Constraints and Innovation in a Biological Model

My students wrote this piece today in response to our first lab exercise.

This model has some constraints due to its materials. Firstly, we are restricted by the amount of space given to build the model--the table. Secondly we are constrained by the zometools--the height, shape and flexibility. These constraints affect the efficiency of our lab and the final look of our model.

  

In evolution, there is no final product. The organism/system is always undergoing change, never reaching a final product, or final phase in which change stops. Different constraints will always offer a chance for a new adaptation and lead the organism onto a new path of evolution.

Nature overcomes the problem of constraints by building everything with a purpose. No materials are wasted on useless parts, and every part gets exactly the amount of material it needs to function. While nature has this happen naturally, we as human builders need to plan out beforehand, and build with purpose, to overcome limitations in material.

The constraints bring species opportunities to evolve because they are trying to be fit for the situation and environment. As we mentioned previously, there are no final products in evolution, so species are constantly getting more fit to deal with the constraints. I would say constraints do nothing but inform the final product, as constraints guide how people work. They inform the decisions we make - how we will adjust. We won't be able to complete tasks if we are not adhering to them.  So, it would be fair to say that the final product is a product of constraints.

                   

An innovation we discovered today was that if you piece together each segment individually, then connect them together as a whole, the building process is much faster and efficient than if each person added pieces one by one to the whole model. In addition, connecting the line segments together in a way that was slightly angled, but not straight increased the surface area of the model.

Connecting with the naturalistic philosophy

Here's a post that some of my students wrote today, in response to our first lab of the semester.

In science, many concepts can be explained by naturalistic philosophy. Causes for events, or phenomenons, can be attributed to natural causes. Nevertheless, this concept does not apply to all cases. According to the mechanistic theory, biological systems are restrained by physical and chemical conditions (in accordance with naturalistic philosophy). In today’s lab exercise, we experienced a plethora of constraints, from our limited time to complete this assignment to limited resources. Had our table been bigger, we would have felt confident creating a larger structure. Had the pieces been easier to put together, we would have been able to create a larger structure without spending as much time on construction. These are just some of the constraints that we faced, and such constraints do well to mirror those found in the biological world. For example, while our table size was only a physical condition, it could well have been a chemical condition – had the limitation acted in the same way, its nature would not matter. The only thing of importance would be the effects on the structure/organism. While our structure was not living and certainly was not aqueous, it is easy to imagine the floor as a space without as much water. If we had time to build downwards and expand, we certainly could have. Yet, it would have been much harder to do so – therefore, if we imagine our structure as a living creature, we can imagine the ground as a chemical limitation.

Our goal for this week’s lab was to build a hypothetical biological surface (with no straight lines) using zometools. While building this table-long structure, our group focused on the idea of pattern and similarity. At first, we attempted to build an uneven planar surface, but our google research on this concept did not go as well. Hence, we decided to build up and long enough to cover the entire table. As we worked on this lab, we realized our tendency to build linear surfaces. For example, the yellow part of the zometools is much more simpler than the rest of the colors in the finished product. The color green includes more physical shapes, such as hexagons. On the other hand, the blue zometools have shapes such as stars, which we found very intriguing and interesting. Lastly, the red zometools have their unique pattern of going upwards and then downwards. 

 

At the end of the day, we realized how easy, yet hard, it is to get away from our comfort zone of building a plane surface. In science, like in any other subject, thinking outside the box and being creative is an arduous task. As students in the 21st century, we are accustomed to being told what to do, which way to build and what way to think. However, this way of learning and living essentially prevents us from growing as intellectual individuals. It is through doubting, questioning and creating that we can design a world where building crooked and sideways is encouraged.

A colloidal origin of life?

Working with ideas about the origin of life and its relationship to the colloidal environment. Scientists figure that the first meaningful step toward life was the development of macromolecules from smaller molecular entities. The RNA world hypothesis posits that RNA was a good candidate for a pre-life molecule. RNA is involved in replication, it can play the role of an enzyme, and it is involved in the production of proteins, which carry out the day to day activities of the cell. All of these activities make RNA a reasonable candidate for a precursor to living cells. RNA activities suggest that it can play a role in controlling its environment. 

RNA might have developed in a meaningful way, that is, in great numbers – populations of which were able to "play around" with their environment until a replicable, sustainable system of life was formed, within the highly ionized colloidal environment of clay deposits. If this is the case then it's possible that the development of probionts, micelle-like bodies that Oparin hypothesized in the mid-1920s makes sense. It's a kind of biomimicry in reverse. That is to say the pre-life RNA molecules began to build an environment similar to the one in which they first arose, an aqueous, protected environment that provided a compartment through which they could interact with their environment. 

If we jump to the present and look at living cells we can consider them broadly as colloidal environments. Within these aqueous spaces are suspended (albeit large) particles like organelles and ribosomes. The organelles themselves can be considered colloidal because of the suspended membrane systems and proteins within them. So many biological features are colloidal. For example milk, blood, tissue systems, and all sorts of bodily fluids are colloidal in nature. 

If we extend our thinking to imagine the first replicating RNA molecules to have built an artificial colloidal  environment around themselves we may get closer to understanding why life took the forms it did and how contemporary living forms relate to our very ancient ancestors of almost four billion years ago. 

No straight lines

One of the things I really want to get across to my students is that the way scientific, and especially biological concepts are depicted is not necessarily the way they are. We tend to get our impressions of how things look from textbooks or from simple image searches. These reflect decades or sometimes centuries of misapprehension. I learned this when I was doing my doctoral work in botany at Harvard and found textbook and scientific images that hailed from medieval depictions of plants that themselves had their source in antiquity! 

While I first learned this lesson as a highly focused graduate student with the world's greatest botany library at his fingertips, I'm thinking a little more generally here. For example, in cells there are no straight lines. But you see straight lines in all kinds of depictions. They connote more than just straight lines. They suggest "solidity" and permanence, conditions that are very rare (if they occur at all) in the cellular environment. Similarly, atoms and molecules are shown with straight lines depicting bonds. Obviously in real life there are no lines there at all. And the bonds of course are invisible, just like the molecules themselves. But as a students (and teachers I think) we tend to take them as a given and come to understand the properties of scientific phenomena within these pre-determined and highly limiting confines. 

The same as there are no straight lines, there is really no "up" or "down" in living systems. Of course there is the force of gravity and this influences structure and function, especially in tissues and organisms, but really, do the organisms have an "up" and a "down" or do they just experience them? Similarly, biological molecules of all sorts are depicted with a "top" and a "bottom." If you look critically at the biological world you see that molecules are not limited in this way. Neither are unicellular organisms. In multi-cellular organisms cells in aggregation are a kind of colloid body within the colloidal medium of tissues. So there is no "up" or "down" there. Just a kind of floating. Even larger organisms, while clearly polar (they have a top and a bottom) are simply organizing their cells and tissues in response to light and/or a perceived gravitational pull. This is obvious in highly plastic organisms like fungi, but it's the case in more "differentiated" organisms as well. Put a plant on its side and it will grow quite well. It will respond to light by growing "upward" shoots and it will respond to soil by growing roots "downward" but the plant can also grow quite successfully upside down. What about in our species? Does a fetus in utero have a particular orientation? If the head is pointed downward is that still the top?

These questions may seem absurd but I think it's important to encourage my students to look in new ways at the world of biology. Not necessarily to understand biology better but to get a new fresh look at their world. 

Our first exercise of the semester will be to construct a model in which there are no straight lines. We'll use Zometools to do it. If you haven't seen these amazing teaching devices you should look them up when you get a spare moment. Each lab group will build what turns out to be an uneven planar surface. It turns out there are lots of scientific applications to this problem. I think there are philosophical implications as well. We'll build table-sized sculptures and then play around then with some questions like, how would water flow on this surface or, how would light move from one point to another along this surface? I'm hoping that students will see patterns in the planar shapes they build. For example if they use repeating same-shapes put together versus random varying shapes how will their creations differ?

I was never taught this kind of exercise in any biology class and I wonder where and if things like this are being taught. It's simple but I think it's also, literally, a kind of rocket science. This is a kind of thinking that may go over the heads of my second-year undergraduates but I see our labs as a kind of incubator for new kinds of thinking that may find their way to other settings. Is it worth it to get students to think outside of the box in this way? Will it influence the way they come to understand the lecture material? Most important, will it help them conceptualize in an abstract way ideas, situations, and structures that they encounter in their future work outside of the classroom?

Music, electron clouds, and mass flow.

Of great importance to me is figuring out how to get my students to make connections. As we work on learning about science I think almost universally, it's more important to conceptualize and connect the material then to get the "facts" right. This is not to say that the content is not important. It's just that the wonderful abstract reasoning that goes into understanding this stuff is a skill students will use for the rest of their lives, way beyond the time when they forget the subject matter along with my name. They pay me the big bucks to gift students with the skill of abstract reasoning. Or at least to introduce it to them. 

In a sense I'm in an ideal teaching situation. My students are non-science majors. I'm not needing to teach them any content for any kind of "professional" exam they'll have to take outside of the assessments I write myself. The other thing is that I teach in an interdisciplinary program at Boston University. My students are used to taking courses in a range of disciplines and we sometimes succeed in connecting our teaching and learning programs among the departments. Next semester we will be focusing on a new and somewhat unusual theme--making the invisible visible. My faculty team is hoping to nurture our students' imagination, trying to get them to play around and build ideas from unconnected, perhaps hidden sources. In general our students don't get enough of this kind of exercise. But it's at the heart  of abstract reasoning. Can we consider this problem within the context of a musical score?

Racing away on the stationary bicycle at my gym this morning I was listening to Bach's Two and Three Part Inventions and following along with a scrolling score. I don't read music but I can follow. And I started to think, with all my recent explorations into the behavior of electron clouds, can we see the notes on a score in a similar fashion? While the actual fingers of the musician hit a particular key at a particular moment (or somewhere around a particular moment), may we consider that that position and that moment are measurable statistically? A slight delay, a hesitation, a stressed note or a trill adding their variable qualities to the physical act? If so, is there is a particular statistical relevance to when and where the musician's fingers will touch the keyboard?

Pretty amazing questions if you consider how close music is to an abstract expression of human cognitive and emotional experience. Abstract reasoning on many levels. The big question is whether I can get my students to think along these lines. Can I have them listen to this music, perhaps in lecture? I thought to myself how strangely cool it would be to tweet the link to this YouTube site to my students, and to ask them to pull out their earbuds and listen to a couple of the Inventions, trying to follow the score just as I have. 

I'd like to take the exercise one step further. Perhaps we could do this as I finish off a short series of lectures on water, where I end with the concept of mass flow. Can the sequence of notes in a score be considered as a series of molecules floating past us? The unique orbitals of each chord and series somehow represented by the black notes against a white screen? And can we conceptualize the flow of the music as comparable to a mass flow of water molecules? I'd love to hear if anyone has done this thought experiment with students. What did you observe? 

Keeping track of learning

Here is the first thing my students in lab will grapple with in a few weeks. Using these instructions it is the students who will be adding to this blog several times a week. 

Each group picks one of the topics below as the focus for the semester's work. The primary focus of the questions is lab work. Each group is expected to report on lab work at the end of lab each week, with a focus on their topic. The secondary focus is lecture. Each group should report on highlights of lecture each week, as appropriate, as they pertain to the group's question. Writing about lab should be submitted at the end of lab each week. Writing about lecture should be prepared during the week and submitted at the end of lab the following week as part of the lab write-up. 

Some weeks people will have more to say about lecture. Other weeks lab may seem more prominent in your thinking. Don't worry about getting it "right." It's about exploring scientific ideas in a new way. As you read the topics and questions below, and add questions of your own, you'll also see that it's about exploring the way we learn, model, and communicate natural systems. Also, while I would like you to focus on the topic you choose, please feel free to reflect and write about any aspect of lab/lecture and the learning process that you see fit. 

One or two people at each table will be responsible for submitting the group's work to the blog each week by the end of lab. These people should be responsible for collecting, assembling, and articulating everyone's ideas at the lab table. 

The blog entry should summarize and discuss the work of the group in a few short paragraphs. Reference to the sub-questions may be made as appropriate, as well as other questions, thoughts, and reflections that arise from the group. The blog should also include photos and sketches made by group members, as well as tweets. 

I expect that you will do some informal, independent outside research to enhance your discussions. For example, googling concepts like "biological shape," "biological surfaces," "molecular behavior" or "uneven planar surfaces" will yield a host of ideas that you can connect to your writing. Even random-seeming terms like "Bioinspiration" will yield great results. I know because I've googled these myself. I strongly suggest you look up these and other topics as appropriate during lab. Instead of starting with articles, find images that interest you and go from there. This can yield amazing, inspiring ideas that you will want to share in your posts. Formal citations are not necessary but ALL images and writing that you suit MUST be your original work.  

Three times a week (after each lab) I will post the blog on Twitter for the perusal of the whole class. This way we will share a running log of our activities, reflections, and inspirations. 

 TOPICS 

1. Shapes and patterns in nature

What patterns do you notice?

How do patterns emerge?

How do patterns interact?

How do patterns inform? 

How does nature build patterns?

How do we mimic natural patterns? Can we?

How do models of nature and natural systems reflect patterns?

How do patterns in nature reflect evolution?

How do patterns reflect evolutionary processes of inheritance and innovation? 

How do patterns reflect nature's way of dealing with physical constraints?

What is a pattern?

How do we detect patterns of surface, shape, line, volume, color and texture in the natural systems we study?

How do physical patterns lead to functional patterns or vice versa?

How do the patterns we find surprise and inspire us?

2. The power of play

How do people play?

What do people discover when they play?

What surprises happen?

What happens to the brain when you play?

What happens to your learning process?

What happens to your process of discovery?

What happens in the group when you play?

Do people like playing together or do they prefer individual "parallel" play?

Does playing preclude work?

Does playing make work happen in a better or different way?

What do we accomplish with play? 

How does nature "play" to solve problems?

How did you play at your lab table today to solve problems?

How does play produce models that communicate about nature?

How can we interpret play within an evolutionary perspective?

How does play allow us to deal with"bigger questions" that are "serious" and not directly play-related?

3. Constraints and innovations

How are natural "constraints" to be interpreted? Only as a bad thing?

How is the model constrained by the materials? For example think back to when we built termite mounds with legos. How do those kinds of constraints affect the work we do each week in lab?

How do we (or how does nature) get around the constraints or use the constraints to its advantage to get the job done?

How do constraints inform the work in progress?

How do they inform the final product?

In evolution is there ever a final product?

How does evolution reflect nature's way of dealing with constraints? 

Are constraints necessarily visible? What about constraints of molecular electrostatic charge, surface characteristics, and shape?

How does nature innovate and/or adjust to physical and molecular constraints in order to carry out its functions?

What innovations did you discover today? This week?

How are constraint and innovation balanced in the evolutionary process? 

What use is innovation?

How can we innovate to learn better?

4. Molecular behaviors

How do different molecules behave? 

How do molecular behaviors influence biological systems?

How are molecular behaviors reflected in biological systems?

How does the shape of a molecule inform us about its characteristics?

How does the shape of a molecule inform its behavior and/or functionality?

How do molecules join to form a surface?

How do molecules join to form a cellular compartment?

How do molecules join to get a particular job done?

How are molecular behaviors reflected in cellular evolution? 

How do molecular behaviors constrain or direct cellular evolution?

How do molecules behave among themselves?

How do molecular interactions determine cellular features?

How do binds and electrostatic interactions affect molecular behavior?

Can we model molecular behavior in a macroscopic study environment?

5. Origins and continuities 

Can we trace a "basis" for the way biological systems behave?

What underlying principles/ behaviors/structures make biological systems similar to one another? 

How do biological systems behave? 

How can we model continuities in biological systems? 

How can biological systems inform human cultural or economic systems?

How is continuity of process reflected in evolutionary outcomes? 

How is evolution part of a continuum?

How do cellular and molecular evolution reflect biological origins?

Are there certain things all biological systems have in common?

Are there certain things all cells have in common?

How are responses to molecular constraints inherited?

How are molecular constraints and behaviors reflected in the cellular environment?

6. Bioinspiration 

How do biological systems give us clues/tools that we can use to build better human systems?

What beauty can we find in biological systems/structures and how do we interpret and communicate that beauty in an effective way?

How do biological systems differ from human systems and what can we learn from these differences?

How do biological systems differ from human systems and what is the significance of these differences? 

What cues and clues can we pick up from nature to inform our perceptions?

How can humans design better systems that are inspired by natural systems?

How can humans design systems that better reflect the constraints and patterns in nature? 

What insights do we gain as we attempt to model nature?

At what levels can we get bioinspiration, cellular? Organismal? How do these differ? How are they the same?

How can bioinspiration inform the future work you'd like to do? How can you apply it to your major outside of this course?

7. Making the invisible visible 

What makes something "hidden" or invisible?

What happens when something hidden becomes "seen"?

Does visibility or invisibility depend on size?

Does visibility or invisibility depend on our perceptions? How? 

How do you know what you're trying to make "visible" when you start an inquiry?

What happens when something is "hidden in plain sight"? How do you find it? 

Can something be hidden behind "visible" signals? 

How does something become visible that wasn't visible before?

What emerges when something previously invisible becomes visible?

If something is "invisible" what is it hidden behind? 

Can a process (like a biological process or a learning process) be "invisible" yet very much present? If so, how do we amplify or communicate that process so that it builds our understanding?

How is molecular and cellular evolution a kind of "invisible hand" and how do we detect that "hand" in our investigations?

Degrees of complexity in a nano landscape

I'm curious about complexity and how it arises from seemingly simple systems. There's probably a large body of work on this question-probably in the field of bioinformatics, which I feel I've been skirting around in my thinking. But I'm not a mathematician or statistician, and it's hard to go into these questions head-on and find something interesting to read so I'm kind of on my own here. Still, interested questions to grapple with. 

One of the early exercises I'll want to do with my students next semester is to have them build a system of repeating subunits. I don't want them to look up polymers or any kind of molecule because I don't want them to get hung up on mimicking any particular feature of their hypothetical molecule. Once when I had the students look up polymers I spent the whole lab trying to address questions like "how do I show a double bond" or "where should I put the ester group" or "I can't get the same angle they're showing in this diagram." The concept is not to show bonds or functional groups or angles. It's to see what kinds of patterns emerge when more or less identical subunits join together. How is the polymer somehow more than the sum of its parts?

In a mental exercise I can imagine the answer for myself. As new subunits are added the growing molecule does more than just get longer. The subunits are attached at some angle, perhaps various angles, probably not in a straight line. As new units are attached they begin to interact with each other. We can see this visually and infer from this that electromagnetic interactions may be occurring. As attractions and repulsions build on the molecule new and less predictable developments take place. Bending or "folding" may ensue, something that adds to the complexity of the molecule because the new emerging shape may take on new characteristics and novel functionalities. Interactions within the molecule and between molecules may arise from this and voila, we have a system that's much different from the collection of non-aggregated subunits we started with. 

I wonder how to equip students to do this mind exercise on their own. Last time I tried this lab I gave the students a big bin of legos and just had them build. The results were pretty much linear and straight-the disturbing straightness partly a constraint of the legos and partly a result of less imagination poured into the project than I might have liked. 

So as we move forward with this concept I think I'll ask students to attach their subunits at some angle. Perhaps I'll ask them as well to compare the results of large vs small subunits. Another possibility is to vary the subunits slightly, something like an array of amino acids instead of a line of glucose molecules. As I think this through (and every lab I build is an extended mind exercise where I try to predict behavioral and cognitive outcomes for my students) I may assign different kinds of tasks to each person at a table. Small subunits, large subunits, identical vs. varying subunits, straight lines, angles, etc. With this kind of set up we can hope for a strongly comparative lab where students actively imagine and build the outcomes that might occur. This way I can have students start to predict complexity and its consequences. 

I guess the next question is a little more complicated. How can I get students to see their creation as a nano landscape in which interactions occur? Can I hope to have students describe complexity that emerges, and do "degrees" of complexity (as the title of this post suggests) matter? Can I expect students, especially early in the semester, to perceive complexities other than what they observe visually? How can I nudge them toward a mental space where the visual outcome is just part of the imaginative process? Can I push for tactile engagement? For a description of "difficulty" in building the molecule? If I ask students to envision their creations as "sculptures" rather than "molecules" can I stimulate some part of their imagination that's not constrained by what they think scientific ideas should be?

These are hard questions that I don't have an answer for. Partly they may be encouraged by the approach I bring to lab. There are two parts to this. First, I generally ask students to tweet me during lab to show me their progress and to answer questions. It's possible that by posing these questions I may elicit imaginative responses. But there's a limit to how much I can ask students to tweet. Sooner or later, if students perceive tweeting as the goal, they start to count their tweets or just send me pat answers as the exercise stales. So tweeting in class is good, very good. But it has its limits. A second part of my approach is that this semester, each week, I'm asking students at each table to reflect on their experience and prepare material for this blog. Each table will choose a different theme like "playing" or "patterns" or our overarching inquiry, "making the invisible visible." Without making the students do too much writing I'm hopeful that these theme-topics will encourage a layer of analysis that goes beyond the tweets but remains fresh, authentic, and informal. We'll see where it all goes. I'd love to hear your responses.