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ChristianKl comments on Should effective altruists care about the US gov't shutdown and can we do anything? - Less Wrong
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So every field has problems, but that doesn't mean those problems are "huge".
Outside view: An entire field which is generally pretty successful at actually finding what is going on is fundamentally misguided about how they should be approaching the field, or the biologists are doing what they can. Biology is hard. But we are making progress in biology at a rapid rate. For example, the use of genetic markers to figure out how to treat different cancers was first proposed in the early 1990s and is now a highly successful clinical method.
You might be but I'm not really.
That's a crude method of measuring success.
The cost of new drugs rises exponentially via Eroom's law. Big Pharma constantly lays of people.
A problem like obesity grows worse over the years instead of progress. Diabetes gets worse.
Even if you say that science isn't about solving real world issues but about knowledge, I also think that replication rates of 11% in the case of breakthrough cancer research indicates that the field is not good at finding out what's going on.
It isn't a metric of success. It is an example, one of many in the biological sciences.
This is likely due largely to policy issues and legal issues more than it is how the biologists are thinking. Clinical trials have gotten large.
A systemic problem, but one that has even less to do with biological research than Eroom's law. Obesity is not due to a lack of theoretical underpinnings in biology.
The question isn't is the field very good. The question is are the problems which we both agree exist due at all to not enough theory? File drawer effects, cognitive biases, bad experimental design are all issues here, none of which fall into that category.
Then at what grounds do you claim that the field is succesful? How would you know if it weren't succesful?
I'm not saying that theory lacks theoretical underpinnings but that the underpinning is of bad quality.
Question about designing experiments in a way that they produce reproduceable results instead of only large p values are theoretical issues.
Enough theory sounds like as attempt to quantify the amount of theory. That's not what I advocate. Theories don't get better through increase in their quantity. Good theoretical thinking can simply model and result in less complex theory.
That's a good question, but in this context, seeing a variety of novel discoveries in the last few years indicates a somewhat successful field. By the same token, I'm curious what makes you think this isn't a successful field?
I've already mentioned the file drawer problem. I'm curious, do you think that is a theoretical problem? If so, this may come down in part due to a very different notion of what theory means.
You seem to be treating biology to some extent like it is physics, But these are complex systems. What makes you think that such approaches will be at all successful?
The fact that Big Pharma has to lay of a lot of scientists is a real world indication that the output of model of finding a drug target, screening thousands of components against it, runs those components through clinical trials to find whether they are any good and then coming out with drugs that cure important illnesses at the other end stops producing results. Eroom's law.
Saying that there's a file drawer problem is quite easy. That however not a solution. I think your problem is that you can't imaging a theory that would solve the problem. That's typical. If it would be easy to imagine a theoretical breakthrough beforehand it wouldn't be much of a breakthrough.
Look at a theoretical breakthrough of moving from the model of numbers as IV+II=VI to 4+2=6. If you would have talked with a Pythagoras he probably couldn't imaging a theoretical breakthrough like that.
I don't. I don't know much about physics. Paleo/Quantified Self people found the thing with Vitamin D in the morning through phenemology. The community is relatively small and the amount of work that's invested into the theoretical underpinning is small.
I think in my exposure with the field of biology from various angles that there are a lot of areas where things aren't clear and there room for improvement on the level on epistomolgy and ontology.
I just recently preordered two angel sensors from crowdsourcing website indiegogo. I think that the money that the company gets will do much more to advance medicine than the average NHI grant.
This seems like extremely weak evidence. Diminishing marginal returns is a common thing in many areas. For example, engineering better trains happened a lot in the second half 19th century and the early 20th century. That slowed down, not because of some lack of theoretical background, but because the technology reached maturity. Now, improvements in train technology do occur, but slowly.
On the contrary. We have ways of handling the file drawer problem, and they aren't theory based issues. Pre-registration of studies works. It isn't even clear to me what it would mean to have a theoretical solution of the file drawer problem given that it is a problem about how culture, and a type of problem exists in any field. It makes about as much sense to talk about how having better theory could somehow solve type I errors.
The ancient Greeks used the Babylonian number system and the Greek system. They did not use Roman numerals.
The file drawer problem is about an effect. If you can estimate exactly how large the effect is when you look at the question of whether to take a certain drug you solve the problem because you can just run the numbers.
The concept of the file drawer problem first appeared in 1976 if I can trust google ngrams.
How much money do you think it cost to run the experiments to come up with the concept of the file drawer problem and the concept pre-registration of studies? I don't think that's knowledge that got created by running expensive experiments. It came from people engaging in theoretical thinking.
Type I errors are a feature of frequentist statistics. If you don't use null hypotheses you don't make type I errors. Bayesians don't make type I errors because they don't have null hypotheses.
LOL. That's, um, not exactly true.
Let's take a new drug trial. You want to find out whether the drug has certain (specific, detectable) effects. Could you please explain how a Bayesian approach to the results of the trial would make it impossible to make a Type I error, that is, a false positive: decide that the drug does have effects while in fact it does not?
I don't. A real bayesian doesn't. The bayesian wants to know the probability which with the drug will improve the well being of a patient.
The output of a bayesian analysis isn't a truth value but a probability.
The earliest citation in the Rosenthal paper that coined the term 'file drawer' is to a 1959 paper by one Theodore Sterling; I jailbroke this to "Publication Decisions and Their Possible Effects on Inferences Drawn from tests of Significance - or Vice Versa".
After some background about NHST on page 1, Sterling immediately begins tallying tests of significance in a years' worth of 4 psychology journals, on page 2, and discovers that eg of 106 tests, 105 rejected the null hypothesis. On page 3, he discusses how this bias could come about.
So at least in this very early discussion of publication bias, it was driven by people engaged in empirical thinking.
I think doing a literature review is engaging in using other people data. For the sake of this discussion JoshuaZ claimed that Einstein was doing theoretical work when he worked with other people's data.
If I want to draw information from a literature review to gather insights I don't need expensive equipment. JoshuaZ claimed that you need expensive equipement to gather new insights in biology. I claim that's not true. I claim that there enough published information that's not well organised into theories that you can make major advances in biology without needing to buy any equipment.
As far as I understand you don't run experiments on participants to see whether Dual 'n' back works. You simply gather Dual 'n' back data from other people and tried doing it yourself to know how it feel like. That's not expensive. You don't need to write large grants to get a lot of money to do that kind of work.
You do need some money to pay your bills. Einstein made that money through being a patent clerk. I don't know how you make your money to live. Of course you don't have to tell and I respect if that's private information.
For all I know you could be making money by being a patent clerk like Einstein.
A scientists who can't work on his grant projects because he of the government shutdown could use his free time to do the kind of work that you are doing.
If you don't like the label "theoretic" that's fine. If you want to propose a different label that distinguish your approach from the making fancy expensive experiments approach I'm open to use another label.
I think in the last decades we had an explosion in the amount of data in biology. I think that organising that data into theories lags behind. I think it takes less effort to advance biology by organising into theories and to do a bit of phenomenology than to push for further for expensive equipment produced knowledge.
If I phrase it that way, would you agree?
No, seeing a bunch of novel true discoveries indicates a successful field. However, it's normally hard to independently verify the truth of novel discoveries except in cases where those discoveries have applications.
This seems like a nitpick more than a serious remark: obviously one is talking about the true discoveries, and giving major examples of them in biology is not at all difficult. The discovery of RNA interference is in the biochem end of things, while a great number of discoveries have occurred in paleontology as well as using genetics to trace population migrations (both humans and non-humans).
So one question here is, for what types of discoveries is your prior high that the discovery is bogus? And how will you tell? General skepticism probably makes sense for a lot of medical "breakthroughs" but there's a lot of biology other than those.
I don't think a flat replication rate of 11% tells us anything without recourse to additional considerations. It's sort of like a Umeshism: if your experiments are not routinely failing, you aren't really experimenting. The best we can say is that 0% and 100% are both suboptimal...
For example, if I was told that anti-aging research was having a 11% replication rate for its 'stopping aging' treatments, I would regard this as shockingly too high and a collective crime on par with the Nazis, and if anyone asked me, would tell them that we need to spend far far more on anti-aging research because we clearly are not trying nearly enough crazy ideas. And if someone told me the clinical trials for curing balding were replicating at 89%, I would be a little uneasy and wonder what side-effects we were exposing all these people to.
(Heck, you can't even tell much about the quality of the research from just a flat replication rate. If the prior odds are 1 in 10,000, then 11% looks pretty damn good. If the prior odds are 1 in 5, pretty damn bad.)
What I would accept as a useful invocation of an 11% rate is, say, an economic analysis of the benefits showing that this represents over-investment (for example, falling pharmacorp share prices) or surprise by planners/scientists/CEOs/bureaucrats where they had held more optimistic assumptions (and so investment is likely being wasted). That sort of thing.
Replication rate of experiments is quite different from the success rate of experiments.
An 11% success rate is often shockingly high. An 11% replication rate means the researchers are sloppy, value publishing over confidence in the results, and likely do way too much of throwing spaghetti at the wall...
Even granting your distinction, the exact same argument still applies: just substitute in an additional rate of, say, 10% chance of going from replication to whatever you choose to define as 'success'. You cannot say that a 11% replication rate and then a 1.1% success rate is optimal - or suboptimal - without doing more intellectual work!
No, I don't think so. An 11% replication rate means that 89% of the published results are junk and external observers have no problems seeing that. Which implies that if those who published it were a bit more honest/critical/responsible, they should have been able to do a better job of controlling for the effects which lead them to think there's statistical significance when in fact there's none.
If the prior odds are 1:10,000 you have no business publishing results at 0.05 confidence level.
Yes, so? As Edison said, I have discovered 999 ways to not build a lightbulb.
Huh? No. As I already said, you cannot go from replication rate to judgment of the honesty, competency, or insight of researchers without additional information. Most obviously, it's going to be massively influenced by the prior odds of the hypotheses.
No one has any business publishing at an arbitrary confidence level, which should be chosen with respect to some even half-assed decision analysis. 1:10,000 or 1:1000, doesn't matter.
You're still ignoring the difference between a failed experiment and a failed replication.
Edison did not publish 999 papers each of them claiming that this is the way to build the lightbulb (at p=0.05).
And what exactly prevents the researchers from considering the prior odds when they are trying to figure out whether their results are really statistically significant?
I disagree with you -- if a researcher consistently publishes research that cannot be replicated I will call him a bad researcher.
So? What does this have to do with my point about optimizing return from experimentation?
Nothing. But no one does that because to point out that a normal experiment has resulted in a posterior probability of <5% is not helpful since that could be said of all experiments, and to run a single experiment so high-powered that it could single-handedly overcome the prior probability is ludicrously wasteful. You don't run a $50m clinical trial enrolling 50,000 people just because some drug looks interesting.
Too bad. You should get over that.
I think our disagreement comes (at least partially) from the different views on what does publishing research mean.
I see your position as looking on publishing as something like "We did A, B, and C. We got the results X and Y. Take it for what it is. The end."
I'm looking on publishing more like this: "We did multiple experiments which did not give us the magical 0.05 number so we won't tell you about them. But hey, try #39 succeeded and we can publish it: we did A39, B39, and C39 and got the results X39 and Y39. The results are significant so we believe them to be meaningful and reflective of actual reality. Please give our drug to your patients."
The realities of scientific publishing are unfortunate (and yes, I know of efforts to ameliorate the problem in medical research). If people published all their research ("We did 50 runs with the following parameters, all failed, sure #39 showed statistical significance but we don't believe it") I would have zero problems with it. But that's not how the world currently works.
P.S. By the way, here is some research which failed replication (via this)