| --- Log opened Sat Jul 23 00:00:05 2016 | ||
| docl | What I was thinking was start with the satellites in orbit at first, but then transfer their momentum onto the pellets until they become relatively stationary. Once they are slowed down to the speed of the earth, you can use them for tethers. | 00:00 |
|---|---|---|
| docl | The pellets would be going faster than orbital velocity (how much faster depends on how many pellets you use). | 00:01 |
| docl | maaku: The ground station idea has the disadvantage that you have to punch the pellets through an atmosphere repeatedly. I imagine that means you can't easily pack them with electronics or tiny mechanical components and expect them to keep functioning reliably. It's not just an energy cost. | 00:08 |
| CaptHindsight | how do magnets work? | 00:18 |
| kanzure | virtual photons | 00:18 |
| CaptHindsight | but I can sees photons so I knows they are there | 00:19 |
| docl | As you add more pellets (mass) to the stream, the trajectory for the pellets can be brought closer to circular, and their velocity slower / closer to orbital velocity. | 00:19 |
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| docl | CaptHindsight: how do you think they work? | 01:04 |
| docl | kanzure: what are 'virtual' photons? what makes those different from real photons? | 01:08 |
| docl | does any of us care about this question? if so, why? | 01:09 |
| docl | Most of what you could possible wish to know about how magnets work was answered 200 years ago by Faraday and/or Maxwell. | 01:12 |
| docl | The rest of it (like say wave/particle duality) is too obscure to do much of anything practical with unless you are doing something very specialized. In that case, you would use your specialized task as an example of why you want to know more so people can target their responses appropriately. | 01:15 |
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| docl | Atoms are all tiny electromagnets. But they tend to line up randomly, so their fields tend to cancel out. But in the case of some materials (like iron) the atoms can line up in a way that permits a magnetic field to be formed. | 01:27 |
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| docl | The movement of an electric charge creates a field that isn't itself an electric field. We call it a magnetic field. Magnetic fields are polar, meaning there are two distinct ends, and depending how you orient the fields, they can attract or repel. If you alter the field strength, that produces an electric field, which can cause electrons to move from one end of a wire to another. | 01:35 |
| docl | So there are a lot of interesting consequences of all that. For example, you can turn a crank at one location (Niagra Falls, say) and use that to vary a magnetic field and produce electrical current, then use that electrical current to vary a magnetic field strength as needed to turn another crank in a completely different location (such as a factory in New York City). As you can imagine, that has trem | 01:41 |
| docl | endous economic implications. | 01:41 |
| docl | But what does that have to do with space stuff? Well, suppose you have a device that ejects pellets at high speeds towards another device. The moving pellets can vary a magnetic field and produce current. That current can be converted back to magnetic field to launch the pellet in another direction. | 01:45 |
| docl | Thus you can have two devices that bounce pellets back and forth endlessly. This doesn't actually extract energy from the pellets unless momentum is imparted to the devices (i.e. they start moving away from each other) | 01:48 |
| docl | Think of it as a lossless version of a ping pong ball bouncing off of a surface. | 01:52 |
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| maaku | CaptHindsight: was that a serious question? | 08:26 |
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| kanzure | r0932jf0qfj0savh08q3rfdsafdka | 08:59 |
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| CaptHindsight | maaku: very serious, I was even frowning and used a low voice when I asked | 10:11 |
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| maaku | CaptHindsight: you can think of a magnet as being coupled to the electromagnetic field around it | 10:16 |
| maaku | changes in this field are transformed into mechanical motions and vice versa | 10:17 |
| maaku | the whole business about virtual photons and such is just notation and a little bit of (incorrect) historical legacy about how physicists and engineers think about magnetism | 10:18 |
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| maaku | i mean virtual photons are incorrect, it's just fitting a square peg (how the world really is) into a round hole (how we're used to thinking about the world) | 10:31 |
| kanzure | polymerase images fixed up, http://diyhpl.us/~bryan/papers2/polymerase/polymerase-images/images.html | 10:31 |
| Reventlov | maaku: well, the characteristic of a model is being incorrect | 10:39 |
| Reventlov | for all we know, there might be no photons at all, it's just that considering photons is a nice way to think about the world, and we can make accurate predictions because of that | 10:39 |
| CaptHindsight | do ferrites attract magnets because they are cuter? | 10:52 |
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| kanzure | yashgaroth: thanks for reading | 11:28 |
| yashgaroth | I still think a heavily modified TdT is gonna be the best way, regular polymerases just ride along a template and wait for the corresponding free base to align | 11:30 |
| kanzure | cool "The strict template-independent activity of TdT appears to be a recent evolutionary event that coincides with the development of V(D)J recombination in mammals." | 11:30 |
| kanzure | i am reading a tdt thing here http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846215/ | 11:30 |
| kanzure | yeah i agree re: waiting for a corresponding base... although if we can determine which base it is trying to incorporate, we can maybe reject until it decides to pick what we want. maybe. | 11:30 |
| yashgaroth | that's a lot of engineering to get pols to be template-free, you're changing the entire core vs. just making TdT respond to light or do some sort of fusion/tether/light-response deal | 11:30 |
| kanzure | well, it's not template-free, it's just "error prone" right :P | 11:31 |
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| yashgaroth | ehh mostly template-free, "random" is the way I'd describe it | 11:32 |
| kanzure | no no i mean, instead of turning taq polymerase into template-free, you just need it to be more error-prone, not template-free | 11:32 |
| kanzure | and then your goal is to control which errors it incorporates | 11:32 |
| kanzure | there are many polymerases that have been engineered to be highly mutagenic | 11:33 |
| yashgaroth | still sitting on a 3'-5' template, and if you're incorporating arbitrary nucleotides it's got nothing to ride on since the mismatches will separate the strands | 11:33 |
| yashgaroth | oh you can make a shitty polymerase real easy | 11:33 |
| kanzure | i think it can be made to hold on to the strand even in the presence of mismatch-induced separation, but i agree that's more engineering work and TdT looks pretty good | 11:34 |
| yashgaroth | as long as you get something that can sit at a free 3' end and add a base, that's a large part of the goal already | 11:35 |
| kanzure | looks like TdT polymerizes at most 50 nt | 11:36 |
| yashgaroth | I'll go read that paper, but that doesn't sound like a hard limit | 11:37 |
| kanzure | i was thinking of writing a few sections on polymerase mechanisms | 11:37 |
| kanzure | i don't see anyone that has done tdt selection experiments. sort of lame.. | 11:40 |
| yashgaroth | if it doesn't relate to cancer, no one's getting the funding to seriously look into it | 11:41 |
| kanzure | wouldn't beter TdT be good for the cancer people? because antibodies? | 11:42 |
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| yashgaroth | you'd think so, but apparently not | 11:43 |
| maaku | Reventlov: gah I' meant "virtual photons aren't incorrect" | 11:47 |
| maaku | you can do the physics that way and it works ... it is just strictly speaking a more complex theory than what we know to be reality -- that the fields are fundamental and what we think of as matter is just propagating waves in those fields | 11:48 |
| maaku | but, engineer hat on, virtual photons are just easier to think about and work with | 11:48 |
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| kanzure | "In the case of Polµ, and assuming an alternative interaction as that seen in TdT, Arg387 acts as a brake for the necessary movement of the primer, to limit nucleotide additions before end bridging. In fact, the single change of this residue for the TdT counterpart (Polµ mutant R387K) showed an increase in untemplated additions that ranged from 10- to 100-fold, reaching levels comparable to those of TdT itself [93]." | 11:57 |
| kanzure | "Why and how the terminal transferase activity of TdT is much higher than that of Polµ? Combined structural and functional evidences for both Polµ and TdT indicate that there is one residue modulating the terminal transferase activity of both enzymes. That residue (Arg387 in Polµ and Lys403 in TdT) tunes the catalytic efficiency of the terminal transferase reaction, by regulating the rate-limiting step." | 11:58 |
| kanzure | "One group of proteins reported to regulate the activity of TdT are referred to as TdT interacting factors (TdiFs). TdiF1 is a protein that binds to the C-terminus of TdT and increases its polymerase activity by ~4-fold [108]. TdiF2 is another protein that binds TdT through its C-terminus, possibly through interactions with the proline-rich and pol β-like domains. However, the interaction of TdiF2 with TdT decreases the polymerase ... | 12:05 |
| kanzure | ... activity of TdT by ~2-fold [108]." | 12:06 |
| kanzure | hrm. | 12:18 |
| kanzure | yashgaroth: could you add text some kind | 12:40 |
| kanzure | nmz787: and you at some point | 12:40 |
| yashgaroth | k | 12:40 |
| kanzure | the one item on my list today was polymerase mechanism but maybe there's other stuff. | 12:40 |
| kanzure | (which i have't gotten to, and would be okay if someone else half-assed it) | 12:41 |
| kanzure | bbiab/afk | 12:41 |
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| nmz787 | kanzure: in the google doc? | 13:05 |
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| kanzure | yes | 13:41 |
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| kanzure | colwiz is a good plugin for google docs, it does inline citations | 15:16 |
| kanzure | but the way it does this is by adding inline citations that are actually hyperlinks to some identifier | 15:16 |
| kanzure | then to generate a bibliography it scans all the links in the documents and reorganizes things so that duplicate citations become more organized under a single entry in a generated bibliography | 15:17 |
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| docl | CaptHindsight: what makes you think magnets are cuter than ferrites? | 16:45 |
| docl | surely you know magnets come in varying physical shapes and thus have differing aesthetic characteristics. | 16:51 |
| kanzure | someone called me yesterday because they thought i was the acs.org sysadmin | 16:54 |
| docl | a magnet cannot fall in love. it is not even biological. its attraction is not sexual or romantic, but purely physical. we're talking about an actual force that is created when the fields interact. | 16:56 |
| kanzure | CaptHindsight is aware of these things | 16:57 |
| kanzure | he was trolling | 16:57 |
| docl | so... why hasn't he been banned yet? | 16:57 |
| kanzure | because he builds hardware and he's good at it | 16:57 |
| docl | like what? | 16:58 |
| kanzure | 6-axis inkjet stuff | 16:58 |
| kanzure | linuxcnc things | 16:58 |
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| docl | got a link? | 17:04 |
| kanzure | you'd have to ask him, i think he's still trying to be pseudonymous or something | 17:04 |
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| docl | why do we think he's good at it? have you seen his work? met him in person? | 17:21 |
| kanzure | want me to ban him, huh? | 17:26 |
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| kanzure | docl: btw see pm | 17:27 |
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| CaptHindsight | oh boy | 17:55 |
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| docl | CaptHindsight: ? | 18:14 |
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| kanzure | andytoshi: hmm getting a ref for ocean dna content turnover rate or half life seems a little more difficult than i thought | 21:53 |
| kanzure | "Ocean viruses may turn over as much as 150 gigatons of carbon per year—more than 30 times the standing abundance of carbon in marine plankton" | 21:54 |
| kanzure | not quite what i was aiming for.. | 21:54 |
| kanzure | you would expect queries like "ocean microbial density" or "ocean bacterial density" to return specific results, but nope. | 21:56 |
| fenn | i wonder if human genetic engineering will become taboo because china's doing it, like how steroids became taboo because the soviets used them | 21:56 |
| kanzure | that's funny because the chinese keep asking us to do it for them | 21:57 |
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| kanzure | "Distributions, abundance, and activities of marine bacteria" http://w3.ualg.pt/~hgalvao/MPOB/BacAbundBiomGrowthActivity.pdf | 21:58 |
| kanzure | 10^6 cells per ml (according to page 19) | 21:59 |
| kanzure | ocean volume is 1.3 * 10^21 liters | 21:59 |
| kanzure | so about 10^27 cells | 22:00 |
| kanzure | oh i was looking for turn over rate. hrm. | 22:00 |
| kanzure | i was probably thinking of stuff like https://www.quantamagazine.org/20150521-ocean-viruses/ | 22:02 |
| kanzure | "Scientists estimate that there are 10^30 virus particles in all the world’s seas. They outnumber all cellular life forms by roughly a factor of 10." | 22:03 |
| kanzure | "Viruses kill vast numbers of hosts. Some researchers have estimated that they kill up to 40 percent of all bacteria in the ocean every day. Paradoxically, though, this daily massacre could actually increase the biomass of the oceans. Mathematical models of ocean ecosystems suggest that by killing so many microbes, viruses could release carbon and other organic nutrients back into the environment, providing an easy source of nutrients ... | 22:03 |
| kanzure | ... for other organisms" | 22:04 |
| kanzure | ah there we go. | 22:04 |
| kanzure | so 40% of 10^27 cells are getting killed by viruses in the ocean every day | 22:04 |
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| fenn | if "they kill up to 40 percent of all bacteria in the ocean every day" that means ocean bacteria have to replicate about once per day, which seems preposterous given how low nutrient density most of the ocean is | 22:31 |
| fenn | i don't think anyone knows very much about ocean bacteria | 22:31 |
| kanzure | andytoshi was asking for a ref re: the claim in the polymerase draft about polymerase replacing the ocean dna content each day (at least for most of the bacteria or something)(not counting extracellular dna) | 22:34 |
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| --- Log closed Sun Jul 24 00:00:05 2016 | ||
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