Friday, April 11, 2008

As I see it: the idiot's guide to the history of animal classification

Chapter 1: Classification is a universal human attirbute. There seem to often be two categories.

Traditional Micronesians seem to classify living things into two groups: Animals and Plants. But remember how german classifies the noun "maedchen" (maiden) as neutral, taking the neutral article "das"? Chuukese does something like that with counting classifiers. English uses counting classifiers trivially; but other languages incorporate explicit syntactic rules for applying them. In Chuukese, the classifier is obligatory (or WAS, because younger speakers don't learn their more sophisticated aspects).

The classifier for a long skinny item is "foch". Like a stick of gum, efoch gum = one stick on gum. ruefoch gum = two sticks of gum.

The classifier for an animal is "men". Emen pik = one pig; emen mwan = one man. Ruemen pik = two pigs, etc. But interestingly, for the octopus, ew kuus = one octopus, it is not given the classifier for animals!

And then, here's a stranger one still, I think: a saw or a knife IS given the classifier "men": Emen ngerenger = one saw.

Chapter 2: Early thinkers also posited two higher categories.

More to come

Friday, March 7, 2008

Monitoring / Red Flags / E. Coli

Beginning from where? My Biology classes have been studying Mitosis. A bit out of sequence, but I stumbled upon several excellent Mitosis videos that clarified the air. Also included were two videos that cleared up confusion about Protein expression. With a self-congratulatory smile, I listened to students, again and again, saying "Now I get it." Just three hours collecting together Google Videos: time well worth wasting.

Along the way, the second day, students were finishing their seatwork on the stages/snapshots of mitosis. I also showed 2 time lapse videos of bacterial fission. One of them concluded that in 48 hours of unbridled division at 20 minute intervals, the progeny of one E. coli would have a mass 4 times that of the Earth.

May I digress?

What is E. coli? Escherichia coli is a symbiont in the human gut:

Escherichia coli (pronounced /ˌɛʃɪˈrɪkiə ˈkoʊlaɪ/) (E. coli), is a bacterium that is commonly found in the lower intestine of warm-blooded animals. Most E. coli strains are harmless, but some, such as serotype O157:H7, can cause serious food poisoning in humans, and are occasionally responsible for costly product recalls. The harmless strains are part of the normal flora of the gut, and can benefit their hosts by producing vitamin K2, or by preventing the establishment of pathogenic bacteria within the intestine.

E. coli are not always confined to the intestine, and their ability to survive for brief periods outside the body makes them an ideal indicator organism to test environmental samples for fecal contamination.

The DEQ posts on line Beach Reports. Red Flags refer to the beaches listed in these reports. Red Flags are also posted in the local newspapers. A separate web page explains the beach monitoring program.

Monday, February 25, 2008

Chicken to the Egg / Egg to the Chicken

Starting from a basic coral reef life cycle, an odyssey.

Why is it relevant to study coral life cycles on Saipan?

  1. Corals are cool
  2. Corals live here: we would have no such island without corals
  3. Coral development parallels development across the gamut of animals
  4. We can allude to various points in the life cycle where corals are susceptible to human activities
    1. Fertilization (chicken first point of view), due to varoius causes
    2. Settlement
    3. Adult life
  5. Leads to animal embryology
  6. Specificity is a ubiquitous theme

Sunday, September 2, 2007

What is a Species?

Starting from a "Biological" definition of species, one soon is convinced that the species idea in itself is flawed. Here I have collected some links and excerpts on this topic. Notes for a digression on species and speciation. These are frequent topics for classroom digressions.

I found an article on line. For the criminally insane price of US$55.87 I could get a copy of this from the cartel at

Márquez L.M.; Van Oppen M.J.H.; Willis B.L.1; Reyes A.2; Miller D.J.2. 2002. The highly cross-fertile coral species, Acropora hyacinthus and Acropora cytherea, constitute statistically distinguishable lineages. Molecular Ecology, Volume 11, Number 8, August 2002 , pp. 1339-1349(11).
Here are some other links:

From Wikipedia article, Definitions of "Species"

Definitions of species

The question of how best to define "species" is one that has occupied biologists for centuries, and the debate itself has become known as the species problem. One definition that is widely used is that a species is a group of actually or potentially interbreeding populations that are reproductively isolated from other such groups.

The definition of a species given above is derived from the behavioral biologist Ernst Mayr, and is somewhat idealistic . Since it assumes sexual reproduction, it leaves the term undefined for a large class of organisms that reproduce asexually. Biologists frequently do not know whether two morphologically similar groups of organisms are "potentially" capable of interbreeding. Further, there is considerable variation in the degree to which hybridization may succeed under natural and experimental conditions, or even in the degree to which some organisms use sexual reproduction between individuals to breed. Consequently, several lines of thought in the definition of species exist:

Typological species
A group of organisms in which individuals are members of the species if they sufficiently conform to certain fixed properties. The clusters of variations or phenotypes within specimens (i.e. longer and shorter tails) would differentiate the species. This method was used as a "classical" method of determining species, such as with Linnaeus early in evolutionary theory. However, we now know that different phenotypes do not always constitute different species (e.g.: a 4-winged Drosophila born to a 2-winged mother is not a different species). Species named in this manner are called morphospecies.
Morphological species
A population or group of populations that differs morphologically from other populations. For example, we can distinguish between a chicken and a duck because they have different shaped bills and the duck has webbed feet. Species have been defined in this way since well before the beginning of recorded history. This species concept is much criticised because more recent genetic data reveal that genetically distinct populations may look very similar and, contrarily, large morphological differences sometimes exist between very closely-related populations. Nonetheless, most species known have been described solely from morphology.
Biological / Isolation species
A set of actually or potentially interbreeding populations. This is generally a useful formulation for scientists working with living examples of the higher taxa like mammals, fish, and birds, but meaningless for organisms that do not reproduce sexually. It does not distinguish between the theoretical possibility of interbreeding and the actual likelihood of gene flow between populations and is thus impractical in instances of allopatric (geographically isolated) populations. The results of breeding experiments done in artificial conditions may or may not reflect what would happen if the same organisms encountered each other in the wild, making it difficult to gauge whether or not the results of such experiments are meaningful in reference to natural populations.
Biological / reproductive species
Two organisms that are able to reproduce naturally to produce fertile offspring. Organisms that can reproduce to almost always make infertile hybrids, such as a mule or hinny, are not considered to be the same species.
Mate-recognition species
A group of organisms that are known to recognize one another as potential mates. Like the isolation species concept above, it applies only to organisms that reproduce sexually. Unlike the isolation species concept, it focuses specifically on pre-mating reproductive isolation.
Phylogenetic (Cladistic)/ Evolutionary / Darwinian species[verification needed]
A group of organisms that shares an ancestor; a lineage that maintains its integrity with respect to other lineages through both time and space. At some point in the progress of such a group, members may diverge from one another: when such a divergence becomes sufficiently clear, the two populations are regarded as separate species. Subspecies as such are not recognized under this approach; either a population is a phylogenetic species or it is not taxonomically distinguishable.
Ecological species
A set of organisms adapted to a particular set of resources, called a niche, in the environment. According to this concept, populations form the discrete phenetic clusters that we recognize as species because the ecological and evolutionary processes controlling how resources are divided up tend to produce those clusters
Genetic species
based on similarity of DNA of individuals or populations. Techniques to compare similarity of DNA include DNA-DNA hybridization, and genetic fingerprinting (or DNA barcoding).
Phenetic species
based on phenotypes
Recognition species
based on behavioral interactions
Species that reproduce without meiosis or fertilization so that each generation is genetically identical to the previous generation. See also apomixis.
Cohesion species
Most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms. This is an expansion of the mate-recognition species concept to allow for post-mating isolation mechanisms; no matter whether populations can hybridize successfully, they are still distinct cohesion species if the amount of hybridization is insufficient to completely mix their respective gene pools.
Evolutionarily Significant Unit (ESU)
An evolutionarily significant unit is a population of organisms that is considered distinct for purposes of conservation. Often referred to as a species or a wildlife species, an ESU also has several possible definitions, which coincide with definitions of species.

In practice, these definitions often coincide, and the differences between them are more a matter of emphasis than of outright contradiction. Nevertheless, no species concept yet proposed is entirely objective, or can be applied in all cases without resorting to judgement. Given the complexity of life, some have argued that such an objective definition is in all likelihood impossible, and biologists should settle for the most practical definition. For most vertebrates, this is the biological species concept (BSC), and to a lesser extent (or for different purposes) the phylogenetic species concept (PSC). Many BSC subspecies are considered species under the PSC; the difference between the BSC and the PSC can be summed up insofar as that the BSC defines a species as a consequence of manifest evolutionary history, while the PSC defines a species as a consequence of manifest evolutionary potential. Thus, a PSC species is "made" as soon as an evolutionary lineage has started to separate, while a BSC species starts to exist only when the lineage separation is complete.

Another article from Wikipedia covers the species problem. A historical review of the idea of the "species" is interesting. The idea of reproductive isolation is paramount.

Quotations on the species problem

"... I was much struck how entirely vague and arbitrary is the distinction between species and varieties" Darwin 1859 (p. 48)[7]

"No term is more difficult to define than "species," and on no point are zoologists more divided than as to what should be understood by this word". Nicholson (1872) p. 20[44]

"Of late, the futility of attempts to find a universally valid criterion for distinguishing species has come to be fairly generally, if reluctantly, recognized" Dobzhansky (1937) p.310 [11]

"The concept of a species is a concession to our linguistic habits and neurological mechanisms" Haldane (1956) [35]

"The species problem is the long-standing failure of biologists to agree on how we should identify species and how we should define the word 'species'." Hey (2001) [39]

"First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require-but cannot be settled by-empirical evidence." Pigliucci (2003) [38]

Reproductive Isolation (Wikipedia):

Reproductive isolation

Adapted from Wikipedia, the free encyclopedia

(wikipedia also has an article on Speciation.

An important concept in evolutionary biology, reproductive isolation is a category of mechanisms that prevent two or more populations from exchanging genes. The separation of the gene pools of populations, under some conditions, can lead to the genesis of distinct species. Reproductive isolation can occur either by preventing fertilization, or by the creation of a degenerate or sterile hybrid, such as the case with the common mule and the hinny.

Three sections:

... Everything from a physical barrier (such as an ocean) formed between two populations, to ethological (behavioral) differences, to errors in cell division that cause incompatibility between populations.

  1. Speciation by reproductive isolation is frequently seen in plants, with errors in division during mitosis doubling the number of chromosomes and thereby preventing even pairing of chromosomes with normal gametes during fertilization.
  2. For various species that bloom seasonally, the time of gamete release can prevent hybridization, a temporal isolation.
  3. For animal species, mating might be stymied.
    1. Incompatible genitalia forms a mechanical reproductive isolation,
    2. members of opposite sexes often fail to recognize one another, due to some morphological difference used to identify a potential mate.
  4. The gametes of different species are frequently incompatible, and do not form a viable zygote.
    1. Sperm may not possess the proper enzymes for penetrating the coat of the ovum, or
    2. have the proper chemical markers to signal the egg cell to accept it.

  • The first is gametic: the gametes successfully combine, but then immediately die .
  • The second is zygotic: the zygote forms but quickly dies.
  • The third is embryonic or larval: which is spontaneous abortion of the hybrid fetus.
  • The fourth is hybrid inviability: the offspring is born but is unfit, quickly succumbs to environmental pressures, and dies.
  • The fifth is hybrid sterility: the offspring can produce no offspring of its own, isolating its genes from both parental groups. Finally, hybrids that do produce offspring can, potentially, produce sterile progeny.

Genes move around on chromosomes, rendering the chromosomes incompatible.

Friday, August 31, 2007

Digression 1: Vestigial structures

One commonly cited evidence for evolution is vestigial structures. Commonly cited vestigial structures are the pegs of snakes, remnants of ancestral legs; wings of flightless birds; and the human appendix.

On Saipan was discovered in about 1995 a blind cave spider. Cave divers have come through Micronesia collecting cave fauna, including blind cave shrimps. We had been studying an evolution video---The Evidence for Evolution---and I needed to explain vestigial structures, one of the evidences for evolution.

An article in Wikipedia about vestigiality.

A burning question is how a vestigial structure loses its functional morphology. Blind cave-dwelling organisms, for example, have eyes, but they are mere suggestions of the functioning eyes of their close allies. How does that happen? What pressures result in this diminution of an organ?

Darwin made some compelling arguments in On the Origin of Species, cited in the Wikipedia article noted above.

Examples of vestigial structures.

Here is a link to a Top Ten Useless Limbs and other vestigial organs, including the nipples of the human male.

The leg bones of a whale.
(found at

Human Vestigial Structures -->
(found at

A blind lobster was mentioned in the fascinating book Within the Deep found on Project Gutenberg: More recently is found a Wikipedia home page for a newly discovered deep sea hairy lobster, Kiwa hirsuta. The picture at left was found on that page.

"The animal has strongly reduced eyes that lack pigment, and is thought to be blind."

A vestigial gene: (from

"Vestigial structures may also be molecular, as in the case of vestigial genes that exist in most species. For example, although humans cannot manufacture their own vitamin C, most other mammals can because they possess a gene enabling them to produce an enzyme (L-gulono-gamma-lactone oxidase) which in turn makes it possible for them to produce vitamin C. Humans possess a defective copy of this gene that does not produce the required enzyme (or any other product). This gene was presumably disabled by mutation at a time in primate evolution when its loss was not a significant disadvantage, and now remains as a vestigial genetic sequence."