DATA MINING

Early camping trip

I have had a lot of fun as a geologist.  I was paid, mind you, to visit all sorts of interesting and beautiful places all over this half of the world.  I worked in the Caribbean (hot, muggy, boring), the Aegean (well worth a visit, especially off the beaten track), Southwestern South America (wonderful), Italy (good food), and half a dozen places in the United States (a mixed bag.)  I even got paid to go to Antarctica, a trip I never could have afforded otherwise.  And all the while I made interesting friends, who enrich my life even now.

But if I had it to do over again, I would study computer applications, with a double major of molecular genetics.  I would become a data miner.

Here is a story about a data miner at UCLA, doing important work, highly regarded research.

https://directorsblog.nih.gov/2018/03/01/creative-minds-looking-for-common-threads-in-rare-diseases/

This young woman – and she looks oh so young – is using computer techniques to comb through existing data bases of DNA information and related data to find “common threads” amongst various rare, “Mendalian” diseases.  She does it in a manner that I don’t fully comprehend, in an effort to accomplish some things I don’t fully understand, either.  Whatever:  NIH is excited enough to fund her handsomely.  (I got this information from the blog of the Director of NIH:  see http://ljb-quiltcutie.blogspot.com/2017/12/frankenstuff.html)

Well, if you do happen to read the rare diseases article you will run on the following useful little ditty:

https://www.genome.gov/20019523/genomewide-association-studies-fact-sheet/

This explains data mining.  I am going to study it, after my morning nap.

THE MURINE CHRONICLES

Linda pretending to be snookered on our Norwegian cruise, 2004

Sometimes I think that the name for this blog ought to be “The Murine Chronicles”, not “Myrl’sBlog”.  Sure, it is written by Myrl, but much of the time it’s about things we humans do to mice and rats.  This posting is strong to rats.

There is a gene known as RAS which is complicit in many kinds of cancer.  When not mutated it produces a protein (RAS), which serves as a signal within cells, telling them when not to divide.  If mutated, RAS can’t do its job and the cell multiplies like sin to produce, in some cases, cancer.  RAS, therefore, is a “proto-onco gene”, one of the worst.  Clearly, if we could develop a drug to prevent screwed-up RAS proteins from doing damage, we’d be way ahead. 

Oh, maybe here is where I should tell you where the name RAS comes from.  Rat sarcoma.  RAS was discovered by abusing our friend, the brown rat.

Well, all this has been common knowledge for more than a decade, and majestic piles of money, effort – and rats – have been expended on developing a drug to counter the malign effect of mutated RAS, to little effect.  Odd though it seems, drugs like this work by “binding” to the subject bad-acting molecule.  Binding requires a precise shape; your missile of death has to fit precisely into some irregularity on the surface of its target.  And not just any old irregularity; as I understand it, it should be the misshapen hole that is causing the trouble!

Hell, I am in way over my head.  Read this link; it is short, relatively easy to understand, and informative. 

https://directorsblog.nih.gov/2018/02/13/kras-targeted-cancer-strategy-shows-early-promise/

And thank God for your little murine friends.

TROUBLE NORTH OF THE BORDER

Linda and Viv Hailwood

On a hike in Yorkshire Dales National Park

Well, here’s one you (probably) can’t blame on Donald Trump:  even the Canadian government is short-changing ovarian cancer research.

https://globenewswire.com/news-release/2018/02/28/1401168/0/en/Budget-2018-Ovarian-cancer-research-funding-still-a-concern-for-women.html

Ovaries and prostates develop from the same swatch of fetal tissue (I seem to have read somewhere), and both are subject to deadly cancers – yet our Northern Neighbors allocate over twice as much money to prostrate problems as to OVCA.  Not good.

Some Canadian women have organized to do something about this.  They want more support for OVCA research (not less for PRCA, for Heaven’s sake!).  Bless their efforts.  What say, Parkfriend?

TECHNOLOGY TO THE RESCUE

Linda and her Mom

At our Rams Hill place, maybe 12 years ago

Multiple myeloma is cancer of the plasma cells.  It is a nasty brute, but can be held at bay and sometimes killed outright by means of bone marrow transplants. 

It transpires that a cancer researcher at UW/Fred Hutch found himself wrestling with just this ugly brute.  With the help of his wife, who is an oncologist, he seems to have conquered it.  But, I guess, this close encounter with mortality led him to think outside the box.  The result was the Center for Cancer Innovation at UW, and later a startup called All4Cure.  Some of the finances for the latter come from Crowd Sourcing (you know what that is, right?).  The whole endeavor relies to an incredible degree on technology (the cloud, next generation DNA sequencing, mathematical data-mining, that sort of thing.   (If you ever doubted the value of $150,000 spent on your kid, and that kid is into tech stuff, doubt no more.)  

  

Well, anyway, this is a happy story and I am happy that Dick Ingwall brought it to my attention.

Read both links; you will be happy you did..

https://www.nytimes.com/2018/02/15/well/live/a-cancer-resarcher-takes-cancer-personally.html

https://www.geekwire.com/2017/health-tech-podcast-researcher-taking-cancer-data-crowdsourcing/ 

AN ANTI-CANCER VACCINE?

Linda and friend

Santorini, late 1980s

Well, dammit! I am sure I have written something about this before, but I can’t find it.  (There are 561 of these little blogs so far.  Have you read them all?)  So, instead of tossing out a Comment I am forced to publish a new blog entry (#562).  But don’t worry, it will be short.  I am scheduled to play some golf in about 30 minutes.

Some people at Stanford are experimenting with what they are pleased to call a vaccine.  On mice, natch – although a human trial seem in the offing.  They inject two molecules (well, squirts containing lots of them) directly into the tumor – which promptly dies.  Better yet, this somehow stimulates the immune system to search out and destroy similar tumor cells throughout the body.

  

Wow!  Good news!  Let’s hope it pans out.

https://www.nih.gov/news-events/nih-research-matters/injection-prompts-mouse-immune-system-destroy-tumors

A NEW, BUT SCARY, RESEARCH ANGLE

Beautiful Linda

Why I write all these things

Boy, this is heavy!  Scientists are examining a mutant protein that is deathly dangerous as a possible cure for cancer!  Yikes!

Okay, so in case you didn’t know (a very likely condition):  There is a condition called Huntington’s disease, or Huntington’s chorea, that is very rare, inherited, invariably fatal and, from some stuff in Wikipedia, a slow and damned unpleasant way to die.  It is caused by a mutation in a gene called Huntingtin, which is transcribed into a protein of the same name that does all sorts of important but – to me and medical science – mysterious things.  In H disease the H gene has a segment with an abnormal number of the three-nucleotide repeats, CAG (cytosine, adenine, guanine,) all in a row.  H disease attacks nerves in the brain.

Well, some researchers happened to notice that victims of H disease rarely, if ever, suffer from cancer.  To explore this observation they infected mice (poor long-suffering little devils – what would we do without them?) with human ovarian cancer, then turned the mutant H protein loose on them.  And - what do you know? - the cancer went away.  Subsequent experiments show that it is equally toxic to cancer cells in general.  Why this is so is not apparent to me, for sure, and I suspect not to the researchers either.

Well, we don’t want to save people from cancer only to turn their brains to mush.  Obviously a lot more money and time, and mice, are required.  But this is intriguing.

As a grumpy aside – why doesn’t Elon Musk spend his countless millions doing something like curing Huntington’s disease, rather than putting a damned automobile into orbit?

IMMUNOTHERAPY MARCHES ON!

LINDA AND BUTCH

                                                       The original "fraidy cat"

There is a type of OVCA known as “hypercalcemic small cell ovarian cancer” that is exceedingly rare, strikes young women, and (heretofore) had been considered incurable.  However, recently four desperate young victims “banded together”, via the internet, and demanded that their doctors try immunotherapy – despite the fact that medical science was certain that it wouldn’t work.  Well, what the heck – it DID work!  The young women are alive and prospering.  Now medical science is scrambling to understand why.  And “they” are testing some ideas.

We’ll beat the sombitch yet!

https://www.nytimes.com/2018/02/19/health/ovarian-cancer-immunotherapy.html?rref=collection%2Fsectioncollection%2Fhealth&action=click&contentCollection=health&region=rank&module=pa ckage&version=highlights&contentPlacement=2&pgtype=sectionfront