links for 2009-06-29

• On our new cousin Ida | A view from the pew
  Earlier this week a fossil Darwinus masillae (nick-named “Ida”) created a bit of a stir and sent creationist websites into deny-everything-about-everything mode. The media has also been pretty unhelpful with it’s “missing-link” labeling and over-hyped rhetoric [...] Ida is NOT: * THE missing link. (Every fossil is transitional in some way; Ida is one link in a very long evolutionary chain.)
  * The only example we have of a transitional fossil. (There are so many … to store and categorise)
  * An example of scientists trying to deceive you.
  * A much needed piece of evidence for the theory. (There’s a mountain of evidence that overwhelmingly supports evolution by natural selection. We don’t even need fossils due to: vestigial organs, embryology, morphological similarities, genomic similarities, observable evolution of micro-organisms and virtually every other discovery in biology over the 150 years.)
  * The work of Satan (!)
  (tags: evolution)

links for 2009-06-26

• The New Economy: And Why This Crisis May Be Our Best Chance :: by David …
  Wall Street is bankrupt. Instead of trying to save it, we can build a new economy that puts money and business in the service of people and the planet—not the other way around. [...]The world of our shared human dream is one where people live happy, productive lives in balance with one another and Earth. It is democratic and middle class without extremes of wealth or poverty. It is characterized by strong, stable families and communities in which relationships are defined primarily by mutual trust and caring. Every able adult is both a worker and an owner. Most families own their own home and have an ownership stake in their local economy. Everyone has productive work and is respected for his or her contribution to the well-being of the community.
  (tags: economy)

links for 2009-06-23

• Capitalism Hits the Fan | Professor Richard D. Wolff
  Watch as Professor Richard Wolff breaks down the root causes of today's economic crisis, showing how it was decades in the making and in fact reflects seismic failures within the structures of American-style capitalism itself. Wolff traces the source of the economic crisis to the 1970s, when wages began to stagnate and American workers were forced into a dysfunctional spiral of borrowing and debt that ultimately exploded in the mortgage meltdown. By placing the crisis within this larger historical and systemic frame, Wolff argues convincingly that the proposed government "bailouts," stimulus packages, and calls for increased market regulation will not be enough to address the real causes of the crisis, in the end suggesting that far more fundamental change will be necessary to avoid future catastrophes. Richly illustrated with motion graphics, this is a superb introduction designed to help ordinary citizens understand, and react to, the unraveling economic crisis.
  (tags: economy)
• Faith and Theology: Why sex tells you nothing about what it means to be human
  This can be especially hard for Christians to grasp, since a very deep part of our moral formation has been the belief that human identity is ultimately wrapped up in the suburban bliss of family life. (On which, see the TV series Mad Men…) This is also why our churches are often so strangely inhospitable to “single” (read: pre-married) people. We simply can’t really believe that these people are fully formed human beings. And so we treat them with all the sympathy or suspicion or indifference that their estate demands; our charity might even compel us to subject them to the peculiar indignity of a “singles” social event, all in the hope that the bright truth of sex will at last dawn in their dark lives.
  (tags: sex church self)

Money and the Crisis of Civilization

• Reality Sandwich | Money and the Crisis of Civilization, by Charles Eisenstein
  In the face of the impending crisis, people ask what they can do to protect themselves. "Buy gold?" "Stockpile canned goods?" I would like to suggest a different kind of question: "What is the most beautiful thing I can do?"
  (tags: economy spirituality society)

Convert Unix timestamp to Date-time format

Working with log files in linux/unix, you’ll inevitably come across the weirdness of a unix timestamp. It’s not intuitive working with the number of seconds since Jan 1 1970, so I rolled a little conversion utility in bash, called “utime2ymd”.

#!/bin/sh
u1="Usage: utime2ymd <timestamp> [local|gmt]"
u2="\n\nConvert 10-digit Unix timestamp to yyyymmdd.hhmmss format"
u3="\n use local time zone (default) or UTC/GMT"
[ $1 ] || { echo -e $u1$u2$u3; exit 1 ; }

unixtime=`echo $1|cut -c -10`

if [ $2 ]
then qual2=`echo $2|awk '{print tolower($1)}'`
    if [ "$qual2" = "gmt" ]
    then thetime=`perl -e "print scalar(gmtime($unixtime))"`
    fi
else
    qual2="local"
    thetime=`perl -e "print scalar(localtime($unixtime))"`
fi 

YYYYMM=`echo $thetime | awk '{print $5 $2}' \
    | sed 's/Jan/01/;s/Feb/02/;s/Mar/03/;s/Apr/04/;s/May/05/;s/Jun/06/;
           s/Jul/07/;s/Aug/08/;s/Sep/09/;s/Oct/10/;s/Nov/11/;s/Dec/12/'`

DD=`echo $thetime | awk '{printf("%02d",$3)}'`
hhmmss=`echo $thetime | awk '{print $4}' | sed 's/://g'`
echo "$YYYYMM$DD.$hhmmss $qual2"

NOTE: There’s a similar script for the Windows environment, called ‘timetool‘. Wonder if I should write a linux version??

Proof that 1=2

Assume and .
Then

obviously:

now, multiply both sides by x:

now, subtract y² from both sides:

now, factorize:

now, cancel (x-y) term:

Therefore,

QED.

RIP Stanley Jaki ~ Scholar and Gentleman

Stanley L. Jaki, OSB was a Benedictine priest and Distinguished Professor of Physics at Seton Hall University, New Jersey since 1975.

Jaki has been an intellectual hero of mine for a long time, I have owned “Science and Creation” for 10 years and explored its riches numerous times. It’s a revelatory book, which gives the reader a feel for the great sweep of religious traditions around the world, and is a brilliant introduction to the development of human thought since history began..

• The Rev. Stanley L. Jaki, Physicist and Theologian, Dies at 84
  The Rev. Stanley L. Jaki, a physicist and theologian whose prolific writings parsed the histories of science and religion and the intertwining of faith and reason, died on Tuesday in Madrid, where he had traveled from Rome after delivering a lecture. He was 84 and lived in Princeton, N.J.

  Father Jaki held doctoral degrees in physics and theology. A relentless scholar, he wrote more than 40 books, including studies of the religious thinking of G. K. Chesterton, the works of the French physicist and historian of science Pierre Duhem and the life of Cardinal John Henry Newman, the 19th-century theologian who famously converted from Anglicanism to Roman Catholicism.

  He is probably best known, however, for works like “Science and Creation” (1974), in which he argued that the scientific enterprise did not become viable and self-sustaining until its incarnation in Christian medieval Europe, and that the advancement of science was indebted to the Christian understanding of creation.

  (tags: faith science)

RE: John Minto | Democracy only for the wealthy in Auckland

• Democracy only for the wealthy in Auckland | John Minto
  Around the developed world there is growing disenchantment with what passes for democracy. The drivers have been the same in each country. For at least five elections from 1984 New Zealanders voted for one set of policies and got another. Despite consistently voting for governments expected to put curbs on corporate control of our economy and keep ownership of community assets in public hands we were betrayed each time by political parties under the effective control of the very corporate sector who benefited from undemocratic decisions.
  (tags: economy)

Psalm 23: English to Maori

The Lord is my shepherd; I shall not want. 2 He maketh me to lie down in green pastures; he leadeth me beside the still waters. 3 He restoreth my soul: he leadeth me in the paths of righteousness for his name’s sake. 4 Yea, though I walk through the valley of the shadow of death, I will fear no evil: for thou art with me; thy rod and thy staff they comfort me. 5 Thou preparest a table before me in the presence of mine enemies: thou anointest my head with oil; my cup runneth over. 6 Surely goodness and mercy shall follow me all the days of my life: and I will dwell in the house of the Lord for ever.

Ko Ihowa toku hepara; e kore ahau e hapa. 2 Ko ia hei mea kia takoto ahau ki nga wahi tarutaru hou; e arahi ana ia i ahau ki te taha o nga wai ata rere. 3 Ko ia hei whakahoki ake i toku wairua: e arahi ana ia i ahau i nga ara o te tika, he whakaaro ki tona ingoa. 4 Ae, ahakoa haere ahau i te awaawa o te atarangi o te mate, kahore he kino e wehi ai ahau: no te mea kei toku taha koe; ko tau rakau, ko tau tokotoko, ko ena hei oranga ngakau moku. 5 E taka ana e koe he tepu ki toku aroaro i te tirohanga a oku hoariri, e whakawahia ana e koe toku matenga ki te hinu, purena tonu taku kapu. 6 He pono e aru i ahau te pai me te atawhai i nga ra katoa e ora ai ahau, a ka noho ahau ki te whare o Ihowa ake tonu atu.

love joy peace faith blessing family

aroha hari rangimarie whakapono manaaki whanau

Taming a Beast called UNIX

The year was 1988. Voices hushed in trepidation, the apprentices gathered in a dingy corner of the Engineering building. In the undergraduate computer lab we assembled to offer sacrifices to the mainframe, hunched over the fading amber or green glow of hesitant dumb terminals, all connected to the mighty UNIX (VAX/VMS) mainframe. Poor first year acolytes we were, learning various complex incantations to extract data from the Beast. We learned to navigate the perils of UNIX: using ed, vi, man, fortran, and other strange spells to tame the Beast. For some of those innocent souls, the Beast caused them to cringe in fear and retreat to a “lesser” academic career, or flee gibbering and drooling in fear. Alas, I was an overconfident youth whose world was shattered by the Beast. So it was that I gave up my dream of conquest and glory.

But fate is fickle, and the world ever turns. So it was that seven years later, after a journeyman’s life, I wandered accidentally back into the nether realms of UNIX. However this time, I was different — stronger in body and mind from years of hard labour — and was wary of the nature of the Beast. Also, Unix itself was a different creature, somewhat mellowed with age, more tractable, less hostile: even unto supporting lower-case symbols and X-windows. So it was that an uneasy truce was forged between Unix and I. We learned to work together. Thus it was that I saw the Beast in a different light: a creature of mankind designed to serve, but only those who prove themselves worthy by mastering its secrets.

One of my greatest masterpieces was written in g77, the GNU port of Fortran. This program applies the Revised Simplex Method in two phases to find the optimal solution to a set of linear equations. I can’t remember all the mathematical theory and strategies involved, but the code still looks cool. For posterity I now give it to the world.

      program main

      implicit none                ! Set up variables..
      integer o,p
      parameter(o=20,p=100)
      integer i,j,m,n,r,s
      integer apos(o),bpos(o)
      real A(o,p),Bi(o,o),b(o),xb(o),cost(p),ca(o+p)
                                   ! Read data..
      open(unit=8,file='lp.dat',status='old')
      open(unit=9,file='lp.out',status='new')
      read(8,*) m,n
      if (m.gt.o.or.n.gt.p) then
        write(9,*)'Exceeded variable/constraint limits'
      endif
      read(8,*) (cost(j),j=1,n)
      write(9,*) 'm    ',m
      write(9,*) 'n    ',n
      write(9,*) 'c''  ',(cost(j),j=1,n)
      write(9,*)
      write(9,*) 'A.x = b'
      do i=1,m
        read(8,*) (A(i,j),j=1,n),b(i)
        write(9,*) (A(i,j),j=1,n),' =',b(i)
      enddo
c ------------------extra bit..-----------------
      do i=1,m
        read(8,*) (Bi(i,j),j=1,m)
        write(9,*) (Bi(i,j),j=1,m)
      enddo
      read(8,*) (bpos(i),i=1,m)
      write(9,*) (bpos(i),i=1,m)
      read(8,*) (apos(i),i=1,n)
      write(9,*) (apos(i),i=1,n)
      do i=1,m
        do j=1,m
          xb(i)=xb(i)+Bi(i,j)*b(j)
        enddo
      enddo
      goto 5
c -----------------------miss out for now------------------------
      write(9,*)
      write(9,*) 'Phase 1'
      do i=1,n                     ! Phase 1
        ca(i)=0                    !  Prepare artificial cost,basis,variables
        apos(i)=0                  !  all original variables are nonbasic
      enddo
      do i=1,m
        do j=1,m
          Bi(i,j)=0                !  initially Bi = identity matrix, I
        enddo
        Bi(i,i)=1
        ca(n+i)=1                  !  artificial cost vector now constructed
        bpos(i)=n+i                !  artificial variables fill the basis
        xb(i)=b(i)                 !  initially xb = b (because xb=Bi.b, Bi=I)
      enddo
      call rsm(m,n,A,Bi,b,xb,ca,bpos,apos,1)
c ---------------------------------------------------------------
5     write(9,*)
      write(9,*) 'Phase 2'
                                   ! Phase 2
                                   !  Now do RSM with the new basis
      call rsm(m,n,A,Bi,b,xb,cost,bpos,apos,2)
      end
C--------------------------------------------------

      subroutine rsm(m,n,A,Bi,b,xb,c,bpos,apos,phase)
      parameter(o=20,p=100)
      integer apos(n),bpos(m),phase      ! variables passed to rsm
      real A(o,p),Bi(o,o),b(m),c(n+m)    !     "
      integer i,j,imax,r,s,note          ! introducing new variables
      real bestrc,bias(m),pi(m),xb(m),z  !     "
      character retval

      imax=2*(m+n)
      tiny=1E-10
      i=0
      call currentsoln(Bi,b,bpos,c,m,xb,z)
1     if (i.lt.imax) then                       ! Iterate Revised Simplex Method..
        i=i+1
        call computedual(Bi,c,bpos,m,n,pi)      ! find pi (initially pi=e)
        call reducedcost(A,c,pi,apos,m,n,s,bestrc)
        if(s.eq.0) then
          if(z.gt.tiny.and.phase.eq.1) then
            write(9,*) '  Infeasibility detected.'
            note=-2
          else
            write(9,*) '  Optimality reached.'
            note=1
          endif
          goto 3
        endif
        call mivitwwbias(A,Bi,m,s,bias)
        call lvratiotest(xb,bias,m,n,r,phase,bpos)
        if (r.eq.0) then
          write(9,*) '  Unboundedness detected.'
          note=-1
          goto 3
        endif
        write(9,*) 'basisupdate:'
        write(9,*) '  bpos',(bpos(j),j=1,m),'   apos',(apos(j),j=1,n)
        call basisupdate(Bi,bias,c,pi,xb,bpos,apos,m,n,r,s)
        write(9,*) '    ->',(bpos(j),j=1,m),'     ->',(apos(j),j=1,n)
        call currentsoln(Bi,b,bpos,c,m,xb,z)
       else
        goto 3
      endif
2     goto 1
3     write(9,*) '  RSM iterations executed: ',i
      end
C-----------------------------------------------------

      subroutine currentsoln(Bi,b,bpos,c,m,xb,z)
      parameter(o=20)
      integer bpos(*)                     ! old
      real Bi(o,o),b(*),c(*),xb(*),z      ! old
      integer i,j                         ! new
      z=0
      do i=1,m
        z=z+c(bpos(i))*xb(i)
      enddo     

      write(9,*) 'currentsoln:  Bi, xb'
      do i=1,m
      write(9,*) ' ',(Bi(i,j),j=1,m),'     x',bpos(i),' =',xb(i)
      enddo
      write(9,*)
      write(9,*) '  --------------------------- Objective value z =',z
      write(9,*)
      end
C-----------------------------------------------------

      subroutine computedual(Bi,c,bpos,m,n,pi)
      parameter(o=20)
      integer bpos(*)                     ! old
      real Bi(o,o),c(*),pi(*)             ! old
      integer i,j,k                       ! new
      do i=1,m
        pi(i)=0
        do j=1,m
          k=bpos(j)
          pi(i)=pi(i)+c(k)*Bi(j,i)
        enddo
      enddo
      write(9,*) 'computedual:    pi ',(pi(i),i=1,m)
      end
C----------------------------------------------------

      subroutine reducedcost(A,c,pi,apos,m,n,s,bestrc)
      parameter(o=20,p=100)
      integer apos(*),s                   ! old
      real A(o,p),c(*),pi(*),bestrc       ! old
      integer i,j                         ! new
      real rc,pian,tiny                   ! new
      rc=0
      bestrc=0
      tiny=-1E-10
      do i=1,n                     !  determine entering var x(s)
        if(apos(i).eq.0) then      !< look at nonbasic columns
          pian=0                   !  (never price artificials)
          do j=1,m
            pian=pian+pi(j)*A(j,i)
          enddo
          rc=c(i)-pian             !< red. cost for nonbasic x(i)
          if(rc.lt.bestrc) then
            bestrc=rc
            s=i
          endif
        endif
      enddo
      if(bestrc.ge.tiny) then      !< This means no ev was found,
        s=0                        !  optimality has been reached,
      endif                        !  so flag s to 0
      write(9,*) 'reducedcost:    x',s,' enters with rc',bestrc
      end
C----------------------------------------------------

      subroutine mivitwwbias(A,Bi,m,s,bias)
      parameter(o=20,p=100)
      real A(o,p),Bi(o,o),bias(*)
      integer i,j,s
      do i=1,m                     !  a quick calculation of bias,
        bias(i)=0                  !  aka. the most important vector
        do j=1,m                   !  in the whole world.
          bias(i)=bias(i)+Bi(i,j)*A(j,s)
          enddo
        enddo
      write(9,*) 'mivitwwbias:    bias',(bias(j),j=1,m)
      end
C----------------------------------------------------

      subroutine lvratiotest(xb,bias,m,n,r,phase,bpos)
      integer bpos(*),r,phase      ! old
      real xb(*),bias(*)           ! old
      integer i                    ! new
      real ratio,rmin,tiny         ! new
      r=0                          ! r=0 returned if no lv can be found
      tiny=1E-10
      teeny=-1E-10
      rmin=10E+10
      do i=1,m
        if(bpos(i).gt.n.and.phase.eq.2) then
                                   ! Artificial present in phase2 basis:
                                   ! Extended lv routine to force out
                                   !   artificial variables..
          if(bias(i).lt.teeny.or.bias(i).gt.tiny) then
            rmin=0
            r=i
          endif
        else                       ! Usual lv routine..
          if(bias(i).gt.tiny) then !   ratio = rate of change of xb(i), as
            ratio=xb(i)/bias(i)    !           xs increases from 0 (enters)
            if(ratio.lt.rmin) then
              rmin=ratio           !   the leaving variable is xb(r), the
              r=i                  !   basic variable which decreases most
            endif                  !   rapidly as xs enters.
          endif
        endif
      enddo
      write(9,*) 'lvratiotest:    xb',r,' leaves.'
      end
C----------------------------------------------------

      subroutine basisupdate(Bi,bias,c,pi,xb,bpos,apos,m,n,r,s)
      parameter(o=20)
      integer apos(*),bpos(*),m,n,r,s        ! old
      real Bi(o,o),bias(*),c(*),pi(*),xb(*)  ! old
      integer i,j                            ! new
      do i=1,m                     ! do gauss-jordan pivot on rth element
        if(i.eq.r) then            ! of bias, and thus also on Bi and xb
          do j=1,m
            Bi(r,j)=Bi(r,j)/bias(r)
            enddo
          xb(r)=xb(r)/bias(r)
        else
          do j=1,m
            Bi(i,j)=Bi(i,j)-bias(i)/bias(r)*Bi(r,j)
            enddo
          xb(i)=xb(i)-bias(i)/bias(r)*xb(r)
        endif
      enddo
      if(bpos(r).le.n) then
        apos(bpos(r))=0              ! xb(r) now nonbasic; 0 in apos
      endif
      bpos(r)=s                      ! xb(r) replaced by xs in bpos
      apos(s)=r                      ! xs located in rth basic position
      end

simplex.f
Note: the above code has not been compiled or executed since sometime around 1998.

Here are some problems solved using this glorious program.