How It All Began



“As well as a flourishing library, the school by 1909 had a wood collection containing specimens of nearly all of Pennsylvania’s native trees and large shrubs. For each species, cross sections and radial and tangential sections had been prepared to show the gross appearance of the wood. The next step was the preservation of samples in alcohol and glycerin so that sections suitable for microscopic examination could be cut. These latter sections were to be especially useful in the study of timber physics (wood technology)." E.H. Thomas, “A History of the Pennsylvania State Forestry School, 1903 – 1929.” p. 67

Monday, September 25, 2017

Backtracking, Once Again

One of the things you get used to as you're documenting a large collection is going back, and starting over. You start out with an assumption about certain things, set up the documentation process accordingly, and then discover that one or more of your assumptions were wrong or incomplete.

This morning I am going back and starting over, with a part of the collection. Since mid-July I've been entering information from Dennis Brett's card index into the database. Once entered, I then planned to begin going through the 100+ boxes of specimens, filing them away in our newly-obtained cabinet system, and noting that new location in the database.

But last week, while grinding my way through the cards, something clicked and I suddenly realized I was messing up my count.

Let's back up a few years. When Mr. Brett donated the collection, he asked for an appraisal for accounting purposes. After checking the options, Penn State decided that I should be the person to perform the appraisal. And I spent the better part of six months doing so.

But in the process, I came across a slight discrepancy. When I first started pondering the size of the collection, I measured the stacks of cards in Mr. Brett's files and estimated that there were 5,000 to 5,500 in the collection. Dennis had performed the same estimation process and concluded that there were 6,000 specimens in the collection. Mr. Brett had been meticulously filling out an index card on every specimen in his collection as they were collected over the years.

Dennis Brett typed out a lot of cards over the past seventy years. Those four cabinets are jammed full.

For the actual appraisal, I didn't use the cards at all, since I needed to examine the actual specimens. Instead, I went through the entire collection, box by box, selected a random specimen from each box, ascertained a value for the selected specimen, applied that value to the number of specimens in that box, and then added the estimated values of all the boxes to arrive at an estimated value for the collection. Over the course of this process, then, I actually determined the true number of specimens in the collection...which was "only" 3,983.

So both Mr. Brett and I had apparently overestimated the number of specimens in the collection by "measuring" the cards. I had no apparent answer for the discrepancy, except that the "measurement" was rough and perhaps a small error could have been multiplied. Dennis also doubted the discrepancy, and felt certain that the actual number was closer to 6,000 than 4,000. After all, he had spent 70 years building the collection, so I took his viewpoint seriously. But...I had counted every piece...could I trust my own tally? I decided to wait until I had the whole collection documented, and the final number would be confirmed. Then I forgot about the issue.

That was back in early 2016. So, by mid-2017, when I started entering the information from the cards into the database in the final documentation effort, the specimen tally issue was really not in the forefront of my thinking. After all, I was ultimately going to match every specimen to a data entry, and reconcile any missing specimens, or eliminate any data entries for which there was no specimen, at the end of the process.

So, I started on the "A's" beginning with Abies amabilis, entering all the data on each card in the appropriate cell in the database. When I reached Abies lasiocarpa, I noticed Mr. Brett had entered a synonym name, A. subalpina. I confirmed that Abies lasiocarpa is the accepted name, entered that in the appropriate column, and moved to the next card...which was for a specimen also labeled A. lasiocarpa, with a synonym of A. subalpina.

This is where fate led me down the wrong road. I briefly pondered if these were the same specimen...but then noticed that each was from a different location. The first was from Oregon, the second from Colorado. So they were indeed different specimens. I made the mental note that Mr. Brett had occasionally entered synonym data on the cards, but made the erroneous assumption, based on the confirmation of different locations in this first instance, that each card represented a unique specimen in the collection.

The fate that worked against me was that these two cards preceded the next two...which were for, I assumed, two specimens of corkbark fir. The first was filed as Abies lasiocarpa var. arizonica, with a synonym of Abies arizonica. The second was for an Abies arizonica, with a synonym of Abies lasiocarpa var. arizonica. I confirmed that the accepted name for the species is A. lasiocarpa var. arizonica, and entered both into the database. As I did, I apparently didn't give enough thought to the source of both specimens...Arizona.

After all, you could assume that a species named A. lasiocarpa var. arizonica would mostly be found in Arizona, so not unusual that two different specimens might be from that state, right? I forged ahead.

But two months and nearly a thousand entries later, it finally dawned on me. By now you've probably figured out my problem, especially if you've built your own card catalogue. Mr. Brett had created multiple cards for those specimens which were labeled with synonym names, so that he could check them against future possible acquisitions under both (or multiple) names. Makes sense.

But it also makes the number of cards in the index larger than the number of actual specimens. In this case, about fifty percent larger.

So, if I was just entering a few hundred cards, I would just keep plunging forward and weed out the multiple entries as I check them against actual samples. But a few thousand? When it takes me about a month to enter roughly 500? Forging ahead at this point would be roughly akin to jumping off the cliff, just because I happened to walk up to it.

Besides, it causes a real problem with my real-time reporting of my progress. If you look at the box on the right, you'll see that I'm reporting that there are currently 5,176 documented specimens in the collection. That number is high...but how much, I don't really know. Meaning I have to go back and clean up the database by deleting the duplicate entries as I pull them from the card file.

So, this morning, I'm doubling back and cleaning up the mess. First, I'll go through the cards I've entered, and as I pull their duplicates, I'll delete those entries from the database, and correct the tally as I go. Then I'll continue through the entire catalogue, until I pull all the duplicate cards. I'll set these aside for later.

Finally, then, when completed with this data entry (which will be two or three months earlier than it would be if I entered all the duplicates) I'll go through the boxes, pull the specimens and match them to their entries. If any of the pulled cards are actually different specimens, I'll find those cards in the stack that I've pulled, and enter the data.

Yes, it sends me back to "Start" today...but it means I'll "Get out of Jail" earlier.


Monday, September 18, 2017

The Acacia Controversy

Entering data today, I stumbled across a naming controversy I had not yet discovered, so I thought it would be a good thing to cover it here.

I've been entering Acacia specimens from the Brett collection, and found that the accepted name for Acacia arabica (with many common names, perhaps the most common being gum arabic), was Acacia nilotica according to my primary reference, ThePlantList.org.  However, a query on Wikipedia for the species re-routed me to Vachellia nilotica. And a further check with my secondary reference, CatalogueOfLife.org, confirmed that Vachellia nilotica is in fact the accepted name. Now, as a finding this is not unusual...I've found that roughly forty percent of our specimens now have newer, different scientific names. But what caught my attention was that The Plant List lists both Acacia nilotica and Vachellia nilotica as accepted names for the species. And neither is listed as a synonym for the other...so when you search for one, you never see the other. This is clearly an inconsistency in their database.

The wood of Vachellia nilotica, formerly Acacia nilotica, originally labled in our collection with a synonym Acacia arabica. A. nilotica was the first Acacia identified by Linnaeus, to give you an idea of how strong that identification is.

The Catalogue of Life site clearly lists Vachellia nilotica as the accepted name, and when I have a difference in these two references, I use the Catalogue of Life listing. That practice started for me when I found that The Plant Lists still uses Leguminosae as the family name, while The Catalogue of Life uses the more modern Fabaceae family name. Still open for discussion, I guess, but that is not unusual in the the of taxonomy, I suppose.

So I use The Plant List as my primary reference simply because it is easier and faster to use (important when you're entering and checking thousands of specimens) but I use the Catalogue of Life when discrepancies become apparent.

Anyway, back to the Acacia thing. The root of this controversy is relatively recent, according to Wikipedia...
"Acacia, commonly known as the wattles or acacias, is a large genus of shrubs and trees in the subfamily Mimosoideae of the pea family Fabaceae. Initially it comprised a group of plant species native to Africa and Australia, with the first species A. nilotica described by Linnaeus. Controversy erupted in the early 2000s when it became evident that the genus as it stood was not monophyletic, and that several divergent lineages needed to be placed in separate genera. It turned out that one lineage comprising over 900 species mainly native to Australia was not closely related to the mainly African lineage that contained A. nilotica—the first and type species. This meant that the Australian lineage (by far the most prolific in number of species) would need to be renamed. Botanist Les Pedley named this group Racosperma, which was inconsistently adopted. Australian botanists proposed that this would be more disruptive than setting a different type species (A. penninervis) and allowing this large number of species to remain Acacia, resulting in the two African lineages being renamed Vachellia and Senegalia, and the two New World lineages renamed Acaciella and Mariosousa. This was officially adopted, but many botanists from Africa and elsewhere disagreed that this was necessary."
So, generally, the Australian region acacias stay as Acacias, while the rest have been changed. A bit messy, but I've found several excellent modern references that follow this convention, including Dyer, James, and James in their fabulous new book Southern African Wood.

Just down my list I discovered that Acacia caffra, another African wood, is now named Senegalia caffra following the modern conventionUnfortunately, The Plant List lists both as accepted names, and again neither is cross-referenced to the other. The Plant List editors clearly have to make some decisions and get to work. The Catalogue of Life again clearly identifies S. caffra as the accepted name, with A. caffra cross-listed as a synonym.

Personally, I wish they were still all Acacias...from a wood standpoint they all look and feel like acacias, and it makes the Acacia family all the more impressive because they are everywhere in the world. Even Linnaeus thought so...but then he was starting with Number One and didn't have to deal with all the thousands of others that eventually were identified in the same Genus as his original Acacia.

Thursday, September 14, 2017

Getting Organized

In the two months since the last post, I've been entering data on the Dennis Brett collection into the Xylarium database. We're now nearing 5,000 specimens as you can see in the block on the right, and I still have about that many to go.

But a couple of weeks ago, an opportunity to get a little more organized presented itself. It began simply enough...I received an email saying that someone in the building was looking to get rid of some old filing cabinets. Now, I've been stumbling around piles of old boxes of wood specimens for a couple of years now, when I moved all of Dennis' samples into stacks around my desk in the lab to make room for the visitors I was expecting during the World of Wood event we hosted back in summer of 2015. These piles of boxes were chest high and were rather daunting. The possibility of bringing in some file cabinets and putting them "away" while I organized the collection sounded like a good one.

But the file cabinets were very, very old, and all different sizes and colors. Looked bad. So I decided against bringing them into the Xylarium. But it got me thinking, and I paid a visit to the Penn State Surplus building a couple of blocks away.

Well, what do you know? Some dorms had been renovated this summer, and they had dozens of identical chest of drawers that had been removed in the process. Not bad, either...light oak plywood sides and fronts, poplar and maple rails, styles, and backs, and thermofused melamine tops. After taking a few measurements of the drawers, I decided they would work. So I bought fifteen of them for $15 apiece, and paid another $10 apiece to have them moved over to the lab. Not too bad, eh?




Each drawer holds 98 standard size samples, stacked in two rows on their sides. With five drawers in each chest, times fifteen chests, I have storage capacity for 7,350 specimens...for only $375!


But not so fast...one slight problem I had not anticipated. When the drawers are loaded as in the picture above, I found that the drawer bottoms began to bow and would certainly creep more over time. With enough creep, they would pop right out of their frames. Then I would have a mess.

But a little wood engineering knowledge provided a relatively cheap and simple solution. I went to the local Big Box and bought two sheets of 19/32 (4-ply) pine plywood that is commonly used for sheathing here in the States. It's strong, and stiff. I was able to get 78 strips about four inches wide and 29-1/2 inches long from the two sheets. I then screwed these braces to the underside of each drawer, and problem solved!





I also bought some 1x2 strips to use as dividers inside the drawers. I was going to screw them in place, but I decided to leave them unfastened, so that they could slide to accomodate other sizes of specimens, since we have so many non-standard specimens in the collection. I call them "sliders" and they work nicely.


This project also differed from your typical woodworking project in one unique respect. One by one, as I emptied the chests to clean them and check for any signs of bugs, I found more than a dozen articles of decidely feminine clothing, most of the underwear and sportswear variety. The chests must have come from the girls dorms. Fortunately, I have daughter who is just starting her freshman year at Penn State, and a few of the garments are her size. Only problem came when I was caught carrying the items out of the building by my boss...at least he acted like he believed my story.

No bugs, but quite a few shorts and shirts, etc., etc.
So another $100 for the modification to the drawers brought the total bill for the project to $475. Custom cabinetry for the same purpose would easily have cost ten times as much, even here in Pennsylvania where every other small business is a cabinet company.

So, storage is in place...problem solved, right? Well...a few of you can guess what my problem is now. How do I efficiently and correctly transfer the 7,000 or so specimens into the drawers? Because even though I moved the boxes (again, for the third time) they still need to go away.



The specimens in the boxes are in no particular order at all. So even though the temptation is to just unload the boxes into drawers and then sort them out over time, you see the problem if nearly all the drawers are filled with random samples. No where to put the ordered samples.

So, patience is once again called for. I have to first enter all the specimens into the database, and once that is done (by the end of the year, I hope) then I'll be able to sort the entries by Family Name, divide them into 98-entry blocks, assign them drawer locations, and then, finally, Finally!...put them away in their proper place.

Yes, after considering several different schemes over the last couple of years, I decided to order the collection by Family Name. The original collection is stored by Accession Number, which is really a bother because that is basically random storage. So if I want to compare several different species of oaks, for instance, I typically have to search them out in that many different drawers. Which is not covenient when I am trying to show something to a Xylarium visitor.

I was leaning toward storing them by geographic region, so that, for instance, I could keep all my Australian specimens together, or that all our Pennsylvania woods would be together in one or two drawers. But I finally decided that following the scheme used at the Forest Products Lab in Madison was the best way to go, especially since the Penn State Collection will be used mostly for research projects. So, hopefully, by 2018, we'll all know how many specimens of each family, genus, and species are in the Penn State collection....and where they are!

Tuesday, July 11, 2017

The Shoulders of Giants

Today is a significant day of accomplishment in the Penn State Xylarium. I've been working for four years, off and on, organizing, validating, verifying, and re-naming specimens that were originally documented by Drs. Wallace White, Richard Jorgenson, Newell Norton, and their predecessors up until Dr. Norton's passing in 1968.

Here are Dr. Wallace White, and Mr. Richard Jorgenson, Professor and Instructor of Wood Technology at Penn State in 1951.

That's Dr. Newell Norton on the right in the tie, seated along with Forestry Instructor John Halberg, in 1951.
And here is what the sum of their work, sixty years in the effort, amounted to.

There were a total of 4,115 specimens organized and documented. These include 2,110 unique accession numbers assigned, but in their original reorganizing that was winnowed down to 2,005 unique specimens. My work on the collection has reduced that number down to 1,760 unique "accepted" species. In addition, there are an additional 31 species for which the proper identification is still unresolved in the scientific community.

The specimens represent 149 different biological families, and have been collected from 130 different countries (or states and provinces in North America) around the world. They were brought together from the collections of 30 different individuals or organizations, and represent the work of hundreds of different collectors. (That number will never be known, as only about forty percent of the specimens have voucher documentation indicating the name of the original collector.)

Practically none of these specimens are what we consider "standard" collector size today, as they were all collected prior to the formation of the "Wood Collectors Society" in the United States from which the final standard evolved. As a result, they are all different sizes, and Dr. Norton decided on four different shape classifications: Type I, which resemble today's standard specimens but are slightly smaller; Type II, which are very small sections, resembling cut-offs from the larger Type I specimens; Type III, which are round or semi-round specimens cut from either very small stems or branches of larger trees; and Type IV, which are blocks, or other odd shapes. I have not yet tabulated how many of each are, a task that remains for another month's worth of work.

All of these specimens have typed documentation (in triplicate!) on file which I used as the beginning of my examination of each specimen. In addition, the 2000 or so specimens from the collection of collector Joseph L. Stearns are all documented by hand by Mr. Stearns in his original notebook, and the 800 or so specimens from the "Project One" distribution by State University of New York have summary sheets and field sheets on file here in the lab.

All of the work is now summarized and available for inspection in the "Database" link in the right-hand column of this blog.

Dr. Norton apparently was the last scientist to work on the collection, his work continuing through the 1960's until his death in 1968. At that time, only about 2/3 of the collection was documented with access numbers. The remaining 1/3 of the collection still sits here, waiting for the next generation of researcher to take it on.

Which I will do, but I have a larger, more pressing task immediately in front of me.

My next line of focus will be to perform the same work on the 4,000 specimen collection of Dennis Brett, who donated his collection of seventy years of collecting to Penn State in 2016. Mr. Brett's collection will become the largest donation to the Penn State Xylarium, double the size of Mr. Stearn's contribution in 1956.

Obviously, I'm eager to get the new collection properly documented and entered into the database. So that comes next.

How long will it take? Well, that depends on any number of factors. Perhaps I will obtain funding that will allow me to step up the resources committed to the work. If not, it will take a while. But in this type of work, the journey is so much more enlightening than achieving the destination.




Wednesday, April 12, 2017

Re-assignment of Family Causes Heartbreak


Hamamelidaceae Liquidambar styraciflua.


Source: Sanchezn - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=3057384

This was my favorite scientific name in dendrology class back in college. We had to memorize about 150 tree names, and a few of them still rattle around in my brain occasionally. But Hamamelidaceae Liquidambar styraciflua pops instantly into my mind every time I pass a sweetgum tree. And they're almost everywhere east of the Mississippi, which means that wonderful name rings in my head all the time.

A Sweetgum in autumn. Source: Ontologicalpuppy - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=36757412
I just came across three specimens of L. styraciflua in my documentation project. Instantly the old satisfaction of allowing those sixteen syllables rolling off the tongue in my brain brought back the pleasant memories of collecting leaf samples in the cool autumn air of Nacogdoches, Texas.

But as I checked into The Plant List to confirm the Accepted Name (yes, it is still Liquidambar styraciflua L.) I received a shock. The Plant List had the Family listed as Altingiaceae! What the heck is Altingiaceae? I quickly clicked over to the Catalogue of Life and confirmed that, indeed, genus Liquidambar has been torn from the bosom of the witch-hazel family Hamamelidaceae, and transplanted into the unknown-to-me family of Altingiaceae.

Altingiaceae Liquidambar styraciflua?! Just doesn't have the same ring, the same rhythm. What were they thinking?

Well, according to Wikipedia...
"The name "Altingiaceae" has a long and complex taxonomic history. Some attribute the name to John Lindley, who published it in 1846. Others say that the authority for the name is Paul F. Horaninov, who described the group in 1841. In the nineteenth and twentieth centuries, the family Altingiaceae was not generally accepted. Most authors placed these genera in Hamamelidaceae and this treatment has been followed in some recent works as well. In the twenty-first century, however, molecular phylogenetic studies have shown that including Altingiaceae in Hamamelidaceae makes Hamamelidaceae paraphyletic. The Angiosperm Phylogeny Group recognizes four families in the lineage including Altingiaceae. Cercidiphyllaceae and Daphniphyllaceae are sister. This clade is sister to Hamamelidaceae and these three families are sister to Altingiaceae. The clade is sister to Paeoniaceae."
-  https://en.wikipedia.org/wiki/Altingiaceae
So, the result of the best thinking on this subject is that the inclusion of Liquidambar in the Hamamelidaceae family is invalid, and the fifteen Liquidambar species have been sent to plant purgatory in the single-genus family Altingiaceae.

So much the worse for modern-day dendrology students, who will never experience the pleasure of committing Hamamelidaceae Liquidambar styraciflua to memory.

A nice non-typical (spalted) specimen of L. styraciflua. Source: Penn State Xylarium.


Monday, April 10, 2017

An Update on Validation of Accepted Names

I've finished going through and finding all the Accepted Names of the species I've entered into the database. The results are in the tally description on the right.

An interesting note was that on my first pass using ThePlantList.org, I had 110 "unresolved" species names. The Plant List Version 1.1 is current as of September 2013. I then thought to check these 110 against a few other sites that I had not been using, and found that the site "CatalogueofLife.org" was current as of March, 2017. Searching these unresolved names on Catalogue of Life changed about 80 of them to "Accepted" names, about half of which were the same as the unresolved names, and the other half were different.

We live in a wonderful time when we can reconcile our areas of research across several online resources, and get a good sense of just how valid our determinations are.

Another note of interest to those of you who may be interested. I've posted a link called "Database" there in the right-hand column that will give you access to the most current version of the Penn State Xylarium worksheet. So you can see what I've entered into the database and keep up with my progress. Hopefully, I'll finish the data entry sometime this year...only about 8,000 to go.

Friday, March 17, 2017

My New Favorite Wood Species

As I confirmed the specimens in the collection with their Accepted Names, I ran across one I had not noticed before, and instantly liked it. The species?

Chukrasia tabularis A.Juss.

Why, you ask? Well, look at that genus name again, and then consider my name. I've got to like a genus named after me, don't I?

Well, maybe it wasn't named after me, but that is a distinguished genus, at any rate. And better yet, C. tabularis is the only accepted species in the genus. The Plant List cites thirteen species of Chukrasia, but the other twelve are all synonyms of C. tabularis.

Now, I halfway expected that any species coincidentally named after me would be some lowly, undistinguished little bush. But not so! Chukrasia tabularis in fact a fine wood. One of its more common names in English is Indian mahogany, and it has many characteristics of the true mahoganies, the Swietenia. In fact, it is a member of the same Meliaceae family.

Chukrasia tabularis (Penn State Xylarium)
Unfortunately, the similarity to Swietenia has caused it to have another more vulgar common name: bastard cedar. We'll ignore that one. It is also called White cedar, East-Indian mahogany, Indian redwood, Burma almond wood, Chickrassy, and Chittagong wood, depending on who is calling it.

From Wikipedia:
The Indian mahogany (Chukrasia tabularis) is a deciduous tree in the family Meliaceae. It is native to Bangladesh, Cambodia, China, India, Indonesia, Laos, Malaysia, Myanmar, Sri Lanka, Thailand, and Vietnam. Also introduced to many western countries such as Cameroon, Costa Rica, Nigeria, Puerto Rico, South Africa, and United States. The plant is widely used in Ayurveda as an important medicinal plant.
The trees are tall with a cylindrical bole and spreading crown. C. [tabularis] leaves are abruptly pinnate or bipinnate with leaflets that alternate or are subopposite, entire and unequal at the base. The erect, oblong flowers, which are rather large and born in terminal panicles, possess four to five petals. Mature fruits are a septifragally three to five valved capsule.
Chukrasia [tabularis] is the provincial flower and tree of Phrae Province, Thailand.
The wood has a texture and weight very similar to cedar and mahogany, with a sweet but slightly distinct odor. Instead of a cedary smell, I get cinnamon and chocolate. So not only is it beautiful, and workable, but it smells like a bakery confection! Can't get better than that.

Chukrasia tabularis, a wood worthy of its name.

Tuesday, February 28, 2017

Penn State Xylarium Makes Public Television

I think it was Andy Warhol who was once quoted as saying that everyone gets fifteen minutes of fame sometime in his or her lifetime. Well, my fifteen minutes was boiled down to less than five, but I'll take it. Our local PBS station, WPSU, did a feature on the Xylarium recently, and after an hour or so of interviewing and shooting video, they produced this four minutes and fourteen seconds of a program. And while I think they missed a lot of the essential facts I shared with them, they showed what interested them, and that's what is important, after all.

Enjoy.


Monday, February 20, 2017

Observations on Updating Scientific Names of Older Specimens

Much of the Penn State Xylarium collection is comprised of very old specimens, those collected in the first half of the twentieth century. I am finding, as I go back and confirm the scientific names of the specimens that a surprisingly high percentage of them are not properly identified with current accepted names.

As I correct these names, I get the sense that somewhere between thirty and forty percent of the specimens are mislabeled. The obvious implication of this is that further collection efforts will be mistargeted unless these names are properly corrected to the modern name. It also means that unless the trading partner, or collection from which I make further acquisitions has been similarly updated, then I must be careful to confirm the specimen name prior to acquisition.

I don't think I have a qay to quickly tabulate the numbers on the whole collection, but here are a couple examples of how many species names are different than their original designation in the Penn State collection.

Quercus matches my original expectations. Only four of forty-two species, about 10%, in the collection had their names altered in the confirmation process (very slight spelling variations are not included). Those were:

  • Quercus breviloba, confirmed as Quercus sinuate var. breviloba
  • Quercus prinus, confirmed as Quercus michauxii
  • Quercus stellata var. margaretta, confirmed as Quercus margarettae
  • Quercus virginiana var. maritima, confirmed as Quercus hemisphaerica
Similarly, Eucalyptus has about a 10% correction rate; six of the 56 species in the collection had to have their name updated. Four of those were the result of the reclassification of several of the Eucalypts to Corymbia.

However, eight of the fourteen Eugenia in the collection had to be corrected to modern names, and most of those had completely different genus names.

Syzygium cumini (L.) Skeels, one of two specimens in the collection originally labeled as Eugenia jambolana.
I also find that if a specimen is a one-only, that is, the only specimen of a species in the collection, there is about a 50-50 chance that the correct modern name is something different, and most likely a different genus.

Overall, I sense that somewhere between thirty and forty percent of the collection is being renamed as I go through the name verification process. Most of those renames are not to other species in the collection, so the overall number of species in the collection is not shrinking by that much...they are mostly being named to other species that are unique to the collection.

At this point, I've confirmed about 2000 of the 3400 names I've entered into the database.
Another week or so, and then I'll be back to data entry of the identified specimens. This time, I'll verify the names as I enter them into the database. It'll go a little slower, but at least I'll have a running tally of the number of unique species in the collection.

I encourage collection curators to perform the same process on their collections, now that the internet makes it so easy. I wonder if this has been done to the really big collections in the Netherlands, Germany, Britain, and Wisconsin?


Thursday, February 16, 2017

Quantifying Anatomical Wood Features in Digital Images

As I work on the collection, I continually ponder the future research direction of the Xylarium. As I think of different issues, such as "How should I outfit the Xylarium lab for specific lines of research?" it is necessary to research the state of each area of research and the technology being used for each.

Which brought me to an excellent video posted by the Swiss Federal Institute for Forest, Snow, and Landscape Research Wood Science Laboratory. They demonstrate the latest in microscopic imaging that they use to perform quantitative analysis of anatomical features of wood samples; that is, they want to be able to perform statistical tests of hypotheses, specifically on climate change, and they need to have precise data on the size of tree cells and growth rings from year to year for the periods they are studying.

This is an introduction to how they do it.



G von Arx, A Stritih, K ÄŒufar, A Crivellaro, M Carrer. 2015. Quantitative Wood Anatomy: From Sample to Data for Environmental Research. DOI: 10.13140/RG.2.1.3323.0169


Most of my thoughts around the use of the Xylarium collection have centered around qualitiative techniques, using macrophotography instead of the microphotography and imaging demonstrated in this video. However, depending on what research partners the Xylarium attracts, we may eventually go in this direction.

Time will tell.

Monday, February 13, 2017

Do You know How Many Oaks There Are?

Still reconciling my partial list of specimens with their accepted names, and working on the Fagaceae family. When I got to the genus Quercus, wow!

According to The Plant List, there are 4,529 named species of Quercus alone. Of course, by far the majority of those are synonyms of the same species. The referees of The Plant List have determined that 633 of that number are legitimate, unique species and have designated them as Accepted Names.

The amazing thing about that, is that those of you who walk the woods often know how difficult many of the oaks are to identify at a glance. Sure, here in America we can tell "red oaks" from "white oaks" pretty easily, but 633 different versions of those?! And to think that botanists originally believe that they had discovered over 4,500 different species? That's a lot of differentiation.

I think that just is a great illustration of how much variation nature provides us with. As the taxonomists and geneticists do their work, they've determined that seven out of eight uniquely named species are really just morphological variants of the same tree.

At this point of my work, I've determined that we have 43 of the 633 different species. I had entered so many oaks into the database that I assumed we almost had them all. Was I wrong!

So many oaks. so little time...

Quercus shumardii, the Shumard Oak. (Penn State Xylarium). From Wikipedia: Quercus shumardii, the Shumard oak, spotted oak, Schneck oak, Shumard red oak, or swamp red oak, is one of the largest of the oak species in the red oak group (Quercus section Lobatae). It is closely related to Texas red oak (Quercus buckleyi), Nuttall's oak (Quercus texana), and Chisos red oak (Quercus gravesii).

Tuesday, February 7, 2017

Reconciling Scientific Names

You have a list of several thousand scientific names, and you want to check each against a reliable authority to determine the correct accepted name.

  1. You decide on a primary authority, such as www.theplantlist.org.
  2. You type or paste each genus name, one by one, into the search bar of the authority, and it lists all the species under that genus.
  3. If your name is the accepted name, you're done.
  4. If your name is a synonym, you click on that name and find the accepted name for that species.
  5. If your name is unresolved, you accept that name and check back periodically to see if there has been a resolution.
  6. Don't forget to check the Family of your accepted name...sometimes they change.
But what if your genus name is not found? Then it gets a little trickier, but you can usually still find your species by using secondary references.

My first response is to consider if there are any logical variants of that genus name. For instance, names ending in -a are often really -um, and vice versa. Do you have others similar names in your list that differ by a letter or two? Check those under the alternate spellings.

I also use a great reference that every serious wood collector should have...The Book of Wood Names, published in 1936 by Dr. Hans Meyer. If I can't find a probable genus name on The Plant List, I use the common name given for the species and go to Meyer. It is amazing that Dr. Meyer and his team could assemble such a staggering list of wood names, much less give the scientific names of all of them back in the days of very slow typewriters. But 98 times out of 100, I find the common name, and the genus...and very often, an alternative scientific name.

If that fails, then I go to Wikipedia and see what results I get there on the unfound scientific name. Sometimes that works. If it doesn't, I go to TAXA (www.woodsoftheworld.org), click on "Woody Genera" and see what is listed there. 

I just used this process to resolve the names of twelve specimens that were labeled with the genus name "Anona" within the family Anonanceae. On The Plant List, no Anona, and no Anonaceae. Meyer gave me "Anona" and "Anonaceae" on all the different common names I searched. Finally, on TAXA, I found the genera "Annona", and when plugging that name into The Plant List, discovered that the correct spelling of the family name is "Annonaceae". Problem solved.

That was clearly a case of a spelling that changed over time, but actual mispellings happen more often that you can imagine. I had four specimens of genus Pistacia, two of which were "Pistacia cera" and "Pistacia "vira". Neither were listed on The Plant List. But I saw that there is a "Pistacia vera", so that was logically the correct spelling of "vira". And that made me think, could "cera" supposed to have been "vera". I went back and pulled the two specimens, and what do you know? They're the same! In fact, checking the original notes, the "cera" specimen was noted as a "root" specimen...and comparing the two, it is easy to see that the two are a root and stem specimen from the same plant.

Pistacia vera, of the Anacardiaceae family. (Penn State Xylarium). The one on the right was originally labeled "Pistacia cera" with one accession number, and the one on the left was labeled "Pistacia vira" with a different accession number, both by the original collector (Joseph L. Stearns) and Dr. Norton in the 1960's. From close analysis in the lab, not much question these were from the same specimen. One was noted as a "root" specimen, so the two specimens were collected separately by the original collector (prior to Stearns) and then the mispellings created confusion and the individual accession numbers.

So that's what I'm doing today!

Monday, February 6, 2017

The Blog is Already Improving the Project

I've simply been going through the colllection, specimen by specimen, trying to settle on a correct identifying scientific name for each. At first, I was just accepting the original identification and labeling of each. Dr. Newell Norton, who had been originally consolidating the collection in the 1950's and 1960's, had been organizing the collection during his work, and having datasheets typed up for each. As he did so, he apparently confirmed the identification and name of each as he went, since some of the specimens had been re-named from their original labeling. And I am not the wood scientist Dr. Norton was, so I accepted the names on the data sheets.

Over the years, though, I've gotten better with references and online tools for confirming the Accepted Name of each specimen, and have begun changing some of the labels as I determine a change to be proper. However, I only started doing that in the last few months; the first 3000 or so specimens or so were simply the accepted name at the time of Dr. Norton's work.

So, when I tried to add an information box on the right-hand side of this blog with the current number of specimens, families, and unique species, I realized I had not reconciled the first 3000 with their current accepted names. Also, in the spreadsheet I'm building (in Google Sheets, so that I can share it online with whomever wants to see it, once it's completed) the genus and species names are entered in separate columns, preventing me from using a function to easily count the number of unique species in the collection.

So, since I'm at this point, I'll break from data entry and go back to the beginning. I've created a new column, called "Accepted Name", and I'll enter the accepted genus and species for each specimen, as determined from The Plant List. For those that have only unresolved names, I'll list those in a separate column. That way, I'll be able to check back every year or so to see if they have been reolved.

Once that's done, I'll use a function on the column to determine the precise number of unique, and correct species in the collection as of my current tally.

Now that I think about it, this is probably a good exercise for all wood collections, if they haven't had their names kept current. There have been a lot of changes in tree species names over the decades, and if specimens are more than a decade old, they probably need to be re-checked. The internet, and advances in genetic research, are really allowing the taxonomists to clean up the family trees of the species. And I'm all for that!

It's a break in my progress on data entry for the collection, but at this point, I'd like to know some good numbers...wouldn't you, if you were in my situation?

The Penn State Xylarium is Live!

It occurred to me today, that after working on the Penn State Xylarium wood collection for nearly three years, I should begin to share the progress and my thoughts on a regular basis. This is the kind of work that is hard to describe and summarize in a single blog post, as I might do on Go Wood, so the logical alternative is to post shorts on a unique site dedicated to the work.

So, to all of you xylophiles, botanists, wood anatomists, and wood specimen collectors who enjoy this sort of thing, here you go. Don't be shy about giving me feedback and requests...this site is for you!

Baikiaea plurijuga, known as African teak, Mukusi, (Penn State Xylarium). Rhodesian teak, Zambian teak or Zambesi redwood, is a species of tree from the legume family, the Fabaceae from southern Africa.
I haven't yet gotten a professional setup to take good photos of the wood specimens, but I'm working on that. Anyone wishing to make a donation to Penn State to help make that happen, please contact me at cdr14@psu.edu.

I'd like to thank Jean-Claude Cerre of Nevers, France, whose groundbreaking work in the field of high-resolution wood macrophotography introduced me to a whole new world of wood, and has inspired me to follow in his footsteps. Merci beaucoup, Jean-Claude!