Comment author: [deleted] 27 July 2012 02:17:24PM 0 points [-]

How do we know whether, by replacing the insert with a random sequence of base pairs the same length, there would be no developmental defect either?

In response to comment by [deleted] on Neuroscience basics for LessWrongians
Comment author: dekelron 28 July 2012 11:04:08AM *  0 points [-]

There are several complications addressed in the article, which I did not describe. Anyway, using a "control vector" is considered trivial, and I believe they checked this.

Comment author: philh 27 July 2012 09:28:01PM 3 points [-]

That's interesting. I guess my next question is, how confident are we that this sequence has been undergoing close-to-neutral selection?

I ask because if it has been undergoing close-to-neutral selection, that implies that almost all possible mutations in that region are fitness-neutral. (Which is why my thoughts turned to "something is necessary, but it doesn't matter what". When you call that unlikely, is that because there's no known mechanism for it, or you just don't think there was sufficient evidence for the hypothesis, or something else?) But... according to this study they're not, which leaves me very confused. This doesn't even feel like I just don't know enough, it feels like something I think I know is wrong.

Comment author: dekelron 28 July 2012 10:34:28AM *  2 points [-]

if it has been undergoing close-to-neutral selection, that implies that almost all possible mutations in that region are fitness-neutral.

There is no "neutral" evolution, as all DNA sequences are subject to several constraints, such as maintaining GC content and preventing promoters from popping out needlessly. There is also large variability of mutation rates along different DNA regions. Together, this results in high variance of "neutral" mutation rate, and because of huge genome, making it (probably) impossible to detect even regions having quarter of neutral mutation rate. I think this is the case here.

This extends what zslastsman written regarding structure.

Comment author: philh 26 July 2012 01:46:59PM 3 points [-]

I'm having trouble working out the experimental conditions here. I take it they replaced a sequence of zebrafish DNA with its human equivalent, which seemed to have been undergoing nearly neutral selection, and didn't observe developmental defects. But what was the condition where they did observe defects? If they just removed that section of DNA, that could suggest that some sequence is needed there but its contents are irrelevant. If they replaced it with a completely different section of DNA that seems like it would be a lot more surprising.

Comment author: dekelron 26 July 2012 10:05:27PM *  2 points [-]

The DNA in the zebrafish was deleted, and the human version was inserted later, without affecting the main DNA (probably using a "plasmid"). Without the human DNA "insert", there was a developmental defect. with either the human DNA insert or the original zebrafish DNA (as an insert), there was no developmental defect, leading to the conclusion that the human version is functionally equivalent to the zebrafish version.

Comment author: Eliezer_Yudkowsky 23 July 2012 10:58:58PM 10 points [-]

Actually, we can guess that a piece of DNA is nonfunctional if it seems to have undergone neutral evolution (roughly, accumulation of functionally equivalent mutations) at a rate which implies that it was not subject to any noticeable positive selection pressure over evolutionary time. Leaving aside transposons, repetition, and so on, that's a main part of how we know that large amounts of junk DNA really are junk.

Comment author: dekelron 26 July 2012 10:19:15AM *  9 points [-]

There are pieces of DNA that preserve function, but undergo neutral evolution. A recent nature article found a not-protein-coding piece of DNA that is necessary for development (by being transcribed into RNA), that had underwent close to neutral evolution from zebrafish to human, but maintained functional conservation. That is, taking the human transcript and inserting it into zebrafish spares it from death, indicating that (almost) completely different DNA performs the same function, and that using simple conservation of non-neutral evolution we probably can't detect it.

Comment author: Alicorn 12 July 2012 05:15:25AM *  1 point [-]

Does distaste for alcohol correlate with anything else?

Supertasting. I strongly suspect I am one. There are only two things on the list of seven things supertasters often don't like which I'll consume (Brassica oleracea cultivars and soy) and I hate the other things.

Comment author: dekelron 13 July 2012 11:49:17PM 0 points [-]

I wonder why it's called "super" if it's a bad thing...

Comment author: djcb 13 July 2012 06:19:57PM 3 points [-]

Well said.

It would actually be interesting to see some research on the biological side of alcohol consumption, say, some studies on the longetivity of rats consuming C2H5OH-containing drinks versus their non-alcoholic controls.

(At the very least, the rats might be saved from less pleasant experiments...)

Comment author: dekelron 13 July 2012 11:10:39PM 4 points [-]

This was already done.

Comment author: Ezekiel 30 December 2011 12:09:47AM 0 points [-]

I'm Israeli, and although my contact with general society in the country is low, I think that's probably a factor. Meme propagation also just takes time.

Comment author: dekelron 30 December 2011 09:50:53AM 1 point [-]

Actually I doubt it's something that complicated. In my opinion, the site is not known because there are few people to publicize it, loop.

Anyhow, ARE there more LWers from Israel? I would really like it if there was a meetup here.

What are good apps for rationalists?

4 dekelron 30 December 2011 08:54AM

The smartphone world is relatively new, so I suspect there are amazing (yet sometimes unknown) apps that can help various aspects of our lives. I cannot think of a better discussion place for this topic. So,

Which app help you optimize life?

Is there an app you keep searching for in vain? (though it might exist!)

For me (I was searching for both apps for months!! until they were finally created):

Anki, A flashcard memorization app with many useful features.

[From the link] Anki is a program which makes remembering things easy. Because it is a lot more efficient than traditional study methods, you can either greatly decrease your time spent studying, or greatly increase the amount you learn.
Anyone who needs to remember things in their daily life can benefit from Anki. Since it is content-agnostic and supports images, audio, videos and scientific markup (via LaTeX), the possibilities are endless.

Simple Counter Widget, A counter widget. Sounds simple, but it's amazingly helpful.
I use it as a tool to better myself. Every time I eat my gum (an annoying mostly unconscious habit), the gum-eating-widget is increased by one. Because the widget is so accessible, I rarely cheat. This gives the habit immediate negative feedback, and allows me to check improvement over time. (Also my desktop looks cool, with many intriguing numbers popping from everywhere)

(less interesting: Record Mic and Call - which includes a useful recording widget, and Waze - which is amazing but well known GPS app (at least here))

 

please share to make this interesting :)

Comments (23)
Comment author: dekelron 26 December 2011 05:25:48PM *  16 points [-]

Hi all,

I'm 25 from Israel. I worked in programming for 4 years, and have recently decided to move on to more interesting stuff (either math, biology, or neurology, don't know).

I'm new in LW, but have read OB from time to time over over the past 5 years. Several months ago I ran into LW, (re)read a lot of the site, and decided to stick around when I realized how awesome it is.

Nice to meet you all!

Ron

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