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Depression-Gene Studies Were Built on Shaky Foundations

theatlantic.com

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Re: Depression-Gene Studies Were Built on Shaky Foundations

#51

Post by thanatropism »

mattkrause wrote: post #50
thanatropism wrote: post #34

I think pop sci rags going wild over papers that claim radical breaks are a part of the problem, even if a small one. There's simply no reason that people who are not technical enough to read scientific papers would be up to date on the latest cancer research. People have a right to knowledge? Then open up the journals.

It’s on a slightly different level. There are strong incentives to find ‘sexy’ results, but this is mostly aimed at getting a paper into Nature, Science, or Cell. Publishing in these journals can have an outsized effect on one’s career, even if the results don’t actually hold up. In contrast, there’s not a huge pay off for getting something into Popular Science or the New York Times science section. Publicity is good…

That's probably a bigger effect.

People have a huge trouble accepting that their wonderful science is a social process.

Re: Depression-Gene Studies Were Built on Shaky Foundations

#52

Post by mattkrause »

rjf72 wrote: post #30
coldtea wrote: post #25

Earlier quoted context omitted.

> what you refer to is not Science,its pseudoscience. Pretty much any crap gets published these days, review standards are abysmal and there is hardly any replication. That's like the argument that USSR was not real communism, etc. At some point, science is as science does. There's no some holier, better checked, domain of practice. It is what it is, and it sometimes has replication, more often than not it doesn't.

One factor you cannot ignore is the exponential increase in the number of 'scientists.' In times past, for better and for worse, college was generally relegated to an extremely small section of generally over-performing society. And of these a tiny minority would then go on to pursue the post-grad level education that would culminate in becoming a scientist. In today's society college has become high school 2.0. And…

I have a hard time believing that the issue is a dilution in the “quality” of scientists, but I would agree that ever-increasing competition for funds and jobs has produced some perverse incentives.

The consequences for publishing something that’s wrong but not obviously indefensible are often pretty low. On average, it probably just languishes, uncited, in a dusty corner of PubMed. It might even pick up a few citations (“but see XYZ et al. 2019”) that help the stupid metrics used to evaluate scientists.

The consequences of working slowly—-or not publishing at all—- are a lot worse. You get scooped by competitors that cut corners, and there’s not a lot of recognition for “we found pretty much what they did, but did it right.” Your apparent unproductivity gets called out in grant reviews and when job hunting. The increasing pace and career stage limits (no more than X years in grad school, Y as a postdoc, Z to quality for this funding) make it hard to build up a reputation as a slow-but-careful scientist.

These are not insoluble problems, but they need top-down changes from the folks who “made it” under the current system....

Re: Depression-Gene Studies Were Built on Shaky Foundations

#53

Post by gpm »

lm28469 wrote: post #44
ekianjo wrote: post #17

Earlier quoted context omitted.

what you refer to is not Science,its pseudoscience. Pretty much any crap gets published these days, review standards are abysmal and there is hardly any replication. Only thru replication can you actually claim there is Science.

The end result is the same. When a big tv channel says "Eating fat is definitely bad because this study says so" nobody will check the actual study and see that it was done on 3 mice for a duration of 10 days with completely unrealistic settings. It's still science, it's just misinterpreted or extrapolated. I see it everyday on HN, people _believing_ we'll all migrate to Mars and terraform it by the end of the centur…

Elon Musk is basically completely unrelated to science. His projects timetables even more so if it's even possible to be less related to science.

Re: Depression-Gene Studies Were Built on Shaky Foundations

#54

Post by mrosett »

fromthestart wrote: post #16
raverbashing wrote: post #8

It's just naive to pin something as complex as depression on a single variable (but that's Popperian scientificism for you) Now it might be that the 1st study identified an effect on a (very specific) subpopulation and in the bigger study case that subpopulation is not present or not identifiable. But who knows Now of course it's not wrong to study a certain gene, but to go "all in on" a very narrow study path is stu…

>It's just naive to pin something as complex as depression on a single variable Why? There are other complex diseases with purely genetic causes, e.g. Huntington's Disease; depression isn't necessarily different. Hindsight is 20/20.

Huntington’s is a very precisely defined disease. Depression has a much wider range of manifestations.

Re: Depression-Gene Studies Were Built on Shaky Foundations

#55

Post by kerbalspacepro »

atomical wrote: post #13
Lazare wrote: post #12

Earlier quoted context omitted.

His identity is hardly a deep secret; anyone who really cares can find it out, and verify his credentials. (Not that those credentials are really relevant here, no?)

I care about reading something written by a professional instead of a Tim Ferriss type. I've found several suspect items in his blog articles. I would like to know his credentials.

You can look them up though? It's not difficult?

Re: Depression-Gene Studies Were Built on Shaky Foundations

#56

Post by skybrian »

unityByFreedom wrote: post #28
Lazare wrote: post #26

Earlier quoted context omitted.

> it is completely relevant here as he's being cited as a real psychiatrist. That's not verifiable without knowing a real name. We're discussing his criticism of how a ton of "real psychiatrists" got some major things wrong. This criticism stands or falls on its merits, not on his status as a "real psychiatrist". You don't need to be a "real psychiatrist" in order to this sort of analysis (and, it turns out, a ton of…

> We're discussing his criticism of how a ton of "real psychiatrists" got some major things wrong No, you replied to me. My comment was it is strange that this Atlantic article cites him as "the psychiatrist Scott Alexander" because that is a pen name, and it isn't verifiable that he is a psychiatrist due to his anonymity. Your refutation of my point is "it doesn't matter that it isn't verifiable", but that was part…

You're assuming without evidence that Ed Yong didn't verify his credentials. How do you know? Maybe ask?

Re: Depression-Gene Studies Were Built on Shaky Foundations

#57

Post by meroes »

coldtea wrote: post #42
bgie wrote: post #37

Earlier quoted context omitted.

You are applying the 'no true scotsman' fallacy wrong. Depending on the definition of X, you CAN say that something is not X Only if you define 'science' as 'the thing that people labeled scientists do', can you arrive at your conclusion. I would define scientists as 'people practicing the scientific method'.

> Depending on the definition of X, you CAN say that something is not X That is a good strategy only if you already have a sample of the thing to derive a definition from. To create a good definition you should examine reality, and see the thing as it actually behaves, first. Only then, once you have a reality-based definition, you can judge other specimens and use the definition to say whether they are X or not. Els…

The concept of science, which is the empirical study of reality, does not change. There are many concepts that can share the same word - is a Scotsman someone born in Scotland, one who moved there, one who shares Scotland's culture and ideals? There should be different labels for each of these concepts but there aren't.

The importance, relevance, trust, and reality of science may change, but the underlying concept does not. Nevermind all the other forces trying to co-opt 'science' for their own purposes.

How many papers and articles describe a purely empirical inquiry into reality and accurately describe all shortcomings and sources of error? 10%? 1? It matters that our trust in "science" may continue to degrade, but none of those change the underlying concept/ideal.

Re: Depression-Gene Studies Were Built on Shaky Foundations

#58

Post by icegreentea2 »

gnoppa wrote: post #39
icegreentea2 wrote: post #27

Earlier quoted context omitted.

Let's not throw the baby out with the bath water. No doubt there's a lot of sketchy stuff going on, but also the fields are very wide with lots of "verticals" going on. Just cause one vertical might be built on a shakey foundation, doesn't mean all of them are (and the converse is also true).

You might be right that not everything in those fields is bad, but most is. Nevertheless, what is so terrible is that all the money is put into research (gene mutation causing cancer) even though it has been proven wrong many years ago. That becomes very clear after reading Thomas Seyfried's work (cell fermentation causing cancer). Sadly, academics have the incentives to publish papers in prestigious journals that ma…

I know you're getting downvoted. I don't think things are as "bad" as you think they are, but it's also impossible to deny that our current incentive structure is not ideal and can lead us to bad results.

That said, with respect with Seyfried's work, I urge you to give something like https://sciencebasedmedicine.org/ketogenic-diets-for-cancer-... a read. Go ahead and skip all of the bits about his chosen associations and focus on just the science parts if you would like. I think you'll find that quite a lot of research as been done on cancer metabolism, and that Seyfriend's work at best can be considered incomplete.

If you find the blog's arguments about lack of clinical trial data to be circular (I guess they kind of are), I don't have any answers for you now, but I suggest you keep on eye out for this guy: https://clinicaltrials.gov/ct2/show/study/NCT01754350

This is one of the studies in early stages that the blog links to (it's been a few years). They just wrapped up the study a few months ago, and hopefully there will be results posted soon. You can also search for that study number (NCT01754350) or study name (ERGO2) for papers when they do come out (again, expect at least a few more months).

Re: Depression-Gene Studies Were Built on Shaky Foundations

#59

Post by logjammin »

searine wrote: post #46
raverbashing wrote: post #8

It's just naive to pin something as complex as depression on a single variable (but that's Popperian scientificism for you) Now it might be that the 1st study identified an effect on a (very specific) subpopulation and in the bigger study case that subpopulation is not present or not identifiable. But who knows Now of course it's not wrong to study a certain gene, but to go "all in on" a very narrow study path is stu…

>It's just naive to pin something as complex as depression No it's not. Twin-based heritability studies show depression risk has about 10% heritability across all cases and 50% heritability among severe cases. There is a genetic component to the disease. That complexity is mediated by dozens of genes, but each one gene contributes a percentage to that heritability. Single genes can and will be found which link genoty…

You don't think you're mixing up "heritable" with "genetic" here? In my family, liking the Yankees is highly heritable across generations, but my grandfather would've laughed in your face if you claimed it was genetic.

Re: Depression-Gene Studies Were Built on Shaky Foundations

#60

Post by joycian »

gpm wrote: post #53
lm28469 wrote: post #44

Earlier quoted context omitted.

The end result is the same. When a big tv channel says "Eating fat is definitely bad because this study says so" nobody will check the actual study and see that it was done on 3 mice for a duration of 10 days with completely unrealistic settings. It's still science, it's just misinterpreted or extrapolated. I see it everyday on HN, people _believing_ we'll all migrate to Mars and terraform it by the end of the centur…

Elon Musk is basically completely unrelated to science. His projects timetables even more so if it's even possible to be less related to science.

Not really true. Tesla is at the forefront of applying machine learning in real-world settings. It's definitely not unrelated to science, in my opinion. If autonomous driving in 2020 is on the timetable, Karpathy (Head of AI) is probably confident that it is possible. Musk is very aggressive on timelines (but always wraps it in "it is probable that", which to him is cautious but to which translates to almost certainly in newspapers), but from what I know, he has delivered most promises (which he sees more as projection of previous trends), albeit a little late.
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