COFFEE TO THE RESCUE? Maybe not

Linda and her Mom, 1980

The NCI Cancer Bulletin is filled with gems of wisdom, interesting curiosities, and useful facts.  The current issue (May 29) has another exchange of fire  in the prostate cancer PSA wars, in which the Feds, in the guise of the USPSTF squares off once again with the hands-on docs, represented this time by the AUA – the American Urology Association.  I’m tired of commenting on this endless debate – if you are so inclined, go read the article yourself.

Of greater interest is a massive study concerning the effect of coffee on health.  Researchers from the NCI followed 402,260 men and women for varying periods of up to 13 years.  They conclude that the drinking of coffee cuts death rates from a host of conditions: heart disease, respiratory disease, stroke, diabetes and infections – but, unfortunately, not cancer.  Moreover, the more coffee you drink, the more the benefit.  Coffee-drinking also reduces the chance of death from injuries and accidents - which you would expect since most coffee consumption is done while sitting down, which is a pretty safe place to spend time.  It turns out, though, that the raw numbers show that coffee-drinkers die EARLY, not late.  This, ostensibly, is because much drinking of coffee occurs while smoking.  Only after ”controlling” for smoking does the drinking of coffee appear beneficial.  No wonder that every cancer lab seems to have a statistician on staff.

The final paragraph of this article raises the question: Cause-and-effect, or merely “associational?  That is:  Maybe something in coffee is actually good for you, or, Maybe coffee drinkers tend to do something healthy that non-drinkers don’t do.  What might that be?

Now I'm going down to the cantina for another cup.

LINDA'S TEAM, Part 2.

We took that truck on our honeymoon.

First day out, I ran it out of gas.

Truck and tent still exist.

Okay, so we have decided to run a northern version of the SummeRun, here in Bellingham.  I will secure a place in a nice park and reserve some kind of shelter for a few hours; I thought, like 10:00 am to 1:00 pm.  I will have some kind of grill going, buy some soda and such stuff, and have a supply of hotdogs, hotdog buns, and maybe potato salad.  Anyone who wants to can bring additional goodies, or healthier things to grill.  We haven’t selected the park yet, but the alternatives Florence and I are considering all are near a trail system so anybody who wants to can walk or run as far as they want to.  The idea is to show up about 10:00, take a walk (or just sit around), then have a group picnic around noon.  If this is a bad idea please let me know:  email me at myrlbeck@msn.com.

This is, after all, a fund-raiser for ovarian cancer research, so I would urge you to donate.    Here the best way to go about it.
      Go to their web site (www.summerun.org) and click on Donate.

                 Type “Linda’s team” in the search block that will come up.

            Fill out the inevitable form, chose the amount you want to give, and finish.  You will need to use a credit   card.

Note:  Do NOT “join” Linda’s team.  If you do they will subtract $30 from whatever you give, for expenses.  As we are not participating in their big race/walk with all the accompanying hoopla, we don’t need to register.

Pretty soon Carolyn will come up with a t-shirt design, and you can order one if you want to. 

I’ll get back to you with more details when I figure out what they are.

ALL IS NOT LOST

Nova Scotia, 2000

That's the Canadian Journal of Serious Literature she's reading

or maybe People Magazine

This was too long for a "Comment", so I'm making it a stand-alone "Post".  It refers to the article about the Stanford Prof I commented on earlier.  

As threatened, I am going to comment on the article about John P.A. Ioannidis which is the cover story of the latest Stanford Magazine.  That story was primarily based on an article that Dr. Ioannidis published in the journal PLoS Medicine, which I presume is an authentic and well respected  outlet for medical research.    Thus, we should  take Dr. Ioannidis’s ideas seriously.  However, after three laborious passes through his “Essay”, I think he blew it.  Here’s why.

In bold type, in the middle of the first page of the PDF containing this article is the phrase “It can be proven that most claimed research findings are false”. That’s scary.   However, to reach most of us the statement should have read  “It can be shown that most claimed research finding are based on faulty statistics”.  To the biostatistical crowd those two statements may be equivalent, but to the rest of us they aren’t.  Maybe readers of PLoS Medicine will get his drift but  the average reader of Stanford Magazine may get the wrong message entirely.  To most of us outside the medical world Ioannidis seems to be saying “So-and-so says that A is a cure for B, but I can prove that it isn’t.”  What he means to say  is “The proposition that A is a cure for B has not been established with proper statistical rigor.”  What we outsiders should realize is that A may still cure B but that formal statistical verification is lacking.  More experimentation may be in order, but the concept is not ready for the trash heap.

Here is a simple example from my field of research.  In paleomagnetism we frequently try to determine whether two mean magnetic directions are or are not “ different”.  To do this we first calculate the two means, as well as things we call “circles of confidence”.  The radius of a circle of confidence (which has as its center the mean direction) is determined by how many samples have been studied, and how much these individual sample directions vary (are scattered).  We also get to choose a “confidence level”; usually 95%, but the choice of confidence level fundamentally  is arbitrary.  If the confidence circles around the two mean directions overlap we state that “at the (95%) confidence level the two directions are not different.”  Note that we do NOT say  that “the two directions are different” because one time in twenty (for 95% confidence, on average) such a statement would be wrong.   We can change the radii of the circles by studying more samples, or by choosing  a different confidence level.  Unless the statistics are improbably, wildly indicative, any  geological conclusions need other types of evidence to be convincing.

I think the same is the case with medical statistics.  They use far more sophisticated  methods than we dumb geophysicists are used to, but they still must face up to the same limitations.  Statistics alone are not capable of establishing truth; they merely give the odds, so to speak.  Thus, don’t lose heart; the bulk of conclusions derived from modern  medical research are not false – in any practical sense of the word.

Ioannidis does give some useful “Corollaries” toward the end of his article that are, in some cases, obvious, but that are true and important nevertheless.  There are six such.  I will comment only on the ones I think I understand:

               The  smaller the study, the less likely it is to be true.  Natch.

2     The smaller the effect size, the less likely the study is to be true.  I take this to mean that if the process            studied has only a minute effect, it is hard to evaluate  correctly.  Natch, again

      The greater the financial and other interests and prejudices on a scientific field, the less likely that the research findings will be true.  Obvious, I think.  Did you know that many critical studies are funded by drug companies that stand to profit from a positive result?  That some of the funds involved are huge?  We need more support from "disinterested" institutions. Never thought I'd advocate for more governmental spending.

      The “hotter” the field, the less likely the findings are to be true.  His reasoning here is a little obscure (to me), but insofar as I understand, I agree.  From my own career, there was a feeding frenzy when Davy Jones introduced the “terrane” concept; lots of the studies done during that frenzy turned out to be crap

.

Okay, that’s plenty.  Thanks to those of you patient enough to read all the way to here.

   

  

ONE YEAR AGO

In our hearts forever

Linda died one year ago today.  I am sure that most of you didn't need to be reminded of that.  I am spending the day in Seattle, helping out at Fred Hutch; tonight I will get together with Florence DiJulio to plan activities for July 22^nd, the day of the Marsha Rivkin Center’s “SummeRun”.  Most likely we will arrange something concurrent, in Bellingham.  The Rivkin Center does good work in the fight against ovarian cancer.  It deserves support.  You should check out their web site.

After the passage of a year I hurt as much as ever.  I never really expect the pain to subside.  However, it helps very much to have something constructive to do, something to occupy my thoughts.  Working with a group doing cutting-edge ovarian cancer research has really transformed my life.  It also keeps my mind active, which (they tell me) is important at this time of life. 

I just got back from checking the Honor Wall in another Hutch building.  Linda will go there, thanks to the generosity of many of you.  She isn’t there yet.  I will keep their feet to the fire.


My gratitude goes out to all of Linda's friends, all her many friends.  Your support throughout that terrible time a year ago was astounding.  i don't know how to express my appreciation.  I know that many of you hurt just as much as Carolyn and I do.   I can't say it too many times: ovarian cancer needs to be wiped from the face of the earth.  

LINDA'S TEAM AND THE SUMMERUN

                                                     Linda and friend, Isle of Sky, Scotland, 1999
                                                 She did all the driving and didn't hit a single sheep!

For 18 years the Marsha Rivkin Center for Ovarian Cancer has sponsored a "SummeRun" as a fund-raising event.  The Rivkin center is attached to Swedish Hospital in Seattle.  The "race" is 5 km - about 3.1 miles - and wends its way through the "pill hill" neighborhood.  Some people will run - some maybe even competitively - but most of us will walk, talk, and sight-see.  Florence DiJulio, Carolyn Joyce and myself are forming a "Linda's Team" for the occasion.   We would like you to participate.  B'hamsters can car-pool; I will drive my new jeep, Carolyn can drive Linda's Subaru, and maybe others will volunteer to drive as well.  A good time is almost guaranteed.  Parking is free!

However, there are drawbacks:
1) It starts at 9 00  am.  I plan to leave at about 6:30.  That's pretty early of a Sunday morning.  (But, see below!)
2) It costs $30.
3) They hope that you will raise money.  I don't like asking people for money, and neither do you.  I'm asking by means of this Post.  Anybody who would like to contribute (and - the Rivkin Center is an important player in ovarian research, closely aligned with Fred Hutch) but can't participate in the event can send me a check, which I will pass on as part of Linda's Team's contribution.  The threshold for me to abscond to Costa Rica is about $5000, so you don't need to worry - we won't get that much.

Other facts:
1) If you raise $50 or more they will give you a T-shirt.
2) Carolyn is designing a Linda's Team T-shirt, which is stunning.  She will inform us of the price and how to order in due time.

To register or get more info, go to www.SummeRun.org.  Or call me:  360 201 1362

OH, DAMN!  I JUST GOT MORE INFO, AND ..... THE RACE STARTS AT 8:15 (!).  I'll have to talk to Florence and Carolyn about what to do. To be sure of getting there in time we would have to leave before 6:00 am.  Maybe we should just hold our own walk, in Bellingham.

NOT OC: Mother's Day

Linda with my mother (1985, top) and her mother (2005, bottom)

I am reading an article about a guy who investigates medical procedures and claims that many (most?) are either ineffective or at least based on flawed experimental evidence.  A crackpot?  Not really; rather, he is a professor at Stanford.  When I get the article digested I will publish my take as a Comment to my last posting, since it seems to fit there.  

P.S.  The Mothers are Hazel Beck and Marion Joyce.  Hazel was about 87 at the time of the picture; Marion was 93.

CANCER CELL CONTAMINATION: a set-back

Linda and the Prince of Darkness, 1978

I returned to Bellingham late yesterday to discover that I had forgotten to stop delivery of the Wall Street Journal.  Sarah, who minds the cats and sees that the house remains standing while I am gone, had placed them in a neat pile – all 39 of them, each with its own red plastic wrapper.  Bellingham is about to begin enforcement of a ban on plastic grocery bags, but the newspapers will still come enclosed in their own wasteful wrappings.  If I were a good environmental citizen I would cancel my newspapers, buy an iPad, and get my news through the ether.  Maybe I will.
 

Anyway, I happened on an interesting and somewhat discouraging article on the front page of the April 21^st issue.  It deals with the problem of “contamination” in the cell lines that some cancer scientists use in their work.  In the Henrietta Lacks book I read that her cells are a well-known contaminate, world-wide.  I somehow visualized her cells surreptitiously escaping from their container, wafting through the air to another cell line, diving in and taking over.  This article makes it less colorful: sloppy lab work, plus mislabeling.  An authority (several authorities, in fact) estimates that between 18 and 36% of all cell lines in use today are not what they are supposed to be.   The results are horrendous for individual cancer researchers and a set-back for cancer research in general

  As an example, one poor duck has worked on breast cancer for 25 years – using cells that probably are melanoma instead.   Apparently many others have discovered that the cells they were probing, rather than representing the cancer in question, were from Henrietta Lacks.  Another mix-up involves a cell line labeled MDA-MB-435, supposedly a breast cancer, being M14, a skin cancer, instead. 

 You can imagine the consequences of this sort of mix-up.  Not surprisingly, lots of these scientists are reluctant to admit that THEIR cells are contaminated, and moreover refuse to test them – even though, the Journal says that the test costs only about $200. Short-sighted, for sure, but completely understandable.

So what do we do?  Well, WE can’t do much of anything about cleaning up the mess.  What we should NOT do is cease advocating for funding of cancer research.  Fortunately, my group at the Hutch uses questionnaires and statistics more than cells, so we will continue to hold up our heads.

Now to the back yard to plant some onions and garlic.  The sun is out, the wind is calm, and there are no rain clouds in sight.  When these conditions describe Bellingham, better get outside and get with it.

      

BOOK REPORTS

                                                  In 1981.  Courtship time.  I was lucky.

I am in Cottage Grove, Oregon, drinking moderately priced red wine (for me “moderate” starts at $4.99), in an okay motel.  The name "Cottage Grove" suggests Mayberry, or perhaps something out of the Little House on the Prairie - but it isn’t.  Last time I was through here I saw a bumper sticker that read, “If it’s Tourist Season How Come We Can’t Shoot ‘Em?” Tonight  I was told not to leave my car unlocked, even for a few minutes.  I’m using the dead bolt.

I have been reading serious stuff lately, and perhaps it would be helpful if I made suggestions.  Previously I wrote that “The Emperor of All Maladies: A Biography of Cancer” was well worth the considerable effort needed to digest it.  I have read it twice, and I may go at it again in a year or so.  It is very hard work in places, but worth it.

Several weeks ago I finished “The Immortal Life of Henrietta Lacks”, by Rebecca Skloot.  This was a huge best-seller.  The NY times book reviewers positively dissolved it in drool.   It won some awards.  So --- why don’t  I like it?  Well, probably because it is more a description of a dysfunctional family and an (inexplicit) condemnation of the current state of education, than it is about science.  It is really two books:  the first about Ms. Lacks cancer and the preservation of her cancer cells, and the second about the painful way in which her family reacted to her cells’ immortality.  The first could have explained why Henrietta’s cells could survive and multiply while other similarly nasty cancer cells croaked in the test tube -  but it doesn’t.  I would have enjoyed hearing about how her cells were used, what they helped discover, why they are an almost universal contaminant in biolabs everywhere, etc., etc.  Probably most people weren’t looking for science, but I was.

The second book was about Henrietta’s family, and I found it hard to read.  Suffice it to say that, if our educational leaders are unable to bring even laggards into the 19^th century, let alone the 20^th and 21^st, they should look for another line of work.

The last chapter of Ms. Skloot’s book is, however, worth reading, because it helps to explain the modern obsession with privacy.

Right now I am reading an excellent book about the 1918 flue epidemic.  It has lots  of science, as well as some interesting history.  More about it later.