Peru: Sure, they want to sell you art when you are a tourist but when you're an anthropologist they'll share their lives for a meal.

Still in Cusco. For some reason I walked down to the plaza de armas (not the real name) to try and find an Internet cafe with wifi. After several attempts at several different restaurants I started seeing the same people. You walk by, say hello and sometimes strike up a conversation if you are looking for something. After they have tried to help you and you still show up it gets kinda funny. The English in the square is excellent, but I like practicing my Spanish when I can. After a time you figure out they like practicing their English, French, or Japanese. It is whatever gets thrown at them really. It's their lively hood. Still, some of them appreciate the attempt. Most of the square is geared towards selling you something. They will sell you a shoe shine, the opportunity to take picture of women dressed in traditional clothing and a baby lamb, random textiles, an Incan massage that is curiously propositioned at night only, and vibrantly colored art. The shoe shine kids tend to be annoying, the massage girls illegal in the states, and the art kids funny. The hosts hang outside the restaurants and pull in whomever they can for a cut of the bill. This makes them particularly veracious. I was in the middle of getting mauled by a mixture of three when I made a sort of contact with a host at a restaurant. An American group walked by that caught his eye and he attempted contact. He wasn't too pushy or rude, but the a particular American girl felt the courage of her group course through her veins and she snapped at him. After the host turned away I apologized to him for the tourists of my country. The result: Instant friendship. The crowd of salesmen dispersed quickly and we chatted for about 20 minutes and his insights became genuine while his manner slackened from the ridged back of someone working hard to pull in affluent clientèle. After we broke off with a Peruvian handshake , fist and elbow bump, I started to walk away. I was instantly overtaken by a pair of art kids. I responded by saying “no, gracias,” as a couple days in the city have taught me, but this too was different. They had apparently been watching me while I talked to the host and they asked me what I was after. I told them a meal with spice and some internet. They were ignorant of the latter but more than happy to show me to the former. For a short time I let these two show me through a couple of narrow streets and I thought I might actually get a chance to use my knives. In reality though they showed me to a Mexican restaurant. The information was not without a catch because they asked if I would pay for a taco for each of them. The exchange rate for US to Sole is 3 to 1 and they had taken me to a fairly well priced place where a taco cost about 2 dollars US. I agreed. The conversation was a mixture of English, Spanish, French, Japanese< and Quechua. It was genuine and open. We asked about how each came to where they are currently and what they planned to do. They were cousins, the younger was 16 the elder 24. They sold art and confessed that none of the many salesmen were the artists. I had guessed this, but they told me there were only two real artists. The elder was going to tour guide school but worried that the government was going to make it a college only enterprise. This was a concern because his Los Angeles living grandfather was paying for his schooling in Cuzco which was not college and previously valid. The Younger had grown up in a small village in Peru and was currently learning Spanish and English because he only spoke Quechua. I learned that the shoeshine crew promise the price is at a sole but afterwards tell you it is a special brush and jack the price to 40 sole. They spoke a lot about the history that they knew, the places they had been, and told many tricks of the city. They were concerned that I was carrying a bag so late and gave me their number just in case I ran into problems, invited me to a soccer game they were playing, offered me an in on touring, and were very free with my anthropological inquiries. They liked the fact that I worked with bones and that I was helping them learn about their own people. In the end they told me the story about the plaza, which I knew, but told me that the local people call it the plaza of tears. They told me the Quechua name, which I forgot, and gave me another Peruvian handshake-fist-elbow-bump and pointed to the best internet cafe they knew. I enjoyed myself today. This must be how cultural anthropologists fell when they start their field work.

Peru: Who needs LSD or Halloween when you have religious certitude.

Mind you, I am not opposed to dressing up and screaming as loud as you can about reconciling the bible with real life. We get that a lot in the states, and I actually find it more entertaining than television. You kill as many brain cells and the crowd response is like caramel on a sundae. Today in Cuzco I spent about ten minuets listening to a group of people dressed as prophets and Semitic tribesmen trying to explain the presence of the Incas in the old world. It took abut five minutes before I had to get my camera out. This, of course, attracted a good bit of attention from the senior screamer and he therefore approached me as I walked away. He spoke some decent English (much better than my Spanish) and handed me a paper written in English that explains what he was all about. I thought it might have been theater, but it wasn't. The sight, should anyone be interested, is http://www.israelcongregaciondejehova.com/. I am certain I could run this through a google translator, but would it make anymore sense then? Probably not. The main thrust of this entry is that I need to see more roots in our crazy sermons. I can't recall the last time I saw an angry anti-gay protester dressed up as the John the Baptist, much less an random Semite circa Roman occupation.

Defecating in Peru: A users guide.

I have been in Peru for a little over two weeks at this point. The largest culture shock was going to the bathroom. As opposed to Japan, no one warned me about going to the bathroom in Peru. You can't wipe and flush it down the toilet. It really isn't all too shocking. It makes sense when you think about the piping here, which isn't very good. It is simply something that you have to think about. Wiping and then throwing the shit-stained paper into a small trashcan placed neatly by toilet. I am certain this is the case in many parts of the world, not just Peru. The rest is pretty much what you will get when you travel outside the United States. People warn you about what can go wrong, but it isn't really much different than what can go wrong at home. You have good people, and bad people. You just know less people when you travel away from home. Depending upon your circumstances this can be a good thing.

I noticed something else about the toiletries here in Peru. Nothing has a child safety mechanism. They aren't nearly as hyper-paranoid about their kids getting into things and liability. It is actually somewhat refreshing. I have been traveling on the bus for a lot of the trip. They don't really have a vast train system or anything like that. Just bus and taxi and motorcycle-three-wheeled-thing. The bus is a very interesting place to meet new people. I was in the middle of this on my first bus when a lady in an official looking uniform came by to videotape me. She moved from seat to seat, zooming in and out of peoples faces. I asked what it was all about in broken Spanish and the girl I was talking to pantomimed a bus going off a cliff. Apparently they hope to identify charred remains with a videotape after the bus crashes and we meet our deaths. This is standard operating procedure. I thought it was nice of them to even think about it, but I also know my forensics. If a bus goes off a cliff they will need dental records at the very least. More than likely they will need DNA. I think it is just there to make the people think that their remains will be properly treated if they die. Eschatology drives humans to some stupid ends, doesn't it?

Nothing can't be something, something can be nothing. The mind

The mind and the brain. A complicated inter web of chemical processes that is desperately attempted at being defined as two separate entities. But is it really? Not necessarily, no. Think of a seed becoming a plant, only as an isolated event. Not how it got there, or why it got there. In order for a plant to exist, it must sprout from a seed. But a seed need not become a plant to exist. The brain is to the mind as a seed is to a plant. The brain can exist without a mind; a seed can exist without becoming a plant. However, a mind cannot exist without a brain and a plant cannot exist without a seed. One may bring up the point of clipping a plant and cloning it to become another plant. But that would fall back on the need for the initial seed to have sprouted. A mind only exists within the brain. It cannot be separated from it. If the mind were indeed separate, then where is it and why would it stay connected to us? We experience our mind behind our eyes, our perception, and our senses. So then would it not make sense for it to be in there, beneath the flesh and within the brain? Our vision comes from our brain, as do our thoughts. Our vision projects out onto the horizon, but it doesn’t exist or occur from without. It is a result of our optical nerve. Our thoughts are to our mind as vision is to the optical nerve. The abstract, the logical, and the radical thoughts that make us who we are cannot exist from outside of us. What’s keeping them separate? What would prevent other people’s minds from bumping into my own and merging mine with their thoughts? If that were the case, bumping minds, would I not feel it? My mind is a part of me; if it is spacial then it should press against things. To imply that the mind exists externally implies that it is something tangible. I can’t grab onto thoughts or emotions, I cannot hold “sad” or “happy” in my hand. If the mind truly was external, should I not be able to touch it? Should I not be able to feel its affects physically against my skin, or find it somewhere near me? The abstract thoughts such as "I wish I was a dragon" come from the same thing that something as simple as "I'm hungry, I want food" comes from. What is the difference between them? Just the complexity really, but they are coming from the same thing which is desire. Both those are expressions of desire. One is simply more blatantly cause and effect from a rumble in our gut. This is the complexity of humans. We go so far out into thought we come up with crazy, insane notions. That may explain why the next jump is that we have a mind separate from the body? Does it need to exist outside of the body? No, it does not. There is no logical conclusion that anyone could come up with for a mind to have to exist, as a necessity, separately from the body. For the mind to exist outside of the body it would have to be spacial. It would have to be something of nothing, in the notions it has been described to me. If it really is there, outside of the brain, it should be able to be seen. One might bring up the point that you cannot see oxygen. The only problem with that point is that the presence of oxygen is a testable situation. If I am breathing, and not turning blue, that is an obvious indicator of the presence of oxygen. If that is not enough, then let us light a match. Does it burst into a flame? Yes it does due to the presence of oxygen. The point I would make to further that it cannot exist externally, is nothing would hold it here. The opposition may state that ideas, thoughts, and memories can exist outside of us. Yes they do, but within a medium. Much like the brain to the mind. I can say “I once hiked on Long’s Peak when I was young.” That idea has no spacial qualities, and I cannot see it. However, I experienced it and other people experienced it. It has a memory to back it, and maybe even a visual document of this. This piece of writing, in fact, is an external representation of my mind. These are my thoughts finding a medium; finding a concrete existence from my brain to my nerves to the black plastic cushioned by my fingertips onto the screen. These phrases, words, and symbols are a result of my mind. In order for them to become something concrete, they are fully dependent on my brain function. If my brain does not work, then my fingers will not work and my ideas would never become ink on paper. These thought and ideas that come from the mind are a product of extraordinarily high brain functions that occurs in the frontal lobes of humans. A cognitive mind is a result of that. It is nothing holy, or supernatural. The mind existing outside the body has no means of being tested and confirmed that it is such, and no visual documentation to back that claim. It is simply a result of a chemical process from within our brain. Furthermore, have you ever noticed that the coma patient or severely mentally ill seem to have lost their mind? The coma patient is completely unconscious, and the mentally ill patient has gone completely into dementia. Both of them have their brains, but the mind is gone. There's no doubt about that. Where did the mind go? Did it not like its person? If the mind was indeed separate, it makes no sense for situations like the previous to be the only case for the mind to disappear. Why aren’t minds just getting up and leaving everyone? Where are they going? How can that be explained rationally along with the dualistic idea? It cannot be. The fact that the mind does not leave the completely healthy person shows that it is in fact dependent on the brains proper function. Therefore, the mind and brain are in fact one and the same and the mind must exist within our brain.

An Introduction

I am a first year student at Front Range Community College, I'm majoring in Anthropology. The reason I chose Anthropology was because I've always had a major fascination with the Ancient Egyptian culture. Eventually, I would like to examine mummies. Identify who they were, see what ailments afflicted them, so on and so forth. Another major interest of mine is Philosophy, I think that stems from the enjoyment I get from arguing and discussing heated topics. The discussions that spur within many a philosophical topic are always interesting. I want to use this blog to post writings I have spent some decent amounts of time on through research and contemplation, and to further my appreciation for science and philosophy.

Darwin's pertubration - Intro to Methylation

This will be the kick off for Darwin's perturbation effect. The first section in a rundown of epigenetic research and its place in evolutionary context. Being that this is an open to everyone (even anonymous) commentators. I am hoping for all types of comments. Bash it, add to it, tell me if it makes sense. This will be a multi-part event, released every few weeks. I am not stupid enough to hold to a schedule I will apologize for not being able to make. On a positive note, I have had some people sign up as authors and we will hopefully see something from them soon.


Darwin’s Perturbation Effect: Natural Selection and the Field of Epigenetics

In 1859, with the publication of On the Origin of Species, Darwin was unsure of the mechanism for heredity. Had he lived to see Mendel’s particulate inheritance be incorporated into this position, eventually giving rise to the modern synthesis, he would have been fascinated by the implications. Over the course of 150 years these two theories have guided the course of research. They have prompted us to sift through the soil in search of ancestral forms, redefined what we know about medicine, and brought our search for origins to a simple four letter code from which variation blooms. Now, advances resulting directly from these lines of inquiry have moved us towards a technological sophistication that allows us to appreciate a new layer of complexity within the evolutionary framework: epigenetics. Paradigms are being refined by advances in methylation, histone modification, meiotic inheritance, imprinting and chromosomal positioning. These studies are currently being driven by new methods developed in order to understand the epigenetic phenomenon. Many of the developing methods within this new field are helping us to comprehend phenomena that are not well understood by classical concepts of genetics (Stam and Chandler, 2004). With this theoretical thrust firmly in mind, it should be noted that as the study of epigenetics expands, so does the definition. This was a central question at the conference held at the Académie des sciences in Paris in May of 2008.

At this conference it was suggested that the definition previously assigned: “the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence (Feil 2008 and Stam and Chandler, 2004).” This definition, though functional, fails on some accounts in the wake of new insights. At the conference a separate definition was suggested: ‘the structural adaptation of chromosomal regions so as to register, signal, or perpetuate altered activity states’” (Feil 2008). At the heart of both of these definitions is the ability for genetic information to be “read” differently depending upon the context of a specific environment. The implication for such a phenomenon is that an environment could produce a phenotypic change by way of an alternate reading of genome depending upon the circumstances an organism is subjected to. This alternative interpretation leaves the genome unaltered and does not require a mutational event to produce variation within a species and could potentially be reversed through a similar epigenetic mechanism (Rassoulzadegan et al. 2007). Such a concept invokes the idea of a nature versus nurture dichotomy which is prevalent in popular media but truly has no bearing in the scientific community. What is apparent is that there is a demarcation problem surrounding which pole of the spectrum has the larger influence in ontogeny. Epigenetics, therefore, could be instrumental in broadening the point of consensus. Before such a revolution takes place, however, we must understand the way in which the genetic code is interpreted by those organelles responsible for transcription and overall phenotypic expression. The best understood method for a cell to achieve this select interpretation is DNA methylation.

A portion of a gene becomes methylated by the direction of the enzyme methyltransferases. Within this enzyme family are two different types, those that maintain methyl patterns and those that create new methyl patterns (Takashima et al. 2008). When a gene becomes methylated it becomes silent and transcription is thought to no longer be possible. It is of note that this pattern of gene deactivation in animals is only found on the dinucleotides Cytosine and Guanine and appears to be essential for the proper development of most eukaryotes. When the gene for methyltransferase Dnmt1, 2, or 3 is knocked out in mice, death or malformation occurs depending upon which combinations remain (Suzuki and Bird 2008). Furthermore, aberrant methylation patterns have been noted in a number of cancers, potentially by way of hypermethylation and oncogene activation (Takashima et al. 2008). Evidence such as this is strong support for the claim that the cause and effect of methylation patterns should be explored. From this several different patterns of methylation have been noted in a variety of organisms.
In invertebrates a ‘mosaic methylation’ pattern is noted. This pattern is characterized by areas of heavily methylated DNA spaced by those that are methylation free. This pattern is also seen in the plant Arabidopsis thaliana (Suzuki and Bird 2008). A separate pattern is evident within vertebrate genomes. This pattern is one of global methylation, where Cytosine and Guanine are universally methylated. This pattern is broken by large unmethylated islands of Cytosine and Guanine (CpG islands) that range from 300 to 3,000 base pairs (bp) long. Unmethylated domain areas account for about 2% of the total. This does not mean that these islands cannot become methylated. It has been observed that somatic tissue can vary in the level of CpG island methylation on genes that are central to development, such as homeobox and paired box (Suzuki and Bird 2008). Even the global methylation pattern remains causally ambiguous, but it is thought that it is established during the implantation and gametogenesis stages of ontogeny (Takashima et al. 2008). Although nothing in vertebrate DNA has yet been uncovered, a variety of non-vertebrate and plant genome assay have exposed a spatial dynamic in which methylation patterns are being revealed in actively transcribed genes, thus denying methylation’s sole property of silencing transcription (Suzuki and Bird 2008). Should this be discovered in vertebrate studies, an entirely new implication for globally methylated patterns could arise. Technological barriers revolving around the relatively large size of vertebrate genomes have thus far dispelled any hopes of mapping the methylated human genome in any great resolution. Still, simultaneous assay techniques and 454 sequencing in parallel with bisulphitetreated DNA are bridging this technological barrier (Suzuki and Bird 2008).

In DNA methylation landscapes-provocative insights from epigenomics by Miho Suzuki and Adrian Bird points out that the unique pattern of vertebrate global methylation landscapes could be a result of an immune system adaptation. It is not difficult to see that a select pressure could be so extreme that an organism could overcome the detrimental consequences of remapping the methylation patterns that are surely ancestral (Suzuki and Bird 2008). The hinge of their argument is that plasmacytoid cells, a type of B cell, can potentially trigger an innate immune response. Specifically “toll-like receptor 9 detects genomes of invading bacterial pathogens by recognizing DNA that is rich in unmethylated CpG moieties (Suzuki and Bird 2008).” Being that methylation is so prominent in vertebrate genomes it would then reduce the risk of an auto-immune response. Potentially lending support to this is the way in which the Epstein-Barr virus (EBV) is linked with auto-immune disorders such as Multiple Sclerosis. A demonstration of DNA methylation may affect B cell behavior in an attempt to evade destruction (Kurtuncu and Tuzun 2008 and Mehler et al. 2008). If this exploitation of epigenetic factors is the case for diseases, then certainly variation in methylation patterns should be a focus of human variation. Past studies, such as the one by Fraga et al. looked at the deviations between methylation patterns of monozygotic twins, demonstrating a significant gap between patterns relevant to age (Fraga et al. 2005). Another study the following year undertaken by Eckhardt et al., was aimed at generating a picture of methylation variance within a large sample size. Groups of people of varying age, between 22-30 and 60 and 76 were examined. The average difference in this group was only .275%, and .1% between the genders. When the cell types were examined in a similar goal a statistical difference did appear, CD4+ lymphocytes versus fibroblasts registering 7.1% (Eckhardt et al. 2006). The seemingly contradictory results of these studies will only be elucidated by improved techniques for mapping epigenetic changes, and better gauges for determining what a significant deviation is.

Not good.

Figuring out what works.

Being that the Blog has been dry for a bit, I have decided to attempt a new formula. As of this post I will be working on a theme arc. This will be a larger body of study, handled in sections, thereafter posted over the course of time. In between these posting there might be a peppering of smaller topics and the occasional rant. Hopefully this will spur me to write more, read more, and think out loud more often, while preserving a more academic tone.

Also, there may be a couple of posts coming in from other people. This is part of the new formula as well. Over time, I hope to get a fairly regular gathering of people to contribute and enrich the blog. The idea of including opposing views is also being tossed around, but only those that are honestly interested in dialectic. This would be an attempt to find common ground. Should you be interested in being a part of this, comment on this or any other section.

So very wonderful.

A post about another blog better than mine.

A nice little blog entry via the slate Human Nature section. The dangers of faith are fairly highlighted, and the point of science in regards to such things as acupuncture are treated in kind.

http://www.slate.com/blogs/blogs/humannature/archive/2009/01/21/faith-and-healing.aspx

Quick Little Post

So this is a simple little article done by the BBC about the detox myth that was passed onto me by a friend of mine. They spend a good deal of time talking about high visibility companies, but this applies triple to mom and pop "shops" that don't have to pass FDA regulation in the United States. This falls into the category of potentially or extremely harmful psuedoscience.


http://news.bbc.co.uk/2/hi/health/7808348.stm

If you want a really good treatment of what something like this can potentially do visit:

http://whatstheharm.net/

Actually, just go there anyway. It is a read that should make you cry like a vegan in a meat packing plant.