DIET AND CANCER: round 3, or maybe 4.

With Coleman, 2004.

In Tucson they say that “the ice broke in the San Pedro River” on the first day of the year that the temperature reaches 100⁰.  Well, the ice was supposed to break in Coyote Creek today  (here in the north Borrego valley) but it only groaned and cracked a little.  Maybe tomorrow.

But, as it reached 99⁰ I did as I had said yesterday – went for a hike early, then spent the bulk of the day indoors.  This gave me a perfect opportunity to investigate a lead sent me by Carolyn, concerning diet and cancer.  Here is the link.  It is remarkably uninformative:

https://www.facebook.com/Alternativehealthsolutions1?hc_location=timeline

This link basically is an ad for a book, by Tamara St. John, the title of which is Defeat Cancer Now:  A Nutritional Approach to Wellness and Other Diseases.  I have not read the book, and probably won’t – but some of you may.  If so, please get back to me.

Ms. St. John says she has had cancer twice, and has been at death’s door since 2009.  She has used diet – apparently very high to vegetable matter – to hold her cancers at bay.  It is very difficult to excavate any concrete information from her blog, which is actually a Facebook page.  She is not a scientist; rather, she is an MBA and motivational speaker. 

Well, dammit!, more power to her!  It goes without saying that none of her suggestions have ever been tested with an NIH-approved clinical trial.  Dr. Ioannidis and his METRICS cohort would smile and shake their collective heads.  But so what?  Just because a hypothesis has never been robustly verified doesn't mean that it's wrong..  Novartis and Pfizer sell drugs to combat cancer; they are, one and all, various kinds of bio-active, mainly organic,  molecules.  So are carrots.  So why can’t a diet of carrots (and brown bananas) help keep cancer at bay?  Maybe they can.  My guess, though, is that – if carrots and bananas are truly effective – their value would have been discovered long, long ago.  So probably this is pseudo-science, and cancer patients certainly should NEVER rely solely on diet.  But, as I've said many times before – what do I know?

TREATS SOON TO COME YOUR WAY

In our home, probably 2010

The blank space on the wall now holds one of Linda's wonderful quilts.

It hit 98⁰  in Borrego Springs today and is supposed to reach new levels  of discomfort tomorrow.  Then it may cool off.  My estimated date of departure is Wednesday, April 23^rd, and (after my usual stay in Eureka), my ETA in Bellingham is April 30^th.  My cats will be happy To see me, and I can begin to put in a garden.  This year I propose to grow lots of turnips.

I am going for a hike tomorrow, in Font’s Point wash – at 6:00 am.

     

Friday of this week I am scheduled  to deliver  two talks to the ABDS Paleontology Society.  The first, The Terrane Concept in  Geotectonics is something I can do in my sleep.  However, the second talk – New Ideas about the Origin of the Grand Canyon – concerns ideas and methods I know almost nothing about.  I took it on so as to force myself to learn something new (besides cancer biology, of course.)  Now I wish I hadn’t, but it is too late.  I will bluff my way through

But not to neglect my blog:  I have several things I want to discuss, but time and energy are lacking right now.  This current blog is something like a Preview of Coming Attractions.  Waiting in the wings are:

1)      Another episode in the series Profiles in Research Excellence.  There is a young scientist at Fred Hutch who has made important discoveries in the field of ovarian cancer genetics.  His name is Jason Bielas.  I would like to meet Dr. Bielas and intend to do so as soon as possible.

2)      I want to do a book report.  The book is The Truth in Small Doses, by Clifton Leaf.  Mr. Leaf is not at all pleased with the way the “war” on cancer is being waged, nor of the way cancer research funds are allocated.  In fact, he is pretty sour on the whole philosophical underpinnings of official anti-cancer activity.  I am nearly through with the book, and so far, reluctantly,  I agree with him.

3)      Finally, Carolyn has sent me a reference to an article on combating cancer through diet.  It appears that bananas – the browner the better – are recommended.  I haven’t read the whole article – but I will.

So, stay tuned.  I have to get back to the Grand Canyon and the mysteries of ⁴He/³He thermochronography.

   

METRICS: Scourge of sloppy science.

Early on - maybe 1981

Back on 11/13/13 I posted a blog entitled “Beware Greeks Bearing Manuscripts”, which featured a very famous bio-statistician named Dr. John Ioannidis.  I had written about Dr. Ioannidis earlier (5/22/12).  Dr. Ioannidis almost singlehandedly has stirred the bio-medical  community into a froth.  His influence seems to have originated with a paper he published in 2005, entitled “Why most published research findings are false.”    At scientific meetings I’ll bet he eats lunch alone.

Dr. Ioannidis seems to turn up everywhere.  A recent article in The Economist:

http://www.economist.com/news/science-and-technology/21598944-sloppy-researchers-beware-new-institute-has-you-its-sights-metaphysicians

informs us that he is starting an institute at Stanford , the purpose of which is to examine bio-medical research and judge how reliable it is.  The name of this menacing creation is the "Meta-Research Innovation Center at Stanford": METRICS for short.  One thing METRICS will do is to troll for studies with faulty statistics; that is, studies  liable to produce “irreproducible results”.  Science is supposed to test the validity of new discoveries or pronouncements by seeing if the results cited can be duplicated.  This process is explicitly performed  very rarely, however, for obvious reasons, mainly involving monehy and professional advancement.  

The goal of METRICS is to hold comfortable scientific feet to the fire.   METRICS also will look for evidence of" publication bias", an evil that is poorly explained in the Economist article, but apparently pretty bad.

The British medical publication Lancet highlights the need for quality control in medical research: they reckon that $200 billion in annual medical research spending (85% of the total) is “squandered on studies that were flawed in their design , redundant, never published, or poorly reported.”  Ioannidis and his METRICS buddies are taking aim at this situation which, if only partly true, is still outrageous.  Good for them.

Better to fund institutions like the Rivkin Center, which awards support only to carefully selected investigators with precisely designed and targeted experiments.  

  

P.S.  Oddly enough, the Greeks and Manuscripts entry has attracted an unusually high number of hits lately.  Why this should be is a mystery to me.  

ONE MORE BATTLE IN THE PROSTATE CANCER WARS. Nuts to this stuff, from now on.

Linda and Ella

About six years ago

Breast cancer and prostate cancer have some things in common.  For one, they are gender-specific: yes, men get breast cancer, but very rarely.  Women don’t get prostate cancer for the good and sufficient reason that they have no prostate.  (This, ladies, is a blessing.  Take it from someone with an old and cranky prostate.)  Each type of cancer is the most prevalent for its respective sex.  Also, breast cancer and prostate cancer generate lots of press:  pink ribbons abound (as well they should), and articles about prostate cancer choke the news.  Now there is even a book about prostate cancer or, more accurately, whether or not to use the PSA antigen as a biomarker.  I wrote about the Prostate Cancer Wars way back on March 27, 2012, and have reported new battles in a bunch of Comments.  Go back and read to get up to speed. 

A few weeks ago The Economist reviewed a book titled “The Great Prostate Hoax: How Big Medicine Hijacked the PSA Test and Caused a Public Health Disaster.”  Read it yourself (the review, not the book) at:

 http://www.economist.com/news/books-and-arts/21598622-furious-debate-over-screening-prostate-cancer-help-or-harm. 

The authors of this book are strongly against using PSA for diagnosis.  They have the creds: the first author is a U. of Arizona professor who claims to have discovered PSA in the first place.  Apparently at times their opposition becomes hyperbolic, even shrill; The Economist firmly dislikes both.  (I cannot comment as I have not read the book, and don’t plan to.)   In spite of any literary deficiencies  the book apparently reports material for several valuable insights.  Two huge clinical studies are cited, one of which reported very little reduction of mortality by PSA screening, whereas the other found a definite benefit for men in 50-69 age range.  Both studies found high quantities of unnecessary worry and medical expense associated with PSA screening.  Many men have elevated PSA but no cancer; further (expensive) tests are required.   Many actual cancers discovered are “indolent”; they pose no real threat, but they scare the hell out of the patient and may result in unnecessary surgery.  A blood marker for cancer avidity is needed, but does not exist.  Maybe all men should get a “baseline” PSA done at age 40.  Or maybe not.

So, what they heck.  As an octogenarian I am going to use “watchful waiting” if my PSA goes up.  As a person mostly interested in ovarian cancer I am going to try to avoid prostate cancer articles in the future.  And as a sloppy eater:  Anybody know how to get peanut butter off your computer keys?

ANOTHER BREAKTHROUGH? Let's hope.

Guess where.  Guess when.  Guess what's in that bottle.

Did I ever tell you that the amount of DNA contained in a human cell, if stretched out, would be about 6 fee long?  Probably not:  I usually save up such gee-whiz facts to use when I am a little low on creativity, like right now.  It must be true; I learned it from a Teaching Company course on genetics taught by one Dr. David Savada , a cancer researcher associated with various institutions in the L.A. area.  It is a very good course, and when you have as much free time as I do I’m sure you’ll buy it. 

Anyway, what I got from Dr. Savada and my previous reading  is that DNA (famously arranged in a double helix) is a very long, fragile molecule that must be protected from damage at all cost.  To accomplish this it is armored with something called chromatin, and to save space tightly wrapped around little nodules called nucleosomes, constructed from histone proteins.   That way you can stuff six feet of DNA into a space much smaller than the head of a pin.  Sounds farfetched to me, but that’s what they say. 

Fragile though it may be, pieces of tumor DNA may be detected, extracted and studied – from the blood.  These things are referred to as ctDNA:  circulating tumor DNA.  In a recent study by a group of about four dozen scientists it has been shown that ctDNA can be used as an easily-accessed (needle in the arm) biomarker for various kinds of cancer.  (Ovarian was mentioned.)  Even early stage disease leaves its molecular signs.  This may be the long-sought early-warning biomarker that my group at the Hutch has pursued for years with, I am sorry to say, not a heck of a lot of success.

These ctDNA things have other uses.  They can help determine disease-stage, for instance.  They can help oncologists determine which drugs will work best, and why a drug – once efficacious – suddenly loses its efficacy.  They can do other things, which I probably don’t understand well enough to try to explain.  In short – a wonderful breakthrough!

But it is possible to be gloomy.  There have been other wonderful breakthroughs, most of which have turned out to be modest advances at best.  Some have turned out to be total flops.. I am reading a book right now that recounts and explains some of these historical things.  So far it has been relentlessly negative; I am sure the author is going to conclude with a wholesale condemnation of cancer research in general.   The book, which I will review sometime in the future, is so depressing that I am going to lay it aside and read a spy novel.      

I was alerted to this article by my friend Kathy O’Briant, mainstay of my group at the Hutch.  Thank you, Kathy.

FINALLY, A COMPUTER I CAN LOVE

Out to dinner.  Where?

Many years ago I was an avid reader of science fiction.  I liked it so much that, while supposedly working

on my M.S. degree in geophysics, I took time out to submit a story to Amazing Stories, which at the time was the premier magazine of that type in the world.  In due course I received a polite rejection from the head editor, who encouraged me to try again.  Real life intervened and I never did.  That’s probably for the better, but who knows?

Anyway, I vividly remember a short story from those days, in which a computer was being awarded the Nobel Prize in medicine – for curing cancer.  It made an acceptance speech, if I recall correctly.  Did it wear a tux?  Or an evening gown?  Can’t remember.

So, maybe that wasn’t such a far-fetched concept.  Dick Ingwall, trapped in his house like me by gale force winds ripping through the Borrego Valley, has studied the NY Times and come up with the following article, which I will comment upon shortly.

http://www.nytimes.com/2014/03/27/science/enlisting-a-computer-to-battle-cancers-one-by-one.html

The deal is, sequencing DNA has become so easy, rapid and cheap that it is possible to take a sample of a tumor and quickly and economically determine which of its genes are mutated.  This doesn’t get you very far, however.  Some of these mutations will turn out to be harmless and should be ignored.  Others are probably harmful, but it isn’t always apparent how they harm, nor what you can do to stop them.  Here is where Watson comes in.  Watson is the IBM super-computer that apparently just starred on Jeopardy.  Watson is busily devouring the abstracts of medical articles – it is up to 23 million or so.  Give Watson a list of mutations and it will spit out a list of drugs, or drug cocktails  that might help.  Then, of course, humans enter the picture.

Obviously, Watson can only make suggestions based on the reported research.  If the research is crap, Watson will mislead.  That’s hardly Watson’s fault.  The familiar adage “garbage in, garbage out” applies, even to a super-computer.  We need lots of basic research for Watson to devour.  Lots of good basic research.

This approach to cancer therapy is going to be tested on a group of 20 victims of a nasty form of brain cancer, glioblastoma.  Prognosis from glioblastoma is dismal.  Let’s hope Watson gets it right.

NOT OC: My grand daughter Olivia Kelly graduates from Western Washington University

I was privileged to participate in Olivia's graduation ceremony.  Despite much trepidation, I did not trip over my own feet and fall off the podium.   The baby is Evelyn Beck Smith, often known as Her Royal Cuteness.