use Perl

http://kitenet.net/~joey/blog/entry/cpan_purity_tester-2006-03-12-22-29.html via http://planet.debian.net/

I'm not sure that's a really useful reuse metric, but it's sure amusing.

Hoping to be helpful, and out of curiosity -- I have always loved math, or at least since 2nd grade -- I clicked on his paste link. It referenced a website by someone I vaguely knew and certainly knew of 20 years ago when our research areas overlapped and have seen in the math literature since then, David H. Bailey. I remember noting his breakthrough on direct computation of digits of pi (in HEX), and his website to search for your name (in ascii) in Pi, but I had not yet played with his new algorithm. I had played with searching for strings of DIGITS in a pre-computed Pi of a mere 10_000 decimal digits with Perl last year. Dave's 5-bit ascii search in Pi searches 4_000_000_000 bits, 5 orders longer.

So I asked Pete_I what was wrong, but the only reply was a punch-line just the facts ma'am from a sniper. So after a short break, I asked him by direct message. It seemed his coding of the algorithm was losing precision after 10-15 decimal places, even though it was using Math::BigFloat.

After several false starts -- and reading the academic paper three links into DBH's pages -- I found that, unless we used the modular arithmetic hacks DBH used to avoid using arbitrary precision packages, we needed to increase the default precision and use BigFloat for all numeric variables, not just $pi. In the process, I refactored the code to compute the sequence of the series first and then evaluate the polynomial by the classical add-and-divide technique.

My final code differs from Pete_I's code primarily in reading in, printing, and subtracting from the comparison value. (And commenting out Acme::Comment ;-)

• Pete_I's node "Pi Generation"
• DBH Home with short description of the new formual for Pi,
• DBH's pi pages
• DBH's Search for your name in Pi page

I looked at Date::Calc and DateTime modules, but neither made it easy to subtract 20 years from a file timestamp from (stat)[9] and reapply with utime. And DateTime.pm required 3 prerequisites, one of which required Module::Build. Eventually I'll hook up the CPANDebian magic, but not until after I upgrade the OS, so that was out.

So, old trick -- separate the problem into easy steps.

perl -MPOSIX=strftime -MFile::Find
  -le 'find( { wanted=>\&foo , follow=>1}, "/");
  sub foo {return if -M $_ > 0;
   my $ts=strftime ("%Y%m%d%H%M.%S",
        localtime ((stat($_))[9]));
   return unless $ts=~s/\b(202[45])/$1-20/e;
   print "touch -t $ts $File::Find::name";}' \
  | tee touch-2025
$ (set -x; . ./touch-2025)
+ . ./touch-2025
++ touch -t 200502052006.08 /
++ touch -t 200412192026.04 /homex
++ touch -t 200412192133.13 /homex/wdr
++ touch -t 200412192026.04 /homex/wdr/.bashrc
++ touch -t 200412192026.04 /homex/wdr/.bash_profile
...

Of course, I tested it as an unprivileged user before running it as root from / (via sudo bash).

I've had fun contributing to Jerrad's YAPerl Advent Calendar this season. I only wish I'd not gotten ill so could have gotten my 3rd submission in a little earlier. Thanks to Jerrad for keeping that fine tradition of Mark's going.

I was reminded by Nat's comment on learning Python and a comment on Boston.PM list referring to a Slash-Dot thread (that strangely claims PHP has defeated Java) that that I had had a revelation at a LUG meeting recently.

I have heard two reasons to prefer Python to Perl that made sense -- and the source and sense of the second one scared me.

• A friend with little remaining wrist does his scripting in Python, since his voice-typer works better with a non-punctuated language.
  (Yes he can reconfigure it to do Perl, but he can do Python with the same training set as email and data files, and it doesn't like switching training sets. If he could switch brands he would, but there's not a good open source alternative in voice-typers yet, there's a very high cost to entry to that market. I assume he uses auto-indent so he doesn't have to say TAB TAB TAB for each line.)
  This is reasonable, limited, and harmless.
• Mark Shuttleworth is pushing to make Python the dominant scripting language of the universe. If I understood Mako correctly at his Ubuntu talk to BLU

  «Python: One goal is "python everywhere." It is the energy that surrounds us and binds us as Jeff Waugh has said.

  «We are working hard to have everything extensible by Python. Mark loves Python.»
  [notes]

  In Q&A, Mako elaborated that having one scripting language for system install, config, startup files and for application customization/integration/scripting is obviously a win. But the reason for preferring Python over Perl in the Gnome+Python+security Ubuntu-preferred feature-set is the simplicity of syntax will make it more acceptable / accessible as a mere scripting language to non-programmers, the desktop users. The minimal subset is perceived to be smaller.

  This is reasonable, potentially pervasive, and thus dangerous. Since he's the millionaire astronaut behind Ubuntu, Mark can do this. If he succeeds in making Ubuntu the replacement for Windows -- and all FLOSS users should hope he does, even Perl Mongers -- Python will be the replacement for WinDos ComManD files and VBA scripting (Visual Basic for Applications), and the replacement for most BASH too.

Modest Proposals Needed

In the sense of Swift, we need some modest proposals to let us see the elephant in the room -- maybe some cup-throwing too, because Jon's comments that Perl is in trouble

« unless we can come up with something that will excite the community, because everyone's getting bored and going off and doing other things»

is still, or again, true. Perl6 is exciting, but what Perl community will be left for it to excite when it is done? They are wandering off -- even Nat is learning Python, though he says it's only a dalliance, not an affair of the heart -- but more seriously, the niches that were once Perl's alone are crowded with too many kinds of finches in one niche.

I'll play Devil's Advocate.(or perhaps Estate Agent and look at our location, location location selling points)

Is Parrot the redemption of Perl, or the path to obscurity? If Parrot makes Python run faster and gives it native access to all of CPAN and 6PAN, does Perl become just the esoteric language for a small band of FLOSS gurus to implement modules for Ubuntu and Open Office users to call from their Python scripts?

So what "ecological" niches has Perl had in the past, and where can Perl5/Perl6 continue expand in the future?

• PHP, a watered down Perl, has colonized the low-end LAMP niche (in spite of mod_perl and FastCGI actually being faster and safer, contrary to mythology).
• Ruby on Rails seems to be gaining mind-share in larger and rich-client (AJAX) LAMP applications, as if Catalyst, Maypole, CGI::Applicaiton, FastCGI didn't exist. Having a cool name that plugs the language is an advantage?
• Java (contrary to the /. article) retains the high ground of stick-build web-apps, thanks in part to the high-profile Apache+Struts library-stack community.
• Python may well get the VBA and Better Shell niche thanks to Ubuntu and the backfeed to Debian (if FLOSS wins all).
• The added academic respectability of the Junctions, Grammar, etc. of Perl6 may give Perl an academic life, but the academic life can be the kiss of death, look at poor Pascal and SmallTalk.
• One liners rule! but the are not a community-building niche.
• CPAN continues to be the "killer app" as the mechanism implementing Cox's Software IC marketplace, but will that be an advantage forever? Python may not have a repository yet, but it will on the Ubuntu side, and must eventually get there for all platforms. PHP and JScript already do. The new Debian.CPAN.org provides automated packaging, which Ubuntu is planning for Python.)
• BioPerl owns not just its niche but its whole microclime, because of a standard SDK.
• Thick-Client programming -- possible with TK or Win32 libs, but this is not "mainstream", and not likely to be competitive
• WebServices -- should be a sustainable niche, but limited growth for the same reason -- largely professional coders, this is more complicated than scripting users usually get.
• Systems Administration -- well established in proprietary Unixes and Linux; likely to remain so in Proprietary and non-Ubuntu Linux. But if Python takes over on Ubuntu and thence Debian and thence DCC- and thence LSB-based distros, perhaps this is a shrinking pool?

In the market place of ideas it's grow or die. The Media new and old -- magazine publishers, slash-dot, book publishers, stock pickers, bloggers -- treat everything as if you aren't growing you must be shrinking, and if you aren't the fastest growing you aren't growing. This is strange logic, but all too often self-fulfilling.

So, where do we grow?

BBC reporting "Gene map points to personal drugs"

"Experts say the study should simplify genetic research Scientists have completed a map of the most common differences in the human genome, which could lead to personalised treatments for diseases."

This is a major ($100M) OpenSource science project -- their CopyLeft License on the data requires foreswearing patenting results of research using the HapMap. Article

Bio::PopGen::IO::hapmap.pm is a part of BioPerl SDK. I'm not sure if only the data is accessed via BioPerl, or if the HapMap was built with BioPerl too. But the whole HapMap website runs on cgi-perl.

Back story -- from 2003 launch of HapMap: 1; 2

1. Always read the release notes carefuly before and during and upgrade.

Luckily there wasn't anything important on the server that I tried to update from Debian 3.0/Woody to 3.1/Sarge withough following the recommended procedure in the platform-specific release note. For the DEC-Alpha platform, it's a just a wee bit more involved than the Ubuntu "just do it". (On DEC-Alpha, everything is a wee bit more complicated ... except Perl is 64bit out of the box, hence my fascination with it.) I tried to just do it and hosed the Alpha ... but since it was a standby system with nothing on it, which is why I was upgrading it first, no harm done expect I had to re-install 3.0 to try the upgrade again.

Upgrading Ubuntu 5.04 Hoary Hedgehog to 5.10 Breezy Badger was pretty slick. Not even in comparison, just slick.

2. If on a ADSL "broadband" not real broadband, doing one upgrade-over-internet is quite enough, don't try to do two different ones at the same time.

3. Math helps with KVM Switches

Knowing modular arithmetic makes using a KVM switch easier ... -1 mod 4 = 3, so to go BACK 1 step on the KVM, advance 3 to wrap around back ... sort of like two wrongs don't make a right, but three lefts do.

« Room-temperature ice is possible if the water molecules you’re freezing are submitted to a high enough electric field. » -- Physics News Update

Light that travels… faster than light!

«A team of researchers from the Ecole Polytechnique Fédérale de Lausanne (EPFL) has successfully demonstrated, for the first time, that it is possible to control the speed of light – both slowing it down and speeding it up – in an optical fiber, using off-the-shelf instrumentation in normal environmental conditions. ... They were also able to create extreme conditions in which the light signal travelled faster than 300 million meters a second. And even though this seems to violate all sorts of cherished physical assumptions, Einstein needn't move over – relativity isn't called into question, because only a portion of the signal is affected. » [emphasis supplied ]

- The Brillouin phenomena apparently involve group velocity, not actual FTL propagation of waves, just of group crests? One of the 3 Google News hits for this story says it's embargoed until Monday 2AM, but two others are out with it, and it's on the university website;... apparently the press release also travelled faster than the speed of light?  

- Ecole Polytechnique Fédérale de Lausanne ( Français ; Deutsch Presskommunique; English press release ) & Applied Physics Letters via EurekAlert
Their previous work.

New method for trapping light may improve communications technologies

« A discovery by Princeton researchers may lead to an efficient method for controlling the transmission of light and improve new generations of communications technologies powered by light rather than electricity. [...] [They] tested whether quasicrystals -- an unusual form of solid -- would be useful for controlling the path of light by constructing a three-dimensional, softball-sized model of such a structure with 4,000 [count of one ] centimeter-long polymer rods.  [...] A quasicrystal is an unusual form of solid composed of two building blocks, or groups of atoms, that repeat regularly throughout the structure with two different spacings. [...] They observed how microwaves were blocked at certain angles in order to gauge how well the structure would control light passing through it. Building the physical model was a breakthrough that proved more valuable than using complex mathematical calculations, which had been a hurdle in previous efforts to evaluate the effectiveness of photonic quasicrystals in blocking light.»  (PR; photo on PU site. )

« [O]ur quasicrystal is far from optimized because it consists solely of thin rods connecting lattice points. A [...] more equal filled/void ratio would reduce polarization effects and enhance the gap overlap while maintaining the nearly spherical Brillouin zone. Laser tweezers used for particle trapping or two-photon polymerization would allow the construction of a quasicrystalline matrix of dielectric components with a photonic bandgap in the visible spectrum.» [Conclusion of preprint]

- Initially this sounds deceptively similar to the above Swiss fiber-optic experiment, and both involve Brillouin Scattering phenomena, but this actually quite different. 
(1) Quasicrystals ( * ) are 3-dimensional analogs of the Penrose tiling  ( * ), both of which seemingly violate the impossibility of 5-fold rotational symmetry -- counter-intuitively, 5-fold symmetry of a sort is possible in an  aperiodic tiling . (Thus providing a simpler counter-example to Wang's conjecture , which held all tilings could be periodic.)  
(2) This is a scaled experiment performed with macroscopic stereolithographic model(s) inspected with microwaves and RF network analyzers, instead of an actual light experiment in light media as with the Swiss study above.
(3) This study is identifying candidates for photonic band-gap nanomaterials, and thus is similar to the negative index of refraction materials. 

- Princeton University PR and Website with preprint from Nature 436 p993ff,  18 August 2005, Letters; via EurekAlert

Saturn's rings have own atmosphere

« Data from the NASA/ESA/ASI Cassini spacecraft indicate that Saturn's majestic ring system has its own atmosphere - separate from that of the planet itself. During its close fly-bys of the ring system, instruments on Cassini have been able to determine that the environment around the rings is like an atmosphere, composed principally of molecular oxygen. This atmosphere is very similar to that of Jupiter's moons Europa and Ganymede.»

- This again reminds me of Larry Niven 's novels The Integral Trees and The Smoke Ring novels, set in a physically plausible torus of atmosphere around a double star  (the physics are quite similar to those for space-tethers in use on modern satellites ) . 
  Note that phrase similar to Europa's -- whose atmospheric pressure is estimated at one-hundred-billionth of Earth's (*) and thus not breathable; what little there is would also be rather cold.

- European Space Agency, Src, via EurekAlert (and also SpaceRef, SciScoop, ...)

Galactic survey reveals a new look for the Milky Way

«With the help of NASA's Spitzer Space Telescope, astronomers have conducted the most comprehensive structural analysis of our galaxy and have found tantalizing new evidence that the Milky Way is much different from your ordinary spiral galaxy. »

- Ordinary? Ordinary may be the wrong word for un-barred in this case. The typical spiral galaxy is barred. The non-barred spirals are less typical, possibly older.  E.g.,
  «Barred spiral galaxies are relatively common, with surveys showing that up to two-thirds of all spiral galaxies contain a bar.»    - Wikipedia

- University of Wisconsin-Madison, Src, via EurekAlert

Too Many Roads Lead to Traffic Congestion

« In all networks, like road or airline traffic networks, the Internet, cancer tumors or industry supply chains, you need to pass packets from node to node, such as cars, information or data. But which are the most efficient, decentralized networks or hub-like centralized ones? According to Technology Research News (TRN), researchers from Oxford University, U.K., have designed a model which maps traffic congestion . This model combines roads going through the center of a city and other ones avoiding it. And they found that, from a cost point of view, it would be sometimes better to close roads going through cities than adding more. They also think that these conclusions can be applied to almost all kinds of networks, biological ones or created by humans. » [RP]

«Researchers from Oxford University in England have tackled the problem [of network optimization] by examining the congestion costs within a network model that combines paths that go around the perimeter of the network and central hubs that provide shorter paths through the network. Real-world networks are too complicated to describe exactly mathematically. The researchers' model is simple enough to solve exactly, yet realistic enough to provide insights into real networks.
The research is aimed at finding ways to ease bottlenecks in networks involving manufacturing, the Internet and traffic, and ways to disrupt networks like tumor blood flow and terrorist supply chains. The findings could also help design better networks. » [OU]

-  That adding a road may increase congestion is not a new result: traffic modellers were aware of this in 1980 if not before. 

- Oxford University, via Technology Research News  and Roland Piquepaille's Technology Trends

African grey parrot is first bird to comprehend numerical concept akin to zero

«A Brandeis Univesity researcher has shown that an African grey parrot with a walnut-sized brain understands a zero-like concept -- an abstract notion that humans don't typically understand until age 3 or 4, and that can significantly challenge learning-disabled children.»

- This is harder than one might expect -- it took a long time for Zero to be accepted in Western mathematics. See, for instance, The History of Zero: Exploring Our Place-Value Number System , or The Nothing That Is: A Natural History of Zero .

 - Brandeis University & the Alex Foundation ; Journal of Comparative Psychology ;
via EurekAlert and World Science News and Primidi ;
and also Science Daily, and Google News

Is my red your red?

«Does society determine the way you see a rainbow? New findings are re-igniting an old controversy.»

- Nice comparitive 2d color map in the linked summary. This debate has been running for 35 years -- interestingly, Paul Kay is cited as the original in color Relativism , so could be significant that he's a co-author in the non-relativist paper, but his 1969 title was "Basic Color Terms: Their Universality and Evolution" , so maybe the relativists took him out of context?

Debi  Roberson (University of Essex in Colchester, U.K), J. Davidoff, I.R. Davies, L.R. Shapiro, 2005.
Color categories: Evidence for the cultural relativity hypothesis . Cognitive Psychology. 50, 378-411.
Terry Regier (U.Chicago), Paul Kay (ICSI), R.S. Cook, 2005.
Focal colors are universal after all . Proceedings of the National Academy of Sciences 102, 8386-91.

ICSI's World Color Survey.

Why Is The Sky Blue, and Not Violet?

«The hues that we see in the sky are not only determined by the laws of physics, but are also colored by the human visual system, shows a new paper in the American Journal of Physics. On a clear day when the sun is well above the horizon, the analysis demonstrates, we perceive the complex spectrum of colors in the sky as a mixture of white light and pure blue. When sunlight enters the earth's atmosphere, it scatters (ricochets) mainly from oxygen and nitrogen molecules that make up most of our air. What scatters the most is the light with the shortest wavelengths, towards the blue end of the spectrum, so more of that light will reach our eyes than other colors. But according to the 19th-century physics equations introduced by Lord Rayleigh, as well as actual measurements, our eyes get hit with peak amounts of energy in violet as well as blue. [...]

The sky's complex multichromatic rainbow of colors tickles our eye's cones in the same way as does a specific mixture of pure blue and white light. This is similar to how the human visual system will perceive the right mixture of pure red and pure green as being equivalent to pure yellow. The cones that allow us to see color cannot identify the actual wavelengths that hit them, but if they are stimulated by the right combination of wavelengths, then it will appear the same to our eyes as a single pure color, or a mixture of a pure color and white light. »

-  Interesting.

- American Journal of Physics, July 2005, via AIP Physics News Update

Scientists get a real 'rise' out of breakthroughs in how we understand changes in sea level

«For the first time, researchers have the tools and expertise to understand the rate at which sea level is changing and the mechanisms that drive that change. ...
“We’ve found that the largest likely factor for sea level rise is changes in the amount of ice that covers Earth. Three-fourths of the planet’s freshwater is stored in glaciers and ice sheets, or about 220 feet of sea level." ...
The latest sea level research conducted by Dr. Steve Nerem, Associate Professor, Colorado Center for Astrodynamics Research at the University of Colorado in Boulder, and his colleagues, published in a 2004 issue of Marine Geodesy Journal, has found that recent TOPEX/Poseidon and Jason satellite observations show an average increase in global mean sea level of three millimeters a year from 1993-2005. This rate is more than 50 percent greater than the average rate of the last 50 years. »

- Comment

- NASA/Goddard Space Flight Center--EOS Project Science Office via EurekAlert  

NASA offers a real-time 3-D look at the inside of hurricanes

«Seeing how rain falls from top to bottom and how heavy the rain falls throughout parts of a tropical cyclone is very important to hurricane forecasters. NASA has sped up the process of getting this data within three hours, and making it appear in 3-D. The new process now gives information quickly enough for forecasters to use.»

- Tropical Rainfall Measuring Mission or TRMM provided some astonishing view of H.Bonnie last year. They're providing similar views in near-real-time to tropical forecasters now.

- NASA/Goddard Space Flight Center--EOS Project Science Office ( http://trmm.gsfc.nasa.gov/ ) via EurekAlert

NRL study finds shuttle exhaust is source of mysterious clouds in Antarctica

«A new study, funded in part by the Naval Research Laboratory (NRL) and the National Aeronautics and Space Administration (NASA) reports that exhaust from the space shuttle can create high-altitude clouds over Antarctica mere days following launch, providing valuable insight to global transport processes in the lower thermosphere. The same study also finds that the shuttle's main engine exhaust plume carries small quantities of iron that can be observed from the ground, half a world away.»

- Days before the next Shuttle launch, they're still getting new science from the ill-fated Columbia. 
"Antarctic polar mesospheric clouds (PMCs)" or Noctilucent clouds form over the antarctic only days later, showing pretty rapid transport in the thermosphere, and bloomed later in the year.

- Naval Research Laboratory, NASA , Geophysical Research Letters,  via EurekAlert 

Experts Explore Science's Unanswered Questions

«Four AAAS symposia tackle overpopulation, string theory, the causes of disease, and what makes us human »

- Science Magazine has full discussion of 25 top questions and 100 more listed.

-  AAAS Science magazine

Simplifying a Nutty Problem -- The Brazil-Nut Problem.

« Swirling marbles may give clues to why larger nuts tend to float to the top of the can. »

-  Includes do-it-yourself experiment link! 

- via AAAS Science magazine 

A Coulomb Experiment for the Weak Nuclear Force

«Physicists at the SLAC accelerator have measured, with much greater precision than ever before, the variation in the weak nuclear force, one of the four known physical forces, over an enormous size scale (a distance of more than ten proton diameters) for so feeble a force. Although the results were not surprising (the weak force diminished with distance as expected) this new quantitative study of the weak force helps to cement physicists’ view of the sub-nuclear world. ... The SLAC work is, in effect, a 21st century analog of the landmark 18th experiments in which the intrinsic strength of the electromagnetic and gravitational forces were measured (by Charles Coulomb and Henry Cavendish, respectively) through careful observation of test objects causing a torsion balance to swing around. The weak force, in the modern way of thinking, is a cousin of the electromagnetic (EM) force; both of them are considered as different aspects of a single “electroweak” force.  »

-  Reuse of a classic experimental design to measure a radically expression of a related force. This experiment indirectly measures the weak force by measuring a parity violation. 

- Slac, via AIP Physics News Update

Two from Saturn - http://news.bbc.co.uk/2/hi/science/nature/4640641.stm - Rings have own atmosphere; and Saturn has gained 7 minutes per day in 20-30 years. (I could use an extra 7 minutes per day.) -- BBC

Einstein ring in distant universe Einstein Ring Using ESO's Very Large Telescope, Rémi Cabanac and his European colleagues have discovered an amazing cosmic mirage, known to scientists as an Einstein Ring. This cosmic mirage, dubbed FOR J0332-3557, is seen towards the southern constellation Fornax (the Furnace), and is remarkable on at least two counts. First, it is a bright, almost complete Einstein ring. Second, it is the farthest ever found. - European Southern Observatory (ESO) ; Astronomy & Astrophysics Letters

Oregon study confirms health benefits of cobblestone walking for older adults

Melting starts at defects in colloidial crystals.
I might have guessed if I'd thought to ask the question, nice to have it confirmed. .
Also at AIP PNU; Contrast with Ultra-fast X-ray pulses reveal how a solid melts into a liquid

"Supernova Olivine from Cometary Dust" -- Rocks for Astronomers

Network theory of getting lost in a strange city ... and why locals' directions make no sense. primidi