Thursday, June 30, 2011

Book of the Week: Serendipity, Twitter, and Louis Agassiz Fuertes

Earlier this week we did a Species of the Day tweet on Twitter (@BioDivLibrary) about the Abyssinian or Ethiopian Wolf - the most endangered canine in the world. For the tweet, we linked to a lovely portrait of the animal in Album of Abyssinian Birds and Mammals (1930), illustrated by Louis Agassiz Fuertes. Little did we know what a fascinating work this actually is. One of our followers on Twitter, John Pittman, known to the Twitter universe as@drhypercube, responded to our tweet with a link to his blog. Made aware of this book on BHL by our tweet & subsequent posting of the illustration to our Flickr account, John's post highlights the genius of this ornithologist and painter - a genius that we had only partially appreciated when we did the original tweet. As John writes,

"This is the peanut butter cup of Biodiversity Heritage Library serendipity - two wonderful things that are even better in combination. Via the BioDivLibrary Flickrstream, the Album of Abyssinian Birds and Mammals from Paintings by Louis Aggasiz Fuertes.

Fuertes, for those who don't know him or his work, was an ornithologist and painter. I've loved his art since I first encountered it (I was maybe 10 years old?) in a coffee table book that was, at that point, way out of my price range. His National Geographic article, Falconry, the Sport of Kings is still a favorite..."

Intrigued by John's post, we decided to feature this work as our book of the week. We started by contacting John to get a little more information about Louis Agassiz Fuertes. He obliged by telling us that, not only was Fuertes an accomplished ornithologist and painter, but he was actually one of the members on the 1899 Harriman Alaskan trip, an expedition that spent two months voyaging from Seattle, along the Alaskan coast to Siberia, and back to Seattle. The accomplishment included discovering approximately 600 new species, 38 of which were new fossil species, charting the geographic distribution of Arctic species, discovering an unmapped
fiord, and naming several glaciers. There were also important studies and documentation done of the indigenous people of the region, including a recording of a Tlingit song on a graphophonic recording machine brought along by Harriman.

This expedition was not the only one that Fuertes took part in. Indeed, our book of the week was the result of Fuertes' involvement in a Field Museum expedition to Ethiopia, for which he not only painted, but personally collected, prepared, labeled and packed "no less than one thousand bird skins" for the Museum. Known as the Field Museum - Chicago Daily News Abyssinian Expedition (1926-27), the participants "traversed a large part of Abyssinia (Ethiopia), making collections which cover a wide range of conditions." Wilfred H. Osgood, a curator of zoology at the Field Museum who wrote the introduction of our book of the week, said of Fuertes,

"The opportunity [the expedition] gave Fuertes for life studies of African birds was varied and unusual. Theretofore engaged solely in painting American birds, he found tremendous enthusiasm in a new field and plunged into it with joyous abandon and tireless energy...The painting was in almost all cases done in the tent, the artist sitting on his sleeping cot and his materials and specimens scattered about him."

Fuertes produced 108 painting and sketches for the expedition. After his death, Mr. C. Suydam Cutting purchased these works and gave them to the Field Museum. As Osgood wrote,

"The great popularity and the prominence of Mr. Fuertes as the leading American painter of birds, together with the opinion freely expressed that these final studies represented the height of his power, brought a demand for their reproduction in some form that would make them available to a wide circle."

Thus came our book of the week, which presents 32 of these paintings "reproduced by offset
lithography." We've featured only a few of these in our post today. We invite you to take some time to look at the rest, and visit John Pittman's blog for more illustrations and information. We send out a special thanks to Mr. Pittman for inspiring this book of the week and providing us with such valuable additional information. There's no limit to the things you can learn via social media conversations!

Thursday, June 23, 2011

Book of the Week: Celebrating Darwin's Library!


Such important words for Darwin, and so revealing to us. They offer us insight into the inner workings of this brilliant mind as he nursed to full fruition an idea that started on the now-legendary Galapagos Islands. Studying the works of the leading scientists of his time was critical to Darwin's development of this idea. By applying, and sometimes countering, the theories of others, he constructed one of our most important scientific foundations - Evolution. He documented this intellectual progression in the margins of the books in his library. And this marginalia, and indeed digital scans of his personal library, are now available for you to peruse at your leisure on BHL in Charles Darwin's Library!

Darwin's personal library, which amounts to 1,480 books, is in the process of being digitized and made available online through BHL. Currently the collection includes 330 of Darwin's most heavily annotated works. But what makes this collection so valuable, and indeed distinguishes it from the other 92,000+ volumes now on BHL, are the transcriptions of Darwin's notes and comments, which are displayed to the right of each annotated page in BHL. These transcriptions, which are the result of work done by Mario A. DiGregorio and Nick Gill, are also fully indexed, meaning that you can search the library for any comments Darwin made in his books regarding a specific subject.


In celebration of the official release of this monumental project, we're featuring the book in which Darwin so aptly summarizes the meat of his theory - Principles of Geology, v. 2 (1837), by Charles Lyell. Within the volume, Lyell postulates that there are definite limits to the variation of species, writing,

"The entire variation from the original type, which any given kind of change can produce, may usually be effected in a brief period of time, after which no farther deviation can be obtained by continuing to alter the circumstances, though ever so gradually; indefinite divergence, either in the way of improvement of deterioration, being prevented, and the least possible excess beyond the defined limits being fatal to the existence of the individual."

In reaction, Darwin wrote in the margin, "If this were true, adios theory," realizing that his proposal of evolution required that, given the right stimuli, organisms can adapt and evolve in infinite degrees as required for the continuation and prosperity of their species. Time and history favor Darwin, as we see that his studies on the variations within species, most famously the bird species he encountered in the Galapagos, ultimately supported the idea that all life originates from a common ancestor, implying unfathomable variations over time from the original.

As we celebrate Darwin, and the fact that he challenged the writings of others rather than saying goodbye to the delicate and sometimes elusive thoughts on adaptation that formed the seeds for his world-changing theory, we encourage you to take some time to look through the books in his library and the notes that he jotted down as he read through them. These notes comprise a history of his work, and provide us a window into those "eureka" moments that forever changed history.

Charles Darwin, we salute you.

Tuesday, June 21, 2011

BHL and Our Users: Dr. Joshua Drew

This week we feature a researcher at the Biodiversity Synthesis Center at the Field Museum of Natural History in Chicago, IL, USA. The Biodiversity Synthesis Group is a component of EOL "dedicated to advancing biodiversity science and the core EOL mission through...diverse meetings, workshops, research programs, and outreach." Our featured user's research focuses on coral reefs and the challenges of both protecting these reefs and discovering new species of coral reef fish. With this brief introduction, meet Dr. Joshua Drew.

Q: What is your title, institutional affiliation, and area of interest?
A: Postdoctoral Researcher, Biodiversity Synthesis Center, Field Museum of Natural History.

Q: How long have you been in your field of study?
A: I've worked as a marine conservation biologist since 2000.

Q: When did you first discover BHL?
A: During my Ph.D. at Boston University in 2008.

Q: What is your opinion of BHL and how has it impacted your research?
A: BHL is a very important part of my research for two reasons. First, as a researcher who is interested in discovering new species of coral reef fish, BHL provides me with easy access to taxonomic literature. This allows me to see the whole history of a species laid out before me. Secondly, much of my work is trying to understand how ecosystems used to look, and using those baselines to evaluate how current conservation measures are succeeding. Having access to historical literature is essential to characterizing what ecosystems used to look like, what species were present and what peoples' opinions of the health of the ecosystem were like throughout time. Since we don't often have old photographic evidence of reef ecosystems, I rely on the historical literature to get a glimpse of how these wonderfully diverse ecosystems used to look.

Q: How often do you use BHL?
A: It depends. When I'm working on a project, I'll use it intensively (two or three times a day); when I'm not actively working on a project, I still find myself accessing it once or twice a week.

Q: How do you usually use BHL (read the titles online/download whole PDFs/Select pages to download/etc.)?
A: For my taxonomic research, I will typically search for a specific name and see how our construction of that species has changed over time. For the historical ecology research I will often search for information about a specific place or places within a region. If I'm lucky, there will be multiple reports on that area throughout time and I can see how species assemblages have changed.

Q: What are your favorite features/services on BHL?
A: I like the ease of having access to the literature anywhere I have access to the Internet. For example, I was teaching a class last semester and it was great to be able to introduce my students to the primary literature with a few clicks on my iPad right in the middle of class.

Q: If you could change one thing about BHL, what would it be, or what developmental aspect would you like the BHL team to focus on next?
A: I think what you are doing is great; I simply would hope that you can further your collaborations with publishers to get more modern content into the BHL.

Q: If you had to choose one title/item in BHL that has most impacted your research, or one item that you prefer above any other in BHL, what would it be and why?

This book was one of the first comprehensive records in the Southwest Pacific, the area where I do most of my work. In it, Jordan and Seale give a great look into what these reefs were like before widespread development. Reading their words is like going through a time machine, and allows us a glimpse into a world that will probably never be again. Additionally, these authors describe for perhaps the first time, a biogeographic pattern of species distributions that still perplexes people to this day - that the islands of the Coral Triangle (PNG, Indonesia, and the Philippines) are much more diverse than those in the Southwest Pacific. People have tried to explain why this pattern exists for over a century, and addressing this question is one of the major challenges I am addressing using molecular systematics.

Thank you, Dr. Drew, for giving us a glimpse into your world and the important oceanic conservation work that you do. These "rainforests of the sea" support twenty-five percent of all marine species, and it is imperative that we work to protect these ecosystems and ensure that they are around for generations, and indeed, millennia, to come.

Learn more about Dr. Drew on his website: www.halichoeres.org

If you would like to be featured on our blog, let us know by sending us feedback, posting on our Facebook page, or sending us a Tweet to @BioDivLibrary. :-)


Thursday, June 16, 2011

Book of the Week: An Experiment in Illustrations

This week we're going to do our book of the week a little differently. We came across this awesome tool on the National Geographic website called Backyard Bird Identifier. By answering some simple questions about a bird that you have seen in either the U.S. or Canada, the application tells you the possible species. We thought that was pretty cool, so we decided to see if this tool could identify birds based on answers that we give solely by looking at the illustrations and associated descriptions in one of the books in our collection. For our experiment, we chose the book Bird-Life: A Guide to the Study of Our Common Birds (1900), by Frank M. Chapman; illustrated by Ernest Seton Thompson. From this book, we chose six illustrations and, answering the questions in the Backyard Bird Identifier using these illustrations and accompanying descriptions, we found out whether the tool could accurately identify the bird. The six illustrations, as well as the answers we gave to the questions, are given below.

Question One: Where did you see the bird?
Answer: Country: United States
Region: Northeast, Virginia
Question Two: When did you see the bird?
Answer: October
Question Three: What color is the bird?
Answer: Black, White, Red
Question Four: How large is the bird?
Answer: 7-11 inches
Application returned 39 results (each possible match has an accompanying picture so that you can determine which of the results was your bird).
Results: Downy Woodpecker was among the possible identities.




Question One: Where did you see the bird?
Answer: Country: Canada
Region: East, Quebec
Question Two: When did you see the bird?
Answer: May
Question Three: What color is the bird?
Answer: Brown, White, Red
Question Four: How large is the bird?
Answer: 7-11 inches
Application returned 42 results.
Results: Fox Sparrow was among the possible identities.







Question One: Where did you see the bird?
Answer: Country: United States
Region: Northeast, Maryland
Question Two: When did you see the bird?
Answer: May
Question Three: What color is the bird?
Answer: Black, Yellow, Orange
Question Four: How large is the bird?
Answer: 7-11 inches
Application returned 38 results.
Results: Baltimore Oriole was among the possible identities.






Question One: Where did you see the bird?
Answer: Country: United States
Region: Northeast, Virginia
Question Two: When did you see the bird?
Answer: August
Question Three: What color is the bird?
Answer: Black, Gray, Red, Brown, White, Yellow
Question Four: How large is the bird?
Answer: 7-11 inches
Application returned 44 results.
Results: Eastern Screech Owl was among the possible identities.





Question One: Where did you see the bird?
Answer: Country: United States
Region: Northeast, New York
Question Two: When did you see the bird?
Answer: January
Question Three: What color is the bird?
Answer: Black, Gray, Red, Brown
Question Four: How large is the bird?
Answer: 7-11 inches
Application returned 22 results.
Results: American Crossbill was not one of the possible identities.





Question One: Where did you see the bird?
Answer: Country: United States
Region: South, North Carolina
Question Two: When did you see the bird?
Answer: April
Question Three: What color is the bird?
Answer: Black, White
Question Four: How large is the bird?
Answer: 6 inches or less
Application returned 32 results.
Results: Black and White Warbler was not among the possible identities.





So, at the end of the experiment, we were successfully able to bring up the identity of the bird in 4 out of 6 cases. Not too bad, considering we were working from a book and illustrations of the species. Try out the tool on your own, preferably from live bird studies :-), and let us know how successful your endeavors are. And be sure to take the time to look at the lovely illustrations in our book of the week. Maybe even try identifying other birds in the book using this tool. If you do, be sure to let us know how it goes! Happy bird identifying!

This week's book of the week, Bird-Life: A Guide to the Study of Our Common Birds(1900), by Frank M. Chapman; illustrated by Ernest Seton Thompson, was contributed by the American Museum of Natural History.

Thursday, June 9, 2011

Book of the Week: 1000 Hints in Gardening

Summer is in full swing and that means all the gardeners have already started coming out of the woodwork to get their hands dirty. We came across this book in BHL and thought it would be an appropriate book of the week for all of our garden-loving friends: 1000 Hints on Flowers and Birds (1917), by Mae Savell Croy.

In case you had any doubts as to whether you should believe anything that Ms. Croy has to tell you in this book, the title page carefully points out that she is the author of "1000 Shorter Ways About the House," "1000 Things a Mother Should Know," and "1000 Hints on Vegetable Gardening." Her obsession with the number 1000 is sure to provide the reader with plenty of tips and ideas for application in their own gardens.

And these tips range in subject from general topics like "The Art of Growing Flowers" and "Essentials in Gardening" to more specific discussions of fertilization, rock gardens, weeds, and house plants. She even includes an entire chapter entitled "The Plea for the Birds," which discusses bird houses, food and water, and a cryptic "Bits of Information" section. For our post, we're going to highlight some of our favorite tips that we gleaned from this title, but there are many more that you can find yourself if you dig a little deeper into the 1000 hints provided.


"While to put it down on paper will be most helpful, the paper design should be made in the garden itself, otherwise there is likely to be confusion when it comes to working out the plan with actual plants. The size of the plants to be grown should always be taken into consideration when setting aside a certain space."


"Draftsmen use a paper ruled in quarter-inch squares, and in using this, each quarter-inch square should represent a foot of ground."


"In a small garden, the seat should be small, but where there is plenty of space, a large seat or a group of seats, a summerhouse or a pergola with seats can be placed to advantage. Let a garden look as if it had human beings taking a personal interest in it."


"They are not only beautiful in themselves but they tend to emphasize the color of the other flowers near. No other one color aids so in emphasizing the color scheme in the garden."


"It should be six months old and be well worked into the soil."


"A seed house which has built up a reputation on the produce from its seed is not going to keep in stock old seed which will tend to endanger its reputation. It pays to purchase the best of seeds."


"House plants often fail to thrive from no apparent reason when what they really need is repotting. Having eaten all the food from the old soil, they require entirely new soil and the addition of fertilizer alone will not answer the problem."


"A pit is simply a large hotbed and is constructed along the same principles, except that as it is in the form of a greenhouse buried under ground, there need be no layers of manure. It should, however, have good drainage and should have a sash covering. It may be made of either concrete or wood, though concrete is highly recommended as it will not permit any water to ooze through the earth surrounding the walls. The depth of excavation depends upon the needs of the individual who is to use it, but it should always be deep enough to give good standing room."


"The strips taken from the boxes should be nicked and the other pieces slid into them, and few tacks will be necessary."


We hope you enjoyed our top 10 favorite tips, a collection of both useful and entertaining tidbits, from our book of the week. Find your own favorite hints from the book and be sure to let us know what they are! We're dying to know what else a pit might be.

Tuesday, June 7, 2011

BHL and Our Users: Rod Page and BioStor

This week, we feature one of our users that has been extraordinarily active in not only using BHL content, but in creating applications that significantly enhance the information and knowledge that can be gleaned from our resources. The creator of BioStor and a huge player in the realm of biodiversity informatics, meet Dr. Roderic Page!

In the beginning..."meh"

I first became aware of the Biodiversity Heritage Library around 2007. To be honest, initially I was underwhelmed. BHL didn't seem to have much literature, what it did have was mostly about plants (I'm a zoologist by background), the interface was a bit clunky, and most of the content was pre-1923, which to me simply echoed the impression that taxonomy is a science that is something of a backwater, obsessed with ancient documents and arcane terminology.

So at the start I wasn't much of a fan. But as BHL grew it started to add more recent content, particularly for museum journals, as well as vital content such as the Bulletin of Zoological Nomenclature, and I realised that it was going to be much more useful than I'd previously thought. So I started playing with ways to visualise content from BHL, such as timelines to plot search results over time, and sparklines to show how the relative frequency of different names for the same organism would change over time (similar to the nice visualisations Ryan Schenk has done recently.)

But where are the articles?

These experiments were fun, but I keep coming up against what for me was the show stopper: BHL had no concept of a scientific article. Because it was a library project the basic unit in BHL was a scanned item, which could correspond to anything from a book, one or more volumes of a journal, or a single article. Whereas librarians deal with volumes on shelves, for most scientists the unit that matters is the article, and there was no easy way to find articles in BHL. To be fair, BHL was well aware of this mismatch between library practice and the expectations of scientists (see Chris Freeland's post But where are the articles??).

I'd spent a lot of time developing a tool called bioGUID, which was designed to find articles online using just the journal name, volume, and starting page. It uses a range of web services to find the article, such as talking to CrossRef to see if it had a DOI (the ubiquitous identifier for modern articles), as well as searching other sources, such as JSTOR. I wanted something like this for BHL, where you could simply take those three things - journal, volume, starting page - and go straight to the article. A common way to provide this service is through a protocol called OpenURL, which takes the journal, volume, starting page for an article and looks for it online.

However, finding articles in BHL is a challenging task, not least because there is little standardisation in how library catalogues record bibliographic information. To give just one example, for the journal Proceedings of the Zoological Society of London here are some of the ways information about a volume is recorded.
  • Part 1- Part 4 (1833-38)
  • 1856
  • 1901, v. 1 (Jan.-Apr.)
  • Jan-Apr 1906
  • 1912 v. 2
  • 1923, pt. 1-2 (pp. 1-481)

So any tool to find articles has to deal with these issues. But after a few experiments I decided it would be possible to find lots of articles in BHL, especially if I had access to all the BHL data on my own computers. So, I grabbed a copy of the data and created BioStor.

BioStor

Below is a screen shot of BioStor, which at the moment has over 31,000 articles from BHL.

There are two main ways to use BioStor. The first is as a website where you can browse or search for articles. You can search for articles about taxa by adding the taxon name to http://biostor.org/name/, for example http://biostor.org/name/Zonosaurus. In addition to displaying the article, BioStor displays the names found in the article as a tag cloud and a classification, and in some cases also shows a map with localities that have been automatically extracted from the text and displayed on the map, such as this example from A revision of the dwarf Zonosaurus Boulenger (Reptilia: Squamata: Cordylidae) from Madagascar, including descriptions of three new species:

The other way you can use BioStor is as an OpenURL resolver. Bibliographic software and websites such as EndNote, Zotero, and Mendeley all support OpenURL, so you can be looking at an article in one of those databases and automatically look for it in BioStor.

BioStor needs bibliographies

One thing I've glossed over is how BioStor has managed to find thousands of articles. Some have been added manually, but this rapidly gets tedious. For the majority of articles what I've done is take an existing bibliography for a journal, or a taxonomic group, and write a small computer programme (or "script") to get BioStor to find the articles automatically. For example, I quickly added most of the articles in the journal Tijdschrift voor Entomologie becase I had an EndNote file containing those references.

I spend a lot of time searching for bibliographies, downloading them or scrapping them from websites, converting them into a readable format, then using scripts to ask BioStor to locate the article in BHL. I'm somewhat taken aback by how hard it is to get these bibliographies. If taxonomists and/or journal editors made these available, we could add many more articles to BioStor. While one approach is to beg, borrow, or steal bibliographies, I'm hoping that the rise of online bibliography databases and associated social networks, especially Mendeley, will generate the bibliographies I need to efficiently find articles in BHL.

What's next?

BioStor has some obvious limitations, notably the assumption that older literature works the same way as modern articles. Whereas today figures, tables, and text are all contained within the page range of an article, it's not uncommon in older (pre-20th centruy) literature for figures and plates to be physically separate from the text. BioStor can't really handle this, so one day I plan to add the ability to have discontinuous page ranges that will include these figures and plates.

Despite the fact that I've spent a lot of time creating and populating BioStor, in reality it is a side project running on a Mac Mini on my desk. At some point it would be nice to feed BioStor's data back in to BHL itself, so users of BHL could more easily find articles without leaving that web site. BHL also has more resources for ensuring the long term survival of data than I do.

What do I think of BHL now?

Despite my initial lack of enthusiasm, I now see BHL as one of the great resources of biodiversity informatics. There's some extraordinary stuff in BHL, and it keeps growing. It's also been great working with Chris Freeland, Phil Cryer, and Mike Lichtenberg, who have all been very helpful, even when I've written blog posts venting my frustration with BHL's limitations. I think it's definitely one of those cases where you only complain about the things you actually care about.

Thursday, June 2, 2011

Book of the Week: Cabinet of Oriental Entomology

It's bugs galore today as we feature the book The Cabinet of Oriental Entomology (1848), by J.O. Westwood. This delightful book is full of gorgeous illustrations of exotic insects. We're picking out some of the illustrations that we particularly love and providing you with an excerpt of what the author had to say about the creatures shown. Enjoy!

1) Papilio icarius

"Assam appears to be pre-eminently rich in the species of Papilio. A number of new species, from this region and the neighboring district of Sylhet, were figured in my 'Arcana Entomologica,' but none of them will bear comparison with the present insect, either for size or singularity of form, owing to the extraordinary elongation of the hind wings and the short dilated tails...Adopting the excellent system of nomenclature proposed with so much taste by Linnaeus, whereby the species of the modern genus Papilio were distinguished by the name of the famous heroes of antiquity, the present species...is named after Icarius, the son of Ebalus and Erigone; who, having been killed by some peasants of Greece, whose companions he had made drunk with wine, (a liquor till then unknown to them, and which from its effects they thought to be poison,) was transformed by Jupiter into a star, which was supposed by some persons to be identical with the celestial Bootes."



2) Eucheirus macleaii
(Figure One: Male; Figure Two: Female)

"India and the adjacent islands offer to us a striking peculiarity in respect to the geographical distribution of the gigantic species of Lamellicorn beetles. Whilst the New World is inhabited by a great number of these fine insects...the tropical oriental regions can boast but of few; these however, are distinguished by their metallic or variegated appearance, of which their American brethren are destitute."








3) Figure One: Saturnia simla

"The female of this fine species has the fore wings comparatively larger and less hooked than in the males...I trust that, in consequence of Captain Boys' arrival in England, I shall be enabled, in a subsequent article, to communicate an account of the early states of this insect."

Figure Two: Saturnia assama





4) Lower Figure: Actias maenae

"The accompanying figure of this very fine insect is copied from a specimen kindly communicated for representation by W.W. Saunders, Esq., F.L.S., which differs in some respects from Mr. Doubleday's description of the species, recently published...This is certainly one of the finest of the recent additions to the list of oriental Lepidoptera; but I am informed that Dr. Boisduval possesses a species of this genus from Madagascar with much longer tails to the hind wings."

Upper Figure: Leucophlebia lineata

"This beautiful insect appears to possess the characters of a distinct genus, in the classification of the exotic Nocturnal Heterocerous Lepidoptera; its elongated body and wings give it an analogy with some of the Sphingidae, as well as to some of the prominent moths, especially to Leiocampa Dictoea."



5) Figure One: Bacteria sarmentosa

"This species of walking-stick insect is longer than any which I have yet seen. It is represented of the natural size, but its full extent is here decreased by unnaturally bending back the fore legs (in order to bring them into the plates) which in the living insect are directed straight forwards...The insect described above is a female; I possess also another female, which I consider to belong to the same species, which is only 7 1/2 inches long, and agrees with it in all its characters, except that the 6th ventral segment has only a minute oval sulcated tubercule at its extremity."

Figure Two: Bacteria virgea

"The proportions and general appearance of this insect indicate that it is most probably the male of the preceding. It is on this account that I have represented them both on one plate."



Take some time to explore the other beautiful plates in this book. The insect world is certainly nothing if not colorful!