The Biosphere

2:55 PM

@Secret Woah! That is not what that study claims! Only very specific mutations can lead to cancer. The study is just pointing out that these specific mutations can happen randomly, not that any random mutation can lead to cancer.

Secret

oops sorry, I overlooked that there are specific ones, thanks for notifying

terdon

It also doesn't claim that most cancers are caused by such random mutation events. Only that most cancer mutations are random. That's a very different thing.

Chris

@Secret Actually most cancers have hotspot regions in some genes where most of the mutations happen-

Secret

Seems I hinged on the word "random" too much, and overlooked anything else

terdon

Heh, that's how headlines are born :)

AliceD

3:40 PM

@terdon You are very likely absolutely right but isn't that with life in general? My wife certainly knows to point the bad things out and overlook the oh-so-many good qualities of me ;-)

terdon

Yes, spouses tend to excel at that :)

AliceD

@terdon oh he&& yeah they do haha

Kiny

As a female, I don't know how i should take that

But i agree that moderators are greatly undervalued by the communities

terdon

@Kiny Note that I used the word spouses which applies to any gender.

And I did so very consciously.

Bryan Krause

Glad to see Biosphere fact-checking at full force :)

terdon

3:49 PM

I also assume Alice is female, given the name. Although that may well be a wrong assumption.

Kiny

@Terdon I apologise xD, I saw Alice talking about his wife, and since I knew You where talking about the same thing i automatically associated

@terdon we should totally ask before we insult anyone! XD

terdon

@Kiny Dunno, I have very little patience for men who consider it an insult to be called women or for women who consider it an insult to be called a man. Not when all we have to go on is a username, anyway :)

Kiny

@terdon XD I've been mistaken for a male multiple times, I have never felt insulted but i still feel the need to correct when such things happen, I good to know your open minded.

terdon

Oh sure, I can understand wanting to correct. I just get pissed off at the (usually male) people who consider it insulting to be called women. I mean sheesh, your own mother is a woman you idiot!

Kiny

I agree, females are a very important contribute to the continuation of the spiecies. If all humans where male xD we wouldn't have a next generation so i actually give both genders equal value

terdon

3:57 PM

Welcome to the site, by the way, I just saw you're new!

Kiny

Joined yesterday! Loving the community so far.

@terdon by the way, how do you experienced members find out i'm new? Is it in my reputation?

terdon

@Kiny Your profile.

Kiny

@terdon I see xD I apologise for my ignorance, I'm new to online comunities. Thanks for telling

terdon

@Kiny No reason to apologize! We were all new once :)

However, I will move these last few messages to the main chat room since this one is supposed to be about the election and we've veered off subject.

Kiny

@terdon your correct, I apologise for going off-topic

terdon

4:05 PM

← 23 messages moved from Biology 2017 Moderator Election Chat

@Kiny hey, I started it :)

Kiny

@terdon started what? XD

terdon

The offtopicness.

Kiny

xD, Whats the theme of this chat room?

terdon

This is just for general discussion, preferably about biology and/or Biology (the site).

Kiny

So going off topic here is acceptable?

skull petrol

4:11 PM

Yup ;-)

Kiny

@skullpetrol Hello =D

skull petrol

Within guidelines of course, and hello!

I'm sure @terdon has much more to say about the "guidelines."

terdon

Not really. This chat room isn't very active so no real guidelines have emerged so far. Just idle chatter.

Kiny

What happens if I want to talk to someone? Off topicness seems pretty much a negative thing across the entire website.

terdon

Apart from the global chat rule: be nice

Kiny

4:16 PM

I like that rule =D

terdon

@Kiny Don't worry about it in chat. The election room is a special case since it is specifically set up to discuss the election and talk to candidates. So it's better to keep the room focused on that subject.

But in general, feel free to chat about whatever you like.

Kiny

@terdon about the election, AliceD tried to explain me about voting but i never really did found out how i can vote too.

lools we speak of Alice and Alice apears

AliceD

@Kiny stop saying sorry! ;-)

skull petrol

Sounds like the "War room" from dr strange love :-)

Kiny

@AliceD edit- My apologies

AliceD

4:19 PM

And Alice Cooper is hardly female.

Kiny

So your a male?

AliceD

Alice is unisex, and can't women have wives too? :-)

Kiny

Of corse they can, I aprove of gay and lesbian marriage!

terdon

@Kiny You can't, I'm afraid. You need a minimum of reputation to be able to vote.

AliceD

Yeah I just found that out too

terdon

4:21 PM

@AliceD Um. No it isn't. Not in English, anyway.

Kiny

@terdon Do you know wich reputation that is?

AliceD

300 rep

Kiny

Thats to bad, nobodys getting my vote then xD

terdon

@AliceD 150 to vote, 300 to nominate.

91

A: There's an election going on. What's happening and how does it work?

What's happening? The community is electing diamond ♦ moderators; those individuals responsible for moderating the site the election is happening on. Moderators are elected by a four-phase process: Phase 0: Announcement and question collection Duration: 7 days An election is announced by a p...

Kiny

Thanks for the link, it is very informative

AliceD

4:24 PM

@terdon that's interesting, partner and spouse it is then (-: After 6 years in English speaking countries still making mistakes

@terdon aha thanks mate

Kiny

My english is full of mistakes too, It has been self tought and is full of holes everywhere.

terdon

@AliceD No, I meant the name Alice isn't unisex in English. Wife is perfectly applicable to a female spouse, the gender of the other spouse is irrelevant (so yes, a married gay woman can refer to her wife).

skull petrol

Alice Cooper?

terdon

@skullpetrol Not his real name. And the whole point of it was precisely to shock the audience with the discrepancy.

Kiny

I also thought AliceD was female due to the name xD

skull petrol

4:28 PM

Right, right.

terdon

> The legend is that the name "Alice Cooper" came from a session with a Ouija board, largely chosen because it sounded innocuous and wholesome, in humorous contrast to the band's image and music. However, in an interview with Mark Radcliffe on the Radcliffe and Maconie show on BBC Radio 2 on 30 November 2009, Alice described the incident with the ouija board as an urban legend: "We literally got that whole story about the witch thing the way you guys got it. It was like just pure urban legend. I heard about the witch thing probably the same day you did, but it was a great story." [16] "Alic…

4

Kiny

I never espected a name change to be considered a career move

skull petrol

TIL

Thanks @terdon

terdon

Same reason Penis van Lesbian changed his name to Dick Van Dyke.

rimshot

skull petrol

So Alice Cooper can never go to wonderland and wonder about his/her gender... :double rimshot:

terdon

4:34 PM

@skullpetrol You know, I think we hang out in the ELU room too much.

skull petrol

You got it pal :-)

Kiny

secretly wants to partecipate in the chat but has no idea what is being said

terdon

@Kiny Don't worry, we're being silly.

skull petrol

Doesn't matter @Kiny just say whatever :-)

Kiny

@terdon being silly is an acceptable and positive traint

well then, what do you guys do when you can't answer any questions? =D

@terdon Can I make a SUPER off topic question?

terdon

4:43 PM

@Kiny In here? Sure. By the way, I'm no authority around here. I am a mod on other Stack Exchange (SE) sites but I'm just a regular user here. You see me answering Alice's questions because I've been an SE user for a while and I know the system.

Kiny

XD

@terdon xD what LINUX operative system would you recomend? (<- it doesn't get moreoff topic than this)

terdon

@Kiny That depends on what you want. If you want something that's easy to use and just "works", go for Mint or Ubuntu. If you want something that is very configurable but takes more work to set up and needs some basic knowledge of Linux, go for Arch. For something in between you can try Debian or Fedora.

Kiny

@terdon Debian or Fedora, got it, i'll take a look online about them later.

terdon

@Kiny If you've never used Linux before, Mint or Ubuntu would probably be better choices.

Kiny

I've used linux before, it was MY operative system as a child, I was forced to change to windows because of school

Although it might have progressed greatly so I might need to releard

Thanks for the feedback

terdon

4:47 PM

Whaaa? That's weird. I switched to Linux in university.

That was in 1999 or so though.

Kiny

My teachers specifically wanted microsoft office files

terdon

@Kiny So? LibreOffice can produce .doc files.

Kiny

Thats strange, When i told my dad the files i needed he switched me to windows, he never mentioned libreoffice

@terdon although to be fair i'll admit the only thing i did on linux all those years was playing games, drawing and writting notes about the games.

terdon

That's weird. LibreOffice, OpenOffice, AbiWord can all do this and all have been available for more than a decade. Well, LibreOffice was forked from OpenOffice less than a decade ago, but Linux has been able to use .doc files for many years now.

Kiny

I tried OpenOffice and some of my teachers hated it

Bryan Krause

4:51 PM

@Kiny I find it hilarious that your very off-topic question was about Linux OS choice - this was a specific topic of conversation here, um, yesterday maybe?

Kiny

I didn't know this chat existed yesterday xD I would very much have liked to join that convo

terdon

@Kiny This has probably improved enormously as well since Word now uses an XML-based open format.

Bryan Krause

Well I think you already have since @terdon was a major participant.

Kiny

Thats awesome, I would still like to be able to open my files even on linux, I been wanting to switch to linux for years.

Who can't ask about linux to terdon after seeing his profile? XD

terdon

@BryanKrause Yeah, for some weird reason everyone seems to think I am some sort of Linux expert.

Kiny

4:53 PM

You should take a look at your own profile xD

" Unix & Linux♦ 97.1k 97.1k 19166289
Ask Ubuntu♦ 47.9k 47.9k 696168 "

Hard to ignore

terdon

:P

Kiny

@terdon I didn't ask for your "expertise" I asked for your opinion. The opinion of users is very usefull to other users or future users.

@terdon Obviously all of your expertise is very welcom.

By the way, why is there a 100 under my name I have 71 reputation?

terdon

@Kiny The chat reputation is the sum of your reputation across all the sites you have an account on. Your total rep is 100.

Kiny

@terdon Does that mean chat wise i can join anything regardless of where is my base reputation?

terdon

?

You need 20 reputation points to chat. Once you have that, you can enter and chat in any public room.

Kiny

5:03 PM

Could I join for example a chat on the academic site?

terdon

Yes. The chat servers are shared across all sites. The only exception is the various Stack Overflow rooms which have their own server.

That's why my name appears in blue here. Any moderator from any site is automatically a chat mod as well.

Kiny

Your a moderator?

terdon

@Kiny Yes. That's what the ♦ you saw in my profile next to my U&L and AU accounts mean.

Kiny

"Elected moderator on Unix & Linux and Ask Ubuntu."

The more obvious the information the easier I miss it. I repent.

terdon

Chris ♦

35k 7 72 126

Chris is a moderator here, so he has a diamond on his profile.

I don't:

terdon, Athens, Greece

10.1k 4 30 63

evolution bioinformatics dna genetics human-biology cell-biology biochemistry

But I do on my U&L page:

terdon ♦, Athens, Greece

97.1k 19 166 289

bash text-processing shell-script awk sed shell grep

Kiny

5:06 PM

O-o Athens? thats very cool

And I didn't really notice those tiny diamonds, I'll try to pay more attention

terdon

Um. Not really. We used to always compete with you guys (Portugal) over the last place in all the statistics lists (either Greece or Portugal was usually the worst in Europe for whatever you were looking for) but now it's always us :(

Kiny

XD I was always taught in school Athens was the city of knowledge

And honestly i don't think Portugal has raised that much

terdon

@Kiny I didn't say it had, but Greece has fallen :P

Kiny

Is the way of living in Greece bad?

terdon

@Kiny it probably was, 3000 years ago.

@Kiny Greece is still stuck in deep depression and financial crisis. I am one of the lucky ones, I have a job, but most people don't. And among those who do, it is common to have salaries at 200€ a month.

Kiny

5:12 PM

If it makes you feel better I'm looking for a job xD and if I don't get one by the end of this semester I'll be forced to drop out of univercity.

terdon

Ouch. :(

Kiny

In my last job i earned 260€

a month

terdon

Part time?

Kiny

I refuse to miss a single class or lecture!

so yes

Theres no point in paying the tuitions if I'm not taking advantage of it =P

terdon

I met someone a few weeks ago who had a university degree (pre-school teacher) and was working as a pre-school teacher, 8 hours a day, 5 days a week and was being paid 200€. And that's not rare in Greece these days, unfortunately.

Kiny

5:15 PM

Well i would die of starvation if i only had 200 a month considering my room costs 200

terdon

Yes. She was still living with her parents for the same reason.

Kiny

Saddly, I can't live with my parents when my univercity is in the other corner of the country with 10 to 12(depends on transport) hours of travel in between

And the city my parents are there's a great shortage of jobs

Otherwise i probably would be living there too and save in advance rather than having to desperately look for jobs during test season xD

But indeed, I wasn't aware Greece had fallen even more, May i ask what job you do?

terdon

@Kiny Where are you from then? Don't tell me you're from Chaves!

@Kiny I'm working as a developer/bioinformatician.

Kiny

Thats my birth city yes xD

@terdon does it say in my profile?

@terdon - developer!!! I have great respect and admiration for developers. specially since i'm going through the struggles to try to be a indie game developer. Can't say i'm having much sucess

Mesentery

@Kiny u have made the Bio chat room alive. It's the first I saw our chat room full of messages when I enter

Kiny

5:28 PM

@Mesentery Its mostly off topic though xD Feel free to join.

terdon

@Kiny Ha! No, but I had some good friends from there.

Kiny

@terdon from CHAVES? XD try me, maybe i'll know some

Mesentery

@Kiny I don't think anything is off-topic in chat.

terdon

Family names: Campos (or, OK, Sarmento Morais de Campos) and Cabeleira.

Kiny

Cebeleira? that's the first I ever heard that one, Sarmento Morais de Campos? I think my dad had an acquaintance of that name.

terdon

5:32 PM

@Kiny Probably. They're a huge family.

Kiny

@terdon xD and my dad knows almost everyone in Chaves, the perks of his job.

@terdon I must say though that I'm very curious about what one does with a job of BioInformatician. Do you develop programs for data analysis?

terdon

@Kiny Bioinformatics is a field of biology.

I recently switched to working in industry as a programmer but before that I was in academia doing research. Just like any other biologist.

Kiny

@terdon I had Bioinformatic class last semester, we where given a DNA sequece to work with

we had to look if it was coding or no coding and making multiple alignements, filogenetic trees, and try to identefy what organism's DNA it was.

@terdon What programming language do you use?

terdon

@Kiny Mostly Perl and bash, some python.

And awk.

Kiny

@terdon So many programming languages! I personally been attempting to learn python.

terdon

5:46 PM

That's a good starting place. If you want to work on biological data, you'll need at least one of Perl, Python or R.

skull petrol

R is the language of choice for sports analysis these days.

terdon

It's great tool for any statistical analysis.

Kiny

I'm afraid I'm already having troubles learning one xD I seem to not be very smart and have difficulties on pretty much everything.

terdon

It's always hard in the beginning.

Kiny

I tried following a free online course, the first assignments where very fun and doable, but soon it became very hard for me to follow and ended up failing to learn further

I joined stack overflow because my BioInformatic teacher sugested I come to the website to learn by reading asked questions and to ask my own, xD wasn't especting it to have a biology website.

@terdon what would you sugest for a complete newbie to learn a programing language?

terdon

5:57 PM

Python, probably. It's an easy language and very popular these days.

Kiny

That's what I'm trying for xD maybe someday i'll earn the rights to be called a programmer!!

Untill then I'll have to work hard at learning.

@terdon Can I ask you something VERY noobish about python?

terdon

You can try, but I doubt I'll know. I've only been using python since last summer.

Kiny

xD what python interpreter do you use? The course I tried to take used a web browser interpreter and I myself only have work done on an engin (which might not even be legitimate python to begin with)

terdon

6:12 PM

Um. Python3

Vanilla python3 as far as I know.

Kiny

Everytime I try to look for one I end up reading stuff about python 2 and python 3 and I honestly have no clue how to use that information to my advantage

terdon

@Kiny Don't. Just install whatever comes with your operating system or is easier to find. Worry about learning the language first, then move on to more advanced stuff.

Kiny

@terdon Don't I need to practice to learn?

terdon

yes, but just get a python interpreter. Don't worry about the fancy ones, go for the simple, vanilla python. In other words, install a Linux distribution and use whatever comes with it.

Kiny

I didn't know linux had a python intrepreter

terdon

6:18 PM

Oh yes. Both Perl and Python are pretty essential to the OS.

Kiny

Thats so cool!

Bryan Krause

6:37 PM

@Kiny Python 2 vs 3 is mostly about library availability - there are a lot of tools/libraries for Python 2 that haven't been ported to python 3, and the scope of the language changes means that they aren't trivial to update; there has been a lot of controversy about that.

Kiny

@BryanKrause so thats why everytime I try to look into it I get stuck with posts about them.

canadianer

7:12 PM

R is a horrible, godawful language. I just wish it wasn't so useful.

Kiny

@canadianer xD Your statements almost look contradictory, would you mind sharing why you dislike R? I've only heard about R today so naturally I'm not very informed about it.

Bryan Krause

@Kiny There are lots of discussions on this topic around the interwebs, for example here is one. A rough tl;dr is that R does not follow conventions that are used by many other languages (which means an experienced programmer can make major mistakes when learning R, whereas for most languages all you need to learn is basic syntax and functions), has a lot of internal inconsistency, and some unnecessary complexity.

However it is also very useful because it can perform so many different analyses and is a commonly used, respected language for statistical analysis, so folks use it despite the drawbacks.

Kiny

@BryanKrause Thanks, that was very informative o.o indeed such a language is bound to frustrate some programmers

canadianer

@Kiny Bryan summed it up nicely. Having learned more conventional languages first, I still find R unintuitive and strange.

fileunderwater

@kiny You could also get a Python install that bundles Ipython, which can be useful for interactive work. The Ipython notebook is a nice to be able to annotate code and to mix code and graphs (again, nice for education/teaching and to easily create standalone documents).

Bryan Krause

7:24 PM

Another way of thinking about it, not sure this is entirely true but I'll go with it anyways...R assumes things are going to be really complex. So it gives you a lot of tools for handling complex problems. But it also provides no real way to handle simpler situations. Whereas in other programming languages you expect to start simple and add on functionality to make more complex problems fit into a simple framework, R is really great for complex problems but makes you make simple problems complex

fileunderwater

On Windows you can get this with distributions from anaconda and enthought, among others

Bryan Krause

The result is that you sometimes get unexpected results when you think R is going to handle a simple problem the way you expect: the simple way.

fileunderwater

I agree with @terdon though, that the most important thing is to get going with something

Kiny

@fileunderwater Thanks for the sugestion!

@BryanKrause I guess that means that, to solver simpler problems, if you have knowledge of another language it might be worth using the other one?

fileunderwater

@BryanKrause At work, Im currently stuck with SAS for different reasons... Now there you have a truly godawful ugly language. R is a supermodel in comparison...

Bryan Krause

7:48 PM

@Kiny Perhaps - like @fileunderwater suggests though, for many purposes there is no alternative. Personally I use MATLAB mostly, which certainly has its own problems (mostly a terrible system of libraries - basically just putting files in a folder and adding it to your path - hope you don't have another function with the same name!, pretty worthless object-oriented ability, variance in behavior between versions that come out quite often, and poor algorithmic documentation)

Matlab is also expensive, and rarely used in industry. I probably wouldn't use it if my university didn't have a site license.

fileunderwater

@BryanKrause I also used MATLAB before, mostly for simulations, but later moved to R for more statistical power (and free licence).

I kind of liked the overall environment in MATLAB though (at least back then), with the integrated environment and a pretty good debugger

Bryan Krause

8:26 PM

@fileunderwater Yeah I don't know if it's just my expertise, but I feel like matlab is a great choice for just manipulating some data in small-to-medium datasets (less than a GB or so of data at a time). It's great for just playing around in the command line and eventually moving your code to a more polished script. I do use matlab for statistics but it is always problematic that the statistical code is all hidden, and some of the functions are poorly documented

For example, a function might spit out a p-value, but nowhere in the documentation does it tell you which test was performed, and the code itself is obfuscated.

Most serious statisticians/scientists aren't okay with just a p-value...

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