Tag: Science
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Explaining Hidden Markov Models (HMMs) using Pac-Man!
The DNA Pac-Man game (https://github.com/HussainAther/dnapacman) can represent how protein sequences are generated (using Hidden Markov Models). We can draw an analogy of how HMMs work in the context of generating protein sequences using the Pac-Man. The next token/letter you eat is the next letter in the sequence of generating a sequence of protein amino acids.
Essentially, if we organize regions of the Pac-Man board representing different hidden states in a Markov Model, then the next letter that Pac-Man eats can represent the next state an HMM selects. We can change the probabilities a certain letter may appear and, when Pac-Man enters the hidden state, then the probabilities would change.
We can observe how the probability for different states changes as people play based on which letter they choose next. We can compare the HMM of Pac-Man to the HMMs in modeling eukaryotic genes following the methods of this manuscript “Hidden Markov Models and their Applications in Biological Sequence Analysis”: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766791/
Full post here: https://github.com/HussainAther/DNAPacManHMM
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Political Virtue of a Virus
A cell infected with a virus in the show “Cells at Work!” Metaphors for a disease can teach us more about them. Coronavirus has become something else. Analogies of COVID-19 being like an evil force of nature, on the edge of life and death just as a virus would be. As alluring as it is to use grandiose metaphors and contemplate their meaning, it’s hard to separate truth from fiction. Any metaphor that lets us understand a deeper or hidden similarity we couldn’t otherwise explain runs the risk of straying from what something actually is. Still, a global pandemic that overturns notions of morality, reality, politics, and everything else can’t be explained without resorting to analogies. With that, the coronavirus is an experimental hypothesis of ethics. It’s a test to our character and morality in how we fight a virus as though it were something evil.
The politics of globalization and communication, like the anonymous force that spreads a viral video spreading, are at their end for this era. The promise of rising living standards and faith in government authority will fall along with them. With them, the experiment of liberalism, in forming unity and common bonds between people, has ended. The virus becomes a test of what can best answer the issues raised by these losses with the mistrust and tension between individualism and collectivism it brings.
When 19th-century Austrian physician Ignaz Semmelweis realized washing hands would prevent the high death rate among pregnant women due to post-partum infections, he was ostracized and sent to a mental asylum where he he would die. Just as Aristotle in Politics described the “exceptional man” who could sing better than the others in the chorus and, as a result, become ostracized by them, we can determine which exceptions we can’t afford to ignore through methods like washing hands and vaccinations.
When philosopher Michel Foucault wrote that modern sovereign power was biopolitical, expressed through the production, management, and administration of “life,” philosopher Giorgio Agamben responded that there was a “state of exception” in which an authority could exercise power in areas law had not otherwise granted to it. During the emergency of the pandemic, we find ourselves in this state. Knowledge itself has become a privilege. Only some voices are valued. Those who choose to spread knowledge and let ideas flourish would be virtuous during this time.
The virus invites us to reflect and meditate upon the world. We are mortal, finite, contingent, lacking, wanting, and many other things. These ideals have been true and will always be, but the virus only further reveals them. Philosopher Baruch Spinoza ridiculed how other thinkers put humans above nature, the idea that man, in nature, is a dominion within a dominion. The coronavirus breaks down solidarity between humans and creates walls between them. It sows divisions and prevents information and righteousness from reaching one another, much the way we self-isolate and quarantine. We must, then, find common solutions that can overcome these obstacles.
We may see the fall of postmodernism. Though nature may seem sinister with how threatening the virus is, we can’t address these issues and help one another without turning to nature. With the rise of “red zone” hotspots, domestic seclusion, and militarized territories, “neighbors” can be “anyone.” Turning to nature for answers and seeking unifying, grand narratives to unite people among one another would bring about a return to modernist ideals. Even fighting against fascism, an ideology that would otherwise welcome barricaded borders and segregation from superior groups, means coming to terms with the idea that the enemy is not some foreigner or outsider. As Agamben wrote, on coronavirus, “The enemy is not outside, it is within us.” Blocking communication with other nations, as sovereignists like Trump may want, won’t solve the problem. Conspiracy theories that Asian individuals or 5G are to blame may also show this xenophobia that attempts to remedy our anxieties.
With certainty, I believe the virus has made politics more of a morality test. There’s a political “virtue” in how we react to it with wisdom and resilience. If the political virtue abandons the “human, all too human,” illusion that we can appropriate nature like a dominion in a dominion, then the morality test of politics means we must learn how to govern nature, not control it. The Greeks would have called political “cybernetic” or nautical, and, like a sailor fighting against a stormy sea, politics means caring about the crew to survive.
Much like the coronavirus was named “corona” for its crown-shape, the authority, legitimacy, and power of individuals who rule nations come into question. Like a virus, neither dead nor alive, we find ourselves in a state of motionless solitude during isolation and quarantine. Teetering on the brink of despair, we have to regain our balance. When governments and economies begin starting up again, we can only fight against the virus so it doesn’t retain its power.
Heuristic 