Tuesday, July 26, 2016

DATA SCIENCE: Or, why you should have studied computers in school.

Our skinny period

Would you have guessed that the U.C. San Diego School of Medicine employs someone described as a “Data Scientist?”  Well, read this article and you will see why. 

Faithful Readers, and there are thousands, already know all about precision medicine – that is, the creation of drugs or drug combinations that target specific mutations.  They also know that before a drug can be marketed it must receive the blessing of the FDA.  The FDA also weighs in on whether a drug approved for, say, colorectal cancer can be used to combat, say, melanoma.  Evidence that such a drug allocation might be useful rests consists of evidence that the misbehaving biological pathways in both cancer types stem from the same mutation(s).

Well, ye gods!  There are hundreds of cancer types involving thousands of mutations.  Moreover there are so many drugs, extant and conceivable, that only God (and the FDA, of course) can keep track of them.  Ergo: a Data Scientist is required. No doubt she drives a Porsche.

This article shows how one goes about determining which drugs will work on which cancers.  The work to date mainly involves yeast; our furry murine friends are threatened.  There is so much work to do that the UCSD people are attempting to farm it out internationally.  ISIS need not apply.

Monday, July 25, 2016


Hiking in Scotland

More and more one reads bits about “personalized medicine.  Often this means using the patient’s genome to determine what went wrong that resulted in cancer.  (This would seem to require sampling the tumor itself.)  Knowing what went wrong then permits study of just how (the “biochemical pathway”) this particular error results in its malign behavior.  Maybe a drug already exists that mucks up or repairs that pathway: if so, use it.  Or, if no such drug is available, persuade a granting agency or drug company to develop one. 

Well, a useful new application of personalized medical techniques allows oncologists to detect the recurrence of cancer very early and very simply.  First, sequence the tumor DNA and pinpoint the tumor-specific peculiarities.  Then, periodically draw a sample of blood (“liquid biopsy”).  Scan the sample for fragments of tumor DNA.  If they are there, the tumor will recur, If not, it won’t.  This works because solid tumors shed fragments of themselves into the blood stream.  The method appears to work particularly well in cases of ovarian cancer.

Yes, I know this was unusually boring (although not unimportant.)  I am still recovering from the energy-drain occasioned by simply WATCHING my two ggrandkids at play.  At least I got to use a cool two-bit word (malign) as well as an inelegant-but-cheering verb phrase (muck up).  Here is the article:

Saturday, July 23, 2016


Quito, Ecuador

That should grab your attention.  This represents a British tabloid’s attempt to suck you into reading an article about some legitimate research performed at Dartmouth University.  Apparently some proteins somehow associated with your ordinary disgusting cat box have been shown to stimulate the immune system to fight cancer.  They have been used on mice with ovarian cancer, to good effect.  There aren’t enough details given to say anything more’ the main purpose of this blog is to announce that I am back at work, after a great holiday in Cordova, Alaska with my family.  Sarah stayed in my house and left it spotless; let’s see how long it takes me to screw it up. 

Sunday, July 10, 2016

STEM CELL CLINICS: Let the buyer beware.

Guess where.
Burning question:  Is there room to add the Donald?

People will attempt to make money out of anything.  Apparently there are over 300 “laboratories” scattered about the country that will “treat” your ailment using stem cells,  They  (purportedly) remove stem cells* from a sample of your tissue (blood, fat, mucus, who knows), cultivate them in vitro, then feed them back into your ailing body – all, of course,  for a whopping fee.  Some anecdotal successes are noted; however, some such enterprises have been forced to flee the country.  The FDA is in hot pursuit.  The bottom line:  read these two articles

and consult an expert  before you send off your package of bottled spit wrapped in a big fat check.

Of course, this is not to say that legitimate stem cell therapy is doomed to expensive failure.  Far from it: induced pluripotent stem cells are a hot item in medical research.  It is possible to “reverse” the differentiation of (some? all?) human cells, in effect turning them back into pluripotent stem cells that are capable of becoming almost anything in the human body.  Theoretically, these induced stem cells can be used – somehow – to repair and/or replace human biological malfunctions.  Legitimate scientific projects to do this are underway.  Legitimate clinical trials presumably are underway, or will be soon.  Again, consult an expert.  And don't look ,at me.. 

*These are not pluripotent stem cells.  Rather, they have differentiated into narrow specialization: for instance, stem cells in bone marrow can produce red blood cells but nothing else.  Even cancers are said to have stem cells, for Christ’s sake!  Another of nature’s bad ideas.

Friday, July 8, 2016


Borrego Springs?  No, Catalina Island

Long ago when I was still active in research the undisputed leader in my field (roughly, paleomagnetism applied to local and regional tectonics) was Ted Irving, an Englishman transplanted to Vancouver Island.  Ted and I shared many ideas and enthusiasms (sharing consisted to a great extent of him talking rapidly on the telephone, and me listening respectfully.)  I remember once asking him if he planned to attend an up-coming conference.  He replied “No.  There are so many conferences these days that, if you attended them all, you would never get any work done.”  I took that to heart.
Well, maybe we should apply that philosophy to cancer research.  On June 29th Joe Biden convened a Moonshot Summit (read: large gab-fest) in Washington, D.C.  Apparently there were 250 simultaneous (and similarly large?) regional Summits scattered across the country.  If this article

is to believed, some important stuff was addressed; you should read it.  Nevertheless, a lot of senior scientists were not in their labs that afternoon – although, presumably, their junior faculty were hard at work..  Or not.

Thursday, July 7, 2016

PNNL: Atomic science to the rescue

Bergen, Norway
For some reason, Linda was not to excited by trolls

Have you ever heard of the Pacific Northwest National Laboratory?  Well, neither had I, until today.  I had heard vague rumors alleging that there was some sort of off-beat research outfit located in the Tri Cities area of central Washington (where all the atomic stuff went on) but –despite having a graduate student working there – I didn’t really know what they did.  As it turns out, we all should be interested in the PNNL: initiated in 1965, it currently employs 4,400 staff and has an annual budget of nearly $1 billion.  It is “the largest single supporter of basic research in the physical sciences in the United States”.  Too bad it’s in Richland.

Turns out the PNNL supports work in cancer biology as well, as this interesting article will attest:

To enjoy this article you will have to remind yourself of several things:

1)      In ovarian cancer there seem to be multiple genetic mutations.  In general, the study of such genes might be referred to as cancer genomics.
2)      Genes “code for” proteins.  Proteins do most of the important work within a cell.
3)      Not every gene in a particular cell is “expressed” (converted into a protein).  Some are expressed massively, some sparely – and most, not at all.  The study of active proteins is known as proteomics.  And so we have, inevitably, ovarian cancer proteomics.
4)      It follows, it seems to me, that it makes sense to study the proteins that are doing the dirty work, and perhaps pay less attention to their associated genes.

Well, the PNNL bio-folks have been studying the active proteins in examples of high-grade serous ovarian cancer (what Linda had.)  They found that they could distinguish between two groups, based on their proteomes.  Members of one group had a much better prognosis than members of the other: 75% 5-year survival rate vs 25%.  Presumably this knowledge eventually may inform individualized therapies.  Anyway, I hope so.

In case you find the web address given above a little opaque, try this:

As an aside: we owe an awful lot to our neighbors across the Pacific.  Japan, we all agree, gives us the  bulk of our better cars.  China, it seems, supplies us with a preposterous fraction of our cancer scientists.  Take the PNNL article, for instance:  it purports to have 47 authors - 23 with unmistakable Chinese surnames. 

Sunday, July 3, 2016


Linda on her 63rd birthday
Boy is Coleman Henner

Here is a good, simple summary of the weapons currently available in our “War on Cancers”.  Several of these were essentially unknown when I commenced my own personal war on ovarian cancer just four years ago.  This rapid advancement underscores Dr. DeVita’s

dictum that one should never give up (on a cancer patient) because some new therapy may be just around the corner.