Santayana, yadda, yadda... This afternoon I'm going to write about Andrew Hamilton and Quentin Wheeler's "Taxonomy and Why History of Science Matters for Science: A Case Study", which derives lessons from the history of numerical taxonomy (phenetics) for the future of DNA bar-coding. I wasn't aware of phenetics, which seems to have been a mid-century attempt to measure living things and then group them without recourse to any overarching theory. This has intriguing parallels to the mathematics of the Bourbaki collective that I won't go into (and don't actually know much about), but I just wanted to throw that out there. The big point here is that the phenetics movement precipitously collapsed after its haphazard data-collecting failed to produce a believable taxonomy, and the authors argue that the same could happen to DNA bar-coding, which uses DNA arrangements to draw relationships between different organisms.

The first point I'd like to address is the use of the lesson from history. In my first post in this series, I discussed the use of history by filmmakers. Here I'm more reminded of the constant use of history in politics, which is notoriously dicey in its deployment of analogies with past events. Here in America we're being subjected to fairly sophisticated historical analyses on a daily basis as the Presidential campaign goes forward. Inevitably, we learn why the strategies being deployed are similar to Reagan vs. Carter in 1980 or Nixon vs. Kennedy in 1960, and so on... I think, as with filmmakers using history, this is both inevitable and healthy, but there's a difference. Here we're not dealing with a flow of ideas and methods over time, but with isolated lessons. It's like studying past Super Bowls or games of chess to provide a palette or menu of possible strategies.

So, I guess this is fair, but what's really going on is the use of history as an illustration of concept. Hamilton and Wheeler are a little apologetic that this isn't really history in a proper sense. The use of historical examples to make arguments about what might or might not constitute valuable work in the present is a tad Whiggish, I suppose, but I have no real qualms about it, since the phenetics example is from a similar enough scientific culture to the present to make the analogy worthwhile. What strikes me is the redundancy of the whole exercise. Isn't it valid from a philosophical or conceptual standpoint just to say, "your data is meaningless because it exists in an intellectual vaccum"? Saying "you're a lot like those phenetics guys, and we all know what happened to them" just seems like belaboring the point.

There are actually more interesting, and possibly more fundamental historical analogies to draw upon here outside the realm of biology. There's a classic debate in economics surrounding a 1947 paper by Tjalling Koopmans called "Measurement without Theory" that could just as easily be used (and which contains a little historical lesson-drawing of its own!).* Actually, that's even a more interesting case, because the theory in question was some pretty abstract stuff. On the other hand, Francis Bacon advocated gathering all kinds of specimens and histories and then playing around with them to see what principles emerged. And that's valid, too.

In the case of DNA bar coding, there are extenuating factors involved that Hamilton and Wheeler are glad to present, but don't really take into account. First is the question of robustness. They point out that DNA bar coding may be useful in cases where species such as bacteria are morphologically ambiguous, but question whether it should be used to make taxonomical statements in areas where the terrain is better known. This, even though the bar coding proponents openly say that their claims are provisional and subject to correspondence with other forms of evidence that are more firmly grounded in evolutionary theory.  (The article left the impression that bar coding advocates suggested that bar coding should be a definitive or sole method, but I'd like to see more before seeing the bar coders as advocating that point of view).

The main sticking point seems to be that there are a lot of species out there that aren't taxonomized (right word?), and that DNA bar coding could aid in the effort to do so. So the question is whether it's better to have an automatically-generated but theoretically-unstable taxonomy or none at all. So long as the means of the organisms' classification remains known, and the method is thought to be fairly reliable (which seems possible or even likely), I don't see the problem, so long as the value of the exercise is deemed worthwhile measured against the expected reliability of the technique and the expense involved.

Hamilton and Wheeler, though, I think are less concerned that the cost-benefit analysis here is inadequate (which is what they claim), and more that the status of the taxonomy created by DNA bar coding will be lost and taken as fact or as giving us information the procedure is not designed to provide, which gets into arguments about scientism. I've always thought concerns about scientism in the history of science have been way overcooked, because the "asserted fact" often seems to be equated with "existence of published text" even though there are loads of sociological means of signaling the status of claims as speculative, likely, certain, etc..., by which, crucially, the bar coders seem committed to abiding. All in all, I call foul on this history lesson. Reading the evidence they themselves present, the authors have not adequately convinced me that we are doomed to repeat history.

*Philip Mirowski has epistemologically linked Bourbaki with Koopmans in his book Machine Dreams, so all this is actually sort of tied together. I'm not going to go into this here (it's incredibly complex); suffice it to say Mirowski loathes both Koopmans and Bourbaki.

The Ferocious Antlion Larva

Antlions live mainly in sandy, warm, arid habitats.  They begin life as eggs, which turn into larvae.  These larvae dig pit traps in the sand.  They bury themselves just under the sand at the bottom of the pit.  When ants, or other arthropods, fall into the pit, they aggressively attack and drag them under the sand to eat them.  This scintillating way of hunting gives the larva the name antlion. 

The larva then go into the pupal stage, where the larva will cocoon themselves in mucus-like saliva and bury themselves.  During this dormant stage, they turn into their adult form.  They will shed their larval skin and grow into a much larger, thinner exoskeleton.  Their winged form is often called antlion lacewings.  In the pupal and adult stage, the antlion will not eat.  Thus, their adult stage is short.  It will only mate and then usually die.  Thus ends and restarts the short yet interesting life of the Myrmeleontidae.

Folksonomies are a very widespread concept today and also a few big magazines have understood their revolutionary approach and value.

What I’m asking to myself is: “Since a year ago, which evolution has emerged? Which new ideas are people working on to improve and empower social distributed classification?”

Before explaining which new features I’m thinking of, I would like to explain why do we need an evolution of tags at all.

I love tags. I really love, as an user, having a way to add a simple powerful metadata layer to my data without having to adopt a centralized hierarchical schema proposed by someone else.

But tags, as we now experience them, don’t satisfy me! They are messy and their widespread adoption is making them also more messy.

Take a look to popular tags’ page on Del.icio.us. How far is this from a hierarchical structure or a nice faceted strategy? Maybe too much. Too much because it’s not easy to extract a mental model out of this stuff and if you cannot use your tags, they will soon loose their power.

Yes we could add an arbitrary structure and semantic to create a better and more powerful UI over these tag clouds, but the rule #1 about folksonomies is: “leave your users free“. Your users act on a personal basis but the aggregation of their mental associations is like a live organism. The structure emerges bottom up by an implicit, quite magical, consensus.

Are you sure that is not possibile to have a better browsing interface without imposing an arbitrary (so limited, restricting, not scalable, biased…) structure?

I’m not sure so I’m here to propose a different more powerful yet not restricting approach.

Continues @ infospace.it

The first step was to search for similar conservation projects on graveyards and their system of cataloging.

Here are some of the resources used:

http://www.gravestonephotos.com/ - from this site I got the table with the codes to specify the relation among those buried in the same gravesite , and other label names to describe a person's details.

http://www.oldcem.bc.ca/ - this site offers a template for those who wish to record graves. The main information I got from it regards the grave itself, such as the material with which was made, its shape, its direction in relation to the church, etc. You can download the recordsheet (pdf file) from the site.

http://connections.smsd.org/csi/Tombs.htm - tomb types

http://www.tngenweb.org/darkside/typology.html - markers

http://www.heritagememorials.com.au/pg_letstyle.php - lettering styles

http://cjstones.com/inscriptions.htm - font types

While building the coding standards I also had to get to know Flickr a bit better, particularly in regards on how it stores additiona information, such as photo's s description and tags.

Useful things to know about Flickr

Flickr offers three main ways to insert content in regards to a photo, its title, its description and its tags.

title - capture the essential information.

description - as detailed as possible.

tags - connect to other objects which are similar to the current one by some particular feature, both within the collection and between the Flickr's community. The tags cannot be more than 75, so which tags to put need to carfully considered.

Flickr also allows to assign the photo to a geographical position.

Flickr allows to create sets. Unfortunately, only the pro account (which has an annual fee) allows for unlimited set, otherwise the user can create a miximum of 3 sets.

Since we want to keep the project at zero cost, we will not make use of this functionality, but decide on an alternative way to organise the photos.

Tags format

label: value

this gets displayed as two separate consecutive tags

i.e.

material:

sandstone

Thus allowing both values to be searchable (Flickr displays the : but discards it when it looks for photos with the same tag), human readable (as by reading the list of tags top-down you get the label followed by its value) and machine readable (it is easy to write code that separates the list into couples according to the : and thus retrieve the different attributes).

However, a discussion of this approach with a friend, highlighted that this way of tagging was still difficult to grasp for those who were not already familiar with the objects described as it is not clear that the label is related to the following value. Plus, sometimes Flickr messes up the order and so you can find a label followed by a different value etc.

Thus, because of the need to keep the label and value together, while at the same time have the possibility to search for photos from other users related to mine, I adopted machine tags (namespace:label=value) for my own descriptions, leaving other users the possibility to Add tags to my photos.

The adopted system

Deciding on content was particularly complex, since it appears to be no standard for the cataloging of gravesites.

There are however guidelines and tips used by different groups, mostly charities, working in the preservation of cemeteries. Thus we thought of integrating them together in one consistent system.
TAGS

To add a machine tag on Flickr, click (as for the other tags) on the Add a tag link, then follow this format:

namespace:label=value

The namespace is churchyardtraveller. If the value is more than one word, you need to put it in "". Flickr will recognize automatically that the new tag is a machine tag and add to your tags a link to show the list of machine tags.

Here are some examples to show correct syntax:

churchyardtraveller:tomb=family(2)

churchyardtraveller:tomb=table

churchyardtraveller:materials=wood

churchyardtraveller:inscription-font="Classic Roman italic"

churchyardtraveller:inscription-style="cut and black painted"

churchyardtraveller:inscription-case="lower case"

churchyardtraveller:mason="Busby&Co., Cumbria"

churchyardtraveller:person(a)="chuYoung George (1822 - 1878)"

TITLE

for a single person:

Surname Initial. (year birth - year death), Church, Place, REGION CODE, COUNTRY CODE "initial inscription..."

i.e. Young G. (1822 - 1878 ), St Margaret, Rottingdean, SXE, ENG "Since thou couldst..."

for 2 people:

Surname Initial. (year birth - year death)/ Surname Initial. (year birth - year death) [relation] , Church, Place, REGION CODE, COUNTRY CODE "initial inscription..."

i.e. Young G. (1822 - 1878 ) / Young M. (1822 - 1873) [wife], St Margaret, Rottingdean, SXE, ENG "Since thou couldst..."

for more than 2 people:

Surname Initial. (year birth - year death) et. al. , Church, Place, REGION CODE, COUNTRY CODE "initial inscription..."

Young G. (1822 - 1878 ) et. al., St Margaret, Rottingdean, SXE, ENG "Since thou couldst..."

DESCRIPTION

"the inscription or part of it, each line separated by / "

It refers to:
in case there are more people buried, but the inscription does not refer to them all

Other information:

...here you copy and paste the info from the tags and add any additional notes...

Think about something as simple as a pair of headphones: where do they belong in the following hierarchy?

Audio Products

• CD Players
• MP3 Players
• Home Theater
• Speakers
• Stereo Receivers
• Accessories

First of all they are an audio product, so from a purely taxonomic standpoint they could exist as a direct child of audio. However if there is one thing we know from endless hours of user testing, its that people love accessory categories and anytime you ask them to find a product that is small in size they will immediately gravitate to accessories.

Ok, so what if we put them under audio, and then, under audio accessories. Great, but people often look for products in categories which they feel are related in more abstract ways. For example, it is not uncommon for users to say things like:

"I Iisten to my MP3 player with headphones so I would look there"

Now imagine other branches of the taxonomy such as Computers or Video Game Consoles. There are lots of headphones made specifically to work with these types of products. Do we place headphones there as well?

I am sure you are starting to get the idea, headphones are becoming ubiquitous in our taxonomy, but is that a problem?

There is no real hard and fast rule or best practice around polyhierarchy. It is an important part of the taxonomists’ toolbox and an essential feature of navigational taxonomies. However in our quest to accommodate a wide variety of users and achieve maximum findability, it can easily be overused.

One of the biggest dangers of overused polyhiearchy is that the principles that govern the framework of the taxonomy become diluted. This can result in the placement of products in categories based on overly abstract associations, and can lead to a whole slew of governance problems as the taxonomy evolves.

Another problem with polyhierarchy has to do with its implementation on websites. In some e-commerce applications of content management, polyhierarchy is achieved through a single master location of a given product that gets linked to from other locations in the taxonomy. This can lead to some very disjointed navigational experiences, especially when the polyhiearchical treatment involves multiple branches of the taxonomy.

For example if the master location of headphones is as a child of Audio, then the following pathway could be possible

Computers > Computer Accessories > Headphones

(select and be directed to a new breadcrumb trail)

Audio > Headphones

All of a sudden the user finds himself in an entirely different branch of the taxonomy. This can be a jarring experience that detracts from the learnability of the taxonomy structure.

The next question then is: does the average user really care? I would argue that most users are more concerned with finding products than the purity of the navigational pathway involved. They can always resort to the ever present “back” button.

That being said, the best way to determine where polyhiearchy should be used is with user testing. Products that are candidates for polyhierachy should be tested with a broad spectrum of users. Analyzing their chosen access points into the taxonomy will give you a clearer idea which associations warrant polyhiearchy and which ones do not.

As a general rule we tend to err on the side of too much polyhiearchy, even though our taxonomist spines may shiver at the thought of some navigational pathways. At the end of the day our goal is to help people find what they are looking for. If that means including headphones in computer accessories… so be it.

]]> http://danbarringer.wordpress.com/?p=38 Mon, 21 Jul 2008 04:46:47 +0000 dbarringer http://danbarringer.wordpress.com/?p=38 July 12, 2008

Dr Kerry Swanson

Department of Geological Sciences

University of Canterbury

from: http://probelog.com/span/

The use of forms from SEM imaging is prolific in today’s architectural schools and in cutting edge built structures. Dr Swanson’s seminar on his work using SEM and taxonomy emphasizes to me that these images are not just pretty forms to be copied into large scale architectural structures. Through taxonomy; the capturing, identifying and study of microscopic forms enlightens us of a whole new world. With only 2/3 of all species categorized, our knowledge of what is possible can still grow. This is not to find forms not yet conceived, but to understand how these forms work: the movement of a spider’s knee, the cutting barbs of a sand fly, the formation of a spider’s web.  The now possible three dimensional images with the understanding of why these shapes exist, can lead to meaningful architecture.

The Three Domains

The organisms living on Earth today are broadly divided into three large domains: Bacteria, Archaea and Eukarya (Protista, Plants, Fungi and Animals). Our understanding of the relationship between the three domains is undergoing big changes right now. The old divisions have been based on morphological and biochemical differences, but recent genetic data are forcing us to rethink and revise the way we think about the three Domains.

It was thought before that Bacteria arose first, that Archaea evolved from a branch off of bacterial line, while the first Eukarya (protists) evolved through the process of endosymbiosis: small bacteria and archaea finding permanent homes within the cell of larger bacteria and forming organelles. It was thought that bacteria were always simple, that Archaea are somewhet more complex, and that Eukarya are the most complex.

Neither Bacteria nor Archaea possess any organelles or subcellular compartments. The chemistry of cell walls is strikingly different between the two groups. The genes of Archaea, like Eukaryia, have introns. Until recently, it was thought that bacterial genes have no introns, however remnants of bacterial introns have been recently discovered, suggesting that Bacteria used to have introns in the past but have secondarily lost them - becoming simpler over the 3.6 billions of evolution. The enzymes involved in transcription of DNA in Archaea are much more similar to the equivalent enzymes in Eukarya than those in Bacteria.

Molecular data, as well as what we know from evolutionary theory how population size affects the strength of natural selection, a new picture has emerged. The earliest Bacteria were simple, hugging the Left Wall of Complexity. While their population sizes were still small, Bacteria evolved greater and greater complexity, leaving the left wall somewhat, evolving more complex genomes, more complex mechanisms of DNA transcription (including introns), and perhaps even some organelles. Likewise, the Archaea split off of Bacteria (or perhaps they even appeared first) and evolved much greater complexity in parallel with the Bacteria. Eukarya also split off of Bacterial tree early on and evolved its own complexity. Thus there were three groups simultaneously evolving greater and greater complexity.

Then, Bacteria and Archaea grew up in population sizes. Instead of small pockets somewhere in the ocean, now bacteria and archaea occupied every spot on Earth in huge numbers. Large population size makes natural selection very strong. Greater complexity is not fit, thus it is selected against. Thus, the originally complex bacteria and archaea became simpler over time - they turned into lean, mean evolving machines that we see today - the dominant life forms on our planet throughout its history. They lost introns, they lost organelles, and lost many complicated enzymatic pathways, each species reducing its genome and strongly specializing for one particular niche.

On the other hand, Eukarya did not grow in numbers as much. The population sizes remained small, thus the selection against complexity was relaxed - the eukaryotes were free to evolve away from the Left Wall. They increased in complexity, engulfing other microorganisms that later became mitochondria and chloroplasts.

Thus, though we, for egocentric reasons, like to think of greater complexity as being better than being simple, the Big Story of the evolution of life on Earth is that of simplification. Natural selection harshly eliminated organisms that experimented with greater complexity - the Eukarya being the exception: an evolutionary accident that happened due to their existence in small, isolated populations in which selection against complexity is relaxed.

Bacteria

Bacteria are small, single-celled organisms with no internal structures or organelles. Bacteria may have cell walls on the surface of their cell membranes, and may have evolved cilia or flagella for locomotion. The DNA is usually organized in a single circular chromosome. Some bacteria congregate into collonies or chains, while in other species each cell lives on its own.

In the laboratory, bacteria can be easily separated into two major groups by the way their cell walls get stained by a particular stain into Gram positive (purple stain) and Gram negative (red stain) bacteria. By shape, bacteria are divided into cocci (spherical cells), bacilli (rod-like shapes) and spirilli (thread-like or worm-like cells).

Bacteria are capable of sensing their environment and responding to it - i.e., they are capable of exhibiting behavior. Bacteria are also capable of communicating with each other - for instance, they can sense how many of them are present in a particular place and they can all change their behavior once the poulation size reaches a sertain treshold - this kind of sensing is called quorum sensing.

Many bacteria are serious pathogens of plants and animals (including humans). Others are important decomposers of dead plants and animals, thus playing important roles in the ecology of the planet. Yet others are symbionts - living in mutualistic relationships with other organisms, e.g., with plants and animals.

The inside of out digestive tract provides a home for numerous microorganisms. The best way to think about out "intestinal flora" is in terms of an ecosystem. We acquire it at the moment of birth and build it up with the bacteria we get from the environment - mostly from our parents. The bacterial populations in the intestine go through stages of building an ecosystem, similarly to the secondary succession. If, due to disease or due to use of potent antibiotics, the balance of the ecosystem is disrupted, it may recover through phases akin to primary succession.

Experiments with completely internally sterile animals (mostly pigs and rabbits) demonstrated that we rely on our intestinal bacteria for some of our normal functions, e.g., digestion of some food components, including vitamins. In many ways, after millions of years of evolution, our internal bacteria have become an essential part of who we are, and there is now a push for sequencing the complete genome of our becterial flora and to include that information in the Human Genome. The composition of the bacterial ecosystem in out guts can affect the way we respond to disease, or even if we are going to get fat or not, thus there is much recent research on individual variation of the intestinal flora between human individuals, so-called "poo print" (yes, scientists do have a sense of humor).

Archaea

Archaea may have been the first life forms on the Earth. Today, they tend to occupy niches that no other organisms can. Thus, they are found living inside the rocks miles under the surface, they are found in extremely cold and extremely hot environments, in very salty, very acidic and very alkaline envrionments as well. The hot water of the Old Faithful geiser in Yellowstone national park are inhabited by a species of Archaea. They are difficult to study as they die in normal conditions in the laboratory - room temperature, neutral pH etc.

Deinococcus radiodurans is one famous Archean. It thrives inside nuclear reactors. Of course, our reactors are a very recent innovations, so the scientists were puzzled for a long time as to what natural environment selected these organisms to be able to survive in such a harsh environment. It turns out that dehydration (drying-out) has the same effects on the DNA as does radioactivity - fragmenting and tearing-up of pieces of the DNA molecule. Deinococcus evolved especially fast and accurate mechanisms for DNA repair. Bioengineering projects are underway to genetically engineer these Archaea in such a way that they can be used to clean up radioactive spills and digest nuclear waste.

Though some Archaea have been found to live inside our bodies, not a single one has, so far, been indentified as a pathogen. Only very recently (i.e., last few weeks) has it been shown that one archaean does have an effect on our health - not as a pathogen but as an enabler. It can migrate into roots of our teeth and set up colonies there. It then changes the environment in the tooth in such a way that it becomes conducive to the immigration and reproduction of a pathogenic bacterium than can then attack the tooth.

Protista

Protists are an artificial group of organisms - every eukaryote that cannot be classified as a plant, a fungus or an animal is placed in this category. Thus, the number of species of protists is very large and the diversity of shapes, sizes and types of metabolism is enormous.

Some protists are microscopic unicellular organisms, like the Silver Slipper (Paramecium), while others are multicellular and quite large (e.g, sea kelp). Some protists, e.g., cellular slime molds, have a single-celled and a multi-celled phase of their life-cycle.

Even some of the unicellular protists can be quite large - an Acetabularia ('mermaid's wineglass', see picture) cell is about 5 cm long, thus perfectly visible to the human eye. Most protists reproduce regularly by asexual processes, e.g., fission or budding, utilizing sexual reproduction (e.g., conjugation, which is gene-swapping) only in times of stress. Some protists are surrounded only by a plasma membrane, while some others form shells of silica (glass) around themselves. Some protists have flagella or cilia, while some others move by pseudopodia (false legs - ameboid movement).

Traditionally, protists have been artificially subdivided into three basic groups according to their metabolism: protists capable of photosynthesis (autotrophs) are called Algae, heterotrophs are called Protozoa, while the absorbers are Fungus-like protists. According to morphology, protists have been divided into about 15 phyla, grouped into six major groups. New molecular techniques are thoroughly changing the taxonomy and systematics of Protista. One group, the Green Algae, has recently been moved out of Protista and into the Kingdom Plantae. Another group, the Choanoflaggelata, has been moved to the Kingdom Animalia as they are most closely related to sponges.

Some protists are parasites that cause human diseases. Most well-known of those are Plasmodium (malaria), various species of Trypanosoma (sleeping sickness, leischmaniasis and Chagas Disease) and Giardia (Hiker's Diarrhea). Dinoflagellates live on the surface of the ocean and are almost as important for absorption of CO2 and production of O2 as are forests on land.

Plants

Plants are terrestrial, multicellular organisms capable of photosynthesis (though some species have secondarily moved back into the aquatic environment or lost the ability to photosynthetize). There are about 300,000 species of plants on Earth today. They are divided into two broad categories: non-vascular and vascular plants. Mosses, liverworths and some other smaller groups are non-vascular plants. All other plants are vascular, meaning that they possess systems of tubes and canals that are used to transports water and nutrients from root to stem and leaves, and from leaves back to the root. Those tubes and canals are called phloem and xylem.

Of the vascular plants, some reproduce by forming spores, while others produce seed. Seedless vascular plants that produce spores are, among others, ferns and horsetails. Seeds are produced by two large groups: Gymnosperms (e.g., conifers) and Angiosperms (flowering plants).

An important evolutionary trend in plants was a gradual reduction of the haploid portion of the life-cycle (gametophyte) and simultaneous rise to dominance of the diploid portion - the sporophyte. In mosses, for instance, almost all of the plant is haploid, except for the diploid spores developing at the very tip of the stem. In flowering plants, e.g., trees, almost all of the plant's cells are diploid (just like in us), while the flowers contain male and female gametes (pollen and egg).

Fungi

Fungi can be unicellular (e.g., some yeasts and molds) or multicellular (e.g, mushrooms). Molecular data show that fungi are more closely related to animals than plants. Fungi are heterotrophs that obtain nutrients from the soil by secreting enzymes into the substrate and absorbing the digested materials. They cannot photosynthetize. Fungi are composed of hyphae, which are thin long filaments. A mass of hyphae is called the mycelium which can build large structures like mushrooms. Spores are the means of reproduction and are formed by sexual or asexual processes.

Fungi tend to enter into symbiotic relationships with other organisms. Some of those relationships are parasitic, as in our own fungal diseases. Other relationships are mutualistic, e.g., lychens, mycorrhizae and endophytes. Lichens are a mutualistic association between a fungus and a photosynthesizer, usually a green algae. Mycorrhizae form mutualistic associations between the fungi and plant roots (e.g., alfalfa). Endophytes are plants that have fungi living inside them in intercellular spaces and may provide protection against herbivores by producing toxins.

Animals

Animals are multicellular heterotrophs (they do not photosynthetize). They exhibit embryonic development and mostly reproduce sexually. One of the important characteristics of animals is movement. While microorganisms (bacteria, archaea and small protists) can move, large organisms (large protists, plants and fungi) cannot - they are sessile (attached to the substrate). Animals are large organisms that are capable of active movement: swimming, crawling, walking, running, jumping or flying. While some animals are also sessile, at least one phase of their life-cycle (e.g., a larva) is capable of active movement.

Some of the major transitions in the evolution of animals are evolution of tissues, evolution of symmetry (first radial, later bilateral), evolution of pseudocoelom and coelom, the difference between Protostomes and Deuterostomes, and the evolution of segmentation.

There are about 37 phyla of animals. Animals can be divided into two sub-Kingdoms: Parazoans and Eumetazoans. Parazoans are choanoflagellates and sponges. They do not have tissues - their cells are randomly organized. A sponge can be pushed through a sieve and all cells get detached from each other during the process, yet they will reconnect and form an intact sponge afterwards. Sponges move by reorganization of the whole body - cells move over each other (pulling the silicate spicules along) and can move as much as 6mm per day. All other animals are Eumetazoans - their cells are organized within proper tissues.

Parazoans also have no body symmetry. Some phyla of animals (e.g, Cnidaria) have radial symmetry - they are called Radiata. Most phyla of animals - the Bilateria - have bilateral symmetry: the left and the right side of the body are mirror images of each other. In bilaterally symmetrical animals, there is early embryonic determination not juts of up-down axis, but also of front-back axis. Bilateral symmetry gives the animal direction - it moves in one direction, the sensory organs and the mouth tend to be in front, while excretion and reproduction are relegated to the back of the animal.

Early during development, the cells of the spherical embryo (gastrula) organize into layers. Some animals (Diploblasts) have only two layers: ectoderm on the outside and endoderm on the inside. Most animals (Triploblasts) have evolved a third layer in between - the mesoderm. Ectoderm gives rise to the skin and nervous system. Endoderm gives rise to the intestine and lungs, among else. Mesoderm gives rise to muscles and many other internal organs. Usually, Radiata are Diploblasts, while Bilateria are Triploblasts.

In more primitive animals, there is no internal body cavity (e.g., flatworms). In others, a cavity forms during the development between the endoderm and mesoderm - it is called pseudocoelom (e.g., nematodes). In most animals, a proper coelom develops between two layers of mesoderm. Our abdominal and chest cavities are parts of our coelom.

In most phyla of animals, the early embryo divides by spiral cleavage. The blastopore - an opening into the cavity of the blastula- eventually becomes the mouth. These animals are called Protostomes. Protostomes are further divided into two groups: in one group animals grow by adding body mass (e.g., annelids, molluscs and flatworms), while others grow by molting (e.g., nematodes and arthoropods).

In Echinodermata and Chordata, the embryo divides by radial cleavage. The blastopore becomes the anus. These animals are Deuterostomes.

Three large phyla of animals - Annelida, Arthropoda and Chordata evolved segmentation, using Hox genes to drive the development of each segment.

You will HAVE to read the three relevant animal chapters in the textbook to learn more about the following phyla: sponges, cnidarians, annelids, molluscs, arthropods and chordates.

Phylum Chordata is the one we are most interested in for egocentric reasons - because we are chordates. The phylum consists of some invertebrate groups and the Vertebrata (all other animal phyla are also Invertebrata). The invertebrate chordates are hemichordates (acorn worms), tunicates (Urochordata - sea squirts) and cephalochordates (e.g., the lancelet - Amphioxus, see picture). The larvae of invertebrate chordates are very similar to the larvae of echinoderms, both groups are also Deuterostomes, and recent molecular data confirm close relationship between chordates and echinoderms as well.

All chordates have, at least at some point during the development, a notochord. The early chordates were aquatic animals. Hagfish and lampreys are two of the most primitive groups of vertebrates. Before the molecular analysis was performed, these two groups were clumped into a single group of Jawless Fish (Agnatha), but have since been split into two separate classes.

'Fish' is the lay term for several different groups of aquatic vertebrates. The most important classes are cartilagenous fish (Chondrichthyes, e.g., sharks, rays and sturgeons), lobe-finned fish (Sarcopterygii, e.g., gars) and ray-finned fish (Actinopterygii - most fish that you can think of). The latter two of those are also sometimes lumped together and called the bony fish (Teleostei). Chrossopterygii, a once-prominent group of lobe-finned fish that survives today with only one living species (Coelacanth, or Latimeria), is the group that gave rise to ancient amphibians - the first vertebrates to invade the land (check out the Tiktaalik website for more information).

Amphibians are frogs, toads, salamanders and cecilians. At least one portion of the life-cycle - reproduction and early development - is dependent on water. They have legs for locomotion and lungs for respiration on land.

Reptilia are a large and diverse class of vertebrates. They include lizards, snakes, tuataras, turtles, tortoises and crocodilians. They have scaly skins that allows them to survive in arid environments. They have evolved an amniotic egg - an egg that contains nutrien-rich yolk and is contained within a leathery shell. Thus, reproduction and development are not dependent on water. Many reptiles live in deserts.

A now-extinct group of ancient reptiles (therapsyds) gave rise to mammals (class Mammalia) about 220 million years ago. The early mammals were quite large carnivores. However, during the 150 million year reign of the Dinosaurs (another extinct group of reptiles) mammals were constrained to a very small niche - that of nocturnal burrowing insectivores. Only after the demise of Dinosaurs (65 million years ago) could mammals embark on a fast evolutionary radiation that produced groups we know now.

Birds and mammals are endotherms - they can control (and keep constant) their body temperature by producing the heat in organs like muscles and liver. This is a metabolically expensive strategy that requires these animals to eat very frequently, but gives them speed and stamina and allows these animals to live in every part of the Earth, incuding polar regions. Other vertebrate classes are ectotherms - they gain their heat from the environment and, if they are cold, they are slow and sluggish.

As it is very difficult for large bodies to lose heat, large reptiles (like dinosaurs), once heated, can retain their body temperature for long periods of time - they are effectively warm-blooded. Some reptiles, notably pythons and iguanas, are capable of producing some of the heat internally. While they cannot keep a constant body temperature, they are capable of some degree of thermoregulation (e.g., becoming somewhat warmer than the external environment). By shivering their muscles, pythons raise their body temperature above ambient and use this heat to incubate their eggs.

There are about 4500 species of mammals, organized into 19 orders. The defining characteristics of mammals are milk ­producing glands and hair.

Monotremes (platypus and echidna) are egg-laying mammals. Their mammary glands are not completely evolved yet - the young lick the milk of off mothers hair.

Marsupials are the pouched mammals (e.g., kangaroo, koala, opossum). The immature newborn offspring crawls up into the pouch and lives inside it until they are large enough to fend for themselves.

Placental mammals (the remaining 17 orders) have a placenta that nourishes their embryos during development. The new molecular data, coupled with a number of exciting newly-discovered fossils, are changing our understanding of genealogical relationships between different orders of mammals, including our new knowledge about the evolution of whales, the relationship between elephants and hyraxes, between Carnivores and Pinnipedieans (seals, etc.) and between rodents and rabbits.

The most recent vertebrate class - the birds (Aves) - evolved out of a branch of Dinosaurs. There are 28 orders of bird in 166 families. Two primary characteristics distinguish birds from reptiles: feathers and flight skeleton. Their feathers are modified reptile scales. Feathers are obviously important for flight, but also insulate as birds are endotherms.

Read:

Audesirk, Audesirk and Byers, Biology, 8th edition., Chapters 19, 20, 21, 22, 23 and 24.

Additional Readings:

New ideas about early evolution of life

Fortify has a taxonomy of coding errors that affect security. The really cool thing is the examples in many different languages.

Its right here, go check it out.

This paper examines user-‍generated metadata as implemented and applied in two web services designed to share and organize digital media to better understand grassroots classification. Metadata - data about data - allows systems to collocate related information, and helps users find relevant information. The creation of metadata has generally been approached in two ways: professional creation and author creation. In libraries and other organizations, creating metadata, primarily in the form of catalog records, has traditionally been the domain of dedicated professionals working with complex, detailed rule sets and vocabularies. The primary problem with this approach is scalability and its impracticality for the vast amounts of content being produced and used, especially on the World Wide Web. The apparatus and tools built around professional cataloging systems are generally too complicated for anyone without specialized training and knowledge. A second approach is for metadata to be created by authors. The movement towards creator described documents was heralded by SGML, the WWW, and the Dublin Core Metadata Initiative. There are problems with this approach as well - often due to inadequate or inaccurate description, or outright deception. This paper examines a third approach: user-‍created metadata, where users of the documents and media create metadata for their own individual use that is also shared throughout a community.

Continues @ Adammathes.com

When I began to become enraptured with Web 2.0 I wanted to find ways to use intelligent, emerging instruments from the semantic web to continually improve findability and search optimization of resources I had gathered over many years, even if my own PC broke down and all my back up systems failed, and my own memory became faulty, or . . . I had hoped that blogging would help me remember where I put things that might someday be useful again.

The catalyst for "Folksonomy: optimizing soul searching" was a question regarding how absent categories impose their presence through their very absence. Faced with closed field category/subcategory options offered by Digg for example, under which I had to place my article, etc I struggled between philosophy or society, finance or economics, environment or politics.

I have also found it enlightening to find under which categories my own Creative Commons blogs, articles, posts and images might appear.

As my own sites grow organically, my categories and parent categories constantly need to be reformulated; new tags added and others deleted or merged. The goal is efficiency and elegance in the ungainly word of "findability" or search engine optimization, potent instruments in the semantic web.

At times I am frustrated by the absence of categories that exclude entire populations and conversations. Recently I came across a site hosted by the Washington Post. In their About page they describe how they use the limitless space of the online world to host a blog entitled "On Faith" which invites "intelligent, informed, eclectic, respectful,fruitful, intriguing and constructive conversation-among specialists and generalists about the things that matter most, religion, the most ancient of forces, the most pervasive yet "least understood topic in global life."

I read comments and the post from David Grant, a junior at Virginia Tech who commenting on his visit to the Baha'i gardens in Haifa,Israel-Palestine (which has recently been named as an International Heritage Site) remarking on the broad reach of the Baha'i religion. "Where else on Earth could you find a family from the Bible Belt, a pair of South Africans currently working in Japan, and a crew of Peruvians all heading to say their prayers at the same spot?"

I wanted to search "On Faith" for more strings on the Baha'i but realized that Baha'i World Faith was not offered in their pop-up menu of "List Posts by Topics" which did include: Anglican, Atheist/Agnostic, Buddhist, Catholic, Christian, Earth-based Spirituality, Eastern Orthodox, Episcopal, Evangelical, Greek Orthodox, Hindu, Jewish, Mainline Protestant, Mormon, Muslim, Native American religion, Protestant, Quaker, Sikh, Taoist, Wiccan.

As of February 2008 there were 5,000,000 Baha'is in the world and 159,692 Baha’is in the United States. I couldn't find a figure for either Taoist or Wiccans but one site at least claimed that in 2001 there were c. 34,000 Wiccans in the US.

Baha'is promote tolerance and moderation and are anxiously concerned with the social issues of the time in which they live. Baha'is around the globe contribute to civil society at locally, regionally, nationally levels on issues and programs related to World Religion Day, interfaith relations, religious freedom, Race Unity Day, race unity, elimination of prejudice, advancement of women (CEDAW), human rights, among others. Baha'is have offices at United Nations as NGO are are prominent in international forums as invited participants acknowledged for civil moderate behaviour in the most volatile situations. Recently the U.S. Bahá’í U.N. representative Jeffery Huffines received a Friendship Award for his work “promoting cultural understanding throughout the world and at the UN Headquarters” and for serving as a “positive, guiding force” to all. It is surprising that Baha'is seem to be largely absent from this forum.

The categories offered under "List Posts by Topics" are confusing since some are parent categories for the others. The Greek Orthodox, Catholics, Protestants and Evangelical are all followers of Christ and are all therefore Christians. Which discussions take place solely under the name of Anglican, Mainline Protestants and Episcopal? In terms of the semantic web it would be far more useful to provide a theme-based "List of Topics" that is inclusive of all the groups and religions mentioned. Tags could be used to facilitate searches for a Quaker, Sikh or Baha'i or Catholic perspective, for example. I would recommend that the blog architects revisit and update their taxonomy using principles of folksonomy: what users do with words.

Years of working with research materials leads to a way of thinking with categories, subcategories; key words (tags); abstracts, descriptions, key concepts, timelines, references in .eml or similar formats. The semantic web revs up that process with powerful tools. So my blogs are always a work in progress, process works.

My own personal blogs are experimental and while I am very conscientious about what is here, I can claim no professional authority in any one field.

At this time in my life I feel as if I live outside linear time. Blog stats soar up suddenly for no apparent reason on a blog posted weeks or month ago. So I tidy it up a little. Then the graph drops sharply again with no apparent reason. I don't need to try to control it.

Outside linear time, I could just pick up threads begun months ago on Milton Friedman, the social history of Inuit, media objectivity or what we do in the name of such concepts as "memory work" or "everyday life." Through creative commons I could share all my teaching, learning and research resources without having to shorten them, tidy them up or make them ready for someone else's deadline. Take what you need and leave the rest. I would still work as hard as I could to maintain my own standards particularly in investigating , acknowledging and referencing sources of information, images, etc.

As I am creating, writing, coding, snurling, twittering, blogging, and uploading to wikipedia, social bookmark accounts, my blogs or others' etc I have absolutely no trust in anyone.

I post knowing that anything I have shared can be misinterpreted, misunderstood, misread. It can be rejected, ignored, criticized. It can be copied and pasted without my name attached. I license all my work under the Creative Commons License 3.0 SA-NC-BY but I know it cannot be enforced in most cases.

So why bother?

What I do is not based on my need to trust others in cyberspace. I do not feel as though I am an embodied link in an embodied network in linear time and space.

This is even more than that. If I use the semantic web effectively, a searcher who is not "now" from a geographic location that is not "here" can still find my arrows, my markers, hotwords and icons, index-mouse-clicks that might just help them a little in their search. Maybe I will be that searcher.

It is more important to me to work hard at providing information that is not misinformation, trying hard to be as close to the truth as is possible, to use the most powerful arguments from the most reliable texts available to me at any given time.

I am not an anthropologist nor a journalist; I am definitely not a churnalist. My responsibility to me and therefore to others in this network or not, is to post that which I believe to be useful in a way that allows others to follow a trail of truth claims should they choose.

Thirteen years ago Francis Fukuyama in Trust: The Social Virtues and the Creation of Prosperity (1995) questioned predictions that the Internet, the computer to computer communication network, unleashed from restrictions imposed by its creator, the Department of Defense, would herald a new organizational network constituted by small firms and individuals that would prove to be superior to large, hierarchical corporations and anarchical market relationships (Fukuyama 1995:195). Fukuyama argued that network efficiency depended on reciprocal moral judgment [1], "a high level of trust and the existence of shared norms and ethical behaviour between network members (Fukuyama 1995:195)." He contrasted the necessity of that network users share social responsibilities and obligations with hackers and other users who were "free spirits hostile to any form of authority . . . vulnerable to certain forms of normlessness and asocial behaviour."

Fukuyama furthered argued that the Internet is a community of shared values using the concept similar to Shumpei Kumon's notion of "consensus/inducement-based exchange." He felt that Internet users in the 1970s and 1980s (mainly government and academic researchers) internalized unquestioned shared values. The Internet could be kept low-cost if users respected certain ethical standards.

In 1994 two lawyers broke the Internet's code of ethics and bombarded news groups with advertisements for their services (Fukuyama 1995:196). The lawyers were not breaking any written laws and were not shamed into retreat. However, the sheer quantity of hate mail they receive, forced their server shut down.

Although the monitization of all things Internet is well underway, there is also exponential growth in cyberworld capital [2] which like cultural capital or academic capital can facilitate access to certain privileges. I am aware of ways in which users of social networking sites strategize to optimize search engine findability, to increase their hits, statistics, and cyberworld capital.

I am not certain if the success in accumulating cyberworld capital or monitizing all things Internet is made more efficient by trust?

Notes

1. Fukuyama compares network as community concept to the Japanese concept of keiretsu and its western reincarnation in American conglomerates like Gulf + West + ITT. keiretsu depends on a high level of trust.

2. Some measure cyberworld capital in terms such as "authority" as with Technorati. Others self-identify as A1bloggers.

After a stroll through a Palo Verde woodland in the Tucson mountains I returned to my car to find this male ant sitting on the roof. I didn't immediately recognize it, and several hours later, after I figured it out, I wished I'd stuck around to looks for queens. What is it? I'll provide the answer next week.

Update: the answer!

Having done user testing on taxonomies I've built a few times, I compare the feeling to what I imagine it's like a being an actor or actress watching yourself in a film.

Imagine you are Scarlett Johanssen (I often do), watching yourself in a film... You cringe at the sight of yourself on the big screen, pick apart your performance, thinking "I could have done it this way...", hear the audience laugh (or not) at jokes... And the pressure of the success of the movie weighs heavily - will it be a bomb? Will the production company go bezerk? Will I ever work again?

Ok, so taxonomy user testing is not quite that dramatic, but there are parallels. Watching users navigate a taxonomy I've built is always teeth clenching for me - I am constantly thinking, why are they clicking there? Are they blind? I should have gone with my first idea for that label... The client is going to freak when they find out that one of their star products is unfindable... Will I ever work again?

Of course, that's the whole point of user testing - to prevent the taxonomy from bombing.

I am always surprised at what I discover in these tests. Categories or labels that I thought were no-brainers can turn out to be black holes of findability. Often this is related to how the taxonomy plays out as a whole in a users' eyes, rather than the specifics of a particular category. When we build taxonomies, we can get very focused on individual labels and categories and neglect the interplay between different terms across the entire structure. The "stickiness" (or lack thereof) of a particular concept or label can severely affect the performance of other seemingly unrelated categories - a ripple effect of sorts.

For example, a recent test on a toy taxonomy had an interesting ripple effect... One of the labels in the taxonomy included the word "pet". This term turned out to be so sticky that users looked for any product that even remotely resembled an animal in this category, regardless of how well it matched the product.

User testing also tends to enlighten stakeholders around the dangers of using internal terminology or organizing principles on the customer-facing web. Sometimes clients can be very reluctant to change categories or terms that they have been using for a long time or that represent how they understand their product line internally. They believe customers think the same way and can't commit to change until hard data proves that users don't care, don't understand, or are just plain wrong about particular terms.

I am big fan of Steve Krug's testing motto: test early and test often. From the taxonomist's point of view, user testing can be a mix of cringe-worthy moments and fist-pumping "I knew it"s. But there is nothing better than getting real users to point out the flaws and successes in your taxonomy.

For more on taxonomy usability testing, you can download our recent webinar on the topic from our site.

This is absolutely hilarious.

Okay it's most likely either fake or a hoax, but it's still damn funny.

For those of you not getting it, click here.

Photo credit: the mad LOL scientist on flickr cc-s

Ini adalah contoh taksonomi berdasarkan teori evolusi (aliran yang mempercayai bahwa manusia itu adalah keturunan monyet - Darwinism). Yang ingin ditunjukkan adalah contoh pemetaan/ klasifikasi jenis-jenis mahluk hidup (tanaman, hewan dan manusia).

One schema that is widely used is for geo- (or location-) tagging, where posts such as my picture of a Kingfisher on Flickr are tagged with (in that case):

• geo:lat=-1.56403
• geo:lon=53.60913

In other words, the coordinates of the place where I took the picture (pages using that schema are also often tagged with "geotagged").

It is then possible for Flickr to display that picture overlaid on a map of the location.

The Flickr page is also tagged:

taxonomy:binomial=Alcedo_atthis

which gives the scientiifc name (binomial or binominal) of the Common Kingfisher, Alcedo atthis.

Another form of tagging, using hash tags, is used by the social media text-messaging service Twitter. Tags in twitter are prefixed with a hash symbol (#), hence the name. A "hash-tagged" message might look like:

I live in #England

Hash tags are parsed by three sites that I know of (there may be others — if so, please let me know): Hashtags (e.g. Hashtags for #blog), Summize (Summize for "#blog") and Twemes (Twemes for "#blog").

All well and good.

It occurred to me recently that it should be possible to use Triple tags in Twitter messages, so I posted these "tweets" as they're called (I find that rather, er, twee):

#tagged post about #Kingfisher #taxonomy
( #taxonomy:genus=Alcedo,
#taxonomy:binomial=Alcedo_atthis )

(See
http://twitter.com/pigsonthewing/statuses/849630924)

and:

Is anyone is parsing #geotagged posts like this: #geo:lat=52.478342 #geo:lon=-1.895389 ( #birminghamuk #rotunda #geo #geotag #tripletag)

(See
http://twitter.com/pigsonthewing/statuses/853592240)

(line breaks have been inserted to inprove readability)

Disappointingly, none of the three hash tag parsers above managed to understand these. They all see "#geo:lat=52.478342" as just "#geo" and "#taxonomy:binomial=Alcedo_atthis" as just "#taxonomy".

Worse still, Hashtags wrongly displays my two posts without the second two-thirds of the tag content, as:

#tagged post about #Kingfisher #taxonomy ( #taxonomy #taxonomy )

(see http://hashtags.org/tag/taxonomy/)

and:

Also wonder if anyone is parsing #geotagged posts like this: #geo #geo ( #birminghamuk #rotunda #geo #geotag)

(see http://hashtags.org/tag/taxonomy/).

See also:

• #geo:lat=52.478342 on Summize
• #geo:lat=52.478342 on Twemes
• #taxonomy:binomial=Alcedo_atthis on Summize
• #taxonomy:binomial=Alcedo_atthis on Twemes

Wouldn't it be great if services which parse hash tags in Twitter messages also recognised "hash-triple-tags"?

Semantic simply means "meaning". We are trying to explicitly define the meaning of Ordnance Survey data, and the knowledge about the world of geography that we as an organisation hold. We are encoding it in a way that's readable, and more importantly, understandable, by a computer: it's like writing a machine-readable version of Ordnance Survey's MasterMap real-world object catalogue.

Why is Ordnance Survey interested in Semantics?

We are investing in semantic technology research to cut the cost and improve the accuracy of data integration. Data integration is widely acknowledged to be expensive and problematic. When such activities involve the inclusion of complex datasets such as OS MasterMap® the challenge becomes that much greater.  The problem is more than a syntactic one and cannot be solved by everyone adhering to one file format or standard. Rather it is also a problem of understanding what the data means:  is the Ordnance Survey definition of a field the same as the way the Government Department for the Environment, Food and Rural Affairs (DEFRA) would understand it? Our definition is spatially delineated by barriers such as fences or ditches, while DEFRA might distinguish a field’s extent by the kind of crops that were grown, as part of their task of calculating farmers’ subsidies. By providing a machine-readable description known as an ontology of Ordnance Survey's data, these semantic differences are made explicit, the impact on the customer’s application can be seen and we can begin to use ontologies to provide bridges between these different world views. As techniques for ontology merging, and ontology to database mapping are developed, it will become easier to semi-automatically integrate our data with our customers'.

Another benefit of semantic technology is that of data repurposing. Our customers have their own terminology for the things they use day to day: and they may not be the same words that Ordnance Survey uses. For example, the Environment Agency uses the term "Flood Defence" - but that doesn't appear as an attribute in our data, although we do capture the Weirs and Flood Walls and so on that are used as flood defences. By authoring an ontology to describe Ordnance Survey data, and one describing the terms a customer does use, we have already shown that it's possible to query an Ordnance Survey database for terms like "Flood Defence".

There are also internal business advantages for Ordnance Survey: with an explicit, machine readable description of the meaning of our data, we can improve quality control and classification decision-making.

In the future this technology will enable our data to be more easily accessed by customers via the Semantic Web (the "web of data").

How do we encode this semantic meaning?

We encode our knowledge using an artificial intelligence technique called an ontology. An ontology is made up of concepts (like a River, a Field or a Building) and relationships between them (for example, a Building is next to a River). We have been developing a method to allow domain experts to capture their knowledge in natural-sounding sentences, in a structured English language called Rabbit, and then the ontology engineer translates these into the machine-readable description encoded in a language called OWL (the Web Ontology Language). We have already produced an ontology for hydrology and are developing ones for Buildings and Administrative Geography. Our aim is eventually to cover the whole of topography.  Our ontologies are available for download both in OWL and as a human-readable description

We are also researching the issues of how to link ontologies to our geospatial database, how to query them, merge them, and how to combine spatial and semantic reasoning.

If you'd like to know more about our research, please have a look at our publications, or contact us at research@ordnancesurvey.co.uk

It's fairly basic, but makes some really good arguments and points about taxonomies and folksonomies. The writing is direct and very accessible--more for non-professionals. But if you're trying to put together arguments for and against taxonomies and folksonomies, she's done a lot of the work for you. Check it out.

Oh, the design is stunning too. Who says library science and information architecture have to be dull and boring?

UPDATE: Here's two books I found online that seem to address what I'm interested in:
Everything is Miscellaneous: The Power of the New Digital Disorder, David Weinberger (2007)
Sorting Things Out: Classification and Its Consequences, Geoffrey C. Bowker and Susan Leigh Star (1999)

Comments still welcome.  Thanks.

When books come to a library they aren’t just put on the shelf for people to use. Resources in a library must first be described and input into a database so users can retrieve the item by performing a search. Social cataloguing is the exact same process except on a smaller more personal scale.

Social cataloguing applications, such as Library Thing, Discogs, and Flixster, allow the user to catalogue their own personal “library” of books, videos, and music. However, the “social” part of the social cataloguing process allows for users to share their catalogues and interact with people who have like catalogues or like interests. Social cataloguing requires user participation and collaboration to function.

Tagging

When librarians catalogue items they catalogue them according to the Library of Congress Subject Headings (LCSH). LCSH are a set of terms, or subject headings, and rules on when to use those terms.

The rules for LCSH make sure that the terms used to describe items stay consistent. This makes it easier to retrieve the items out of a catalogue. This kind of system is called a taxonomy. Taxonomies are systems that use “controlled vocabulary” to describe material.

Social cataloguing is a folksonomy. Folksonomies, a term coined by Thomas Vander Wal, do not use controlled vocabulary but keywords, or tags, which are chosen and generated by users. Folksonomies rely on the collaborative creation of tags to categorize content.

Have you heard of the term “metadata?” Metadata is simply data about data and tagging is a form of metadata. Tagging is the process of assigning a keyword or term to information such as a picture, webpage, piece of music, or file. The tags are assigned by the user according to what they believe the information is about and how they will be able to retrieve it through searching. For example, take a look at this comic.

How could this be tagged? This comic can be tagged using these words: humor, comic, blogging, web 2.0, social software, and netgen.

However, the interesting thing about tagging is that everyone can tag however they want. Each item can be tagged in a variety of ways. How would you tag this comic? Your keywords may be very different from the ones listed but just as valid.

Tag Clouds

In social cataloguing applications, once something is tagged it can be retrieved in a search or can be displayed in a tag cloud. A tag cloud looks something like this:

One kind of tag cloud is one that represents by size the number of times a tag has been used for a particular item. Another kind of tag cloud represents by size the number of times the tag has been used on any item. This is a Library Thing tag cloud and represents the second style mentioned. The tags in a tag cloud are usually linked and will bring you to a list of the item(s) that are connected with that tag.

Social Bookmarking

Social bookmarking uses the same principals and structure as social cataloguing. Social bookmarking is also a folksonomy and requires participation, collaboration, and tagging but, unlike social cataloguing, the user does not catalogue collections. Social bookmarking is the organization, describing, and storing of webpages.

Unlike simply bookmarking your favourite sites on your web browser, social bookmarking searches tags that people have used to describe a webpage. Once the user has searched and found websites of interest, they can bookmark them on a hosted site and share their favourite sites with others. Users can also tag the websites to add to the collaborative nature of the application.

Activities

• Create and account with LibraryThing
• Create a profile
• Create a catalogue of a few books you own
• Tag the books with descriptive words

Readings

Leptogenys attenuata

In spite of the southern winter, the coastal forests of Kwazulu-Natal had plenty of ant activity to keep me occupied last week. In addition to the beautiful Polyrhachis I posted earlier, here are portraits of a few of the species I encountered.

Crematogaster tricolor

Platythyrea cooperi

Myrmicaria natalensis

Plectroctena mandibularis

Anochetus faurei

Oecophylla longinoda (African Tailor Ant)

Cataulacus brevisetosus

Dorylus helvolus

Pachycondyla (Bothroponera) mlanjiensis

Atopomyrmex mocquerysi

Pheidole megacephala (Big-Headed Ant)

Solenopsis geminata (introduced from South America)

Cephalotes rohweri, the Arizona Turtle Ant.  Workers like like this: