Our microbiome challenges our concept of self | Hacker News Reader

Our microbiome challenges our concept of self

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100 pointsWalterSear66 comments

Whether or not your concept of self is challenged depends on your current concept. If you think biology is applied chemistry, and chemistry is applied physics, you're just fine.

You articulated my thoughts perfectly, thanks.

I think it's useful to draw a distinction between the concept of self and the sense of self. The concept of self refers to the physical being. That's purely a physical consideration: i.e. the physics you mention.

OTOH, the sense of self refers to sentience. It's more "who am I?" than "what am I?" For instance, it's what is fractured in dissociative disorders.

So, here, you can have your concept of self challenged without your sense of self being affected.

Are you referring to the difference between the subjective experience of feeling like a "self" vs your knowledge of being a "self" (or the illusion of being a self)? If that is the case, I actually disagree that the experience of being a self would remain unchanged indefinitely if you change your belief of what you are as a self. If you are mindful of your new concept of self, the character of your daily experience will be changed as you reframe your experiences in to your new concept of self. To take this to an extreme, you could practice mindfulness meditation to the point where you lose the experience of a sense of self.

Well, the first I referenced is just the physical notion of self, more attuned to the article. If I realize that I am x % bacteria, then it may change my perception of that physical self. But, I don't believe that it would, per se, cause me to question my very existence as a self.

However, I agree that if I were inclined, then it could certainly be one of any number of factors (including mindfulness meditation or any serious conscious consideration) that prompts me to start thinking about or questioning my "self" as a sentient entity beyond just my physical being.

I just don't believe that such an outcome is inevitable or that those two experiences of self necessarily converge. That is, one can certainly question the former without ever considering the latter. In fact, I would wager that most who encounter an article such as this would fall into that category.

Gotcha. I was a bit confused by your "physical self" terminology as the relevance of the term "physical self" depends on whether you believe in some non-physical self or if you believe that consciousness and thus the self is just some emergent property of a particular configuration in your "physical self" (and thus there is no such thing as a non-physical self). There is a lot of evidence that if you change some configuration of your physical self that your experience of self will change.

As long as you understand that "you" don't exist, you are just fine.

Sure I do, the limitation is in peoples failure to recognize reality not a static notion of self.

People think of themselves as a living organism but skin makes use of dead cells. At the other end people think of non organic tattoos and dental fillings as part of who they are. Beyond that, when driving you don't think in terms of this giant extra thing, it's also part of the fuzzy self.

Really, the core failure is the rather western insistence on clear separations and concrete ideas. I would posit that self as those resources under your control is probably a better fit for how people think than a simplified biology.

I think most people don't have a use for thinking of reality in these terms until they struggle with something that brings them to this line of questioning or unless they are just naturally very curious and have a lot of free time. As far as I know, the practice of mindfulness (which I'm assuming is a necessity for getting a more objective view of the world) is just as esoteric today in the East where these practices originated from.. only the philosophy underpinning the practice may be seen as less foreign over there.

What are the practical consequences? Should I revoke your status as a being I have general moral obligations to? Or should I extend my moral obligations to all objects animated or not?

You should extend your moral obligations to all animated objects.

You have a moral obligation to the Universe inclusive of everything it comprises, not any isolated parts of it.

Interesting philosophical questions on how oneself views oneself, especially if you go back to the source paper at http://journals.plos.org/plosbiology/article?id=10.1371/jour... rather than the linked extract. “[W]e have never been individuals...”

Microbiome is one of the things we're including in the Arivale program. Early days on the research front, but fascinating stuff - our clinical team have written up two less philosophical, more scientific articles re. correlations of microbiome to health at https://www.arivale.com/gut-microbiome-tmao-heart-heath/ and https://www.arivale.com/gut-microbiome-crohns/.

I posted this comment (https://news.ycombinator.com/item?id=15923695) about the microbiome about 2 months that is related, of course I was down voted into oblivion.

But essentially my point was that human genes are not determinative and work hand in hand with the microbiome, where an analogy I used (though not my original thought) is that the human (genes) are like a piano and the microbiome is like the player.

One of the more interesting studies I have read included identical twins in Africa, where obviously genes are identical, so is environment and diet, yet one twin would be healthy while the other was malnourished. The conclusion was it was the difference in the twins microbiome that was determinative and the cause.

I'm not sure, but it might be the use of the phrase "leaky gut". Some people will have a knee-jerk reaction against that term vs. the term "intestinal permeability".

That's a weird reason to downvote. Most people don't know what either of those terms means.

I only became aware of it after seeing the edit war on Wikipedia. It may not be the reason for downvotes but it's apparently a controversial topic among some people.

Will you are a lawyer (quite a good lawyer by my estimate), but you should be careful when moving outside of your sphere of competency. Biology is very, very complex.

Identical twins are not genetically identical (they typically all have small genetic difference), but even if they were the cause for any difference could be due to factors outside of the microbiome. There is no way any careful scientist could conclude from one set of twins what the cause of any difference between them was.

Edit. I apologise for my tone. I am just trying to explain why you got downvoted.

>There is no way any careful scientist could conclude from one set of twins what the cause of any difference between them was.

The twin study wasn’t n=1 it was multiple sets of twins throughout the continent. Either way the twin study wasn’t in my original comment, so it wasn’t the reason for my being downvoted.

My comment regarded the fact that humans have relatively very few genes compared to many other life forms, yet are obviously more complex, that should’nt be controversial or downvoted. But I continued that the microsbiome can explain some of that complexity, for example here is article from Cleveland Clinic regarding a study that concludes the microbiome can change the way genes express themselves, not changes to dna, but the microbiome can turn genes on and off. https://www.google.com/amp/s/health.clevelandclinic.org/2016...

Humans don't have relatively fewer genes compared to other life forms. Humans have less DNA than some species (salamandas are an example), but all animals have around the same number of genes. The extra DNA in some organisms seems to be (mostly) non-functional.

Yes the microbiome influences which genes are expressed.

In the example I was given was wheat vs humans. A quick google search shows wheat has 164,000 to 334,000 genes, compared to 20,000 to 25,000 for humans.

The way it was expressed to me at the time it’s scientifically surprising much simpiler life forms have fewer genes. “This paradox has vexed scientists since the discovery of DNA about 45 years ago,” notes Dmitri Petrov of Harvard Universitys Society of Fellows, when discussing amoeba’s with a genome 200 times the size of a human. See: https://news.harvard.edu/gazette/story/2000/02/why-onions-ha...

As you suggest I should probably avoid topics outside my expertise, and genetics certainly is, but I am passionate about health and nutrition, on the edge of those topics the microbiome and genetics come up. Anyway I think was I contribute on these topics deserves a conversation (reply) like you have engaged in and not just downvotes.

> But essentially my point was that human genes are not determinative and work hand in hand with the microbiome

I think what's more generally accepted is that genes work in concert with environment, of which the microbiome plays but one part.

The boundary at which the self ends and the environment begets another philsophical point that Alan Watts spoke at length about, essentially stating there is no dividing line, it's all a spectrum upon which we place arbitrary boundaries because of our need to put things in boxes and that the concept of self that we create of ourselves is a complete fiction.

Also, is the autonomic nervous system or the unconscious and nonconscious considered part of the self?

All good questions, but none of these facts necessarily entail that there is no self, they simply change what we could possibly mean by the "self".

For instance, cars and jobs don't actually exist at the level of particles and fields, and yet we can say with certainty that I have a car that I drive to my job almost every day. These terms have sensible and precise meanings, even if we don't yet know their precise meanings.

>On the contrary, it means that the stakes of the natural sciences exceed the expertise of the natural sciences and reach over into the arts. This makes a close collaboration of the life sciences with the human sciences imperative.

Why do new findings like this lead people to conclude that “science needs philosophy” It’s never the philosophers that make the findings.

And it’s not like the laws of physics will need to be re-written.

To be generous this sentence could be interpreted as meaning the humanities need to take notice of what science is finding, not the other way around.

Unless we metaphorically neutron bomb the humanities and start again nothing science discovers will have any influence on humanities.

Edit. Humanities graduates how about engaging rather than knee jerk down voting anything that questions your world view.

> Humanities graduates how about engaging rather than knee jerk down voting anything that questions your world view

I have a degree in mathematics.

Not quite the engagement I was looking for :)

Science needs phillosophy as one source of inspiration for new research. Many of humanities greatest scientists were also brilliant philosophers.

There would be no science without philosophy.

The scientific method _is_ philosophy.

I think it's very important to retain the ability to postulate above scientifically proven things.

>postulate above scientifically proven things

That's just what theory is. Unless you mean postulating about things which are fundamentally unreachable by evidence, in which case I challenge the claim that they're ever important. (If they were important in a situation, then that situation would be an experiment that could confirm or deny them.)

Not all philosophy is like that, of course. For example this comment, which is definitely philosophical and I hope not wrong!

Indeed. Epistemology aside, I'm definitely not arguing for religion or insanity.

"Philosophy is dead" - Stephen Hawking.

Philosophers haven't bothered to learn modern science, they do not have the expertise necessary to do anything but pontificate on vagaries. Philosophy these days seems more about finding clever places to hide religious beliefs than it is about explaining the world as it is and answering questions in useful and productive ways. Scientists do that now.

> Philosophers haven't bothered to learn modern science

Incorrect.

> they do not have the expertise necessary to do anything but pontificate on vagaries

Also incorrect.

> Philosophy these days seems more about finding clever places to hide religious beliefs than it is about explaining the world as it is and answering questions in useful and productive ways.

3 for 3, congratulations!

Excellent points. I stand refuted and corrected. Wonderful.

There's nothing to refute, your statements had just as little substance as mine. If only there was some field of study which could discern valid logical arguments and how persuasive we ought to find them. Someone really ought to start such a field of study.

How arrogant.

It is philosophy that gave birth to science is it is today. In fact, "science" was once known as "natural philosophy".

Science is a practical philosophy based on experimentation via the scientific method. It is a philosophy, that is, a way of looking at the world.

> Philosophy these days seems more about finding clever places to hide religious beliefs than it is about explaining the world as it is and answering questions in useful and productive ways.

What about Scientism, the religion that considers science to be the "One, True Way"? It usually incorporates the reductive materialist belief system quite heavily.

And it is Scientism that arrogantly dismisses philosophy as some outmoded system, when in fact, Scientism is ironically a philosophical position itself, a religious one at that.

Meanwhile, philosophy as a whole continues to explore different ways of looking at the world unabated, because it doesn't get side-tracked by ridiculous religious dogma.

Meanwhile, science and the scientific method, those practical philosophical tools that have been very useful in the hands of those who care about positive and beneficial progress for all of mankind, continue marching on proudly, unconcerned by ridiculous religious dogma.

Arrogance isn't a fallacy in reasoning. Rejecting a belief because it sounds arrogant is particularly stupid kind of vanity.

Arrogance is rooted in self-importance. In fact, if one can glean common themes from science, it's that there is a distinct lack of self importance, that humans are special . The Earth is not the center of the universe, the sun and stars do not revolve around it, there is no center of the universe as every point can be considered the center, all motion is relative, etc.

Noam Chomsky is the father of modern linguistics, and his theories hold that the principles underlying the structure of language are biologically determined in the human mind and hence genetically transmitted. The 1984 Nobel Prize laureate in Medicine and Physiology, Niels Kaj Jerne, used Chomsky's generative grammar model to explain the human immune system, equating "components of a generative grammar ... with various features of protein structures." Chomsky's work contributed substantially to the decline of behaviorist psychology. In addition, some arguments in evolutionary psychology are derived from his research results

I've read less of Daniel Dennet, but he has been influential in the theory of mind and the direction that some AI research has taken.

When I think of modern philosophers, these are the giants.

> Philosophy these days seems more about finding clever places to hide religious beliefs than it is about explaining the world as it is and answering questions in useful and productive ways.

It's funny that you mention that. While at undergrad I took a biology class taught by Robert Sapolsky (I consider him equal parts scientist and philosopher) where he philosophized on the origin of religiosity using scientific findings and research. Would you like ot know more: http://www.openculture.com/2014/12/robert-sapolsky-explains-...

They're not completely distinct fields of study, they operate on a spectrum as science and philsophy go hand in hand. The big questions in philosophy are somewhat neatly summed up in 4 questions: Who am I? What do I want? Why am I here? Where am I going? Substitute we for I, and then that pretty much sums up the questions science tries to answer.

I think this misses a major fact which is that many revolutionary scientists were extremely philosophical people and developed new theories by thinking out of the box and reimagining the way things work instead of accepting the ideas of their time. There are people who were simply diligent and bright, like Karl Von Frisch, but, for example, Stephen J Gould basically started the entire field of developmental biology through his philosophical exploration of the idea that ontogeny recapitulates phylogeny.

Philosophy is about asking questions, which eventually lead to separate disciplines, once frameworks for answering those questions have been created. Many discrete departments at a modern university have their roots in philosophy.

I'm not arguing with your initial point, articles like this and the subsequent claims about science and philosophy are usually wrong. But I realise, from the responses to you claim that a lot of people are quite ignorant about philosophy and its history in science.

There is a great quote in a Daily Nous article, about this: "many new disciplines have sprung forth from philosophy over the years: physics, psychology, logic, linguistics, economics, and so on. In each case, these fields have sprung forth as tools have been developed to address questions more precisely and more decisively. The key thesis is that when we develop methods for conclusively answering philosophical questions, those methods come to constitute a new field and the questions are no longer deemed philosophical."

[0] http://dailynous.com/2017/08/23/intellectual-achievement-cre...

Because the concept of the conscious self being just a small part what constitutes one unit of homo sapiens has been part of philosophy for thousands of years. As I see it, philosophy is there to ask the big questions, having a say in the prioritization of the direction of R&D. Elon Musk asked himself what was most needed to ensure a prosperous future for humanity, and his answers were PayPal, SpaceX, Tesla, SolarCity, Neuralink and the Boring Company. They also happen to double at what a functioning Mars colony would need :)

I came across some of the microbiome research in the recent years, I know about the hacker culture interest in fermented foods and do drink kefir semi-regularly myself. But there appears to be a quite some correlation between microbiome and, well, diet: https://www.nature.com/articles/nature12820 Aparrantly you can change your microbiome rapidly by eating differently.

When discovering effects for the whole organism, can’t it be that these are correlations that have been found before in nutrition studies? Why is / isn’t this a problem? Maybe I’m missing something.

I wonder if these new discoveries about the microbiome can explain why on disciplines like Zen meditation (Zazen), one has to focus her mind on a point at the gut level.

Could these techniques somehow be aware of the gut-mind connection?

https://www.health.harvard.edu/diseases-and-conditions/the-g...

Just an info: Focusing mind at the gut level is not specific to Zen meditation but is instead part of Yoga Sutras of Patanjali (https://en.wikipedia.org/wiki/Yoga_Sutras_of_Patanjali) from which all these techniques are derived from. Specifically it is focusing on the 7 centres of energy called Chakras. The gut level thing you talk about is called the Manipura in Sanskrit or the Solar Plexus Chakra in English transliteration.

I've read that the microbiome can and does influence our sense of taste, altering it in such a way that the foods that certain species of bacteria prefer to metabolize end up tasting better. Although I've anecdotally found this to be true, I think it is commonly accepted that the gut affects the mind whether the conscious self is aware of it or not. A lot of the mindful meditation I've practiced doesn't have the goal of making the mind quiet. Quite the opposite, it is a technique to quiet conscious thinking that takes effort so that one can be more aware of thoughts that seemingly arise out of nowhere...like when you're stuck with a difficult problem only to have a solution pop into your head over the weekend while going out for a run, without any conscious effort

Your gut contains the second largest collection of neurons in your body, and has a large influence on our behaviour...

https://www.scientificamerican.com/article/gut-second-brain/

That's where the concept of soul fits right in. We cannot delineate between "us" and the "environment" either - we constantly lose and acquire molecules from it.

Any examples of molecules acquisition and losing?

Every inhale and exhale, for two.

There is a lot of truth in that - the microbiome is a key factor affecting out nutritional intake. It affects how effective we take up energy but also affects us through a multitude of chemicals all influencing the cells in our body. Our health, out intellectual capabilities and our moods depend on it.

If the ego is part microbiome and we are consequent then we should have laws that declare antibiotics tools for partitial mass murder or suicide.

Warren Ellis, as usual, is ahead of the curve.

One of the most interesting characters in Normal is a (seriously mentally ill) futurist who conceives of her microbiome as a separate entity and talks to it like she suffers from DID. It's a whole book about how a sufficiently-obsessive focus on the future can break your identity, so this is a nice fit.

Is this worth reading if I loved Transmetropolitan?

The results from this study will probably be interesting: https://www.nasa.gov/mission_pages/station/research/experime...

GMO BT bacteria gets in your gut, kills your flora, releases toxins (pesticides). Your body struggles, serotonin levels decreases. You can't sleep, get depressed. Your doctor prescribes SSRIs. It interferes with your reproductive system and quality of life.

You go online, read a comment on HN that gives you a hint of what happens. It goes against your confirmation bias, you get triggered, you down vote. haha sorry

You should consider expanding your source of news beyond naturalnews.com.

  A car is not a car without the human, with the keys to the car, sitting in the driver's seat, in a state ready and capable to operate the vehicle, and in possession of valid paperwork in good-standing, proving that they are legally entitled to operate the vehicle.
  A car is not a car without the human, with the keys to the car, sitting in the driver's seat, in a state ready and capable to operate the vehicle.
  A car is not a car without the human, with the keys to the car, sitting in the driver's seat.
  A car is not a car without a human sitting in the driver's seat.
  A car is not a car without a human to drive it.
  A car is not a car without a human inside it.
  A car is not a car without an animal inside it.
  A car is not a car without an object inside it.
  A car is not a car without an engine inside it.
  A car is not a car without something inside it.
  A car is not a car without anything inside it.

Doesn't hold up. The car remains a car, so long as it is actually a car.

If you really want to challenge views about being a human, consider that each of us all have been single celled animals for at least a couple of seconds, if not minutes or hours, of our lives. It didn't stay that way, but it's an incontrovertible fact for every last one of us, and indeed also for lots of other organisms.

Plenty of passengers ride the bus, but the bus is not redefined by this.

each of us all have been single celled animals for at least a couple of seconds

That seems wrong to me because it conflates different identity concepts. That cell wasn't me, but more like a seed from where I was built. Actually, if I'm not mistaken, identical twins come from a single embrio that gets splitted, so with that reasoning both twins were the same person at one time. I don't think so.

That's exactly what I mean about proposing a notion that serves as a challenge to a point of view. I was pretty confident I was putting forward a statement that someone would take issue with, even if it's part of a sentiment I buy into.

Anyway, the original atoms and molecules of that first cell are long gone, yet here we are. In terms of qualifying one's semblance of self, I think infant amnesia also represents a significant developmental boundary, for "counting" as a self aware human. If you don't remember learning to walk, was it "you" that learned? It's a pretty fluid and blurry line for human existence.

Speaking of challenges to a point of view:

Plenty of passengers ride the bus, but the bus is not redefined by this.

Smell, sickness, graffiti, background noise, and even the occasional pleasant conversation.. all things passengers bring to the bus that may not actually redefine it but do potentially have lasting impact on the bus itself and shape the experience for all parties involved.

The whole problem is anthropomorphism. There is no bus, there am just I, and the bus is part of my experience. There are no other people, even -- only me and that which looks and behaves similar to me. So I rationalize exterior events as just as involuntary as my own thought. When I rationalize that as free will, I must rationalize other exterior stimuli as expected, wanted and willed, too, but then there is no interior left. Which is a contradiction, so nihilism is the only solution. If that sounds like bollocks, I will still find a way to rationalize that.

> Plenty of passengers ride the bus, but the bus is not redefined by this.

The busriding-experience is shaped, which is all that matters. How many parts of a ship can you change until it's not the same ship anymore? There never was a ship to begin with. Just a build. Perhaps this is why Americans love the gerund. "building" is a process and an object at the same time.

> ... lasting impact on the bus itself and shape the experience for all parties involved

This prompted me to answer. I couldn't say it better.

I remember the time before I could walk or talk but can listen and communicate with body language... just FYI.

"Your honor, if I was asleep when my car ran off the road, can it truly be said that 'I' ran over the deceased?"

I often think that the person I was years ago is dead. But when I read what I wrote then, it's surprising how identical the "voice" is, how little the feelings changed in so many years.

We're the shape, not the matter, even if the shape is built on matter. Memories are part of the shape, but you can lose memories, same as you can lose an arm and it's still you, for the most part.

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