Biology / Cognitive Science / Musings / Philosophy / Science / Uncategorized

A Walk through the Forest – Sources of Structure

File:20140227Hedera helix03.jpg

A few minutes away from the place I am living, there is the Eilenriede forest area, right in the middle of the city. Some part of it is left to its own. No trees are felled there, rotting branches are not cut away, and fallen trees are left to themselves. The area is returning bit by bit to the state of a primeval forest. A few tracks are criss-crossing this areas, narrow, probably unofficial paths.

Following one of these paths, what strikes me is the irregularity of life forms. Our own bodies have shapes determined mainly by our genes, and with many animals it is the same. This might cause us to assume that living things in general have a systematic structure, but going through this small patch of forest shows me that this is not really so. The shape of the ivy plant creeping up a tree follows the shape of the tree trunk and its branches. The shape of the tree itself is quite irregular.

There seem to be three components contributing to the shape or structure of each organism, with varying shares of each in any particular organism. There are aspects of the structure that are completely under the control of the genes. For example, the shapes of the leaves of the trees seem, to a large extent, to be genetically determined. Secondly, there seem to be some random components. For example, the branching patterns of the trees show a lot of irregularity. No two trees look the same. However, this irregularity must be under some genetic control since each species has its typical pattern or statistics. Now that the trees have shed most of their foliage and their branches are clearly visible, I have no difficulty to identify an oak tree or a linden tree, although each of them is different in detail. If I think of my own body, this element of controlled randomness is probably also there, maybe in the exact pattern of the capillaries and the microscopic distribution of cells. In trees, it is just more visible.

The third component consists of those aspects of an organism’s structure or shape that develop in response to its environment. I have already mentioned the shape of the ivy plant that traces the tree or rock it is growing on. The branching of the trees probably also responds to available light (and thus to other trees) and to the prevalent direction of the winds. A tree’s roots will have to respond to other roots, to the stones embedded in the soil and to the availability of minerals and water.

File:Fungi in Lady Spencer's Wood - geograph.org.uk - 112004.jpg

The path is passing along the rotting remains of a tree trunk. Fungi are sprouting from its side. The mycelium, the fine hyph of such a fungus is growing through the tree trunk, maybe following the wood fibers and the yearly layers of wood cylindrically stacked into each other. That network of hyphae of the fungus develops a shape that does not at all depend on its genes, except in its microstructure. If one could edge the wood away and make the mycelium visible on its own, it would trace the shape of its wooden substratum in much detail, a shape that was determined by the genes of the tree, not those of the fungus.

We can see the same in a rotting fruit. A rotting rose hip changes into a mass of bacteria whose shape reproduces that of the former fruit. One could argue that the bacteria are many individual organisms, not one organism, but that is a matter of definition.

What we see in the ivy, in the light-searching branches of trees, in their roots, as well as in the fungus and maybe in the blob of bacteria as well is that the shape these organisms take is, to a large extent, not determined by their genes, but by their environment. The genes equip them with possibilities of reacting to their environment and these reactions then determine the actual forms they take.

Among animals, we see such reactive growth mainly among sedentary forms, like for example, sponges and corals. Those animals that are free floating (or flying) or moving across (or burying into) the ground, on the other hand, seem to lack such adaptive components in their structure. The structure of such animals (and we belong into this group ourselves) seems, to a large extent, to be genetically determined. However, adaptive aspects of the shape are there (even if we do not consider the growth of muscles in response to exercise, and similar changes). We find them inside the nervous system.

Simple animals might just have a limited range of possible reactions to their environment. They don’t learn, so their nervous systems do not change according to the environments. Normally, they are present in large numbers, and if they have to adapt, they do it in terms of that other great learning process, evolution. Evolution however, also does not follow any fixed path. Like the growth of the mycelium and the creeping ivy stalk, it adapts its shape to whatever it finds.

While this evolutionary, genetic adaption also occurs in complex animals, these are able to adapt as well by learning. To some degree, less in some species and more in others, they change the structure of their neuronal networks in response to the environment. As a result, they change their reactions and behaviors. This applies to humans as well, and even to the most extreme extent. Unlike the ivy plant or the fungus in the tree trunk, we do not change our outside shape much in response to our environment, but our brains change, and the results are dramatic.

The sky is gray today and dusk is setting in early this time of the year. It’s time to leave the forest and return home. Due to some little change somewhere in my brain, I manage to find my way back, out of the forest, through the allotments at the edge of the forest, and back to the house where I am living. And due to some little change somewhere in my brain, I am able to write down some of the traces of the thoughts I had during that walk.

(The picture showing the ivy is from https://commons.wikimedia.org/wiki/File:20140227Hedera_helix03.jpg, not from Eilenriede, but I have seen something like that there today. The “reactive structure” of the plant is clearly visible here. The second picture, showing fungus growth on a piece of wood, is from https://commons.wikimedia.org/wiki/File:Fungi_in_Lady_Spencer%27s_Wood_-_geograph.org.uk_-_112004.jpg, also not from where I am, but fine to illustrate my point.)

14 thoughts on “A Walk through the Forest – Sources of Structure

  1. One aspect of this article is that it is partially a partial response to http://selfawarepatterns.com/2015/12/02/discovering-the-architecture-of-the-mind/. In that interesting article, the author writes about his view that the human mind has a fixed architecture. We read:

    “I often get push-back on this idea. One of the arguments I commonly hear is, perhaps the mind doesn’t have a structure. Maybe it’s just an unstructured mess from which our consciousness arises, or the structure may be so complicated that it’s forever outside of our ability to understand it.”

    Then he presents arguments for his view. The first is:

    “The first broad one is that everything else in biology follows recognizable systems and subsystems and has a systematic structure that we’ve been able to discover. (Think organs in a body or cell machinery.) Many of these systems are profoundly complex, but they haven’t shown themselves to be undiscoverable. Arguing that the mind is unstructured is arguing that everything is systematic until we get to the mind, then the rules change. It’s possible, but doesn’t seem likely to me.“

    I think that this is not so. As pointed out in the article above, the structure of organisms is only partially determined by their genes, so not all of their structure is “systematic”. If you think of archetypical animals (bilaterians moving around, like ourselves) it might seem so, but only until we get to learning and brain plasticity.

    Thanks to selfawarepatterns to have put my thinking on this track. Once you look for it, you can see adaptive or reactive aspects of organism’s structure and behaviour everywhere.

  2. Nannus, interesting post.

    I think you might have read some things into my views that aren’t there. “Systematic” to me doesn’t necessarily mean “determined and fixed by genes”. I know it’s both nature and nurture, genetics (and epigenetics) and environment. And environment begins in the womb.

    For instance, fetuses reflexively kick and move in the womb, and it turns out that the kicking and moving is crucial for healthy joint development. The eyes of a fetus spontaneously generate signals, which help the developing brain wire appropriately.

    But despite all this dependency on environmental contingencies, it’s striking how similar the final forms are, how similar animals of the same species are in their development. Human brains are remarkably similar in their functionality. As I noted in my post, there are variances between individuals, but the overall structure is similar in healthy individuals.

    In the case of brains, we all have the same lobes, the same sub-cortical structures, the same connections, and mostly the same functional locations. We all have similar primal behaviors, although the range of human behavior learned from the environment is vast.

    So, I don’t disagree with anything you observe in this post, but I would disagree that our posts disagree, if that makes sense🙂

  3. What I find intriguing is that you chose photos from Wiki Commons and didn’t use your own? I have a sense of a private moment, or needing to preserve some aspect of your walk through the forest by not taking your own pics? I know I do.

    • The point is that at the moment I don’t have a camera. For me the point of this article was not so much to document that particular forest or walk, but to get across some insights I had while going through the forest. That is probably the difference between a photographer/artist and sombody like me who is more philosophy-inclined. I have considered starting photography, but I think I would not have the patience for it. I also never had a very good camera and after my last one spoiled, getting a new one was not a priority for me.
      That is the reason why I am following the blogs of artists and photographers. They do something I am not god at.🙂

    • That was not really the topic here. The Fibonacci sequence emerges from certain branching patterns, as a result of their recursive structure, but it does not explain them. There also can be different recursive patterns. I think it has also been over-hyped somehow, see http://www.lhup.edu/~dsimanek/pseudo/fibonacc.htm.
      My main topic here is instead that some aspects of the structure of organisms are not a result of their own genetics but the result of a response to their environment.

  4. Here in the desert I get to see some very interesting adaptations to the environment (I’m can totally see you getting into desert plants). The saguaro generally grows under a “nurse” plant—something that protects it while it’s young from animals and such. I bought a small 6 inch saguaro when we first visited Tucson, then took it back home with me to Vermont. I thought for sure it would die, but it didn’t. I kept it in a pot and took it in and out all the time, depending on the weather. Then we decided to move to Tucson, and I brought the saguaro with us. We then planted the saguaro in our backyard. I thought it would be nice to plant it under the mesquite tree so it would look like it had grown under a nurse plant. Then I put a hanging pot on one of the limbs of the mesquite (just for some annuals). After a while, the hanging pot got stuck because the mesquite grew around it somehow, so the hook on the planter is embedded in the branch. I planned to move the pot because I thought the saguaro underneath it might be getting too much water, but since the pot is now a permanent fixture, I just left it and continued planting in it. That saguaro has grown a lot faster than they usually do. It’s now about three feet tall and fat. I often wonder what factors played into my saguaro’s growth, and how my thoughtless positioning of the hanging plant might’ve affected it. Not to mention the saguaro’s move from Tucson to Vermont and back.

    On the human body…the other day I happened to notice the veins in my hands. I usually can’t see them, but for some reason they were bulging out this day. I noticed that the pattern of the veins was not the same on both hands and I called my husband in. “My veins are different on each hand! Look at this! I’m a freak!” He laughed and said that was true for everyone. I still find it fascinating and mysterious. (I know, I probably sound like a total idiot, but oh well.)

    • I find desert plants very fascinating (and desert animals as well). It is interesting to see what solutions emerge in extreme conditions.
      It is a fascinating idea to have a large cactus growing in your back yard.

      I actually used to have a small cactus for many years (don’t know the species) and it used to produce a wonderful flower every year but then it somehow did not prosper again and eventually died. I don’t know what was the reason, maybe I had given it too much water. Normally only desert plants survive in my home because an appartment is essentially a desert. It is dry, it is warm and it never rains. Since I forget watering the plants, the others tend to die.
      I only know the large ones from greenhouses of botanical gardens. There is one in the old botanical garden in Hamburg that has a desert department but that is, of course, a quite unnatural place since they are sqeezing lots of plants from different areas into a tiny space.

      I guess our vein patters are partially genetic and partially random. I don’t know if anybody has ever investigated how those patterns are generated. Scientifically thats an interesting question.

      • I’m lucky to be living next to the Saguaro National Forest and my neighborhood is a certified wildlife habitat:

        http://www.aguadulcehoa.com/item_list.asp?subcat=35&subtitle=Backyard+Wildlife+Habitat

        I was reluctant to move into a suburban community with an HOA, but this place has a lot of good rules. We’re not allowed to have bright lights (for stargazing) and only native plants are allowed in public areas. (No stupid palm trees…we don’t want this beautiful desert turned into something that looks like a golf resort.) Most people have saguaros on their property here. We might have one at the end of our lot, but that’s way over by the wash. I’d love to have one in the front, but I guess I should consider myself lucky to have our beautiful mesquite tree. (It’s the largest one I’ve seen in our neighborhood.)

        I didn’t want any cacti in our backyard because it seems that any time my husband steps out, he brings back a piece of jumping cholla or prickly pear, which then gets smashed into various carpets and the little needles end up sticking me for the next few months. The saguaro was the exception. (No pieces that break off.)

        If you were here, I’d send you home with some cacti to keep. A lot of them are easy to give away since it only involves breaking off a piece and sticking it in dirt. I have this amazing succulent that looks like a cholla, but you can pick it up with your bare hands. I’ve never seen this plant anywhere before. I got it while I was in the hospital waiting for my husband to come out of surgery. There was some sort of plant sale, and this guy bent over to pick this plant up out of a box and I hollered, “Don’t touch that!” He laughed and showed me that the spines were not actually needles. I love this plant. I have no idea what it’s called, but I try to give away a few pieces to everyone and spread it around to keep it going in case I happen to kill one. I doubt I’d be able to find it again. It flowers sometimes and these are waxy magenta blooms.

        I would recommend a Christmas cactus for you. Have you seen those?

        https://en.wikipedia.org/wiki/Schlumbergera

        I don’t know if they are prevalent in Germany, but they do well indoors. We had ours in Vermont for years, decades, actually. It was my husband’s before I came along. They do really well indoors. Ours sat in some corner with little sunlight, I forgot to water it, and it survived. We brought it with us to Tucson and right now it’s giving us some beautiful blooms.

        I was so surprised by the vein patterns. If I’d had to guess, I would have supposed that everyone’s was the same. It is an interesting question how those patterns are generated.

        • Christmas cacti are common here as indoor plants and I have one in my place in Cologne. However, I think that is not a desert species but they grow on trees somewhere in Brasil. I will post something about tropical plants on the Kellerdoscope later because that was one of my grandfather’s hobbies and there are some drawins about those plants and some letters.
          The rules about native plants make sense because introduction of foreign species to ecosystems is one of the main reasons for extinctions because some species are invasive. And what is the use of having grass lawns in a desert area. You either waste water or you have to paint them green, as some people now do in California. Very crazy, especially since there are so many beautiful plants adapted to the dry conditions.
          I wonder what your soft-spined cactus is. Googling for “cactus with soft spines” yields some results, including some I have seen here in greenhouses in botanical gardens. But you would really need some expert to find out exactly what it is.
          I like to eat prickly pears, but I don’t like their needles. They sometimes sell them here in supermarkets with the needles removed but in most cases, some are still there.

          • Yeah, the X-mas cactus is native to Brazil.
            The Christmas cactus is not something I would put in the ground here in Tucson since we do get some freezes and I doubt it would survive the summers.

            I know what you mean about California. But I guess people like that look. I prefer the natural Sonoran desert…why change something that’s so lush and magnificent on its own? Plus, I love not having to mow the lawn anymore.

            On the other hand, if you have a dog, you start to want grass. I feel sorry for Geordie sometimes…those damned pokey plants are constantly getting caught in his paws. Most people here in Tucson avoid planting a lot of grass unless they have a lot of money and don’t mind seeing astronomical water bills. Usually you see small patches here and there with landscaping rock. Plus I see a lot of ads for fake grass here. That makes some sense…it’s one of those things you start to miss once you’ve lived here for a while.

            I’d post a picture for you of the cactus-looking succulent here, but I don’t know how to do that.

            You eat prickly pear? Wow. What do you do with it? I can’t believe they sell them there. I’ve never eaten them. I could go outside and get one if I wanted, but the needles are indeed obnoxious. The funny thing is, I see them in supermarkets here too. I guess not having to take out the needles justifies buying them (otherwise you could just step outside and take them.)

            The mesquite pods are apparently an expensive item if you want to buy mesquite flour. I never think to make my own. I prefer to let the coyotes eat them…they do a nice job of cleaning up the yard.🙂

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