.

blog_target_couponOne day, a Target manager got a very irate call from a father. He was upset that Target sent his teenage daughter a coupon book for expectant mothers. He assured the manager that his daughter was pure and nowhere near pregnant. The Target manager apologised profusely and said they meant no disrespect…much groveling ensued

So, what happened is Target knew from feedback that just sending out coupons for baby products had a negative effect on many women…it’s like “WHAT you’re not pregnant, what’s wrong with you” or something.

Anyway, Target wanted a better way to target its advertising. In steps Big Data. It seems that based on your purchasing habits…like deodorant, moisturizer, etc…they could target the expectant mother market exclusively.

Well, back to our father. As it turned out a few days later the father called the manager again and this time offered an apology. It turned out that after a very intense and frank conversation, the daughter in question was pregnant and had not yet told her father.

So Big Data was right in the fact, but was it wrong in using that information?

In the next part we will see how Big Data has allowed science to see the universe like never before.

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Raising the Black Death from the Dead

Posted by Ethan Clow on October 13, 2011

Scientists have recently pieced together the DNA of one of history’s greatest killers, the Black Death. The New York Times has an article documenting the process and explaining the science behind this amazing advancement. You can read the actual science paper here.

To summarize, a group of scientists, led by Kirsten I. Bos of McMaster University in Ontario and Johannes Krause of the University of Tübingen in Germany, began to sample DNA from human remains in graveyards and cemeteries across Europe that dated back to the 14th century.

Specifically, they used DNA from teeth. Dr. Bos explains the process:

“If you actually crack open an ancient tooth you see this dark black powdery material and that’s very likely to be dried up blood and other biological tissues.

“So what I did was I opened the tooth and opened the pulp chamber and with a drill bit made one pass through and I took out only about 30 milligrams of material, a very very small amount and that’s the material I used to do the DNA work.” – source

So that’s pretty cool, they were able to reconstruct the DNA of an ancient pathogen by examining old bones and dried blood. By analyzing the DNA of the old Bubonic plague, scientist can learn a bit more about the current variation of it. Obviously bacteria will evolve over time like all living things but it turns out that this particular bacteria is a slow evolver. Of the bacterium’s chromosome, which is about 4.6 million DNA units long, only 97 of these DNA units have changed and only a dozen of these changes occur in genes and therefore would affect the organism’s physical properties.

The goal is to create a living version of the ancient Bubonic plague. Wait, what?

“Such a microbe could be handled only in special secure facilities. But even if it did infect a person, the bacterium would be susceptible to antibiotics, like its living descendants, said Hendrik Poinar of McMaster University, a team member.” – source

So aside from the troubling question of why these scientists are playing Frankenstein with the Black Death, this is pretty cool research. Here’s another question arises, if the ancient bacterium is so closely related to the current strain, why does the current strain seem to be far less deadly? What does “less deadly” mean? Apparently the modern plague has a mortality rate of 1-15% in treated cases and a 40-60% mortality rate in untreated cases.  Additionally from 1987-2001,the World Health Organization has reported an annual average of 38,876 cases of the plague with 2847 deaths worldwide.

Granted, that’s not the most reassuring numbers but when you compare the way the plague cut through the population of Europe, it was like a hot knife through butter.

How to explain this discrepancy? What we need is some Historic Context!!

When the Black Death hit Europe in the 1300’s things weren’t going well for the average European. The average person was extremely malnourished. Food was scarce and what little food you got wasn’t particularly healthy for you. Major famine had repeatedly struck western Europe at this time, which was only exasperated by the climate getting colder (the Little Ice Age)

Economically, Europe was in trouble (sound familiar?) there is evidence that the average person was basically scrapped for cash and having trouble making ends meet. People couldn’t buy enough food or live in great conditions. And then to make matters worse, a giant war broke out. The Hundred Years’ War (although it didn’t last 100 years) between England and France broke out in 1337 and left the countryside of Europe decimated.

It was a perfect storm for an invading microbe. When the Black Death hit, people thought it was the end of the world. It almost was. People would get infected and if they didn’t die within hours, would be dead in a few days. Since the disease (pasteurella pestis) was spread by fleas who liked to hang out on rats, the unsanitary conditions of medieval Europe were like a smorgasbord for the bacteria.

It’s estimated that the Black Death killed off about 30 – 60% of Europe’s population. The disease spread fast as well. It entered Europe in 1347 and by 1352 it had spread all across the continent and into Russia.

If for some reason you ever travel back in time to this period and want to escape the plague, head to central Europe, somewhere between Prague, Cracow and Warsaw, for some reason, we aren’t too sure why, the plague didn’t really spread there and those areas remained largely uninfected.

Getting back to the science of the Black Death, this research also solves a few debates over the origins of the plague. The majority of scientists accept the theory that the plague was caused by pasteurella pestis however, some have maintained that could not be the case. Other theories suggesting the culprit was an Ebola-like virus or perhaps something related to Anthrax. For many of these theories, the evidence often comes up that the description of symptoms doesn’t match what Bubonic plague does. I’m skeptical of such claims for a few reasons.

A) Medical science wasn’t very good back then. Doctors, if you want to call them that, for the most part stood around and when “duuuhhhhh” at the mountain of bodies that piled up during the plague. So I’m not surprised that descriptions of symptoms are spotty or appear inconsistent.

Duuuhhhhhh

B) People weren’t really aware of disease as communicable in our sense of the word. Sure they would isolate people who had the illness but they didn’t get the idea of washing your hands or not living in squalor. The treatments they did have, like bloodletting were just making things worse. So again, people might also be dying from treatment, let alone the Black Death.

But this new research really points to pasteurella pestis being the culprit here. DNA doesn’t lie and this is really a slam dunk in that department. Especially if they are able to take the DNA code and make a living sample of the ancient plague.

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