Precision medicine: Hype over hope?

"I urge you to take part in the Twitter chat happening next week

Thanks, Adam. I think I will attend this. There are the standard questions of course but there are additional questions I wish to ask about which have only been briefly alluded to here such as the accuracy of my EHRs. I know mine contain errors, and I also know that it's very difficult to fix them.

"When someone pointed out that this would involve very large numbers, I immediately refined the concept."

The trouble is that your refining of the concepts appears to be based on you being able to make yourself look as if you were correct all along and very seldom is it on your coming to an understanding.

Side note because you've mentioned this analogy more than once on the blog: Most of those here do bash anti-vaxxers and alt med proponets but they have information upon which to back up their claims how ever abrasive they may come across. But when someone just comes across as abrasive with only smoke-and-mirrors to defend their position it is a real turn off. That is why it would benefit you to read up on this subject. At this point you wouldn't be able to convince me of joining PMI because it's obvious you don't know the subject you are discussing.

bluff WRT claim of expertise is called.

No, I just don't have the desire or patience to explain the value of covariates in a genetic association model to you. Have you ever taken an upper level stats class on regression?

zebra@485

Now, I don’t see the utility in saying “nyah-nyah that’s not what ‘study’ means to me”, as long as we both understand the intent– do we need to invent new words to communicate?

Isn't that what you just did? You're the one who is using a non-standard definition of study.

Those are the issues that I’m really interested in better understanding through your expertise, but I just want to point out that my position on privacy and security is being misrepresented in a ridiculous way

How exactly were your views misrepresented? You said multiple times that privacy concerns weren't a big deal and security wasn't a significant risk. Didn't we already go over countering cherry-picked quotes? Please provide the additional context that changes the quotes I've used.

I would vote, in so far as I have a vote, for very stringent restrictions to prevent misuse of the information, and for resources to be committed to aid in that. That was asked and answered more than once, so any report to the contrary is not to be believed.

This is the first I recall you not dismissing privacy and security concerns or simply asserting that your idea is secure without any specifics. In fact, I doubt it's coincidence that privacy and security have only become concerns for you after AdamG and I pointed out that the PMI working group takes them very seriously. Just in #465 you laughed at my use of the term "infosec" instead of making a substantive rebuttal of my point. Please provide evidence to the contrary.

perhaps because ann and I had a more philosophical discussion about morals and laws that was too difficult for some to understand.

Including yourself. You're deluded if you think that did anything but provide ample evidence that philosphy is yet another subject of which you have a minimal knowledge and an even more minimal awareness of your lack of knowledge.

Here's an interesting note. AdamG came into this pretty neutral but your obstinance seems to have changed that somewhat.

AdamG@502

If you really want to learn, you have to do the work.

This. 100 times this. I've been saying it all along and zebra still has yet to even skim any reference. But zebra is more concerned with proving his superiority than learning. Doing the work would only be an admission that there's something he doesn't know.

zebra@503

Aww, bluff WRT claim of expertise is called.

Seriously? Do you want him to teach you an intro to genetics class through RI comments? Can you see how your past behavior might be responsible for AdamG choosing not to answer your questions? Rhetorical question. Of course you don't; you're infallible in your own eyes.

AdamG,

You mean you don't want to explain the value of covariates in a genetic association model as it pertains to the question of whether we have free will or not? That's not very accommodating of you.

I bet I could get it out of you over a few beers...or a few pitchers. Maybe a keg?

#507...i was responding to zebra's "Why do I need the information about the abuse to detect the genetic correlation?" at 496.

505,

Please, spare me the standard internet practices of deflection and distraction, huffing and bluffing, and just act like a grownup if you think you can explain it to us poor uneducated types.

In this context, as described more than once, explain why I would need to know about the abuse in order to detect the genetic correlation.

I'm willing to be found in error if it helps educate people-- I don't like it, but there's always a cost to reducing one's ignorance.

How does being abused or not as a child inform us about the genetic correlation, or not, with some physiological condition that develops later

Because the relative risk for developing antisocial behaviors is modulated both by MAOA allele and previous abuse. Can you define relative risk in your own words?

I'm done here. Go read the original paper, zebra, and let us know what you've learned.
http://www.ncbi.nlm.nih.gov/pubmed/12161658

Adam G #508.

In my prior comment at #507, I was making a very poor joke regarding the discussion of science delving off into philosophy - of which there is a time and place for either and for both.

Both usually goes with late night drinking in my experience.

Zebra,

The effort given by those here in educating you always educates me. It's just that I think there must be an easier way than the one-up-manship involved. Maybe not, and I'll take what I can get. As long as they're willing to put with it.

AdamG,

Can you describe the difference between

"why do I need the information about the abuse to determine the genetic correlation"

and

"why do I need the information about the abuse to determine the 'relative risk' once I have determined that there is a genetic correlation"

Haystack, needle. Asked and answered already.

But by being genuinely open to the possibility of a misunderstanding, I have realized that in the future I should use "detect the correlation" rather than "determine". It would require a convoluted reasoning to make that mistake in this context, but anything is possible.

And this is the problem with the endless quotemining; I lose track of even my own language-- I did say detect, but I think I used determine earlier. Anyway, I am not going to keep scrolling back to check these things.

If RP responds to my couple of questions, I will appreciate it. That's it.

Oh, and capnkrunch-- I found multiple comments where I responded to you about security. Disagreeing with you is not the same as not answering, quite the opposite. And in exchanges with ann, Grey Falcon? and perodatrent, it was clear that I favored laws discouraging abuse in studies. Laws, not moral pronouncements.

Aww, bluff WRT claim of expertise is called.

And he acts all butt-hurt when people treat him like a ill-mannered twit?

502

Aww, bluff WRT claim of expertise is called.

I think Krebiozen started that in post #4, to be honest.

Oh, and capnkrunch– I found multiple comments where I responded to you about security. Disagreeing with you is not the same as not answering, quite the opposite.

I never said that, did I? Read carefully.

This is the first I recall you not dismissing privacy and security concerns or simply asserting that your idea is secure without any specifics.

Prove me wrong.

And this is the problem with the endless quotemining; I lose track of even my own language– I did say detect, but I think I used determine earlier. Anyway, I am not going to keep scrolling back to check these things.

This is a word game that only you are playing. The reason data on abuse is necessary is because that's the population in which MAOA modulates risk of antisocial behavior. It's right there in the title of the study that AdamG linked to, which you would have known if you made even a minimal effort to educate yourself. But instead you choose to play word games and whine about being misrepresented and insult people who actually work in the field.

Forgot to close the italics. Should have ended after "behavior".

AdamG,

"That’s not very accommodating of you."

Just to be clear this comment of mine was meant as sarcasm. I can understand perfectly well why you wouldn't want to go into a basic education of genetics on this thread.

I got it NaT, no worries :)

Tone via text is harrrrrrd

Why do I need the information about the abuse to detect the genetic correlation?

Hm. Well. The answer to the question as phrased is:

Because absent the abuse, there's nothing for it to correlate to. The gene variant alone doesn't express itself that way if nothing turns it on.

It's one of them there epigenetic factors about which one hears so much loose talk these days, in short.

But that's not really a different answer than the one I already gave. So I have a feeling there may be some kind of miscommunication that I'm not picking up on. Let me know, if so.

I will see if ann can apply her rabbinical inclinations to the question.

I prefer to think of myself as Talmudic. Just to demonstrate I have them.

ann, you disappoint me. I was under the impression you had been raised to the archbishopric.

OK. Having read back through the comments looking for clues as to what the question was, I came up with this:

We’re not talking about what we know, but what we might find out. Haystack first.

In which case the answer is:

In order to find most such things out, you need information about environmental factors that's as close to comprehensive as you can get. Because epigenetics count. Genotypes and phenotypes alone don't actually constitute a haystack that contains needles in many -- possibly most -- cases.

For example: Although there's high concordance in monozygotic twins for schizophrenia and autism, it's not 100 percent. So something apparently sometimes causes the genetic predisposition to zig rather than zag in one twin.

Plus of course, it might be more than one something. And/or more than one gene variant.

I mean, there are an awful lot of chronic, incurable little-to-partially understood conditions that are thought to have a genetic component that's contingent on some other thing and/or things, but who knows exactly what?

I would imagine you'd have to cast a pretty wide net wrt environmental factors. Not that I'm an expert. But it makes sense to me.

ann,

You are the only one who could suck me back in, other than RP on this and the other question.

Instead of "missing", how about "you are letting knowledge get in the way of knowing"? (trying to be Talmudic or Eastern Mystical here, since you didn't get the haystack/needle point.)

In my database, there will be abused children who have this gene. So a researcher would detect a correlation between the negative subsequent behavior and the gene.

How could it be otherwise? And this is one of the things that recommended my approach to me in the first place.

I’m willing to be found in error if it helps educate people–

Oh. My. G-d.

I don’t like it, but there’s always a cost to reducing one’s ignorance.

See above.

Read the paper, zebra. It's free to access and addresses many of your questions.

You're even more D-K than I thought given you don't seem to know the difference between a gene and an allele. Everyone has MAOA, moron. Read a f-ing book before you try to design genomic databases-but-not-studies.

In my database, there will be abused children who have this gene. So a researcher would detect a correlation between the negative subsequent behavior and the gene.

Maybe.

But let's say for the sake of argument that he or she did:

Since searching the database for that polymorphism would show that there was no correlation between the negative subsequent behavior and the gene in all the non-abused children who had it, it wouldn't look like -- and, in point of fact, genuinely wouldn't be -- a meaningful correlation until the environmental factor was identified.

This is (at least as I understand it) exactly where research on a lot of conditions that are thought to have a genetic component that's kinda-sorta-maybe already been identified has run aground. It's not possible to point to the anomalies and say "This is the cause," because lots of people without the condition also have that anomaly.

How could it be otherwise?

Well. Since the existence of unidentified environmental factors is a known obstacle research progress on the genetic causes of illness, you could make an effort to include as many of them in your database as you reasonably and possibly could.

Because otherwise you'd basically just end up stuck where you already were except on more fronts until you put together a complementary database, anyway. And why borrow trouble?

To use an example where knowledge won't get in the way:

There are a number of autoimmune disorders -- MS, rheumatoid arthritis, Addison's -- that are associated with changes to one or several genes. But not everybody with the disease has those changes. Not everybody who has those changes has the disease. And even among those who do, not everybody has the same one. Or the same course. And so on and so forth.

Just genotypes plus phenotypes don't get you all that far. I mean, the goal is to find out something that facilitates prevention, ideally. Right?

@#AdamG --

I don't know. I used "gene" the same way @#526 -- ie, to mean the variant in question -- and I do understand the distinction. It's just that although my reading fluency is adequate, my understanding is too superficial for true speaking fluency.

You know how it is.

Zebra @466: "You would have to elaborate. Everyone is in the same birth cohort. Are you talking about the difference of <1 year?"

A birth cohort is all of the people born during a specific time period. That time period (and sometimes place, like a specific hospital) is defined at the beginning of a study, to determine who will be recruited into the study.

So if I say that a birth cohort is everyone born in a specific calendar year, then you and I are not in the same birth cohort.

You do not define who you mean by "everyone" when you say that "everyone is in the same birth cohort". Everyone in the world? No. Everyone in the study group? Yes, because that is how they were chosen.

Since you are such a stickler for precision of language, please define your terms, particularly when you are using them to mean things that they do not mean in the technical context of the conversation.

JustaTech@529

Since you are such a stickler for precision of language

And yet (as you alluded to) he's also the most egregious abuse of it (not just words but punctuation too!). He's like the living embodiment of projection. Speaking of projection and word games, he accused everyone of being unable to admit mistakes yet he was unable to admit that his definition of study was wrong (instead choosing to claim that we were the ones at fault). Quite frankly that would have been an incredibly minor point to concede.

In my database, there will be abused children who have this gene. So a researcher would detect a correlation between the negative subsequent behavior and the gene.

Oh, wait, now it magically has some sort of behavioral records, too? Do schools and parents and juvenile courts all now have to report to your fever dream as well? Are you under the further delusion that you're going to get psychiatric records? And where are the records of childhood adversity or abuse going to come from?

How could it be otherwise?

You really haven't picked up a single clue from all the time people have wasted replying to you, have you? Did it ever occur to you that there are all kinds of reasons for antisocial behavior? The fact that you could even ask this question pretty clearly reveals that your pig-ignorance has left you with no refuge but magical thinking.

It's been pointed out before, but you're doing it backwards. Since you're obviously too damned lazy or incompetent to do it yourself, do you know where that signal came from in the first place? Here. Not by saying, "Computer, give me all genetic variants associated with data that you don't have."

And this is one of the things that recommended my approach to me in the first place.

What is? Be specific. It certainly isn't MAOA, which you've just heard of. After all, given that you just blurted it out in the second comment of the thread, one might suspect that not only did nothing "recommend" it to you, but that you didn't put a f*cking bit of thought into it in the first place and are now just stupidly digging in your heels, with a concomitant increase in your trademark obnoxiousness.

Are you under the further delusion that you’re going to get psychiatric records? And where are the records of childhood adversity or abuse going to come from?

To be fair, in this particular case, there might be some indirect signs of both the maltreatment and the conduct/oppositional defiant disorder in the regular old medical records, since both are correlated with higher rates of accidental injury. (And ODD is correlated specifically with hospital admission for burns and poisoning, per one study, I just now learned from the internet, which is a very poignantly distressing little piece of quasi-knowledge, if true. Those poor kids.)

But there might not be. And obviously, it wouldn't be specific enough to draw any clear inferences from even if there were. Kids with ADD also have higher rates of accidental injury. And so do any number of children for any number of social and/or environmental reasons, including -- potentially -- none.

You can't really correlate without correlates. In a nutshell. At some point, somehow, you'd need to dredge them up from somewhere.

This is not my bailiwick at all, so if someone who knows what they're talking about could enlighten me, I'd appreciate it. But am I wrong in thinking that for stuff like schizophrenia (and maybe autism?) there's the additional complication of figuring out what's genetic and what's just innate -- ie, the possible result of prenatal viral or bacterial exposure and so on?

Genetics, genomics and neurology are the three fields I most regularly come away from muttering, "Nobody's ever going to understand this and trying will probably just end in tragic irony due to unanticipated consequences, like an episode of the Twilight Zone."

That's very 20th century of me, I readily admit. But I don't really mean it. It's just the kind of thing I say to myself before throwing my wooden shoe into a lace-making machine or whatever. Although that's actually 19th century, I guess.

@ ann:

For a start, you can look at websites like schizophrenia.com and Wikip---- ( schizophrenia entry) for details about causation from genetics, other causes and ( possible) overlap with other neurodevelopmental condition.

To be fair, in this particular case, there might be some indirect signs of both the maltreatment and the conduct/oppositional defiant disorder in the regular old medical records, since both are correlated with higher rates of accidental injury....

But there might not be. And obviously, it wouldn’t be specific enough to draw any clear inferences from even if there were....

I don't think that this rises to being fair. Sure, there's going to be some related data, but it's going to be signal-poor and buried in noise as far as this example is concerned.

Z. apparently thinks that the way to arrive at study populations is to randomly shake huge barrels of data and hope that one pops out. One might note that – somewhat like the flirtation with "ontology" – Z. has elected to appropriate* the "needle in a haystack" observations directed his way and, bizarrely, do this:

We’re not talking about what we know, but what we might find out. Haystack first.

It's almost some sort of Flannery O'Connor approach demand.

If I had Gaist's talent for dialogue, I'd add it here.

* To truly grotesque proportions.

That video is unavailable to me. :(

Interestingly, "Haystack First" was the name of the O'Connor/Welty/McCullers salon/roundtable.

Ann, it is indeed nice to disagree with someone who knows what the f I'm talking about and can articulate a rational counterargument. (however right or wrong it may be).

Since searching the database for that polymorphism would show that there was no correlation between the negative subsequent behavior and the gene in all the non-abused children who had it, it wouldn’t look like — and, in point of fact, genuinely wouldn’t be — a meaningful correlation until the environmental factor was identified.

"Meaningful correlation" is a little Scotsman-like for my taste.

The question is whether we would have a high degree of confidence in its validity. And the answer again is "of course we would", not "maybe" as you say. You know that.

Because otherwise you’d basically just end up stuck where you already were except on more fronts until you put together a complementary database, anyway.

Just genotypes plus phenotypes don’t get you all that far. I mean, the goal is to find out something that facilitates prevention, ideally. Right?

Let's look at three things.

-my often repeated statement that I am talking about basic research
-Eric Lund's commentary on accuracy and precision
-Orac-- yes, Orac, who wrote the OP which I actually read carefully, apparently unlike everyone else- saying:

what has been called an “arms race” or “gold rush” among academic medical centers to develop precision medicine initiatives, complete with banks of NGS machines, new departments of bioinformatics and genomics, and, of course, big, fancy computers to analyze the many petabytes of data produced, so much data that it’s hard to have enough media upon which to store it and we don’t know what to do with it.

So, what you think of as a problem, I see as an advantage. On multiple fronts.

zebra@536

Ann, it is indeed nice to disagree with someone who knows what the f I’m talking about and can articulate a rational counterargument. (however right or wrong it may be).

Ah... would that we could experience the same from this side of the fence. Anyone else note the parallels to See Noevo? Impervious to reason, not able to back up claims, ignores/insults people who disagree, and a weird fixation on ann.

The question is whether we would have a high degree of confidence in its validity.

No. The problem is that the correlation appears in the subpopulation of abused children. If you don't have that data you don't see the correlation. This would have been obvious to you if you had read the paper. It's even in the title.

Seriously though, with a minimal skimming of some of the references provided you cluld have given a reasonable defense. Hint: check the PMI working group draft. In your immunity to education though you picked the clearly losing horse and made the unsupportable claim that the correlation between MAOA and antisocial behavior in abused children would be visible in the general population absent any environmental data (i.e. history of abuse).

-my often repeated statement that I am talking about basic research

Oft repeated, never supported. Recall that malia told you that mass quantities of data is not what we need for basic research. I know you asserted otherwise but never supported that assertion. I'm inclined to believe the geneticist over the layperson even absent your numerous failures of basic concepts.

-Orac– yes, Orac, who wrote the OP which I actually read carefully, apparently unlike everyone else- saying:

Did you really? I fail to see how that quote offers you any support. In fact take a look at the last bit:

... so much data that it’s hard to have enough media upon which to store it and we don’t know what to do with it.

IDK. I don't think you addressed Ann's last point. I got the impression from this statement that you would disregard collecting information about child abuse in your database/study.

"Related to that, I am having a hard time understanding the reasoning about acquiring all this other information. How does being abused or not as a child inform us about the genetic correlation, or not, with some physiological condition that develops later?"

So, great, you have identified a correlation (not a causation) of an outlier gene change to antisocial behavior, but is there any other information available?

To use an analogy which I hate to do, but please bear with me. Several people have food poisoning. It is discovered that the majority of them but not all of them ate lettuce in the past two days. Yet others have eaten lettuce and haven't gotten sick. So whats missing and what do you need to do next?

So I question the utility of your database/study beyond a certain point. If that's how you envision it, that's fine; it's your invention. However, PMI is a very different beast and after reading more at AdamG's link I'm fairly well intrigued by it now.

capnkrunch, we cross posted. Regarding your concern with the missing data of child abuse as you described:

"made the unsupportable claim that the correlation between MAOA and antisocial behavior in abused children would be visible in the general population absent any environmental data (i.e. history of abuse)."

I think he was blowing off knowing about the abuse because this particular gene (is it polymorphism?) is an already known correlation. It's not as if we are starting from scratch in this case. Personally, I don't agree with this because at the very least it would be confirmation of this correlation perhaps even leading to causation, but it's his monster.

"Meaningful correlation” is a little Scotsman-like for my taste.

We can just make it "correlation."

The question is whether we would have a high degree of confidence in its validity. And the answer again is “of course we would”, not “maybe” as you say. You know that.

No, I really don't. Correct me if I'm wrong. But as far as I can see:

A hypothetical researcher would initially either be looking at the subset of children with an MAOA variant, or the subset of male children with antisocial behavioral disorders. Right?

If the latter, they'd see that maybe 45% of them had a low activity allele.

In order to be confident in the validity of the association, they'd then have to look at a group of non-antisocial controls. And when they did, they'd see that maybe 34% of them also had a low-activity allele.***

Further complicating matters, 20-ish% of the antisocial sample has a high-activity allele. And while that would be much lower than the non-antisocial group's 60-ish%, the high-activity allele kids in both groups would appear to have a significant predisposition to ADD and depression.

So. The researcher now has several suggestive and potentially significant indications that genetically determined variations in MAOA activity correlate to something neuropsychiatric. But it's not completely clear what.

However, when 55% of the subset does not have the polymorphism, confidence in its validity would definitely be very rash. At the very least, you'd need to replicate the result several times before you could say the correlation was valid.

And even then, you would have to identify the swing factor that turned the correlation into causation.

If our hypothetical researcher instead started out looking into the genetic side of the equation -- ie, all children with all MAOA variants, or boys with any MAOA variant, or whatever -- it would be even more of a mess.

So. How do you figure differently? It seems pretty unambiguous to me. There's not enough to hang your hat on and too many potential confounders for confidence.

***Wherever there's no reference given for prevalence, I checked several studies and estimated the range. I could be somewhat off, though.

ann,
It's worth noting, perhaps, that without childhood abuse those with low MAOA activity are less likely to exhibit antisocial behavior than those with high MAOA activity (Figure 1). That might well be enough to mask the correlation in the whole population.

So z*bra wants to give researchers access to child protective service records WITH IDENTIFYING INFORMATION? Jesus H Christ on a hyper speed pogo stick! I worked for 30 years in social services, with some of that time in MIS, and this idea is hypercube level craziness. These databases include unproven allegations of criminal activity, information about victims who are minors and information about siblings of those in our pseudo-cohort. What could ever go wrong with putting all that in one database?

Incidentally, if an additional reason for exercising caution wrt premature conclusions about validity is needed:

There evidently might be considerable racial and ethnic variation in the frequency of these alleles. And it would really be kind of dire to go around confidently proclaiming that there was a valid association between antisocial violence and an allele that appeared to be more common among African Americans than it is among Asians/Caucasians before you'd looked into it enough to know how, why and if it really expressed itself that way.

The maltreatment is really not an incidental or secondary factor. And neither are other cultural/environmental factors. At a glance, there also appears to be an association between low MAOA activity and male alcoholism in Scandinavian populations, for example.

@Krebiozen --

Thanks! I actually meant to mention that.

But that reading-vs-speaking fluency thing I mentioned @#528 is a real handicap. Stuff gets lost in translation. I probably miss a lot, too.

So corrections and additions are much appreciated.

Opus,

I don't think zebra was/is saying that's what he wanted social services data in his database/study. Rather the opposite. But he presumed to be able to make connections without this knowledge (not necessarily social services records but the knowledge someone was abused) and that's where he ran aground IMHO.

Not a Troll@539

I think he was blowing off knowing about the abuse because this particular gene (is it polymorphism?) is an already known correlation.

So he is talking about taking an already known correlation in a subpopulation and trying to see if it can be generalized to the general population? In that case, ann's comment #540 is more on point (as well as Krebiozen@541).

This all started because someone (Narad maybe?) said that it would be difficult to collect environmental and psychiatric information. No matter how you a
slice it, saying we don't need that data k
is a weak defense. Had he at least skimmed the PMI draft he would have seen that behavior health and environmental behavior will be among the data collected. Pointing that out would have been a far stronger counterpoint.

Of course, I'm sure DCFS records won't be collected but abuse will probably be asked about in the self-reported data and may show up in medical records too. The psychiatric history is another animal given that release of psychiatric history usually requires an additional consent on top of the general one. From what I've read (admittedly not the whole report yet) this isn't addressed specifically. Howeever, they do talk about granularity in the consents and I think it's fair to assume that such granularity would include psychiatric/behavior health.

There you go zebra. Try doing the work yourself next time instead of blurting out the first thing that comes to mind and then digging your heels in. Your obstinance would be more understandable if there was more than a modicum of thought behind the things you say.

... There's clearly some letters and line breaks in the second paragraph that shouldn't be there.

So he is talking about taking an already known correlation in a subpopulation and trying to see if it can be generalized to the general population?

As I understood it, the question was whether the correlation between genotype and phenotype would show up without knowledge of/information about the abuse, assuming that the antisocial behavior was known.

And as far as I can see, the answer to that is maybe, but it wouldn't necessarily be obvious that it was the signal worth following up on. And even if it was, it wouldn't be at all clear what it signified. Meaning:

Theoretically, assuming you were starting at square one and detected the correlation, you couldn't confidently conclude that it was genetically dispositive at all, per se. Maybe it would turn out that children of alcoholic mothers were likelier to have that allele, as well as likelier to be poor and malnourished, hence the antisocial behavior. Etc.

Or at least I think so. But maybe I've gotten the whole thing wrong. Anything's possible.

Also, though I don't know whether this is true or not:

The percentages are not that high. And there's a lot more than that one allele. Conceivably you'd be looking at other comparably suggestive correlations, just by the numbers.

Is that right, someone who knows?

I suspect explaining anything that a “mature, rational (non-paranoid), non-Authoritarian adult” might do would go right over your head. Let’s try this: how would you like it if it your genome was publicized and it was revealed that you had a constellation of genes associated with tiny-penis-syndrome or intractable-pig-headed-disease?

forget about that, let me plant his genome on a rape & murder crime scene. Then, if that doesn't convince him of the need for ethics & privacy, it will leave me to ponder at the question: is he trying very hard to be a stubborn pigheaded id10t or does these qualitative come naturally to him.

Al

ann@548

As I understood it, the question was whether the correlation between genotype and phenotype would show up without knowledge of/information about the abuse, assuming that the antisocial behavior was known.

Ah. Yup, I see that now. Your "maybe" is a much better answer than my "unsupportable".

Maybe it would turn out that children of alcoholic mothers were likelier to have that allele, as well as likelier to be poor and malnourished, hence the antisocial behavior. Etc.

Makes sense. I think earlier in this thread (though I can't find it) someone mentioned how without correcting for confounders it looks like coffee correlates with cancer but it is actually that smokers are disproportionately coffee drinkers. You need data about both things to reach an accurate conclusion.

Even if the specific instance being discussed turns out that environmental data is unnecessary there are likely others where it is. That's why I think 'environmental data is not impossible to collect; AdamG and friends are going to do it' is a much more tenable position than 'environmental data is unnecessary'.

"Anything’s possible."

In genetics, and on this thread apparently.

Regarding the complexity of this particular gene and variants, I found two articles that may be of interest

http://www.nature.com/mp/journal/v14/n8/full/mp200944a.html

http://www.geneticliteracyproject.org/2014/11/04/does-the-human-warrior…

If Retro Pump didn't convince anyone already, I think this one example alone highlights the massive questions/issues involved in genetic research. Even though the PMI will be knee deep in this as well I'm beginning to see it as much more than just a collect and sort through volunteers' genomes study. It's more like a pool of research subjects with as much information captured so they can be selected for further studies.

"As I understood it, the question was whether the correlation between genotype and phenotype would show up without knowledge of/information about the abuse, assuming that the antisocial behavior was known."

ann, I took this into consideration of what he was saying for his database/study in general but when he kept emphasizing "what we already know" for this particular gene discussion, I took it one step further in that this was an already in-the-bag correlation that could be worked. I have no idea if I'm correct or if I was at t one time and now things have changed or if it is something entirely different.

You seem to speak zebra's language so I will defer to your interpretation.

The question is whether we would have a high degree of confidence in its validity. And the answer again is “of course we would”....

No, you wouldn't. You were too lazy to read the Corsi et al., weren't you? Your blob of genomes is filled with just about every confounder imaginable, plus it doesn't contain the requisite data.

"Until this study's findings are replicated, speculation about clinical implications is premature. Nonetheless, although individuals having the combination of low-activity MAOA genotype and maltreatment were only 12% of the male birth cohort, they accounted for 44% of the cohort's violent convictions, yielding an attributable risk fraction (11%) comparable to that of the major risk factors associated with cardiovascular disease (37). Moreover, 85% of cohort males having a low-activity MAOA genotype who were severely maltreated developed some form of antisocial behavior. Both attributable risk and predictive sensitivity indicate that these findings could inform the development of future pharmacological treatments."

“Meaningful correlation” is a little Scotsman-like for my taste.

Why? You're perfectly happy to emit complete gibberish such as this:

The issue, which is probably above your heads, is what constitutes a significant sample, because of the noisiness of the genomic information.

I think he was blowing off knowing about the abuse because this particular gene (is it polymorphism?)

It's a two-repeat polymorphism in the MAOA promoter region. A really quick glance suggests that three or more repeats are OK on this front, but don't hold me to that.

^ Oh, but naturally, the way to tease this out is by starting from a pile of whole genomes. Haystack first, people!

You seem to speak zebra’s language so I will defer to your interpretation.

Z., quite simply, can't take heat. Imagine this performance made incarnate, say, as the Q&A of a routine weekly departmental colloquium. "This week, we have a guest from the Department of Blobular Globularism, Professor Zebra...."

Actually, I've been there; a genuine comparison would require that the doors to the hall be locked for two hours. After frothing for a while at the questioners in the audience, Z. would be left with simply ignoring them, and then the poor bastard who introduced him would be left trying to deal with the awkward silence by signle-handedly trying to get him to fill the time or, perhaps, requiring that the increasingly impatient audience write their questions on 3-by-5 cards so that they could be translated into appropriately kowtowing terms.*

* This would be an example of what "interlocutor" actually means, Z.

It’s more like a pool of research subjects with as much information captured so they can be selected for further studies.

Exactly right. Don't bother listening to the folks doing the overhyping ("we'll fix all the cancers!"), who are largely not involved and mainly just ego boosting. Everyone involved in PMI currently is on the same page about what we aim to create: 21st century Framingham.

Let’s look at three things.

"Let's"? "Look"? This sort of construction is usually a prefatory remark meaning "I'm going to examine these things," not left hanging in the air.

Oh, wait, you imagine yourself to be in a pedagogical role.* Gotcha.

-my often repeated statement that I am talking about basic research
-Eric Lund’s commentary on accuracy and precision
-Orac– yes, Orac, who wrote the OP which I actually read carefully, apparently unlike everyone else-

OK, you bootstrap that accuracy-and-precision bit. I'm sure it will be eminently thought-provoking.

* Child psychologists don't necessarily have fixed outcomes in mind.

Oh, Narad, you bring back frightening memories of Quarterly Meetings with the CEO of our small division. Most real questions were unwelcome so HR started the 3 x 5 card thing to review them beforehand.

But there was that time right after we were newly acquired by a different company when the one of their talking heads didn't play that game. He took all questions. It was quite funny to watch the disarray of the HR people then. Although, it still wasn't funny being locked in a room with them for hours.

Did you work in academia or something that just sounds like it, like the government?

It’s a two-repeat polymorphism in the MAOA promoter region. A really quick glance suggests that three or more repeats are OK on this front, but don’t hold me to that.

My impression was that two-repeat is low activity and high-risk but rare; and that most of what they're looking at is three-repeat (low) and four-repeat (high).

I also saw something about 3.5R and 5R. But I made an executive decision not to think about it.

Corsi et al.

Campi. But I know that you meant that.

ann@562

Campi. But I know that you meant that.

Caspi actually ;)

Also your link in #540 was broken and I forgot to mention it before. Could you repost it please?

@NaT:

Regarding the complexity of this particular gene and variants, I found two articles that may be of interest

The latter one has an interesting bit:

"I have read that MAOA-L is pretty common–one paper says 40 percent of the population possesses it. It gave no reference, and I haven’t been able to nail that number down for sure, but let’s assume it’s true."

That paper, from EMBO Reports, is unpromisingly titled "The Psycho Gene." I mention it only because I ran across Beaver et al. (PDF) earlier, which pegs the 2R allele at 0.1% of its Caucasian population.

Referring back to my caveat in comment 556, I suppose that leaves 3R to take up the slack.

@capnkrunch:

This all started because someone (Narad maybe?) said that it would be difficult to collect environmental and psychiatric information. No matter how you a slice it, saying we don’t need that data [] is a weak defense. Had he at least skimmed the PMI draft he would have seen that behavior health and environmental behavior will be among the data collected. Pointing that out would have been a far stronger counterpoint.

Of course, I’m sure DCFS records won’t be collected but abuse will probably be asked about in the self-reported data and may show up in medical records too.

I'm not entirely certain about the antecedent of "he" here, but I at least was talking about Z.'s brilliant idea of shaking study populations out of randomly poking a giant whole-genome database with a stick. "Abusive environments" don't simply reduce to things that are going to appear in medical records.

Z.'s "how could it be otherwise" was simply the impressive physical feat of putting the final nail in one's own coffin.

You need data about both things to reach an accurate conclusion.

Yes. But in reality, I imagine that most of the queries to such a database would be by researchers on a quest to find out the effect of low-activity MAO on dopamine in the nigrostriatal pathway as it relates to tardive dyskinesia.

Or what have you. It could be anything. My point is just that specialists specialize, so they'd have some idea of what they were looking for and at, presumably.

Campi. But I know that you meant that.

Caspi actually

Thanks; I'm not sure where that one came from.

Oh, wait, no, that's not the proper response:

I’m willing to be found in error if it helps educate people– I don’t like it, but there’s always a cost to reducing one’s ignorance.

Then again, I'm not sure what this automaton would actually emit in this situation.

Narad@565

I’m not entirely certain about the antecedent of “he” here, but I at least was talking about Z.’s brilliant idea of shaking study populations out of randomly poking a giant whole-genome database with a stick.

My bad. Poor pronoun use on my part it was zebra I meant. And I went back through the thread and the route to where we are know was actually much more convoluted than I remembered (and the hole zebra's in now was entirely dug by himself).

What I was commenting on was #531 where you said:

Oh, wait, now it magically has some sort of behavioral records, too? Do schools and parents and juvenile courts all now have to report to your fever dream as well? Are you under the further delusion that you’re going to get psychiatric records? And where are the records of childhood adversity or abuse going to come from?

Had he not dug in his heels on that data being unnecessary I think we could have mounted a reasonable defense using Table 5.1. There's a number of categories from which psychiatric history and family environment could come from. History of abuse would be much less reliably obtained because the main source would be self reporting.

“Abusive environments” don’t simply reduce to things that are going to appear in medical records.

Yeah, that's why I figured it would more likely come from self reporting by the participants. Depending on the data gathered it could be gleaned from medical records; narratives*, repeated history of suspicious injuries or malnutrition, visits to abuse counselors, etc. Not a wide net nor a particularly reliable one, but it could supplement self reporting.

*Though it's unlikely that they will get psychiatric notes it's possible hints could be found in other providers' notes. I document it in my PCR's whenever I contact DCFS.

Though I'm generally skeptical of gene-environment-behavior associations in humans, this is one of the more believable ones.

As usual, the real meat of this paper is in the supplement (PDF). It's important to remember that what they're really associating here is antisocial behavior and MAOA (the protein's) activity, but they're using MAOA (the gene's) alleles as a proxy for protein activity. This means that though there are several different alleles that can combine into a number of distinct genotypes, they can be generally grouped into 2 distinct phenotype categories, high and low activity.

This is especially true because the polymorphisms we're talking about in particular involve a VNTR, which is a spot in the genome with a bunch of small repeats close together that is prone to mutations that alter its length, as illustrated here. Since only a small bit of sequence gets added or removed each time, some alleles end up having somewhat similar effects on the promoter region, and therefore transcription.

In this case, we have 5 distinct common alleles but only 2 phenotypes. There's pretty solid evidence that these alleles directly alter expression and fall into these two groups, so it's a pretty good proxy. Allele frequencies in the Caspi study are in Figure S1: 95.7% of their study population had one of the two common alleles, 3 (low) or 4 (high).

Perhaps zebra would like to explain how his database would be able to identify this association, given that the 3 groups in Figure 1 would be essentially collapsed into one.

Comment in moderation with some Saturday Afternoon Genetics...

@capnkrunch #563.

I don't remember what I linked to. But I think it was this:

http://www.nature.com/npp/journal/v30/n9/full/1300785a.html

Or this:

http://archpsyc.jamanetwork.com/article.aspx?articleid=482035

Or maybe this:

http://www.nature.com/mp/journal/v11/n10/full/4001851a.html

There’s a number of categories from which psychiatric history and family environment could come from.

The need for this sort of inference from an incomplete data set just goes to show how abysmal Z.'s Grand Idea is. Psych records? How about juvenile criminal records? Do the "more rational" Canadians treat these in a more freewheeling fashion than the "USA paranoid group"?

One of the first remarks that Caspi et al. make about DMHDS is that it is free from population stratification. Z., on the other hand, thinks it's a better idea to smear biases all over the place and try to sort them out later, once the a priori inevitable result for which "we [sic] would have a high degree of confidence in its validity" pops out of the magic box.

I almost wrote that it would take more time to list the things that Z. for which has demonstrated a wholesale lack of understanding than the items of the complementary set, but then I realized that it's not clear that the latter is nonnull.

Keep in mind that Z. has refused to so much as describe the imaginary interface to his magic box or the protocols, including comparisons with the VSD. The PMI report addresses forms of access, but reading is hard, or something.

I mean, I'm no great expert on computational complexity, but at least I've T.A.'d introductory algorithms for a bunch of master's students.* Z. cannot be bothered with such minor issues – a haystack of things that reduce to the traveling-salesman problem must cause an NP= P needle to spring into being among them, or something.**

Christ, Eric Lund pointed out way back in
comment 62 that this is a whole lot of underpants gnomes.

Nothing has changed.***

* While I was in a nonacademic position. Long story. Cormen et al. as text.
** The comparison to S.N. is not inapropos; check out its recent performance at EvolutionBlog. This footnote has also been randomly moved up because I needed the final one at the last moment.
*** It doesn't compare closely enough to "The Ballad of Frankie Lee and Judas Priest" to allow the phrasing that I reflexively desired.

^ "the things that Z. for which Z. has"

I think. I'm going to go clean the cat boxes and the ceiling fans to cleanse my palate.

there’s always a cost to reducing one’s ignorance.

Sometimes one is even expected to read papers.

OK, I mopped the bathroom ceiling and am moving on to the dishes, but this is another good one:

Remember, we, the wealthy USA, and I would hope the rest of the world, are paying the [Canadians] to do this. I would throw in even a couple more F-35’s if need be. And someone mentioned that the Brit NHS was doing something along these lines with phenotypically distinct populations. Rational healthcare systems do have advantages.

Oops.

With apologies to gaist.

At the annual International Genomics Conference in Fernando Po, a disheveled figure is on stage in one of the lecture theaters, rooting through some overhead projection transparencies. Projected onto the screen behind him, upside down, is an overhead stating 'THE ZEBRA GEGNOMICS DATABASE PROJECT (NOT "A STUDY")', hand-written in marker pen, upside down. A small audience of professional geneticists watch with curiosity.

SCIENTIST 1: Who is this guy? Who uses an overhead projector these days. I'm surprised they even have one. Doesn't everyone use PowerPoint these days?

SCIENTIST2: No idea, the program doesn't say what his field is or where he works, just that he has an revolutionary and innovative idea that will, he claims, revolutionize genomics. Might be good for a giggle.

On stage zebra is ready to begin.

ZEBRA: Fellow scientists, good afternoon. Today I want to present to you my new idea for revolutionizing gegnomics. What I propose... [he pauses for effect] is to sequence the gegnomes of every child born in the US in a single year. This will give us a database of genes that we can simply match to obesity, autism and other conditions, [Zebra pauses beaming, looking for the adulation and
applause he anticipates. He is greeted with silence.]

SCIENTIST1: Your slide's upside down, and you spelled genomics wrong.

ZEBRA: [Quickly removes transparency and replaces it with the next one.] Irrelevant non sequitur, and it's out of context. That's how I spell gegnomics, obviously, try to keep up. Any relevant comments?

SCIENTIST2: How are you going to fund this project?

ZEBRA: Easy, we just take it out of the defense budget.

SCIENTIST2: Does the Department of Defense know about this?

ZEBRA: Nitpicking, next.

SCIENTIST1: This will generate a vast amount of data, and we are having trouble storing and processing the data we already have. What do you propose to do with all this data?

ZEBRA: It will be a resource for researchers. It will stipulate research and answer all the gegnomic questions ever asked. You scientists are clearly too stupid to have thought of this before, so you need someone like me who can think out of the box.

SCIENTIST2: I think you mean 'stimulate'...

SCIENTIST1: [sotto voce] Someone's out of his box...

ZEBRA: More irrelevant nonsense - does anyone actually knowledgeable have any comments?
[A shocked gasp goes up from the audience]

SCIENTIST1: You do know this is Professor Craig Venter?

ZEBRA: Who?

SCIENTIST1: He's one of the biggest names in genomics!

ZEBRA: Nonsense, appeal to Authority, and it's gegnomics, I can make any word mean whatever I like. Anyway that's an ad hominem, attacking me just because I don't have a formal education in genetics. Typical Authoritarian fools. You wouldn't treat President Obama like this, he gets it.

HECKLER: You know nothing about genetics, you're an idiot!

ZEBRA: That's typical of this meeting, you are all prejudiced against zebras from the start. I encounter intolerant idiots like you wherever, so I must be getting under their skin and making them realize how blinkered they are. Any sensible, knowledgeable comments?

SCIENTIST2: How are you going to get IRB approval for this project? You need to specify experimental design, do a risk assessment, show how the data will be secured...

ZEBRA (triumphantly): I don't need IRB approval because it isn't a study so the law doesn't apply. No IRB, problem solved.

SCIENTIST2: Does it use human subjects?

ZEBRA: Well, yes, but just to create a gegnomics database.

SCIENTIST2: You take blood samples?

ZEBRA: Yes, but...

SCIENTIST2: Then it's human research and you will need IRB approval, unless you do it in some country where there are no human rights..

ZEBRA: Why do I need IRB approval? Why are you picking on me?

SCIENTIST2: There are ethical issues you need to address, privacy for one.

ZEBRA: Ethics? Privacy? Vacuous concepts.

[Zebra frantically leafs through the overhead slides until he finds the one he is looking for - he places it on the projector and gestures at it triumphantly - it is titled 'ETHICS - A VACUOUS CONCEPT' clearly copied and pasted from a philosophy 101 text book.]

ZEBRA: We can safely ignore a vacuous concept like ethics, or do you clever scientists believe in God? [He smirks mockingly at the assembled throng]
You wouldn't care about privacy or human rights if you were locked in a cell with a broom handle up your ass, would you? Thomas Pynchon wrote a novel about that, something about Broomhandle's Rainbow - a bunch of geneticists steal blood samples from the world's politicians, clone them all, and then send them to London in a V-2 rocket or something.

SCIENTIST1: It's Gravity's Rainbow, and that isn't the plot, even if it was in any way relevant., which it isn't What does privacy and human rights have to do with having a broom handle up your butt? Anyway, you can't just ignore ethical issues! Just because they don't exist doesn't mean we don't have a duty to create them? Look what the Nazis did!

ZEBRA: See! See! Now you are calling me a Nazi! This always happens, I make a sensible suggestion and people are so jealous they have to make up some stupid objection or compare me to Hitler. It's 20th century thinking at its very worst.

[Realizing that the lecture is being held by a lunatic, people start filing out of the lecture theater.]

ZEBRA: Wait, come back, you haven't heard the most brilliant bit yet, you fools! Ethics and privacy are very important, as I said, but my database overcomes all those ethical problems.

[Only a few scientists remain, retained by a horrified fascination at the bizarre spectacle.]

SCIENTIST1: You said ethics and privacy are vacuous concepts!

ZEBRA: No I didn't.

HECKLER: It says so on the screen behind you you dickhead!

ZEBRA: [Immediately changes the slide] You're taking that out of concept, and anyway that's a non sequitur.

SCIENTIST2: [Realization dawning] You don't know what a non sequitur is, do you? Or anything at all about genetics, or anything else from the look of it.

ZEBRA: You're trying to change the subject. This database is not, I repeat not, any kind of study or any kind of human research that requires IRB approval, which it would get, obviously, though ethics is of course of immense importance as I keep saying if only you idiots would listen, this database solves all the problems that you fools have run into with genomics.

SCIENTIST1: How does it do that?

ZEBRA: By having such a large database. You see the risk of any individual patient's data being exposed is reduced. Brilliant, you see.

SCIENTIST1: But by having such a large database you make it more likely that someone will have their privacy compromised.

ZEBRA: Yes, but it is much less likely to be me, I mean any specific person, because an individual's likelihood of having their confidential health data exposed is reduced because there are so many other targets. It's brilliant, why can't you see that?

SCIENTIST1: [Laughing.] That's a novel approach to data privacy I suppose...

SCIENTIST2: Why would you need an entire year's birth cohort? That's about 5 million children in the US. Wouldn't it be better to focus on people with specific conditions?

ZEBRA: OK, I'm changing my project, now it's going to be an entire year's birth cohort from Canada, and it will have IRB approval, and we won't sequence the genome, we'll just keep blood samples, and if anyone opts out we will replace them with other people who opted out by er.. look a squirrel!

SCIENTIST3: What about Iceland?

ZEBRA: Iceland, of course, excellent point, er... One moment! [Zebra frantically taps at his phone for a minute.]

ZEBRA: Iceland, excellent idea. They sequenced every person, exactly as I suggested.

SCIENTIST3: No they didn't, they sequenced a few hundred thousand and the project collapsed because of the privacy and ethical issues you said were vacuous concepts.

ZEBRA: I never said that, you took me out of context. I said that ethics and privacy are very important.

SCIENTIST3: What about phenotype data? How are you going to collect that?

ZEBRA: Pheno what? One moment! [Zebra consults his phone again] Phenotype data will go in the same database, obviously. Yawn.

SCIENTIST3: But where will it come from? Doctors records? Hospital records? An interview?

ZEBRA: Yes, yes, all of those, obviously. Duh. Yawn.

SCIENTIST1: Hold on a minute. You didn't even know what a phenotype was until you Googled it just then, did you? You don't have the faintest clue what you are talking about.

ZEBRA: Yes I did and yes I do. How hard can genetics be anyway? I've read the Wikipedia entry and it seems pretty easy to me.

[Exeunt remaining scientists shaking their head in disbelief ]

ZEBRA: Wait, come back you fools, you don't understand. You are all stuck in a blinkered mind-set and only I have the vision, imagination and intelligence to help,,you see the error of your way? Hello?
[Crickets...]

Krebiozen, you've outdone yourself. Maybe stand-up is your second calling; this is hilarious. And I would say this even if you had written it about my comments had they been the same. It's that good.

Now, now. Z. is "willing to be found in error," so long as it "helps educate people" – viz., demonstrate that Z. is right. (In fact, he's the href="http://scienceblogs.com/insolence/2015/09/08/precision-medicine-hype-over-hope/#comment-416862">only person here capable of the very task, qualification aside.)

^ Ahem.

Now, now. Z. is “willing to be found in error,” so long as it “helps educate people” – viz., demonstrates that Z. is right. (In fact, he’s the only person here capable of the very task, qualification aside.)

Time for me to make a shopping list before it's too late.

Narad

Would you get us...some sour cream and onion chips with some dip, man, some beef jerky, some peanut butter. Get some Häagen-Dazs ice cream bars, a whole lot, make sure chocolate, gotta have chocolate, man. Some popcorn, red popcorn, graham crackers, graham crackers with marshmallows, the little marshmallows and little chocolate bars and we can make s'mores, man. Also, celery, grape jelly, Cap'n Crunch with the little Crunch berries, pizzas. We need two big pizzas, man, everything on 'em, with water, whole lotta water, and Funyons.

Thanks much!

Who uses an overhead projector these days. I’m surprised they even have one. Doesn’t everyone use PowerPoint these days?

He who acetates is lost!

"He who acetates is lost!"

LOL. If you breath that stuff in you certainly are. For hours.

Alright, I'm going to go now. I've overstayed my welcome for tonight. I think I'm just in an odd mood because Orac has been back for almost a week and still nothing about the bats. I'm hoping they're ok.

Who uses an overhead projector these days. I’m surprised they even have one. Doesn’t everyone use PowerPoint these days?

My Russian students, especially the ones in STEM fields, always get a kick out the fact that there is a behemoth of an electric typewriter (circa 1980-something, I'd say) sitting amongst the four computers in the computer lab.

I'm not sure why it's there, although I've heard several explanations, but it's been there since I started and doesn't seem to be going anywhere. (Still works just fine, too.)

^Russian language students, I should probably specify, not students from Russia.

JP -- we keep an IBM Selectric D in the office, next to the superduper hi-speed, low-drag printers, because every so often somebody shows up with a form that can't be filled in by computer.

It should surprise no one that two of the last five non-computerized forms were from the DOD.

@shay:

I've heard that theory; an alternate explanation that I've heard is that a certain (now late, sadly) Professor Emeritus used to use it for various things.

It can type in Cyrillic, evidently; there are mostly-worn-off Cyrillic stickers on the keys. The non-computerized form theory makes the most sense for me, especially if one considers that we deal with ex-Soviet countries on a regular basis, and not by any means only Russia.

It is kind of funny that it's in the grad student lab, though. Doesn't clutter up the main office that way, I guess.

Not a Troll,

Krebiozen, you’ve outdone yourself.

That's kind, but I'm sure could have done a lot better if I was willing to spend a bit more time on it. There is, after all, no lack of additional material :-)

With apologies to gaist.

None required. In fact, I'll happily direct to you, duly, the undeserved overflow of internets I got in the other thread.

There is, after all, no lack of additional material :-)

I admit that trying to pick and choose which inanities to highlight seemed the biggest task with See Noevo the dishonest misanthrope, the jokes on him pretty much wrote themselves.

It's weird how some people unwittingly keep roasting themselves with almost every comment they make.

Ann 540,

You are wandering a bit here. Remember, basic research. As I have said, lots of little grad students adding lots of bits of knowledge.

The "researcher" is just doing that one thing. Finding a correlation between one genetic characteristic and one phenotype. So, you can't bring in all these other pieces of information that you know.

By doing that you confuse the validity of the correlation with its significance (not statistical).

You haven't made a case that we wouldn't have confidence in the detection of the correlation. On what possible basis would you challenge it? I would really like an answer to that, since I want to improve my database if necessary.

With respect to your points, separate from the above question: If I were doing research in this field, and I discovered this one correlation, I would then continue to look for others in the genome, until I was confident that I had well-characterized the relationships. I wouldn't start chasing squirrels.

If I understood Retro Pump correctly, s/he said something like " initially we all got excited thinking we were going to find magic cures and get rich and famous, but it sure didn't work out that way".

I wonder, if the gratis, expansive, clean, database I suggest had been available, how many resources would have been better spent.

Gratis?

Expansive??

Clean???

It looks like you have stopped your pseudo-cogitation and are now just throwing out material for Krebiozen.

You haven’t made a case that we wouldn’t have confidence in the detection of the correlation.

My comment, still in moderation, does exactly this. Aside from the fact that the above statement is pretty close to stats word salad, the short answer is you have no statistical power to detect the association. This is because in your database, it would be impossible to separate cases into the 3 groups used by Caspi et al. for the analysis as shown in the x-axis of Figure 1.

Perhaps you'd like to tell us specifically what statistical method you would use on this "gratis, expansive, clean" (???) database to detect this association, given that low activity MAOA alleles are associated with less antisocial behaviors in individuals who fall in the most common subcategory (no maltreatment).

Later that day, the two Scientists are having dinner.

SCIENTIST1: I really enjoyed the presentation by Dr. Eric Green this afternoon.
SCIENTIST2: Indeed, an excellent presentation. Unlike, you know... [He points towards a table nearby, where Zebra is inserting himself, interrupting a lively discussion].

ZEBRA: No need to get up, we're among friends here. Real scientists among peers.
DINER1: Quite. [clears throat, turning back to the others] So, as I was saying about the concerns that raises for the information security applic-
ZEBRA: Yes, yes, no doubt a fine subject, but rather peripheral to the real issue, I think.
DINER1: Excuse me?
ZEBRA: Infosec, silly acronym, and wholly unnecessary.
DINER2: But we were just discussing-
ZEBRA: Peripheral points of little interest, I'm afraid. Whereas the main point, quite clearly, is the utility and accessibility of my project. On gegnomes.
DINER1: On what?
ZEBRA: Gegnomes. Pay attention.
DINER2: What on earth are you talking about?
ZEBRA: I'm surrounded by idiots, again. My project, the Great Zebra Gegnomic Database.
DINER1: The what?
ZEBRA: You must be slow, I won't bother explaining it to you.
DINER2: You're being rude, sir, and I would like for you to le-
ZEBRA: It's a wonderful project, much appreciated and applauded by the real experts in the field, like the esteemed Professor Greg Venter-
DINER2: Craig.
ZEBRA: Greg Venter, the esteemed Professor of Gegnomics personally complimented me on my project, and lamented how there are so called experts in the field who have not yet realized the full potential of my gratis, expansive, clean databa-
SCIENTIST2: Evening.
DINER1: Evening, Mr. Venter...
DINER2 Hello Craig.
SCIENTIST2: Hello.
ZEBRA: What? Who?
SCIENTIST2: I couldn't help overhearing Mr. Zebra here, and I feel I must make it clear that I most certainly did not-
ZEBRA: So you disagree with some minor details, no biggie, there's no shame in being wrong sometimes, even for an esteemed expert such as yourself.
SCIENTIST2: They are not minor details I disagree with, I assure you. Your project is ill-thought, gravely misrepresented even by you, and wholly untenable.
ZEBRA: It's obvious there is some ungrounded hostility here, towards novel thinkers. I know when I'm not welcome. [stands up]. It's a pity none of the real numerous experts who greatly appreciate my database showed up. Your "opinions" aren't needed anyways. [Exits]

The “researcher” is just doing that one thing. Finding a correlation between one genetic characteristic and one phenotype. So, you can’t bring in all these other pieces of information that you know.

By doing that you confuse the validity of the correlation with its significance (not statistical).

I don't understand.

How can a valid correlation between a genetic characteristic and a phenotype be established if you don't look at anything apart from the rate at which they co-occur? Even the most bare-bones inquiry would have to have a control group.

So at a minimum, assuming the inquiry had been in the form most favorable to you -- ie, the researchers weren't just looking for any genetic characteristic corresponding to antisocial behavior, but specifically for MAOA 3R and nothing else -- what they'd get would be 45% in the sample, versus 34% in the controls.

There's no way to say whether that's valid without looking at a lot of other stuff. I mean, I'm assuming that "valid" means "validly shown to be among the causal or contributing factors for the behavior." So that would actually be the case even if the numbers were more eye-popping. You'd need to have some testable idea of how it worked.

But never mind that.

You haven’t made a case that we wouldn’t have confidence in the detection of the correlation. On what possible basis would you challenge it?

I don't really know enough about it to make a case one way or the other. I believe that if the sample was large enough, you could confidently conclude that the result represented something. Whether it was something that was valid for the purposes of your inquiry would be another question.

But my understanding of such things is basic at best.

AdamG 592,

We wouldn't have confidence in the detection of a correlation we couldn't detect?

Jeez, back to the drawing board. What was I thinking? Of course this idea is useless if it can't detect the undetectable!

sigh

zebra:

I wonder, if the gratis, expansive, clean, database I suggest had been available, how many resources would have been better spent.

Please stop. You are making an even bigger fool of yourself now. You are clearly showing you know nothing about IT.

With respect to your points, separate from the above question: If I were doing research in this field, and I discovered this one correlation, I would then continue to look for others in the genome, until I was confident that I had well-characterized the relationships. I wouldn’t start chasing squirrels.

Again, I don't understand. There could be any number of correlations that had no relationship to each other, the behavior, or anything else. Plus if you did that, either you'd find the other stuff I mentioned or I have no idea what you're talking about.

Ann 594,

So we are on the same page in using this particular correlation as an example of something a researcher might discover-- AdamG doesn't seem to get that.

How can a valid correlation between a genetic characteristic and a phenotype be established if you don’t look at anything apart from the rate at which they co-occur? Even the most bare-bones inquiry would have to have a control group.

Of course, no problem. I wasn't questioning what you said about that.

But

I’m assuming that “valid” means “validly shown to be among the causal or contributing factors for the behavior.”

Not at all. Valid means "I can publish this and someone isn't going to point out that my sample size is insufficient, or there are confounding factors, or I engaged in selection bias..."

And since I am saving you the expense of buying one of those machines Orac talks about, you can put your funds into analyzing a sufficiently large sample. And if another underfunded researcher wants to challenge/verify the result for some reason, they have gratis access to a different set of data from the same cohort, if that suits their experimental design.

Is that making sense yet?

What do you even mean at this point? You asked:

You haven’t made a case that we wouldn’t have confidence in the detection of the correlation

What specifically do you mean by 'the correlation' here? If you mean the association between low MAOA activity and antisocial behaviors in a history with maltreatment, I already explained in 592 why it could not be confidently detected, as you ask. We would not be able to separate individuals into the 3 groups necessary to detect the association.

If what you're trying to argue is 'any results gleaned from my database would be significant, and robust' that is incredibly naive, especially because you have yet to comment on precisely how any phenotype data would be collected. It's not like you can just copy and paste this stuff, honey...
http://www.ncbi.nlm.nih.gov/pubmed?term=24987407

using this particular correlation as an example of something a researcher might discover
Sigh indeed. Why didn't you just say "You haven’t made a case that we wouldn’t have confidence in the detection of any correlation" if that's what you meant.

And as I just said, you're putting the cart miles before the horse here. First tell us specifically what phenotype information would be used to detect such a correlation, and how that would be collected.

It is apparent, to this reader at least, that the incredibly perspicacious musings of Mssrs gaist and Krebiozen are deserving of much praise: indeed they are seemingly meritorious beyond measure.

I should be SO pleased - if they were ever appear in either a serialised web-based format or in print- to submit a preface and/ or introduction to this important work. AND I can assure you most confidently that my own efforts OBVIOUSLY will be intrinsically more thought-provoking and intriguingly apropos compared to anything written prologueally by Kennedy, McCarthy, Haley, Olmsted or Sears
( who habitually precede blather written by their comrades with blather all their own).

At the very least, it will be reality-based and spelt somewhat realistically: can you ask for more? I can't.

Perhaps you’d like to tell us specifically what statistical method you would use on this “gratis, expansive, clean” (???) database to detect this association, given that low activity MAOA alleles are associated with less antisocial behaviors in individuals who fall in the most common subcategory (no maltreatment).

Then there's that. And there would be that. Because realistically speaking, the bare-bones search parameters I described only make even rudimentary sense if you already know there's a correlation, contingent on some external factor.

Even then, they don't make much sense. Though.

ann and Adam G:

what you say is precisely why so many amateurs get caught .

AdamG,

Since the genetics involved in antisocial behaviors is a hot mess* right now, would you speak to something simpler such as how zebra's database could be used (or not) for finding the genes and alleles correlated to eye color? Assuming that we are starting from scratch and there is no knowledge of what genes impact eye color.

*my entirely unscientific phrase.

Denice,

You went high end. I'd be happy with a Krebiozen and gaist cartoon.

And that is something that is entirely possible (with the name changed to protect the anonymity of the pseudonymous of course).

So we are on the same page in using this particular correlation as an example of something a researcher might discover– AdamG doesn’t seem to get that.

I think he does, in the sense that he would grant that it's possible to design a search of the database that might discover it.

But that's not saying much. If a researcher who was just using the database to look for some (or any) correlation between some (or any) genetic factor and a particular phenotype would probably always find something.

And a researcher who was using it to look for some (or any) correlation between a low-activity MAOA allele and some (or any) behavioral or mental disorder would also probably find something most of the time.

But it still wouldn't mean much. MAOA affects several neurotransmitters. One or more of them is implicated in virtually all major mental illnesses. That's already known.

In order to find out anything validly of interest in relation to the object of your inquiry, you'd need to do more than query a database for a correlation.

Not at all. Valid means “I can publish this and someone isn’t going to point out that my sample size is insufficient, or there are confounding factors, or I engaged in selection bias…”

Someone could point out that since you hadn't looked for confounding factors, the validity of your finding was unknowable. And they'd be right.

Eye color is not the best example here, as it requires careful attention to subtle gradations in phenotype. For a super cool example of how this complexity can be unraveled, see http://www.ncbi.nlm.nih.gov/pubmed/23555287

A more straightforward example here would be a rarer, severe disease linked to a single event. For example, let's say I knew absolutely nothing about Down Syndrome. Since DS would certainly be noted in the medical record, it would be easy to separate your data accurately into true cases and true controls. As it's unlikely for someone to be misclassified clinically as having DS, even without a chromosomal assay, comparing genome-wide SNP genotypes would instantly reveal that nearly all your cases and none of your controls carry what appear to be 3 alleles for every variant on chromosome 21...boom, disease mapped.

Again this is a straightforward one...trisomy 21 was identified as the cause of DS in the 50's as all it took was the development of the first technology that could routinely detect large chromosomal abnormalities: karyotyping.

@ Not a Troll:

I regularly emulate the queen's English-
however I'm not saying *which* queen.

Unfortunately, Jameson at AoA is today spouting the erroneous belief that because something co-occurs it MUST be causative.
e.g. 20 years ago there were less vaccine as well as less autism, ADHD, obesity etc.
There are also more organic food stores, more natural health advocates, more social networks, University of G--gle degrees and more thinking moms.

Ann #607,

" If a researcher who was just using the database to look for some (or any) correlation between some (or any) genetic factor and a particular phenotype would probably always find something. "

Maybe, maybe not. Remember, we are not assuming things we already know. But why is that a problem anyway?

"Someone could point out that since you hadn’t looked for confounding factors, the validity of your finding was unknowable. And they’d be right."

What would be a confounding factor when using my database?

"a researcher who was just using the database...would probably always find something" But why is that a problem anyway?

What would be a confounding factor when using my database?

1. False positives.
2. What wouldn't be? I dunno, because you haven't said what phenotypes you'd measure and how.

If you really want to learn something, do the minimal amount of effort and watch this video on statistical power:
https://www.youtube.com/watch?v=aEvrqfTV3cQ

Unless you'd rather stick to your usual reading material.

Though I’m generally skeptical of gene-environment-behavior associations in humans, this is one of the more believable ones.

I agree. I always wish that such studies looked more at factors like education, literacy and intellectual stimulation or exercise in childhood generally. As distinct from intelligence.

But that's not a criticism of Caspi et al. I personally would just like to see it.

AdamG,

Let's go as simple as I think is possible - or not. I have no idea.

The phenotypes in zebra's database would be a person's physical characteristics and the ICD-10 codes of any diseases they've had or currently have. Understanding that we'd have to pay 1,000s of Canadian and American grad students to capture and enter all of this data, and that some of the information will just be incorrect for various reasons.

Would this be a good resource for researchers? Worth the effort involved?

What would be a confounding factor when using my database?

Potentially anything. Correlation by itself could always be due to either coincidence or factors unrelated to the inquiry.

Or maybe almost always. If you were looking at a nice straightforward single-gene disorder with a conveniently unmissable Mendelian pattern of inheritance, finding the single gene would do the trick.

But you wouldn't need the database for that. You could just test the affected people and their immediate family. And it's usually not the case.

Not A Troll,

You are making an excellent effort to clarify things-- good question with eye color.

Just a point-- there are no grad students involved in creating the original database. The samples get collected and processed. The data on phenotypes comes from the healthcare system.

Ann 615,

Ann, seriously. it might be coincidence? You're rejecting all of statistics?

So, look, if "it could be anything", just give me a couple of examples.

As it’s unlikely for someone to be misclassified clinically as having DS, even without a chromosomal assay, comparing genome-wide SNP genotypes would instantly reveal that nearly all your cases and none of your controls carry what appear to be 3 alleles for every variant on chromosome 21…boom, disease mapped.

I'd be curious about the time complexity of this if actually carried out from scratch in the brute-force manner that Z., by default, envisions. Enumerating multiple-locus combinations scales intractably (PDF).

You’re rejecting all of statistics?

EMP-hardened irony meters all around!

Just a point– there are no grad students involved in creating the original database. The samples get collected and processed.

By magic? It's impressive that you're still willing to say something this profoundly dense at this stage of the performance.

Understanding that we’d have to pay 1,000s of Canadian and American grad students to capture and enter all of this data

Not actually true. Most large health networks conducting research these days consent patients broadly to be part of biobanks for this exact sort of work. Since their EMR is already filled out by their physician, the data's all there.

Then it's just a matter of comparing the IC9/10 codes of people with a certain genetic variant to those without to see if the folks with the variant are more likely to have a certain code in their EMR.

Would this be a good resource for researchers? Worth the effort involved?

not only is it a good idea, but it's already been implemented rather successfully:
http://www.ncbi.nlm.nih.gov/pubmed/20335276

This approach is a cornerstone of PMI. One of the things that makes it work is an initial baseline exam with findings coded into a patient-accessible EMR. See the section starting on page 58 of the PMI document labeled "Recommendations for an initial PMI core data set"

as for zebra...

The samples get collected and processed.

Finally, the true role of the gegnomes is revealed!

The paper you cite has to do with detecting associations that underlie primarily driven by three loci (here meaning three different polymorphisms)...If your goal is 'discover which specific genes cause features of DS when found in triplicate' then yes, you'll have to do a much different study that models these relationships.

I was actually talking about using sequencing as a counting method in order to diagnose trisomy 21...this works by looking at the stoichiometry of fragments of cell-free fetal chr21 in the mother's blood. It's super neat!

More on this here: http://www.ncbi.nlm.nih.gov/pubmed/26332378

or an excellent lecture for those who prefer:
https://youtu.be/6P9AVGp6R5w?t=73

Ok, my mistake. In the US at least, I thought there would still need to be an effort involved for the switch from ICD-9 codes to ICD-10.

^Also, my point would be moot if starting from a brand new just born birth cohort. So, never mind.

an effort involved for the switch from ICD-9 codes to ICD-10.

This is indeed a challenge, but more in the scope of a single smaller workgroup tasked to build an algorithm to automate this than an undertaking of thousands. I'm simplifying here though...honestly neither ICD system is great, I'm glad there's an increasing move towards using SNOmed codes which make everything a lot more comprehensible...ICD is a mess.

https://www.nlm.nih.gov/research/umls/Snomed/snomed_main.html

My previous comment regarding DS was directed to Narad if not obvious...

I was actually talking about using sequencing as a counting method in order to diagnose trisomy 21…this works by looking at the stoichiometry of fragments of cell-free fetal chr21 in the mother’s blood. It’s super neat!

Right, but I was proceeding from the starting point of not knowing anything about the cause of Down Syndrome and getting it to fall out of Z.'s magic box, the interface to which he has proved unable to describe other than to intimate that people will be able to randomly query medical conditions and simply be handed whole genomes.

people will be able to randomly query medical conditions and simply be handed whole genomes

Actually, simply running mPileup on your mapped case genomes would instantly reveal not only that chr21 had way higher coverage on average than the cases, but your heterozygosity for the entire chromosome would be way off in cases.

The technology to do this is already extraordinary. Assuming the most basic type of database, a warehouse of raw genome sequencing data with annotated disease status, this could be done in about a day using freely available tools over the web:
https://usegalaxy.org/

Believe me, I'm not giving zebra any credit here, but the resources out there these days are kind of amazing.

"The samples get collected and processed."

A simple lesson learned from a career in government: Assume that any proposal which cannot be expressed in simple sentences (subject/verb/object)is worthless.

Ann, seriously. it might be coincidence? You’re rejecting all of statistics?

I don't think so. We're not talking about overwhelming numbers or a huge sample. It's kind of hard to calculate overall prevalence for "antisocial behaviors." But responsibly defined, they're not all that common.

So, look, if “it could be anything”, just give me a couple of examples.

I already gave one. It could be that boys born to women who drank or used drugs during pregnancy are likelier to have that allele (as a mutation, either as a direct result of the alcohol/drug use or something associated with it) as well as likelier to be exposed to one or more environmental factors that are (in turn) associated with higher rates of antisocial behavior, which would (in that case) not be genetically determined at all.

It could also be that boys with that allele are prone to some other behavior or have some other trait that predisposes them to sleep deprivation, which in turn predisposes them to yet another type of behavior, which in turn makes them prone to conflict, which in turn has an effect on endocrine function, which makes them even more prone to conflict, which (in conjunction with other factors) leaves them biopsychosocially prone to violence as adults at a disproportionate rate.

I believe, although I'm not certain, that you could also be looking at a genetic factor that was correlated to the behavior but didn't appear to be because...Well. I think I read something about Alzheimers and epigenomics that suggested it was more about what you did with your genes than what they did with you. Maybe.

But I'm hazy on the details, due to having virtually no clue what I'm talking about. So never mind. I guess my point is just that I imagine that there are also probably scenarios I can't even begin to conceive of. However, although I know what I don't know, I still don't know it. So I can't elaborate.

The thing I don't know is whether that kind of thing would be evident if you didn't look for it, or whether looking for it is standard, and so on.

I mean, I can follow a line of reasoning if somebody else has already done all the work of layin. But as I've already said, my understanding is shallow.

Those last two paragraphs were an attempt to elaborate, on which I gave up.

Just ignore them.

Most large health networks conducting research these days consent patients broadly to be part of biobanks for this exact sort of work.

By default? I had to sign off on several pages (presented by a chirpy grad student who also waltzed into the procedure room to see if she could score a brushing as well)* when I sent bits of my latest colonoscopy to be embalmed and sent forever to the Great Colon Bank in the Sky down the street.

Since their EMR is already filled out by their physician, the data’s all there.

Anyway, I was reminded again of the VSD, the participating HMOs in which have their own IRBs for independent researchers. Z. of course has specified that he would need a more compliant "rational" population to ultimately have his Grand Vision come to fruition and spread its nutritive seeds far and wide to desperately hungry flocks of graduate students, but I was also reminded that he can't even bring it to the Power—t level of description.

* None of them said you got to watch, Peaches, and there's no reason for you have been wearing a lab coat.

ann 629,

I appreciate that you are really trying to answer. I just don't see how you think that would be a confounding factor. What would it be confounding?

We would still observe the correct correlation between the genetic information and the phenotype, even if the genetic information is the result of mutation.

It there really were some way that there would be confounding factors, someone would have suggested it by now.

I think AdamG pretty much sums it up with his disclaimer:

"Believe me, I’m not giving zebra any credit here, but the resources out there these days are kind of amazing."

or

"Believe me, it pains me terribly to give zebra any credit here...."

AdamG,

I was actually talking about using sequencing as a counting method in order to diagnose trisomy 21…this works by looking at the stoichiometry of fragments of cell-free fetal chr21 in the mother’s blood. It’s super neat!

I spent ten years running the laboratory end of a prenatal Down Syndrome screening program that used serum AFP and beta HCG to estimate risks of a Down Syndrome pregnancy (using multivariate analysis), so that's of great interest to me. If I generated a positive screen result the woman would be advised to have amniocentesis and cytogenetics would karyotype the fetus, so she could make an informed decision as to whether to continue with the pregnancy. Even with fine tuning we only had a 75% true positive rate and a 5% false positive rate, so it wasn't very good, though better than nothing. I always knew that some better and less invasive method would become available eventually, so it's nice to see that happening.

I recently read (in 'Mutations' by Leroi) that the gene for superoxide dismutase 1 resides on chromosome 21, so people with Down Syndrome have three copies of the SOD1 gene. A simplistic view might assume that this would be a good thing, since SOD1 mops up oxygen free radicals, but we know that the free-radical theory of disease and ageing is flawed. It is thought that it is the extra copy of the SOD1 gene that has some of the most destructive effects of Down Syndrome the mental retardation associated with it may be because SOD1 may have a role in pruning neuronal architecture, which is also where autism may have its roots. Interesting, or at least I thought so. No doubt it will provoke a yawn form zebra.

Believe me ... the resources out there these days are kind of amazing.

I'm impressed, thank you. I imagine the fact that I'm thinking about computational complexity makes it obvious that I'm trying to work from first principles.

This has its pros and cons, and help bootstrapping things greatly ameliorates that latter.

It there really were some way that there would be confounding factors, someone would have suggested it by now.

I believe that I've already mentioned that you've built in nearly every confounder imaginable.

You have a "haystack" of genomes and a needle-sparse set of hypotheses to be examined against an information-sparse set of medical records. You may have noted that I'm not the only person here to have paired the words "cart" and "horse."

I also find it interesting that it is a mutation in the SOD1 gene that leads to ALS (aka Lou Gehrig disease), "a particularly ferocious neurological disease in which the motor neurons of the spinal cord, brain stem and motor cortex are progressively destroyed, leading to paralysis and death".

These kinds of single gene mutations appear to be in a tiny minority. Most genetic disorders are likely to be caused by MAGOTS, which are far harder to discover. The human genome consists of over 3 billion base pairs CG, GC, AT or TA, so finding correlations between human conditions (whether physiological or otherwise) and variations in these base pairs that may be modulated by environmental factors seems mind-bogglingly complex to me. I'm glad there are some amazing resources out there to deal with this!

Krebiozen, check out this paper.

"I think AdamG pretty much sums it up with his disclaimer:"

Or it could just be that they don't give credit here for wild a** guesses. They may give credit for educated guesses but probably not after you've alienated them with difficult to decipher writings and arrogance.

If you pay attention, you can see that the credit goes to those who have some solid ground on the subjects they are speaking to either from experience, training or researching it and to those who have done the work such as creating the mPileup program.

^ Then again,

The SAM format consists of one header section and one alignment section. The lines in the header section start with character ‘@’, and lines in the alignment section do not. All lines [sic–'fields'] are TAB delimited. An example is shown in Figure 1b.

That is so COBOL 20th century. I still await the details of the post-"sorting" Z. object-oriented data structure.

Narad,

Um. was that for me? I did learn COBOL long ago in what seems like another lifetime. All I remember is to make sure to put the period at the end of the sentence, dummy.

AdamG,

Krebiozen, check out this paper.

Thanks, that was interesting too, though I always take cell culture findings with a pinch of salt. You can to buy SOD in health food stores, and I seem to remember claims that copper salicylate mimics SOD. If so, and if any of it is actually absorbed, some people may be doing themselves more harm than good.

Zebra (616)

I don't have time to comment here much, but thought I'd toss in a note tonight.

You state:

The samples get collected and processed.

Thanks for offering a perfect example of why the course in writing for clarity I took 25 years ago included the rule

Use active voice, not passive voice.

It's because in passive voice, it's so easy to drop the subject entirely. (which you manage to do in a different context quite often IMHO)

You left the key part, by whom?

Who does all the work of collecting and verifying the data and who pays them to do it?

And that's just the start-up cost of your little brainstorming exercise. Then of course you have yet to even describe a plan likely to achieve useful results from that start-up cost, etc.

'nuff said.

We would still observe the correct correlation between the genetic information and the phenotype, even if the genetic information is the result of mutation.

No, you wouldn't. (Also, it's immaterial that it was a mutation. That was just a narrative flourish.) You would observe what appeared to be a correlation between the genetic information and the phenotype, when in fact it was a correlation between the genetic information and one or more unknown, unidentified confounds, which were correlated to the phenotype.

Narad@635

I believe that I’ve already mentioned that you’ve built in nearly every confounder imaginable.

I think I know why zebra thinks otherwise. He's operating on the "if I can't see it it's not there" principle. His database doesn't contain data on confounding factors (it's just a medical record linked to a genone) so there's no confounders there. He's conflating data on confounders with the confounders themselves.

This is, of course, wrong. The confounders are there either way, the difference is that if you have data on them you can identify and control for them.

@Krebiozen and gaist
That alone made this whole thread worth it. I'm Not a Troll. A webcomic on the RI trolls would make for a fine read.

Ahem. I'm with Not a Troll. We are, in fact, two different people.

Dear gegnoramus Z.

If I look at your quote here:

“Believe me, it pains me terribly to give zebra any credit here….”

Iiiiii don't think that's the interpretation I understood from AdamG and I have my own idea about why you shouldn't give yourself any credits here:

You don't know what's out there 3:)

even more so, you argue out of gegnorance 3:) (i.e. talking out of where the sun don't shine).

why not getting a bit of education on the topic?

https://www.coursera.org/specializations/genomics

https://www.coursera.org/specializations/jhudatascience

Your friendly Gunnery Sergeant Hartman :D

That alone made this whole thread worth it. I’m Not a Troll. A webcomic on the RI trolls would make for a fine read.

May I recommend this pharmadog (woof) for the drawing?

http://lepharmachien.com/produits-naturels/

Gunnery Sgt. Hartman

Zebra @617: Correlation and confounders:
As was mentioned by capnkrunch up at 550, there is a simple, classic example of a spurious correlation (a confounder).
In epidemiology studies of cancer coffee consumption will often appear to be strongly positively correlated with cancer and cardiovascular disease. The reason that coffee has this correlation is that most smokers drink a lot of coffee. Thus, while coffee is correlated to cancer, it is not the mechanism of action (that would be smoking), it is just a confounder.

So for ann's example, the anti-social behavior in the boys could be caused by that gene mutation, or it could be caused by a violent upbringing. You would need to do more studies to determine if either is the sole cause of the behavior.

Confounding factors are always a huge issue in all research. That's why studies are so carefully controlled.

Ann (et al):

If there is no mutation, there is no correlation.

Everyone keeps making-- whether because of ZDS or simply unclear thinking-- this fundamental error.

Said multiple times now: Basic research. Accumulating valid (robust) information. Not gold-rush looking for the miracle cure, as described by Orac in that quote I gave.

If I'm looking for a correlation, I'm looking for a correlation, not causality. So, there are no confounding factors, except as I have already suggested.

I mean, I mentioned an actual example of how the data might be distorted (in a minor way) at least a couple of times, and you people can't even work from that to find some similar possibilities to beat me over the head with. That would be constructive.

AdamG,

Well, I did my part in the Twitter chat. The team did a good job and most of my questions were answered. I could have done without all of the cheerleading but that is to be expected.

Thanks for letting us know about this.

Said multiple times now: Basic research. Accumulating valid (robust) information. Not gold-rush looking for the miracle cure, as described by Orac in that quote I gave.

If I’m looking for a correlation, I’m looking for a correlation, not causality. So, there are no confounding factors, except as I have already suggested.

Dining. Room. Table.

If I’m looking for a correlation, I’m looking for a correlation, not causality. So, there are no confounding factors

zebra, I just want to make sure I am understanding your argument. Do you believe this statement to be true or false:

Confounding factors need only be considered in this context if one is trying to establish causality, and play no role in finding correlations.

Please, correct me if this is not what you are advocating.

NaT...thanks for chiming in. I'll probably still be around here when it comes time for folks to start signing up...

If I’m looking for a correlation, I’m looking for a correlation, not causality. So, there are no confounding factors, except as I have already suggested.

There is no such thing as looking for a correlation while blind to confounds. That's not research, basic or otherwise. It's....I don't know what it is, actually. It's essentially a game of chance of some sort. Roulette. Slot machines. Something like that.

A correlation doesn't necessarily have to be causal, exactly. But in order for an association between two variables to be correlative, A has to at least be demonstrably dependent on B in some way. If that can't be demonstrated, it's not one.

All of those things are non-optional. If you use the words "correlation" and "research," that's what you're talking about.

I mean, they're not my rules. But they're not yours either. The words mean what they mean.

ann@653

It’s….I don’t know what it is, actually.

Haystack first ann. It's looking for hay in a haystack. You're always successful but in the end you haven't accomplished much.

"I’ll probably still be around here when it comes time for folks to start signing up…"

That's good, AdamG. To clarify most of my questions asked in the chat were answered. I'm sure my questions will be a work in progress if I decide to sign up. But don't worry, I don't plan to abuse your presence here to answer them. There will be a contact for that through NIH, I'm sure.

For zebra's conundrum, I think he is just looking for correlations between Col A (genomes/alles or however granular he plans) and Col B (coded medical conditions). I am not sure he grasps how far that will not get you or for the presence of red herrings.

Anyway, that's my best guess.

The more I think about, the more this seems like the crowning moment of Z.'s "proposal." An enitre birth cohort is going to be sequenced, magically have its members' medical records thoroughly tracked* in a perfectly secure yet easily accessible fashion, and, at long last, the goal is to aimlessly churn out false positives. After burying them in noise for good measure, and ensuring that one has no way to easily identify screaming confounders such as, oh, say, population-level data. And this will cause people to flock to graduate study of this mess because, well, there's no better way to get tenure than to spend years picking sh*t with the crows.

One could almost just say "The Aristrocrats" and stop there, but there is so much else wrong that it's enough to drive a person to distraction.

Perhaps Z. would like to address this failure mode, and what it has to say – yet again – about the arrangement of carts and horses. L-rd knows he never got around to stating whether it has more than one dimension or not.

* BTW, returning to antisocial behavior, how complete is medical documentation of concussions?

^ "think about it"

(I was reminded of concussions by a truly impressive "data set" that Puliyel has on his Web site, but that's for another time or, more likely, place.)

Relocated, although the monument to the gag reflex that is Z.'s comment 503. Allow me to review:

Why do I need the information about the abuse to detect the genetic correlation?

What's the "correlation" with, again? Sweet G-d. Anyway....
-----

You know what? Since Z. didn't have the damn sense to take advantage of an opportunity to stop publicly making a fool of himself, there's another bit of utter fraudulence that I don't believe I've commented on previously:

I would oppose them [undefined, but apparently supposed to be related to comments 412 and 414] I empathize with people suffering, and because, even if I am not directly involved, it causes disruption in the society. You can’t really be isolated from things– it’s like when the cop shoots the black guy for no good reason. Everyone picks up the tab, in multiple ways.

This is more than faintly insane, but I'll write the bulk of it off to Z.'s situation at this juncture.* Resorting to weird persecution fantasies (which, as is par for the Zourse, are "concretized" and "defined" by virtue of being assigned acronyms) is beyond the scope of where I intended to go.

The garden-variety Bodhisattva concept is prima facie dualist, hydraulic, and pathognomic of Not Getting It, but here, Z. horks up some sort of freakish "operational definition" of empathy.

This reminds me of a story.

"'You don’t understand,' said the master. 'My mind and the fawn’s mind are the same. It was very hungry. It wants milk, I want milk. Now it is dead. Its mind is my mind. That’s why I am weeping. I want milk.'"

Protip, Z.: Don't try dropping the word "empathy" when your
entire, grotesque** sh*ttrip boils down to plain indignance over the failure of the perceived world to affirm your own glowing self-appraisal.

* Imagining how he would react to stopping up – or, better, causing to overflow late at night – the toilet at the home of somebody whom he was visiting for the for the first time, with first impressions on the line, is offered as a light-hearted exercise for the reader. Then again, he's apparently now a septuagenarian or something.

** In the vernacular sense.

^ "although also having taken note of"

Hell, allow me to gratuitously call attention to a strange (to say the least) yet enthusiastic Z. tic:

- - -

I just finished logic101, so I think I will call that reductio ad absurdum. (sarcasm)

- - -

If I have to end up sounding like philosophy101, perhaps it’s because everyone else sounds like they never took that class, and it is necessary to (re-)state the obvious?

- - -

I really don’t want to spend my time being philosphy101 professor

- - -

There is something very simple going on, Z., but for some reason, you can't figure it out:

1. "It" is not all about you.
2. "It" is all about you.

I am not a developmental psychologist, but my friends and neighbors have kids, and we hang out and work a little (or more if necessary) at enjoying our time together and so forth. I would guess, on this basis, that most 12-year-olds could authoritatively dispense with this "insolubilium" in passing between bites of carrot stick or whatever.

I mean, it would be vastly more interesting if you yourself would embark upon some "basic research," by which I mean something along the lines of getting under a haystack and starting a bona fide blog about all the shiny things that you find and how you figure out whether they're "needles" or random bits of leftover baling wire or something.

I cannot imagine any way that Dispatches from the Haystack could underform this wretchedness.

Idly advancing the notion that "hey, maybe we should sequence a U.S. birth cohort" is bullsh*tting. This is a good thing where I come from. Freaking right the f*ck out when people start kicking the idea around and finding it, ah, lacking in certain respects and then, in consequence, making up insane sh*t-brained "syndromes" might, briefly, have passed as a bit of horsesh*tting on the side, but this is ridiculous.

Not only have you been indulging a humorless, thoughtless, petulant tantrum, you apparently just couldn't bear the notion that it might stop being reinforced to some sort of minimal gratification threshold.

Not all parasitism is truly obligate, Z.

^ Bit of close-ital failure, but it'll do.

I am eager to see zebra's response to AdamG's question at #652. I won't hold my breath though.

I would oppose them [undefined, but apparently supposed to be related to comments 412 and 414] I empathize with people suffering, and because, even if I am not directly involved, it causes disruption in the society. You can’t really be isolated from things– it’s like when the cop shoots the black guy for no good reason. Everyone picks up the tab, in multiple ways.

I have to say, I not only don't see the problem with that, I think it's an ingenious and viable work-around for the objectivist-libertarian tendency towards callous indifference -- ie, it's in your self-interest to oppose bad acts against.others because it could be you.

He cited Niemoller as a way of saying the same thing @#219. But you could also use "An injustice anywhere is a threat to justice everywhere." And the Golden Rule would also do it. It comes off as more sanctimonious, but it's the same principle.

I agree with it.

I have to say, I not only don’t see the problem with that, I think it’s an ingenious and viable work-around for the objectivist-libertarian tendency towards callous indifference — ie, it’s in your self-interest to oppose bad acts against.others because it could be you.

In Buddhist philosophy, this is considered the "conventional" or "relative" view: your actions or inactions affect others, which directly or indirectly comes back and affects you. We're all in a complex web of relationships that can't be untangled.

Narad is evidently speaking from the "absolute" viewpoint, in which It is me. Tat tvam asi, in so many words.

A reference to Sandokai is perhaps in order:

The spiritual source shines clear in the light;
the branching streams flow on in the dark.
Grasping at things is surely delusion;
according with sameness is still not enlightenment.
All the objects of the senses
interact and yet do not.

Adam 652:

In what context?

Ann:

It's not easy being green. Thanks.

JP.

"In Buddhist philosophy." Whoa, dude, that's some deep shit.

In what context?

In exactly the context you mean when you stated

I’m looking for a correlation, not causality. So, there are no confounding factors

Again, True or False:

Confounding factors need only be considered in the analysis of the database zebra has proposed if a researcher is trying to establish causality, and play no role in finding correlations.

If I'm misrepresenting your views on this, please feel free to to clarify your exact position.

AdamG,

If you don't want to be accused of quotemining (taking a partial quote out of context), then don't do it.

Said multiple times now: Basic research. Accumulating valid (robust) information. Not gold-rush looking for the miracle cure, as described by Orac in that quote I gave.

If I’m looking for a correlation, I’m looking for a correlation, not causality. So, there are no confounding factors, except as I have already suggested.

I mean, I mentioned an actual example of how the data might be distorted (in a minor way) at least a couple of times, and you people can’t even work from that to find some similar possibilities to beat me over the head with. That would be constructive.

Did you miss the last paragraph?

BTW, Orac appears to be putting me at least in moderation. If he is growing impatient with this thread, it represents yet another thing he and I have some agreement on.

How would your database aimed at "accumulating valid (robust information" deal with false positives?

And BTW, silly zebra, it's you typing "shit" without circumventing the word filter that put you in moderation, not Orac singling you out - for that you're not significantly whiny a troll yet.

If I’m looking for a correlation, I’m looking for a correlation, not causality. So, there are no confounding factors, except as I have already suggested.
[...]
If you don’t want to be accused of quotemining (taking a partial quote out of context), then don’t do it.

I can't think of any context in which that paragraph makes any sense, so I await zebra's explanation with interest.

zebra, your continued dodges are highly amusing. This time with no quotes whatsoever so nothing is 'mined:'

True or False:

Confounding factors need only be considered in the analysis of the database zebra has proposed if a researcher is trying to establish causality, and play no role in finding correlations.

Great article Narad linked to @656 but over my head. Is there a relatively simple example of what the issues would be if an particular allele in Col A of zebra's database was found to be a match with an illness in Col B for a significant percentage of the number of those with the illness?

Please don't ask what percentage would be significant as I have no idea what that would be. Thanks.

AdamG,

I never said that. Here's what I said.

So, there are no confounding factors, except as I have already suggested.

I mean, I mentioned an actual example of how the data might be distorted (in a minor way) at least a couple of times, and you people can’t even work from that to find some similar possibilities to beat me over the head with. That would be constructive.

Do you understand the meaning of the word "except"?

Do you understand "work from that to find some similar possibilities" ?

Why don't you tell me-- what is your interpretation of the actual comment? Do you think it says what you are paraphrasing it as: "no confounding factors except" means "no confounding factors"? "Work to find some similar possibilities" means "don't bother looking for similar possibilities"?

You're getting positively desperate-whacky trying to elicit some little turn of phrase or interpretation that will Put That As*hurt On Zebra! because well, back here he used this word and over there he used that word blah blah blah.

This from a supposed expert in the field.

At this juncture I'm reminded of something I read recently about the growth of PoMo in the social sciences and the attack on natural sciences (from 'Higher Superstition: The Academic Left and Its Quarrels With Science' by Paul R. Gross and Norman Levitt, please forgive the longish quote, but I think it's apposite):

Natural science is one of the last major features of Western life and thought to come systematically under the critical gaze of the academic left. The reason is obvious. In order to think critically about science, one must understand it at a reasonably deep level. This task, if honestly approached, requires much time and labor. In fact it is best started when one is young. It is scarcely compatible with the style of education and training that nurtures the average humanist, irrespective of his or her political inclinations.
[...]
A curious fact about the recent left-critique of science is the degree to which its instigators have overcome their former timidity or indifference toward the subject not by studying it in detail but rather by creating a repertoire of rationalizations for avoiding such study. Buoyed by a “stance” on science, they feel justified in bypassing the grubby necessities of actual scientific knowledge. This is not because any great number of science apostates has flocked to their banner, although a handful of figures with scientific credentials, as well as the occasional refugee from an unsatisfactory scientific career, can be found on the movement’s fringes.

The assumption that makes specific knowledge of science dispensable is that certain new-forged intellectual tools—feminist theory, postmodern philosophy, deconstruction, deep ecology—and, above all, the moral authority with which the academic left emphatically credits itself are in themselves sufficient to guarantee the validity of the critique.
Thus we encounter books that pontificate about the intellectual crisis of contemporary physics, whose authors have never troubled themselves with a simple problem in statics; essays that make knowing reference to chaos theory, from writers who could not recognize, much less solve, a first-order linear differential equation; tirades about the semiotic tyranny of DNA and molecular biology, from scholars who have never been inside a real laboratory, or asked how the drug they take lowers their blood pressure. We speak not only from an acquaintance with the literature, but from regular experience of lectures, seminars, and symposia, where speakers tend to say more directly what they think than they do in print, and whose reigning attitude is that the cultivation of an authentically postmodern cultural critique requires the avoidance of dialogue with anyone who happens to be a working professional scientist. Above all, it demands a principled refusal to learn the substance of the science one proposes to criticize.

This is for Ann, if you are still there, and that is indeed it unless she replies or someone can rise to her level.

Ann, I think your problem again is in not "separating" things, as with so-called natural rights, and legal rights.

There are sources of error at different stages of the process. It isn't that there aren't confounding factors that might distort the data that is initially collected; one point of doing it my way is to eliminate what would normally be common sources of error.

Let's consider schizophrenia, or, since I don't want to get a lecture about how little I know about schizophrenia, some hypothetical similar diagnosis. So, in the usual way of doing things, what we do is go around finding people who have a condition, which may result in their being incompetent to make such a decision, and ask them if we can sequence their DNA.

The obvious problem with this is that we may then for example only get the DNA of patients for whom drugs work to make them competent to make such a decision, which of course is decided by the ethics committee of which everyone is so fond.

So, if I use that database, I am not completely confident that the statement (for example) "65% of those with the diagnosis have the genetic characteristic 1 (GC1), [while, say, only 35% of those without the diagnosis have GC1."] And so on for GCn. It may well be that those who respond poorly to medication have different GC's. That's the kind of thing you are talking about, right?

But let's say we do my project. We eliminate that source of potential bias, as well as the ethics question, because we have already asked: can we use your genome even if you become schizophrenic? So we can be much more confident in that statistical statement, made with respect to the cohort, absent some unlikely phenomenon like what I suggested earlier, or whatever someone can come up with, as requested.

BUT

This does not mean that [schizophrenia] might not also be correlated to environmental factors, for example, or that we don't have to do much more work to sort things out.

It does mean that all the researchers trying to do that are working with the same "[people with schizophrenia] genome range" *, in which they can have more confidence than if they had to use a less comprehensive (and potentially contaminated) sample they collected themselves, to establish it themselves. And gratis, because it is published.

*Developed by the swarm of little "basic research grad students", who got the database information gratis.

So, if you still disagree about the merits of my proposal, that's OK, but that's my best exposition of what we are disagreeing about.

And again, you have my gratistude for providing a coherent counterargument.

@Krebiozen:

At this juncture I’m reminded of something I read recently about the growth of PoMo in the social sciences and the attack on natural sciences

I'm pretty deeply invested in the humanities, and I suppose I'm a "leftist," and I see no evidence that this "growth" exists. As in, I have not come across a single person who quibbles with the scientific endeavor in this manner. Maybe there are a few people out there engaged in such a thing, but I have never met a single one.

Granted, when friends start talking about queer theory or "hegemonic something blah blah blah," my eyes kind of glaze over, as it's just not my thing, but I don't really see how "feminist theory" is anti-scientific. It doesn't properly apply to the study of, say, physics, sure, unless we are talking about the study of the culture of physics departments and why they are so heavily male, for instance.

And this:

It is scarcely compatible with the style of education and training that nurtures the average humanist, irrespective of his or her political inclinations.

doesn't even make sense. Or the terms are so vaguely defined as to render the statement meaningless, whatever.

But anyway, if you are referring to zebra, he still hasn't stated what his higher educational experience is in; I doubt he knows any more about postmodernism than he does about anything else.

I'll say it again...if you want to learn, you have to do the work.

You do realize there are people whose entire career is based on unraveling confounding factors inherent in GWAS, right? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1852732/

By the way that article has an actual, real life example of a spurious genotype/phenotype association that was published. This stuff CAN'T be explained via a few comments here. That's why I linked you to a textbook that I legitimately think you would get a lot out of, if you are willing to do the work of reading it.

What you're doing here is the equivalent of going to a particle physicist and saying "I have THE BEST idea! Let's build something that smashes atoms together, wouldn't that be helpful! And it would be gratis for basic research swarms!"

^ I mean, if you take a look at, say, the average university's annual budget, and any budget cuts that have been made over the past ten years or so, the notion that science needs to defend itself from the humanities is pretty hilarious. We would just like to be allowed to exist, mostly. That would be nice.

In any case, a lot of the "scientific" arguments disparaging "humanists" or whatever just strike me as anti-intellectual and absurdly utilitarian*; I wonder if it has ever occurred to any of these guys (and they are mostly all guys) that if you are not interested in something or don't get it, maybe it is not because you are too smart for it.

*I am reminded of a conversation I was having with an engineer friend of mine in which I mentioned that anthropology students often take at least a decade to get a PhD, since they have to do years of field work. His reaction: "That's ridiculous! That means you'll be in your thirties when you get a PhD. And sure, I mean, I guess it's cool that you'll have a PhD and all, but it won't be useful or anything. I mean, come on."

As though the only reason why one might study a culture and make a significant contribution to a field of knowledge is because it will have an immediately practical use...

*I am reminded of a conversation I was having with an engineer friend of mine There's your problem right there.

Krebiozen, I think I can sum up the attitude referred to in your post above in just one sentence.
"We don't understand this, but we're smart, so we don't need to understand it to critique it."

JP,
I don't agree with everything the authors say, and to be honest I got bored with the book after the first couple of chapters (its language reminded me of some impenetrable pomo texts, ironically). It's an oldish book, and I'm aware that it somewhat indignantly tars too many with the same brush, but it has an element of truth in it and I found those passages amusing which is why I shared them.

It does seem snobbish to tell people that they don't understand science well enough to criticize it, but it is also true that it takes years of study to properly understand things like statistics and genetics. It's irritating to those of us that have spent years of hard work learning this stuff to encounter someone who thinks they can simply bluff their way through with the help of Google and Wikipedia.

Hopefully things in the unnatural sciences have improved a bit (post-Sokal) but I was surprised by some of the examples they gave in the book, though they are presumably extreme ones chosen for effect. I experienced some of this in the late 80s when I took a few years out of clinical biochemistry to study social anthropology, and had several heated arguments about whether science is just 'another way of knowing'. I was surprised several times by the scientific ignorance of some of my fellow students and even my tutors.

There really are people who claim that Newtonian and Einsteinian physics were merely expressions of the social conditions at the time (see Stanley Aronowitz's 'Science and Power'), and bear no relation to 'reality'. The number of social scientists who have horribly misunderstood quantum physics and especially the uncertainty principle is depressing.

There is also Bruno Latour whose anthropological studies of scientists are fun, but also contain gnomic statements such as, "“Since the settlement of a controversy is the Cause of Nature’s representation, not the consequence, we can never use the outcome—Nature—to explain how and why a controversy has been settled.” It seems that some people interpret science as nothing more than a cultural construction, but when you ask them how it is that science has led to so many technological innovations they usually fall silent.

BTW, regarding anthropology students taking a decade, I was offered a place to do Master's and a PhD. but I couldn't get a grant because the previous years' students hadn't completed theirs, and the funding body blacklisted my university until they did. I had a wife and child to support so I went back to lab work instead (after a brief sojourn working as a research anthropologist, but that's another story).

It does seem snobbish to tell people that they don’t understand science well enough to criticize it, but it is also true that it takes years of study to properly understand things like statistics and genetics.

This wasn't my point; it takes years of study to understand a lot of things, for one thing, and this:

It is scarcely compatible with the style of education and training that nurtures the average humanist, irrespective of his or her political inclinations.

Still doesn't make any sense. What do they imagine the "education and training that nurtures the average humanist (sic)" to be, and how on earth is it supposedly incompatible with understanding science? I have known "humanists" who went on to get advanced degrees in science or mathematics. They didn't seem to be hobbled in any way by their prior education. (Which also belies the claim that one must "begin young" in scientific training if one is ever arrive at an understanding of a scientific subject.)

As regards snobbery, it does come off as rather self-congratulatory and clueless: we studied science, and it was a lot of hard work, and you just don't realize that. It is as though they are assuming that people in the humanities don't work hard, or don't want to work hard, or don't even understand how hard science is, or something. It's childish and silly.

RE: Bruno Latour: It kind of depends on what era of his writing one gets into. I'm a fan of several of his books, but not so much his earlier work.

I experienced some of this in the late 80s when I took a few years out of clinical biochemistry to study social anthropology, and had several heated arguments about whether science is just ‘another way of knowing’. I was surprised several times by the scientific ignorance of some of my fellow students and even my tutors.

I dunno, maybe things have changed in 30 years, but like I said, I haven't come across this argument. I mean, except perhaps in the rather obvious sense that there are other ways of knowing or ways of studying things; one does not study a sonnet (or whatever) in exactly the same way as one studies a chemical reaction, but it doesn't mean there is no way to study literature, or that the endeavor isn't valid. (It's also the case that there are certain similarities between the study of a poem and the study of a chemical reaction, but that's another subject.)

It seems that some people interpret science as nothing more than a cultural construction, but when you ask them how it is that science has led to so many technological innovations they usually fall silent.

I dunno about the "nothing more" part, but I have a hard time seeing how science could possibly not be interpreted as a social construction. I mean, unless one believes that it was handed down from a pure Platonic realm of reason or something. Clearly science is the product of humans and their culture. I also can't grok the notion that there's any contradiction between the fact that it's a cultural construction and the fact that it's led to so many technological innovations; it's a cultural construction that has led to a lot of technological innovations. That's the only way to think of it that makes any sense, at least as far as I can see.

Oh:

I was surprised several times by the scientific ignorance of some of my fellow students and even my tutors.

And I am often surprised by, say, the ignorance of STEM students and even faculty when it comes to history, literature, art, all kinds of subjects. :) There are a lot of things out there to study: nobody is an expert in everything. Which is to say that I don't see STEM people as being any less prone to stunning Dunning-Kruger effect than humanities types when it comes to "alien" fields of study. Hubris is an equal-opportunity character flaw, I'm afraid.

JP,
I entirely agree that:

It is scarcely compatible with the style of education and training that nurtures the average humanist, irrespective of his or her political inclinations.

is a ridiculous statement. I'm well aware of the excellent work that the majority of social scientists do and of the hard work involved; I'm proud of my social anthropology degree. I'm also sure things have changed in 30 years (thanks for reminding me!) and I think the more extreme pomo attitudes were particularly prevalent in the late 80s at SOAS (where I studied).

It wasn't science itself so much as the model of the universe that science has generated that some people claimed had no relation to 'reality'. I honestly had arguments with people who claimed that the origins myths and other explanations of the world around them related by a hunter gatherer tribe were as valid as what scientists tell us about the universe, and that I was ethnocentric, Eurocentric and racist to argue otherwise.

I have no doubt that cultural factors sneak into science all the time, but claiming that Einstein's equations were merely an epiphenomenon of bourgeois early 20th century society (as Aronowitz appears to do) seems ludicrous to me. I think the scientific method transcends culture (insofar as that is possible).

WRT to the people and science, viewpoints matter*.

Personally, I don't think the Left handles this any better than the right' it is a human failing. The anti-psychiatry crowd is largely left of center with some who identify as Marxist. They're a very intelligent group as a whole and many are found in academia.

However, at many of their blogs, I've seen it too many times to count where scientific studies are critiqued as lies, manipulation, obfuscation or poor methodology as long as it is a point the community disagrees with. Yet they are more than happy to cite studies that agree with their viewpoints without ever looking into the same issues. I would feel more confident of their position if they would acknowledge the flaws in the research that agrees with them as much as they dissect the ones one the opposing side.

A more extreme example of an agenda flipping off science is the push to make carnivores into vegetarians and to stop animals from killing each other. Granted not mainstream environmentalism but who would think of such a thing to begin with. I doubt years ago people were entertaining this thought, and if it continues, it will be a laugh a minute for me until they get hold of a politician or two.

Forgot my footnote @684.

*This discussion fits really well ideas discussed on Orac's most recent post)

@ Not a Troll:

re the "push to make carnivores into vegetarians"

Ha!
I just heard ( PRN) that Paleolithic folk REALLY weren't meat eaters so much because they ate oats! ( Nearly vegan!)

and about 10 years ago, teach your cat to go vegan!**
Seriously. The cat will live to a grand old age!

Someone must have corrected that stupidity because he stopped and changed it to raw diets including fish.

HOWEVER the anti-psychiatry movement just explains itself if you catch my drift.

** don't try this until you want one less cat.

I honestly had arguments with people who claimed that the origins myths and other explanations of the world around them related by a hunter gatherer tribe were as valid as what scientists tell us about the universe, and that I was ethnocentric, Eurocentric and racist to argue otherwise.

Hmm. I guess I can see where a more tempered version of this attitude could be useful in a field like anthropology; certainly origin myths of hunter-gathering tribes, say, are as valid to them as the scientific explanation of the world, if not moreso. I mean, if you are actually studying a culture on its own terms, you can't just dismiss myths as silliness; they're hugely important cultural artifacts, and they have hugely important cultural functions.

Pitting one against the other (i.e., myths vs science) seems more like a category to me than anything else.

I have no doubt that cultural factors sneak into science all the time, but claiming that Einstein’s equations were merely an epiphenomenon of bourgeois early 20th century society (as Aronowitz appears to do) seems ludicrous to me.

I haven't read Aronowitz on Einstein (and likely never will), but if that is indeed his position, I agree that it is silly. I mean, Einstein's equations indisputably are a product of early 20th century society (I dunno about the "bourgeois" part), but they also describe the physical world accurately.* Which is a grand thing.

I think the scientific method transcends culture (insofar as that is possible).

Insofar as that is possible, I guess; but it's still a product of culture. It wouldn't have arisen in a culture that didn't allow for free inquiry, for example. It's not so much that culture sneaks into science, at least from my vantage point, as that the two things can't really be separated. The political climate determines to a large extent what kind of science is funded, for example. And so on.

But yeah: the scientific method is really the only method we have to accurately describe and understand physical, "objective" reality. I'm glad that people came up with it.

*As far as they go, of course, like anything else in science.

**The quotation marks are just the epistemologist in me asserting itself. Sorry/not sorry.

have no doubt that cultural factors sneak into science all the time, but claiming that Einstein’s equations were merely an epiphenomenon of bourgeois early 20th century society (as Aronowitz appears to do) seems ludicrous to me.

I would be astonished if he made that claim, and utterly unsurprised if the word of someone who thought it worthwhile to write a book attacking the academic left was completely unreliable on that point. And probably on most others.

I mean, this...

t is scarcely compatible with the style of education and training that nurtures the average humanist, irrespective of his or her political inclinations.

...is what I would call ludicrous. Good scholarship is good scholarship.

Obviously, some -- indeed many -- academics are fools. But that's not any commoner or less common in any department or discipline than it is in any other, in my experience and observation.

Furthermore, it doesn't reflect very well on the training and education that nurtured the authors that they think this is an A-OK tactic:

We speak not only from an acquaintance with the literature, but from regular experience of lectures, seminars, and symposia, where speakers tend to say more directly what they think than they do in print,

Oh, really? You have secret knowledge of stuff that's not in print? Please allow me to join your cult!

...

There really are people who claim that Newtonian and Einsteinian physics were merely expressions of the social conditions at the time (see Stanley Aronowitz’s ‘Science and Power’), and bear no relation to ‘reality’.

Seriously, do you have a quote that bears that out? I just glanced at a little bit of Science as Power online, and it does not look any likelier to contain statements that daft than I would have expected.

I give up. I'm surprised this thread has gone on so long. I don't have the stamina to try and educate Zebra on the genomics of birth cohorts or the difficulties in linking complex diseases that have a gene-by-environment flavour.

So you collect genomic data on millions of kids. You don't see the need to collect any other data aside from health records and let’s say on of your diligent grad students decides to study the association between schizophrenia and genes at age 25. How will you explain that less than half of your identical twins with schizophrenia have their twin also develop schizophrenia? Maybe it's because one of the twins smoked too much pot when they were 17. Maybe it's because the twins were adopted out at birth and were raised in different families, thus had different socioeconomic upbringings, different schools, different???. Maybe one of the twins suffered more traumatic events than the other (car crashes, divorce, death of a child, job loss...). Most of the time you will never know, as you haven’t actively monitored environmental and socioeconomic info. Maybe you should try to better familiarise yourself with the concept of 'complex diseases', which are in fact most diseases except some rare Mendelian ones. Though NGS data is a wonderful thing, we still need a lot more basic biology and environmental understanding to make the best use of it. We need better diagnostic criteria for sure. Is all heart disease the same? Is high blood sugar and insulin resistance a single disease? Is all schizophrenia, depression or bipolar disorder the same disease? Is all breast cancer the same? The clear answer is no.

This is aside from all the ethical issues involved, which are many.

Seriously, do you have a quote that bears that out?

There was this:

Harding referred to Newton's Principia Mathematica as a "rape manual" in her 1986 book "The Science Question in Feminism"

Sokal and Bricmont accused Luce Irigaray of describing E=mc2 as a "sexed equation" because "it privileges the speed of light over other speeds that are vitally necessary to us" -- but it's not clear whether she actually wrote that.
https://www.reddit.com/r/askphilosophy/comments/2hu5sb/did_luce_irigara…

@#690 --

I meant "a quote from Aronowitz."

I don't doubt that it's easy to find stupid quotes from identity-politics-oriented leftist academics. Or to cherry-pick them,, as the case may be. And while I'm not sure that's a fair characterization, I'm not sure it's not. Because I am sure that left-wing humanities professors are not actually any kind of threat to science.

However. Be that as it may. It's been a long time since Sokal's little exercise in trolling. The menace to progress that was Social Text has evidently been tamed. Everything's fine. Why is it necessary to keep stomping the queer and feminist theorists?

What bothers me is really that from what I know of Aronowitz, which is limited, he's a perfectly good thinker whose most prominent distinguishing characteristic is that he's unreconstructed, old-school left, through and through. That he's such a favorite target makes me suspicious. I find it very hard to believe that it's not just a political act, masquerading as something else.

Also, as I've said before, Sokal made a bad impression on me from the get. I feel that if he really wanted to do something for science, he should have published something in his own damn field.

That the feminist theorists are always in there also raises a little bit of a red flag, tbh. There's certainly no shortage of idiotic feminist theory. But feminist-bashing does not have a good pedigree.

I actually know the work of Aronowitz's late wife, Ellen Willis, better than I know his. Speaking of feminists. She did very good work.

Sokal and Bricmont accused Luce Irigaray of describing

Well. Burn her, I say!

Come on. If they're so fragile that they're threatened by what some French feminist theorist that virtually nobody has ever heard of wrote in 1974, the problem is not on the academic left's side. I mean, how did that statement injure science, precisely? Sokal and Bricmont probably did more to promote it than she did..

Sokal and Bricmont accused Luce Irigaray of describing E=mc2 as a “sexed equation” because “it privileges the speed of light over other speeds that are vitally necessary to us” — but it’s not clear whether she actually wrote that.

The Speculum of the Other Photon? Perhaps this really comes down to polarization.

Simply put, my take on Sokal is basically:

I don't doubt that NYU gives Stanley Aronowitz all kinds of love and attention that it doesn't give Sokal. But as far as I can see, that isn't because leftist gangs got together and devalued science. It's because Stanley Aronowitz is a much more accomplished and productive academic than Sokal is.

I mean, it's not the Cultural Studies department's fault that he hasn't done star quality work. They didn't even exist for most of the time he wasn't doing it.

If they’re so fragile that they’re threatened by what some French feminist theorist that virtually nobody has ever heard of wrote in 1974

I read some Irigaray as an undergrad, almost a decade ago; my recollection is that I found her work interesting, if obnoxiously essentialist, which I think was my general feeling toward a lot of French feminism of the era. I confess to not having them revisited them recently; it could be an interesting exercise.

Speaking of anthropology, I actually read Irigaray in a class taught by an Evergreen professor who had gotten her PhD in anthropology in the 70s-early 80s, if memory serves. She got interested in feminism, epistemology, post-colonial theory, etc., because of her experience in anthropology; she related stories of having male colleagues pour out all kinds of personal difficulties they'd encountered in field work, sometimes literally crying in her lap.

The question of how possible it is to be "scientifically objective" during serious anthropological field work is certainly an interesting one. It definitely comes up in discussions over drinks with anthropology PhD student friends, especially wrt to sticky and sometimes traumatic experiences during field work.

Oh, and wrt to anthropology students taking a decade to finish (at least), that's come up in discussions recently as well, with the university administration having recently decided to attempt to push a five-year finish time for PhD students across many fields. The issue is that it is generally understood that a PhD in anthropology will take substantially longer than this, and that current candidates entered the department under that general understanding.

Academics of the world unite: you have nothing to lose but your administrators!

@Not a Troll #684:

A more extreme example of an agenda flipping off science is the push to make carnivores into vegetarians and to stop animals from killing each other. Granted not mainstream environmentalism but who would think of such a thing to begin with. I doubt years ago people were entertaining this thought.

You've never seen the 1989 film "Shirley Valentine", I assume. One of the jokes has Shirley Valentine (Pauline Collins) pet-sitting a bloodhound. Said bloodhound's owners say that the dog is vegan. Now, I know life sometimes imitates art, but I would guess that that is at least partly based on reality.

@ Denice #686

I just heard ( PRN) that Paleolithic folk REALLY weren’t meat eaters so much because they ate oats! ( Nearly vegan!)

Wait, aren't cereals of any type definitively NOT paleolithic diet?
I think PRN got confused when someone told them that paleolithic people were huge believers in sowing their wild oats.

@ JP, ann and a few others

Speaking of anthropology

Nothing meaningful to add to your discussion, but to say I am learning lots about anthropology and other social sciences, beyond the clichés. Please continue :-)

I'm going to restore the original boldface here:

I would oppose them [undefined, but apparently supposed to be related to comments 412 and 414] because* I empathize with people suffering, [sic] and because, even if I am not directly involved, it causes disruption in the society. You can’t really be isolated from things– it’s like when the cop shoots the black guy for no good reason. Everyone picks up the tab, in multiple ways.

I have to say, I not only don’t see the problem with that, I think it’s an ingenious and viable work-around for the objectivist-libertarian tendency towards callous indifference — ie, it’s in your self-interest to oppose bad acts against.others because it could be you.

My real ire was drawn by Z.'s nonsensical assertion that he "empathize[s] with people suffering." This literally doesn't mean anything, and Z. immediately abandoned it in favor of "discovering" some sort of monetized or convenience-oriented version of... the categorical imperative.*

This isn't, in legal terms, "field preemption." It's stark idiocy. Nothing has gone before in Z.-land, or if so, it's The Wrong Century, or Needlessly "Compicated," or stop writing about this distraction from the Z. vision, stupid Orac.

Z.'s enthusiastic construction of what he imagines to be monuments to his pure brilliance at this point reminds me of neither more nor less than the beginning of The Monkey Wrench Gang, with the caveat that I'd be much more charitably inclined toward a billboard for an independent podiatrist.

* I inadvertently omitted this "because" in the original quote.

Now, I know life sometimes imitates art, but I would guess that that is at least partly based on reality.

Yah, dogs. I would strongly advise against inadvertently bringing up Camille Marino.

sticky and sometimes traumatic experiences during field work.

I don't want to behalf in this drunken and erratic way, but in the interests of the fieldwork I must try to blend into the milieu.
The ship was supposed to arrive and take me home but it is long overdue. Getting worried here.

I wish I hadn't posted those quotes from Gross and Levitt, as I have no real interest in supporting their attack on what they term 'the academic left' They do spend some time (perhaps a little too much) explaining that they are not taking a political stance, and I should perhaps add that my personal politics are mostly leftist-liberalish. It was just that their exasperation with those attacking science without understanding it resonated with how I felt about zebra's attempts to bluff his way through genomics and then statistics.

However, since I have stumbled down this road, I may as well be hung for a sheep...

Gross and Levitt don't give many direct quotes (understandable given Aronowitz's somewhat impenetrable style) but they paraphrase Aronowitz as follows:

To take but one example from among several dozen—and we stress that it is entirely typical in its pugnacious illogic—we hear Aronowitz denounce the idea that Einstein conceived special relativity by sitting around the cafes of Bern and meditating upon the Michaelson-Morley experiment. It is an idle legend, Aronowitz asserts, a mystification designed to conceal how the social, political, and economic currents of late-nineteenth-century European capitalism and imperialism brought to birth the theory now famously associated with Einstein. Similarly, he tells us how the development of celestial mechanics by upper-class gentlemen-scientists such as Newton cannot be understood apart from an analysis of seventeenth-century mercantilism.

Without reading the passages they refer to it is impossible to assess the accuracy of this claim. I did find this in Chapter 12 of 'Science and Power' (the only part I can find online), as perhaps one example of what Gross and Levitt claim:

Since we can only calculate effects and infer causes, control and predict behavior by constituting the object of knowledge theoretically and changing it in the process of our intervention, I argue that the so-called laws of nature are better described as laws of science. Scientific theory describes the relation of humans to the object of knowledge, not the objects themselves, taken at a distance. Further, our knowledge of effects is always mediated by the logic of scientific discovery, e.g., by its concepts of causality as a part of the apparatus of discovery.

I find it hard to conceive of gravitational theory, for example, as describing the relation of humans to gravity, not gravity itself.

Here's another quote from 'Science and Power':

That scientific facts are constituted socially as well as technologically infers that science is an intervention in both senses. This means that the object is constituted as a relation between the ends of scientific inquiry and its means. As Fleck demonstrates, facts are produced, not discovered.

To be honest I'm not entirely clear what Aronowitz is suggesting here (despite having spent three years learning to understand that kind of language). It does appear to me that he is claiming facts have no objective reality, whereas I would argue E=MC^2, for example, is indeed "discovered" not "produced". If that particular equation was "produced" out of whole cloth, how is it that nuclear fission works?

I also noticed a footnote in Chapter 12 that states:

Werner Heisenberg, Physics and Philosophy (New York: Harper and Row, 1958), p. 9: “we know the object of scientific knowledge only by the speculative means of axiomatic theoretic construction or postulation: Newton’s suggestion that the physicist can deduce theoretical concepts from the experimental data being false.” This theory, in common with the Duhem-Quine hypothesis discussed in chapter 9, has, nevertheless, escaped most natural and social scientists as well as their philosophical acolytes.

That didn't sound right to me, so I tracked down the quote here. What Heisenberg actually wrote was, in context (my emphasis) :

But, why, it may be asked, should the concept of probability be introduced into the theoretic definition of the state of a mechanical system at any statical moment t1 in principle? In making such a theoretical construct by axiomatic postulation, do not Heisenberg and quantum theoreticians generally beg the question at issue between themselves and Einstein? This book makes it clear that the answer to these questions is as follows: The reason for the procedure of quantum mechanics is thesis (1) above, which Einstein himself also accepts.
Thesis (1) is that we know the object of scientific knowledge only by the speculative means of axiomatic theoretic construction or postulation; Newton's suggestion that the physicist can deduce our theoretical concepts from the experimental data being false. It follows that there is no a priori or empirical meaning for affirming that the object of scientific knowledge, or, more specifically, the state of a mechanical system at a given time t1 , must be defined in a particular way. The sole criterion is, which set of theoretic assumptions concerning the subject matter of mechanics when pursued to their deduced experimental consequences is confirmed by the experimental data?
Now, it happens that when we theoretically and in principle define the state of a mechanical system for subatomic phenomena in terms solely of numbers referring to position and momentum, as Einstein would have us do, and deduce the consequences for radiation from black bodies, this theoretical assumption concerning the state of a mechanical system and the subject matter of atomic physics is shown to be false by experimental evidence. The experimental facts simply are not what the theory calls for. When, however, the traditional theory is modified with the introduction of Planck's constant and the addition in principle of the second set of numbers referring to the probability that the attached position-momentum numbers will be found, from which the uncertainty principle follows, the experimental data confirm the new theoretical concepts and principles.

Firstly Aronowitz omits the word "our" from the quote, changing its meaning substantially from referring very specifically to subatomic phenomena, to experimental data in general. Heisenberg makes it clear that when Planck's constant is introduced "the experimental data confirm the new theoretical concepts and principles". It does look to me as if Aronowitz has misquoted and grossly misinterpreted Heisenberg in precisely the way Gross and Levitt claim.

Oops, only "subatomic phenomena" was supposed to be bold.

@ Helianthus:

Heh. Exactly.

PRN's head honcho has however, an agenda which involves re-writing all scientific fields to fit his hobby horse's needs so why not change this as well?

Supposedly scientists have got it all wrong:
- the paleo diet included oats ground with a pestle, little meat
- the Mediterranean diet is REALLY vegan
- cats can be vegan ( Oooops! Fix that one)
- if everyone became vegan, it would have a great impact upon AGW's effects
- veganism prevents/ cures cancer and all other ills

.

I can't believe I wrote "hung for a sheep", I meant "hanged", not "hung". It isn't important but it's one of my bugbears - my neurological functioning isn't at its best at present.

I read some Irigaray as an undergrad, almost a decade ago; my recollection is that I found her work interesting, if obnoxiously essentialist,

I'm not 100% sure whether it's really essentialist or merely unfortunately capable of being understood that way. But that might be an excessively nuanced distinction, in that the latter case would just mean the essentialism was reflexive and unexamined.

I agree that it's interesting. In fact, IIRC, some of it's incredibly good. It's been a while, though.

Based on the parts of the essay from which Sokal/Bricmont chose to pick a statement by her at which to laugh and point that are freely available on line, I would say that they're doing exactly what they're accusing her of -- ie, throwing rocks at something they know little about and aren't qualified to understand, out of purely personal hostility and arrogance.

It would not surprise me if the same was true for most of their targets.

But even without reading the whole thing, it's completely clear that she's not saying "Mass-energy equivalence is an artifact of the patriarchy! Take back the universe!" She's talking primarily about how culture informs language, and hence perception.

It's somewhat subjective. But as I read it, at least, that thing about the speed of light being privileged is not intended to be taken entirely serious. She's being provocative.

There's a defense of her work here:

http://www.newstatesman.com/voices/2014/05/jane-clare-jones-luce-irigar…

"entirely seriously"^^

I find it hard to conceive of gravitational theory, for example, as describing the relation of humans to gravity, not gravity itself.

That's not what he means. I'm running out now, and I don't want to express it imprecisely. But I'll give it a (probably inadequate) go:

He's just saying that the way people perceive/conceive of the world is culturally informed. There is thus an inherent distinction between the world as it is (nature) and knowledge of the world as it is (science).

^^Just as I thought. Inadequate. I'll give it another try later.

It does appear to me that he is claiming facts have no objective reality,

No. He's claiming that they acquire a subjective dimension when they're discovered/described. But he's not saying they're objectively untrue or non-factual, therefore. He's just saying that all human endeavor occurs in the context of culture, including human understanding.

Or maybe "human knowledge" -- ie, science.

It's not as hostile as you think it is. He's on the side of knowledge.

The last quote appears to be a mistake, though. And probably a stupid one on his part. I'd say that overall, Sokal's thinking is exponentially sloppier however.

Retro Pump @689.

Yes, this thread is still going. It's not possible for me to learn genetics on this forum or most likely any other method, however, where I was leading in acting for a simpler example of where cofounders make/made all the difference is a question of logic and an educated guess.

It appears that zebra would be happy to learn almost half of the identical twins both have schizophrenia and then have some grad students launch into a research project on why this is so or why isn't this percentage higher in identical twins. To him this wouldn't even be known without the existence of his database and the brute force of numbers he is counting on to generate leads to research projects.

The logic question comes into play on where the tipping point is between a streamlined database with less data that can be matched but less time spent on teasing out correlations and more time spent on research projects vs one with enough data so that technology and statistics can be used to narrow down true correlations as much as possible before a research project is begun but where there are more security and ethical issues.

Who knows where that tipping point is but it appears that the PMI is aiming for the more robust database.

where I was leading in asking

Apologizes for my atrocious typos of late. Not exactly sure why that is.

ann,

"It does appear to me that he is claiming facts have no objective reality,"
No. He’s claiming that they acquire a subjective dimension when they’re discovered/described. But he’s not saying they’re objectively untrue or non-factual, therefore. He’s just saying that all human endeavor occurs in the context of culture, including human understanding. Or maybe “human knowledge” — ie, science.
It’s not as hostile as you think it is. He’s on the side of knowledge.

I understand what you are saying but I'm not at all convinced. Aronowitz may be on the side of knowledge, but he doesn't seem to think that science is capable of uncovering any. What else does he mean when he says scientific facts are "produced" not "discovered"? I'm pretty sure the planets were obeying Newton's laws of motion long before he "produced" them. Then he comes out with statements like this:

Speculative philosophy refuses to go away, despite its intentions, because physics, mathematics, and biology, the three sciences that have generated the controversy, are themselves rent. Nonclassical physics continues to make discoveries, but the actors cannot agree on what they have found. Or, to be fair, they are unable to render clearly the significance of the products of scientific discovery because the framework of understanding is in contention.

It does look as if he is claiming that "physics, mathematics, and biology [...] are rent" (i.e.torn into pieces), because of Heisenberg's uncertainty principle. I wasn't aware that quantum physics had led to the entire framework of understanding of science to be in contention.

He also writes:

The imputation to nature of characteristics that are nothing more than the objectivization of the table of organization of the social world has imparted to both the appearance of natural facts as well.

So science "produces" the appearance of "natural facts" that are really "nothing more than the objectivization of the table of organization of the social world". I struggle to find any other way to interpret this than that Aronowitz is claiming that science doesn't discover real facts about objective reality.

BTW, I had forgotten just how frustrating this kind of writing is. It really seems to me that it deliberately makes its meaning obscure, and to make people feel dumb if they can't make sense of it. Presumably I can't be too dumb in this area since I got a decent grade and was encouraged to continue my studies, but who knows?

The last quote appears to be a mistake, though. And probably a stupid one on his part. I’d say that overall, Sokal’s thinking is exponentially sloppier however.

I think it's worse than that. He seems to have utterly misunderstood quantum physics and is basing a large chunk of his writing on that misunderstanding.

I’d say that overall, Sokal’s thinking is exponentially sloppier however.

Are you referring to his hoax, or his writing generally?
Personally I find Sokal's more usual style of writing, for example this article about his notorious hoax, to be far clearer and more incisive than Aronowitz's (for example the chapter of 'Science and Power' I linked to above), but of course YMMV.

That scientific facts are constituted socially as well as technologically infers that science is an intervention in both senses. This means that the object is constituted as a relation between the ends of scientific inquiry and its means. As Fleck demonstrates, facts are produced, not discovered.

To be honest I’m not entirely clear what Aronowitz is suggesting here (despite having spent three years learning to understand that kind of language).

I was following it in the sense of Representing Electrons (book review; PDF) up until the last sentence.

It does appear to me that he is claiming facts have no objective reality, whereas I would argue E=MC^2, for example, is indeed “discovered” not “produced”. If that particular equation was “produced” out of whole cloth, how is it that nuclear fission works?

Speaking of fission (PDF),

"If we are to doubt the findings of the empirical sciences, we need to be given better reasons than that they have arisen from and been a necessary adjunct to capitalist social relations. Even if this latter is the case (and I doubt that it is, at least in the global, undifferentiated manner Aronowitz asserts), scientific discoveries could still give correct descriptions of (certain features in) nature. That the nuclear-power industry has attempted to impose on us a grossly undemocratic and capital-intensive form of energy production [If you say so] is no grounds for thinking that controlled fission reactions are just a capitalist plot."

Are you referring to his hoax, or his writing generally?

I'm referring to his thinking, as reflected in both. But that's kind of awkward, because you agree with him. Although your iteration of it is honest, warm and intelligent, which does make a difference. And not a small one.

I really don't want to bicker with you, or offend others here who admire and/or agree with Sokal. But fwiw, briefly:

What else does he mean when he says scientific facts are “produced” not “discovered”? I’m pretty sure the planets were obeying Newton’s laws of motion long before he “produced” them.

I sincerely do not understand Aronowitz to be disputing or questioning that.

I think that that when he says facts are "produced" not "discovered," he most probably just means that they're a form of capital -- ie, science is the means of production, facts are the product. If so, it has no implications for their factual-ness, one way or the other.

I would have to read the whole book to be sure, though. That's just the meaning that seems likeliest to me.

The imputation to nature of characteristics that are nothing more than the objectivization of the table of organization of the social world has imparted to both the appearance of natural facts as well.

It's almost impossible to say what that means, absent context. And I'm not sure how much context would help, tbh.

However, I would again read that as simply meaning that objective facts acquire subjective dimensions and connotations when they're described and formulated by human beings operating within the boundaries of the culture to which they belong.

It would really be such an enormous departure from form for him to be saying anything remotely like "facts don't exist!" as to border on too bizarre to be credited. I mean, he's a Marxist activist-intellectual. You can''t really count on his ideas being sensible. But you can at least count on their being oriented to three, wrt basic reality-testing.

Maybe I'll read the book. But I'm almost sure that his target is power, not science. Because Marxism.

BTW, I had forgotten just how frustrating this kind of writing is. It really seems to me that it deliberately makes its meaning obscure, and to make people feel dumb if they can’t make sense of it. Presumably I can’t be too dumb in this area since I got a decent grade and was encouraged to continue my studies, but who knows?

It's difficult to get through. And I agree it's frustrating. Hateful, even. But I don't think it's deliberate, in his case. I think he's actually trying for clarity and precision, believe it or not.

Personally I find Sokal’s more usual style of writing, for example this article about his notorious hoax, to be far clearer and more incisive than Aronowitz’s

It's clearly stated. But it's the opposite of incisive. He's fine through to the "So what?" But after that, it's unknowing bias all the way.

I realize that he probably doesn't know what he doesn't know. Even still, though. He's making fun of stuff he doesn't understand, which he's selectively quoting for that very purpose. He's going out of his way to do it. And that's just not admirable, imo. It isn't and can't be productive of anything good.

I would personally say that some of his subjects are quite dreadul -- even arguably fraudulent -- on their own terms. I think Lacan is just awful, for example. But, you know, nobody has to read him if they don't feel like it.

I frankly agree with Andrew Ross, as quoted by Sokal at that link. Maybe he himself (Sokal) doesn't realize it, though. I don't know.

@Narad --

Speaking of fission (PDF)

It was nice to see Richard Rorty's name. I knew him growing up. I don't think he was a big deal yet at the time, but I might not have known. I was only, like, eight.

I tried to read an essay by him ten years or so ago. But I couldn't understand one word of it.

That the nuclear-power industry has attempted to impose on us a grossly undemocratic and capital-intensive form of energy production [If you say so] is no grounds for thinking that controlled fission reactions are just a capitalist plot.”

Maybe I'm the only person on earth who thinks it. But nevertheless. I do think that he's not asserting that they're just a capitalist plot in the sense of "they are nothing but an abstract illusion, invented by capitalism for capitalist purposes." He means functionally.

ann,
I'm more than happy to agree to disagree about Aronowitz and Sokal. I have no strong feelings either way, and in some ways I agree with Aronowitz more than I do with Sokal. Despite being very funny, I think Sokal's hoax was a nasty trick for a physicist to play on social scientists who understandably assumed he was sincere. I also think that far more of our experience and our beliefs are culturally constructed than we generally realize, that metaphors (and the reality) of power, privilege and (white, older) male domination visibly and invisibly pervade our culture. I think you can find traces of that hegemony (cringe) in all sorts of cultural artifacts and detritus, including which scientific subjects exist and are studied, what gets published, which scientific findings are easily accepted, which are not etc. etc..

However, I struggle to see the influence of 17th century mercantilism in Newton's equations, or of early 20th century Europe in Einstein's. Would those equations be any different if an Arabic, Japanese, Russian or Indian scientist had "produced" them?

I remember during my anthropological studies, when we looked at Freud our professor (a woman who had studied as an Indian Saddhu and chain-smoked bidhis while she lectured) suggested we assess his work as if it were fiction, as literary critics, rather than fact, which I think helped. I wonder if the work of scholars like Aronowitz is better read as a sort of intellectual poetry.

I can follow the passages Narad linked to, though the first gives me nasty flashbacks to the semiotics class* I took, and what I read of the second before wearying baffled me a bit (WTF does "underlabour " mean?). Do physicists still regard electrons as "theoretical entities"? I struggle to see why writing a biography of the electron is any different to writing a history of the scientific understanding of the electron. I can see some products of science, like the technological process to produce aluminum for example, as products in the Marxist sense, but the concept of an electron (cloud)?

* Perhaps I have a somewhat simplistic view of the signified, the signifier and the signal - is it really enough to base an entire field of study on? I had the very strong sense that the semiotics texts I read were simply trying to confuse me with long words of which I had learned to understand the meaning, but still couldn't parse into anything meaningful in the sentences they were arranged in. Coming from a natural science background I was used to words and sentences having specific, unequivocal meanings, and found this confusing. I still have the uncomfortable, lingering feeling that there is some meaning in there that I have failed to grasp; I get a similar feeling reading zebra's utterances at times. I can't help wondering if some social scientists (and some commenters here) look at the sometimes impenetrable language of the natural sciences and construct a sort of cargo-cultesque simulation.

I think Lacan is just awful, for example.

I feel that I should be defending Lacan here, out of sheer contrarian perversity, because everyone hates him, but I can't.

@Krebiozen --

You're not only very smart and very gracious, but a better writer than Sokal, Aronowitz and myself at their best combined. There's very little in your last post that I disagree with, although I diverge from most of it somewhat, just as a function of having my thoughts and not yours, if you know what I mean.

So although it's very minor, the only thing I'd humbly ask you to reconsider is this:

However, I struggle to see the influence of 17th century mercantilism in Newton’s equations, or of early 20th century Europe in Einstein’s.

Per Gross and Levitt, what Aronowitz actually said about Newton was that he "cannot be understood apart from an analysis of seventeenth-century mercantilism."

There is nothing PoMo about Stanley Aronowitz's work. He's a Marxist theorist. Marxist analysis is socioeconomic. That he said that Newton could not be understood apart from an analysis of seventeenth-century mercantilism therefore almost couldn't be more Marxist.

It has nothing to do with the influence of mercantilism on Newton's equations, and suggests no such relationship. It's just straight-up historical materialism.

And that's as good an example as any of what I dislike about both Sokal and Sokal's popularity in the skeptical community. He has a bias. It caused him to misconstrue the evidence he was examining. He created a myth based on his misconstruction. And as people are wont to do when myth-making, he invested it with emotional properties that he and others who see the world more or less as he does are bound to find both compelling and gratifying.

So naturally, they subscribe to it. And that's really what I care about. Because it's a myth based on personal bias, and that's never helpful.

That leaves me in kind of an odd position, in that I end up defending a kind of work that I myself have no real affinity for and frequently dislike, in many regards.

But what can you do? If the worst consequence of it is that you now read Aronowitz in a state of Marxist-theory blindness that leaves you unable to imagine what he means by "produce" if it's not what Sokal et al. think it is, I suppose that's not so bad.

But fwiw, seriously. I'm 99% sure that he means "produce" in the Marxist sense of the word. Because he's a Marxist.

The fancy, excessively complicated French theorists are up to something else entirely. And while (funnily enough), I personally think Freud can best be read from a quasi-Marxist perspective, I agree with you generally that that sort of thing works better in art. Ceci n'est pas une pipe. Pale Fire. Etc.

Everybody should therefore have artistic talent bordering on genius. Problem solved!

ann,

You’re not only very smart and very gracious, but a better writer than Sokal, Aronowitz and myself at their best combined.

I'm gobsmacked at that - you are too kind! If you are correct in your interpretation of Aronowitz then I agree with you - of course Newton wouldn't have been in a position to study science at all absent his social, economic and historical context - but I will still grumble that Aronowitz could have made himself a bit (or a lot) clearer.

Incidentally, Newton was not the 'gentleman scholar' of independent means I always assumed, He was a farmer's son who worked as a subsizar (a sort of servant) at Trinity College to fund his studies before getting a scholarship.

Oh, what the hell. I really do object to it. So. Again. Simply put:

That Sokal doesn't (and evidently can't) distinguish Marxist theory from deconstructionism makes him guilty of exactly what he's accusing his targets of doing -- ie, swaggering into an unfamiliar field and saying "Oh, pish-tosh, what errant nonsense," when, in fact, he has no idea what he's talking about and doesn't understand the material at even an elementary undergraduate level.

To make matters worse, as far as I can see, most of the time his targets actually aren't doing what he accuses them of.

Therefore, the difference between Sokal on the academic left and Stanley Aronowitz on Heisenberg is that Heisenberg is not Aronowitz's primary focus or -- properly speaking -- his subject. So his work doesn't rise or fall on the error.

Kreb says:

"- is it really enough to base an entire field of study on?"

No.

Hilariously, I had to translate stuff like that as a degree requirement. And I was hoping for Piaget- silly me

At any rate, wouldn't it just be easier to say that our thoughts/ words don't correspond 1:1:1 to "reality" ( whatever that is) and we should just be aware of it and call it a day?

That to which we attend acquires increased significance to US but maybe not others. Cultures do that as well.

I am reminded of an old Confucian saying which states it much more eloquently which I suspect catches the drift but I never could get the words straight.

I'm not being entirely serious.

but I will still grumble that Aronowitz could have made himself a bit (or a lot) clearer.

Most academics are not particularly gifted writers, sadly. I was really being way too snippy about Sokal in that regard before. He writes quite well. The problem is really that he's not a gifted reader.

I'm inclined to believe that his intentions were more innocent than his actions. And I suppose it's possible that he targeted the political left because it was there.

But I can't really say much else about him that's good. There were (and still are) plenty of people both within the academy and elsewhere who'd like to see cultural studies go away because they don't like having their campuses sullied by what I once heard somebody characterize as "professors of hip hop." Which meant "black people," in context.

So, you know. He's entitled to his opinion, that goes without saying. But where there are real consequences, there are also real responsibilities. Intellectuals aren't exempt from that. At the very least, he could have been more diligent.

At any rate, wouldn’t it just be easier to say that our thoughts/ words don’t correspond 1:1:1 to “reality” ( whatever that is) and we should just be aware of it and call it a day?

I actually very recently came to realize that there was more to semiotics than I'd been condescendingly thinking, lo these thirty-plus years. But I think the reason I underrated it was that completely idiotic and unnecessary semiotic analysis was so vogueish when I was in school.

So I think I agree with you.

makes him guilty of exactly what he’s accusing his targets of doing — ie, swaggering into an unfamiliar field and saying “Oh, pish-tosh, what errant nonsense,” when, in fact, he has no idea what he’s talking about and doesn’t understand the material at even an elementary undergraduate level.

Exactly.

Additionally, I am somewhat confused as to why many people seem to be offended by the notion that, say, Einstein's equations are the product of early 20th century culture. It's something that seems to me almost trivially true; Einstein was a product of early 20th century culture, for one thing. A real-life Mowgli would hardly be a practicing physicist, I think, what with the difficulty in acquiring language after the critical period.

It doesn't make Einstein any less brilliant or his equations any less correct. I can't really see how describing something accurately is an "attack" on it.

I mean, we are all communicating with each other by means of the Roman alphabet, which is a product of culture. We are products of culture. Almost everything we use, interact with, eat, etc., on a day-to-day basis is a product of human culture.

Like I said: the plain fact of it is almost trivially true. The specifics, I think, could be a worthy and interesting thing to study, if somebody were so inclined.

@ ann:

Believe it or not, I have an undergrad degree in a *liberal art*, although it also includes a great deal of life science/ social science, it was loaded with lit/ writing, visual arts and philosophy.
While I was later pursuing degrees in social science, one prof encouraged me to write about the psychology of visual arts which I did in order to fulfill independent study/ seminar requirement and up my street cred.

Thus I read semiotics and Gestalt works about art - graphic representations of emotions, some aesthetic styles and personality etc etc. At least HE liked it.

I do maintain a fond place in my heart for 'culture and cognition' but it is far more mundane than what is usually considered- purely that we pick and choose what we include in our own construction of the world- which exists quite independently despite our efforts.

I know that Eskimaux/ Northern Aboriginal People? have many words for snow but I don't think that that necessarily changes what they actually SEE in a physical sense but they do attend to snow more and spend more time thinking about snow in all of its variability.

OBVIOUSLY there's a lot more about Pomo ** which I have dis-remembered with great effort.
-btw- you can selectively forget but it ain't easy.

** but not the tribal folk who make baskets

I know that Eskimaux/ Northern Aboriginal People? have many words for snow but I don’t think that that necessarily changes what they actually SEE in a physical sense but they do attend to snow more and spend more time thinking about snow in all of its variability.

Eskimo or Inuit, mostly. It depends on which people you're talking about.

But anyway: are you sure about that? What does it mean to see something? We are not camcorders, after all. Vision is something that happens in the brain, although the eyes are of course a necessary component.

Russian, for instance, has two words for what we would call in English "blue": sinii and goluboi. The first one refers to a darker blue, and the second one to a lighter blue, but they are two different colors to a Russian speaker, the same as red and pink are to us. As it turns out, Russian speakers actually can distinguish shades of blue more quickly and accurately than English speakers can. Certainly the physical properties of whatever colored thing they are looking at are real physical properties "out there,"* but are Russian speakers and English speakers really seeing the same thing?

There are languages which use cardinal directions (PDF) rather than relational directions when describing where something is, and when thinking about where something is. I imagine speakers of those languages see things rather differently than I do.

*I had best not get started on this.

JP,

Additionally, I am somewhat confused as to why many people seem to be offended by the notion that, say, Einstein’s equations are the product of early 20th century culture.

I don't think that's the notion people are offended by, it's the notion that Einstein's equations bear no relation to any objective reality. Whether that notion exists other than as a misunderstanding of some dense Marxist or pomo texts I am still unsure. I shan't lose any sleep over it :-)

Sapir-Whorff hypothesis?

Or even Sapir-Whorf hypothesis.

Sapir-Whorff hypothesis?

More or less, yeah. I mean, I would say that languages differ primarily in what they force people to attend to, like the gender of people doing verbs in Slavic languages, cardinal directions in certain aboriginal languages etc., rather than what they can express. But it does seem to me that language sort of inescapably shapes our cognition, perception, etc., at least to an extent. And of course our communication.

@ JP:

Sure. The language might lead a person to differentiate more; similarly an English-speaking artist might be more attuned to differences although there are not two words I English ( he/ she uses *qualifiers*- lighter/ darker- more, as well as other dimensions).
Still, the proximal stimulus is a particular tone of blue - some may attend to its particular-ness more or less. Similarly, skiers see different snow/ ice conditions. It's what is attended to that determines the situation and labels, not just what is seen physically.

We use the word "see" to stand for different levels -
what's on the retina, what we perceive it to be, then, as an opinion ( how we imagine/ surmise it)- " I see that he's on to his usual routine again".**

Then again, there's See Noevo.

** I shouldn't get into this either.

JP:
Ha! We crossed paths in cyber space.
Way to go!

And I must GO as I am expected elsewhere and need to do something about my hair.

"That the nuclear-power industry has attempted to impose on us a grossly undemocratic and capital-intensive form of energy production..."

Hm? How's that again? How many non capital-intensive forms of energy production can support modern society's 24/7 electricity needs?

I know that Eskimaux/ Northern Aboriginal People? have many words for snow but I don’t think that that necessarily changes what they actually SEE in a physical sense but they do attend to snow more and spend more time thinking about snow in all of its variability.

Eskimo or Inuit, mostly. It depends on which people you’re talking about.

I thought the snow trope – which involves Whorf starting the game of Telephone from Boas – had been laid to rest some time ago (certainly when I was in grad school).

But anyway: are you sure about that? What does it mean to see something? We are not camcorders, after all. Vision is something that happens in the brain, although the eyes are of course a necessary component.

This is more HDB's area, but most visual processing actually occurs in the retina.

^ Oh, it also turns out the W—dia mention of the Himba under "Color Vision" is, y'know, plain dumb.

I thought the snow trope – which involves Whorf starting the game of Telephone from Boas – had been laid to rest some time ago (certainly when I was in grad school).

I'm not the one who brought it up, and I thought about mentioning that it is more of a cliche than anything, but I was mainly responding to what seemed like a question of what is the "correct" thing to call speakers of Eskimo languages, which can be answered differently depending on where you are. "Eskimo" is an umbrella term including Inuit and Yupik peoples, some people find it offensive, it's not used in Canada, but it is used in Alaska. There are also Aleuts, who speak a language which is part of the Eskimo language family, but are not considered to be culturally Eskimo.

Anyway. The "Russian blue" phenomenon which I did bring up is real.

That Sokal doesn’t (and evidently can’t) distinguish Marxist theory from deconstructionism makes him guilty of exactly what he’s accusing his targets of doing — ie, swaggering into an unfamiliar field and saying “Oh, pish-tosh, what errant nonsense,” when, in fact, he has no idea what he’s talking about and doesn’t understand the material at even an elementary undergraduate level.

"In fact, the word 'deconstruction' appears only once in my article, in the wry (wasn't that clear?) confession that 'I'm an unabashed Old Leftist who never quite understood how deconstruction was supposed to help the working class.'"

^ "My article" being the afterword, to which Aronowitz was responding.

^^ So, yah, I get the point now.

This is more HDB’s area,

Indeed.

but most visual processing actually occurs in the retina.

Huh. I am still under the impression, though, that vision is constructed, not physiologically direct; we don't notice our blind spot, for instance.

but most visual processing actually occurs in the retina.

I don't know if anyone has *quantified* the information-processing contributions of retina vs. lateral geniculate nucleus vs. visual cortex, there is *so much* of the brain given over to visual cortex, I suspect it's doing most of the work.

I am still under the impression, though, that vision is constructed, not physiologically direct

That way lies the 'homunculus' fallacy, with a little JP inside your head, looking at the retinal image projected on a screen.

That way lies the ‘homunculus’ fallacy, with a little JP inside your head, looking at the retinal image projected on a screen.

How so?

I thought most processing occurred in the brain. Or is that only the interpretation? Or did I totally miss the point?

http://www.theguardian.com/education/2012/nov/12/improbable-research-se…

^^ So, yah, I get the point now.

Does that mean I don't have to point out that he's being disingenuous and evasive with that "In fact, the word "deconstruction" only appears once" routine?

That's not a rhetorical question. I'm really not sure what you're saying.

I don’t know if anyone has *quantified* the information-processing contributions of retina vs. lateral geniculate nucleus vs. visual cortex, there is *so much* of the brain given over to visual cortex, I suspect it’s doing most of the work.

Bear in mind that the people I got mixed up with long ago would have assigned facial recognition to a Yale T predicate and hoped for the best.*

I did at least casually follow things from the LGN to V1, but in retrospect, I was relying on a subterranean, imaginary perceived visual realm in which nothing made sense. In retrospect, this still presumes object recognition.

* I wouldn't say that the infiltration of Common Lisp was the beginning of the end, but nobody much seemed to use the Lisp Machine once it was procured.

Does that mean I don’t have to point out that he’s being disingenuous and evasive with that “In fact, the word “deconstruction” only appears once” routine?

That’s not a rhetorical question. I’m really not sure what you’re saying.

I was at an intermediate point in reminding myself of the order of things and thought I had figured out "Sokal doesn’t (and evidently can’t) distinguish Marxist theory from deconstructionism" referred to Aronowitz's statement that "Social Text was founded, and remains within, the Marxist project."

My "thinking out loud" enshrined in that final comment was an ill-formed mile marker.

That way lies the ‘homunculus’ fallacy, with a little JP inside your head, looking at the retinal image projected on a screen.
How so?

For me at least, it is an insidious mental model, easy to fall into, best avoided by not thinking too much about the end results of visual processing. Perhaps it is a cultural construct.

http://www.theguardian.com/education/2012/nov/12/improbable-research-se…
In the middle of the 20th century, an Austrian professor turned a man's eyesight exactly upside-down. After a short time, the man took this completely in his stride.

Marc Abrahams made a real dogs breakfast of that bit of Gosh-Wow fluff. Kohler's study of mental plasticity and inverted vision was an attempt to *replicate* an original claim from Stratton, in 1897. And his collaborators did not describe a correction for the effect of the prism; they learned to adapt for them... but the world still looked upside down (or ambiguous).
There's a been a series of inverted-vision attempts to replicate Stratton's claim (because prism glasses are easy and fun), and this is the consistent result... the world stays looking upside-down.
http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.294.9093&rep=r…

Glad to see the genome question is settled and we are back to the fun philosophy stuff.

It should be noted that if you look at the development of physics over the centuries, there's an awful lot of just the kinds of insulting back-and-forth disagreement that takes place on the internet, albeit written out in fine cursive on fine parchment, I suppose. This between the revered "giants" that preceded Newton, as well as those who followed.

But understanding that history, one has to recognize that talking about "objective reality" is a dangerous business. You know, we built that LHC partially with the hope that it would "break" physics, so there would be something for really clever physics grads to do besides creating financial disasters. Are we so sure that this might not have led to a different model of "reality" from the one we have now, had it happened? Are we quite sure that the dark matter/dark energy path might not lead us to a new construction of cosmology?

With respect to Ann's interpretations, I would agree almost entirely, and I would just point out that social/economic structures are very much intertwined with the extant technology, and that technology informs physics. The "giants" who did the math were beholden, much as it irked them, to the "engineers" of their time, for the problems they had to solve.

So, was it the socio-economic structure that brought Einstein to his creation, or trains and clocks and telegraphs? Correlation, causality, complex symptoms/systems oh my. Perhaps that's what some of these writers are missing.

# 739, 740
Indeed, I can confirm Italians use 3 different words for various hues of what in English is called "blue".
Examples from football (soccer) jackets, which you could find on some video files:
Società Sportiva Lazio: "biancocelesti" (whiteblues)
Italian national team: "azzurri" (blues)
Bologna Football Club: "rossoblù" (redblues)

I was at an intermediate point in reminding myself of the order of things and thought I had figured out “Sokal doesn’t (and evidently can’t) distinguish Marxist theory from deconstructionism” referred to Aronowitz’s statement that “Social Text was founded, and remains within, the Marxist project.”

Aha.

That was a reasonable inference, but incorrect. I hadn't seen that statement until you linked to it.***

I was speaking from personal observation, having...well, observed that Aronowitz was a Marxist in the course of encountering his work here and there (mostly in the popular press) over the years.

Same for Andrew Ross.

I think I've said this here in comments before. But one of the reasons I always thought Sokal was a troll was that I had some glancing familiarity with the work of both Ross and Aronowitz, which, though not extensive, was plenty enough to make it clear that he was definitely misrepresenting them.

I can no longer recall precisely why, but at the time, it seemed to me that Sokal's principle target was actually Ross, not Aronowitz. NYU had just hired him to be the director of a big, new graduate program, and he was kind of a rock star -- young, good-looking, sexy, sought after, and (in short) exceptionally glamorous for an academic.

Additionally, although some of his work was on conventionally weighty subjects -- labor, class, etc. -- he was unlike Aronowitz in that he also wrote about the kind of low pop-culture subjects that people love to hate. And not at all badly, I might add. Which is unusual.

In any event. At the time, it seemed to me that he was gunning for Ross because he was a player-hater, plain and simple.

Irrespective of which, what I said before still stands.

As far as I can tell, there's no evidence whatsoever that the phenomenon he was purportedly exposing with his hoax even existed prior to it. Or ever has apart from it.

It therefore appears to me that he intentionally harmed a number of his colleagues for no good reason at all, simply in order to aggrandize himself beyond his real deserts.

And he not only got it completely wrong, he also refused to admit it, and -- in fact -- has been doubling down on the error out of sheer arrogance, plus either ignorance or something worse ever since.

*** It actually caused me to revise my opinion of Sokal, to his detriment.

For me at least, it is an insidious mental model, easy to fall into, best avoided by not thinking too much about the end results of visual processing.

That would be a serious hardship for me. Especially in museums.

Perhaps it is a cultural construct.

If "it" is "the homunculus fallacy," it definitely is. And I know that because one encountered it frequently in the movies and film strips they used to show middle-schoolers in health class, back in the day.

Or I did, at least. It might not have been specific to vision. But we definitely saw (IIRC) movies featuring a little man at a control board in the brain, turning stuff on and off.

Hormones, probably. Now that I come to think of it. But I would maintain that it still counts as evidence of cultural construction.

Hey! That reminds me of an excellent example of science repeatedly overlooking established facts out of cultural bias that's been going on for centuries and persists even to the present day:

Historical, social and scientific factors appear to be responsible for the poor presentation of clitoral anatomy even in current textbooks. Active deletion of the clitoris as a labeled structure from an early version of Gray’s Anatomy compared with subsequent versions indicates the influence of social factors over science.5 The medical profession has also had a major influence on female sexuality throughout history, particularly in the 19th century. The widespread practice in Western medicine of clitoridectomy for indications as diverse as epilepsy, hysteria and catalepsy is relatively recent.6 In addition to such factors, anatomists have compounded the poor display of clitoral anatomy by revealing it only in 1 plane. While the sagittal plane may suit the display of an essentially linear structure such as the penis, the clitoris is not well displayed in this plane. The axial plane is the most useful. As a multiplanar modality, MRI reveals each component of the clitoris and complements the information obtained at dissection.

(Link).

In another paper, the same author gives a detailed account of the recurrent disappearance of the clitoris from medical texts each and every time anyone (re)discovered it over the centuries. But I can't find a free online full-text version, atm.

I'm reasonably sure it's still nowhere to be found in the diagrams and other materials used for most present-day health classes all across America. However.

That's actually the same kind of thing that Luce Irigaray was trying to point out about language, more or less.

Summary from Psychology Today, two years ago:

It’s a mystery worthy of Miss Marple herself. The clitoris vanishes every few generations and then needs to be rediscovered. Sometimes, this rescue from obscurity is to considerable fanfare. Why does this keep happening?

First, don’t panic. A vital anatomical structure is not really vanishing--it just disappears from anatomical textbooks every so often. Second—don’t just take my word for it--test this for yourself. Go into any decent bookshop and check out the medical anatomy section. Look up “clitoris” in the pictorial index. I guarantee that roughly half of the medical textbooks—ones that are used to train doctors--will disagree with the other half. One half will label, as if complete, a structure they will call the clitoris that is actually a wholly external organ. This is in fact the clitoral glans--a highly sensitive part of the clitoris—but definitely not the whole thing. The remaining textbooks will detail a far more complex structure, about four inches in length, mostly internal, and with a variety of nerve pathways, complex mapping onto the sensory cortex of the brain, and a host of integrated organelles. Are half the female population notably different from the other half? No, they are not.

That's some pretty culturally determined science, you do have to admit.

Perhaps it is a cultural construct.

If “it” is “the homunculus fallacy,” it definitely is. And I know that because one encountered it frequently in the movies and film strips they used to show middle-schoolers in health class, back in the day.

Yeah, I was sort of confused by the idea that it must be a natural way of thinking of things that is easy to fall into. I looked it up on the Gazoogle, and saw one of those pictures of a little person inside a person's head, looking out. Come to think of it, I may have seen a similar representation somewhere once or twice, but I certainly didn't encounter it enough for it to stick; it's honestly not something that occurred to me at, in terms of ways one might think about the mind or vision or what have you.

I definitely don't think about (or experience) vision that way either.

My thoughts sometimes first occur as images or patterns in my mind's eye rather than words, especially if I'm thinking about something complex. And that does feel more like I'm watching something happen than like I'm doing something, I guess.

I'm assuming that's not super-duper unusual. So if it comes from within, maybe that's where it comes from.

754 ann,

How do you know that they are thoughts?

My thoughts sometimes first occur as images or patterns in my mind’s eye rather than words, especially if I’m thinking about something complex. And that does feel more like I’m watching something happen than like I’m doing something, I guess.

I think in images sometimes if I am working on visual art, or thinking about working on visual art. I think in words if I'm sitting down to write something or if I'm having a conversation. Otherwise, I don't really know how to describe my "thoughts" - and, actually, a lot of the time, if I'm not deliberately thinking about something, I am just perceiving things and not really thinking at all. I gather that this is in fact unusual, or that people who do not experience life this way can't imagine it, because I have had people react in an incredulous way if I say it.

I actually find it very hard to imagine going through life with a constant monologue-type thing your head, which some people evidently experience.

This might have something to do with meditation practice, but it is also just sort of generally how things have always been for me, I think.

Incidentally, I think this is why I have never really found cognitive behavioral therapy to be particularly helpful. When I am really depressed or distressed or whatever, it is not because of negative thinking; it's because I feel a certain way, often in an overwhelming way, and it seems to just be a background thing that's there for no reason in particular. (Well, I'm sure there are reasons, but it isn't typically triggered by thoughts.)

One of the times when my mind does get into a wheel of verbal-type thought is when I'm particularly anxious, though. But even in that case, it feels like the feeling of anxiety is there first, and then my mind goes crazy ruminating about all sorts of things and I guess looking for things to pin it on.

More things in heaven and earth...

http://www.bbc.com/news/health-34039054

@JP --

Word to all of that, especially this:

Otherwise, I don’t really know how to describe my “thoughts” – and, actually, a lot of the time, if I’m not deliberately thinking about something, I am just perceiving things and not really thinking at all. I gather that this is in fact unusual, or that people who do not experience life this way can’t imagine it, because I have had people react in an incredulous way if I say it.

I too find it incredible that other people have some other kind of thought.

But that's not what I meant. What I meant was:

@zebra:

How do you know that they are thoughts?

It happens when I'm trying to solve a problem or figure something out from a starting point of little information, if that makes sense. I see images and/or patterns that represent the possibilities, then they either (a) dissolve, which = "I don't know" (usual); or (b) cohere, which = "Wait! I know, I know!" (infrequent, but quite thrilling).

That's when I'm most aware of it, anyway. It's not something I do on purpose. It just happens sometimes. I think it maybe used to happen more when I was a child. But maybe I was just more frequently in situations about which I had little information.

@#757 --

Cool! Neither of those is me. But I do have ordinal linguistic personification synesthesia. And that's kind of similar to the non-verbal thought, in that I see/perceive/recognize the personal qualities of (let's say) 5 x 5 = 25*** rather than think them. Because I just do.

***Red, yellow, boisterous, noisy, a clattering sound, a happy little boy running downstairs, autumn, balloons.

Two is yellow, five is red, both are male. Etc.

@ann:

That's interesting. I have a slightly similar thing, where I have a kind of feeling of a 3-D map in my mind (sounds weird, it's hard to explain) and sometimes things "click" into place. I don't "see" an image, though.

I too find it incredible that other people have some other kind of thought.

I think this is the first time I have actually sat down and tried to explain it before; usually it has just come up in the context of people asking me, "What are you thinking?" and me responding "nothing." They usually interpret it as me being evasive or stoic or something, I think, but a few times they have interrogated further. Once was when I was seeing a therapist who asked me what I was thinking, like right at that moment, and I said "nothing really," and he didn't believe me - I think his words were "Come on, you're not just having some kind of Zen moment," and I tried to explain that no, I was aware of sitting in a chair and a room and looking at him and all, but I wasn't thinking anything.

Man, other people are weird.

Ann 758,

I asked about the term "thoughts" because I have a similar phenomenon when encountering more complex math-- an unconscious conversion to some kind of "mapping" that involves shapes arranged in a plane, with variations in hue and saturation.

But I can't know whether the image contains actual information, or is just a "message" that my unconscious or mathematical intuition or whatever we call it has arrived at a conclusion about "where the answer lies". (And it does only happen when I get that right.)

Perhaps it isn't surprising that abstract inputs give abstract outputs; if the problem is verbal or more concrete, I often spontaneously see schematized versions on that screen behind the eyes. Still, there are no "steps" or consciousness about what I am seeing or how I am solving it.

More things in heaven and earth...

people asking me, “What are you thinking?”

Thoughts *happen* but I'm not sure that I can claim credit for thinking them.

@ JP and ann:

Believe it or not, people study stuff like that.

I interviewed people about their experiences with verbal thought vs imagery which was preliminary for something else.

Offhand, I'm trying to think about what would be interesting to look up. I always enjoy reading about how people use imagery or facility in language/ bilingualism to aid memory. Ability for mental rotation of images. Also the therapeutic implications for imagery/ language in meditation ( JP hints a little about this). Self regulation through inner speech. Day dreaming. The book, Memory Observed, may have something. Vygotsky?

@#761 --

That's not dissimilar to what I'm talking about, actually. I see it like an equation, almost. And it is one, more or less. Logic is math, and it's basically verbal logic without the words.

Maybe it's just a mild form of the same phenomenon that enables people with savant syndrome to make complex calculations instantly. I believe that's also said to be about "seeing" the answer. And it definitely does happen instantly -- ie, before I've really formulated the question I'm trying to answer, on a conscious level.

It's really never seemed like all that big of a deal to me. I mean, maybe it's not universal. But I'm sure it can't be exceptionally uncommon.

However, I didn't realize I had synesthesia until well into adulthood because it simply never crossed my mind that everybody didn't perceive that 16 was green and white/female. (I mean, that's just who 16 is. Are they blind?)

So what do I know.

ann,

But I do have ordinal linguistic personification synesthesia.

I was just reading about that ('Dueling Neursosurgeons', Kean); you might find it interesting too:

Synesthesia probably has a genetic component, since it runs in families and pops up in most cultures. Importantly, too, neurologists have ruled out the idea that synesthetes are just talking metaphorical jive, the way the rest of us speak of “loud shirts” and “sharp cheddar.” These people’s brains actually work differently, as tests reveal. One experiment involved filling a piece of paper with a bunch of alarm-clock fives (5), but also scattering a few blocky twos (2) in there. Normal people find it nearly impossible to pick out the 2s without hunting one by one. To synesthetes, each 2 pops out in Technicolor, instantly. (It’s similar to the way numbers pop out automatically on color-blind tests.) As another trick, if you show a synesthete, say, a giant numeral 4 made up of rows and rows of tiny 8s, the figure’s color will flip depending on whether she focuses on the whole (the 4) or the pixels (the 8s). Other tests make synesthetes squirm. Normal people have no trouble reading text of basically any color. For synesthetes, numbers or letters that are the “wrong” color can disorient or repel them, since the colors on the page do battle with the colors in their minds.

On the Sapir-Whorf perception thing, some years ago I read of an experiment that involved discharging an electroscope, but historically scientists reported seeing what they expected to see, i.e. what the prevailing theory said should happen, rather than what 'really' happens (either the foil arms of the electroscope fell instantly or slowly, I forget which). It would be an interesting example of belief affecting scientific practice, but sadly I have been unable to locate it since.

I may experience a minor, limited form of synaesthesia in that I "see" ( in my mind's eye) certain musical passages as moving patterns of light that relate qualitatively to the music ( e.g. parts of Glass' work "look" like spinning wheels of light/ sustained notes may "look" like a beam of light)
Go figure.

764 ann,

"And it definitely does happen instantly — ie, before I’ve really formulated the question I’m trying to answer, on a conscious level."

Putting aside the matter of visual effects, "creative insight" or "the shower effect" or "intuition" is very likely the moment when you figure out, consciously or unconsciously, what the question is.

As to the prevalence of the actual visualization part, I don't know, but actual problem solving as opposed to following algorithms or pattern recognition has been rare in my experience with students. It needs to be developed, rather than stifled, which is what happens with most of the population.

Synesthesia probably has a genetic component, since it runs in families

Yes. I discovered that there are some grapheme-color synesthetes in mine. I have that with numbers, though not letters.

But it's really the personification that's the most prominent -- ie, if six was orange, that would be wrong and I wouldn't like it, but it would still have six-ness. If it was male, however, it just wouldn't be six. It would be some interloper using six's form and name. And I would be hostile to it.

Happily, that circumstance doesn't really arise.

@Denice --

There's an instance of something like that in the lyrics to "Lola," by the Kinks. ("I asked her her name and in a dark brown voice she said 'Lola'.")

That's always just seemed very non-figurative to me. Unlike "silver bells," for example.

Putting aside the matter of visual effects, “creative insight” or “the shower effect” or “intuition” is very likely the moment when you figure out, consciously or unconsciously, what the question is.

I don't think so. When it fails, it's just a non-thing. When it works, it's more like the answer to a question that wasn't asked. So an insight, I suppose.

Wait. Scratch that, I misunderstood you.

Yes, I agree.

@ ann:

It makes me wonder if people with this ability express it somehow- I might imagine business/ finance as a series of pathways or "see" social interactions as a matrix- all in motion of course. I use visual metaphors often..

My thinking is a complex mixture of rapidly moving images, numbers, letters and dialog, but I can only see it dimly and fleetingly, though I can readily retrieve information from it, if that makes sense. I can put together a complex plan of action in detail, such as a complex computer program, or a work project, but may have trouble putting it in writing as it tends to be moving and in three dimensions. I have tried many different mind-mapping methods, but none seem to suit my style of thinking.

As for synesthesia, here's the passage preceding the one I posted earlier, which may also be of interest:

The most common type of synesthesia produces a symphony of color, especially when people hear certain sounds or see certain letters and numbers. Richard Feynman saw ecru j’s, indigo n’s, and chocolate x’s inside equations. Vladimir Nabokov once said that for him, the long vowel aaah has “the tint of weathered wood,” while the shorter ah “evokes polished ebony.” Franz Liszt used to berate his orchestra—who could only stare back, bewildered—for playing his music the wrong color: “Gentlemen, a little bluer, please, the tone depends on it!” Another time he implored: “That is a deep violet [passage]!… Not so rose.”

Also the therapeutic implications for imagery/ language in meditation ( JP hints a little about this).

Hmm. I can't say as I've ever done much meditation which involved imagery or language. I guess I tried a few Tibetan-type meditation practices a long time ago, but they didn't really catch me; it felt like more of a mental exercise than like, well, zazen. (The style of meditation I practice is called zazen or shikantaza in Japanese; I'm not sure what it is called in Korean, although by all rights I suppose I should know.) But it in any case, it is just sitting. That's it. You're aware of the breath, any passing thoughts, any emotions, etc., but you're not fixating on them. Or at least that's the idea. I've read somebody else who reported that after a couple decades of zazen (I've been at it since I was 15, with some hiatuses? hiati?), he started going through long periods in day-to-day life where no specific thoughts were really coming up. So the idea isn't to try to stop thoughts on purpose - I can only suppose that would be some sort of psychological repression - but just to kind of let them subside on their own.

And of course I have random thoughts that come up and now and then, but even when I'm thinking, it's almost never an "internal monologue." I always thought that was just a voice-over device used in movies and TV, until I found out that a lot of people actually experience it, and even define it as consciousness or something. But anyway, say if I think about having a cup of coffee or something, I don't think "Gee, I'm kind of tired, and a cup of coffee sounds nice." I notice that I'm tired, and then maybe I imagine holding a cup of coffee and drinking it, and then I head to the kitchen.

As far as imagery goes, I can imagine things quite vividly, and I tend to recall what things look like with a high degree of accuracy, what color things are, etc. But when I imagine a thing, I don't actually see it. When I close my eyes, all I see is black. So other people actually see things, like literally, when they imagine them?

^ Heh; tangentially how I tend to remember what things look like quite well, I also get tend to really absorbed in looking at things. The first or second time I saw the psychiatrist I'm seeing, he asked me what I like to do for fun, and I think one of the main things I said was "walk around and look at things." Which probably sounds pretty weird, I suppose.

@ JP:

I meant the therapeutic use of meditation-like states which focus upon an image or words/ sounds in order to divert attention away from disturbing thoughts/ images that arise spontaneously or excessive worry. Paying attention to breathing or observing the external world is another method.

Right. People can use inner speech as well as imagery as rehearsal or planning as well as for repetition of past events. They also vary in how much they use imagery and how clear those images are..I haven't really kept up with this research.

Personally I can sometimes evoke very clear images of what've I've already seen - it's almost like 'seeing' but not exactly. "Mind's eye' is a good descriptive, I have excellent memory for maps and diagrammed material which means that I often function as navigator or instructor. People loved me in anatomy and physio classes. It's easy for me to reproduce what I learn this way altho' the maps may not really be in perfect proportion, the relationships between items are usually correct. Frequently I recall disturbing images better than I would choose .I can also plan things like creating an image with drawing materials or camera.

I discovered when studying that sometimes I would recall where a particular phrase or passage was located upon the page ( top/ bottom, left'right) even though I never intended to recall that.

I practice is called zazen or shikantaza in Japanese; I’m not sure what it is called in Korean, although by all rights I suppose I should know.)

Cham-seon, I guess, but it's not really the same, as Korean meditation practice is koan-oriented – observing "the critical phrase," not breathing. Sitting meditation also tends to be focused around seasonal retreats, rather than being a core practice (full-time meditation monks are a distinct minority).

hiatuses? hiati?

Fourth declension; the nominative plural would also be "hiatus," but with a long 'u'.

Cham-seon, I guess, but it’s not really the same, as Korean meditation practice is koan-oriented – observing “the critical phrase,” not breathing.

Hmm. That explains all that stuff Haju was saying about thinking "Who am I," etc. I remember the first time I went for an "interview" with her, she asked me to "practice out loud," and I just sort of boggled and said I had no idea what that meant. It took a while to explain what I "do" in meditation.

In any case, though, although Ann Arbor ZBT is a Korean temple (sort of, I mean it's a bit ecumenical and Americanized, you can look them up), they still definitely do at least morning and evening sitting meditation. And lots of bowing. Seriously, 108 full bows is kind of a b*tch on the knees. (One reason that I haven't gone to early morning meditation there in a while...)

Japanese Zen also has retreats, actually - sesshin - but again, the meditate quite a bit every day as well. I'm really only familiar with the Soto school in practice, but I understand that the Rinzai school practices zazen as well, and after the student "finishes" koan study, they "move on" to shikantaza.

But anyway, yeah, it's kind of funny that I think I have actually been associated with A2 ZBT probably for the longest chunk of time of any temple, but I still come at things in a very Soto way. I suppose that my introduction to Zen as a teenager was also in the Soto vein, through a book or two.

Fourth declension; the nominative plural would also be “hiatus,” but with a long ‘u’.

Ah.

The first or second time I saw the psychiatrist I’m seeing, he asked me what I like to do for fun, and I think one of the main things I said was “walk around and look at things.” Which probably sounds pretty weird, I suppose.

Again, not to me.

Hmm. You know how you're sometimes unaware of how much time has passed when you're very absorbed in something?

Would you say that's characteristic of you?

@Ann:

Yep, for sure.

My thinking is a complex mixture of rapidly moving images, numbers, letters and dialog, but I can only see it dimly and fleetingly

"My mind is a raging torrent, flooded with rivulets of thought cascading into a waterfall of creative alternatives."

In any case, though, although Ann Arbor ZBT is a Korean temple (sort of, I mean it’s a bit ecumenical and Americanized, you can look them up), they still definitely do at least morning and evening sitting meditation. And lots of bowing. Seriously, 108 full bows is kind of a b*tch on the knees.

Yah, the Providence Zen Center, which is Kwan Um Central and thus nominally Chogye, seems to do the same sort of thing. A quick glance at this, which I have to hand, suggests nothing of the sort in the monastic environment, though.

Morning service (which the meditation monks skip) is three prostrations, a standard chant, brief prayer, recitation of the Heart Sutra, a bit of bowing, and off to the day. Then again, these Zen centers are largely nonvocational, so perhaps something has to substitute for more realistic temple rules.

One difference in Korean koan (hwadu) practice is that a student typically gets just one – it's subitism, after all – so this can still be focused on outside of sitting-walking* meditation.

* These are paired; I don't really know much of anything about Japanese-style practice.

^ "these Zen centers" meaning the U.S. ones.

There’s an instance of something like that in the lyrics to “Lola,” by the Kinks. (“I asked her her name and in a dark brown voice she said ‘Lola’.”)

That’s always just seemed very non-figurative to me. Unlike “silver bells,” for example.

There are different accounts of the precise inspiration for the lyrics, but I'm inclined to take this line as indicating that Lola's black.

Wrt that pesky security issue. Received a letter in the mail today about this http://www.modernhealthcare.com/article/20150909/NEWS/150909880

It sucks.

One difference in Korean koan (hwadu) practice is that a student typically gets just one – it’s subitism, after all – so this can still be focused on outside of sitting-walking* meditation.

* These are paired; I don’t really know much of anything about Japanese-style practice.

Sitting and walking meditation are paired in Japanese-style practice, too. Typically you'll have a 25-40 minute sitting period (depends on the temple), then 10 minuted of walking meditation (kinhin), then another zazen period, and so on. I think the typical Sunday morning routine at DRZC in Portland was 40 minutes sitting, 10 minutes walking, 40 minutes sitting, 15 minute chanting/bowing thing, coffee or whatever, then a Dharma talk. Similar thing at Olympia Zen Center, except it was much less well-attended, possible because it actually happened at 7:30 or so on Saturday morning. It was nice though; we would typically eat breakfast after sitting and then "study" after breakfast, which could get silly.

The Sunday service at AAZBT is like 20 minutes of sitting, I think, then Yebul and a little more sitting and a Dharma talk. Wimpy, I say, but I can always go for the more substantial Wednesday evenings and so on.

The Japanese monastic environment is kind of its own thing; mainly young monks go there for a period of time, then go back and run their dad's temple or whatever. One hears from the Japanese teachers who came to America that they left in large part because there wasn't much serious zazen practice going on in Japan, and they were sick of the bureaucracy and whatnot, the Soto-shu had just become a funeral guild, etc. Which I suppose explains the emphasis on sitting in American Japanese-style Zen.

There's an interesting thing going on in American Zen wrt monks/priests, too, and how exactly people make it work in an American context. But I could go on for a long time in this vein.

^ Oh: in Soto Zen, at least (I dunno about Rinzai), one is also expected/encouraged to keep practicing outside of "formal" sitting and walking meditation practice.

I asked about the term “thoughts” because I have a similar phenomenon when encountering more complex math–

Such as?

an unconscious conversion to some kind of “mapping” that involves shapes arranged in a plane, with variations in hue and saturation.

What does it look like when presented with the question what it could possibly mean to raise e to an imaginary power, as in Euler's identity?

Anyway, more in the direction these comments have gone, I'll mention – quite separately from internal dialogue, etc. – that I know there's an opportunity to defeat an item of MDD anxiety when the somatic element rises from my solar plexus to my throat.

Whereas I'm just disappointed that nobody commented on my example of culturally determined science.

It is kind of a conversation stopper, I guess.

But seriously. Anatomy texts.

One would hope.

@ann:

I'm actually just sort of gobsmacked that there are anatomy textbooks that DON'T include the clitoris. And I totally agree that the oversight must be... culturally constructed.

Plural = 'clitorides'. Before anyone asks.

@JP --

I know, it's shocking. And yet, there are not. (Well. They include part of it.)

I gather that before Helen O'Connell MD began to agitate about it in 1998, it was even worse.

I mean, regular folk can figure out what they need to know without an illustration. But I would want a surgeon (for example) to be educated to know what the what was. For mercy's sake.

@ ann re @791:

Oh I meant to say something along the lines that perhaps that explains why it is often overlooked in ...er.. OTHER contexts.
BUT I am glad that you mentioned it.
-btw- way back in the mists of time, wasn't there a feminist movement that .um.. focused its attention on it?

Not that I recall.

I mean, there was Our Bodies, etc. And Shere Hite, if she counts.

I'm a little too young for that stuff, though.

Oh I meant to say something along the lines that perhaps that explains why it is often overlooked in …er.. OTHER contexts.

Only by jerks and totally clueless lovers at this point, I think? I mean, I remember being like 15 or 16, shortly before I moved away for school, riding around in a car with some friends (I slipped a lot of things past my mom, plus I think she gave up and stopped caring at some point) and talking about sex and my buddy Dylan remarking that "there's always time to go for the clit."

But anyway, I digress.

@ Narad

There are different accounts of the precise inspiration for the lyrics, but I’m inclined to take this line as indicating that Lola’s black.

My interpretation was always that her voice was low and perhaps had a rough edge.

@ JP and ann:

OBVIOUSLY you missed my sarcasm signal.

@ Renate:

I read that as she was a guy trying to sound like a woman somewhat unsuccessfully.
It was in " old Soho" so most likely white but could be black.

@ Denice, etc

way back in the mists of time, wasn’t there a feminist movement that .um.. focused its attention on it?

Not sure about a real feminist movement, but in a strawman one in a movie or something... Although I'm not daring to search this on the internets.

It was at lest tangentially mentioned as one of the three things men were always missing (the other two being the toilet's seat and birthdays).
Since I read it, I'm pleased to report I have become much better with one out of the three. Still have to work on the birthdays.

@Narad, Renate, re: "Lola":

I've always taken it to mean that she had a husky or deep voice, prefiguring the "talk like a man" line two verses later.

re: malia @79

Well, I went out to see my sister, and we sat around and spit into a test tube. There were a few interesting things to come out, but mostly what we already suspected.

The big thing that I was looking for happened just as I expected - neither of us have any sign of Native American DNA, family stories to the contrary. 99.3% European for me, 99.6% for her. I know this doesn't prove there is no Native American in my family tree, but if there is any, it's way back, just as I expected.

One disappointing result is that I'm only 2.8% Neanderthal, and my sister clocked in at 3.1%. I was hoping to come in with a higher score than that, or at least higher than her. I understand that the 2.8% is about average for European stock.

The most unexpected result is that I'm descended from an Irish king (well, we share a Y, anyway). I am Haplogroup R1b1b2a1a2f2, very common in Ireland (and not uncommon on the west coast of Britain).

I guess that's why I like a Guinness every now and then.