The Biosphere - 2015-07-08

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5:15 AM

@AliceD I removed the comment regarding my personal experience with ketamine and animal experiments but what is it about people receiving threats. That was not a valid reason. The method that I described was the one that was approved by the Animal Ethics Committee.

6:13 AM

Should we push this to Health.SE

0

Q: How calorie intake affects weight gain?

There are ton's of textbooks and websites that say that if you want to gain weight you have to increase your calorie intake. My question is how is it possible for a body to take in more calorie than it needs because overeating is the same as not absorbing and the body will not cooperate to gain m...

physiology digestive-system

@Chris

6:33 AM

@WYSIWYG Probably not a bad idea. I think it is on topic there as well.

@Chris They would like this kind of question.

Then let's move it. How do we do this?

Close and migrate

select the option "this belongs to another site" option in the off-topic section

ah. ok.

I have never done this.

I migrated 3 questions. To travel, English and chemistry.

8 hours later…

2:10 PM

Bler de bler bler. Come on computer count faster.

In my experience 90% of bioinformatics is learning what to script and what not to script

I think I should have scripted more of this

@WYSIWYG - are Pedram and Nimba nicks for the same user?

Just wondering :)

@WYSIWYG that's great work! What do you think of the pond question? I think it's great for Gardening?

@AliceD Do you have links to the user profiles?

2:33 PM

@AliceD That is not something we usually reveal in public

2:44 PM

@AliceD I don't think the G&L community has that level of expertise.

3:13 PM

@Resonating And what language to script in. You said you know CL. Do you ever use it for scripting?

Hi @WYSIWYG

@FaheemMitha Goodness no. It's lovely but no.

@Resonating Why not?

3:29 PM

@FaheemMitha My workflow tends to be "write heavy-lifting tool in the best language for it. Then: script its behavior with python"

@Resonating I'm not quite sure I follow that. So you think CL doesn't cut it? And if so, why? Just curious.

@FaheemMitha Languages influence thinking, see the weak sapir-whorf hypothesis

@Resonating Never heard of it.

Sounds like a made-up thing, but is actually real.

@FaheemMitha more concretely, writing a relatively sophisticated propositional logic solver in CL is absurdly easy, it's maybe 100 lines. Writing a specifically asynchronous script where you have to think about threading and so forth really calls for python's multiprocess library. most CL are thread-safe and compiled multithreadedly so it's not a huge gap in performance but python allows for tighter granular process controls

If I want to run this process on this core for this amount of time, it's way easier in python than in CL

also: biopython is lovely

@Resonating I thought CL has thread libraries now. Never used them though.

3:35 PM

@FaheemMitha it almost certainly does, even though if you ask me it's a bit silly. Most of the functions in lisp should be pure, and therefore the compiler should thread things for you because it can

@Resonating Dunno, never given it much thought. But isn't it about multiple processes rather than threads? So you can run on multiple processors?

The difference turns out to be less important than you think. Scheduling several threads on one core and many processes on many cores is fundamentally the same problem, so they share a lot of the solutions

Let's talk multiprocessor vs multithreading.

@Resonating Multiprocessing is less trouble-prone. You don't have to worry threads writing over each other in the shared memory area.

But I don't really think it is that important. Bottom line, you think Python is more effective than CL?

@FaheemMitha The principle is the same. you have private resources and public resources, and whether those are private/shared memory for threads or cores and files for processes doesn't make much of a difference in the long run

python doesn't thread well because it has a GIL but whatever, what I really want to do is multiprocess anyway

@FaheemMitha Sure, if you put a big asterisk by more effective. More effective at what?

@Resonating In my experience it does make a difference.

@Resonating More effective at whatever you are doing.

Which I assume is bioinformatics type stuff.

I'm actually interested in using CL for scientific computation, though I realise I'm seriously in the minority.

3:44 PM

@FaheemMitha Yes. It's more effective at scripting the kind of things I want to script right now. there's only one sliding scale of programming language power, and it is <everything except fortran tied for 1st> <all the kinds of fortran tied for last place>

@Resonating I don't follow the second sentence. Can you elaborate?

Don't be scared! I'm doing a lot of blast and sequence validation and so on, which means lots of IO, which means lots of multiprocessing and child processes that run blast and so on and so forth

CL is very fast for problems that can be structured a certain way

Uh, Fortran sucks. Everything that isn't fortran doesn't suck

except PHP

PHP also sucks

In theory CL should be good for things like text processing, which bioinformatics does a lot of.

@Resonating Amen to that. But are there lunatics out there using PHP for scientific computation?

@FaheemMitha No. but there are lunatics out there using PHP. Does it really matter what they're using it for?

I'd like to write a tree alignment solver or something in CL. That would be fun

@Resonating Fair point.

@Resonating So you think CL is not a reasonable choice for scientific computation? Or does it just depend on the problem/area?

3:54 PM

@FaheemMitha Depends on the problem/area.

@Resonating ok

4:41 PM

@Resonating you said "lovely" twice. I thought that was a British thing. Apparently not.

4:52 PM

@FaheemMitha Sorry. It might be? I'm forn to Urbana, my family is from english colonies.

5:05 PM

@Resonating forn? And no reason to apologise. It's just an observation.

5:18 PM

@FaheemMitha you know. Foreign. 'forn'

It's always fun to talk to you because we both speak fluent english but we clearly don't speak the same language all the time

@Resonating Oh, definitely not. In any case, I've never heard that particular variation. And the US is an English colony.

@Resonating if you do happen to use CL for "real" work, I'd be interested to hear about it.

6:06 PM

@MadScientist or @WYSIWYG Hi! Pardon the intrusion into your room, but I'm hoping to check if a question is on-topic, and how to know! It's a simple "identify this mushroom" question. I asked if it was o/t at Great Outdoors, and I got different responses. One said it was ok, as I found it while on a hike, and the other said it should be asked here. You guys do have some, but if I'm only seeking a name, is it too pedantic?

@Sue Identification questions are on-topic, just try to provide as much relevant detail as possible (e.g. location)

@Sue This is a public room, no need to apologize.

@MadScientist Hi! Thanks. My primary SE experience is on GL, but this is not a back-yard mushroom. I've seen plant id questions here, but I also found an old meta post here that seemed to indicate a preference for migrating such questions elsewhere. I didn't know if the same was true with the mushroom. I don't want to post something boring on a scientific site!

@FaheemMitha Hi and thanks :)

meta.biology.stackexchange.com/questions/181/…... and meta.biology.stackexchange.com/questions/151/…... are the meta questions I was referring to. Do you think your people would want to learn about the mushroom, or would it be wasting space?

6:50 PM

@Sue As long as sufficient details are provided species identification is a valid question. Details include location, size, climate, geology and any other details that could be observed.

A good resolution photograph is must.

By good res I mean that the main feature in discussion should be clearly visible and not blurred or zoomed out.

@WYSIWYG Ok-thanks! Would I ask here about an id for a bird's egg I found? I'd like to understand some of the material I found inside, so it's a more scientific question than the mushroom.

7:17 PM

@Sue Sounds reasonable to me. Don't worry too much about it - if it is not considered suitable it will be closed or moved somewhere else, but it is no big deal.

People ask terrible questions on these sites every day without a second thought.

Stack overflow is a cesspool. People with thousands of rep asking "I typed this and it didn't work plz help"

0

Q: Can double sumata be pleasurable?

Just to be clear what I mean by "double sumata": double intercrural sex, double interfemoral sex, double pussyjob, double pussyrub, double rubjob, pussy sandwich, cock in between tribbing pussies. My friends showed me some animated porn videos, wherein one male puts his erect penis in between th...

uh. What is supposed to happen to this kind of question?

7:33 PM

@FaheemMitha Cool, thanks!

@Resonating I'm happy to see that gone so fast! You guys have had your share of disgusting lately :(((

@Resonating Deletion with extreme prejudice.

@FaheemMitha Does that mean bye-bye to the user too?

@Sue I'm not sure. Hopefully they'll get the message? In five year's time when they are old enough to drive maybe they'll come back and ask a real question.

@Sue I might be alone in this because I've only ever answered one species-identification question and that was by accident, but I love species-identification questions. Pictures and location are vital but they're definitely on-topic here.

At least until we get a speciesidentification.stackexchange.com

7:51 PM

@Resonating Yay-a species lover! Thanks for the support. Nature fascinates me! I love to learn about how things behave, but at the very least-what they're called :)

We found this cool thing on a hike recently which is a "poison-ivy rope." I wish I had taken pictures. The sign said it lives, and is toxic, for up to 50 years! It was literally wrapped like a rope around a tree.

@Sue Around here there's some kind of poison ivy thing that grows in huge ropes on trees. It's a pest. It chokes out the tree and it's a devil to remove because it's poisonous. It can't even be burned because the smoke is worse than contact

Aww WYSIWYG closed-as-duplicate a question on phylogenetics

Is there a word for a relationship between two questions where question A is answered by question B's existence?

A and B are not duplicates, but "does Y exist" is answered neatly by the existence of "X and Y: which is better?"

@Resonating That's probably what we saw. I didn't realize it's dangerous to the tree.

8:07 PM

@Sue In properly-managed forests periodic fires burn it off and the trees are fine, but the woods near here have passed through the controlled burn stage. There's feet of lumber on the ground, covered in poison ivy. Any controlled burn would require evacuation of the nearby town.

At least, probably. Maybe they just don't burn it off because they don't want to disturb the photographers

@Sue Usually not unless it's spam, I think.

@Resonating :) I was looking at your profiles to see where you live. I didn't find it, so it might be private, but if not, I'm curious...

@FaheemMitha Oh-I know sometimes I see things in the Meta chat room about blacklisting users. I thought extreme rude/offensive was included. Is there a warning process instead?

@Sue I don't really know the details. I've seen users deleted when the user has not history and the account was just created, so it is obviously just a spam delivery system.

@Sue btw, @Resonating's town is mentioned "upstream' in the chat. :-) Seek and ye shall find. And where are you from?

Oh, I see your profile says MA. Assuming that is still current.

@Resonating I was just musing on how the use of words change. Once upon a time, and for centuries, the word Madonna probably referred to a certain lady in the New Testament. Now, if you use the word, people assume you mean a different person entirely.

Even though (and I think this is called irony) Person B was probably named after Person A.

8:31 PM

@FaheemMitha Okay-I found Urbana, which either puts him in the country of Bangalore, the state of Illinois, or at a Christian conference in Canada, any of which would be cool! Yup, I'm Massachusetts born and raised, although if I had my choice, I'd live someplace warmer!

@Sue It's IL. :-)

"country of Bangalore"? Not sure what you mean. :-)

There are far worse places to live in than MA. Do you live in an urban area?

@FaheemMitha I meant some type of township in Bangalore India called Urbana urbana.ozonegroup.com/official_nri/…...

@Sue Oh, I see.

Luckily for him, he lives in Illinois, I'm reasonably sure. I think we talked about it earlier.

Though there is always room for confusion; I occasionally get people I talked to here mixed up, since I have never met any of them, nor do I even have an idea of what they look like or sound like. So there is not a lot to hang a memory on.

@FaheemMitha Suburban, actually. I was raised in the city of Brookline, just outside of Boston. I've moved around some, including a few years in a country town where we were able to have pet goats, but now we're in a suburb near the center of the state, and my pets are my indoor cats, and outdoor birds, chipmunks, skunks, squirrels, bugs, bees, etc. and flowers. I know what you mean about forgetting things about people. It's natural in this setting. Where do you live?

@Sue Bombay, India.

8:43 PM

@FaheemMitha Do you like it there?

That sounds like a reasonable place to live in. Though cold, of course. I imagine Boston must be pretty lively.

@Sue Not really, no.

Are you asking about Bombay as a place, or my personal circumstances?

@FaheemMitha Does that change the answer?

@FaheemMitha Actually, both are pertinent-whichever you'd like to tell me about.

@Resonating Certainly.

@Sue Hmm, well, what would you like to know? :-)

@Resonating have you read The Way of All Flesh?

@FaheemMitha What don't you like about your circumstances? Do you wish things were better in Bombay, or that you lived elsewhere?

8:49 PM

@FaheemMitha Nope. It sounds metal, though. Enlighten me?

@Resonating metal?

@Sue Well, Bombay is a nasty hellhole, like the rest of India, though more developed. That's the short version.

But my personal circumstances are nothing to complain about, by international standards.

@Resonating I accuse you of making up words, or at any rate, new meanings for them.

Unless you are sharing the latest Illinois slang.

metal like death. buzzfeed.com/ailbhemalone/…

@Sue So I guess you do a lot of gardening then? I saw you are active on the Gardening SE.

@FaheemMitha I promise I am mutually intelligible with some human beings!

Appearances to the contrary

@Resonating good grief. Just google The Way of All Flesh. You should read it, time permitting. It's a good novel. And famous too. Or it used to be.

8:53 PM

@FaheemMitha That's what I thought, I'm sad to say. I shouldn't be complaining just because it's cold here-rather inconsiderate of me. I just looked up that book-it seems interesting.

@Sue It is. Though as reviewers comment, the narrator does go on a bit.

I read it as a child and admired it very much. But rereading it as an adult he does make me feel a trifle restive.

@Resonating just think, someone spent probably hours of their life putting together this totally pointless list. It's so sad.

@Resonating I have been in a few new chat rooms recently, and found very few Americans!

@FaheemMitha I think you overestimate the effort that went into this. I could bash out a list like that in half an hour while playing candy crush

@Resonating Clearly you should get a job on Buzzfeed.

Whatever that is.

@Sue There are tons of Americans here. You can't go a foot without tripping over one. Where have you been?

@Sue I'm one of the only regulars in here in GMT-fingers. Nearly everyone else seems to be in india or similar time zones

I'm overhearing a pretty wonderful debate in approximately .3 of a shared language about some kind of nitrogen tank order

9:00 PM

@FaheemMitha For the past year, mostly on GL, where the chatters are from the US, but many users are in the UK. Now in the rooms here, Great Outdoors, and Health, I'm meeting mostly people from the UK.

@Sue Hmm, well there are a lot more rooms than that.

@Resonating It surprises me how global SE is!

I see I am currently in 8 "main" rooms. And that is only a small fraction of the SE rooms.

@Sue Why?

@FaheemMitha Yup-I notice you've been in the Frying Pan. There are a number of people there from other countries too, but also Americans.

@Sue yes, the Frying Pan is a wild and wacky place.

Are you relatively new to SE?

9:05 PM

@FaheemMitha I think because I've never been involved in something like this, and always assumed these types of things were more regionalized. I think the global thing is awesome, I just didn't realize it until recently.

I just assume everyone's american until proven otherwise. Normally I'm right, but I like this all india all the time room

Everybody talks about hiking in the ghats and not US politics which are impossibly silly at the moment

@FaheemMitha Almost a year! I found the site through SA, but settled in at GL because I love plants, etc., and because the kind people there have taught me about the system. My first SE answering experience was on a site where I was asked for more information, and didn't know how to add it. I was warned that the answer would be closed, but not taught how to keep it open-sad. My goal is to make life easier for new users, but it's hard. That's why I like chat rooms-people genuinely want to help!

@Resonating Hardly all india all the time. It's just me and @WYSIWYG.

@Resonating U.S. politics are crazy is right!

@Sue Yes, most people tend to settle into one home site, at least at first. I'd consider mine U&L, but it tends to be a little slow.

9:14 PM

@FaheemMitha Who else comes in here on the reg? AliceD and mad scientist sometimes

@Resonating you

@FaheemMitha So that's like 2/3 india all the time. I'm rounding up.

And @SolarLunix. Haven't seen here for a bit, though.

Oh I forgot about SolarLunix. :( You can round up from .5 though

@Resonating Lol. But I don't talk about India. Nor does WYSIWYG really.

There was some talk about biking a while back. WYSIWYG likes to bike.

Also @rg255 has been around a fair bit. Trying to remember where he is from...

9:17 PM

Huh. I think I found a way to reliably crash ncbi.

@FaheemMitha The tech-y stuff is way over my head. My son is a computer engineer, so he's the tech in the family. I see you're active in the Android room. That is a sad site indeed. Nobody votes at all, even if people have been helpful. Ask Different's the same way!

Ah, English, but lives in Sweden. Or is it Norway?

@Sue I'm not really active in Android. I've talked to people a bit there.

I have an Android phone (purchased it recently) but I don't use it much - other than as a phone.

No, Sweden.

@FaheemMitha Oh-I just saw it in your list of chat rooms. You and @Resonating are really smart :)

@Sue based on what? :-)

Someone said in a motivational lecture that humans can't keep track of more than 5 things at the same time. It certainly seems to be true of my brain.

@FaheemMitha Based on your posts!

9:24 PM

@Sue I learned something really wise recently. If you're not sure you know what you're talking about, don't say anything at all. If you can't think of anything wrong about what you're about to say, you don't know what you're talking about.

Makes you a terrible conversationalist, but boy do you look smart

@Sue Any particular ones? :-)

@Resonating That's an excellent principle to live by. There is a friend of mine I wish you would tell it to.

I don't quite get the second sentence, though.

"If you can't think of anything wrong about what you're about to say, you don't know what you're talking about."

Mostly it's to avoid dunning-kruger

If you're an expert on the subject 99% of the time there's no way to compactly express anything true without abstracting away something or ignoring an exception

@Resonating Cute! You're intelligence is obvious. I just found your real name-very American! All three of us are "keeping an air of mystery." That text is one of the many things on the profile page about which I'm quite irate.

"all atoms fill their valence shells according to the triangle rule" for instance

True: except for copper. Chemistry is a mystery.

@Resonating Oh, I see what you mean.

9:30 PM

@Sue American? Really? I'm second-generation and the rest of my extended family is from south africa or england

Time to go to sleep. Bye, guys.

And ladies.

@FaheemMitha Lots of highly voted stuff on many sites. Bye and sleep well!

@Resonating I'm second generation too, though both sides were Russian.

@Resonating I guess I'll go too-it's time to feed my cats and they know it. My husband works nights, so whatever chatting I do is usually after 3. Thanks for your help, and company. Keep up the good work!

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