Cat

Here's a picture of Magic that I took recently:

Scarab Ring

Clarissa finally inspired me to take pictures of this ring, which I bought on Etsy maybe a year ago, and which is currently my favorite ring.

Here's a shot of my whole hand, so you can see about how big it is:

My hand

Here's a close-up, for detail:

Close-up view of scarab ring, index finger

Three-quarter view, with a clenched fist:

My index finger, balled into a fist. Scarab ring takes up entire length of first finger joint

Side view, so you can see 1) how flat it is, and how thin and light the metal is; and 2) the intricate designs worked into the band:

Where'd the beetle go?!

All Science Is Microbiology

As with any major news story, there has been a wave of editorial cartoons referencing the discovery of the Higgs boson. But I noticed something funny about the way some of these cartoonists have chosen to depict this event: the kinds of lab settings that they draw, from the equipment being used to depictions of (what is apparently supposed to be) the particle itself, suggest to me that the field of science in which this discovery occurred is not theoretical physics but microbiology.

Here is the cartoon (from my own local paper, the Kansas City Star) that made this obvious to me:

I don't know where that speech bubble is supposed to be coming from, but the things inside the circle (which looks a lot like the view through a microscope to me) are obviously cells of some kind. Except for the one on the right, which seems to be a grossly outsized mitochrondrion ...

Once I saw that, I remembered this earlier cartoon, where the visual non sequitur had gone right by me the first time, but after seeing the above cartoon, with the amoeba-looking thing labeled "God particle," it finally clicked for me.

I hope he's using the highest possible magnification on that thing ...

The microscope. The guy in this cartoon is looking through a light microscope. Light microscopes use visible light passed through a series of glass lenses to magnify whatever's on the slide; the greatest degree of magnification possible with this technology is an image 1,000 times the actual size of the object.


According to this webpage, the smallest thing you can see with just your eyes is 0.1 mm (100 micrometers, or 100,000 nanometers) long; that would mean, I think, that the smallest thing you could see at 100x magnification would be 0.001 mm (one micrometer, 1,000 nanometers) long. That same webpage lists the size of the smallest thing visible by light microscopy as 500 nanometers; another website gives the theoretical limit as 200 nanometers, which is approximately equal to the wavelength of visible light.


The webpage I cited first in the above paragraph, the "Cell Size and Scale" page, further states that the most powerful electron microscopes (microscopes that don't rely on visible light, but which use a beam of electrons to illuminate whatever they're pointed at) can resolve individual molecules, even individual atoms.


Here is a page on CERN's website that does a decent job of conveying just how small the particles they're trying to learn about are:

The infinitesimal scale of particle physics is mind-blowing, and rather abstract to imagine. If we enlarge an atom to the size of the Earth, then the protons and neutrons that make up the nucleus of the atom would each measure the length of an Olympic stadium. Smaller still are the quarks. If we consider our hypothetical atom blown up to the size of the Earth, then a quark would be smaller than a tennis ball. 

However, this does not give us a very good idea of the size of the atom itself. So staying with the same analogy, but scaling things in the opposite direction, if an atom was the size of the Earth, then an amoeba would be as big as our solar system. Going even further, the distance from the centre of Geneva to CERN (about 10 km) would stretch across the entire Milky Way galaxy.  

So if, as mentioned above, a single atom represents the smallest thing that can be seen by any microscope, these subatomic particles are smaller than that by many orders of magnitude. So the possibility of seeing even one of the larger subatomic particles through a light microscope makes the idea of me taking off my glasses, peering into a cup of coffee and watching individual molecules of sugar dissolve sound plausible by comparison.

More examples of cartoons showing people looking through light microscopes at the "God particle:

Whatever you do, don't blink!

 Here's one showing the "God particle" in what appears to be a petri dish:

This one is from England, so at least it's not just Americans who don't know how big the Higgs is!

... and, finally, here's one showing it in a test tube:

This one is visible to the naked eye!

(People might associate the test tube more with chemistry than with microbiology, but you can indeed grow cultures in a test tube. Bacteria cultured in a test tube are going to be suspended in a liquid growth medium, rather than spread across a solid one, but they can live there just as well.)


Anyway, I got a huge kick out of these cartoons, seeing as how they unconsciously nudge you toward the conclusion I named in my post title: All Science Is Microbiology. Even when it's theoretical physics. 


I have no idea if anyone besides me finds this funny; of anyone who reads, or might read, here I'd be most confident of thevenerablecorvex sharing my appreciation of it. Hopefully if I name her, she will see this post and laugh, too.

Occupational Hazards

I'm working on a fairly technical post about MMS, and this verse has been running through my head for some time now:


Johnny was a chemist,
He isn't anymore
'Cause what he thought was H₂O
Was H₂SO₄ 

Post #300

Numbers:


Blog founded - 9/4/2007


100th post - 1/1/2009
Interval between blog founding and 100th post: approx. 1 year, 5 months


200th post - 9/20/2010
Interval between 100th post and 200th post: approx. 1 year, 9 2/3 months


300th post - 6/30/2012
Interval between 200th post and 300th post: approx. 1 year, 9 months


Amazing. I was sure I was getting slower, was taking longer to write fewer posts. Looks like that's not really the case, though. 

New Medicaid Regulations Are Open to Public Comment

A little over a month ago, the Centers for Medicare and Medicaid Services proposed some new rules for home- and community-based services for people with disabilities, trying to ensure that states do everything they can to make sure that disabled people covered by Medicaid can actually get the services they need in their own homes, or in supported residential settings where they have the same amount of freedom and control over their own lives that they would if they were living on their own.


That's the spirit of the law, anyway. Lots of advocacy groups made up of people whom this law is supposed to benefit have written recommendations for wording that makes sure the letter of the law honors the spirit --- that health-care providers receiving Medicaid funding to give people supportive housing don't just take the money and throw the intended beneficiaries into a group home that reproduces all the restrictions, power dynamics, and other bad things about institutions in a somewhat different setting.


The rule change is open to public comment until Monday; I'd like to add my voice to a chorus of voices emphasizing just how important autonomy and freedom from restriction are. If you have anything to say about it, especially if you've got any concrete ideas or relevant personal experiences, go here, click the big blue "Comment Now!" button, and let loose.


The Autistic Self-Advocacy Network and the Administration on Intellectual and Developmental Disabilities have both written about this proposed rule change; AIDD's page  is an easy-to-read summary of what the rules entail, while ASAN's page is more of a critique.


Here is the proposed definition of "home and community-based setting":

(i) The setting is integrated in, and facilitates the individual's full access to, the greater community, including opportunities to seek employment and work in competitive integrated settings, engage in community life, control personal resources, and receive services in the community, in the same manner as individuals without disabilities. 

(ii) The setting is selected by the individual from among all available alternatives and is identified in the person-centered service plan. 

(iii) An individual's essential personal rights of privacy, dignity and respect, and freedom from coercion and restraint are protected. 

(iv) Individual initiative, autonomy, and independence in making life choices, including but not limited to, daily activities, physical environment, and with whom to interact are optimized and not regimented. 

(v) Individual choice regarding services and supports, and who provides them, is facilitated. 

(vi) In a provider-owned or controlled residential setting, the following additional conditions must be met. Any modification of the conditions, for example, to address the safety needs of an individual with dementia, must be supported by a specific assessed need and documented in the person-centered service plan: 

  (A) The unit or room is a specific physical place that can be owned, rented or occupied under another legally enforceable agreement by the individual receiving services, and the individual has, at a minimum, the same responsibilities and protections from eviction that tenants have under the landlord tenant law of the State, county, city or other designated entity; 

(B) Each individual has privacy in their sleeping or living unit:         (1) Units have lockable entrance doors, with appropriate staff having keys to doors;         (2) Individuals share units only at the individual's choice; and         (3) Individuals have the freedom to furnish and decorate their sleeping or living units. 

(C) Individuals have the freedom and support to control their own schedules and activities, and have access to food at any time; 

(D) Individuals are able to have visitors of their choosing at any time; and  

(E) The setting is physically accessible to the individual.

They also spell out what a "home and community-based setting is not:

Home and community-based settings do not include the following: 

(i) A nursing facility; 

(ii) An institution for mental diseases; 

(iii) An intermediate care facility for [people with intellectual disabilities] 

(iv) A hospital providing long-term care services; or 

(v) Any other locations that have qualities of an institutional setting, as determined by the Secretary. The Secretary will apply a rebuttable presumption that a setting is not a home and community-based setting, and engage in heightened scrutiny, for any setting that is located in a building that is also a publicly or privately operated facility that provides inpatient or institutional treatment, or in a building on the grounds of, or immediately adjacent to, a public institution, or disability-specific housing complex.

And here is the definition of "person-centered service plan": 

The person-centered service plan must reflect the services and supports that are important for the individual to meet the needs identified through an assessment of functional need, as well as what is important to the individual with regard to preferences for the delivery of such services and supports. Commensurate with the level of need of the individual, and the scope of services and supports available under the State plan HCBS benefit, the plan must: 

(1) Reflect that the setting in which the individual resides is chosen by the individual. 

(2) Reflect the individual's strengths and preferences. 

(3) Reflect clinical and support needs as identified through an assessment of functional need. 

(4) Include individually identified goals and desired outcomes. 

(5) Reflect the services and supports (paid and unpaid) that will assist the individual to achieve identified goals, and the providers of those services and supports, including natural supports. Natural supports cannot supplant needed paid services unless the natural supports are unpaid supports that are provided voluntarily to the individual in lieu of State plan HCBS. 

(6) Reflect risk factors and measures in place to minimize them, including Individualized backup plans. 

(7) Be understandable to the individual receiving services and supports, and the individuals important in supporting him or her. 

(8) Identify the individual and/or entity responsible for monitoring the plan. 

(9) Be finalized and agreed to in writing by the individual and signed by all individuals and providers responsible for its implementation. 

(10) Be distributed to the individual and other people involved in the plan. 

(11) Include those services, the purchase or control of which the individual elects to self-direct, meeting the requirements of [earlier section] of this subpart. 

(12) Prevent the provision of unnecessary or inappropriate care. 

(13) Other requirements as determined by the Secretary. 

... and rules for how the service plan should be drawn up:

Based on the independent assessment required in [earlier section] of this subpart, the State must develop (or approve, if the plan is developed by others) a written service plan jointly with the individual (including, for purposes of this paragraph, the individual and the individual's authorized representative if applicable). The person-centered planning process is driven by the individual. The process: 

(1) Includes people chosen by the individual. 

(2) Provides necessary information and support to ensure that the individual directs the process to the maximum extent possible, and is enabled to make informed choices and decisions. 

(3) Is timely and occurs at times and locations of convenience to the individual. 

(4) Reflects cultural considerations of the individual. 

(5) Includes strategies for solving conflict or disagreement within the process, including clear conflict-of-interest guidelines for all planning procedures. 

(6) Offers choices to the individual regarding the services and supports they receive and from whom. 

(7) Includes a method for the individual to request updates to the plan.

(8) Records the alternative home and community-based settings that were considered by the individual.

(That has got to be the greatest number of time I have had to type the word "individual" on any given day.)


I think this all sounds fairly complete, and airtight, but then I have zero experience actually living in this kind of environment.  


What do you, my readers, think? Do any of you have anything you would add, or change, to the above specifications? Without your input, I'm pretty much going to be echoing ASAN's recommendations in my comment on regulations.gov, but I'll hold off on commenting until, say, tomorrow night or Monday morning to see if I get any additional recommendations from comments here.  

Two Quick Links about Why the Fight over Evolution Matters

So, apparently Kevin Drum, a political commentator I don't read but who is apparently somewhat well-known, has written an article for Mother Jones declaring the fight over how whether biology is taught in public schools an irrelevant sideshow. 


I was nonplussed by this. Obviously, it's not the most important issue in the world --- it doesn't pose an existential threat the way climate change, peak oil/peak everything, overpopulation and hunger do, and it doesn't have the dire social consequences (or moral urgency) of, say, restricting access to contraception, the mass incarceration of people of color and poor people, increasing economic inequality or the deliberate demolition of the welfare state --- but I still felt like it had some importance that went beyond mere cultural border-policing*.


Amanda Marcotte at Pandagon and PZ Myers at Pharyngula both responded to Drum's article, and each of them made points that rang true for me, and helped explain why his statement bothered me.


Amanda:

I have to admit, I'm boggled at Kevin Drum's reaction to the news that nearly half of Americans are young Earth creationists ... . He completely misreads the situation and frankly does so in a way that I personally felt thrown under the bus.

... 

Kevin takes it as a given that fights over what's taught in high school are strictly about symbolism and have no real importance. I suspect that's a much easier view to take if you're the beneficiary of a good public school in a blue area or lucky enough to have gone through or been able to put your own kids through private school. For someone who went to a rural high school in Texas, the notion that high school doesn't matter strikes me as ridiculous in the extreme. 

The reason conservatives target high schools (and junior high schools and elementary schools) isn't because they're playing for peanuts. On the contrary, conservatives understand something liberals don't, which is that if you get people while they're young, you usually have them for life. This is also, incidentally, why conservatives pay more attention to pop culture than liberals. Liberals are great people --- I'm one of them! --- but  we have a tendency towards preening individualism and therefore discount the importance of things like what's in the classroom and what's on TV because we personally feel we're iconoclasts who aren't affected by it. Which can, in this case, cause us to neglect to remember that in fact this is the air that most people breathe, and the quality of that air matters. 

I also had strong feelings of no you're wrong when I read the paragraph in Drum's article where he dismisses "a 10th grade understanding of evolution" as something so piddling as to be dispensed with entirely, so much does it pale in comparison to the understanding of evolution one gets (presumably) in college, or in books on evolutionary biology. PZ, along with a slew of other biology professors in his comments and at Mother Jones, takes him to task for this; they write that, no, actually, they have noticed a change in how readily their students grasp what they have to teach. Almost as if high school curricula were geared toward preparing the students for college ... 


Anyway, what felt unfair to me was his assumption that, if people needed the knowledge, they could always pick it up elsewhere. This made me angry, because for many people there is no "elsewhere," or at least not one that is immediately accessible without guidance. 


(Who has tried to teach themselves a completely novel subject by checking out books on it from the library? Isn't it hard to figure out which books will be the ones you need? Technical books are often overly specific and assume you've already got a grounding in the subject, and are interested in exploring a particular question within it, and books for laypeople might not be thorough enough, and also might not be trustworthy). 


As for college, well, not everyone goes there, most of the people who go there will never encounter evolution in the classroom --- I didn't, and I majored in a biological science! --- and, again, college professors have enough to do without having to burn up lecture time with remedial material and correcting misinformation. Plus, not all colleges are created equal; some 


To top it off, what you know before college helps determine where you go, whether you go at all, and what you study! College is expensive, and for many prospective students (I know I felt this way when I was applying to colleges) the size of the scholarship you can get makes the decision for you. Scholarships for merit, as opposed to need (and there will always be more people who can't really afford college than there are people officially deemed too poor to afford college on their own), depend on how one performs on standardized tests. And what does standardized test performance depend on? What you learned in high school.


There's more: as Amanda also points out, what you're exposed to in high school shapes your interests and aspirations:

[M]y high school biology course didn't teach evolution. Without evolution, biology actually doesn't make sense, and instead it's just an anatomy class. ... I had no idea how fascinating biology actually was until I was an adult, and long past any chance of starting on that as a career path. Not that I think I would, but you can easily see someone like me making that choice as a young woman, but not really being able to because I was never offered that option in a realistic sense to begin with. 

(As someone who did study biology, and who loves Amanda's writing about science- and skepticism-related topics as much as I do her feminist writing, I can see it. Her interest in the subject is obvious, as is her commitment to find out what's true and how we know it's true. While she won't --- can't --- go into the kind of technical details I sometimes do here, her grasp of general, foundational principles is firm enough that I can easily forget she does not possess a biology degree herself.)


To shift to another aspect of why Drum's assessment is so horribly, horribly wrong, I quote PZ:

[T]his is going to be the century of dependence on the sciences. Climate change is going to hit us all; environmental crises are going to rise up all over the place; we're going to face shortages of energy and fresh water; emerging diseases will be a major concern; new biomedical technologies will cause cultural shocks; the whole world is going to change. Most people, I agree, will not be doing the research that leads to changes, and most of these problems will require political and social changes to correct, but how are you going to convince people to, for instance, change their fuel consumption habits when they're in complete denial of basic facts? How can you expect people to appreciate the importance of ecology and global interactions when you tell them that evolution doesn't matter? How will you get them to make rational decisions to control pandemics when they can't comprehend probability, epidemiology, and viral/bacterial evolution on even the most basic level? 

Most importantly, though, this utilitarian attitude that all that matters is what people can directly use in their day-to-day life is a denial of the Enlightenment and principles on which our country was founded. It's a rejection of the liberal idea that human beings should be well-rounded and informed individuals --- the informed citizenry that should be the foundation of a democracy. We can't expect everyone to be biologists or poets or political scientists, but we should expect that one outcome of a public education is an appreciation of the breadth of human endeavor, and at least a smattering of the fundamentals of a wide range of subjects, sufficient that, to make it practical again, students can make informed career decisions and understand a basic argument from evidence from an expert. We lack that now. And to wave away a simple but essential starting fact about our existence as unimportant is deeply offensive.     

I would add to his first paragraph that you don't have to wait for some futuristic nightmare scenario for these things to affect people's lives. Disease-causing bacteria are already becoming resistant to a whole lot of the antibiotics we use to fight them; lots and lots of species have disappeared or are disappearing; sensitive ecosystems are already being stressed, some to the breaking point by human activity, and humans are already failing to see why they should care***.

The picture he paints in that first paragraph has already come to pass, in the way that the proverbial camel is already in the tent, he just needs to take a few steps forward before it becomes obvious to everyone.

I would also add something else that I think denying evolution does: it makes it easier to think of humans as separate from, and above, the natural world and all those other animals. It allows us to think that what we do to it, to them, will never get back to us. 

(You don't have to deny evolution to get to that mindset, though: I see it arising just as readily from the erroneous view of evolution as a teleological process of development from simple to complex organisms, with humans sitting triumphantly at the apex. I've posted before about my annoyance with this picture of evolution.)

*This is what Andrew Sullivan, another famous political commentator whom I know to be obtuse, thanks to driftglass, an obscure political blogger who is quite acute**, has called belief in creationism a "cultural signifier" that describes the group membership of the believer rather than what that person actually believes about reality. That whole line of reasoning makes me queasy, but even if he is right that no one actually believes the Earth is six thousand years old and every animal species living on it was molded from clay and animated with the breath of a god, if that is what they decide shall be taught to children as fact, in place of the full history of life on Earth (as much of it as we know, anyway) and an explanation of how life on Earth has changed as Earth itself has changed, then those children grow up with a much poorer understanding of the world around them. An idea can have consequences in the real world whether people truly believe it or not; all they need to is act as if they believe it. Also, Andrew Sullivan is dumb.

**Hee. I made a geometry pun.

***This is not, at all, meant to be an exhaustive list, or even a primer on any of those subjects. I just put a recent news/research story in every link to make the point that, yes, this stuff is happening, and it's not just one or two isolated incidents. 

Hilarious.

Don't know how I got there, but I found my way onto this Tumblr and there beheld something truly awesome:

This Avengers cover mock-up.


It originally came from Comics Alliance, concocted by blogger Chris Sims and artist Kelly Callen.


In case you can't see it, the image shows seven Avengers --- Captain America, Thor, Nick Fury, the Incredible Hulk, Hawkeye, Iron Man, and a black-gloved redhead I think is Black Widow (hard to tell since we're just seeing the top of her head, from behind) --- all holding the worst possible gift someone could ever give them. Cap's got a pair of pink socks covered with swastikas; Fury (who has one eye) has a 3-D movie and a pair of 3-D glasses, which he is holding up to his single eye; the Hulk has a chemistry set; Iron Man has a book on running a successful business by his old enemy and competitor Obadiah Stane; Hawkeye (an archer) has a box of bullets; the Russian Black Widow has a DVD of "Rocky IV"; and Thor has a copy of Richard Dawkins's book The God Delusion*.


Captain America's speech bubbles say, "ONE OF US is responsible for these horrible gifts! And nobody's leaving until I FIND OUT WHO!"


I love the look on Thor's face.


*This is especially funny because, not only is the book an argument that gods in general don't exist, but Thor in particular is one of the author's favorite examples of gods no one believes in anymore. (See this video for a collection of clips where he refers to Thor in this way.)

Calling All Amateur Botanists

I found this wildflower growing on the bank of the creek running through my backyard: 

It's got small, star-shaped white flowers with a cluster of short yellow stalks in the center; almost like a narcissus, only with very different stem and leaf structure. (See, it's got one stem, with all the leaves coming off of it, and two flowers at the top).

Its leaves are kind of weird-looking, too --- they're much larger than the flowers, longer than they are wide, with edges that I'm not sure whether to call serrated, because the "points" are so rounded. 

Here's a close-up of the flower: this picture isn't as clear as the others, because I had to move closer to the plant to take it, and the flower is growing out of a fairly steep creek bank. Thus I was in an unstable position when I took it, and wasn't really able to steady the camera. 


(I notice, though, that while the flower in that picture might be out of focus, the thorns on the stem show up beautifully. Auto-focus can be a very strange thing.)


So, does anyone know what this is?

Blog Changes in Blog Owner's Lengthy Absence

So I leave the blog unattended for a couple months, and when I come back to it I find I can't even get on it anymore! I have to download a whole new browser before I can use it.


Now that I've done that, it seems to work well enough; the post editor screen is a little different, but not by much. And on the dashboard, where you can see a list of all your posts, they have a little counter next to each post showing how many pageviews it has! I really like that feature; now I can see which topics people are most interested in seeing me write about. (Of course, the high view count for some posts may simply reflect the fact that some of my posts are more widely syndicated than others ... but still, that's more information than I had before.)

So, Feministe has a pretty interesting post (responding to this article in the New York Times) about family dinner conversations, and how they shape a person's rhetorical style.


Here's how Jill describes her family's dinnertime ritual:

Even when I go home, still, a sit-down dinner and a long discussion is non-negotiable. The TV gets turned off. We don't answer the phone. There are no cell phones allowed at the table. There isn't a structured conversation --- we just talk. And since I come from a family of political junkies, the conversation inevitably turns to politics; since I also come from a family of people who like to push boundaries and challenge each other, the conversation inevitably turns into an argument. No one yells --- we aren't a yelling family --- but voices get raised and sarcasm gets thrown around and even though we're all lefty liberals we get deep into it.

And then we clean up and we watch some CNN and we all move on with our lives. It never occurred to me that dinner-time arguments over, say, farming subsidies or the proper legal treatment of child molesters could create lasting wounds or ongoing anger. Which is maybe why it's taken me years to figure out that, in the blogosphere, you can't come at someone hard in a comment section and expect that they understand you're challenging them because you respect them and find their views interesting, and that they will respond to your challenges and heated critiques with the same, and you'll both walk away still liking each other and not thinking about it much beyond, "Well that was an interesting discussion." Most people just think you're a flame-throwing asshole. I blame my parents.

One person, in comments, mentioned how they felt like the absence of any dinnertime conversation (or, really, any conversation at all beyond the most perfunctory) while they were growing up deprived them of the chance to develop any kind of rhetorical or conversational skills.


My own experiences are like Jill's in a lot of ways: my family, too, sits down for a home-cooked meal and unstructured conversation every night, and does not really consider any subject to be taboo. Certainly not politics, which is discussed frequently. But we don't argue like Jill's family does; we're more conflict-averse, we're not very emotionally expressive (indeed, we tend to be uncomfortable with strong emotions), and, for me at least, argument is not a style of discussion that I am very good at. My mind works slowly, taking time to unfold and absorb every aspect and ramification of whatever I have just been told (besides the fact that I don't think in words and need to "translate" something into the pictorial/abstract colors-and-shapes milieu of my thoughts, and auditory-processing issues mean it takes me longer to decode spoken language than written language, so in conversation I have a particularly long lag time between hearing and understanding), and any thoughts I might have in response to whatever I've just been told also take time to form themselves. I am thus in the position of not yet knowing what I think when it is time for me to speak. I may not even know what you've just said by the time you're done saying it and waiting for me to respond. 


To accommodate this, I tend to treat discussion less as a contest between ideas than as a process of discovering what each person's ideas are. 


Because I have often found that people's ideas are interconnected in unpredictable ways (including my own), just stating what one thinks about something isn't always enough. Sometimes if you say one thing, the person you're talking to proceeds as if you had said that thing, and a whole bunch of other things you haven't said and aren't sure you even understand. I have also made these assumptions about other people, thinking that I had found a word or phrase to express a bundle of concepts and then finding that, in the other person's lexicon, that word didn't come with all the connotations it carried in my head. So I try and identify the premises I am starting from, and the premises that I and my interlocutor hold in common. From there, I will try to explain how I get to whatever proposition we're debating from those premises, and will also listen to my friend (I can pretty much only do this with friends) draw me a similar map of his or her reasoning.


What Jill's post got me to realize is that this style of conversation, which it has taken me years to develop, might not solely be an accommodation of my cognitive and communicative quirks. It might also be something I have carried with me from childhood, modeled somewhat on the kind of dinnertime conversations my family has.


(Obviously, it couldn't be an exact copy of my family's conversational style, or I wouldn't have had to develop it, but I do feel that what I have jerry-rigged together for myself probably has roots in how my family communicates. It's an adapted version, but I am starting to see some shared features).


Anyway, if you were going to describe my family in terms of what kind of people they are (like Jill describes her family as political junkies), you'd probably call us science nerds. As much as we talk about politics, it's not the thing we talk about most. Most of our dinnertime conversation is of a technical nature, drawing on whatever field each of us is trained in (electromagnetics, chemistry, biology, medicine). Because we are not all trained in the same things, we often have to include a lot of background information leading up to whatever it is we want to discuss. (When my siblings and I were children, this was almost always our dad explaining something about electromagnetics, but now that I have my own body of knowledge and experience, I will sometimes find myself holding forth about chemistry or biochemistry). So my family tends to explain rather than argue, because many of the things we talk about require explanation before they can be discussed in any depth. 


I think now that habit, as much as my needing to slow conversations down and check repeatedly to make sure everyone is on the same page, has predisposed me to prefer a collaborative, expository conversational style to an adversarial, argumentative one, and to feel myself disadvantaged when I do find myself in the middle of an actual debate.     

Magical Thinking about Food

This appeared in an ad insert for Hy-Vee (a grocery-store chain, if you didn't know) bundled in with the Kansas City Star on Wednesday; the text says "Kiwi fruit is a 'good sweeper' that assists to sweep off the unwanted substances and toxins out of your body. Kiwi also has a perfect NuVal score."

What I thought was weird about the ad copy was this idea that some foods have this incredible power to remove "toxins" from your body. It's not that I'd never seen that before, but previously I'd only ever seen it in contexts much fringier than an advertisement for a supermarket chain.

I have other thoughts about this odd and superstitious notion --- for one, I suspect that the fear it speaks to, the fear of things getting into one's body without one's knowledge and doing horrible things once they're in there, is very old --- but they're not in order and I haven't done any research yet, so I will wait and deal with them in another post. For now, I'm just going to point out this apparent crossover of an idea common in New Age circles into the mainstream.

Everything Old Is New Again

I recently inherited a copy of a book I've wanted to read for a long time: Richard Hofstadter's Anti-Intellectualism in American Life.

(I've wanted to read this book for a long time because when I was a teenager two things happened: I came to the understanding that what I really wanted to do with my life was be a scientist, preferably in some flavor of biology; and there was a periodic eruption of anti-evolution crusading here in Kansas. That those two things happened so close together made me especially eager to find out why people were so hostile to evolution, and later I figured the answer must lie somewhere in American history, as this seems to be a particularly American bit of unreasonableness.)

Anyway, I got my hands on one of my uncles' old copy of this book (it's from 1966! The physical book is that old! Isn't that neat?), and am now reading it.

It's hugely interesting, and I might review it here if I can organize my thoughts about it sufficiently to do so, but right now I want to point out one particular thing that astonished me.

What astonished me was that a strain of magical thinking that I had thought mostly emerged in recent decades, and whose roots must lie in the 1960s counterculture-derived New Age movement, is really a whole lot older:

As late nineteenth-century America became more secular, traditional religion became infused with, and in the end to some degree displaced by, a curious cult of religious practicality. If we accept the evidence of a long history of best-selling handbooks, from Russell H. Conwell's "Acres of Diamonds" to the works of Norman Vincent Peale, this cult has had millions of devotees. It has become, by all internal evidence and everything we know about its readership, one of the leading faiths of the American middle class. It is, as I hope to show, a rather drastically altered descendant of the older self-help literature, but it affords, in any case, striking evidence of the broad diffusion in American life of the practical motif. Modern inspirational literature takes its stand firmly with the world: what it has to offer is practical. "Christianity," writes Norman Vincent Peale, "is entirely practical. It is astounding how defeated persons can be changed into victorious individuals when they actually utilize their religious faith as a workable instrument."
...
Modern inspirational literature builds upon the old self-help tradition and bears a general resemblance to it, but it also has major differences. In the old self-help system, faith led to character and character to a successful manipulation of the world; in the new system, faith leads directly to a capacity for self-manipulation, which is believed to be the key to health, wealth, popularity, or peace of mind. On the surface, this may seem to indicate a turning away from the secular goals of the older self-help books, but it actually represents a turning away from their grasp of reality, for it embodies a blurring of the distinction between the realms of the world and the spirit. In the old literature these realms interacted; in the new they become vaguely fused. ...

It is what Raymond Fosdick calls "power for daily living" that the success writers purport to give. In the nineteenth century the primary promise of success writers was that religion would bring wealth. Since the early 1930's there has been a growing emphasis on the promise of mental or physical health; inspirational writing has been infused with safe borrowings from psychiatry and has taken on a faint coloration from the existential anxieties of the past twenty years. Although success literature has given way to a literature of inspiration, its goals remain largely everyday practical goals. For more than a generation, the metaphorical language of this writing has been infiltrated and coarsened by terms taken from business, technology, and advertising; one often gets the sense that the spiritual life can be promoted by good copy and achieved like technological progress by systematic progressive means. Louis Schneider and Sanford M. Dornbusch, in their illuminating study of the themes of inspirational books, have spoken of this as "spiritual technology." One success writer tells us that "God is a twenty-four-hour station. All you need to do is plug in." Another that "religious practice is an exact science that ... follows spiritual laws as truly as radio follows its laws." ... "Conduct the affairs of your soul in a businesslike way," exhorts Emmet Fox. Prayer is conceived as a usable instrument. "A man," says Glenn Clark, "who learns and practices the laws of prayer correctly should be able to golf better, do business better, work better, love better, serve better." "Learn to pray scientifically," commands Norman Vincent Peale. "Employ tested and proven methods. Avoid slipshod praying."

... What the inspirational writers mean ... is that you can will your goals and mobilize God to help you release fabulous energies. Fabulous indeed they are: "There is enough power in you," says Norman Vincent Peale in an alarming passage, "to blow the city of New York to rubble. That, and nothing less, is what advanced physics tells us." Faith can release these forces, and then one can overcome any obstacle.

All of the stuff about instrumental faith --- faith that was supposed to make good things happen for you in this world, particularly to bring you riches --- rang some bells for me, as I'd read about something called the Prosperity Gospel that pretty much said the same thing, but was held to be a recent development coming out of the megachurches.

I was also somewhat reminded of The Secret (an appalling bit of woo popularized in a mega-best-selling book from 2006, where if you want something badly enough, "the universe" will bring it to you --- poor, innocent quantum mechanics is horribly abused in attempts to explain how this supposedly works) by the mentions of willing what you want into being, particularly in a long paragraph following the passage I quoted, where Hofstadter describes a nineteenth-century quasi-spiritual movement called the New Thought, which apparently held that "... one could have whatever one wishes by 'sending out a requisition to the great subconscious'." That nailed it down for me; except for what they call the mysterious, all-pervading cosmic sugar daddy, the Handbook of New Thought and The Secret might well be interchangeable*.

I also got a chuckle out of the throwaway reference to "advanced physics" in the last Norman Vincent Peale quote. I suppose that, back then, the physics that people misused to justify their magical thinking was either electromagnetics (those newfangled radio and TV waves!) or nuclear fission (I imagine this is where the bizarre comment about New York is coming from --- all that energy, lurking inside atoms! Never mind that only a few elements are fissile, and even then only under a very specific set of conditions; it's not like common household objects will explode if you look at them while thinking explodey thoughts), while today, of course, it's quantum mechanics.

*Apparently this is only news to me, as Wikipedia mentions the New Thought on its page for New Age philosophy, and their page for prosperity theology mentions both New Thought and the mid-20th-century writers that Hofstadter was talking about.

"I Don't Care If They Hit You; You're Not Supposed to Hit Back!"

(Photo by Allison Long, for the Kansas City Star)

A recent article in the Kansas City Star covered a group with a different sort of anti-bullying campaign: it's a boxing-based fitness class just for teenagers who've been bullied or whose friends have been bullied.

It's called Fight Club, and in general I think it's awesome. It sounds, in a lot of ways, like exactly what I needed in middle school.

There's only one thing that bothers me about the program: it's not an actual self-defense class. The article stresses that the kids taking the class are encouraged not to fight back against their abusers, and that the boxing serves more as an outlet for emotions than as practical training:

It's not a self-defense class. Holly Reynolds, the woman who started the program, can't call it that for legal reasons. It's not about fighting, either, though Reynolds gave it the same name as the 1999 Brad Pitt movie about underground fight clubs.

This Fight Club is about getting fit, feeling strong and fighting the good fight, she said.

These teens don't spar with each other. They spar with their feelings.

It's not that the things the classes do offer --- improved physical fitness, confidence, an emotional outlet, a roomful of other people who are having the same experiences as you, along with adult trainers and mentors who are clearly on your side --- aren't also hugely important; I just worry that explicitly discouraging these kids from fighting back if they're assaulted undermines what the program is supposed to do. It's supposed to give you confidence and enable you to stand up for yourself or your friends; how can you do that if you freeze up once the confrontation escalates?

We have a serious problem in mainstream American culture, in that we tend to put all the blame on victims of violence --- especially certain kinds of violence. If you were raped, you must've done something to draw attention to yourself, or gone somewhere you shouldn't have, or trusted someone you shouldn't have trusted. To use some philosophical terminology, the rapist may have been the immediate or proximate cause, but you were the ultimate cause of your own rape.

It's the same with bullying, whether of children in school or of adults in the workplace or in their communities. If one or more people decide to harass you, stalk you, follow you around in groups yelling things at you, try to scare you, subject you to unwanted, gross and insulting sexual advances, physically attack you or vandalize your property, it's bad, but you must've done something to make them choose you as their target.

And with school bullying, adults tend to tell children very stupid, unhelpful things when those children ask for help, like, "Just ignore them; they'll go away if you don't respond." (More victim-blaming: you're only being bullied because you let them get a rise out of you!) They also hold victims of bullying to a much higher moral standard than the bullies themselves: no matter how in-your-face, menacing or even violent they get, if you hit them back, you're just as bad as they are. They ignore bullying until it does turn into a physical fight, and when that happens, they act as if all combatants are equally at fault*.

So, against that kind of cultural backdrop, I don't think it's doing the kids any favors to try and convince them they don't want to hit the people who are abusing them. Of course they do. Telling them they don't, when they know perfectly well that they do, would (I think) just work to undermine any impression you've made of being the rare adult who understands what they're going through.

Don't get the wrong idea; I know teaching kids self-defense won't magically enable every one of them to win a fight with a bully (especially those who are bullied by a whole pack of people), and I know it's not fair to expect victims of bullying to solve the problem on their own. In my ideal school environment, teachers and bystanders would play a much more active role in defusing incidents of bullying; I just think physical self-defense is also a tool kids need to be given, without shaming or second-guessing them when they use it.

*That happens to grown women, too, when they try to defend themselves against rape or domestic abuse.

Signal Transduction in Autism

EXECUTIVE SUMMARY: A study published this past summer analyzed tissue extracts from 20 donated brains, half (10) of which came from autistic donors. Half (5) of those people had histories of regression --- that is, they started out developing normally, speaking and everything, but then they lost some of the skills they had gained.

The brain tissue extracts were analyzed using a technique I describe in the main body of this post, that tests for the presence of a certain enzyme (protein kinase A, here) by giving it an opportunity to react with a sort of dummy peptide that can't really do anything except sit there and let the enzyme (and only that enzyme) act on it, and then introducing antibodies that will "tag" the altered peptides with an enzyme that will change a solution's color under certain conditions. This allowed the researchers to measure the relative activity of the enzyme across subjects or across brain regions; a similar measure, but using antibodies to the enzyme itself, rather than to its product, was used to measure the amount of enzyme present in each extract.

Using this method, the researchers found differences in protein kinase A activity and expression only in the frontal lobes, and only between the autism-with-regression subgroup of the autism group and both the controls and the rest of the autism group.

Protein kinase A is involved in intracellular signaling; it's one of the signal-boosting enzymes that helps the cell react quickly to changes in its environment. It modifies other proteins, affecting their activity. Some of its targets are proteins involved in neurotransmission (signaling between brain and nerve cells) and long-term potentiation (reinforcing those connections between neurons that are frequently used). It's this latter process that the study authors think may be disrupted in regressive autism.
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SFARI News posted some time ago on a study published on August 31 in PLoS ONE, comparing the amount of a certain enzyme present in tissue extracts from different regions of the brain between deceased subjects with and without autism who had donated their brains to the National Institute of Child Heath and Development Brain and Tissue Bank for Developmental Disorders.

The enzyme in question is protein kinase A, which plays a hugely important role in the cell, helping mediate a process called signal transduction, through which the cell is able to react to its changing environment, or to signals from other cells. In signal transduction, a molecule from outside the cell (usually a hormone) attaches to a receptor outside the cell and causes the receptor to change shape, thus altering the part of the receptor that's inside the cell and triggering a chain reaction of changes in enzymatic activity within the cell.

Protein kinase A participates in one particular signaling pathway: the one involving a class of receptors called G proteins, which are actually clusters of several smaller proteins that split apart whenever something attaches to its extracellular binding site. The now-mobile subunits then go on to do other things in the cell, most importantly to activate* an enzyme responsible for turning adenosine monophosphate (AMP) into cyclic AMP, which works as a signaling molecule inside the cell.

(Here is a cartoon from Nature Publishing Group's Scitable website illustrating that splitting apart of the G protein after a signaling molecule binds to its associated receptor; I adapted the image somewhat to make it less busy)

(Cyclic AMP)

Cyclic AMP is part of a class of molecules called "second messengers," which are small molecules that can bind to, and either activate or inhibit, a wide range of enzymes. Also, the enzymes responsible for making these molecules are regulated by receptors on the surface of the cell, so that when a signaling molecule binds to the receptor, the enzyme gets switched on (in the case of adenylyl cyclase, which is what turns regular AMP into cAMP) and starts churning out second-messenger molecules, which then go on to tinker with their target enzymes. In this way --- by coupling receptor binding with synthesis of these second-messenger molecules --- the cell can amplify the signal it receives, allowing it to react more quickly to changes in its environment.(Cartoon showing signal transduction using cyclic AMP as a second messenger, taken from this community college's Anatomy & Physiology II webpage. You can see how a hormone binding to its receptor frees up the receptor-coupled G protein to exchange its GDP for GTP and then go off and --- depending on the hormone --- either activate or inhibit adenylyl cyclase, which either starts or stops churning out cAMP, which goes on to do lots of different things, like activating enzymes, telling the cell to secrete various things, opening ion channels, etc. The only thing I don't like about this cartoon is that it only shows one cAMP molecule as the output of all the running around happening in the cell membrane, when really cAMP is being continuously produced by every active adenylyl cyclase. So, what that looks like, relative to the amount of hormone coming to the cell from outside, is more like this other cartoon, down below) (See, look at the arrows coming out of that yellowish triangle. One arrow splits into five, then 25, then more than you can clearly see. This table from the Memorial University of Newfoundland's cell biology webpage lists the number of molecules affected by each step in a cAMP-dependent signaling pathway, from the one molecule changed when a single molecule of hormone binds to its receptor, to the 10,000 molecules changed by the time adenylyl cyclase starts producing cAMP).

Anyway, protein kinase A is one of the enzymes activated by cAMP binding to it, and it is also mostly a regulatory enzyme --- that is, it activates or deactivates other enzymes. Protein kinase A does that by transferring a phosphate group from ATP (a small molecule made up of a sugar, a nucleotide base and three phosphate groups) to certain amino acid residues on any of its target proteins.

What kinds of proteins does protein kinase A regulate? Well, that depends on what kind of cell all this is taking place in. Every cell in the body contains a complete human genome; the differences between cell types are differences in which genes are expressed --- i.e., which proteins are present. So each cell type is going to have a different mix of proteins whose activity needs to be coordinated.

Some of its targets are proteins expressed in almost every cell type: these include a histone, one of a large family of proteins whose function is to condense chromosomal DNA that is not actively being transcribed or replicated; transcription factors (most notably, from the CREB family); a metabolic enzyme involved in storing energy for later use; ion channels; and other kinases (enzymes that alter the activity of other proteins by transferring phosphate groups onto them from ATP).

Although protein kinase A performs specialized functions in just about every cell type, I'm only going to talk about what it does in the brain, since that is the cell type relevant to this post. There, in addition to the stuff mentioned above, protein kinase A 1) helps regulate the synthesis of a common precursor to a variety of neurotransmitters, 2) helps form synapses by guiding the specialized proteins that allow the membranous sacs that deliver neurotransmitters from one neuron to the next toward the tip of the developing axon, and 3) with another protein kinase, regulates the ion-channel activity of the NMDA receptor, which is involved in strengthening the more frequently-used conntections between neurons. There may be more, but this is what I've been able to find.

For all that background information, the experiment I'm going to describe is actually pretty simple: like I said above, the researchers took tissue samples from five different regions of donated brains from autistic and non-autistic subjects, homogenized them (basically, ran them through a blender) and tested each sample for protein kinase A activity. The test they used is called the ELISA (for Enzyme-Linked ImmunoSorbent Assay --- see why people would rather call it Eliza?), which is a plastic plate covered with small circular wells (0.7 cm across by 1 cm deep) with, in this case, short peptides containing either serine or threonine (the two amino acids to which protein kinase A can attach a phosphate group), anchored to the bottom. (ELISA is most often used to test for the presence of antibodies --- that's how HIV testing is done --- so for that, the thing stuck to the bottom of the well would be the antigen to which whatever antibody you're testing for responds). They added their brain tissue extracts one by one to each well, along with a small amount of ATP dissolved in water (for the protein kinase to "borrow" phosphate groups from), then waited an hour and a half before emptying out the wells (the substrates, which were permanently affixed to the bottoms of the wells, would stay, along with, presumably, any phosphate groups that had been attached to them during the previous 90 minutes) and introducing an antibody specifically designed to bond with the phosphorylated form of the substrate peptide. Next, they washed the wells out thoroughly (to weed out everything that was not chemically bonded to the fixed substrates) and added a second antibody, chosen for its ability to bind to the first antibody, and which was also attached to an enzyme known for producing dramatic color changes as a side effect of its interaction with certain organic molecules. (A solution containing the molecule in question was also added, so that the wells in which the greatest proportion of the well-bottom peptides had been phosphorylated, and thus had the whole antibody rigmarole sticking off of them, would have the deepest color. There is even a way to measure color --- a device that can measure the degree to which something absorbs light at a given wavelength --- so that you don't have to rely on just your eyes to tell you whether this well or that one is a darker shade of yellow).

They used a somewhat similar technique, called Western blotting, to compare the amount of active protein kinase A between groups for each brain region. They injected their tissue samples from each of the different brain regions into a polyacrylamide gel, and ran an electric current through the gel to get the proteins to move through it. Since the gel resists having things move through it, different size proteins will travel through it at different rates. After a while, most of the proteins will separate themselves into bands along the gel, by size. Once this happened, the researchers transferred the proteins to a nitrocellulose membrane, and added antibodies specific to the catalytic (active) subunit of protein kinase A. Just like with the ELISA, there was also a secondary antibody coupled to a color-producing enzyme.

One thing that's a bit unusual in this study is that the researchers divided their brains from autistic donors into two groups, based on the developmental history of the donors. They had a "regressive autism" group, whose members started out developing typically but then lost some of the skills they'd acquired: speech was the most common skill that was lost, but some of the donors in this category also lost social skills and interest in social interaction. There was also a "non-regressive autism" group, whose members were delayed in language and social development from birth.

Subtyping autism is an increasingly popular thing for researchers to do, since "autism" is such a broad, flexible category that encompasses people with a very wide range of developmental and medical histories. It makes sense that researchers would want to subdivide this large, diverse group further to make sure they're comparing apples to apples when they look at different studies of "the autistic brain" or "the autistic immune system" or whatever.

The thing that's strange about subtyping in this study is that the number of brains being looked at is already so small. Each big group (autism, both regressive and not, and controls) had samples from ten people in it, and the researchers couldn't always get a sample from every point of interest on every brain, so sometimes the number of samples in a given category (brain region + donor neurotype) was less than ten; the smallest n for any category was 7. But that means that, with subtyping, the biggest n possible for either autism subgroup is 5, which looks more like a case study than a comparison across populations. But then, histological studies of donated brains always have to deal with smaller sample sizes, since there isn't exactly a superabundance of donated brains, and I guess if you have big differences among your subjects, you might as well sort them into subcategories, even if your subcategories are tiny.

At some point in this post I should probably mention the results of this study I've gone to such lengths to describe. The authors only found differences in protein kinase A activity in one region --- the frontal cortex --- and this difference was largest between one subgroup of the autistic group --- the autism-with-regression subgroup --- and both the non-regressive autism subgroup and the control group. The regressive autism subgroup had maybe a little less than half the PKA activity of the controls and the non-regressive autism subgroup (those two groups did not differ). Taken as a whole, the autism group had about 35% less PKA activity in the frontal-lobe samples than the control group.

The results were similar for the Western blot; the only region that showed any differences in PKA expression was the frontal lobe, and again, it was only the regressive autism subgroup that differed. Tissue extracts from that group had siginificantly less PKA in them than extracts from either the control group or the non-regressive autism subgroup; the unified autism group did not differ from the control group.

The researchers also looked for a correlation between their measure of PKA activity and various possible confounding factors, like how long each donor had been dead, the age of the donors when they died, whether they had any history of seizures, and what medications they were taking; they didn't find any relationship between any of these things and either outcome variable. Their measure of PKA expression also involved measuring how much of another protein was present in each tissue extract, both because that protein is about the same size as PKA, and thus cannot be separated from it using electrophoresis, and also to have a protein whose expression is not expected to vary across groups with which to compare relative amounts of the protein that is expected to vary.

Here is a picture of the Western blot showing both PKA (top row) and the other protein, a structural protein called beta-actin (bottom row), from all tissue samples:(Figure 2A, in Ji et al., 2011 - samples from autistic donors are on the left, and subdivided into non-regressive and regressive subtypes. Controls are on the right. You can see that, in the bottom row, the blobs are all approximately the same size, indicating expression of beta-actin is more or less the same across groups. You can also see that the blobs in the top row are a lot thinner - one space has nothing at all in it - in the regressive autism group than they are in either the non-regressive autism group or the control group. It looks like PKA expression is a bit more variable within the control group than beta-actin is, though.)

So, for a couple of reasons --- the extreme smallness of sample size, and also the degree of variation in PKA expression within the control group --- I am a bit skeptical as to whether this finding will hold up. It definitely needs to be tested a few more times, with bigger donor pools.

Leaving that aside, though --- what are the implications of this finding, should it be substantiated? The study authors refer to earlier literature that describes a role for cAMP signaling pathways in both brain development (obviously germane to a study about developmental disability) and long-term memory formation and learning (relevant to the question of how people can lose skills they once had). But it's not clear yet exactly what that role is; if you search for "protein kinase a brain" on BioNOT (a database of negative experimental results), you find an article claiming to find no difference in PKA activity between tissue samples taken from donors with Alzheimer's disease and those taken from healthy donors. So that complicates things a bit, as Alzheimer's is, even more than regressive autism, characterized by a loss of learned skills and memories.

Sources:
Ji, L., Chauhan, V., Flory, M., & Chauhan, A. (2011). Brain Region–Specific Decrease in the Activity and Expression of Protein Kinase A in the Frontal Cortex of Regressive Autism PLoS ONE, 6 (8) DOI: 10.1371/journal.pone.0023751

*What does it mean to activate an enzyme? Well, an enzyme is a kind of protein, and like all proteins, it has a range of three-dimensional configurations** it can assume, and only some of these possible shapes leave the binding site for the molecule the enzyme acts upon freely accessible. So when an enzyme is in one of those arrangements, and molecules of its particular substrate can just drift along and come into contact with the binding site(s), that's when the enzyme can be considered active. Binding of a phosphate group or some other small molecule at a different binding site will usually trigger a shape change; that is how enzymes can be activated or deactivated by other enzymes.

**I have this idea that proteins are called proteins just because of this shape-changing ability they have, in which they resemble the mythical Proteus.