Monday, November 02, 2015

Evolution as a foundational concept in biochemistry and molecular biology

The American Society for Biochemistry and Molecular Biology (ASBMB) has been promoting a new way of teaching undergraduate courses. The idea is to concentrate on fundamental principles and concepts rather than on trivial details. The various working groups came up with a list of these fundamental concepts under five main headings: Evolution; Matter and Energy Transformation; Homeostasis; Macromolecular Structure & Function; and Biological Information.

I've discussed the concepts before [ASBMB Core Concepts]. There are problems.

Various committees continue to meet in order to build a "concept inventory" to guide the new curriculum. There have been a series of workshops organized around the main themes. The participants in the workshops are, for the most part, teachers at small universities and colleges. They have lots of experience teaching undergraduate courses but they aren't necessarily experts in the subject material.

I saw this clearly when I attended a session at the last Experimental Biology meeting in Boston last April. The purpose of the meeting was to review the major concepts in Evolution and Homeostasis. I met a great deal of resistance from the workshop leaders when I tried to explain the concepts of neutral alleles and random genetic drift and show them why they were so important when comparing sequences and constructing phylogenetic trees.
INTEGRATING EVOLUTION AND HOMEOSTASIS WITH THE CORE CONCEPTS OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
Symposium Tues. 9:45 am Boston Convention & Exhibition Center, room 256

Chaired: E. Bell

9:45 RCN-UBE: Integrating Evolution and Homeostasis with the Core Concepts of Biochemistry and Molecular Biology J.E. Bell, A. Aguanno, P. Mertz, M. Johnson and K.M. Fox. Univ. of Richmond, Union Col., NY, Univ. of Alabama, St Mary’s Col. of Maryland and Marymount Manhattan. (559.2)

Presenters:
Small Group Work: Integrating Evolution and Homeostasis into the Core Concepts E. Bell, Univ. of Richmond A. Aguanno, Marymount Manhattan Col.

Group Discussion on Core Concept integration with Homeostasis A. Aguanno, Marymount Manhattan Col.

Small Group Work: Question Development Involving Evolution and Homeostasis M. Johnson, Univ. of Alabama

Group Presentations and Discussion on Question Implementation K. Fox. Union Col.
This same group has published some of their findings in the July/August issue of the education journal, Biochemistry and Molecular Biology Education (BAMBED)1 (Aguanno et al. 2015).

Here are the learning objectives they have developed under the "Evolution" concept.
  • central importance of the theory of evolution
  • Darwin's theory of evolution
  • process of natural selection
  • evidence for the theory of evolution
  • molecular basis of natural selection
I really think this misses the boat in a biochemistry context where molecular evolution plays such an important role. It will be hard to discuss genome organization and junk DNA, for example, if students don't know about population genetics and random genetic drift. It will be hard to explain (correctly) why different proteins in different species have different amino acid sequences if students don't know about neutral alleles.

I pointed this out to the authors at the meeting and stimulated a discussion about these concepts. The authors, and the other teachers in the room, were pretty certain that the differences in amino acid sequences were all due to natural selection. Most of them had never heard of random genetic drift.

The problem here is that the learning objectives and the "capstone experiences" are being developed by teachers who don't really understand evolution. It is assumed that the best people to work on the new curriculum are experienced teachers but that's demonstrably false. (It applies to the other concepts as well.)

It turns out that biochemistry professors are not as knowledgeable about core concepts as you might imagine.

The authors surveyed 161 teachers in 143 institutions across the USA to find out what are the most important concepts in a biochemistry and//or molecular biology course.

The results, right, indicate that less than 8% of the respondents thought that evolution was an important concept.

This could be due, in part, to the fact that biochemistry courses are often taught by professors who are members of a chemistry department but no matter what the explanation it looks like we have a lot of work ahead of us if we are going to convince our colleagues to make evolution a core concept.

I'm pretty sure that many of the people who teach our introductory biochemistry courses at the University of Toronto don't see evolution as a core concept and don't understand modern evolutionary theory.


1. Disclaimer: I am on the editorial board of that journal.

Aguanno, A., Mertz, P., Martin, D., and Bell, E. (2015) A National Comparison of Biochemistry and Molecular Biology Capstone Experiences. BAMBED 43:223-232. [doi: 10.1002/bmb.20869]

13 comments :

  1. This was quite a interesting thread for many reasons.
    The lack of knowledge of these teachers/professers should lighten charges about ID/YEC creationists. If these creationists are expected to have a higher understanding at least they are as good as these teachers/professors.
    In fact most ID/YEC readers of origin blogs do know about genetic drift and company since its heavily promoted.

    Again all this shows these are complicated subjects and most people, even in academia, are not up on them. Its small circles.
    Creationists are only fighting small circles for the prize and NOT THE SCIENTIFIC COMMUNITY. Or educational institutions
    , It also shows evolutiony biology is taught in North america by those not up on it. so why can't creationists say they are not up on it at all in seeing its errors??

    If UoT Biochem profs don't understand modern evo theory or evolution as a core concept then creationists can say its not a core concept or needed in understanding biochem. We do say that.
    Evolution is a subject of history of the natural world but not relevant to the present working natural world. One can conquor, discover, invent in nio subjects without agreement with or attention to evolution.
    Evolution is not a core concept in biological subjects of any species.
    Creationism isn't either. Biology is just there right now.

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  2. I am reminded that children prefer teleological explanations for things. For example when asked "Why does it rain?", they might answer: "It rains so that the plants can grow".

    Some people don't fully grow out of this mode of thinking and it is this type of thinking that ultimately gives rise to concepts like intelligent design.

    It is also this type of thinking which influences the view that if a particular nucleotide is a C instead of a G then there must be a teleological reason for that.

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  3. "central importance of the theory of evolution"

    Yet the evolutionary camp cannot get their act together on just what the theory is. They are all squabbling with each other over that.


    "process of natural selection"

    Evolutionists can't even get their story straight on what Natural Selection is.

    Some say it is a process, some say it is an outcome etc, Look at Jerry Coyne, he is confused about what it is because of all of the confusion in the evolutionary camp.


    Jerry Coyne-"In principle, natural selection is simple. It is neither a "law" nor a "mechanism.

    Jerry Coyne "and the mechanism for most (but not all) of evolutionary change is natural selection."

    hahaha

    Some say it is survival of the fittest, Some say the fittest are the strongest,the fastest etc

    Some say that fitness is defined by the number of offspring, So somebody that is terminally ill but who has children would be fitter than a just so story telling evolutionary biologist who is in excellent health but has no children.

    hahahaha

    "evidence for the theory of evolution"

    Yet the evolutionary camp cannot get their story straight on just what the theory is.

    "molecular basis of natural selection"

    They can't even get their story straight on what natural selection is,


    Dr Marc Kirschner, founding chair of the Department of Systems Biology at Harvard Medical School states:

    “In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, physiology, have not taken evolution into account at all.”


    Students of Molecular Biology etc do just fine without evolutionary just so stories filling their heads with crap. If evolutionists want to fill peoples heads with evolutionary just so stories then maybe they should sell them to the sci fi channel.

    hahaha

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    Replies
    1. Jack Jones says,

      In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, physiology, have not taken evolution into account at all

      Can you find me a single college-level biochemistry textbook or a molecular biology textbook that doesn't discuss evolution and use our knowledge of evolution to explain and extend fundamental concepts in their disciplines?

      It's a simple question. Let's see if you are up to it.

      If not, retract your lie.

      Delete
    2. It wasn't Jack's lie. It was Dr. Marc Kirschner's. And you know he must be right, because he has "Dr." in front of his name and a prestigious title after it. But oddly enough, if you look at his web page, there's quite a bit of evolution on it. It turns out that Jack was just cutting and pasting a quote mine, and the quote is Kirschner complaining about something he thinks is pernicious.

      Delete
    3. A follower of Professor Moran says "quote mine"

      Quote Mine-Code for any quote that destroys the position of the evolutionist and leaves him with no valid rebuttal.

      Here is a little rhyme for you.

      Evolutionists rely on the quote mine label when they cannot handle quotes that destroy their fables.

      Professor Moran says " Jack Jones says,

      In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, physiology, have not taken evolution into account at all"

      Nope, I quoted a prominent Evolutionist called Dr Marc Kirschner.



      It is your own people that you should be angry with for revealing the truth

      This is what H Allen Orr said in a review of Michael Behe's book.


      "there's a striking asymmetry in molecular versus evolutionary education
      in American universities. Although many science, and all biology,
      students are required to endure molecular courses, evolution-even
      introductory evolution-is often an elective. The reason is simple:
      biochemistry and cell biology get Junior into med school, evolution
      doesn't. Consequently, many professional scientists know surprisingly
      little about evolution."


      H. Allen Orr is University Professor and Shirley Cox Kearns Professor of Biology at the University of Rochester.



      This is what Ernst Mayr the famed Evolutionary Biologist said "Evolutionary biology, in contrast with physics and chemistry, is a historical science…[where] Laws and experiments are inappropriate…
      ….
      Instead one constructs a … narrative"

      the word narrative is a politically correct substitute for the term just so stories.

      Mayr still probably made his colleagues mad with his confession.

      So it is your own people that you should be mad at for revealing the truth.


      Dawkins attacks Ben Carson for being ignorant on Evolution and yet if that is true as Dawkins says then Carson pursued his career and became a leading Neurosurgeon just fine without believing one type of Creature gave rise to a different type over many generations or that life evolved from non living matter in nature by chance.

      hahahaha





      Delete
    4. A follower of Professor Moran says "quote mine"

      Quote Mine-Code for any quote that destroys the position of the evolutionist and leaves him with no valid rebuttal.


      If so, you should be able to tell us where the quote comes from so its context can be checked to see if it means what you claim it means. You were using it to support your claim that "Students of Molecular Biology etc do just fine without evolutionary just so stories filling their heads with crap." But Kirschner was arguing just the opposite: that they don't do just fine, and that these sciences should incorporate more evolution into their methods. That's what a quote mine is: using a quote to say something quite different from the author's intention.

      Delete
    5. @Jack Jones

      I notice you forgot to answer my challenge.

      I assume you're working on it, right?

      You do realize, don't you, that you will look pretty silly if it turns out that major textbook authors think evolution is important and they are trying their best to get it into biochemistry courses.

      Not to mention the fact that this very post documents a case where the American Society for Biochemistry and Molecular Biology specifically advocates evolution as a fundamental concept that all biochemistry students should master.

      You're an Intelligent Design Creationist. Surely you don't want to look silly?

      Hmmm .... on second thought ....

      Delete
    6. I gave you the words of Prominent Evolutionists who admit it is not needed for medical students, they knew about the textbooks.



      Now...Your biggest achievement in the debate seems to be coming up with the term IDiot on a blog.



      hahahaha

      All those years of study and your achievement when it comes to the evolutionary debate is to play on words.

      They know what is in the textbooks and they said what they said. So you need to take up your complaint with them.

      I noticed that you didn't explain in your reply to my post why medical students would need to believe one type of animal gave rise to a different type of animal over many generations or believe life evolved from non living matter by chance to treat their medical students.

      hahahahaha

      I assume you're working on it, right Professor Moran?

      hahahaha

      "You do realize, don't you, that you will look pretty silly if it turns out that major textbook authors think evolution is important and they are trying their best to get it into biochemistry courses."

      And yet if they do start or have used the term then you know it is either as narrative gloss or used in a generic sense, You wouldn't use a word in one sense deceptively and equate it for a meaning in another sense would you Professor?


      hahahahaha



      "Not to mention the fact that this very post documents a case where the American Society for Biochemistry and Molecular Biology specifically advocates evolution as a fundamental concept that all biochemistry students should master."

      That is an admission that they have been getting on without it. I wouldn't be surprised if some evolutionists wanted to push their faith on to medical students though.

      PZ Myers in Evolution vs God "Humans are still fish"

      Tell me Professor, why would Doctors need to believe they are fish in order to treat the medical conditions of their patients?

      "You're an Intelligent Design Creationist."

      Wow, Is that meant to be some kind of put down that I believe my brain was intelligently designed and you believe your brain was the result of dumb chance.

      hahahahahaha

      You surely are a Professor of sticking your foot in your mouth.

      hahahahahaha





      "Surely you don't want to look silly?"

      You believe Humans are nothing more than determined matter in motion As you believe that then why would you think that which is determined could be silly?

      You're not using language consistent with your faith Professor.

      Furthermore, You believe yourself to be a fish, You need to worry how you look.

      I suppose you are going to go into denial mode and throw your colleague PZ under the bus just like you threw the other Evolutionists under the bus.

      hahahahaha



      "Hmmm .... on second thought ...."

      Thoughts on Materialism would be nothing more than chemical reactions, it makes no sense to say that chemical reactions are true or false. If you shook up a bottle of mountain dew and a can of Pepsi then it wouldn't make sense to say one was fizzing more correctly than the other.

      If your faith were true then some brains would fizz design and others would fizz chance.

      It makes no sense to say chemical reactions are true or false.

      Clearly, Even second thoughts are difficult for you as you have not thought your position through properly in your reply, and you are a Professor.

      Standards must be slipping.

      hahahahaha

      You believe humans are nothing more than matter in motion.

      As Material things can be resolvable in terms of chemical elements. Which do you tell your students are free?

      Is sodium free?

      What about Potassium, What about Iron? What about Lead?

      Seeing as you believe in free will, You must do for your judgements of others to have merit then you are holding conflicting views Professor.

      The standards are really slipping in academia for you to have become a Professor.


      hahahahahahaha

      Delete
  4. I must confess, as a college biochemistry professor who uses Dr. Moran's excellent tome, "Principles of Biochemistry", in a one-semester introductory biochemistry course, that I assume my students have had more than a smattering of evolution in their previous coursework at the university. Time constraints necessitate the paring-down of evolutionary discussions. Could you provide some suggestions as to how I could bring home the message for further and deeper understanding of evolution without missing out on sequential ordered kinetic mechanisms? (I do point out that natural selection is a major mechanism, but not the only mechanism, for observed evolutionary changes)

    (I didn't think it was possible to use the word 'biochemistry' more than three times in a sentence.)

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    Replies
    1. Could you provide some suggestions as to how I could bring home the message for further and deeper understanding of evolution without missing out on sequential ordered kinetic mechanisms?

      Discuss why the same proteins from different species have different amino acid residues.

      Discuss which came first, glycolysis or gluconeogensis and how you would go about testing your hypothesis.

      Ask the students to explain where chemisomotic species get their energy and make sure you teach them the answer.

      Discuss why humans can't make vitamin C and several amino acids when they are an essential part of the diet.

      Describe photosynthesis in green sulfur bacteria and purple bacteria then show how the two photosystems were combined in cyanobacteria. Show them how chloroplasts are related to cyanobacteria.

      Same with mitochondria.

      Describe the evolution of metabolic pathways (Chapter 10) and give some examples.

      Ask your students how an irreducibly complex pathway like the Krebs cycle could have evolved.

      Talk about promiscuous enzymes and the evolution of enzymes.

      Get them to debate the existence of junk DNA.

      And last, but not least, don't bother teaching about sequential ordered kinetic mechanisms, The students will forget everything you said the day after the exam. :-)

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    2. Thank you. These are great starting points for classroom discussions with students. I actually do use variations of some of these as exam questions (chloroplast/mitochondria relationships to bacteria, vitamin C, and protein similarities).

      My favorite part of kinetics is confusing the students with the different types of reversible enzyme inhibition. It's fun and evil, but that's because I flow...

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