Thursday, April 21, 2011

Core Concepts: Pathways and Transformations of Energy and Matter

The AAAS document, Vision and Change in Undergraduate Biology Education, defines five core concepts for biological literacy. One of the core concepts is Pathways and Transformations of Energy and Matter. This is an important one for biochemistry since we are the people charged with making sure undergraduates understand the basic core concept that life obeys the laws of physics and chemistry.

Here's how the authors of Vision and Change describe the core concept.
4. PATHWAYS AND TRANSFORMATIONS OF ENERGY AND MATTER:

Biological systems grow and change by processes based upon chemical transformation pathways and are governed by the laws of thermodynamics.


The principles of thermodynamics govern the dynamic functions of living systems from the smallest to the largest scale, beginning at the molecular level and progressing to the level of the cell, the organism, and the ecosystem. An understanding of kinetics and the energy requirements of maintaining a dynamic steady state is needed to understand how living systems operate, how they maintain orderly structure and function, and how the laws of physics and chemistry underlie such processes as metabolic pathways, membrane dynamics, homeostasis, and nutrient cycling in ecosystems. Moreover, modeling processes such as regulation or signal transduction requires an understanding of mathematical principles.

For example, knowledge of chemical principles can help inform the production of microorganisms that can synthesize useful products or remediate chemical spills, as well as the bioengineering of plants that produce industrially important compounds in an ecologically benign manner. These are topics of intense current interest.
At first glance this seems like an adequate description of a core concept but the more you think about it the more you realize that it's just a bunch of motherhood statements without any real teeth. It sounds very nice to say that students need to understand kinetics and thermodynamics but the recommendation has no substance unless you explain exactly what it is that they are supposed to understand. We all know that both these concepts are poorly taught in undergraduate courses.

When I was teaching introductory biochemistry I always asked my students the following question to make sure they had grasped the concept of where cellular energy comes from.
There are species that are autotrophs. They grow and reproduce using only inorganic molecules as their only source of essential elements. Carbon usually comes from CO2. Some of these species are capable of photosynthesis (photoautotrophs) but others are not (chemoautotrophs). Where do chemoautotrophs get the energy to grow and reproduce if they can't carry out photosynthesis and they don't require organic molecules as food sources?
Let's look at the AAAS Project 2061 Science Assessment Website to see how they treat the topic of Matter and Energy in Living Systems. This site is for high school biology but it's the only place I know where we can assess what AAAS thinks is important in basic concepts. Students are expected to know that...
All organisms need food as a source of molecules that provide chemical energy and building materials.
  1. Food consists of carbon-containing molecules in which carbon atoms are linked to other carbon atoms.
  2. Carbon-containing molecules serve as the building materials that all organisms (including plants and animals) use for growth, repair, and replacement of body parts (such as leaves, stems, roots, bones, skin, muscles, and the cells that make up these structures) and provide the chemical energy needed to carry out life functions.
  3. If substances do not provide both chemical energy and building material, then they are not food for an organism.
  4. Chemical energy from carbon-containing molecules is the only form of energy that organisms can use for carrying out life functions.
  5. Carbohydrates (including simple sugars and starch), fats, and proteins are molecules that are food.
  6. Light is not food because it is not made of atoms and therefore cannot provide building material, and even though substances such as water, carbon dioxide, oxygen, and various minerals provide atoms for building materials for some types of organisms, they are not food because they do not contain carbon atoms that are linked to other carbon atoms and cannot be used as a source of chemical energy.
Oh dear. If this is an example of core concepts then we need to add one more item; namely "7. According to item #3, chemoautotrophs are not organisms."

I'm sure most of you recognize the problem. The focus is on plants and animals, ignoring protozoa and bacteria. This is not how to teach basic concepts in biology and it certainly isn't how to teach if evolution is supposed to be an important core concept. Complex plants and animals did not just poof into existence with specialized metabolic pathways.

But not to worry. Although the six statements above seem wrong, they are soon clarified in the next section ...
Plants make their own food in the form of sugar molecules from carbon dioxide molecules and water molecules. In the process of making sugar molecules, oxygen molecules are produced as well.
  1. Unlike animals, plants do not take in food from their environment.
  2. Plants make their own food in the form of sugar molecules by means of a chemical reaction between carbon dioxide molecules and water molecules. Oxygen molecules are also a product of this reaction.
  3. The process of making sugar molecules involves linking together carbon atoms that come from molecules of carbon dioxide.
  4. The chemical reactions by which sugars are made takes place inside the plants. In most familiar land plants, the carbon dioxide molecules that are used come from the air that enters the plant primarily through its leaves, and that the water molecules that are used in the reaction enter the plant through its roots.
Here's the core concept as I teach it. I'd appreciate feedback on which way is better.
Photosynthetic organisms, such as bacteria, algae, and plants, can use light as a source of energy. They convert this energy into chemical energy in the form of ATP and other cofactors. These "high energy" molecules are used to provide energy in biosynthesis reactions that make all of the important molecules in the cell including amino acids, proteins, nucleotides, nucleic acids, fatty acids, lipids & membranes, carbohydrates, and polysaccharides.
Note that point #2 above is absolutely wrong. Oxygen is NOT produced as a result of a reaction between CO2 and H2O. That is a major misconception. The oxygen given off by some photosynthetic species is derived directly from water as part of the photosynthetic electron transfer reactions. Some photosynthetic species don't produce oxygen yet they are perfectly capable of synthesizing nucleic acids, proteins, lipids, and carbohydrates. How do they do it? You need to understand the answer to that question if you are going to understand how eukaryotic photosynthesis evolved.

My main criticism of undergraduate biology education is that the core concepts are not being taught and, when an attempt is made, they are often taught incorrectly. The Vision and Change document doesn't make a contribution toward fixing this problem. The "core concepts" it describes are not specific enough to be helpful and when they are specific they turn out to be wrong or misleading.


22 comments :

  1. It looks like they are saying that all biological functions can be reduced to physics and chemical reactions.

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  2. That entire teaching scheme is a lot of guff about 1970s energy transformations models.

    Modern students want to know (a) why there here and (b) where they're going.

    This brings into question human origins, which directly comes into conflict with the dominant morality system of the world.

    It's nice and quaint to tell students that thermodynamics governs all systems atoms to humans, but when you begin dig into the meat of the issue, heated debate immediately springs to the fore.

    These are the things students need to be taught. The meat. Visit Hmolpedia to see some of the meat and spread the word.

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  3. Larry, I think you are demanding too much in this case. Sure there are mistakes but they are not incorrigibly bad mistakes. Fact is, 98% of biological science professors and 99% of biological sciences students biology would make the same or worse mistakes.

    My bar is much lower because of the students admitted to the graduate program in biochemistry, an very clear majority never had a course in physical chemistry, statistics or genetics. Good half of them can't solve quadratic equation. On that background forgetting about existence of chemosynthesis seems pretty minor problem.

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  4. DK says,

    On that background forgetting about existence of chemosynthesis seems pretty minor problem.

    Perhaps. But if you're writing a critique of undergraduate education in biology and a major part of that critique is teaching basic concepts, then don't you think it's a good idea to get them right?

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  5. if you're writing a critique of undergraduate education in biology and a major part of that critique is teaching basic concepts, then don't you think it's a good idea to get them right?

    You have the point! :-)

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  6. Is there agreement here that the report is saying that all biological functions can be reduced to physics and chemical reactions?

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  7. People here are either not sure if the report is saying that all biological functions can be reduced to physics and chemical reactions,
    or
    they do not want to acknowledge that the report is saying that.

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  8. Anonymous,

    My guess is that nobody is answering because the report is not saying that biological phenomena can be "reduced" to physics and chemistry.

    Perhaps your complain is that they describe biological phenomena in terms of physics and chemistry. If so, well, that is correct, biological phenomena can be explained in terms of physics and chemistry. If you want to see some mention of magic, well, that belongs to prehistory.

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  9. If events cannot be reduced to physics and chemistry then there must be some additional element involved.

    Let's take your actions.
    In addition to physics and chemistry there is intelligence involved.
    Similarly with the actions of the cell.
    See Dr. James Shapiro's work.

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  10. Hey anonymous, if you are the same one (wouldn't it be useful to have some constant nickname, or whatever they call these thingies?)

    The intelligence involved is a consequence of those physics and chemistry. Shapiro's work looks interesting but I would not go too much beyond the metaphors. In other words, that Bacterial communication and colony growth, and whatever, might "involve" some "computation" is but a metaphor, and the real deal is understanding how that works. If you looked closely what you would find is that bacterial computations work mechanically. No magic involved. Their workings can be perfectly explained with physics and chemistry, just like our computers work with physics and chemistry. Evolution itself can be thought of as an algorithm (and has been applied as such). That does not mean that an "intelligence" other than the laws of nature (if you want to think of them as intelligence, but I would not try and go too far with the metaphor), would be required to build any of it.

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  11. Hi Negative Entropy.
    You posted:
    "Evolution itself can be thought of as an algorithm (and has been applied as such)."

    Where did that algorithm come from?

    Was it the inevitable result simply of the "workings of physics and chemistry"?

    Please think about that.
    There is an issue here whether you acknowledge it or not.

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  12. Hey anonymous,

    Where did that algorithm [evolution] come from?

    Was it the inevitable result simply of the "workings of physics and chemistry"?


    It sure was.

    Please think about that.

    I have. My work demands me to continually think about that and more.

    There is an issue here whether you acknowledge it or not.

    Sure, the issue seems to be your lack of understanding of science in general, and/or of complexity and natural ways towards it in particular.

    Think about this (trying to use an example that should be easy and non-challenging to your beliefs, whichever they are, so you get the idea):

    1. Start with gravitational forces. Put just two objects, let us say, the sun and our planet. Now, the orbit of our planet around the sun is quite simple, and does not break any natural laws. Right? It should be an ellipse, right? You would not claim that their not going randomly through the universe breaks any laws of nature. Gravity is what makes this possible, right?

    2. Now, let us add another planet, let us say mars. Now both orbits, ours and mars' can be described by ellipses, but we notice a few kinks here and there. We check our equations, and the kinks we did not anticipate are due to the very fact that we have three objects. Our description of the system, to be accurate about those little kinks requires us to take into account this very fact, that we have three objects. We have a more complex system. The complexity is not random, yet is perfectly explainable by natural laws and properties. Gravitations, masses, three objects.

    3. Continue adding planets, and we get a pretty complicated, non-random, system. It is very hard to model accurately to the point that we are forced to rely on approximations. Yet, our inability to model the whole system does not mean that the system requires superhuman-like intelligence to work.

    See? Complex systems can be explained very well naturally. You can use similar principles to understand the workings of other systems without forcing any "magical intelligence" to the soup. Think ocean currents, winds, their basic forms, then their shaping because of the uneven distribution of rocks, depths, mountains, and such. Then you can go a few steps further and perhaps, after long studying, notice that the same applies to biological systems.

    This is it about this theme from me to you my friend. I anticipate your almost instantaneous further complains with little if any digestion of my explanation. I can only show you the way. Following it further requires your willingness to learn. I can't do anything if you lack it.

    Best,
    N.E.

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  13. Negative Entropy says,

    Evolution itself can be thought of as an algorithm (and has been applied as such).

    I don't agree that evolution can be thought of as an algorithm.

    Start with lungfish. What kind of algorithm do you apply that will result in kangaroos?

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  14. Hey Larry,

    Start with lungfish. What kind of algorithm do you apply that will result in kangaroos?

    Who are you and what did you do to Larry? You left me wondering where to start. I shall try though. The "problems" that this "algorithm" might solve depend on the inputted variables. Sometimes it will be no more than keeping some kinds of mutations out of the soup (too deleterious?), sometimes it will be the problem of adapting life to some new conditions, et cetera. The algorithm does not have such a precise "purpose" as making kangaroos out of lungfish. The kangaroos would be a "secondary effect" of solving rounds and rounds of these kinds of problems.

    But let us not forget that this is metaphorical. As for applications "as such." I meant both, genetic algorithms (and its siblings), and "wet-lab" directed evolution.

    Best,
    N.E.

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  15. @ Negative Entropy,

    If you're looking for a good metaphor then "algorithm" isn't it. In fact, that's just about the worst metaphor Daniel Dennett could have come up with.

    I prefer to think of evolution as a sloppy purposeless random path through time. The history of life is marked by countless accidents and historical contingencies making it about as far removed from "algorithmic" as you can possibly get. Life would look very different if there hadn't been several mass exinctions, for example. How do you factor in random meteor strikes when creating an algorithm for evolution?

    I call it evolution by accident.

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  16. Larry,

    I call it evolution by accident.

    It would be lots of fun to continue this. Lots of fun indeed. But, besides I don't want to troll your blog, let us just say that I did not say that the "implementations" of this "algorithm" lacked any bugs.

    :)

    P.S. I was not looking for a metaphor. No doubt "algorithm" has served very good purposes in my courses and presentations. However, I mentioned it here as an illustration that metaphors might be useful, but that such metaphors don't mean that life needs an intelligence to work. That you don't like the metaphor should reinforce this very point to this Anonymous person.

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  17. Larry,

    If you feel like I am trolling, please just ignore this comment and we leave it there. Or else, let me know if I should just stop. I continue here out of wanting to give you a real answer, rather than the unsatisfactory one that I gave you before.

    I prefer to think of evolution as a sloppy purposeless random path through time. The history of life is marked by countless accidents and historical contingencies making it about as far removed from "algorithmic" as you can possibly get. Life would look very different if there hadn't been several mass exinctions, for example. How do you factor in random meteor strikes when creating an algorithm for evolution?

    But you seem to be conflating the results of the algorithm, and the situations where it has run, with the algorithm itself. While I agree with you about the situations and results of evolution, evolution can indeed be thought of as an algorithm. An heuristic one at that. It solves problems as they come by, sometimes problems created by the algorithm itself. Those countless accidents and historical contingencies, those random meteor strikes, are variables that get the algorithm running one way or another. If you kill most of life, then the algorithm has little to run with, but lots of directions where to run, and run it does.

    Best,
    N.E.

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  18. Does anyone think that intelligent human actions can be reduced to just physics and chemistry?

    In other words, if we consider only the laws of physics and chemistry we have enough to explain human action?

    But the laws of physics are just a set of laws and chemistry is just a set of laws. How can sets of laws themselves determine how someone uses those laws.
    For example, I pick up a ball and drop it on the floor. The ball's movement follows the law of gravity. But did the law of gravity or some other law determine that I would drop the ball?

    If someone thinks so, please tell me what that law is.

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  19. @Anonymous,
    Have you ever heard of the fallacy of composition?

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  20. It looks like Negative Entropy is not all that interested in understanding this.
    Does anyone else?

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  21. Pterosaur,

    Did you go and check the meaning of a fallacy of composition?

    Your rant is mainly one of such fallacies, but also contains other categorical errors. Of course, I am not saying that you used such a fallacy, and such categorical errors, on purpose. But check and think for yourself.

    I think I understood much better than you. Maybe it is you who is not interested in understanding.

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  22. Negative Entropy is not interested in anything but silly attacks. Is anyone else interested?

    ReplyDelete