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Topics - Kai

#201
This is where you supply photographs of unidentified arthropods and notes like "I found this bug in my bathtub, what is it!?" Then I give you a good answer at some level and a wild guess when it comes to the species.

Go!
#202
Or Kill Me / Slack, or something.
February 15, 2010, 10:32:32 PM
My advisor has left for the day, hell, the building is nearly all empty by now. Only people left are die hard professors and graduate students like myself.

I've had a shitty day, to be honest. The physiology exam this morning was less than enjoyable, done more or less on an empty stomach, which was promptly followed by a 3 hour seminar and a lunch discussion with the speaker. And I'm feeling like an idiot the entire time. Not that this isn't a normal occurence for me.

This afternoon I was supposed to work on more of the bad ass physiology project but apparently the bacteria got thrown out so....I'm left sitting in my office, all my plans for today out the window.




WHAT THE FUCK AM I DOING HERE?!?! I'm not getting a fucking thing done, I haven't done SHIT this afternoon. I have 8 samples and god knows how many microcaddisflies to identify before the end of the month, I have reading to do up the wazoo, I have a discussion to prepare for tomorrow, a lab to write for wednesday, there's a seminar tonight, and I haven't accomplished a damn thing.

The worst part is, I don't even feel good about it. I don't feel satisfied. I don't feel happy with sitting around feeling tired and depressed and anxious because I feel like my collegues just want to throw me down a hole. Complete paranoia I know, but I'm living in a shell of fucking isolation here. I have maybe one meaningful conversation a day and it just feels like all the minds around me are getting more and more distant.

If I go home, I'm just going to fucking masturbate, probably. Not that schlicking isn't fun, but its about as productive as what I'm doing here, which is to say, not at all.

Also, fuck you.

~Kai
#203
Aneristic Illusions / Oh FUCKING SHIT.
February 13, 2010, 10:26:00 PM
Department of biology professor at Alabama university murders chairman of the biological sciences department and two associated professors.


FUCK.





FUCK!





I heard about this just now, and I really have no words.

More here: http://membracid.wordpress.com/2010/02/13/tragedy-at-uah/ if you want it.

For gods sakes though, at least look here: http://membracid.wordpress.com/2007/07/28/academia-is-a-cult/

Bug Girl says it much better than I could. Right now I'm just reeling.
#204
The title is refering to a rather exciting paper which just appeared in Nature Journal a couple days ago. The authors have used 62 genes from 75 species representing all the major clades of arthropods (and therefore the greatest diversity of life on this planet) to infer a phylogeny of the Arthropoda.

The results are interesting, to say the least.

http://blogs.discovermagazine.com/loom/2010/02/10/blind-cousins-to-the-arthropod-superstars/ and

http://myrmecos.wordpress.com/2010/02/11/the-most-ambitious-arthropod-phylogeny-yet/

weigh in on the coolness of this whole paper. With the snow still on the ground outside, its like christmas for an arthropod systematist.


Some particularly interesting aspects of the phylogeny:

- Insects are clearly nested within the crustaceans, no way to bow out of it this time. We can infer that insects and other hexapods are simply terrestrial adapted crustaceans. The big problem with this for carcinologists is that it renders the crustaceans paraphyletic, so we can no longer talk about crustaceans but the clade Pancrustacea, which includes the insects.

-The closest living relatives of the insects seem to be the Xenocarida, the "strange shrimps". Time for the morphologists to go wild.

-The chelicerates, including spiders, are still a mess. I wouldn't trust any clades with bootstraps under 90 in this. The analysis has been done with maximum likelyhood, a phenetic, distance related measurement, and not parsimony. So, things like "paleoptera" I'm not willing to accept.

-It's interesting how the phylogeny largely vindicates morphologists in their earlier decisions. This seems to be a trend, and it speaks of the ability of molecular systematics to independently corroborate traditional systematics.

#205
Two vast and trunkless legs of stone / HEY APUT!
February 13, 2010, 12:19:47 AM
Thanks for making southeastern roads even more dangerous for pedestrians.

Oh, and making me walk home because the buses are shut down. Cheers!
#206
Yesterday, I was sitting in my insect behavior class. We were talking about altruism and mutilevel selection, and I asked the question, can these ideas of kin selection be applied to our species, since it seems we react in altruism for not only kin. My professor paused for a moment in his characteristic way, and motioned with his chalk. They do apply, he said, but talking about it gets very muddy. Applying behavioral study to humans is often difficult because the basic activities are obscured by culture, although culture can be considered a behavioral adaptation, but more often it is obscured by sensitivity.

He went on, Roger, to tell a story about the great sociobiologist EO Wilson. Back in the 70s, Wilson had proposed that racism in humans may be a sort of kin selection. Kin, in this case race, have to be recognizable to be considered same with self. And since the so called differences in skin color and surface features of different groups of humans are so immediately obvious, its very easy to see how racism could be a sort of kin selection, a selfishness related to passing on ones own genes and the shared genes of others.

Now, he was completely villanized for this, Roger. He would go to scientific meetings and people would pour water over his head while he was speaking and should "DR. WILSON, YOU'RE ALL WET!" It didn't matter if the science was there, people were so sensitive to the topic of racism in any way that they wouldn't hear a word of it.

But thats the issue, isn't it? People grasping to hypotheses and treating them like absolutes of a moral code. If Wilson was right, they would think, then that makes racism /okay/, wouldn't it?

Now, what kind of silly thought is that, Roger? Yes, there is kin selection in humans, and yes, it seems very likely that racism would be some form of group selection. BUT. BUT! That does not mean that racism is morally acceptable. That's the difference, the stupid, easy to see difference between the objective knowledge of science and the 'Truth' of society. We are dirty apes, Roger, but we live together in relative suprising harmony, considering. Just because racism has happened as an extention of biology, doesn't make it good. Just because, for example, fireflies attract mates with lights, doesn't mean we should all wear christmas tree lamps when going to the bar.

It's such a great and fatal mistake to believe that just because something has happened to be one way, that we are somehow stuck to it, that it's some sort of absolute. We might as well be practicing Christianity in the 12th century. Just because it's wrong to be racist, doesn't mean that Wilson isn't right.
#207
Literate Chaotic / Making time for nothing.
January 23, 2010, 10:15:58 PM
Since this isn't really a rant, and more a statement, I'll leave it here.

People are constantly rushing about. It's from one thing to the next to the next until the end of the day there's nothing left to do except collapse and sleep. I see this often in academia, with fellow students and professors.

People are often surprised when I can remember conversations I've had years ago, or even five minutes ago, whereas I'm surprised when they cannot! True, I have difficulty with proper names, and words often escape me. But when it comes to visual memory, and concepts, I have no trouble. My adviser, on the other hand, is unable to remember a conversation he had with me two days before, a paper he read just last week.

I think I understand the trouble here. He tells me, "I'm burning the candle at too many ends" riding in the car one time after dozing off in front of his laptop, filled with the 16 NSF grant proposals he had to read and comment upon in three days time. Everyone is constantly in mental motion, if not physical motion, absorbing everything, being involved in every possible activity. If there is one spare moment in the day, it must be filled with something! Idle moments are considered unproductive. And yet, their memory suffers. This to me seems very confused.

In addition to eating an optimum diet, sleeping a solid 7 hours every night and daily low impact excessive, the mind does need stimulation. But it also needs quiet time. I don't mean "I'm going to sit down and quietly read these 300 papers in three hours" quiet time. I mean, literally, doing nothing. Simple, quiet yet alert relaxation, not focused on any particular thing, and not in the process of heavy absorption.

Antero Ali (how many times can I reference Angel Tech in one day? Lets find out!) speaks of "absorption, integration and communication". It's not enough to simply absorb all day long. The mind needs space to integrate all this information, space that is not already filled with something else. Idle time. Einstein suggested that every new graduate find a job which doesn't take a lot of thought, and just think for a while.

So, my suggestion. Read a little, write a little, communicate a little, and do nothing (just a little nothing) every day. Sit (not in front of the computer!) or walk without any goal in mind. Let your mind wander, to what happened today already, to imaginative thoughts. This is integration time, space forming time as AA calls it.  I guarantee, this time will increase your ability to remember more than anything else, assuming you live an already intellectually active life.

And if not, why the hell not?
#208
This morning, I had my first experience with Ekbom's Syndrome, or what is more often called Delusional Parasitosis. A pest control man came to my lab, looking for someone who could look at some "insect samples". I said I wasn't the curator (we don't have a museum curator/diagnostician at the moment, since our last one left for a better paying position), but would take a look, regardless of whether I could identify the sample or not.

But, there was nothing even the closest bit insect looking in the sample. Dust specs, plant parts, debris and dirt. Nothing I could say was a leg or a head or abdomen, or any sort of chitinous arthropod part. He told me that he had a client, an older woman, who SWEARS that there are bugs infesting her house that bite her. He had some cell phone pictures to show me.

Now, I made a point to say I'm not a medical doctor so I can't diagnose these things, but just from my experience I was pretty sure what this was. Delusional Parasitosis is a mental illness where the sufferer believes they and/or their residence is infected with parasites. This is one of the few medical conditions that the average entomologist comes into contact with on a regular basis, especially if they are a diagnostician or work at a museum. I've heard stories of people who won't take no for an answer, who bring samples every week (always no insect parts), and who have a large number of welts and open sores from scratching and picking at their skin, to "let them out" they say. No matter what you tell these people, they will likely continue to believe they are parasitised, even when there is no evidence for such. They don't often go to medical doctors either, instead bringing the "specimens" to us. It's a very sad condition since there is, as far as I know, no cure. Again, not a medical doctor (I know I keep saying this, but you can get in big trouble for diagnosing without a license).

I mention it today because this is the first time I've ever personally seen it. I gave the man a notecard with a link to the wikipedia article, and said he should tell her to go see a doctor about it. He just hoped that it would help her come to terms with that it's "all in her head".

For more information on Ekbom's Syndrom: http://en.wikipedia.org/wiki/Delusional_parasitosis
#209
Or Kill Me / A Rant.
January 17, 2010, 06:34:04 PM
Just yesterday I overheard a conversation, just a portion of it, between a young man and a young woman.

"But yeah, I have absolutely no problem with gays. Gay marriage is another story"

"Well, its not really marriage, yeah"

"Well, what it really is, is that it fucks up the nuclear family, which America is based on. And I have a problem with that."



Excuse me for a moment, I'm going to just step in to your conversation about "tolerance" here for a minute.

Your bastion of the Nuclear FamilyTM, that glorious wondrous unit of ONLY One ManR, and One WomanR and 2.5 children, the cornerstone of The America, is as good as a coin toss. Or didn't you know that, didn't you know that 50% of all marriages end in divorce, you fucking hypocrite, that this so called monolith is as good as me rolling a die to see if it works out. These are all STRAIGHT people fucking up, mind you, not those glorious faggots you have no problem with. Oh NO, you have gay friends, you love gays, just keep them the hell out of your sacred coin toss, you irredeemable schmuck, you ignorant fucktard.

How about this? How about I sit here and make you un-fucking-comfortable as possible for a while. I've got a male body, and I've fucked men. That's RIGHT, I've played with penis. Never mind that I'm somewhat trans-ish and I've played with pussy as well. How does that make you feel, shithead? How tolerant do you feel right now, when I'm shoving it in your face just like you shove your GLORIOUS UNION in mine and all my friends constantly, how fucking special it is. LIsten, shitneck, we all see through your veil of tolerance right down to the intolerance that is at it's core. You want to look tolerant while actually inside your a homophobic fucking asshole. You like seeming tolerant, it makes you look fucking fine to all the other posers out there, the so called Moderate White America crowd, all of them ignorant shitheads just like you.

Also, Fuck You,

~Kai
#210
It sorta looks like a glob of lumpy pudding from this far above.



But when you look closer you can see its just jam packed full of Trichoptera.



Thats not water either, its 80% ethyl alcohol.



Then I put them in a smaller dish and under the scope they go!



After identification, VIALS.



Good eatin'n. But this "bowl" has barely been dented after 9 hours work.
#211
Or Kill Me / I'd like to redefine a word.
January 09, 2010, 03:13:28 AM
If that's alright with you all. I know how some of you all really hate the mushy headed redefinition of words and think it transforms language into a bunch of meaningless garble, so I had to ask.


No, wait...fuck it. I'm co-opting this bitch.

I'm taking the word spiritual, and all of its modified versions.

You see, I'm a bit fed up with supernatural religion. I'm tired of being told IT DOESN'T COUNT unless it includes some sort of bullshit mythos. I don't need the supernatural for my worldview so I'm trashing it. And I'm fucking taking this word back.

Spirit. When I consider that word, I visualize an outpouring of purposeful directed energy. It, for me, is a metaphor for that telos in mind and body that the Japanese call iki gai, literally "the thing that gets you out of bed in the morning". Spirit is metaphor for the expression of purpose, and therefore meaning (because purpose comes from what is meaningful).

Therefore, spiritual co-opted pertains to that which is personally meaningful and purposeful in ones own understanding of the human experience, making spirituality a personal system through which one finds meaning and purpose.

I was thinking about this today while watching Sagan's Cosmos, and thinking back to this video of Neil DeGrasse Tyson speaking before a lecture hall filled with psychologists. I remember most what he said near the end of his talk. He said he feels that the same region of the brain that lights up when he considers the universe might be the same region that lights up when people have numinous experiences of god and whatnot, that he wants someone to test that, because then he could offer people the universe.

Way to go Tyson, you fucking nailed it. I don't need deities or celestial beings or fear of eternal punishment or rebirth or ANY of those things to derive SPIRIT in my life. I can commune with life, with the universe, I can consider what is understood about everything rather than taking someone elses assumptions and I can most definitely find meaning and purpose just as powerful and numinous and mystic as all those other fuckers with their robes and beards and holy writ. I am spiritual, I have a spirituality, and damn if I'm not full of spirit, MY spirit, my purpose and meaning, my interpretation of human existence, MY GODDAMN FUCKING RELIGION.


I'm taking that word, and you can pry it from my cold dead claws.

Also, fuck you.

~Kai
#212
Lets all get drunk tomorrow and celebrate!  :banana:

For those uninitiated, Perihelion is the day the earth passes along it's ellipse closest to the sun, this year on January 3rd. It cycles between 1 to five of January every few years. Aphelion, the day the earth is furthest from the sun, is in July.



And if you ask me why, why, Kai, is it cold in the winter if the earth is /closest/ to the sun, then I will kill a motherfucker.  :argh!:
#213
Literate Chaotic / Metaphorically speaking.
January 02, 2010, 05:18:23 PM
A TED Talk by James Geary, about metaphor and it's impact on thought and decision making.

http://www.youtube.com/watch?v=2cU56SWXHFw
#214
That is all. Discuss.
#215
The prediction thread for the year 2010. Call it NOW rather than later!

My first prediction:

-Cure for prostate cancer will be discovered.
#216
I saw the dead sea scrolls, GS. They were on display at the Royal Ontario Museum when I was in Toronto and took a special trip to see them. The whole experience was very well done from the perspective of the entire exibit, with artifacts and 600 years of history of the Levant displayed with care and excellence, starting with Sepphoris in the 3rd century BCE, through Jerusalem in the Hasonean and Herodean dynasties, and to the 2nd century CE and the possible reasons behind the scrolls. The artifacts built nicely too, with the nearness to the scrolls themselves increasing on to the end of the exhibit. And there in the darkened room at kiosks behind panes of glass were fragments of hand written documents nearly two thousand years old. But by that point, I wasn't totally there.

Well, I was there, physically. My body was there. But as I moved through the exhibit something incredible was happening. I was loosing touch with all the yammering humans all around me, and reaching a place of quiet, and it was just me, and the artifacts. As I increased in this cathexis (I know now thats what this emotional connection is called, such a useful term) I wasn't really all there inside. I was torn across time and space, I was the one wearing the sandals or weaving the cord, or filling the amphora. I became those people, saw through their eyes and here I was thrust back and forth, in both places at once. My body was there but the cathexis had cause my mind to conjure up these visions.

By the time I reached the scrolls I was shuddering, and upon seeing them I was crying. There I was standing before the fragments, yet at the same time I was at the community on the Dead Sea, seated on plaster and writing HVHY in Hebrew. These things, the objects of those who had lived so long ago, were so powerful an experience that I sat in the hall of the Buddhas for twenty minutes trying to catch my breath.

Do you know what I mean, GS? Do you, in the process of a dig, pick up a flint shard or a bone, and are suddenly transported across time and space in your mind to where you are the one using or making or being that object your are holding? Are you overwhelmed by this feeling of connection to our holy and wretched species, and does it make you pause and reflect on how we could be both so wholly beautiful and wholly ugly at the same time?

I'm writing this letter to you because I thought you maybe would understand this more than anyone I know, because you work with these remains, these objects every day, and it must have SOME pull for you. Something. Some connection to a greater humanity that is awesome and terrifying and exists beyond the mundane stupidity of what passes for a persons existence in this country and day. Something beyond a view of humanity covered in McDonald's logos, not romanticized, but not vilified either, just real.

And I felt it there, and just like staring at the stars it was both empowering and draining at the same time, but more importantly it made me feel HUGE, and gave me some perspective. Those sandals...mine too.
#217
GASM Command / SCIENCEGASM
December 28, 2009, 07:12:40 PM
(A subset of POSTERGASM. via my friend Leda)

1. Purchase old science textbooks. Medical and biology texts are best, with lots of line drawings and diagrams.

2. Cut out diagrams and drawings.

3. Make some wheat paste, or get some tape.

4. Poster the shit out of a neighborhood with these.

5. PROFIT!


I did this when I was in Toronto, and aside from the cold it was honestly the coolest thing ever. It would LIGHT UP MY DAY to walk down the street and see a random diagram of ATP, or the citric acid cycle, or a phylogeny of amniotes pasted up on a pole.
#218
MERRY SOL INVICTUS YOU BEAUTIFUCL FAGGOT FUCKERS!
#220
This is a bit of interesting silliness from me, biological and systemic.

In biology, when a species is described, the specimen the description is based on is called the type, or more specifically, the holotype. If more than one specimen is necessary to describe it, these are called syntypes, and any supplemental specimens are called paratypes. Later, a better specimen may be found to represent the species, and would be designated a lectotype. In the event that a holotype specimen is damaged, lost or destroyed, a neotype may be named to replace the holotype. The idea is, species are actually represented by real, physical specimens (or cultures, in the case of microorganisms) to which the name is attached. When I say Cheumatopsyche analis, for example, I mean that there is a physical specimen of a male designated in 1903 by Nathan Banks and deposited in the Museum of Comparative Zoology at Harvard University. HH Ross determined that the original descriptions weren't adequate and published a work in 1938 designating new lectotypes, also deposited in the MCZ. Species are very real in that sense of having a physical analogue for the conceptual name. And while some will argue that there are many different types of species concepts, they will all agree that a description refers to an individual, the holotype, and a hypothesis in relation to other individuals, both described and undescribed.

So my silly question is this: who was/is the holotype specimen for the species Homo sapiens, and where is it stored?


The original description for H. sapiens was in the first publication recognized by the international code of zoological nomenclature (well, second really, but thats another story), the tenth edition of Linnaeus's Systema Natura, published in 1758. It turns out that Carl von Linne never declared a type specimen for the species, although the myth is he designated /himself/ as the type. In 1959, WT Stearns formally designated Linnaeus as the type. Unfortunately, there still was no type specimen, as Carl von Linne was buried and not deposited in a museum.

In 1994, the paleontologist Robert Bakker supposedly described the skull of deceased paleontologist Edward Cope, but unfortunatly I can't find a copy to verify. Funny arguments ensue. Is the Sterns lectotype valid without a specimen holding? Or is it the (possible) publication of Edward Cope's skull that makes him the lectotype? Does it even MATTER that there is no type specimen for Homo sapiens, since the species is "so well known"? What is with this whole TYPE thing anyway; isn't it a throwback to the concept of natural kinds and essences, and should be discarded?

It makes me wonder if some biologists should go dig up Linnaeus's grave in the middle of the night and deposit it in a museum to be done with it once and for all. A formal lectotype description will ensue.


Or maybe Bakker had the right idea and a neotype should be described. Either way, as far as the International Code of Zoological Nomenclature is concerned, Homo sapiens doesn't exist.
#221
I'm on the Graduate Academic Integrity Committee. By volunteering, I am not only required to be familiar with and understand the GAI Policy, but I also sit on hearings for graduate students who have violated the policy. Level one offenses are mild while level three can result in suspension and level 4 as a permanent termination from the university.

This Thursday I will sit with four other people and hear the case of one who is charged with committing a level 3 violation, a flagrant and intentional plagiarism on a significant portion of an important paper in his class. After hearing the case, the committee decides and recommends the punishment.

I'm not really sure how I feel about this anymore. Is it just me, or are people assholes, out to bring down anyone they perceive as unworthy? I've looked at the letter and syllabus of the accusing professor, and it seems to me he is an asshole who I wouldn't associate with in public. Regardless of what this student has written, this guy is a jerkface. But then, this IS an MBA program we're talking about here. What is it you've said about MBA's before, Roger? Fucking useless? Worthless wasteful degrees? Something like that.

I know this kid is sunk, even if he does come out clean somehow. Maybe he actually has no problems with plagarizing to get the grade, or maybe he made a simple mistake and forgot to put in quotation marks. Perhaps he grew up in a culture where using the best information was rewarded, where using someone else's words was seen as the smart way, especially if they were good words.

I don't know, Roger. The kid did plagiarize, and quite a bit too. Not only did he copy words verbatim, but he didn't quote them or cite his source. Paragraphs worth, Roger. Maybe he deserves to burn. Maybe I'll be dolling out justice, you know, fairness and equity and returning whats payed out and all those other meaningless sayings. I'll suspend his ass, because he is a badwrong person, and he deserves it, the little badwrong student. SEND HIM BACK TO HIS COUNTRY, WE DON'T WANT HIS KIND HERE!

Maybe the professor manipulated the paper and is doing this to get him kicked out.

I can't really tell. All I have is the word of one professor and a couple scanned PDF's, with handwritten notes. His fate is in my hands. I judge, I'm THE Decider. I Decide.



To be honest, I feel pretty filthy.
#222
I'm told by several people, including my adviser, that the use of molecular sequence data to infer phylogeny is a sort of phenetic interpretation. The argument is that, not only is the method of aligning sequences obscured and semi-mystic in the final publication, a sort of art, but that the phylogeny is inferred by overall sequence similarity and not by homologous characters.

I agree that molecular systematics is not cladistics, but neither is it phenetics.

Cladistics as a school places high emphasis on the use of special shared characters called synapomorphies or homologues to infer a phylogeny, so the thought of using something like a sequence, with no obvious characters or homologues other than the four base pairs as a way to generate a tree topology is a poor alternative. It is not surprising that a cladist would call molecular systematics like phenetics because algorithms such as maximum likelihood seem to mimic the overall similarity matrices of phenetics.

To understand why molecular systematics is not phenetics, one needs to return to the central premise of the phenetics school of thought. Phenetics was the reaction of strict empiricists to the earlier system of evolutionary taxonomy. The pheneticists wished to create a system with strict codes for determining hierarchy. They determined that the phylogeny of an organism is near impossible to be correctly inferred and therefore taxonomic hierarchy should not try to represent phylogeny.

Since molecular systematics at its heart is working to represent accurate phylogeny, it cannot be phenetics. So, if molecular systematics is neither cladist nor phenetic, what is it?

It seems to me that the combination of phylogenetic inference and some level of art mimics a /gradist/ school of thought, most similar to the early evolutionary taxonomy. I don't necessarily see it as a bad thing, to have two different schools of thought working together. Obviously phenetics is out, because I believe a topology should represent correct phylogeny as often as possible. Once we agree that taxonomy should include phylogeny, then there are two ways to go about inference. Either we work with the morphology, employing cladistic methods including parsimony and synapomorphy, or we work with molecular data, employing maximum likelyhood, baysian analysis, and other neogradist methods to derive phylogeny. Both are useful toolsets.
#223
Discordian Recipes / Thanksgiving for One.
November 24, 2009, 08:50:44 PM
I'm thinking of making a cornish game hen in crock pot for thanksgiving dinner. I was wondering if anyone here had done that before and if they had any suggestions. Also, suggestions for other things (vegetables, etc) to put in with it.
#224
Looks like I'll be in the city from the 14th to the 22nd of December. Make plans to worship my holy visage now.
#226
Techmology and Scientism / OFAUK 3D MANDELBULB
November 15, 2009, 10:53:59 PM
http://www.skytopia.com/project/fractal/mandelbulb.html

It looks like so many biological micro and macrostructures, it would take a lifetime to list them all. The most obvious one is coral polyps.

SO FUCKING COOL.
#227
Techmology and Scientism / Parataxonomists.
November 13, 2009, 04:26:41 AM
http://findarticles.com/p/articles/mi_m0GER/is_2000_Fall/ai_66240361/

Think of it like paralegals or paramedics. A /very/ cool idea.

My colleague and I were talking about how cool it would be to say SCREW THE DEGREE and just take off into the field somewhere remote and do parataxonomy. I mean, I think she was serious about it; I'm a horrible field biologist, and I like the work I'm doing. This idea has the whole "scientific monastics" feel to it though, which appeals to me. I'm thinking most about these lines:

QuoteCosta Rica's forty parataxonomists are beginning to solve a long-standing problem: "the taxonomic impediment," otherwise known as "the taxonomic bottleneck." The fastidious process of finding, collecting, preparing, identifying, naming, labeling, describing, and publishing new species can get bogged down at any step. But the biggest bottleneck of all is this: Today's taxonomists cannot pass on, to eager new students, the patient pursuit of taxonomy, because there are none. The best students are being lured into well-funded, high-tech, molecular taxonomy, leaving the job of collecting and naming new species underfilled, underfunded, under-respected, and fading into history.

Primary taxonomy, the science (and somewhat of an art) of describing "new" species, is as important now as ever. The science part of describing species deals with the question, "what is a species?"; the art and technology part deals with communicating both linguistically and visually the characters that determine and diagnose the species. There is also a level of parataxonomy involved; for example, I may see a specimen that looks like a particular described species but something isn't quite right, the look of it strikes me as odd and differs somehow from the gestalt visual I have in mind. This may lead me to look closer and do some visual comparisons, from which I end up determining I have a specimen in hand from a previously unpublished lineage of organisms.

Unfortunatly, as stated in the quote above there are fewer and fewer primary taxonomists willing to take the time to do real down and dirty cladistic type character analysis, and take the molecular route. Many systematists have argued sequence alignments by maximum likelyhood is a return to the days of phenetics and numerical systematics based on overall similarity rather than special shared characters (synapomorphies and synapotypies). Just like the ecologists who spend all their time in computer models, a systematist who spends all day doing multiple sequence alignments doesn't really KNOW what they're studying. Again, its all reductionism versus holism, but doesn't every argument come down to The One and The Many anyway? The solution is knowing when to use which.

I think that parataxonomists are an excellent resource for primary taxonomy as well as taxonomic inventories for the monitoring of biodiversity. I hope to see more of this sort of work in the future, much much MUCH more.
#228
Dear Roger,

The pills have finally started to kick in. I wake up in the morning and feel refreshed, go in to the university and work all day happily. I used to keep the windows shut and blinded, but these days I open them as often as possible, letting the light stream in. I've started taking walks in the afternoon sun and spending more time outside in general. Misery loves more misery, but happy people don't like being cooped up inside.

The world hasn't changed any. We're still in a costly economic recession, more than half the country denies the validity of evolution, 2 (maybe soon three) foreign wars, bailouts to the wealthy, the poor becoming even poorer, and it seems we're headed towards a thousand year cultural/social dark age. I'm still in the south, I still observe bigoted bullshit every day, I'm still in a town where the buildings are like rotting mausoleums. Homecoming is tomorrow, and with halloween, this town will be /packed/ with hundreds of thousands of screaming yahoos.

However...it doesn't bother me as much now. Even though I can contemplate the horrors listed above, even though I walk with a colleague past the big muddy field where all the frat houses are making a mess building their floats (which will take 2 weeks for the school to clean up after this weekend, and it won't look the same till next spring). She says to me, "this is whats wrong with America...no no, its just a symptom..." I ask what its a symptom of, and we can't quite put our fingers on this complex thing which is driving the insanity. Who is driving insanity? Certainly not HIMEOBS. But I'm well, I'm not so dead inside, because there was something wrong with me and suddenly the things I knew I enjoyed are enjoyable again. Remember caddisflies? Remember how excited I was? I have that same excitement again, except instead of the short lived burst ending in anxiety it's this steady flame of passion and pleasure, calm and confident. The past three days have been the most wonderful since I arrived in this decrepit town, because now I can finally ignore the decrepitude, or at least shove it out of the way while I consider more exhilarating things. There are millions of screaming yahoos, but they don't have to bring me down. I can fight now, I can stand my ground, I can LAUGH as I kick them in the nads.

Yes, the pills have made me "HappyTM", and I don't think I want to go back.

Sincerely,

Kai
#229
Techmology and Scientism / Symphony of Science
October 25, 2009, 05:32:11 PM
Remember that Sagan autotune vid, Glorious Dawn? Well, the same guy has come out with a new one, featuring ND Tyson, Feynman, Sagan and Bill Nye, and it seems like hes planing on doing more.

http://www.youtube.com/watch?v=XGK84Poeynk

http://www.symphonyofscience.com/

This is really beautiful and religious stuff for me.
#230
Or Kill Me / Jibbering monkeys.
October 15, 2009, 11:54:31 PM
Yes YOU, I mean you. All of yous. Fucking jibbering monkeys. Its like something straight out of "They're Made of Meat", all flapping and squirting and waggling and spitting out your anus like mouths, spewing horrendous nonsense, lies, ignorance and just plain STUPID TALK. I hear you all in my sleep, I hear you all day long, you maniac retard monkeys, on the street and in the office.

Its gotten so bad I can't even understand speech anymore, all the talk, even the most coherent is rendered into hoots and howls and high pitched screeches. When I go for a walk, I don't see a mother and her child walking for ice cream, I see a gorilla and a smaller gorilla  grunting and throwing their shit straight out of their assholes and picking every orifice, I SEE IT DAMN YOU ALL. A bunch of business men in suits become a squawking caterwalking maniac bunch of chimpanzees licking each others dicks. Its like I've put on one of those special pairs of movie glasses except instead of seeing the world in 3-d I see it in MONKEY VISION.

And as much as I want to take them off they won't come off, they're stuck to my face and the only way to remove them is to rip my face off! Did you hear me, I'M GONNA RIP MY FACE OFF! YOU WON'T KNOW WHAT HIT YOU!


Also, fuck you, Kai.
#231
Or Kill Me / Whats that gray puddle?
October 15, 2009, 10:37:40 PM
Sometimes you see these grey puddles laying around. In classrooms, on vinyl kitchen floors, on buses and even on the sidewalk on the way to work. You know what I mean right? The puddles are a grey goo when fresh, and over a weeks time dry and harden to an oily gray stain, like a car just took a gas dump on the floor. And you know what they are, right?

That's where someone's brain dribbled out.

You see, the brain is a sensitive organ. We THINK with it for fucks sake, it /has/ to be sensitive. And though it does just fine under normal levels of stressors, it can't handle dissonance too well. And I'm not talking filter switching and reality selection you spags do. I'm talking out of phase dissonance. I'm talking, the world tells you one too many lies. Suddenly the truth is revealed, and the strain sends it pooling out the nose like a pudding. Poor brains, its not their fault. They didn't choose to live in a world where everything makes so little sense, where everything is bombarding with conflicting ideas and it just can't tell which is right and which is bullshit.

Eventually, after too much tv, too much Happy PillsTM and pictures of Beautiful People, the poor thing just gives up. I've seen it happen before, saw a guy eating his morning bagel, reading his newspaper, and suddenly his brain started dribbling out his nose into his coffee. I tell you, it was like one of those Egyptian embalmers had taken a hook inside and liquified it, just like that.

Took about five minutes for the gray nose"bleed" to stop. Funny though, the guy didn't notice, just kept on reading his newspaper and eventually left the shop. I wonder if he ever misses his brain....no, I guess not. Without your brain, thoughts are pretty simple. And thats just how They like it.
#232
Two vast and trunkless legs of stone / Roger, it HURTS.
October 13, 2009, 09:55:03 PM
My heart is bleeding,
bloody tears of blood,
red and purple out my eyes and ears,

The pain, I never knew,
the horror, all due
to her dark heart full of blackness
and evil.

And I thought she was better,
not so hateful, not so hurtful,
a giant boot stomping, forever.


I'mma go listen to Linkin Park now.




Also, fuck you Kai.
#233
Techmology and Scientism / Scientific Monastics?
October 12, 2009, 05:46:49 PM
From the latest Nature. They run this section called Futures, which often contains some interesting literature.

QuoteLife in a monastic lab

Joost Uitdehaag

The bell rang for evensong as Jorge attached the power-pack and started his gel. He smiled. He liked it when everything was exactly in time. He left the lab and walked towards the chapel. On the way he met his older friend, Anselm, who hurried along as usual.

"Slow down," Jorge whispered. "What's the use?"

"What's the use of being slow?"

"Slow is about taking aim."

"Where did you get that from?"

"A penitence session."

"Don't mention those."

"You mean they are counterintuitive to a fearful old individualist. Really, you should join. Maybe even tonight?"

Anselm just smiled. They stopped talking as they entered the chapel. It had a pleasing retro ambience — its design influenced by Le Corbusier's famous Chapel of Notre Dame — amid the lab complex of the Benedictine Order for Oncology, set in a remote valley in the Ardennes.

For Jorge, his lab was one of the good things the great crisis had brought: a total reshuffling of drug research, an injection of idealism in a world of self-interest. That the injection had come from religion was no surprise for Jorge. Management gurus had been courting religious rules long before the crisis. Live for yourself or for your community, that was the post-crisis choice, and science and religion were both community efforts. Scientific monasticism was a new synthesis, the ultimate way of serving society.

All the scientists had gathered in the chapel, and they started a medieval hymn. Singing together was supposed to stimulate collaboration and equality, but Jorge was still bad at it. During the hymn he worried about Anselm. His friend had started to complain again about giving up the 'self' side of science. He was a former academic and had this all-pervading desire to compete and establish his name, but within the Order that would get him into trouble. They gave you a permanent contract and a budget so there was no need to worry about grants or tenure, but in return the Order demanded no double work, no egos and no secrecy.

If only Anselm had been a pharma man. Novices from industry generally had less trouble giving up the self-side. But then again, those who had worked through the Barren Years had generally less passion for their jobs than a zebrafish for a barcode.

Jorge wondered why people could not simply decide if they really wanted to live their undergraduate dreams and work on curing disease, or if they wanted something else. Anselm always said he was naive.

"Idealists have a history of getting hurt," he would say.

"Isn't that the whole point," Jorge would reply, "that contributing costs you?"

"You just haven't suffered yet."

Anselm had been damaged by his time in academia; that much Jorge knew. That's why doing penitence tonight would be good for him. It would give him that perfect feeling that all was well and that he was living a good life. If only Jorge could convince him.

The singing finished and Abbott Fra Paolini spoke about the Barren Years. That was the time when ever larger pharma companies and a society ever more hostile to them together had driven the cost of developing a drug to $2 billion. And what was considered worse: to the cost of a thousand scientific careers. It had been the scientific equivalent of the Somme offensive.

With a wide movement of his hands, Fra Paolini spoke of the day when seven ex-pharma scientists had taken up vows in a monastery to continue a 'killed' project. It was a golden move. Their vows of poverty (no patenting, no bonuses), chastity (do nothing that satisfies only yourself) and obedience (listen to what patients want) were the right guarantees for patient organizations and health insurers to pour money into monastic research labs. In the past year, these labs had developed and published the majority of new therapies (generics companies usually took up marketing them).

After the ceremony, Jorge waited for Anselm.

"Why do you fear a penitence session? You know they did this all the time in the old days: remember Borel and cyclosporine? It's part of our tradition. It is why the public likes us."

"I don't fear it. I just don't think it's rational. It's hysterics."

"I'm not hysterical."

"But you're not joining tonight are you?"

Jorge did not answer. Anselm stopped walking and gave him an angry look.

"You are! That would be what, the second time in a month? You're wasting yourself."

"The supervisory committee allowed me."

"Sure they do. Bunch of vampires, they are."

"It has nothing to do with them and all with me," Jorge hated being berated.

"I won't allow you," Anselm said.

"What do you want to do? Swap places?"

"If that's what it takes."

Jorge was amazed. Was getting Anselm to do penitence really this simple? Was he really going to give up his principle for a worry about a friend? Anselm never ceased to surprise him.

"All right," he said.

In the monastery, most clinical trials were carried out in the infirmatorium, on a veranda filled with the evening's sunlight. Jorge was sitting at Anselm's bed.

"You are getting chimidinib," Jorge said, "the first inhibitor of the Chung-Mi variant isomerase. Have you seen the preclinical data?"

"Yes. They're ok."

Jorge rolled up Anselm's sleeve as a nurse prepared the drip.

"You want some blood for western blotting tomorrow?"

Anselm nodded. "Don't worry," he said as the compound started to enter his body.

But Jorge felt guilty. That night he did the only sensible thing: he lit a candle for his friend.
#234
Or Kill Me / The amazingness of transcription factors.
September 25, 2009, 04:13:26 AM
Sitting here, preparing for a molecular biology exam tomorrow morning, I am struck with the utter beauty and simplicity that gives way to the emergence that is organized structure of tissues, organs, and all of that in relation to each other positionally, in animals especially. And the reason this is, the greatest reason that we are all beings constructed of great precision rather than just big blobs of randomized flesh and particles of different types of tissue all over,

Is Transcription Factors.

This /is/ a rant. Its a rant about how fucking awesome this shit is. And I'm going to try to explain it now, so you all can share in its complete awesomeness.


So, in higher eukaryotes (organism that have cell nuclei, like tripanosomes, earthworms and humans for example), unlike bacteria, have a whole lot of junk in their DNA. In fact, only about 30 % of our DNA sequence codes for proteins. The rest USED to be called "junk DNA", because it just all looked like random junk. Now, upstream of a coding sequence, there are all these little areas called enhancers. Enhancers can interact with proteins very specifically, and specifically, they interact with transcription factors.

Now, when you were conceived, your mother (or your mother's body really) kick started your development with a bunch of transcription factors. One she put at one end of the blobby embryo, another she put at the other end, and the back, and the belly. The diffusion of these transcription factors causes a gradient.

If you've ever seen a grid before, one of those number graphing grids, its pretty similar to how this all works. Go to one area of the grid and one transcription factor might be in high amounts (close to the butt end) but another might be in low amounts (far from the "head"), and two more are in equal amounts. You can see how this would sorta set the embryo out as a three dimentional grid with each little square having different amounts of transcription factors of different types.

Now, these original transcription factors bind to the enhancers of a specific gene in one particular area of the embryo, and for whatever reason, the interaction of the enhancers and the transcription factors and the DNA and the RNA Polymerase (the protein that transcribes the DNA to an RNA strand which can then be processed, sent out of the nucleus and made into Protein via ribosome), because this transfactor inhibits this one which enhances this one which inhibits two others which enhances this other one and feedsback and enhances the first one....

Because of this, the Polymerase binds on and takes off, makes the transcript. Now, turns out that THIS transcript codes for another transcription factor protein. See where I'm going with this?

The whole of the body is set out in a network grid of interacting transcriptions factors for which the whole of the body plan sets down on.

So, you have a gene for keratin, and you want your fingernails to be in the right place, but not for example on your forehead, or your cock.

The transcription factors at the end of your fingers during development are at just the right levels and types to interact just right with the enhancers on the gene that codes for keratin, and whoila! you've got fingernails in the right place!

So, from an initial few transcription factors from your mother, the embryo sets off a cascade of TFs flying up and down the body, compartmentalizing, segmenting, and all the right materials are getting made in all the right places.

So, what if you change one transcription factor sequence, or one enhancer sequence? Maybe it does nothing. Maybe you end up with brown eyes instead of blue, or blond instead of black, or you're missing your veriform appendix or your ears are a little lower. Or maybe its lethal, no survivors. Or MAYBE, something really novel, the idea that theres some latent gene in there somewhere that codes for the digestion of cellulose, and one transcription factor gets turned on and suddenly your stomach can breakdown wood pulp. THIS IS THE STUFF THAT EVOLUTION IS MADE OF. The genes for things like melanin, or keratin, or specific tissues are highly conserved, they don't differ much between species. But you change a TF here and an enhancer here and suddenly your organism of choice is looking completely different.

Most genes aren't expressed in a given tissue. Which ones are determines the structure and function. The transcription factors determine the location of the how and the why, starting from just a few at conception.

Kai,

Is in fucking AWE. You motherfuckers best bow to the universe in it's awesomeness.
#235
Techmology and Scientism / Lose/Lose
September 24, 2009, 12:13:02 PM
Lose/Lose is an indy galaxian/galaga style video game where you play as a space captain piloting through uncharted and alien space. Alien ships come towards you but never fire on you, and every ship you destroy gives a point. However....in the real software of the computer those ships represent files, and when you destroy one a file is permanently deleted. Likewise, when your ship is destroyed, the game is deleted. So much for little 1s and 0s. Not only is there the moral quandary in the game of destroying ships that never fire on you, there is also every time you do, you delete a file, possibly a book you were reading, a report you wrote for work or school, system files that make your OS work....yet, these /are/ all just binary code of switches, and never really exist in the sense that a piece of paper exists. When you wipe a file of all the switch organization, there's nothing left there. There's no physical possesion in files on computers. Yet I certainly wouldn't shoot down the aliens, because somehow the software is still /my stuff/, even though physically it's just on and off switches in a particular combination.

http://www.stfj.net/art/2009/loselose/

Just want to reiterate, this game /will/ delete your files. Play at your own risk.
#236
Or Kill Me / Wishywashy minds.
September 23, 2009, 03:03:11 PM
The minds of the American people have become so wishywashy. Words that used to be useful in description are no longer useful anymore. For example, a nazi used to be someone who promotes censorship, book burning, tolitarian indoctrination, genocide and eugenics, torture and other fascist characters. Now a nazi is someone who bans clove cigarrettes.

It used to be that bigot meant a clearly intolerant and discriminatory person who bases their opinions of someone on broad aspects of identity rather than the content of their character. Now a bigot is someone who thinks torture is morally abhorent.

It used to be that racist meant someone who judged people initially by the color of their skin and based all other opinions of a person around that. These days, the word racist means anyone who doesn't give the white man special treatment.

It used to be religious persecution was the inquisition, the crusades, mass murder and genocide, economic and social exclusion, forced emmigration. Now religious persecution is refusing to put up a christmas display on public property, or removing the ten commandments from a court house.

Cause the tv god can't be wrong can it? It wouldn't be broadcasting 24/7 into your living room if it was false, a just society wouldn't allow it. Yet we don't live in a just society, and we certainly don't live in a clear and competent society. Might as well start all talking in gibberish, because thats what public discourse has become, a string of gibberish and meaningless syllables, like some sort of chant which lulls the mind into euphoria. All the clear words of communication have gone to shit, and the whole of the nation are like chickens with their heads cut off. This is the disgusting world we live in, where political opinions are coddled, especially of the "poor little defenseless" white man. This is a world where I can't even call out someone on human mistreatment so deplorable it makes my blood boil.

Fuck you, Kai.
#237
Okay, just made this up today.

Start out by sauteeing minced onion and garlic in olive oil (you'll need a good sized pot.

add in a spoonful of cumin.

cut up some chicken breast and sautee that with the above and a little bit of Nam Pla. NOT TOO MUCH. Don't worry about the smell, it'll go away.

Add in 2 spoonfuls of tomato paste, can of whole peeled tomatoes, can of corn, can of chillies and tomatoes, cubed carrot and green pepper. Fill up with water (you'll want a bit more for what comes next).

Add in a cup of dry lentils.

Stir that all together with a pinch of sage, thyme, basil, oregano and a bay leaf. Also, cayenne pepper and coriander. Also also, salt and pepper (freshly ground of course) to taste.

Let it all sit and simmer for 45 min to an hour. Add more water for preferred thiness/thickness. Eat.


This soup has honestly awesome flavor. Was an experiment. Got the idea from all the lentil soups I've been making recently, and a chilli I make in the cold season. Sorta combined the two.
#238
The channel was CNN.


All you monkeys need to get the fuck off my planet.  :argh!: :argh!: :argh!:
#239
Aneristic Illusions / Someone explain to me...
September 18, 2009, 07:39:04 PM
...the reasoning in the statement:

"Getting rid of public schools and moving to private will increase the standard of education and remain affordable due to competition."

Because I just can't wrap my head around the idea that businesses would have the best interests of the people in mind, or that everyone would be able to afford private education.

~Kai,

Knows a very annoying socialist hating libertarian.
#240
Techmology and Scientism / DNA to RNA Transcription.
September 11, 2009, 02:18:57 PM
Or, how the double stranded DNA in the nucleus is transcribed to the single stranded RNA that will later serve as a template for protein manufacture.

I just had a class on the complexity of transcription factors in relation to enhancers and how ridiculously complex this whole network of additive factors is. I understood about a quarter of it.

Maybe this will help: http://www.nature.com/nature/supplements/insights/transcribing/index.html A whole segment in Nature about transcription.

Right now, however, I am feeling /very stupid/.
#241
Aneristic Illusions / You know what day it is.
September 11, 2009, 11:43:44 AM
I'm staying far away from the news and people who watch tv today.
#242
Principia Discussion / NIGEL, YOU JERKFACE!
September 11, 2009, 01:38:45 AM
YOU SUCK SO MUCH! I HATE YOU, YOU JERKFACE, AND YOUR HORRIBLE SPAGGY JERKISHNESS FOR ABSOLUTLY NO REASON AT ALL. JERK.  :evilmad:

Also, fuck you Kai.
#243
Think for Yourself, Schmuck! / Extended Mind.
September 06, 2009, 02:03:32 PM
Have any of you'all heard of this? The philosophy of extended mind addresses the minds interaction with the environment and where the boundary between the two exists.

http://consc.net/papers/extended.html

I understand that consciousness actually extends to the limit of our sensory systems (and not just located in our brains) but I hadn't considered that, for example, a notebook as an external store of memory could be considered a part of that.
#244
Apparently, there is evidence to suggest that Glenn Beck, Fox News anchor and radio host murdered and raped a young girl in 1990. I don't know the truth, only that there is a rumor flying around that Glenn Beck murdered and raped a young girl in 1990. People want to know if they have a murderer rapist in their midst, and if Glenn Beck did indeed murder and rape a young (black) girl in 1990, the world has a right to know.

The most troubling thing is, if Glenn Beck can deny the claim that Glenn Beck raped and murdered a young girl in 1990, why doesn't he come forward? Why does he not provide evidence of his innocence as to the claim that he murdered and raped a young girl in 1990? WHAT IS HE AFRAID OF?

http://glennbeckrapedandmurderedayounggirlin1990.com/
#245
http://catalogue-of-organisms.blogspot.com/2009/09/amoeba-much-wierder-than-you-think.html

The weirdness of the 5 species of Amoeba doesn't stop at pseudopods. Their DNA has over three hundred billion base pairs. That's 100 times more sequence than human (our DNA is around 3 billion base pairs). They have this radial stage where they turn into this spikey ball when detached from the substrate. Eukaryotes with absolutely no sexual reproduction; all reproduction of Amoeba species is by fission. There are these stellar aggregations of protein and RNA inside the nuclear envelope that no one has any clue what they do. Most of their biology remains completely unknown. Can you imagine how long it takes to sequence 500 chromosomes?  :x

WHAT HATH EMERGENCE WROUGHT?!  :eek:
#246
Was thinking about that old thread by LHX today, that went down when the Discordian Network database was lost back in...early 2006? Anyway, can't remember what the details were but I remember it was amazing. Anyone else remember better than me? I know X did some drawings.

Was trying to remember...
#247
http://news.bbc.co.uk/2/hi/uk_news/8216604.stm

I wonder about the result of this. Will there be a large split and new denominations from the Lutheran Church? Is this a slowly snowballing effect that started with the Anglicans ordaining a gay man? Will we see more measures like this pass in the next several years in denominations such as the Presbyterian Church?

Or, most importantly, is this going to cause the moral majority Movement to become even more crazy and dangerous?


I'm not quite sure where my opinions lie.
#248
Or Kill Me / Skeptics and dismissiveness.
August 23, 2009, 02:28:00 PM
Skeptics and skeptic websites and talk don't interest me particularly.

In part, it's because skeptics are often preaching to the choir. I understand the need for extraordinary claims to be backed by evidence and a willingness to change one's beliefs based if evidence arrives. The debunking of homeopathy, UFO's, creationism and the like are uninteresting because I already understand why these hypotheses are false. I also don't enjoy arguing with people over their personal beliefs in the above held topics (in public, anyway) so the need to internalize the argument is largely useless. I can get by with understanding what is false, and why, and not think much along those lines because there is nothing interesting going on there.

The other reason skeptic talk doesn't interest me is that it tends to be dismissive. Take religion for example. I am facinated by religion. It's a very human activity, and there are very few cultures (if any) on this planet that don't have some sort of binding central myth. I find that by studying religion and engaging in religious activities I am a better person, with greater understanding and a greater well-being. Many skeptics dismiss religion. I don't mean to say they actively bash religious beliefs and activities (although sometimes they do) but they tend to dismiss it as something to be avoided.

Why is that? I find that particularly facinating. Here we have this entirely human activity, so central to the lives of so many people, and while often destructive it is just as often creative, and a skeptic will avoid taking part. Is it because religion has burned them in some way? Is it because they can't rationalize religious activities and therefore it is meaningless? And then sometimes I wonder if there isn't a sort of religion in rationality...but I won't go that direction. I will say that human existence is rather amazing and religion is part of that. There is so much interesting stuff happening in religion, worthy of investigation not just to "show how wrong it is".

It seems to me that when a skeptical person is shown evidence that, for example, auras do not exist in the physical energetic sense, they will do either one of two things. A, they will conclude there is nothing interesting to investigate in people who do individual "aural work", or B they will actively talk and type and podcast how much of a bunch of hooey aural work really is. Both endings have a real dismissive tone. I say, lets look at this more closely. There doesn't seem to be this thing called aural energy which sits around a person and can be manipulated by thought. However, this mental excercise has some interesting results, it seems the thought process of imagining this field around oneself and manipulating it changes the way the person reacts to reality, and THAT is very interesting.

"But it's /just/ the placebo effect".

Just? /Just/ the placebo effect you say? That's like saying that the reason photosynthesis continues to function on this planet is /just/ because of photons from the sun. There's something interesting here, in psychosomatic and somatopsychic connections, something so profoundly useful and meaningful that it is, well, STUPID to dismiss.

Which is why I tend to hang out with "New Agers" more than Skeptics. The weird stuff has interesting results.

~Kai
#249
Techmology and Scientism / The science of naming.
August 18, 2009, 08:43:37 PM
I don't know if you all would be interested, but I've been thinking quite a bit about taxonomy recently. Specifically, the naming, classification and organization of living organisms into a hierarchical structure. It's sorta what I do in school and in research so the subject finds it's way into my mind space quite often.

Traditionally, there were four schools of thought on the basic reasons for classifying organisms. The first was the essentialist school, which held via Plato that all living things were reflection of divine eidos set down by god, immutable types. Around the time of Darwin, a second school called phenetics came about, which classified organisms via overall similarity. Both of these two systems have been more or less abandoned, though the Linnaean hierarchy is still used to this day.

Post Darwin, two basic systems have come about, the Cladist system ala Will Hennig which held taxa (the holder of a name) to be monophyletic (have one common ancestor) clades, and the other, the Evolutionary Synthesis system which borrowed from both cladistics and phenetics. Both try to place organisms in an evolutionary hierarchy, but Cladistics puts a high emphasis on monophyly and strict branching events based on genetic and morphological evidence, while Evolutionary Synthesis (ES) alows for paraphyletic taxa (groupings that include the common ancestor but not all of the descendents), with higher emphasis on apomorphies (specially unique characters; this is in contrast to plesiomorphies, more general shared characters).

For an easy example, Cladists would consider the Clade Aves to be part of Clade Reptilia, as the former is nested within the other via fossil and genetic evidence; as Reptillia would need to include all of the descendants to be monophyletic, and as birds are descended from the same ancestors as all other reptiles, then a bird would be considered a reptile. ES considers Class Aves to be distinct enough in it's apomorphies (feathered wings, for example) to give it "higher importance" in the classification, and therefore place it outside of Reptilia in it's own group, equal in the hierarchy; this is a paraphyletic grouping, which is completely okay under ES.

Obviously neither of these work well in situations where horizontal gene transfer takes place (bacteria, for example); in this case a more traditional phenetic approach is favored.

Now, if you looked at the example above, you can see the two systems are at odds much of the time. The Cladists and Synthesist get into big arguments over what is right and what is wrong. The cladists argue for a strict phylogenetic system where names are matched to clade which occur at branching events and follow lineages; they believe the synthesists system to be far too vague as far as evolutionary relationships go, and completely disregard lineages in their hierarchy. The synthesists argue for a more easy naming system communication wise, putting more emphasis on unique characters and the Linnaean naming system; they believe the cladist system to be an affront to the traditional taxonomy and ease of communications about organisms. Both complain of the other's "taxonomic inflation" (I've also heard the term "taxonomic terrorism" before), of the cladist's "excessive naming" of clades, and of the synthesists "excessive raising" of taxa (from genus to family for example) as "some sort of political exercise".

Some of these arguments get quite nasty. This: http://www.mapress.com/zootaxa/2008/f/zt01950p086.pdf is one of the more mild ones. The writer is coming from a synthesists background, claiming that the use of clades violates Linnaean hierarchical naming systems.

Okay, theres another argument I should cover, one that I'm a bit less neutral about, but I'll try anyway. Due to the way the International Code of Zoological Nomenclature is worded, whenever a rank change occurs the name assigned to that particular taxon must change as well. This tends to be quite political, with people raising names associated with pet projects and deleting names that they don't care for. Only the specific name (Genus species) is somewhat fixed. So, with people changing names of higher taxa all over the place, this pisses a whole bunch of people off. The ranking system which leads to the tendency to put more importance on some taxa than others is the culprit.

The alternative to this is the PhyloCode (http://www.ohio.edu/phylocode/). Many many taxonomists hate this (and will say so in rather vile language). People have a love affair with Linnaeus, what can I say. Phylocode will destroy traditional taxonomy and kill your cat, its the end of the world as we know it, or so goes the argument. People who like phylocode for being rankless with higher taxa having fixed names similar to the way species are handled under the ICZN believe it works, and will avoid all the political name changes and confusion associated with them. The understanding is thus: If we know via evidence that a particular taxon is monophyletic (thereby being a clade) why not fix the name until someone comes along with evidence to the contrary, thus saving us the confusion of the other system? I'll admit, I like PhyloCode, even with the current issues (it doesn't cover species names, for example, only higher taxa).

So the people who love Linnaeus argue with the people who love PhyloCode, and the Cladists argue with the Synthesists. And the problems continue. Names have a lot of power, and just like the person who has the gold makes the rules, the person who names taxa tends to have power and respect within the scientific community.

#250
http://www.faqs.org/patents/app/20090030925 wut

O.o

Kai,

Thinks MS is getting way too big for its own britches.

also,

.....yeah, patenting a whole biological method. Riiiiiiiight.