We have a winner!

The winner of the mnemonic contest for the geological table, is the poem inspired by Lord of the Rings.... We had over 100 votes. Congratulations - and 5 extra credit points go to the winner!


Cruel Mordor, perilous place
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quest too crucial, jeopardous task,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Persistently pursuing Mount
[Permian, Pennsylvanian, Missisippian]
Doom, Sauron’s orcs challenge.
[Devonian, Silurian, Ordovician, Cambrian]

Sex, drugs, and macroevolution

I've been meaning to try this for a while, but finally pulled it off this year. The idea is to have students in my Macroevolution course invent a mnemonic to remember the geological table. This was not my original idea, rather SJ Gould wrote in his book Wonderful Life that he did the same thing in a class at Harvard. Gould presented his favorite of all time, which was a poetic review of a pornographic movie called Cheap Meat:

Cheap Meat performs passably, [Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quenching the celibate’s jejune thirst, [Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Portraiture, presented massably, [Permian, Pennsylvanian, Missisippian]
Drowning sorrow, oneness cursed [Devonian, Silurian, Ordovician, Cambrian]


I told the class I'd give extra credit to the mnemonic voted as the favorite. There are 160 students, so the TAs and I have selected a few of our favorites to be nominated for the voting. We were looking for creativity, humor, and grammatical and logical wording. So here are a few to choose from. Please vote by April 25 to decide the winner!


Perhaps not too surprisingly, especially given that these students are mostly ~21 year-old undergrads, and given that the example given to them was a review of a porno, many of the mnemonics were sexual in nature. Two were just plain X-rated - I indirectly told the students in lecture about these, but I decided it may not be appropriate to present them in their full glory a public lecture. Instead, I will paste them below - if you are not over 18, if you are easily offended, or if fellatio is illegal in your state, read no further!!

Call my penis pappa
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Quit talking crazy just
[Quaternary, Tertiary, Cretaceous, Jurassic]
Tongue pappa please
[Triassic, Permian, Pennsylvanian]
Make daddy shoot out come
[Missisippian , Devonian, Silurian, Ordovician, Cambrian]

Your favorite? Then vote for "pappa"


X-Rated number 2:
Come over sexy damsel, my pocket pride tolerates juicy candy ticklers quite prevalently.
[Cambrian, Ordovician, Silurian, Devonian, Mississippian, Pennsylvanian, Permian, Triassic, Jurassic, Cretaceous, Tertiary, Quaternary, “Periods”]
Your favorite? Then vote for "pocket pride"


X-Rated number 3:
Penises, Constantly Quiver Through, Muscle Contractions, Just The, Pleasant Peripheral Pleasure Most Drunken Students Obtain Casually
[Phanerozoic,
Cenozoic Quaternary Tertiary,
Mesozoic, Cretaceous, Jurassic, Triassic,
Paleozoic, Permian, Pennslyvanian, Mississippian, Devonian, Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "casual pleasure"


Here is an X-rated pair from one young lady:
1) College Male Pricks Pick
Quick-Tongued Chicks, Jumbo Tits,
Porn Portraying Massive Dicks, Sex, Orgasms, Clits

2) College Makes Promiscuity Permissible:
Quick, Take Chances! Just Try…
Produce Passionate Memories: Davis, Storke Orgasms Call!
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
[Permian, Pennsylvanian, Mississippian, Devonian, Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "college males"


Here's an R-Rated trio of mnemonics by one author - perhaps borderline NC-17, depending on how violent the "dutifully stimulating mastication" gets. Number One is a nicely worded political statement and Number Three the NC-17 device. All three follow the same order for the periods and eras of the Phanerozoic:

1. Present circumstances merit precaution quick thinking can justify. The problematic president’s mal-action does seem oddly classified.

2. Pleasingly cunning my Penelope queen Took care, justly, to preserve; preventing malicious dudes Stealing Odysseus’ crown.

3. People copulate making progeny. Quiet touching can joyfully turn pleasing palpation. Mastication dutifully stimulates - overcoming common-sense.
Your favorite? Then vote for "triple threat"



While we're on the theme of political statements, here is a passionate plea for world peace:
Can men practice peace?
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]
Question the chaos, justify truth,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Pacify people’s malice,
[Permian, Pennsylvanian, Missisippian]
Discontinue struggle, operation ceasefire
[Devonian, Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "world peace"


And a little more on politics - nice rhythm, nice rhyme:
Clinton’s Quivering Tricks,
McCains Charlatan Jingoist Tics,
Poles Predicting Pennsylvania
Do Sense Obama's Campaignia
Your favorite? Then vote for "Obama"



A brief plea for a pants-off dance off:
Pants Can Obstruct Sex
[Paleozoic, Cambrian, Ordovician, Silurian]
Do Make Pantless Party
[Devonian, Mississippian, Pennsylvanian, Permian]
Your favorite? Then vote for "dance off"


More on dancing:
Quality Tequila Caused Jessica To Playfully Perform Many Dances Standing On Chairs
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian, Mississippian, Devonian, Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "tequila"


I announced this as one of my early-submitted personal favorites in class, a mildly sexual, perfectly sensical mnemonic for the seven periods of the paleozoic:
“Cocktails on second dates make people promiscuous”
[Cambrian, Ordovician, Silurian, Devonian, Mississippian, Pennsylvanian, Permian]
Your favorite? Then vote for "second dates"


It was not only sex, but drugs also, that dominated the mnemonical themes. Here's word from a discriminating smoker:
Cruddy Marijuana Producers Provoke Quarrels That Continually Join The Pissed Purchasers,Depleting Student's Obsessive Cravings.
Your favorite? Then vote for "crud"


And finally, some of my favorite miscellaneous devices:


Here's a dialog on the anti-evolution debate:
Can monkeys produce people? Questions timelessly clashing justly together People perpetually meditating Does science overrule creationism?
Your favorite? Then vote for "science rules!"


Even though I am a fairly rabid Green Bay Packers fan, having grown up in Wisconsin (a Brett Favre statue stands on my office shelf right next to my Charles Darwin bobble-head), I like this NFL mnemonic, with only a few extra - mostly minor - words, by an obvious Chargers fan:

Charger Quarterback Throws,
[Cenozoic, Quaternary, Tertiary]
Catches &, Jumps, Touchdown for More Points.
[Cretaceous, Jurassic, Triassic, Mesozoic, Paleozoic]
Packed Crowd, Delighted,
[Permian, Carboniferous, Devonian]
San diego Offense Conquers.
[Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "Go Chargers!"

A frustrated student of quantum mechanics:
Quantum theory creates jumbles that permeate pensive minds, destroying semblances [of] order completely.
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic, Permian, Pennsylvanian, Mississippian, Devonian, Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "Quantum Theory"


An exuberant ad:
Close Out Sale! Don’t Miss Practical Prices!

(Cambrian, Ordovician, Silurian, Devonian, Mississippian, Pennsylvanian, Permian)
Totes, Jackets, Clothes!
(Triassic, Jurassic, Cretaceous)
Top Quality!
(Tertiary, Quaternary)
Your favorite? Then vote for "Close out sale"

A couple of literary mnemonics:
Ode to Fawkes the Phoenix (Dumbledore’s pet from Harry Potter)

Crying marks phoenix’s palingenesis.
(Cenozoic, Mesozoic, Paleozoic, Proterozoic)
Quills turn crimson jubilantly,
(Quaternary, Tertiary, Cretaceous, Jurassic)
Time passes, phoenix majestically develops
(Triassic, Permian, Pennsylvanian, Missisippian, Devonian)
Sacred opulent coat.
(Silurian, Ordovician, Cambrian)
Your favorite? Then vote for "Fawkes"

and Lord of the Rings:

Cruel Mordor, perilous place
[Cenozoic, Mesozoic, Paleozoic, Proterozoic]

Quest too crucial, jeopardous task,
[Quaternary, Tertiary, Cretaceous, Jurassic, Triassic]
Persistently pursuing Mount
[Permian, Pennsylvanian, Missisippian]
Doom, Sauron’s orcs challenge.
[Devonian, Silurian, Ordovician, Cambrian]
Your favorite? Then vote for "Tolkein"


But after all is said and done, I think this one gets my own personal vote:
Certain Old Sedimentary Deposits Move Pure Paleontologists To Jaunty Celebration
[Cambrian, Ordovician, Silurian, Devonian, Mississippian, Pennsylvanian, Permian, Triassic, Jurassic, Cretaceous]
Your favorite? Then vote for "Pure Paleo"

Darwin - Thought of it all

I just was reading parts of Origin of Species again for an encyclopedia entry that I am writing. As usual, it's abundantly clear that Charles Darwin was thinking clearly, in this case about tree thinking versus linear thinking. In Chapter 6 (Difficulties on Theory), he clearly distinguishes linear thinking and tree thinking.

"In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition."

Today, we have statistical methods that we use for making inferences about lineal ancestors, which depend on the phylogenetic relationships among the collateral descendants. But, as I've written in other posts, people often confuse collateral descendants with the actual lineal ancestors.

Textbook linear evolution

I presented my ideas on the limitations of linear evolution, versus tree thinking, in a presentation to a Department of Ecology and Evolution, and got an interesting comment. A colleague challenged my statement that the "morphological series" of eyes (at the time I presented a specific figure from Salvini-Plawen and Mayr on gastropod eyes, which will be the subject of a future post) was presented as a model of evolution. The commenter was actually was a colleague of Mayr at the time, and the commenter stated that Mayr and people at that time weren't thinking of this as a model for how evolution actually proceeded.

Well I am very grateful for this comment, because others may be thinking the same thing - that the linear series of eyes are not meant to represent a model of evolution per se. In fact, I believe this may be true, at least for the time when it was authored. However, as I will explain below, people do currently use eye series as models for how eyes actually did evolve.

So, why do I believe that there initially could have been different intent? Well, all these morphological series do is to test an ancillary assumption of the hypothesis that natural selection drove the origin of complex eyes. If natural selection did and could drive eye evolution, an ancillary assumption is that a series of intermediate steps exists between a simple and complex eye. This was Darwin's strategy in Origin - to point out support for this ancillary assumption by highlighting eyes of living animals at many different levels of complexity. Salvini-Plawen and Mayr refined Darwin's idea by providing such series in closely related groups of animals. True, a test of an ancillary assumption of natural selection may not have been intended as a model of how evolution actually proceeded. Incidentally, another ancillary assumption that natural selection produced complex eyes is that there was enough time for the process to work. Nilsson and Pelger tested this with a morphological model, and several calculations, but that is a topic for another post. Perhaps, Salvini-Plawen and Mayr were not equating the eyes of living animal eyes with ancestral states of extinct animal eyes (although this is not uncommon). Certainly testing an ancillary assumption is good science, but it also may not represent the proposal of an actual model.
Nevertheless, these morphological series are now taken as models of how evolution actually proceeded. For example, I just came across such a series in the textbook I use for my Macroevolution course. The text is Ridley's Evolution, 3rd Edition. Note that the caption begins, "Stages in the evolution of the eye".

At this point, I need to re-iterate, there is value to these series, in testing an ancillary assumption. But it could be dangerous to equate the eyes of living species, with those of species in a progessive series of evolution, from simple to complex eye. Furthermore, these series ignore the origins of variation. For example, the caption states "An eye is protected by adding a transparent cover of skin and part of the cellular fluid has differentiated into a lens." How does an eye add a transparent cover? Where does the variation come from? How does fluid differentiate into a lens?

Studying natural selection at the level of morphology alone is silent on these points, because it assumes variation is abundant, and that variation is then left to be anonymous. But exciting times are upon us, because we are know beginning to uncover the molecular basis for phenotypic changes. There is no designer - it is all mutation and natural selection - but by looking at the molecules, we can gain a new level of detail in our understanding of how complex traits evolve.

For one example, where we've gone beyond a morphological series, see a previous post of mine on the evolutionary origin of a cephalopod lens....

Linear Thinking in Ostracod Eye Evolution

People often ask me how I came to study something as obscure as ostracod crustaceans. The answer is a funny story.

The spring/summer before moving to Duke University to start working for my PhD, I was thinking about what I would do for my thesis. At that time, I was already interested in testing comparative methods aimed at estimating what extinct species might have been like, the methods are called "ancestral state reconstruction". Well, one part of the project was to work on a phylogeny of viruses that was evolved in the lab. The actual ancestors were preserved in the refrigerator, so I could estimate these ancestors using the existing methodologies.

In addition to the virus study, I wanted to do a similar exercise with a group of organisms that have a good fossil record, and compare estimated ancestors to the fossil record. So, I wrote my advisor-to-be, to ask if he could recommend a group with a good fossil record. The email came back with the title "Ostrocads are it!!". Cliff had accidentally inverted the o and the a in "ostracods".

Once I figured out what is an ostrocad, the first paper I came across was by Andrew Parker, who would later help me in many ways by email, as well as in person when I collected ostracods in Australia. Here is a news story about us, with a photo taken near Sydney.

Andrew's paper was entitled "Discovery of functional iridescence and its coevolution with eyes in the phylogeny of Ostracoda (Crustacea)". In it, he suggested "The myodocopid lateral eye probably evolved at a similar point in time as iridescence, possibly to detect iridescence. The graduations by which the ostracod compound eye has developed are suggested. These findings challenge current theories which demand a single evolution of the compound eye."

These provocative statements would lead to the bulk of my dissertation, which tested Andrew's ideas using molecular phylogenetics and ancestral state reconstruction.

The "graduations" Andrew suggests are illustrated in his figure 5. His caption begins "Possible means of derivation of the myodocopid compound eye."



This is a perfect example of linear thinking, versus tree thinking. Laid out are 3 living species of myodocopid ostracods; all from the same family. These are used to represent a linear, graduated series from a simple eye in Azygocypridina, to a complex compound eye in Macrocypridina.

The deep history of genes and irresponsible reviews

For reasons I won't go into, I was looking up an old review of a paper of mine, that is now published (after originally being rejected a few times). I don't know if I have bad luck, or bad technique, but most of my papers are rejected several times before they are published. I do believe strongly that I've gotten my share of incompetent and irresponsible reviews. One example of an incompetent review is quite relevant, and related to other posts.

In the manuscript in question, I reported finding multiple opsin visual pigment genes in ostracod crustaceans. I concluded that these genes were the result of gene duplications. The reviewer, who admitted not being a molecular biologist, took issue with concluding that multiple genes were due to gene duplication, writing:

"...while humans indeed have 3 opsin genes, it is not certain that they all arose from duplication - the rod, blue, and red/green lines have been separate for millennia, and it is possible that some have entered the genome by other mechanisms."

When I get reviews back, I often take notes (meant only for myself), such that I summarize the reviewers comments, and can understand and remember them later more easily. In response to this reviewer's comments, I wrote:

"True, aliens just MIGHT have come down and put opsins in our genome. Short of that ALL GENES ARISE BY DUPLICATION!!! (He did say he was not a molecular biologist)."


As I wrote on a previous post the dogma among evolutionists now is that most genes originate by duplication. My reviewer had a pre-1950's view of gene evolution. He failed to understand, as Ingram had done as early as 1961, that genes likely have a long history, and a deep common ancestry. The reviewer has failed to come to grips with the common ancestry of genes. Just as pre-Darwinian biologists believed that each species was created independently, my incompetent reviewer, and pre-Ingramian biologists believed that genes may be independently created. I wonder how many other people fail to understand the deep common ancestry of genes.

I wonder how many people fail to grasp the deep common ancestry of all biological entities, united by a deep history, diverging through new combinations, and through specialization of duplicated entities.

Questions about evolution

I just had a student ask me some questions about evolution. Since I spent a little time on this, I thought I would post it here, in case someone else might find it useful. I left the student as anonymous.


STUDENT:

Hi professor Oakley, I had your Macroevolution course last year, and am now in Ken Kosik's Neurobiology course this quarter. We've been talking a good deal about the evolution of the nervous system, and I had a few questions I figured you would be most qualified to answer.

Professor Kosik brought up your research on the genes conserved from sponge to human that, in humans, are important in the formation of eyes. I remember you mentioned this during Macro, too, and that, despite being used by Creationists as evidence for Creation, it is, in fact, further evidence for evolution.

OAKLEY
Well, the bottom line is that creationism is not science, it is a faith. My own philosophy is that faith and science are completely separate, "non-overlapping magisteria". One can have faith in a creator and also accept the scientific facts of evolution; I know several people who fit this precise description. (I personally am agnostic, I don't care if there is some sort of creator or not, I don't see any reason why it should matter to my life).

Creationism is simply not a science, it does not present testable hypotheses, because one can always say "that is how the designer made it". I prefer to use the term "anti-evolutionists" to describe people who twist logic to call into question the scientific facts of evolution. My goal is to distinguish the magisteria - divine creation is not impossible, but it is unscientific.

See this article for what I mean by non-overlapping magisteria, in SJ Gould's words:
http://www.stephenjaygould.org/library/gould_noma.html


In contrast to creationism, science presents hypotheses. One hypothesis of evolution is global common ancestry, the hypothesis that all life is derived from a single common ancestor. This hypothesis is supported when we find highly non-random similarities among organisms - like a nearly universal genetic code, for example. We could find scientific facts that contradict universal common ancestry, such as a non-DNA form of life - therefore it is a testable hypothesis.

There are many other testable hypotheses in evolutionary biology, such as "natural selection is a primary mechanism driving evolutionary change". We talked in macroevolution about how people test for the requirements of natural selection (variation, super-fecundity, heritability, and differential survival due to or correlated with the heritable trait). We also talked about inferring selection on genes using neutral theory as a null model.

STUDENT

Why is this? Also, where can I find your paper on this topic online?

OAKLEY
Here is a good blog about our eye research:
http://www.tuibguy.com/?p=209

Here is the paper:
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001054

and a news story that was in many newspapers:
http://www.mcclatchydc.com/staff/robert_boyd/story/21106.html



Regarding the synapse research, that Ken probably talked about in your class, here is a news article:
http://blog.newsweek.com/blogs/labnotes/archive/2007/06/06/irreducible-complexity-is-reducible-afterall.aspx

Here is the original paper for that:
http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0000506


STUDENT:

We covered the topic of "exaptation" in Neuro and this, too, makes me wonder about evolution. If we don't know the original purpose of a gene that eventually helped us make an eye, who's to say that it ever had a purpose?

OAKLEY:
We can make inferences about the functions of genes using phylogeny and comparative biology. If two genes share the same function, then likely their ancestral gene had the same function. There are statistical models for working out more complicated cases, too.

So, in the case of our eye research, we do have a good idea of the previous function. Eyes use phototransduction, which is a GPCR-based transduction pathway. We can see by inferring the history of genes used in eyes, that they are closely related to other GPCR pathways. GPCR pathways very generally transmit signalls from outside cells to inside cells, and "tell" that cell to do something. In the case of vision, a gene (called opsin) evolved light sensitivity. But opsin is related to other GPCR genes that transmit signals, but not light signals. In this way, we can see that light perception evolved from other signaling genes.


STUDENT:

It seems like assuming that the gene DID once have a purpose implies evolution - isn't this a circular argument?

OAKLEY:
In the case of opsin visual pigment genes, we can infer that the ancestral gene did have a function.

STUDENT:
I'm not sure I've worded this incredibly clearly, but I'm sure you get a lot of questions like this, so you probably have a good feeling for the problems people tend to have with evolution. Evolution, since taking your course, has pretty much become the entire basis on which I understand biology, but in these cases I'm not so sure it makes sense.

OAKLEY:
Your thoughts on the centrality of evolution are shared by some great scientists (I didn't know he was Russian Orthodox Christian, supporting my point above): Theo. Dobzhanski