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Wednesday, January 7, 2015

HAPPY Mapping and Happy Mapping: Whales, Genomes, and Meandering

           HAPPY Mapping, first proposed in 1989 by Paul Dear and Peter Cook, is a method used to study the linkage between two or more DNA sequences. It is mapping based on the analysis of approximately HAPloid DNA samples using the PolYmerase chain reaction. In genomics, HAPPY mapping can be applied to assess the orientation of various DNA sequences across a particular genome in the generation of a genomic map.





            I stumbled on HAPPY mapping after watching this TED talk about happy mapping. Daniele Quercia talks about finding that more beautiful route to travel along. It may add a minute or two to your commute, but adds immeasurably to your happiness factor.

            Here's a piece of a happy map through Denver:




            All of this brings us to the Bowhead Whale. 




               Researchers are looking at the genome of  Bowhead Whales, the longest-living mammals, to see why they live to over 200 years without a higher risk of cancer or other diseases despite having more than 1000 times the number of cells as humans. According to the article published January 6, 2015, in Cell Reports and described in Science News:

              "The scientists discovered differences, including mutations and duplications, in the whale genes that are tied to cancer, aging and cell division. The results suggest that the whales are better than humans at repairing their DNA and keeping abnormally dividing cells in check. The whales do not accumulate damaged DNA, allowing them to live longer without developing age-related diseases like cancer, says coauthor João Pedro de Magalhães, a gerontologist at the University of Liverpool."

              I can tell them why they are so good at DNA repair and longevity. These great cetacean beasts SWIM all day. . .and they take the HAPPY, happy route.






Off to a happy swim,
Steph




39 comments:

  1. Replies
    1. ... although any app that beeps me once or more a day to ask me how I'm feeling, who I'm with, what I'm doing, etc, is gonna make me pretty unhappy very fast.

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    2. Right there with you on that one, jan.

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  2. Hmmm.... My wife tells me that some of the cycle computers on the spinning bikes at the Y are "happier" than others, reporting higher calorie burn for the same effort. I wonder if Fitbit could spread happiness and increase the density of happy routes around the world by just telling sweet little lies on occasion: "Oh, you fitness maniac, you just burned a Double Whopper and set a new land speed record for that jog around the block!"

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    1. That is partly why I swim-- no blinking numbers, no data (happy or not), just me and the water. It's the best outside, of course, with a sea, lake, or kettle pond to enjoy.

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  3. Steph,
    You probably don’t need this in the Rockies, but, is it even a good idea? I have heard that people who exercise regularly increase the size of their hearts. Is that so? Their heart muscle is well-developed. I have also heard that people who have difficulty breathing because of an ailment, such as emphysema, develop large hearts just because their heart must work harder to keep the body alive. But then they might die of an “enlarged heart.”

    I am serious about the above paragraph (I want information), but not the one below.

    Whenever I’m on a treadmill I always wear a feedbag in order to replenish the calories I am burning. (I could not find the SNL clip on YouTube. Sorry. I did find this Onion ripoff, however.)

    LegoNotSoBighearted

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    1. The explanation in Wikipedia is good:

      Healthy cardiac hypertrophy (physiologic hypertrophy or "athlete's heart") is the normal response to healthy exercise or pregnancy, which results in an increase in the heart's muscle mass and pumping ability. Trained athletes have hearts that have left ventricular mass up to 60% greater than untrained subjects. Rowers, cyclists, and cross-country skiers tend to have the largest hearts, with an average left ventricular wall thickness of 1.3 centimeters, compared to 1.1 centimeters in average adults. Heart wall thickness can be measured by ultrasound; computed tomography is more accurate, though it is more expensive and has risks of exposure to radiation.

      Unhealthy cardiac hypertrophy (pathological hypertrophy) is the response to stress or disease such as hypertension, heart muscle injury (myocardial infarction), heart failure or neurohormones. Valvular heart disease is another cause of pathological hypertrophy. It has also been suggested that the root cause of many heart ailments is cardiac hypertrophy, which in turn is caused by hypoxia due to atmospheric CO, particulate matter, and peroxyl acyl nitrates, which reduces ATP synthesis in cardiac mitochondria. Pathological hypertrophy also leads to an increase in muscle mass, but the muscle does not increase its pumping ability, and instead accumulates myocardial scarring (collagen). In pathological hypertrophy, the heart can increase its mass by up to 150%.

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    2. Yes, it's a good explanation. . .and a good question, Lego.

      As to the feedbag/feedback thing, that's where I came into Blaine's two years ago. Ah, the days of AbqGuerrilaBoy! Thanks for the laugh, Lego.

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  4. Ever run into Dana Gocheski on any of your Denver happy walks? Fellow Denverite, librarian, and respectable Jeopardy! contestant this week.

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    1. I looked up Ms. Gocheski but do not know her or of her.

      In addition to happiness this week how about coffee nappiness? Has anyone tried this and found it useful?

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    2. The only way I could ensure falling asleep in a twenty minute time frame would involve hitting myself in the head with a hammer. Probably counterproductive.

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    3. Don't do it, Paul.

      There's something about counting with 4's and 7's and 8's and breathing for a quick nap but it never worked for me.

      Wonder if "counterproductive" is ever used at the Formica factory. . .

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  5. Replies
    1. Oh, yeah. None of the medical people I know would go for much end-of-life medicine. Absolutely no one wants CPR or intubation. In my mind, defibrillators are for young, healthy people who get electrocuted or hit in the chest with a baseball. Otherwise, you're getting robbed of the quick, easy death everyone says they want. (Obviously, this is simplified, and my opinion only; your mileage may vary.)

      A larger question is how to handle the long, slow decline that often precedes a natural death. For a much deeper and informed perspective, see Atul Gawande's latest book, Being Mortal.

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    2. I will check it out; looks quite good. Handling the long, slow decline with grace and dignity is my wish.

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    3. Grace and dignity are hard to come by once debility and dementia have robbed you of your ability to control your bowels and bladder, bathe, dress, and feed yourself, recognize your loved ones, or remember what was being discussed five minutes ago, and even harder after you've burned through your life savings in a few months paying someone to handle those things for you,

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    4. Surely not everyone goes through such debility and dementia. Although, I have a friend whose husband was diagnosed with early-onset Alzheimer's disease at 58 and that is tough on her. So far, he seems to be mostly pretty happy still, enjoys music and walking the dogs with a companion, thankfully.

      My grandmother was mowing her own lawn at 90 so I'm hopeful that I have good genes. And my 84-year-old mom is doing yoga and traveling to Europe still. I know that's no guarantee, though. I do want to read that book.

      Hoping we all have good genes, good mobility, and quickish wit as we age! Happy trails, indeed. . .

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  6. Replies
    1. jan,
      I am no doctor, nor do I play one on TV. I normally leave all the medical discussion to you, a medical professional, and Steph, who seems to be very healthy, and smart about a lot of stuff.

      But my prescription (Rx it for what it is worth, about two cents, and your health insurance might even cover it.) for a long and happy life is to drink lots of Buttermilk and avoid pulling Triggers...

      ...Oh yes, and also avoid butchers wielding knives.
      Q.: What do you call lamb fillets laid out on paper towels?
      A.: Muttony on the Bounty

      LegoLambdaMD(DoctorOfMutton)

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  7. Replies
    1. Swimming is great, but it's not weight-bearing, so it doesn't do much to maintain bone strength. I think a "balanced diet" may be important in your exercise regimen, as in your food intake.

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    2. Yeah, it's a good thing I have Maizie who likes her two-a-days.

      Has anyone heard the term "postural sway" before? I thought of postural swaying during our morning perambulation. Swimming helps walking and walking helps swimming and. . .

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    3. ... and exceeding the limits of pastoral sway helps cow tipping.

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    4. hahahaha

      15% is customary, no? ;-)

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  8. Being a bit obsessive, especially about maps, I'm trying to figure out point A, above. Another place you work with kids?

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    1. My first apartment in Denver, the top attic floor of an old Victorian at 13th and Race. I had to lean to the left in the bathroom and lean to the right in the kitchen. But, good times!

      The route was a happy map from my original community garden at the Denver Botanic Gardens to Rosedale Community Gardens near Kunming Park where I now garden. The route was pretty linear as you approached Point B so I cropped that out.

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  9. Replies
    1. Wild, but what's the significance? Do healthy cells do this? In humans? Or do only certain mouse tumor cells do this? Who makes the microtubules -- the mtDNA deficient cell or the donor cell? Just when you thought you had some clue about how things work....

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    2. But, just a moment of wonder before the questions perhaps. . .

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    3. I wonder if bacterial conjugation is relevant here. Stupid question, perhaps.

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    4. Not a dumb question at all. Looks pretty similar to me.

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    5. I agree, jan and Paul. So many more questions for me now. About plants. About animals. . .

      Lego, any inside scoop on Lambda phage.

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    7. I'd ferreted out Max Delbrück before your link appeared. Waaaay too much fascinating stuff out there.

      Tonight I am careening between bats (inspired by the recent New York Times article and incredible photos, sharks and their oily livers which take up to 90% of their body cavities by volume, Annie Smith Peck who first climbed the tallest mountain in Peru, and recent Ebola developments.

      And then there's the fact that some shark species continue to ovulate while pregnant in order to provide a ready source of food to their offspring. So they take great care of their young in utero. . .but then have been observed eating their young after they were born.

      Ahhhhhh, decisions. . .

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  10. Great day at "College For A Day" in Denver. 9 colleges and their grads and these great topics:

    Dr. Catherine M. Stock
    Professor of History - Connecticut College
    Red Power: How the Occupation of Wounded Knee Shaped Conservative Politics in Rural America
    How the white community in South Dakota responded politically to the American Indian Movement’s (AIM) Occupation of Wounded Knee in 1973.
    http://www.conncoll.edu/directories/faculty-profiles/catherine-stock/


    Dr. Kim Yi Dionne
    Assistant Professor of Government - Smith College
    The Challenges in Responding to Ebola
    Why have West African governments and the international community struggled in responding to Ebola? Review the outbreak to date, the responses and the obstacles faced when trying to contain an epidemic.
    http://www.smith.edu/gov/faculty_dionne.php

    Dr. John F. Morrissey
    Professor of Biology - Sweet Briar College
    Sharks are People Too!
    The common knowledge about sharks is wrong! Learn about the diversity, anatomy, reproduction, and feeding behavior of sharks.
    http://www.biology.sbc.edu/faculty/HomePageJMor.html

    Unifying theme: the "Underdogs"--AIM, healthcare workers, and sharks.






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  11. Monkey Cage Blog/Washington Post

    New post is up. Bats prevailed (and hopefully, they will again soon).

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