"Linkage Disequilibrium Tutorial" written by Tinypliny on estrip.org

10/31/10 03:35 - 43.ºF - ID#53042

Linkage Disequilibrium Tutorial

A guest messaged me to say:

Hey. I just wanted to say thank you for writing about how to read LD blocks. My teacher failed to mention the details and you have solidified what I thought was going on. Thank you again

How cool is that?! I am so glad at least one person found the post on how to interpret LD maps and blocks useful!

The post on how to interpret and read Linkage Disequilibrium maps and blocks:

Permalink: Linkage_Disequilibrium_Tutorial.html
Words: 91
Location: Buffalo, NY
Last Modified: 10/31/10 03:35

Category: science

10/26/10 12:26 - 61.ºF - ID#53013

Soda is the new cigarette

Back in the 1940s, this Phillip Morris advert interrupted TV programming and annoyed the heck out of people:

{Though why anyone would want to follow that creepy looking "doctor" in his rickety car just to see him smoking is beyond me... unless you are a shoddy-noir fan.}

Fast forward to 2010 and this is what is happening, quite literally, in our backyards.

::Download Flash Video::

From

We saw a similar disturbing story last year:

Full marks to whoever sees the ominous similarities here.

I was going to preach on pedantically about how the Center for Disease Control (and Prevention) -- CDC has come out with findings that show that 1 out of every 3 of us are going to get Type II diabetes in 2050 (1) and how eerily similar is the fact that, currently, 1 out of every 3 of us is clinically obese (2) - 5% of which is directly and squarely attributable to soft drinks, colas and other dodgy carbonated what-nots (3, 4). I was also going to throw in research findings about how sweetened beverages cause diabetes, metabolic syndrome (5), hypertension and cardiac diasease (6) and finally, how obesity and diabetes are increasingly being linked to an increased risk of cancer as well as poorer cancer-related outcomes (7, 8).

But I guess, we will all be cold in our comfy plus-size graves by then. So, I am just going to splash this post with some time-machine acccelerant and serve up the punchline from 2050.

However, feel free to ignore this post and all the evidence and drink up those colas. Because you see, history does repeat itself and it will probably be 2050 before we will get to see the surgeon general's message on cola cans, pepsi cans and other members of this aggressively marketed ilk.

The full-text of all the references for the pedantically inclined:

1. The CDC diabetes prediction making news-waves: Boyle J et al. Projection of the year 2050 burden of diabetes in the US adult population: dynamic modeling of incidence, mortality, and prediabetes prevalence. Population Health Metrics. 2010;8(1):29+. Available from:

. PDF Link:

2. The dramatic obesity charts, statistics and trends in the US:

3. National Cancer Institute's report on where all the excess energy-intake in the US population is coming from. PDF Link:

4. A systematic review of all the epidemiological studies, clinical trials, prospective studies and retrospective studies that have investigated the associations between obesity and the consumption of carbonated drinks (and yes, the vast majority of the reliable studies have very consistently damaging findings against cola): Woodward-Lopez G et al. To what extent have sweetened beverages contributed to the obesity epidemic? Public health nutrition. 2010 September;p. 1-11. Available from:

. PDF Link: ::READ PDF::

5. Hu FB et. al. Sugar-sweetened beverages and risk of obesity and type 2 diabetes: Epidemiologic evidence. Physiology & Behavior. 2010 April;100(1):47-54. Available from:

. PDF Link: ::READ PDF::

6. Chen L et. al. Reducing Consumption of Sugar-Sweetened Beverages Is Associated With Reduced Blood Pressure: A Prospective Study Among United States Adults. Circulation. 2010 June;121(22):2398-2406. Available from:

. PDF Link: ::READ PDF::

7. Renehan AG et. al. Interpreting the epidemiological evidence linking obesity and cancer: A framework for population-attributable risk estimations in Europe. European Journal of Cancer. 2010 September;46(14):2581-2592. Available from:

. PDF Link: ::READ PDF::

8. Pal SK et. al. Impact of Age, Sex, and Comorbidity on Cancer Therapy and Disease Progression. Journal of Clinical Oncology. 2010 September;28(26):4086-4093. Available from:

. PDF Link: ::READ PDF::

Bonus reading: The guide to healthy-eating from Harvard:

tinypliny writes at 08:56:18 10/29/10 - Comment #59079: Gaaahhh spellos spellos and omissions!

What I meant was:

Poor eating habits quantitatively/qualitatively change your brain so much that smoking cessation become THAT much more difficult in a smoker who eats junk food compared with a smoker who is eating healthier food.

tinypliny writes at 08:51:30 10/29/10 - Comment #59078: (e:metalpeter), yes, exactly. It's a bunch of cumulative unhealthful behaviour that is throwing the main spanner into the works of disease prevention in this country... or any country for that matter.

tinypliny writes at 08:49:29 10/29/10 - Comment #59077: (e:Paul), I was at this tobacco control talk given by Dr. Giovino :::link::: recently. Interestingly, he believes that the common notion that smokers are poor eaters is not true. His hypothesis is that the poor eating habits cause changes in receptor biochemistry and kinetics in the brain and this in turn, prevents smokers from quitting successfully and for long. So the poor eating habits quantitatively/qualitatively change your brain so that smoking cessation become THAT much difficult that in a smoker who is eating healthier food.

I thought it made so much sense. We are fostering a generation of easy addicts with no public awareness of what healthful food actually is.

Maybe I need to go out of control on a post about the dietary guidelines next.

tinypliny writes at 08:43:36 10/29/10 - Comment #59076: lol, it this looks like out of control, I wonder what you would have said had you seen the emails, docs etc I threw at this workplace faux pas.

Unfortunately, "the man" didn't think it was worth his time though.

paul writes at 12:26:27 10/29/10 - Comment #59072: You know whats crazy is the warnings on the cigarette boxes in canada even have those explicit photos on them and people still smoke.

mike writes at 10:47:31 10/28/10 - Comment #59070: i love me my doctor pepper or pepper md as i like to call it

mike writes at 10:47:12 10/28/10 - Comment #59069: you're out of control

metalpeter writes at 04:52:26 10/27/10 - Comment #59055: First of all Hope some other people jump into this.....

Where we agree: Soda is Bad for you. Any science that is funded by someone who could benefit from that science should never be trusted completely and is most likely biased towards one of there causes.....

Where we disagree (I think): I think most people know that it is bad for you (or at least a lot of people). There has been a big movement to get it out of schools.. But what I see is that it isn't the Soda. It is the lifestyle. Drinking pop is part of the unhealthy way of living. It goes with all the bad for you snacks and all the bad for you food. Most people who eat healthy and good know to cut out or keep the Soda Pop.

It is kinda like when people at bars didn't smoke but once they had a drink they had to have a smoke. That both things are bad but they go together for a cumulative effect and make two things that are bad a lot worse....

Distractions made me lose my train of thought.....

tinypliny writes at 09:45:16 10/26/10 - Comment #59049: (e:metalpeter), I just want to emphasize that soda:
-- is PURELY responsible for more than 5% of calorie intake of the US population today.
-- is the STRONGEST indicator of impending clinical obesity
-- CAUSES hypertension and cardiac disease (yes, CAUSES, in a controlled, prospective, randomized clinical trial)
-- is strongly implicated in temporal pathogenesis of Type II diabetes.

Please don't be under the misconception that soda is harmless - because it is not.

In the 1940s, people said much the same thing for smoking that it is just "linked" to lung cancer and doesn't cause it. I don't know how much more proof does public policy need to convince people that it is not really a harmless little treat. I am so disappointed that people are encouraged to treat sodas as if they were just a little indulgence. Please take a look at the last book link from Harvard written by Dr. Walter Willett. It is written very well and lays out clearly why colas are such an insidious evil.

Giving money and accepting money leads to conflict of interest. This is a BIG issue in medical science. Take a look at all these studies that were published when the authors and their parent institutions were funded by the American Beverage Association, Coca Cola and Pepsi: :::link:::

As you can see, most of the studies conclude that there is no link between sweetened beverages and obesity and even argue against changing vending machine contents in schools. However, when a research team from Harvard pulled down most of these studies and re-analyzed the meta-analysis conducted by the coca-cola funded authors, they found that they had mis-analysed all data to favour coke and other sodas. The coke-funded authors responded to the Harvard team with a very weak reply --> :::link::: , but by that time, one of the authors was actually under the PAYROLL of the American Beverage Association. Since the Harvard rebuttal was published in a reputed journal the coke-funded team were forced to declare their conflicts of interests:

"The original research was conducted while all of the authors were affiliated with the University of Maryland and was supported with funding from the American Beverage Association (ABA). RAF is currently a Senior Risk Assessment Expert with the US Food and Drug Administration (FDA), Center for Biologics Evaluation and Research. MLS is currently a Senior Vice President for the ABA. PAA is a consultant for the ABA. The views expressed in this article are those of the authors and may not represent those of the University of Maryland, the ABA, the FDA, or any other organization with which any of the authors may have been affiliated in the past. RAF declared no conflicts of interest other than the original source of funding for the project. MLS is employed by the ABA but had no other conflicts of interest. PAA is a consultant for the ABA but had no other conflicts of interest."

You don't want to be working somewhere that takes money from the cola industry - that will put any future work of yours under the cloud of conflict. This is exactly how science is diluted and distorted.

And they have been successful. The public at large still believe that coke is so harmless when a good 500+ well-carried out studies squarely assign blame to soda. :/

this study which got published in peer reviewed journals. It completely clears coke of any harmful effects - the ONLY study to do this in the face of 70+ studies that show just the opposite.

metalpeter writes at 07:07:35 10/26/10 - Comment #59046: A couple of things ok maybe a few....
1. That first ad is great cause doctors don't say they are good for you (there are ones where they do) they just say that most doctors use that brand so people may think they are good for you.

2. I like coke and Pepsi and love how it tastes....

3. There is nothing wrong with drinking some Soda Pop but it shouldn't be all you drink.....

4. Soda Pop may be linked with obesity but that doesn't mean it causes it....

5. I don't think soda causes it at all. It is that people who have it as there drink of choice also have the big mack and the big plate filled with all other kinds of food like Bacon Burgers and things like that....

6. In Terms of the giving money thing you have to remember that giving money alone doesn't make them guilty of anything, they also Own Minute Maid and have Dasani Water. Pepsi owns Sobe and at one time not sure if this is still true the same company that is lays/doritos ....

All that being said there is the mentality that Diet pop is good for you so if you have all this high calorie high fat food and a big giant diet soda that off sets it... Yes there is stuff in Cola that Kids should not have more importantly girls. I forget what it does something about pulling calcium away from bones so you then need even more or something I can't remember.....

The thing with Soda Pop is that it is fine as a treat or to have sometimes but it shouldn't be a what you drink with dinner every night thing. On a side note is one good thing it does do is keep Dentists in Business ......

Permalink: Soda_is_the_new_cigarette.html
Words: 690
Location: Buffalo, NY
Last Modified: 10/26/10 12:36

Category: science

10/20/10 12:02 - 46.ºF - ID#52984

Did you know? (Facts against smoking.)

A recent debate on (e:dcoffee)'s journal - (e:dcoffee,52972) about smoking prompts me to remind everyone about how evil smoking actually is. Did you, for instance, know that:

Approximately, 30 percent of all cancer is caused directly by smoking. It is a risk factor for cancers of not only the lung, but also the larynx, the oral cavity, esophagus, bladder, kidney, pancreas, stomach and cervix.

And if that was not enough, 100% of Smokers inevitably end up with either emphysema or chronic bronchitis.

Admittedly, cancer is a rare disease, but 30% of all deaths due to cardiac disease is also directly attributable to smoking. Cardiac disease is the #1 killer in this country.

Children exposed to secondhand smoke in households are more likely to get asthma, chronic respiratory disease, middle ear infections and cardiac disease as adults, . More than a 3rd of all the children who have ever tried even one cigarette will become regular daily smokers before they leave high school.

US spends at least $100 billion every year for health care addressing smoking-related issues in its hospitals and clinics. The state makes payments of over $20 billion in smoking-caused Medicaid payments every year.

It is SO hard for me to sympathize when someone defiantly brings up smoking as an excusable recreational habit instead of feeling guilty about it. I just cannot see their point of view and maybe deep inside, don't want to. It is on par medically with all of the other hard drug addictions, simply because of the massive medical and financial impact it causes. As I write this, some MORON smoking in my building and hanging their cancer-sticks out their window is causing smoke to drift into my living space. You will excuse me if I feel this intense urge to go right up to them, scream in their face and choke them to death.

Blatant admission: All of this is completely plagiarized from various sources on the net. It is comforting to know that infinitely wiser people have arrived at these various damaging conclusions against smoking and that it is not some personal ill-supported propaganda of mine. Google each sentence on this blog and you will likely find a million peer-reviewed research documents in support.

tinypliny writes at 10:06:10 10/21/10 - Comment #58983: Hee Hee.

jason writes at 08:57:55 10/21/10 - Comment #58982: Okay Tiny, so don't smoke.

libertad writes at 12:07:39 10/21/10 - Comment #58980: @(e:metalpeter), I don't think I could have said it better myself. Addiction, and I think this one in particular are very complex. Tobacco use is done at a much more frequent rate than other addictions. Most other addictions could not sustain the frequency of abuse that smoking can for as long a period of time. In other addictions, use at such a high rate would result in either an inability to function normally, lethal overdoses or incarceration. This is, in my belief, the reason why illegal drug addicts have a harder time kicking cigarettes than the street drugs.

@(e:tinypliny), most people who are current smokers that enter a hospital for treatment (smoking related or not) are offered the nicotine patch. When the patient is released they will often remove it, most likely due to liability issues, because they are no longer under medical supervision. When people are released it is also very often a time of relapse for many very legitimate reasons. Smoking with the patch can be particularly dangerous to people who have already experienced some type of health trauma.

I don't believe inpatient smoking cessation is an option for probably 99% of smokers. Can't back that up scientifically but I believe it is an accurate guess. From what I have heard, the only type of treatment that people who are hospitalized for anything that can be linked to smoking is the patch and very rarely is behavioral counseling offered except for maybe a referral to the their state's quit line services.

metalpeter writes at 06:37:51 10/20/10 - Comment #58977: Just want to add something about the smoking addiction. I think there are a few factors to why it can be so hard to stop and it all comes down to multiple addictions and habits....

Yes there is the Addiction to the chemicals in them. But it is more then just that there is the addiction/habit of smoking. If you are at work you have a pattern and go out side at certain times. That is a habit at those times that you used to smoke what do you do. Hey everyone else is smoking and here you are alone or vice versa when you went out there you got to escape from everyone. Humans are creatures of habit. As an example at work when I work with certain people I right down their Name (PD, RF) but then when they take a day off habit makes me write them in even though my mind knows not to. I think that physical part is a big factor that habit, it is more then just the nicotine. I have heard of people using wooden cigarette or pencils so that they can get used to the feeling of holding them...... It is a very complex issue and what works for one person might not work for another in terms of quiting....

tinypliny writes at 07:26:23 10/20/10 - Comment #58972: Thanks for writing and adding to the post (e:libertad). It definitely balances the point of view and presents some hard facts about how we, as a medical community and political system are ALSO in a state of denial about the need to take and treat smoking more seriously.

I was not aware that taking off the nicotine patches was something that was forced on patients. I don't think it is a medically sound move because addictions cannot stop that abruptly and come back with even more force if nicotine patches are not slowly graded down. Surely everyone who has the faintest medical knowledge knows this.

Are the patients told that they have to continue treatment as an inpatient if they don't remove their nicotine patches? If they refuse to remove their patches, are they then given inpatient treatment for their addiction? Why is that a bad thing? I am not sure I understand the logic behind this remove-nicotine-patches or we won't let you go threat. What kind of diseases are we talking about? Is this true for all the spectrum of smoking-related hospitalizations? Why would they be still smoking when they enter the hospital if they are wearing the nicotine patch? We are missing something in this picture.

Political will is a non-existent thing. I have NO faith in politicians. They are scum who leech money out of people and go on egotistical trips from the power they have. If politicians and people in power had any intention of doing good, we would be a vastly better planet instead of a planet that is dying and in denial. :/

libertad writes at 05:09:56 10/20/10 - Comment #58971: I think we all do know this information, it would be very hard not to. You mentioned in your comment about the need for the addiction to be treated clinically and it already is. Nicotine addiction is listed in the DSM IV and treated in much the same way as other ailments. Unfortunately, this does not usually go beyond the writing of a script.

While almost any former illegal drug user will tell you that cigarette smoking is the hardest to stop they received more support getting of the street drugs. We offer very little mental health counseling to someone who needs/wants to stop. Please don't assume that people do not know what they are doing to themselves or that they don't really want to quit. Telling someone to quit or telling them they are going to get cancer or COPD is not enough to stop. There often is strong denial which is just a way to cope with their inability to stop. We do not offer inpatient care for smoking cessation which I firmly believe is needed for many seriously dependent individuals.

Do you know how many patients I have spoken to who are hospitalized for smoking related illnesses that are released but only first after they rip the nicotine patch off of their arm? The medical profession is setting these people up to fail at a time when they are most vulnerable. Then *we* look down on them and think of how foolish they are to continue to smoke. How weak and selfish they are to burden everyone else with the costs of their illnesses.

My job can only provide so much help. I can provide up to a half hour of phone counseling for an addiction that starts when people are still children. Many I talk to have been smoking for 40 to 50 years and the only counseling they will ever get is going to be less than 30 minutes on the phone. Often people are humiliated by their addiction and therefore do not ever even get the brief counseling we give over the phone.

So here is the big picture. We have a government that is now dependent on the sale of cigarettes cutting what little help is available in smoking cessation. They will never make cigarettes illegal in our lifetimes. It didn't work with prohibition of alcohol and it isn't going to work on cigarettes. I also believe that they need to stop manipulating the tobacco to make it more addictive. The time to do this is now. This is something that can be done politically unlike making them illegal. We can do this without making them appear safer. It will make it easier to stop and harder to get hooked if they would just regulate the production. The answer is never going to just lie with just one solution.

Permalink: Did_you_know_Facts_against_smoking_.html
Words: 369
Location: Buffalo, NY
Last Modified: 10/20/10 12:20

Category: simple pliny

10/16/10 03:52 - 57.ºF - ID#52959

Sick of clutter.

My flat is in a dreadful state of preventable clutter and it's annoying! There is always this small corner in my flat that has a big laundry box with piled up papers, journals, books and whatnots. I am determined to get rid of that pile today. I really like the idea of a floor level "bookshelf".

My floors are not grey but they are due for a thorough cleaning and polish. It's been 7 months since I polished them last.

tinypliny writes at 08:04:07 11/20/11 - Comment #66332: That is a really nice space.. How terrible. My corner clutter has built up ONCE AGAIN! AAArgh I made that floor level floating bookshelf work for about half a year and then I started throwing everything on top of it till it became a pile.

I think my floors are somewhat okay now - polishing them makes them very orangey but they need a clean up too. NO time till december end.

I don't like those chairs in that flat. I would sit on the floor near the windows with the low table. :)

tinypliny writes at 01:30:26 10/18/10 - Comment #58917: I would be in heaven if that was my flat!! Sadly, it is not.
Anyway, mission accomplished. I managed to get rid of every little sheet of paper that I won't be reading, gave away a zillion journals to the unofficial Mayflower basement freecycle, washed the grime off my keyboard, washed all the piled up dishes and scrubbed the sink, polished the floors so much that I think they are rather slippery now, populated a "floating" almost-floor level bookshelf with books that I will actually read, rounded up the books that I have always hated to be sold, packed up folders and old statistical methods notes to be given away, found (e:jbeatty)'s Lebanese cooking book that I never gave back (despicable me!), found a credit card that I thought I had lost and a cheque for $11!

Next weekend: Bathroom cleanup and polishing.

LOL, I guess this makes me sound psychotic, but you have no idea how much of a clutter a pile of random paper and cardboard can make. I guess this is part of how I get ready for a gloomy winter ahead - by making the flat so shiny that I can ignore the terrible weather even though I have no curtains. :-)

What I really want is the Philips LivingColours :::link::: but at $199, it's a bit too expensive to justify as a "winterizing" purchase.

dimartiste writes at 05:25:51 10/17/10 - Comment #58914: You would actually have a heart attack to enter my humble abode. I have years worth of paperwork to file (thankfully I already have the filing cabinets);Things that need to be gone through, thrown out and reorganized to my new thought processes. Beautiful flat BTW! Very neat and organized. Space as a great deal to do with your perspective. If you had a small closed flat with separate rooms your clutter would not be the same kind of noticeable. Your open floor plan makes the littlest thing out of order come to your attention. I was less curious about the rugs versus white chairs, how do you keep them White?

metalpeter writes at 10:04:45 10/17/10 - Comment #58906: great comment by (e:libertad) .... It sounds like what you need is One Filling Cabinet That could maybe be in like a corner or some type of thing to hold things you need but hide them away (I need about 7 of those).... Here is the thing that is odd. Books you read on the floor is clutter but books on the table displayed for people to look at or magazines in that half circle are part of home decorating.........

libertad writes at 06:59:27 10/16/10 - Comment #58905: Only pyschotics live in places like those. I like to have some clutter. Books on the floor?

Permalink: Sick_of_clutter_.html
Words: 81
Location: Buffalo, NY
Last Modified: 10/16/10 03:54

Category: the odes

10/13/10 10:43 - 53.ºF - ID#52949

So what did you do today?

And now I just want to sleep for 100 hours.
Good Night.

Permalink: So_what_did_you_do_today_.html
Words: 14
Location: Buffalo, NY
Last Modified: 10/13/10 10:43

Category: e:strip

10/10/10 08:27 - 59.ºF - ID#52932

The votes are in.

One of my three faithful readers thinks I sound like a super-boring, pedantic, self-aggrandizing and basically, obnoxiously patronizing prick on my blog.

Yes, thanks very much mum, for sharing all of that. Your honesty is refreshing.

Permalink: The_votes_are_in_.html
Words: 38
Location: Buffalo, NY
Last Modified: 10/10/10 08:27

Category: i-tech

10/09/10 09:58 - 55.ºF - ID#52923

Classmate Tablet

What I really want is this. The design screams "Education!!" - like no other tablet can.

Plus of course, I want to able to toss the laptop on my desk in moments of frustration and not have to repent later. And how cool is that 180 deg swivel camera?!

So instead of this conversation:

Me: Mum, it's snowing here!
M: Really?
Me: Yeah! Look! *Twist Twist*
{Major twisting, silent cords tangling and..}
Me: Damn! Sorry. Unfortunately I cracked my LCD screen with the power plug. Let's talk later.

I could have this one:

Me: Mum, it's snowing here!
M: Really?
Me: Yeah! Look! *Swivel Swivel*
M: That is lovely! Are you wearing a sweater? I hope you are wearing a muffler. Did you have some tea? Are you eating well ... or anything at all? I can clearly see your bones sticking out.
Looks like you have a cold...
Me: Wait. How can you see all that when you are looking at the snow?
M: Don't change the subject.
Me: Damn! Sorry. The connection is awful. Let's talk later.

Permalink: Classmate_Tablet.html
Words: 179
Location: Buffalo, NY
Last Modified: 10/09/10 10:13

Category: the odes

10/09/10 09:47 - 55.ºF - ID#52922

A little wicked wicket gate.

Completely annoyed with the new wicked wicker wicked gate that has sprung up blocking the small concrete path that leads around the LinNor building.

It was the only way to avoid jumping over or falling into the gaping holes of construction all around the North, N.Pearl and Franklin intersection.

Which means I have one more fence I really want to learn to jump.

And this time it's not even an option. I would rather jump this fence than strategize my way around and across a muddy slushy pit... and possibly fall in. The trouble is I am not sure jumping that fence is going to be easy to begin with, let alone jump with a long coat on or in the rain or snow - when that shortcut path REALLY helped. Damn you. LinNor.