Palaeontology 2.0

Maastrichtian Dinosaur Provinciality

mvavrek — Fri, 23 Apr 2010 17:42:08 +0000

Hans Larsson and I had our paper published recently in PNAS on the low beta diversity of Maastrichtian dinosaurs in the Western Interior. Hopefully a few people will read the methods and notice that we used the fossil package to do a lot of the stats in it, and others might start using it as well. If you have any questions about the paper or the package, feel free to contact me any time.

Teaching

mvavrek — Thu, 11 Mar 2010 07:24:41 +0000

I have been reading a bunch of articles lately on education, and how to improve it. It’s been making me think a lot about my own education, especially in university. I just want to know if the major universities are ever going to give education more than a fleeting thought. Obviously, research is very important, but at what point should it be to the exclusion of teaching? If you never take the time to teach others what you know, then what? Knowledge not passed along is knowledge lost. I would hate to have toiled away at my research, uncovering new things, but not have shared that with others before I died. And I mean more than what can be passed along in a journal article. Too many journal articles are never read anyhow; if you actually take the time to teach someone what you know, then you know that knowledge will have been passed on. And when I talk about teaching, I mean more than just standing in front of a room and saying words. There was a class in university that I went to less than half the time, and I did better for it because I didn’t get confused by the abysmal teacher reading nothing but equations off a Powerpoint slide. I think that too often, profs forget that the people they are teaching could become some of the most important people in their lives: namely, politicians. If these future politicians (and their constituents) a never taught how exciting or amazing a subject is, that subject might not get as much funding the next year, because nobody cares about it. Teaching can be in your own self interests.

Building a Better Teacher (NYT)

Why We Must Fire Bad Teachers

Fixing US STEM education is possible, but will take money

fossil Package Updated to 0.2.4

mvavrek — Wed, 20 Jan 2010 23:37:28 +0000

I just uploaded a new version of fossil to the CRAN website, with a number of changes. There are some fixes in the way the spp.est() function was handling abundance data, and I’ve added a small species/locality dataset that I used for a number of new examples in the package. I’m also currently working on a new clustering method to include, but it’s still being worked on at the moment. Hopefully it’ll be in the package before too long.

Enjoy!

LaTeX and Palaeontologia Electronica

mvavrek — Mon, 18 Jan 2010 05:56:16 +0000

I’ve been trying to prepare a manuscript for submission to Palaeontologia Electronica (PE), and as my workflow at the moment has been revolving around LaTeX, I took te plunge into creating my own custom bibliography style file in PE format. Luckily for me I could use the great makebst.tex file by Patrick W. Daly which simplified the process to a series of multiple choice questions. I somehow doubt that there is that many other palaeontologists using LaTeX for manuscript submissions, but anyhow here’s the palelec.bst file (I can’t upload .bst files to this site, so just copy and save the text in a text editor as palelec.bst). Hopefully it works, as I’ve been fighting a bit with WordPress to get it to render properly, but if need be, you can always contact me and I can send out a copy of the original .bst file.

%%
%% This is file `palelec.bst',
%% generated with the docstrip utility.
%%
%% The original source files were:
%%
%% merlin.mbs  (with options: `ay,nat,nm-rvvc,keyxyr,dt-beg,yr-per,yrp-per,note-yr,vnum-x,num-xser,ser-ed,pre-edn,edpar,pp,ed,xedn,nfss,')
%% ----------------------------------------
%% *** Reference style for Palaeontologica Electronica ***
%%
%% Copyright 1994-2008 Patrick W Daly
 % ===============================================================
 % IMPORTANT NOTICE:
 % This bibliographic style (bst) file has been generated from one or
 % more master bibliographic style (mbs) files, listed above.
 %
 % This generated file can be redistributed and/or modified under the terms
 % of the LaTeX Project Public License Distributed from CTAN
 % archives in directory macros/latex/base/lppl.txt; either
 % version 1 of the License, or any later version.
 % ===============================================================
 % Name and version information of the main mbs file:
 % \ProvidesFile{merlin.mbs}[2008/10/04 4.30 (PWD, AO, DPC)]
 %   For use with BibTeX version 0.99a or later
 %-------------------------------------------------------------------
 % This bibliography style file is intended for texts in ENGLISH
 % This is an author-year citation style bibliography. As such, it is
 % non-standard LaTeX, and requires a special package file to function properly.
 % Such a package is    natbib.sty   by Patrick W. Daly
 % The form of the \bibitem entries is
 %   \bibitem[Jones et al.(1990)]{key}...
 %   \bibitem[Jones et al.(1990)Jones, Baker, and Smith]{key}...
 % The essential feature is that the label (the part in brackets) consists
 % of the author names, as they should appear in the citation, with the year
 % in parentheses following. There must be no space before the opening
 % parenthesis!
 % With natbib v5.3, a full list of authors may also follow the year.
 % In natbib.sty, it is possible to define the type of enclosures that is
 % really wanted (brackets or parentheses), but in either case, there must
 % be parentheses in the label.
 % The \cite command functions as follows:
 %   \citet{key} ==>>                Jones et al. (1990)
 %   \citet*{key} ==>>               Jones, Baker, and Smith (1990)
 %   \citep{key} ==>>                (Jones et al., 1990)
 %   \citep*{key} ==>>               (Jones, Baker, and Smith, 1990)
 %   \citep[chap. 2]{key} ==>>       (Jones et al., 1990, chap. 2)
 %   \citep[e.g.][]{key} ==>>        (e.g. Jones et al., 1990)
 %   \citep[e.g.][p. 32]{key} ==>>   (e.g. Jones et al., 1990, p. 32)
 %   \citeauthor{key} ==>>           Jones et al.
 %   \citeauthor*{key} ==>>          Jones, Baker, and Smith
 %   \citeyear{key} ==>>             1990
 %---------------------------------------------------------------------

ENTRY
  { address
    author
    booktitle
    chapter
    edition
    editor
    eid
    howpublished
    institution
    journal
    key
    month
    note
    number
    organization
    pages
    publisher
    school
    series
    title
    type
    volume
    year
  }
  {}
  { label extra.label sort.label short.list }
INTEGERS { output.state before.all mid.sentence after.sentence after.block }
FUNCTION {init.state.consts}
{ #0 'before.all :=
  #1 'mid.sentence :=
  #2 'after.sentence :=
  #3 'after.block :=
}
STRINGS { s t}
FUNCTION {output.nonnull}
{ 's :=
  output.state mid.sentence =
    { ", " * write$ }
    { output.state after.block =
        { add.period$ write$
          newline$
          "\newblock " write$
        }
        { output.state before.all =
            'write$
            { add.period$ " " * write$ }
          if$
        }
      if$
      mid.sentence 'output.state :=
    }
  if$
  s
}
FUNCTION {output}
{ duplicate$ empty$
    'pop$
    'output.nonnull
  if$
}
FUNCTION {output.check}
{ 't :=
  duplicate$ empty$
    { pop$ "empty " t * " in " * cite$ * warning$ }
    'output.nonnull
  if$
}
FUNCTION {fin.entry}
{ add.period$
  write$
  newline$
}

FUNCTION {new.block}
{ output.state before.all =
    'skip$
    { after.block 'output.state := }
  if$
}
FUNCTION {new.sentence}
{ output.state after.block =
    'skip$
    { output.state before.all =
        'skip$
        { after.sentence 'output.state := }
      if$
    }
  if$
}
FUNCTION {add.blank}
{  " " * before.all 'output.state :=
}

FUNCTION {date.block}
{
  new.block
}

FUNCTION {not}
{   { #0 }
    { #1 }
  if$
}
FUNCTION {and}
{   'skip$
    { pop$ #0 }
  if$
}
FUNCTION {or}
{   { pop$ #1 }
    'skip$
  if$
}
FUNCTION {new.block.checkb}
{ empty$
  swap$ empty$
  and
    'skip$
    'new.block
  if$
}
FUNCTION {field.or.null}
{ duplicate$ empty$
    { pop$ "" }
    'skip$
  if$
}
FUNCTION {emphasize}
{ duplicate$ empty$
    { pop$ "" }
    { "\emph{" swap$ * "}" * }
  if$
}
FUNCTION {tie.or.space.prefix}
{ duplicate$ text.length$ #3  }
    { s nameptr
      "{vv~}{ll}{, jj}{, f{.}.}"
      format.name$
      bibinfo bibinfo.check
      't :=
      nameptr #1 >
        {
          namesleft #1 >
            { ", " * t * }
            {
              s nameptr "{ll}" format.name$ duplicate$ "others" =
                { 't := }
                { pop$ }
              if$
              numnames #2 >
                { "," * }
                'skip$
              if$
              t "others" =
                {
                  " " * bbl.etal *
                }
                {
                  bbl.and
                  space.word * t *
                }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
  } if$
}
FUNCTION {format.names.ed}
{
  'bibinfo :=
  duplicate$ empty$ 'skip$ {
  's :=
  "" 't :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr
      "{f{.}.~}{vv~}{ll}{ jj}"
      format.name$
      bibinfo bibinfo.check
      't :=
      nameptr #1 >
        {
          namesleft #1 >
            { ", " * t * }
            {
              s nameptr "{ll}" format.name$ duplicate$ "others" =
                { 't := }
                { pop$ }
              if$
              numnames #2 >
                { "," * }
                'skip$
              if$
              t "others" =
                {

                  " " * bbl.etal *
                }
                {
                  bbl.and
                  space.word * t *
                }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
  } if$
}
FUNCTION {format.key}
{ empty$
    { key field.or.null }
    { "" }
  if$
}

FUNCTION {format.authors}
{ author "author" format.names
}
FUNCTION {get.bbl.editor}
{ editor num.names$ #1 > 'bbl.editors 'bbl.editor if$ }

FUNCTION {format.editors}
{ editor "editor" format.names duplicate$ empty$ 'skip$
    {
      " " *
      get.bbl.editor
   "(" swap$ * ")" *
      *
    }
  if$
}
FUNCTION {format.note}
{
 note empty$
    { "" }
    { note #1 #1 substring$
      duplicate$ "{" =
        'skip$
        { output.state mid.sentence =
          { "l" }
          { "u" }
        if$
        change.case$
        }
      if$
      note #2 global.max$ substring$ * "note" bibinfo.check
    }
  if$
}

FUNCTION {format.title}
{ title
  duplicate$ empty$ 'skip$
    { "t" change.case$ }
  if$
  "title" bibinfo.check
}
FUNCTION {format.full.names}
{'s :=
 "" 't :=
  #1 'nameptr :=
  s num.names$ 'numnames :=
  numnames 'namesleft :=
    { namesleft #0 > }
    { s nameptr
      "{vv~}{ll}" format.name$
      't :=
      nameptr #1 >
        {
          namesleft #1 >
            { ", " * t * }
            {
              s nameptr "{ll}" format.name$ duplicate$ "others" =
                { 't := }
                { pop$ }
              if$
              t "others" =
                {
                  " " * bbl.etal *
                }
                {
                  numnames #2 >
                    { "," * }
                    'skip$
                  if$
                  bbl.and
                  space.word * t *
                }
              if$
            }
          if$
        }
        't
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {author.editor.key.full}
{ author empty$
    { editor empty$
        { key empty$
            { cite$ #1 #3 substring$ }
            'key
          if$
        }
        { editor format.full.names }
      if$
    }
    { author format.full.names }
  if$
}

FUNCTION {author.key.full}
{ author empty$
    { key empty$
         { cite$ #1 #3 substring$ }
          'key
      if$
    }
    { author format.full.names }
  if$
}

FUNCTION {editor.key.full}
{ editor empty$
    { key empty$
         { cite$ #1 #3 substring$ }
          'key
      if$
    }
    { editor format.full.names }
  if$
}

FUNCTION {make.full.names}
{ type$ "book" =
  type$ "inbook" =
  or
    'author.editor.key.full
    { type$ "proceedings" =
        'editor.key.full
        'author.key.full
      if$
    }
  if$
}

FUNCTION {output.bibitem}
{ newline$
  "\bibitem[{" write$
  label write$
  ")" make.full.names duplicate$ short.list =
     { pop$ }
     { * }
   if$
  "}]{" * write$
  cite$ write$
  "}" write$
  newline$
  ""
  before.all 'output.state :=
}

FUNCTION {n.dashify}
{
  't :=
  ""
    { t empty$ not }
    { t #1 #1 substring$ "-" =
        { t #1 #2 substring$ "--" = not
            { "--" *
              t #2 global.max$ substring$ 't :=
            }
            {   { t #1 #1 substring$ "-" = }
                { "-" *
                  t #2 global.max$ substring$ 't :=
                }
              while$
            }
          if$
        }
        { t #1 #1 substring$ *
          t #2 global.max$ substring$ 't :=
        }
      if$
    }
  while$
}

FUNCTION {word.in}
{ bbl.in capitalize
  " " * }

FUNCTION {format.date}
{ year "year" bibinfo.check duplicate$ empty$
    {
      "empty year in " cite$ * "; set to ????" * warning$
       pop$ "????"
    }
    'skip$
  if$
  extra.label *
  before.all 'output.state :=
  after.sentence 'output.state :=
}
FUNCTION {format.btitle}
{ title "title" bibinfo.check
  duplicate$ empty$ 'skip$
    {
      emphasize
    }
  if$
}
FUNCTION {either.or.check}
{ empty$
    'pop$
    { "can't use both " swap$ * " fields in " * cite$ * warning$ }
  if$
}
FUNCTION {format.bvolume}
{ volume empty$
    { "" }
    { bbl.volume volume tie.or.space.prefix
      "volume" bibinfo.check * *
      series "series" bibinfo.check
      duplicate$ empty$ 'pop$
        { swap$ bbl.of space.word * swap$
          emphasize * }
      if$
      "volume and number" number either.or.check
    }
  if$
}
FUNCTION {format.number.series}
{ volume empty$
    { number empty$
        { series field.or.null }
        { series empty$
            { number "number" bibinfo.check }
            { output.state mid.sentence =
                { bbl.number }
                { bbl.number capitalize }
              if$
              number tie.or.space.prefix "number" bibinfo.check * *
              bbl.in space.word *
              series "series" bibinfo.check *
            }
          if$
        }
      if$
    }
    { "" }
  if$
}

FUNCTION {format.edition}
{ edition duplicate$ empty$ 'skip$
    {
      output.state mid.sentence =
        { "l" }
        { "t" }
      if$ change.case$
      "edition" bibinfo.check
      " " * bbl.edition *
    }
  if$
}
INTEGERS { multiresult }
FUNCTION {multi.page.check}
{ 't :=
  #0 'multiresult :=
    { multiresult not
      t empty$ not
      and
    }
    { t #1 #1 substring$
      duplicate$ "-" =
      swap$ duplicate$ "," =
      swap$ "+" =
      or or
        { #1 'multiresult := }
        { t #2 global.max$ substring$ 't := }
      if$
    }
  while$
  multiresult
}
FUNCTION {format.pages}
{ pages duplicate$ empty$ 'skip$
    { duplicate$ multi.page.check
        {
          bbl.pages swap$
          n.dashify
        }
        {
          bbl.page swap$
        }
      if$
      tie.or.space.prefix
      "pages" bibinfo.check
      * *
    }
  if$
}
FUNCTION {format.journal.pages}
{ pages duplicate$ empty$ 'pop$
    { swap$ duplicate$ empty$
        { pop$ pop$ format.pages }
        {
          ":" *
          swap$
          n.dashify
          "pages" bibinfo.check
          *
        }
      if$
    }
  if$
}
FUNCTION {format.journal.eid}
{ eid "eid" bibinfo.check
  duplicate$ empty$ 'pop$
    { swap$ duplicate$ empty$ 'skip$
      {
          ":" *
      }
      if$
      swap$ *
    }
  if$
}
FUNCTION {format.vol.num.pages}
{ volume field.or.null
  duplicate$ empty$ 'skip$
    {
      "volume" bibinfo.check
    }
  if$
  eid empty$
    { format.journal.pages }
    { format.journal.eid }
  if$
}

FUNCTION {format.chapter.pages}
{ chapter empty$
    'format.pages
    { type empty$
        { bbl.chapter }
        { type "l" change.case$
          "type" bibinfo.check
        }
      if$
      chapter tie.or.space.prefix
      "chapter" bibinfo.check
      * *
      pages empty$
        'skip$
        { ", " * format.pages * }
      if$
    }
  if$
}

FUNCTION {format.booktitle}
{
  booktitle "booktitle" bibinfo.check
  emphasize
}
FUNCTION {format.in.ed.booktitle}
{ format.booktitle duplicate$ empty$ 'skip$
    {
      format.bvolume duplicate$ empty$ 'pop$
        { ", " swap$ * * }
      if$
      editor "editor" format.names.ed duplicate$ empty$ 'pop$
        {
          " " *
          get.bbl.editor
          "(" swap$ * "), " *
          * swap$
          * }
      if$
      word.in swap$ *
    }
  if$
}
FUNCTION {format.thesis.type}
{ type duplicate$ empty$
    'pop$
    { swap$ pop$
      "t" change.case$ "type" bibinfo.check
    }
  if$
}
FUNCTION {format.tr.number}
{ number "number" bibinfo.check
  type duplicate$ empty$
    { pop$ bbl.techrep }
    'skip$
  if$
  "type" bibinfo.check
  swap$ duplicate$ empty$
    { pop$ "t" change.case$ }
    { tie.or.space.prefix * * }
  if$
}
FUNCTION {format.article.crossref}
{
  word.in
  " \cite{" * crossref * "}" *
}
FUNCTION {format.book.crossref}
{ volume duplicate$ empty$
    { "empty volume in " cite$ * "'s crossref of " * crossref * warning$
      pop$ word.in
    }
    { bbl.volume
      capitalize
      swap$ tie.or.space.prefix "volume" bibinfo.check * * bbl.of space.word *
    }
  if$
  " \cite{" * crossref * "}" *
}
FUNCTION {format.incoll.inproc.crossref}
{
  word.in
  " \cite{" * crossref * "}" *
}
FUNCTION {format.org.or.pub}
{ 't :=
  ""
  address empty$ t empty$ and
    'skip$
    {
      t empty$
        { address "address" bibinfo.check *
        }
        { t *
          address empty$
            'skip$
            { ", " * address "address" bibinfo.check * }
          if$
        }
      if$
    }
  if$
}
FUNCTION {format.publisher.address}
{ publisher "publisher" bibinfo.warn format.org.or.pub
}

FUNCTION {format.organization.address}
{ organization "organization" bibinfo.check format.org.or.pub
}

FUNCTION {article}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.title "title" output.check
  new.block
  crossref missing$
    {
      journal
      "journal" bibinfo.check
      emphasize
      "journal" output.check
      format.vol.num.pages output
    }
    { format.article.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  format.note output
  fin.entry
}
FUNCTION {book}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
      editor format.key output
    }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  format.date "year" output.check
  date.block
  format.btitle "title" output.check
  crossref missing$
    { format.bvolume output
      new.block
      format.number.series output
      format.edition output
      new.sentence
      format.publisher.address output
    }
    {
      new.block
      format.book.crossref output.nonnull
    }
  if$
  new.block
  format.note output
  fin.entry
}
FUNCTION {booklet}
{ output.bibitem
  format.authors output
  author format.key output
  format.date "year" output.check
  date.block
  format.title "title" output.check
  new.block
  howpublished "howpublished" bibinfo.check output
  address "address" bibinfo.check output
  new.block
  format.note output
  fin.entry
}

FUNCTION {inbook}
{ output.bibitem
  author empty$
    { format.editors "author and editor" output.check
      editor format.key output
    }
    { format.authors output.nonnull
      crossref missing$
        { "author and editor" editor either.or.check }
        'skip$
      if$
    }
  if$
  format.date "year" output.check
  date.block
  format.btitle "title" output.check
  crossref missing$
    {
      format.bvolume output
      format.chapter.pages "chapter and pages" output.check
      new.block
      format.number.series output
      format.edition output
      new.sentence
      format.publisher.address output
    }
    {
      format.chapter.pages "chapter and pages" output.check
      new.block
      format.book.crossref output.nonnull
    }
  if$
  new.block
  format.note output
  fin.entry
}

FUNCTION {incollection}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.number.series output
      format.edition output
      format.chapter.pages output
      new.sentence
      format.publisher.address output
    }
    { format.incoll.inproc.crossref output.nonnull
      format.chapter.pages output
    }
  if$
  new.block
  format.note output
  fin.entry
}
FUNCTION {inproceedings}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.title "title" output.check
  new.block
  crossref missing$
    { format.in.ed.booktitle "booktitle" output.check
      format.number.series output
      format.pages output
      new.sentence
      publisher empty$
        { format.organization.address output }
        { organization "organization" bibinfo.check output
          format.publisher.address output
        }
      if$
    }
    { format.incoll.inproc.crossref output.nonnull
      format.pages output
    }
  if$
  new.block
  format.note output
  fin.entry
}
FUNCTION {conference} { inproceedings }
FUNCTION {manual}
{ output.bibitem
  format.authors output
  author format.key output
  format.date "year" output.check
  date.block
  format.btitle "title" output.check
  organization address new.block.checkb
  organization "organization" bibinfo.check output
  address "address" bibinfo.check output
  format.edition output
  new.block
  format.note output
  fin.entry
}

FUNCTION {mastersthesis}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.btitle
  "title" output.check
  new.block
  bbl.mthesis format.thesis.type output.nonnull
  school "school" bibinfo.warn output
  address "address" bibinfo.check output
  new.block
  format.note output
  fin.entry
}

FUNCTION {misc}
{ output.bibitem
  format.authors output
  author format.key output
  format.date "year" output.check
  date.block
  format.title output
  new.block
  howpublished "howpublished" bibinfo.check output
  new.block
  format.note output
  fin.entry
}
FUNCTION {phdthesis}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.btitle
  "title" output.check
  new.block
  bbl.phdthesis format.thesis.type output.nonnull
  school "school" bibinfo.warn output
  address "address" bibinfo.check output
  new.block
  format.note output
  fin.entry
}

FUNCTION {proceedings}
{ output.bibitem
  format.editors output
  editor format.key output
  format.date "year" output.check
  date.block
  format.btitle "title" output.check
  format.bvolume output
  format.number.series output
  new.sentence
  publisher empty$
    { format.organization.address output }
    { organization "organization" bibinfo.check output
      format.publisher.address output
    }
  if$
  new.block
  format.note output
  fin.entry
}

FUNCTION {techreport}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.title
  "title" output.check
  new.block
  format.tr.number output.nonnull
  institution "institution" bibinfo.warn output
  address "address" bibinfo.check output
  new.block
  format.note output
  fin.entry
}

FUNCTION {unpublished}
{ output.bibitem
  format.authors "author" output.check
  author format.key output
  format.date "year" output.check
  date.block
  format.title "title" output.check
  new.block
  format.note "note" output.check
  fin.entry
}

FUNCTION {default.type} { misc }
READ
FUNCTION {sortify}
{ purify$
  "l" change.case$
}
INTEGERS { len }
FUNCTION {chop.word}
{ 's :=
  'len :=
  s #1 len substring$ =
    { s len #1 + global.max$ substring$ }
    's
  if$
}
FUNCTION {format.lab.names}
{ 's :=
  "" 't :=
  s #1 "{vv~}{ll}" format.name$
  s num.names$ duplicate$
  #2 >
    { pop$
      " " * bbl.etal *
    }
    { #2  }
    { s nameptr
      "{vv{ } }{ll{ }}{  f{ }}{  jj{ }}"
      format.name$ 't :=
      nameptr #1 >
        {
          "   "  *
          namesleft #1 = t "others" = and
            { "zzzzz" 't := }
            'skip$
          if$
          t sortify *
        }
        { t sortify * }
      if$
      nameptr #1 + 'nameptr :=
      namesleft #1 - 'namesleft :=
    }
  while$
}

FUNCTION {sort.format.title}
{ 't :=
  "A " #2
    "An " #3
      "The " #4 t chop.word
    chop.word
  chop.word
  sortify
  #1 global.max$ substring$
}
FUNCTION {author.sort}
{ author empty$
    { key empty$
        { "to sort, need author or key in " cite$ * warning$
          ""
        }
        { key sortify }
      if$
    }
    { author sort.format.names }
  if$
}
FUNCTION {author.editor.sort}
{ author empty$
    { editor empty$
        { key empty$
            { "to sort, need author, editor, or key in " cite$ * warning$
              ""
            }
            { key sortify }
          if$
        }
        { editor sort.format.names }
      if$
    }
    { author sort.format.names }
  if$
}
FUNCTION {editor.sort}
{ editor empty$
    { key empty$
        { "to sort, need editor or key in " cite$ * warning$
          ""
        }
        { key sortify }
      if$
    }
    { editor sort.format.names }
  if$
}
FUNCTION {presort}
{ calc.label
  label sortify
  "    "
  *
  type$ "book" =
  type$ "inbook" =
  or
    'author.editor.sort
    { type$ "proceedings" =
        'editor.sort
        'author.sort
      if$
    }
  if$
  #1 entry.max$ substring$
  'sort.label :=
  sort.label
  *
  "    "
  *
  title field.or.null
  sort.format.title
  *
  #1 entry.max$ substring$
  'sort.key$ :=
}

ITERATE {presort}
SORT
STRINGS { last.label next.extra }
INTEGERS { last.extra.num last.extra.num.extended last.extra.num.blank number.label }
FUNCTION {initialize.extra.label.stuff}
{ #0 int.to.chr$ 'last.label :=
  "" 'next.extra :=
  #0 'last.extra.num :=
  "a" chr.to.int$ #1 - 'last.extra.num.blank :=
  last.extra.num.blank 'last.extra.num.extended :=
  #0 'number.label :=
}
FUNCTION {forward.pass}
{ last.label label =
    { last.extra.num #1 + 'last.extra.num :=
      last.extra.num "z" chr.to.int$ >
       { "a" chr.to.int$ 'last.extra.num :=
         last.extra.num.extended #1 + 'last.extra.num.extended :=
       }
       'skip$
      if$
      last.extra.num.extended last.extra.num.blank >
        { last.extra.num.extended int.to.chr$
          last.extra.num int.to.chr$
          * 'extra.label := }
        { last.extra.num int.to.chr$ 'extra.label := }
      if$
    }
    { "a" chr.to.int$ 'last.extra.num :=
      "" 'extra.label :=
      label 'last.label :=
    }
  if$
  number.label #1 + 'number.label :=
}
FUNCTION {reverse.pass}
{ next.extra "b" =
    { "a" 'extra.label := }
    'skip$
  if$
  extra.label 'next.extra :=
  extra.label
  duplicate$ empty$
    'skip$
    { "{\natexlab{" swap$ * "}}" * }
  if$
  'extra.label :=
  label extra.label * 'label :=
}
EXECUTE {initialize.extra.label.stuff}
ITERATE {forward.pass}
REVERSE {reverse.pass}
FUNCTION {bib.sort.order}
{ sort.label
  "    "
  *
  year field.or.null sortify
  *
  "    "
  *
  title field.or.null
  sort.format.title
  *
  #1 entry.max$ substring$
  'sort.key$ :=
}
ITERATE {bib.sort.order}
SORT
FUNCTION {begin.bib}
{ preamble$ empty$
    'skip$
    { preamble$ write$ newline$ }
  if$
  "\begin{thebibliography}{" number.label int.to.str$ * "}" *
  write$ newline$
  "\providecommand{\natexlab}[1]{#1}"
  write$ newline$
}
EXECUTE {begin.bib}
EXECUTE {init.state.consts}
ITERATE {call.type$}
FUNCTION {end.bib}
{ newline$
  "\end{thebibliography}" write$ newline$
}
EXECUTE {end.bib}
%% End of customized bst file
%%
%% End of file `palelec.bst'.

Reproducible Results: Not Likely

mvavrek — Tue, 22 Sep 2009 04:26:17 +0000

A PLoS article this week puts some numbers (small, though they may be) on how truly free and open scientists are in sharing their data. For the article, the authors sent information requests for data previously published on in PLoS journals. The thing about these journals is that they have an explicit data sharing policy, which makes it clear that the raw data sets they use in their analyses must be made available to other researchers.

Just a little history about the PLoS journals: they were originally set up with the ideal of Open Access as a founding tenet. This included not only sharing your data but making the journal itself freely accessible to anyone, free of subscription.

But back to the article itself. THe authors found that out of 10 requests for data, they recieved only one dataset. In fact, some of the data holders seemed rather indignant in the thought that someone might actually want to look at THEIR data, as I’m sure they thought the only reason why would be for the requesters to scoop the next big story to come out of these datasets.

In the end, this study only really serves to emphasize the fact that science is still a very closed (and I would say, closeminded) place to work in.

Evolution Essentials

mvavrek — Sun, 20 Sep 2009 04:00:01 +0000

A great summary on Ars Technica about 5 essential things that most people don’t understand about evolution. It’s a good read even if you do think you know a lot about evolution, as it emphasizes some points that I think are often muddled in a lot of scientific discussions (subobtimal solutions being better than no solution, for example).

Patented Phylogenetics

mvavrek — Sun, 13 Sep 2009 06:23:30 +0000

Ars Technica has a story about how Microsoft tried to patent clustering phylogenetic methods. If the patent would have gone through, it could have meant that anyone who wanted to use a phylogenetics clustering program (PAUP, Mesquite, etc) would have suddenly found themselves unable to do so, at least not without paying Microsoft first the associated fees for licensing their patent (or else by pirating the software, which seems to be a common theme in cash strapped labs). Luckily, there is plenty of prior art (meaning, Microsoft was obviously not the first person to do it), so they won’t be granted the patent in the end. Something like this makes an (arguably) good case for scientists to release any code and programs they produce under an Open Source license, which in effect would preserve their work in the public domain for future scientists to use.

Creationism 2.0

mvavrek — Fri, 11 Sep 2009 06:20:33 +0000

If you happen to take William Dembski’s course on ‘Intellient Design’ at Southwestern Baptist Theological Seminary, you will be pleased to know that you can get an easy 20% of your mark from simply posting replies defending creationism ‘Intelligent Design’ on ‘hostile’ websites (presumably, that means ANY scientific website). Richard Dawkins (who is very intelligent while simultaneously arrogant, or at least so he seemed from the talk I saw) mentions this as well as plucking out some other gems from the course, such as a question from the Christian Faith and Science module which reads:

Trace the connections between Darwinian evolution, eugenics, abortion, infanticide, and euthanasia. Why are materialists so ready to embrace these as a package deal? What view of humanity and reality is required to resist them?

Remember kids: don’t evolve.

Zombie Defense: Strike Hard, Strike Often

mvavrek — Sun, 16 Aug 2009 21:43:29 +0000

Most people should remember from elementary school how we were supposed to create a fire escape plan for our house and practise it with our families, but what about other equally dangerous and deadly situations? I always found my school lacking in it’s zombie plague contingency plans; luckily we now have a better idea of a plan of action. Four students from Carleton and University of Ottawa have run different outbreak and response models (PDF) for zombie infection. Unfortunately, the news is not great. Only one scenario works in favour of non-zombies, that of a strike hard and strike often approach. Even at that, the authors are not entirely convinced the plan would be successful, especially as coordinating attacks during a time of turmoil would be very difficult. So remember to be on the lookout for zombies at all times, as the earlier the infection is caught, the more likely the human race may survive.

Death of the Dead Tree Journal

mvavrek — Sat, 15 Aug 2009 07:24:01 +0000

Ars Technica has a story on the American Chemical Society and their plans for switching most of their journals over to electronic format only. In some ways, the news may seem surprising, but at the same time, it does seem somewhat inevitable. I know that personally I do virtually all of my research online in some fashion. Anymore, if the article isn’t online and isn’t that vital to the work I’m doing, I’m not going to waste my time tracking it down when there are likely other papers that will work as well and are online, and I think this kind of attitude is (for better or worse) fairly common among my generation in the sciences. The days of the printed article are likely numbered. This is not to say that books will stop being published, but I see books (and by this I mean something I read for enjoyment) and journals (something I read for my job) as two different things. Journal articles are more useful to me if they are electronic, as then I can have them instantly in front of me without having to search through a filing cabinet, I don’t have the clutter of papers that I print of to skim once and never use again, and I can search with various tools to find what I want even if I can’t remember the specific paper. Books, on the other hand, I want to be able to enjoy slower and away from the distractions of a computer. I don’t need to search the text of a book and I like taking them to places where I have no power source, such as the park or camping. Books are more useful to me in dead tree format, and I will continue to buy them in that format. But I can honestly say that so long as I can access journals on line in high quality PDF format, that I won’t miss the fact that they’re no longer being printed. In fact, not printing them means lower costs for me in a couple of ways: research libraries no longer need to spend money building larger and larger buildings to hold journal collections that are rarely looked at; and (hopefully) journal subscription costs come down because of the savings of not having to pay for printing. Let the future begin.