Dramatic wars begin with a grievous setback that makes everyone desperate to fight back, right?

I isolated myself in a coffee shop, buckled down, and pounded straight through my grading. I got it done! Early even! The students…well, umm, there were some rough spots. The mean was about 65%, brought down by one specific page where they had to do some math, and it was a massacre. I was imagining that page soaked in blood, with more pouring out of my wicked pen, and was getting a little uneasy. I know what we’re going to be going over in the next class!

Now, though, I get to go home, where my wife has some chore involving the picket fence I’m supposed to do, but once that’s over, I’ve got to honor the completion of one onerous task (if not the outcome).

I’m thinking I’ll sit back and read the new Joe Abercrombie, A Little Hatred. It seems appropriate, very grim-dark, with lots of close-fought bloody battles. For that 65%, you know, which is barely passing and means half the class is getting Ds or worse so far.

(The title does not reflect my feelings towards the students, who are my brave compatriots in the struggle to master cell biology.)

Behe…yeah, he’s over and done with

When Michael Behe published Darwin’s Black Box, there was a loud “Huzzah!” from the creationists — they had new buzzwords, like “irreducible complexity”, for the first time in 50 years, and they had a scientist with a legitimate Ph.D. to cite as an authority claiming evolution couldn’t happen. The “science” was crap, but it was a strong rhetorical play, and we had to respond vigorously to it. It was garbage, but all the back-and-forth enhanced Behe’s reputation. I read it thoroughly and contributed to online discussions about the fallacies in it.

Then he came out with a second book, The Edge of Creation, and the creationists all went “huzzah?”, because there was nothing new in it, no spark of rhetorical flourish they could use in debates, but there was an implication that caused them worries. Behe was claiming you could see the hand of the Designer in ongoing processes, and that It was actively engineering diseases and parasites to kill us right now. Whoops. It was still garbage, but it didn’t trigger a surge of creationist activity that needed refutation. I skimmed it, threw it aside, ignored it.

Now he has a third book, Darwin Devolves, where he returns to the same old stagnant, tainted well and says the same old things, and it’s only going to inspire the die-hard Behe fanchildren, and isn’t going to challenge any scientists at all. I’m not going to pick up a copy. Not going to read it. Not going to critique it. Everything has already been said, he has nothing new that we need to refute, and he’s nothing but yet another crackpot…just one who has a tenured position at a legitimate university, even if he is something of a pariah to his colleagues.

But because he got creationists excited 20 years ago, someone had to suffer through his book for Science magazine, and the sacrificial victims are Nathan Lents, Joshua Swamidass, and Richard Lenski, who write that a biochemist’s crusade to overturn evolution misrepresents theory and ignores evidence.

Behe is skeptical that gene duplication followed by random mutation and selection can contribute to evolutionary innovation. Yet there is overwhelming evidence that this underlies trichromatic vision in primates, olfaction in mammals, and developmental innovations in all metazoans through the diversification of HOX genes. And in 2012, Andersson et al. showed that new functions can rapidly evolve in a suitable environment. Behe acknowledges none of these studies, declaring an absence of evidence for the role of duplications in innovation.

Behe asserts that new functions only arise through “purposeful design” of new genetic information, a claim that cannot be tested. By contrast, modern evolutionary theory provides a coherent set of processes—mutation, recombination, drift, and selection—that can be observed in the laboratory and modeled mathematically and are consistent with the fossil record and comparative genomics.

Deja vu, man. These are exactly the complaints everyone made about Darwin’s Black Box: he didn’t seem to understand modern evolutionary theory, he ignored the multiple mechanisms of evolutionary change, he blithely pretended the evidence against his thesis didn’t exist, and he just sailed on, smug in his ignorance. Nothing has changed. His formula is the same. The same counter-arguments still apply.

Let’s all just ignore this rehash, OK?

A rip-roaring horror story

I picked up this book (actually, my brother gave it to me), and I couldn’t put it down. It’s got everything. It’s got a brave heroic protagonist. It’s got a god-soaked repellent psychopath for a villain who could have stepped straight out of a Steven King novel. It’s got establishment schemers who make everything worse. And most of all, it’s got grisly body horror. I kept reading because I had to know what abomination would be perpetrated on the innocent victim next.

Only it’s not a novel. It’s Candice Millard’s Destiny of the Republic: A Tale of Madness, Medicine and the Murder of a President, and it’s about the assassination of James Garfield.

The protagonist: James Garfield was one of those forgotten, minor presidents I didn’t know much about, because he served less than a year and months of that was was spent slowly dying in agony. But, I learned, he was a rather progressive candidate who accepted a nomination by popular acclaim reluctantly, and was a vigorous defender of civil rights who campaigned for dignity and equality for all races. He was a Republican. That tells you how much the party has declined in the last 140 years.

The assassin: Charles Guiteau was a cheap grifter, a narcissist with delusions of grandeur. He wanted to exploit the spoils system, whereby an incoming administration would freely hand out jobs and high ranking positions to their pals and people with money (hey, so the system hasn’t changed that much). Guiteau talked himself into thinking he deserved to be ambassador to France and that he was good friends with various politicans (he wasn’t), and when he didn’t get his due, decided to murder the president for the fame.

The real assassin: Guiteau pulled the trigger, but the real killer were the swarm of incompetent doctors who wanted the acclaim that would fall on whoever saved Garfield. Worst of the bunch was Dr. Doctor Bliss — his first name was actually “Doctor”, which would have been improbable in a novel — who seized control of the patient and limited what could be done, all the while issuing enthusiastically optimistic daily progress reports as the President spent months in steady decline. A later analysis of the treatment found the aphorism “Ignorance is Bliss” appropriate.

The body horror: the American doctors did not believe in the germ theory of disease, and rejected Lister’s antiseptic technique. So, as Garfield lay bleeding on the filthy train station floor, what did Bliss do? He stuck his unwashed finger in the bullet hole. He pulled out a series of non-sterile probes and poked them in there. He’s looking for the bullet in the worst way possible, and further, he ends up misdiagnosing him. The bullet had gone through to the left side of Garfield’s body, but Bliss was confident it was on the right, and so he kept probing on the right — every day, he seemed to be torturing Garfield further with this pointless insertion of his finger into the open wound — and eventually got the confirmation he wanted: an abscess formed, and a river of pus ran through the track he’d made with his dirty tools.

Really, you will learn more about pus than you ever wanted to know in this book. Pools of the stuff form in Garfield’s body, streams of it drain out of him, boils full of pus erupt all over his body as sepsis sets in. It is not for the squeamish. I probably just ruined everyone’s breakfast by mentioning it.

It doesn’t have a happy ending. Garfield dies. Bliss is disgraced. Guiteau is hanged. Oh, sorry, spoilers.

The one glimmer of optimism at the end is in Garfield’s vice-president, Chester Arthur, another of those easily forgotten presidents. He is a product of the spoils system, and a minion of a scheming senator who opposed Garfield and who groomed Arthur as a tool to serve his ends. Arthur was also something of a bumbler who’d lucked into appointments without actually getting elected, and who was terrified at the idea of taking over the job. He spends most of the book offstage, blubbering in fear, aware of his own incompetence. But then, when the president dies, he steps into the role, tells the scheming senator to take a hike, and rises to the occasion. His main accomplishment is the reform of the civil service, doing his best to end the spoils system.

I guess that sort of counts as a happy ending.

Anyway, if you’re one of those people into horror novels, who enjoys harrowing, gut-twisting tales of nightmarish experiences, try reading some history. It’s far scarier than anything fictional.

Daniel Mallory Ortberg has a new book, and he’s a man

He’s transitioning to be a man, and while he was working through that, he wrote a book, The Merry Spinster: Tales of Everyday Horror.

On the one hand, it’s very much a work of fiction. It is not a thinly veiled retelling of relationships and experiences I have had personally. And yet I also began thinking very seriously about my gender identity and the possibility of transition about halfway through writing it. And the title, the idea of a merry spinster — the idea of jolly, self-sufficient female solitude — that’s very dear to me. And in some very real ways, that’s no longer mine.

There’s a line in one of the stories in the book, Cast Your Bread Upon The Waters, where the main character – whose gender is never clarified – refers to their son, against whom they’ve been plotting murder, like this: “My son Johnnie was very beautiful, and I loved him.” It’s one of the first unmitigated statements they make about a person they very clearly loved but are trying to build a case against. Only after they’ve done the deed can they honestly say, I loved him. I don’t want to cheapen the story by saying, “Ah, yes, I too have released someone I love into the sea, it is a point-by-point allegory for transition.” But man. That merry spinster, that Toastified Mallory Ortberg — she was beautiful, and I loved her. And she is! And I do! And she is not gone, there has been no death, no act of violence, no act of disavowal or abnegation or dismissal. And yet she’s not herein the way that she was. Anyhow, it’s a good book, I think, and I’m glad we wrote it.

And still the same writer. It looks good!

Moors are lovely places, no werewolves at all

This may be my last bit of pleasure reading for a while, as the storm of a new semester strikes. But I’m happy to say I finally got to On the Moor: Science, History and Nature on a Country Walk by Richard Carter, and it was wonderful. Science and history and geography and evolution and culture all tangled up in musings while walking about the moors around Hebden Bridge — I got to visit that place a while back, and it was lovely and dense with a feeling of history. Now you too can sample it! Then get on a plane or train and go visit it! I’m sure Richard will be happy to give everyone a tour.

It’s also interesting for me since part of my paternal family came from that region in the Beforetimes, in the Long Long Ago. Maybe I should pick up a copy for my Out West family.

The Human Story Retold Through Our Genes

Now there’s an ambitious title: Adam Rutherford’s A Brief History of Everyone Who Ever Lived. It’s a substantial book, but I would have thought it would have had to be a bit longer to cover everyone, and really, a biography of every individual who ever lived would probably get a bit repetitious.

Fortunately, this isn’t a collection of actuarial tables and obituaries. It’s something much more useful: a description of how we know what we know about humanity, from the perspective of genetics, with a solid awareness of the limitations and capabilities of such an approach. That’s helpful — one of our big problems right now is the abuse of genetics by the ignorant to advocate for an impossibly deterministic and racist view of human history. This book counteracts that by describing the methodology accurately, and you’ll learn a lot by reading it. But don’t panic, it’s not a textbook — it does tell the stories and is a good read.

If you doubt me, a revised chapter has been made freely available, A New History of the First Peoples in the Americas, just for us provincial Americans (the full book has a far more global perspective). This one focuses on some of the historical and scientific controversies around efforts to pigeonhole American Indians into one ill-fitting racial category or another.

The idea that tribal status is encoded in DNA is both simplistic and wrong. Many tribespeople have non-native parents and still retain a sense of being bound to the tribe and the land they hold sacred. In Massachusetts, members of the Seaconke Wampanoag tribe identified European and African heritage in their DNA, due to hundreds of years of interbreeding with New World settlers. Attempting to conflate tribal status with DNA denies the cultural affinity that people have with their tribes. It suggests a kind of purity that genetics cannot support, a type of essentialism that resembles scientific racism.

The specious belief that DNA can bestow tribal identity, as sold by companies such as Accu-Metrics, can only foment further animosity—and suspicion—toward scientists. If a tribal identity could be shown by DNA (which it can’t), then perhaps reparation rights afforded to tribes in recent years might be invalid in the territories to which they were moved during the 19th century. Many tribes are effective sovereign nations and therefore not necessarily bound by the laws of the state in which they live.

When coupled with cases such as that of the Havasupai, and centuries of racism, the relationship between Native Americans and geneticists is not healthy. After the legal battles over the remains of Kennewick Man were settled, and it was accepted that he was not of European descent, the tribes were invited to join in the subsequent studies. Out of five, only the Colville Tribes did. Their representative, James Boyd, told The New York Times in 2015, “We were hesitant. Science hasn’t been good to us.”

Data is supreme in genetics, and data is what we crave. But we are the data, and people are not there for the benefit of others, regardless of how noble one’s scientific aims are. To deepen our understanding of how we came to be and who we are, scientists must do better, and invite people whose genes provide answers to not only volunteer their data, but to participate, to own their individual stories, and to be part of that journey of discovery.

A book about human genetics with a humanist perspective? That debunks 19th century dogma about race and intelligence? Yeah, it’s good. I’ve been trying to think of ways I could fit it into my already packed-full genetics course, or whether I could offer a non-majors course that incorporated it as a text.

But at least I can tell you all that you need to read it.

There will be a test. Not that I’ll be giving it, but rather that our entire culture seems to be testing you on this subject right now. You should read the book so you can answer it correctly.

Hooray for random mail deliveries!

It must be Christmas. Got a pile of packages in the mail all at once today, including some lab stuff (not shown).

I’m looking forward to Twilight of the Gods (maybe this weekend, if I’m a good boy and get my grading done), but does anyone know anything about the Theodora book? I’m always up for learning about Byzantine empresses, but this is one of those things where I didn’t request it, a prescient publisher just thinks I should take a look at it.

You’re telling me dinosaur reconstructions contain assumptions?

They do, and they always have. Here’s an interesting way to illustrate that: make reconstructions of modern animals as if we had no idea about the expected distribution of fat and other soft tissues. Here’s a baboon drawn from its bones while pretending ignorance of hair and lips and such unfossilized stuff:

This is from a book by John Conway, CM Kosemen, and Darren Naish, called All Yesterdays: Unique and Speculative Views of Dinosaurs and Other Prehistoric Animals. I’m going to have to add it to my list.

Unburying some Secrets: Peter Godfrey-Smith’s evolution of consciousness

This is a guest post by Joshua Stein, a doctoral student at the University of Calgary and @thephilosotroll on Twitter.

Peter Godfrey-Smith’s Other Minds: The Octopus, the Sea, and the Deep Origins of Consciousness is, like it’s subject, a strange animal. It is accessible to a broad and general audience; it also deals with a lot of technical literature in comparative psychology and philosophy of mind. I think the book can be deeply enjoyable for a broad lay-audience, but it is even better with a little bit of background and explanation of where Godfrey-Smith fits into the literature and what he’s saying about consciousness. I want to provide some of that background, to illustrate why this book is so interesting and show some colleagues in philosophy and psychology why the book should be regarded as a philosophical success.

There are some things about mind and consciousness that Godfrey-Smith takes for granted. The first is that we can study and discuss consciousness as an empirical issue. Most folks are probably familiar with the claim that “we can’t study consciousness” for some reason or other. The claim comes up an awful lot, even in some philosophical literature. (The most noteworthy advocate is the disgraced Colin McGinn.) I won’t get into the objections to this position, but it is basically set aside by most philosophers.

There are two approaches to evaluating minds; one is to look directly at the nervous system and extrapolate about how it works from the internal mechanisms, while the other is to look at how the organism behaves in the environment. There’s a long history around these two approaches, often regarded as in tension; it is increasingly common, though, to use both methods in order to a build a more satisfying theory. Godfrey-Smith uses both throughout the book: he’ll often discuss the ways he sees octopuses behave, and then shift to talking about mechanisms in the central and peripheral nervous system.

Godfrey-Smith uses the book as an opportunity to offer a rich, and technically sound, story about consciousness. There are two features that he discusses at length in the book, returning to them over and over, and these two features are pretty prominent in modern theories of consciousness. The first is that consciousness involves the integration of different sorts of sensory information (pp. 88-90); the second is that consciousness involves the temporal ordering of events (91-92), and allows those orderings to be made available in action.

Godfrey-Smith writes. “I see ‘consciousness’ as a mixed-up and over-used but useful term for forms of subjective experience that are unified and coherent in various ways.” (97) Unlike many contemporaries, Godfrey-Smith doesn’t offer a specific theory of consciousness; however, he does involve existing theories and shows how they play a role in discussing consciousness in radically different minds; obviously, in the book, he’s concerned with cephalopods.

There are some other features that show up in Godfrey-Smith’s story of consciousness that make the story so satisfying, but before I get to this, I think it is useful to note that the two prominent features play a part of an old philosophical tradition. The Anglophone philosophers David Hume and John Locke each came up with stories about what consciousness is that involved rich experience and temporal ordering, respectively.

For Hume, consciousness was about the vivid and integrated character of experience; an auditory experience isn’t a two-dimensional thing. It has pitch and timbre and tone, and there’s noise that has to be filtered out. Part of what it is to have a conscious experience of a piece of music is to experience the different dimensions of that piece, all laced together into a multidimensional sensory experience.

For Locke, consciousness was about the autobiographical constitution of identity; people are continuous over time and have a unified psychological story that extends back into their pasts, and includes certain features of possible futures. This gives us something like the temporal ordering feature.

Godfrey-Smith isn’t committal to any such view being decisive. Rather, he’s open to the possibility that both of these things are true of and involved in facilitating consciousness. His story rather illustrates that many of the inherited theories (now far more technical and closely aligned with certain findings in neuroscience and cognitive psychology) are mutually reinforcing in valuable ways.

Because Godfrey-Smith isn’t committed to a particular theory about consciousness, he’s open to pointing out how different theories illustrate different features of consciousness. One instance, present from the very beginning of the book, is the role of attention; an organism that attends to a feature of its environment for a period of time illustrates both features of consciousness (because they perceive the feature over time and integrate information about changes in that feature). He notes that this is common with octopuses who see and attend to him when he is diving to watch them; it comes up regularly in his anecdotes.

Initially, I wondered if Godfrey-Smith considered that attention is instrumental in a popular theory of consciousness (actually, the one I more-or-less subscribe to). He invokes things that look curiously like classic tasks in joint-attention (57-58), only performed by octopuses instead of children or chimpanzees; the giveaway that he’s taken this into consideration is his invocation of Jesse Prinz (91-91), whose 2012 book The Conscious Brain articulates and explores the attentional theory of consciousness.

Another feature is embodiment. While Godfrey-Smith expresses skepticism of a certain view of embodiment (74-75), he also gives a lot of the stock arguments for why embodied cognition is so important. For example, cuttlefish can’t process color visually (due to a lack of individuation in light receptors used for color vision) but still respond to differences in color in their environment through features in the skin; a version of this approach (though for object-vision and not color) has been used to develop vision substitutes for the blind. (80-81) Even as a skeptic about certain strong views of embodiment, Godfrey-Smith shows how many theories that focus on embodiment as something that shapes conscious experience get certain bits right.

I could go on with the various different features that Godfrey-Smith picks up and illustrates, but at that point I would risk summarizing a huge portion of the observations he makes in the book; it’s worth reading for yourself to see how these different elements fit together and provide a broad and interesting theory of consciousness.

The last point I want to make, which is of special interest to readers here familiar with PZ’s various criticisms of evolutionary psychology, is something that I think Godfrey-Smith does particularly well.

One way of criticizing a lot of the literature in evolutionary psychology is that it puts together a specious “just-so story” about how certain features of the brain (and therefore the mind) evolved in ways that are not as responsive to things like the environment, interaction with conspecifics, and other features that we know (from developmental psychology) play a huge role in how any particular member of a species develops.

Claims about the evolutionary history of a particular behavior, for example, and selection pressures influence the development of tools and their prospective role in reproductive success (just google “sexy handaxe theory” if you’re wondering what I’m talking about) are difficult to evaluate, for both philosophical and scientific reasons, but Godfrey-Smith’s constant focus on the contemporary role of the various functions for octopuses (for example, the way that attention helps them to interact with their environment, or the way that peculiarities in the peripheral nervous system help in hunting) makes the story much more plausible, and much easier to evaluate, rather than focusing on the buried secrets.

The 2017 Hugo awards are out

The winners have been announced, and they are NK Jemisin, Seanan McGuire, Ursula Vernon, Amal El-Mohtar, Ursula K. LeGuin, and Marjorie Liu…hey, wait a minute, those are all lady names. Obviously, this must mean that women are genetically predisposed to write the best science fiction and fantasy. The evidence is right there! I’m sure the people who argue that existing sex differences in anything can’t possibly be caused by socio-cultural factors will agree because they hate that kind of stuff. They’re just going to have to acknowledge that women are biologically better writers.

Oh, there was the usual effort by the Sad/Rabid Puppies to get some of their nominees on the ballot, and they did have a few works they pushed — none of them won. Not even the transparent attempt to steal credit from good authors by naming them succeeded. They nominated, for instance, China Mieville, Neil Gaiman, and the movie Deadpool…they lost, too. I suspect there might be some weak negative effect, even, where attaching Vox Day’s recommendation to an otherwise good book causes some negative votes. Not that it matters; all the winners were rewarded fairly on their own merits.

One interesting twist: the Puppies, for some reason, really really hate Rachel Swirsky’s If you were a dinosaur, my love, which was nominated for a Hugo in a previous year. I like that story a lot, so I don’t quite get the hatred, but OK, they’re allowed…but this year they intentionally went looking for an opposing story, something with dinosaurs in it, so they could simultaneously sneer at both Swirsky and Chuck Tingle. They picked Alien Stripper Boned From Behind by the T-Rex, by Stix Hiscock. You can’t hold that against Hiscock, though.

Hiscock also said she didn’t know anything about Beale, and seemed to be unaware (before the interview) that he was responsible for Alien Stripper getting on the ballot. She was a little hurt that he would use her novelette as a way to mock the Hugos, especially since it doesn’t seem like he’s even read it. (It’s possible Beale picked it specifically because of the Rabid Puppies’ hatred of the award-winning novelette If You Were A Dinosaur, My Love.) “I guess I’ll cry a little, laugh a little. But I’ll be ok. Jokes are pretty hilarious sometimes,” Hiscock said.

Still, Hiscock said it’s an honor to be nominated, even though she probably won’t be able to attend the ceremonies in Helsinki because of the expense. And even though Beale might’ve gotten Alien Stripper on the ballot due to sheer pettiness, the bank error is definitely in Hiscock’s favor. Book sales of Alien Stripper Boned From Behind by the T-Rex are through the roof.

It didn’t win, even though the author is a woman, and we now know that women naturally have superior writing skills.

But I ordered a Kindle copy of Alien Stripper Boned From Behind by the T-Rex anyway. It was free. The author seems nice. Besides, I’ve already read all the winners.