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Tuesday, October 15, 2013

ASBMB Core Concepts in Biochemistry and Molecular Biology: Evolution


Better Biochemistry
Tansey 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.

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]


whimple said...

"matter and energy transformation"

This term is reserved by physics for the equivalence of mass and energy. Even if interpreted separately as "matter transformation and energy transformation", what does "matter transformation" mean? Does that mean chemistry? If so, please just call it 'chemistry'.

W. Benson said...

Why is there no mention of development and biochemical differentiation?

John Harshman said...

Yeah, the complete emphasis on selection is weird, especially at the molecular level. I would also expect, in addition to neutral and nearly neutral evolution, some kind of recognition of the treelike nature of descent, as well as the exceptions -- horizontal transfer and lineage sorting, chiefly, and of gene duplication, paralogy, and such.

Robert Byers said...

If such things are stressing evolution as the guiding creative force for the complexity and diversity in biology then it must demonstrate the methodology to justify it all as a intelligent investigation. Or a scientific one.!
Are they really just looking at minor rare examples of selection within species and then extrapolating one size fits all??
On behalf of the public and creationists I think any evidence presented for evolution is not scientific and rather all they do is look at present biological mechanics and guess about unobserved and past processes and events.
Evolution is unrelated to the present world and all speculation.
Its just a hypothesis that all is interrelated by evolutionary ways.

Anonymous said...

I know this is a tangent, but I always have this question when I see endosymbiosis mentioned.... How is it a "principle of evolution?" Isn't endosymbiosis simply something that organisms do - like eating, sleeping, social living, or any other behavior? Does endosymbiosis have a special effect on allele frequencies over time?

Tim Martin

John Harshman said...

The endosymbiotic origin of eukaryote organelles certainly has had a big influence on allele frequencies over time. And if it didn't, I would still say that it was evolution. How about you? Endosymbiosis is just as much or as little a thing that organisms do as is replication, reproduction, or gene duplication. I think those are principles of evolution too.

whimple said...

drift, horizontal gene transfer, Neutral Theory, symbiosis, adaptation and natural selection...

Should probably add something about synthetic gene transfer as a mechanism of evolution such as glyphosate resistance in soybeans etc.

SRM said...

Isn't endosymbiosis simply something that organisms do - like eating, sleeping, social living, or any other behavior?

It's not clear, when you describe endosymbiosis as above, that you are aware of the nature and ramifications of endosymbiotic events.

Firstly, I think it is a fairly rare event in the scheme of things and is not so common as sleeping and is not normal (so to speak) for one cell type to take up residence in another cell type. But that it occurs, it has had an enormous effect on the history of life on earth.

Secondly, it may be rather transient such as during an acute infection process, or it may be much more stable such as when nitrogen-fixing bacteria infect plant root cells which has a profound effect on both the endosymbiont and the host for the lifetime of the host, or it may be entirely fixed with the mitochondria and plastids being the best examples of this. There are several examples of where it appears a free-living bacterium is in the process of becoming what could one day be called an organelle should there exist human biologists in several tens of millions of years (which I suspect is doubtful).

Its ranges from tough to impossible to imagine that in any of the above cases that this will not effect evolutionary outcomes in both the endosymbiont and the host. Once fixed into gametes and thus subject to stable vertical transmission, an endosymbiotic event represents a massive horizontal gene transfer event at the very least.

judmarc said...

Something I've got very little idea of as a layperson is what the relationship (if any) is between random genetic drift and speciation, versus other mechanisms of genetic change in populations and speciation.

I can picture (I hope correctly) how random genetic drift will change allele frequencies over time to the extent that a modern population might not be able to interbreed with one of the same lineage from, say, a million years ago. And again I can picture how the same process might result in speciation if members of what was a single population are divided by, e.g., geological events and the now separated populations drift apart over time.

But is there a process (that we currently understand) based on drift that could result in speciation within a single, undivided population? Or would that be (at least as currently understood) exclusively the province of processes like adaptation, endosymbiosis, etc.?

Larry Moran said...

Speciation is a complicated issue. The genetic changes that distinguish one species from another are not the same as the genetic changes that lead to true speciation, i.e. the inability to exchange genes through sexual reproduction.

I think you are asking about sympatric speciation. Read the Wikipedia article to see how complicated it can be.

judmarc said...

Thanks for the reference, that's indeed what I was thinking of. I recall reading about the apple maggot example, but "magic traits," sexual conflict, and allochrony are all new and interesting concepts for me.

John Harshman said...

If you're interested enough, there's a great book by Jerry Coyne and H. Allen Orr, appropriately entitled Speciation. Short answer: most speciation is allopatric; drift can cause speciation if you give it enough time, but selection (though purely as a byproduct) can cause speciation much more quickly. And you should also understand that here we're talking about at least facultatively outcrossing eukaryotes, almost certainly a minority of what we usually call "species".

John Harshman said...

I will note that, in addition to the cellular organelles, Wolbachia infections can have a big influence in evolution.

Anonymous said...

Regarding structure and function I have found another paradox in this article that sounds very interesting:

“Close to a miracle”

"Researchers are debating whether function or structure first appeared in primitive peptides."

What do you think? I'd say both and that must have been a miracle.

Anonymous said...

Oh man, I think I actually had endosymbiosis confused to regular old "symbiosis" somehow.... I don't know how I did that.

Thanks for the explanations! This makes more sense now :)

Tim Martin

Andre said...

Yes time and chance can do anything!

Andre said...

And speciation is so complicated that most of it pure thumb suck in any case... I'm still waiting for that indisputable proof of this said speciation, it is a major selling point of the chance and time can do anything religion......

If you close your eyes and imagine, it's not that hard to believe that birds descended from dinosaurs, just ignore the actual structural change difficulties, and the couple of 100 million mutations that had to be good even though most are usually bad and lastly how information that can build these body plans have the ability to just magically poof into existence.... just ignore these insignificant problems and if you do, you'll see that evolution is true!

Larry Moran said...

I am certain that you are lying when you say that "you have found" something in that article. All you have done is demonstrate that you are reading the creationist blogs.

judmarc said...

This is something I've never understood: How someone's ignorance of a fact can make it untrue in their world. Gravity doesn't care that you don't know about relativity theory or even Newtonian mechanics, or whether you believe them - you still can't flap your arms and fly. Similarly, your colossal ignorance (and proud - since when was wilful ignorance a source of pride?) of a wealth of corroborating facts such as feather imprints on fossils, even down to details of genetics (it's known not only that "dinosaurs" became birds, but which lineage of dinosaurs), doesn't make those facts go away in the real world the rest of us inhabit.

You're certainly welcome to live in your fantasy world, but one wonders why, when there is so much going on - information about dinosaur feather coloration beginning to emerge, for example. So you can tell your kids and grandkids that this wonderful, amazing stuff isn't actually true, and hope to heck none of them go to a college with a good paleontology or evolutionary biology department, if you're truly so hung up about this that you'd deprive them of the excitement and fascination.

steve oberski said...

you close your eyes and imagine

That's the problem, isn't it Andre ?

Anonymous said...

Really? Prove it Larry. If you don't its you failure again and again

SRM said...

...and lastly how information that can build these body plans have the ability to just magically poof into existence....

it always cracks me up when creationists talk disparagingly about things "magically poofing into existence".

Really Andre, are you so lacking in critical faculties (and so completely indoctrinated) that you can't see what is wrong in your argument.

Anonymous said...

I read less often than you do Larry from what I can perceive. Lately they ran this fascinating story that should lift up the spirits of all the believers after my nagging requests for the obvious.

" Complete skull of an adult male Homo erectus creates shock waves"


the shit you dont like:

Cheers, Love Quest :)

Faizal Ali said...

Thanks, Quest. Like you, I don't frequent UD all that often. It's reassuring to know they can still put out the comedy like always. And, if not for you, I would have missed this priceless gem from Mr. Robert Byers:

Brain stuff again.
I insist. We have no brain, I don’t, for thinking. its just a middleman between our thinking soul and our physical body.
There is no evidence otherwise or show it.

Difficult to know if by "we" he was referring only to present company....

Faizal Ali said...

BTW, here's what seems to be a good, measured discussion of the skull finding, which makes reference to the ENCODE hooplah for good measure:

Linzel said...

I always value the opinions brought forth here. I would like to defend the NGSS somewhat and state that if neutral theory, HGT and more were in the standards we would not have time for everything. As much as I agree these are important concepts, especially drift [which I will attempt to use somehow] the biology [life science] NGSS standards are grade 10 material. Any student considering life science in college should be taking an additional biology course before going to college. Any AP biology teacher should incorporate these into the AP course as there are many opportunities to do it.