"Your mamma's so dumb she can program in Arduino!"

Interesting and slightly amusing letter from IEEE Spectrum Editor-in-Chief Susan Hassler:

Dear Members and Readers,

Please accept our sincere apologies for the headline in today's Tech Alert: "With the Arduino, Now Even Your Mom Can Program." The actual title of the article is "The Making of Arduino."

I'm an IEEE member, and a mom, and the headline was inexcusable, a lazy, sexist cliché that should have never seen the light of day. Today we are instituting an additional headline review process that will apply to all future Tech Alerts so that such insipid and offensive headlines never find their way into your in-box.

Spectrum's insistence on editorial excellence applies to all its products, including e-mail alerts. Thank you for bringing this error to our attention. If you have any additional comments or recommendations, do not hesitate to contact me or other members of the editorial staff.

Sincerely yours,

Susan Hassler
Editor in Chief
IEEE Spectrum

[ the article that caused the fuss: http://spectrum.ieee.org/geek-life/hands-on/the-making-of-arduino ]

Why symbiosis is not a good example of group selection

[ In a Google+ post, someone asked whether symbiosis was a good example of group selection. I responded in a comment, and another comment asked me to expand my response a little bit in my own post. So here is a copy of that post (with a few more hyperlinks). ]

Part 1: What is group selection?

Typically "group selection" doesn't cross species boundaries. That is, group selection refers to the proliferation of a particular form of a gene, otherwise known as an "allele", due to its benefits to groups of individuals which share that allele despite the individual costs of having that allele. It may help to consider the basic group-selection argument for the evolution of altruism (i.e., the evolution of behaviors that are costly to an individual and yet beneficial to a different unrelated individual). Before that, consider why we wouldn't expect altruistic alleles to have strong representation in a population.

For every gene or group of genes, there can be many different variations (alleles). Some of those variations will be deleterious to an individual, and so you would expect the relative representation of those deleterious variations to decrease over generations. So imagine if one of those alleles encoded an altruistic trait that caused an individual to do something costly for the benefit of another (e.g., helping a stranger understand group selection with no expectation of future payoff). Individuals with that allele are suckers. Those without that allele instead focus on tasks that return direct benefit to themselves, and that direct benefit would payoff with greater productivity of offspring that share that non-altruistic allele. When an altruist met a non-altruist, the benefit from the altruist would increase the non-altruist's alleles representation in the next population while decreasing its own alleles' representations. So we would expect that altruistic alleles would fade away into obscurity. Moreover, the benefit from all of the altruists would diffuse across the variety of alleles rather than being concentrated on just the altruistic ones.

However, what if that altruistic allele also encoded a behavior that would seek out others with that same allele. This non-random association means that each individual who helps another does actually help to increase the productivity in that allele. That is, even though there is a cost to the individual doing the altruistic task, the benefit going to the other individual is felt by the other copy of the same allele in the different (and unrelated) person. So when these altruists group together, altruistic benefits do not diffuse. They are captured within the group. Moreover, the group's synergy can cause it to be more productive than the remaining groups of non-altruists. Consequently, the altruistic allele not only persists in the population, but its representation can grow because there is a differential benefit between altruistic and non-altruistic groups. It is this differential benefit between groups that is group selection.

Part 2: Symbiosis and Mutualism

A symbiotic relationship between members of different species is not group selection (in general) because it does not posit that there is a mutual allele that may be deleterious in an individual but beneficial in a group. That is, there is no group synergy that is mitigating individual costs by generating benefits elsewhere that help to support alleles that would otherwise naturally decay. When species are mixed within a population of interest, the analysis is a bit different because alleles cannot flow across the species barrier (except for special cases).

For example, consider an allele that existed across species (e.g., an allele for a gene shared between humans and bonobos), the speciation in general would prevent the sort of group selection gains because there would be no way for increased numbers of alleles in one species to transfer to the other species. Imagine that altruists in one species seek out altruists in the other species. The result could lead to more increases in the altruist representation in one species than another, and so there would be an altruist surplus. Those surplus altruists would have no choice but to associate with non-altruists in the other species. However, if the group was all of one species, then there would not be surplus altruists. Altruistic benefit need not diffuse across non-altruists too.

However, most examples of symbiosis are not altruistic. Instead, they are mutualistic. That is, the behavior does benefit another, but that is a possibly unavoidable side effect of an action that benefits the individual doing the behavior. For example, if I'm driving through a parking lot looking for an empty space to park, I am revealing information to my competitors (other drivers) about where empty spots are not. I don't want to help the competing drivers, but it is unavoidable because they can see me go down an isle of the parking lot and not find a spot. Consequently, they do not go down that same isle. Of course, I use their searching behavior to inform my choices of the next isle. So we are doing "cooperative search" only because the behaviors have mutual benefits. The same goes for many symbiotic relationships among individuals of different species.

Consider a remora ("sharksucker"). It's a small fish that essentially attaches to another host (fish, whale, turtle, etc.). It can receive nutrients from on or around the host. It can also be protected from predators that avoid the host. In some cases, the host could eat the remora, but the remora is so small that it may not be worth the effort. Some hosts actually receive a small benefit (cleaning, for example) from the remora. Regardless, the remora experiences very little cost and plenty of benefit. Moreover, the host experiences very little cost and possibly some benefit. So there's no surprise that this behavior evolved. You don't need any fancy mathematical model to show how this is possible – when the benefits align like this, it's natural to assume that it is going to be favored by natural selection.

Part 2.5: Symbiosis and Co-evolution

Having said all of that, symbiosis can lead to elegant examples (or at least suggestions) of co-evolution, which describes how a change in one species can lead to a change in other species. In particular, natural selection on different species creates a feedback across species. One species is the ecological background for another species, and so as each species changes it creates new niches (and destroys old ones) for other species. So the evolution of one species can guide the evolution in another. But I think this post is long enough. :)

More information

Wikipedia does a pretty good job on these particular subjects. Check 'em out there.

( I have also mirrored this content on a post on my website. )

Duplex Printing from the Command Line to an HP LaserJet Printer

My department has several HP LaserJet printers available to access within the department via LPR and SMB. However, if you are working from a personal laptop connected to the university wireless, those servers will not be available to you. Instead, you must print by piping your documents through SSH to a department server that does have access.

Unfortunately, doing duplex printing (i.e., two-sided printing) to an HP LaserJet printer from the command line is not trivial. So, using the GSview documentation as a guide, I put together a small bash script (available for download as hplj_duplex_print) that does the trick.

#!/bin/bash

declare -a input_file
if test $# -eq 0; then
    input_file=("-")
else
    input_file=("$@")
fi

( echo -e "\e%-12345X@PJL JOB"
  echo "@PJL ENTER LANGUAGE = POSTSCRIPT"
  echo "<< /Duplex true /Tumble false >> setpagedevice"
  gs -sDEVICE=psmono -sPAPERSIZE=letter -q -sOutputFile=- \
    -dNOPAUSE -dBATCH "${input_file[@]}"
  echo -e "\e%-12345X@PJL EOJ"
  echo -e "\e%12345X"
  ) | lp -d your_HP_printer_spool_name

You should replace the your_HP_printer_spool_name with your printer's spool name. You might want to tweak some of the options (details below), but the general structure will remain the same. The opening and closing escape sequences communicate to the HP LaserJet printer that a PostScript file is coming. Then the setpagedevice PostScript directive instructs the printer to use its duplex module.

Regarding tweaking:

• Again, make sure to change your_HP_printer_spool_name to your spool name. You may also want to change lp to lpr, but you will likely have to change -d to -P then.
• You may want to change the gs (GhostScript) options to suit your purposes. For example, you can change the psmono device to one of the other GhostScript devices like psgray or psrgb.
• The Tumble switch determines whether to do short-edge (true) or long-edge (false) duplex printing, and so this script defaults to the latter case. If you prefer vertical flipping, change the /Tumble false to /Tumble true. You might also make this a configurable command-line switch on the script.

"Dark Matter is an Illusion" summary in National Geographic News gets something a little wrong

There was an interesting article from National Geographic News yesterday:

"Dark Matter Is an Illusion, New Antigravity Theory Says"
by Ker Than

I thought I'd post a link to the primary source here. I also wanted to point out that the explanation Ker Than gave got something really important wrong and consequently diminished the elegance of the proposed theory.

Here's the primary source:

"Is dark matter an illusion created by the gravitational polarization of the quantum vacuum?"
by Dragan Slavkov Hajdukovic
Astrophysics and Space Science 334(2):215--218
DOI: 10.1007/s10509-011-0744-4

Ker Than, the National Geographic News reporter, got it a little mixed up in this part of the NatGeo article:

All of these electric dipoles are randomly oriented—like countless compass needles pointing every which way. But if the dipoles form in the presence of an existing electric field, they immediately align along the same direction as the field.

According to quantum field theory, this sudden snapping to order of electric dipoles, called polarization, generates a secondary electric field that combines with and strengthens the first field.

This electric analogy states that electric dipoles align and strengthen electric fields, but that's incorrect. Electric dipoles weaken surrounding electric fields. In particular, the positive end of the dipole goes toward the "negative end" of the field and the negative end of the dipole goes toward the "positive end" of the field. So the two fields subtract from each other, not reinforce. This is summarized in the primary source (that I'll quote below).

[ note that magnetic dipoles align and reinforce surrounding magnetic fields because there are no magnetic monopoles. That is, magnetic field lines are continuous; they don't terminate. Consequently, magnetic dipoles are torqued to align their fields. Electric dipoles are driven by the motion of their monopolar ends ]

What Ker Than missed was that in this model of "gravitational charge", it is the case that opposites repel and likes attract. That's why you (matter) are attracted to earth (also matter). However, anti-matter and matter would repel each other. Moreover, if you had a matter–antimatter virtual pair (as quantum field theory says you do in a vacuum of space), that dipole would align because its "positive" end would be pulled toward the positive end of the gravitational field (and vice versa for its negative end). This alignment would strengthen the resulting field.

Here's the relevant snippet from the bottom of the first column of page 2 of the article:

In order to grasp the key difference between the polarization by an electric field and the eventual polarization by a gravitational field, let's remember that, as a consequence of polarization, the strength of an electric field is reduced in a dielectric. For instance, when a slab of dielectric is inserted into a parallel plate capacitor, the electric field between plates is reduced. The reduction is due to the fact that the electric charges of opposite sign attract each other. If, instead of attraction, there was repulsion between charges of opposite sign, the electric field inside a dielectric would be augmented. But, according to our hypothesis, there is such repulsion between gravitational charges of different sign.

Why GMail's show-if-unread is NOW useless with nested labels

Once upon a time, when they were both in "GMail Labs", the show-if-unread feature and nested labels features worked together seamlessly.

• nested labels: You could create a nested label (like a subfolder) by adding slashes in folder names. You would create two folders called "Parent/ChildA" and "Parent/ChildB", and they would be displayed as "ChildA" and "ChildB" underneath a single "Parent" that you could collapse and expand.
• show-if-unread: Only labels that had unread messages in them would show up in the left bar. To see all of your labels, you could use the "more" link which would show you a full list.

In the case where a nested label had unread messages in it, it would show up in its flat form (if I recall correctly) in the list. So you'd see "Parent/ChildA" but "ChildB" would still be nested under "Parent" in the "more". That was fantastic.

However, eventually both labs features became integrated into production GMail, and they messed it all up. Now, ostensibly to avoid revealing the slash form and to avoid having parent labels repeated in both the unread and read lists, they've made it impossible to apply show-if-unread to nested labels. Consequently, if any nested labels have unread messages in it, the parent and all of its nested labels show up in the unread list. So you get things like this (click for larger):

Obviously, that defeats the whole purpose of show-if-unread. I'm forced to look at all of those read nested labels just because some of their "sublings" are unread.

So Google has gone from taking two nice features and combining them into one terrible and useless and awful thing.

Electric Sheep on KDE 4.6.5 with Fedora 15 (using Intel graphics card)

---

This post begins with a few important updates; scroll down to see the bulk of the original post.

Fedora 16 update: If you are using Fedora 16, then see updates from a newer post about how to get ElectricSheep built and running.

DPMS Update (getting monitors to sleep/standby/suspend/turn off on schedule again): It turns out that electricsheep is preventing my monitors from getting DPMS sleep/standby/off signals because of a bug in mplayer that was fixed today in SVN r34074. If you pull down the updated mplayer and build it yourself, your DPMS problems with electricsheep will be fixed. If you aren't willing to pull down the SVN source and build the fixed binary, you could use something like this sample electricsheep-wrapper script that starts both electricsheep and a secondary process that reads waiting times from xset q, sleeps for those times, and then issues the appropriate xset dpms force commands. To use the hack, all references to electricsheep in KDE or xscreensaver configuration files must be changed to electricsheep-wrapper and the electricsheep-wrapper script has to be installed in a directory in the PATH. Or, again, you can just wait for mplayer to get patched in your Linux distribution.

KDE update: electricsheep's SourceForge SVN includes a Desktop file for KDE, and so I've updated the stuff below to use it instead. It's probably a good idea to check out their updated SVN repository at GoogleCode to see if the support files have improved.

Multiple Monitors update: KDE will stretch one electricsheep across all of your monitors. Instead, if you want electricsheep to put a different instance on each monitor, use xscreensaver instead of kscreensaver. To do so, you'll have to follow the instructions for using xscreensaver on KDE, which are also on the xscreensaver man page. I modified step 4 to use my own custom system-level kscreenlocker that doesn't force everyone on the system to use xscreensaver. Additionally, to get electricsheep to show up in the xscreensaver-demo menu, you need to not only install the relevant electricsheep.xml file (find it in the source repo's or built it yourself), but you also have to add a line to your own ~/.xscreensaver configuration file. I don't know why the former doesn't generate the latter. On one of my machines, it does. On the other, it doesn't.

Of course, YMMV.

---

I installed electric sheep today because I was bored of my ASCIIQuarium KDE screensaver and not thrilled about the other options (some of which bail out on my dual screen Intel setup). [ If you're not familiar with Electric Sheep, you should check out the Electric Sheep Wikipedia page which discusses how the screensaver evolves over time. It's a distributed computing project, and the genetic algorithm that guides the evolution actually takes input from Electric Sheep users (well, not me, because I don't have the keyboard support to "up" and "down" the sheep I see). So the screen saver is constantly downloading and processing new AVI's, generating new content, and contributing it back to the network. I like it because it's pretty screen saver diversity at the cost of a few computing cycles and some disk space. ] It wasn't so bad, but it also wasn't trouble free. Here's what I did (which almost worked entirely without me having to do anything special):

1. Use the Fedora-specific script from Tait Clarridge's page on downloading and installing electric sheep in Fedora (if you are running Fedora 16, see my updated script instead).
2. Learn from Giulio Guzzinati about the need to add an electric sheep KDE Desktop file to get the screensaver into the KDE Screen Saver configuration tool.

Unfortunately, Giulio Guzzinati's desktop file didn't work for me, and so I had to build my own use the desktop file inside the electricsheep distribution. Here the file that ended up "working" for me (which is downloadable as electricsheep.desktop, but I copied from electricsheep.desktop.kde in the SVN repo).

[Desktop Entry]
Exec=electricsheep
Icon=kscreensaver
Type=Service
X-KDE-ServiceTypes=ScreenSaver
TryExec=xscreensaver
Actions=InWindow;Root;Setup;
X-KDE-Category=Fractals Screen Savers
X-KDE-Type=xv
Name=ElectricSheep

[Desktop Action Setup]
Exec=electricsheep-preferences
Name=Setup...

[Desktop Action InWindow]
Exec=electricsheep -window-id %w
Name=Display in Specified Window
NoDisplay=true

[Desktop Action Root]
Exec=electricsheep -window-id %w
Name=Display in Root Window
NoDisplay=true

X-Ubuntu-Gettext-Domain=desktop_kdeartwork

As explained in Giulio Guzzinati's post, you can place that file in

/usr/share/kde4/services/ScreenSavers/

You can probably put it in

~/.kde/share/services/ScreenSavers/

as well (you might have to create that directory first) if you'd rather do something local. That put the Electric Sheep across both of my monitors. If you'd rather put a separate electricsheep in each monitor, use xscreensaver instead of KDE's screen saver. If you're having trouble getting your monitors to go to sleep while electricsheep is running, then you need to get an updated mplayer that fixes the bug that causes that problem (see the updates at the top of this post for more information). Alternatively, you can use a hack like this electricsheep-wrapper script to re-enable DPMS-like timeouts during the screensaver. To use the hack, all references to electricsheep in KDE or xscreensaver configuration files must be changed to electricsheep-wrapper and the electricsheep-wrapper script has to be installed in a directory in the PATH. However, it probably won't be too long until the mplayer DPMS fix reaches your Linux distribution.

3mindme is shutting down! Old owner recommends NudgeMail

Today I received the quoted e-mail below from David Barrett (@quinthar). His work as CEO of Expensify and some complications with maintaining the longevity of 3mindme have made him decide to shut down the 3mindme service effective immediately. He recommends the very similar but commercially operated service NudgeMail as a substitute. You can find other substitution options at an old post of mine discussing these services.

Hi! I'm David, the guy who made 3mindme. I'm very sad to inform you that I'm shutting down the service permanently, starting immediately. I strongly encourage you to check out a similar service at http://nudgemail.com -- it's essentially the same thing as 3mindme, but better.

Q: What will happen to the emails I've scheduled for the future?
A: After I send this email to all users, I'm going to send all future-dated emails immediately. My goal has always been to return every email at precisely the right time. Unfortunately, I'll need to make due with simply returning them at all.

Q: Can I do anything to convince you to keep 3mindme alive?
A: Probably not. It's been a fun service to operate these many years, but as CEO of Expensify (https://expensify.com - Expense reports that don't suck!) I just don't have the time to devote to 3mindme.

Q: Why now, after years of continuous operation?
A: Spam. I recently learned that many users (myself included) were having their emails silently dropped, meaning they got no error response, but the message was never scheduled for future delivery. Solving this problem is very difficult and time consuming, and I'd rather shut down 3mindme than leave it in a non-functioning state.

I think that's all. If you have any questions, feel free to respond to this email and I'll do what I can to help. Otherwise, give NudgeMail a shot, and keep Expensify in mind for your next expense report!

-david
Follow me at http://twitter.com/quinthar

So that is very sad. 3mindme was a nice server-side mail-me-back reminder service that didn't have the ugly commercial taste of pretty much every other alternative.

So bye-bye 3mindme; we'll miss you.

Using \gobblepars to prevent LaTeX from adding empty lines at gaps

While searching for something else, I came upon a StackOverflow question from a while ago that asked how to prevent LaTeX from adding a \par at particular blank lines in the source code. The asker didn't want to remove blank spaces everywhere; he just wanted to get rid of the paragraphs at certain spots.

Of course, you can use comments to do this:

\somemacro{}
%
Some text

However, a lot of people don't like the look of that. Some of the responders on StackOverflow gave some alternatives that seemed ugly and half baked. So I came up with \gobblepars, which is a macro you can add to the end of your own macro definitions to cause them to eat up all trailing pars, or you can use explicitly. For example:

\somemacro{}\gobblepars

Some text

would do the same as the commented stuff above. Moreover, if you had control over \somemacro, you could build \gobblepars into it (in fact, even if you didn't have control, you could use \let and \def to augment an existing macro with a trailing \gobblepars, but that's a different topic).

Here's the simple definition of \globblepars (you put this in the preamble of your LaTeX document):

\makeatletter
\newcommand\gobblepars{%
    \@ifnextchar\par%
        {\expandafter\gobblepars\@gobble}%
        {}}
\makeatother

So that's pretty simple. It checks for a \par (which includes a blank line in the source) trailing it. If it finds one, it gobbles it up (i.e., gets rid of it) and then calls itself again. This process will continue until it finds something other than a \par. Hence, it "gobbles" strings of "pars".

Update to my LaTeX CV templates: Space allowed after sections now!

In preparation for setting up MultiMarkDown (MMD) to write my CV for me, I've been thinking about ways to refactor my old résumé/CV LaTeX templates to make them look a little cleaner. A fix I came up with tonight should help with that, and I think it will also make the templates easier for others to work with even if they're not doing anything with MMD.

In particular, the \section macro used to be renewed as a \marginpar with some other ugly stuff. Putting the sections in the margins caused problems because people like to put spaces after the sections, which generates a \par that means the section content will not be aligned with the section heading in the margin note. So the old way I got around that problem was to force people not to use spaces between \section and the section content. If they needed visual space in their source code, they could use comments to do that.

Well, I've swapped out that ugly definition for a slightly less ugly one that uses \llap (with a \smashed \parbox) and some creative gobbling. In particular,

% The section headings
%
% Usage: \section{section name}
\renewcommand{\section}[1]{\pagebreak[3]%
    \hyphenpenalty=10000%
    \vspace{1.3\baselineskip}%
    \phantomsection\addcontentsline{toc}{section}{#1}%
    \noindent\llap{\scshape\smash{%
        \parbox[t]{\marginparwidth}{\raggedright #1}}}%
    \vspace{-\baselineskip}\par}

The \vspace and \par combination should ensure that an additional \par isn't added by LaTeX. So before you were restricted to things like...

\section{Stuff} \begin{bibsection} %...

and

\section{Stuff}
%
Junk

But now you don't have to be so careful about the whitespace. You are allowed:

\section{Stuff}

\begin{bibsection} %...

and

\section{Stuff}

Junk

So that's cool. Much more readable.

You can get my most recent LaTeX CV templates at their page on my website. You can find a detailed history of the source code changes within my Mercurial repositories of documents.

(updated: new \gobblepars allows for arbitrary amount of space after each \section)
(updated: replaced \gobblepars with \par hack that still allows for arbitrary amount of space after each \section but also prevents lists from adding a \par when placed directly after a \section; consequently, adjusted all of the lone-lists to get rid of their leading negative vertical space (probably can get rid of them now, actually). I'm trying to shift toward using conventional lists (or perhaps conventional modifications of them from paralist or enumitem))

The maximum number of matrix dimensions in MATLAB

[ Background: I was asked what the maximum number of matrix dimensions was in MATLAB today. I responded as follows. ]

You are only limited by the amount of memory available and the maximum number of ELEMENTS (as opposed to dimensions) in a matrix. The actual number of dimensions is just a detail about how the memory is indexed. You can reshape any existing matrix to any number of dimensions (I'll give details below). You can only create a new matrix if it abides by the memory and element limits that vary by computer.

To find out the maximum number of elements for a matrix on your computer, use the MATLAB command "computer" (do "help computer" for details). For example:

[~,maxsize,~]=computer

tells me that I can have 2.8147e+14 elements in matrices on my computer. So I better be sure that:

(number of rows)
   × (number of columns)
   × (number of cubes)
   × (number of 4-th dimensional thinggies)
   × (...)

is less than that number.

To find out about memory limits on your system see, the command "memory" ("help memory" or "doc memory"). Unfortunately, memory may not be available on your system. Alternatively, you can see:

http://www.mathworks.com/support/tech-notes/1100/1110.html

for information about memory limits in MATLAB. For information about the maximum number of elements (and the command "computer" that I discussed above), see (UPDATE: MATLAB has moved this page, and this link doesn't land in the right spot anymore):

http://www.mathworks.com/support/tech-notes/1200/1207.html#15

Regarding dimensions, you can use the command "reshape" to re-index any existing matrix. For example, if I start with the column vector:

A=ones(100,1)

I can turn it into a row vector:

newA = reshape(A, 1, 100)

or a matrix of any number of dimensions so long as the number of elements is still 100.

newA = reshape( A, 2, 2, 25 )
newA = reshape( A, 1, 1, 1, 1, 1, 1, 1, 1, 1, 100, 1 )
newA = reshape( A, 1, 1, 1, 2, 1, 50, 1, 1, 1, 1, 1, 1, 1, 1 )
% etc.

Now, I'm assuming you're using regular MATLAB matrices. Alternatively, you can use sparse matrices so long as you limit yourself to functions that work with sparse matrices:

help sparfun

A sparse matrix stores an index with every element. That lets it "skip over" the 0 elements of the matrix. Consequently, you can store VERY large matrices with an abstract number of elements far larger than anything you can work with in MATLAB... however, most of those abstract elements will be 0.