Sunday, January 29, 2012

Microclimates in action

No matter how many times I come back to this trail, the Hendrie Valley Loop at the Royal Botanical Gardens always has something new to see. Birds of many different colours flutter by, catching insects and gobbling up birdseed left behind by people from every walk of life. Muskrats, squirrels, beavers, and mice are some of the many animals you can see on this trail... even deer! The amount of motion, colour and life here can easily distract you from the bigger concepts at work on this trail. But on the boardwalk, there is something fantastic to look at, something to see...


If only you zoom out, so to speak, and see the forest for the trees.

The following photos were taken on December 24th, 2011 within a minute of one another. Let's compare them. The first one was taken looking south-east from the bridge. As you can see, there is frost on the ground, ice on the creek banks, and the sun is well on its way to setting. Take a look at the forest composition. There's a high percentage of conifers, and the deciduous trees have very skinny growth patterns.


This picture, taken within a minute of the previous one, is of the northern, south-facing slope of Hendrie Valley. To take this photo, all I did was turn 180 degrees; I did not do any walking. As you can see, this side is still getting sun, has no frost on the grass, and has no ice on the creek beds. Moreover, there is only a single, seemingly out-of-place conifer to be seen here. Most of the trees are deciduous, and much more lofty than the ones in the previous photo.

It is a well-known fact that north-facing slopes get less sun than south-facing slopes in the Northern Hemisphere. Go south, and the pattern is reversed. These two patches of forests are characterized by a completely different species composition, which is in turn affected by their respective geography.

And that, ladies and gentlemen, is microclimates in action.

The Frameshift Conundrum

This was supposed to be a one-sentence response for a question asked in my Genetics course BIO260

For those of you with an interest in molecular biology, this might be of interest:

-------------------------------------------------------------------------


During the translation process (currently happening in every cell in your body), proteins are assembled using an RNA template that codes for amino acids three letters (one codon) at a time. For example, the RNA letters AGA code for Arginine, while the letters UGA tell the ribosome to stop translating the string of RNA and cast aside the chain of amino acids for further processing.

This complex mechanism is not without its drawbacks. Certain mutations, namely the insertion or deletion of one or two letters, can cause what are known as frameshift mutations. In short, all of the letters downstream of a frameshift mutation are shifted in a way that makes them code for different amino acids than what would normally be coded for, resulting in dud proteins, some of which may even be harmful.

Here's where it gets interesting. If the coding of amino acids was due entirely to chance, we would expect a frameshift to result in stop codons in a way that is proportional to the percentage of stop codons in the table of amino acids. In other words, a frameshift mutation should result in a string of base pairs that codes for a stop codon only once every 21 codons on average (64 possible codons / 3 stop codons). In reality, the occurence of a stop codon is much more frequent following a frameshift, usually within just a couple of codons downstream of the mutation.

This means that amino acids are coded strategically, so as to be able to respond to frameshift mutations with a quick termination of the translation process.

This may be due to the evolutionary pressure (i.e. natural selection) for stop codons following a frameshift. From a survival standpoint, this makes perfect sense. If stop codons are more common following a frameshift mutation than what would be found at random, an organism will make much shorter dud proteins. This means that less building blocks (amino acids) are wasted in the making of these dud proteins. I imagine dud proteins are also less likely to tangle into harmful messes if they are short rather than long.

This is a fantastic example of evolution acting on even the most basic processes of life.

Sunday, January 15, 2012

Sprouts


Winter is a time for dormancy. Annual plants have given their lives for the next generation, dispersing seeds into sheltered crevices. Perennials are tucking deep into the soil, pulling themselves away from the oppressive weather. Even the trees, mightiest of giants, have shed their leaves; the ones that haven't find their growth reduced or altogether stopped, holding out for warmer times.

Despite the subzero temperatures and the reduced sunlight, however, my windowsill is teeming with life. In quiet coalescence, a handful of mung bean seeds, turn into a tangle of mung bean sprouts.



The easiest method, in my opinion, is the jar method. It works for most types of sprouting seeds.

Jar Method
1) Take a big, clean jar and fill it with lukewarm (not warm!) water
2) Wash a handful of sprouting seeds and put them in the jar of water
3) Use a strainer lid or a cheese cloth (held in place with a jar ring or a rubber band) to "cap" the jar
You must allow proper air flow and drainage through the lid
4) Let soak for 6-8 hours, then drain. This is the only time you soak the seeds.
5) Drain, rinse, drain, and lay the jar on an angle so that any remaining water drains out
6) Rinse and drain twice daily (once in the day, once at night)
7) Repeat step 5 until you get some sprouts

My current equipment consists of an upcycled instant coffee jar with a hole cut out of the screw-top lid, "capped" with some cheese cloth.



Sprouting is one of the easiest ways to get nutrients and enzymes into your diet. It costs next to nothing (two to twenty cents per jar of sprouts), requires no fancy equipment, and can be done in any part of the house.

Keep in mind, however, that not all seeds can be sprouted. Even more importantly, not all seeds that can be sprouted should be sprouted! There are sprouts that are downright poisonous (e.g. anything in the tomato family) and seed sources that are likely to be treated with harsh chemicals (e.g. mercury-coated seeds). It is also important to be aware that clumps of wet seeds in the process of sprouting are extremely susceptible to bacterial infections. E. coli, Salmonella, and other dangerous microorganisms may get to your sprouts before you do.

Indeed, there are various things to learn before starting your sprouting adventure. This post is not meant to be a resource for all the necessary knowledge, only a blurb to get you interested in the process.

For a more detailed analysis of the world of sprouting, go to sprouting.com; the website has a vast array of educational and commercial resources at your disposal. Use it wisely, however. You might not necessarily need a $130 sprouter when a couple of jars will do the job. You may not want to order their seeds, either, if you can buy them at your local health food store. As with anything, make sure you know what you're getting yourself into.

As for me, I'm about to enjoy a peanut butter and mung bean sprout sandwich :D

That's all for now,
--Ioni

Sunday, December 4, 2011

Essay - False accusations: Reactions to Darwin’s On the Origin of Species


A couple of weeks ago, I fished reading Charles Darwin’s On the Origin of Species. I'm taking an interesting class right now, JHE353: The History of Evolution. In contrast to all of my other classes, this class is not considered a science course, though it undoubtedly deals with scientific theories. By the same token, it deals with very many unscientific theories as well. The course examines popular notions about evolution from ancient times up until the 1950s. The evaluation is divided between two tests and a 2000-word essay, as well as nominal participation marks for showing up to the tutorials.

Having long wanted to read On the Origin of Species in its entirety, I took the essay portion of the course as an opportunity to read the fantastic and controversial work. It led to an essay that has brought me a much deeper understanding of Darwin, and of both the brilliance and erroneousness of different aspects of his theory of Evolution by Natural Selection. Reading his book and writing my essay also allowed me to finally finish an artwork I had left on the back burner for too long of a time.

Without any further ado, I present to you my essay. Please ignore the hyperlinked endnotes.

---------------------------------------

Ionatan Waisgluss
November 30, 2011
JHE353

False accusations:
Reactions to Darwin’s On the Origin of Species

Throughout the history of evolutionary thought, man’s perceived relationship with nature has undergone significant changes, each geared towards the mentality of its respective era. Intuitively, these relationships can be split into those which are descriptive and those which are prescriptive. The distinction is based on whether they employ the naturalistic fallacy, viz whether they make the assumption that nature provides a model for human affairs. Prescriptive relationships with nature can be found all throughout history, but experience an especially strong resurgence after the publication of Charles Darwin’s The Origin of Species and towards the turn of the 20th century. Around this time, eugenic references to the natural ways, laws, or order can be found in countless publications of popular culture, such as magazines, letters, or pamphlets. Without a doubt, the age after Darwin’s publication represents a turning point in man’s relationship with nature. There is ample documentation of Victorian and post-Victorian reactions to Darwin’s work, particularly in the form of sensationalist caricatures. A concerningly large number of these responses react to Darwin’s work as if it held a prescriptive model of nature (i.e. employed the naturalistic fallacy). In this essay, I will prove that Darwin’s work was by no means prescriptive. The following paragraphs will show that Darwin did not believe, state, or otherwise imply that man should follow the example of nature, since he did not support the ideas that might makes right, that man should take evolution into his own hands, that man is reducible to an animal, or that man and nature are entirely one and the same. For this purpose, published works, including various collections of cartoons and articles, have been retrieved and included with the essay when appropriate. Proof of the descriptive nature of The Origin of Species have been derived from Darwin’s work1 and journals2, as well as various secondary sources.

A common doctrine attributed to Darwin is that of might makes right, where morality is decided by power (for instance, strength and influence). A very immediate attribution of this doctrine to Darwin can be found shortly after the publication of his famous work. In 1896, an extremist book by the name of Might is Right: The Survival of the Fittest was published under the pseudonym Ragnar Redbeard. The book begins with a quote from The Origin of Species, that "inferior organisms succumb and perish or are enslaved. Superior organisms survive, propagate, and possess."3 Might is Right goes on to employ the naturalistic fallacy full-force, arguing that it is right for the sun to shine, since it is observed doing so, and that since Darwin’s laws are observable, they must be right as well.4 The logical error comes from assuming that man should base his actions on what happens in nature. Might is Right argues that nature favours the fittest, and that man should become more fit, as nature (and Darwin) commands.5 However, Darwin’s definition of the fitness of a given organism is not based on power (i.e., might) but in “infinitely complex relations to other organic beings and to external nature.”6 Moreover, Darwin clearly states that he uses the concept of struggle for existence in a metaphorical sense; survival of the fittest can be a function of mutualistic interactions between organisms, or even success despite a harsh climate.7 It has more to do with success in leaving progeny behind than with any other observable trait on which one would intuitively (though erroneously) base fitness. Stephen J. Gould has called Darwin’s principle of fitness a tautology, since survival of the fittest refers to "the survival of those who survive."8 Indeed, Darwin’s definition of fitness has nothing to do with the axe and hammer insignia associated with Might is Right, or to the dog-eat-dog mentality associated with Darwinism. The idea that might makes right does not echo Darwin’s thoughts, but merely applies the naturalistic fallacy in anthropocentric ways which Darwin does not.

Might is Right is often labelled a Social Darwinist work, since it applies the principles of Darwin to society. In contrast to Darwin’s descriptive work, it advocates the idea that the human species should take its evolutionary fate into its own hands. It is worth noting that The Origin of Species does not make any mention of improving human fitness; this is not accidental, but a consequence of Darwin’s beliefs about the limitations of man. Darwin states that natural selection is “immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art.”9 A prescriptive interpretation of Darwin’s natural laws overlooks his obvious preference for the hand of nature over that of man, and that as a consequence, a prescriptive application of his natural laws would not only go against his sense of aesthetic (an minor point), but very importantly, against the improvement of the species. In The Origin of Species, Darwin challenges the reader to consider how he would go about improving the fitness of a given animal in the wild, for the sole cause of “[convincing him] of our ignorance on the mutual relations of all organic beings.”10 Clearly, Darwin does not believe that the human species could be improved by anthropocentric selection. Realizing this is key to separating Darwinism from Social Darwinism, Nazism, and Eugenics.

Another reaction to The Origin of Species is well-documented in the form of sensationalist caricatures, articles and other social artefacts. Cartoons about evolution had been around since before Darwin,11 but became even more prevalent after Darwin’s controversial book. It is also worth noting that no other Victorian evolutionist was as frequently or intensely caricatured as Darwin.12 Darwin’s proposal of man’s place in nature, wherein man shares the same types of selective pressures, and parts of an evolutionary history with every other animal on earth, was misrepresented by sensationalist media as a proposal that men are reducible to animals. Three social artefacts have been drawn from Darwin Online13 and included with this essay (Images 3, 20 and 26 from the database). These images show variations on people’s idea of man as animal as interpreted from Darwin. Image 20 is a very literal interpretation, wherein Darwin’s theory is satired by showing its author as an ape. Image 26, a poem about the implications of Darwinism, is much more metaphorical, drawing on human characteristics given to different animals (e.g. the courage of a lion, the lowliness of a snake), and attributing them to a believer of Darwinism. Image 3 shows yet another take on man as animal, wherein Darwin is portrayed as being an inhuman beast by way of what he is alleged to do to his son in the name of science. Here, it becomes important to take into account Darwin’s personality, as the labels “ape-like” or “inhuman” seem ill-suited to a man who sees “beauty and infinite complexity [in] the coadaptations between all organic beings”14, or who manages to include a beautifully poetic Tree of Life analogy in a book of science. Even in talking about the struggle for life, characterized by its brutality, he sugar-coats it by claiming that we may “console ourselves with the full belief, that the war of nature is not incessant, that no fear is felt, and that death is generally prompt,”15 all of which are assertions without a scientific basis, and on which he does not elaborate. He goes on to say that the organisms which get to multiply are those which are vigorous, healthy, and happy.16 Such examples of anthropomorphism riddle this famous work; Darwin’s charming personifications are far from the work of a heartless animal. Natural selection gets a similar treatment, alleged to reject the bad and preserve the good in each species, tirelessly improving it over time, for “the good of each being.”17 Darwin even goes as far as to call slave-making in ants a wonderful instinct.18 Here, any allegations of inhumanity by way of Darwin’s reaction to slave-making in ants should be quickly quelled by his labelling of the slave-making instinct (independently of ants) as odious.19 This reaction is likely brought on by Darwin’s travels to South America— particularly his visit to Brazil, which prompted him to exclaim in his journal Voyage of the Beagle that he would never again visit a slave-country.20 Darwin is as much of a Humanist as anyone else; he writes and thinks beautifully (at least in the opinion of the author of this essay.)

The ambivalent treatment of the slave-making instinct brings to mind another point about Darwin’s placement of man in nature. The only strong reference to mankind’s place in nature in The Origin of Species is late in the book, where he nonchalantly states that his theory will throw light on the origin of man and his history.21 There is much more to be inferred, however, from the way in which Darwin defines what is natural and what is not. In various parts of the book, Darwin uses the word unnatural to contrast the way in which things develop in nature. A good example of this is when he talks about organic beings produced by unnatural conditions and unnatural crossings,22 referring to experimental conditions produced by humans. The concept of varieties of organisms as a result of domestication is a big theme throughout this book, particularly in Chapter I. In a later chapter, the subject matter of Chapter I is referred to in passing in an interesting term that continues to be used today: artificial selection.23 This term could easily be replaced with human-mediated selection, as one could call the evolution of certain fungi ant-mediated, but Darwin chooses not to do that. Darwin’s usage of unnatural and artificial in reference to human intervention tells us a great deal about the relationship between man and nature in the mind of this famous author; namely, that man is different enough from the rest of nature to be able to intervene. If this is the case, then the claims that Darwin’s work reduces humans to animals is not at all justified, as he makes an implicit, yet pervasive distinction between nature and man. Darwin implies that man is part of nature, but different enough for his constructs to be unnatural, and his behaviour artificial. This implicit disjunction of nature and man leaves no room for the naturalistic fallacy; why should man behave like nature when he is implicitly different?

In closing, it is important to realize that in order to truly understand a work that deals with man’s place in nature, one must be able to account for whether it is descriptive or prescriptive. It seems that because Darwin’s theory is so consequential to our perceived place in nature, critics have overlooked the fact that Darwin’s work does not tell us what we should do, but only how nature changes over time. Failure on behalf of contemporaries and later interpreters of Darwin to categorize his definition of nature correctly is likely, due to the sensationalist nature of the media, and to the agendas of the groups which draw their unsound support from Darwin. Hopefully, it will be clear to the reader of this essay that The Origin of Species does not employ the naturalistic fallacy, as Darwin claims that the definition of fitness is beyond human understanding, and that nature is much better at evolving a given species than would be man left to his own devices. Additionally, Darwin does not believe that man is reducible to an animal, since he has very Humanist and anthropocentric ideals. Most importantly, Darwin believes man to be distinct enough from nature so as to not be able to take his morality from it. All of this being the case, we should perhaps reconsider such terms as Social Darwinism and Post-Darwinism, especially in the contexts of eugenics and social engineering, which draw fallaciously from nature, and which have little to do with the views of Charles Darwin.

1DarwinOn the origin of speciesvarious
2DarwinVoyage of the Beaglevarious.
3Redbeard, Might is Right, preface
4Redbeard, Might is Right, 94
5Redbeard, Might is Right, 95
6DarwinOn the origin of species61
7DarwinOn the origin of species62
8Gould, Darwin's Untimely Burial
9DarwinOn the origin of species61
10DarwinOn the origin of species78
11Clark, You are Here
12Browne, Darwin in caricature
13Wyhe, The Complete Work of Charles Darwin Online
14DarwinOn the origin of species109
15DarwinOn the origin of species78
16DarwinOn the origin of species78
17DarwinOn the origin of species84
18DarwinOn the origin of species219
19DarwinOn the origin of species220
20Darwin, Voyage of the Beagle, [see works cited]
21DarwinOn the origin of species488
22DarwinOn the origin of species265
23DarwinOn the origin of species109



Works Cited

Browne, Janet, “Darwin in caricature: A study in the popularisation and dissemination of evolution,” Proceedings of the American Philosophical Society 145(4): 496-509, 2001, accessed November 21, 2011, http://dash.harvard.edu/bitstream/handle/1/3372264/Browne_Darwin_Caricature.pdf?sequence=1

Darwin, Charles, On the origin of species. A facsim. of the 1st ed., with an introd. by Ernst Mayr (Cambridge: Harvard University Press, 1964), various pages.

Darwin, Charles, Voyage of the Beagle: Journal of researches into the geology and natural history of the various countries visited by H.M.S. Beagle (Online: Project Gutenberg, 2008), accessed November 20th, 2011, http://www.gutenberg.org/cache/epub/3704/pg3704.txt. [Ctrl+F: “On the 19th of August we finally left the shores of Brazil”]

Clark, Constance A., “You Are Here: Missing Links, Chains of Being, and the Language of Cartoons,” FOCUS—ISIS, 100:3, 2009, accessed November 22, 2011, from http://www.kean.edu/~bregal/docs/You%20Are%20Here.pdf

Gould, Stephen J., “Darwin's Untimely Burial,” Natural History 85: 24-30, Oct. 1976, accessed November 8, 2011, from http://www.stephenjaygould.org/library/gould_tautology.html.

Redbeard, Ragnar, Might is Right (Online: Archive.org Community Texts, 2001), accessed November 20th, 2011, http://www.archive.org/details/MightIsRightByRagnarRedbeard, various pages.

Wyhe, Dr John van, The Complete Work of Charles Darwin Online, 2002, accessed November 8, 2011, from Darwin Online: http://darwin-online.org.uk/content/frameset?itemID=CUL-DAR140.4&viewtype=image&pageseq=1. [Images attached to bibliography]

Image 3

Image 20

Image 26


Monday, September 12, 2011

Hidden alleyway (Bathurst & Bloor)


Since moving to Borden Street at the start of September, I’ve been continuously exploring the Bathurst & Bloor area, always on the lookout for interesting shops, venues, places to practice parkour, and, of course, street art!

Bathurst & Bloor is a fantastic intersection. Most people know it for the iconic Honest Ed’s, which now incorporates Sonic BoomHero Burgers,and The Wine Rack; it’s worth visiting for its sheer size, if not for its fantastic deals. For additional awesomeness near this intersection, check out Midoco’s incredible selection of arts & crafts novelties, have a drink at a bar named after a disorder of your choice (Insomnia or Amnesia), or see what’s playing at the Bloor Cinema.

Walk west for tasty meals in Koreatown, east towards UofT, north through the Annex, or south through Mirvish Village. Indeed, Bathurst & Bloor is a heck of a hub!

For those interested in street art, I found an absolutely fantastic alleyway with extraordinary graffiti. The alleyway is in between Borden and Brunswick, and starts just south of Bloor. The best way to get here from Bathurst and Bloor is to walk east to Borden St., walk south past Kilgour’s, make a quick left, and then a quick right. There are some painting styles in this alleyway that I haven’t seen elsewhere. The place is a graffiti museum, and I’m lucky enough to pass through it every day on my way to and from home! The nearby establishments The Green Room, and Tranzac, are also elaborately decorated with street art, and are great for drinks and atmosphere after a day of wandering around alleyways.

Below are some of the art pieces you may see, though keep in mind... street art is ephemeral, which is part of what gives it its charm.








Happy exploring,
--Ionatan Waisgluss

Tuesday, September 6, 2011

Rush Lane

If you happen to find yourself in the Queen and Spadina area, just south of the magic of Chinatown, you’re only steps away from a guerilla art gallery of astounding proportions. Half a block south of Queen St., stretching from Spadina Ave. west to Portland St,, there is a series of laneways known as Rush Lane, or Graffiti Alley. Within this very walkable area, you can find all shapes, sizes and styles of guerilla art on surfaces ranging from the railings of fire escapes to oh-so vulnerable brick façades.

According to various sources, a group called Style in Progress is given a 24-hour period by the city to legally paint Rush Lane each summer. Their website is currently down, but the group can be reached via their facebook site. In reality, a significant portion of the art that is up on Rush Lane is not affiliated with Style in Progress at all, but is done illegally at other points in the year. The result is a hodgepodge of contrasting styles that gives the alley an ever-changing, very unique quality that is a must-see for all street art enthusiasts.

The space, intended for delivery trucks, is frequented by a mix of pedestrians, street art enthusiasts, photographers, and (of course) graffiti artists. Rush Lane also happens to be the filming location for Rick’s Rants, of The Rick Mercer Report fame. Below are some photos I took while wandering west along the alley.










If looking at so much amazing art has left you hungry, you can always have a some cheap, delicious food at Java House (Queen & Portland, where Rush Lane ends), or go for a reasonably-priced Venezuelan specialty at Arepa Cafe (490 Queen St. W.).

Happy exploring,
--Ionatan Waisgluss