Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
Micheal Eisen, a well known geneticist at UC Berkeley, has weighed in on genetics and l’affaire Mukherjee on his website It is Not Junk. As you’ll see from his post (click on the screenshot below to go there), he thinks that Mukherjee way overrated the significance of epigenetics in his New Yorker piece. I like the title of his post, and love the subtitle, which you’ll recognize as a variant of Arthur Clarke’s Third Law.
Just a few excerpts (indented) and my comments:
Biologists now invoke epigenetics to explain all manner of observations that lie outside their current ken. Epigenetics pops up frequently among non-scientists in all manner of discussions about heredity. And all manner of crackpots slap “epigenetics” on their fringy ideas to give them a veneer of credibility. But epigenetics has achieved buzzword status far faster and to a far larger extent than current science justifies, earning the disdain of scientists (like me) who study how information is encoded, transferred and read out across cellular and organismal generations.
True, and I’m not quite sure why it’s become a buzzword. One explanation is that it somewhat circumvents genetic determinism by suggesting that the environment, your behavior, or even (à la Chopra) your will can change your genes, perhaps in a heritable way. That makes it appeal to those Leftists who don’t like genetic determinism. Also, epigenetics has been construed as eroding the modern theory of evolution by suggesting (wrongly) that evolution can occur in a Lamarckian way—through the inheritance of environmentally acquired “DNA marks. People always love the notion that “Darwin was wrong”—although in this case it wouldn’t hold, as Darwin himself had a Lamarckian view of inheritance. But “epigenetics” is a buzzword among geneticists, too, and I’m not quite sure why.
In one way this debate is incredibly important because it is ultimately about getting the science right. Mukherjee’s piece contained several inaccurate statements and, by focusing on one aspect of Allis’s work, gave an woefully incomplete picture of our current understanding of gene regulation.
Any system for conveying information about the genome – which is what Mukherjee is writing about – has to have some way to achieve genomic specificity so that the expression of genes can be tuned up or down in a non-random manner. Transcription factors, which bind on to specific DNA sequences, provide a link between the specific sequence of DNA and the cellular machines responsible for turning information in DNA into proteins and other biomolecules. Small RNAs, which can bind to complementary sequences in DNA, also have this capacity.
But there is scant evidence for sequence specificity in the activities of the proteins that modify DNA and the nucleosomes around which it is wrapped. Rather they get their specificity from transcription factors and small RNAs. That doesn’t render this biochemistry unimportant – the broad conservation of proteins involved in modifying histones shows they play important roles – but ascribing regulatory primacy to DNA methylation and histone modifications is not consistent with our current understanding of gene regulation.
Yes, and count on a scientist, rather than a journalist (unless he’s Carl Zimmer) to report the science accurately. It is the specificity of gene action that Mukherjee is interested in: after all, he began his piece with a discussion of cellular differences—between identical twins and, later in the piece, between cells within a body, all of which start with a single undifferentiated cell, the egg. And we know that specificity of gene action is conferred by small RNAs and transcription factors. We don’t know the same for histones or epigenetic markers.
But I digress. I see there are now a lot more articles on the Internet about this argument, which in the end IS about getting the science right (although it seems to also be about not looking bad if you’re famous). But I can’t be arsed to talk about every piece. Just Google “Mukherjee epigenetics” if you’re interested.
“Because it lags slightly behind reality, consciousness can “anticipate” future events that haven’t yet entered awareness, but have been encoded subconsciously, allowing for an illusion in which the experienced future alters the experienced past.” —Adam Bear
In discussions about our idea of “agency” (or, if you will, “choice” or “free will”), I’ve described experiments showing that you can, to a substantial degree, predict what kind of binary choice—a choice between two actions—someone will make up to 7 seconds before they report having made a conscious choice. This has now been shown in several experiments, and it suggests this: your brain makes “choices” for you before you’re conscious of having made them. And that comports with determinism: the view that our feeling of free agency is illusory, for at any moment when we face a “choice” there is only one choice we can make: the one the laws of physics dictate, acting via your genes and environmental influences. Yet we feel otherwise, and strongly so.
That’s really not much of a surprise, though those who believe in libertarian free will, or even in compatibilism (i.e., free will is compatible with physical determinism) don’t like those experiments.
What is surprising, though, is the suggestion that your consciousness of having made a choice comes not only after your brain has made the decision, but after you’ve actually made the choice.
That’s really not all that surprising, though—not if the notion of having chosen something freely is a confabulation: a part of our neuronal circuitry, perhaps evolved, that makes us feel as if we’ve chosen something when the result of the “choice”—the action—has already occurred. If it’s the case, it seems like a spooky reversal of time. But it’s really not. It’s just our brains fooling us by giving us an experience, or implanting a “memory”, that is in an incorrect time sequence with respect to an action.
This is one of the conclusions you can draw (there are others; see below) from a nice new paper in Psychological Science by Adam Bear and Paul Bloom at Yale (see reference below; free access). Bear has also written a very good and comprehensible summary of the results at Scientific American, “What neuroscience says about free will.” (Answer: you don’t have it, at least in the libertarian form.)
The experiments were clever, and came from the hypothesis that if conscious choice was illusory, you could think you’d made a choice after the choice was actually made and acted upon.
The first thing the authors did was expose the subjects (who had been trained) to five randomly-placed circles on a computer screen, asking them to choose one circle quickly. Then, after intervals of time ranging from 50 to 1000 milliseconds (0.05 to 1 second), the computer randomly turned one of the circles red.
The subjects were then asked if their chosen circle turned red. They had three choices: “yes”, “no” and “I didn’t have time to choose before the circle turned red”, all indicated by pressing one of three keys on a keyboard.
Without any “postdictive bias” of the kind I described above, one would expect “yes” to be answered about 20% of the time when subjects reported that they did make a choice, because the circle that turned red was one of five chosen randomly by the computer. Instead, regardless of the interval before the circle turned red, the probabilities that you said “yes, my chosen circle turned red” was always higher than 20%. That’s shown in the graph below, which plots “probability of a yes answer” against the interval after which the circle turned red.
What’s important about this plot is not only that the probability was higher than 20%, which means that people were saying that their “choice” turned red more often than they should, but that that probability was higher when the interval between the start of the experiment and the circle’s turning red was shorter. That is, people’s bias—that they had “chosen” the circle that later turned red—was higher when they had less time to “make” a choice:
Fig. 3 (from paper) Results from Experiment 1: probability that participants chose the red circle on trials in which they claimed to have had time to make a choice. The error bands denote 95% confidence intervals. Also shown are the results of the best-fitting logistic model of responses as a function of the reciprocal of time delay.
That makes sense, for according to the author’s model of choice confabulation (below), your memory bias would be greater for the shortest delay between the start of the experiment and the circle’s turning red. Confabulation is likely limited to a short window of time, simply because it’s less likely you can reverse your experience or rewrite history after a longer period. The authors describe this as “the window of unconscious processing”. Note that you wouldn’t expect a negative relationship of the sort shown above people were simply lying about whether they chose the red circle, as such lying shouldn’t show any time dependence.
There are other controls described as well, like seeing if the degree of confidence a subject had in his/her choice affected this relationship (it didn’t); but you can read the short paper yourself.
Here’s the authors’ model (be sure to read the caption):
Fig. 1 (from paper). A model of postdictive choice in Experiment 1. Although choice of a circle is not actually completed until after a circle has turned red (choice time > delay), the choice may seem to have occurred before that event because the participant has not yet become conscious of the circle’s turning red (choice time < delay + lag in consciousness). The circle’s turning red can therefore unconsciously bias a participant’s choice when the delay is sufficiently short.
The authors thought of one problem with the experiment above. If the subjects were confused about whether they had chosen the circle that turned red, they might simply randomly press the “yes” or “no” button. That would drive the “yes” answers, expected to be 20%, towards 50%, giving the higher-than-expected “yes” rate shown above.
To deal with this, they used an experiment in which they showed TWO randomly positioned, and colored, circles on a screen, with the two colors chosen from an array of six. The told the subjects to choose one color. They then added a third circle between the two that had a color randomly chosen from the two initially displayed. And, as in the five-circle experiment, the third circle appeared at intervals ranging between 0.05 and 1 second. This way a random punch of “yes” and “no”—”I chose the right color” or “I chose the wrong color”, respectively—a randomness due to confusion, would not bias the results. With only two circles, a random punch would just make the probabilities of “yes” and “no” closer to 50%, which is what they should be anyway.
And again, the same bias was shown: subjects generally reported that they chose the circle of the same color as the one that appeared later with a probability of higher than 50%: as high as 63% at short time intervals. And again, the shorter the time interval, the greater bias was seen in the self reports. Here’s the graph of probability of saying “yes” against the time delay. The overall pattern is statistically significant (p = 0.002):
Fig. 5. (From paper). Results from Experiment 2: probability that participants chose the circle that matched the color of the middle circle on trials in which they claimed to have had time to make a choice. The error bands denote 95% confidence intervals. Also shown are the results of the best-fitting logistic model of responses as a function of the reciprocal of time delay.
What both of these experiments seem to show is that, as Bear wrote in the Scientific American piece, “Perhaps in the very moments that we experience a choice, our minds are rewriting history, fooling us into thinking that this choice—that was actually completed after its consequences were subconsciously perceived—was a choice that we had made all along.” The paper with Bloom cites earlier experiments that also support this result. We have to face the possibility, just as we now realize that choices can be made by the brain before we become conscious of them,” that choices may actually be carried out before we become conscious of having made them; and yet that we feel that the sequence was the opposite of what really happened.
Three issues remain:
How common is this phenomenon? This is the first experiment I know of that tested the “confabulatory choice” idea, and we clearly need more and differently designed studies to test the robustness of the conclusions.
Could there be another explanation? Yes, the authors mention at least one. They describe an alternative to their explanation that having made a choice subliminally biases you into thinking you made it before you did, and in fact after the choice was enacted. The alternative is that you experience the choice at the correct moment you made it (i.e., after the circle had turned red), but that the time of that choice is “immediately afterward encoded into memory incorrectly, which subsequently biased their reports of what they had chosen.” Thus we have a memory-revision versus a misperception hypothesis. To me this is a distinction without much difference, for it leads to the same phenomenon: we think we make conscious choices not only after they’re unconsciously made by our brain, but also after we actually carry out the actions. I should add that the authors give three other limitations of their conclusions, but they’re not the kind that invalidate their results; and you can see them by reading the paper.
Why does the brain work this way? Under determinism, there is no problem with us becoming conscious of having made a choice only after our brains have made it for us. Nor is there a naturalistic problem in accepting that, in short intervals, our actions could actually precede our having the sense of “choosing” to do them. What we don’t understand is why we have the illusion of being conscious agents: an illusion of having made the choice at the moment our brains made it, and of having performed an action only after we’re conscious of having decided to do it. All the experiments suggest that these “feelings” don’t represent the real temporal sequence of decision-making.
As I mention in my lecture on free will, the illusion of agency could be either an epiphenomenon of our complex brains, or it might be evolved, and for various reasons. One is that we would leave more copies of our genes if we hold others and ourselves responsible for making choices—for deceiving ourselves into thinking that we could have done otherwise. This could lead to a schema of reward and punishment that could allow one to function better in a small social group. But that’s just a guess, of course. In his Scientific American piece, Bear speculates along these lines, and I’ll leave the last word to him:
Perhaps the illusion can simply be explained by appeal to limits in the brain’s perceptual processing, which only messes up at the very short time scales measured in our (or similar) experiments and which are unlikely to affect us in the real world.
A more speculative possibility is that our minds are designed to distort our perception of choice and that this distortion is an important feature (not simply a bug) of our cognitive machinery. For example, if the experience of choice is a kind of causal inference, as Wegner and Wheatley suggest, then swapping the order of choice and action in conscious awareness may aid in the understanding that we are physical beings who can produce effects out in the world. More broadly, this illusion may be central to developing a belief in free will and, in turn, motivating punishment.
The unstated implication here is that a belief in free will and motivation for punishment (and I’ll add “reward”) leads you to leave more copies of your genes than do individuals without such beliefs and motivations.
We have miscellaneous photos from regulars today. First, from Mark Sturtevant:
While going over some old pictures, I suddenly realized I had never sent you pictures from the batch of ‘hickory horned devil’ caterpillars that I had raised some years ago. These grow to become the longest caterpillar in the U.S., and later they become the lovely regal moth (Citheronia regalis), which, perhaps surprisingly, is not our largest moth. Anyway, here is a picture of these babies. They were quite a handful. This was, so far, from the only time that I reared this species, although it was very easy and I hope to do it again one day. I had over a dozen of them (!), but sadly none survived to the adult stage. I think the problem was it was too cold for them in my refrigerator where they spent the winter.
Some things to note here are that the blue-ish ones have stopped feeding, and they would very much prefer to be looking for a place to burrow underground to form a pupa. You can see the brownish color of the future pupa is already inside them. Another thing to note is that the second one from the right is pooping. Look at the size of that turd!
To get an idea of the size of these things, I recommend to zoom in so that my hand is about the size of your hand.
And two photos from Diana MacPherson, who sent snaps of an American Red Squirrel (Tamiasciurus hudsonicus). Her notes:
Notice the weird fur colour in the second picture (near the bum). This is the same red squirrel that visits my feeder all the time. I watched where he/she went and it was along the horse fence, to the front of my yard and into an evergreen tree on my neighbour’s property near the fence.
Finally, I had asked readers to send me a photo of Mercury’s transit across the Sun a few days ago, and finally one obliged: the indefatigable Ben Goren, who sent notes:
You could maybe title it, “Spot the planet!”
To put things in perspective…Mercury is about 3,000 miles across, bigger than the Moon. Roughly, you could fit Asia in that dot…and it’s not even as big as the very small storm (sunspot) near the center….
Photographed with a Canon 5Ds mounted to a Canon 400mm f/2.8 II with a 2x teleconverter, and a Baader filter in front.
It’s Hump Day (due to decrepitude, this was originally posted as “Tuesday: Hili Dialogue”), and the gray weather and sloppy rain continues in Chicago. Further, the fog in Hyde Park is about the worst I’ve seen in 20 years. Here’s a photo taken from my crib at 5:30 a.m., looking toward the skyline of Chicago. You can’t see even a block ahead, and flights are being canceled at Midway Airport:
But Philomena is on tonight at 10 pm on BBC2, and at least some of you will be able to watch Cunk on Shakespeare. Don’t miss it, UK readers!
On this day in history, the HMS Beagle was launched in 1820, the ship that would take Darwin around the world a decade later; and you know what happened then. On May 11, 1960, the Mossad captured Adolf Eichmann and brought him to Israel for crimes committed when he was a Nazi. Those born on this day include Irving Berlin (1888), Salvador Dali (1904) and Richard Feynman (1918). Those who died on May 11 include Bob Marley (1981) and Douglas Adams (2001).
Meanwhile in Dobrzyn, Hili is either misunderstanding humans or trying to cadge more free noms:
Hili: Why did you pick these lilies-of-the-valley?
A: They are for Malgorzata.
Hili: She would probably prefer the pâté from my can.
In Polish:
Hili: Po co zerwałeś te konwalie?
Ja: Dla Małgorzaty.
Hili: Ona pewnie wolałaby taki pasztet z puszki z jedzeniem dla kotów.
Born March 26, 1986, Scooter lives with his owner Gail Floyd, who was there the day the kitten was born – and he’s been right by her side ever since.
As a kitten, Scooter liked to play in Gail’s hair and even became accustomed to riding on her shoulder, going with her wherever she went. Nowadays, nothing has changed. He wakes Gail up every morning at 6 AM, “talking” and jumping around, and is always waiting by the door when she arrives home from work.
. . . He enjoys getting blow dried after a bath and his favourite snack is chicken – which he’s treated to every other day.
Meet teacher Tonya Andrews in Joshua Texas, who was sad because her beloved 16-year-old cat had just died. She said she’d replace it, but almost immediately several of her students did it for her, giving her two kittens. The video showing it, as tw**ted by one of her students, is priceless (click the blue arrow).
This restores my faith in humanity—at least for a few hours.
[‘JAC: There was a formatting problem with the photos in this post (Cunk broke the site), so I’ve eliminated them, and things are back to normal.]
by Matthew Cobb
“I’ve always wanted to make people laugh,” she says. “It’s been my only ambition, ever since my dad introduced me to the genius of the great comedians: Tony Hancock, Woody Allen, people like that. While other kids were into New Kids on the Block, I was into Harold Lloyd and Stan Laurel. I’m still like that. I don’t have any hobbies.”
Cunk argues with Paul Taylor, head of collections at the Shakespeare Birthplace Trust, when he fails to provide her with white gloves for examining a First Folio. “Simon Schama gets to wear gloves,” moans Cunk. “But he doesn’t get to wear them here,” snaps Taylor.
There had been doubts that Cunk could sustain the gag for 30 minutes, but the show works, not least because it satirises the structure of a hosted BBC history documentary. “I have to go on a journey,” says Morgan. “Everybody doing this kind of programme does. It’s the law.” Morgan revels in the role. “It’s like wearing a suit of armour. If you’re Cunk, nothing can harm you. I can say anything and it’s fun. I have absolutely no social skills. I love creating awkward moments.” For instance, Cunk argues with Paul Taylor, head of collections at the Shakespeare Birthplace Trust, when he fails to provide her with white gloves for examining a First Folio. “Simon Schama gets to wear gloves,” moans Cunk. “But he doesn’t get to wear them here,” snaps Taylor.
Jerry’s venturing downtown this afternoon, and spotted this and asked me to post it.
My first thought was “There’s a play about Neil deGrasse Tyson?” But of course, it isn’t a play but a talk, although Chicago Theater is particularly coy about saying what he will be talking about.
It is heartening to see that talks by scientists can and do fill theaters. I am sure it will be highly enjoyable, Tyson has a remarkable gift for communicating his love for science.
![[ Color corrected by ArgyllCMS ]](https://whyevolutionistrue.com/wp-content/uploads/2016/05/mercury-transit.jpg?w=500)
