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!