I'm going to get my genes tested!
Early Christmas gift
+ savings
+ donation from wonderful person
+ black friday sale
= 🤗
Huh, it seems Tim Ferris is into 3 day water fasts. I have that on my short list as a possible way to hard reset my microbiome. I'm planning to do that after I know how my body responds to serotonin ala the gene test.
It's funny that I haven't seen a single thing mentioning gut bacteria in his stuff but he's doing the same things I've found that fight infections like h pylori. Even his weighing of poop can be construed as a way to track dead bacterial load.
If you didn't know, your appendix has a use: it repopulates your gut after extreme stomach issues. Not much use in modern civilization as we've mostly conquered diarrhea. However I'm finding all sorts of examples where maybe it still might be useful. Like in fasting.
Did you know that SSRIs cause diarrhea because your colon's movement is also serotonin based? And opioids constipate you for similar reasons.
Since I'm resisting the urge to add to my threads on twitter today... I thought you might like to know:
I was really curious if the sun could make my poop hurt a while back.
It seems there is a direct connection between vitamin D and the sun
https://theconversation.com/the-sun-goes-down-on-vitamin-d-why-i-changed-my-mind-about-this-celebrated-supplement-52725 and that can have a major effect on the gut microbiome. https://blog.frontiersin.org/2016/12/22/vitamin-d-improves-gut-flora-and-metabolic-syndrome/
Now to find out how long I need to be in the sun given what I think I have for genes. Reflections from snow might boost Vitamin D generation.
I wonder what the normal turn around is for this.
Seems they're really popular for the holidays due to the sale. 1.5 million vials of spit or something?
Anyway, Soon(TM)
My current obsession: Steelmaning social constructionism using gametheoretic models of risk/reward systems. Trying to merge it w/ evo-psych and the emerging understanding of gene/culture feedback loops.
Exploring epigenetics as verticle transfer of microbiome + other forms of contagion when splayed against food norms.How cultural ritual + memetics adapt to resource density & environment.
Hunch: astrology "science" historically acted proxy for personality changes due to food scarcity & disease?
I spent most of the evening curating content I've collected on twitter about vagal nerve stimulation.
Yes... My internet search history is full of search terms involving how butt sex can cure hiccups and the odd sexual interest of john harvey kellogg inflating people's bladders to induce vagal stimulation.
Enjoy:
https://are.na/ultimape/vagus-nerve-vagal-response-stress-breathing-pooping-and-dog-butts
I had an old thread on birdsite exploring how hunger causes changes in various organisms, particularly interesting was how serotonin is a hunger driven feature in most, and that it plays a role in aggressiveness of locust behavior.
Imma just leave these two studies here.
Oh hey, I can use google to search my own content.
Here's an older thread I lost related to the topic of the one you're reading.
Sometimes I see a weird article while I am looking stuff up that seems to hit every single "hmm" factor in my brain, the topic instantly becomes a focus of mine.
I am now going to spend a few hours looking up studies on baby poop and IQ/behavior.
https://www.fatherly.com/health-science/baby-poop-science-iq-tests-microbiome/
Now you may be asking yourself, "is he just saying this as a stunt?"
No, I did a similar thing 3 months ago based on http://www.independent.co.uk/news/science/sausages-made-with-baby-poo-are-completely-normal-and-super-healthy-say-scientists-9153895.html
Ah it seems the only big study on microbiome changes as we age was done on a japenese population, and didn't really track how diet and lifestyle affected it. Darn.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879732/
Not sure how many people will use it, but if you're interested in getting your genes tested with 23andMe, if you use this referral link: https://refer.23andme.com/s/apeinago It will give me a $20 amazon gift card when you place an order.
If 10 people use that link, I can feed myself for a month while working on tools to help with analyzing the raw data i'm getting from the test.
23andMe genetic test results are in. I did a quick look thru for SNPs in my list of "high confidence" genes (maybe 20 or so) and I was 100% accurate and they all fit my diagnosis and observed symptoms right on the nose.
Once I get the full data download I'm going to be diving into specifics about my dopamine and serotonin receptor characteristics and start tweaking my diet toward a microbiome that helps me create what I need.
I'm going to be shitting myself... for SCIENCE!
I'm planning out what I might want to eat after my fast. I found some kefir, actual saurkraut, and there seems to be a reputable brand of kombucha I can source locally, but I don't know where to find kimchee or natto yet.
Any other good "live and active cultures" foods I might want to look into?
My hope is that my appendix will do most of the work of repopulating, I'm going to be using these other ones to bias the process a bit toward certain kinds & make sure I have a good ecosystem starter.
Does anyone know how to translate this https://www.wikigenes.org/e/ref/e/14699425.html into the snp system 23andMe's raw data reports (or chromosone+position)? I have my IMPA2 genes, but don't know what system this is using.
(currently investigating sleep issues as possible autism overlap with bipolar)
Hey, I wonder what strains of bacteria are in kombucha.
Oh weird, different brands use different ones.
Oh neat, lack of Lactobacillus rhamnosus seems to be a risk factor for autism.
I wonder where it comes from...
Oh gross. 🤮
TL;DR: why my search history now contains the phrase "vagina yogurt".
#nsfw https://motherboard.vice.com/en_us/article/mgbx9q/how-to-make-breakfast-with-your-vagina
I found out what that gene description format means
https://ghr.nlm.nih.gov/primer/howgeneswork/genelocation
Looks like they use an entirely different coordinate system and frame of reference. Pain the butt, but I think I need to figure this out well enough that I can write a translation library.
It is slightly confusing because I'm not sure how this system encodes stuff like gene knockouts and stuff like duplication.
So I'm I'm going to do that 3 day fast net month. Any tips on how to avoid catastrophe?
Ooh, I can hook up an old wii-fit scale to my computer https://github.com/aelveborn/Wii-Scale This looks fun.
I've decided that I need to take some steps to get cheaper food and that means figuring out some way of cooking despite not being in control of my environment / careless roommates.
I found a silicon "sponge" that should let me boil it to keep it sanitary. And I think I can afford my own pan and spatula + store it all separately. I don't have the mental fortitude for playing "why is the spatula in the bathroom" or "why is the pan under all the mail in the living room".
Changing diets on a budget is hard. Its harder dealing with executive function troubles. When I'm in my own space I can set up routines that help me function. Where I'm at now what should take me 10 minutes (like cooking an egg and some toast) will often take two hours and exhaust me.
For past year or so I've been mostly living on fake soylent because I get burned out finding everything I need to cook when they wander away. Playing a 25 step towers-of-hanoi game when I just woke up = 
I'm in a rock/hardplace scenario because I need to improve my diet to function better, but I can't function well enough improve my diet. I'm under constraints that make everything more difficult than they should be.
I'm an interloper here and don't have much say in on-goings. We can't share food b/c I need a different diet and my sleep schedule is all over the map. Even if I could articulate issues clearly, It would be a major pain for them to overhaul their entire lifestyle just for me.
I'm beyond thankful for my current situation. I've been able to stabilize here and have even been able to concentrate on my issues. Since I got my gene test back I confirmed exactly what I need to do to 'fix' myself.
I'm at a point where I can't move forward without difficult changes. It sucks having a solution right in front me, but struggling with the last mile.
I become depressed & anxious because my brain fixates on my roadblocks to not being so depressed + anxious any more.
Stupid brain.
I'm dehydrating as I struggle to find my way in this last stretch of my personal death labyrinth. I've been wandering for years. Too Long.
A claustrophobic passage in a pitchblack cave. I'm thirsty. The path is narrowing. Lightheaded. Crevasses to each side. Fear is making me dizzy. One wrong step could send me tumbling into the abyss. Panic: don't panic.
The end in sight: a cure to claustrophobia, a fully charged flashlight, and a clean water spring.
I drink my tears.
http://www.rhizome.solutions/2017/10/rhythms-of-poetry.html
I have a pan, sponge, and drying area now. Next step is freeing up space in the fridge.
In a fit of frustration I ended up cleaning up one of the ominous piles in the kitchen and it's really helped with my mood. Turns out there was a shelf in the basement that had been sitting there for years unused and still in the box.
Doesn't look like I'll be able to do my Fast this month - stuff I needed to pick up was little more expensive than I hoped, but I'm still working toward it as my interim goal.
Instead of being disappointed with another failure, I'm choosing to see it as an opportunity to get into a routine with my new cooking stuff.
This will also give time to order specialty items from amazon and have them shipped before I do it. I wasn't able to source water filter, for example, but found a cheap one online.
Joke, but abnormally vulgar gross commentary on food stuff. Show more
Joke, but abnormally vulgar gross commentary on food stuff. Show more
I've been mostly joking with my "Vagina yogurt" framing of infantile infection. But its funny because it might be true.
"Babies who ate the microbes for a week — along with some sugars to feed the microbes — had a dramatic reduction in their risk of death and sepsis. They dropped by 40 percent, from 9 percent to 5.4 percent."
https://www.npr.org/sections/goatsandsoda/2017/08/16/543920822/probiotic-bacteria-could-protect-newborns-from-deadly-infection
So for ~$6000 I can get a shot-gun sequence test of my (blood, swab, urine, fecal, tissue, semen) and get a report of bacteria, virus, parasites, and fungi that might be causing me trouble. https://aperiomics.com/
Amazing!
Oh hey, another study coming out confirming my own findings just by reading science papers like a nerd.
https://www.npr.org/sections/thetwo-way/2018/02/08/584330475/major-psychiatric-disorders-have-more-in-common-than-we-thought-study-finds
Everytime I find a good food that might have pro-micorbiome properties, it turns out its because its been made with microbes. Like apparently cacao is processed thru bacteria and is why dark chocolate is full of stuff like polyphenols and other antioxidants.
https://www.youtube.com/watch?v=9yswzITbAbA
On the 'how to make everything' channel, they go into detail on the process of fermenting cacao. https://youtu.be/r6Q2Vr1JUGo?t=1m39s
In other news, Kombucha taste like stinky feet.
I've been looking for a detailed food tracking app for #quantifiedself purposes since I found out fitbit's app could scan barcodes natively. I have a prototype rigged up in air-table based on my old grocery shopping app design, but I never had motivation to actually rig up the scanning system.
I just read @sonya 's article on going carnivore ( https://www.inc.com/sonya-mann/carnivory-zero-carb-experiment.html) and saw she recommend https://cronometer.com
I bought the ad free version for my phone using google survey credits.
It is 👍
@ultimape It looks like a really good app, but...no AU database from what I can find through searching.
I did see a forum post asking about JSON versions of one existing Australian dataset (AUSNUT) so I'm guessing there's a way to pipe it in. (And I'm guessing the same method can be used to pipe in self-recorded data for prepared stuff.)
Unfortunately, the CSIRO database (which is bigger and more up-to-date) seems to only be accessible through an API.
@dartigen ooh yeah, back when I was working on the shopping app prototype even localizing across state lines was tricky. Customizing it to adapt to different countries entirely sounds like major pain.
Was reading about nutrient density yesterday a bit. A bunch of the stuff I want to make sure is in my diet seems to not be recorded. (sulforaphane, choline, betaine). And can vary wildly. Its frustrating.
Its also disturbing to read about how nutrients are in decline: http://journals.sagepub.com/doi/abs/10.1177/026010600701900205
@dartigen There's also some evidence that the form of niacin commonly used as an additive isn't bioactive. I've got genes that prevent me from getting a niacin flush so I wanna get ahold of the real stuff. The app doesn't' seem to distinguish between the two.
@ultimape For me, I'm more after tracking macros at first - I want to check if I've got those right first, in volume and balance. (I had it very, very wrong to begin with - not enough carbs, and not nearly enough food overall. Explains a few things.)
I'm frustrated by most diet plans too - if they're not far too much food, then they're full of my IBS triggers. I figured that looking at more detailed nutritional analysis would help me work around that and find better substitutions.
@dartigen Similar for me regarding food intake being way too low and not balanced. Tho I have the reverse problem vs IBS (chronic constipation) despite having many IBS associated genetics.
The nutrients are more for reduction in brain-fog issues and reducing autism associated meltdown states. Combined w/ more overall serotonin production i'm hoping to reduce my anxiety/ depression to the point where I can function like when I was in college.
I wrote more on my plan here https://are.na/block/1734936
@ultimape Ah, I'm more focusing on trying to smooth out energy through the day when active, since I'm apparently active enough to render my usual eating inadequate. I have to at least maintain my weight; too much change without obvious other causes and I'll be kicked off my meds, which won't be good.
I haven't looked at my genetics in that area yet, but I'll see if anything new has been turned up...it'll be interesting to update my profile too.
@ultimape (It's also frustrating how many guides and plans out there are focused at weight loss, when I'm trying to avoid that.
I'd use the CSIRO guide, but it doesn't exclude my IBS triggers, and it doesn't provide much advice on substitution in those recipes.)
@ultimape It looks like most people here use MyFitnessPal...which has features I really need locked behind a subscription. And has very questionable privacy controls, as well as being corporate-owned (and by UnderArmor, which makes it a double ugh).
But, reviews I'm finding are saying that Cronometer is better for fresh foods, and I guess there can't be much difference between countries there...
Ooh, I just found my old list of cheap food provisioning on Trello. I had tried to get people to contribute to it, but only one person ever bothered to comment. https://trello.com/b/cLFeDFxy/provisioning
Going to have to mine this and see if there is stuff I missed on my shopping list.
Going over notes, it seems a lot of my 'go to' food items are also chock-full of stuff that is probably really good for me. Esp since I found I do have the mutations associated with methylation pathways. https://www.hindawi.com/journals/aurt/2013/578429/
If anyone is curious what I ate today to see what cronometer does: https://imgur.com/a/2CYhB
I also found it has a setting to show estimate choline intake. It seems the 4 eggs was just about enough to push it to 90%. Sadly the data on the peanut butter brand didn't include any details on that kind of things so I might need to replace that entry with a more accurate estimate. 🤓
I'm loving the scanning feature too. It let me put things into the log really quickly.
This talk by Rob Knight is very dense, but does a wonderful job as an overview of state of the art in Microbiome Research. https://www.youtube.com/watch?v=2iKHMyWzclM
At a little before the 21 minute mark he mentions the Weizmann institute. I just picked up their book; https://www.amazon.com/gp/product/B06XZM4XJG/ and am slowly reading thru their research findings: https://genie.weizmann.ac.il/selected.html directly. The have a short video overview here: https://www.youtube.com/watch?v=hZWLy7FLvZ4
Their research fits independent findings, stuff like https://www.nature.com/news/2011/110420/full/news.2011.249.html
Meet Your Microbiome!
https://www.youtube.com/watch?v=Ybk7E7SLbWw
Your Microbiome and Your Brain
https://www.youtube.com/watch?v=2ycHwcV9MvM
Your Microbiome: The Invisible Creatures That Keep You Alive!
https://www.youtube.com/watch?v=xEo3N9EOpgw
You Are Mainly Microbe… Meet Your Microbiome!
https://www.youtube.com/watch?v=4BZME8H7-KU
How our microbes make us who we are
https://www.youtube.com/watch?v=i-icXZ2tMRM
You are your microbes
https://www.youtube.com/watch?v=1X8p0vhsWRE
How Bacteria Rule Over Your Body – The Microbiome
https://www.youtube.com/watch?v=VzPD009qTN4
The Antibiotic Apocalypse Explained
https://www.youtube.com/watch?v=xZbcwi7SfZE
I've spent the past hour trying to figure out how to get enough potassium in my diet. it seems impossible.
Like, to get 100% I'd have to eat almost half of my day's calories on just lentils or something. And they have really good DV/calorie ratios.
Looks like I'll need supplements for the magnesium / potassium.
Looking up the topic, the DV recommendations for potassium are based on guess work https://discourse.soylent.com/t/why-is-the-rda-of-potassium-so-high/13064/9
Issues with these six: they need to be balanced in particular ratios on top of having sufficient amounts.
zinc <-> copper
potassium <-> sodium
calcium <-> magnesium
But I don't know what proportions I need, or if I gotta tweak for my genes.
Will be a pain in ass to confirm. I was trying to avoid looking up ion channels.
I can't seem to find a single example of anyone studying a Fasting regimen as a way to change microbiome to fight anxiety and depression. Weird to me because it makes sense given all the other studies on using Fasts to treat stuff like Crohns and Multiple Sclerosis.
Though there seems to be an open study on eating poop (FMT) for depression. But they seem to exclude people with bipolar and schizophrenia so while I'm not diagnosed with those, I prob don't qualify anyway.
https://clinicaltrials.gov/ct2/show/NCT03281044
@ultimape everyone is qualified to eat shit at least once in their life. On a serious note, stay away from shitty food 😆, and eat stuff heavy in good flora like kimchee.
I found out that Ed Yong has a google talk https://www.youtube.com/watch?v=MbTntA0kLZ4 and teamed up with PBS to publish a bunch of interesting explorations on youtube.
Remember, even you are alone, your microbes will always be there for you, watching over you (like santa).
Anyone wanna crowdsource measuring the stuff in my poop?
https://ubiome.com/consumer/explorer/
I've been exploring the concept of Vagina Yogurt powered by breastmilk and baby vomit. Somewhere along the way I started looking up drinking goats blood rituals, and smelling nursing women's armpits as an aphrodisiac.
My insatiable quest for knowledge knows no bounds. I wrote a bit more about it here if you're curious:
https://are.na/block/1801523
I just realized that I'm basically trying to live blog a quest to improve the quality of my farts.
I'm tooting about it as I go.
A semi-tangent to my research on autism/Microbiome is an interest in Alzheimer's Disease.
I used to work at a nursing home and dug into the topic because of trying to explore possible causes of my brainfog/memory loss. I read that diet changes can improve AD symptoms at about the time I seriously started investigating my own symptoms (my gram has Multiple Sclerocis and it was the same diet).
Anyway, I finally put pieces together after years of exploring the idea space.
https://www.are.na/block/1808140
TFW: running circles around slatestarcodex
I'm a computer obsessed autistic nerd w/ executive function disorder. I am effectively agoraphobic. I'm so fucked with anxiety/depression/sensory issues that I can't even manage to get on disability.
I'm living on a donation of $100 a month, and by grace of some girl I met on the internet.
I spend most of my time reading science pubs in quest to fix myself, hundreds a day. I have an operating model of disease that lets me make predictions that end up panning out months+years later.
What do?
I told the person donating me money that I was going to use it to drink copious amounts of wine until I shit myself and then go on a 3 day fast...
I got my donation early this month 
My sleep schedule shifted again at the end of last month. This seems to coincide with access to food and going back on my psudo-soylent diet that I'll admit is woefully lacking. It was worse this time because I was out of vitamins and the household food was 90% carbs.
Pain in the ass: I wanna start my Fasting regimen but I can't go to the store at midnight since they're closed :(
I gotta do it quickly otherwise I won't be able to sync my budget with it and will end up having to wait a month.
Finding detailed information about probiotic strains on a blog post for a Chinese Herbal Medicine and accupuncture clinic.
I feel a bit disgusted. And yet...
"Chinese medicine has a certain model for viewing the world and the body. It is ancient wisdom and extremely valuable. But it is just one viewpoint / one lens. Western medicine and science has a different lens and has discovered incredible new information about health. It is also valuable."
http://www.chinesemedicinedoc.com/want-gut-health-take-prebiotics-not-probiotics/
I've been digging into pro/prebiotic supplements a bit to explore if there are custom strains I could get at somepoint, but 90% of what i'm finding is bullshit.
Seems to me that he's at least done his research and has enough details that I can verify his claims independently. A lot of what he's saying already aligns with stuff I've read elsewhere on places that i'd trust more.
http://www.chinesemedicinedoc.com/probiotics-strains-are-important/
I wish I had enough money to get the 3 sample kit from here: https://ubiome.com/consumer/explorer/ to be more confident on it working.
Chicken & Egg Scenerio. I gotta not be anxious and depressed to be able to hold down a remote job. But having an income would make all of this so much easier.
Bootstrapping sucks.
My sleep schedule is really wonky. Kindergarten starting again will help to whack it into better regularity.
@ultimape That chronometer demo for WFPB was really useful. Thanks for sharing that!
@brianpoe @sonya it's definitely weird, but I found it extremely useful. I read through a bunch of the source material for the idea and found out that I actually have the genetics where I don't produce enough cholesterol and I have to get it from my diet.
Whereas most people can produce cholesterol directly from fats thru a calcium related process in bile, it seems my system is impaired. In an odd sort of way it's helped me eat less meat because I can focus on that particular issue.
@brianpoe @sonya Im big on plant based stuff, but I've been using eggs since it seems potentially the least harmful on the environment. I tend to prefer sustainable sources and thats my focus versus something like the ethos behind veganism. It seems a lot of the diets like lacto-vegetarianism or vegiterian+fish might be due to this weird qurik some populations have.
I'm hoping that stuff like eating insects might do the same thing and then I could reduce the load even further.
@ultimape Genuinely curious; how do you know your cholestrol synthesis system is impaired?
There is so much crosstalk, industry bias, and cultural identity tied up in diet. I've found it a difficult subject to navigate. But if we stick to the studies (and sometimes drill down into studies to identify weak or slanted studies), I think we can find the truth.
May I share a source that I've found to be scientifically verifiable? This one is on ideal cholesterol:
https://youtu.be/lakaozfALho
@brianpoe it fits symptoms and genes, and explains why I feel better when I focus on liver condition.
Found in a subset of autism
https://www.kennedykrieger.org/overview/news/autism-new-study-discovers-statistically-significant-link-between-abnormally-low-chole
And in a subset of schizophrenia, even in studies all the way back in 1950
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1822429/
I have a genetic profile that sits in the overlap.
@brianpoe there's two parts to this, one part is the binding of cholesterol with calcium to be transported in the blood where it's needed and then the other part is actual deposition of such in the usage of by body. That seem to related to inflammation factors. The Binding stuff happens in the bile and gallbladder, and the bile acid is secreted by the liver and also partially controlled by a local microbiome and feedback w/ diet.
I have issues with both. Accounting for them help me get better.
@brianpoe the calcium binding factor is also tangentially related to genetics that I have that code for a different insulin profile than typical people (the kinds that reduces bone loss), as well as serotonin processing system that suggests it's been adapted to higher natural blood acidity. I have a really hard time getting enough protein in my diet without eating meat, but I've managed that so far at least.
@brianpoe side effect of all of this is that my immune system seems to be more on the knife-edge, and very selective when it comes to the kind of microbiome I support. It also means Rick factors leading toward the multiple sclerosis, and possibly a certain kind of Alzheimer's or Parkinson's if I'm not careful with my diet.
My family history includes crohn's disease multiple sclerosis, as well as widely varying and irregular cholesterol levels.
@brianpoe Ah, just remembered I got bloodwork done that showed I had high levels of cholesterol and yet I had no sources of cholesterol in my diet. It was really strange.
I went looking about stuff like HDL and LDL and found all sorts of things that affect it in an interesting way if you're autistic or schizophrenic and found the processing issue and my cholesterol levels dropped once I fixed it. But then they got too low.
turns out blood cholesterol is a poor proxy for health.
@brianpoe A lot of the popular stuff around omega3s and cholesterol seem to be based on bad studies and poorly educated doctors just parroting stuff from seminars. I actually predicted this kind of thing last year: https://vitals.lifehacker.com/omega-3s-aren-t-so-great-for-your-heart-after-all-1823578728
But with the caveat that it does seem to help schizophrenia: https://www.forbes.com/sites/emilywillingham/2015/08/12/can-fish-oil-arrest-psychosis-onset-in-schizophrenia/#5f667f792396
and plays a role in MS issue in the brain.
https://www.semanticscholar.org/search?q=Omega%E2%80%936%2FOmega%E2%80%933%20Ratio%20and%20Brain-Related%20Functions&sort=relevance
It makes sense, the brain is like 25% cholesterol.
I'm not aiming to go carnivore myself, but the app is very flexible and even lets you set custom goals.
Their birdsite feed had a review of a Vegan's food breakdown if you wanna understand it: https://www.youtube.com/watch?v=BCqKo-tT0RE
I'm going to be using it to track - hopefully the knowledge alone will help nudge me into a better diet, or at least confirm what I'm missing when the end of the month rolls around and I start getting sad.
Its going to be a big help with retrofitting my gut after my big fast.