ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution

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Better BiochemistryTansey et al. (2013) have described the five core concepts in biochemistry and molecular biology. These are the fundamental concepts that all biochemistry instructors must teach and all biochemistry students must understand.

The five core concept categories are:

1. evolution [ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution ]
2. matter and energy transformation [ASBMB Core Concepts in Biochemistry and Molecular Biology: Matter and Energy Transformation]
3. homeostasis [ASBMB Core Concepts in Biochemistry and Molecular Biology: Homeostasis]
4. biological information [ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information]
5. macromolecular structure and function [ASBMB Core Concepts in Biochemistry and Molecular Biology: Molecular Structure and Function]

I'm glad that evolution is on the list because I favor teaching biochemistry from an evolutionary perspective. I think that the core concepts of evolution are important and they need to be emphasized in a biochemistry course with a focus, of course, on molecular evolution. This is what I try to do in my textbook.

Let's see how ASBMB describes the core concept of evolution.

The Central Importance of the Theory of Evolution to All Biological Sciences

As it is for all biological sciences, evolution is a foundational concept in biochemistry and molecular biology. An understanding of the shared evolutionary history of all living systems on our planet is thus critical for any student of these disciplines. Evolutionary theory guides experimental efforts across biochemistry and molecular biology. This ranges from the comparison of related enzymes from different species by the identification of key active site residues to the use of interspecies comparisons in the determination of gene functions to the search for genes responsible for genetic diseases using phylogenetic approaches to the study of the regulatory mechanisms that guide development. Our attempts to understand human molecules and processes are enhanced immeasurably by our understanding of their counterparts in other organisms. Our efforts to address a new human pathogen–viral, bacterial, or eukaryotic–are enhanced immeasurably by previous studies of viruses or organisms related to the pathogen.

That's not too bad, although I don't like the emphasis on trying to understand human molecules by comparing them with molecules from other species. Surely, we are trying just as hard to understand bacterial and yeast molecules? I would not have made it sound like the goal of a biochemistry course is to understand humans. That does not seem consistent with a concept-based approach to teaching and it's certainly not consistent with an evolutionary perspective on teaching biochemistry.

Students should be able to describe examples of evolution to a lay audience, value the principles of evolution through natural selection as foundational to biochemistry and molecular biology, and defend these principles in their work, schools, and communities.

I agree that students (and instructors) should value the principles of evolution by natural selection. However, they should also value the principles of evolution by random genetic drift and they should also value the other principles of evolution—such as Neutral Theory, horizontal gene transfer, and endosymbiosis. I hope this doesn't mean that ASBMB is going to concentrate on natural selection to the exclusion of other concepts in evolution.

The Basics of Darwin’s Theory of Evolution

The earth is 4.6 billion years old. All known life on the planet has descended from a common ancestor that existed over 3.5 billion years ago. Differentiation into the myriad of extant species has occurred by a process of slow evolution driven by natural selection.

I think it's wonderful that students have a knowledge of Darwin's Theory of Evolution by Natural Selection. It would be horrible if ASBMB thinks that this is all there is to evolution. That would be propagating one of the major misconceptions about evolution; namely, that "evolution" and "natural selection" are synonyms. Let's hope they aren't making that mistake ... it's not looking good.

The Process of Natural Selection

Slight, random, heritable changes (mutations) produce diversity in a population. Alterations may decrease, increase, or have no effect on fitness in a particular environment. Deleterious mutations are more common than advantageous ones. Those alterations that increase fitness give some members of a population a survival advantage. Adapted individuals are more likely to reproduce, and thus, are more likely to contribute genetically to the next generation. Over generations, this process gradually leads to an increase in fitness for the population in that given environment. Natural selection is manifested at all levels of biology including ecosystems, speciation, population dynamics, physiology, cell biology, and molecular biology.

All this is true and it's a fundamental concept that needs to be taught in biochemistry and molecular biology courses, with examples. But there's more to evolution than that, especially molecular evolution which is an important part of biochemistry and molecular biology.

I fear that ASBMB has bungled the most important concept.

Students should be able to use the tools of biochemistry and molecular biology (including databases of biological molecules and functional assays) to explain changes in traits, adaptations, and the success or failure of organisms and species.

This is a pretty good example of a learning outcome but it's not perfect. I would change the last part of the sentence to say that students should be able to "... explain the molecules, pathways, and cellular organization of modern species in terms of their evolutionary history." The language in the ASBMB statement puts too much emphasis on adaptation.

Evidence for the Theory of Evolution

The theory of evolution is broadly supported by an internally consistent and intersupporting array of millions of studies that have accumulated over the past 150 years (since Darwin). The studies come from biochemistry, genetics, molecular biology, modern genomics, astronomy, geology, paleontology, prebiotic chemistry, the macroecology of islands, developmental biology, and many other disciplines. The shared history of organisms on this planet is evident in their common genetic code, metabolic pathways, chemical approaches to catalysis, and processes of information transfer. Evolution is directly observed in the laboratory in long-term evolution trials with microorganisms, in medicine as pathogens adapt to common therapies, and in agriculture, as plants and pests adapt to human efforts at control. Evolution is not just a set of unifying principles; it is an ongoing process and challenge affecting human health and prosperity.

This is a little bit confusing since I don't know what the authors mean by "theory of evolution." The only "theory" they've mentioned so far is Darwin's theory of evolution by natural selection. Surely they don't think that's all there is?

I fear that this is exactly what they mean. This entire core concept is based on a flawed adaptationist view of evolution.

Students should be able to analyze pre-existing or novel data and relate the findings in light of the theory of evolution.

Well, they can't do that, can they, if they don't understand evolutionary theory in the first place? Let's say a group of students learns for the first time that a particular budding yeast protein differs from that of a fission yeast protein at five positions. How are they ever going to correctly explain that if they don't understand Neutral Theory and fixation of alleles by random genetic drift.

The Molecular Basis of Natural Selection

Selection is driven by challenges inherent to an environment. The heritable genotypes of different individuals of the species change over time through random, heritable changes (alteration of the sequence of nucleotides; mutations) in an organism’s germ line DNA, or germ line RNA in some cases (e.g. RNA viruses) and arise during DNA replication or via unrepaired DNA damage. These contribute to population diversity. At the molecular level, evolution and natural selection are manifested in terms of altered gene expression or gene product function resulting from these physical alterations in the heritable genetic information. Acquisition of new traits or structures is facilitated by gene duplication, wherein one copy of a gene can evolve to acquire a new function. Diversity in a population renders individuals in that population more or less fit in a given environment. Genetic alterations that improve fitness tend to increase in frequency within a population in succeeding generations.

This section on an evolutionary core concept covers only natural selection. If we look at evolution at the molecular level—an important perspective in biochemistry and molecular biology—then something like 99% of all significant increases in allele frequency (and eventual fixation) is due to random genetic drift.

It seem to me that mentioning the 99% might be an important part of the core concept.

Students should be able to describe what a mutation is at the molecular level, and how it comes about, be able to predict how changes in a nucleotide sequence can influence the expression of a gene or the amino acid sequence of the gene product (protein) and be able to translate these findings into a conclusion about how said mutation would impact the general fitness of an organism or population.

Students should also be able to identify those changes that DO NOT affect fitness and explain how they come about. Students should be aware of concepts like non-adaptive evolution of complexity and even if they aren't taught in an introductory course they should be prepared to consider them in more advanced courses. They can't do that if they've never heard of random genetic drift.

Students should be able to understand where mitochondria and chloroplasts came from and what happened to the original proteobacterial and cyanobacterial genomes. Not all of that can be explained by natural selection. Students should be able to think critically about the tree of life and recognize that the simplistic Three Domain Hypothesis is no longer valid. That requires an understanding of horizontal gene transfer and the ability to consider nonadaptive mechanisms.

Students should be able to think critically about genomes and junk DNA. They can't do that if they only know about natural selection.

It's true that the Next Generation Science Standards [Biological Evolution: Unity and Diversity] don't cover drift, horizontal gene transfer, Neutral Theory, or symbiosis. The focus is on adaptation and natural selection. If those standards are adopted, then high school students will not be prepared to understand evolution when they enter college. Hopefully, these misunderstandings will be corrected in their first year biology class.

Thus, by the time students take biochemistry and molecular biology they will probably know more about evolution than what is covered here under "core concepts." That's going to be embarrassing if students know more than the instructors.

There are many ways of teaching evolution but not all of them are valid. Now that we are in the 21st century. it's important to recognize that modern evolutionary theory has progressed well beyond what Charles Darwin thought in 1859. Modern evolution should be based on population genetics, or should, at the very least, contain a healthy dose of population genetics. There is general agreement about this among evolutionary biologists. (You will see the exceptions speaking out in the comments below.) There is unanimous agreement that the two most important mechanisms of evolution are random genetic drift and natural selection See, for example the University of California, Berkeley website: Mechanisms: the processesof evolution, and Mechanisms of change. We've gone long past the time when natural selection is the only game in town. That's a relic of mid-twentieth century thinking

There are plenty of examples of non-adaptive evolution on the best websites. The evolution site at Berkeley (University of California Berkeley, USA), for example, has a page devoted to Not an adaptation under their list of misconceptions. The authors of that site include genetic drift, accidents, and exaptations. Modern 21st century students need to understand this. Students studying biochemistry and molecular biology need to understand this concept more than most since so much of those subjects involves non-adaptive evolution.

Tansey et al. don't specifically equate evolution with progress but by concentrating on natural selection and emphasizing that evolution leads to an increase in fitness, they do little to dispel the common misconception that evolution is progress. This misconception is shattered when students realize that random genetic drift is a major mechanism of evolution. The Berkeley website addresses this misconception: MISCONCEPTION: Evolution results in progress; organisms are always getting better through evolution.

I don't think this is a very good way to start describing core concepts. I think the authors' view of evolution is flawed and incomplete. I think it's important for biochemistry students to understand WHY the sequences of gene and proteins in different species are not the same. It's mostly because neutral, or nearly neutral, substitutions have been fixed in the different lineages by random genetic drift.

I think it's important for biochemistry students to understand WHY you can construct phylogenetic trees from those sequences and why the trees demonstrate an approximate molecular clock. It's because the rate of fixation of neutral alleles by random genetic drift is the same as the mutation rate and the mutations rates in different lineages are relatively constant over long periods of time.

That level of understanding goes way beyond the simplistic view of evolution presented in Tansey et al. (2013).

I don't know why the authors of this report choose to describe the core concept of evolution in this way. Is it because they think that a simplified, adaptationist, version is all that's required in a biochemistry/molecular biology program? Or is it because they disagree with my perspective and think that their description is accurate? I hope they will participate in the discussion.

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Tansey, J.T., Baird, T., Cox, M.M., Fox, K.M., Knight, J., Sears, D. and Bell, E. (2013) Foundational concepts and underlying theories for majors in “biochemistry and molecular biology”. Biochem. Mol. Biol. Educ., 41:289–296. [doi: 10.1002/bmb.20727]