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November 19, 2013

MathCAD and Livescribe Desktop on a Linux Machine

I"ve finally found a version of Linux that meets most of my needs, out of the box, without a lot of fuss. Meeting "all my needs" requires the occasional use of Windows programs, either by dual-booting to Windows or running Windows in a virtual machine. Neither was very difficult; see below.

I've been using WIndows and Microsoft Office for many years, but have been finding them increasingly annoying, with "updates" that were worse than the versions they replaced -- forced on us by their use of new file formats (docx, etc.), GHz computers running slower than MHz computers used to because of all the bloatware, etc. Sticking points in earlier versions of Linux I've tried were:

* Support for two monitors on my desktop PC, one requiring rotation for portrait mode.
* Support for WiFi on my Acer Aspire One netbook.
* Support for a few Windows-only applications, notably MathCAD and Livescribe pens, which record handwritten notes in a proprietary format, which can be exported to PDF bitmap images and text or spreadsheet files, as I've discussed before.

Linux Mint handled both of these with ease.

On my desktop, I decided on a dual-boot configuration, to keep all my old XP programs, settings, and files, for now. I followed these instructions, using a $6 Linux Mint 15 MATE DVD from OSDisc.com.

Linux Mint comes with LibreOffice, which handles some things (e.g., importing from various spreadsheet file formats) better than Microsoft Office. It even imports and exports docx, which I suppose will just enable people to keep using that evil format. I'm not sure .odt is better, though. If I can't edit a document file with a plain-vanilla text editor, it's harder to process it with Python.

I also used Linux Mint's package manager to install VirtualBox, installed Windows XP within VirtualBox, and installed MathCAD (one of the few Windows programs I can't do without) on the XP virtual machine. I couldn't get the VirtualBox version of XP to use my second monitor, but if I need two monitors for a Windows program I can still boot to my old copy of XP. Within Linux Mint itself, setting up the two monitors and rotating one was easier than it had been in XP.

I used the same DVD (and an external drive) to replace the aging operating system on my Acer Aspire One with Linux Mint, encouraged by this video. Mint seems to connect to Wifi faster than Linpus did, though other operations seem slower. Mint found my video camera but not the microphone, so I may have to use an external headset for Skype or Google Hangout -- but I couldn't get either of those to work at all with the previous operating system. Mint doesn't respond to tapping the touchpad either, but the buttons work. The netbook seems to lock up more often than it did with the less-capable older version of Linux, so I may be pushing the limits of what you can do with 500 Mb of RAM.

Maybe these minor problems can be solved, but I'm really impressed by how well Mint worked out of the box on both desktop and netbook.

Getting Livescribe Desktop working was a bit of a challenge:
* Installed VMware (may be possible with VirtualBox, but maybe harder)
* Installed WindowsXP as virtual machine, from original CD.
* Installed .NET framework 2 (otherwise Livescribe Desktop installs, but won't run)
* Downloaded and installed Livescribe Desktop.

Once I did all that, it was able to upload and display pages from my Livescribe Echo smartpen, a very useful tool for lab notes, as I've discussed elsewhere.

November 17, 2013

Evolving-multicellularity lab exercises

If you're a teacher looking for a couple of great lab exercises on the evolution of multicellularity, see this website.

Why did it take so long for unicellular organisms to evolve multicellularity? Is evolving even simple multicellularity (groups of cells staying together, with little or no division of labor) so difficult, perhaps requiring several simultaneous mutations? Or were conditions such that there was little or no advantage to simple multicellularity?

My colleague Mike Travisano and his postdoc Will Ratcliff (my former PhD student) reasoned that selection for rapid settling through liquid would favor clumps over individual cells. Sure enough, they were able to evolve simple multicellular clusters from unicellular yeast, in less than a month. Mark Borrello and I participated in the discussions and were coathors on an open-access paper describing this work. This paper generated a lot of interest, as I've discussed previously.

If simple multicellularity can evolve so easily, why did it take so long? One explanation is that rapid settling in liquid wouldn't usually have been beneficial. What factor(s) would give simple clusters of cells a reproduction or survival advantage over single cells? One possible advantage would be resistance to predation by larger single-celled organisms. A brilliant pioneering paper by Boraas et al. (1998) showed that, faced with predation, unicellular algae evolve simple multicellular clumps that are too big for the predators to eat. An earlier post links to a movie Will Ratcliff made, showing a unicell-gobbling rotifer "flinching" when it encounters a multicellular yeast cluster.

Last summer, high-school teachers Tami Limberg and Nicholas Beerman worked with Will to develop a lab exercise showing how predation can favor multicellularity. Will's snowflakeyeast.com website has all the information you need to 1) evolve multicellular yeast, or 2) explore the effects of predation on multicellular versus unicellular yeast.

Will is starting a faculty position at Georgia Tech. Ryoko Oono, my other recent PhD student, is starting a faculty position at UC Santa Barbara. The only other person to earn a PhD with me so far is Toby Kiers, who has just accepted a University Research Chair at Vrije Universiteit Amsterdam. Past results do not guarantee future results.

November 1, 2013

Time for a grand bargain to fire bad doctors, bad teachers, bad politicians, and bad CEOs?

In response to today's article in the New York Times discussing differences in skill among surgeons -- and reader comments asking why dangerously incompetent surgeons are allowed to keep working -- I am reposting below my 2010 essay on analogous problems in various professions.

Retention based on seniority is, in effect, a conspiracy between teachers' unions and people for whom lower taxes are more important than quality education for the kids in their community.

This post is inspired by two recent New York Times stories. One reports the battle between teachers' unions (favoring pay and job retention based on seniority) and educational reformers who want pay and retention to be based on other criteria, such as student test scores (Brill 2010). The other story reports that some incumbent politicians in the US lost primary battles to challengers in their own party (Zeleny and Hulse 2010). This is news because it hardly ever happens.

I want to make two points. First, US teachers and US politicians are in similar situations. Once they've been in the job for awhile, they can be hard to get rid of, even if their performance falls well below average. This is also true of university professors, medical doctors, and business executives, although pay in those occupations may depend more on current or past performance than it does for politicians or teachers.

Second, random changes to the current system could make things worse rather than better, for an economic reason I haven't seen discussed. More-thoughtful changes are another story.

How do poorly performing people manage to keep their jobs in these very different occupations? For teachers, basing retention on seniority makes it difficult or impossible to fire a poorly performing senior teacher, even if their contract doesn't explicitly promise the life-long employment that college and university professors typically enjoy.

What about politicians, doctors, and business executives? For politicians, seniority often translates into committee appointments that let them funnel government money ("pork") to their districts. So voters are reluctant to oust them, even if they are corrupt or incompetent. Business executives often appoint the boards that determine their salaries and job retention. Bad doctors (Kolata 2005; Leonhardt 2006) are presumably responsible for more than their share of the 120,000 Americans a year who die each year due to medical errors (Levy 1996), although fully 84% of all doctors can't be bothered to change their gloves to keep from transferring pathogens among patients (Yoffe 1999). But, like rapist priests, having to move to a community with less oversight is about the worst bad doctors have to fear.

Before eliminating tenure, seniority, or incumbent-politician advantage, however, consider their positive aspects. I would argue that the rights of incumbents to continued employment are trumped by those of thousands of students, citizens, stock-holders, or patients, but that doesn't necessarily mean we should reduce employment security.

If security of employment isn't a right, it is certainly a major perquisite. So, if we reduced the job security of teachers (or doctors, etc.) we would need to increase salaries or other benefits to attract equally qualified applicants. (And don't we want even more-qualified applicants than we have now?) Retention of teachers based on seniority is, in effect, a conspiracy between teachers' unions and people for whom lower taxes are more important than quality education for the kids in their community.

As alternatives to tenure or higher salaries, we could consider perquisites that would particularly appeal to the sort of person we want to attract to teaching. Consider sabbaticals. Someone who is really excited about teaching French or in biology might take a job that paid for summers in France or expenses to participate in lab or field research, even if their salary were lower.

Suppose we eliminate seniority as the sole criterion for retention? How would this affect the type of people who apply for teaching positions? It would depend on what the new criteria are.

Letting principals or deans fire teachers or professors at will would select for ass kissers. Furthermore, we would have to raise taxes, to pay more than the many lucrative ass-kissing positions in the private sector. A fellow faculty member once suggested that my project would get more money from the dean if I started going to his church. Someone else suggested that a major reduction in our budget might have had something to do with my public criticism of the dean's biotechnology-only approach to hiring. I don't want to believe either of those claims, but I was glad that I had tenure. If deans or principals could fire at will, students would be exposed to less diversity of opinion.

What about test scores as a criterion? If pay or continued employment for teachers depended on the absolute test scores of their students, then school districts with poorly prepared students would have trouble hiring any teachers at all, because they wouldn't expect to survive more than one year.

But why not base pay and retention on how a teacher's students perform on a test at the end of the year, relative to other students who had similar scores at the beginning of the year? This seems more promising, but it depends on the test. If the test were based only on memorization, than potential teachers who are good at helping students develop critical thinking skills or creativity would look for another profession. If there were tests that measured the full range of student's intellectual progress, however, then "teaching to the test" could be a good thing. This wouldn't be easy, but it might be possible.

University faculty are hired to produce new knowledge that benefits society, not just to transmit existing knowledge. It's probably easier to set minimum expectations for this function than it is to evaluate the quality of teaching in specialized fields. The quality and quantity of published research is already a major factor in determining pay raises for university faculty. But, if a professor hasn't published for several years, maybe he or she should be fired. Again, this risk would make university positions less attractive, so we would have to increase salaries or improve working conditions, to attract people as qualified as the current pool.

Similar arguments apply to other professions. Term limits are a really stupid idea, given the real benefits of experience. But reducing the ability of more-senior politicians to direct funds to their states would reduce the incentive for voters to re-elect a politician who is not representing their other interests. Pay-for-performance for doctors seems like a good idea, but it should be based on long-term patient outcomes, not numbers of procedures performed. Business executives would take a longer-term view if much of their compensation came in the form of dividends from stock that could never be sold, and which reverted to the company on their death. If the company prospered over the long-term, they'd get dividends for life.

The key point is that the criteria we use to determine salary and job retention will affect what type of people are attracted to a job, as well as how motivated they are to excel.

Brill S. 2010. The Teachers' Unions' Last Stand. New York Times 17 May.
Kolata G. 2005. When the Doctor Is in, but You Wish He Weren't. New York Times 30 Nov. 2005.
Leonhardt D. 2006. Why Doctors So Often Get It Wrong. New York Times 22 Feb. 2006.
Levy D. 1996. Medical groups act to curb errors. USA Today, 14 October 1996 .
Yoffe E. 1999. Doctors are reminded,' wash up!'. New York Times 9 November 1999.
Zeleny J., and C. Hulse. 2010. Specter Defeat Signals a Wave Against Incumbents. New York Times 18 May.