Evolution of Scientific Theory/Hypothesis: Lamarckian? (Ironic or just amusing?)

Random thought of the day (may or may not become a daily occurrence):

For those of you without a biological background, a primer. Evolution is the study of the development of new species from older species (ex. from ape-like beings to humans). During the development of evolutionary theory there were two competing theories. Both theories involve the transfer of traits from the parent generation to the next. Both theories also state that the accumulation of these changes/traits will eventually lead to the formation of new species. The two theories differed in where the traits came from. The first theory, largely discredited now, states that these new traits arose from an organisms own ability to change itself. A famous example of this would be the giraffe gaining its long neck via stretching. Giraffe-ancestors would not be able to reach foliage in high up places (they were vertically challenged), so they would stretch their necks. This self-inflicted change would be passed on to their offspring, eventually leading to the creation of giraffes. This theory was labelled as Lamarckian evolution. The second theory states that these traits originated among the population already and that environmental pressures would give individuals with certain traits an advantage and these traits would be passed on. While a famous example of this would be moths in Europe during the Industrial Revolution, I prefer to look at the evolution of antibiotic resistance in microbes. Many species of bacteria are susceptible to penicillin. If we take a large population of a species of bacteria and expose them to penicillin, you'll find that some of the bacteria will survive and form new colonies. In this case, the environmental pressure would be the antibiotics and the trait would be the resistance. This theory would be called Darwinian evolution.

Okay primer over, back to my story. I was reading an article about cancer and the article mentioned HeLa cells. I remembered what HeLa cells were, but I was curious as to any new research on them. Ironically, I came across a fairly old article (1991) that proposed that the HeLa cells had evolved into a new microbial species. This then made me think about evolution, and then about science itself when I came to the conclusion that scientific theories evolve in a Lamarkian manner.

Take a fictional scientific theory stating that liquid water makes aliens explode. With each new discovery the theory changes a little bit. At first it becomes liquid water makes aliens explode because they are made of lithium. In the end you have a theory about how alien physiology created a new flexible lithium. Now inspecting how this theory/hypothesis evolved, you see that with new challenges to the theory, the theory adjusts itself, becoming a new, slightly different explanation.

Looking into this further we are aware that sometimes there are competing theories that try to explain the same phenomenon. There are two outcomes to this. One, the theories merge and become a new theory (this would be akin to two species evolving into a single species [I can't think of a biological equivalent]). The second outcome would be that one of the theories is discredited. One could argue that this is textbook natural selection, but I disagree. In this case the theories adjusted themselves in different directions. The key here isn't the survival of the fittest concept but rather the origin of the differences in the theories. The theories may have started the same but they diverged by changing themselves. If the theories didn't start the same it is more akin to two different species competing for the same ecological niche.

Anyways, I'm not expecting, or even wanting the current scientific method to change. I was just amused by how scientific theories evolve in a way that is not parallel to biological evolution.

Standing desks

I converted my desk to a standing desk this morning (couldn't sleep and there was nothing better to do). Already I can feel the difference to my posture. I do understand what some people say when they complain about the pain in their feet but I think the benefits outweigh the drawbacks. You expend more energy, meaning it's one extra step in preventing obesity. Your posture doesn't slouch. Finally, since you aren't sitting, you can't really relax and do nothing. Standing desks force you to be doing something, otherwise you're just standing there.

Humans evolved a long way to stand on two feet, there's no reason why we shouldn't take advantage of that.

An empirical analysis on visual stimulus addiction.

Anime and TV shows have ruined me. I really have no one to blame but myself. Hours of constant visual stimulus via my computer has really warped me in many ways. There are three main observations I would like to point out about this 'addiction' of mine.

1. Whenever you're away from the visual stimulus, you feel like there's something missing.
2. The stimulus isolates you. There's so many reasons to go back to it and leaving it almost painful.
3. It warps your sense of time.

The first two are fairly standard in terms of addiction, but I think the third is the most interesting of all. You know what I caught myself doing one day? I started cooking an egg (hard-boiled) and I started an episode of anime. An anime episode is approximately 1/4 h long excluding intros and endings, so it serves as an ideal timer for hard boiling an egg. I was fast forwarding through the episode like I usually do and I found myself expecting actual time to speed up as well. From here I noticed that other things seemed to have changed about my sense of time. My patience has dropped almost exponentially and activities that take more than 1/4 h now seem to be lengthy and not worth it.

I've decided to wean myself off of anime and tv shows for a while (watching only an hour or so a day). I'll do this for a few weeks to see if I can reverse the time warp that has already occurred. Incidentally, this means that I'll have a lot more time to do stuff like my novel, so you might see me posting a lot more. If not, be sure that I'm still getting stuff done.

Revision software revisited

So I decided to switch away from git and to start using bazaar. For some reason git wouldn't do commits for me (probably me being stupid). I find that working with bazaar is very intuitive. Perhaps this ease of use can be attributed to the fact that I'm not publishing my work via bazaar. This means that I don't have to worry about things like pushing the changes to a server etc. For those of you who use Windows, I suggest using Mercurial (Hg). Mercurial is apparently better for extremely large projects and installation on Windows isn't very difficult, also the syntax is the same as bazaar.


Bazaar Quickstart guide:

1. bzr whoami "name "
2. bzr init (run in project folder)
3. bzr add (add all project files in project folder to bzr)

 You've now started using bzr

• bzr commit -m "Short description of change" (this commits your changes to the next revision (ie from revision 1 to 2))
• bzr revert -r# (this changes the project back to revision #)
• bzr status (see what files have changed since your last commit)
• bzr diff (see what has changed IN the files since your last commit)
• bzr log (see history of changes)

edit: It suddenly occurs to me that this would be a good way to share the project. However, this would work well if I intended to share it so as to create a novel/story that was written by a social community. My intent is more that my writing can provide inspiration (a bit conceited of me, I know) to others, rather than creating a collaborative novel.

Brilliant ideas

So I was talking to a friend about pumps. In particular, we were talking about membrane-bound pumps (cellular biology). I thought about it for a moment and I could think of no examples of a non-membrane-bound pump. Of course, with my limited knowledge, that by no means indicates that there are none. At first I thought that the whole concept of a non-membrane-bound pump was kind of odd. If the pump didn't connect to the membrane, then what was the purpose? To keep the fluid that it was floating around in circulating? I tried thinking of non biological examples of pumps and then it hit me. Perhaps the most iconic pump of all is not membrane bound. A bike pump is a perfect example of this. It is a unattached pump that attaches to a membrane pore.

This is where my 'brilliant' idea came in. As a thought exercise, I thought of practical applications of a bike pump-like pump in terms of biology. I thought that it would be a great way to deliver drugs. You could use the pump as a way to target specific cells. In essence, a pill would contain two different compounds. One compound would be the pump. This pump would be a custom designed protein with two to three functional parts. The first would be a tissue-specific ligand that would bind to a pore or channel of sufficient size for the drug to pass through. The second part would forcefully open/activate the channel. Finally, the third would be a pump specifically designed for unidirectional transfer of the active drug. The second compound in the pill would, of course be the drug.

It seems like a no brainer when you think about it on the surface and it seemed, at least in my head, to work really well. Then when you delve deeper into it there are a variety of problems to overcome. First would be that making the custom pump would be ridiculously expensive and time consuming, probably better just to make a wide acting drug and let people deal with the side effects. The second problem would be finding a receptor or pore that is ONLY on the tissue you want. Another problem would be finding a way to make sure that you're pump doesn't attach permanently. This might actually solve itself, as some receptors are internalized after activation (which might be a problem in and of itself). Of course the biggest obstacle would be the fact that many drugs act on the receptors themselves, tricking the cell into doing a desired effect, which means that there is no need of a delivery system. Sigh so much for these brilliant ideas of mine.

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Another 'brilliant' idea I had recently was a slot machine dim sum restaurant. I figured that it would be a great way to introduce newbies into the world of dim sum. By leaving the choice to chance, they get an unbiased variety of dishes. Rather than being limited to the dishes that their friends or family want, they can try out more exotic dishes. Of course, this kind of defeats the purpose of dim sum whereby you choose the dishes as they come by but it doesn't have to be used by everybody. In addition to the slot machine dim sum, a rotation-sushi-like delivery system would be nice. It is unfortunate, though that such a delivery system kind of makes the dining experience kind of impersonal due to the fact that the participants are facing the conveyor belt rather than each other. Still, despite the problems, I think it would be a cool thing to do and not necessarily limited to dim sum. I could definitely see something like this used in conjunction with Microsoft Surface in restaurants.

Feeling dumb

So as some of you know, I wrote a little script to make my life easier during the process of writing this novel. The purpose of this script was to facilitate multiple versions of my novel. I have a nasty tendency to rewrite parts of my story and I wanted to be able to keep track. This was the script:

#!/bin/bash
IFS="
"
function findfile {
for word in $filetype; do
    case $word in
        .tex) find /home/ray/ -name *.tex | sort;;
        .odt) find /home/ray/ -name *.odt | sort;;
        .doc) find /home/ray/ -name *.doc | sort;;
        .html) find /home/ray/ -name *.html | sort;;
    esac
done
}

function editfile {
for word in $filetype; do
    case $word in
        .tex) gedit $response;;
        .odt) oowriter $response;;
        .doc) oowriter $response;;
        .html) oowriter $response;;
    esac
done
}

function makerevisions {
if [ -d $directory/Revisions/ ];
then
    echo "Revisions directory exists"
    mkdir $directory/Revisions/$(date +%F-%R)
    cp $response $directory/Revisions/$(date +%F-%R)/
else
    echo "Revisions directory does not exist"
    mkdir $directory/Revisions/
    mkdir $directory/Revisions/$(date +%F-%R)
    cp $response $directory/Revisions/$(date +%F-%R)/
fi
}

filetype=$(zenity \
--list \
--title="Select filetype" \
--column="Filetype" \
    .tex \
    .odt \
    .doc \
    .html)   
if [ "$filetype" == "" ]; then
    exit 1
fi

response=$(zenity \
--list \
--title="Select file" \
--column="File" \
    $(findfile))
filename=${response##/*/}
directory=${response%/*.***}
if [ "$response" == "" ]; then
    exit 1
fi

editfile $*
makerevisions

echo $filetype
echo $response
echo $filename
echo $directory

unset IFS

Anyways, to continue my story, I found out that I was being extraordinarily dumb. In many ways I was simply trying to reinvent the wheel. I forgot that there were many tools out there that did the exact same thing. Basically, what I was trying to do was a primitive version control script. I realized relatively recently (to may shame) that I could use things like git and svn to do the exact same thing, except better. So I took a look at a few different tools and I finally decided upon using git. I chose git because, well simply, it appeared to be the easiest to learn and I could use it offline. Now I have a script that I worked so hard on (a symptom of my amateurish scripting abilities) that's, for all intents and purposes, useless.

As a side note, it should be mentioned that git these 'software revision control' tools work particularly well because I am using LaTeX. I am unsure as to whether or not it would track changes just as well if it were regular doc, odt... etc. files.

Choosing a Perspective

When I started this endeavor I thought that it would be nice to write the bulk of the story in first person perspective. This would give the readers a unique look at the world while making sure that the narrator does not know everything. However, I found that my narrator knew too much about the story. There were thing that I, the writer, did not want to disclose but the character narrating had no reason to hide. This, of course, makes writing the part difficult and some of the scenes awkward. Therefore, I am contemplating whether or not to rewrite the sections in third person. While this perspective allows the narrator of the story to know everything, there are no constraints against what may or may not be disclosed.