Friday, July 29, 2011

Random Thought: A Response to Carcinogenesis as Speciation.

In a recent article that has been making its rounds in layman news media, Duesberg et al. (2011) have been proposing that carcinogenesis should be considered speciation. In other words, this means that cancers should be considered new species and that the formation of cancers are, in fact, the creation of new species. This paper is both intriguing and shameful at the same time.

Tuesday, June 7, 2011

Random Thought: Genetics, Evolution, & Eugenics

A recent slew of articles in Science caught my attention. All the papers highlight the effect of epistatic interactions between beneficial mutations can cause a decline in the rate of increase of fitness of the population1,2,3.

A little background first. Evolution is the process by which a population changes in order to adapt to some selective pressure. This usually occurs by the weeding out of individuals who are not as fit as the others. As this occurs the fitness of the population as a whole increases.

In the lab we can study evolution in bacteria. We expose bacteria to a selective pressure and see how they adapt and evolve. With gene sequences we can tell exactly which genes have been altered/selected. The researchers of these papers did exactly this. In the one paper, researchers took, the bacteria and exposed it to low glucose (main food source) environment and looked at the adaptations that resulted2. The saw that there were five mutations that were being incorporated into the bacteria.  They showed that the decreases in the increases in the fitness could be attributed to negative epistatic (gene-gene interactions) effects between the beneficial. While I did read the paper I didn't really understand, it seems they did some math magic and some other stuff (not an evolutionary biologist, didn't really get everything they were talking about).

Anyways, this got me thinking about the current state of human evolution. In my opinion, humans are currently in a state of evolutionary limbo. Our technology, medicine (courtesy of our intellect) have overcome any environmental stimulus in place of any biological adaptations.People of all shapes, sizes, intellects, colours, dispositions, et cetera are breeding without regard to the increasing fitness of the human population (some breed merely for the concept of 'love'). There could, of course, be selective pressures that I am not taking into account (irony will probably have radio waves or some such man-made thing become our next selective pressure). Some have presented the solution to this problem: artificial selection.

Eugenics is process by which humans select traits that they wish future populations to have and breed accordingly. Eugenics also includes the selective breeding out of certain traits/diseases. Using this, we could theoretically, artificially evolve humanity. This is an impractical method though, for all of humanity would have to abide by the eugenics program (or at least one large enough to branch off into its own species). I'm of two minds on this topic.

On one hand, I wouldn't mind humanity evolving into a bunch of beautiful genius olympic-level athletes. By doing this we could accelerate our technological advancements as well as increase our physical preparedness for disaster. One of my fears is that our brains will become a limiting factor in our technological development. What happens when to advance the current state of science we have to study for 40 or 50 years just to get caught up. What happens when the 'basics' are beyond the capacity of the human brain. If we do not either become more intelligent and have higher brain capacity, eventually our technological development may not grow either. We could also rid ourselves of a number of genetic diseases, securing the medical future of our race.

On the other hand, I fear the repercussions. Evolution itself requires that there be variability in a population. Eugenics, is in essence a program in which we decrease the variability of our population. We remove those traits that we dislike or find unattractive and we keep only those that we like. Should we take this too far, we may face the same problems that our monoculture crops currently face. If a disease or other selective pressure comes in the future and we've removed so much variability in our species that no one individual has an immunity, we will have caused our own extinction. Furthermore, I don't believe we have enough knowledge of our bodies that we can make educated assumptions about what traits are truly beneficial. On its face, sickle cell anemia is a very detrimental disease, whereby red blood cells are deformed. This causes poor oxygen transport, which leads to a wide variety of symptoms. However, it does confer upon the individual an increased immunity to malaria. What if, in some future we discover that a gene that increases the risk of leukemia actually grants protection against HIV (or some other disease), but we've eliminated it from our population. We'd have lost a valuable, yet seemingly negative trait.

The obvious solution to this would be genetic engineering (another way we could artificially evolve). We keep track of all current traits and their various genetic permutations, and when we find one we want tor bring back, we just engineer it into our populations again. I didn't mention gene therapy/engineering in the same breath as eugenics due to the fact that the technology just isn't on par. We can and are (sperm/ova banks) implementing eugenics, but gene therapy for the purposes of evolution are far beyond our current capabilities. Setting aside the moral dilemmas that eugenics might create, I think we should hold off until we require it, or until we have a near complete understanding of the human body at a molecular level (all pathways mapped).
    1. Kryazhimskiy, S; Draghi, JA; and Plotkin, JB. 2011. In Evolution, the Sum is Less than its Parts. Science. 322:1160-1161
    2.Chou, HH; Chui, HC; Delaney, NF; Segre, D; and Marx, CJ. 2011. Diminishing Returns Among Beneficial Mutations Decelerates Adaptation. Science. 322:1190-1192
    3. Khan, AI; Dinh, DM; Schneider, D; Lenski, RE; Cooper, TF. 2011. Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population. Science. 322:1193-1196

Wednesday, April 6, 2011

Random Thought: Statistics in science

I was conversing with a friend of mine about the research project that she was doing and we both came to an agreement. Statistics should not be done by the researcher. There are two main reasons why I think that statistics on a set of data should not be done by the researcher who gathered the data.

Wednesday, March 30, 2011

Disney deaths

I know I'm not the first one to notice this but a lot of Disney villains die by falling. I recently watched the movie "Tangled". The movie was a fun romp but I didn't like the ending...


Sunday, March 27, 2011

Random thought: Greenhouse effect and solar energy

Comparing the effects of greenhouse effect and solar energy. I was thinking and I came to an odd thought: is it hypocritical/counter-intuitive to use solar energy to combat greenhouse effect.

Primer: The greenhouse effect that some believe is contributing climate change. Light penetrates the glass and heats the interior of the greenhouse (heating the surfaces it touches upon), the heat is then radiated into the air. Rather than letting it pass through the heat is absorbed into the greenhouse gases and then re-radiated outwards, sometimes back into the surface. End result is that the greenhouse is warmer than expected. More of the sun's energy remains upon the Earth rather than being reflected/radiated back into space.

The basis for solar energy is capturing sunlight and converting it into electricity. I know of two methods that they do this. The first is through photovoltaicism (probably spelled that wrong), whereby photons are absorbed by a metal and a current is generated. This is what you see on lawn lights and calculators. The second I know heats up a medium and then converts the heat energy into electricity, in much the same way as conventional electricity generation. This method uses mirrors instead of panels, to focus, rather than collect, the sunlight onto one spot. This spot is usually inhabited by something with a high specific heat capacity. something like molten salts. This way the energy is stored long after the sun has gone down. The heat is then used in some sort of engine to drive a turbine or otherwise generate electricity.

Overly simplistic thought: Greenhouse gases (CO2, CH4, etc.) trap the sun's energy and convert it into heat. Solar power traps the sun's energy and converts it into heat, and then into electricity or directly into electricity. This electricity will likely be used and will, eventually produce heat. So Is using solar power contributing to the problem rather than helping it.

The other green power sources don't run into this problem. Wind, geothermal,and tidal utilize energy already absorbed by the planet. This energy comes from within the earth, from the movement of the earth, from the movement of the moon around the earth, and from the sun (only the energy that would have originally been absorbed by the earth)

So, is solar power adding to the problem rather than solving it?

Edit/Update:  Something I forgot to mention. A relatively recent solar power idea that I've read about is to beam energy collected from space down to earth. This would likely be done from a geostationary satellite that gathers the sun's rays and transmits them down to a receiver platform on earth via laser or microwave. This is, in many ways worse than conventional solar power with regards to this article as solar energy that would have normally passed the Earth by would then be transmitted to the planet.

Earth hour

So, at 20:30 today it was Earth Hour. When you try to do your best to turn off all your electronic appliances and lights in order to save the planet just a little. Or at least something to that effect. By the end of the hour I realized that I probably wasn't really making a dent. Other than the otherwise minimal light-pollution that I emit, my other footprints didn't exactly shrink. Turning off all my lights and my computer saved a measly 5*13 (CFL lights) + 400W (computer assuming max power usage [unlikely]). A drop in the bucket compared to the other things in my house, the stove and the oven. While I realize that in the end my computer and my lights are on a lot longer, I doubt I made an impact. To be honest I think that the future of energy savings is in increased efficiency rather than reduced usage. I'm lazy. I'm much less likely to actively reduce the amount of time my electronics are on, rather I'm much more willing to upgrade my hardware to increase power efficiency. LED light bulbs, efficient computers, induction stoves... these are the future.

Sunday, March 20, 2011

On Jell-O (I'm dumb)

So the stores that I visit sell two versions of Jell-O. The sugar free-and the normal Jell-O. They are approximately the same in price. However, the unit price of one is FAR better than the other.

Sugar free:


As far as I can tell they both taste EXACTLY the same. I just recently bought a bunch of regular Jell-O. The reason: cuz I was caught off guard by the unit price. I thought that it might make more Jell-O. They both make 500 mL of Jell-O. In reality, I was just paying for sugar filler.

Chapter 1, Section 2

Wind and Sand

The sound of wind and surf woke him. The water ebbed up and down his legs. He lay there enjoying the feeling of the water on his legs and the sand beneath him. His eyes remained closed and the world around him was a mystery. This was a mystery that he was less than anxious to solve. What lay beyond the thin layer of flesh separating him from the outside world? The sand beneath him was hot and the water coursing up and down his legs was cool. The world could still be on fire and he did not want to wake up to such a world once more. A man can not stay in his dreams forever, though. Eventually, he would have to open his eyes and face whatever appeared before him. Still, he decided to lay there for a moment more, determined to put off such a confrontation for as long as he could.

When his eyes opened he almost wanted to shut them once more. The fire island had been teeming with unnatural life, where new rock and sky were constantly being born. Here, in this new land, there was a complete absence of life. Had the fire island been given life at the cost of life in other lands? He had washed upon a land contrary to the one where he woke up in. All around the world was barren. An abnormal quiet had festered in this place. Even the seas seemed muted, devoid of life. He should have heard the wind rusting among the reeds and grasses near the shore. There should have been the sounds of birds screaming for food, and fish splashing in the water. This was a new world. So full of life, and yet devoid of life at the same time. Before his lengthy slumber he thought he had seen all the world had to offer. In truth, he had only scratched the surface. Endless desolate seas, empty barren beaches, flaming scorching islands inhabited the world now. Perhaps the only thing that gave him hope was that the sky did not reflect the land. Stars still dotted the celestial landscape and the moon still hung in the sky. What other astonishing things awaited him? What other horrors?

For a moment he expected the gods to answer him. For a moment all was still. The gods were toying with him, no doubt they would wait until his guard was down before raining down destruction upon him once more. For now, nothing calamitous appeared to be coming his way so he began to decide upon the myriad of decisions that befell him. In truth, there was only one real option. The remaining decisions were merely of the where, the when and the how. The direction; now or later; by water or by foot, these were the choices. Each of these choices were equally valid. He could only hope that what he chose would lead him to civilization, or at the very least a place where the old rules of the world still hold true. His journey began with this hope planted firmly in his mind.

He waited a day before leaving. He slept during the day. He had already seen what daylight had to offer, now was the time to see what surprises night had in store. He awoke to the sun on his face, something that relieved him more than he had expected. Since his initial awakening he had not seen the sun. He had suspected that it still illuminated the world above the clouds of smoke and ash, but he had had no real evidence. The shore stretched towards the rising sun and, as far as he could tell, so did the barrenness. He chose his direction. He would follow the setting sun. This way he would have more daylight with which to explore this new land. Since this direction ran parallel to the shore, he would not be in short supply of water. That is of course, if he could find a way to remove the salt.

He did find a way to freshen his water. A clever system using large stones from the sea and the sun's powerful rays. This though, did not make his trek any easier. In fact, the system reversed his earlier decision to journey through the night. Since he had to wait during the day for the water to collect, his movements were restricted to the night time. Travelling in the night was cold and dark. He would injure himself upon unseen obstacles and often found himself having words with the ground. There was one unexpected boon about this though. He did not have to see the barren wastelands around him.

As far as he had gone, he had still not found anything that could be considered food. Either there was nothing there, or they were very adept at hiding away from him. A week passed and he was finding himself increasingly fatigued and lethargic. Stomach pains plagued him throughout the day. He began to see hallucinate. At first, he was amused by these visions. They would relieve his loneliness. That would soon change when the images began to taunt him. He would see food off in the distance. He would chase after, only to find that nothing but swirling sand.

The sand too was a danger. Some days, dark days, the wind would pick up and the sand would pierce his body. No travelling was done these days. He would hunker down and pray for the wind to stop. Sometimes he would be lucky and there would be a dune, under which he could take shelter. Other days he would weather the storm as best he could. Not a great deal of time passed before he realized he was dying. Either the sand would kill him or the hunger would. He tried to drive these thoughts away, but he longer he stayed in the desert the more persistent the thoughts became. He found solace and no little amusement in a single idea. The idea that his death would provide evidence to future peoples that there was life in this land. His corpse might one day be the source of academic discourse. A barren land with a single life.

His dreams of being an anomaly would end abruptly. In the distance grew a settlement of some sort. Unlike any he was familiar with. The closer he came, the more he realized that this was no mirage of his mind or of the desert. At first he was irked. One dream had died and he could not paint an ironic picture in the history of the land. This feeling passed, and it passed very quickly. This was solid proof that there were others besides him. He was going to live, and he would no longer be alone. He arrived in the dark of night, and he would not truly see the city until the next morning. When he did, the sight took he breath away.

Great stone buildings littered the land. Each building was exquisite. Each seemed to be carved from a single stone. The buildings were diverse in design. Despite the diversity, there was a harmony among the buildings. Towards the centre of the settlement the buildings rose higher and higher, culminating in a single spire that seemed to touch the sky. He had difficulty comprehending the sheer size of the city. Even the largest of his peoples' cities paled in comparison. This city must have housed many hundreds of thousands, perhaps more. And so many houses. Each inhabitant must have been given their own abode. This would be unheard of in his society. This city was so strange, yet so wonderful at the same time.

He would later learn that the appearance was not the only wonder the city had to hold. The central spire's apex was obscured as the spire pierced the clouds. He couldn't fathom why people would want to build so high. The air above the clouds was thin and cold, the wind especially strong. Then he heard it and he understood everything. It, in this case, was the song of the city. The spire acted as colossal flute. The gods would play the flute using the wind itself. A powerful melody swept the city. Though the purpose was unknown, the music was beautiful. He could imagine with ease the people of the city stopping to savour the sound.

The thought brought him back to the moment. He had still not seen anyone. He was not surprised though there were plenty of explanations. A civilization such as this could build down as well as they could build up. They would likely be underground, shying away from the searing sun. They would come out when the sun set. He did not wish to offend them by invading their abodes before then. So he waited. Darkness was a long time in coming. He wasn't sure if he minded. The anticipation was intense. Did he mind the anticipation? Not in the least. Even if there were no people here, he knew that the world had not been remade anew. Here was proof that there people still dwelt on this world. He would find them.

Using gaming software for map generation

One of the games that I play is a turn-based strategy called Battle for Wesnoth. It's a free game (GPL'd) and it comes with a map editor. I found this to be a superior way to make maps for my storyboarding. I've yet to find a good way to convert it to an image file... I'll get back to you with the results.

UPDATE: figured it out (I'm dumb, there was a map screenshot hotkey).

UPDATE: I forgot that the textures are GPL'd as well... can't post it here

Grab it from here:

Or here


I'm not really an artist so the things that I post here will most likely look fairly crude. Anyways, here's a potential map for my setting. You'll notice that it was sketched on the back of a piece of scrap paper. I'll get around to cleaning it up later.

UPDATE: retraced over lines in GIMP (Gnu Image Manipulation Program)

Saturday, March 12, 2011

Preliminary thoughts on the Enlightenment desktop (E17)

OS: Arch Linux
Architecture: x86_64

So I had to reinstall my computer the other day. For some reason, likely my haphazard tinkering, My home partition wouldn't mount. This is a big deal because everything is on my home partition and really I made my root partition too small. I knew it wasn't a problem with the partition itself, rather a problem with the operating system. I COULD mount the partition when I booted up into other OS's (ex. Ubuntu 9.10 and Arch setup disks). I was hesitant at first about reinstalling. I actually wanted to find out what was wrong and fix it for future reference. So I headed off into the world of linux forums. I posted my problem along with the output of of several commands (mount /dev/sda4 /home, dmesg | tail, fdisk -l, blkid, fsck.ext4 -fv /dev/sda4) as well as a few files (/etc/fstab). The help I received there was swift, within minutes of posting someone already responded. However, the help I got was of little use. While I probably could have gotten it fixed eventually with the help I was receiving, I'm impatient and decided just to reinstall. One thing though. I did as a bit of a stupid question and I got a bit of a sarcastic remark, but that's kind of to be expected. Looking back on a few things, I think it may have had something to do with an invalid journal inode.

So I was reinstalling when the thought occurred to me that this was a golden opportunity to try out the Enlightenment window manager v 0.17. I had heard good things about it and I was unsure as to whether the path that GNOME was taking was what I wanted. One of the first things I noticed was the lack of good user-level documentation on their website. This could have been due to the fact that their wiki was in migration, but I'm not totally sure. Installation was easy, a single command through the terminal.

Starting up the desktop for the first time a quick questionnaire pops up asking you for things like what you want in your quicklaunch. Once that was over you are shown a mundane desktop with a single dock/panel (they call it a shelf). I must say Enlightenment has a bit of learning curve. First of all, switching desktops is triggered by moving the mouse to the edge of the screen. This is a hassle if you aren't used to it. Don't know how many times I've switched desktops trying to close a window. But this kind of behaviour has benefits too. Making the switch easier, fewer buttons etc. The next thing you notice is that clicking on the desktop opens the application menu. This is kind of nice. This gives a previously unused space into something useful. Middle clicking the desktop opens a list of windows. This means that so long as you've a piece of desktop open, you can access any opened applications as well as open anything. The window menu (right clicking on the title bar) gives a wide variety of options, including: adding to the quickstart, always on top, lower, raise, pin to desktop. You can even customize the window borders for that particular window. This makes the look of Enlightenment very customizable. One thing I have to say about it though is that it takes a lot more to 'always on top' a window, it's nested in a few menus).

Now onto the 'shelves'. You can have as many as you wish but there are only 12 spots to place them (one on each side). I guess you could have individualized panels for each of your desktops but that's probably excessive. The shelf itself is a bit glitchy. Trying to remove 'applets' will cause the whole desktop to freeze. As a workaround one can disable the module associated with the applet.  These applets are pretty standard, sound, taskbars, quicklaunch, weather, time, etc. Most of these work really well.

Finally, there's the settings manager. Here you can configure almost EVERYTHING. It's nice to have a graphical way to access all your desktop settings.

Overall I think that with enough tinker time, I can get this desktop to look and behave jsut the way I want it to. I think I'll keep using it until I find something better. I wonder what it will be like once it's out of beta stage of testing.

Friday, March 11, 2011


First I would like to extend my sympathies to those living in and around Japan.  I hope that all that are missing and injured are found and that they recover.

It's funny. I initially started this blog to get story ideas out of my head and now it's focus has diversified quite a bit. Today's topic food. Lots of ground to cover actually.

Let's start with the context. We had hotpot at home and in the end we had leftovers, a little bit of everything. As usual, I started to put a plan together to use up the leftovers. So I thought I'd share how I clear out hot pot left overs.

In my house we eat hot pot with rice (I know it's kind of odd), seafood, beef, lettuce, tofu and whatever else is in the fridge that would go well in hotpot. Usually we have a little bit of everything save the rice left over. The easiest way to clear out all of this is to make noodle soup. Basically, you boil the noodles, and then dump them in the hot pot broth. Instant noodle soup. Now this maybe undesirable because it's really like eating the same thing you ate the night before. Separately, it takes a bit more work.

Let's start with the sea food. I find the best option here is to make salt and pepper sea food dishes. The reason for this is that the seafood is already shelled and cut into little pieces. What you do here is you mix the seafood with a little bit of lemon juice/wine/vinegar, soy sauce, cornstarch and oil. Then you fry it in some hot oil. Take them out just before they're done and set them aside. Next fry up some sliced peppers and onions. Throw in your seafood, salt (I like five spice salt), pepper, chilli pepper to taste.

The beef and the tofu is just asking to be made into mahpoh tofu. Just stir fry with oyster sauce, soy sauce and spices and you're done. Lastly the lettuce and the hot pot broth can be a side dish used to temper the saltiness and the spiciness of the above dishes. The final thing you have left then is the dipping soy sauce. If you were smart you would have used them cooking the above dishes and you'll only have a bit left. It would be a waste to just throw it away so I usually just add it to my batch of soy sauce chicken broth/sauce.

And that's how I clear out hot pot leftovers (nothing left).

Wednesday, March 9, 2011

Chapter 1, Section 1

A short note before you read. The following is mostly a third person re-write. The prologue will be the same as before.

Fire and Water

He awoke with a start, shivering despite the heat of the day. The terror and despair of the vision lingered even as the memory began to fade. These dreams fatigued him emotionally. While the dream would only last the night and the memory quickly disappeared, the feelings, especially the intense ones, stayed and tainted his mornings. Once the last vestiges of the dream ebbed away, he found his body torn and tattered. Lacerations, small and large, ragged and straight, clean and dirty, all evidenced a night spent rolling around scratching at himself in a vain attempt at extinguishing illusory flames. He cursed. Already, his nights were filled with horror, did they have to taint his days as well?

As if in answer to his unvoiced question, the ground underneath him burst outward. He was showered in scalding hot debris, blasted with with a wave of hot air and shocked into attention at the sheer fury of the event. For the first time of the day, he focused his attention outward rather than inward. He looked around, taking in his surroundings. Shaking his head he closed his eyes. He took a deep breath. When his heart slowed, he dared to open his eyes again. When he did, dread filled his heart.

He dreamt of terrors that infected his body well into the day, now he found that his dreams had grown into reality. All around him the world was aflame. The ground seemed too hot to touch. Wisps of smoke rose from the blackened land, rising to merge with the dark miasma above. Smoke and ash filled the air filled the air creating a false night, lit only by the sporadic bursts of reddish lightning. Pools of steaming liquid, surrounded by orange, yellow and green crystals dotted the blackened land. Behind him sat a vast lake, unlike any he had ever seen. The lake sparkled, not with the reflections of the sun but with its own internal illumination. Yellow and orange with a thin layer of broken black covering the surface, the lake roiled and bubbled and burst. Sometimes there would be small geysers of the viscous, golden fluids, spewing forth high into the sky before darkening, stained by the soot and falling back into the lake. Those drops that did not quite return to the lake would splatter against the earth and give rise to new rock amidst a torrent of smoke and steam.

The sounds of the land were everywhere. There was a tremendous roar emanating from the lake, much like the ocean but much much louder, only the thunder from above was louder. The rumble from the ground was palpable. As the stones rained down from the fountain of gold they chattered, announcing their conception. Some, not read for the world, fell back into the glowing lake with an audible thwack. There were other sounds, sounds that he could not quite place. A crashing perhaps? Hissing? He was unsure whether the sounds were unknown to him or that they were being obscured by the dominant noises of the area.

A thousand fragrances floated through the air. Burned rock and ash were ubiquitous, and made the air difficult to breathe. The air was hot but not dry. In fact, the air was humid, something that he found quite unusual. Though the crystal-lined pools steamed, they did not seem to dissipate and were unlikely to have caused the amount of moisture in the air. A smell, reminiscent of rotten eggs, emanating from these crystalline pools, turned the air rancid. Rotten though they may have been, the scent of eggs stirred within him a fierce hunger. For a moment, he lost himself in his hunger and let himself dream of nicer things. He dreamt of honey soaked bread and a cold mug of mead. He shook himself. He could not be entrapped by his daydreams.

Leaving took top priority. The ground was frying him and the hot and humid air was steaming him; he was being cooked alive. He began to walk away from the molten lake, towards one of the crystalline pools. He leaned down to the foul-smelling water and touched his lips to the water. He scrambled away from the water, wiping his lips with his hands like a mad man. Looking down upon his hands, he saw blood. The water had burned him! Even his arm was beginning to burn, the hair shriveling and his skin curling. What kind of cursed land was this where even the water burned? There was no alternative. He had to escape and he could not dally. He ran away from the lake, dodging any of the burning pools that came in his way. He had not gone twenty steps before the ground cracked and gave way. His foot slipped into the hole, as if he had stepped on thin ice. Underneath the thin sheet of rock hid a reservoir of water. He screamed as his foot was enveloped in pain. The land was intent on killing him. He crawled, burning his hands upon the ground. At last he came upon the end of the land. He found the source of the mysterious sounds and scents, he had come upon an ocean.

Looking around him, he discovered that he had awoken upon an island of fire, surrounded by the sea. The ocean crashed upon shore. Where the water touched upon the land, vast columns of steam would be born and sometimes, the land would crack. The smell of salt and water displaced the smoke and the ash and burning rock. He began to despair. How could he escape? The land was too hot to bear and the water burned like liquid fire. Was he expected to fly? Once more he began to wonder what this land was. Had the Sun descended, burning away the water and giving birth to new land while willing its properties upon the water? Perhaps he had not been only been cursed but honoured as well. He could be witnessing the Sun reenacting the miracle that began the world.

Miracle or not, he was still stranded. He could neither stay upon the land nor swim away. That is what he thought. That is, until the mist from the surf met his skin and did not burn. He inched forward, unwilling to risk the possibility that his senses were misbehaving. When he felt the splash of water again, and observed that his flesh was still whole, he rejoiced. Not wasting another moment, he dove into the sea. In his haste he forgot one important thing. Sea water makes wounds sting. Upon entering the water, he was inundated with pain. His face, arms, and foot were afire anew. The world darkened and the pain disappeared.

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.

Saturday, March 5, 2011

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.

Friday, March 4, 2011

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.

    Wednesday, February 23, 2011

    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.


    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:

    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;;

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

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

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

    response=$(zenity \
    --list \
    --title="Select file" \
    --column="File" \
    if [ "$response" == "" ]; then
        exit 1

    editfile $*

    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.