The Human Microbial System
TAPP Radio Ep. 47 TRANSCRIPT
The A&P Professor podcast (TAPP radio) episodes are made for listening, not reading. This transcript is provided for your convenience, but hey, it’s just not possible to capture the emphasis and dramatic delivery of the audio version. Or the cool theme music. Or laughs and snorts. And because it’s generated by a combo of machine and human transcription, it may not be exactly right. So I strongly recommend listening by clicking the LISTEN button provided.
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Episode 47 Transcript
The Human Microbial System
Kevin Patton: In their book Microcosmos: Four Billion Years of Microbial Evolution. Lynn Margulis and Dorion Sagan wrote, “Life did not take over the world by combat, but by networking.”
Aileen: Welcome to The A&P Professor, a few minutes to focus on teaching human anatomy and physiology with host Kevin Patton.
Kevin Patton: In this episode, I tell you how you can prevent robots from taking your teaching job. I discuss the human microbial system, and I reveal an upcoming series of special episodes.
Kevin Patton: Some of you may have seen a post not long ago at Getting Smart. It was written by Raj Shah and it’s 3 Necessary Skills for Educators in the Era of A.I. AI is artificial intelligence and it’s coming soon to your school. If it’s not there already. AI will be replacing some of the tasks normally done by teachers. And that can be really good, freeing us up to focus on the stuff that humans do better.
Kevin Patton: But, it could end up displacing us. That is if we don’t focus on improving our skills in the areas where humans are much better than AI. And we need to make sure that students, administrators, policy makers, everyone realize that some aspects of teaching really do need living humans to work well, to have the outcomes that we’re looking for. But hey, we’re teachers. We know how to educate. So let’s make sure we’re doing that starting now before it becomes a regret that we didn’t start it when we should have, so that everybody knows that yeah, we still need humans to be teachers, at least for some of it.
Kevin Patton: So what are the three skills that Raj Shah recommends that we get ready for AI? Well, number one is the skill of generating ideas. That is creativity. And you may not have thought of that as a skill. You may have thought of that as something innate, but it is a skill that we can develop. And you probably already do this a lot, but just don’t think of it in those terms. For example, if you’re a regular listener, you probably brainstorm a bajillion great ideas after listening to every episode. You’re thinking yeah, I get what Kevin just said, but I can think of two ways that would work better. Wait, three ways. No. Make that four ways. I can do it better than Kevin does it. Or maybe you’re saying to yourself or the person in the seat next to you on the train, that new discovery I just heard about on The A&P Professor podcast, that could be incorporated into my course here, or maybe there, or in this way, or in that way.
Kevin Patton: Hey, you might think. Maybe this gives me an idea for framing this or that concept a little differently, or maybe I could change the order of topics presented in my course. Creativity is simply thinking outside the box a bit. We do it when we see things are not going so well in our classroom, or maybe things are going well but could be better. And then we innovate. That is we try some other things. We do it when we read an article or participate in a workshop or presentation, at HAPS, or AAA, or APS, and think through some ways we could use that idea we just heard in our own teaching. Or maybe we just pull it out of our memory at some unexpected moment in the classroom and we need it, which is what they call improvisation. It’s just another form of creativity in teaching.
Kevin Patton: I find myself improvising a lot in lab class for example. I might be working with a small group trying to help them figure out what’s going on in their dissection, and then some new way of describing something pops into my head, or some new way of finding it in the first place hits me. It’s usually not an overly original idea that never occurred to anyone else, but it’s more often an application of something I heard or saw somewhere in some way. But that application at that moment to solve that problem, that’s the creative part of it. That’s the improvisational part of it.
Kevin Patton: So skill number two that Raj Shah talks about is the skill of storytelling. Well, this one is not new to regular listeners of this podcast. I first brought this up way back in episode 12, and I often riff on the idea that teaching is a form of storytelling. And that if we think of ourselves as the tellers of the story of human structure and function, all the rest just flows naturally.
Kevin Patton: There are many aspects to telling a story, and one of them is actually making up stories like we do when we use analogies. For example, in episode 15, I related an abbreviated version of the love story I tell involving actin and myosin, with a subplot of the love story between calcium and troponin. So any time we use an analogy, we’re doing storytelling in a very concrete and obvious way. And we use storytelling when we’re constructing case studies, or many case test items. Or just giving examples of practical scenarios where knowing some concept of A&P is necessary.
Kevin Patton: But another aspect of storytelling is having students explore concepts in a logical sequence. That is a sequence that tells a story. An intelligent machine can relate all the facts of a story, even the story of human structure and function. And an intelligent machine can even try to fit them into any of a library of different plot patterns. But I’m not so sure a machine will ever be able to figure out how to tell a compelling story about how urine is formed in the nephron.
Kevin Patton: But I can, and I think that even in the age of AI coming to higher education in the near future, I can take my renal stories to the bank. Well, what’s skill number three that the author identifies in this article?
Kevin Patton: The third skill is the skill of professional improvement. Now, of course you’re doing that right now, right? By listening to this podcast, you’re engaging in professional development. Maybe you never thought of it that way, but you need to, if for no other reason than you need to be entering this into your professional development plan or professional development log, or whatever you have at your school. A lot of schools have that, and you’re most often thinking of courses you take, workshops you attend to, things like that. But put this podcast down. There are many hours … I hope there are many hours, it’s not just a few minutes. There are many hours over the course of a year that you’re listening to this podcast and you’re doing professional development.
Kevin Patton: That’s a skill you want to continue to improve and that is getting new information all the time. If you’re constantly out there getting more information and looking at new and other ways of doing things, it’s going to feed into those other skills of storytelling and generating ideas. Creativity, the improvisation that I talked about. That all overlaps and fits together, doesn’t it?
Kevin Patton: Now, there are a lot of other ways that you’re already doing professional development. As I said, workshops and seminars and so on. Reading articles, that’s professional development. Do as much of that as you can. Read books from the A&P Professor book club for example.
Kevin Patton: And another way of improving your professional development is by broadening it out beyond just the core of what we need for teaching anatomy and physiology. I mean, here’s some examples of things that I’ve done that some of them overlap, some of them don’t overlap my teaching of A&P.
Kevin Patton: For example, I’ve been spending a lot of time in the last few years, the last many years trying to learn as much as I can about accessibility. Now, of course that directly ties into teaching, but it affects other areas of life as well. I took a course not long ago in osteoarchaeology. I think that’s a fascinating topic and I’ve picked up little bits here and there, but I never took a course in it before and I did. And wow, it was amazing, and it really stretched the way I think. And now it gives me more examples, more applications in anatomy than I ever had before.
Kevin Patton: For quite a while now ever since I started teaching A&P, I’ve been dusting off as much of my old Latin training as I can and really diving into scientific terminology. It’s just really fascinating to me in and of its own even if I wasn’t using that in my teaching and writing.
Kevin Patton: And podcasting. Yeah, okay. I’m doing podcasting related to teaching, but I’m learning all kinds of new things about the whole process of podcasting. I’m learning about marketing, I’m learning about audio engineering. Clearly I’m not learning enough about audio engineering, but give me time. I’ll keep stretching myself and I’ll learn more and more.
Kevin Patton: I’ve taken art classes, I’ve taken classes in American sign language. I’m working on mastering tai chi chuan. I’m thinking maybe I should take a course in artificial intelligence now. There’s all kinds of things and I’m sure you have them too. And the more of these things that some of them might be related to teaching. Probably a lot of them aren’t related to teaching. We should keep doing that and as many different things as we possibly can.
Kevin Patton: I think learning anything new extends our ability to do all of the things I already mentioned in terms of being creative and being good storytellers. In then post that I mentioned at the top of the story here, Raj Shah mentions the idea of a t-shaped skillset. That is where you gain some general knowledge and skills across many different disciplines and interests, and that broadness forms the cross bar of this imaginary T at the top of that T. But also develop a deep knowledge in one field such as A&P, and that forms the upright or middle part of this imaginary T.
Kevin Patton: So we have the broad part across the top or the deep part right in the middle. And now that I’m saying all this out loud, I’m recalling that liberal arts approach I chafed under as an undergraduate. I went to an institution that believed strongly in a liberal arts approach. And even though I was a biology major, I had to take enough philosophy and theology for a minor. And I had to take languages and art. Oh my, the art classes I had to take. And I was a science major and I didn’t see the point back then. But now I realize that it has enriched my life a lot, and I think it has made me a better thinker, and probably a more human and humane thinker.
Kevin Patton: Now I think I’d add one more skill, at least one more skill to Raj Shah’s list of three. And that is the human skill of empathy and compassion. Yep. That’s another of my go-to topics of discussion in this podcast, as many of you know. But really, I truly believe that students learn best in a nurturing environment facilitated by an empathetic and compassionate teacher. I think an intelligent machine can mimic that, but I find it hard to believe that it could do so as convincingly or effectively as a human can. So for that reason, or maybe just because it’s what makes teaching worth the frustration and effort, and gets us up in the morning looking forward to another day, I think we ought to develop our skills of empathy and compassion.
Kevin Patton: Perhaps the overall lesson here is that we are facing yet another factor that’s changing the landscape of college teaching in a very dramatic way. And this is a change that threatens overall employment in teaching roles, and the employability of individual teachers. But I think that if we pay attention to what’s happening and learn to surf this wave rather than trying to resist it, we’re going to be successful. And I’m thinking that a good way to do that is to get better in ways that AI cannot, or at least will not for a very long time. And that is get better at the uniquely human skills and ways of thinking. And perhaps we also need to make sure that society gets educated on what AI can do and cannot do when it comes to teaching.
Kevin Patton: So to practice this, I have this challenge for you. Call into the podcast hotline and give your thoughts on this topic, and let’s brainstorm some ways. Let’s think outside the box and brainstorm some ways that we can all promote creativity, storytelling, and humanity and teaching anatomy and physiology. Just call 1-833-LION-DEN. That’s 1 (833) 546-6336. Or visit us at theapprofessor.org.
Kevin Patton: This podcast is sponsored by HAPS, the Human Anatomy and Physiology Society, promoting excellence in the teaching of human anatomy and physiology for over 30 years. And keeping you creative to keep your job in the age of artificial intelligence. Go visit HAPS at theapprofessor.org/haps. That’s HAPS.
Kevin Patton: Hey, I have a favor to ask. The amp professor podcast has been entered into the People’s Choice Podcast Awards, but I need a lot more nominations from listeners to get this podcast into the final slate of nominees. It only takes a minute or two to nominate, and it must be done by the last day in July. Just go to podcastawards.com and nominate The A&P Professor. That’s it. And you’ll also have the opportunity to opt into the pool of judges if you want if that’s something you might find to be fun and interesting, who knows? That’s podcastawards.com or just click the link in the show notes or episode page before the end of July. I really appreciate your help with this.
Kevin Patton: A searchable transcript and captions for the audiogram of this episode are funded by AAA, the American Association of Anatomists at anatomy.org. Yep. AAA is another great way to keep your human intelligence nimble and up to date.
Kevin Patton: In the preview episode released a few days prior to this full episode, we dissected the term microbiome in anticipation of discussing it in this segment. Microbiome is an ecosystem of microorganisms that not only lives on or in our bodies, but interacts with our bodies. That is with the cells, tissues, organs, and systems of our body. And for that reason, I sometimes call it the human microbial system. Or occasionally I’ll call it the human microbiome system to more closely align with the current lingo.
Kevin Patton: The reason I often add the word system is because I think it underscores the role of the human microbiome alongside the other body systems that we traditionally recognize operating together in the human body. Because it’s become such an integral part of how we understand human structure and function, I think it’s time we started treating the microbiome like a normal body system, don’t you?
Kevin Patton: Now I’m going to circle back to this idea in a few minutes. You’re either going to have to skip ahead in the audio, or suffer through a few minutes of reviewing some ideas about the human microbial system first.
Kevin Patton: And the reason I’m thinking about this today especially is that the journal Nature recently had a series of articles about NIH Human Microbiome Project. It’s been carried out over 10 years in two major phases, the second of which was recently completed. The first phase mapped out the basics by trying to find out what constitutes a normal healthy microbiome, and the second phase is called the Integrative Human Microbiome Project because its goal has been to study the dynamic changes in the microbiome and host in different scenarios.
Kevin Patton: Now the three scenarios that they chose to study are number one, pregnancy and preterm birth. Number two, inflammatory bowel diseases. And number three, stressors that affect people with prediabetes. Now keep in mind that this is all a set of first steps. It’s gonna take forever to get a complete picture of what’s going on. If that’s even possible. As with the rest of humans structure and function, I certainly hope we never completely figure it out. That would take all the fun out of it. That’s like a favorite series of novels or films. I don’t really want to reach and end to it. I want the story to progress, I just don’t want it to end.
Kevin Patton: By the way, I have links to the Nature material in the show notes and episode page if you want to dive a little more deeply into this. And of course there are a bajillion other sources that you can use to catch up on what we know so far about the human microbiome. There’s just too much to review in this episode or even 100 episodes. But for now, I’ll list a few basic ideas about the human microbiome mentioned in the nature articles and elsewhere.
Kevin Patton: But before I do that, I want to get something out there that really excites me about this microbiome thing. One of my first loves in biology was ecology. Like all of you, when I was a kid, I did not have a dream of being an A&P professor when I grew up. I wanted to be a wild animal veterinarian or zoologist, and then later a lion tamer, but that’s a story for another day. So I studied zoology, and part of that involved ecology. And I’ve met a lot of you who came to A&P along a similar road, and there are others of you that came through maybe a more clinical channel. And I don’t know, maybe some of you started out wanting to be a poet or a rock star. At least I want to believe that’s true. But I came to it along a road that started with ecology.
Kevin Patton: Anyway, it’s just so exciting for me to see that my newer found love of human anatomy and physiology is brought me right back to one of my first loves, ecology. This whole microbiome thing is essentially a study of the structure and function of ecosystems in and on the human body. Right? I’m doing ecology again. So here’s what we have some evidence for so far.
Kevin Patton: First of all, there are many ecological niches in the human body. The Encyclopedia of Ecology defines a niche as a term for the position of a species within an ecosystem, describing both the range of conditions necessary for persistence of the species and its ecological role in the ecosystem. The ecological niches of the microorganisms that make up the human microbiome are spread across many different body regions. For example, different regions of the gut, regions of the urogenital tracks, of the skin, of the respiratory track. Even in the eye, the conjunctiva of the eye and different parts of the ear and just all over the place.
Kevin Patton: I want to emphasize that there are many unique localized regions within the areas I just listed. For example, there are different sets of conditions in which microbes species may be found and persisting in many different regions of the body’s skin. That is the conditions and typical organisms found in the armpit is different than on the face, and it’s different near the nose than it is on the forehead. And the conditions and microbes in the follicles of your eyelashes are different than in the follicles of your pubic hair. By the way, please don’t tell my mother I’m talking about pubic hair in public. Her heart’s not strong.
Kevin Patton: Now many of the principles of ecology apply to the human microbiome. One of the many things that fascinated me as an ecology student was the fact that one little change in the environment, like a little change in temperature or a little change in pH, could cause a little or even a big change in the makeup of the communities of organisms in that region.
Kevin Patton: Likewise, a change in the population of just one kind of organism can disrupt the structure of the whole set of populations of different organisms in any region. Food sources for organisms is a big player in ecology, and that’s true in the human microbiome as well. In the gut, dietary fiber feeds many keystone species of microorganisms. And when the fiber content of our diet changes, we might see changes in the function and the overall health of our digestive system.
Kevin Patton: Which brings us to another thing we know about the human microbiome. Disruptions can cause major problems. There have been links between differences in microbial populations and various health conditions such as inflammatory bowel diseases, diabetes, inflammatory conditions of many kinds, and many areas of the body. In parkinsonism, in the autism spectrum, even how we think. Heck, your microbiome may be influencing how you’re processing what I’m saying right now. And my microbiome might be influencing what I’m saying to you right now. Maybe if I eat a bit more oatmeal, these podcasts won’t be so goofy.
Kevin Patton: Something that keep in mind though is that we’re just at the very, very beginning of understanding these relationships. We all know that correlation does not equal causation. Some of the microbiome characteristics unique to particular states of health may be caused by an issue in the microbiome itself, or they may be a result of the health state. Which is the egg and which is the chicken?
Kevin Patton: And the more we learn about the human microbial system, the more it looks like any other system of the body. It’s complicated. There are all kinds of interdependencies and intertwining of structures and functions. For example, the function of the human microbial system seems to always intertwined with the immune system, which makes sense, right? I’m starting to think of the immune system as more of a broad spectrum microbe wildlife manager rather than the bounty hunter kill off the bad ones, protective model of immunity that I was originally taught.
Kevin Patton: One last thought on the role of the human microbial system. As if I ever stop with just one last thought, but I’ll try hard this time. I think what we’re learning about the human microbial system is showing us that we need to expand our thinking about how we define what it is to be a human in the biological sense. We cannot function without a healthy microbial system. So really, isn’t that system an integral part of us? Is it really necessary to limit who we are as a biological organism to just our human cells and their cellular genome? Can’t we also include the cells and genomes that are in and on us that also interact with the various parts of our body to keep us alive and healthy?
Kevin Patton: You know how folks are now thinking that living birds are essentially the current form of dinosaurs? Well, I’m thinking that all organisms alive today, including humans, are essentially the current forms of the network of microbes that first appeared as life on our planet. Okay. That was my last thought on the role of human microbial system, so I’ve kept my promise, but I do need to circle back to keep an earlier promise about discussing how we deal with this in our A&P course. As usual, I don’t have a definitive answer. Of course. That’s how I roll. I want to know what you alls think about how to deal with the human microbial system or should we even call it that?
Kevin Patton: I’ll go ahead and tell you how I’m doing it and honestly it’s working pretty well for me. What I do is I introduce this concept very early in the course when I’m talking about levels of organization, specifically when I’m discussing the body systems. I talk about this emerging idea and how we’re just on the cusp of understanding it, and maybe we should think of it as another one of our human systems, our human body systems. And then I bring it up every time I can route the next two semesters, because it really fits in just about everywhere. And as I do with many topics in A&P course, I bring in current news, especially headlines that my students may have seen in the national news outlets. Like a recent one that linked unique microbiome characteristics to being an elite athlete. And then we can assess it a bit. For example, finding out that behind the headline is the fact that we’re talking about mouse athletes, not human athletes. So yeah, that kind of changes the story a little bit, doesn’t it? We haven’t found that in humans yet. We may never find it in humans. And how do you define an athlete in a mouse anyway?
Kevin Patton: And then we look at the numbers of individuals that were studied and the test conditions and so on and see, is this some reliable information, or do we need to wait a little bit until more tests have been done, more kinds of testing, maybe some better technology in understanding this? So we’re learning science as we do this. Doing all this helps get the concept of the microbiome out there, but it also helps students interpret scientific information and evaluate new information. And it kind of engages them in a really exciting cutting edge area of biological discovery that’s happening right now all around us. So okay, really, those were my last thoughts.
Kevin Patton: The free distribution of this podcast is sponsored by the Master of Science in Human Anatomy and Physiology Instruction. The HAPI degree. You’ll definitely have an edge on even the most intelligent AI tools with HAPI. Check out this online graduate program at nycc.edu/hapi, that’s H-A-P-I, or click the link in the show notes or episode page
Kevin Patton: Well, here’s something new and different. For the next few weeks, I’m going to be releasing a special summer series of podcast episodes. Now, each of these specials will be focused on a single topic or at least on a couple of closely related topics. And some of them may be quite a bit longer than a typical episode. But hey, you can always hit pause, take a nap, and pick up where you left off.
Kevin Patton: Now the content of these specials will be mostly selected from individual segments from past episodes released over the last 18 months. So yeah okay. It’s sort of like summer reruns, but it’s repackaged in a thoughtful way that helps us review some of the major ideas and themes that we’ve discussed. And not just review them, but reflect on them. We know that revisiting prior learning, spacing it out helps us consolidate these ideas and firm them up in our conceptual framework, just like dreaming does for us. So think of these special episodes as a compliment to all those nightmares that this podcast has been giving you.
Kevin Patton: I think this series may also be helpful for newer listeners, who can get caught up on all those recurring themes so that they can benefit from them as we pick them up again when we resume normal programming in a few weeks, without having to binge on all 46 of the prior episodes. Not that I discourage binge listening to this or any other podcasts.
Kevin Patton: Okay. Really this is all a strategy to give me some time to catch up on my favorite podcasts. Okay, not really, but hey it’s a good idea now that I think of it. There won’t be preview episodes for these weekly specials by the way. But the word dissections, the book club recommendations, and the other features that you love in the preview episodes will all return in a few weeks. And don’t forget, there are a lot of ways to listen to upcoming or past episodes. Just go to theapprofessor.org/listen and there’s all kinds of options listed there. And you can call in with your questions, your comments, and your ideas that the podcast hotline, it’s 1-833-LION-DEN, or 1 (833) 546-6336. Or send a recording or a written message to firstname.lastname@example.org. I’ll see you down the road.
Aileen: The A&P Professor is hosted by Kevin Patton. Professor, blogger, and textbook author in human anatomy and physiology.
Kevin Patton: Please do not use this episode if the safety seal is broken.
This podcast is sponsored by the
Human Anatomy & Physiology Society
This podcast is sponsored by the
Master of Science in
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