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Comment Re:graphical Harvard museum effort not available (Score 1) 72

When the American Museum of Natural History in New York redid the fourth floor exhibits about dinosaurs, they chose to arrange the specimens in a tree-like structure representing their phylogeny (well, subject to the constraint that it's basically a big loop with a few bumps and nooks and crannies.) At the time (this was the late 1990s,) it was controversial because most museums grouped specimens by function (carnivores, herbivores, etc.) instead of by their evolutionary path. In fact, the AMNH welcoming film to the dinosaur floor (the Meryl Streep-narrated one) really does quite a nice job explaining the tree and the museum visitor's path through the tree as they walk the halls.

Comment Re:graphical Harvard museum effort not available (Score 1) 72

It's really too bad that the fabulous museum exhibit display Deep Tree isn't more broadly available. .

Aha, happy to be mistaken and outdated on this one- I looked and found that now there is a web page via NOVA with a good interesting subset of the data. It's nicely done and at the DeepTree link at this link.

Comment graphical Harvard museum effort not available (Score 2) 72

It's really too bad that the fabulous museum exhibit display Deep Tree isn't more broadly available. There is a lovely display, with graphical interface, which is just enchanting to wander through much of the tree of life. It does a great job conveying the scale of the diversity of life and the boggling number of species, and it's aimed at the general public. It has nice pinch/zoom/etc. touch-screen functionality on a table-sized display. Unfortunately, for years, there was exactly one place on earth where you could play with it: at the Harvard Natural History Museum. And unless you are there at a particularly empty time, you will have to squeeze a fair number of kids out of the way to actually play with it for more than about two minutes. Now, things have improved a bit and it looks like there are a grand total of four museums that have the exhibit. (You should visit if there is one near you, try to avoid a time when school field trips are likely to be there!) The development was supported by a $2.3 million US National Science Foundation grant so public money was used to develop it, and it seems feasible to implement it or at least a scaled-down version of it on what are now much more common multi-touch displays like tablets or at least be available on the web, but as far as I can tell, it's been years since the grant and still the only place you can use it is in these four museums. I see this as a missed opportunity for a dramatic broader impact on understanding evolution and the scale of the diversity of life.

Comment available current data overstates non-vaccinated c (Score 1) 616

One of the issues that isn't addressed in these debates is the poor data about truly unvaccinated children. One thing to be aware of is that some of the "personal belief exemption" data may have some flaws related to poorly-interpreted data. In some cases, it may overstate the presence of anti-vaccination communities. That is, some of those listed as PBE are still vaccinated but nevertheless chose the "PBE exemption."

I know of at least a dozen fully-vaccinated children in public school in an affluent school district in California, whose parents are scientists, engineers, and medical researchers, who have moved to California for work. Enrolling a child in a California public school is a often morass of paperwork. In particular, there needs to be documentation of vaccination or you need to select the "PBE" exemption. (Or other exemptions, including the genuine medical exemptions for compromised immune system, etc.) The requirements of documentation are onerous, particularly for people who are busy getting settled with new housing, new jobs, and many other issues. Vaccination records from an out-of-state doctor are generally not considered sufficient. It is possible, upon moving to CA, to get new primary care physicians for your children, make appointments, and get the proper certification. However, that takes a good deal of time (months in many communities) and is considered by many people a waste of resources. A number of school administrators recommend to arriving parents that rather than deal with the documentation (and keep their children at home until the paperwork is all sorted out), they merely check the "PBE" box on the form, which takes one second and no money. The "personal belief" was simply that the documentation was overly onerous for people who had better things to do than waste time satisfying unusually specific documentation requirements.

The media reports of "anti-vaccination communities are common in affluent school districts" may instead be merely that a number of affluent school districts have clued in the new arrivals that they can avoid trouble by claiming the PBE. A school district where the enrollment staff informs people about the PBE option as a way to avoid paperwork appears, when looking at the data, to be a school district filled with anti-vaccination morons.

There is much more reliable data about incoming kindergartners- these children, sometimes new to school of any type, are generally already California residents with California doctors, and the chance that a PBE exemption for them does indicate that their parents are nutballs is much higher. But the overall data needs to be viewed with a more critical eye.

Comment Re:"Beneath Apple DOS" was available then (Score 1) 211

My memory was that the scrolling Terminator listings were assembly source code from Nibble magazine. I'm not sure what particular program, but it was a very recognizable format even when it just flashed on the screen briefly. I think there was some checksum code that came with the printed Nibble magazine that could you could check to make sure that you'd typed in things correctly. So I was probably one of the few people in the theatre who was amused that just as the Terminator robot was about to hunt and kill something (or whatever it was), he appeared to be doing a quick check to make sure that the "Hunt and Kill Something" code that had been typed in from the magazine was typed correctly.

The internet is good at these types of things: here is a site with screenshots from the Terminator movie and indeed it was Nibble magazine source code, and the checksum program was KeyPerfect. The source appears at a quick look to be for some kind of disk utility, perhaps a RAMdisk or something. The code seems to be named OVLY (overlay?) and I recognize VTOC as a virtual table of contents on a disk sector.

Comment Re:"Beneath Apple DOS" was available then (Score 2) 211

My memory was that the scrolling Terminator listings were assembly source code from Nibble magazine. I'm not sure what particular program, but it was a very recognizable format even when it just flashed on the screen briefly. I think there was some checksum code that came with the printed Nibble magazine that could you could check to make sure that you'd typed in things correctly. So I was probably one of the few people in the theatre who was amused that just as the Terminator robot was about to hunt and kill something (or whatever it was), he appeared to be doing a quick check to make sure that the "Hunt and Kill Something" code that had been typed in from the magazine was typed correctly.

Comment "Beneath Apple DOS" was available then (Score 1) 211

There was Beneath Apple DOS, a fabulous book from the time which was invaluable for figuring out what was going on. My understanding was that Don Worth and Peter Lechner disassembled the shipped code and sorted out how things worked, with great explanations. Those were a great guide and helpful for writing all kinds of software. I suspect that a similar effort these days would not be resolved without legal intervention- I have no idea if they even asked permission or if it would have occurred to people that you might want to ask. (This PDF of the book says that Apple was not in any way involved in the book, did not endorse it, etc right on the title page.) Then again, the source code for important parts of the ROMS at the time (Woz's Sweet16) was distributed with the computer in hard copy manuals. I learned a great deal from reading the Sweet 16 source for that and also from Beneath Apple DOS. Beneath Apple DOS wasn't full source code, but it did explicitly identify what blocks of code did what in a way that made it easy to understand what was going on and how to change things.

Comment National Science Foundation disruption (Score 3, Informative) 1144

As a researcher in mathematics, I am fortunate to have a great position and supportive research environment. I still get a paycheck and my day-to-day life continues more-or-less the same, but there are a number of thoughtless consequences indirectly for me, mainly due to the National Science Foundation being currently unfunded. My NSF grant money was delivered some time ago to my grants office and I can spend money as usual for my postdocs and students, so it isn't affecting me there directly. Instead, we have the following consequences:

  1. The NSF webpages are down. That means no reports on existing grants can be filed, not a big deal. But it also means that no new grant submissions can be filed. There are many deadlines in the fall and this is usually a very busy time for grant submissions. I expect that deadlines will be shifted, but that is a huge hassle as in my fields, generally there are once-a-year deadlines and there is a big buildup and plan to time things around the deadlines. Deadlines are carefully distributed throughout the year to avoid congestion with grants offices and to avoid proposing researchers getting overwhelmed. That is all out the window with no idea about how things will be resolved.
  2. No NSF review panels are meeting. In my fields, being asked to do a panel is both an honor and a serious burden. It is a lot of work to read proposals, often in related areas not exactly in areas of primary expertise. Twelve people are asked (per panel) to consider dozens of proposals, each hundreds of pages long (total, most of the important stuff is in about 50 pages.) These are essentially volunteers, top-level researchers from around the world who feel it is important to choose wisely which researchers are funded. Panels are scheduled to meet at the NSF with travel arrangements made by them. Generally it is a very intensive time with tight timelines. All of that is on hold. No new panels are being scheduled, existing panels are in limbo despite people having already read proposals and begun to evaluate them, and panels that already met can't have any further progress on funding decisions. Scheduling panels is a pain and there will be massive congestion and chaos once things get going again, assuming there is again a budget.

To my mind, these are a big disruption. For people in the lab sciences whose funding is disrupted, projects that have been ongoing or building up can be seriously affected. For people whose funding record will have a big role in their hiring, tenure, and promotion situation, this is a huge stress-inducing situation.

Blegh. This is a completely unnecessary disruption to thousands of scientists and researchers. Science research funding in the US has always been a pain, even when things go smoothly. Excellent researchers have left for Europe over the years due to frustrations with the NSF system, and things like this will exacerbate that problem.

The National Institutes of Health (NIH) research grant system is even larger scale and is also totally on hold, with consequent disruptions. And with the life sciences, uncertainty in projects can be more problematic as it is often harder to put things on hold. I feel sorry for people whose funding needs to be renewed, is under consideration, or needs adjustment now as this is a huge hassle.

Comment Re:Alternative Metrics (Score 4, Insightful) 273

Good summary, speaking as another tenured faculty member. There are a number of things which are not addressed in the study which complicate any analysis:

  1. Younger tenure-track faculty tend to rarely teach introductory courses as large lectures in institutions I have been at. Generally, young, untenured faculty are given teaching reductions during their probationary periods to focus on research and getting grants, which are the primary determinants of whether or not they get tenure.
  2. Tenured active researchers who are enthusiastic and productive about their research generally teach less overall and are less likely to teach intro courses. There are some active research faculty who relish the large-lecture environment and the "showmanship" aspects that it entails, but in my experience those are not typical and most researchers prefer to teach upper-division and graduate courses.
  3. From the study The freshmen who got the biggest boost tended to be less academically qualified students, judged by SAT scores and such, in the hardest subjects. To me, this indicated that the talents being measured are reflective of more basic level information, and perhaps related to improving student organization and study skills. Some adjuncts are excellent at giving the structure and feedback that weak students need (their livelihood may depend upon such skills) whereas other faculty may not have the patience to help get poorly-prepared students up to speed, and their livelihood depends upon other skills such as research, mentoring graduate students and postdocs, and so on.

The first two points result in a biased sample- tenured faculty teaching intro classes may well be dominated by "dead wood" faculty who have to teach more because they are no longer as productive in research, and are more likely to teach intro courses. I have been in departments where one strategy to get unproductive faculty to retire is to assign them to large intro lectures for non-majors. That is not a recipe for learning success and may be sufficient to bias the results downward as seen in the study. It appears there is just one institution in the study (Northwestern, a private university in the American midwest) and if that is a common practice there, that makes the whole thing pretty moot.

Another point is that it does take a while for junior faculty to find their teaching footing, particularly in the large lecture-theater classes. Often, small changes in administrative or organizational methods have a big impact on how happy the students are or how much time they put into the class. With greater instructional experience, particularly in large lectures, it is not surprising that a seasoned adjunct instructor may do better by these metrics that a hotshot excited untenured researcher, no matter how enthusiastic the latter is.

Comment excellent criticism from knowledgable rail expert (Score 2) 533

There is a great discussion from Alon Levy at Pedestrian Observations. Alon is a mathematician who is very knowledgable about transit issues and rail alignments in particular.

In stark contrast to most media (which seems incapable or disinterested in addressing the engineering issues and is basically repeating a press release) he has a number of specific issues:

  • The cost per mile of construction estimates are way too low, probably by a factor of 10.
  • At the planned speeds or even a fraction of them, the alignments would result in much higher passenger G-forces than any existing transit (although lower than many roller coasters) (.5g allegedly for Hyperloop, although it isn't clear how they could keep it that low, versus less than half that for Shinkasen and less for European HSR.
  • The throughput is completely unrealistic
  • The energy use estimates are not fair comparisons
  • The increased speed would not result in significantly faster times than traditional HSR to downtown destinations, due to Hyperloop ending in Sylmar, quite a distance from LA.

Comment sharelatex and scribtex good options (Score 1) 160

Two good options I'm surprised that haven't been mentioned are sharelatex https://www.sharelatex.com/ and a former rival (now subsumed into sharelatex) scribtex https://scribtex.com/ Both are a "Google Docs meets LaTeX" solution that work well for various settings. I've had good luck using them with student collaborators who may not want to learn all the ins and outs of LaTeX for a joint project but who can edit text, draw figures, etc. and learn at least some of LaTeX without just starting with a blank page. They work well with the main features being that they are TeX-aware and the collaborators can just edit online and then typeset to PDF online without having to install TeX, style files, BibTeX, various graphics packages etc. on their own machines. The "diff" capability and the "revert to version of July 15" features are great when working with less-than-expert-LaTeXers as there are inevitable screwups and it has served me well both for writing academic papers with students and for collaborating on research grant proposals with people who give blank stares when the word "github" comes up. It is a great improvement over the "one author has the token and people email each other the latest version" method that is quite common and usually results in a couple of screwups along the way.

Comment Re:TeX for Math (Score 1) 300

Absolutely- the proper typesetting gave airs of polish and correctness. The effect is long-gone now, but I do remember seeing mathematical preprints, typeset nicely in TeX, which had as the first line something to the effect of: "Warning: although this looks like a final result, do not be fooled by its appearance. It is really preliminary and should be gauged as if it were haphazard handwritten scribbles rather than polished typeset mathematics." These days people are used to seeing all kinds of mathematical tripe typeset nicely (perhaps generated automatically, in fact) so those kind of disclaimers are no longer needed!

Comment details matter, unclear (Score 1) 44

It's hard to tell from the summary or article what is going on here. I suspect a decent fraction of these may be people submitting proposals under different programs for similar or overlapping projects. Sometimes a scientific project will kind of fall between programs and people will submit more-or-less the same proposal to two different parts of the NSF, hoping for funding from one. Given the low funding rate and the great deal of uncertainty about funding (thanks, oh-so-functional Congress!) it is pretty common for people to submit to multiple programs or to have several co-Principal Investigators, each with a component of a larger-scale project. And people definitely recycle their earlier proposals, funded or not. There are also often required sections on ``broader impact'' that are important in many fields that may not have much in common with the specific proposal and may be copied from other proposals. To me, there is a huge difference between ``self-plagarism'' or duplication, between recycling a broader impact statement from a colleague, and between outright plagiarism, unknown to the person who is being copied, with genuine scientific theft of ideas. From what is described, it sounds like they aren't yet distinguishing between these cases.

There was a good description on the arXiv about good plagiarism detection methods and tuning parameters for efficient detection of duplication and plagiarism, applied to a good part of the body of arXiv submissions. That algorithm is run now, which is why you see those ``article has significant text overlap'' messages, detailed here.

Comment Re:Why tenure? (Score 1) 193

Thanks, and I agree that many associate profs do just continue full-strength out of momentum and self-motivate. The system and general academic research culture encourages complete devotion to your research and you get used to it. Going into academic research is a terrible idea if you don't truly love what you do, and get your own internal rewards from research success as well as the external ones.

Glad you like the username, I have fond memories of the Apple ][, though that was a while ago. I have a lot of brain cells still (uselessly) remembering old commands...

You've been Berkeley'ed!