Archive for: November, 2015

Do I need to say more [Coffee Drinkers edition]?

Nov 18 2015 Published by under Uncategorized

I shall keep the very large title pasted from the journal CIRCULATION:

Association of Coffee Consumption with Total and Cause-Specific Mortality in Three Large Prospective Cohorts


I shall also keep the list of authors and the links to their articles

Ming Ding;Ambika Satija;Shilpa N. Bhupathiraju;Yang Hu1Qi Sun;Jiali Han;Esther Lopez-Garcia;Walter Willett;Rob M. van Dam;Frank B. Hu*

It is worth noting that Dr. Hu has 111 hits when you click on his link. Dr. Hu is a Professor of Nutirtion and Epidemiology at Harvard SPH. He received his PhD in 1996. That is less than 20 years ago. I know that 111 pubs is not so much in epidemiology. Not because I am an epidemiologist with over 100 pubs. But  I know epidemiologists. It used to be that all you need was one or two big papers (like the original epidemiological study of breast cancer and your career was made). Now you have to publish 100 of those papers to get your h-index up that high.

Anyway, I do not come to bury Dr. Hu, but to praise him:

From the abstract:

Background—The association between consumption of caffeinated and decaffeinated coffee and risk of mortality remains inconclusive.

This is true. And a source of great gnashing of teeth and rending of clothes.

Methods and Results— blah blah blah.

So, I have extracted the important points for you from the methods and the results:

N= 74,890 women and  93,054 women and 40,557 men.

The data includes 4,690,072 person-years of follow-up.

That's 4.6 million years of follow up. I do not want to live 4.6 million years. Probably 2-3 million would be sufficient for all I want to do.

In this time 19,524 women and 12,432 men died.

One presumes these deaths were not from terrorist attacks but from various natural causes. Since the study was based in America, and Indigenous Peoples are a very small part of US population (one source: listed as American Indian/Alaska Native are 0.9% of the US population, or in combination with other races, 1.7%; the US Census lists AI/NA as 1.6%), one can assume that most of these 200K+ people had some immigrant ancestry, and someone at some time decided that it was OK to let them into the country despite what was perceived as their inferior "stock" at that point. Just saying. Most of us can trace our roots back to somewhere else, and ultimately, we're all from Africa anyway and ape-ish ancestors (~10^6-7 years) at that. Just a bit of perspective.

Now on to the important stuff:

Consumption of total, caffeinated, and decaffeinated coffee were non-linearly associated with mortality. [my bold] Compared to non-drinkers, coffee consumption one to five cups/d was associated with lower risk of mortality, while coffee consumption more than five cups/d was not associated with risk of mortality.

There's more there - about smoking and decalf vs. calf. You can read the whole thing if you like. But, to the main point:

Significant inverse associations were observed between coffee consumption and deaths due to cardiovascular disease, neurological diseases, and suicide. No significant association between coffee consumption and total cancer mortality was found.

It's good to know that coffee is neutral on cancer. But the suicide point is important.

Conclusions—Higher consumption of total coffee, caffeinated coffee, and decaffeinated coffee was associated with lower risk of total mortality.

I consider this to be carte blanche to consume up to five cups of marvelous stuff. I just wonder if triple espressos count as a one or three.

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Quote of the Day (my life in chaos version)

Nov 17 2015 Published by under Uncategorized

I have so many great ideas. For posts. For projects. For grant proposals. For more projects. For teaching improvements.  hahahaha. Here is a quote from Leonard Bernstein that seems appropriate:

To achieve great things, two things are needed; a plan, and not quite enough time.

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More on choosing a mentor

Nov 13 2015 Published by under Uncategorized

I just received a link from GWIMS (Group on Women in Medicine and Science, part of the AAMC- Association of American Medical Colleges) for the GWIMS Toolkit. This toolkit is:

a series of presentations designed to provide practical guidance on a variety of topics relevant to women faculty in academic medicine. Each presentation provides an overview of the topic, relevant best practices, tips on implementation, and useful references for more information. We encourage you to share these resources with interested colleagues at your organization.

First, much of the information is valid for sub-disciplines other than academic medicine and life sciences. I think these pages are public, and anyone can go and download any of the toolkits, which are pdfs of presentations. One of the ones announced today is "How to Identify Mentors Committed to the Professional Success of Women in Medicine and Science". I'm not sure that I can immediately link to the pdf, but you can go to the toolkits link above and use that. They make a couple of good points that are worth emphasizing (hence this post as a follow-up to the last). In places it gets wordy & academic-ese, but its easy to skip. For example, they list three different roles: a coach, a sponsor, a counselor.  I don't think the lines among these is particularly obvious (advice on personal/professional life vs general career guidance?).

It is important to figure out what you want or need from a mentoring relationship. Ask yourself, "with what do I need help?". Sometimes, its just someone to listen to you without comment (such people are often called "friends"). Sometimes its someone to teach you how to pipette better (such people are often called "postdocs"). And sometimes its a template to write a letter for a job application. The main point is that rather than feeling a vague need that is difficult to articulate, thinking about what you want and need may make finding it a lot easier. This applies to shopping in a grocery store, also.

One minor point on one slide about finding mentors underlies a whole world of trouble.  If you are junior faculty, your department chair can and may function as a mentor. However, using the person to whom you report, i.e., your direct boss, as a mentor can present a problem because of "potential conflict of interest".  I think every PI is rife with COI. It can be especially tough when, as a young PI, you need to produce papers/grants/data and you rely on your trainees. You are training them, but they are also "working" for you. Therein, of course, lies thousands of tweets about the abuse of Postdocs and the perversion of the NIH system to provide cheap labor. I had a discussion years ago, with a good department chair, who really supported women and really wanted to mentor them. But he also had to evaluate all the junior faculty and I tried to explain that for some aspects of mentoring that by nature of his role as "boss", they just weren't always going to be comfortable in coming to him. I remembered this the other day when talking with my postdoc. He's on the cusp of leaving the lab. Of course I want him to stay, he's brilliant and hard working. But of course I want him to go get a great job and establish his own lab. For me, the best I can do is point out that I have this COI, and make him aware that I see both sides. At the end of the day, COI is almost always there when you work with other human beings, as they almost always have their own agendas. Those agendas may or may not overlap or conflict with your agendas. Caveat emptor.

Here is the list of tips for searching for a mentor:

  • Look for individuals as mentors who enjoy their roles and responsibilities
  • Look for individuals as your mentors who are experienced yet willing to listen to your concerns and needs
  • Look for individual mentors with whom you can build a relationship on trust, mutual respect and confidentiality
  • Consider any personal and/or professional biases that they may bring to your mentoring relationship

This all may be obvious, but reading it once and sticking it somewhere back in your hindbrain is worthwhile.

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quote of the day: choosing an advisor or mentor

Nov 11 2015 Published by under Uncategorized

Erma Bombeck was a thing way back when. A housewife-humorist with a column about suburban life. When she strongly supported the Equal Rights Amendment in the 70s, a lot of more conservative papers pulled her column. She was also a breast cancer survivor, but didn't talk about it. Here is a quote of hers I came across about "spouse shopping"

People shop for a bathing suit with more care than they do a husband or wife. The rules are the same. Look for something you'll feel comfortable wearing. Allow for room to grow.

 Leaving aside the problems with the concept of "spouse shopping", or rather using shopping as a metaphor for choosing, I think the same applies to finding a thesis or postdoc mentor. People, students or trainees, are concerned with the specific topic and whether they are going to work on a particular problem that has caught their interest. There is nothing wrong with using that as a first criterion for narrowing the field.

But far more important are a host of other factors that have nothing to do with the actual science being done in the lab.

What is the reputation of the mentor? How do they treat their trainees? How often does the mentor talk with the trainees? How much is the mentor around to talk to trainees. Does the mentor's style match yours (do you need to talk with them all the time, would you rather be left alone to work out problems, how do you feel about micro-management)? You can find these things about by talking to the trainees. You can ask some pointed questions along these lines. You can also ask more subtle questions: what is the turn-over in the lab? How long did the last phd student/undergrad/post doc last? Will the mentor ask for the current trainees view of applicants? How does authorship work in this lab?

Ask yourself: am I going to learn something new, even if I'm going to Lower Podunk University instead of The University of Big Swinging Genitalia? Will a project I do in this lab make me more employable, make me understand science better, help me work on those bigger things that interest me?

In short: can you see yourself being comfortable in this lab? Is there room for you to grow?

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Being a Friend

Nov 06 2015 Published by under Uncategorized

The words "friend" and "community" and "ally" get thrown around a lot. I've got a lot of responses to the various deep thoughts that I read on the matter, but they generally fall into two categories. The first is the scrooge response of "screw them all". The second is the ultra-scrooge-response "really screw them all". No, not really. I guess it can be unicorns farting rainbows. Just not often.

One of my oldest and most wonderful friends sent me an upworthy article. We joke that we have to be friends, because we know where the bodies are buried. One of the nicest things about getting older is that there are people in your life that you have known for 20 or 30 years.

Here is the link to the article she sent me. It got past my scroogy-little heart. In part because it demolishes one of my least favorite things to hear: "everything happens for a reason". No one who has lost someone, really lost someone to death, departure, disease, or drugs believes that. Of course you can grow from bad things, but that's not why it happened.

My personal model of the universe is that it is a very, very large dice game. Any individual event can be traced from proximate to more distal causes. This person chose to have a drink or six and get in his car and drive recklessly through the streets, and arrived at a particular corner at exactly the same time as this other person crosses the street. We can follow the path backwards to the decision to drink and why that happened in this person's life. We can follow the path that made the other person leave their apartment at exactly the wrong time, deeply thinking about something that had happened the day before. We can look at what happened the day before and the problems that the alcoholic had. But, to the outside world, to me moving through life, and importantly to each of the people involved, its just chance, a throw of the dice, that the other arrived at exactly the same place at exactly the same time.

If by "things happen for a reason" you mean that trace of events that led two people, one of them drunk and driving the wrong way up a small street at a dreadful speed, to be in the same place, then yes, there is a reason. But that's a trivial interpretation of "for a reason" If you, however, say this to the spouse or the parent or the child of the person who was killed, it may be true in the most trivial sense, but it is cruel beyond reason.

Say you discover someone you were supposed to protect was being abused years ago. It happened despite your conscious and instinctive efforts to protect. In fact, at the time all your efforts went well beyond what your "friends" think you should have done. "It happened for a reason" sounds awfully like:  "You fucked up. You are a dreadful person". You didn't know. It isn't an excuse. It is what was at the time. (Let's not argue about "really knowing and pretending" versus "not knowing". There's a range there. Accept what I'm saying here.) That someone, particularly a young person, should have suffered for a reason that involves grown-up growing up, is beyond contempt. Justifying this on religious grounds (your deity has a greater purpose for you, and using this child as a pawn so you can progress in life) is the ultimate relinquishing of what makes us human: responsibility for one's own life in the face of that randomness.

The randomness of the world makes it cruel. There are billions of people doing things for their own reasons that have nothing to do with whatever reasons you have for doing things. And sometimes people intersect, at random. What the person who lost needs to hear is not some admonishment to grow. They do not need to be told to let the event sink in as a fucking good thing.

One of the quotes from the article:

But loss has not in and of itself made me a better person. In fact, in some ways it's hardened me....  my pain has never gone away, I've just learned to channel it.

This is so very true. I have gotten harder as I get older. The part of the message that hit me hardest (and I think the message from my friend):

I've grieved many times in my life. ... The ones who helped — the only ones who helped — were those who were simply there.


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quote of the day

Nov 04 2015 Published by under Uncategorized

I like video games, but they're really violent. I'd like to play a video game where you help the people who were shot in all the other games. It'd be called 'Really Busy Hospital. - Comedian Demetri Martin

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Women of the Supreme Court

Nov 03 2015 Published by under Uncategorized

I am a big fan of the Supreme Court as an entity. It has huge power, and tends to get overlooked, except when they're appointing a new justice.

I am particularly a fan of the Notorious RBG (see here and here).

There is a new picture / painting of the women of the Court. It's very nice and all. They look very good, and serious and like people you'd like to be making important decisions about the future of, well everything.The Four Justices by Nelson Shanks


But here are some pictures of them at some thing celebrating (this picture?). In this first one, the three sitting justices actually look like they are having fun.

supreme court women


But this one? I want to party with Sotomayor. She reminds me of a good friend, who in fact, is a marvelous person. The notorious RBG looks like my sister when I am talking too loud in public.

supreme court women2

Here are a few links to read about the Supreme Court.

10 cases that impact all of us. Easy to read and easy to understand.



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