…the noyau, an animal society held together by mutual animosity rather than co-operation
Robert Ardrey, The Territorial Imperative.
[to work around page bug]
…the noyau, an animal society held together by mutual animosity rather than co-operation
Robert Ardrey, The Territorial Imperative.
[to work around page bug]
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Hi, Sal.
I am happy for you that you are getting good grades in grad school, but I am not particularly impressed. Two reasons: 1) I’ve taught similar classes, so I am aware of grade inflation. 2) Your writing here, and your inability to express yourself clearly and coherently, suggest that you are, at best, deeply confused.
It’s nice that you think that you “wiped the floor with [my] tongue over the chromatin discussion”, but when you say stuff like that, you are making my point for me: you are clueless.
You fail to comprehend. Here you are re-phrasing what I wrote, mischaracterizing it in order to try to score rhetorical points. Real scientists avoid this behavior.
I haven’t said ANYTHING about SRY & chromatin, except to note that your characterization of Nishino 2014 as showing that “it is a fact that SRY is regulated by chromatin” is wrong. I have said, all along, that the TIMING of SRY expression involves 16 other transcription factors (see, no mention of chromatin).
Then your hopeless logic fail. Just because X is required for SRY or MAT expression, does not in any way detract from the fact that they sit atop a regulatory hierarchy. You cold just as well claim that because MAT expression requires ATP, CTP, GTP and UTP and a temperature between 23 and 36 C, it therefore does not sit atop a hierarchy.
Still wrong, Sal.
“through chromatin modification” ? When you keep making this shit up, you keep making my point for me.
Between the misrepresentation and the sloppy writing (and thinking) there isn’t much point in continuing a conversation with you. I had been assuming that your writing was merely a display of D-K stupidity, but now I think that you are fundamentally dishonest. And D-K stupid.
I pity the poor teachers who are holding their noses while giving you your grades.
Been there, done that.
Here to praise Gregory (who seems to have whooshed in and then left again) for FINALLY making a comment which did not deserve immediate guano-ing.
Way to go, Gregory! I knew you could do it if you really tried. I knew your slavering paranoia and anti-Semitic anti-KN ranting was – at least – partly within your own control, and you could keep it down if you wanted.
Too bad, Gregory, that you had to stain your effort with a gratuitous slam against atheists. But you gotta start with baby steps in improvement, I guess. Keep trying – you’ll become a decent human being yet!
I was breast fed. Makes all the difference.
Are you independently stupid?
Patrick and Neil still suck at moderation.
Oops. Nothing new about that at all.
I think Sal is finally getting it. All posts here at TSZ belong in Noyau.
Where they disinfected afterwards?
Postmilking Teat Disinfection
I’m guessing no.
Here’s another research paper you ignored.
Take that, man, you’re way behind the curve in terms of available literature.
Nishino paper mentions DNA methylation, DNA is a chromatin modification, and another researcher interpreted the methylation changes as follows:
Oh I get it, you refuse to acknowledge DNA methylation is a chromatin modification that allows chromatin to control gene expression. Too funny.
But since you seem bent on arguing chromatin doesn’t regulate genes, get a load of this:
http://www.nature.com/scitable/ebooks/Chromatin-in-eukaryotic-regulation-16549786
So you still want to argue Chromatin doesn’t regulate gene expression? Laughable.
Oh dear Sal, do at least try to read for comprehension.
At no point have I claimed that Sry is NOT regulated by methylation, or by histone modifications, or by that wonderfully fuzzy concept “chromatin”. My “see, no mention of chromatin” was pointing out to you that YOU had mischaracterized what I had written, putting words in my mouth. Read slowly now: the only comment I made regarding SRY and chromatin was to point out that your concluding based on Nishino that it is a “fact that SRY is regulated by chromatin” was wrong, and I offered to disabuse you of that error. That offer still stands. Would you like to describe in your own words the methods Nishino used? Quoting what some other random scientist concluded from the paper is , err, underwhelming.
When you quoted Darasi 2002 as saying “After demethylation SRY gene expression was restored”, what technique did Dasari use to measure the demethylation?
Also, if (as you appear to be claiming) differential methylation is responsible for the differences in expression observed by Dasari, why didn’t SRY show up in Wang et al. 2005, given that both studies looked at LNCaP and PC3?
You seem to have a fundamental blind-spot regarding the nature of evidence.
In case you still don’t get it, I am not claiming that SRY is not regulated by methylation, I am poking holes in the “evidence” that you have offered to date, and thus testing whether you are competent to defend your use of this evidence.
You were getting an “Incomplete”, until that howler about hepatocellular carcinoma in yeast. Now it’s a “F”.
Addendum:
Multiple times dear Sal has claimed that “[Francesc Piferrer] has interpreted the methylation changes as follows:”
But what Dr. Piferrer actually wrote was more nuanced.
That’s dishonest, Sal.
Of course, using the same logic we can take Wang et al 2005 as “suggesting that Sry is NOT controlled epigenetically by a mechanism involving DNA methylation.”
So you might want to explore that the researchers actually did. Or not. Your choice.
So are you admitting SRY is regulated by DNA methylation, therefore SRY is regulated by something else. Hahaha!
Yet another logic fail from Sal.
I know this may be difficult for you to comprehend, but I am not making any claim or admission one way or the other.
Even after pointing out two papers that show DNA methylation regulating SRY.
For the reader’s benefit, since there is a long list of genes, I’ll put an ellipsis in the above to help get the point across:
There you have it both in this study and backed up by the Nishino study and my interpretation confirmed by Francesc Piferrer.
The DNA methylation state regulates SRY expression.
The problem with you DNA_jock is you can’t admit you made a mistake. I can since I don’t have to save face like you do.
Thanks for the free-of-charge tutoring on yeast MAT not being the same as human MAT. I thought the two having the same name made them homologous as is usually the convention for gene names.
But even with you pointing that out, I should your claim that MAT unambiguously at the top of the regulatory hierarchy can be only true by omitting the fact MAT is regulated by other things like the HO endonuclease.
But HO is regulated also by MAT domains.
http://europepmc.org/articles/PMC545453
There is a loop apparently. As I said, hard to characterize things with a strict hierarchy.
Heh.
Wow, just wow!
I pointed out to you that HO “regulates” MAT. And that MAT expression requires ATP, CTP, GTP and UTP.
None of these facts, all of which I pointed out to you, detract from the fact that MAT sits atop a regulatory hierarchy.
DO try to keep up.
How are the alleles of MAT found at HML and HMR kept silent? (Careful, it’s a trap!)
So are you admitting that, in heterothallic yeast, MAT sits atop a regulatory hierarchy. Hahaha!
Scenario where professor DNA_jock teaches.
Professor DNA_jock pauses and considers how his response will affect his saving face at TSZ:
Sal, you are the person making claims. When you write a paper at university and you are challenged on some of the points it makes, will you insist the challenger presents their version of events? If not, why not?
Actually, my response would be:
Why on earth would Professor Jock make a claim one way or the other? This isn’t middle school, where students are spoon-fed the answers. Grow up and think for yourself, ferchrissakes!
You may or may not notice that Prof. Jock’s first question here was part of my original response to you regarding Nishino — ‘what techniques did the researchers use’…Of course, Sal concluded that it was a fact that SRY was regulated by “chromatin” — sloppy ambiguous language that any professor should beat out of his student. I notice that the hypothetical student here avoided that particular mistake.
That’s progress, I guess.
Oh I get it, your point was that if you omit the fact MAT is controlled by things like chromatin and other genes (and the proteins they code for), one can argue MAT sits atop one regulatory hierarchy even though it’s not the atop the other regulatory hierarchies.
If one is free to omit or include what sits at the controlling top, then a hierarchy is in the eyes of the beholder. Then what’s the point of arguing. You have no right then to declare someone else’s view of the order of control is unequivocally wrong.
If someone wants to argue epigenetic memory is stored and therefore gene expression is regulated by chromatin modifications (as in Turner’s book), that’s not really wrong is it?
But that doesn’t really help your insinuation that transcription factors have absolute priority in the scheme of things, maybe in a regulatory network topology, it is inappropriate to say one class of molecules takes absolute priority over all others.
But you said:
So is there ambiguity then over what controls MAT and therefore some ambiguity as to which hierarchy we should take as defining what ultimately rules epigenetic inheritance (somatic and/or transgenerational).
But if chromatin can be modified by non-Transcription Factors, it sort of weakens the claim Transcription Factors are solely in control. By the way, for the benefit of the readers is 10-HDA a transcription factor or not? 🙂
Because DNA_jock claims SRY is unambiguously at the top of a regulatory hierarchy.
But If the hierarchy where SRY is placed at the top is only because other things possibly regulating SRY are omitted in the conception of the hierarchy, it only shows the hierarchical model is somewhat in the eyes of the beholder.
The paper suggests that the claims “SRY is at the top of a regulatory hierarchy” is only due to the omission consider molecules and systems that possibly regulate SRY.
We’re kind of waiting for you to respond, Sal.
For the reader’s benefit, here is an electron micrograph photo of chromatin as published from the DNA learning center of Cold Spring Harbor Labs.
https://www.dnalc.org/view/16637-Gallery-29-Electron-micrograph-of-chromatin-1-.html
Well that took a lot longer than it should have. Phew.
Still with the howlers though. MAT is not controlled by “things like chromatin”, although I will grant you that it needs pol-II (i.e. “other genes”, LOL) for its expression. So?
Or are you looking to discuss the HDAC-mediated silencing of HML and HMR?
(It’s a trap!)
TGTKOG
stcordova,
I worked with Jon Widom. I knew Jon Widom. Jon Widom was a friend of mine. You, Sal, are no Jon Widom.
</Lloyd Bentsen mode>
That’s the 30nm fiber, duckie. Calling it merely “chromatin” is more overly vague and fuzzy language.
That’s a 30nm fiber of Chromatin. 30nm fiber is one of the ways Chromatin is organized in vitro, but it is still chromatin. Your comment is as stupid as saying when a string coils into an x-sized conformation it is no longer a string.
From wiki article on Chromatin:
From wiki:
https://en.wikipedia.org/wiki/Chromatin
Apparently DNA_jock was having problems when I stated the gene expression of SRY was controlled by chromatin, but there you have it in wiki that gene expression is controlled by chromatin, and I cited 3 peer-reviewed papers that specifically said the SRY gene was regulated by chromatin — specifically DNA methylations which are a chromatin mark.
As far as DNA_Jock’s comment:
A Nobel Prize was awarded for elucidating some of the structure of chromatin:
So even on the Nobel Prize website, the word “chromatin” is used. It’s not that fuzzy a concept, what may be fuzzy are the list of all the components of chromatin at any given time, but that is true of living things in general.
Sal:
Yes, yes it is.
That’s right! Very good that you chose to add the caveat “in vitro”. That’s being specific.
But that is NOT what I wrote, now, is it? Again with the mis-representation.
I wrote
See the difference? No? Okay, My comment is as stupid as saying when a wire is coiled into an spring, calling it merely a “wire” is overly vague and fuzzy language. Yes, Sal, it’s still a wire, I never said it was not, but you really, really need to work on the specificity of your use of language. The fuzzy terms “epigenetic” and “chromatin” are both frequent sources of confusion and misunderstanding for you. You would be well advised to avoid their use. Be more specific, and you might thereby reduce your tendency for equivocation. Sadly, I suspect that you find your equivocations beneficial, not detrimental. Your failure to distinguish between mitotic “inheritance” and “inheritance” across generations has been particularly long-running, and self-serving.
Anyhoo, do you have any interest in actually discussing how Nishino tested the effect of methylation, or how Darasi measured demethylation? Or how you would reconcile Darasi with Wang et al. 2005, given that both studies looked at LNCaP and PC3? Y’know, discussing the actual science?
I thought not.
As you put it yourself:
Yeah.
I never called the photo “merely” chromatin. You’re attributing something to me that I didn’t say.
Baloney, I made a distinction here for example in just a few posts above:
Oh Sal, you called the 30nm fibre “chromatin”, without any qualification. I pointed out that that was overly vague use of language. You accused me of claiming that the 30nm fibre was NOT chromatin.
Your misrepresentations are quite transparent.
Likewise, only Sal could distinguish between somatic and transgenerational inheritance by lumping them together.
LMAO
It’s still chromatin.
If I showed a picture of a man and said “that’s a picture of a human”, I don’t have to put a qualifier saying he’s 6 feet tall, it’s still a picture of a human.
The photos is an example of chromatin that happens to be in a 30nm conformation, but it’s still chromatin. The point of the photo was to falsify your argument that chromatin is a fuzzy concept. That photo refutes your claim pretty easily. The fact it is in the 30nm conformation is not relevant to the fact it is still chromatin and that chromatin is not a fuzzy concept since it evidently can be seen in a photograph (vs. some conceptual diagram).
I was listing the two forms of epigenetic inheritance, not lumping them together as the same thing. You’re just laughing at your ability to misread.
There are two forms of epigenetic inheritance:
1. somatic
2. transgenerational
Note wiki lists them the same way in the article on epigenetics:
https://en.wikipedia.org/wiki/Epigenetics
and
So wiki lists:
1. somatic epigenetic inheritance
2. transgenerational epigenetic inheritance
Compares well with what I said:
You’re just laughing at your misreadings, not what I actually said.
Holy shit, Sal, do you ever read what you write?
So, if I were to claim that “British man” is a fuzzy concept, you could “refute my claim” merely by posting a photograph (not a painting, an effing photograph) of Oscar Wilde!
Wow! Sal-logic(tm) is even more fun than I originally suspected.
Since DNA_jock is having some trouble understanding this phrase
let me render the phrase in an alternate way along with some bolding to help him better comprehend:
The wiki article on epigenetics uses the phrases:
1. somatic epigenetic inheritance
2. transgenerational epigenetic inheritance
DNA_jock is eager to misread a simple statement since he can’t bring himself to admit that he was wrong to accuse me of not making a distinction between the two types of epigenetic inheritance. He’ll find ways to delude himself that I actually never made that distinction at TSZ in this thread or others.
Correct me if I’m wrong , Sal, but I have asked a number of times whether you are asserting that any of the changes you are worked up about survive more than a few generations.
Aww!, dateline= 18th October 1982, a day I remember well, thank you for the trip down memory lane!
You wildly underestimate yourself, dipshit. But hate is the wrong word. You are this tragic yet comedic figure who gets everything wrong.
Want to place a wager?
Mung,
I’ll take the same bet Joe F offered you.
His bet was that intelligence offers better results than ignorance. You agree with Joe that intelligence offers better results than ignorance. You want me to bet what, exactly? You want me to wager that ignorance offers better results than intelligence?
What odds do you offer?
Mung,
The bet was very simple Mung. You keep changing things. You wanted a test . You got one. Now you’re moving the goalposts. Pathetic.
I’m willing to put up $10,000.00 dollars. What odds do you offer?
Is 10k a special number for Internet idiots?
Ah, so the coward never intended any sort of actual bet! What a surprise.
Seems so.
So, Mung, remind me what you are whining about regarding that trivial learning example that IDists are so obsessed with refuting called WEASEL?
If you cared to restate your position and then state your bet you might actually win some money. As it is it just seems like you’ve whined about something you don’t understand then when called on it you create a “bet” that you’ve no genuine intent of taking regarding something you’ve invented yourself based on a mangling of something someone else said.
So either you can refute WEASEL as is or you can’t. Either cumulative selection is demonstrated or it is not. Either you have honor or you do not (you don’t).
OMagain, to Mung:
He can’t. And it bugs the crap out of him.
Here’s a typical example of what is so counterproductive from Keiths.
@ Keiths
That you pepper your comments with snark and insult means people avoid dialogue with you. It also loses TSZ members. I’m sad about that.
“He can’t. And it bugs the crap out of him” is pretty mild, Alan, not to mention truthful. (It refer’s to Mung’s failed attacks on Weasel.) How many people here haven’t exceeded that rather tame level of snark?
In any case, I thought you were going to answer my question about the interaction with Neil:
Alan:
keiths:
What I think is funny is that, while I’ve regularly disagreed with keiths about this or that, my own most recent dust up with him involves some (ridiculous) thing that we AGREE on–Elon Musk’s hot tub estimation that it’s highly likely that we’re in a simulation. I just said I’d “put” something differently than Keiths did. And keiths told me I was wrong about that. The headline of the interview is
I said I’d call that a billions-to-one shot. Keiths felt it important to correct me on how I’d put that.
Anyhow, while he’s thinking about his crucial OP, I want to mention that it could be that some people display what might be called a “fear of being wrong” when they assiduously refuse to answer questions about or objections to their own views, utilizing a preferred MO of “Always Attack.” (Could call that “Double A” but it’s already been used in Season 2 of Silicon Valley). So I’m hoping keiths’ promised OP treatise on internet psychological failings that people besides him have will get into those aspects as well.
I note with sorrow, however, that Keiths has a history of promising posts that he doesn’t deliver. (Of course, how COULD he give us all that he might? We may wish it, but….do we DESERVE it?) And since this one is such a big topic, and one that keiths has considered so carefully, I know that he may be forced to focus on just one of his own virtues instead of covering the vast waterfront of them, which would probably require at least weekly entries on his own blog for a couple of years.
My prediction that this would be a mistake was not mistaken. :sad face:
Alan,
You wrote:
I asked:
You replied:
And I said:
Well, here we are, and now you don’t want to answer the question.
There must have been something about my exchange with Neil that prompted you to write this:
What was it? Quote, please.