Sunday, May 11, 2014

Crowdsourcing Taxonomy

Crowdsourcing is an old idea. All of the plants in Botanica Caroliniana are the result of a large effort to crowdsource taxonomy.

James Petiver (1665-1718) was an apothecary in London. Petiver was a member of the Royal Society and a collector - of all sorts of things. Except for a brief period studying entomology in the Netherlands, Petiver worked in London. He kept a shop "at the sign of the white cross in Aldersgate, London."

Somehow Petiver got into the business of collecting natural history specimens, especially insects and plants. Ships were visiting all parts of the world, and Mr. Petiver and his friends evidently had an insatiable appetite for the curiosities they might bring back. So he started printing pamphlets asking for contributions to his collections, with explicit directions for collectors to follow for collecting and storing herbarium specimens. The collectors - Lord, Lawson - would package up their materials and send them to London when they could. Petiver then organized them according to some taxonomic scheme - if you look at the order of Lord's specimens, they are pretty much arranged by current families - and bound them in books.  By the time he died in 1718, Petiver had the largest collection of dried plants in the world.

Hans Sloane (1660 - 1753) jumped on this opportunity, purchasing Petiver's collections and many others, which eventually became the basis of the Natural History Museum, London. Sloane himself spent some time in Jamaica and is famous for his descriptions of Jamaican natural history, but the vast majority of his collection - some 120,000 specimens - came from people he never met and places he never visited. Catesby was one of his contributors. William Sherard (1659 - 1728), another of Catesby's sponsors, was doing much the same thing in Oxford.

The big man himself, Carolus Linnaeus, used this same business model. His travels were mostly restricted to places close by - Lapland, central Sweden, the Netherlands - and he did most of his work from his comfortable facilities in Uppsala. To fill his coffers, he sent his students on voyages of discovery. Daniel Solander and another student traveled around the world with Captain Cook. Others visited Japan, the Americas, Australia, and anyplace else they could reach. The ones who survived gave their specimens to Linnaeus, who worked them into his Systema Naturae.

Why do it this way? Well, for one thing, traveling was dangerous. Lots of Linnaeus' students died on their journeys, cutting short their aspirations for scientific discovery.

But more practically, you can't do two big things at once. Exploring and collecting specimens is one job. Assembling a collection is another. To make a collection, you have to be physically present at your research site, and you are encumbered by lots of stuff - camping gear, the specimens themselves. You can visit only a restricted area, and you might have to visit that area repeatedly to catch your subjects in bloom.

Assembling a collection, on the other hand, requires peace and quiet, a large flat surface and a roof overhead, lots of paper and glue, and reference materials. It's not easily done in the field. More importantly, a good collection requires a large body of specimens. Specimens from multiple collectors can offer perspective that the work of a single collector cannot. If you want to organize the world's plants, you need lots of contributors in lots of different places. You want to see the big picture.

This is how crowdsourcing works today. Project Budburst, the Great Backyard Bird Count, and NASA's Disk Detective program (sorting out stars with disks from nebulae and galaxies) all use non-scientist volunteers to collect and process data. The professional scientists then process what the citizen scientists send them, and the result is much better than they could achieve trying to gather data alone.

Like our historic collectors, today's citizen scientists are motivated by a desire to be part of something bigger - to make a contribution to science and maybe learn a little more science themselves. Lord and Lawson collected for Petiver out of interest in the world around them and the hope that what they saw might be of use - and as a way of making contact with London intellectual life, in short supply in the Carolinas in 1700. And their contributions did turn out to be real, useful both to the botanists creating modern taxonomy and to those of us studying them today.

Wednesday, May 7, 2014

Winchester Wedding

In A New Voyage to Carolina, John Lawson records this scene:


        Next Morning we set out early, breaking the Ice we met withal, in the stony Runs, which were many. We pass'd by several Cottages, and about 8 of the Clock came to a pretty big Town, where we took up our Quarters, in one of their State Houses, the Men being all out, hunting in the Woods, and none but Women at home. Our Fellow Traveller of whom I spoke before at the Congerees, having a great Mind for an Indian Lass, for his Bed-Fellow that Night,

Page 41 spoke to our Guide, who soon got a Couple, reserving one for himself. That which fell to our Companion's Share, was a pretty young Girl. Tho' they could not understand one Word of what each other spoke, yet the Female Indian, being no Novice at her Game, but understanding what she came thither for, acted her Part dexterously enough with her Cully, to make him sensible of what she wanted; which was to pay the Hire, before he rode the Hackney. He shew'd her all the Treasure he was possess'd of, as Beads, Red Cadis, &c. which she lik'd very well, and permitted him to put them into his Pocket again, endearing him with all the Charms, which one of a better Education than Dame Nature had Bestow'd upon her, could have made use of, to render her Consort a surer Captive. After they had us'd this Sort of Courtship a small time, the Match was confirm'd by both Parties, with the Approbation of as many Indian Women, as came to the House, to celebrate our Winchester-Wedding. Every one of the Bride-Maids were as great Whores, as Mrs. Bride, tho' not quite so handsome. Our happy Couple went to Bed together before us all, and with as little Blushing, as if they had been Man and Wife for 7 Years. The rest of the Company being weary with travelling, had more Mind to take their Rest, than add more Weddings to that hopeful one already consummated; so that tho' the other Virgins offer'd their Service to us, we gave them their Answer, and went to sleep. About an Hour before day, I awak'd, and saw somebody walking up and down the Room in a seemingly deep Melancholy. I call'd out to know who it was, and it prov'd to be Mr. Bridegroom, who in less than 12 Hours, was Batchelor, Husband, and Widdower, his dear Spouse having pick'd his Pocket of the Beads, Cadis, and what else should have gratified the Indians for the Victuals we receiv'd of them. However that did not serve her turn,but she had also got his Shooes away, which he had made the Night before, of a drest Buck-Skin. Thus dearly did our Spark already repent his new Bargain, walking bare-foot, in his Penitentials, like some poor Pilgrim to Loretto.        After the Indians had laugh'd their Sides sore at the Figure Mr. Bridegroom made, with much ado, we muster'd up another Pair of Shooes, or Moggisons, and set forward on our intended Voyage, the Company (all the way) lifting up their
Page 42 Prayers for the new married Couple, whose Wedding had made away with that, which should have purchas'd our Food.

Stole his shoes! That's cold!

This story seems to be a popular one. I've found it in this blog and mentioned in this book on humor and the American Indian. The author of the essay in question suggests that portrays himself and his fellow European explorers as the greenhorn butt of jokes, and the Winchester Wedding as a big joke by the Indians on the whole expedition.

So what is a "Winchester Wedding"? Just what it looks like, apparently - a hookup. The term appears in broadside ballads from the time. Lawson wrote more on the subject of Indians and Winchester Weddings in a description of Indian women (scroll down a bit; these pages are undifferentiated, so the links aren't that useful):

"As for the Indian Women, which now happen in my Way; when young, and at Maturity, they are as fine-shap'd Creatures (take them generally) as any in the Universe. They are of a tawny Complexion; their Eyes very brisk and amorous; their Smiles afford the finest Composure a Face can possess, their Hands are of the finest Make, with small long Fingers, and as soft as their Cheeks, and their whole Bodies of a smooth Nature. They are not so uncouth or unlikely, as we suppose them; nor are they Strangers or not Proficients in the soft Passion. They are most of them mercenary, except the married Women, who sometimes bestow their Favours also to some or other, in their Husbands Absence. For which they never ask any Reward.
As for the Report, that they are never found unconstant, like the Europeans, it is wholly false; for were the old World and the new one put into a Pair of Scales (in point of Constancy) it would be a hard Matter to discern which was the heavier. As for the Trading Girls, which are those design'd to get Money by their Natural Parts, these are discernable, by the Cut of their Hair; their Tonsure differing from all others, of that Nation, who are not of their Profession; which Method is intended to prevent Mistakes; for the Savages of America are desirous (if possible) to keep their Wives to themselves, as well as those in other Parts of the World. When any Addresses are made to one of these Girls, she immediately acquaints her Parents therewith, and they tell the King of it, (provided he that courts her be a Stranger) his Majesty commonly being the principal Bawd of the Nation he rules over, and there seldom being any of these Winchester-Weddings agreed on, without his Royal Consent. He likewise advises her what Bargain to make, and if it happens to be an Indian Trader that wants a Bed-fellow, and has got Rum to sell, be sure, the King must have a large Dram for a Fee, to confirm the Match. These Indians, that are of the elder sort, when any such Question is put to them, will debate the Matter amongst themselves with all the Sobriety and Seriousness imaginable, every one of the Girl's Relations arguing the Advantage or Detriment that may ensue such a Night's Encounter; all which is done with as much Steadiness and Reality, as if it was the greatest Concern in the World, and not so much as one Person shall be seen to smile, so long as the Debate holds, making no Difference betwixt an Agreement of this Nature, and a Bargain of any other.
If they comply with the Men's Desire, then a particular Bed is provided for them, either in a Cabin by themselves, or else all the young people turn out, to another Lodging, that they may not spoil Sport; and if the old People are in the same Cabin along with them all Night, they lie as unconcern'd, as if they were so many Logs of Wood. If it be an Indian of their own Town or Neighbourhood, that wants a Mistress, he comes to none but the Girl, who receives what she thinks fit to ask him, and so lies all Night with him, without the Consent of her Parents."

Tuesday, January 21, 2014

Spontaneous trefoil?

On the lower left of HS 242 f. 110, one of Lawson's collections, is a label covering what appears to be a plant specimen. It's quite small, and the bit that appears most clearly looks like a trifoliate something-or-other. A Desmodium, perhaps? Who knows. Weakley includes the common name "trefoil" in eight different plant entries - anything with leaves clumped in threes can merit it.

The intriguing thing is the label, which is evocative. (At least, my attempt at deciphering it is evocative.) It appears to read:

"Jan. 27th 1710. Spontaneous [?] trefoil of Carolina growing on the fork of Neus River and in other places having shed [?] from flower like drops of blood a sweet herbage[??] all spontaneous trefoils are more hairy here than in England."

I may have gotten that completely wrong.

But what if I'm right, and it does refer to "spontaneous trefoil"? Did people believe plants could grow spontaneously? Is trefoil a particular weed, common in England?

I found this account in The Farmer's Magazine, London 1851 (MDCCCLI - I hate Roman numerals!) describing a case of trefoil growing in fields sown with clover. Because the seed produced pure clover in most fields, the farmers concluded that the trefoil must have grown spontaneously. The author refuses to believe this, noting that seeds could lie dormant for years until conditions were right for them to germinate, but it is intriguing, no?

Then there's this, from the Annals of Agriculture, and Other Useful Arts, published London 1804: "Gypsum has also another very singular property, that of encouraging the growth of spontaneous trefoil on spots where seed had never been sown, particularly of the yellow and white trefoil. In Alsace I have seen many instances of this singular circumstance."

And this, on the adulteration of forage plants, another author recognizing that yellow trefoil seeds can last a long time.

What is trefoil? I'm not going to attempt to identify this specimen, but I can speculate more on my musings. This UK lawn weed site identifies Trifolium dubium as the noxious weed Lesser Trefoil - it's a Eurasian native, and is introduced to our area, so maybe not that. Plant identifies it as Medicago lupulina, also introduced to our area. Weakley includes the common name "trefoil" in eight different plant entries - anything with leaves clumped in threes can merit it.

Sadly, our photographs do not allow us to see through that unfortunate label to further examine the plant specimen. So the mystery will have to stop here for now.

Friday, January 17, 2014

Taxonomic hierarchies

How do we sort things? Let me count the ways....

Modern scientific taxonomy got started with Carl Linnaeus (1707-1778). He was the man, I must say. After spending his younger years exploring the botanical biodiversity of Sweden and northern Europe, he dedicated his mature years to sitting in Uppsala and organizing the pieces of the world that came to him in the mail. Explorers went out to sea at his behest, and some of them - the ones that survived - sent him specimens of plants, animals, stones, whatever.

Linnaeus decided to organize everything. At the time the world must have seemed suddenly knowable, all things coming clear. Everything must belong to a type, and all types must fit into a hierarchical structure. (Could it be Latin grammar that gave him this idea?)

Linnaean organization especially emphasizes two things: kingdom and genus. Kingdom defines the nature of the beast. Genus names a category and allows specification to produce a binomial - a scientific name.

To start with the binomial: The scientific name of a species consists of two names, genus and species. The genus is its generic name, or category. The species is the name of a specific type of organism within that category.

Take the lion, Panthera leo. The generic category is panthers. What kind of panther? The "lion" kind. You could also have the "tiger" kind of panther, Panthera tigris, or the leopard kind of panther, Panthera pardus, which actually means "Panther panther." (The word "leopard" comes from two Greek words meaning "lion panther," so our common name for leopard means the same thing as the scientific name for lion. Haha!)

All those generic panthers belong to the cat family Felidae. So do generic little cats, in the genus Felis, "cat" in Latin. Linnaeus named our domestic cat Felis catus. Catus is another Latin word for cat. So a domestic cat is the "cat" kind of cat. Another little cat is called Felis silvestris, the kind of little cat that lives in the forest. Simple!

Now kingdoms. Linnaeus created three kingdoms - Plants, Animals, and Minerals - to encompass everything in the world. Anything missing? Minerals fell by the wayside pretty quickly, but they weren't the real problem.

The invention of the microscope suggested that microorganisms didn't fit into either Plants or Animals. In the 1860s biologists added a new kingdom, Monera, for all single-celled organisms. But all single-celled organisms aren't alike. Some are small and primitive with no nucleus, and others are large and well-organized with nuclei and membrane-bound organelles. Scientists started calling them prokaryotes and eukaryotes. In 1938 they added another kingdom, Protista, to hold single-celled eukaryotes. The prokaryotes - bacteria and cyanobacteria - stayed in Monera.

Now, fungi are really not at all similar to plants - no chlorophyll, chitin cell walls - so in the 1960s they got taken out of Plantae and put in their own kingdom Fungi. And animals, plants, and fungi are all eukaryotes, so it was kind of important to put them with single-celled eukaryotes if cell structure was going to be a category. But they were ALREADY kingdoms. We needed another level of taxonomy. So that led to the short-lived empires - Prokaryota and Eukaryota. Kingdom Monera went into Prokaryota. Eukaryota got everyone else - Animalia, Plantae, Protista, and Fungi.

But in the 1970s and 1980s, biologists started focusing on common ancestry instead of physical similarity. Microbiologists announced that prokaryotes were not all bacteria, and that some were in fact very very different - so different they deserved their own kingdom. In the 1990s they got rid of Monera and replaced it with Bacteria and Archaea. The empires were changed into domains called Prokarya and Eukarya.

And that didn't even last very long. Now there are three domains. Eukarya still contains animals, plants, fungi, and protists. But the kingdoms Bacteria and Archaea are now in domains called Bacteria and Archaea. This leaves room for more discoveries.

Do we still need kingdoms? Does the genus-species naming structure still work? Clearly many things don't fit into the Linnaean schema. Plant taxonomy is full of subspecies and subfamilies and things just called clades or tribes. Hominin (human ancestor) taxonomy got stuck with a family called Homidae - all the great apes - and several named genera, but then has had to fit lots of categories in between them for extinct taxa. (Chimpanzees are currently grouped in a tribe called ... Panini. That's funny.)

And don't even get me started on the slime molds and water molds! Poor Phytophthora, dumped by Fungi. My kingdom for a kingdom! At least they still fit in Eukarya.

One obvious problem with imposing an organizing structure on the world is that one then forces the world to conform to the structure, rather than the other way around. (It's not an animal, and it's not a mineral, so it MUST be a plant....) On the other hand, we have to be able to talk about stuff. It will be amusing to watch this process unfold over the next decades. Will Linnaeus disappear entirely?

Monday, January 13, 2014

Catesby's bison, Darwin's Scotch Firs, and Roan Mountain

Every fall Patrick McMillan takes his Plant Taxonomy class on a field trip to Roan Mountain, TN, to study island biogeography and the ecology of high grassy balds. He talks about the importance of ecosystem engineers in keeping things stable - in this case, keeping the grassy balds grassy.

Grass won't just stay grassy on its own. Left to its own devices, it often will go back to forest, probably through an ugly transitional stage involving lots of brambly bushes. What keeps the bushes and trees from growing? Large animals. In the case of our grassy balds, it was the bison and Indians that used to roam the Appalachians. (Before that - maybe mammoths? But that's a very long time ago.)

There were bison up in the South Carolina mountains in Catesby's time. He writes about them:

Preface, viii.
"I then went to the upper uninhabited parts of the country, and continued at and about Fort Moore, a small fortress on the banks of the River Savanna, which runs from thence a course of 300 miles down to the sea, and is about the same distance from its source, in the mountains. I was much delighted to see nature differ in these upper parts, and to find here abundance of things not to be seen in the lower parts of the country; this encouraged me to take several journeys with the Indians higher up the rivers, toward the mountains, which afforded not only a succession of new vegetable appearances, but most delightful prospects imaginable, besides the diversion of hunting buffelo's, bears, panthers, and other wild beasts."

In his entry on the Pseudo Acacia, he also mentions the bufello:

Vol. 1, Appendix p. 20, Bison americanus and Pseudo Acacia hispida floridus roseis
"I never saw any of these trees but at one place near the Appalachian mountains, where Bufellos had left their dung; and some of the trees had their branches pulled down, from which I conjecture they had been browsing on the leaves.... I visited them again at the proper time to get some seeds, but the ravaging Indians had burn'd the woods many miles around, and totally destroyed them, to my great disappointment; so that all I was able to procure of this specious tree was some Specimens of is which remain in the Hortus siccus of Sir. H. Sloane, and that of Professor Dillenius at Oxford."

As it happens, there are no Pseudo acacia in the Sloane specimens today, but there are two (00087396X and 00087400J) in the Oxford collections. Patrick has identified them as Robinia hartwigii Koehne, Granite dome locust.

There are no bison roaming the grassy balds today (no Indians burning the locust trees either), though Patrick would love to see them restored. Instead, there are cattle grazing in some areas. The grazed parts are empty and grassy. Just beside those grazed bits are areas with the same basic ecological components but no cattle. Those parts are overgrown with brambles, bushes, trees - no grassy balds there.

Charles Darwin described this phenomenon in On the Origin of Species, in Chapter 4, "Struggle for Existence:"

"How important an element enclosure is, I plainly saw near Farnham, in Surrey. Here there are extensive heaths, with a few clumps of old Scotch firs on the hill-tops; within the last ten years large spaces have been enclosed, and self-sown firs are now springing up in multitudes, so close together that all cannot live. When I ascertained that these young trees had not been planted, I was so surprised at their numbers that I examined hundreds of acres of the unenclosed heath, and literally I could not see a single Scotch fir, except the old planted stumps. But on looking closely between the stems of the heath, I found a multitude of seedlings which had been perpetually browsed down by the cattle. In one square yard I counted thirty-two little trees; and one of them, with twenty-six rings of growth, had during many years, tried to raise its head above the stems of the heath, and had failed. No wonder that, as soon as the land was enclosed, it became thickly clothed with vigorously growing young firs."

"Here we see that cattle absolutely determine the existence of the Scotch fir...."

Monday, July 8, 2013

Rattle snakes and Alexipharmacal plants

Our intrepid Carolina explorers were always worried about rattlesnakes. What does one do about snakes that make frightening noises and whose bites can result in pain, bleeding, nausea and vomiting, low blood pressure, blurred vision, tissue damage, etc. (Although apparently not all rattlesnake bites even deliver venom; it's possible to get bitten and come to no serious harm.) The main effective treatment these days is antivenom, which wasn't around in the early 1700s. Catesby worried quite a bit about rattlesnakes - see his descriptions of their bites in the Natural History (vol. 2, p. 41), and in his plant collections.

Joseph Lord, living in coastal South Carolina in 1704, was also concerned. Three of his specimens contain labels mentioning the use of plants against rattlesnake bites. My favorite is this one, Eupatorium rotundifolium on H.S. 268 f. 35. His label reads:

“This (I think) I have sent you formerly without a name, as now it comes: but I desire you would please to let me know it’s name. Besides that an Indian told me of it's use in feavers, its found to be Alexipharmacal, & an admirable antidote against the Poison of Rattle-snakes in particular, conquering the Venom of their biteing. Gathered, Aug. 15, 1704, having been near a month in flower. It grows common in our woods, both in high & low land. There are divers other plants growing commonly that seem to be varieties of this.”

Alexipharmacal? I had to look that one up. It means an antidote, from the Greek words “ἀλέξειν, alexia,” meaning “to ward off,” and “φαρμακός, pharmakos” for “drug.”

Lord’s label makes it appear that the Indians and the Colonials who arrived here after them were all looking for the same thing as modern doctors - an antivenom. So would this plant work? Well, the closely related Eupatorium perfoliatum goes by the common name “boneset” or sometimes “ague-weed.” It was historically used to treat fevers and other assorted ailments. So maybe this one would work too.

One of the other rattlesnake plants is a specimen of Ageratina aromatica on H.S. 268 f. 33. Common name? “Small-leaved white snakeroot” or “Lesser snakeroot.”

Ageratina used to belong to the genus Eupatorium - of massive snakebite treatment fame. And Lord describes this one as “of the Tribe … of whose vertue against the biting of the rattle-snake I have made mention.” Sounds like taxonomy to me - long before Linnaeus.

Monday, June 24, 2013

Joseph Lord, a new 18th-century buddy

When I was in London a couple of weeks ago, I spent a day at the Natural History Museum, photographing a few more collections from the Sloane Herbarium. I had found three collectors we'd missed with our first round of photography. They are Joseph Lord, Col. Halsteed, and George Franklin - three guys who were in South Carolina between 1700 and 1710. That makes them the earliest collections we've worked with so far.

Joseph Lord is by far the most important of these three. Lord was a true American, born in Massachusetts in 1672 and educated at Harvard, after which he became a minister. (Did anyone from Massachusetts become anything else?) In 1695, Lord took a group of parishioners to South Carolina and founded the town of Dorchester. He built a house there and developed a plantation, which he mentions repeatedly in the notes to his plant collection.

Ah, yes, the plant collection! And the notes! Lord made his plant collection in 1704, and sent it to London to James Petiver, an apothecary who assembled a number of the collections in the Sloane. Lord's handwriting is beautifully legible, and he recorded useful details - things like color of flowers (a detail that is lacking in many herbarium specimens, which tend to be shades of brown), growing conditions, type of soil, and collection date. Patrick has already made good use of Lord's notes in the determinations we've begun.

We've already found something super cool - a specimen of Schwalbea americana, American Chaffseed, in the lower right corner of H.S. 158 f. 245.This is almost certainly the first collection of this plant, which is now in danger of dying out completely. This plant was listed as a federally endangered species in 1995.

American chaffseed is native to the longleaf pine ecosystem. It's a hemiparasite, or partial parasite - it performs some photosynthesis on its own but gets some of its nutrients and water by attaching itself to host plants with specialized roots called haustoria. It's not particular about hosts - American chaffseed parasitizes longleaf pines, hollies, and various grasses and composites. It's a fire-adapted species that depends on periodic fires to clear out vegetation to allow seeds to germinate and seedlings to establish themselves. Fires were regular occurrences in the longleaf pine savanna that was common in South Carolina before European settlement, but that has nearly disappeared from the region today.

This is one of the rarest plants on earth today. The 2008 5-year review noted 33 occurrences in South Carolina, 12 of which were considered protected but none with formal protection agreements and only one with a formal management plan. Almost all occurrences were in the Francis Marion National Forest. Total numbers had dropped between 1995 and 2008; and remember, those 2008 numbers are based on surveys done prior to 2008. So we don't really know how many of these plants are left. Some of these areas are being managed with controlled burns, which benefits a whole range of fire-adapted species. But there's not much space for them, and small populations are prone to getting smaller.

So it's neat that Lord picked an American chaffseed.