Not being part of the rumor mill

I had something happen today that made me stop and think. I repeated a bit of ‘knowledge’ – something science-y that had to do with a celebrity. This was a factoid that I have repeated many other times. Each time I do I state this factoid with a good deal of authority in my voice and with the security that this is “fact”. Someone who was in the room said, “really?” Of course, as a quick Google check to several sites (including snopes.com) showed- this was, at best, an unsubstantiated rumor, and probably just plain untrue. But the memory voice in my head had spoken with such authority! How could it be WRONG? I’m generally pretty good at picking out bits of misinformation that other people present and checking it, but I realized that I’m not always so good about detecting it when I do it myself.

Of course, this is how rumors get spread and disinformation gets disseminated. As scientists we are not immune to it- even if we’d like to think we are. And we actually could be big players in it. You see, people believe us. We speak with the authority of many years of schooling and many big science-y wordings. And the real danger is repeating or producing factoids that fall in “science” but outside what we’re really experts in (where we should know better). Because many non-scientists see us as experts IN SCIENCE. People hear us spout some random science-ish factoid and they LISTEN to us. And then they, in turn, repeat what we’ve said, except that this time they say it with authority because it was stated, with authority, by a reputable source. US. And I realized that this was the exact same reason that it seemed like fact to me. Because it had been presented to me AS FACT by someone who I looked up to and trusted.

So this is just a note of caution about being your own worst critic – even in normal conversation. Especially when it comes to those slightly too plausible factoids. Though it may not seem like it sometimes people do listen to us.

Maybe Mild Buffalo Chicken Bites

I had a problem- I had a craving for buffalo chicken (wings or pieces or something, but you know- with the sauce!) but I have kids who have varying levels of tolerance to heat, from 0 to just a little bit is OK. So I did what I love to do sometimes when I’m cooking and looked at about 4 different recipes then combined them to make what I wanted. Most recipes for buffalo chicken have a sauce that is based on Frank’s Red Hot hot sauce- pretty much a non-starter for me. So what I did was to get a lot of the same flavor without using the hot sauce, partly based on some other recipes, partly based on what I thought should work. I’ve now tested this recipe once after writing it down and it seemed to work just fine. An added bonus is that you can separate the sauce prior to serving and mix in as much hot sauce as you’d like for the heat lovers in your family!

Maybe Mild Buffalo Chicken Bites

Sauce

  • ¼ cup butter
  • ½ cup tomato sauce (I used tomato soup, which worked great- very smooth)
  • 3 T red wine vinegar (to taste)
  • 1 t garlic powder
  • 1 t onion powderDSC_6480
  • 1 t salt
  • ½ t mustard powder
  • 1.5 T smoked paprika
  • 1 T yellow mustard
  • 1.5 T maple syrup
  • 1 T Worcestershire sauce
  • hot sauce to taste

Melt butter in a saucepan over medium heat. When butter starts to bubble add onion and garlic powder, mustard powder, and paprika. Cook for another minute or two but do not overcook. Add remainder of the ingredients, whisk and cook for another 5-7 minutes.

Chicken

  • 1.5 lbs chicken breast cut into small-ish pieces
  • 1 t salt
  • 2 t smoked paprika
  • 1 t garlic powder
  • ½ t coriander powder
  • ½ c flour

Toss chicken pieces with paprika, salt, garlic powder, and coriander. Add flour and toss coating evenly. Place in a single separated layer on a well-oiled pan. Place in 450° F oven for 10 minutes. Flip each piece over and cook for 4 more minutes.

Remove from oven and put in bowl. Toss with about 2/3 of the sauce and serve. Mix in extra/any hot sauce to part of the sauce here to adjust heat if you’d like.

Chopped the chicken in fairly small sized bites.

Chopped the chicken in fairly small sized bites.

Coated chicken ready to go in the oven

Coated chicken ready to go in the oven

Cooked chicken bites should be browned on both sides.

Cooked chicken bites should be browned on both sides.

The finished product served with celery stalks, ranch dressing (should be blue cheese, I know), and pan fried potato chips. YUM!

The finished product served with celery stalks, ranch dressing (should be blue cheese, I know), and pan fried potato chips. YUM!

 

 

The first day of the rest of your career

I remember well what that day felt like. Actually there were two days. The first, most exhilarating, was when you went into mortal, hand-to-hand combat with a bunch of seasoned veterans (your committee) and emerged victorious! Well, bruised, battered, downtrodden, possibly demoralized, but otherwise victorious! After years of toil, and months of writing, and weeks of preparation, and days of worrying you’d survived, and maybe even said something semi, halfway smartish.

Then there’s the graduation ceremony. The mysterious hooding. It has to be special because it’s a HOOD for god’s sake- and nobody knows WHY! (OK- I’m sure there are lots of people who do know why if I’d bother to Google it, which I won’t. Leave the mystery). Your family and/or loved ones afterward to welcome you and elbow you saying (slyly) “Doctor?” Feels awesome.

When the smoke and mirrors clear and the buzz has died down you might ask yourself: what next? Most will already have a post-doc lined up but not everybody. But even if you do your newly minted PhD isn’t the entire world. Let me tell you what that amazing, splendiferous, wholly unmatched in the history of science-dom PhD looks like to a future employer:

Square One.

This is the first day of the rest of your career. Revel in it. Be proud of it. But know what it means: a foot (barely) in the door. No doubt a very important foot in the door- but it’s just so you can compete in the next round(s).

PhD_comic2

The work-social activity: How not to be exclusionary

“We definitely don’t want to be exclusionary here. We just want to be selective about who we invite.”

A couple of years ago my friend from work and I started going out for beers at local brewpubs, often on Friday afternoons after work. After we’d done this awhile I started inviting others from work- first post-docs working with me, then others working on projects I worked on. These became semi-regular, maybe once a month, and I gave them a name: Mad Scientist Friday Afternoon Beer or MSFAB. I gathered a list of usual suspects who were on the email list when we had one of these and included “Please feel free to invite anyone you’d like along too” in the emails.

At some point I realized that this disclaimer/invite didn’t cut it. The MSFAB had taken on a bit of a life of its own. Not that it is so popular or anything, but we have a group of maybe 10-12 people who have shown up more than a few times. I didn’t want to be exclusionary, but realized that by selecting a group (casually done as it was) that I was at least in danger of setting up an exclusionary situation.

You might think- “this isn’t a big deal, just some guys going for drinks after work”- and you’d be partly right. But I realized that these kinds of work-social activities are where a lot gets done. People meet in a relaxed environment and talk about projects, proposals, ideas, as well as things non-work related. Social connections forged in this way can have a large influence on how work is done, who goes to who when they have funding

"Curse you tiny beer!"

“Curse you tiny beer!”

opportunities, etc. This is important stuff. This is also the stuff of back room deals and old boys clubs.

So, my intention is to be inclusive if people want to come. But if I leave it up to social connections to get word out this semi-organized fun activity does run the risk of becoming exclusionary and cliquish. So I’ve started to change how I handle these invites. I try to cast a broader net. These are still work people that I have a connection with, but I don’t limit my list of people who are specifically invited. My email now still has the “invite friends” message, but also has an opt out message: if you don’t want to be on this list just let me know.

In a way it is impossible to not be somewhat exclusionary – I often find myself unable to schedule one (and would be unable to attend if I were an invitee) because of family obligations – but making it as inclusionary as possible is a good goal. Of course this is most pertinent to recurring activities and I’m not trying to make a work-social activity into a fully work activity and suck the fun out of it.

The intention of these outings is to build work connections and teams and to bring different people together in new ways- well, actually MY motivation is so I can drink good beer with a group of interesting people on the occasional Friday- but the rest is important too. So I’ve made a short list of some things to keep in mind for these kinds of activities (really just notes to myself as I’ve been developing my thinking about this topic).

  1. Think about it. Awareness that this could even be an issue is a good startpub_photo_3
  2. Be inclusive. Don’t simply be not exclusive.
  3. Be diverse. Don’t assume that people wouldn’t want to be included because of your preconceptions about their gender, culture, religion, or any other factor.
  4. Allow an opt-out. If people don’t want to be contacted tell them it’s OK.
  5. Be fun. This isn’t a duty or a job, it’s just being reasonable and thinking about other people.
  6. Don’t worry too much about the mixing and interpersonal relationships between people you might invite. This really isn’t your problem to fix and leads to cliquishness.
  7. If you are a manager or otherwise responsible for other employees make it as clear as possible that this is an optional, fun, social activity and that attendance is completely optional (if it is- if it’s not then it’s not really a social activity, it’s work). Actually if you’re a manager you should be extra careful with all these things.
  8. Be welcoming. When someone new shows up say hi and provide some introductions where appropriate.

I think this is actually the tip of a larger iceberg very pertinent to several different important topics- but I’ll let these be an exercise to the reader. Please leave any comments below.

Spaghetti plots? Sashimi? Food-themed Plots for Science!

For whatever reason bioinformaticians and other plot makers like to name (or re-name) plotting methods with food themes. Just saw this paper for “Sashimi plots” to represent alternative isoform expression from RNA-seq data.

Sashimi plots: Quantitative visualization of alternative isoform expression from RNA-seq data

That prompted me to post this from my Tumblr http://scieastereggs.tumblr.com (growing collection of funny bits in scientific publications):

————————————————————————————————

Spaghetti plots? Lasagne? OK then I can do rigatoni plots

This possibly somewhat satirical paper makes the case for “lasagne plots”, following on the spaghetti plots that are popular in some fields for representing longitudinal data. Lasagne plots are presented as an alternative for large datasets though the authors state: ”To remain consistent with the Italian cuisine-themed spaghetti plot, we refer to heatmaps as ‘lasagna plots.” The remainder of the paper is a pretty straight-on discussion and demonstration of why and when these plots are better than the spaghetti plots.

Lasagna plots: A saucy alternative to spaghetti plots

Bruce J. Swihart, Brian Caffo, Bryan D. James, Matthew Strand, Brian S. Schwartz, Naresh M. Punjabi

Interestingly, a recent paper reimagines heatmaps as “quilt” plots (though less satirically so). This opens whole new doors in the thematic renaming of methods for plotting data.

(h/t @leonidkruglyak)

But, in keeping with the Italian cuisine-themed spaghetti and lasagne plots: Now introducing Rigatoni plots!

(no pasta was harmed in the making of this plot. Well, OK. It was harmed a little)

Need to show outliers? Tasty, tasty outliers? No problem! (thanks @Lewis_Lab)

(capers. They’re capers)

via Spaghetti plots? Lasagne? OK then I can do rigatoni plots.

What peer review feels like

Sometimes, getting reviews back on a paper feels a bit like this. I’ve actually had this happen, reading through reviewer 1 and 2’s comments and feeling pretty good. Then scrolling down to find the last reviewer has totally chewed it up. Surprise!

Of course, reviewer 3 is (most of the time) not an actual person/reviewer position- but rather represents the bad, unfair, or just plain wrong-headed reviews that we frequently get on papers and grants. Sometimes the part of reviewer 3 is played by the editor too. And sometimes reviewer 3 is actually right.

 

Reviewer3Attack

The uncanny valley of multidisciplinary studies

This was inspired by a conversation with a colleague today who suggested the term, as well as a particularly thorny paper that has now been in review for going on two years, and has been reviewed by four journals (and one conference)- and of course the wonderful xkcd for the format. Ugh! Sometimes it really does feel like I’m a zombie. A multidisciplinary undead. Blarg.

Arrgh - I'm a zombie. Brains!

Arrgh – I’m a zombie. Brains!

Here’s a link to the Wikipedia entry on “uncanny valley“. It’s from robotics and it describes how robots make us feel increasingly uncomfortable, uncanny, as they get more and more human like. It’s not a completely appropriate analogy to link it to publishing computational biology studies, but I think it actually makes a lot of sense. From the reviewers’ point of view the methods, language, format, and sometimes even goals of a multidisciplinary paper become more and more foreign as they move further into the territory of the other field. If they are too far one way or another they won’t be seen by the other side’s reviewers. Of course, there are those reviewers who are completely familiar with the middle ground- we’ll call them zombie-lovers, who have no problems. But getting a review like that is an exception rather than the rule.

What if fuel efficiency followed Moore’s law

At current rates by the year 2026 we will be able to drive, on average, 37 miles on one gallon of gas in the US. Wow. If that number strikes you as underwhelming then just consider, as a comparison, growth in the computer industry over a corresponding time period. Most portions of the computer industry have followed Moore’s law, a doubling in speed, capacity, efficiency every one to two years. This has proceeded since the 1970s to today, pretty much unabated.

Historical fuel efficiency trends in the US

Historical fuel efficiency trends in the US. Note that on the scale from the graph below, this would be a straight line.

PC hard disk capacity (in GB). The plot is logarithmic, so the fitted line corresponds to exponential growth.

PC hard disk capacity (in GB). The plot is logarithmic, so the fitted line corresponds to exponential growth.

My late grandfather, Gideon Kramer, was a very forward thinker- a futurist even. He was not very tolerant of lack of progress in some areas. He would have said “there’s just NO EXCUSE for this kind of thing”- actually, I think he probably did weigh in on exactly this issue. But really, IS there an excuse for this kind of thing? I’m sure there are sound practical reasons why fuel efficiency hasn’t increased much- at all- since before the 1970s. Even the most cutting edge fuel efficient vehicles, hybrids, and electrics don’t really do all that great. But there were likely very sound practical reasons why humans would never travel into space, never come close to eradicating polio and smallpox, we would never have hand-held communication devices with computational power unimaginable 30 years ago in our pockets. And yet we have done all these things.

So this raised the question: What if fuel efficiency DID follow Moore’s law? Where would we be?

If fuel efficiency in the US started following Moore’s law, with a doubling time of two years, in 1980- about the same time the computer industry really took off, we would have been able to drive from LA to New York on 1 gallon of gas in 1994. By 2002 we could have climbed in our cars, driven around the WORLD, and THEN had to refill our 1 gallon gas tanks. In 2009 we could have driven our cars to the moon- the frickin’ MOON- on, you guessed it, 1 gallon of gas. By the year 2026 we would be able to drive to the SUN- 93 million miles- MILLION MILES- on 1 gallon of gas. (this was, I should mentioned, not overlooked by Gordon Moore himself).

Calculations based on a doubling time of two years.

Calculations based on a doubling time of two years.

 

 

 

Here’s another way of thinking about it. If I drove 25,000 miles a year, which is about twice the national average, I would be able to buy a car- put one gallon of gas in it and drive it for forty (40) years without refueling. This is making a couple of assumptions- the first being that engine life would also follow Moore’s law and my car would actually last that long, and the second limitation is that the gas in the tank would actually go bad long before it got used up. In a few years we would be able to hand down the family gallon of gas to our kids and grandkids- a family heirloom that could continue to be used by generations to come.

So don’t get the wrong idea, not everything in the automotive industry has failed to follow Moore’s law. Apparently the tire pressure used in cars has obeyed Moore’s law, albeit with a longer time period for doubling. Really. That’s the best you can do automotive industry?

Clearly, there are technical and theoretical reasons why fuel efficiency hasn’t followed Moore’s law and probably can’t. However, it seems clear that the potential for fuel efficiency in vehicles is simply not being realized. Is this due to technical or practical constraints, or just simply because the demand isn’t there? I tend to believe that we just don’t want it or need it bad enough to make it happen. But I believe we can do better and we will be forced to in the near future.