"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.
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.
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?
>> 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.
"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.
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?
Thanks for the enlightening reply! It definitely helps to understand what is going on in the mind of a biologist when they encounter a computer scientist.
I think what draws me most to the field of biology, and the prospect of biological computing, is that there are insane uncertainties and super complex pathways; the fact that the same test run 10 times in a biological machine may not yield the same result each time.
My main challenge is in starting a dialog with people in the field. Perhaps I will try communicating in scientific method lingo and see how that fares.
Overall, the feeling I get is that biologists fear the commoditization of their field, and I observe that even the progressive bio startups are still sticking to the (closed) pharmaceutical model of business.
We at uBiome would LOVE to work with you on a citizen science study of the microbiome in Turkey. Please write to studies@ubiome.com and we'll get you set up. (Our website is www.ubiome.com.)
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 y...
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.
Can you point me to some resources about fermentation? I make my own milk kefir, and it turned my life around, but I'm considering adding in more diverse stuff.
The following book, the first 3 chapers explores the bio chemistry of the microbes. Citing research not as much as the other book I recommended, but has a solid base to understand your gut bacterium.
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:
(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.
17 comments
[ 3.2 ms ] story [ 52.2 ms ] threadI 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.
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.
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?
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.
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.
Crunching the numbers is the means to refute them, then. I don't know what you think CS folks are doing all day?
I think what draws me most to the field of biology, and the prospect of biological computing, is that there are insane uncertainties and super complex pathways; the fact that the same test run 10 times in a biological machine may not yield the same result each time.
My main challenge is in starting a dialog with people in the field. Perhaps I will try communicating in scientific method lingo and see how that fares.
Overall, the feeling I get is that biologists fear the commoditization of their field, and I observe that even the progressive bio startups are still sticking to the (closed) pharmaceutical model of business.
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 y...
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.
http://www.amazon.com/The-Art-Fermentation-Exploration-Essen...
Here in China, fermented foods are numerous. One of the tastiest is https://en.wikipedia.org/wiki/Furu though the Wikipedia page doesn't show the cheesey sauce-like kind that is common around here. I might just upload a shot shortly! Check out https://en.wikipedia.org/wiki/Yunnan_cuisine
A short talk covering the paper: 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
The actual paper "Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders": http://www.cell.com/abstract/S0092-8674(13)01473-6
http://onlinelibrary.wiley.com/doi/10.1111/j.1440-1819.1984....
(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.