stormsewer: (the rock)
Last time I talked about gene drives (genes that remove competing versions of themselves from the genome) in yeast. Now a group has published doing essentially the same thing in flies. Using this technique you can force 97% of the offspring to lose the gene variant you're targeting. Things are moving fast...
stormsewer: (the rock)
I don't often read about scientific advances that give me a sense of vertigo, but it did happen recently. And no, actually, it's not the idea that we may soon be editing the genomes of human embryos, which has gotten people quite riled up [1]. It is work out of a lab working towards the same or similar goals, though: the Church lab at Harvard [2].

The article is entitled "RNA-guided gene drives can efficiently bias inheritance in wild yeast" [3]. I'm fond of saying that humans will soon be taking control of their own evolution, but the work here was a punch in the face for me regarding with how very possible that is going to be in the near future. Read more... )
stormsewer: (death)
So, I've been thinking a lot about death lately.Read more... )
stormsewer: (the rock)
Graduate school is a great experience... to have had in the past. On this, my official graduation day, I've decided to write down some of what I learned, about being a scientist and a human being.1 (The TL;DR might be this.)
Read more... )
stormsewer: (death)
So, I subscribe to a mailing list about peak oil. Sometimes the people on there annoy me. Most of the time these days I just ignore that. But recently people on there were arguing about entropy and the second law of thermodynamics and how that plays out in the context of biological systems, which seem to go against the Law. However, no one there really seemed to know what they were talking about, and I find a lot of people generally have misunderstandings where this is concerned. But as a molecular biologist and as a human it's something I think about a lot. It's foundational to how the universe operates. For your edification, I present my involvement (thus far) in the conversation. Face your imminent heat death! )
stormsewer: (the rock)
The size of the human haploid genome (one of the two genome copies each person contains in each of their 10 trillion cells) is about 3 billion bases. Each base can be one of four, so the total possible number of DNA sequences of 3 billion base pairs is 43,000,000,000, which is about 1 x 101,800,000,000. You, snowflake, constitute one of those. Well, two, actually. (Not counting all the varied mutations I'm sure you've picked up on the way.)

While genetic algorithms are cool, this does point to a limitation as far as considering them as models of biological evolution- they're not going to do well with a 3-billion-value genome. The number of actual "genes" is something like 30,000, not counting the extra variation you get from alternative splicing, and the number of theoretically possible identities of each of those DNA stretches is... very large. Our genome is rather different from the genome of a workable genetic algorithm in other ways, too. It is not just a list of predetermined responses to a set of predetermined stimuli. It is instructions for coding an information processor. For example, those 3 billion base pairs contain instructions for building a brain containing 100 billion neurons. This kind of hierarchy (DNA bases -> genes -> cells -> organs -> organisms -> societies) is a hallmark of truly complex systems. If we think of each neuron as a bit (either on or off, 0 or 1), the number of possible brain states is 2100,000,000,000, which is about 1030,000,000,000. One of those brain states, snowflake, is exactly what you're thinking and feeling right now.
stormsewer: (power lines)
So, I've been toying with genetic algorithms a bit. Making a genetic algorithm basically involves making a list of responses to every situation the algorithm might encounter. Typically you start with a random pool of algorithms, compete them, mutate and mix and match the winners' genomes to make a new generation, and then repeat indefinitely. (Does this process sound familiar?) The idea of encoding a response for every possible situation works well for some problems, but not for others. For instance, it would never work for teaching a computer to play go. Why not? )
stormsewer: (graveyard tree)
Of course the next chapter in the book is about evolutionary computation, though of course that's rather different from what I'd really like to see. Absolutely fascinating stuff, of course, so now I want to try my hand at writing a genetic algorithm...
stormsewer: (graveyard tree)
So, I've been thinking about life lately. Not in the who-am-I-why-am-I-here sense, but in the what-is-the-difference-between-alive-and-not-alive sense. Now I'm certain that my cogitations are pretty infantile compared to those of certain others, but I'd like to tell you some of what I've been thinking. Let me philosophize you, baby. )


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