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Thursday, April 24, 2014

ASBMB Core Concepts in Biochemistry and Molecular Biology: Biological Information


Better Biochemistry
The American Society for Biochemistry and Molecular Biology (ASBMB) has decided that the best way to teach undergraduate biochemistry is to concentrate on fundamental principles rather than facts and details. This is an admirable goal—one that I strongly support.

Over the past few months, I've been discussing the core concepts proposed by Tansey et al. (2013) [see Fundamental Concepts in Biochemistry and Molecular Biology]. The five concepts 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]
So far, I've highlighted several problems with the core concepts of evolution, matter & energy, and homeostasis. It seems as though it is easy to identify broad categories but quite difficult to agree on the core concepts within each category. It some cases, I think the "core concepts" described by Tansey et al. (2013) are incorrect or, at best, misleading.

Let's look at "Biological Information." We can all agree that information and information flow is a very important topic and there should be many important concepts within that topic. Tansey at al. (2014) start off with "The Genome."
The Genome

Two key conditions for life include the presence of powerful biological catalysts, and heritable information to guide the production of those catalysts. The information for an organism's enzymatic catalysts, as well as for proteins and RNA molecules with structural, transport, signaling, and ligand-binding functions, is stored in its genome. The genome is comprised of linear polymers of four nucleotides, called nucleic acids, assembled into unique sequences that encode the information needed to specify the macromolecules particular to that organism. An organism's genome is usually encoded in double-stranded deoxyribonucleic acid (dsDNA) polymers but the genomes of some microbes are comprised of single-stranded or double-stranded ribonucleic acid (ssRNA or dsRNA) polymers. The dsDNA polymers may be very long and encompass millions of nucleotides in each strand. Complete polymers are called chromosomes. The nucleotides of one strand of a DNA chromosome form complementary base pairs with the nucleotides of the other strand, with adenosine residues paired with thymidine, and guanosine paired with cytidine.

Hereditary information passed on from one generation of a species to the next may include all of the genome of the organism (asexual reproduction) or a portion of the genome (sexual reproduction). The heredity of multicellular organisms also depends on the transmission of mitochondrial or chloroplast dsDNA from parent to offspring. The transmission of epigenetic imprinting from one individual to the next is also important.

Students should be able to define what a genome consists of, and how the information in the various genes and other sequence classes within each genome are used to store and express genetic information.
I believe that all introductory biochemistry & molecular biology courses should spend a considerable amount of time on the structure of nucleic acids. I would have added a number of other core concepts to the description. Of course students should know about complimentary base pairs but they should also know the structure of DNA and, especially, what holds the double stranded helix together. The fact that the strands run in opposite direction is essential for understanding DNA replication, repair, and recombination.

This is one of the few times where I support teaching a specific structure in some detail. The idea here is to prove that "information" is contained in well-understood chemical structures. (Cells obey the laws of physics and chemistry.) Students should know that there's nothing magical about biological information.

This is also one of the few times where I support teaching history. The history of the discovery of DNA as the carrier of heritable information is one of the best examples of how science works. Some history is important in teaching science as a way of knowing. Most educators agree that we should be teaching students about the nature of science.

I agree with teaching the concept that the genome contains heritable information but I would make sure to cover specific information other than genes for RNAs and proteins. Students should know about information for regulating gene expression and for things like origins of replication, telomeres, etc.

I would avoid using the word "encode" unless you are referring specifically to reading frames. I would explain that a genome is defined as one complete copy of the collection of large DNA molecules in a cell. It refers to the haploid DNA content. It is not technically correct to say that sexually reproducing species pass on only a "portion of the genome."

If teachers are going to talk about transmission of heritable information outside of the normal chromosomes, I would make sure to include plasmids along with mitochondria and chloroplasts. Otherwise, it look like a course that only covers eukaryotes. (I'm not sure this is a core concept.)

If students are really going to "be able to define what a genome consists of" then one can't avoid talking about the C-value paradox and junk DNA [Five Things You Should Know if You Want to Participate in the Junk DNA Debate]. I think the structure and size of genomes are important core concepts because they help focus student's attention on biological information and what part of the genome is essential.

"Epigenetic imprinting" is a fad. It is not an important core concept. It can be covered in upper-level courses [What is epigenetics?].
Information in the Gene: Nucleotide Sequence to Biological Function

The unit of genetic information in a nucleic acid that specifies some macromolecular product (protein or RNA) is called the gene. The information in a gene is converted into single-stranded RNA in a process called transcription. Those RNAs derived from protein-encoding genes (called "messenger RNA" or mRNA), are then "translated" by ribosomes into protein molecules. Proteins consist of linear sequences of amino acid residues whose order is determined by the sequence of mRNA nucleotides, utilizing a universal genetic code (minor exceptions to code universality are readily explained by evolutionary theory).

All known organisms–bacteria, archaean, or eukaryote–utilize the same pool of 20 "standard" amino acids for protein synthesis, the same genetic code to translate mRNAs and guide that synthesis, and the same set of four nucleotides to constitute genomic nucleic acids.

Students should be able to explain the central dogma of biology (the message in DNA is transcribed into RNA and translated into protein) and relate the commonality of the process to all of life.
This would be an excellent time to teach a very fundamental concept: "what is a gene?" [What Is a Gene? ] This is a fabulous topic for a student-centered learning approach. You can have students come up with their own definitions and then try and reach a consensus. There is no universal definition that works in all cases but by the time students arrive at that conclusion they will have learned a lot.

Students need to understand the basics of information flow from DNA to RNA and protein (Sequence Hypothesis). They should understand the difference between this information flow and the real meaning of the Central Dogma of Molecular Biology [Basic Concepts: The Central Dogma of Molecular Biology]. I hope there will be a time in the future when we don't need to teach this but, for now, we need to teach it because students will have misconceptions about the meaning of the Central Dogma. Tansey et al. share those misconceptions.

I don't know how much of the mechanisms of transcription and translation are basic concepts and how much is detail. I have a tendency to over-emphasize concepts in this part of the course.

The genetic code is important. You can't say that it's "universal" because that's not exactly true. Once you qualify that statement you are obliged to mention that there are exceptions. However, it wrong to say, as Tansey et al. (2013) do, that "minor exceptions to code universality are readily explained by evolutionary theory." I don't know what part of evolutionary theory they are referring to but I can't think of any easy explanation for the genetic code variants found in some species.

Furthermore, if you are going to mention the minor exceptions (variants) then surely you have to mention the codons for the three non-standard amino acids. Don't you?

Two important topics have been neglected. First, we need to teach the important concept that there are multiple types of functional RNAs. In addition to ribosomal RNA, tRNA, and mRNA, there are many smaller RNAs that are catalysts and regulatory molecules.

Second, I think we have to cover RNA processing and modification. The core concepts are that RNA can be post-transcriptionally processed by adding or removing nucleotides and by modifying existing nucleotides. (This includes splicing and the organization of many eukaryotic genes.)
Genome Transmission from One Generation to the Next

Passing a copy of the genome to a new cellular generation requires genome duplication, a process called replication. Each strand of the double-stranded DNA comprising a chromosome is used to direct the synthesis of a complementary strand, leading to the generation of two identical dsDNA products. One copy of the replicated genome is passed to the daughter cell when the cell divides.

Students should be able to illustrate how DNA is replicated and genes are transmitted from one generation to the next in multiple types of organisms including bacteria, eukaryotes, viruses, and retroviruses.
This sounds okay to me.

The important concepts are that DNA replication is semi-conservative, the two strands are never separated, synthesis of new DNA on both strands is coordinated by assembling a molecular machine at the replication fork, synthesis occurs in one direction only, the energy for synthesis is derived from the incoming nucleotide triphosphates, DNA replication begins at specific sites in the genome called origins, and the termination of synthesis at the ends of linear chromosomes presents a problem.
Genome Maintenance

Because genetic mutations can be quite deleterious to an organism and/or its progeny, there is a low biological tolerance for genomic alterations. For this reason, the nucleic acids in chromosomes are nearly unique in that they are the objects of elaborate and energy-intensive repair processes. Repair affords a high degree of genomic stability in most organisms, and limits the rate of evolutionary processes. In higher eukaryotes, including mammals, defects in DNA repair processes produce genomic instability and can lead to cancer.

Students should be able to state how the cell insures high fidelity DNA replication and identify instances where the cell employs mechanisms for damage repair.
The important concept here is that DNA replication is error-prone even though it is extremely accurate compared to transcription and protein synthesis. Students need to understand some, but not all, of the DNA repair mechanisms and their intrinsic error rates. They should be able to understand overall error rates in different species and the implications for understanding evolution.

The basic biochemistry of recombination is an essential concept.

Teachers should avoid using the term "higher eukaryotes" and any other descriptions of species using the words "higher" and "lower."

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]


The Lorax said...

I don't know what part of evolutionary theory they are referring to but I can't think of any easy explanation for the genetic code variants found in some species.

Not sure it qualifies as an easy explanation or is an aspect of evolutionary theory, but a fair amount of work has gone into studying the CTG Leu --> Ser variant found in Candida albicans (and related spp.), which provide some explanatory insights. Admittedly no definitive tests have been done, but the current evidence suggests that the variation can tolerate both Leu or Ser encoding in protein, albeit with phenotypic effects on the cell. (some recent refs)
Molecular reconstruction of a fungal genetic code alteration. Mateus DD, Paredes JA, Español Y, Ribas de Pouplana L, Moura GR, Santos MA. RNA Biol. 2013 Jun;10(6):969-80
Candida albicans CUG mistranslation is a mechanism to create cell surface variation.
Miranda I, Silva-Dias A, Rocha R, Teixeira-Santos R, Coelho C, Gonçalves T, Santos MA, Pina-Vaz C, Solis NV, Filler SG, Rodrigues AG. MBio. 2013 Aug 30;4(4)
Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Bezerra AR, Simões J, Lee W, Rung J, Weil T, Gut IG, Gut M, Bayés M, Rizzetto L, Cavalieri D, Giovannini G, Bozza S, Romani L, Kapushesky M, Moura GR, Santos MA. Proc Natl Acad Sci U S A. 2013 Jul 2;110(27):11079-84

Jonathan Badger said...

Also, I'm not sure if they really meant that the variants themselves could be easily explained -- I interpret more to be more saying that the fact that the variants are just minor modifications from the universal to be easily explained as cases of descent with modification. It isn't as if there any organisms where the code is completely different.

Jonathan Badger said...

"Epigenetic imprinting" is a fad
I don't like the way some people confuse it with evolution either, but it is kind of absurd to call it a fad. There are real phenotypic associations with imprinting such as obesity. Do you think the agouti mouse model is going to overturned or something?

Robert Byers said...

I don't agree evolution is in any way relevant to biochemistry knowledge.
One could get 100% in biochem in understanding and knowledge of what is here and now and NO NEED to memorize about its origins.
One is just learning how something before our eyes works, as far as they know, and how it got there is irrelevant to it. Its another subject.
then its all speculation and not very good at that.
In fact I suspect very few people need to know this stuff at all. i don't think the knowledge of it would make any difference to a doctor and so on.

Jem said...

"In fact I suspect very few people need to know this stuff at all. i don't think the knowledge of it would make any difference to a doctor and so on."

This is right, but also ridiculous. I'm sure you could function as a paralegal if you thought that the US Constitution had appeared magically in 1986, halfway through Reagan's second term. I'm sure you could come up with all sorts of rationalizations explaining away the evidence of amendments and references to it in the historical record.

But the creationist position is 'you have to teach in schools that it magically appeared in 1986', and your proposed 'compromise' is 'well, just avoid the subject of when it magically appeared'. How about, instead of that, we just ignore you because you're very stupid?

The Lorax said...

If I understand you correctly, I would argue that the variants are not easily explained by descent with modification as changing the code essentially changes every protein sequence simultaneously. In fact, I will argue that the fact the code isn't all over the place argues that it is extremely difficult to vary the code.

The Lorax said...


Tom Mueller said...

Larry – I was surprised to discover your definition

What is a gene?

A gene is a DNA sequence that is transcribed to produce a functional product.

Call me an old fashioned classicist – but I reckon if the mutation of some stretch of DNA results in a heritable change in phenotype (constitutive super-expression of the lac operon let’s say) than we are talking about a "gene".

In the Dark Ages when I first studied Genetics – genes were identified by zapping hapless organisms with mutagens or ionizing radiation and checking for observable mutations. That was pretty straight-forward and particularly rigorous - or at least it used to be.

To belabor the point - if we can discuss “enhancer genetics” – does that not imply that enhancers must ipso facto be “genes”?

In other words - non-transcribed sections of DNA can be genes: a case in point would be some categories of cis-acting regulatory genes as defined by their mutations.

How would Mark Ptashne respond - I wonder?

Piotr Gąsiorowski said...

But Jem, there are also Old Constitution Creationists who are prepared to accept that the US Constitution appeared much earlier, possibly even in the 1930s (if not the 1880s!), and that some of the amendments may have been added since. Its age is not the issue, as long as we agree that the earliest version appeared magically.

Tom Mueller said...

Is epigenetics overhyped?!

Absolutely YES!

Is epigenetics (when correctly understood) rendered trivial or unimportant? … nothing more than a “fad”?

Absolutely NO!

Epigenetics remains a subset of what Mark Ptashne deems self-perpetuating changes of gene regulation and development.

To cite Mark Ptashne:

For as long as I can remember, the word has been used to imply memory: A transient signal or event triggers a response that is then perpetuated in the absence of the original signal. I have mentioned IMPORTANT [emphasis mine] examples of such epigenetic effects…

Ptashne’s issue is not with the significance of epigenetics as an important biological phenomenon, but rather the confusion surrounding the entire notion, in particular the specious suggestion that nucleosome modification drives gene regulation and not the other way around!

To cite Mark Ptashne yet again: “…memory effects are important for development, and the question will arise as to how they are achieved.”

There arises yet a separate question: Does epigenetics play a significant role in evolution?

PZ Myers summed it more succinctly and eloquently than I could ever hope:

We say epigenetics is really important [emphasis mine] in development and in physiological adaptation -- it's good to know more about it, and is essential[emphasis mine] for understanding the state of the organism. But evolution? Meh. Acquiring the process of semi-permanently modifying the cell state is something that was a key innovation (OK, many innovations) in evolution, but it's been overhyped as an information transfer process on evolutionary timescales.

So I must respectfully disagree with Larry – somewhat that is. Yes current textbook sound-bite renditions of epigenetics are flawed and guilty of hubris. That said; epigenetics remains an important biological phenomenon that merits placement amoung the Core Concepts.

Back to Epigenetics vis a vis Evolution.

The Methylation status of CpG islands together with their peculiar propensity to mutation seems to me to represent an excellent candidate for Joe Felsenstein's "Canalization" and surprisingly rapid "Genetic Assimilation".

Ptashne deliberately ignored DNA Methylation: I ignore DNA methylation in the remainder of this article because its possible role in development remains unclear, and it does not exist in, for example, flies and worms—model organisms the study of which has taught us much of what we know about development.

OK – as a an epigenetic mechanism maybe DNA methylation remains important in some lineages (ours perhaps) and not in others.

The ubiquity of presumed “functional” CpG islands as upstream regulatory elements would also seem to indicate that they may play a significant role in evolution; yes, an information transfer process even on evolutionary timescales… maybe.

I can sympathize with those who feel that epigenetics still play an important (albeit diminished) role in evolution.

How to build a Neanderthal

Joe Felsenstein said...

Correction: not Joe Felsenstein's "Canalization" and "Genetic Assimilation" but Conrad Waddington's "Canalization" and "Genetic Assimilation".

Tom Mueller said...

Hi Joe - correction duely noted.

Fact remains - I still remain in your debt!

ITMT - I was wondering if the absence of methylation in flies and worms may reflect a derived peculiarity of ecdysozoan divergence from a more basal default setting common to lophotrophora and deuterostomes.

It would appear that such conjecture has merit - although it is not quite that simple.

I stumbled across this interesting review when searching for an answer

best regards,

Larry Moran said...

As you saw from my post on "What is a gene?", the issue is complicated and there's no universal definition that doesn't have exceptions.

But there are some definitions that don't seem to be very useful. One of them is to define as a "gene" any part of the genome that's functional. This would mean that origins of replication and telomeres are "genes," to use just two examples. It would also mean that including enhancers and regulatory sites in the definition of a gene would result in ill-defined genes with bits and pieces (e.g. enhancers) separated from the rest of the gene by large stretches of non-genic DNA.

It's better to think of enhancers as bits of DNA required for regulating the expression of a gene and not as part of the gene itself. But, some people disagree. That's why biology is so much more difficult than physics!

Tom Mueller said...

Hi Larry – I agree with you …That's why biology is so much more difficult than physics!

I thought you would like this article:
What is a gene, post-ENCODE? History and updated definition

Regarding your contention - …there's no universal definition that doesn't have exceptions.

I beg to differ.


My definition of a gene paraphrases of Morgan’s, Sturtevant’s and McClintock’s: “… if you can mutate and map it - it’s a gene!”

Why not!?

That would make “regulatory genes” a subset of “genes” - even when no transcript is produced.

Call me an old fashioned classicist – but I reckon when the mutation of some stretch of DNA that results in a heritable change in phenotype (constitutive super-expression of the lac operon let’s say) then we are talking about a "gene".

On the subject of BASIC concepts: How is it that some alleles are dominant and others recessive? What are the molecular mechanisms?

That question comes up every year in my class! BASIC stuff!

The answer: dominance can be cis-dominant or trans-dominant. I consider the concepts of cis and trans as basic and crucial.

Trans-dominant is easy to understand. For example, in the lac operon, constitutive expression of the lac genes as a result of faulty repressor protein (so-called i- mutants) could be masked by making partial diploids (with a plasmid) that encoded functional repressor protein.

A second class of constitutive expression of the lac genes expression could not be masked. These oc mutants mapped to a different stretch of genome and were shown to be cis-dominant; i.e. they represented regulatory DNA that controlled only their adjacent operon.

Two somewhat similar phenotypes – completely different genetics and map as different loci on in the genome!

We are talking G E N E T I C S ! ! !

Forgive me… I need to catch my breath. I just got carried away there for a minute. As you can see, I am quite passionate about the subject.

I say we all pay homage to the giants who first understood Genetisc in molecular terms and defer to their original definition.


Tom Mueller said...

@ Joe

This is where I start scratching my head:

The human version of the enhancer HACSN1 was discovered because of the remarkable difference between the human and chimp versions of the enhancer - 13 nucleotide differences in a stretch of 81 nucleotides (a far larger number of changes than would be expected had the mutations been the result of drift rather than positive selection).

Far more than when comparing comparing Chimpanzees to mice, rats, dogs or chickens,for example.

Positive selection clearly increased the prevalence of an adaptive trait

What would a population geneticist call HACSN1, if not a gene?

Larry Moran said...

I thought you would like this article:
What is a gene, post-ENCODE? History and updated definition

That's Mark Gerstein's paper from 2007. He wants to redefine the word gene because he thinks his group has discovered wonderful new things about the genome through ENCODE. I don't think anyone paid attention and that must have really pissed him off.

My definition of a gene paraphrases of Morgan’s, Sturtevant’s and McClintock’s: “… if you can mutate and map it - it’s a gene!”

No problem. You can use any definition you like as long as you spell it out in discussions and papers. In the classroom, you are obliged to teach other definitions and you MUST tell your students that very few scientists agree with the definition you use.

Larry Moran said...

Tom asks,

What would a population geneticist call HACSN1, if not a gene?

I can't speak for population geneticists but I call it an enhancer.

Tom Mueller said...


Larry - I strongly suspect that in a previous lifetime you were a Jesuit!


Tom Mueller said...

That was a compliment BTW...

Tom Mueller said...


Tom Mueller said...

Lets try this again without typos:

re: That's Mark Gerstein's paper from 2007. He wants to redefine the word gene because he thinks his group has discovered wonderful new things about the genome through ENCODE. I don't think anyone paid attention and that must have really pissed him off.

Larry - Thank you for the update... I misread the link and thought it was the current edition. I did get the author was a propagandist for ENCODE and I did not agree at all with his summation. Fora like this allow a hopelessly out-of-date HS teacher to stay current.

Thank you.

re: My definition of a gene paraphrases of Morgan’s, Sturtevant’s and McClintock’s: “… if you can mutate and map it - it’s a gene!”

LM No problem. You can use any definition you like as long as you spell it out in discussions and papers. In the classroom, you are obliged to teach other definitions and you MUST tell your students that very few scientists agree with the definition you use.

And yet again - thank you... will do. ITMT - how alone am I when employing such a classical definition of "gene"? Would silver-haired classical geneticists define "gene" like myself.

ITMT - I note that a minimum of google-whacking generates hits for "operator gene"

Would these represent vestiages of usage no longer current?

Tom Mueller said...

@ Larry

Re: Teachers should avoid using the term "higher eukaryotes" and any other descriptions of species using the words "higher" and "lower."

Advocatus diaboli on

I agree – somewhat… Yes, this is a very important distinction that must be stressed with our students. There is no distinction between MODERN organisms that are more primitive vs. more evolved. There is no such thing as a living fossil! Each MODERN organism is as MODERN as the next.

For example – modern coelacanths are just as modern as modern humans – neither is more primitive with respect to the other!

For an excellent article

Ditto Sharks

That said – some organisms can appear to be more “basal” vs “more derived”

How can we explain this to students such that they can better understand such subtleties?

Examine a vertebrate cladogram

Compared to Lampreys - Mammals may have acquired more bells and whistles (and often subsequently lost) that we (as mammals) find particularly interesting. Such thinking betrays a mammal-centric bias on our part. Modern Lampreys have also acquired (and often subsequently lost) many bells and whistles compared to their ancestors that from a Lamprey’s POV are even more interesting.

That all said – I maintain there is an intuitively apparent cogency to the notion that some modern species can still indirectly represent modern ambassadors of some more basal evolutionary stage, a stage that preceded more derived evolutionary stages (Darwin’s descent with accumulated modifications).

That is why cladograms are such powerful tools! Cladograms reveal probable relationships and degrees of relationships between groups of organisms, along with the relative times when different lines branched off (speciation occurred), showing common ancestry.

I like to explain it to my students this way – Let’s describe the Last Common Ancestor to Eumetazoa; it most likely had a dorsal nerve cord, indeterminate radial cleavage during embryogenesis and employed methylation as an important mechanism for gene regulation. Are Deuterostomes in fact “basal’ when compared to Ecydysozoa? From an insect’s POV, aren’t humans less derived? Wouldn’t insect high school students regard us in the same condescending light that human high school students regard jawless fish?

Now wouldn’t that be a nice rejoinder to toss a Creationists’ way? I will leave that up to you. I just wanted my students to avoid some common misconceptions inherent in misunderstanding cladograms.

See where I am going with this?

Advocatus diaboli off

Unknown said...

Well, the contention is with applying terms like "higher", "lower", "primitive" and the like to species or clades. There's no issue with using these terms for character states, meaning pretty much the same thing as "retains the plesiomorphic state" or "is apomorphic", provided you are adressing an audience that has a firm enough grounding in phylogenetics to get that. It's not useful to think of insects as less derrived than humans or the reverse, because of course any clade has apomorphies. But it is useful to think in terms of character states that remain plesiomorphic.

If you want to retain the mind-blowing aspect, tell your students that humans are a transitional form between insects and starfish. Echinoderms have a couple of apomorphies that arose after their common ancestor with insects and humans being closer related to them allows us to divide up the apomorphies into those that arose prior to the human-starfish split and those that arose later. By providing information about the sequence in which the apomorphies evolved, humans fulfil the criteria for being transitional.

Piotr Gąsiorowski said...

We are also transitional (in this broad sense) between earthworms and blackbirds, and between dandelions and bumblebees, and generally between any X and Y if we are more closely related to Y than to X.

Unknown said...

Yup. How would you define it in a more narrow way? Being a transitional form basically means to be informative about the sequence of character evolution. The reason it's emphasized in some cases is that we don't know this sequence in a lot of cases and thus a newly discovered species can provide new insight.

Piotr Gąsiorowski said...

I did not mean to criticise you definition or reduce it ad absurdum. It's OK as far as I'm concerned.

Just helping Tom to blow his students' minds.

Tom Mueller said...

Hi Piotr – Hi Simon

I thank both of you.

On the subject of
common misconceptions regarding evolution in general and cladograms in particular

Misconception #1: Higher and Lower
Misconception #7: Different Lineage Ages for Modern Species
Misconception #8: Backwards Time Axes
Misconception #10: Change Only at Nodes

… seems to be particular problematic.

I wanted to adopt an approach that made my students understand that deuterostomes (including humans) were basal to eumetazoa but not “primitive or lower” no differently than jawless fish can be considered basal but not "primitive or lower" to vertebrates.

The mind-boggling notion that Insects would occupy the apex of any putative Scala Naturae is of course an amusing hook to grab students’ attention and pique their imagination.

Let others take that battle to Creationists...

dziękuję! ;-)

Tom Mueller said...

Simon - I am in the process of constructing a wroksheet where my students are provided a quick and easy molecular cladogram employing echinoderms and chordates are are clearly basal when compared to Ecydysozoa and Lophotrochopra.

The problem is finding a suitable outgroup!!!! It would appear that Porifera could be derived from more ancestral versions of Ctenophores.

That suggestion I find mind-boggling

Unknown said...

Well, both Porifera and Ctenophora would make a decent outgroup. If you include both you of course run into the question of which of them is closer related to the Bilateria. A paraphyletic Ctenophora doesn't seem to be supported by anything really. There's the recent paper by Ryan et al. suggesting that Ctenophora are the sister group to all other metazoans, but the Comb Jellies are monophyletic according to their analysis.

Tom Mueller said...

Hi Simon

I am not so sure... Ryan’s diagram has Ctenophora root Porifera, Placozoa, Cnidaria and Bilateria.

“If ctenophores evolved before sponges, the sponges probably lost some of their ancestors’ complexity. It’s also possible that sponges have a complexity that has yet to be defined.”

In other words, Porifera are closer to Bilateria than Ctenophora!

Some taxonomists had already argued that Cnidarians are descendants of ancient bilateral coelomates and not the other way around. Biologists have known since the 1920s that Cnideria had a directive axis which gave them right and left-hand sides. Volker Schmidt went on to argue that non-radially organized hydrozoan larvae have an anterior concentration of sensory and ganglionic nerve elements, suggesting that a fundamental genetic toolkit for the establishment of bilateral and polarized anatomies was already present before the Cnidaria-Bilateria divergence. He went so far as to suggest that diploblastic status of adult Cniderians is derived and that true mesoderm can be even be detected during Cniderian embryogenesis. That last argument is particularly contentious.

In any case, I always regarded adult Cnidaria as having Bilateral synmetry... well actually two perpendicualr axes of bilateral synmetry

I am not even completely convinced that Choanoflagelates are a reliable outgroup to Porifera!

Allow me to cire Allow me to quote PZ Myers:

“While complete, recognizable homologs of important signaling genes like hedgehog and Notch are not found, fragments of them are found scattered about.”

Boy does this echo and perhaps parallel Ryan's placement of Ctenophora as sister ot Porifera along with Eumetazoa.

In other words, so-called “outgroups” cannot be presumed but rather need to be deduced. False presumptions about outgroups can really mess up data analysis

John Harshman said...

What exactly do you mean by "basal" here?

Unknown said...

"Porifera are closer to Bilateria than Ctenophora!"

Yup, if the results hold, that's true. But that does not imply that "Porifera could be derived from more ancestral versions of Ctenophores.", it just implies that
(Ctenophora (Porifera,Bilateria)) holds, rather than (Porifera(Ctenophora, Bilateria)).
If sponges were derived Ctenophores, then Ctenophora would be paraphyletic with regard to the Porifera. There's a lot of evidence that Crustacea is praraphylietic with regard to Hexapoda (i.e. the Pancrustacea hypothesis) and that says that insects are derived crustaceans. That's quite different from the results Ryan et al. got for the metazoa.

"Some taxonomists had already argued that Cnidarians are descendants of ancient bilateral coelomates and not the other way around."

Make that precise. Is that an argument about character evolution, or about phylogeny? Do they argue that Bilateria is paraphyletic? Is anybody supporting "the other way around"? That seems to say that Cnidaria is paraphyletic with regard to the Bilateria. Misconception #5 might be at work here.

"False presumptions about outgroups can really mess up data analysis"

Outgroups don't do an awful lot. They root the tree, but your unrooted tree still carries most of the phylogenetic information. And in general you pick your outgroups based on existing larger scale phylogenies (one of the reasons we won't get a rooted tree for the domains). Unless you think Bilateria is paraphyletic, either Ctenophora or Porifera or Placophora or Cnidaria are outgroups you could use.

John Harshman said...

Porifera, at least, is probably paraphyletic. Last I saw there were three different clades of sponges, none of them sister to any of the others.

Unknown said...

But in these phylogenies Ctenophora aren't the sister clade of all other metazoans. In the Ryan et al. paper Porifera is recovered as monophyletic. It's likely that it'll take some more time until there's a consensus about the relationships among metazoan clades and it wouldn't surprise me if one or more of them were paraphyletic.

Tom Mueller said...

Hi John

I reckon characters or traits are considered “derived” if they are absent in a “basal group”, but present in presumed "later" groups because these traits emerged later on along the cladogram as it were.

I understand “basal group” to be some version of a modern ambassador representing the last common ancestor of the group. The clade jawless fish would be basal to mammals. That is not to say that modern jawless fish are identical to the last common ancestor of jawless fish and mammals.

Along these lines, the last common ancestor to Eumetazoa could have had a dorsal nerve cord, indeterminate radial cleavage during embryogenesis and employed DNA-methylation as an important mechanism for gene regulation.

Alternatively, the last common ancestor to Eumetazoa could have had a ventral nerve cord, determinate spiral cleavage during embryogenesis and avoid DNA-methylation as an important mechanism for gene regulation.

In other words, perhaps Protostomes were basal and Deuterostomes derived… or alternatively the reverse. I prefer the reverse not out of obstinacy but because I accumulated much evidence to support Deuterostomy as basal and Protostomy as derived.

Frankly, I find the whole notion of paraphyletic vs polyphyletic distracting and try to avoid those terms as much as I can.

Tom Mueller said...

I get the distinct impression we are not all employing vocabularly the same way...

...can we please avoid the use of paraphyletic/polyphyletic?

Either Ctenophora root Porifera, Placozoa, Cnidaria and Bilateria or they don't. That seems to be the question here.


Tom Mueller said...

@ Simon

I remind you that I am an aging high school teacher out of his depth. Your answer really confused me!

But that does not imply that "Porifera could be derived from more ancestral versions of Ctenophores.", it just implies that
(Ctenophora (Porifera,Bilateria)) holds, rather than (Porifera(Ctenophora, Bilateria)).


If (Ctenophora (Porifera,Bilateria)) holds

Then indeed "Porifera [would] be derived from more ancestral versions of Ctenophores.

The key word here is "ancestral" implying that modern Ctenophores could be a lot more complicated than the last common ancestor that gave rise to both modern Ctenophores and modern Porifera.

Just the same - this data seems to imply that Porifera must have lost a lot of complexity along the way - or possess much more complexity than is apparent - or some combination of both alternatives.

Please tell me I got that right.

I fear I may be confused yet again.

Unknown said...

I'm not sure we can avoid them, when we are discussing phylogenetics. The only type of question we really ask in phylogenetics is: Is this group of organisms monophyletic? And the possible answers boil down to "Yes", "No, it's paraphyletic" and "No, it's polyphyletic".

We can go through a list of claims in this vein the Ryan et al paper makes:
Porifera: Monophyletic
Ctenophora: Monophyletic
Bilateria: Monophyletic
Acrosomata: Polyphyletic
Epithelozoa: Paraphyletic
Coelenterata: Paraphyletic
Parahoxozoa: Monophyletic

And so on.

Unknown said...

"The key word here is "ancestral" implying that modern Ctenophores could be a lot more complicated than the last common ancestor that gave rise to both modern Ctenophores and modern Porifera."

Well, Sponges and Ctenophores go back to a common ancestor. That's trivially true for any two taxa. I assumed your statement to actually make a substantive claim, which in this case would be that this common ancestor was a Ctenophore. Since a principle of phylogenetic systematics is that if an ancestor of some species was a member of a clade, then that species is as well, this would imply that Porifera is a subclade of the the Ctenophora and thus the Ctenophora excluding Porifera is paraphyletic.

And yes, of course the phylogeny of Ryan et al. substantially changes how character evolution would have occured - though it's not clear whether this means reduction in sponges (possibly multiple times) or parallel evolution.

John Harshman said...


I think that's confused. Modern species can't represent the last common ancestor of a group, and jawless fish aren't a clade. I think you are conflating characters and taxa. Taxa are, or are supposed to be, clades. Characters may or may to diagnose clades.

Now, I think you're using "basal" to mean "primitive", which I would consider poor usage. Characters (or character states) may be primitive, but it's unclear what it would mean to say that a taxon is primitive. Perhaps that all or most of its characters are? But that would be highly subjective and would depend on which characters we wanted to pay attention to.

Now if you want to talk about characters we do have ways of inferring which states are primitive and which derived using a phylogenetic tree, most simply through parsimony: we infer the ancestral state that requires the fewest transformations over the tree. But two taxa aren't enough, as in your conundrum regarding the primitive position of a nerve cord in Eumetazoa. That would also be true regarding the characters of Ctenophora in Ryan's tree. Characters shared by Ctenophora and the out group would reasonably be considered primitive for Metazoa, as would characters shared by other metazoans and the out group. But we have no way to determine whether characters not shared by either group with the outgroup are primitive. So your speculation that the metazoan common ancestor resembled a ctenophore is problematic.

Incidentally, "basal" is a problematic term in general. It suffers from the problem you exemplify here. It's usually used to refer to the less diverse of two sister taxa with the implication that that less diverse taxon is somehow primitive and representative of the ancestor. But such assumptions are unwarranted and can't be justified in the general case.