Software Simulates an Entire Organism

For the first time, software simulates the lifespan of an entire organism, a single-cell bacterium called Mycoplasma genitalium. This means that the simulation shows how the cell comes in existence, develops metabolic processes and executes them, which allows it to grow and reach the state where it divides and two other cells result from it. Running the computer simulation for this process takes 10 hours and generates 500 MB of data. (Here is the article in The New York Times.)

It is interesting and strange to be able to measure a lifespan of a cell in this way. It is not exactly clear what it tells us–it doesn’t mean that the process itself (when a cell is truly developing) takes 10 hours, that’s just how long it takes for our computers to run a similar process. And the 500 MB of data generated don’t mean that a cell or a body has a hard drive of some sort which stores all the generated cell lifespans (what a huge hard drive it would be–as there are approximately 50 trillion cells in the body, it would take 25 trillion GB to store all their lifespans! and that isn’t even considering the fact that many of them divide constantly). It means that this is how close we, humans, are at this point to creating a life form artificially (i.e. without having sex and giving birth to a baby because at that we’re pretty good)–by using computer software, we can simulate an organism’s lifespan. This helps us understand it better from a computational point of view on the mechanics of the process of life. It is incredible that we can do this; and yet, we are being pushed further by everything we don’t know, that we can’t do yet, for example create an actual life form artificially, understand so much about it that we can actually create it.

It seems that there is some structural aspect that we haven’t grasped yet. We know the ingredients of the cell–how many carbon molecules, oxygen, hydrogen, maybe flourine molecules go into making it–and we also know what the separate organelles of the cell are made of and how they exchange things to make that cell alive. What we are missing, it seems, is how we go from the ingredients to the quality of “aliveness,” and I (and a number of other people) would argue that there is something about the structure of those organisms which we are missing and that this specific structure makes it in some way possible for these ingredients (for example, molecules) to function the way they do and reach a state we call “aliveness.”
Or, the other option is that we are the ones calling things “alive” and that there is nothing about them that makes them “alive,” nothing about their structure or anything else. As fellow human beings, we can’t escape our own perceptions, so we can’t bypass our definition of “alive,” look at the way that the cell objectively exists, poke around, and definitively conclude “ahhh, the cell is alive” or “arrrghhhh, the cell is not alive.” That’s how it goes when we’re human. Cheers!

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A Metro Catastrophe

“A Metro Catastrophe”–a new short story I wrote about experiencing the metro and the city here in DC. Enjoy.

A Metro Catastrophe

Ridges of trees surround Washington, DC—yellow and green trees in lines one after the other. The first lines are bright, each following line more and more bluish, gradually swallowed by the horizon’s constant blueness. High buildings are still sometimes visible with the trees; streets—not at all, people’s faces—not at all.

People walk those streets nevertheless. Many of them are making their way down the sidewalk, hoping to find some shade and let their panting bodies cool down. Even in the shade it isn’t truly cool. The heat is in the air, in the asphalt, in the cars, in the buildings, in the people, and it’s not going anywhere. The heat is always on our faces, there in every breath, no matter taken through the nose or through the mouth, fills our lungs. It covers our bodies like an extra layer of skin, and sweating becomes the natural state of being, sweat drops make rivers down the back of our legs, down our backs, between our breasts, down our foreheads. It’s not embarrassing anymore to have moist spots on one’s shirt under the armpits—you don’t belong to the community if you don’t have them. Everyone wants to leave this heat and enter an air conditioned building or bus or metro. When the air conditioning on one metro train gives up and the train becomes a luxurious oven, people leave it and get on another train—only to discover that its air conditioning has given up too. Then they sit and sweat, making their own little sweat puddles on the seats. The heat settles in, we accept it, and let it envelop us like the favorite woolen blanket.

A catastrophe took place on the metro yesterday. A train was derailed, and five stations were left with no train service. Including my station, College Park—University of Maryland.

It was Friday afternoon, and I had left half an hour early from work, at 4.30pm. My mind was full with nothing-thoughts. It was my turn to cook tonight, and I was wondering what I should make. Sure, we had cauliflower and broccoli at home, but we always cook those. What else should I make?

As I said, a mind filled with nothing, oblivious.

I had been waiting at the College Park—University of Maryland metro station on the Green line for a while now, about fifteen minutes, and no train was even scheduled to come. Every five minutes, a very sweet-sounding lady would announce that they were experiencing delays in both directions on the green and yellow line, that they were hoping to resolve them soon, that they apologized for the inconvenience, and, most importantly, that they thanked us for riding metro. None of us at that time was thankful for riding metro, and we weren’t hiding it: people were pacing and looking at their watches and staring in the direction of the train’s arrival, as though concentrating would bring the train faster, just as little kids stare at the sky to make it rain. After I had waited for more than half an hour, the same sweet-sounding lady, who sounded to me like a slightly chubby, round-faced, almond-haired girl, informed us that no trains were running in our direction now, so we should exit the station and look for a bus or free shuttle which would transport us to Fort Totten, the station at which the Green and Red lines intersect for the first time. Usually, I would get off at that station from the Green line and get on the Red line, so yes, I needed to get there, but with no trains running, I would have to get on a bus. The bus I would need to get on was F6. On its bus stop, there were about fifty people. No, that would be too much waiting, I though. What about the free shuttles? Oh, yes, the free shuttles are supposed to arrive here, a metro worker told us, but we don’t know when that will be happening, maybe in half an hour, maybe in an hour. At that moment, I saw a bus headed for Prince George’s Plaza—the metro station after ours. They already had shuttle service there, the metro worker said. Awesome, I’m getting on that one, Prince George’s Plaza is only about three minutes away by metro, it can’t be too far by bus.

Oh yes, it can, I found out later.

I got on the bus to Prince George’s Plaza and asked the driver before I swiped my card, “Does this bus go to Prince George’s Plaza?” “Yes,” he said. I swiped my card, confirming that this was indeed the bus I needed, and sat in an open seat. There wasn’t one near the window, so I had to sit by the aisle. Sitting by the aisle makes me uncomfortable because I’m in the middle of the space in the bus, while, in order to feel comfortable, I need to sit on one side, either side, of the bus and be one with it. In this way, I am a part of the outline of the space, like a point on the side of the geometric figure, and can observe the space—otherwise, I am somewhere inside it and am being observed.

Sitting somewhat in the middle of the bus space, I felt uncomfortable and texted the world away to my boyfriend. “Do you want to go to a theater and watch a play tonight?” I said. I wanted to do something different, to escape from the everyday lives we had been living for a while. I was tired of the heat and the daily commute and the chores, I was growing apathetic towards my repetitive tasks at work and towards cooking a delicious meal and reading a good book. I wanted to do something crazy, I wanted to run and jump about the world, catch the wind in my skirt, cover the sidewalks with dance. I didn’t know whether I wanted people with me or not—my initial plan was to go home, change, and leave, without telling my boyfriend anything. I would walk and talk and dance until my legs couldn’t hold me up anymore; then I would come back and land into bed with all my love for the world and for my wide-eyed boyfriend.

I decided he didn’t deserve that, though—he had been a good boyfriend all along and it wasn’t fair to treat him like that. So I invited him, I said, “Let’s go to a theater tonight,” I was waiting to see his response. Almost certainly he would say he wanted to stay at home, he didn’t feel like wasting his time at a theater, and then I’d be free to roam the nightly streets. And then came his response: “The Blue Dragon sounds good, what do you think? It’s at Odley theater, it’s a little far, but I can drive there. It starts at 8.” What an amazing boyfriend I have! I thought. Okay, so we are going to a play. And I started looking up plays, but I couldn’t keep my eyes on the screen. Around me, shabby houses were all I could see, the bus would turn right and left and go straight, and poor, shabby houses was all I could see. Was it worse than Maine, I don’t know. In Maine, it’s mostly sad, fat, white people, here, in Maryland, right next to DC, it was mostly sad, many of them fat, black and Hispanic people. Same difference. There was still no light in their eyes, no purpose to their motions. It’s the same image that scared me in my first November in Maine: moderate cold, a man with a miserable jacket, ballooned up by the spherical mass of his body, cigarette in his mouth, and a dirty, bored, hopeless look in his eyes. I have seen many sad and poor people in Bulgaria, but I still got scared, scared and hurt, as though something had pinched my soul and torn away a little piece of meat from my body. Why did these people look so sad and how did they find strength to get on the bus, I didn’t know. I wanted to get out of that neighborhood, leave and forget, or pull all these people in an earth-wide embrace and weep with them all.

After a full hour of swinging back and forth along streets and alleys, we reached the station. Salvation was there for us all now that we were there, the station workers would set up the red carpet for us and send us off flying to Fort Totten because every last person on this station had been waiting for us, oh, so impatiently.

Swarms of people were trying to make their way here, and there, and then back here again, darting and searching as though for their own heads, desperately. There was no sign of the usual unwritten rules in the metro: when one gets off the train, she comes up here and then walks up here; if she needs to stop and do something, she would step aside in this area in order not to obstruct anyone’s way; from here, you come here and you get on the elevator and you stand here, no, not here, unless you’re walking. In busy mornings and evenings, there would be rivers of people walking and flowing on the elevators, through the machines to read their cards, on the hard floor tiles, into the world. No sign of such purpose and implied organization now, no sign of respect for who got there first. Giant crowds of people waiting for something, so annoyed by modern inconveniences that they are about to go back to natural order.

A station worker yelled, “Bus to Fort Totten, Bus to Fort Totten!” I asked “Where, where?” He pointed over there; I looked over there but couldn’t see a bus, I only saw people; I move a little bit to the side and then a little more until I saw one lonely bus sitting there and saying “Fort Totten.” Of course the bus would be there—where the largest, loudest, most impatient crowd was. It was the people who were tired of waiting and simply wanted to go home. There was no way I could get on this bus and I knew it. I tried not to care too much, but I was angry, I was angry and helpless, angry because I was ridiculously helpless in this post-modern world where our will should count as something. This wasn’t even a real disaster like an earthquake, and we saw how our world of technological advances and blown up expectations crumbled in a matter of seconds; it seemed like a subtle reminder from nature or fate or luck—“Hey, you humans, careful with all the planning—things don’t exactly work that way.”

Someone yelled, “Bus on the other side!” And the entire crowd ran, ran like one, like a slim antelope, our muscles one in a well-toned body. And yet, we weren’t one. We tried to outrun each other, looked back to see whether everyone was running or whether it had been a lie, looked forward to find the bus before everyone else found it. I saw the Fort Totten bus with people trying to get on, almost raiding it, and I saw another bus, to the side, a smaller one. I walked over and got in line for the second bus because its line was smaller, but no one was getting on yet. A formal-looking official was importantly looking at some papers and checking off tiny boxes. A lady turned to me and said, “You should go to the other bus; you can’t get on this one.” I had no idea what this meant and I wanted to respond to the arrogance; but I saw that the first Fort Totten bus had opened its back door too—hope for me to get on! I landed there, just as hens do when they fly over short distances and land at the end point with disheveled feathers. I did get on the bus, I even found a seat! I couldn’t believe it! I asked two, three people, “Is this the bus to Fort Totten?” “Yes,” they all answered and nodded their heads with fatigue. I’d even made it to the right bus, I’d found a seat, and I would finally get there!

We stayed at the station a little longer while as many people as possible got on. The driver spent five minutes yelling that some people needed to get off because the doors wouldn’t close, and if they didn’t get off, the whole bus would be unloaded. Just as a few people reluctantly got off, a few other people from outside saw some space freeing up and jumped on the bus. The doors wouldn’t close again. The driver yelled again. The newcomers got off. The doors closed, finally, and sealed us off, the people on the bus who were leaving this world of natural order and were heading out to the world of the privileged, of civilization.

The Privileged were sealed off from the Primitive, those still in the mud of natural order, the dirty ones, the lowly ones, waiting for their salvation—for the next bus.

Finally on the bus, people began talking. They talked and laughed like they never would on a bus with strangers but it was the common misfortune, the common catastrophe that brought us together. The two women in the seats in front of me told each other their lives on that bus ride, pulled out their cell phones to show each other pictures of their dogs, husbands, children, and in the end they went their separate ways after expressing the most sincere wishes I’ve heard in a while. No phone numbers exchanged; that was for the better, to honor the memory.

I listened to music on that bus ride. The songs took me higher, and I listened with all my might, following wherever they took me. My awareness climaxed while Dido’s Worthless played—while the tandem of voices poured into my ears like a sorrowful, angelic choir, rays of white light were coming out of a center and rising, rising. I felt joy and sorrow then, and understood why those two work together so well and are always present: now joy, now sorrow, appearing to us as two separate entities but truly the two shades of one long dance, intertwined and slithering along. I, a human, could maybe bypass my inborn bias against pain and for pleasure and experience the world for a little bit, the way it truly is. Even if I am late for work next Tuesday.

After about an hour on the bus, we arrived at Fort Totten. It reminded me of a battlefield after the fact: buses parked and out of service, exhausted from rushing to transport such masses of people, women and men, resigned, sitting in the grass with suitcases and backpacks, trying to call someone; survivors. I left the bus and walked into the metro station, swiped my card, up the escalator, got on the train. A transition zone had been passed—I was in the regular, post-modern world again where trains ran and dropped off passengers at stations. Just when I thought that the transition world was over, I noticed that one of the women who had sat in front of me on the Fort Totten bus was riding on the train too in the same car as me. A thrill went through me when I saw her: she knew what it was like to have a little catastrophe for the afternoon, just like I did. She, too, saw the clouds of thoughts and worries that we carry around our heads, and she let them disperse for a bit.

Maybe she did, maybe she didn’t.

Posted by Mariya Manahova

Writing: Early Morning

I wrote a poem this morning–I don’t usually write poems.

 

Early Morning

In the dusk and in the silence

of 5.30 in the morning,

I sit on the toilet—

I listen to the muffled sounds

of pipes and plumbing,

I search

for another sink with water,

for another toilet flushing,

for another soul awake.

I hear nothing

—but muffled pipes—

and I pee

straight into the toilet water.

Like a cry in a fog-blinded night,

my pee tears into

the early morning.

 

Posted by Mariya Manahova

by David Renshaw

Purpose and Architecture in the National Museum of the American Indian

Just yesterday, I went to the National Museum of the American Indian. Very intriguing content and very well presented.

I was fascinated by how much thought had been put in arranging the exhibits. My usual idea of a museum is a series of halls with things along the walls. In this museum, it was completely different: halls were divided into corridors and from corridors stemmed little rooms of exhibitions for a specific Native American nation. Those rooms were made up of walls like paravans, shaping them into triangles or irregular quadrangles. There were main paths that led through the halls and smaller paths that you could take and still get around but look at all the exhibits, the details, and pass secretly between paravans. In one exhibition, “Our Lives,” I walked in what I thought was a curvy line that was going forward, and then suddenly I was back at the beginning–it was a circular path. Granted, spatial orientation has never been my strong skill.

There were also very thoughtful examples of film and multimedia across the museum. My favorite was the welcoming film in the Lewene or Levene theater (I am certainly misspelling it) because it projected on three different surfaces, and it was evident that someone had thought very intently about how to involve the viewer to a larger extent.

It was a very pleasant experience to see how much purpose can be put in the design and architecture of the exhibits in the National Museum of the American Indian. It’s a shame that the website doesn’t follow this manner of expression–otherwise I would have shared more. But visiting is easy, and the architecture and the purpose in the design made it a pleasure to visit because one didn’t simply feel like an observer but could feel that her train of thought was being guided and eased into this new knowledge, as though it was a game, finding one’s way through a maze, spatially and informationally, discovering the details in the big picture.

Posted by Mariya Manahova

Presentation: Models of Categorization

I made a short presentation the other day comparing models of categorization. I read a book called Formal Approaches in Categorizationwhich presents a number of approaches to categorization. It also talks about comparing models, but, unfortunately, does not provide too much information on that probably because it was beyond the scope of the book and/or because not too many comparative studies have been performed (according to the authors). After reading the book, I realized that my knowledge about categorization was still a mess, so I put things down and organized them. Then, I organized them a little better in the presentation. In the end, it answered some questions and raised others, which means it was a successful activity.

Here is the presentation:

Presentation on Models of Categorization

Let me walk you through it. At first, I go through the organization of the presentation. Then I note the book’s definition of a model of categorization and mention the quantitative measures that we use currently. Next, I list the issues in categorization modeling I will be discussing.

First is the issue of supervised vs unsupervised categorization, whether categorization happens with our without feedback from other people or machines, and it seems that it can happen in both ways both in the “real” world and in the lab; I discuss how that is implemented in different models.

Then I discuss the problem of one or multiple systems–whether we fundamentally have one or more categorization systems; I think that we have one overall system that can be divided in sub-systems that categorize different types of stimuli.

Next, I talk about psychological similarity, which is a useful way to measure how similar (and how different) two stimuli are and thus to measure the person’s reaction; the bottom line is that all models need to use this in order to refer to some type of categorization because in its essence things are categorized depending on how similar (or different) they are.

The following issue is a major distinction in categorization theories, exemplars vs prototypes. Exemplar theory believes that categories are formed because all the instances (or exemplars) falling into a category you have ever experienced are stored (but the brain doesn’t have so much computational power to store them all and compare every thing you are currently experiencing to all previous instances). Prototype theory claims that categories are formed around a prototype which is an average of all those exemplars you have witnessed (but how is that average produced exactly?). It seems most reasonable that categories would be formed around something in between exemplars and prototypes, like an average of the most characteristic instances of the category, e.g. the most dog-like dogs, or maybe even a few stored instances that are the most representative.

Category representation, the next issue, is very, very interesting, so we have many theories about it. Unfortunately, we can’t really know what category representations the brain is using because we don’t have actual ways of testing them yet (yes, I may be skeptical but also realistic). But it’s ridiculously interesting!!! The representations of categories and how those function in the brain is probably my favorite topic among these!

Then I note that the context in which stimuli are presented needs to be taken into account as well as the sensory input (visual, auditory, tactile, etc.) by which it is delivered. Pretty straight forward but necessary to keep in mind.

Neuroscience also provides some useful insights. Most of the observed diseases in categorization are ones that affect specific domains, for example a person can’t categorize animals but can categorize everything else. This suggests that categorization processes are domain-specific–when you damage one domain, the animal one for example, it is the only one damaged. This may mean that different categorization processes take place for different domains–animals, humans (even though we are technically animals too), food, man-made objects, and others. This may be a problem for categorization models because they don’t account, generally, for different domains, i.e. the theories are domain-general. This means that they postulate the same categorization process across different domains. Now, neuroscience does not necessarily tell us that different categorization processes are taking place in different domains, but it tells us that there may be something else going on. Maybe the different domains are situated in different brain regions, which is why when you injure one region, you can’t categorize things in that region. Maybe the categorization process lies in the connections between the neurons or in the patterns of firing of those neurons across all domains. Or it may be something else. It is certainly an important insight that neuroscience brings in and we should integrate it in theories and models but it doesn’t necessarily shatter our world to pieces.

I end with two questions. Are the distinctions between categorization models fundamental? It seems to me like they are all getting at the same thing from many different angles but because they generally use different computational methods, we can’t really compare across models (with some exceptions). Also, debate is focused on the specific models, which were supposed to model the brain and the mind’s ability to categorize. It seems like we may be forgetting those primary sources and targets: the models are not the most important thing in themselves; the process of categorization which takes place in the brain, in the mind, in the heavens, whatever you’d like to call it, is what we are studying.

Comments, thoughts, and objections are more than welcome!

Posted by Mariya Manahova

Log of the S.S. the Mrs Unguentine

What a weird, amazing book! Log of the S.S. the Mrs Unguentine by Stanley Crawford is a story about a husband and wife living on a boat for forty years. They have fruit trees, vegetable gardens, goats, ducks, dogs, filtered water–a mini ecosystem on a boat. They tend their garden and they tend the boat, and they scarcely speak to each other.

In the beginning, we are caused to hate the husband and sympathize with the wife because, it seems, he doesn’t take heed of her opinion and has taken her almost as a prisoner on this boat, she wants to go on land but he always brings her back, she works all day long on the boat and only has one day off per year. As the book progresses, however, she doesn’t want to see land anymore, says that she couldn’t have lived a life other than this, so we begin to see real, honest love in that relationship of theirs. we see how peculiar and ingenious her husband is, how caring and gentle he is to his wife and how witty. “Kind man,” she calls him at one point later in the book which almost made me fall out of my seat with surprise (I read a lot on the metro): a chapter ago, she would have never, ever given him a direct compliment.

Many, many colors and smells filled the book. I didn’t know the sea could have so many colors, but now I feel like I’ve seen them all.

“The barge, magnificent barge, a jewel cresting upon the high seas those thirty to forty years when the weather was still a true marvel, when one could see stars at noon, when rare clouds were so fine and gauze-like and so much more transparent to moons, when rains were frank and without whining drizzle and cleared without lingering–such was the bright and empty space we sailed across seemingly to no end, and where my simple chores could have gone on for days and days without me minding.” (p. 75)

“…every bone and muscle ceaselessly active and fresh, my skin tanned to a glowing sienna with only a vein surfacing here and there near a breast, a wrist, an instep, to indicate the warm blood which sometimes seemed to flow out and beyond, to feed the rainbow colours of it all, dishpan and stern deck, our lake, the sea, back to the sun.” (p. 76-77)

” Unguentine was in his prime those days, he was more present, more carnal, his body exuding the manly aromas of ripe glands so strongly I could nose out his shifts in mood, the nature of his work, for hours at a time even though he might be at the far end of the barge. He never spoke, no longer wrote me notes. I didn’t need them. I would read his face and body, and he mine, to know what thoughts were to traverse the narrow band of air which separated our flesh.” (p. 77)

I didn’t know what to think of those lives and that love until the very end, but what I know is that the book painted a full portrait of what it means to live a life, not only on a boat but any life.

Posted by Mariya Manahova

Meditation: watching how reactions happen

I watched reactions today.

While I was meditation, there was a loud noise, I perceived it, and a startled reaction occurred within me.

A stimulus, an interval of perception, and an emotional response. Classic.

But the interval of perception was too apparent, too apparently separate in its own length. Quite clearly, the noise was being classified as a startling stimulus, then a search was initiated for the appropriate response to that particular stimulus, and then a startled response was identified as the most appropriate, so it was set into motion. Which means that if instead of that startled response I identify a neutral response as the correct reaction, my brain would put that into motion.

So it’s a matter of habit—which reaction has my brain learned to associate with this stimulus. If I, gradually, teach my brain to associate a different reaction as the appropriate to this stimulus, that’s what my brain would do. And once I’m conscious of that interval of perception during which the appropriate response is being searched for, I can modify the search results a little bit and, gradually (to keep expectations from sky rocketing), identify a calmer reaction as the best one for the startling loud noise.

It gives me peace to know I can observe the way I think on such a level. But am I implying that I can control it as well, modify it, exert my will power over it? How can my will power be so separate from the habits I’ve learned when those are both interconnected? How do we speak of will power affecting things anyway?

Is it true that I can affect the way I myself think, my learned habits which define my thought frames? Or am I changing a belief about the way I think—are they fundamentally different?

Probably not. Probably the key lies in a teeny, teeny, tiny rift between some two big questions, so it is unnoticeable but nevertheless there for anyone who knows how to find it. And the key is probably shaped something like this: one should observe how those thoughts happen, see the process of thoughts appearing as one whole and understand it from the center to the outermost curves and tunnels. Then the intent alone will shape them when one thinks she is looking away.

Posted by Mariya Manahova