Tuesday, August 27, 2019

bad science

In my last post, I noted that there were, among the projects, a number of studies of how family history affected risk of various diseases. These were built around some methods that Liz and I developed for querying genealogical databases, primarily the Utah Population Database, fondly referred to as the UPDB. The UPDB provided huge numbers of connections between people over multiple generations, but was hit-or-miss with the disease data that was needed to connect people with the same condition. The cancer data was excellent, thanks to longstanding connections to the statewide cancer registry. Heart disease, stroke, diabetes, Alzheimers, and many (most) others, though, were only available with the help of clinical enterprises, most of which had financial and competitive interests that frequently impeded research.

Over time, we developed some approaches that allowed for reasonable conclusions to be drawn about smaller clinical datasets, and a steady trickle of physicians brought data to us for analysis. Among these were a number of fine physician-scientists with whom it was a pleasure to work.

Not all of them, however. Shortly before we left Utah for Louisville, I worked with an ophthalmologist who had a fairly typical clinical series of patients with age-related macular degeneration, a leading cause of visual impairment and blindness among older folks.

As was the norm, I identified the relatives of his patients, including which of them were also affected, and computed the relative risks (compared to controls), and the usual supporting statistics, wrote the bulk of the Methods and Results sections of the resulting paper, and contributed commentary about the wider implications. For some reason he felt my contribution was not worth noting, however, and he sent off his draft, got it accepted and published, without my name on the author list.

If you're not listed as an author, of course, you don't participate in any correspondence with the journal or its editors. Nor is it the practice of any university oversight committee to query all the faculty not listed as authors to make sure no one was left off the list. So I didn't see this paper until it came out. I wrote a strongly-worded email to this ophthalmologist (he's the senior author--the one listed last), cc'd to higher-ups at the university, and extracted a promise to revise the online publication to correctly reflect my contribution. The principle mattered more to me than this particular publication, and I promptly forgot about the entire incident.

Until I saw this headline. It seems that what goes round comes round, at least if you go far enough around. I especially liked this line from The Scientist: "Zhang’s poor record of disclosing conflicts of interest accompanies a sketchy past of putting patients and research participants at risk during his work." 

That and apparently being some kind of spy. In comparison, my beef about authorship is pretty small. But I think the view into his character afforded by that minor incident was clear enough, and I was not at all surprised that someone who can so easily step on a colleague has no compunction about abusing his patients.

[By the way, it's clear in the first link above that he lied about contacting the journal. Saves me the embarrassment of having co-authored a paper with him.]

Monday, August 26, 2019

Projects

The reality of my projects has been called into question--recently, but also on many prior occasions--and, as a more-or-less recently retired professor, I am here to defend them.

In academics, as in life, projects can take many forms. For me and many others in biomedical research, the classic pattern has been: 1) develop an idea; 2) do some preliminary research at little or no cost; 3) if the idea seems to have some support, try to get funding to do a larger-scale study; 4) publish the results; 5) iterate steps 3 and 4 for as long as possible, perhaps an entire career.

For the record, you can see how this looks in my case by clicking here. The number of publications is less important than the number of citations, which indicate that someone has read your paper and thinks that the research that they have done is in some way indebted to the previous work described in your paper. They may disagree vehemently with your conclusions, but they can't ignore your work. Scientific consensus arises from scientific argument; nothing gets you ahead in your career faster than disagreeing with the conventional wisdom and actually being right. Actually, "faster" isn't the right adjective. "Farther" is better. Lister, Mendel, Gallileo, McClintock, and many others did not achieve success in the short term. (The trick is that the conventional wisdom in science is very often right.)

I've started, finished, and contributed to all kinds of scientific projects over the years, ranging from assessments of the degree to which fallout from nuclear weapons testing caused cancer and other diseases in Utahns living downwind, to (many) studies of the utility of family history as a predictor of disease risk, to studies of molecular markers of aging . . . and numerous other projects inspired by collaborations with physicians, fellows, and students over the years.

The majority of projects don't get past step 1 or 2, but that doesn't mean they don't have merit. In fact, the early stages of putting together ideas and data, doing preliminary statistical analysis and seeing early results is usually more fun and rewarding than writing up papers for publication, preparing grant proposals, and even getting an award and making the dream project a reality.

At present, Liz and I are working on preliminary data and writing up results for several projects that have been or will be turned into grant proposals. We're doing this pro bono, which gives us the freedom to pick our spots and keep our priorities straight.

Of course I've had lots of projects over the years that didn't have anything much to do science: co-raising children, managing finances, house and yard maintenance, travel, pointless tinkering with electronics and software, etc.

Being a cancer patient is also a project--make no mistake: there are daily, weekly, monthly, and annual cycles of medications, blood tests, X-rays, and consultations. Every month requires a new prescription, a telephone order complete with nurse consultation, a check of the insurance status for said order, and a consideration of any travel plans for the next month, since a street address and delivery signature are required. The process is not especially hard or complicated, but it is always front and center and cannot be ignored.

And then, sometimes, I write about my experiences and associated thoughts. At Christmas I took all the posts from the beginning of this blog and formatted them into a book, to give to my mother and others who weren't going to be reading blog posts. The result was a slender volume of about 100 pages--not monumental, to be sure, but a satisfyingly tactile indicator of having done something.

Dog raising is another project. I'm pretty sure that it becomes less of a project as your dog becomes better trained. Suffice it to say that Sunny is still a small dog, but a big project.
And we've added a new project/family member: a tiny teardrop trailer ready for road trips. Mostly it won't require much work on our part, but I will need to improve my trailer-backing skills.



Thursday, August 15, 2019

N of one

It turns out that N-of-one trials are a thing. Back in the early days of this blog, I described the basic idea and naming principle--that my experience with treatment would be its own experiment, controlled to some degree by my pre- and post-treatment experiences.

I have been carefully recording many variables, but not quite with the rigor that would be required to do a formal trial. I've been focused on labs, and thinking about exposures, but haven't been good about recording exposures (diet, alcohol, probiotics, dog, travel, weather, etc.). I expect that, soon, N-of-one trials will answer lots of questions about how individual variation (in genetics, epigenetics, microbiome) interacts with exposures to make people sick (or not).

But the labs are good! Here's a picture, very much like the last (many) pictures, but produced by a website, all4cure.com, started by an oncologist who found himself diagnosed with multiple myeloma. The data transfers are definitely not as easy as they could be, but it's working, to what effect I'm not quite sure. The graphs are fairly nice, though.


I don't know how long this particular drug regimen will continue to be effective--no one does, because I was an early adopter. If Medicare and marrow continue to support it, I am not going to complain.

Thursday, June 13, 2019

Re-mindfulness

One consequence of the continuous chemotherapy regimen is sleeplessness. It's not extreme, and it can be managed with drugs that (probably) don't have terrible long-term consequences, notably Benadryl. But at certain points of the cycle, I can get almost exactly 4 hours of good sleep--and then I am awake, as if I'd just had a double Americano and a slap in the face.

Possibly because of previous experience with the above-named therapies, I am not distressed to find myself in this position at 3 or 4 AM. Sometimes I welcome the quiet and have thoughts that are useful and constructive. Sometimes I reflect on a dream (inevitably weird). Sometimes I can't be totally sure what I've got.

So--I have been introduced to the concept of mindfulness on many occasions, and it has always seemed like the right approach to pretty much everything in life. Especially to driving a car, though that is rarely mentioned. It also has, at various times, seemed just like some cultural buzzword worthy of derision by the broletariat. In any case, mindfulness is not always achieved (I suppose) even by its most enlightened practitioners, and is less often, rarely, achieved by those of us who practice whatever it is we practice.

One recent night, my eyes open in the dark, I thought about several specific moments when I should have been mindful but was not. The consequences of having not been mindful, the possibility that life might have been altered positively had I been so, etc.

Remindfulness! OK, maybe this has been done. I think psych therapists have spent some decades here. But maybe I could do a TED talk? Otherwise, watch out--there could be a whole lot blog posts on this theme. Sorry.

Thursday, June 6, 2019

Love Poems

The late 1970s was in some ways the ideal time to go to college. No one cared about anything (sex, drugs, and rock ‘n roll excepted). There was no war to oppose. There was no war to be called up for. The economy was a mess, but I remember few discussions of what people would be doing when they graduated, with the exception of premeds and the few aiming for Wall Street.

At some point, I found the pond to be too stagnant for my taste. I ran a two-line ad in the college paper that said something like “Tired of apathy? Join Bedrock!” and gave some contact information about a meeting. I think we got 8 people to that first meeting, only 3 were of which were my roommates. The agenda was to get people on campus talking about the global environment, cultural conflicts, energy and feminism.

The name Bedrock came from a poem by Gary Snyder. It’s a love poem, and I’m going to say I knew that, but I have it on better authority than that. I managed to arrange a visit to Kenyon by Snyder some months after founding Bedrock. He was giving a reading at Oberlin and all we had to do was get him a ride from Oberlin to Kenyon on the appointed date. I had a car and a friend, and we snapped to it. I think that was the only longish car trip my ‘73 Audi Fox ever made without breaking down, and I remain slightly, grudgingly grateful for that.

Gary Snyder was the first “famous” person I’d ever met. He’d featured (as Japhy Ryder) in Jack Kerouac’s The Dharma Bums, he’d won a Pulitzer for his poetry, and he was cool beyond belief. He had a hip flask of bourbon—he preferred Rebel Yell, but was settling for J.W. Dant while in Ohio—and he shared with us. Could be the first moment when I though bourbon was worthy of my attention. Oh well.

He asked me about the name Bedrock, noting that it was a love poem. Lamely, I explained that I was trying to establish some kind of foundation for even getting started to get people involved in thinking about what was going to happen next in the world and whether we could do anything to make it better.

He said: “Why the Hell are you guys so diffident?”

We were all that, but maybe that was the difference between 1978 Ohio and 1978 California, and the difference between him and us. And maybe this sounds even more lame, but I am proud of several moments in Bedrock’s history, notably when we had a great panel discussion (40 years ago!) of the conservative case for carbon taxes.

So, love poems. The Kenyon Review had just been revived during those years. I asked Philip Church, poetry editor of the Review, if I could do an independent study with him, and to my surprise he agreed. I had a set of poems I’d written, wrote some more, and met with him weekly in his office. He was generous in his criticism (probably this was not a good sign, although I didn’t get it back then), and we had great, wide-ranging conversations about music, evolution, and even poetry (Loren Eiseley was a touchstone for both of us).

One week I brought him a poem called “Scotch Symphony.” It was a memory of an event from late Spring of my Junior year, when a friend soon to graduate took me to a lake where great blue herons nested. The language in the poem was abstract enough to get Dr. Church intrigued. When I told him it was basically a love poem he was deflated. It did feature whiskey and birds as well, but I guess the love was problematic. To say the least, but that was not in the poem.

I’ve buried the lede again. Love is what it’s all about, people! As I’ve confronted my own mortality (sure I’ve been granted a reprieve, but all we’re--any of us--going to get is a reprieve of one kind or another), I’ve done a fair amount of reflecting on what all the noise and confusion of my life has amounted to: I’ve made some contributions to science, passed some genes on to the next generation, had a few transcendent moments in some sport or other, viewed some spectacular scenery, and so forth. The real experience of life, though, has been to love. The other emotions leave a mark, of course, but when I am lying in a bed and drawing my last, I am hoping to remember the love I’ve felt for all the others: family, friends, colleagues. Romantic love is its own thing, of course—I can’t compare Liz to anyone—whatever shape my brain is in by the end, I know right now that our love is flying out into the universe at 186,000 miles per second and can never be erased. I didn’t even write her a love poem until we’d been married 17 years, but I think there is other evidence out there.

The same goes for my children, both of them. If you truly love your partner, the love you feel for the spawn of that relationship is every bit as intense, if differently conceived. I don’t know how it is if you have less positive feelings for your partner. Might not make that much difference, but I’ve only experienced it the one way, and I am beyond grateful for that.

It’s certainly true that hateful people are frequently remembered long after they die. Who cares about them? We care because we don’t want to follow their example. We may or not be remembered—I would like to be remembered—but it will make no difference to we who are deceased. Better, I think, to feel love in your last moments. I’m going to try.

Sunday, June 2, 2019

CR



I made a quick trip to Mayo just before Memorial Day, a routine follow-up with blood and urine samples and a C/T scan to make sure my bones were still holding together. The original plan was to drive up to Rochester, with the dog in tow, and continue from there out West as far as Salt Lake City for a wedding and some long-overdue visits with friends. After a quick overnight test trip of ~200 miles, though, we decided that we couldn't do the dog-and-drive thing for two weeks straight without driving ourselves crazy, so we decided we'd better board the dog and fly. We're going to practice traveling with Sunny, and hope to get her as far as Wisconsin, at least, this Summer.

The visit to Mayo was happily uneventful, and confirmed the fact that I am still essentially disease-free at this point. My hematologist (third author on this paper) noted that I now meet the criteria for "complete response," and we figured that I've been there for about a year now. The kappa and lambda numbers keep edging close to one another, and both are in the normal range. The other lab values look fine across the board (platelets a little low, but not alarmingly so). Even my hard-pressed red blood cells have rallied to boost my hemoglobin up into the normal range. My bones are holding together, too--nothing new going on there.

Lots of patients would have treatment stopped at this point, but it's not something we're contemplating now. The "high risk" 17p deletion argues against stopping, as does the fact that I'm tolerating all the drugs pretty well. The only change is that I'll start getting Zometa (that's what's keeping my bones together) every 6 months instead of every 3 months. It seems to be making my teeth a little bit brittle.

The wedding, visits, etc. were great. We're not in the habit of enumerating friends, so it was kind of a surprise to me just how effortlessly we filled up every available minute of the week with great friends, while still sadly failing to see many others. We'll have to come back again soon.

Wednesday, May 15, 2019

Down to Earth

We've been back in Louisville for a few weeks now, absorbing the rainfall, and maintaining our so-far perfect record of not attending the Kentucky Derby.

I have been working a little medical mystery. I've become accustomed to a kind of gastrointestinal rhythm as the chemotherapy cycle rolls on. It's a 28-day cycle, with all the major drugs delivered on days 1, 8, and 15, and dexamethasone continuing on day 22 as well. All those days are Thursdays. The standard weekly pattern has been 2-3 days of constipation, followed by a day or two of something kind of "normal" (by chemo standards), and then a day or two of diarrhea. But it varies, and I've developed a tolerance for the variation that may be a little too tolerant.

Somewhere in the run-up to the wedding, it finally dawned on me that I'd had the diarrhea for a while, but not the constipation. In fact, the diarrhea was getting pretty bad, to the point where a longish dog walk could become a (mercifully--so far--internal) drama. I tried some probiotics, fiber (bad idea), and so forth. The impending wedding presented a potential Waterloo (sorry!), but the gods continued to be merciful and I thought perhaps the whole thing had passed.

When we returned to Louisville, though, the pattern resumed. Liz reminded me that Sunny tested positive for Giardia when we adopted her (Giardia can be transmitted from dog to human directly). She was treated at the time, of course, and tested negative afterward, but just try to stop a hound from drinking out of puddles, ponds, and the worst parts of streams. I have. I tried to schedule an appointment with my primary care doc to have a stool sample run. He couldn't see me for two weeks, which seemed excessive. His assistant suggested urgent care, or my hematologist. Urgent care seemed to be the better fit, so we headed over to a place we'd used before, conveniently operated by the same organization as my hematologist.

It turns out that this urgent care doc couldn't run a stool sample(!), because he couldn't do follow-up(!!), but he could prescribe flagyl, as if the Giardia diagnosis had been made (!!!). So he did. I bit my tongue, as I do, not being able to imagine how any critique of this system I leveled at him would get communicated back to the higher-ups at whatever meeting of whatever group he next attended. So I effectively agreed to do the experiment the wrong way around.

Meanwhile, it occurred to me that it was easy to get the dog re-tested. I picked up a stool sample kit at the vet's, and by the next day had a result back (cheap, too!)--negative for everything. Giardia was no longer looking like a strong contender, but I dutifully continued with my course of treatment, even though the early results were not promising. At my next hematology appointment, I asked if they could do a stool sample (they could), so I gave them one. C. diff. is the main concern for cancer patients, but hey, why not check everything? Negative there, too, although I'd like a little more detail on what exactly was tested.

Meanwhile, nothing has really changed, except my weight, which has declined, and my blood pressure, which has increased. I need to keep my fluid/electrolyte intake up, and take enough Imodium to manage my life in the interim. I have recently come to believe that the chemo cycle is the driving factor, probably the Revlimid (lenalidomide). The 28-day chemo cycle that I'm on is 3 weeks of Ninlaro + Revlimid, and 4 weeks of dexamethasone. Lately I've noticed that the 4th week has been better than the rest. Within the first 3 weeks, it seems the end is worse than the beginning. Within each of those weeks, I take Ninlaro at the beginning, and Revlimid every day, so the ratio of N/R declines through the week, and the diarrhea gets worse.

Tonight, as I was finding links to help with the technical stuff, I stumbled upon something that might explain the problem (if this were a podcast, I'd say it "rocked my world," but that seems overwrought in print). It turns out that Revlimid (for reasons I don't currently know) contains lactose. As a white guy, that wouldn't be likely to draw my attention, but it seems that I am lactose intolerant, according to
23andme:


Over the last few months, I've been trying to reduce my consumption of dairy products, with mixed results. but I had no idea that for 75% of each month I've been compromising my efforts (and paying handsomely for the experience!) with one of my go-to drugs.

I'll have a lot to discuss next week, when I have my annual follow-up review at Mayo.