Wednesday, November 25, 2015


Heron Island clambake, 2019
Heron Island is in Maine
Note large crustacean by my right foot
I am beginning to pack for Borrego Springs.  I plan to leave Bellingham on December 2nd and, after a pleasant layover in Eureka with Linda’s sister Carolyn, to arrive in the desert on December 10th – where I will remain, God willing, until the end of March.  This means that I will not be posting any more movie reviews until spring.  (I assume this will disappoint a few of you, although I have watched as the number of “Likes” each review stirs up has dropped from about 30 to about three.   No, my feelings are not hurt.  Not much, anyway.)  Also, I won’t be posting any new blogs for some time, although I will take it up again when I am settled in B.S.  I don’t even know whether my computer works, or whether I have cable, or even if I have running water down there, so “getting settled” may take a while.
But here are some articles to tide you biology aficionados over for a few days, at least.
The first discusses probable developments in cancer treatments during 2016.  It comes from a publication of the Economist called The World in 2016, which – as a subscriber – I get free.  It is a delightful collection of analyses of present circumstances worldwide, together with predictions of where various aspects of human endeavor are headed next year.   You apparently can buy it for $13.95.  Canadians get it for C$13.95, which means that they get a break of maybe 50 cents.  Gloat, Parkfriend.
Anyway, this article is a comprehensible summary of what is going on in immunotherapy.   All of you who are eager to learn more about checkpoint inhibitors will enjoy this little essay:
The second article is wisdom straight from the horses’ mouth: the NCI.  It elaborates on recent research showing just how dammed complicated cancers are, and how knowing precisely which genomic mistakes are involved in each can help.  This comes under the category of targeted therapy, I guess.  There is nothing particularly new here, but this is a good summary.  Note particularly the number of acronyms showered upon you – this seems to be typical of biology, or maybe just molecular biology.  (If I had referred to “margin-parallel crustal displacement caused by oblique convergence” as MPCDOC  I would have been tossed out of the American Geophysical Union and showered with rotten fruit.)
Also, it helps to know that a tyrosine kinase is an enzyme that slaps a phosphate group on a tyrosine molecule, thereby providing the energy needed for a biochemical “cascade”.   Here is the article:
Try to make do until I get back on line.

Friday, November 20, 2015


On a bridge somewhere
Deception Pass?
Somewhere recently I mentioned that Big Pharma spends more on advertising than on research and development.  I’m not sure how to react to this fact (if it is a fact – I suppose somebody might have made the whole thing up.)  My gut-level response is mostly a blend of anger and disgust.  The disgust portion stems from the annoying nature of TV ads touting new drugs, which invariably end with the words “ask your doctor if Fidoplex could be right for you.” Characteristic of most of these ads is the obligatory two minute litany of side effects, usually ending with “death”. I particularly like the one that always terminates with two people, of opposite sex, in adjacent bathtubs!  These prime time ads must cost a fortune!  Why not spend that fortune searching for new drugs or therapies? 
Not so long ago there were people called drug reps.  These guys each represented some particular drug company, and they were tasked with bringing the new pharmaceutical marvel of the moment to the attention of the clinicians who wrote prescriptions.  Before Linda became a physical therapist she worked at the front desk of a group of physicians; one of her primary responsibilities was to keep these gentlemen from totally disrupting the daily flow of business.  Still, the drug reps got in, spoke directly to the doctor, explained their new wares, and left samples.  The doctor then made up his or her mind.
I suspect that the earlier way of disseminating news of new therapies (drug reps and free samples) cost a hell of a lot less than today’s  big, splashy TV ads, and did the job better.  Surely the med people must have preferred it: imagine how annoying it would be to have half a dozen patients every day ask “What about this Fidoplex stuff doc?  Sure sounds like a world beater.”
I acknowledge that there has to be a means of disseminating news of new therapies.  Ideally, the meds involved would read about them in professional journals, or learn about them at professional meetings.  Ideally, yes, but our modern doctors are far too busy to read all those journals, or go to all those meetings.  They deserve to put up their feet and watch Jeopardy when they get home, if that’s what they want to do.  They are, after all, human.
So, bring back the drug reps.  I don’t know where they went, nor why. (As an aside: I used to get scads of free pills, and now I have to buy ‘em.)   Finally – Big Pharma – quit annoying me with your stupid, splashy ads, and plow the money you save into something useful.

Tuesday, November 17, 2015


Glacier Bay, Alaska
Do you know what a “metabolite” is?  Well, like me you probably could guess that is something that has to do with metabolism – the messy and biochemically complicated way that we turn thing like berries, butter, bread and bacon into the energy that runs our bodies and the stuff that makes them up.  The products of metabolism are known as metabolites.  How a biochemist would categorize them is something I don’t know – but it is pretty clear from this article that they are not proteins.
So, anyway, people at Georgia Tech have used some clever chemistry and computational tricks to recognize a group of 16 metabolites that are elevated in ovarian cancer patients, but not in the rest of the population.  They attained a specificity of over 90%, meaning that the test was 90% accurate in distinguishing women with cancer from women without cancer.  And the really good news is:  The cancer patients were in either stage 1 or stage 2 – meaning that metastasis had not begun.  As always, more testing is required, but still – maybe we have here the Holy Grail:  genuine early detection.
The Georgia Tech test would operate from a simple blood sample.  The group I attempted to help at
Fred Hutch also sought a blood test, but they were looking at proteins exclusively (I believe.  Remember, I’m just a dumb geologist.)  Some proteins definitely are elevated in ovarian cancer patients – CA125 and HE4 are examples.  Sadly, they don’t rise until the cancer is fairly far advanced.    Our work seems to have fizzled out.  I will keep an eye on these Georgia Tech people.  I am encouraged.

Saturday, November 14, 2015


Wild guess:  Chile, mid 1980s
Trapped inside by bad weather and lethargy, I found this web site while piddling around with the computer:
I bring it to your attention because it has an abundance of important information about ovarian cancer, in an easily accessible format.  I was inspired to join a local chapter (of the National Ovarian Cancer Coalition) but, it turns out, the nearest is in Sacramento, California.  And, don't ask: I am too old and lethargic to start a new one.

Thursday, November 12, 2015


We were thin once
Cat is Whiskers
Confused about mammography?  Sure you are.  Most everybody who cares a fig about it must be a little confused.  Not only do guidelines/recommendations change every few years, but the latest “revisions” to come out, from two noteworthy organizations, do not agree.  The organizations are ACS (American Cancer Society) and USPSTF (our old friend the United States Preventative Services Task Force.)  Their recommendations are not radically different, but they do not agree on everything.  Two things they do agree on, however, are: (1) Mammography saves lives; (2) You don’t need quite so much of it.  They also seem to agree that the individual woman should make up her own mind.  Here is the article that inspired this:
All women should read this, then decide. 
Personally, if I were female I would say “To hell with false positives” & get checked frequently.

Sunday, November 8, 2015


Linda on a typical Bellingham summer day
Well, we have ten or twelve of them most any year
While fumbling around in the depths of the internet seeking enlightenment on checkpoint inhibitors (q.v.), I stumbled on an article I actually could understand.  It had nothing to do with checkpoint inhibitors, though – it was a report of NCI awards for SPORE grants.  NCI you recognize: a SPORE is alternatively a way that some plants reproduce, or – as in this case – a type of NCI award called a Special Program on Research Excellence, or (as I am sure recipients regard it – the jackpot).  These grants last for five years and (currently at least) are worth $2.85 million annually.  At the moment there are four active SPOREs in the field of ovarian cancer research.  Mayo Clinic received one this year.  I am going to study the Abstract for their proposal, and if I can make any sense of it I will report.
Needless to say, Mayo Clinic is top drawer.  I am encouraged.
Sadly, the program I attempted to help at Fred Hutch was not funded.  I don’t think it was my fault.

Friday, November 6, 2015


Part of the reason we bought the place in Borrego Springs
Most of you already know that having babies lowers a woman’s risk of developing ovarian cancer.  You probably also are aware that this is a correlation, not proof of cause-and-effect.  (But I think it is.)  Well, Oxford University has just verified what you already knew; they studied 5700 British women for (well, hell, they don’t say how long), and found that having one child lowered the probability of developing OVCS by 20% - and the more kids you have, the lower the probability. For some (rarer) kinds of OVCA the risk reduction was even greater.   (My grandmother had nine kids – and didn’t develop OVCA.  Anecdotal evidence, you say, and you are right.  Raising all those kids, and in Cripple Creek Colorado at the turn of the last century, left her exhausted, but healthy.  She spent the last 20 years of her life sitting in a comfortable chair, smiling.)   Anyway, the same study showed that women who have their fallopian tubes removed are at a considerably lower risk of OVCA than otherwise.  You already knew that, too.
So why am a telling you all this, if you already know it?  Well, first of all it’s a big deal: journals from Nature to the sleaziest British tabloids are writing about it.  In case you have nothing better to do, read this:
And also, I suspect that a few of you need to be reminded.
Finally, this finding has profound demographic consequences, which you can work out for yourself.