Monday, May 24, 2021

The most poisonous wood?

Continuing in my progress of labeling and filing the wood specimens, I came across this one...
As you can see, it carries a most ominous warning on the lower label. It was also wrapped tightly in plastic wrap. I checked with my Kingsbury, Poison Plants of the United States and Canada. Sure enough...
Early literature dealing with the exploration and botanical characteristics of tropical America contains many references to the actual and supposed toxic characteristics of the manchineel tree. All parts of the plant contain a milky sap which is extremely caustic. Cases involving severe skin irritation and blindness (usually temporary) in human beings and animals were not unusual. Probably from the severity of the reaction, the tree gained the unfounded reputation of bing able to poisin persons who merely came under its shade. The fruit is not offensive in odor or taste and has been the source of poisoning in human beings. At the time of the Spanish explorations, the Indians used the juice of the machineel tree as an arrow poison. It also served as an ingredient in many native medicinal preparations. The wood was prized in furniture making, but it was found necessary to scarify and burn the surface of the trunk before cutting or handling.
Well, I'm glad of that reference to furniture making. The way I read that last sentence, the poisonous sap was retained in the sapwood and was eliminated by the destruction of the outer surfaces of the log. Which is good, considering I had already handled and filed this specimen several times without knowing the story behind the species...
I think I'll go wash my hands now.

Friday, July 19, 2019

Making Progress in Organization

Well, last year I reported that the majority of the specimens had been documented in our database. The next step was to begin organizing them physically in the Xylarium.

The first step was kind of tough. I had to empty all the specimens out of the old cabinets so that I could begin loading them up in the correct order (by Family, Genus, Species). So I had specimens stacked everywhere, and empty cabinet drawers all. Then I had to print out new labels from the database. Got that done a couple of months ago. Since then, I've been going through the specimens, finding their appropriate labels, and putting them in the correct drawers. This is what that looks like...

Specimens stacked everywhere...

Starting to go back in...

Starting to look organized...

Easier to just leave drawers partially open as I go...

Over 11,000 labels.

Well, I have no idea how long this is going to take, since other people seem to think I ought to be doing other things :-) Oh, well, my goal is the end of the year. I just won't say what year.

Thursday, October 18, 2018


Yesterday was a big day for the Xylarium. After five short years, I've completed validaton/verification and data entry on the 10,753 wood specimens that have some form of original documentation, including about 1,000 that are fully vouchered with field collection sheets. About 90% of the specimens were collected between 1900 and 1960. There are an additional 3,000 - 4,000 undocumented specimens that await identification and data entry.

A quick review of the collection:

Specimens Documented to Date:
Total: 10753
Angiosperms: 9616
Gymnosperms: 1137
Unique Families: 193
Unique Accepted Genus/Species: 3872
Unique Unresolved Genus/Species: 63
Continent of Collection: Total (Unique Species)
Africa: 641 (237)
Asia: 1701 (867)
Australia: 1477 (630)
Central America: 1563 (538)
Europe: 280 (113)
North America: 3559 (880)
South America: 876 (430)

The reason I felt compelled to share this with you is that the database has at least two unique features that may occasionally be helpful to you.

The first is that all the assigned scientific names are "Accepted" in current online plant databases. In the process of building the database, I found that about 40-50% of the original names were either misspelled or had changed since original identification. So, the database is a quick check on Accepted names of practically any species you may have an interest in...without your needing to check against several online databases...which I've already done for each species. And I've noted which reference source I ultimately used for final determination of "Accepted" status.

The other is that most of the specimens were documented with at least one common name. Common names are a lot harder to find in one place for a specific species...Wikipedia and the Catalogue of Life have some of them if you know the scientific name, but if you're starting out with a common name, the process can be a lot tougher. This database gives you the option to either start out with a common name and work backwards, or start with a known Genus and scan possibilities. For instance, if someone asked you about "silver fir", a quick scan of the Abies entries or sort of the database tells you that Abies alba, Abies amabilis, Abies concolor, and Abies spectabilis all are at least occasionally called "silver fir" in their part of the world....which is also noted in the database.

The link to the database is in the right-hand column where you'll see a "Database" link. If I have the access set up correctly, you can sort as you like, but can't modifiy the database. Please let me know if you discover otherwise.

So, that's where the Penn State Xylarium is at, today. Now that the database is completed to this point, I can sort by Family and begin to reorganize and file all the specimens in a convenient way. So, if  someone asks me about the physical differences between different oak woods, for example, I can simply open one or two drawers and show them.

Most importantly, I can generate detailed stories derived from the collection specimens for research, teaching, or Extension proposals. So the drudgery is over, and the fun begins. Let me know if you have any ideas...

Tuesday, December 19, 2017

The Season of Giving...

I couldn't let this holiday season pass without mentioning to followers of this blog the generosity of three prodigious wood collectors to the Penn State Xylarium.

You know of course, that last year Mr. Dennis Brett, IWCS #257, donated his wonderful collection to Penn State, increasing the number of documented specimens in the collection by 3,981 specimens and nearly doubling the number of unique species in the collection from 1,760 to over 3,100. I've been busy validating and entering his collection into our database, and I can see the finish line on that project.

But just as if to ensure I don't catch up on my work, the University has recently received two more excellent donations to the Xylarium. But you'll hear no complaints from me.

Last month, Mr. John Colwell, IWCS #4698, donated his collection of 2,825 specimens to the Xylarium, and I picked it up a few weeks ago. It is a wonderfully documented collection, and Mr. Colwell, who is a Penn State alumnus, has the entire collection entered on a spreadsheet, which means that I'll be able to incorporate it into the Penn State collection in a mere matter of weeks.

Mr. Brett's donation increased the size of the Penn State collection from 4,115 to 8,096 documented specimens, and Mr. Colwell's donation pushes that number to 10,921 documented specimens, with around 4,000 unique species represented.

And just for a little icing on the cake, two weeks ago Penn State received another wonderful donation. Mr. Rejean Drouin, IWCS #3589, donated a badly-needed collection of Vietnamese wood specimens to our Penn State Xylarium. His donation consisted of 298 specimens of 182 different species of woods from three different regions of Vietnam.

So, the Penn State Xylarium has been blessed abundantly in this season of giving. It now contains over 11,000 documented specimens of over 4,000 species, with another 3,000 to 5,000 waiting for validation and documentation. Plenty of work to do there.

The three donations almost ready for filing away. Boxes on the floor at left are part of John Colwell's collection; the white box in the middle are the Vietnamese woods of Rejean Drouin; and the stacks of boxes on the right are Dennis Brett's former collection.

All this activity at the Xylarium is generating quite a bit of excitement at the University, as you may imagine. I have several researchers in different areas of investigation interested in collaborating on research projects and wanting to use the Xylarium specimens as part of the justification for pursuing research funding in wood chemistry, medical research, plant systematics, and genetic research.

And Mr. Brett, Mr. Colwell, and Mr. Drouin are now members of the fraternity of wood collectors who are helping make this research possible through their donations. All told, I believe there have been at least ten other IWCS members who've donated to the Penn State collection over the past seventy years, including some names you may recognize...Richard Jorgenson, Ken Bassett, Ron DeWitt, Mark Peet, and yours truly. All are names that will live in posterity through the research of folks not yet born.

That is truly the Spirit of Christmas Yet-to-Come.

Merry Christmas...

Tuesday, October 17, 2017

Digging Into a Name Validation

For those few of you who have an interest in this blog, you'll probably be interested in the minutae of things others could care less about...for instance, the detail of validating a scientific name when things don't go smoothly.

This morning I've run across a specimen card labeled "Dalbergia foliosa - Rosewood - Brazil". OK, looks pretty straightforward. But a check with The Plant List under Dalbergia gives me a moment of pause.

Yes, there is "Dalbergia foliosa (Benth.) A.M.Carvalho" listed as an Accepted Name. OK, nothing to see here, move along, right? Well, I should have...but to do this job right, you have to expend at least a minimal level of intellectual curiosity when something catches your eye.

And what caught my eye this time? Well, the entry right above Dalbergia foliosa is "Dalbergia foliolosa Benth.", also listed as an accepted name. Look closely...only two letters difference, and both with the same primary authority.

Now, this happens from time to time, and when it does, I always wonder..."Why would the authority give a name so similar to another species that it could be confused by a simple misspelling?" This is a relevant, and I believe, valid question from my experience...about one of every ten specimen records I've entered has a slight spelling variation from the Accepted Name. So when I see two Accepted species names, one foliosa, and the other foliolosa, from the same primary authority, and one with a secondary authority, I suspect that a typo or misspelling has been confirmed as a separate Accepted Species. And I don't know which one is correct, as in this case.

So, how do I investigate this question? Well, next I checked the database I've been using as my final reference, The Catalogue of Life. And what do I find? Accepted Names of both species. My suspicion is growing that this second name may in fact be a second, separate species.

Both of these sources cite the source of their listings as  the International Legume Database & Information Service. So I go to the site and try to access the records for Dalbergia. Unfortunately, all I get in response to my queries is a screen that says "404 Not Found. The resource requested could not be found on this server!" And that seems to be the response for every page of the site that I try to access. I've had this trouble before with the site, and hope that the site hasn't permanently gone down due to lack of funding, or lack of an adminstrator, or something like that. Because we have an awful lot of databases that use this database as their source.

So I dig into the contacts for the database, which seems to be one Richard White at Cardiff University. Unfortunately, an email to his listed address returned this message:

"Message not delivered
There was a problem delivering your message to See the technical details below, or try resending in a few minutes.
The response from the remote server was:
550 5.7.1 recipient <> unknown #292 (y9GFMO008515648400)"

So, at least for the time being, I'm going to have to make a decision without the benefit of the International Legume Database and Information Service. What else can I try?

Well, the huge collection of specimens at Kew Gardens in London has an online database of its specimens. So, if I can go there and see that they in fact have specimens of both D. foliosa and D. foliolosa, then I will trust that they are in fact different species.

Unfortunately, their collection of over 42,000 wood samples includes neither D. foliosa or D. foliolosa. However, their Herbarium collection of over 7 million specimens contains one herbarium voucher of D. foliosa...and this one voucher tells an interesting story.

If you examine the voucher in the link above, you'll see that the specimen was originally collected in 1854 as Ecastophyllum foliosum, with a synonym name of Ecastophyllum glaucam. The name was then updated to Dalbergia glauca in 1939, and confirmed as such in 1988...before being updated to Dalbergia foliosa (Benth.) A.M.Carvalho by Carvalho in 1997. Which is interesting...The Plant List shows D. glauca as a synonym for three species...D. foliosaD. ovata, and D. obtusifolia, depending on which authority you believe.

So, am I confirmed that my specimen record is in fact D. foliosa? True, Kew has a specimen with that label...that was only labeled as such after a couple name changes with the last change in 1997. But...they have 49 vouchered specimens of D. foliolosa!

And what do you know? The second of these that I happened to pull up was this one. And you'll notice that the original labeling of the specimen as collected in 1931 was Dalbergia foliosa! Collected in Brazil, where our Penn State specimen in question also came from.

So, what is my conclusion? Well, I suppose I'll stay with D. foliosa for now. Even though it looks suspiciously that the two species are the same, and that the D. foliosa in the Kew collection may possibly have been mislabeled, I don't have a direct basis for changing my label. So, Dalbergia foliosa it is. At least, until I can determine something different at the next stage, verification of the identy of the species from the wood sample. That may be even more interesting. One thing I know for certain...I'll be trying to acquire several specimens of each before I tackle that project. And talking with some Dalbergia experts, like my friend Mihaly Czako down in South Carolina. Maybe we can straighten this one out. If we do, I'll update this post.

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,  However, a query on Wikipedia for the species re-routed me to Vachellia nilotica. And a further check with my secondary reference,, 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 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.

The most poisonous wood?

Continuing in my progress of labeling and filing the wood specimens, I came across this one... As you can see, it carries a most ominous ...