What’s in a (gene) name

Last autumn, Microsoft made a subtle change to its Excel spreadsheets, one which flew under the radar for normal mortals. Unlike many other software tweaks, this one made it easier to stop the software automating certain tasks. Specifically, its tendency to automatically convert input into dates. One major reason for the change was the havoc this automation had wreaked on geneticists needing to populate Excel with gene names like MARCH 1 and SEPT1. “Stop helping me,” one commenter pleaded in the Verge writeup: “Never automate anything without providing an easily discoverable means to de-automate it.” From your lips to god’s ear, mate.

This change from Microsoft was a welcome olive branch, as the human genome has had more than enough problems getting its naming conventions into the 21st century. Here’s my writeup about that from a couple of years ago.

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Look, no one is trying to get a dick joke into the human genome. If it happens, it won’t be by design. No one even really thought it was a possibility until the late 1990s, when the physical chemistry professor Paul W. May was having a beer with some other science friends and they got around to talking about funny molecules. Everyone knew about the ring-shaped molecule called Arsole. It didn’t take long to conjure up several more funny science terms. May began to collect these, and soon had so many that he turned the collection into a blog. By 2008 the blog had become a book. (NB: both blog and book are written in Comic Sans. And he commits to the bit. Main text, table of contents, acknowledgments, and references – all Comic Sans. References!) The book has a whole separate section on gene names, and here you will find some of the spiciest names in science. By the time the book was published, however, some of them were already out of date – the Human Genome Nomenclature Committee had begun to take a keen interest in what geneticists were calling their new genes, and by 2006 had put the kibosh on 10 names deemed the most offensive. But if they thought their work was done, they didn’t know how much stranger it could get.

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SNAPSHOT: This Horseshoe Crab

I was in Assateague, Virginia, some weeks back, doing the summer beach thing. The wild horses, standing hoof-deep in the chilly saltwash, were lovely, as they always are. They’re one of the truly special things about this national seashore. The horseshoe crabs? Lovely in their own way, I suppose, and definitely special. Especially this one, with its crustacean backpack. The host was deceased, unfortunately, but its riders were still with us, holding on tight.

I knew a few things about horseshoe crabs before spotting this one, including that they’ve been around for more than 400 million years, that they haven’t changed much in that time, and that their blood–which happens to be blue because of a copper-based respiratory pigment called hemocyanin–is used in human medicine. Why/how that last bit? I looked up the details: Scientists discovered a protein in the crab’s blood called limulus amebocyte lysate that clots when it come into contact with endotoxins (toxic bacteria). So the substance can be used as a toxin-detection system that helps ensure vaccines, drugs, and medical devices aren’t contaminated before they’re put inside people.

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Where We First Blew Up the Bomb

This week is the 79th anniversary of two nuclear weapons used on a human populace. In remembrance, I look to the region where the first bomb was set off as a test, less than a month before it was used against the Japanese people.

Where this devastation begins is hard country, Jornada del Muerto, which means journey of the dead. The name came before “Trinity Site,” and was taken for the bones of a horse and rider found there by a Spanish party more than 350 years ago, as if some poor fool and his horse had stumbled into the Book of Revelations. 

I can only imagine the test site was chosen for its emptiness. Hardly a soul lives around here even today. Downwinders still pay, and for many, the government that did the deed won’t cover the cost. My family is from a town a hundred miles west, downwind in southern New Mexico. We don’t talk about it. 

The basin is now marked with a hot crater half a mile across. An event of such magnitude in human history resonates in all directions through time. In the Pleistocene, the detonation site would have been under a lake, part of a chain of sparkling mirrors, some taking up the whole horizon. The next big basin south is now occupied by an active bombing range, a perfectly flat geography called Ancestral Lake Otero, a place that no longer has a lake. Its once muddy shorelines have produced a litany of Ice Age tracks, Columbian mammoth, big cat, giant ground sloth, human. Now it is barren, nearly lifeless. When the wind blows, the sky turns to zinc.

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What to expect when you’re transforming

I’m not on TikTok, so I had to be told about pregnancy nose. Whereas in the 1960s, women sat down together and discovered the political underpinnings of their personal struggles, now we do things like congregate online and discover, via selfies, phenomena we were never told to expect in ‘What to Expect When You’re Expecting.”

The same hormones that orchestrate a whole new placenta and get the blood flowing there also dilate blood vessels and produce fluid retention elsewhere. It can lead to a giant, unrecognizable nose. Perhaps we didn’t notice before because weight gain can, itself, reshape the face, but taken together on TikTok, it’s clear: pregnancy nose is a thing.

What about the more permanent effects of pregnancy? Our society tends to pathologize these, or rather, to focus on the pathologies that arise. But I wish someone had told me sooner about the coolest permanent change. It happens whether you carry the baby to term or suffer a miscarriage or abortion. It persists for decades, until you die.

You become a chimera.

 For as long as a little one and a mother share a body, they are exchanging cells. The fetal cells that circulate in a mother’s blood cross the blood-brain barrier (which is more permeable at that time) and stay in our brains. They don’t just accrete there like so much flotsam, either. They properly differentiate into neurons, colonize the heart and help it beat, and regenerate the liver. Sometimes when they reach a new organ, the baby’s cells fuse with the mothers’.

Studies often look for the clearest indication of this—cells with male chromosomes in women who have had sons—but you can also get those indirectly from an older male sibling, because your mother can pass them back to you in the womb.

The whole idea is just beautiful to me, that both my son and my brother quite literally live in me forever. I find meaning in it. And it makes me wonder what other magic is at work when we bring our ancestors to life, through birth.

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This week, a mourning dove has started to build a nest in the walnut tree outside my office window. I see it flying back and forth with twigs in its beak, perching on a piece of webbing, waiting for the right moment to swoop in.

Why is a mourning dove building a nest in August? I’m not sure. I think I once interviewed a researcher who said that mourning doves are “dumb as rocks”–but I can’t remember when, or who.

But it did remind me of a post I wrote in 2016, which was the first time one of my kids was traveling without me. This summer, more fledglings winged away on their own, and there is part of me that always–not worries, exactly, but wonders how they could possibly be out in the world, so far away. Sometimes when I’m traveling, I feel like this, too–weightless and winged, granite replacing grey matter, unable to stop turning my head to look at what’s behind me.

Then, yesterday, I saw a crow start to harass one of the neighborhood doves. After a moment, the dove turned and chased the crow off into the trees. The dove returned, cooing contentedly. The crow did not.

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We came back from vacation earlier this month to find that someone else had moved in. I didn’t realize it at first—the house seemed just as we had left it, and we were busy emptying the car and starting the laundry and repopulating the house with the things we’d taken with us.

It was later, when two of the boys were in the bathtub, that I saw piles of bird poop around the floor in the dining room. The dining room is a small space underneath a greenhouse window, and it’s always attracted birds. I froze, wondering if I’d find a bird huddled in the corner. When I didn’t hear anything, I started looking around for a dead bird. I wanted to find it before the kids did. Their toys are in this greenhouse room, too, and I imagined the unhappy surprise of finding a still, small creature when you’re reaching for a wooden train track.

I crouched down to look closer. And that’s when I saw the tiny white ball beneath the table.

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Oh God, Another Meaningless List

Recently, and to much engagement-baiting fanfare, the New York Times published its list of the best books of the 21st century. As with any such list, it was riddled with omissions, both benign (whither Anthony Doerr, Madeline Miller, and Lauren Groff?) and insidious (outrageously, not a single Native American author made the cut). I was irked to note that only one nonfiction book about nature and/or the environment appeared on the list, the worthy H Is for Hawk. I love George Saunders, but did he alone pen three books that were better than anything anybody wrote this century about climate change?

Anyway, the Times’s cynical exercise got me wondering — if an outlet was to compile a list of this century’s best nature/environment books, what would be on it? On the platform formerly known as Twitter, I threw out some suggestions of my own, and solicited others from the gaggle. Some of those books are compiled in this post.

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Spotted Lanternfly Epiphany

This picture creeps me out too but less so than actual living spotted lanternflies.

Y’all know about spotted lanternflies, right? I don’t have to explain them? (invaders, hordes over-running the landscape, even government officials say to just kill ’em?) Last summer I had a lot of them and I killed every one I was able to kill, given that they’re fast and cunning. This summer, the tree guy inspected my 2 red maple trees — maples are among spotted lanternflies’ top choices for setting up camp. I went outside to ask what the tree guy found, and he told me with some excitement that my property was the only one he’d inspected that had no spotted lanternflies. Not only that, but also not even any egg masses.

This turns out to be not strictly true: the same day I saw a spotted lanternfly on the outside of a window screen three stories above pavement so I couldn’t get to it. And two days later, I saw several more in the maple tree and around thereabouts. And I just now killed one in my house. But never mind because good news, even if temporary, is still heartening; like, it gives you heart. Plus as a savage predator, I enjoy it: grab the flyswatter, smack, it drops, track it down, smack smack smack smack, dead as a doornail, VENGEANCE IS MINE!

Flyswatters work and the reason I know is that the neighborhood kids use them; I buy them, they use them. Back to the tree guy: I think the kids are the reason he found (relatively fewer) of them — in fact, the minute he told me that, the heavens opened and I had an epiphany.

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