Usher syndrome, Part I: an introduction to sensory perception

Guest Blogger Danio:

In my introductory post I mentioned that my research focuses on the genetics of hereditary deaf-blindness, specifically Usher syndrome. As it’s likely that many of you have never heard of it, I thought I’d kick it up a notch with some sciency posts on what we know about Usher syndrome and what we think we can contribute to the diagnosis and treatment of the disease.

Usher syndrome is a genetically recessive condition characterized by hearing impairment, usually from birth, which is due to the degeneration of sensory neurons in the inner ear, and blindness due to retinal degeneration, which begins to occur in childhood or adolescence and progresses through several decades. Additionally, some Usher patients have balance problems associated with the sensory cell loss in the ear. There is a great deal of variation in the clinical presentation of the disease, and three clinical subtypes can be classified by the severity and age of onset of the symptoms. Usher syndrome affects about 1 in 17,000 Americans, and there are a number of populations around the world where the incidence is higher due to founder effects or intermarriage.

To begin to understand the pathology of this disease, one needs to focus on the affected cell types: mechanosensory hair cells and photoreceptors. Both are highly specialized types of sensory cells, but they’re performing essentially the same function, namely receiving an environmental stimulus and converting it into an electrical signal that is transmitted to the brain for interpretation. Although the nature of the stimuli–sound and light–are quite different, they are processed in much the same way, and thus it is not surprising to find a number of structural and functional similarities between photoreceptors and hair cells.
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It’s got a good beat and you can dance to it

My first of several posts about sensory cell neurobiology will be appearing shortly. To get you warmed up, here’s a movie showing a mechanosensory hair cell responding to a low frequency sound played through the glass pipette you can see in the image. *Caution*: low frequency sound may not be appropriate for work. Earphones recommended.

Also, the Scienceblogs Survey is now open again, and will remain so until 11PM EST Friday, August 15th.

~Danio

This nasty war

Brought to you by guest blogger LisaJ:

Canada lost two soldiers serving in Afghanistan this week. This marks the 89th
and 90th Canadian soldier to be killed since starting our peacekeeping mission in Afghanistan in 2002. Master Corporal Josh Roberts leaves behind his fiancé in Manitoba, and Master Corporal Erin Doyle leaves behind a wife and a young daughter. These stories are just heartbreaking. They are both very young men, and they’ve had their lives just ripped right out form underneath them. Their families’ lives have undoubtedly been shattered. What’s more, breaking news this morning tells us that a female British-Canadian aid worker, along with two American and Trinidadian colleagues, were also killed in a militant attack in Afghanistan yesterday. This is sickening. This is three of my own fellow citizens in one week, and I know that doesn’t even compare to the countless others, largely civilians and American soldiers, who will have lost their lives in Afghanistan and Iraq this week.

Everytime I hear of one of these stories I just find it so tragic, and so I should. These people have selflessly given up their lives for the rest of us. In this case, I find it especially selfless since it’s not really our war that the Canadian soldiers serving in Afghanistan are fighting. I imagine that most people here will agree with me when I say that I find the death of any soldier, of any nationality, serving in Afghanistan or Iraq right now to be an awful, tragic, horrible, sickening, unfair and unnecessary loss. It just makes me so angry every time I hear of another death or injury, because what the hell are they all doing there anyways? (Note: the previous statement was not meant to imply that I don’t know what their role is in Afghanistan. I understand that they are there to protect the Afghan citizens, and I am not trying to undermine their role here in this statement. I just think it’s unfortunate that they were sent there in the first place). I have so much respect for these soldiers, and I just cannot imagine how heart breaking it must be for themselves and their families every day, not knowing what may happen to them at any moment. Just imagining having to say goodbye to a loved one who is heading off to serve in such dangerous battlefields makes me sick to my stomach. The pain and grief they must feel everyday must be unimaginable. For all of you here who have served or who have loved ones serving, my hats off to you, you are strong, wonderful people and I feel for you everyday.

I know a lot of us here have strong opinions that this war shouldn’t even be taking place. It’s this aspect of the whole damn thing that, for me, makes these deaths all the more horrible. What saddens me more is that even I, who is so horrified every time I hear of another dead or injured soldier, find myself grieving pretty quickly and putting the faces and details of these soldiers lives to the back of my mind. This is an unfortunate adaptation of the escalating death count in this war. I guess as the numbers pile up it just gets harder and harder to remember them all, so their stories slip away much more quickly. This is a sad fact, but not entirely unnatural. I mean, we can’t all walk around grieving for our lost soldiers every day, that would prohibit us from functioning normally, but it’s just sad when their names and faces start to get lost in the shuffle. What we should be able to take some tiny amount of solace in, however, is that soldiers who are badly injured will be well taken care of when they return home by the government who sent them to war in the first place. Now I’ve heard a lot of stories of injured American soldiers who have to fight tooth and nail to get any kind of medical compensation for their injuries, and many don’t ever get the payments they are entitled to. But this can’t also be happening in Canada, right? Well reports this week show that Canadian reservists, which reportedly make up 20% of the 2500 Canadian troops deployed in Iraq, who suffer significant body trauma, such as the loss of a limb, receive sub-par long term medical care and compensation upon their return home. Apparently they’re getting it right with some soldiers, the ‘career soldiers’, but not these reservists who have apparently made the mistake of just selflessly stepping in to help out in this particular war. It looks like they’re working on fixing this issue, but I’ll believe it when I see it. Just another example of how our society and government has its priorities really screwed up. These soldiers should get nothing but respect from our governments. You lose a limb for your country, you should be adequately compensated and given as much care as you need, end of story.

Anyways, here’s to all of our soldiers and their families who are giving the ultimate sacrifice in this war. And here’s hoping that our governments get it together one day and treat these soldiers, aid workers, diplomats, and everyone actively involved in the war and relief efforts the respect and honour that they deserve.

Putting the cracker in context … again

Guest blogger Sastra:

When I log into Pharyngula, as a matter of habit I usually glance at the little Recent Comment bar on the side, to see who has just responded to what. It helps to show which threads are particularly lively at the moment. Every now and then there’s someone responding to an “old” post – one that’s been otherwise inactive for days, weeks, months, or, in very rare cases, years. Given the recent major fuss caused by “Crackergate,” we can still notice the occasional newcomer weighing in on the contents of PZ’s kitchen garbage can. Presumably they’ve followed one of the many links still hanging around out there. The cracker threads are not quite ready to die.

I don’t think the issue and its moral ramifications (or the interest in them) are quite finished and over yet, either, so – here ya go — I’m going to bring it up again. Those who are sick and tired of the topic may lightly skip to the next post.

I have, like most (though not all) of the regular Pharyngulites, been – by and large – supportive of PZ’s action, and the rationale behind it. However, I think it’s simplistic to see this as a simple issue, which is easy to explain or defend. There are some good, hard, and reasonable points on the other side, as well as arguments which sound reasonable, but are only superficially plausible. But, judging by the continued reactions, our replies and responses are not always getting through, and we can’t just assume it’s because the other guys aren’t listening. I don’t know — maybe a new approach might help.

So I thought it might be interesting then to take another stab at trying to explain the why behind it, by coming at it from a different perspective.
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Here’s to the teachers!

MAJeff here with his espresso.

A few years ago, when I was teaching back in Minnesota, there was a group of us first-year faculty who got together every Wednesday night for beer, pool, and chat. We had to switch bars a couple times–once because some folks weren’t feeling very comfortable with the war-mongering in our usual bar when we were there during the invasion of Iraq, and another because I spent an hour getting harassed by some of the locals (it was an hour because I refused to give up public space, but threats of violence told me an hour was long enough)–but we kept at it for the year. Several of us ended up leaving town after the spring, so I don’t think it kept going. I’ve not found something like since.

One of the things conversation turned to every night was teaching. Of course, some of it was complaining about our students. But a lot of it was of the, “What do you do when…?” or “How do you…?” or even “Class rocked today!” I don’t have the citation handy, but one of us even published an article based on those weekly drinking excursions. (In the literature, it became about “peer-mentoring.”) Coming from Sociology, Biology, English, Art Education, Math, Women’s Studies, and Computer Engineering we often didn’t have topical course information we could share. But, we talked about our classroom time, students with difficulties, difficult students, and the fact that none of them had ever heard of Billie Holliday. Those Wednesday nights with colleagues were honestly some of the best experiences of my teaching career.

I was reminded of those evenings recently. A few years ago, I was asked to put together a “Nuts and Bolts of Teaching” workshop for new Teaching Fellows where I’m doing my PhD. These are grad students who’ve spent time as Teaching Assistants but are preparing to teach their own classes for the first time. I didn’t do the workshop this year (I created it and taught it the two previous years), but had to find my materials for the Professor who was taking it over. The department used to have a semester-long course on teaching, but it had fallen by the wayside. Now, there’s a one-day workshop.

I’ve taught at six schools in the past 7 years. Other than that one year–when I was an Assistant Professor who had to go through orientation, where I met all those drinking teachers–I’ve never had the kinds of opportunities to engage in that “teaching talk.” My best friend here in Boston and I used to have those conversations quite a bit. But since the Department moved me from our shared office to one in a hallway all by myself, we don’t see each other as often, and rarely get to spend that kind of time talking about our teaching.

Now, one thing going on here is simply being adjunct. As I’ve described it to my students when they asked why I wasn’t sure if I’d be back the next year, we adjuncts are nothing more than “temps.” We have the same lack of job security and, generally, non-benefit status. We’re easily exploitable labor. And, we’re evidence of how little value teaching has. Regular faculty can get time-off for research; then we temps get hired. We may not contribute much in terms of building up departments, but to managers concerned with the fiscal bottom line, we’re a bargain. Some of us are pretty good, too.

My best friend here in the city teaches with me. We used to share an office, but because of scheduling issues, I got moved to another office; I’m now the only person in an entire basement wing of the building. We don’t get to talk much about teaching, like we used to, because we just don’t see each other as often. I admit that my friend and I are somewhat exceptional in being among the best instructors in the department. (I’ve got the evals to back it up.) But, there’s often very little opportunity for adjunct people to work on improving our teaching skills. I’m starting my sixth and final year at this school. Several of the places I’ve taught, including, this one, have any number of programs put in place to assist faculty in improving their teaching. Often, adjunct aren’t even made aware of such opportunities, and even if we were, we wouldn’t be eligible for them. More of the people teaching students aren’t provided opportunities to improve their skills. We’re teaching more and more of the classes, and the primary concern often isn’t our teaching ability, but the cost of our labor.

I’m not complaining too hard here. Adjunct positions have allowed me to teach at a wide variety of schools, to gain incredible experience, and–because I love teaching–to work on my own skills (albeit on my own). It’s frustrating, though, to have very strong skills in an area that is so devalued.

Teaching is a wonderful profession.

I really, really like my students. It’s an amazing experience to every year watch a new group of young people discover new things, about themselves and the world around them. It’s a little overwhelming, sometimes, to be a part of that process. And, it’s cute as hell when you can see the “EUREKA!” moment on their faces, as are the contorted facial expressions during exams. It’s heartbreaking when they come to my office to chat about their relationship problems or being denied and apartment because of their race. It’s a bit overwhelming to realize the role we often play in this young people’s lives.

The classroom is my happy place. And that seems to come through to my students. I’m still amazed when I run into them on the train or at a conference or when I receive an email out of the blue. It’s incredible to hear how I’ve touched people, even those who just sat in the back of the room being quiet.

So, here’s to teachers and to teaching. Here’s to the people that moved the folks reading this. Here’s to my HS science teacher, who was actually able to interest me; here’s to my undergrad Voice Instructor, who let me break down crying when I was struggling with coming out of the closet; here’s to my MA and PhD advisors, who taught me about being actively engaged scholars; and here’s to the folks I TA’d for in my PhD program, who taught me it’s ok to be me when teaching. Here’s to the folks toiling away, doing good work, inspiring and instructing.

Here’s to teachers. Who are the teachers for you, and how did they inspire you?

Giving up the ghost

Guest Blogger Danio:

When I began to seriously question organized religion, years ago, it didn’t take long to conclude that the myths I had been taught as a child were no more tractable than any of the other thousands of belief systems that have come and gone throughout human history. While I quickly and cheerfully discarded all god-belief without regret, the concept of the soul, a consciousness of some kind that could persist beyond the physical life, was significantly harder for me to relinquish. The idea that the essential ‘me’ would cease to exist upon my death was not nearly as disconcerting as the realization that my departed family members, of which there are, regrettably, many, were no longer present anywhere, in any form.

Science and reason helped me overcome this sense of loss, and appreciate the importance of accepting life, brutal and exquisite as it is, as an ephemeral, purely biological process. Reading Dawkins’ A Devil’s Chaplain and various other works helped me to clarify my feelings on mortality. PZ has also written eloquently on the subject, when, for example, he discussed the brevity and relative insignificance of human life on a geological time scale.

Most of all, I have arrived at this acceptance as a lover of science, contemplating the wonders of genetic transmission through lineages. I can easily envision a connection, a common thread that runs through the years, linking my life to thousands of others. I see the ghosts of countless ancestors flit across the faces of my children, with all their various expressions of youthful joy and consternation and everything in between, and recognize that my offspring represent the distillation of innumerable contributions to the molecular constitution our flourishing family tree–the joining together of humanity at its most elemental.
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Complete Scienceblogs Survey; Win valuable prizes!

Guest Blogger Danio:
Orac has posted a directive from the Seed Overlords regarding a survey they’d like us to conduct. As my distinctiveness has been temporarily added to the collective (I’ll be implanting the “sleep” command into their subroutines next week though, oh yes…) I am dutifully passing it on. It takes less than 10 minutes to complete and you can enter to win stuff at the end of it.

_______________________________________________________________________
Whoops! The survey has been closed already. Sorry about that. Here’s a pointless poll instead.

A victory for rationalism in California

Guest Blogger Danio:

Stand up and cheer for the academic standards at UC, and the LA Federal Judge whose ruling on accrediting courses taught in Christian schools upholds these standards.

A federal judge in Los Angeles has thrown out the remaining claims of Calvary Chapel Christian School, which sued the University of California alleging university officials rejected some courses for credit because of their Christian viewpoint.

What a bunch of sticklers those UC guys are! In order to qualify as an accepted college preparatory course, the UC standards require the course content to be largely reality based:

a UC professor who reviewed Calvary’s proposed Christianity’s Influence on America class said the course used a textbook that “instructs that the Bible is the unerring source for analysis of historical events,” “attributes historical events to divine providence rather than analyzing human action,” and “contains inadequate treatment of several major ethnic groups, women and non-Christian religious groups.”

Oh, the uppity secular progressivness of it all! Surely indoctrination into batshit insane bigotry shouldn’t affect one’s admission into a state university, right? Right?

That, apparently, was the basis of the lawsuit filed on behalf of Calvary by the Advocates for Faith and Freedom. The lead counsel for the plaintiffs, of course, plans to appeal, and is playing up the discrimination angle for this poor, embattled majority faith for all it’s worth:

Tyler…fears schools will become afraid to teach from a Christian perspective. “We’re worried in the long term, Christian education is going to be continually watered down in order to satisfy the UC school system,” he said.

That’s right, you tool. Churches and church-sponsored schools are free to teach all the nonsense they want to willing, tuition-paying participants, but they must not be free of the consequences of setting their egregiously misinformed students loose in the real world.

Promoting a scientific mind

Posted by LisaJ

I find it astounding in this day and age, with the many grand scientific discoveries and advances we’ve seen and in our increasingly technologically dependent world, that a large proportion of our population (at least in Canada and the US, with which I have more personal experience) seems uninterested in understanding and learning about science. We have a wealth of information available at our fingertips and an educational system with the potential to accommodate any type of scientific mind, but yet we science-minded individuals are not in the majority. We are a culture that largely breeds an aversion to science. Now I know that I’m generalizing here, and that some individuals living in North America aren’t able to access these opportunities so easily, but that of course is part of the problem.

Now I’m not saying that I think everyone should become a Scientist, I just think it’s sad that more people aren’t embracing the wonders of science into their daily lives. Science is everywhere. It has the power to explain anything you want to know about the world, and it opens our minds up to bigger and bigger possibilities everyday. Science is beautiful, and to embrace it is to enrich your life dramatically. But so many people aren’t doing this, and they are really missing out in life. I see it myself everyday with many of my friends and family members who choose to tune out whenever science is brought up or who quickly cut me off with the ‘oh, you’re so smart, that’s too hard for me’ line. And they’re entirely comfortable to just walk away, carry on, and not understand.

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