DIYPS

Infection is not inevitable: how to stop the spread of infections like COVID-19, flu, RSV, colds, and more in your house

by Dana Lewis

I observe a number of people who seem to think it’s inevitable that once someone gets sick, the rest of the house is going to get sick with 100% certainty.

Nope.

First of all, household transmission rates are less than 100% for all of these conditions, even if you didn’t take any precautions or make any behavior changes.

Secondly, with knowledge about how these things spread and some mitigation measures, you can reduce this a lot – and in some cases to nearly zero.

I will caveat: that of course depending on the situation some of these precautions may not make sense or be possible. For example, if you have kids, your exposures may be different. We don’t have kids in our house, so we are dealing with adult to adult possible transmission. That being said, some of these things may still be worth doing to some degree, to cut down the risk of exposure and/or to limit the viral dose you are exposed to, even in a situation that is less straightforward like a parent taking care of sick kids.

PS – if you’re reading this in January 2025 and don’t read the rest, make sure you’ve gotten your flu shot (yes, it helps) for the 2024-2025 flu season. No, it’s not too late. If you’re >65, you should also check about the RSV vaccine (which like the flu shot is a seasonal vaccine). It’s not too late and given the current high rates of RSV and flu (and soon to be uptick in COVID), they can help prevent getting or limit the severity if you do get exposed.

Our experience preventing the spread of RSV and the common cold

I can speak with recent, practical experience on this.

Twice.

First, let’s talk about RSV.

Before Thanksgiving, Scott and I were exposed to a nibling (aka a niece or nephew – of which we have 10 plus several honorary ones!) who had what we thought was a lingering cough from a cold from a few weeks ago. Because I am avoiding infection, I wore a mask inside and did not get up close to the nibling, so as a result of all of this likely had minimal exposure. Scott did not mask and had spent a lot more time with this nibling hanging all over him and coughing near or on him. Within 48 hours, he started to get symptoms of something.

We activated our plan for household transmission avoidance. Well, with a rolling start: Scott recognized by Thanksgiving evening that he was starting to feel unwell and had a tiny bit of coughing. I thought I could hear something in his chest differently, in addition to the occasional cough, so I went into full precaution mode while Scott did a partial precaution mode. This meant we set up air purifiers by each of our beds, and a fan pointed in my direction so all air was blowing away from me. I also wore a mask to go to sleep in. (This was super annoying and I don’t like doing this, especially because I usually take a shower and go to bed with wet hair. Wearing an n95 with head straps on wet hair plus having a fan and purifier blowing on me is chilly and unfun.) I would’ve preferred Scott to mask, too, or go to the guest bedroom to sleep, but it was late in the evening; he wasn’t convinced he was really sick; and I was too exhausted to argue about it on top of the fact that we were leaving on a trip the next morning. So he did not mask that night.

The next morning, though, he was definitely sick. He tested negative for COVID, and the nibling and everyone else from that house had been testing for COVID and negative, so we were fairly confident based on serial testing that this was not COVID. At the time, the thought was this was a common cold.

Since we were planning to mask in indoor spaces, anyway, including in the airport and on the plane, we felt comfortable going on our trip as planned, because we would be unlikely to infect anyone else. (This includes no indoor dining: we don’t take off our masks and eat inside.)

Because Scott realized he was sick, he masked from that point forward (with a non-valved N95). We both masked in the car, in the airport, on the plane, and again when we arrived while driving in the rental car. Then a challenge: we needed to eat dinner (we got takeout), and we were sharing a hotel room overnight. We switched from a hotel room with a king bed to a room with two queen beds, which would give us some more space overnight. But we took turns eating dinner unmasked in the hotel room (it was too cold to be outside) with the far-UVC lights on and the purifiers around each of us when we ate. While we ate, the other person was masked. (And I went first, so there was no unmasked air from Scott while I was eating and he went second). We also took turns showering, again with me going first and him not having been in the bathroom unmasked until after I had gone in. Other than that, we stayed masked in the hotel room including overnight, again with purifiers between us and the far-UVC lights running.

(This hotel did not have windows that opened to outside, but if there had been windows I would’ve eaten in front of the open window and we would’ve likely kept it cracked open and the heat turned up, to improve the room’s ventilation).

The next day, we had more of a drive, and again we masked. We also slightly rolled down the windows in the backseat to improve ventilation. Scott sometimes took his mask off for comfort stretches, because he was driving, but put it back on fully and sealed it before coughing. I kept my mask on without ceasing. We did a 4.5 hour drive this way.

Luckily, once we arrived at our destination, there was a spare bedroom, so that became Scott’s headquarters. He stayed masked in the living room/shared areas. He sat downwind outside and masked up when coughing if anyone was outside. We left the sliding door to the outside cracked open, in order to keep the air in the common areas well-ventilated. This worked, because we were able to keep CO2 levels (a proxy for ventilation) down below 700 ppm most of the time.

Because we had separate bedrooms, we did not mask while sleeping the rest of the week, because we each had our own rooms (and own airflow). I did keep a purifier running in my room all week, but that’s my habit regardless because I’m so allergic to dust.

And guess what? It all worked. We masked again on the drive back to the airport and in the airport and on the plane and again once we got home.

I never got RSV. The four other adults we spent time with and shared a house with….also did not get RSV. So we are pretty confident that the transmission chain stopped completely at Scott.

In summary, what worked:

  • Masking in shared spaces, and two-way masking when it wasn’t possible to ventilate
  • When we had to sleep in the same room, two-way masking even for sleeping overnight
  • Scott masking in shared spaces that were well ventilated, and often left the room to go cough even when masked (or coughing outside). This often meant he masked, but the rest of us did not mask inside the whole time.
  • Generally keeping distance. Droplets were managed by the N95 mask, and we were ventilating to reduce aerosol transmission risk, but still keeping physical distance to further reduce the risk.

RSV is *very* transmissible especially with aerosols, and Scott was coughing a lot all day and night. (At one point, his Sleep Cycle app was estimating 18 coughs per hour). It took a long time for that to get down to normal, so he continued to sleep in our guest room when we got back and we continued to ventilate well even when we gradually reduced masking once he stopped coughing. It took about 10 or so days for all of his biometrics to normalize, and about 14 days for his cough to completely go away. It probably was closer to three weeks before he finally felt all recovered.

So with that timing in mind, you know what happens 4 weeks after Thanksgiving? Christmas/other end of year holiday gatherings.

We had plans to see 8 kids and 8 adults (plus us) for Christmas. And at Christmas, it seemed like everyone had a cold already. So again, I went in and mostly masked except for when I was in front of an open window and the room was well ventilated, without anyone coughing actively in the room. (If anyone was in the room with me and coughing, especially the kids, I would mask even with the window open).

I did not get the cold that 8-10 (out of 16) people eventually got.

But…Scott did. And this time, he was mostly masked, but he still spent more time up close with kids who were coughing quite a bit. And this is where some of the dynamics of knowing WHAT people have is helpful. You can’t always know, but you can sometimes use the symptoms to figure out what people have.

For example, based on symptoms of the nibling who passed on germs to Scott around Thanksgiving, and Scott’s symptoms (instant, incredible chest cough but no runny nose, sore throat, fever, or aches) we had ultimately guessed that Scott had RSV. We then knew that the biggest risk was either droplets from coughing (especially because the volume of coughing), which could be reduced drastically by masking, or aerosols, which again would be helped by his masking and also ventilation, and in closed spaces, two-way masking (me masking).

For the Christmas germs, everyone seemed to have mild symptoms with congestion, runny noses, some coughs. But no fevers or aches and it seemed less severe. Given our recent experience with RSV, we narrowed it down to likely being a cold (rhinovirus), given again everyone testing repeatedly negative for COVID.

Given that, we knew the risk was going to be highest for us from droplets and fomites. So we again masked in shared spaces; Scott went to sleep in the guest bedroom as soon as he started getting symptoms; and we both did a lot of hand washing. Scott washed his hands before touching any of my things and regularly wiped down the kitchen. I tried not to go in the kitchen much (our main overlapping shared space), but also wash my hands after any time that I did. He didn’t have much of a cough and it was more controlled, so he would hold his cough until he could cover it with a mask or be in the room by himself. We also did our usual running of purifiers and opened windows and ran fans to increase ventilation to keep CO2 low.

And again? It worked. I did not get the cold, either from any of the ~8+ folks who did across the holiday period, or from Scott. Scott’s vitals all returned to normal at the five day mark, although we continued to mask in the car through day 7, to be more cautious (due to my personal situation).

So, infection is not inevitable, even in small houses and apartments.

Here’s what we’ve taken away from these experiences with more aerosol-based (RSV) transmission diseases and more droplet and fomite-based (cold) experiences:

  1. Two-way N95 masking works. Mask in the car, run the fan, keep the windows cracked, run purifiers at home, and ventilate spaces, but you still want two-way masking when something is aerosolized and you’re in the same spaces. This can prevent transmission.
  2. Keep distance when someone is coughing and sneezing (and if they have a cough or sneeze type illness, you want 6 foot distance even when they’re not actively coughing or sneezing, because they make droplets just from breathing and talking). The person who’s coughing and sneezing should mask, even inside, unless they are in their own room in private (and it’s not a shared room).Keep your air ventilated (if you haven’t, read my post about ventilation and using a Co2 monitor)Depending on the illness, to fully protect yourself you’ll need to commit to wearing a mask at all times indoors to protect yourself if the person who is sick is not masking. (Eg, Scott got a cold while mostly masked around heavily coughing niblings, but not throughout the whole house the whole day). With adults, the adults who are sick should definitely mask if they’re in shared spaces with other adults. (It’s harder with kids, and it should be a conversation depending on the age of the kids about them masking in shared spaces, such as if they want to play with Uncle Scott, or help them understand that someone may not want to play up close if they’re sick and coughing and not willing to mask. That’s fine, but that’s a choice they can make when kids are old enough to understand.)
  3. Have the infected person sleep in a different space (on the couch or in another room if you have a spare bedroom). If you have to share a room, both should mask.
  4. Use cleaning wipes to wipe down shared surfaces (e.g. fridge handles, microwave, counters, bathroom surfaces like the flush on the toilet or sink faucet, etc) and wash your hands after using these shared spaces every time. Fomites can last longer than you’d expect.
  5. Use metrics from your wearable devices (eg Apple Watch or Oura ring or similar) to track when your temperature, respiratory rate, heart rate, cough rate, etc. return to normal. That tied with symptom elimination can help you determine how long you’re likely most infectious for. The general estimates of contagiousness for each condition generally seem to be right (e.g., two weeks for an adult with RSV and 5-7 days for a cold) in our recent experiences. I would continue precautions for at least those minimum time frames, if you can.
  6. Yes, there’s a cost to these precautions, in terms of human contact. There was no hugging or hand holding or kissing or any touch contact during these time periods. I felt pretty lonely, especially because it was me we were trying to protect (because I am at high risk for bad outcomes due to immunosuppression right now), and I’m sure Scott also felt lonely and isolated. That part sucked, but we at least knew it was a fixed period of time, which helped.

What we’d do differently next time

Infection is not inevitable -how to reduce transmission of illness in your household (including COVID-19, RSV, flu, and the common cold), written by Dana M. Lewis from DIYPS.orgThis basically has been our plan for if either of us were to get COVID-19 (or the flu), and it’s good to know this plan works for a variety of conditions including RSV and the common cold. The main thing we would do differently in the future is that Scott should have masked the very first night he had symptoms of RSV, and he has decided that he’ll be masking any time he’s in the same room as someone who’s been coughing, as that’s considerably less annoying than being sick. (He really did not like the experience of having RSV.) I obviously did not get it from that first night when he first had the most minor symptoms of RSV, but that was probably the period of highest risk of transmission of either week, given the subsequent precautions we took after that.

Combined, everything we did worked, and we’ll do it again when we need to in the future, which should not be very often. We went five full years without either of us getting any type of infection (yay), and hopefully that continues from here on out. We’ll also continue to get regular COVID-19 boosters; annual flu shots; and other annual shots if/when they become available (e.g. when we reach the age, getting the RSV vaccine).

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Remember, if you’re reading this in January 2025, RSV and flu levels are very high in the US right now, with COVID-19 expected to pick up again soon. It’s not too late to get your boosters and given the rates of respiratory illness, consider situational masking even if you don’t typically mask.

Power outage, winter heat, battery, and other tools and solutions

by Dana Lewis

We recently had a multi-day power outage. Ugh. It luckily wasn’t so cold we needed to go find a hotel to stay in (or stay overnight with family elsewhere), but it was chilly, inconvenient, and annoying. We have done a lot of preparation for power outages, though, because we often get a handful a year during really windy storms around here. We found ourselves pleasantly surprised with the utility of a couple of things and wanted to share with other folks. Most of these serve two purposes, but work really well in a power outage situation. I’ll describe what we got them for originally and how we use them in a power outage. (PS – we bought all of these on Amazon, and I’m sharing these links as Amazon affiliate links).

Lights
Sure, your phone has a flashlight, but if you’re spending hours without power, it makes a surprising psychological difference to have at least a little light in the room(s) you’re spending time in.

Our first go-to is the fact that our bigger batteries (more details on them below) have decent lights that can be turned on. Point it toward a wall or set it upright and point to the ceiling, and you have enough light to see the room by. And your brain is going to be less stressed. Win.

The other lights we have had for years are high powered, rechargeable LED waist or head lamps. I *love* these, which I got for ultrarunning. The ones we got come in a pack of two, and what I do is deconstruct them and link the two bands together, essentially making one band that has both lights and backlights on them. I point one toward the front, and one to the back. The battery pack and red light part that usually goes on the back is facing the sides. These are really bright, and good enough to wear around my waist when running or walking in the dark, and I don’t use a headlamp with them. So that’s why we had them, and they’re usually the second light source we go to in a power outage. Scott will wear one as a waist lamp or pendant lamp as he moves around. The other thing we realized this time is that you can hang it over a standing lamp and the light reflects off the wall really well (and at height), which is a nice complement to any other lower light sources you have.

Some of our small battery power banks we use for charging phones or little electronic devices have lights, too, that are more similar to your phone’s flashlight. I wouldn’t buy these for the sake of these lights, but it’s handy to know if any of your power banks have lights so you can use them in a power outage, too.

The last set of lights I’ll mention are new in our collection this year. We got them for our pantry, which doesn’t have lights. These are motion sensor lights that trigger when we open our pantry door and stand there looking in the pantry. They flip off after a few seconds in auto mode. They are rechargeable, but we found that they lasted for months on auto without needing recharging. Once we hit the power outage, Scott pulled one out of the pantry and realized it magnetically attaches to the light fixture in our bathroom. There’s four brightness settings, and you can also switch it to stay on. So if you are in the bathroom and using that room, you can switch it to “on” and it’s a great light source, then switch it back off (to motion sensor mode) when you’re done in there. We thought they were so useful that we went ahead and ordered a second set to use in the house and leverage for a future power outage.

Heat

We were lucky this time that it was only 40-50F for most of our power outage. That being said, we did get chilly and it got chillier every day. I tend to run cold anyway and use a heating pad at the foot of my bed normally, so without that…brrrr. We’ve gotten all of these things over the years to make hiking and walking and skiing in the cold and wet more comfy, so like the lights these all have primary uses beyond power outages, but they doubled up nicely to serve us during the outage, too.

(By the way, heating pads have changed since we were kids. I resisted getting another or a new heating pad for about a year. Because the heating pad I had was ~10-15 years old and one of those old style plasticky ones with a blue scratchy fabric cover over it. I hated the plastic. Then I finally looked online and was shocked that they come in different colors – I could get purple! – and sizes and they aren’t plastic anymore. Woohoo! So, I now own multiple heating pads in different colors and sizes. Mentioning that in case anyone else has a historical heating pad and doesn’t know there are better options now! The one I got isn’t listed anymore, but this one looks similar, other than color choice (which might be under a different listing).)

A heated vest is one of the things Scott used the most. We originally chose this one (there are a ton of options from different brands and different styles) because we wanted one that could heat the back as well as the front. This one you can turn on each of those independently, and there are also three different levels of heat. If you’re chilly but don’t want to be bundled up inside in a coat with sleeves, this is a great choice. (I wear it a lot on wet days for outside activities, putting it on under a rain jacket).

The other thing we use a lot and used in the outage to stay warm is fingerless heated gloves. We have big, full finger heated gloves, too, but those are more like bulky ski gloves and don’t work well for me (because I have especially small hands). In fact, we have two sets of full finger heated gloves, because last year we bought a small pair for me to use for cross country skiing…and they were way too big for me. Scott adopted that pair, and we found another pair that was a smidgen smaller. They’re still bulky and make it hard to do anything, but when hiking or skiing in the rain, they’re perfect. Otherwise, when on walks where I want to use my phone or at home in power outages, I like the new fingerless heated gloves we got. Again, if you have small hands like I do, measure your hand and check the measurements on heated gloves (fingerless or full finger) when you order, most of the “small” to “small/medium” or “one size fits all” are huge on me. The ones I got are a little big through the palm and wide on the fingers, but because they’re fingerless, they’re still functional. I’ve actually surprised myself with how often I’ve been wearing them on slightly wet days when heading out for a walk and are on the list of “I can’t believe it took me so long to discover/figure out I should buy these”, just like the modern era heating pads. If you get cold at work and your hands get really cold, these are the kind I would look for. But I also highly recommend them for outdoor activities, too.

Food prep and heating

Speaking of heat, let’s talk food. After multiple days, even if you have available ready to eat food, it gets old. We bought a 12 volt DC hot plate in a zipper bag (check the picture if that description doesn’t make sense) to use on long car trips and for after big hikes and ultramarathons, when I wanted to be able to eat and refuel on a long drive home. It works awesome in the car for things like a frozen dinner or a shallow tupperware container of stew or chili (check the size of your tupperware to make sure it fits; shallow square ones work best in the one I got); but also warming up savory biscuits or sandwiches or scones or leftover pizza. Pretty versatile, and easy to clean even when using between a gluten eater (Scott) and someone with celiac. This is also one of our go-to’s for if we have an extended power outage and want hot food if there’s nothing in the area and we don’t want to or can’t drive to an area with power. Ready to eat canned soup or stew into a tupperware into the hot plate container, and like light in the room…it’s just going to make everything else feel a little less stressful than it would be otherwise.

Battery and batteries and batteries galore

We have two large (250Wh+) power stations, and lots of smaller (5-30Ah / 20-100Wh) power banks. One of the power stations has a working AC inverter, allowing us to power a heating pad for a few hours, recharge the more portable power banks, or keep all of our electronics powered/charging all night. The other used to have an AC inverter, but its cooling fan sounded like a helicopter, so we weren’t too sad when its AC outlet broke. Now we just use its built-in light, its 12V DC auto outlet (e.g. for the hot plate), its USB ports for charging electronics, lights, or smaller power banks, and/or its 12V DC barrel plug outlet to charge the power station whose inverter still works.

The smaller “phone charger” power banks are pretty much interchangeable with the ones you probably already have. Some of them (like the Anker one) support wireless phone charging, and serve nicely as a plugged-in wireless charger until you want to unplug them and take them with you. A couple of the larger ones (like this one, which we recently got) support USB-C PD at high enough wattage to keep my laptop’s battery from draining while I use it, or even (slowly) charge it.

Keeping batteries topped off is a bit of a chore during a long outage. What we found works best with two power stations is:

  • Keep a 12VDC to AC inverter in the car, and use it to recharge one of the large power stations at a time (via its AC to 15VDC adapter), and any smaller power banks that you’ve used up (via USB). (You probably don’t want to try to plug in multiple 15VDC adapters at once, or you risk blowing your car’s 12VDC fuse/breaker.)
  • Keep the other power station in the house for AC needs, to keep other electronics, lights, and small power banks topped off. When its battery gets low, swap the two power stations.

If you live in a sunnier climate, these kinds of power stations can be recharged via solar panels, but for a Western Washington November windstorm, we didn’t even bother getting our solar panel out of our camping bag. If you plan to use PV, you might want to buy an integrated kit to ensure optimal compatibility between the PV panel and the power station’s charge controller.

Outside of a power outage situation, Scott mostly uses these power stations as range extenders for his e-bike. He has two e-bike batteries, so can take both of those and a power station in the saddle-bags and charge one battery off the power station while using the other one. On a long ride without too much pedal assist, he can fully drain a power station to get an extra ~15mi of range.

Ice and keeping things cold (and safe)

While we are talking about power outages, we’ll share some of what we found works for us in terms of managing our fridge and freezer, too. This is less on the “here’s things you can buy” list and more “here’s information your brain can consider in the future” if you have an extended power outage.

Before the power goes out, we make sure we have lots of frozen ice packs (and/or ice) scattered around your freezer.

When the power goes out:

  • Eat ice cream until you’re full. The ice cream will be a lot tastier before it melts.
  • Take a hot shower: the hot water won’t stay hot for more than a few hours.
  • Put a few of the ice packs in the fridge to keep it cold.
  • Leave the fridge door mostly shut. You can quickly grab things out as needed: just don’t stand there with it open deciding what you want to eat. The objective is to keep the temperature from rising too much at once, as it takes a lot longer than normal to cool back down just from ice packs.
  • When you’re tired of ice cream and get hungry, eat leftovers, etc. out of the fridge (cold, or heated up on the 12VDC hot plate).

If the power is still going to be out by the time your ice packs melt:

  • Drive to a nearby area that still has power, and buy a few bags of ice from a convenience store, Walmart, etc.
  • Pour the bagged ice out into gallon ziploc bags: the bags it comes in will leak when it starts to melt.
  • Put at least two gallons of ice in the fridge and two gallons in the freezer.

When the power comes back on:

  • Check that you still have un-melted ice in both the fridge and freezer. If not, your remaining food may not be safe. (40F is when bacteria can start to grow, which is why if you’re in doubt, you should toss it out. But if you keep frozen packs frozen… you may not have to toss everything out.)

Electric vehicles as a power assist

We have an EV (a used 2018 Tesla Model 3), and it worked quite well. It can’t power the whole house like an F150 Lightning or a Cybertruck, but with a 12V to AC inverter, can recharge power banks of all sizes, without having to worry about running the battery down or idling the engine to avoid it. The battery lasts for weeks if we don’t drive it, or longer if we leave Sentry off. If we go anywhere, we can charge at our destination or Supercharge on the way. And even with 500k people without power, the nearest powered Supercharger was only a 10m drive from here.

What we wished we had (and didn’t, yet)

The main thing we were missing was having fast enough Internet. We had cell service, so we could hotspot with our phones, but during the day when everyone’s doing that it’s unusably slow for working from the laptop. Zoom still worked via phone, but in order to get any “real work” done, we wanted “real” Internet. This time around, we got that (and hot showers) by driving up to Scott’s parents’ house, where they never lost power. But to be ready for next time, and for back country hikes and long road trips, we ordered a Starlink Mini. It’s a bit pricier than a regular Starlink dish, but is only about the size of a laptop, works off a power bank, and can be easily used in the car. We got the $50/mo 50GB plan, which we can pause and reactivate at any time, paying $50 only for the months we want to use it. We’ll likely post an update later once we use it a bit. (If you want a Starlink referral code for either a regular Starlink or a Starlink mini, this referral code gives you one month of free service.)

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TLDR: it’s nice when you have things that can pull double duty in regular life and in power outages. Our list includes a lot of lights; a lot of heating options; batteries galore; and strategies for keeping our food cold or hot as desired.

If you have any favorite double duty tools or solutions we should get, that you love for power outages and other use cases, please comment and describe them so we – and everyone else – can check them out!

Multi-day power outage: batteries, power sources, heating, and other things that worked well

Pain and translation and using AI to improve healthcare at an individual level

by Dana Lewis

I think differently from most people. Sometimes, this is a strength; and sometimes this is a challenge. This is noticeable when I approach healthcare encounters in particular: the way I perceive signals from my body is different from a typical person. I didn’t know this for the longest time, but it’s something I have been becoming more aware of over the years.

The most noticeable incident that brought me to this realization involved when I pitched head first off a mountain trail in New Zealand over five years ago. I remember yelling – in flight – help, I broke my ankle, help. When I had arrested my fall, clung on, and then the human daisy chain was pulling me back up onto the trail, I yelped and stopped because I could not use my right ankle to help me climb up the trail. I had to reposition my knee to help move me up. When we got up to the trail and had me sitting on a rock, resting, I felt a wave of nausea crest over me. People suggested that it was dehydration and I should drink. I didn’t feel dehydrated, but ok. Then because I was able to gently rest my foot on the ground at a normal perpendicular angle, the trail guides hypothesized that it was not broken, just sprained. It wasn’t swollen enough to look like a fracture, either. I felt like it hurt really bad, worse than I’d ever hurt an ankle before and it didn’t feel like a sprain, but I had never broken a bone before so maybe it was the trauma of the incident contributing to how I was feeling. We taped it and I tried walking. Nope. Too-strong pain. We made a new goal of having me use poles as crutches to get me to a nearby stream a half mile a way, to try to ice my ankle. Nope, could not use poles as crutches, even partial weight bearing was undoable. I ended up doing a mix of hopping, holding on to Scott and one of the guides. That got exhausting on my other leg pretty quickly, so I also got down on all fours (with my right knee on the ground but lifting my foot and ankle in the air behind me) to crawl some. Eventually, we realized I wasn’t going to be able to make it to the stream and the trail guides decided to call for a helicopter evacuation. The medics, too, when they arrived via helicopter thought it likely wasn’t broken. I got flown to an ER and taken to X-Ray. When the technician came out, I asked her if she saw anything obvious and whether it looked broken or not. She laughed and said oh yes, there’s a break. When the ER doc came in to talk to me he said “you must have a really high pain tolerance” and I said “oh really? So it’s definitely broken?” and he looked at me like I was crazy, saying “it’s broken in 3 different places”. (And then he gave me extra pain meds before setting my ankle and putting the cast on to compensate for the fact that I have high pain tolerance and/or don’t communicate pain levels in quite the typical way.)

A week later, when I was trying not to fall on my broken ankle and broke my toe, I knew instantly that I had broken my toe, both by the pain and the nausea that followed. Years later when I smashed another toe on another chair, I again knew that my toe was broken because of the pain + following wave of nausea. Nausea, for me, is apparently a response to very high level pain. And this is something I’ve carried forward to help me identify and communicate when my pain levels are significant, because otherwise my pain tolerance is such that I don’t feel like I’m taken seriously because my pain scale is so different from other people’s pain scales.

Flash forward to the last few weeks. I have an autoimmune disease causing issues with multiple areas of my body. I have some progressive slight muscle weakness that began to concern me, especially as it spread to multiple limbs and areas of my body. This was followed with pain in different parts of my spine which has escalated. Last weekend, riding in the car, I started to get nauseous from the pain and had to take anti-nausea medicine (which thankfully helped) as well as pain medicine (OTC, and thankfully it also helped lower it down to manageable levels). This has happened several other times.

Some of the symptoms are concerning to my healthcare provider and she agreed I should probably have a MRI and a consult from neurology. Sadly, the first available new patient appointment with the neurologist I was assigned to was in late September. Gulp. I was admittedly nervous about my symptom progression, my pain levels (intermittent as they are), and how bad things might get if we are not able to take any action between now and September. I also, admittedly, was not quite sure how I would cope with the level of pain I have been experiencing at those peak moments that cause nausea.

I had last spoken to my provider a week prior, before the spine pain started. I reached out to give her an update, confirm that my specialist appointment was not until September, and express my concern about the progression and timeline. She too was concerned and I ended up going in for imaging sooner.

Over the last week, because I’ve been having these progressive symptoms, I used Katie McCurdy’s free templates from Pictal Health to help visualize and show the progression of symptoms over time. I wasn’t planning on sending my visuals to my doctor, but it helped me concretely articulate my symptoms and confirm that I was including everything that I thought was meaningful for my healthcare providers to know. I also shared them with Scott to confirm he didn’t think I had missed anything. The icons in some cases were helpful but in other cases didn’t quite match how I was experiencing pain and I modified them somewhat to better match how I saw the pain I was experiencing.

(PS – check out Katie’s templates here, you can make a copy in Google Drive and use them yourself!)

As I spoke with the nurse who was recording my information at intake for imaging, she asked me to characterize the pain. I did and explained that it was probably usually a 7/10 then but periodically gets stronger to the point of causing nausea, which for me is a broken bone pain-level response. She asked me to characterize the pain – was it burning, tingling…? None of the words she said matched how it feels. It’s strong pain; it sometimes gets worse. But it’s not any of the words she mentioned.

When the nurse asked if it was “sharp”, Scott spoke up and explained the icon that I had used on my visual, saying maybe it was “sharp” pain. I thought about it and agreed that it was probably the closest word (at least, it wasn’t a hard no like the words burning, tingling, etc. were), and the nurse wrote it down. That became the word I was able to use as the closest approximation to how the pain felt, but again with the emphasis of it periodically reaching nausea-inducing levels equivalent to broken bone pain, because I felt saying “sharp” pain alone did not characterize it fully.

This, then, is one of the areas where I feel that artificial intelligence (AI) gives me a huge helping hand. I often will start working with an LLM (a large language model) and describing symptoms. Sometimes I give it a persona to respond as (different healthcare provider roles); sometimes I clarify my role as a patient or sometimes as a similar provider expert role. I use different words and phrases in different questions and follow ups; I then study the language it uses in response.

If you’re not familiar with LLMs, you should know it is not human intelligence; there is no brain that “knows things”. It’s not an encyclopedia. It’s a tool that’s been trained on a bajillion words, and it learns patterns of words as a result, and records “weights” that are basically cues about how those patterns of words relate to each other. When you ask it a question, it’s basically autocompleting the next word based on the likelihood of it being the next word in a similar pattern. It can therefore be wildly wrong; it can also still be wildly useful in a lot of ways, including this context.

What I often do in these situations is not looking for factual information. Again, it’s not an encyclopedia. But I myself am observing the LLM in using a pattern of words so that I am in turn building my own set of “weights” – meaning, building an understanding of the patterns of words it uses – to figure out a general outline of what is commonly known by doctors and medical literature; the common terminology that is being used likely by doctors to intake and output recommendations; and basically build a list of things that do and do not match my scenario or symptoms or words, or whatever it is I am seeking to learn about.

I can then learn (from the LLM as well as in person clinical encounters) that doctors and other providers typically ask about burning, tingling, etc and can make it clear that none of those words match at all. I can then accept from them (or Scott, or use a word I learned from an LLM) an alternative suggestion where I’m not quite sure if it’s a perfect match, but it’s not absolutely wrong and therefore is ok to use to describe somewhat of the sensation I am experiencing.

The LLM and AI, basically, have become a translator for me. Again, notice that I’m not asking it to describe my pain for me; it would make up words based on patterns that have nothing to do with me. But when I observe the words it uses I can then use my own experience to rule things in/out and decide what best fits and whether and when to use any of those, if they are appropriate.

Often, I can do this in advance of a live healthcare encounter. And that’s really helpful because it makes me a better historian (to use clinical terms, meaning I’m able to report the symptoms and chronology and characterization more succinctly without them having to play 20 questions to draw it out of me); and it saves me and the clinicians time for being able to move on to other things.

At this imaging appointment, this was incredibly helpful. I had the necessary imaging and had the results at my fingertips and was able to begin exploring and discussing the raw data with my LLM. When I then spoke with the clinician, I was able to better characterize my symptoms in context of the imaging results and ask questions that I felt were more aligned with what I was experiencing, and it was useful for a more efficient but effective conversation with the clinician about what our working hypothesis was; what next short-term and long-term pathways looked like; etc.

This is often how I use LLMs overall. If you ask an LLM if it knows who Dana Lewis is, it “does” know. It’ll tell you things about me that are mostly correct. If you ask it to write a bio about me, it will solidly make up ⅓ of it that is fully inaccurate. Again, remember it is not an encyclopedia and does not “know things”. When you remember that the LLM is autocompleting words based on the likelihood that they match the previous words – and think about how much information is on the internet and how many weights (patterns of words) it’s been able to build about a topic – you can then get a better spidey-sense about when things are slightly more or less accurate at a general level. I have actually used part of a LLM-written bio, but not by asking it to write a bio. That doesn’t work because of made up facts. I have instead asked it to describe my work, and it does a pretty decent job. This is due to the number of articles I have written and authored; the number of articles describing my work; and the number of bios I’ve actually written and posted online for conferences and such. So it has a lot of “weights” probably tied to the types of things I work on, and having it describe the type of work I do or am known for gets pretty accurate results, because it’s writing in a general high level without enough detail to get anything “wrong” like a fact about an award, etc.

This is how I recommend others use LLMs, too, especially those of us as patients or working in healthcare. LLMs pattern match on words in their training; and they output likely patterns of words. We in turn as humans can observe and learn from the patterns, while recognizing these are PATTERNS of connected words that can in fact be wrong. Systemic bias is baked into human behavior and medical literature, and this then has been pattern-matched by the LLM. (Note I didn’t say “learned”; but they’ve created weights based on the patterns they observe over and over again). You can’t necessarily course-correct the LLM (it’ll pretend to apologize and maybe for a short while adjust it’s word patterns but in a new chat it’s prone to make the same mistakes because the training has not been updated based on your feedback, so it reverts to using the ‘weights’ (patterns) it was trained on); instead, we need to create more of the correct/right information and have it voluminously available for LLMs to train on in the future. At an individual level then, we can let go of the obvious not-right things it’s saying and focus on what we can benefit from in the patterns of words it gives us.

And for people like me, with a high (or different type of) pain tolerance and a different vocabulary for what my body is feeling like, this has become a critical tool in my toolbox for optimizing my healthcare encounters. Do I have to do this to get adequate care? No. But I’m an optimizer, and I want to give the best inputs to the healthcare system (providers and my medical records) in order to increase my chances of getting the best possible outputs from the healthcare system to help me maintain and improve and save my health when these things are needed.

TLDR: LLMs can be powerful tools in the hands of patients, including for real-time or ahead-of-time translation and creating shared, understandable language for improving communication between patients and providers. Just as you shouldn’t tell a patient not to use Dr. Google, you should similarly avoid falling into the trap of telling a patient not to use LLMs because they’re “wrong”. Being wrong in some cases and some ways does not mean LLMs are useless or should not be used by patients. Each of these tools has limitations but a lot of upside and benefits; restricting patients or trying to limit use of tools is like limiting the use of other accessibility tools. I spotted a quote from Dr. Wes Ely that is relevant: “Maleficence can be created with beneficent intent”. In simple words, he is pointing out that harm can happen even with good intent.

Don’t do harm by restricting or recommending avoiding tools like LLMs.

Meet me in the gray area: beyond prevention, before progression

by Dana Lewis

Two things can simultaneously be true:

  • Doctors may wish they had more opportunities to help patients prevent having worse/later stage outcomes of a disease.
  • Doctors may struggle when a patient seeks health care at an early stage, asking for strategies and intervention support against developing worse/later stage outcomes of a disease.

The struggle may be for a few reasons. There’s often a lack of systemic infrastructure to support patients who show up earlier rather than later in a disease progression, especially when the frequency/timeline of care is much quicker than the system is currently resourced for. There’s often a lack of research for these earlier stages and what effective strategies are for preventing progression and treating earlier stage outcomes.

When a clinician struggles with this, it’s not a moral failing of the clinician if they don’t feel equipped to tackle those challenges. However, I do wish clinicians would more often clearly communicate to patients about these struggles. The patient might have a choice: do they pursue another clinician who might have different resources (including time/energy) or expertise in navigating the unknown? Or do they work with the existing clinician to navigate the murky waters together, figuring it out as they go? But patients only have a choice if they realize it themselves and are equipped to pursue alternative paths – or are told that this is a fork in the path.

The challenge is this is a gray area for all of us – patients and clinicians alike. But the reality is, the gray area (for a patient) betwixt and between prevention and progression is our life. The black and white that may emerge after the gray space can be as significant, literally, as life and death. We as patients are highly motivated to navigate the gray area and reduce suffering and possibly try different or new strategies that have shown early promise (although maybe haven’t yet been tested to RCT or the ideal standard, or in the specific disease or stage of the disease in question). We as patients may not have time to wait for the evidence to evolve further.

Clinicians may be aware of the gray space that the patient has landed in. The reality that many clinicians may not know or forget – or have slipped out of their mind – is that the gray space is even more daunting to face alone. If the instinct is to simply shoot down every patient idea with “that’s not approved for use in this disease” without forthrightly contextualizing against a recognition “there’s nothing tested or proven for this part/stage of the disease”, it can begin to put cracks in a relationship. What clinicians might not realize is that a patient may not have time to be in the gray space with a clinician who simply says no to trying anything, because no one has ever studied it before and when little study is being done at all about the gray area the patient is within. Or maybe clinicians do realize it, and sometimes rely on the power of the broken systemic infrastructure that keeps a patient from finding a clinician who does feel equipped to walk through the gray area with them.

What I wish is for clinicians to be equipped to identify this situation, standing on the edge of the gray area with a patient. And to say up front, then and there, if they don’t feel comfortable pursuing off-label strategies when there are zero documented on-label strategies beyond waiting for the worse outcomes to progress. I don’t like that (because why wait for permanent damage to do something, when permanent damage is not inevitable if action is taken sooner), but I very much highly respect and appreciate a clinician who is forthright and willing to say they don’t have time/energy/feel equipped to do so.

Why? Because if I’m already in the gray space, past prevention and before serious progression, it gives me a better opportunity to find someone else who can partner there. It might take a try or two, but it keeps me from wasting time and energy and trying to invest in developing a relationship with a clinician who has already decided they can’t help me until I cross over into black and white worse outcomes.

When we talk about prevention, it’s often about preventing a disease. In the world I live in, and the body I live in – now inhibited by five autoimmune diseases, I don’t have a choice about disease prevention for the most part. My body is clearly equipped with a superstar hyperactive immune system. While I’ve seen some research working on addressing autoimmune stuff, it’s likely decades away from any cure of any one condition that I have (let alone all of them) or fixing the hyperactivity of my immune system and preventing additional autoimmune diseases. Sure, I can work to prevent other diseases that aren’t autoimmune (exercising, staying in as best health overall that I can, etc.), but my focus right now is keeping each of my five autoimmune conditions from being bigger headaches than they already are.

(As a side note, I recently read this paper looking at rates of autoimmune conditions after T1D, based on a registry analysis in Sweden of people with T1D. It’s interesting that the risk of “one more” condition following T1D is 17%, two more is essentially the square of that, etc. etc. all the way down…so the risk is typically about 17% and it’s not additive; having two does not mean you’re more likely to get three, it means you have about the same 17% chance of something else. That’s a useful mental model to me, understanding that I got unlucky 4 more times…and that combination of luck is rare among people with T1D. They went all the way to the category of “three or more” autoimmune conditions after T1D, calculating that 0.3% of people with T1D have 3 or more autoimmune conditions after T1D. They stopped there, but you can extrapolate by multiplying by 17% again and estimate it’s 0.08% for four or more…which is where I’m at. This shows me that I’m not alone in dealing with so many things, but it puts me at about 1 in 1,250 of people with T1D or around one in a million – heh – in the general population if you extrapolate based on global population estimates and assume similar rates/risks of autoimmune conditions in the general public.)

Four of the five are easy enough (although, the fourth took about a year and a half to get to ‘easy enough’, overlapping with the third taking two to three years). The fifth, though, is the gray area that I currently inhabit. Possibly because I am in tune with my body because of the experience with these other autoimmune conditions, I have been presenting to the healthcare system to address this fifth autoimmune condition earlier than most people. Like many autoimmune conditions, it takes years to decades for some people to get diagnosed. Many are diagnosed after systemic manifestations have fully kicked in, e.g. these later stage worse outcomes I referred to above. I’m in a gray area, at the edge of seeing systemic activity, and able to identify it as a red flag, but before – I hope – permanent irreversible damage has been done. The question remains, however, for me to figure out how to navigate this gray area and with which clinicians, in order to achieve care that will possibly prevent or delay or reduce the severity of the outcomes that I will end up with.

I speak from personal experience with this gray area. It’s not fun to navigate, even if you do have a really great clinician partner. But it’s infinitely more challenging to stand there in the gray, unsure of the ability or willingness of a clinician to partner with you.

Meet me in the gray: beyond prevention, before progression - a blog written by Dana M. Lewis on DIYPS.org

How I Use LLMs like ChatGPT And Tips For Getting Started

by Dana Lewis

You’ve probably heard about new AI (artificial intelligence) tools like ChatGPT, Bard, Midjourney, DALL-E and others. But, what are they good for?

Last fall I started experimenting with them. I looked at AI art tools and found them to be challenging, at the time, for one of my purposes, which was creating characters and illustrating a storyline with consistent characters for some of my children’s books. I also tested GPT-3 (meaning version 3.0 of GPT). It wasn’t that great, to be honest. But later, GPT-3.5 was released, along with the ChatGPT chat interface to it, which WAS a big improvement for a lot of my use cases. (And now, GPT-4 is out and is an even bigger improvement, although it costs more to use. More on the cost differences below)

So what am I using these AI tools for? And how might YOU use some of these AI tools? And what are the limitations? This is what I’ve learned:

  1. The most frequent way I use these AI tools is for getting started on a project, especially those related to writing.

You know the feeling of staring at a blank page and not knowing where to start? Maybe it’s the blank page of a cold email; the blank page of an essay or paper you need to write; the blank page of the outline for a presentation. Starting is hard!

Even for this blog post, I had a list of bulleted notes of things I wanted to remember to include. But I wasn’t sure how I wanted to start the blog post or incorporate them. I stuck the notes in ChatGPT and asked it to expand the notes.

What did it do? It wrote a few paragraph summary. Which isn’t what I wanted, so I asked it again to use the notes and this time “expand each bullet into a few sentences, rather than summarizing”. With these clear directions, it did, and I was able to look at this content and decide what I wanted to edit, include, or remove.

Sometimes I’m stuck on a particular writing task, and I use ChatGPT to break it down. In addition to kick-starting any type of writing overall, I’ve asked it to:

  • Take an outline of notes and summarize them into an introduction; limitations section; discussion section; conclusion; one paragraph summary; etc.
  • Take a bullet point list of notes and write full, complete sentences.
  • Take a long list of notes I’ve written about data I’ve extracted from a systematic review I was working on, and ask it about recurring themes or outlier concepts. Especially when I had 20 pages (!) of hand-written notes in bullets with some loose organization by section, I could feed in chunks of content and get help getting the big picture from that 20 pages of content I had created. It can highlight themes in the data based on the written narratives around the data.

A lot of times, the best thing it does is it prompts my brain to say “that’s not correct! It should be talking about…” and I’m able to more easily write the content that was in the back of my brain all along. I probably use 5% of what it’s written, and more frequently use it as a springboard for my writing. That might be unique to how I’m using it, though, and other simple use cases such as writing an email to someone or other simplistic content tasks may mean you can keep 90% or more of the content to use.

2. It can also help analyze data (caution alert!) if you understand how the tools work.

Huge learning moment here: these tools are called LLMs (large language models). They are trained on large amounts of language. They’re essentially designed so that, based on all of those words (language) it’s taken in previously, to predict content that “sounds” like what would come after a given prompt. So if you ask it to write a song or a haiku, it “knows” what a song or a haiku “looks” like, and can generate words to match those patterns.

It’s essentially a PATTERN MATCHER on WORDS. Yeah, I’m yelling in all caps here because this is the biggest confusion I see. ChatGPT or most of these LLMs don’t have access to the internet; they’re not looking up in a search engine for an answer. If you ask it a question about a person, it’s going to give you an answer (because it knows what this type of answer “sounds” like), but depending on the amount of information it “remembers”, some may be accurate and some may be 100% made up.

Why am I explaining this? Remember the above section where I highlighted how it can start to sense themes in the data? It’s not answering solely based on the raw data; it’s not doing analysis of the data, but mostly of the words surrounding the data. For example, you can paste in data (from a spreadsheet) and ask it questions. I did that once, pasting in some data from a pivot table and asking it the same question I had asked myself in analyzing the data. It gave me the same sense of the data that I had based on my own analysis, then pointed out it was only qualitative analysis and that I should also do quantitative statistical analysis. So I asked it if it could do quantitative statistical analysis. It said yes, it could, and spit out some numbers and described the methods of quantitative statistical analysis.

But here’s the thing: those numbers were completely made up!

It can’t actually use (in its current design) the methods it was describing verbally, and instead made up numbers that ‘sounded’ right.

So I asked it to describe how to do that statistical method in Google Sheets. It provided the formula and instructions; I did that analysis myself; and confirmed that the numbers it had given me were 100% made up.

The takeaway here is: it outright said it could do a thing (quantitative statistical analysis) that it can’t do. It’s like a human in some regards: some humans will lie or fudge and make stuff up when you talk to them. It’s helpful to be aware and query whether someone has relevant expertise, what their motivations are, etc. in determining whether or not to use their advice/input on something. The same should go for these AI tools! Knowing this is an LLM and it’s going to pattern match on language helps you pinpoint when it’s going to be prone to making stuff up. Humans are especially likely to make something up that sounds plausible in situations where they’re “expected” to know the answer. LLMs are in that situation all the time: sometimes they actually do know an answer, sometimes they have a good guess, and sometimes they’re just pattern matching and coming up with something that sounds plausible.

In short:

  • LLM’s can expand general concepts and write language about what is generally well known based on its training data.
  • Try to ask it a particular fact, though, and it’s probably going to make stuff up, whether that’s about a person or a concept – you need to fact check it elsewhere.
  • It can’t do math!

But what it can do is teach you or show you how to do the math, the coding, or whatever thing you wish it would do for you. And this gets into one of my favorite use cases for it.

3. You can get an LLM to teach you how to use new tools, solve problems, and lower the barrier to entry (and friction) on using new tools, languages, and software.

One of the first things I did was ask ChatGPT to help me write a script. In fact, that’s what I did to expedite the process of finding tweets where I had used an image in order to get a screenshot to embed on my blog, rather than embedding the tweet.

It’s now so easy to generate code for scripts, regardless of which language you have previous experience with. I used to write all of my code as bash scripts, because that’s the format I was most familiar with. But ChatGPT likes to do things as Python scripts, so I asked it simple questions like “how do I call a python script from the command line” after I asked it to write a script and it generated a python script. Sure, you could search in a search engine or Stack Overflow for similar questions and get the same information. But one nice thing is that if you have it generate a script and then ask it step by step how to run a script, it gives you step by step instructions in context of what you were doing. So instead of saying “to run a script, type `python script.py’”, using placeholder names, it’ll say “to run the script, use ‘python actual-name-of-the-script-it-built-you.py’ “ and you can click the button to copy that, paste it in, and hit enter. It saves a lot of time for figuring out how to take placeholder information (which you would get from a traditional search engine result or Stack Overflow, where people are fond of things like saying FOOBAR and you have no idea if that means something or is meant to be a placeholder). Careful observers will notice that the latest scripts I’ve added to my Open Humans Data Tools repository (which is packed with a bunch of scripts to help work with big datasets!) are now in Python rather than bash; such as when I was adding new scripts for fellow researchers looking to check for updates in big datasets (such as the OpenAPS Data Commons). This is because I used GPT to help with those scripts!

It’s really easy now to go from an idea to a script. If you’re able to describe it logically, you can ask it to write a script, tell you how to run it, and help you debug it. Sometimes you can start by asking it a question, such as “Is it possible to do Y?” and it describes a method. You need to test the method or check for it elsewhere, but things like uploading a list of DOIs to Mendeley to save me hundreds of clicks? I didn’t realize Mendeley had an API or that I could write a script that would do that! ChatGPT helped me write the script, figure out how to create a developer account and app access information for Mendeley, and debug along the way so I ended up within an hour and a half of having a tool that easily saved me 3 hours on the very first project that I used it with.

I’m gushing about this because there’s probably a lot of ideas you have that you immediately throw out as being too hard, or you don’t know how to do it. It takes time, but I’m learning to remember to think “I should ask the LLM this” and ask it questions such as:

  • Is it possible to do X?
  • Write a script to do X.
  • I have X data. Pretend I am someone who doesn’t know how to use Y software and explain how I should do Z.

Another thing I’ve done frequently is ask it to help me quickly write a complex formula to use in a spreadsheet. Such as “write a formula that can be used in Google Sheets to take an average of the values in M3:M84 if they are greater than zero”.

It gives me the formula, and also describes it, and in some cases, gives alternative options.

Other things I’ve done with spreadsheets include:

  • Ask it to write a conditional formatting custom formula, then give me instructions for expanding the conditional formatting to apply to a certain cell range.
  • Asking it to check if a cell is filled with a particular value and then repeating the value in the new cell, in order to create new data series to use in particular charts and graphs I wanted to create from my data.
  • Help me transform my data so I could generate a box and whisker plot.
  • Ask it for other visuals that might be effective ways to illustrate and visualize the same dataset.
  • Explain the difference between two similar formulas (e.g. COUNT and COUNTA or when to use IF and IFS).

This has been incredibly helpful especially with some of my self-tracked datasets (particularly around thyroid-related symptom data) where I’m still trying to figure out the relationship between thyroid levels, thyroid antibody levels, and symptom data (and things like menstrual cycle timing). I’ve used it for creating the formulas and solutions I’ve talked about in projects such as the one where I created a “today” line that dynamically updates in a chart.

It’s also helped me get past the friction of setting up new tools. Case in point, Jupyter notebooks. I’ve used them in the web browser version before, but often had issues running the notebooks people gave me. I debugged and did all kinds of troubleshooting, but have not for years been able to get it successfully installed locally on (multiple of) my computers. I had finally given up on effectively using notebooks and definitely given up on running it locally on my machine.

However, I decided to see if I could get ChatGPT to coax me through the install process.

I told it:

“I have this table with data. Pretend I am someone who has never used R before. Tell me, step by step, how to use a Jupyter notebook to generate a box and whisker plot using this data”

(and I pasted my data that I had copied from a spreadsheet, then hit enter).

It outlined exactly what I needed to do, saying to install Jupyter Notebook locally if I hadn’t, gave me code to do that, installing the R kernel, told me how to do that, then how to start a notebook all the way down to what code to put in the notebook, the data transformed that I could copy/paste, and all the code that generated the plot.

However, remember I have never been able to successfully get Jupyter Notebooks running! For years! I was stuck on step 2, installing R. I said:

“Step 2, explain to me how I enter those commands in R? Do I do this in Terminal?”

It said “Oh apologies, no, you run those commands elsewhere, preferably in Rstudio. Here is how to download RStudio and run the commands”.

So, like humans often do, it glossed over a crucial step. But it went back and explained it to me and kept giving more detailed instructions and helping me debug various errors. After 5-6 more troubleshooting steps, it worked! And I was able to open Jupyter Notebooks locally and get it working!

All along, most of the tutorials I had been reading had skipped or glossed over that I needed to do something with R, and where that was. Probably because most people writing the tutorials are already data scientists who have worked with R and RStudio etc, so they didn’t know those dependencies were baked in! Using ChatGPT helped me be able to put in every error message or every place I got stuck, and it coached me through each spot (with no judgment or impatience). It was great!

I was then able to continue with the other steps of getting my data transformed, into the notebook, running the code, and generating my first ever box and whisker plot with R!

A box and whisker plot, illustrated simply to show that I used R and Jupyter finally successfully!

This is where I really saw the power of these tools, reducing the friction of trying something new (a tool, a piece of software, a new method, a new language, etc.) and helping you troubleshoot patiently step by step.

Does it sometimes skip steps or give you solutions that don’t work? Yes. But it’s still a LOT faster than manually debugging, trying to find someone to help, or spending hours in a search engine or Stack Overflow trying to translate generic code/advice/solutions into something that works on your setup. The beauty of these tools is you can simply paste in the error message and it goes “oh, sorry, try this to solve that error”.

Because the barrier to entry is so low (compared to before), I’ve also asked it to help me with other project ideas where I previously didn’t want to spend the time needed to learn new software and languages and all the nuances of getting from start to end of a project.

Such as, building an iOS app by myself.

I have a ton of projects where I want to temporarily track certain types of data for a short period of time. My fall back is usually a spreadsheet on my phone, but it’s not always easy to quickly enter data on a spreadsheet on your phone, even if you set up a template with a drop down menu like I’ve done in the past (for my DIY macronutrient tool, for example). For example, I want to see if there’s a correlation in my blood pressure at different times and patterns of inflammation in my eyelid and heart rate symptoms (which are symptoms, for me, of thyroid antibodies being out of range, due to Graves’ disease). That means I need to track my symptom data, but also now some blood pressure data. I want to be able to put these datasets together easily, which I can, but the hardest part (so to speak) is finding a way that I am willing to record my blood pressure data. I don’t want to use an existing BP tracking app, and I don’t want a connected BP monitor, and I don’t want to use Apple Health. (Yes, I’m picky!)

I decided to ask ChatGPT to help me accomplish this. I told it:

“You’re an AI programming assistant. Help me write a basic iOS app using Swift UI. The goal is a simple blood pressure tracking app. I want the user interface to default to the data entry screen where there should be three boxes to take the systolic, diastolic blood pressure numbers and also the pulse. There should also be selection boxes to indicate whether the BP was taken sitting up or laying down. Also, enable the selection of a section of symptom check boxes that include “HR feeling” and “Eyes”. Once entered on this screen, the data should save to a google spreadsheet.” 

This is a completely custom, DIY, n of 1 app. I don’t care about it working for anyone else, I simply want to be able to enter my blood pressure, pulse, whether I’m sitting or laying down, and the two specific, unique to me symptoms I’m trying to analyze alongside the BP data.

And it helped me build this! It taught me how to set up a new SwiftUI project in XCode, gave me code for the user interface, how to set up an API with Google Sheets, write code to save the data to Sheets, and get the app to run.

(I am still debugging the connection to Google Sheets, so in the interim I changed my mind and had it create another screen to display the stored data then enable it to email me a CSV file, because it’s so easy to write scripts or formulas to take data from two sources and append it together!)

Is it fancy? No. Am I going to try to distribute it? No. It’s meeting a custom need to enable me to collect specific data super easily over a short period of time in a way that my previous tools did not enable.

Here’s a preview of my custom app running in a simulator phone:

Simulator iphone with a basic iOS app that intakes BP, pulse, buttons for indicating whether BP was taken sitting or laying down; and toggles for key symptoms (in my case HR feeling or eyes), and a purple save button.

I did this in a few hours, rather than taking days or weeks. And now, the barrier to entry to creating more custom iOS is reduced, because now I’m more comfortable working with XCode and the file structures and what it takes to build and deploy an app! Sure, again, I could have learned to do this in other ways, but the learning curve is drastically shortened and it takes away most of the ‘getting started’ friction.

That’s the theme across all of these projects:

  • Barriers to entry are lower and it’s easier to get started
  • It’s easier to try things, even if they flop
  • There’s a quicker learning curve on new tools, technologies and languages
  • You get customized support and troubleshooting without having to translate through as many generic placeholders

PS – speaking of iOS apps, based on building this one simple app I had the confidence to try building a really complex, novel app that has never existed in the world before! It’s for people with exocrine pancreatic insufficiency like me who want to log pancreatic enzyme replacement therapy (PERT) dosing and improve their outcomes – check out PERT Pilot and how I built it here.

4. Notes about what these tools cost

I found ChatGPT useful for writing projects in terms of getting started, even though the content wasn’t that great (on GPT-3.5, too). Then they came out with GPT-4 and made a ChatGPT Pro option for $20/month. I didn’t think it was worth it and resisted it. Then I finally decided to try it, because some of the more sophisticated use cases I wanted to use it for required a longer context window, and in addition to a better model it also gave you a longer context window. I paid the first $20 assuming I’d want to cancel it by the end of the month.

Nope.

The $20 has been worth it on every single project that I’ve used it for. I’ve easily saved 5x that on most projects in terms of reducing the energy needed to start a project, whether it was writing or developing code. It has saved 10x that in time cost recouped from debugging new code and tools.

GPT-4 does have caps, though, so even with the $20/month, you can only do 25 messages every 3 hours. I try to be cognizant of which projects I default to using GPT-3.5 on (unlimited) versus saving the more sophisticated projects for my GPT-4 quota.

For example, I saw a new tool someone had built called “AutoResearcher”, downloaded it, and tried to use it. I ran into a bug and pasted the error into GPT-3.5 and got help figuring out where the problem was. Then I decided I wanted to add a feature to output to a text file, and it helped me quickly edit the code to do that, and I PR’ed it back in and it was accepted (woohoo) and now everyone using that tool can use that feature. That was pretty simple and I was able to use GPT-3.5 for that. But sometimes, when I need a larger context window for a more sophisticated or content-heavy project, I start with GPT-4. When I run into the cap, it tells me when my next window opens up (3 hours after I started using it), and I usually have an hour or two until then. I can open a new chat on GPT-3.5 (without the same context) and try to do things there; switch to another project; or come back at the time it says to continue using GPT-4 on that context/setup.

Why the limit? Because it’s a more expensive model. So you have a tradeoff between paying more and having a limit on how much you can use it, because of the cost to the company.

—–

TLDR:

Most important note: LLMs don’t “think” or “know” things the way humans do. They output language they predict you want to see, based on its training and the inputs you give it. It’s like the autocomplete of a sentence in your email, but more words on a wider range of topics!

Also, the LLM can’t do math. But they can write code. Including code to do math.

(Some, but not all, LLMs have access to the internet to look up or incorporate facts; make sure you know which LLM you are using and whether it has this feature or not.)

Ways to get started:

    1. The most frequent way I use these AI tools is for getting started on a project, especially those related to writing.
      • Ask it to help you expand on notes; write summaries of existing content; or write sections of content based on instructions you give it
    2.  It can also help analyze data (caution alert!) if you understand the limitations of the LLM.
      • The most effective way to work with data is to have it tell you how to run things in analytical software, whether that’s how to use R or a spreadsheet or other software for data analysis. Remember the LLM can’t do math, but it can write code so you can then do the math!
    3.  You can get an LLM to teach you how to use new tools, solve problems, and lower the barrier to entry (and friction) on using new tools, languages, and software.
      • Build a new habit of asking it “Can I do X” or “Is it possible to do Y” and when it says it’s possible, give it a try! Tell it to give you step-by-step instructions. Tell it where you get stuck. Give it your error messages or where you get lost and have it coach you through the process. 

—

What’s been your favorite way to use an LLM? I’d love to know other ways I should be using them, so please drop a comment with your favorite projects/ways of using them!

Personally, the latest project that I built with an LLM has been PERT Pilot!

How I use LLMs (like ChatGPT) and tips for getting started

How to Pick Food (Fuel) For Ultramarathon Running

by Dana Lewis

I’ve previously written about ultrarunning preparation and a little bit about how I approach fueling. But it occurred to me there might be others out there wondering exactly HOW to find fuel that works for them, because it’s an iterative process.

The way I approach fueling is based on a couple of variables.

First and foremost, everything has to be gluten free (because I have celiac). So that limits a lot of the common ultrarunning fuel options. Things like bars (some are GF, most are not), Uncrustables, PopTarts, and many other common recommendations in the ultra community just aren’t an option for me. Some, I can find or make alternatives to, but it’s worth noting that being gluten free for celiac (where cross-contamination is also an issue, not just the ingredients) or having a food allergy and being an ultrarunner can make things more challenging.

Then, I also have exocrine pancreatic insufficiency. This doesn’t limit what I eat, but it factors in to how I approach ideal fueling options, because I have to match the enzyme amounts to the amount of food I’m eating. So naturally, the pill size options I have of OTC enzymes (one is lipase only and covers ~6g of fat for me, the other is a multi-enzyme option that includes protease to cover protein, and only enough lipase to cover ~4g of fat for me; I also have one much larger that covers ~15g of fat but I don’t typically use this one while running) influence the portion sizes of what I choose.

That being said, I probably – despite EPI – still tend toward higher fat options than most people. This is in part because I have had type 1 diabetes for 20+ years. While I by no means consume a low c-a-r-b diet, I typically consume less than the people with insulin-producing pancreases in my life, and lean slightly toward higher fat options because a) my taste buds like them and b) they’ve historically had less impact on my glucose levels. Reason A is probably the main reason now, thanks to automated insulin delivery, but regardless of reason, 20+ years of a higher level than most people’s fat consumption means I’m also probably better fat-adapted for exercise than most people.

Plus, ultrarunning tends to be slower than shorter runs (like marathons and shorter for most people), so that’s also more amenable to fat and other nutrient digestion. So, ultrarunners in general tend to have more options in terms of not just needing “gu” and “gel” and “blocks” and calorie-sugar drinks as fuel options (although if that is what you prefer and works well for you, great!).

All of these reasons lead me toward generally preferring fuel portions that are:

  1. Gluten free with no cross-contamination risk
  2. ~20g of carbs
  3. ~10g of fat or less
  4. ~5-10g of protein or less

Overall, I shoot for consuming ~250 calories per hour. Some people like to measure hourly fuel consumption by calories. Others prefer carb consumption. But given that I have a higher tolerance for fat and protein consumption – thanks to the enzymes I need for EPI plus decades of practice – calories as a metric for hourly consumption makes sense for me. If I went for the level of carb intake many recommend for ultrarunners, I’d find it harder to consistently manage glucose levels while running for a zillion hours. I by no means think any of my above numbers are necessarily what’s best for anyone else, but that’s what I use based on my experiences to date as a rough outline of what to shoot for.

After I’ve thought through my requirements: gluten free, 250 calories per hour, and preferably no single serving portion size that is greater than 20ish grams of carbs or 10g of fat or 5-10g or protein, I can move on to making a list of foods I like and that I think would “work” for ultrarunning.

“Work” by my definition is not too messy to carry or eat (won’t melt easily, won’t require holding in my hands to eat and get them messy).

My initial list has included (everything here gluten free):

  • Oreos or similar sandwich type cookies
  • Yogurt/chocolate covered pretzels
  • PB or other filled pretzel nuggets
  • Chili cheese Fritos
  • Beef sticks
  • PB M&M’s
  • Reese’s Pieces
  • Snickers
  • Mini PayDays
  • Macaroons
  • Muffins
  • Fruit snacks
  • Fruit/date bars
  • GF (only specific flavors are GF which is why I’m noting this) of Honey Stinger Stroopwaffles

I wish I could include more chip/savory options on my lists, and that’s something I’ve been working on. Fritos are easy enough to eat from a snack size baggie without having to touch them with my hands or pull individual chips out to eat; I can just pour portions into my mouth. Most other chips, though, are too big and too ‘sharp’ feeling for my mouth to eat this way, so chili cheese Fritos are my primary savory option, other than beef sticks (that are surprisingly moist and easy to swallow on the run!).

Some of the foods I’ve tried from the above list and have eventually taken OFF my list include:

  • PB pretzel nuggets, because they get stale in baggies pretty fast and then they feel dry and obnoxious to chew and swallow.
  • Muffins – I tried both banana muffin halves and chocolate chip muffin halves. While they’re moist and delicious straight out of the oven, I found they are challenging to swallow while running (probably because they’re more dry).
  • Gluten free Oreos – actual Oreo brand GF Oreos, which I got burnt out on about the time I realized I had EPI, but also they too have a pretty dry mouthfeel. I’ve tried other brand chocolate sandwich cookies and also for some reason find them challenging to swallow. I did try a vanilla sandwich cookie (Glutino brand) recently and that is working better – the cookie is harder but doesn’t taste as dry – so that’s tentatively on my list as a replacement.

Other than “do I like this food” and “does it work for carrying on runs”, I then move on to “optimizing” my intake in terms of macronutrients.  Ideally, each portion size and item has SOME fat, protein, and carbs, but not TOO MUCH fat, protein and carbs.

Most of my snacks are some fat, a little more carb, and a tiny bit of protein. The outlier is my beef sticks, which are the highest protein option out of my shelf-stable running fuel options (7g of fat, 8g of protein). Most of the others are typically 1-3g of protein, 5-10g of fat (perfect, because that is 1-2 enzyme OTC pills), and 10-20g of carb (ideal, because it’s a manageable amount for glucose levels at any one time).

Sometimes, I add things to my list based on the above criteria (gluten free with no cross-contamination list; I like to eat it; not messy to carry) and work out a possible serving size. For example, the other day I was brainstorming more fuel options and it occurred to me that I like brownies and a piece of brownie in a baggie would probably be moist and nice tasting and would be fine in a baggie. I planned to make a batch of brownies and calculated how I would cut them to get consistent portion sizes (so I would know the macronutrients for enzymes).

However, once I made my brownies, and started to cut them, I immediately went “nope” and scratched them off my list for using on runs. Mainly because, I hate cutting them and they crumbled. The idea of having to perfect how to cook them to be able to cut them without them crumbling just seems like too much work. So I scratched them off my list, and am just enjoying eating the brownies as brownies at home, not during runs!

—

I first started taking these snacks on runs and testing each one, making sure that they tasted good and also worked well for me (digestion-wise) during exercise, not just when I was sitting around. All of them, other than the ones listed above for ‘dry’ reasons or things like brownies (crossed off because of the hassle to prepare), have stayed on the list.

I also started looking at the total amount of calories I was consuming during training runs, to see how close I was to my goal of ~250 calories per hour. It’s not an exact number and a hard and fast “must have”, but given that I’m a slower runner (who run/walks, so I have lower calorie burn than most ultrarunners), I typically burn in the ballpark of ~300-400 calories per hour. I generally assume ~350 calories for a reasonable average. (Note, again, this is much lower than most people’s burn, but it’s roughly my burn rate and I’m trying to show the process itself of how I make decisions about fuel).

Aiming for ~250 calories per hour means that I only have a deficit of 100 calories per hour. Over the course of a ~100 mile race that might take 30 hours, this means I’ll “only” have an estimated deficit of 3,000 calories. Which is a lot less than most people’s estimated deficit, both because I have a lower burn rate (I’m slower) and because, as described above and below, I am trying to be very strategic about fueling for a number of reasons, including not ending up under fueling for energy purposes. For shorter runs, like a 6 hour run, that means I only end up ~600 calories in deficit – which is relatively easy to make up with consumption before and after the run, to make sure that I’m staying on top of my energy needs.

It turns out, some of my preferred snacks are a lot lower and higher calories than each other! And this can add up.

For example, fruit snacks – super easy to chew (or swallow without much chewing). 20g of carb, 0g of fat or protein, and only 80 calories. Another easy to quickly chew and swallow option: a mini date (fruit) bar. 13g carb, 5g fat, 2 protein. And…90 calories. My beef stick? 7g of fat, 8g of protein, and only 100 calories!

My approach that works for me has been to eat every 30 minutes, which means twice per hour. Those are three of my favorite (because they’re easy to consume) fuel options. If I eat two of those in the same hour, say fruit snacks and the date bar, that’s only 170 calories. Well below the goal of 250 for the hour! Combining either with my beef stick (so 180 or 190 calories, depending), is still well below goal.

This is why I have my macronutrient fuel library with carbs, fat, protein, *and* calories (and sodium, more on that below) filled out, so I can keep an eye on patterns of what I tend to prefer by default – which is often more of these smaller, fewer calorie options as I get tired at the end of the runs, when it’s even more important to make sure I’m at (or near) my calorie goals.

Tracking this for each training run has been really helpful, so I can see my default tendency to choose “smaller” and “easier to swallow” – but that also means likely fewer calories – options. This is also teaching me that I need to pair larger calorie options with them or follow on with a larger calorie option. For example, I have certain items on my list like Snickers. I get the “share size” bars that are actually 2 individual bars, and open them up and put one in each baggie. ½ of the share size package (aka 1 bar) is 220 calories! That’s a lot (relative to other options), so if I eat a <100 calorie option like fruit snacks or a date bar, I try to make it in the same hour as the above average option, like the ½ snickers. 220+80 is 300 calories, which means it’s above goal for the hour.

And that works well for me. Sometimes I do have hours where I am slightly below goal – say 240 calories. That’s fine! It’s not precise. But 250 calories per hour as a goal seems to work well as a general baseline, and I know that if I have several hours of at or greater than 250 calories, one smaller hour (200-250) is not a big deal. But this tracking and reviewing my data during the run via my tracking spreadsheet helps make sure I don’t get on a slippery slope to not consuming enough fuel to match the demands I’m putting on my body.

And the same goes for sodium. I have read a lot of literature on sodium consumption and/or supplementation in ultrarunning. Most of the science suggests it may not matter in terms of sodium concentration in the blood and/or muscle cramps, which is why a lot of people choose sodium supplementation. But for me, I have a very clear, distinct feeling when I get not enough sodium. It is almost like a chemical feeling in my chest, and is a cousin (but distinct) feeling to feeling ketones. I’ve had it happen before on long hikes where I drank tons to stay hydrated and kept my glucose levels in range but didn’t eat snacks with sodium nor supplement my water. I’ve also had it happen on runs. So for me, I do typically need sodium supplementation because that chemical-like feeling builds up and starts to make me feel like I’m wheezing in my chest (although my lungs are fine and have no issues during this). And what I found works for me is targeting around 500mg/hour of sodium consumption, through a combination of electrolyte pills and food.

(Side note, most ultrarunning blogs I’ve read suggest you’ll be just fine based on food you graze at the aid station. Well, I do most of my ultras as solo endeavors – no grazing, everything is pre-planned – and even if I did do an organized race, because of celiac I can’t eat 95% of the food (due to ingredients, lack of labeling, and/or cross contamination)…so that just doesn’t work for me to rely on aid station food to supplement me sodium-wise. But maybe it would work for other people, it just doesn’t for me given the celiac situation.)

I used to just target 500mg/hour of sodium through electrolyte pills. However, as I switched to actually fueling my runs and tracking carbs, fat, protein, and calories (as described above), I realized it’d be just as easy to track sodium intake in the food, and maybe that would enable me to have a different strategy on electrolyte pill consumption – and it did!

I went back to my spreadsheet and re-added information for sodium to all of my food items in my fuel library, and added it to the template that I duplicate for every run. Some of my food items, just like they can be outliers on calories or protein or fat or carbs, are also outliers on sodium. Biggest example? My beef stick, the protein outlier, is also a sodium outlier: 370mg of sodium! Yay! Same for my chili cheese Fritos – 210mg of sodium – which is actually the same amount of sodium that’s in the type of electrolyte pills I’m currently using.

I originally had a timer set and every 45 minutes, I’d take an electrolyte pill. However, in the last year I gradually realized that sometimes that made me over by quite a bit on certain hours and in some cases, I ended up WAY under my 500mg sodium goal. I actually noticed this in the latter portion of my 82 mile run – I started to feel the low-sodium chest feeling that I get, glanced at my sheet (that I hadn’t been paying close attention to because of So. Much. Rain) and realized – oops – that I had an hour of 323mg of sodium followed by a 495mg hour. I took another electrolyte pill to catch up and chose some higher sodium snacks for my next few fuels. There were a couple hours earlier in the run (hours 4 and 7) where I had happened to – based on some of my fresh fuel options like mashed potatoes – to end up with over 1000mg of sodium. I probably didn’t need that much, and so in subsequent hours I learned I could skip the electrolyte pill when I had had mashed potatoes in the last hour. Eventually, after my 82-mile run when I started training long runs again, I realized that keeping an eye on my rolling sodium tallies and tracking it like I tracked calories, taking an electrolyte pill when my hourly average dropped <500mg and not based on a pre-set time when it was >500mg, began to work well for me.

And that’s what I’ve been experimenting with for my last half dozen runs, which has worked – all of those runs have ended up with a total average slightly above 500mg of sodium and slightly above 250 calories for all hours of the run!

An example chart that automatically updates (as a pivot table) summarizing each hour's intake of sodium and calories during a run. At the bottom, an average is calculated, showing this 6 hour run example achieved 569 mg/hr of sodium and 262 calories per hour, reaching both goals.

Now, you may be wondering – she tracks calories and sodium, what about fat and protein and carbs?

I don’t actually care about or use these in real-time for an hourly average; I use these solely as real-time decision in points as 1) for carbs, to know how much insulin I might need dependent on my glucose levels at the time (because I have Type 1 diabetes); and 2) the fat and protein is to make sure I take the right amount of enzymes so I can actually digest the fuel (because I have exocrine pancreatic insufficiency and can’t digest fuel without enzyme pills). I do occasionally look back at these numbers cumulatively, but for the most part, they’re solely there for real-time decision making at the moment I decide what to eat. Which is 95% of the time based on my taste buds after I’ve decided whether I need to factor in a higher calorie or sodium option!

For me, my higher sodium options are chili cheese Fritos, beef stick, yogurt covered pretzels.

For me, my higher calorie options are the ½ share size Snickers; chili cheese Fritos; Reese’s pieces; yogurt covered pretzels; GF honey stinger stroopwaffle; and 2 mini PayDay bars.

Those are all shelf-stable options that I keep in snack size baggies and ready to throw into my running vest.

Most of my ‘fresh’ food options, that I’d have my husband bring out to the ‘aid station’/turnaround point of my runs for refueling, tend to be higher calorie options. This includes ¼ of a GF PB&J sandwich (which I keep frozen so it lasts longer in my vest without getting squishy); ¼ of a GF ham and cheese quesadilla; a mashed potato cup prepared in the microwave and stuck in another baggie (a jillion, I mean, 690mg of sodium if you consume the whole thing but it’s occasionally hard to eat allll those mashed potatoes out of a baggie in one go when you’re not actually very hungry); sweet potato tots; etc.

So again, my recommendation is to find foods you like in general and then figure out your guiding principles. For example:

  • Do you have any dietary restrictions, food allergies or intolerances, or have already learned foods that your body Does Not Like while running?
  • Are you aiming to do carbs/hr, calories/hr, or something else? What amounts are those?
  • Do you need to track your fuel consumption to help you figure out how you’re not hitting your fuel goals? If so, how? Is it by wrappers? Do you want to start with a list of fuel and cross it off or tear it off as you go? Or like me, use a note on your phone or a drop down list in your spreadsheet to log it (my blog post here has a template if you’d like to use it)?

My guiding principles are:

  • Gluten free with no cross contamination risk (because celiac)
  • ~250 calories per hour, eating twice per hour to achieve this
  • Each fuel (every 30 min) should be less than ~20g of carb, ~10g of fat, and ~5-10g of protein
  • I also want ~500mg of sodium each hour through the 2x fuel and when needed, electrolyte pills that have 210mg of sodium each
  • Dry food is harder to swallow; mouthfeel (ability to chew and swallow it) is something to factor in.
  • I prefer to eat my food on the go while I’m run/walking, so it should be all foods that can go in a snack or sandwich size baggie in my vest. Other options (like chicken broth, soup, and messy food items) can be on my backup list to be consumed at the aid station but unless I have a craving for them, they are secondary options.
  • Not a hassle to make/prepare/measure out into individual serving sizes.

Find foods that you like, figure out your guiding principles, and keep revising your list as you find what options work well for you in different situations and based on your running needs!

Food (fuel) for ultramarathon running by Dana Lewis at DIYPS.org

Functional Self-Tracking is The Only Self-Tracking I Do

by Dana Lewis

“I could never do that,” you say.

And I’ve heard it before.

Eating gluten free for the rest of your life, because you were diagnosed with celiac disease? Heard that response (I could never do that) for going on 14 years.

Inject yourself with insulin or fingerstick test your blood glucose 14 times a day? Wear an insulin pump on your body 24/7/365? Wear a CGM on your body 24/7/365?

Yeah, I’ve heard you can’t do that, either. (For 20 years and counting.) Which means I and the other people living with the situations that necessitate these behaviors are…doing this for fun?

We’re not.

More recently, I’ve heard this type of comment come up about tracking what I’m eating, and in particular, tracking what I’m eating when I’m running. I definitely don’t do that for fun.

—

I have a 20+ year strong history of hating tracking things, actually. When I was diagnosed with type 1 diabetes, I was given a physical log book and asked to write down my blood glucose numbers.

“Why?” I asked. They’re stored in the meter.

The answer was because supposedly the medical team was going to review them.

And they did.

And it was useless.

“Why were you high on February 22, 2003?”

Whether we were asking this question in March of 2003 or January of 2023 (almost 20 years later), the answer would be the same: I have no idea.

BG data, by itself, is like a single data point for a pilot. It’s useless without the contextual stream of data as well as other metrics (in the diabetes case, things like what was eaten, what activity happened, what my schedule was before this point, and all insulin dosed potentially in the last 12-24h).

So you wouldn’t be surprised to find out that I stopped tracking. I didn’t stop testing my blood glucose levels – in fact, I tested upwards of 14 times a day when I was in high school, because the real-time information was helpful. Retrospectively? Nope.

—

I didn’t start “tracking” things again (for diabetes) until late 2013, when we realized that I could get my CGM data off the device and into the laptop beside my bed, dragging the CGM data into a CSV file in Dropbox and sending it to the cloud so an app called “Pushover” would make a louder and different alarm on my phone to wake me up to overnight hypoglycemia. The only reason I added any manual “tracking” to this system was because we realized we could create an algorithm to USE the information I gave it (about what I was eating and the insulin I was taking) combined with the real-time CGM data to usefully predict glucose levels in the future. Predictions meant we could make *predictive* alarms, instead of solely having *reactive* alarms, which is what the status quo in diabetes has been for decades.

So sure, I started tracking what I was eating and dosing, but not really. I was hitting buttons to enter this information into the system because it was useful, again, in real time. I didn’t bother doing much with the data retrospectively. I did occasional do things like reflect on my changes in sensitivity after I got the norovirus, for example, but again this was mostly looking in awe at how the real-time functionality of autosensitivity, an algorithm feature we designed to adjust to real-time changes in sensitivity to insulin, dealt throughout the course of being sick.

—

At the beginning of 2020, my life changed. Not because of the pandemic (although also because of that), but because I began to have serious, very bothersome GI symptoms that dragged on throughout 2020 and 2021. I’ve written here about my experiences in eventually self-diagnosing (and confirming) that I have exocrine pancreatic insufficiency, and began taking pancreatic enzyme replacement therapy in January 2022.

What I haven’t yet done, though, is explain all my failed attempts at tracking things in 2020 and 2021. Or, not failed attempts, but where I started and stopped and why those tracking attempts weren’t useful.

Once I realized I had GI symptoms that weren’t going away, I tried writing down everything I ate. I tried writing in a list on my phone in spring of 2020. I couldn’t see any patterns. So I stopped.

A few months later, in summer of 2020, I tried again, this time using a digital spreadsheet so I could enter data from my phone or my computer. Again, after a few days, I still couldn’t see any patterns. So I stopped.

I made a third attempt to try to look at ingredients, rather than categories of food or individual food items. I came up with a short list of potential contenders, but repeated testing of consuming those ingredients didn’t do me any good. I stopped, again.

When I first went to the GI doctor in fall of 2020, one of the questions he asked was whether there was any pattern between my symptoms and what I was eating. “No,” I breathed out in a frustrated sigh. “I can’t find any patterns in what I’m eating and the symptoms.”

So we didn’t go down that rabbit hole.

At the start of 2021, though, I was sick and tired (of being sick and tired with GI symptoms for going on a year) and tried again. I decided that some of my “worst” symptoms happened after I consumed onions, so I tried removing obvious sources of onion from my diet. That evolved to onion and garlic, but I realized almost everything I ate also had onion powder or garlic powder, so I tried avoiding those. It helped, some. That then led me to research more, learn about the categorization of FODMAPs, and try a low-FODMAP diet in mid/fall 2021. That helped some.

Then I found out I actually had exocrine pancreatic insufficiency and it all made sense: what my symptoms were, why they were happening, and why the numerous previous tracking attempts were not successful.

You wouldn’t think I’d start tracking again, but I did. Although this time, finally, was different.

When I realized I had EPI, I learned that my body was no longer producing enough digestive enzymes to help my body digest fat, protein, and carbs. Because I’m a person with type 1 diabetes and have been correlating my insulin doses to my carbohydrate consumption for 20+ years, it seemed logical to me to track the amount of fat and protein in what I was eating, track my enzyme (PERT) dosing, and see if there were any correlations that indicated my doses needed to be more or less.

My spreadsheet involved recording the outcome of the previous day’s symptoms, and I had a section for entering multiple things that I ate throughout the day and the number of enzymes. I wrote a short description of my meal (“butter chicken” or “frozen pizza” or “chicken nuggets and veggies”), the estimate of fat and protein counts for the meal, and the number of enzymes I took for that meal. I had columns on the left that added up the total amount of fat and protein for the day, and the total number of enzymes.

It became very apparent to me – within two days – that the dose of the enzymes relative to the quantity of fat and protein I was eating mattered. I used this information to titrate (adjust) my enzyme dose and better match the enzymes to the amount of fat or protein I was eating. It was successful.

I kept writing down what I was eating, though.

In part, because it became a quick reference library to find the “counts” of a previous meal that I was duplicating, without having to re-do the burdensome math of adding up all the ingredients and counting them out for a typical portion size.

It also helped me see that within the first month, I was definitely improving, but not all the way – in terms of fully reducing and eliminating all of my symptoms. So I continued to use it to titrate my enzyme doses.

Then it helped me carefully work my way through re-adding food items and ingredients that I had been avoiding (like onions, apples, and pears) and proving to my brain that those were the result of enzyme insufficiency, not food intolerances. Once I had a working system for determining how to dose enzymes, it became a lot easier to see when I had slight symptoms from slightly getting my dosing wrong or majorly mis-estimating the fat and protein in what I was eating.

It provided me with a feedback loop that doesn’t really exist in EPI and GI conditions, and it was a daily, informative, real-time feedback loop.

As I reached the end of my first year of dosing with PERT, though, I was still using my spreadsheet. It surprised me, actually. Did I need to be using it? Not all the time. But the biggest reason I kept using it relates to how I often eat. I often look at an ‘entree’ for protein and then ‘build’ the rest of my meal around that, to help make sure I’m getting enough protein to fuel my ultrarunning endeavors. So I pick my entree/main thing I’m eating and put it in my spreadsheet under the fat and protein columns (=17 g of fat, =20 g of protein), for example, then decide what I’m going to eat to go with it. Say I add a bag of cheddar popcorn, so that becomes (=17+9 g of fat) and (=20+2 g of protein), and when I hit enter, those cells now tell me it’s 26 g of fat and 22 g of protein for the meal, which tells my brain (and I also tell the spreadsheet) that I’ll take 1 PERT pill for that. So I use the spreadsheet functionally to “build” what I’m eating and calculate the total grams of protein and fat; which helps me ‘calculate’ how much PERT to take (based on my previous titration efforts I know I can do up to 30g of fat and protein each in one PERT pill of the size of my prescription)

Example in my spreadsheet showing a meal and the in-progress data entry of entering the formula to add up two meal items' worth of fat and protein

Essentially, this has become a real-time calculator to add up the numbers every time I eat. Sure, I could do this in my head, but I’m usually multitasking and deciding what I want to eat and writing it down, doing something else, doing yet something else, then going to make my food and eat it. This helps me remember, between the time I decided – sometimes minutes, sometimes hours in advance of when I start eating and need to actually take the enzymes – what the counts are and what the PERT dosing needs to be.

I have done some neat retrospective analysis, of course – last year I had estimated that I took thousands of PERT pills (more on that here). I was able to do that not because it’s “fun” to track every pill that I swallow, but because I had, as a result of functional self-tracking of what I was eating to determine my PERT dosing for everything I ate, had a record of 99% of the enzyme pills that I took last year.

I do have some things that I’m no longer entering in my spreadsheet, which is why it’s only 99% of what I eat. There are some things like a quick snack where I grab it and the OTC enzymes to match without thought, and swallow the pills and eat the snack and don’t write it down. That maybe happens once a week. Generally, though, if I’m eating multiple things (like for a meal), then it’s incredibly useful in that moment to use my spreadsheet to add up all the counts to get my dosing right. If I don’t do that, my dosing is often off, and even a little bit “off” can cause uncomfortable and annoying symptoms the rest of the day, overnight, and into the next morning.

So, I have quite the incentive to use this spreadsheet to make sure that I get my dosing right. It’s functional: not for the perceived “fun” of writing things down.

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It’s the same thing that happens when I run long runs. I need to fuel my runs, and fuel (food) means enzymes. Figuring out how many enzymes to dose as I’m running 6, 9, or 25 hours into a run gets increasingly harder. I found that what works for me is having a pre-built list of the fuel options; and a spreadsheet where I quickly on my phone open it and tap a drop down list to mark what I’m eating, and it pulls in the counts from the library and tells me how many enzymes to take for that fuel (which I’ve already pre-calculated).

It’s useful in real-time for helping me dose the right amount of enzymes for the fuel that I need and am taking every 30 minutes throughout my run. It’s also useful for helping me stay on top of my goal amounts of calories and sodium to make sure I’m fueling enough of the right things (for running in general), which is something that can be hard to do the longer I run. (More about this method and a template for anyone who wants to track similarly here.)

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The TL;DR point of this is: I don’t track things for fun. I track things if and when they’re functionally useful, and primarily that is in real-time medical decision making.

These methods may not make sense to you, and don’t have to.

It may not be a method that works for you, or you may not have the situation that I’m in (T1D, Graves, celiac, and EPI – fun!) that necessitates these, or you may not have the goals that I have (ultrarunning). That’s ok!

But don’t say that you “couldn’t” do something. You ‘couldn’t’ track what you consumed when you ran or you ‘couldn’t’ write down what you were eating or you ‘couldn’t’ take that many pills or you ‘couldn’t’ inject insulin or…

You could, if you needed to, and if you decided it was the way that you could and would be able to achieve your goals.

Looking Back Through 2022 (What You May Have Missed)

by Dana Lewis

I ended up writing a post last year recapping 2021, in part because I felt like I did hardly anything – which wasn’t true. In part, that was based on my body having a number of things going on that I didn’t know at the time. I figured those out in 2022 which made 2022 hard and also provided me with a sense of accomplishment as I tackled some of these new challenges.

For 2022, I have a very different feeling looking back on the entire year, which makes me so happy because it was night and day (different) compared to this time last year.

One major example? Exocrine Pancreatic Insufficiency.

I started taking enzymes (pancreatic enzyme replacement therapy, known as PERT) in early January. And they clearly worked, hooray!

I quickly realized that like insulin, PERT dosing needed to be based on the contents of my meals. I figured out how to effectively titrate for each meal and within a month or two was reliably dosing effectively with everything I was eating and drinking. And, I was writing and sharing my knowledge with others – you can see many of the posts I wrote collected at DIYPS.org/EPI.

I also designed and built an open source web calculator to help others figure out their ratios of lipase and fat and protease and protein to help them improve their dosing.

I even published a peer-reviewed journal article about EPI – submitted within 4 months of confirming that I had it! You can read that paper here with an analysis of glucose data from both before and after starting PERT. It’s a really neat example that I hope will pave the way for answering many questions we all have about how particular medications possibly affect glucose levels (instead of simply being warned that they “may cause hypoglycemia or hyperglycemia” which is vague and unhelpful.)

I also had my eyes opened to having another chronic disease that has very, very expensive medication with no generic medication option available (and OTCs may or may not work well). Here’s some of the math I did on the cost of living with EPI and diabetes (and celiac and Graves) for a year, in case you missed it.

Another other challenge+success was running (again), but with a 6 week forced break (ha) because I massively broke a toe in July 2022.

That was physically painful and frustrating for delaying my ultramarathon training.

I had been successfully figuring out how to run and fuel with enzymes for EPI; I even built a DIY macronutrient tracker and shared a template so others can use it. I ran a 50k with a river crossing in early June and was on track to target my 100 mile run in early fall.

However with the broken toe, I took the time off needed and carefully built back up, put a lot of planning into it, and made my attempt in late October instead.

I succeeded in running ~82 miles in ~25 hours, all in one go!

I am immensely proud of that run for so many reasons, some of which are general pride at the accomplishment and others are specific, including:

  • Doing something I didn’t think I could do which is running all day and all night without stopping
  • Doing this as a solo or “DIY” self-organized ultra
  • Eating every 30 minutes like clockwork, consuming enzymes (more than 92 pills!), which means 50 snacks consumed. No GI issues, either, which is remarkable even for an ultrarunner without EPI!
  • Generally figuring out all the plans and logistics needed to be able to handle such a run, especially when dealing with type 1 diabetes, celiac, EPI, and Graves
  • Not causing any injuries, and in fact recovering remarkably fast which shows how effective my training and ‘race’ strategy were.

On top of this all, I achieved my biggest-ever running year, with more than 1,333 miles run this year. This is 300+ more than my previous best from last year which was the first time I crossed 1,000 miles in a year.

Professionally, I did quite a lot of miscellaneous writing, research, and other activities.

I spent a lot of time doing research. I also peer reviewed more than 24 papers for academic journals. I was asked to join an editorial board for a journal. I served on 2 grant review committees/programs.

I also wrote a lot.

*by ton, I mean way more than the past couple of years combined. Some of that has been due to getting some energy back once I’ve fixed missing enzyme and mis-adjusted hormone levels in my body! I’m up to 40+ blog posts this year.

And personally, the punches felt like they kept coming, because this year we also found out that I have Graves’ disease, taking my chronic disease count up to 4. Argh. (T1D, celiac, EPI, and now Graves’, for those curious about my list.)

My experience with Graves’ has included symptoms of subclinical hyperthyroidism (although my T3 and T4 are in range), and I have chosen to try thyroid medication in order to manage the really bothersome Graves’-related eye symptoms. That’s been an ongoing process and the symptoms of this have been up and down a number of times as I went on medication, reduced medication levels, etc.

What I’ve learned from my experience with both EPI and Graves’ in the same year is that there are some huge gaps in medical knowledge around how these things actually work and how to use real-world data (whether patient-recorded data or wearable-tracked data) to help with diagnosis, treatment (including medication titration), etc. So the upside to this is I have quite a few new projects and articles coming to fruition to help tackle some of the gaps that I fell into or spotted this year.

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And that’s why I’m feeling optimistic, and like I accomplished quite a bit more in 2022 than in 2021. Some of it is the satisfaction of knowing the core two reasons why the previous year felt so physically bad; hopefully no more unsolved mysteries or additional chronic diseases will pop up in the next few years. Yet some of it is also the satisfaction of solving problems and creating solutions that I’m uniquely poised, due to my past experiences and skillsets, to solve. That feels good, and it feels good as always to get to channel my experiences and expertise to try to create solutions with words or code or research to help other people.

Replacing Embedded Tweets With Images

by Dana Lewis

If you’re like me, you may have been thrilled when (back in the day) it became possible to embed public social media posts such as tweets on websites and blogs. It enabled people who read here to pop over to related Twitter discussions or see images more easily.

However, with how things have been progressing (PS – you can find me @DanaMLewis@med-mastodon.com as well), it’s increasingly possible that a social media account could get suspended/banned/taken down arbitrarily for things that are retrospectively against new policies. It occurred to me that one of the downsides to this is the impact it would have on embedded post content here on my blog, so I started thinking through how I could replace the live embedded links with screenshots of the content.

There’s no automatic way to do this, but the most efficient method that I’ve decided on has been the following:

1 ) Export an XML file of your blog/site content.

If you use WordPress, there’s an “Export” option under “Tools”. You can export all content, it doesn’t matter.

2 ) Run a script (that I wrote with the help of ChatGPT).

I called my script “embedded-links.sh” and it searches the XML file for URLs found between “[ embed ]” and “[\embed]” and generates a CSV file. Opening the CSV with Excel, I can then see the list of every embedded tweet throughout the site.

I originally was going to have the script pair the embedded links (twitter URLs) to the post it was found within to make it easier to go swap them out with images, but realized I didn’t need this.

(See no. 4 for more on why not and the alternative).

3 ) I created screenshots with the URLs in my file.

I went through and pasted each URL (only about 60, thankfully) into https://htmlcsstoimage.com/examples/twitter-tweet-screenshot’s example HTML code and then clicked “re-generate image” in the top right corner under the image tab. Then, I right-clicked the image and chose “Save As” and saved it to a folder. I made sure to rename the image file as I saved it each time descriptively; this is handy for the next step.

I did hit the free demo limit on that tool after about 30 images, and I had 60, so after about 20 minutes I went back and checked and was able to do my second batch of tweets.

(There are several types of these screenshot generators you could use, this one happened to be quick and easy for my use case.)

4 ) I then opened up my blog and grabbed the first link and pasted it into the search box on the Posts page.

It pulled up the list of blog posts that had that URL.

I opened the blog post, scrolled to the embedded tweet, deleted it, and replaced it with the image instead.

(Remember to write alt text for your image during this step!)

Remember to ‘update’/save your post, too, after you input the image.

It took maybe half an hour to do the final step, and maybe 2-3 hours total including all the time I spent working on the script in number 2, so if you have a similar ~60 or so links I would expect this to take ~1-2 focused hours.

Replacing embedded web content with images by Dana M. Lewis

Understanding the Difference Between Open Source and DIY in Diabetes

by Dana Lewis

There’s been a lot of excitement (yay!) about the results of the CREATE trial being published in NEJM, followed by the presentation of the continuation results at EASD. This has generated a lot of blog posts, news articles, and discussion about what was studied and what the implications are.

One area that I’ve noticed is frequently misunderstood is how “open source” and “DIY” are different.

Open source means that the source code is openly available to view. There are different licenses with open source; most allow you to also take and reuse and modify the code however you like. Some “copy-left” licenses commercial entities to open-source any software they build using such code. Most companies can and do use open source code, too, although in healthcare most algorithms and other code related to FDA-regulated activity is proprietary. Most open source licenses allow free individual use.

For example, OpenAPS is open source. You can find the core code of the algorithm here, hosted on Github, and read every line of code. You can take it, copy it, use it as-is or modify it however you like, because the MIT license we put on the code says you can!

As an individual, you can choose to use the open source code to “DIY” (do-it-yourself) an automated insulin delivery system. You’re DIY-ing, meaning you’re building it yourself rather than buying it or a service from a company.

In other words, you can DIY with open source. But open source and DIY are not the same thing!

Open source can and is usually is used commercially in most industries. In healthcare and in diabetes specifically, there are only a few examples of this. For OpenAPS, as you can read in our plain language reference design, we wanted companies to use our code as well as individuals (who would DIY with it). There’s at least one commercial company now using ideas from the OpenAPS codebase and our safety design as a safety layer against their ML algorithm, to make sure that the insulin dosing decisions are checked against our safety design. How cool!

However, they’re a company, and they have wrapped up their combination of proprietary software and the open source software they have implemented, gotten a CE mark (European equivalent of FDA approval), and commercialized and sold their AID product to people with diabetes in Europe. So, those customers/users/people with diabetes are benefitting from open source, although they are not DIY-ing their AID.

Outside of healthcare, open source is used far more pervasively. Have you ever used Zoom? Zoom uses open source; you then use Zoom, although not in a DIY way. Same with Firefox, the browser. Ever heard of Adobe? They use open source. Facebook. Google. IBM. Intel. LinkedIn. Microsoft. Netflix. Oracle. Samsung. Twitter. Nearly every product or service you use is built with, depends on, or contains open source components. Often times open source is more commonly used by companies to then provide products to users – but not always.

So, to more easily understand how to talk about open source vs DIY:

  • The CREATE trial used a version of open source software and algorithm (the OpenAPS algorithm inside a modified version of the AndroidAPS application) in the study.
  • The study was NOT on “DIY” automated insulin delivery; the AID system was handed/provided to participants in the study. There was no DIY component in the study, although the same software is used both in the study and in the real world community by those who do DIY it. Instead, the point of the trial was to study the safety and efficacy of this version of open source AID.
  • Open source is not the same as DIY.
  • OpenAPS is open source and can be used by anyone – companies that want to commercialize, or individuals who want to DIY. For more information about our vision for this, check out the OpenAPS plain language reference design.
Venn diagram showing a small overlap between a bigger open source circle and a smaller DIY circle. An arrow points to the overlapping section, along with text of "OpenAPS". Below it text reads: "OpenAPS is open source and can be used DIY. DIY in diabetes often uses open source, but not always. Not all open source is used DIY."