Nature did not intend that you put those colors there!

Oh, my. Some researchers have discovered that pigments in tattoo inks can, over the years, wander out of the tattoo into places like lymph nodes. They have not, however, identified any danger or harm from this phenomenon. All I can muster is a weary, “So?”. This shouldn’t be at all surprising.

Next up: scientists will discover that the skin texture under your tattoo will change with age, that the shape of your body can distort the shape of your tattoos, and most horrifyingly, that people with tattoos have pigmented inks permanently discoloring their skin!

Building a sex is harder than most people imagine

Now will you believe me? I keep saying that sex and sex determination are far more complex than just whether you have the right chromosomes or the right hormones or the right gonads, and now here’s a lovely diagram that illustrates some of the steps in sex determination.

The biology is set up to favor driving an individual to one side or the other, but there are so many detours that can be taken en route that it is ridiculous to ignore all the people who end up following a more unique path.

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.

Dunning-Krueger and evolutionary biology fandom

A graphic designer, Katherine Young, redesigned a girls’ magazine cover to highlight the implicit assumptions we all tend to make about women:

I ran across this on Facebook, where someone posted it approvingly, and I agree — why shouldn’t girls and boys be reinforced for a wide range of abilities? You can be pretty, or you can be smart, or you can be strong, or you can be brave, or you can be sensitive…or you can be all of those things at once, even, although then I’ll hate you for being so much better than me. No! That’s not it! We should give everyone opportunities to be all those things, and others as well, and avoid channeling them down a single acceptable path.

But then someone commented on that post, and it was fascinating. I’m used to criticizing creationist for appallingly bad reasoning abilities and misuse of scientific theories, but here’s a magnificent example of someone babbling pretentiously in favor of some narrow scientific concepts, and applying them as a justification for his gender biases. It’s kind of horrifying. It’s also painfully common.

So this person (all names removed to protect the guilty) asks for a clarification. He doesn’t get one, but that doesn’t matter, he’s on a roll.

it seems to me that you are suggesting that is immoral or at least somehow improper for females to be evaluated using physical characteristics that highlight fertility such as facial symmetry, skin texture, hip to waist ratio, etc. and that instead they should be judged on mental abilities that enable them to have a career. is my understanding of your intent correct?

The implication being that the females should be judged on the basis of their potential fertility, where fertility is the most desired quality, but things like intelligence make no significant contribution to their maternal abilities.

I wonder if he’d make the same demands on boys: we should be evaluating them on symmetry, penis length, sperm count, and combat ability, because those contribute to men’s purpose in life, which is to crush their competitors and impregnate females. I didn’t ask, because I was afraid that he’d say yes, and also think those are good things.

Because of course what he claims to be driving his ideas is an objective position on evolution.

given the great demands placed on the female body during homo sapiens’ lengthy gestation and lactation period, would it be wrong for me to suggest that encouraging males to select mates based on characteristics that enable the female to generate wealth independent of a mate rather than on their ability to bear children may have long term negative effects on the species. or is that just the crazy in me talking?

Oh, man. A couple of problems here: evolution doesn’t care what’s “good” for the species. It’s all about short term responses for individuals and their progeny, and different strategies work for different individuals. One size fits all is not a smart plan for a diverse population.

Humans have complex lives and a difficult maturation process. It also wouldn’t benefit us if females were reduced to a shapely, symmetrical uterus perched atop some wide, sexually attractive hips. Maybe benevolent evolution should be shaping men to be uxorious and devoted stay-at-home fathers so their mates can focus on that beauty thing, for the good of the species?

I should also point out that this idea that we men, from our limited perspective, can actually assess what traits are “good for the species” has an unpleasant history. That’s the basis of eugenics, the idea that we can control the complex genetic interactions involved in our development, physiology, and behavior, and that we can predict what traits will be directly beneficial for future generations. We can’t. That we can’t doesn’t stop people from over-simplifying the problem and pretending that they know exactly what’s best for everyone else.

It’s pointed out to him that he’s making the fallacy of composition. Does he care? Of course not! Because evolution. And because he cares about these girls <shudder>.

that may be true but i would caution throwing the baby out with the bath water and ignoring the evolutionary reasons behind our obsession with beauty, not just because of the long term impact on the species as a whole, but also because of the individual impact on the mental well being of young girls

Again with the “species as a whole” argument! How does he know what’s good for the species as a whole? For example, right now we’re seeing a long term pattern of decline in sperm counts in many human populations. Would he favor artificial selection for fecundity in boys for the “good of the species”?

He also seems to think he knows best what is good for the mental well being of young girls, and that is to focus on beauty and appearance and fashion. Some girls will be happy with that, and of course they can follow that course…but others are not. What are we to do with them, for the good of their mental health? Tell them to shape up and memorize cosmetics brands, so they’ll be happy and well-adjusted? I never faced that specific pressure, but I was told as a kid by my peers and teachers that I, as a boy, was supposed to like sports, and should turn out for baseball and football. I was judged because I wasn’t good at sports (maybe some of you experienced the same phenomenon), and it wasn’t good for my emotional well-being. I liked to read books instead. All I needed in my life was some jerk trying to explain to me that my interests in science were not good for the species, and that they had an evolutionary justification for why I needed to butt heads with the big boys on a grassy field.

But now we get into the religious argument. This is an example of uninformed religious dogmatism.

it seems to me that you always turn the natural order of things upside down! sometimes i am not sure if you are serious or just playing with me :)

not everyone can be smart and win the google science fair. suggesting to young girls that they have to be smart in order to have a meaningful and successful life might not be the best way to go.

natural order of things is a dead give-away. How do you know? Why is it that the natural order of things is always a matter of a guy informing girls that they are supposed to make themselves attractive to him?

And that last line…has he considered that suggesting to young girls that they have to be pretty in order to have a meaningful and successful life might not be the best way to go? Probably not.

One last quote…

when i was young and naive, the vanity of women frustrated me. especially because i was a slob, i could not understand their obssession with adorning themselves with all kinds of paints and bows and ribbons and shiny trinkets, but now that the passions of youth that blind objective contemplation have been reduced a few dimly glowing embers buried in a pile of ashes, i understand there are evolutionary forces behind these obssessions and i can accept them as the natural order of things.

The hypocrisy…he was a slob, but he knows best what women should do. He thinks women as a whole are vain. But now that he has found Jesus evolution, he understands the reason why women should be working so hard to make themselves beautiful — it’s to enhance his ability to reproduce, and theirs, too, because the only way a woman can improve their fitness is with a good hip-to-waist ratio, while he can get away with being a pompous slob.

I am not fooled at all. This is a man using poorly understood sciencey buzzwords to justify his culturally supported biases.

Mary Schweitzer and the mysterious dinosaur soft tissue

Science has an overview of Schweitzer’s work. You may recall that she published descriptions of cells and soft tissue imbedded deep in fossilized dinosaur bone. That work is much beloved by creationists (it means those bones must be young, they say), but despite starting out as a creationist, she does not support that claim of a young age. She’s a theistic evolutionist.

She went back to school at Montana State University in Bozeman for an education degree, planning to become a high school science teacher. But then she sat in on a dinosaur lecture given by Jack Horner, now retired from the university, who was the model for the paleontologist in the original Jurassic Park movie. After the talk, Schweitzer went up to Horner to ask whether she could audit his class.

“Hi Jack, I’m Mary,” Schweitzer recalls telling him. “I’m a young Earth creationist. I’m going to show you that you are wrong about evolution.”

“Hi Mary, I’m Jack. I’m an atheist,” he told her. Then he agreed to let her sit in on the course.

Over the next 6 months, Horner opened Schweitzer’s eyes to the overwhelming evidence supporting evolution and Earth’s antiquity. “He didn’t try to convince me,” Schweitzer says. “He just laid out the evidence.”

She rejected many fundamentalist views, a painful conversion. “It cost me a lot: my friends, my church, my husband.” But it didn’t destroy her faith. She felt that she saw God’s handiwork in setting evolution in motion. “It made God bigger,” she says.

I’ve read her papers, and they’re real head-scratchers. She seems to do good work; she documents everything carefully; she interprets the results cautiously. They don’t jibe well with expectations — chemistry ought to show more decay — but heck, data is data, if there are sound observations we’ve got to conform the theory to the evidence, not the other way around. She is reporting stuff that seems colossally unlikely, though.

Schweitzer’s most explosive claim came 2 years later in two papers in Science. In samples from their 68-million-year-old T. rex, Schweitzer and colleagues spotted microstructures commonly seen in modern collagen, such as periodic bands every 65 nanometers, which reflect how the fibers assemble. In another line of evidence, the team found that anticollagen antibodies bound to those purported fibers. Finally, they analyzed those same regions with Harvard University mass spectrometry specialist John Asara, who got the weights of six collagen fragments, and so worked out their amino acid sequences. The sequences resembled those of today’s birds, supporting the wealth of fossil evidence that birds descend from extinct dinosaurs.

It’s difficult to believe, but then there’s another dilemma: we expect extraordinarily strong evidence before it should be accepted, but how strong does it have to be? Is this too nitpicky?

She needs more fossils to quiet a continuing drumbeat of criticism. In addition to raising the specter of contamination, Buckley and others have argued that antibodies often bind nonspecifically and yield false-positive results. Critics also noted that one of the six amino acid sequences reported in the 2007 paper was misassigned and is likely incorrect. Asara later agreed and retracted that particular sequence.

“That’s worrying,” says Maria McNamara, a paleontologist at University College Cork in Ireland. “If you are going to make claims for preservation, you really need to have tight arguments. At this point I don’t think we are quite there.”

The biggest problem, though, is this one: all these results come from one and only one lab.

But no one except Schweitzer and her collaborators has been able to replicate their work. Although the study of ancient proteins, or paleoproteomics, is taking off, with provocative new results announced every few weeks, most findings come from samples thousands or hundreds of thousands of years old—orders of magnitude younger than Schweitzer’s dinosaurs.

“I want them to be right,” says Matthew Collins, a leading paleoproteomics researcher at the University of York in the United Kingdom. “It’s great work. I just can’t replicate it.”

That’s something I wish the creationists who bring up her work could understand: we want her to be right. I want to be able to go to a databank and download protein sequences from T. rex. I want to see a molecular phylogenetics comparison of Stegosaurus and Hadrosaurus osteocyte proteins. I think it would be awesome to compare sequences from different ceratopsians and assemble a family tree.

What I want and what we’ve got are two different things, though, and if only Schweitzer has the magic hands to extract this information, I’m not going to trust it. I don’t reject it out of hand, but damn,
it really needs more replication. At this point I don’t want to see another paper from her — I want to see it coming from another, unaffiliated lab. That would be better confirmation.

Cassini must die

It’s happening tomorrow: the Cassini probe is being ordered to destroy itself by crashing into Saturn. It seems harsh. You’ve sent a tourist to an exotic location to go crazy taking vacation snaps, and then instead of a return trip, you reward them with a request to send more pictures of their suicide. I guess it is a spectacular way to go.

And then you learn that those photos were taken with a one megapixel camera. No, really. It’s got some fancy filters to extract more information from its photos, but otherwise, I’ve got better cameras in my electronics junk drawer. It was launched in 1997, so I guess that is to be expected.

Clearly, what this means is that NASA must launch more robots into space with more up-to-date fancy cameras. I know, the budget is tight, but if it will help, I’ll give them the phone out of my pocket — it has a higher resolution camera on it.

Until that next robot goes skyward, you can watch the final moments of Cassini early tomorrow morning. The timing is perfect: it looks like I can just check in right around the time I get up and watch the death of a space probe before I have to go off to work.

Climate change is happening now

You can’t deny it — or rather, you can, but you have to ignore all the evidence. Here’s a list of seven climate hotspots where the shifts are already obvious: southern Spain, Bangladesh, Malawi, the Svalbards in Norway, Brazil, the Philippines, and so the Americans don’t wander off and wonder where those places are, New York. They’re all depressing, but I found the news about the Amazon to be most discouraging.

Perhaps most ominous is the fact that a positive feedback loop appears to be in play. As the Amazon dries, Nobre says, tropical forest will gradually shift to savanna, releasing carbon dioxide into the atmosphere and further adding to global warming.

“When we see a dry season of over four months or deforestation of more than 40 percent then there is no way back. Trees will slowly decay, and in 50 years we would see a degraded savanna. It would take 100–200 years to see a fully fledged savanna.”

The Amazon then would be unrecognizable, along with much of Earth.

We don’t know what all the global consequences of losing the Amazon rain forest would be, but apparently, we’re going to do the experiment and find out.

Meanwhile, there are still people who believe it’s not a problem, and that market forces will compensate for our new hot, dry, stormy, flooded reality. The scientific research is 97% in agreement, which is already remarkable, given how much scientists like to argue. And the other 3% is junk science.

But what about those 3% of papers that reach contrary conclusions? Some skeptics have suggested that the authors of studies indicating that climate change is not real, not harmful, or not man-made are bravely standing up for the truth, like maverick thinkers of the past. (Galileo is often invoked, though his fellow scientists mostly agreed with his conclusions—it was church leaders who tried to suppress them.)

Not so, according to a review published in the journal of Theoretical and Applied Climatology. The researchers tried to replicate the results of those 3% of papers—a common way to test scientific studies—and found biased, faulty results.

Katharine Hayhoe, an atmospheric scientist at Texas Tech University, worked with a team of researchers to look at the 38 papers published in peer-reviewed journals in the last decade that denied anthropogenic global warming.

“Every single one of those analyses had an error—in their assumptions, methodology, or analysis—that, when corrected, brought their results into line with the scientific consensus,” Hayhoe wrote in a Facebook post.

But of course it is that flawed 3% our elected officials have chosen to accept, and we don’t have a mechanism for removing deluded idiots from office.