Tuesday, February 28, 2017

Botany in Congress

Now more than ever before in our history it is incongruous to see a botany bill in Congress (intentional pun). But here it is: a bill that promotes botany, botany education, and plant conservation! The Botanical Sciences and Native PlantMaterials Research, Restoration, and Promotion Act has a Democratic and a Republican sponsor. See here for a summary of the main points of the bill.

Right now, at the university where I teach, I have two students who are beginning research projects with an endangered tree species the bark of which has antibacterial properties. One of them already develops and sells botanical skin care products and wants to develop one that incorporates extracts from this species (without knowing anything about the active ingredient/s). The other is a chemistry major who knows how to conduct research on the active ingredient/s. Despite the depressing overall political climate, I am encouraged by the (what appears to me sudden) interest in botany and conservation among some of my students. This bill, in the unlikely event that it passes, will come too late to help my botany majors with their student loans etc.

Thursday, February 23, 2017

My Public Apology to the Neanderthals

I have also posted a YouTube video on this subject here.

If there are any Neanderthals reading this blog, I must ask, can you possibly forgive me? I had you all wrong. My voice joined in with the scientific establishment, led by such great scholars as Chris Stringer, in claiming that Neanderthals had no culture. This is very much the image that I presented in my Encyclopedia of Evolution. Apparently we were wrong.

Of course, my dear Neanderthals, I could not believe that a hominin with a brain as large as yours could be stupid. I never said you were stupid—put down that club, I’m trying to explain myself here—but just that you used your intelligence for something other than culture. Like maybe figuring out better ways of hitting each other over the head with clubs—oops, I think I went a little too far right then. But I wrote a novel manuscript (as yet unpublished) in which the heroine was an intelligent Neanderthal woman who lived in Minnesota in the late twentieth century. I can prove that I wrote this! I have a notarized copy of the manuscript from [date]. I’ve been defending your dignity, after a fashion, for many years now. But, you gotta admit, Neanderthals left no cave paintings or artifacts that might suggest art and religion, in stark contrast to the thousands of artifacts and massive painted caves of the Cro-Magnon modern humans.

But the accuracy of the non-cultural view of Neanderthals depends to a large extent on the interpretation of a set of artifacts that are not exactly part of American discourse, not even of intellectual snobs like me—the Châtelperronian artifacts. These artifacts, found in France, date to about forty thousand years ago, right about the time that dark modern humans came up from Africa and encountered the light-skinned, red-haired Neanderthals. The artifacts were found in a deposit that appeared to be of Neanderthal origin. They included some really well-made stone tools and, most fascinating, various bones and shells with holes drilled in them, which were apparently used in necklaces. Most of us scientists preferred to believe that such decorations could not possibly be Neanderthal. We wanted to think that the deposit was actually of modern Homo sapiens origin. Or, if the deposit was from Homo neanderthalensis, we speculated that you Neanderthals stole them from modern humans, or if you made them you were just imitating modern humans.

If we could get DNA from the human bones at this site, we could maybe settle the question. Svante Pääbo has elucidated the Neanderthal genome. But apparently thirty thousand years is about the limit to get DNA from old bones. To get enough DNA from the Châtelperronian bones, it would be necessary to almost completely destroy them. But it turns out that collagen (the protein in cartilage) does not decompose as readily. It was collagen that Mary Higby Schweitzer found in 70-million-year-old T. rex bones. Geneticists Matthew Collins and Frido Welker were able to get enough collagen from the Châtelperronian bones to analyze (Science, 23 September 2016, page 1350). Previous studies have shown that human collagen is rich in the amino acid aspartate, while Neanderthal collagen is rich in asparagine. The Châtelperronian bones had asparagine-rich collagen, identifying them as Neanderthal.

Of course, errors are possible in the reasoning used above. But the most straightforward interpretation, according to Jean-Jacques Hublin, Collins’s and Welker’s collaborator, is to say that Neanderthals made the artifacts.

Please forward a link to this essay to any Neanderthals you know.

Friday, February 17, 2017

Heeeeeeere's Connie!

Note: I have also posted a YouTube video about this.

When software changes the spelling of names, sometimes it’s a hoot, and sometimes noot.

Let me introduce you to Connie Maculatum, the poison hemlock plant.

Actually, the name is Conium maculatum, but apparently certain Microsoft programs automatically change scientific names into words that the programs think should be there. One of the best-selling books of the Christmas 2016 season, and one which I received as a present, contained this error. I doubt that the authors or editors intended the text to read “Connie.” But apparently, even after the correct name is written, Microsoft changes it from scientific accuracy to one of its standard, approved list of words. This might happen even after an author reverses the change.

It gets personal sometimes. One of my lab students last fall had the last name Cotten. In case your software changed it, the name ends with an -en. I had to write this twice in order to get Word to accept this spelling. But when we recorded her grades in Excel, it kept changing the spelling to Cotton no matter how many times we tried to correct it. We apologized to the student. She, however, has had this experience so many times that she hardly reacted. Her birth certificate, the IRS, and the university might have her name with the correct spelling but, dammit, Microsoft is determined to change her name to Cotton.

Science magazine reported that twenty percent of genetics articles that have been published online contain incorrect names of genes because Excel automatically changed them—and refused to unchanged them. One example is the gene septin-2, abbreviated SEPT2, which Excel changed to September 2. This happens even in the top journals. Notice: twenty percent of papers.

Technology is supposed to be our servant, but it determines the framework of reality. You have no choice but to enter information into Microsoft software in a prescribed format and to accept whatever form it comes out.

For centuries, people have had to accept occasional and embarrassing misspellings. The nineteenth-century report that Edgar Allan Pee had published a new book is probably apocryphal; in fact, I might have made it up. But at least newspaper and book publishers had the option of spelling it correctly.

I studied, and am now trying to rescue, an endangered plant species: the seaside alder, Alnus maritima. If I see this plant referred to on websites as Alnus maritime one more time, I think I am going to scream.

I don’t mind Microsoft underlining words that it “thinks” are misspelled, so long as I have the option of overriding its “decision.” It’s the automatic, silent, and unstoppable changes that I hoot.

Tuesday, February 14, 2017

Popechick, or, St. Colonel Sanders

Okay, this title is going to take some explaining. It comes from a web link publicized by Science magazine.

Apparently, until about 1000 CE, the Catholic Church did not make a big deal about eating meat on Fridays and certain holidays. But after that time, probably as a direct result of the papal edict, there was a market for chickens. Farmers bred chickens that were plumper and which laid eggs all year long rather than just seasonally. These characteristics are associated with a gene variant known as thyroid stimulating hormone receptor (TSHR), which is now found in virtually all commercial chickens. Archaeologists (for whom DNA sequencing is now a standard tool) sampled twelve sites in Europe ranging from 280 BCE to the eighteenth century and found that the TSHR allele was rare in chickens before about 1000 CE.

Is it too much of a stretch to say that the whole modern chicken industry exists as a result of papally-enforced religious dogmas from a thousand years ago? Just remember the Law of Unintended Consequences: this is certainly not what the Catholic Church was trying to do.

Wednesday, February 8, 2017

Maybe There Will Be a Mass Exodus

In an earlier essay, I speculated that, despite Trump’s attack on science education and research, insisting that both education and research should be focused entirely on his loudly-stated beliefs rather than on any data from the real world, there would probably be no mass exodus of scientists out of the United States into (for example) China. But events of recent weeks have caused me to rethink this.

Trump announced the appointment of his chair of a task force that will recommend reforms for higher education. That man is Jerry Falwell, Jr. Yes, the president of Liberty University, and the son of its late former president, Jerry Falwell. Jerry Falwell Jr. has said that he will redesign higher education so that it is focused on the Bible, and will bring higher education “back to some form of sanity.” And what this undoubtedly means is that, in order for students to receive loans to attend colleges and universities, they will have to attend colleges and universities that promote the utter and absolute truth of Creationism. Science education will quickly collapse, and therefore science educators will quickly leave the United States (this is my plan) or else find some other kind of job (I have not ruled out the possibility of being a science-education supermarket produce stocker, leading customers on economic botany tours in the produce section). If the entire function of science education is to indoctrinate college students in creationism, then scientific research will quickly collapse in the United States. Other countries, more welcoming to science, will benefit immensely from the inevitable brain drain.

What could possibly go wrong?

The creationists do not really want to see God, Jesus, or the Bible exalted in science education. They do not want the Bible to be taught. They want their interpretation of the Bible to be taught. Creationists consider themselves personally inerrant, incapable of error, when they open a Bible and start talking. There have been many interpretations of Genesis 1, for example, and the history of these interpretations goes back hundreds of years. But creationists consider all these other interpretations of the Bible to be wrong. The creationists, and they alone, are chosen by God to tell people what to believe about the Bible. Jerry Falwell Jr. thinks that we should all bow down and revere Him, Falwell, as the single approved explicator of God’s truth.

I don’t have a problem with Jesus. I don’t have a problem with the Bible, which may be inspired by God or may be an historical record of people trying to understand God. I have a problem with creationist Republicans elevating themselves to Godlike status and pushing God out of the way. This is the “form of sanity” that Falwell intends to impose on all scientists, educators, and students.

I teach about evolution, biodiversity, and global warming. Will I soon be considered an enemy of the state? History is full of scientists who have been crushed by religious power, from Galileo to Vavilov.

Thursday, February 2, 2017

Scientific Honesty

Scientists may not be naturally more honest than other people, but the scientific method enforces honesty when it is followed, as it usually is, at least in the underfunded ecological and organismic sciences. Actually, scientists are, on average, more honest partly because the scientific enterprise attracts honest people—that is, people who do not want their reputations tainted by dishonesty. For preachers and presidents, of course, the more taint the better. So keep grabbing that p***y, Trump! And all you evangelical Christians, keep praising Trump for doing so!

One of my major projects is that I have kept records on the spring budburst dates of almost 400 trees (22 species) for the last twelve years in southern Oklahoma. While my data set is not the biggest in the world, it is one of the major on-the-ground data sets (as opposed to satellite imagery), and certainly the best one for hundreds of miles around where I live and work. On January 30 and 31 of this year, almost all of the sweetgum trees (Liquidambar styraciflua, in the Altiginaceae family) burst their buds—that is, the bud scales separated enough that I could see the green underneath. But there was one tree I missed. It was way over across campus, not close to any other trees in my data set. Since it is surrounded by brick walls, creating a warm microenvironment, I assumed that its buds had opened also. This was a statistically valid assumption. But if I wanted to make this tree a data point (datum) in my study, I had to go look at it. I did so—it was a nice 73 degree F day, like many other winter days in southern Oklahoma (itself an indicator of global warming)—and found that, indeed, I was correct. All this, for one datum out of several thousand.

This honesty is in striking contrast to the ruling junta in Washington, where the worshipers of Donald Trump believe that they can just make up “alternative facts”, assertions that God Himself is obligated to accept. My data clearly show that budburst over the past twelve years has occurred about three weeks earlier—more in some, less in other, species. But Trump can just make up an alternative fact, and say that this has not happened, and that simply sweeps aside my thousands of data and the millions of data worldwide not only of global climate change but of organism responses to it. I fear—and I hope I am wrong—that Trump and his junta will force federal research facilities to make up data to prove that global warming is not occurring, and cut off grant funding for anyone who does not agree with Him. This won’t hurt me; I just keep records on the trees I see when I walk to work or drive down to the park. All I need is statistical software, which the university provides (don’t tell Trump). The ascendancy of “alternative facts” or Trump-truths is one reason I believe that the very scientific way of thinking is under assault in America.

Maybe not in France. They have their own political mess right now, but even the right-wingers over there appear to accept global climate change and the importance of doing something about it. There is more than one way of being wrong. You can be in error, or you can be abusively wrong. The former, in French, is se tromper (to deceive oneself) (Trump le trompe), I think. The latter is avoir tort (Trump a tort). Perhaps the best description of Trump is Trump nous trompe—Trump deceives us. He should be ashamed, but Trump n’a jamais honte.