Filed under: Brave New World, Connections, General Musings, Genetic Testing, Health, NPR, Science, tech, Wired | Tags: Allen Institute for Brain Science, blogging, BRAIN Initiative, health, jim downey, Katie M. Palmer, NPR, Rob Stein, science, technology, Wired
Two brief news items in the last day or so illustrate just *how much* fundamental knowledge we don’t have about our own biology.
The first is this good article from Wired about building a comprehensive model of the human brain: A First Big Step Toward Mapping the Human Brain
Relevant excerpt:
The Allen Cell Types Database, on its surface, doesn’t look like much. The first release includes information on just 240 neurons out of hundreds of thousands in the mouse visual cortex, with a focus on the electrophysiology of those individual cells: the electrical pulses that tell a neuron to fire, initiating a pattern of neural activation that results in perception and action. But understanding those single cells well enough to put them into larger categories will be crucial to understanding the brain as a whole—much like the periodic table was necessary to establish basic chemical principles.
Consider that: we’re just now really building a good map of how the different neurons interact within one small component of the brain. And not even the human brain, at that.
And this news story, which came as a shock to me when I heard it on NPR: Seasons May Tweak Genes That Trigger Some Chronic Diseases
From the story:
The seasons appear to influence when certain genes are active, with those associated with inflammation being more active in the winter, according to new research released Tuesday.
* * *
Other researchers say the findings could have far-reaching implications.
“The fact that they find so many genes that go up and down over the seasons is very interesting because we just didn’t know that our bodies go through this type of seasonal change before,” says Akhilesh Reddy, who studies circadian rhythms at the University of Cambridge but was not involved in the new research. “And if you look at the actual genetic evidence for the first time, it’s pretty profound really.”
Again, this is a really basic bit of science — akin to understanding how the sequence of gene expression leads to the development of an organism. Learning that your genetic activity changes during the year means that illnesses are much more dynamic than anyone realized previously.
Not to get too Rumsfeldian, but it really is important to know what we don’t know, as seen between the two items above. In the first case, researchers set out to build a model because they knew that they needed the basic knowledge. In the other, it was investigation of a mystery which led to an unexpected discovery.
And in both cases, it’s science at work. And very cool.
Jim Downey
Filed under: Alzheimer's, Amazon, Connections, Health, Hospice, Kindle, Marketing, Promotion | Tags: Alzheimer's, blogging, care-giving, dementia, direct publishing, Ether One, free, game, health, Her Final Year, hospice, jim downey, John Bourke, Kindle, memoir, Michael Thomsen, promotion, The New Yorker
OK, a bit flip, there. Sorry. This actually sounds like a really interesting game, and the people who are involved with it seem to understand about the limitations inherent in it:
Ether One: The Video Game That Tries to Simulate Dementia
Ether One, a first-person puzzle game made by a six-person team at White Paper Games, in Manchester, England, is about the slow dissolution of the brain. The game casts the player as an employee of a futuristic memory-retrieval company called the Ether Institute of Telepathic Medicine. Your job is to dive into the mind of Jean Thompson, a sixty-nine-year-old woman diagnosed with dementia, and retrieve a series of lost memories. Using scans of the woman’s brain, the Ether Institute reconstructs 3-D simulations of what remains of her memory. Players must reassemble the story of her life using the oddly alien artifacts (the symbolic significance and basic operation of which remain a mystery) left behind in the fraying simulation of her past home and work places.
* * *
Ether One is built around a central control room from which players access the four main areas of Jean’s past—a seaside town in England, an industrial mine, a processing factory, and a lighthouse overlooking the ocean. Each area is filled with hundreds of tchotchkes, mementos, and mundanities that could hold some long-forgotten significance. Players are asked to “collect” the memories and are limited to carrying only one object at a time. At any point in the gameplay, they can instantaneously teleport back to the control room, which is lined with empty shelves to hold anything they collect. As a player, you’re never sure what’s important and what isn’t, so the system encourages you to take everything.
This hoarding is repaid with periodic puzzles, such as a door with a numeric lock whose code can be found on the bottom of a previously collected mug. As the game progresses, these puzzles increase in complexity, as does the array of random objects filling the shelves. The collection gradually overwhelms the player’s ability to remember just where all of these things came from and why they seemed important enough to retrieve. Why did I bring this plate all the way back here? Whose hat is this supposed to be again? It’s a tidy simulation of the cognitive degradation of dementia.
The author of the piece, Michael Thomsen, has first-hand experience with a family member who suffered with dementia. Here’s his concluding insight about Ether One:
Playing Ether One, I can’t say I felt any new illuminations about the disease. Most of the things I watched my grandmother go through were missing in its simulation, but I was reminded of the helplessness I felt. After solving the first few puzzles in Ether One, I realized that I’d been storing way too many items back in the hub world. It reminded me of my grandmother’s stuffed bookshelves in her nursing home room—old books, half-used perfume bottles, porcelain ferrets, a piece of Bohemian glass I’d given her once—we’d kept as much as we could when she moved in, trying to guess what might mean something to her and what might be lost for good. If video games indulge in a fantasy of objects—swords, spaceships, and the like—it’s one that’s hard to translate into a room filled with forgotten things. In Ether One, I found that the distance between these seemingly incompatible worlds lessened just a little. Even though I couldn’t quite forget myself inside its artifice, it was comforting to have the space to try.
May be worth checking out.
Also worth checking out: the Kindle edition of Her Final Year will be available for free download next week, from Monday through Wednesday.
Jim Downey
Filed under: Book Conservation, Connections, Failure, Health, Marketing, Publishing, Survival, U of Iowa Ctr for the Book | Tags: appendectomy, appendicitis, art, blogging, book conservation, bookbinding, bookbinding techniques, bureaucracy, health, jim downey, Legacy Bookbindery, mortality, survival, teaching, training, University of Iowa Center for the Book
The summer before this past one I almost lost my wife to appendicitis.
All my adult life I have known that sudden, unexpected death can strike those we love. And I have tried to live my life accordingly.
The flip side of that, of course, is that I know I could die suddenly, as well. And while I have done a number of crazy and stupid things, I’ve always tried to keep an eye on the real risks involved. It’s not smart to lose track of the fact that you’re mortal.
But being there in the hospital with my wife, as she recovered from an emergency appendectomy, reflection on my own mortality took a slightly different direction. Rather than just thinking about what I had accomplished, and whether it had been a full life, I got to thinking about what I had to offer. And one thing I started thinking about was that I had accumulated a lot of very specific experience which was fairly rare: my book conservation skills.
Now, there are some really good schools out there to train conservators. As well as professional organizations, and workshops and all the sorts of things you would expect. But not a lot. Certainly not enough to meet the need for trained conservators; a need which will only continue to grow as more and more books and articles are published only in electronic format, and the current inventory of printed material starts to age and grow fragile.
Since I have been in private practice as a conservator for 20+ years, I haven’t done a lot of just low-level routine repairs. Rather, I’ve worked on the more valuable items from both private and public collections — the sorts of things which individuals and institutions felt it was worth paying me for my expertise. In other words, I’ve been fortunate enough to work on the cream of the crop from multiple collections, as it were, which has given me the opportunity to further hone a wide range of techniques and demanded that I do my very best by the books and documents entrusted to my care. And with that experience came judgment about what techniques are appropriate in what cases, what will work and what won’t. Judgment which often isn’t even conscious, but lives in my fingertips and can only be shared by close example and repetition.
That’s what I have to offer. And that’s what would be lost were I to die suddenly.
That’s what I got to thinking.
As luck would have it, about the same time I started working with an old acquaintance who had developed an interest in medieval bookbinding. He doesn’t live close, so we had to discuss things online and over the phone, with his coming to visit for weekend training now and then. Because *nothing* compares to hands-on, face-to-face training.
And working with him reminded me of how much I enjoy sharing my skills and love for my craft. Oh, I’ve taught plenty of bookbinding classes over the years, and that has been enjoyable. But there is nothing like working with a student who shares my intense passion for caring for historical texts, rather than someone who just wants to make some blank books for Christmas gifts or needs to have another example for their arts portfolio.
So I got to thinking of how I could find another mechanism to share my skills with people who already share my passion. And I decided to sound out a local institution about perhaps training some of their staff (many large libraries and archives have one or a few preservation technicians, who do the valuable basic repair work on the collection). I knew that while the budget environment wasn’t good, there might be a way for us to work out an arrangement for long-term, careful training in depth of some of their staff, allowing me to transfer both specific skills but more importantly nuances in judgment through hands-on work of items in their collection.
The institution was certainly receptive, and for a while we worked hard to see how to bring my initial thoughts into reality within their system. Meetings were held, brain-storming sessions conducted. Lots and lots of meetings, involving lots of different people and departments, different budget lines and facilities. The prospects were very promising, and I was very excited about the possibilities to begin a new phase of my book conservation career, teaching others part-time. But ultimately the bureaucracy proved too hard to overcome; rather than starting a long-term, fairly permanent training program, the bureaucracy could only accommodate a temporary ‘pilot’ program within its usual rules and guidelines for professional development.
And here is where the title of this post comes into play: knowing when to walk away.
Because when all was said and done, there was a chance … but only a chance … that the temporary pilot program teaching two or three people might find a home (and funding) within the institution. Maybe.
What should I do?
I considered and consulted with some close friends. After all the discussions, after all the meetings and brainstorming, I was deeply vested in seeing this work out.
But I had to take a step back and think about my initial goals, and rationally assess whether or not this would accomplish what I wanted. I decided that it didn’t — that I would be committing too much time and energy to trying to meet the needs of the bureaucracy rather than my own needs, and that I would have too little control over what I could teach.
I can’t blame the bureaucracy; it exists for a reason. Trying to change it, to get it to do something unique and risky, was probably a fools errand from the start.
So, failure.
Maybe.
There’s more than one way to skin a cat, though. The bureaucracy at the institution in question, as well as the bureaucracy at many such institutions, is already set up to handle another version of training for their staff: specific workshops conducted by outside consultants, lasting from a few hours to a few days.
So that’s what I am going to do. In the next couple of months I will put together the initial offerings of training workshops for specific conservation techniques. All will have detailed descriptions of what the workshop will include. All will include plenty of hands-on practice under close supervision. All will be completely modular, so that any institution can select from the menu of offered workshops without being committed to other workshops.
I may not be able to do in-depth training of a small number of people, but I can share my skills and judgment with a much wider selection of institutions. It’ll be a lot more work on my part, but will hopefully also accomplish more.
We’ll see. I’ll keep you posted as to developments as things happen.
Jim Downey
Filed under: Alzheimer's, Health, Humor, Wales | Tags: blogging, cats, health, humor, jim downey, St. Cybi's Well, Wales
(See postscript at the bottom.)
She’s named after Sir Edmund, because when she was young she always wanted to climb things. She’s no longer a youngster, and just turned 14.
For the most part, she’s been in good health, though in the last year she started losing her eyesight, and just recently she’s had some minor strokes. The results of this are that she’ll just get confused for a while, sometimes tend to walk in small tight circles, and occasionally throw up. But our vet says that she’s not in any real pain, and as long as she continues to bounce back from those episodes, there’s no reason why we can’t keep her and love her with a little extra care. We’re used to caring for people and pets which need a little additional attention, so it’s no big deal.
This is Mel:
As you can see, she also likes climbing on things. But she’s named ‘Melyn’ for the color of her eyes. It’s Welsh. Yeah, as you might gather from St Cybi’s Well, we enjoy Wales, and my wife has been learning the language for a decade or more. Mel’s about 4 years old, and a bit more of a rascal. The two cats get along tolerably well.
Our bed is on top of a stack of drawers. One of Mel’s favorite games is to pull open those drawers. And in particular, the one which is right where my foot needs to go when I swing my leg out of bed. This is especially fun when it’s the middle of the night and I’m just getting up to go to have a pee (ah, the joys of middle age … ). I’ve cracked the side of my bare ankle on the side of that drawer too many times to count. But even *I* will learn eventually, so I’ve gotten into the habit of swinging my leg out even further, and then sweeping it in slowly so as to push the drawer closed if it has been left open by dear Mel.
Sometime last night, Hil seems to have had another minor stroke. And after getting down from the bed, threw up. Fortunately, she did so on a small throw rug (hmmm … ). It woke my wife up, so she dealt with it, and then took Hil in to where the litter box is, thence to the water bowl in the bathroom. Since Hil was a little confused, and my wife wanted to get back to sleep rather than sit and watch the cat while she decided whether or not to have some water, she just left Hil there. This is fairly normal — give Hil a reference point, and she’ll manage to sort out where she wants to go eventually.
Usually, by the time I get up in the morning (I get up first), Hilary has made her way downstairs and is politely waiting for breakfast. Mel is more … demanding. And serves as a very effective wake-up clock if I try and sleep in. As the saying goes, there’s no snooze button on a hungry cat. So this morning we went through the usual routine. I got up, swung my leg over, closed the drawer, and put on some clothes. My wife told me that Hillary had had an episode earlier, but that she had dealt with it. Mel noisily demanded breakfast.
So I went downstairs, Mel close at heel the whole way. Got the catfood out, took it to where their feed bowls are. Mel dug in, but Hil wasn’t to be seen. I checked around, didn’t see her downstairs, but figured that since she had been sick in the night, she might not be hungry and was probably curled up somewhere in the upstairs, would come down when she felt like it. No biggie — I could check on her later if she didn’t appear.
I got coffee, and went about my wake-up routine. Normally this includes getting in a walk, but today we have heavy thunderstorms and I am not THAT dedicated to getting in my exercise. Same for my wife, who thought she’d just catch a little extra sleep after her disrupted night.
After an hour or so of coffee and reading online, including a lot of attention from Mel but no sign of Hil, I figured I’d pop upstairs, see if I could find Hillary, and see how she was doing and whether she wanted some food yet.
I went upstairs. My wife was waking up, doing a little reading in bed. She said she hadn’t seen Hil yet this morning. I checked around upstairs in all her usual haunts. No luck.
Hmm.
Yeah, you guessed it. I thought to check the drawer below our bed, which I had closed without looking earlier. There she was, happily snoozing in amongst the clothing.
I brought her downstairs, got her some food. Mel watched, yellow eyes glinting. And I think I detected a slight smile on her face, as well.
Jim Downey
A postscript: Hillary had another and much larger stroke about 12 hours after I posted this. She passed away peacefully in the early hours of the next morning.
Filed under: Connections, Emergency, Failure, Flu, Government, Health, NPR, Pandemic, Predictions, Preparedness, Science, Science Fiction, Survival, Travel | Tags: blogging, CDC, Ebola, flu, health, Homeland Security, influenza, jim downey, NPR, pandemic, predictions, science, Science Fiction, St. Cybi's Well, survival, The Atlantic, TSA, WHO, writing
… St Cybi’s Well, what with an incompetent theocratic government in place:
So imagine the scenario. A deadly flu pandemic is beginning in the northeast. TSA agents are asked to report for work in the germ incubators that are airports to keep the transportation system running. And while their bosses in Washington, D.C. can’t supply them with reliably functioning respirators to protect them from infection, they’re keeping thousands that may not work on hand, thinking they may hand them out for “employee comfort,” like security theater karma for those who make us remove our shoes and take our water.
But sadly, scarily, it isn’t. Rather, that passage is from the following news item:
The Department of Homeland Security Is Not Prepared for a Pandemic
As the Department of Homeland Security endeavors to prevent another 9/11, a terrorist attack that killed nearly 3,000 Americans, it is worth remembering that there are far deadlier threats out there. I speak not of ISIS or Ebola, but the influenza virus. The flu pandemic that began in 1918 killed 675,000 Americans. That is to say, it killed about as many Americans in a couple years as the AIDS virus has in decades. Worldwide, that same flu pandemic killed an estimated 30 to 50 million people. It would take 16,000 attacks like 9/11 to equal that death toll. Those figures powerfully illustrate the case for redirecting some of what the United States spends on counterterrorism to protecting ourselves from public health threats.
Of course, money only helps if it isn’t squandered. Take the extra $47 million dollars that Congress gave the Department of Homeland Security in 2006 to prepare for a pandemic. As a recent Inspector General report explains in depressing detail, a lot of that money was wasted. And one darkly hilarious passage in the audit reveals what may be the most galling example of security theater ever.
Oh, joy.
But it’s OK, because the rest of the world is ready to step up and fight against a viral threat which could explode into millions of cases in just a few weeks, right?
Um …
Dire Predictions On Ebola’s Spread From Top Health Organizations
Two of the world’s top health organizations released predictions Tuesday warning how bad the Ebola outbreak in West Africa could get.
Both the Centers for Disease Control and Prevention and the World Health Organization agree that the epidemic is speeding up. But the CDC’s worst-case scenario is a jaw-dropper: If interventions don’t start working soon, as many as 1.4 million people could be infected by Jan. 20, the agency reported in its Morbidity and Mortality Weekly Report.
*sigh*
Sometimes it feels less like I’m writing a cautionary work of fiction and more like I am looking back and writing an historical account …
Jim Downey
Filed under: Bad Astronomy, Fireworks, Gardening, Habanero, Health, Humor, Music, Phil Plait | Tags: Bad Astronomy, blogging, Carolina Reaper, gardening, Habaneros, health, humor, jim downey, music, Phil Plait, volcano, Wikipedia
… but *do* have a very healthy respect for it.
The SMOKIN’ ED’S CAROLINA REAPER® pepper, that is. Here’s a bit about it from Wikipedia:
The Carolina Reaper is a hybrid cultivar of chili pepper of the Capsicum chinense species, originally named the “HP22B”, bred by cultivator Ed Currie, who runs PuckerButt Pepper Company in Fort Mill, South Carolina, United States. It’s the world’s hottest hybrid pepper. The original cross was a red naga pepper and a red savina pepper. [1] The “Carolina Reaper” was rated as the world’s hottest chili pepper by Guinness World Records according to 2012 tests,[2] averaging 1,569,300 on the Scoville scale with peak levels of over 2,200,000 Scoville Heat Units (SHU). The previous record-holder was the Trinidad Scorpion Butch T.[3]
There are some included in today’s harvest of peppers:
How are they? Oh, baby!
No, seriously, trying one of these peppers is sort of the equivalent of seeing a live, active volcano. Sure, it’s insanely hot (I ate the smallest little piece, about the size of an apple seed, and it did the whole ‘mouth numb, face flushed, lips melting, nose running’ thing). But it’s also insanely cool to just experience the thing … if you exercise a little respect for its power.
And they have the same flavor profile as other super-hot Habaneros, which is actually why I like them. It’s a deep, smokey, lasting peppery flavor.
I’ve only harvested about 60 peppers from my plants so far this season. For some people, that would be about 59 too many. But if the weather holds, perhaps I’ll have a total harvest along what I’ve gotten in years past.
Jim Downey
*Of course. And if you would like to order your own fresh super-hot peppers, you can do so from the same place I get my seedlings each year.
Filed under: Art, Bipolar, Connections, Depression, Health, Predictions, Science, Slate | Tags: apophenia, art, bipolar, blogging, creative process, depression, health, jim downey, Katy Waldman, Lancaster University, medicine, mental health, Northwestern University, predictions, Rick Nauert, science, writing
Since this blog has recently picked up a bunch of additional followers, I’m going to reiterate something I’ve said in the past: I’m mildly bipolar. Have been all my adult life. My ‘natural’ bipolar cycle is about 18 months, though that can be influenced by outside factors. It’s mild enough that I’m able to manage my bipolar swings without medication, but I keep a close eye on it. I’m thankful that I can manage it without medication, because I have always perceived a connection between this bipolar condition and creativity.
And increasingly, science agrees with me:
Professor Steven Jones, co-director of Lancaster University’s Spectrum Centre, said, “It appears that the types of inspiration most related to bipolar vulnerability are those which are self-generated and linked with strong drive for success.
“Understanding more about inspiration is important because it is a key aspect of creativity which is highly associated with mental health problems, in particular bipolar disorder.”
“People with bipolar disorder highly value creativity as a positive aspect of their condition. This is relevant to clinicians, as people with bipolar disorder may be unwilling to engage with treatments and therapies which compromise their creativity.”
Bingo.
And then there’s this, from an article on apophenia:
Another possible culprit in apophenia is dopamine. A 2002 experiment revealed that people with high levels of dopamine more often extract meaning from coincidences than those with lower dopamine levels. And when self-described skeptics (team “UFOs are fake”) were given the drug L-dopa, which ups the brain’s dopamine supply, they began to perform more like self-described believers (team “I can speak to spirits”) on the same pattern-finding tasks. Likewise, when Brugger and his colleagues administered dopamine to a group of healthy adult men, that group proved more likely than a control group to notice visual similarities between random pairs of shapes.
Personal accounts from manic patients fizz with an almost compulsive meaning-making, but the research on connections between apophenia and bipolar disorder is thin. One clue: Just like people with schizotypal tendencies, people at risk for bipolar disorder often ace creativity tests. They seem to excel especially at the type of “intuitive, open-minded thinking” that results in surprising associations. (Though he hasn’t studied apophenia and bipolar disorder, Brugger says he would “assume that you see connections everywhere in a manic state.”) A symptom of mania known as clanging, in which ideas are strung together not in a logical order but because of how the words sound, has an apophenic aura.
Related, this news about another scientific discovery concerning depression:
The first blood test to diagnose major depression in adults has been developed by Northwestern Medicine scientists, a breakthrough approach that provides the first objective, scientific diagnosis for depression. The test identifies depression by measuring the levels of nine RNA blood markers. RNA molecules are the messengers that interpret the DNA genetic code and carry out its instructions.
* * *
“This clearly indicates that you can have a blood-based laboratory test for depression, providing a scientific diagnosis in the same way someone is diagnosed with high blood pressure or high cholesterol,” said Eva Redei, who developed the test and is a professor of psychiatry and behavioral sciences at Northwestern University Feinberg School of Medicine. “This test brings mental health diagnosis into the 21st century and offers the first personalized medicine approach to people suffering from depression.”
I suspect that it won’t be long until some similar test is developed for markers indicating bipolar condition.
Oops, there I go, drawing connections again …
Jim Downey
Filed under: Connections, Emergency, General Musings, Health, NPR, Pandemic, Predictions, Preparedness, Psychic abilities, Science Fiction, tech, Writing stuff | Tags: bats, blogging, Ebola, health, jim downey, NPR, pandemic, predictions, science, Science Fiction, technology, White Nose Syndrome, writing
News item on NPR this afternoon:
Ebola In The Skies? How The Virus Made It To West Africa
The Ebola outbreak in West Africa is the most explosive in history. One reason the virus spread so fast is that West Africa was blindsided. Ebola had never erupted in people anywhere close to West Africa before.
The type of Ebola causing the outbreak — called Zaire — is the deadliest strain. Until this year, it had been seen only in Central Africa, about 2,500 miles away. That’s about the distance between Boston and San Francisco.
How did it get there?
Disease ecologist says scientists don’t know for sure. But they have a top theory: The virus spread through bats.
Many signs point to bats as the main source of Ebola. Scientists have found Ebola antibodies in bat species that are widespread throughout Africa. The virus infects and replicates inside bats, but it doesn’t kill the animals. So bats can easily spread Ebola.
And bats get around. Some can migrate hundreds, even thousands of miles.
Combine that with the item I posted about earlier … and my mind went in a very odd direction as I was doing some routine work in the bindery this afternoon: what if …
… what if a few years ago someone with some limited precognitive ability (either technological or psychic) was able to foresee an Ebola epidemic which made it to the US and then was spread by our native bat population?
And then what if they decided to do something to stop that epidemic before it ever happened … by decimating the bat population?
Yeah, sometimes the ideas I get kinda scare even me.
Jim Downey






