
Chasing the Link Between Gut Bacteria and Autism - jessaustin
http://www.theatlantic.com/health/archive/2015/11/how-microbes-shape-autism/416220/?single_page=true
======
nyc111
"Gilbert and his colleagues aim to recruit a thousand people with autism as
part of a large study called American Gut."

I have been planning to do the same type of investigation here in Turkey. I
see this as a big data problem. You don't have to be a medical doctor to match
gut flora to diseases. This is a database problem.

I contacted several microbiologist here in Turkey to ask their support but
none replied. Academics and professionals do not like to talk to non-
professionals.

Anyone who is interested in this subject and would like to discuss please
contact me.

I consider this discovery of the microbiome and its role in the human body to
be the greatest revolution in human history. And There is a lot we can do as
citizen science projects.

~~~
epoxyhockey
_Academics and professionals do not like to talk to non-professionals. I
contacted several microbiologist [...] but none replied_

I have also experienced this. Biologists keep their cards very close to their
chest and don't seem to be fans of our software culture, let alone the open
source software culture. They don't even respond to inquiries.

There is great opportunity for biologists that do open up to the larger
community of software engineers.

~~~
teekert
As a biologist and open source/Linux nerd, I can tell you it is because the
biologists don't understand you or what you can do. And they find it annoying
that you pretend to understand their field.

Biologists do things "knowledge based", they love to quote stories in which
data-driven research ended in the conclusion: "ATP is an important molecule".
They love terms like datarrhea. They love the Google Flu fiasco. They know
what over-fitting is but never heard of random forests.

And I can tell you, quite often they are right. Computer scientists often
don't understand and appreciate the complexities of a signalling pathway, the
insane uncertainties, the lack of reality in any of the models biologists use
to illustrate connections, the ease with which models are discarded.

So tell me, what are your hypotheses and how do you think your algorithms can
prove them right or wrong?

~~~
manmal
>> Computer scientists often don't understand and appreciate the complexities
of a signalling pathway

Do they have to? If I understood OP right, he just wants to crunch some
numbers and find out whether there is a correlation between specific bacteria
types and diseases. It's a stochastic approach to the problem.

I don't like rants like yours that basically say "don't talk about this
subject, you don't have the necessary background". Problems sometimes _are_
solved by people foreign to a field.

~~~
teekert
"he just wants to crunch some numbers and find out whether there is a
correlation between specific bacteria types and diseases."

I don't think he is, he is specifically looking for biologists.

I don't like your: "he just wants to crunch some numbers". So what if you find
a correlation? You can always find a correlation when the number of parameters
is much greater than the number of experiments, that is the problem with
knowledge-less Big Data. Suppose you do find a correlation. Is it because of
the bacteria? Or is it because of the Genomic similarities between the
persons? Is it because those persons were breast fed? Do the hate milk? Or
when there is no correlation, is it because the microbiota has no effect? Or
is it because the bacteria in one gut are continuously exchanging plasmids?
Again, what is your hypothesis?

I like the computer scientists that reach out to other field and help in
_generating_ hypotheses. Just crunching some numbers sound like a recipe for
nothing.

I mean, when you do find a correlation? Are you going to advice people
medically based on a correlation? I know the FDA for one does not like that.

~~~
manmal
Are you accusing computer scientists of not being able to apply scientific
methods? I'm not sure, and I don't want to setup a strawman. Of course there
would have to be hypotheses, and they would be tested. Scientific methods are
not exclusive to biology. In the study or citizen study I imagine here, a
questionnaire would include questions like yours.

Crunching the numbers is the means to refute them, then. I don't know what you
think CS folks are doing all day?

------
popsomoa
My friend Dr. Elaine Hsiao of Caltech and UCLA was the lead author of the
paper mentioned in the article regarding the effects of B. fragilis in mouse
models of autism. It was her doctoral work. If you find it interesting here
are some talks and papers by her to check out:

A short talk covering the paper:
[https://www.youtube.com/watch?v=FWT_BLVOASI](https://www.youtube.com/watch?v=FWT_BLVOASI)

A longer talk about the field of microbes and behavior:
[https://www.youtube.com/watch?v=mY_fRFjteAw](https://www.youtube.com/watch?v=mY_fRFjteAw)

The actual paper "Microbiota Modulate Behavioral and Physiological
Abnormalities Associated with Neurodevelopmental Disorders":
[http://www.cell.com/abstract/S0092-8674(13)01473-6](http://www.cell.com/abstract/S0092-8674\(13\)01473-6)

------
cpncrunch
This seems a little bit speculative. Studies have already shown abnormal HPA
axis activity in autism:

[http://onlinelibrary.wiley.com/doi/10.1111/j.1440-1819.1984....](http://onlinelibrary.wiley.com/doi/10.1111/j.1440-1819.1984.tb00793.x/abstract)

(The HPA axis is one of the main modulators of bowel motility).

So basically there is already research showing that the brain is influencing
the gut in autism, but the idea that the gut might be influencing the brain in
autism is speculative.

------
napperjabber
Being someone who has had to deal with a number of issues that I inherited
from a horrible childhood experience. I was one of the lucky ones. I only had
habbit issues to overcome.

What it came down to was diet. Obviously, but the tone of this article. Gut
Bacteria is what I was missing most I found. Between forgetting what I thought
was good three days later(early age dementia) and not creating a food log. I
knew I was having trouble in my mid-twenties.

In my early twenties, I bought into the Drinking Culture. I'm not going to
talk much about that here, but I can assure you that It was not a good phase
of my life. ( As a disclaimer, didn't do anything that hurt anyone, I was that
guy that would listen to everyone. Jesus people, wake the fuck up and move on
with your lives. )

After I was spent, I missed the days of being able to work out for two hours
every 4 days with an off day on the 5th. It was a great routine that I got
myself into, but I feel out of when I deadlifted 275lbs incorrectly. I was on
my back for 3 days after that. It wasn't until years later that I learned the
reason why I was so off on my deadlifts was because of the type-of-
food/nutrition that displaces my organs within my body. - Growing up, I was
taught that I needed to eat as much as possible as I wont be guaranteed a meal
in the coming days. Thing is, I always had a meal in the coming days. The
concept of fasting was so alien to me that I was not only appalled by the idea
of losing a meal, but I felt like I want have lost something of myself if I
did miss a meal.

After spending sometime hanging out with 'really healthy people', I was
introduced to the Raw Food Diet. I started training myself to follow the Diet.
There was a 4-5 week period where I was able to stay 100% raw. Over the course
of 6-8 months, I lost nearly 70lbs and increased my biking range from 10 miles
to 60 miles three times a week. ( Riding a $320 diomondback bike. It was
awesome. ) I was considering buying a real bike for the 2016 Olympics.

My work-place changed bosses and my entire life destabilized as I couldn't
handle someone who didn't have an apparent objective, yet had a political
goal. The man further insulted me by ignoring me and not really asking me what
the problem was. I realized that I had to leave the company in order to
understand why people act they way the act. For my entire life, people had
protected my when I hadn't asked for it and I was at the end of my patience
with groups of people protecting me. - I moved to Chicago. In between quitting
that job and moving, I found my now Wife.

When getting to Chicago, I was in love with the idea of getting back to my
half centuries, but all I could do was Bike the Coast of Lake Michigan or the
streets of Chicago. Immediately, the first people I meet were not only proud
to be meat eaters, but they tried to convert me from a vegetarian back into an
omnivore. It's annoying, having people promote their eating style yet not
listening to what your dietary conditions are...and so begin my natural
reluctance to the Chicago mentality. Over the next ten months, I was slowly
mentally beatin down by the boy who hired me and the community that I thought
I needed to be a part of. - I moved to L.A.

After a three month sabbatical and an additional $30,000 in debt to re-jult my
diet and workout routine, I relocated to L.A. with the mentality to make
money. Within a 12 month I make my way back up the developer foodchain into a
position that can finally finance me and it all begins again. Once I got bake
into the elite-circle, I start to experience the mentality that I need to eat
what others offer me. The misconceptions that sugar and coffee is good for you
go deep into the mentality of the elite. There is one difference between me
and the others that they don't get. They begin to resent me because I'm eating
an orange rather than poisoning myself with sugar coated cookies. After a
while, I succumb to the peer pressure(Probably only in my mind at this point,
thank you Chicago.) and start downing multiple cups of coffee and eating a ton
of sugar. I eat the sugar to keep my body temperature up and the coffee is to
keep me focused. As a result, it kills my sleeping cycle and my eating cycle.
Months later, after the company doesn't give me any work, they 'lay me off'. -
Luckily I saw it coming and had a backup plan.

Right now, my focus is working off the debt. I've found a job that pays me
well and allows me to work remote. As a result, I've lowed my cost of living
by moving out of LA. My next house will be next to a trail so I can get into
my half centuries again.

How does fermentation mix in with this book I just wrote? Fermentation is my
current culinary pursuit. Maintaining a raw food diet is a lot of effort. You
have to make mental decisions every day and spend large sums of money for food
that you use for just the water within. With fermentation, you can ferment
rice, beans, fish, cabbage, anything. Store it in a mason jar for days, weeks,
or even months. The cost of food goes down from $50/day to $10/day. You're no
longer 'gluten intolerant'. Your brain is 'always on' when you want it and you
can 'always turn it off' when you want to. ADD, ADHD, all that is just another
way of saying 'to much sugar' for me. This coming from someone who has been
labeled with Autism, Tourettes, ADD, ADHD, Aspergers, and Dyslexia. - It
wasn't until I took the initiative and spent years understanding how my body
reacts to diet.

Living in America, I'm starting to find hints of Isolationism in everyday
situations. A nation protected by water, we've instilled this into our
culture. The belief that we need to build a group of friends, a cliques, a
group of fellow thinkers. Rather than learning how to communicate with others.
If someone had taken the time to explain to me that diet is about finding the
right fuel for your body and not a selfish endeavor of pleasure, I would have
been able to communicate with others better.

\-- How to measure ones self --

Programming, as my primary source of income is helpful. It allows me to count
the keystrokes I make on a screen and the corrections of said keystrokes. I do
this mentally, as it helps me slow down my mind and I've yet to take the time
learn how to write a VIM plugin.

How much time does it take you to write a story? If it takes longer than avg,
you're probably not getting enough sleep or you're eating to much sugar
inducing a higher ADD state.

Energy drinks help you focus, but you have to eat dense food so that it
doesn't kill your liver. Sugar without fiber is the worst for you. It'll
destroy your liver the fastest.

Do you just read short articles? When was the last time you finished a book?
It's not because you can't, it's because you haven't yet balanced your diet.
Decrease the amount of meat/sugar you consume and increase plant-fiber intake.
You'll notice a change within days.

When you do this for the first time, the plants will not taste like anything.
I spent 3-4 weeks forcing myself to eat food that tasted like cardboard or
sawdust. Kale, spinach, roman lettuce, cilantro, parsley. It all tasted the
same to me. I spent a considerable about of time re-training my taste-buds. I
now enjoy steamed veggies more then something fried, sauteed, or prepared in
some other kind of sauced-uniform fashion.

The pace of me writing this book as recently slowed from this point.

Lastly, at the start of this book, I woke up very mentally balanced. While
writing this, I have consumed one Blueberry Coffee Cake and two Cappuccinos. I
anticipate that my grammar and writing has become worse while writing this
book. Confidences is not a mental feat, is the result of a proper diet.

\- Hope this helps in your research, if you have questions, feel free to ask.
I will answer in more detail in a private session then I would in public.

\- For anyone with the same struggles, I started here(This book cites
research/studies for all of it's assertions.):
[http://www.amazon.com/Vegetarian-Sports-Nutrition-Enette-
Lar...](http://www.amazon.com/Vegetarian-Sports-Nutrition-Enette-Larson-
Meyer/dp/0736063617/ref=sr_1_5?ie=UTF8&qid=1448139485&sr=8-5&keywords=vegetarian+athlete+nutrition)

~~~
abledon
After reading this, A part of me wishes / wonders what it would be like
reading any docs/readmes/code you write for your day job.

~~~
napperjabber
Hah, the shakyness of the grammer is a clear indication of the pressure I
'feel' like I'm under. My readmes are simple and to the point, I expect the
reader to understand the cli and to explore the codebase. I don't spend much
time communicating the architecture for the fact that I know I will litter it
with grammatical errors. Instead, I write comments for every algorithm I
compose.

Alas, your reluctance is a result of my poor education and forced isolation
pushed upon my by an institution. Something that takes a lot of patience of
mine to force myself to understand people that I classify you with; will not
understand because they too have been through this gauntlet, but have had
better guidance than I.

