Posts with Comments by amnestic

Get off your ass and start this project: Viral videos

  • interesting. i was wondering about how to go studying these 'viral' phenomena after looking at this article in Fast Company, which I'm certain you'll enjoy for multiple reasons.
  • Studying stem cells in vivo via inter-species chimeras?

  • Yeah. There is also a physical boundary/filter between the blood and the brain that serves to keep a great deal of the immune system out. 
     
    By the way, the current issue of Cell is all reviews on stem cells, and the Research Channel has four lectures from the HHMI Holiday lectures 2006: 
     
    Understanding Embryonic Stem Cells 
    An overview of embryonic development, and properties of stem cells. 
     
    Adult Stem Cells and Regeneration 
    The role of stem cells in regeneration. 
     
    Coaxing Embryonic Stem Cells 
    Coaxing stem cells to become specific cell types. 
     
    Stem Cells and the End of Aging 
    Finding factors is experimentally enhanced, muscle regeneration improves.
  • Podcastiness

  • here's the archive: 
    http://www.itstherub.com/radio.htm#history
  • Time to take another look at your (third) cousin?

  • btw, wuz talking to outrageous p-vaues with some people the other day. see one on the order of exp(-129). lol. 
     
    seen this curmudgeon? 
    The earth is round (p
  • Resonance and plasticity

  • I just wonder why this only getting attention recently. 
     
    It might be because its PITA to understand all these electronic analogies for a biologist or psychologist. At least that's why it's taken me a while to get into it.. 
     
    Also the ability to record from many neurons at once in live behaving animals is relatively recent (maybe 10-20 years). The other techniques are fairly technical as well and may have required greater precision micromanipulators. Aaaand recording from neurons generates tons and tons of data that has to be stored somewhere and that is getting easier and easier..  
     
    some guesses anyway
  • What makes human populations different?

  • 5' utrs often regulate the initiation of translation. two of the major features that can affect translation are mRNA secondary structure and upstream open reading frames. 
     
    the ribosome loads onto the 5' end of the mRNA and scans in the 3' direction to find the start codon. obstructive secondary structure near the 5' end or at the start codon might make this more difficult. the simplest form of secondary structure is a stem loop wherein a reverse-complementary sequence is just downstream a little bit and the mRNA basepairs with itself, so it'd be interesting to know if there were reciprocal mutations in the divergence that maintain (or fail to maintain) a structure. 
     
    also, upstream open reading frams are start codons with in-frame stop codons encoded in the mRNA upstream of the true start codon. these can act very much like roadblocks or decoys tricking the ribosome into thinking its job is done before it has even begun.. so that type of regulation predicts mutated AUGs or stop codons. the distance between uORFs and the true start codon matters as well.
  • Super Tuesday

  • does it matter to anybody about ron paul and evolution? 
     
    "" mccain and torture? 
     
    did anybody watch paul on meet the press, because he lost some luster on there for me.. missing a lot of details.. it sounds grand, but sweeping reforms would require meticulous planning, n'est-ce pas? does the president even have the power to do the junk he wants to do?
  • Kibra up in the air

  • From the Need et al. non-replication: 
     
    From Papassotiropoulos et al. we can infer that the genotype explains 6.2% of total variation for the 5-min delayed verbal recall in Swiss cohort 1, and 4.1% for the 30-min delayed VLMT in the US cohort. We note that our Genetics of Memory cohort was 90% powered to detect an effect size of 3.2% at a significance of 0.05, and the German cohort was 90% powered to detect an effect size of 3.0%. Any effect size greater than 1.7% should have produced a P-value less than the observed one with a probability of at least 95%.
  • The importance of book stores

  • i agree. i go to the bookstore for mental rejuvenation. tonight i found four books that i wouldn't have seen otherwise: 
     
    Paul Ricoeur - Memory, History, Forgetting 
    Lisa Saltzman - Making Memory Matter 
    Mark Danielewski - Only Revolutions 
    David Shenk - The Forgetting: Alzheimer's - Portrait of an Epidemic 
     
    i'm trying to see if i can get any unique perspective on memory from outside the literature and the hackneyed Proust references.
  • Former Miss Universe contestent weighs in on the Watson Affair

  • Razib, can you set up your blog to support video comments? Thanx. 
     
    http://xkcd.com/322/
  • Andy Samberg + Mahmoud Ahmadinejad → MSM (?)

  • LL Cool J - I need love 
     
    http://youtube.com/watch?v=Tq1eABGnO78
  • RNA regulons

  • well i haven't made much of an effort to understand premature termination codon detection. but what little i've read about nonsense-mediated decay has pointed me in that direction. 
     
    according to this review 
    (doi:10.1146/annurev.biochem.76.050106.093909) 
    it looks like mammals do the pioneer thing but cervisiae doesn't. 
    It remains to be determined whether yeast and mammals truly differ with regard to what rounds of translation triggers NMD. It is possible, for example, that yeast NMD is more often triggered during early rather than later rounds of translation. Conversely, mammalian NMD may occur to some extent in later rounds. Consistent with this, the substrate for mammalian NMD does not absolutely require using a CBC-dependent mechanism because mRNAs containing internal ribosome entry sites can be degraded by NMD (129, 130).
  • A modern classic text

  • wow.. i hadn't heard of this guy but i've been obsessing over biological oscillations and timers and Alon is doing it rigorously. and the network analysis mirrors some of the ideas from Buzsaki's book from last year.  
     
    here's the google book preview. 
     
    i'm thinking that this allows you to figure out which analogies are realistic. i guess i'm really referring to this paper. They find the same network motifs in transcriptional and neuronal networks. "The feedforward loop motif common to both types of networks may play a functional role in information processing. One possible function of this circuit is to activate output only if the input signal is persistent and to allow a rapid deactivation when the input goes off." so now when a new feature of feed-forward neuronal signalling is discovered does it make sense to look for that in transcriptional networks? Like if subpatterns in stimulus-induced firing rate produce different downstream effects in neurons is there an analogous function in transcription?  
     
    anyway, no matter how much the above is nonsense, i'm looking forward to reading the book and getting a more concrete grasp on his conception.
  • Incarceration Nation

  • according to u.s. census data from 2000 and the national household survey on drug abuse summary report (1998)..  
    whites are 75.1% of population and 72% of users 
    blacks are 12.3% of population and 15% of users 
     
    this may be a better place to start evaluating the evidence regarding whether blacks use more drugs than whites. 
     
    ziel's comment points us to statistics on which races get AIDS through intravenous drug use.. 1) that's just heroin. 2) i'm not sure you can guess the amount of drug use from the amount of AIDS transmission. do whites and blacks share needles at the same rate for instance? 
     
    i'm not really aware of where to start looking for statistics, but it might be worth looking at marijuana use in particular. i think the imprisonment statistics might be more difficult than that to explain.
  • dareano - the policies differ to the extent that iq fails to predict incarceration. 
     
    dudeman - are you suggesting that blacks pushing for a policy is evidence that the policy is not racially biased?
  • Felons usually have low IQ's, and too many unintelligent people vote as is. Lagriffe showed that it was idiocy that got bush elected, not the fact that lots of idiots were in jail, a 
    It seems like if you want to stop low IQ voting then you shouldn't use prison as a proxy. You should use IQ itself. Using prison appears to bias you towards disenfranchising blacks with low IQ. So we let a lot more white idiots vote for bush than black idiots vote for gore. 
     
    Personally, even though we may suffer from stupid voters I can't think of a way to make a just system that excludes them. Aside from being just, I'm just not sure how you ensure that intellectuals are deciding who can vote for all eternity. Maybe better to have a blanket rule that everyone gets a voice.
  • Neuroscience, cancer/biology, math videos

  • oops. i'll fix that.
  • Nerds

  • yeah.. if you wanna make yourself sad, watch the guy start waving his arm around during this performance 
    http://www.thefader.com/blog/articles/2007/07/11/video-quik-live-at-the-fader-summer-music-party 
     
    Speaking of the term tard... quote from Mavado from the same site.. 
     
    "I?m not asking for trouble, I?m just askin / Lawd? / When my enemies come to send me to the graveyard / Let the first shot they fire blaze my heart hard / Cause I?d rather be a memory than a retard??
  • What use are male friends anyway? Women friends are useful, attractive, they smell good, and they have lots of other female friends to meet. Men fail on all four. 
     
    That hit me when I was around 20. I haven't had a serious male friend since. Never missed them either.
     
     
    This type of talk makes me sad. I have a lot of great male friends and they are useful for bouncing ideas off of, working on creative projects with, and venting frustrations with to name a few. I guess if your whole life is about improving your chances with women, then skip the friends and aim for the money, but whats the matter with a little personal enrichment? And is there such a thing as a purely platonic female friend or is there always that angle you're workin? 
     
    Re: nerdcore. It's a hoax. These cats aren't even smart, they're worker bees who know the jargon enough to get by and they got the right software for beats. There is no emotion and the delivery is all tongue-in-cheek.  
     
    Anyone familiar with the backpacker phenomenon in hip-hop? I think it's like the Guitar God worshippers of yesteryear and probably a lot like baseball statistic memorizers. It's a weird level of nerddom because you can sneak in acting like you are cool and into rap music, but after a while the truth becomes apparent. You've just been analyzing the lyrics and the allusions made by the samples instead of having parties and dancing to it.
  • Homo amygdala?

  • now that i look.. the authors of the amygdala study aren't all that fond of the prefrontal cortex story for humans. 
     
    We tested this idea and found that humans have only 2% plusminus 28 more prefrontal white matter than expected for a primate of similar prefrontal gray matter volume (Fig. 1b). On the basis of a prediction calculated from only great ape data, the human values are actually 17% plusminus 35 lower than expected. Given these results, it is difficult to make a strong claim for the evolution of specialized human enlargement of prefrontal white matter beyond simple allometric scaling to maintain functional interconnectedness at a larger overall brain size. Specialization of cortical neuron types8 and elevated gene expression associated with metabolism and synaptic plasticity9 in humans suggest that subtle modifications of architecture, function and connectivity10 may have been critical in the evolution of human cognitive capacities.
  • temporal lobe is famous for memory and maybe navigation.. higher cognitive functions are more often put up front..?
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