bad news

I'm writing this because it's a lot of nuance to tell everyone individually. To summarize, a few weeks ago my blood counts started to drop so they did a biopsy last Tuesday and today I got the results: it looks like I still have some leukemia cells. There are a variety of possible treatments they're looking at (they choose depending on the details of what is happening). The rest of this is a more detailed explanation of those points.

(Also the original title of this post was "less than ideal news" until I realized I used that same title last year when I relapsed. So this post is more blunt instead.) 

My appointments were cut back to monthly in mid-August. The September appointment went fine, but in the first week of October my counts had declined, and my doctor was concerned. So the next week they did a bone marrow biopsy, and today he told me the preliminary results, which is that I have myelodyplastic syndrome, which is a fancy way of saying that my body isn't producing blood cells in the right amounts, which is probably because there are still leukemia cells floating around. (MDS and leukemia are not identical, I think there are a variety of causes of MDS, but since I had leukemia a year ago that's the obvious conclusion. Sometimes MDS become leukemia later. Also, I already knew about MDS a little because I know Carl Sagan had it. Turns out he died of pneumonia, but I think it was probably as a complication. Huh, he had three bone marrow transplants from his sister. The two things I have going that he didn't are, I'm almost 30 years younger than he was, and there has been an extra 20 years of learning in the medical community. In spite of those, we still haven't gotten that good at this.)

As a little review, the cells in our bone marrow produce our blood, red blood cells that carry oxygen, white blood cells that fight infection, and all sorts of other stuff, like platelets, which form clots when we're bleeding. Leukemia is the result of one of those bone marrow cells dividing out of control, instead of maturing into an adult blood cell. The immature cells are called blasts, and I think typically you don't really see any blast cells in the "peripheral blood" (the blood in your veins). To diagnose leukemia they do a bone marrow biopsy, they use a needle to get a sample of my bone marrow (from the bones in my lower back, which are easy to get to, cause I'm boney), and then they count up the blast cells.

A leukemia diagnoses is when 20% or more of the cells in the bone marrow sample are blasts (normally they expect 5% or less to be blast cells). My biopsy last week had about 6% blasts, so it's not exactly considered a relapse, and that's why it's considered MDS. (When I was diagnosed last year it was 100% blasts, and at that point they were circulating through my peripheral blood too, so a hematologist that I still have never met knew when he saw it that I had leukemia, and he called me and told me I needed to go to a big hospital right away. After the first chemotherapy I still had 5% blasts, which is why they did a second "induction" chemotherapy.)

So what will we do about it?

To start we'll try and induce some graft-vs-host-disease. Since the transplant last November, the main concern (besides the leukemia coming back), was that the new donor cells I received could attack me as if I were a foreign invader (this is what HLA typing is for; my donor was a half match). So until today I've been taking some immunosuppressant drugs, which slow down the white blood cells and make them less likely to attack me. The upside is that sometimes they see a graft-vs-tumor effect, where the new donor cells attack any remaining leukemia cells as invaders. That's the plan right now.

Next week we'll see if that's helping, and they'll probably do another biopsy in a few weeks. There are a lot of other options, but which we pursue might depend on how things go in the near future. There are some new drugs that might help, some new chemotherapy drugs, and some that might help induce graft-vs-host (and hopefully also graft-vs-tumor). Another possibility is that they might collect some adult T cells from my donor (a cousin on my dad's side). It'd be a small amount, because they can be quite dangerous to me, and once they put them in they can't take them back out. 

That's pretty much all we discussed.

I mentioned how the results were preliminary, the other part is called cytogenetic analysis, which involves sequencing the genome (probably just part of it), in the leukemia cells, to see which mutations they might have. Some mutations are known to be vulnerable to certain drugs, so if any such mutations are identified they will likely dictate how we respond. They cytogenetics should be complete sometime over the next week or so.

Short digression, I'm watching a David Attenborough BBC show about predators, and the first episode just ended with cheetahs, following a mother with four cubs, and they mentioned that 90% of cheetah cubs don't survive to their second birthday. 

The original cytogenetic analysis from last year found an inversion on chromosome three, which is associated with a poor prognosis, and not long ago I read on quora how leukemias are among the fast cancers, which is both good and bad. Good because chemotherapy drugs are specifically chemicals that interfere with cell division (since that's what cancers are), and by dividing so rapidly they're more vulnerable to chemicals that are really good at killing young cells. The downside is that because they divide so rapidly, they also develop resistance quickly. When I relapsed last summer they used a different chemotherapy drug, because whatever cells survived the previous treatments were most likely to have some mutation that made them resistant to the previous chemotherapy drugs.

That's pretty much all I have to say about my health situation.

The second episode of that show (I think it's called Hunt?), I think he just said polar bears are only successful in 1 out of every 20 hunts. A failure rate of 95%!

So in light of this (my health), I'm focusing my work and time on things I enjoy, and which I think are achievable. Which has meant more curved-crease origami, and less programming. (Because a lot of my programming projects I'm unsure will ever pan out.) Spending time with friends. I should probably order a bunch of 3D models printed.

Okay, now a polar bear is climbing around an incredibly steep cliffs, eating bird eggs & hatchlings. First I was really worried for the bear, he's so high up, and it's ridiculously steep and crumbly. But then I'm watching him just slowly eating every egg and bird he can get near, and the birds are helplessly squawking at him, inches away as he eats their babies. I think there is something I find comforting about being reminded of how nature works. No matter how much time I have left, it's really unlikely I'll be eaten alive, or starve to death, which is what most animals deal with every day for their entire lives.

I've always loved nature programs. Though even as a little kid I remember feeling really bad seeing animals get caught. I'm not sure when it occurred to me that the animals chasing them had to eat too. 

long Time No Update!

Haven't updated since... May 25th‽ Lots has happened, my appoints went from weekly, to every other week, to monthly (next week will be my second monthly appointment). I think my next bone marrow biopsy is around a year, so mid to late November. I've had a few therapeutic phlebotomies (bleedings) so far, but I'll probably need to continue them for a bit over a year. 

Went to Wyoming (flew to Chicago with Collin, where we met Corey, and we drove to Wyoming!) to see the solar eclipse in August. All I wanted for my birthday was for the Sun to block out the Moon for about two minutes, and I got it!

Also, we watched the eclipse on a hilltop in Wyoming, on a lake shore, with about 10 other people, I think maybe all of them were from Colorado. Jenny was one of them, she left a comment on my main page, and then I did something that messed up the comment section on the main page, and I haven't figured out how to fix it yet.

I spent a lot of time trying to motion stabilize the footage of the eclipse, with mixed results. I shot it in 4K with a Sony A7S ii and a 150-600mm Sigma lens (with a Canon to Sony E-mount adapter) I rented from lensrentals.com. I used opencv to find circles, but that didn't quite work as well as I hoped. Then I used contour detection, with fairly good results. And then there is the issue of cropping. A month has already gone by since the eclipse, so I've set that aside and the video is here now.

And the plane crossing it, that was incredible! In the video, shortly after the eclipse starts, the screen goes black. I was watching the LCD when that happened, and my first thought was, "did the camera just die‽ how could it die right now‽" You can hear, I think Collin, saying how the plane is headed straight for it. I looked at the lens and saw that the breeze had blown the solar filter back in front of the camera, and I managed to flip it back off the lens just in time to get the plane crossing. Later Collin looked up flights for that area and we found two commercial flights that went directly over us during the eclipse, and in the video there are, I think, a couple times where you hear someone mention there are two planes. Collin once, and one of the other women later I think. She also says something about how the plane looks like it's steering to see the eclipse, and I think at the time both Collin and I thought she meant they had flown into the shadow, and we figured that was planned. But looking at the flight paths later, it looked as if one of the planes banked sharply to one side, then the other, and then back again, possibly to show the passengers? The result looks like a big bump in the flight path, which otherwise is headed north east to south west across the country. 

I ended up buying the Sony I rented, and they're notorious good at shooting video in low light (the reason I rented it). The night before I returned the lens I decided to look for Andromeda, and I didn't know how easy it is to spot. The app I was using to look for it was so filled with stars I had trouble orienting it right, and decided to look at the Pleiades star cluster first, and I happened to catch a meteor on camera.

Recently I've been working on another variation of minesweeper again, and I just now learned a little tiny bit more of Swift, which is actually what prompted me to post. I figured if I write about what I learned I'd be more likely to remember it. It involves the concept of in-out parameters for functions. I had run into them in the past, but didn't understand what they were doing, but the examples I just read were clear. 

I also started by trying to figure out what was meant by some code, a class named Array2D<T>, which it turns out is a generic type. Generic types (apparently) let you write code that will be more flexible than normal, like the way an array type can take integers, floats, strings, etc., as members, that's what makes them generic. The explanation of generic types involved in-out parameters, which if my understanding is right, are sort of like functions that will change the values of parameters. I think they're kind of like a shortcut of having a function return modified values and setting the variable you pass into the function equal to the returned value. To use an in-out parameter you must write inout after the parameter name in the function declaration, and when you call it you use an ampersand to denote the inout variable. Here's the documentation for in-out parameters. And here is the documentation for generic types.  (Generic code I guess.)

I also revisited an idea I've had for a long time, and worked on quite a bit a few years ago, involving trying to generate point clouds from a video with a pull focus. I managed to get an iPhone app working that would perform a pull focus, and then wrote some opencv code to pull out the in-focus parts, but it does a terrible job. After the bad first attempts I remembered how years ago I read about a simple method for focus stacking (a related problem), that consisted of blurring the photo and subtracting the blurred result from the original. The idea being that the in-focus parts change the most during blurring, and the out-of-focus parts don't change much, so the result is mostly the parts that were in focus. But the results of that were pretty horrendous too. I also had the color off when I made the video below. 

When I return to it again I'll try implementing something like the contrast-based approach to autofocusing. I suppose something I should keep in mind is that, ideally, each pixel will result in only one point, so I really want to look through the "column" of pixels (a single pixel over the duration of the video), and select the one with the highest contrast? That doesn't sound terrible...

Current Events

So I haven't written any updates in a quite a while again. Things have been going well. I had my first therapeutic phlebotomy (blood letting!) a couple weeks ago and it went fine, turns out they take about 500 mL, and they'll keep doing that monthly as long as I am healthy and iron levels remain high. The actual procedure only took maybe 10 minutes, but then there was some waiting before and after, mostly to make sure I felt okay. 

They also made an appointment for me to get an IVIg (intravenous immunoglobulin) infusion in another few weeks. I guess immunoglobulin is the antibody our immune systems use to attack invaders, and it's pretty common for post-transplant patients to have low levels, so this is all still pretty routine. 

They started giving me vaccinations too, which they had told me I would need eventually, around 6 months post transplant (which is about where I am). 

Otherwise things seem to be proceeding about as well as can be expected. They've been reducing the immunosuppressants and I'm on pretty low levels now. I think I've had very minor signs of graft-vs-host, some rashes on the backs of my hands that come and go over the course of a few days. Last fall, before the transplant, I was watching videos and reading about the process, and many patients mentioned how some small signs of GvHD are encouraging because it means the new immune system is working, and there is even a graft-vs-tumor effect whereby the grafted immune system can attack any leukemia cells that remained. 

The one minor weak point is that I still haven't gained any weight, but my appetite is pretty much back to normal, I just need to focus more on eating more constantly. Small meals still but more frequent.

Outside of health issues, I renewed my drivers license finally! And I've been working on modeling polyhedra of all sorts, and getting many more models printed. Right now I have some earrings and pendant designs being made, hopefully this iteration is nice enough that I can start making them for sale!

These are some of the objects I've been working on: stellated polyhedra derivativespolyhedra addiction, and crisscrossed tetrahedron

I also started working on a game involving hyperbolic geometry, but I quickly realized I didn't know enough of the geometry to make what I needed, so I have to go back and learn a lot more before I can return to that.

Health Update: Day 142 Post-Transplant

It's now been 142 days since the transplant on November 18th, looks like this is only the second time I've written about this since I came home in early December.

Around day 30 they did a chimerism test, to look at my white blood cells and see how many were from me and how many were from the donor, and it was good, indicating all donor. On day 102 they did a bone marrow biopsy and another chimerism test, and both had good results: no sign of leukemia cells, and again, all donor, no me.

So things have been going about as well as can be expected for all this. I've been gaining weight, though slowly, two steps forward one step back. They've been slowly reducing the amount of immunosuppressants I take and I should be off them completely in a few months, unless I get some of the more severe symptoms of graft-vs-host-disease. They also reduced my visits from weekly to every-other-weak recently, which is nice.

A few appointments ago the doctor told me I have very elevated levels of iron, maybe 10 times a normal amount, though he said it wasn't cause for concern. He explained how our bodies hold onto iron pretty well because meat is difficult to get in nature, and with all the blood transfusions I had last year my body accumulated a lot of excess iron. So the solution apparently is to donate blood, except in my case they'll have to throw the blood away, so it's basically blood letting. So I immediately thought of that SNL sketch with Steve Martin as the medieval barber/doctor who uses bloodletting for everything — "Gilda, get the leeches!" (And according to that wikiepdia article this sketch was done a few times, which might explain why that quote I just used isn't in the transcript I found. Or my memory might be wrong.)

So we haven't started doing that yet but it'll be once a month for a while until my iron is in a more normal range.

In general I'm feeling alright. I've been working on modeling jewelry again and am working to better organize how I share it here, I'm enjoying that a lot.

I'm trying to embed that SNL sketch below but it doesn't seem to work, I can't even get it to play when I go to the site, but here is a link if you're interested. Or if you have Hulu apparently it's on there too.

Edit: figures, now that I'm ready to post this the embedding seems to be working, thanks NBC! (Or maybe not, seems touchy.) (Click the "read more" link below to see it... maybe.)

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The Trimmed Progeny of a Small Stellated Dodecahedron

I think this started as a dodecahedron, then small stellated... this seems right though. Except maybe I should try to smooth out the remnants of the haircut.

Brief Thoughts on The Brain

So I've been thinking lately about some different ways to view the brain, and causality, and I think there is an unsettled question.

I recall reading about a study of London cab drivers that suggested the part of the brain that stores directions was proportionally bigger in the brains of cab drivers who had been working longer, and I think the natural conclusion was that like muscles being exercised becoming stronger and healthier, exercising the "directions" part of the brain made it bigger and stronger as well. Which would make a lot of sense. But there is an alternative explanation, which would be that some people are born with bigger "directions" parts of the brains, and those people naturally become more long-term cab drivers. This doesn't fit quite as well if there is correlation between the length of time they've been a cab driver and the size of that brain part, because you'd expect to find young cab drivers with varying sizes, and the ones with the biggest being the ones you'd expect to last the longest. I'm not sure what the research found, I should probably be looking it up.

The reason I bring this up is that this second view tends to be how we view mental illnesses, as problems with the brain that cannot be reversed through "exercise". I find this particularly concerning with diagnosing children with mental illnesses, as their brains are still developing and I think we don't yet know enough to safely say a developing brain truly has a problem (in most instances), or if its merely a stage in the maturing process. I watched a documentary on medicating children for mental illness a few years ago on Netflix and was astounded by the fact that some children were diagnosed as young as five, put on drugs that affected their brain chemistry, and believed they could never function without them. I'm not saying that maybe isn't true in some cases, but I think it would take some pretty hefty evidence to convince me.

I've also been thinking for quite a while now that if we truly understood mental illness, we'd be able to cure it reliably, which we cannot, and that's an indicator we don't yet understand the problem. PTSD for example is cured in some people, but it seems that most that suffer from it continue to suffer from it indefinitely, suggesting we don't really know how to cure it. As opposed to traditional illnesses like bacterial infections or bone fractures.

Anyway, I'm not necessarily siding with one view or the other, just noting that there are two competing views on how the brain works, and while I want to lean towards the one, I think we still need more evidence to really know which. I suppose there is the possibility that both are true to varying degrees, but teasing apart the strength of each one would still be ahead of us as well. I guess just keeping in mind the fact that "practice makes perfect" is well established, and remembering that our brains are plastic and nothing is set in stone, are good things to know when dealing with mental illnesses.

Transplant Complete (Sort of)

So I came home last Monday from the transplant process, the hospital stay wasn't quite four weeks long. I think I went in on November 11th and left on December 5th.

So far things have been going about as well as can be expected, I'm still having some issues but that's normal. The transplant process itself went fine, and the next 100 days will be careful watching for symptoms of graft vs. host disease, so I'll have a couple appointments a week for a while, if things keep going well it'll drop down to once a week. 

I'm sort of quarantined a little bit, they want me to avoid crowds and school aged kids, but I can have visitors, they recommended keeping it to no more than 2-3 at a time. 

My sense of taste is probably the worst symptom at the moment, it makes it pretty hard to eat. Oddly I can still smell food pretty well, but most of it tastes kind of bad. Sweet things are decent, but salt is very absent. 

That's about it for now. Just a lot of waiting and taking my time with things.

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Home Again for Now

So I was released on Wednesday, the 19th, and have been home the last two days. My ANC was 320 Wednesday morning, which was really discouraging, since it had been 400 the day before and they had told me if it remained at 400 I could go home. So I spent a few hours thinking I'd be stuck there at least a few more days. But then later in the day they told me that they don't think anything weird is happening, my numbers are just kind of bouncing around a bit, which is fairly typical, and since I've been through all this repeatedly they trust me to look for signs of infection and seek medical help if I have any complications. And since I was just waiting around to recover, I might as well do that in the comfort of my own home. So I got to go home! They wanted to give me a blood transfusion before leaving, cause my hemoglobin was like 7 something, and outside the hospital they want it to be at least 8, so they did a transfusion and then another blood count and it was really good news, my ANC had gone up to 370, my hemoglobin was 9 I think(?) and my platelets had ticked up a little bit from the morning as well. 

They did a bone marrow biopsy on Monday, but it was kind of too early, there were blast cells, which could potentially be leukemia cells, but they may also just be normal healthy cells that haven't matured yet. So they'll want to perform another biopsy sometime soon, this week probably, and if that looks good I should be all ready to start the transplant process at MGH. On Monday I'll go in for a more routine checkup to make sure the numbers are looking good, and then my hope is, if all that checks out, we can go into the transplant process as soon as is possible. I'm nervous about it, but I'm more nervous that any waiting is giving the leukemia cells more time to regrow.

Someone contacted me about reworking the octopus to be smaller. I've wanted to redesign a lot of things about it for a long time, so I might actually try to do that finally. It has me digging through old project files trying to decide how to go about it. I had also begun a cuttlefish model not long ago, so I might just start with that instead. I think I should learn about rigging the model up this time, so I can more easily rearrange the legs in the future.

An End Within Sight

So my ANC has started to bounce back the last few days, 0 to 40 to 30 to 80 to 90 and then 160 today, and so I'll probably be going home sometime in the next few days, maybe Wednesday Thursday or Friday (not likely tomorrow).

I had an infection last week, my temperature briefly spiked to about 102, so they put me on antibiotics and started taking blood cultures to look for bacteria — usually when they've done that for past fevers they never find anything, in this case they found two species of bacteria, one associated with the guts and the other associated with the skin. I had bit my lip kinda bad a few days earlier, and possibly burned a little bit of my lip and tongue on some hot dinner, so it's possible that was part of it. But my PICC (the catheter that goes in my arm to deliver the chemotherapy drugs more directly into my blood stream, near my heart), started feeling sore so they pulled it out and figured it might have developed an infection, which is where the skin species of bacteria might have come from. It also developed a clot, superficial, but for a while kind of uncomfortable. They're not really worried about it being a problem, I guess pumonary embolisms tend to be clots in your legs that dislodge and travel to your lungs, often causing serious problems. Being in my arm, and not being so bad as to actually block blood flow out of my arm, are good signs it shouldn't be as troublesome. But as a result I'll have to stay on an anticoagulant until my body naturally destroys the clot with enzymes. (To prevent the clot from getting bigger as my platelets return.) So I'm not real excited about that.

The other thing I'm a bit bummed about is they're saying I'll have to stay on IV antibiotics for a few more days, till Monday, so they'll probably want to put another PICC in me to deliver the antibiotics, instead of the perhiphial IV they're using now. I'm still trying to convince them if the IV is still working when I leave that should be enough, but we'll see. The IV nurse who put it in took some extra steps to make it better, like using an ultrasound to find a bigger vein, and putting a special dressing on it to help kill bacteria, like they normally would with a PICC. And the nurses have been keeping me on a slow drip of saline to keep the vein open. Still, the doctor didn't seem very open to the idea.

I'm not sure about the longer term plans. This morning the doctor said they'd probably have me come in for one more outpatient biopsy to make sure I'm clean before going to Boston for the transplant process. Which made me a little nervous that with all the time in between I could get stuck in this perpetual state of needing re-induction chemotherapies, which cause complications, which delay the transplant, which gives more time for the leukemia cells to return — but I'm pretty sure that's just fear getting the best of me. It must be pretty obvious to them the importance of getting to the transplant as soon as possible.

In any case, I'm anxious to get it started, I don't want it to be delayed any more. 

So most of the last week I felt pretty immobilized, the last few days I've started to come out of that, eating solid food again (I was avoiding it for a while, it was irritating my tongue and lip too much). Now that I'm feeling more normal again I'm trying to get going with programming again, to explore some cellular automata type approaches to drawing, and if I can figure that out maybe I'll start pursuing the variations to minesweeper I had been contemplating for the last couple years. If only for my own entertainment. 

I'm feeling pretty burnt out about politics — I wish I didn't feel so obligated to be vocally political, but if Hillary loses I'll blame myself for not doing more early on. And it would be so great to see a Supreme Court dominated by justices that value reality over ancient superstitions (Scalia believed the devil exists and was trying to actively discourage people from belief in his god). It'd be nice to see them stand up for voting rights, for the right to abortion, and gay rights, healthcare, firearms, campaign finance, and on and on... My whole life it's been a sharply divided court, mostly along the party lines of the presidents who appointed them. With Scalia dead, Ruth Bader Ginsburg 82, and two more justices aged 78 and 79, it seems possible the next president will appoint as many as four new justices. It'd be depressing to see them be the expression of the same tired old ideas that should have been dead and buried last century.

Anyway, rant over.

Biopsy Good!

I thought about titling this post “biopsy negative!” but decided that could be misinterpreted, and “biopsy positive” could definitely send the wrong message, so I went with the primitive sounding “biopsy good”.

So this morning the doctors came in to tell me they didn't find any signs of the leukemia in my bone marrow, so I'm back in remission. Now it's a matter of waiting likely another 11-21 days (could be shorter, or longer), for my immune system to regrow enough to fight off infection on it's own. Then, assuming I'm in good health (which seems likely right now, I walked three miles last night without difficulty), then I'll head to Boston to begin the transplant process. I guess there's a chance I could get a fever, as I did in the past, before my immune system is mature again, in which case that would delay things a bit, but once I'm strong and healthy we'll try the transplant.

I'm nervous about the transplant process, there's a lot of uncertainty, but in my favor are my age and health, and this is the best shot at curing me, or at least prolonging my life for a good while, so I'm also anxious to begin — the sooner it starts the sooner I'll be able to work on recovering and finding out if it worked or not. And also the less likely the leukemia cells will regrow into a problem again.

I guess I could mention too, I'm at the stage where the later chemotherapy effects are starting to happen, my hair is just beginning to fall out, and my sense of taste seems to be changing again, though it's hard to explain exactly how. In both cases they seem like relatively harmless effects, I've been lucky that my digestive tract has remained pretty healthy, and my mouth too. Sores in the mouth are a common symptom and so far I haven't really had that, though a couple days ago my platelets were very low and I apparently accidentally bit my cheek while eating a cookie, and a blood blister formed right away. But I got a platelet transfusion the next morning and I'm not much of a bleeding risk again for now, and the blood blister is going away quickly.

Chris, the Creative Visual Artist for the Norris Cotton Cancer center, (where I've been treated all this time — which just reminded me, someone asked for my address and I forgot who...), asked me to share some of my photography for an artshow later in October, so I need to write up an artists' statement and get a couple pictures printed, and framed, to be hung. That'll be fun. And after I post this I'm going to go back to fiddling around with some programming ideas, see if I can get back into the programmer mindset.

Thanks for reading!