A funny link from CPP

Warning, much offensive profanity to be found here, but useful if you have problems with people who like to write nasty comments anonymously.

Note that this is not something I'm in need of currently, nor am I asking for obnoxious comments. I just think that sometimes CPP's insane ranting stream of &*#$(#)@! is hilarious in a very un-PC way. I always find myself wondering if I met CPP in real life, would I know it was CPP?

Personality splitting.

Literally spent an hour writing a paragraph on a friend's FB page this morning, only to delete it after realizing it sounded too much like YFS and maybe not appropriate for FB.

Meanwhile, things at work are progressing in both potentially good and severely bad ways, leading me to wonder if I'm going to be leaving my current position even sooner than I thought. But I still think that if I leave, I won't be coming back.

Kind of sucks because I'd like to blog about it, but the whole anonymity thing is getting to me lately. I'm going to back to thinking I might compile a book, FSP-style, but also augment it with the details I couldn't blog about from my current position.

Still mulling this all over. Meanwhile, I hope everybody is having a good hump day.

It's the little failures every day.

Becca's comment that some people like to tell you

"It should work! It always works!"

on the last post made me think I should respond on the topic in general.

So, here is my feeling on the day-to-day failure we experience regularly as scientists.

Yes, most of the new things we do are not going to work consistently right away.

Sometimes they don't work for the first few tries, and then we tweak it a little and it goes.

Sometimes it works the first time, doesn't work for ten more, and eventually we completely change what we're doing to get it going again.

How we handle it depends on what kind of bench scientist you are. There are different kinds of people doing science (even if diversity could be considered an overstatement for some variables). Seems to me there are at least 4 different kinds of bench scientists.

1. Follows a protocol and it generally works.

These people are good at taking directions, even if they don't always follow them to the letter. They will often 'interpret' the protocol in such a way that makes it work, but they won't tell you that when you get the protocol from them. They might not even realize they're doing it. If you ask them why they do something a certain way or if a certain step is necessary, they sometimes have a rationalization, but they usually don't know.

They don't consciously vary their approaches or generate new ones.

However, they tend to get a lot done, so long as their project involves just cranking out data using mostly established methods.

2. Golden hands.

These people can make anything work. I can't say I've ever worked with one, but I hear they exist. According to legend, they have a deep understanding of fundamental concepts and can apply these to any problem on the fly, generating new methods as they go.

Personally, I'm not sure if I believe in the Myth of Golden Hands. I have certainly worked with some people who were very good at some things, and who knew their limits. If you needed help with something outside their area of expertise, they would tell you who else to ask. I guess this lowers their chances of exposing what they don't know.

I think this is smart- knowing your limits is important, even if people call you a "genius", enough failures will make people question that label.

Alternatively - and I have seen this - they themselves do not actually have The Golden Hands, but their wife (it's always the wife in this scenario) does.

Sometimes people know that it's actually the wife doing all the work, and sometimes they don't. It usually becomes obvious when the wife leaves her post as Supportive Tech to get her own PhD, or stays home with a new baby.

3. Sloppy struggler.

The sloppy struggler does not take good notes, so even if something works, this kind of person has no idea how to reproduce the result. They know how to do a few things, maybe because someone showed them repeatedly and they practiced a lot, but they aren't good at following protocols and they don't understand the basis of what they're doing. If something goes wrong, they're lost. They tend to extremes: either refusing to try any new methods, or trying new things all the time in search of one that works. They sometimes try to ask others for help, becoming leeches and pests.

Most of us go through this as a stage in training, but some never leave it.

If this fails, they refuse to ask anyone anymore and become secretive and paranoid.

Many of these people end up becoming PIs, because what they lack in bench skills they make up for by
a) working harder than anyone else, or at least putting in more face-time at the bench
b) charming the pants off the boss (and anyone else within range).

These are the ones who are later tempted to fake data or lie and say something has been reproduced three times, when it only gave the desired result once.

4. The bedrock.

These people often end up as career techs or lab managers, if not PIs. They keep all the lab protocols, they remember the history of where the techniques came from; what worked and what didn't. They troubleshoot because they don't have golden hands, but they are only willing to struggle for so long before they try to find an expert or co-worker to help them brainstorm other approaches.

They will usually take the time to show you how to do something, but usually not more than once. They will happily answer your questions, so long as you're not rude about it. They will say "I don't know" when they don't know, and nobody accuses them of having golden hands, because we all know they struggle like normal human beings do at the bench.

They often spend large chunks of their careers getting new projects off the ground, although the projects don't always work out and they don't always get credit for it. Without these people, science would not exist.

Eventually they all retire or leave academia to follow their spouse or take care of a dying parent. And then all that lab memory is lost, leaving behind the protocol books. If this person was the lab manager or career tech, they also leave behind a completely helpless PI.

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Having defined these categories, then, how do these different types of people deal with failures?

Follows a protocol tends to just repeat and repeat, assuming any problems are their own fault. There's a certain humility and patience here to be admired. But if that fails for long enough, they eventually will be called to the PI or the bedrock, since their sudden lack of consistent productivity will be noticed.

Golden hands, if such people exist, would presumably not need to ask anyone to help them troubleshoot. According to legend, everything they do always works, so they would never find themselves in this scenario? I guess if by some stroke of fate they ran into a problem they couldn't fix immediately, they would ask google or go back to their textbooks and figure it out? Secretly go find someone else who knows better? My guess is that they'd be most likely to drop the project, to avoid looking stupid. They would be most likely to declare that "it doesn't work" and most people would believe them.

The sloppy struggler has a serious case of insecurity, but they deal with failure by banging their heads against the problem. Eventually, if desperation peaks, they might make an effort to get organized; if they do, that usually prompts growing out of this stage. The sloppy struggler is usually his or her own worst enemy at the bench, and everyone else's enemy in the lab. But this often isn't realized until it is too late, particularly if the person has that lethal weapon of charm on their side. If they can get someone else to help them (by choice or by PI mandate), they will often exploit that person into doing their work for them.

The bedrock is used to failure, might have been a sloppy struggler or a protocol-follower in their earlier days. They pack it in for the night, go home and look some things up, maybe ask their friends over a beer what else they should try. And then they try again the next day. Failure is taken in stride; it's part of the job.

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Obviously, this is oversimplified for the purposes of analysis. Most of us have some of these characteristics, and deal with failures in more than one way. A lot of it depends on environment.

In the best scenarios, The Sloppy Strugglers would learn how to keep a notebook early on, and learn some humility about how to ask for help while respecting other people's time, and then much of the danger would be averted before it begins.

Follows-a-protocol would be taught to ask questions, forced to understand every step of their protocols and why they're doing it that way. This could build a good habit for the long-term, instead of just blind obedience.

Don't count on it.

We've discussed the possibility of more jobs opening up when the baby boomers retire.

Hasn't happened yet. Might not ever.

This beautifully written article in the Chronicle has quite a bit to say on the subject, and is well worth the time to read completely.

One excerpt on the subject of history repeating itself (because no one was listening the first time):

Mr. Ehrenberg thinks the majority of academic retirements will occur naturally. "I don't think colleges are going to be in such a hurry to kick people out," he says. He and others say that young Ph.D.'s should not count on a windfall of jobs as their elders turn emeritus. Cost-conscious colleges, for instance, could shift some jobs off the tenure track. And past predictions of waves of retirements helping out the academic job market have flopped: A major study published in 1989 by William G. Bowen, then president of the Andrew W. Mellon Foundation, predicted that colleges could face severe faculty shortages by the end of the 1990's, largely because of retirements. But the expectations raised for an improving job market in the arts and sciences did not materialize.

I think there is no way these retirements are going to happen naturally. The numbers just don't add up. Scroll to the bottom of the article for several useful tables citing percentages of institutions that say they want to recruit new faculty (96%) but are clearly not thinking about where they'll put us how we'll be paid, since many fewer institutions say they are thinking about retiring old faculty (19%).

How can that be? Here's another excerpt explaining why this is more of a problem now than ever before:

The average age of retirement in the general population is 62. But in academe, faculty members appear to be retiring at 66, on average, and that age is drifting upward, although retirement data is not always as crisp as demographers might like. The August telephone survey found that about one-third of those responding expected to retire at age 70 or later. The ability of colleges to enforce a mandatory retirement age of 70 ended in 1994, when an academic exemption for a federal age-discrimination law expired.

Maybe the academic exemption wasn't such a bad idea. Maybe they shouldn't have retired it!

Screw you guys, I'm staying home.

Got a much-needed pep talk from a friend today who insists I should start on the job application process, even as I'm agonizing over publications, publications, publications.

So I swore I'd try to get in the mode of moving forward, not worrying about past mistakes, not being afraid of the worst possible outcomes.

Bite the bullet, make the leap, that sort of positive thinking!

But then I checked my junkmail folder, and found that an abstract I submitted a couple months ago for a meeting got assigned to a Poster.

I am somewhat amused that my email program knew exactly what to do with an email like that!

I hate posters. And this work, IMHO, deserves to be presented in a talk.

And I always hate this meeting.

So I'm thinking I'd rather not go.

It's supposed to be good to go to these things, for networking, blah blah blah.

But this meeting is big enough that it's really hard to meet anyone new.

And most of the people I know who go religiously every year are people I don't really ache to see. You know how it goes, you go out and drink with them because that's what you're supposed to do, but you find yourself having to drink just to numb the pain of having to talk to them?

Yup, this is one of those meetings that makes me question if I'm in the wrong field. It's that bad. It's one of those meetings that makes me remember why sometimes I really hate scientists and science.

So I think I'll take a line from Cartman on Southpark and just skip the whole thing.

I'd much rather stay home and like science than go to this meeting and hate it.

It will be the second abstract I've withdrawn this year for lack of getting picked to give a talk, so I'm wondering if that looks bad.

Somehow I doubt anyone who relegated me to poster status would even care.

What is academic freedom?

In response to a comment on the previous post, and a note in the
Chronicle of Higher Education about a professor at Virginia Tech who used the massacre as a example in a lecture and then got reprimanded for it, let's use this as an excuse to talk about academic freedom.

Oh, and let me just say that the idea of locking the doors of all the classrooms at Virginia Tech seems a little extreme in some ways, and just common sense in others. Thoughts, anyone? Would you want to be the student or the teacher if there was a chance you could be trapped in the room if there were a real emergency?

In science, academic freedom is usually not nearly as complicated as it is in the humanities.

I think the best recent example is the dispute about whether or not to teach evolution (science) vs. "intelligent design" (humanities).

With the separation of church and state, one might expect that religious studies would be kept out of public schools, but it's not quite so black and white as that.

Although it was never explicitly described to me in any lecture or textbook while I was in school, I always understood academic freedom to be the freedom "to study what you want."

Maybe this also includes "to lecture on what you want" and "to publish what you want", but my understanding is that in most cases it doesn't include those two things at all.

Nor does it include "to get funded to work on what you want."

I guess in the ideal situation, parents would never complain, and no one would worry about what anybody else worked on. Maybe in a scenario where money was endless and jobs and schools were plentiful?

So, not what we have right now.

I'm a little puzzled by this commenter who says you can't have academic freedom until much later in your career. I presume what is meant by this is that, until you're really established, it can be extremely difficult to work on anything outside the mainstream, be that alternative hypotheses or totally weird systems like some kind of primitive octopus.

There aren't any rules saying you can't work on what you want, except for the kinds of rules that say you shouldn't be using some stem cells (thank you, President's religion).

And you shouldn't be implanting them into animals or people without approval, or working on P3 level viruses without a P3 level containment facility. That kind of thing that is as much in the interest of safety as it is research.

Seems to me that in public schools, and especially in the humanities, it can be much more gray. Some books, at some schools, are considered too racy. Etc. But again that gets back to restrictions on teaching, not on studying.

Here is the Wikipedia definition, which basically says that a range of activities should be covered in pursuit of knowledge, which I take to mean that lecturing and publishing should be allowed, but then they add this clause about avoiding controversial matter unrelated to the subject.

And I love the line where they say that tenure protects academic freedom. That made me laugh.

Use your power for good, tenured people, not evil!

So how do you define controversial? Is this stuff about not teaching evolution really controversial, or is it just a bunch of fanatical nonsense? Should we take it head on as a serious threat, or just try to maneuver around it and outlast it?

Should we be moving to Canada? At what point do we declare science in the US lost to the religious nutjobs?

Q: What's controversial?

A: Ever read the comments on this blog?

note added in proof: when trying to publish this post, I got an error I've never gotten before: Your request could not be processed. Please try again.

What, so the censor can get a better look at it? Or did I say something controversial??

Fact-checking and Freedom of Speech

Had an interesting chat yesterday with a friend who heard a recent NPR report on how- i.e. the mechanism of - journalism has degraded to the point of widespread inaccuracy.

This is third-hand, but apparently many media sources are now requiring 'story quotas' from journalists, which creates pressure to 'produce'. I'm not sure if there's any metric for quality of these stories- it would appear not.

This got me thinking about how public media is not that different from scientific media, and how some of the changes proposed recently would make scientific publishing more like public media sources.

We've discussed here on many occasions how arbitrary scientific peer-review can be. If you happen to get 3 reviewers who know your senior author, for example, and they all think he's a great guy, your paper- however stellar or crappy- is much more likely to get into Top Tier Journal than if your co-authors are all nobodies.

Similarly, it's much more difficult to get a High Impact paper if you're a nobody, or if everybody hates your boss, because the bias among all scientists seems to favor prior reputation over the current data at hand. Why reward someone you hate for a job well done?

It's probably a weakness inherently human and psychological that even scientists can't rise above in our supposed Supreme Objectiveness.

Having said that, what if we let everyone publish everything in One Big Journal, and then let everyone comment on everything, and posted all the comments for everyone to see? Kind of like One Big Science Blog (with the obligate filter for obscenities, a.k.a me, for this site).

If we assume that scientific discourse will follow a similar path to public media sources (and I'm including both mainstream and 'alternative' sources in that group), we can assume a few things will happen:

1. The amount of information available will skyrocket.
2. The amount of crappy information will also skyrocket.

Anybody want to come up with an equation to determine whether those two things are at all interdependent? That would make for an interesting math problem.

Anyway, the question on everyone's mind is, how are we going to sort through all of the crap to get to the good stuff?

I've seen the following three behavioral responses from scientists at all levels:

1. Scientist reads Almost Everything.
2. Scientist reads Almost Nothing.
3. Scientist reads only what's absolutely required- i.e. only what's directly related to their own area of research.

We've all been all three of these at various times, but I'm most concerned about #2. We really don't want very many - or any- scientists like that getting advanced degrees. Or, god help us all, their own labs.

But isn't that what the average American is doing these days? Most of us have stopped watching the news because it either

a) has no worthwhile content
b) is totally inaccurate
c) is too depressing.

And doesn't that also apply to most of the science publishing out there?

I've taken to watching Face the Nation and Meet the Press on Sundays, and listening to the occasional short burst of NPR or CNN when I'm lucky enough to flip by the station when they're actually reporting news. It's not enough, and if it were my job to be aware of wordly goings-ons I would be in big trouble.

But I'm also way behind on my reading for work. I'm too busy during the week and can't face doing it at night or on the weekend, the way I did in former years.

There are a variety of highly biased resources for keeping up with literature, like Faculty of 1000. Less biased tools have what I call a high 'clutter-factor' or CF, such as having journals email you the new table of contents (TOCs) every week or month when the new issue comes out. Another method with a high CF that hasn't worked well for me is having journals sent to my house ("I"ll read them on the toilet!") instead of to my lab.

The point of all this musing is the alarming conversations I've been having with people at all levels lately, wherein it becomes frighteningly obvious that most scientists don't read outside their immediate area at all. PIs are gifted at appearing to know all the latest research- because they go to meetings, but they don't know it in any depth.

The interesting side-effect of this is that most PIs don't know whether the correct controls have been done unless they're threatened enough to wait for the paper and examine it in detail. So PIs go around dropping names and results left and right, without ever bothering to verify the verity of their claims.

This feeds back into the media frenzy style of news communication- where word spreads like gossip, without any supporting evidence, and without any fact-checking.

So my question is, are we as scientists lacking the right to express our freedom to speechify? Shouldn't we be allowed to run off at the mouth like everyone else does?