More Recent Comments

Wednesday, October 07, 2020

Undergraduate education in biology: no vision, no change

I was looking at the Vision and Change document the other day and it made me realize that very little has changed in undergraduate education. I really shouldn't be surprised since I reached the same conclusion in 2015—six years after the recommendations were published [Vision and Change] [Why can't we teach properly?].

The main recommendations of Vision and Change are that undergraduate education should adopt the proven methods of student-centered education and should focus on core concepts rather than memorization of facts. Although there has been some progress, it's safe to say that neither of these goals have been achieved in the vast majority of biology classes, including biochemistry and molecular biology classes.

Things are getting even worse in this time of COVID-19 because more and more classes are being taught online and there seems to be general agreement that this is okay. It is not okay. Online didactic lectures go against everything in the Vision and Change document. It may be possible to develop online courses that practice student-centered, concept teaching that emphasizes critical thinking but I've seen very few attempts.

Here are a couple of quotations from Vision and Change that should stimulate your thinking.

Traditionally, introductory biology [and biochemistry] courses have been offered as three lectures a week, with, perhaps, an accompanying two- or three-hour laboratory. This approach relies on lectures and a textbook to convey knowledge to the student and then tests the student's acquisition of that knowledge with midterm and final exams. Although many traditional biology courses include laboratories to provide students with hands-on experiences, too often these "experiences" are not much more than guided exercises in which finding the right answer is stressed while providing students with explicit instructions telling them what to do and when to do it.
"Appreciating the scientific process can be even more important than knowing scientific facts. People often encounter claims that something is scientifically known. If they understand how science generates and assesses evidence bearing on these claims, they possess analytical methods and critical thinking skills that are relevant to a wide variety of facts and concepts and can be used in a wide variety of contexts.”

National Science Foundation, Science and Technology Indicators, 2008

If you are a student and this sounds like your courses, then you should demand better. If you are an instructor and this sounds like one of your courses then you should be ashamed; get some vision and change [The Student-Centered Classroom].

Although the definition of student-centered learning may vary from professor to professor, faculty generally agree that student-centered classrooms tend to be interactive, inquiry-driven, cooperative, collaborative, and relevant. Three critical components are consistent throughout the literature, providing guidelines that faculty can apply when developing a course. Student-centered courses and curricula take into account student knowledge and experience at the start of a course and articulate clear learning outcomes in shaping instructional design. Then they provide opportunities for students to examine and discuss their understanding of the concepts presented, offering frequent and varied feedback as part of the learing process. As a result, student-centered science classrooms and assignments typically involve high levels of student-student and student-faculty interaction; connect the course subject matter to topics students find relevant; minimize didactic presentations; reflect diverse views of scientific inquiry, including data presentation, argumentation, and peer review; provide ongoing feedback to both the student and professor about the student's learning progress; and explicitly address learning how to learn.

This is a critical time for science education since science is under attack all over the world. We need to make sure that university students are prepared to deal with scientific claims and counter-claims for the rest of their lives after they leave university. This means that they have to be skilled at critical thinking and that's a skill that can only be taught in a student-centered classroom where students can practice argumentation and learn the importance of evidence. Memorizing the enzymes of the Krebs Cycle will not help them understand climate change or why they should wear a mask in the middle of a pandemic.


  1. My undergrad years are 40 years behind me but I remember the first 2 plus years being nothing but memorization and regurgitation. But in my third year I had a prof that loved to teach by starting a lecture with a presumably simple question. And then spend the entire lecture making the students figure it out using their own reasoning ability.

    One question was “why are there no trees in the ocean?” Another was “Why can’t a protozoan be the size of a whale?”

    1. Hi William Spearshake,

      my biophysics teacher gave some of his students a 100 DM bill between their open thumbs and forefingers in his lecture - with the announcement that you can keep the bill if you catch him immediately after he released it. Nobody succeeded (the trick is to juke it), but nobody has forgotten what he taught about membrane biophysics.

      One of my teachers in ecology used to demonstrate the eggs from the last nesting box in the open hand during the hole-nesting birds excursion. With a big gesture he then devoured them to the horror of his students. He defended himself by saying that this helped him in his love life despite his age. Of course these were eggs made of white chocolate. No one forgot what he taught about population biology - yes, love life...



  2. What a boring way of teaching (straight lecture with students memorizing pathways). I am using COVID-19 forced online to completely flip my class room for my metabolism course. I have always done the active exercises during class but now it is significantly expanded. Students watch mini-lectures ahead of synchronous sessions. In the latter, they work in small groups (breakout rooms) on questions that engage them in thinking about the metabolic pathways. Some of the best questions are the ones that get them to think about how the pathways could have evolved which forces them to really think about the chemistry. In addition to the working questions, they do reflections on each module. They really enjoy it. Once back in person, it will be even better. A number of students for their reflections on the Citric Acid Cycle commented very favorably about the focus on understanding and not memorization given the horror stories they have read about online regarding the cycle in biochemistry courses.

    1. Good questions for the citric acid cycle are ...

      How did it evolve?

      Given the high standard free energy change for the citric synthase reaction, why is it not coupled to ATP production?

      Why do so many textbooks and websites show FADH as a product of the succinate dehydrogenase reaction?

      The glyoxylate pathway is extremely important in most species but not in mammals. Why?

      Predict the flux for each reaction.

      Why are anaplerotic reactions necessary and important?

    2. I forgot ...

      How can most bacterial species survive without a citric acid cycle?

    3. Hi Larry Moran,

      another one of this kind: In which direction does the citrate synthase reaction proceed under physiological conditions? ;-)

      Mall A. et al. (2018): Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium. Science 359, Issue 6375, pp. 563-567; DOI: 10.1126/science.aao2410



    4. All are questions my students have to think about.

      Off topic - Is there a good biochemical reference for why ketoacidosis occurs? The ketone bodies of acetoacetate and D-beta-hydroxybutyrate are bases so the explanation adding them to blood causing the blood to acidify doesn't make sense.

    5. Hi KStRNA!

      Acetoacetic acid and β-hydroxybutyric acid are responsible for the acidification of the blood in ketoacidosis. This is caused by a long-lasting insulin deficiency:

      (1) Lipolysis as well as gluconeogenesis is ultimately disinhibited, resulting in the formation of acetyl-CoA and NADH.

      (2) The acetyl-CoA can now not be utilized in the citrate cycle as usual: On the one hand it is inhibited by the high NADH concentration, on the other hand the oxaloacetate is missing as a reaction partner of the acetyl-CoA, because the uninhibited gluconeogenesis has consumed the oxaloacetate as a substrate for glucose production.

      (3) As a consequence, the energy-rich acetyl-CoA accumulates in the cell. It cannot be used for fatty acid synthesis either, as this is not sufficiently stimulated by the lack of insulin.

      (4) In order to be able to use the acetyl-CoA nevertheless, the mitochondria of the hepatocytes now synthesize ketone bodies.

      (5) During the formation of acetoacetate and β-hydroxybutyrate, one proton is released each, since these are weak organic acids.

      (6) The pH value of the blood decreases.



    6. Lamarck,

      Why would putting weak bases into the bloodstream lower the pH?

      Acetoacetate and β-hydroxybutyrate are weak bases and are what are synthesized in the liver. When protonated then they are acids but what is synthesized are bases!

      Over the course of ketone body synthesis, an acid is generated - the HMG-CoA. Given its pKa, it will deprotonate in the cell and the HMG-CoA will have a negative charge. The cell's buffering system will absorb much of proton absorbed.

      HMG-CoA lyase catalyzes the conversion of the anionic HMG-CoA to the anionic acetoacetate and acetyl-CoA. Acetoacetate then can be reduced to β-hydroxybutyrate in a process where a proton is consumed but β-hydroxybutyrate is still an anion, a weak base.

      The simplest explanation is acetoacetate and β-hydroxybutyrate are transported out by monocarboxylate transporters (MCTs), which could that to moving a proton in the same direction, which would acidify the blood/ However, to bring acetoacetate and β-hydroxybutyrate into other cells, a proton also must be transported into the cell, so if balanced it would be no net change in pH. However, if more ketone bodies are exported out of the liver than can be absorbed by the rest of the body, there would be a net transport of protons into the bloodstream due to the transporters moving the ketone bodies out of the liver cells. The ketone bodies are weak bases so don'y really absorb many of those protons. However, is there anything else going on? For example, given protein breakdown is also likely going on, is bicarbonate being absorbed from the blood for the urea cycle? As bicarbonate levels are diverted to the urea cycle, carbonic acid would deprotonate to bicarbonate to maintain equilibrium, decreasing the pH. It would also mean more CO2 will react with water to form more carbonic acid to once again maintain equilibrium.

      With regards to the MCT moving protons, isn't that what happens in lactic acidosis? Lactate is generated in the cell during homolactate fermentation. Lactate is a base and would actually increase the pH. However, when transporting out of cells via MCTs protons would also be moved out into the blood. If the liver is functional that is ok, as the liver cells when taking up lactate will also be removing protons from the blood. When the liver is not functioning properly, there isn't balance. Protons are being transported out of cells into the blood but won't be readily absorbed by the liver.

    7. Hi KStRNA!

      »Why would putting weak bases into the bloodstream lower the pH?«

      So procatively formulated, the question does lead to a slight uneasiness in my mind... ;-)

      Textbooks of human physiology have the systemic view of differential diagnostics due to their medical target group. Therefore, some of the descriptions here might mislead to assume that ketosis is the cause of acidosis or the like. However, the use of the terms is basically identical. Actually no problem, but it is a task of biochemistry to draw attention to it.

      Of course, ketone bodies are not formed here as acids, but as their conjugated bases. So we have to look at what happens to the protons.

      Basically, the black box approach shows that the protons ingested with food are excreted net via the kidneys. Essential here H⁺ results from the decomposition of sulfur-containing amino acids to sulfuric acid - in the process, urinary protons of the order of 100 mmol/d are produced. Now the blood circulation in between with its acid-base homeostasis plays the decisive role as the hub of physiological control mechanisms. Thus, the pH value in arterial blood is close to 7.40 (= ~40 nmol/l H⁺). Deviations from this have an effect on the degree of protonation of the proteins, changing their conformation and thus influencing body functions in a variety of ways.

      In some metabolic situations, however, organic acids occur more frequently as intermediate products of energy metabolism, such as lactic acid in cases of oxygen deficiency or 3-hydroxybutanoic acid and acetoacetic acid in hunger metabolism.

      Therefore, we only need the appropriate basic route for situations where fatty acids need to be mobilized. Fasting will therefore reduce insulin levels and lead to increased activity of fatty tissue lipolysis. Et voilà: The fatty acids released in this process ionize rapidly and release protons.

      In this context interesting from an evolutionary-biological point of view:

      Jebb, David & Hiller, Michael (2018): Recurrent loss of HMGCS2 shows that ketogenesis is not essential for the evolution of large mammalian brains.



    8. Lamarck - once again lactic acid is NOT produced during fermentation - lactate is as our host has pointed out.

      3-hydroxybutanoic acid and acetoacetic acid are not synthesized during ketone body production, their conjugate bases are. You went from saying that acids aren't formed to then saying acids are formed. In between you talked about protons from ingesting food.

  3. Science is under attack all over the world? In this worlds thats impossible. Instead what might be meant are conclusions SAID toi be science proven that are rejected and opposed. Then very little and probaly some right and there shoulkd be some more.creationists know that.
    Everybody forever says they are against mere memorization. GOOD. However actually all science knowledge requires memorization unless someone newly figured something out.
    There are serious problems in schooling in North America for a long time now but I still think kids generally know more, of what can be known, then ever before in history of education. surely teachers are better now, man for man, then ever before
    The bible says there is wisdom, understanding, knowledge. The first two are the difficult ones to teach kids.
    its most likely true then in former days it tended to be the upper classes kids who went to higher education and so brought with them/gained understanding and wisdom from thier circles. Today everybody goes and so mere memorization of info , knowledge, is notived by everyone. something isv wrong it seems.
    I see higher education today as just finishing school for high school.
    Finally teaching kids to think harder/critically, is difficult or not possible really in mere classes.
    I think one can not distance the education of a kid from the intelligence level of the kid. this because they are kids barely pass puberty. They are really just members of demographics without having yet had interests/passions kick them into higher thinking/learning.
    Finally case in npoint is the state censorship of creationism in North America in schools. no claim to thinking/teaching to think critically when the most important subjects have a state sponsered conclusion that may boy be questioned.God and Genesis and religion was the historic conclusions on many subjectsv and the censorship today proves critical thinking is not welcome if its result is different from if one did not do critical thinking. not just creationism but these days great demands on obedience is made.
    To sum. Great problems in education and great problems in how educating and things have never been better regarding teachers and students abilities.

    1. Hi Robert Byers!

      »Science is under attack all over the world?«

      Take a look at the March for Science, for example.

      »Instead what might be meant are conclusions SAID to be science proven that are rejected and opposed. Then very little and probably some right and there should be some more. Creationists know that.«

      Science doesn't care what you believe. That's your main problem, isn't it?

      »However actually all science knowledge requires memorization unless someone newly figured something out.«

      Then also a parrot would be a knowing one. What is meant here can be best understood by watching videos on YouTube of lectures by Richard Feynman. In the style of Joseph Schumpeter: Science is creative destruction. And already we are at an Evolutionary Epistemology.

      »There are serious problems in schooling in North America for a long time now but I still think kids generally know more, of what can be known, then ever before in history of education.«

      Hopelessly lapped by Europe, Japan and South East Asia. Make America think again...

      »I think one can not distance the education of a kid from the intelligence level of the kid.
      God and Genesis and religion was the historic conclusions on many subjectsv and the censorship today proves critical thinking is not welcome if its result is different from if one did not do critical thinking. Not just creationism but these days great demands on obedience is made.«

      LOL: You want to keep the kids stupid, but allow them to ask certain “critical” questions? Now that is a really big performative contradiction. But he who knows nothing must believe everything...

      No one is bothered by critical questions. But be honest: You can't stand that science means freedom. And the true historical insight followed from the Age of Enlightenment.

      Summary: You are not part of the solution, you are part of the problem.

      BTW: You should still learn something. Let's start in the classic way: Did Adam and Eve have a bellybutton?



    2. The belief that random DNA copy errors can accumulate until a functional, integrated, role-specific organ or bio-system appears is stupid. Nobody has any business teaching such nonsense.

  4. Hello Dr Moran I wanted to inform you that sciencedirect published an article 5 years ago that supposedly solves the paradox of value c

    I would like to ask you if you have time to read the article and write me an opinion in your comment answer

  5. Hey Larry, I recenty found this paper

    Adaptation in plant genomes: Bigger is different (

    and was wondering your thoughts on the paper, given your commitments to genome size evolution being neutral.