Thursday, November 8, 2012

DIY Publishing with DocBook, Saxon, and Apache FO

Overview


Diagram Showing Build Process


This post is about simple, single source publishing using DocBook, that is, starting with DocBook XML markup you can transform it into other formats (like HTML and PDF) using freely available tools. DocBook is a common markup language for producing documentation.

Disclaimer: If you are serious about single source publishing using DocBook then what we show here is probably not for you ultimately. Rather, you'll want robust DocBook authoring tools like the the ones given here: DocBook Authoring Tools. We've had lots of experience with one of these tools, Oxygen XML Editor, and can say that after preparing this post we can appreciate what goes into it and tools like it are worth the money.

Should you keep reading? Keep reading if you are interested in playing around with DocBook to see what it is and how you use it, and you are moderately savvy around installing and running things on your computer. The goal of this post is to show a simple build process workflow for building DocBook into other output formats using free tools.

Motivation: Our original intent was to take the output from this blog (an RSS or Atom feed) and convert that to DocBook and then from there convert to whatever format we wanted like HTML, PDF, or epub. But before we can achieve that lofty goal we needed to step back and look at the simpler problem of transforming simple DocBook content into other formats. There are other sites, such as at vogella.com and cuddletech.com, that show this. So what do we add here? Here, we try to focus on a workflow that makes sense in addition to showing the tools that enable it. The basic workflow is this: author, transform, review, and repeat.

The project we develop here can be downloaded here.

Tools and Libraries Used

  • Eclipse
    • What is it?
      • Eclipse is a free toolset for software development.
    • Why use it?
      • It's free and easy to get. It has basic XML editing capabilities as well as many plugins you can get to help out with development and other tasks. For example, you can use the Vex editor for working with DocBook. Vex has command completion, but what we found is after a while working with DocBook you have pretty good idea of what tags go where.
      • Eclipse as an organizing principle of your workflow is a good concept since you can keep everything together in a project. With a project, sharing or moving the project is relatively easy using importing and exporting paradigms.
      • Also, ANT (a Java build tool) is built into Eclipse which makes developing a build process workflow easier. And, ANT tasks can be run at the command line for more flexibility.
  • Saxon.
    • What is it?
      • Saxon is a collection of tools for processing XML documents like DocBook source files.
    • Why use it?
      • There is a Saxon-HE - Home Edition that is free to use.
      • In our tests, it turned out to be flexible and have the least amount of things to download and assemble. There are just two JAR files to download. (Only one is really needed.)
      • It also was able to deal with XInclude which is a approach for merging many XML documents into one. XInclude allows you to include the contents of one XML document in another. In this post we use many XML files in a hierarchical arrangement to represent the source content. Again, it’s about workflow, so the ability to deal with many XML files was important. For more on processing modular documents, see the Sagehill book Chapter 23. Modular DocBook files.
      • Other options? We tried out the XSLT library and it worked, but Saxon seemed easier to use - just one JAR. We did not try Xalan.
  • Apache FO.
    • What is it?
      • Apache FOP http://xmlgraphics.apache.org/fop/ (Formatting Objects Processor) is software that can be used to process an intermediate stage of the transformation of DocBook markup to PDF. The intermediate stage are XSL formatting objects (XSL-FO) a markup language for paged media.
    • Why use it?
      • There doesn't seem like much else is available that is free.
  • DocBook Stylesheets
    • What are they?
      • We are transforming XML documents using XSL stylesheets (used in an XSLT engine like Saxon) to our desired output. The stylesheets are the instructions for performing the transformation. They stylesheets we'll use in this post are the ones that transform our source markup to HTML and to FO (formatting objects).
    • Why use them?
      • Required: these are the transforms. We downloaded them from Sourceforge and used docbook-xsl-doc-1.77.1.zip.
  • DocBook DTD
    • What is it?
      • The DocBook DTD defines how DocBook markup must be written.
    • Why use it?
      • Required: the rules of the road in regard to DocBook. We downloaded from www.oasis-open.org at http://www.oasis-open.org/docbook/xml/4.5/. We used version 4.5. You don't have to have the DTD local to your project, but it helps if you are working offline. The examples shown here assume the DTD is local.
A Note About the DocBook Version
We tried hard to use DocBook 5 but couldn't get it to work properly and ended up using DocBook 4.5. We followed the transition guide to make that leap from V4.X to V5.0 but little problems kept arising when we tried to put all the tools we mention above together. We suspect that it should be easy to move to V5.0 and we'll try to look at that in the future.

Example DocBook File Directory Structure


So let's say we are going to produce a best-of this blog's posts for the last three years. In this case one strategy for organizing the content would be to have a chapter for every year and keep the content of each year in a separate file. A master "book.xml" file will manage the ordering of the separate entries. So our files might look like this:

book.xml
    entry1.xml
    entry2.xml
    entry3.xml
    …
In book.xml we would have the (simplified) markup:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN" "../lib/docbook-xml/docbookx.dtd" [
<!ENTITY % myent SYSTEM "entities.ent"> %myent;
]>
<book>
 <bookinfo>
  <title>Travelmarx DocBook Example</title>        
  <author>  
   <firstname>Travelmarx Blog</firstname>
   <affiliation>
    <address>
     <email>&email;</email>
    </address>
   </affiliation>
  </author>
  <copyright><year>2012</year> <holder>Travelmarx</holder></copyright>
  <abstract>
   <para>Selected Travelmarx posts.</para>
  </abstract>
 </bookinfo>
 <chapter id="chapter2012">
  <title>2012 Posts</title>
  <para>Interesting posts from 2012.</para>
  <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="entry1.xml"/>
  <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="entry2.xml"/>
  <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="entry3.xml"/>
 </chapter>
 <chapter id="chapter2011">
  <title>2011 Posts</title>
  <xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="entry4.xml"/>  
 </chapter>
</book>


Setting Up the Eclipse Project


Here's the order we are going to do things:


  • Create a Java project in Eclipse. 


    • Create folders to help organize how we'll author and build.
    • Copy the Saxon JARS into the project and modify the build path of the project.
    • Copy the Apache FO Library into the project and modify the build path of the project.
    • Copy the DocBook stylesheets into the project and use them in book.xml.
  • Create DocBook source files.
  • Create a build file.
  • Run a build.



Basic Project Setup


After Step 2 (left) and After Step 7 (right) in Setup



1. Create a new workspace, for example, workspace_travelmarx, or use an existing.

2. Create new Java Project.

3. Set view to Project Explorer if needed.

4. Create a new folder \lib\saxon and put saxon9he.jar here.

5. Create a new folder \lib\apachefo and put all the contents of the Apache FOP (1.1) distribution files here. Not all of it is needed, but it's easier to just copy it all for now.

6. Create a new folder \lib\docbook-xsl and put all the DocBook XSL files from the ZIP here.

7. Create a new folder \lib\docbook-xml and put all the DocBook DTD files from the ZIP here.

8. Create a new folder \input, \output, and \css. The input folder will contain source DocBook files. The output folder will contain transformed output. The \css folder will contain optional style sheets for HTML. You don't have to put anything here. We generated a css file by viewing source of this blog and grabbing the style. Not perfect, but a start.

9. Create a new folder \tmp. This will be a temporary staging area. In the transformation from DocBook to PDF there is an intermediate stage in the form of Formatting Objects (FO). This directory contains the intermediate FO files.


Create DocBook Source Files


Book.xml File in Markup (left) and Book.xml file and Related Files (right)



1. All of the source input is in the \input folder and all the following folders and files should be created inside this folder.

2. Create an \images folder. We want to include images so we'll put them here.

3. Create book.xml. Using book.xml is a convention. The build.xml script below expects book.xml.

4. Create entry1.xml, entry2.xml, entry3.xml, and entry4.xml. This arrangement of book.xml to entry files is arbitrary. You can select what you want.

5. Create entities.ent. This file contains data (reusable text) that can be used in any file that declares an ENTITY that references the entities.ent file. It is one way centralize common text.


Build


Instead of building the build.xml file piece by piece, we’ll show the completed file. It has the following pieces:


  • Property definitions
  • MacroDef - macro definition to run the saxon transform
  • TaskDef - task definition to run the ApachE FO transform to get final PDF
  • Targets that define what action you want to perform. For example, there are tasks for building HTML and one for building the PDF.

The build.xml file has a default target, build HTML.

Build.xml Markup (left) and Running Build.xml at the Command Line (right)



Run the build.xml File


 

1. Select the build.xml and Run As, Ant Build (without the ellipsis) to run the default target. Or, select the Ant Build with the ellipsis to change the target.

2. Use shortcut keys, Alt+Shift+X, Q

3. Or, if the build file is what is open, click the Run icon or use the Run menu.

4. Or, run it from the command line.


The output of the HTML or the PDF is in the \output folder.  Here is the build.xml file:
<?xml version="1.0"?>
<project name="DocBookTest" basedir="."  default="build-html">

  <description>
      Transforms DocBook XML to HTML and PDF output.
  </description>

  <!-- Configure basic properties that will be used in the file.
  -->
  <property name="input.dir" value="input" />
  <property name="output.dir" value="output" />
  <property name="fo.dir" value="tmp" />
  <property name="src.tmp" value="tmp"/>
  <property name="docbook.xsl.dir" value="${basedir}/lib/docbook-xsl" />
  <property name="html.stylesheet" value="${docbook.xsl.dir}/html/docbook.xsl" />
  <property name="fo.stylesheet" value="${docbook.xsl.dir}/fo/docbook.xsl" /> 
  <property name="saxon.jar" value="${basedir}/lib/saxon/saxon9he.jar"/>
  <property name="fop.home" value="${basedir}/lib/apachefop"/> 
 
  <macrodef name="saxon">
    <attribute name="in" />
    <attribute name="out" />
    <attribute name="style" />
    <attribute name="classpath" default="${saxon.jar}" />
    <element name="params" optional="true" implicit="true" />
    <sequential>
        <java classname="net.sf.saxon.Transform"
              classpath="@{classpath}">
            <arg value="-s:@{in}" />
            <arg value="-xsl:@{style}" />
            <arg value="-o:@{out}" />
            <arg value="-xi:on"/>
         <arg value="html.stylesheet=css/master.css"/>
            <params />
        </java>
    </sequential>
    </macrodef>
 
 <taskdef name="fop" classname="org.apache.fop.tools.anttasks.Fop">
   <classpath>
     <fileset dir="${fop.home}/lib">
       <include name="*.jar"/>
     </fileset>
     <fileset dir="${fop.home}/build">
       <include name="*.jar"/>
     </fileset>
   </classpath>
 </taskdef>
 
  <!--
      - target:  usage
      -->
  <target name="usage" description="Prints the Ant build.xml usage">
    <echo message="Use -projecthelp to get a list of the available targets." />
  </target>

  <!--
      - target:  clean
      -->
  <target name="clean" description="Cleans up generated files.">
    <delete dir="${output.dir}" />
  </target>

  <!--
      - target:  depends
      -->
  <target name="depends">
    <mkdir dir="${output.dir}" />
  </target>

  <target name="xinclude">
     <xsl.xinclude in="${input.dir}/book.xml" out="${src.tmp}/book.xml" />
  </target>

  <!-- target:  build-html
  -->
  <target name="build-html" depends="depends" description="Generates HTML file from DocBook XML">

   <delete>
      <fileset dir="${output.dir}" includes="*"/>
   </delete>

   <saxon in="${input.dir}\book.xml"
        out="${output.dir}\book.html"
           style="${html.stylesheet}"/>   
   
    <!-- Copy the stylesheet to the same directory as the HTML files -->
    <copy todir="${output.dir}/css">
      <fileset dir="css">
        <include name="*.*" />
      </fileset>
    </copy>

    <!-- Copy images to the same directory as the HTML files -->
    <copy todir="${output.dir}/images">
      <fileset dir="${input.dir}/images">
        <include name="*.*" />
      </fileset>
    </copy>

  </target>
 
  <!-- target:  build-pdf
  -->
 <target name="build-pdf" depends="depends" description="Generates PDF file from DocBook XML">

   <delete quiet="true">
      <fileset dir="${fo.dir}" includes="*"/>
       <fileset dir="${fo.dir}/images" includes="*"/>
   </delete>

   <saxon in="${input.dir}\book.xml"
        out="${fo.dir}\book.fo"
           style="${fo.stylesheet}"/>     
  
    <!-- Copy images -->
    <copy todir="${fo.dir}/images">
      <fileset dir="${input.dir}/images">
        <include name="*.*" />
      </fileset>
    </copy>
  
  <fop format="application/pdf" 
    basedir="${fo.dir}"
    fofile="${fo.dir}\book.fo"
    outfile="${output.dir}\book.pdf"/>

  </target>
 
</project>  

Monday, November 5, 2012

Good People of Seattle Mural

Good People of Seattle Mural Panorama (left) and Front Shot (right)
Good People of Seattle Mural Panorama Good People of Seattle Mural Straight On

Good People of Seattle Mural Faces
Good People of Seattle Mural - Pioneer SquareGood People of Seattle Mural - Pioneer Square

Here’s another eye-catching mural by Jeff “Weirdo” Jacobsen and Joey Nix. This one is on the 2nd and Main Cannery Building in Pioneer Square, Seattle, and is dedicated to the Good People of Seattle. The mural features four people: Michael Trapp, Ana Dyson, Michael Doucett, and Taylor. Trapp and Doucett are by Weirdo and Dyson and Taylor are by Nix. Ana (Bender) Dyson was a musician and graffiti artist who passed away earlier this year. Her portrait in this mural joined with her tag “Aybee”.

One panel of the mural reads: “Dedicated to the Good People of Seattle 2012” with FranklinAndThomas.com written nearby. 

Around the corner are some pieces by Baso Fibonacci and Jean Nagai. Fun stuff on the Flatcolor Mural Wall at 3rd Ave. S., 2nd Ave. Ext. and S. Main Street.

The Old Cannery building, you guessed it has something to do with canning. The Department of Neighborhoods has more background on the building, what its features are and why there is a discrepancy between the two facades (east and north) - hint, a street cut through it. An interesting tidbit: “the building was occupied by the Cannery Workers of ILWU Local 37. On June 1, 1981, Silme Domingo and Gene Viernes of Local 37, who were trying to reform the conditions for cannery workers and also had actively opposed President Marcos of the Philippines, were gunned down in this building.” 

Ana (Bender) Dyson and Michael Doucett (left) and Across Main Street Looking at the Mural (right)
Ana (Bender) Dyson and Michael Doucett  Good People of Seattle Mural

Good People of Seattle Mural Dedication (left), Taylor (middle), and Michael Trapp (right)
Good People of Seattle Mural Dedication   Good People of Seattle Mural, Taylor Good People of Seattle Mural, Michael Trapp 

Flatcolor Mural Wall: Jean Nagai ‘12 (left) and Baso Fibonacci ‘12 (right)
Flatcolor Mural Wall: Jean Nagai ‘12 Flatcolor Mural Wall: Baso Fibonacci ‘12

“Did you see that raccoon?”
Baso Fibonacci ‘12

Monday, October 22, 2012

Books: Charles Darwin and the Mystery of Mysteries, Journal of Disappointed Man, Fordlandia, and Beak of the Finch

Charles Darwin and the Mystery of Mysteries Book Cover (left), The Journal of a Disappointed Man Cover (right)
Charles Darwin and the Mystery of Mysteries Book CoverThe Journal of a Disappointed Man Cover

Mystery of Mysteries

Charles Darwin and the Mystery of Mysteries by Niles Eldrege and Susan Pearson is book for kids (ages 9 and up) that does a good job of talking about who Charles Darwin was and what his life was like in England in short, easy to understand passages. It includes short vignettes with pictures of the people that were important in Darwin’s life. The title of the 2010 book comes from a phrase that Darwin wrote in his travel journal while on his famous five year sea voyage: “Hence, both in space and time, we seem to be brought somewhat near to that great fact—that mystery of mysteries—the first appearance of new beings on this earth.” (see Voyage of the Beagle (Illustrated) for example).

The cast of characters in the Mystery of Mysteries are introduced as they more or less made in appearance in Darwin’s life: Robert Waring Darwin (his father), Susannah Wedgewood Darwin (his mother), Erasmus Darwin (his brother, also the name of his grandfather), mentor Reverend Adam Sedgwick, Captain Fitzroy, Joseph Hooker, Emma Wedgewood (his wife), and Annie (his daughter) to name just a few. About half of the book is spent on Darwin’s famous voyage and is a very approachable introduction to the journey.

Life’s Mysteries and the Disappointed Man

Darwin died in 1882 - toward the end of the Victorian era (1837 - 1901). A few years later, in 1889, Bruce Frederick Cummings was born and lived his adult life in the Edwardian era (1901 - 1910) and World War I era (1914 - 1918). Under the pseudonym W.N.P. Barbellion he authored the work The Journal of a Disappointed Man: An Intimate Edwardian Diary. Cummings was diagnosed with a disease today known as multiple sclerosis in 1915 and he died in 1919.

The diary is chatty, pithy, introspective, and sad. At times, it’s hard to read - as if you are eavesdropping in someone’s mind and you don’t have the complete context. Then, you get the zingers that keep you lingering, reading them over and over. Here are some that stood out to me:

“As for me, I am proud of my close kinship with other animals. I take a jealous pride in my Simian ancestry. I like to think that I was once a magnificent hairy fellow living in the trees and that my frame has come down through geological time via sea jelly and worms and Amphioxus, Fish, Dinosaurs, and Apes. Who would exchange these for the pallid couple in the Garden of Eden?”
Barbellion, W.N.P. (2011-06-01). The Journal of a Disappointed Man : An Intimate Edwardian Diary (Victorian London Ebooks) (Kindle Locations 376-378). Victorian London Ebooks. Kindle Edition.

“I have discovered I am a fly, that we are all flies, that nothing matters. It's a great load oft my life, for I don't mind being such a micro-organism — to me the honour is sufficient of belonging to the universe — such a great universe, so grand a scheme of things. Not even Death can rob me of that honour.”
(Kindle Locations 928-929)

“Life opens to me, I catch a glimpse of a vision, and the doors clang to again noiselessly. It is dark. That will be my history.”
(Kindle Locations 1038-1039)

“My life has always been a continuous struggle with ill-health and ambition, and I have mastered neither. I try to reassure myself that this accursed ill-health will not affect my career. I keep flogging my will in the hope of winning thro' in the end. Yet at the back of my mind there is the great improbability that I shall ever live long enough to realise myself. For a long time past my hope has simply been to last long enough to convince others of what I might have done — had I lived. That will be something. But even to do that I will not allow that I have overmuch time. I have never at any time lived with any sense of security. I have never felt permanently settled in this life — nothing more than a shadowy locum tenens, a wraith, a festoon of mist likely to disappear any moment.”
(Kindle Locations 1725-1731)

“If only I had the moral courage to play my part in life — to take the stage and be myself, to enjoy the delightful sensation of making my presence felt, instead of this vapourish mumming.”
(Kindle Locations 2191-2192)

“My purpose is to move about in this ramshackle, old curiosity shop of a world sampling existence. I would try everything, meddle lightly with everything.”
(Kindle Locations 2384-2385)

Fordlandia Book Cover (left), Fordlandia Album Cover (right)
Fordlandia Book Cover Fordlandia Album Cover

Fordlandia: Disappointment in the Jungle

Speaking of sadness and disappointment, I also finished the 2010 book Fordlandia: The Rise and Fall of Henry Ford’s Forgotten Jungle City by Greg Grandin. The book describes Henry Ford’s attempt to create a large rubber plantation in the Amazon jungle from 1928 until it was sold in 1945 by Ford’s grandson. It was a failure for many reasons and the more it failed, the more the reasons for carrying on became idealistic.

The primary goal of the plantations (there were two plantations) was to produce rubber cheaply at a time when there was a British monopoly on rubber production most of which was coming from Asia. Ironically the rubber plantations in Asia were started from seeds smuggled out of the Amazon years earlier. Cheap rubber would help Ford since cars needed tires. (In the early 1930s large scale production of synthetic rubber was years in the future, and Thomas Edison, a friend and advisor to Ford, debunked reports that appeared at the time that it was possible. A guess a light bulb didn’t go on in Edison’s head?)

The plant in question at the center of the failure of Fordlândia (in Portuguese) is the rubber tree, Hevea brasiliensis, which is native to South America. Growing plantation-style rubber seems like it should be possible since it was being done in Asia? From the book (Chapter 21: Bonfire of the Caterpillars) Grandin explains why that wasn’t the case at all:

Hevea is what botanists call a climax plant, meaning that it developed in an ecosystem— in this case the Amazon— that was at the apex of its complexity. Unlike relatively new pioneer crops like wheat, corn, or rice, which grow rapidly and throw off many fertile seeds and flourish in a variety of habitats, including large plantations, Hevea is not so adaptable. Its genetic composition is as old and evolved as the jungle that surrounds it. To use a metaphor associated with human behavior, Hevea is set in its ways. It grows slowly, its girth is thick, its seeds need coaxing, and it likes to hide from predators by mixing with other jungle trees. Yet despite these survival strategies, rubber, like many other tropical plants, can be a successful commercial crop when completely removed from its home environment, freed from the pests and plagues that evolved and adapted with it. While Southeast Asia was similar enough in climate to the Amazon, its native insects, parasites, and spores ignored South American rubber and so trees could be planted in close rows. In their original context, on the other hand, rubber trees grown near one another proved susceptible to pestilence, as Weir put it, with “every change of humidity.”
Grandin, Greg (2010-04-27). Fordlandia: The Rise and Fall of Henry Ford's Forgotten Jungle City (p. 318). Macmillan. Kindle Edition.

The Benson Ford Research Center, a library and archive located at the Henry Ford, has historic images of Fordlandia.

The 2008 4AD release, Fordlandia, by the Icelandic composer and producer Jóhann Jóhannsson, was inspired by the failed Ford project. Strangely, I’ve listened to this album for years before finding out the story about Fordlandia and always found the music haunting and sad. It is interesting to have a story that goes along with it.

Evolution You Can See: Disappointed Creationists

For less time than it took for the folly of Fordlandia to become evident, and decades later, a husband and wife team methodically studied birds over twenty years and showed that you can see evolution in progress much to the disappointment of creationists. The Beak of the Finch: A Story of Evolution in Our Time [1995] by Jonathan Weiner tells the story. It is a story about evolution, the Galápagos Islands, finches, and in particular the story of that husband and wife team, Rosemary and Peter Grant, and their work in the Galápagos studying those finches. I read this book after we returned from the Galápagos and many of Weiner’s descriptions of Daphne Major evoked fond memories. The Beak of the Finch is one of the most interesting books I’ve read in a long time. Weiner weaves facts and story together smoothly all the while making complex science concepts accessible to the reader.

The central idea in the book is this that we can watch evolution at work: “…that Darwin did not know the strength of his own theory. He vastly underestimated the power of natural selection. Its action is neither rare not slow. It leads to evolution daily and hourly, all around us, and we can watch.” Daphne Major - the island the Grants returned to year after year - offers a perfect laboratory to study evolution of the finches (primarily Geospiza).

In the last few chapters, Weiner takes the idea of watching evolution at work and applies it to the issues of the growing resistance of insects to insecticides and bacteria to anti-bacterial drugs (The Resistance Movement) and global warming (A Partner in the Process). These are issues that all readers can surely relate to, right?

The Beak of the Finch Book Cover Front (left) and Back (right)The Beak of the Finch Front CoverThe Beak of the Finch Back Cover

Sunday, October 21, 2012

Binomen Art - Vitis

Vitis Spelled with Concord Grapes (left) and Concord Grapes (right)
Vitis Spelled with Concord GrapesConcord Grapes

This year we had a good harvest of our Concord grapes. We harvested about 35 pounds of grapes of which 10 pounds was made into jam.

Two weeks ago we harvested the bulk of the grapes and took the binomen-themed pictures with the genus name Vitis spelled out with grapes arranged on a leaf. Today, on a brisk fall morning, we took photos with the jam jars and yellow-brown-green leaves.

Vitis is a genus of vining plants in the family Vitaceae. Concord grapes are a cultivar derived from the grape species Vitis labrusca. V. labrusca has thick leaves with a hairy underside with brown or white hairs. The slip-skin of the Concord grape is easily separated from the pulp ball.

Vitis labrusca has the common name of “Fox grape”. At first we thought it might derive from the Aesop Fable The Fox and the Grapes. But, it seems that the common name refers to the strong smell, “candied-strawberry/musky,” of the Concord grape. The Wikipedia entry for Vitis labrusca mentions that in the 1920s scientists identified the aroma as methyl anthranilate. This compound is secreted by the musk glans of foxes and dogs apparently. So which came first, the common name or the identification of the compound? In the book General Viticulture, the following appears (2nd Edition, page 167):

The foxy aroma of Vitis labrusca is among the most pronounced odors of grapes, and probably this fact attracted the investigators who some years ago isolated and identified the aroma substance as methyl anthranilate (Power and Chestnut, 1921). A well-matured Concord grape, ground under favorable conditions, may contain as much as 3.8 mg. of this aroma substance per liter of juice.

Quattrocchi says of Vitis etymology:

The Latin name for the grapevine, Latin vieo, -es, etum, ere “to bend, plait, weave,” Akkadian ebitu “to be tied, girt”; see Carl Linnaeus, Species Plantarum. 202. 1753 and Genera Plantarum. Ed 5. 95. 1754; Giovanni Semerano, Le origini della cultura europea. Dizionario della lingua Latina e de voci moderne. 2(2): 613, 616. Leo S. Olschki Editore, Firenze 1994.

On a side note, we learned that ampelograhy is a field of botany that deals with the identification and classification of grapevines, Vitis spp. Wikitionary gives the eytmology as deriving from the Greek ampelos for “vine” and graphē for “writing”. In older literature, the family name Vitaceae can be referred to as Ampleidaceae.

Jars of Concord Grape Jam on Colored Grape Leaves (left) and Grape Slip-Skin on Fall Leaf (right)
Jars of Concord Grape Jam on Colored Grape LeavesGrape Slip-Skin on Fall Leaf 

Jars of Concord Grape Jam on Colored Grape Leaves (left) and Vitis Spelled Out in Grapes (right)
Jars of Concord Grape Jam on Colored Grape Leaves Vitis Spelled Out in Grapes

Close Up of Vitis Leaf Underside Showing Brown Hairs
Close Up Up Vitis Leaf Underside Showing Brown Hairs

Tuesday, October 16, 2012

Binomen Art - Punica (Pomegranate)

Punica Spelled Out with Pomegranate Seeds (left), A Clump of Seeds with Arils (right)
Binomen Art - PunicaA Clump of Seeds with Arils

Here we go again playing with food. It’s pomegranates this time. Pomegranates (Punica granatum) just arrived in the local grocery store as we wind down from the summer fruit and move into fall. We like to sprinkle the pomegranate seeds over muesli. Unfortunately, the seeds of these pomegranates (or more correctly, the aril of the seeds) in this post do not have the deep ruby color that we’ve seen in the past.

From Quattrocchi the origin of the generic term Punica is given as:

The Latin name, malum punica “Carthaginian apple,” Punicus, a, um, from Poenus, i “a Carthaginian,” Poenus, a, um “Punic, Carthaginian,” Poeni, orum “the Phoenicians, the Carthaginians,” Greek Phoinix “Phoenician”; see Carl Linnaeus (Carl von Linné) (1707 - 1778), Species Planatarum. 472. 1753 and Genera Planatarum, Ed. 5. 212. 1754.

Punic refers to a group of people from Carthage in North Africa (today, Tunisia). Carthage was a Phoenician city-state founded in 814 BC. The Phoenicians came from the western, coastal part of the Fertile Crescent. The high point of Phoenician culture is said to be from 1200 - 800 BC. The Wikipedia entry for Phoenicia traces the word punicus to the term for blood red or crimson and referring to the Phoenician monopoly on the purple dye of the Murex snail.

The specific epithet, granatum, means seeded, which is self-explanatory.

Punica Spelled Out with Pomegranate Seeds and A Split Pomegranate (left), Pomegranate Seeds Removed from the Fruit (right)
Punica Spelled Out with Pomegranate Seeds and A Split Pomegranate Pomegranate Seeds Removed from the Fruit

Monday, October 15, 2012

Lake Wenatchee Misty Fall Day- Plants We Noticed on a Sunday Morning


View Over Lake Wenatchee Looking South
View Over Lake Wenatchee Looking South
We stayed over one night at a friend’s cabin nearby the lake and on Sunday morning we had a chance to walk around and explore and identify some plants*. It’s fall and the rain has started, finally and well, thankfully this year. The leaves of the Big Leaf Maple (Acer macrophyllum) show interesting patterns in green and gold as they** prepare to drop. The smaller Vine Maples (Acer circinatum) stake out red on the color spectrum. On the edge of a drive way, we spot what we think is Blue Elderberry (Sambucus cerulea): blue dried up berries with a white bloom. Well, at least we are pretty sure of the Sambucus part. Nearby on a dirt road we spot some pine drops (Pterospora andromedea) looking very sticky. Finally, the trees around the cabin have a healthy supply of Wolf Moss (Letharia vulpina) - an almost fluorescent green dues to the vulpinic acid they contain. Cool!

* We probably said it before, but the (Revised) Plants of the Pacific Northwest Coast: Washington, Oregon, British Columbia & Alaska is a good general reference to carry around.

** We use they because we always thought of the tree controlling the show, but it seems the leaves have a part to play. In a book we are currently reading, Botany for Gardeners, author Brian Capon describes it this way: “Leaf senescence, prior to abscission, includes the breakdown of chlorophyll and weakening of cell walls at the base of the petiole, in a narrow band of cells called the abscission zone. In spring and summer, auxin produced in the leaf keeps the abscission zone intact. But low night temperatures and short days in autumn cue the leaves to reduce auxin production and increase the liberation of ethylene.” The ethylene destroys the cells in the abscission zone and the leaf falls away. Who is doing what?

Big Leaf Maple (Acer macrophyllum) leaf with smaller Vine Maple leaf, red (Acer circinatum) (left), Big Leaf Maple Seeds (right)
Big Leaf Maple (Acer macrophyllum) leaf with smaller Vine Maple leaf, red (Acer circinatum) Big Leaf Maple Seeds
Big Leaf Maple (Acer macrophyllum) Spotted Leaf 

Wolf Lichen (Letharia vulpina) on Douglas Fir (Pseudotsuga menziesii)
 

Pinedrops (Pterospora andromedea) – fall colors
Pinedrops (Pterospora andromedea) – fall colors Pinedrops (Pterospora andromedea) – fall colors

Blue Elderberry (Sambucus cerulea) berries (left) and leaves (right)
Blue Elderberry (Sambucus cerulea)Blue Elderberry (Sambucus cerulea)

Plants of the Pacific Northwest (left) and Botany for Gardeners (right)
Plants of the Pacific Northwest Botany for Gardeners