The 'Weird' Male Y Chromosome Has Finally Been Fully Sequenced (theconversation.com) 145
An anonymous reader quotes a report from The Conversation: The Y chromosome is a never-ending source of fascination (particularly to men) because it bears genes that determine maleness and make sperm. It's also small and seriously weird; it carries few genes and is full of junk DNA that makes it horrendous to sequence. However, new "long-read" sequencing techniques have finally provided a reliable sequence from one end of the Y to the other. The paper describing this Herculean effort has been published in Nature. The findings provide a solid base to explore how genes for sex and sperm work, how the Y chromosome evolved, and whether -- as predicted -- it will disappear in a few million years. [...]
Spoiler alert -- the Y turns out to be just as weird as we expected from decades of gene mapping and the previous sequencing. A few new genes have been discovered, but these are extra copies of genes that were already known to exist in multiple copies. The border of the pseudoautosomal region (which is shared with the X) has been pushed a bit further toward the tip of the Y chromosome. We now know the structure of the centromere (a region of the chromosome that pulls copies apart when the cell divides), and have a complete readout of the complex mixture of repetitive sequences in the fluorescent end of the Y.
But perhaps the most important outcome is how useful the findings will be for scientists all over the world. Some groups will now examine the details of Y genes. They will look for sequences that might control how SRY and the sperm genes are expressed, and to see whether genes that have X partners have retained the same functions or evolved new ones. Others will closely examine the repeated sequences to determine where and how they originated, and why they were amplified. Many groups will also analyze the Y chromosomes of men from different corners of the world to detect signs of degeneration, or recent evolution of function. It's a new era for the poor old Y.
Spoiler alert -- the Y turns out to be just as weird as we expected from decades of gene mapping and the previous sequencing. A few new genes have been discovered, but these are extra copies of genes that were already known to exist in multiple copies. The border of the pseudoautosomal region (which is shared with the X) has been pushed a bit further toward the tip of the Y chromosome. We now know the structure of the centromere (a region of the chromosome that pulls copies apart when the cell divides), and have a complete readout of the complex mixture of repetitive sequences in the fluorescent end of the Y.
But perhaps the most important outcome is how useful the findings will be for scientists all over the world. Some groups will now examine the details of Y genes. They will look for sequences that might control how SRY and the sperm genes are expressed, and to see whether genes that have X partners have retained the same functions or evolved new ones. Others will closely examine the repeated sequences to determine where and how they originated, and why they were amplified. Many groups will also analyze the Y chromosomes of men from different corners of the world to detect signs of degeneration, or recent evolution of function. It's a new era for the poor old Y.
Just discovered (Score:1)
Re: Just discovered (Score:2)
The future (Score:2)
According to Reddit this is going to be used for quick DNA test strips for identify people's true gender identity when there's a question.
Re: The future (Score:3)
The genius of Reddit. This is biology, not ideology. Biological testing for gender identity would be akin to a CAT scan to determine a patient's preferred colour of cat.
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Neither.
Gender is now about forcing other people to accept the delusions of the mentally ill as reality upon threat of physical or economic force or just good old fashioned harassment.
Re: The future (Score:5, Informative)
If your born with a dick, your gender is male
Time to read up on how genetics work. Because the Y chromosome doesn't even do that. It might activate the genes that do that. Usually. There are plenty of XY with vaginas due to androgen insensitivity. There are other things besides Y that trigger some of the other genes, so you might see differentiation in brain development that doesn't appear physically.
The default human form is female and only differentiates based on hormone signals that may or may not work correctly. You can call it mental illness, but it's less like illness and more like differentiated biology through gene and hormone activation.
Your "dick" is just an extended clitoris that has enveloped your longer urethra and your testicles descended down a proto vagina after differentiating from ovaries. Your labia fused into a scrotum.
Even the psychologists that think gender dysphoria is a mental illness would agree that transition would actually help because the mental disconnect causes that amount of trauma.
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Y chromosome is not indicative of gender, scientifically speaking.
It is a strong statistical hint, though.
Re: The future (Score:2)
> There are XX biological males, as well.
>Y chromosome is not indicative of gender, scientifically speaking.
It is a strong statistical hint, though.
Ridiculous. XX syndrome is something like 0.05% of live male births. That's more than a hint, it's a near perfect p value.
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A perfect p-value would be ~3*10^-7. ~1 person per 3.5 million.
You're an idiot.
Re: The future (Score:2)
0.05 (i.e. 5%) is the benchmark in testing the null hypothesis. 0.05% is 0.005 - even more significant. Incidentally, it'd be 10 people in 2000. You're welcome.
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It is not even fucking remotely the "benchmark" for demonstrating that something is not a scientific truth. You'll note that chromosome arrangements don't have anything even remotely approaching a normal distribution.
The benchmark for a scientific truth is 5 sigma, or ~3*10^-7.
Males have XY chromosome arrangements is scientifically false.
Males normally have XY chromosomes is undeniably
Re: The future (Score:2)
I didn't say scientific truth. These are probabilities, which for done reason you think 0.05% overturns what is accurate for 99.5% of a population.
However you're misunderstanding this, it does explain your confusion over sex.
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0.5% of a population is a massive error rate, scientifically speaking.
If the burden of proof for any finding was a p-value of 0.05, we could argue albinos don't exist while we're at it.
Explaining that a rare, but not that rare percentage of human males are XX does not represent confusion over sex.
Rather, I think you're very upset by the idea of people not adhering to your particular take on gender and are desperately reaching for any way you can to show these people as aberr
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Exceptions are human beings (Score:2)
Born with a dick: male.
Born with a vagina: female.
Everything else is mental illness or exception spewing academics and meaningless on a social scale of billions.
Human beings born with ambiguous bits are exceptions, and they are also human beings. For example, a boy with defective SRD5A2 can have ambiguous or feminine-looking bits at birth and become clearly a boy at puberty. (A search keyword is "guevedoces".) Who decides which bathroom exceptional human beings must use?
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Of course they are human beings. We don't need to make sweeping grand societal changes for the tiny number of special people who honestly truly have something different going on. They don't need a special bathroom in every building. They don't need a special sports team. They don't need a special check box on government forms.
Exceptions do not make the rule nor do we need a special rule throughout all of society for exceptions.
Indiana restroom trespass bill (Score:2)
We don't need to make sweeping grand societal changes for the tiny number of special people who honestly truly have something different going on. They don't need a special bathroom in every building.
Indiana state legislators appear to disagree with that. A "restroom trespass" bill has been introduced in several recent sessions of the Indiana General Assembly. It defines a "female" as someone with XX chromosomes or who was apparently female at birth, defines a "male" as someone with XY chromosomes or who was apparently male at birth, and bans "males" from female restrooms and "females" from male restrooms. A strict reading of this particular bill would deem XY AFAB people (5-ARD, Swyer, CAIS) and XX AMA
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We don't need to make sweeping grand societal changes for the tiny number of special people who honestly truly have something different going on. They don't need a special bathroom in every building.
Indiana state legislators appear to disagree with that. A "restroom trespass" bill has been introduced in several recent sessions of the Indiana General Assembly. It defines a "female" as someone with XX chromosomes or who was apparently female at birth, defines a "male" as someone with XY chromosomes or who was apparently male at birth, and bans "males" from female restrooms and "females" from male restrooms. A strict reading of this particular bill would deem XY AFAB people (5-ARD, Swyer, CAIS) and XX AMAB people (de la Chapelle) simultaneously male and female, banning them from both restrooms. It would in effect ban about 1,200 Hoosiers from using the restroom at all in places that lack a unisex restroom.
That's Indiana for you: The same idiots that sought to Legislate Pi to 3.2 !
https://www.forbes.com/sites/k... [forbes.com]
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Exceptions do not disprove the rule.
Let's just pretend they don't exist for your sake. Clearly it's too much for you to handle.
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Nah, let's instead force all of human civilization to completely alter fundamental aspects of how it's structured including all human communication in order to make this microscopically small minority feel slightly better about themselves.
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False dichotomy.
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I can't believe this is such a hardship for you.
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Born with a dick: male.
Born with a vagina: female.
Everything else is mental illness or exception spewing academics and meaningless on a social scale of billions.
Prove it; or STFU and FOAD.
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"There are currently no laws requiring me to accept Christianity."
Don't give the Republicans ideas...
Re: The future (Score:2)
That a water scorpion can breath underwater through a 'snorkel' at their tail has little bearing on a discussion of human respiration. The modern concept of gender applied to humans has no relevance outside of humans.
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The male pattern baldness teacher at my kid's school showing up in a leather mini skirt and red silk top to teach class was 1 too many. Knowing that if I called him Michael instead of Michelle my kid would get punished so I had to play along with his disturbing sickness displayed in front of the kids every day until I could get her out of there.
Thanks for the useless life advice, Mr "I make grand and boldly false assumptions about strangers on the internet".
How about you step back and loo at your own arrog
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Why is any teacher showing up in a mini skirt, much less little kids' school?
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I see this approach far too often. Demanding some new, radical change, and then acting like those who oppose it are the ones trying to make a change. No. There are delusional people out there who are obsessed with making everyone accept their delusional views of biology and society. They are abnormally obsessed, not the people who call them out for their
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Re: The future (Score:2)
Look at Monopoly guy here! Not all of us can afford healthcare that doesn't come with a haircut and a shave.
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The genius of Reddit. This is biology, not ideology. Biological testing for gender identity would be akin to a CAT scan to determine a patient's preferred colour of cat.
Wait!
Isn't that what they're for?!?
Re: The future (Score:2)
Definitely, although PET scans are better if you have other kinds of animals to do.
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Definitely, although PET scans are better if you have other kinds of animals to do.
Naturally!
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Not really.
You do get individuals with XY chromosomes who look very much like women, and can get pregnant and so on. That is due to chromosomes elswhere not doing what they usually do in the presence of a Y chromosome.
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You also get individuals who suffer from Galactosemia and cannot be breastfed.
We don't redefine the taxonomy class Mammalia to account for the fact that these specific individual members don't conform to the normal definition. Nor do we suddenly pretend that humans aren't mammals because these individuals exist. Yes, you can get people with genetic abnormalities who develop in extremely unusual ways. That doesn't mean that male and female don't exist in nature. That doesn't mean that they don't have well un
Re:The future (Score:5, Informative)
The Y chromosome contains almost none of the information to define what makes a body male or female. It has a big toggle switch in it to activate genes that everyone - XX and XY have. And since there are other activation triggers to some of these genes, you get a lot of characteristics activated differently than just whether there is a Y chromosome present.
So we aren't sequenced yet? (Score:2)
All that noise a couple of decades ago about sequencing of the human genome... What did that effort sequence?
What still remains to be sequenced?
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It sequenced all the obvious stuff.
It was done by sequencing lots of little bits of DNA, putting that all in a massive database, then matching sections at each end of the small sequences to others, to join them all together.
The problem with this is that when there are lots of long repeating sections, that couldn't be accurately matched.
Also there are lots of sections that don't seem to code for any known proteins or enzymes, so they were called "junk" DNA - though they might actually not be junk at all, but
Re:So we aren't sequenced yet? (Score:5, Informative)
The issue was that the Y chromosome contains very long sequences of repeating junk DNA and the old sequencing methods were producing very small pieces.
Here is an analogy with all letters instead of just the four ATCG found in DNA.
Let's imagine that sequencing gives you a lot of small pieces of no more than 10 characters such as ...
(1) eThatIsT
(2) ToBeThatI
(3) eOrNotToB
(4) ToBeOr
(5) hatIsThe
(6) OrNotToBe
(7) BeThatIs
(8) Question
(9) IsTheQuest
Overlapping of (7), (1) , (5), (9) and (8) produces the longer sequence BeThatIsTheQuestion
Similarly, (4), (3) and (6) produces ToBeOrNoToBe
And finally (2) connects those 2 sequences to form the full genome ToBeOrNotToBeThatIsTheQuestion
That this technique does not work well if you have a lot of repeating sequences in the genome.
Imagine that the genome contains ToBeOrNoToBe repeated a few hundred times.
Sequencing would produce a lot of fragments such as ToBeOr, eOrNotT, ToBeOrNo, rNotToBeToB, ToBeToBe, eOrNotToB, oBeToBeOr, eToBeXrNotT, oBeOrN, oBeOr, BeOrNotT , ...
It would be easy to figure out that ToBeOrNoToBe is repeating itself but not how many times.
Also, some fragments may contain single mutations like the X in one of the fragments above there would be no way to figure out where that X occurs in the repetition.
The new sequencing methods produce longer fragments and so make decoding a lot easier.
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https://phys.org/news/2023-08-... [phys.org] says the old techniques sequence fragments about 100 bases long, but the new ones can handle "thousands".
https://en.wikipedia.org/wiki/... [wikipedia.org] says the trade-off with long-read techniques is a higher error rate (compared to previous sequencing techniques) that goes up as a function of the read length, which perhaps explains why it's not qualified very clearly.
Re:So we aren't sequenced yet? (Score:4, Funny)
So basically it's that typical man thing of never wanting to throw old junk away "just in case".
I'll tell my wife it's not my fault, it's in my DNA!
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So you're saying our genes are typewriters and we are the monkeys writing Shakespeare..
Actually, that might make plenty of sense. We only need one good copy of X. The Y is a truncated mutated copy that may not matter for a lot besides turning on sex-specific genes on other chromosomes. But we won't know until we analyze the sequence. Sequencing might have been hard but it still might be because it is mostly junk.
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"Weird" ? (Score:2)
determine maleness ... junk DNA (Score:2)
If you're going to repeat everything, this is going to take a long time.
But do you know why (Score:2)
When tons of people say you have to find your why... This dude went out and did it literally
I will ask the unasked question... (Score:2)
Did they find the gene for penis size and has someone figured out how to adjust it via crispr?
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1. You need SRY gene to get testicles (you can't have penis without them, because it would look stupid)
2. You need AR gene. When embryo develops a tube, AR creates receptors for testosterone to attach.
3. You need MKRN3 and KISS1R for androgen production. It might be interesting to see what happens if you leave one out, but it might not be what you want.
4. You need SRD5A2 to convert testosterone into DHT (dihydrotestosterone) which affects the penis growth.
Simply inactivate SRD5A2 to get smaller penis and yo
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It's not in Y. Virtually nothing that makes you male is in the Y other than the toggle switch.
What about other forms of life? (Score:2)
Most of the complex lifeforms (plants, animals) have sexual reproduction, and have done for hundreds of millions of years, Is that all done with the same X and Y chromosome?
Re: What about other forms of life? (Score:2)
No [wikipedia.org].
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Interesting, but "many" do. It would be interesting to see if all mammals had it, then it evolved away, some must be very close to that point.
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Most of the complex lifeforms (plants, animals) have sexual reproduction, and have done for hundreds of millions of years, Is that all done with the same X and Y chromosome?
No, there are other methods of sex selection. For instance reptiles use incubation temperature.
About 'junk' DNA (Score:5, Interesting)
A lot of what is apparently still labelled 'junk' DNA is sequences scientists thought did nothing because it didn't code proteins.
They were wrong - it turns out DNA does a lot more than just create proteins. Which really seems like something they should have figured out right away, but maybe that's just me.
Crazy Sexist (Score:2)
The idea that women biologists would be less interested in animalian sexual reproduction than men is the most mysogynistic thing I've read in edited content here.
This site is devolving into telling us how to feel, not what to know. Stick to news.
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When my kids tell me I'm weird (Score:2)
I tell them it's genetic.
Now science has proved it!
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Hey, I own it, I am weird.
And if you're human, you are too.
Why does this keep happening? (Score:2)
NO Reason - At All (Score:2)
Q: This being the lowest level, the machine code if you will, was any excuse for women to love men found?
A; Nothing to see here. Please move along.
The Y chromosome will disappear in a few million.. (Score:2)
Sure. Because sexual dimorphism is just a passing fad...
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Okay.
Didn't know this was a communal sci-fi novel writing workshop...
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Name one programmer who worked on code that didn't have at least some level of intelligence behind it.
Re:junk code?!? (Score:4, Informative)
Since we're blurring the line between code and hardware here, I'll offer up this example:
"Dr. Thompson peered inside his perfect offspring to gain insight into its methods, but what he found inside was baffling. The plucky chip was utilizing only thirty-seven of its one hundred logic gates, and most of them were arranged in a curious collection of feedback loops. Five individual logic cells were functionally disconnected from the restââ" with no pathways that would allow them to influence the outputââ" yet when the researcher disabled any one of them the chip lost its ability to discriminate the tones. Furthermore, the final program did not work reliably when it was loaded onto other FPGAs of the same type."
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The intelligence behind that code was what some people call "front-loaded": the conditions were set up (by an intelligent actor, Dr. Thompson) to produce a result. You don't get FPGAs in nature, the thing that evaluates the fitness function and creates the next generation was intelligently designed, and the FPGA loading and execution were all arranged by a human.
(Where cdesign propronentsists go off the rails is that they claim that's why people evolved.)
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Name one programmer who worked on code that didn't have at least some level of intelligence behind it.
And some level of junk in their code?
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Re:junk code?!? (Score:5, Interesting)
A lot of "junk code" on other chromosomes, on closer examination, turned out to be not so junk: Introns that when cut out became feedback signals to indicate the segment had been transcribed into RNA so it could be skipped now, signals to activate transcription of helper enzymes on other sections of the genome, RNA enzymes to do some related thing, etc. Of course some WAS junk - viral remnants, tracks of jumping genes, etc. And some was still WTF: Who knows if it's junk or gold? Seems to me this is likely for the Y also.
One theory of why the Y is so short: The shorter it is, the less likely a selection-restriction could develop on it. On other chromosomes this is bad but not insurmountable with time. On the Y (if a countermeassure doesn't evolve lightning-quick) all the first mutant's children are male, all their children are male, and so on until there's an all-male generation, after which the species disappears into the dustbin of extinction.
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A lot of "junk code" on other chromosomes, on closer examination, turned out to be not so junk: Introns that when cut out became feedback signals to indicate the segment had been transcribed into RNA so it could be skipped now, signals to activate transcription of helper enzymes on other sections of the genome, RNA enzymes to do some related thing, etc.
Ie, spaghetti code. There's a reason we software engineers despise Windows, systemd, or php, and I see no reason why biologists wouldn't share the sentiment.
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Java is the most spaghetti like. 14 classes and 40 functions deep with calls to 35 different "factories" - It can take days to find code that actually does anything or has any logic in it in a Java codebase (or any object oriented language for that matter). It is also dreadfully inefficient and environmentally irresponsible at scale.
What's wrong with having a ViewFactoryFactoryFactoryFactory? :-D
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As soon as I see the word factory in a codebase, I know the whole thing is shit.
John Smith 2319, John Smith 2294?!?
Good God, man; just how many Sock Puppets does it take?!?!???
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Seems to me this is likely for the Y also.
One theory of why the Y is so short: The shorter it is, the less likely a selection-restriction could develop on it. On other chromosomes this is bad but not insurmountable with time. On the Y (if a countermeassure doesn't evolve lightning-quick) all the first mutant's children are male, all their children are male, and so on until there's an all-male generation, after which the species disappears into the dustbin of extinction.
The way I remember it is since only half of children have the Y chromosome, there is selection pressure from the genes on the X chromosome to remove it or make it non-functional producing more XX children. Genes on the Y chromosome have their functions taken up by genes on other chromosomes to make the attack surface of the Y chromosome smaller.
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Imagine you were to use a random word generator, and compile trillions of outputs until you got one that did what you want it to do.
What would that code look like?
That's essentially what has happened with DNA.
46,XX testicular aka "de la Chapelle" (Score:4, Informative)
all the code is already elsewhere, the only that matters on Y is a small bit of config (SRY) that can be just as well stored on an X chromosome instead with no adverse effects.
Some male humans have been deployed with the SRY on an X chromosome. They call it a "de la Chapelle" configuration [wikipedia.org]. Some legislators are not amused, telling these 46,XX men they should use the women's.
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Re: junk code?!? (Score:2)
Re: Something something nonbinary (Score:5, Interesting)
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He's posting red pill content about traditional male societal roles as if that has anything to do with the physical/chemical make up of rhe Y chromosome.
I think he's just amusing himself.
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What does that even...? Shut the fuck up.
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In this context:
- Cis is short for cisgender, meaning an individual's gender identity matches the individual's apparent sex at birth.
- Het is short for heterosexual, meaning preferring sexual interactions with the opposite sex/gender from oneself.
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Re: Something something nonbinary (Score:2)
Oh boy...this guy had his feelings hurt really bad, somebody call a waaambulance.
And you can put away your sock. I only have one account I actively use dude. I have an older one as well but haven't even used it since 2013 I think.
Re: Something something nonbinary (Score:2)
And yet I'm not the one bitching about it.
I never really care where the moderation on my comments goes. I just comment and whatever happens happens. I get mod points all the time but I basically never use them.
When you get downmodded, your feelings get hurt so you make another account. When I get downmodded, which happens all the time, I really couldn't care less. Sometimes I even make a post knowing full well it's going to get downmodded quickly, and again I don't care.
TBH I don't know why my that post got
Re: Something something nonbinary (Score:2)
Dude you only need one account to continue posting. Quitchyer bitchin.
Re: Something something nonbinary (Score:2)
Censored how? Because your karma is shit? Just don't be a dick dude, and you won't have a problem.
Re: Something something nonbinary (Score:2)
But you don't ever say anything either truthful or factual. If you're at zero, you're basically AC, which people respond to all the time. I personally always browse at -1, especially given some of the best posts are there.
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What the hell are you talking about? Why would I defend my troll behavior? Trolling is what I do. That would be like saying you're preoccupied with defending your mouthbreathing behavior. And no, I don't always try to get the last word, very often I won't even reply to somebody's response, the fact that I pissed them off is usually enough. While I've already succeeded here, you're one of those cases where you actually believe in the shit coming out of your mouth, which is entertaining.
Re: Something something nonbinary (Score:2)
I get that you think I'm sexy and all, but I'm not into dudes, dude.
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This post is a classic example of slashdot "moderating" cowards and the use of sock accounts. This asshole is a straight up troll, modded +4. The system DOES NOT work.
Only made worse by the oft-abused "Anonymous Coward" Karmic Shield.
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Well she does like the tip, especially if you lightly tease her with it.
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