Replication Isn’t Enough

I bang on about statistical power because it indirectly raises the odds of a false positive. In brief, it forces you to do more tests to reach a statistical conclusion, stuffing the file drawer and thus making published results appear more certain than they are. In detail, see John Borghi or Ioannidis (2005). In comic, see Maki Naro.

The concept of statistical power has been known since 1928, the wasteful consequences of low power since 1962, and yet there’s no sign that scientists are upping their power levels. This is a representative result:

Our results indicate that the average statistical power of studies in the field of neuroscience is probably no more than between ~8% and ~31%, on the basis of evidence from diverse subfields within neuro-science. If the low average power we observed across these studies is typical of the neuroscience literature as a whole, this has profound implications for the field. A major implication is that the likelihood that any nominally significant finding actually reflects a true effect is small.

Button, Katherine S., et al. “Power failure: why small sample size undermines the reliability of neuroscience.” Nature Reviews Neuroscience 14.5 (2013): 365-376.

The most obvious consequence of low power is a failure to replicate. If you rarely try to replicate studies, you’ll be blissfully unaware of the problem; once you take replications seriously, though, you’ll suddenly find yourself in a “replication crisis.”

You’d think this would result in calls for increased statistical power, with the occasional call for a switch in methodology to a system that automatically incorporates power. But it’s also led to calls for more replications.

As a condition of receiving their PhD from any accredited institution, graduate students in psychology should be required to conduct, write up, and submit for publication a high-quality replication attempt of at least one key finding from the literature, focusing on the area of their doctoral research.
Everett, Jim AC, and Brian D. Earp. “A tragedy of the (academic) commons: interpreting the replication crisis in psychology as a social dilemma for early-career researchers.” Frontiers in psychology 6 (2015).


Much has been made of preregistration, publication of null results, and Bayesian statistics as important changes to how we do business. But my view is that there is relatively little value in appending these modifications to a scientific practice that is still about one-off findings; and applying them mechanistically to a more careful, cumulative practice is likely to be more of a hindrance than a help. So what do we do? …

Cumulative study sets with internal replication.

If I had to advocate for a single change to practice, this would be it.

There’s an intuitive logic to this: currently less than one in a hundred papers are replications of prior work, so there’s plenty of room for expansion; many key figures like Ronald Fisher and Jerzy Neyman have emphasized the necessity of replications; and it doesn’t require any modification of technique; and the “replication crisis” is primarily about replications. It sounds like an easy, feel-good solution to the problem.

But then I read this paper:

Smaldino, Paul E., and Richard McElreath. “The Natural Selection of Bad Science.” arXiv preprint arXiv:1605.09511 (2016).

It starts off with a meta-analysis of meta-analyses of power, and comes to the same conclusion as above.

We collected all papers that contained reviews of statistical power from published papers in the social, behavioural and biological sciences, and found 19 studies from 16 papers published between 1992 and 2014. … We focus on the statistical power to detect small effects of the order d=0.2, the kind most commonly found in social science research. …. Statistical power is quite low, with a mean of only 0.24, meaning that tests will fail to detect small effects when present three times out of four. More importantly, statistical power shows no sign of increase over six decades …. The data are far from a complete picture of any given field or of the social and behavioural sciences more generally, but they help explain why false discoveries appear to be common. Indeed, our methods may overestimate statistical power because we draw only on published results, which were by necessity sufficiently powered to pass through peer review, usually by detecting a non-null effect.

Rather than leave it at that, though, the researchers decided to simulate the pursuit of science. They set up various “labs” that exerted different levels of effort to maintain methodological rigor, killed off labs that didn’t publish much and replaced them with mutations of labs that published more, and set the simulation spinning.

We ran simulations in which power was held constant but in which effort could evolve (μw=0, μe=0.01). Here selection favoured labs who put in less effort towards ensuring quality work, which increased publication rates at the cost of more false discoveries … . When the focus is on the production of novel results and negative findings are difficult to publish, institutional incentives for publication quantity select for the continued degradation of scientific practices.

That’s not surprising. But then they started tinkering with replication rates. To begin with, replications were done 1% of the time, were guaranteed to be published, and having one of your results fail to replicate would exact a terrible toll.

We found that the mean rate of replication evolved slowly but steadily to around 0.08. Replication was weakly selected for, because although publication of a replication was worth only half as much as publication of a novel result, it was also guaranteed to be published. On the other hand, allowing replication to evolve could not stave off the evolution of low effort, because low effort increased the false-positive rate to such high levels that novel hypotheses became more likely than not to yield positive results … . As such, increasing one’s replication rate became less lucrative than reducing effort and pursuing novel hypotheses.

So it was time for extreme measures: force the replication rate to high levels, to the point that 50% of all studies were replications. All that happened was that it took longer for the overall methodological effort to drop and false positives to bloom.

Replication is not sufficient to curb the natural selection of bad science because the top performing labs will always be those who are able to cut corners. Replication allows those labs with poor methods to be penalized, but unless all published studies are replicated several times (an ideal but implausible scenario), some labs will avoid being caught. In a system such as modern science, with finite career opportunities and high network connectivity, the marginal return for being in the top tier of publications may be orders of magnitude higher than an otherwise respectable publication record.

Replication isn’t enough. The field of science needs to incorporate more radical reforms that encourage high methodological rigor and greater power.

Steven Pinker and his Portable Goalposts

PZ Myers seems to have pissed off quite a few people, this time for taking Steven Pinker to task. His take is worth reading in full, but I’d like to add another angle. In the original interview, there’s a very telling passage:

Belluz: But as you mentioned, there’s been an uptick in war deaths driven by the staggeringly violent ongoing conflict in Syria. Does that not affect your thesis?

Pinker: No, it doesn’t affect the thesis because the rate of death in war is about 1.4 per 100,000 per year. That’s higher than it was at the low point in 2010. But it’s still a fraction of what it was in earlier years.

See the problem here? Pinker’s hypothesis is that over the span of centuries, violence will decrease. The recent spike in deaths may be the start of a reversal that proves Pinker wrong. But because his hypothesis covers such a wide timespan, we’re going to need fifty or more years worth of data to challenge it. [Read more…]

Veritasium on the Reproducibility Crisis

It’s a great summary, going into much more depth than most. I really like how Muller brought out a concrete example of publication bias, and found an example of p-hacking in a branch of science that’s usually resistant to it, physics.

But I’m not completely happy with it. Some of this comes from being a Bayesian fanboi that didn’t hear the topic mentioned, but Muller also makes a weird turn of phrase at the end. Muller argues that, as bad as the flaws in science may be, think of how much worse they are in all our other systems of learning about the world.

Slight problem: there are no other systems. Even “I feel it’s true” is based on an evidential claim, evaluated for plausibility against other competing hypotheses. The weighting procedure may be hopelessly skewed, but so too are p-values and the publication process.

Muller could have strengthened his point by bringing up an example, yet did not. We’re left taking his word that science isn’t the sole methodology we have for exploring the world, and that those alternate methodologies aren’t as rigorous. Meanwhile, he explicitly points out that a small fraction of “landmark cancer trials” could be replicated; this implies that cancer treatments, and by extension the well-being of millions of cancer patients, are being harmed by poor methodology in science. Even if you disagree with my assertion that all epistemologies are scientific in some fashion, it’s tough to find a counter-example that effects 40% of us and will kill a quarter.

My hope doesn’t come from a blind assurance that other methodologies are worse than science, it comes from the news that scientists have recognized the flaws in their trade, and are working to correct them. To be fair to Muller, he’d probably agree.

Ignorance and Social Justice

“Why are you a feminist?”

Because it lets me sleep at night. Think about it: let’s say it’s true that over half the human population is burdened with a systematic disadvantage compared to the rest. Having learned of that, can you honestly shrug your shoulders and ignore the problem? I certainly can’t, so I’ll do what little I can to correct this injustice.

You may not agree, which is fine. But the corrolary of this view is that you cannot be opposed to feminism without also misunderstanding it. This sets up a prediction we can test: people who oppose feminism and other forms of social justice must be ignorant of it, must invoke straw-people, and must be resistant to learning or understanding it, if my stance has some truth to it.

The evidence suggests it has more than a little.

For instance, after offering to debate Martin Hughes, TJ Kirk cowardly backed out. Stephanie Zvan has an excellent blog post up pointing out that this is a common theme: people opposed to social justice aren’t keen on actually debating the subject.

That’s the real function of “You don’t want to debate” in this context. It isn’t to get you to debate. It’s there to say there’s something wrong with you. That’s why the offer disappears once you drag the argument into the reality of terms and conditions and making sure no one profits from the debate. It wasn’t real to begin with.

To do well in a debate, you really have to know the other side in depth. If you do that homework, though, you might learn the other side’s arguments are correct. So if you are hoping to sleep well at night, you don’t debates. I popped into the comment section to point out an exception to this:

Some of the hardcore haters would disagree, and say they’re perfectly fine with a debate. They have a very peculiar definition of “debate” in mind, though, where both sides shout slogans into the night without critically appraising their merits. It’s an extension of what I’ve called the “treadmill of lies:” By endlessly cycling from myth to lie, they avoid having to consider any one in detail and thus can convince themselves they’re just a bunch of skeptical satirists.

When this actually happens during a debate, we call it a “Gish Gallop.” This technique is a big problem with traditional, in-person debates, and I don’t think it’s a coincidence that TJ Kirk was pushing for this format instead of a more leisurely exchange of blog posts. He knew he had nothing but slogans against Hughes’ arguments, and he knew those wouldn’t convince anyone but those already convinced. Unless there was some sort of reward involved, like cash or a raised profile, there was no point in “debating” Hughes.

I go into a little more detail on the treadmill here. But as luck would have it, this data point was followed by yet another. Possibly in response to the controversy kicked off by Kirk, a number of atheist YouTubers joined with him to fire back a challenge: “QUESTIONS WHITE MEN HAVE FOR SJWs!

Others in the atheo/skeptic community have been responding back, in between bouts of muffled laughter and obvious eyerolls. I’ll add my two cents at some point, but for now I’d like to point out a common theme in the questions.

3. Do you want women to be equal or do you want women to be a protected class? You can’t have both.

Protected class: “A group of people with a common characteristic who are legally protected from employment discrimination on the basis of that characteristic. Protected classes are created by both federal and state law. … Federal protected classes include: Race. Color. Religion or creed. National origin or ancestry. Sex.

4. What are you afraid will happen when you leave your “safe space”?

A Safe Space is a place where anyone can relax and be able to fully express, without fear of being made to feel uncomfortable, unwelcome, or unsafe on account of biological sex, race/ethnicity, sexual orientation, gender identity or expression, cultural background, religious affiliation, age, or physical or mental ability.

5. How can you possibly justify the idea that it’s somehow racist to disagree with black lives matter?

When we say Black Lives Matter, we are broadening the conversation around state violence to include all of the ways in which Black people are intentionally left powerless at the hands of the state.  We are talking about the ways in which Black lives are deprived of our basic human rights and dignity.

6. Are you aware the present is not the past? Are you familiar with the concept of linear time? Because you seem incredibly comfortable traveling back through time by talking about how bad things were for women, or black people, or whomever. And then by using some form of SJW magic, you then claim or imply that those problems in the past exist today. Are you aware that this trick that you’re doing is not working? Why do you think that would work?

Results: In the United States, an estimated 19.3% of women and 1.7% of men have been raped during their lifetimes; an estimated 1.6% of women reported that they were raped in the 12 months preceding the survey. The case count for men reporting rape in the preceding 12 months was too small to produce a statistically reliable prevalence estimate. An estimated 43.9% of women and 23.4% of men experienced other forms of sexual violence during their lifetimes, including being made to penetrate, sexual coercion, unwanted sexual contact, and noncontact unwanted sexual experiences. The percentages of women and men who experienced these other forms of sexual violence victimization in the 12 months preceding the survey were an estimated 5.5% and 5.1%, respectively.

8. Did you know there are 13% more women in college right now than men? So if the whole goal of feminism is “equality,” shouldn’t we have some men-only scholarships in order to equal everything out?

The strength of this unconscious bias is quite astonishing – even for a relatively objective measure such as promptness, students rated a “female” professor 3.55 out of 5 and a “male” professor 4.35, despite the fact that they handed work back at the same time.

The implications are serious. In the competitive world of academia, student evaluations are often used as a tool in the process of hiring and promotion. That the evaluations may be biased against female professors is particularly problematic in light of existing gender imbalance, particularly at the highest echelons of academia. According to the American Association of University Professors, in 2012, 62% of men in academia in the US were tenured compared to only 44% of women, while women were far more likely to be in non-tenure track positions than men (32% of women in academia compared to just 19% of men).

When there are answers to the questions those YouTubers fired off, it only takes a few minutes of Googling to get an answer. Want scientific studies? They’ve been done by the hundreds, on nearly all the topics pushed by “social justice warriors.” Decades of research have been done, untold thousands of words have been spilled, and yet these people opposed to social justice are completely ignorant of it all. Had they put in the time to educate themselves, like some others have, they’d become social justice warriors too.

But as Zvan would have predicted, some of those questions aren’t actually questions.

7. Why do you think that you can spend your entire life in a state of perpetual emotional immaturity? Do you actually imagine that you’ll be able to stretch out your adolescence for your entire existence?

10. What do you hope to gain by bringing back racial segregation?

12. Why do you think every cis white male is born racist?

14. Would you rather be right, or popular? It seems like your primary objective is to score social points and get public validation.

These questions were never meant to be answered, they’re just empty talking points that form the treadmill’s belt. They’re meant to protect you from educating yourself, from breaking the wall of ignorance.

Because you might not sleep well, once you find out what’s on the other side.

A Computer Scientist Reads EvoPsych, Part 4

[Part 3]

The programs comprising the human mind were designed by natural selection to solve the adaptive problems regularly faced by our hunter-gatherer ancestors—problems such as finding a mate, cooperating with others, hunting, gathering, protecting children, navigating, avoiding predators, avoiding exploitation, and so on. Knowing this allows evolutionary psychologists to approach the study of the mind like an engineer. You start by carefully specifying an adaptive information processing problem; then you do a task analysis of that problem. A task analysis consists of identifying what properties a program would have to have to solve that problem well. This approach allows you to generate hypotheses about the structure of the programs that comprise the mind, which can then be tested.[1]

Let’s try this approach. My task will be to calculate the inverse square root of a number, a common one in computer graphics. The “inverse” part implies I’ll have to do a division at some point, and the “square root” implies either raising something to a power, finding the logarithm of the input, or invoking some sort of function that’ll return the square root. So I should expect a program which contains an inverse square root function to have something like:

float InverseSquareRoot( float x ) 
{

     return 1.0 / sqrt(x);

}

So you could imagine my shock if I peered into a program and found this instead:

float FastInvSqrt( float x )
{
    long i;
    float x2, y;
    
    x2 = x * 0.5;

    i = * ( long * ) &x;
    i = 0x5f3759df - ( i >> 1 );
    y = * ( float * ) &i;

    y = y * ( 1.5 - ( x2 * y * y ) );

    return y;
}

Something like that snippet was in Quake III’s software renderer. It uses one step of Newton’s Method to find the zero of an equation derived from the input value, seeded by a guess that takes advantage of the structure of floating point numbers. It also breaks every one of the predictions my analysis made, not even including a division.

The task analysis failed for a simple reason: nearly every problem has more than one approach to it. If we’re not aware of every alternative, our analysis can’t take all of them into account and we’ll probably be led astray. We’d expect convolutions to be slow for large kernels unless we were aware of the Fourier transform, we’d think it was impossible to keep concurrent operations from mucking up memory unless we knew we had hardware-level atomic operations, and if we thought of sorting purely in terms of comparing one value to another we’d miss out on the fastest sorting algorithm out there, Radix sort.

Radix sort doesn’t get implemented very often because it either requires a tonne of memory, or the overhead of doing a census makes it useless on small lists. To put that more generally, the context of execution matters more than the requirements of the task during implementation. The simplistic approach of Tooby and Cosmides does not take that into account.

We can throw them a lifeline, mind you. I formed a hypothesis about computing inverse square roots, refuted it, and now I’m wiser for it. Isn’t that still a net win for the process? Notice a key difference, though: we only became wiser because we could look at the source code. If FastInvSqrt() was instead a black box, the only way I could refute my analysis would be to propose the exact way the algorithm worked and then demonstrated it consistently predicted the outputs much better. If I didn’t know the techniques used in FastInvSqrt() were possible, I’d never be able to refute it.

On the contrary, I might falsely conclude I was right. After all, the outputs of my analysis and FastInvSqrt() are very similar, so I could easily wave away the differences as due to a buggy square root function or a flaw in the division routine. This is especially dangerous with evolutionary algorithms, as Dr. Adrian Thompson figured out in an earlier installment, because the odds of us knowing every possible trick are slim.

In sum, this analysis method is primed to generate smug over-confidence in your theories.

Each organ in the body evolved to serve a function: The intestines digest, the heart pumps blood, and the liver detoxifies poisons. The brain’s evolved function is to extract information from the environment and use that information to generate behavior and regulate physiology. Hence, the brain is not just like a computer. It is a computer—that is, a physical system that was designed to process information. Its programs were designed not by an engineer, but by natural selection, a causal process that retains and discards design features based on how well they solved adaptive problems in past environments.[1]

And is my appendix’s function to randomly attempt to kill me? The only people I’ve seen push this biological teleology are creationists who propose an intelligent designer. Few people well studied in biology would buy this line.

But getting back to my field, notice the odd dichotomy at play here: our brains are super-sophisticated computational devices, but not sophisticated enough to re-program themselves on-the-fly. Yet even the most primitive computers we’ve developed can modify the code they’re running, as they’re running it. Why isn’t that an option? Why can’t we be as much of a blank slate as forty-year old computer chips?

It’s tempting to declare that we’re more primitive than they are, computationally, but there’s a fundamental problem here: algorithms are algorithms are algorithms. If you can compute, you’re a Turing machine of some sort. There is no such thing as a “primitive” computer, at best you could argue some computers have more limitations imposed on them than others.

Human beings can compute, as anyone who’s taken a math course can attest. Ergo, we must be something like a Turing machine. Is it possible that our computation is split up into programs, which themselves change only slowly? Sure, but that’s an extra limitation imposed on our computability. It should not be assumed a-priori.

[Part 5]


[1] Tooby, John, and Leda Cosmides. “Conceptual Foundations of Evolutionary Psychology.The Handbook of Evolutionary Psychology (2005): 5-67.

A Computer Scientist Reads EvoPsych, Part 3

[Part 2]

As a result of selection acting on information-behavior relationships, the human brain is predicted to be densely packed with programs that cause intricate relationships between information and behavior, including functionally specialized learning systems, domain-specialized rules of inference, default preferences that are adjusted by experience, complex decision rules, concepts that organize our experiences and databases of knowledge, and vast databases of acquired information stored in specialized memory systems—remembered episodes from our lives, encyclopedias of plant life and animal behavior, banks of information about other people’s proclivities and preferences, and so on. All of these programs and the databases they create can be called on in different combinations to elicit a dazzling variety of behavioral responses.[1]

“Program?” “Database?” What exactly do those mean? That might seem like a strange question to hear from a computer scientist, but my training makes me acutely aware of how flexible those terms can be. [Read more…]

What is False?

John Oliver weighed in on the replication crisis, and I think he did a great job. I’d have liked a bit more on university press departments, who can write misleading press releases that journalists jump on, but he did have to simplify things for a lay audience.

It got me thinking about what “false” means, though. “True” is usually defined as “in line with reality,” so “false” should mean “not in line with reality,” the precise compliment.

But don’t think about it in terms of a single thing, but in multiple data points applied to a specific theory. Suppose we analyze that data, and find that all but a few datapoints are predicted by the hypothesis we’re testing. Does this mean the hypothesis is false, since it isn’t in line with reality in all cases, or true, because it’s more in line with reality than not? Falsification argues that it is false, and exploits that to come up with this epistemology:

  1. Gather data.
  2. Is that data predicted by the hypothesis? If so, repeat step 1.
  3. If not, replace this hypothesis with another that predicts all the data we’ve seen so far, and repeat step 1.

That’s what I had in mind when I said that frequentism works on streams of hypotheses, hopping from one “best” hypothesis to the next. The addition of time changes the original definitions slightly, so that “true” really means “in line with reality in all instances” while “false” means “in at least one instance, it is not in line with reality.”

Notice the asymmetry, though. A hypothesis has to reach a pretty high bar to be considered “true,” and “false” hypotheses range from “in line with reality, with one exception” to “never in line with reality.” Some of those “false” hypotheses are actually quite valuable to us, as John Oliver’s segment demonstrates. He never explains what “statistical significance” means, for instance, but later on uses “significance” in the “effect size” sense. This will mislead most of the audience away from the reality of the situation, and in the absolute it makes his segment “false.” Nonetheless, that segment was a net positive at getting people to understand and care for the replication crisis, so labeling it “false” is a disservice.

We need something fuzzier than the strict binary of falsification. What if we didn’t compliment “true” in the set-theory sense, but in the definitional sense? Let “true” remain “in line with reality in all instances,” but change “false” from “in at least one instance, it is not in reality” to “never in line with reality.” This creates a gap, though: that hypothesis from earlier is neither “true” nor “false,” as it isn’t true in all cases nor false in all. It must be in a third category, as part of some sort of paraconsistent logic.

This is where the Bayesian interpretation of statistics comes from, it deliberately disclaims an absolute “true” or “false” label for descriptions of the world, instead holding them up as two ends of a continuum. Every hypothesis in the third category inbetween, hoping that future data will reveal that its closer to one end of the continuum or the other.

I think it’s a neat way to view the Bayesian/Frequentism debate, as a mere disagreement over what “false” means.

A Computer Scientist Reads EvoPsych, Part 2

[Part 1]

the concept of “learning” within the Standard Social Science Model itself tacitly invokes unbounded rationality, in that learning is the tendency of the general-purpose, equipotential mind to grow—by an unspecified and undiscovered computational means—whatever functional information-processing abilities it needs to serve its purposes, given time and experience in the task environment.

Evolutionary psychologists depart from fitness teleologists, traditional economists (but not neuroeconomists), and blank-slate learning theorists by arguing that neither human engineers nor evolution can build a computational device that exhibits these forms of unbounded rationality, because such architectures are impossible, even in principle (for arguments, see Cosmides & Tooby, 1987; Symons 1989, 1992; Tooby & Cosmides, 1990a, 1992).[1]

Yeah, these people don’t know much about computer science.

You can divide the field of “artificial” intelligence into two basic approaches. The top-down approach outlined modular code routines like “recognize faces,” then broke those down into sub-tasks like “look for eyes” and “find mouths.” By starting at a high level and dividing these things down into neat, tidy sub-programs, we can chain them together and create a greater whole.

It’s never worked all that well, at least for real-life problems. Take Cyc, the best example I can think of. It takes basic facts about the world, like “water is wet” or “rain is water,” and uses a simple set of rules to query these facts (“is rain wet?”). What it can’t do is make guesses (“are clouds wet?”), nor discover new facts on its own, nor handle anything but simple text. Thirty years and millions of dollars haven’t made a dent in those problems.

Meanwhile, the graphics card manufacturer NVidia is betting the farm on something called “deep learning,” one of several “bottom-up” approaches. You present the algorithm with an image (or sound file or object, the number of dimensions can be easily changed), and it maps it to a grid of cells. You toss a slightly smaller grid of cells on top of it, and for each new cell you calculate a weighted sum of the nearby values in the previous grid, weights that are random to start off with. Repeat this several times, and you’ll wind up with a single cell at the end. Assign this cell to an output, say “person,” then rewind all the way back to the start. Wash, rinse, and repeat until you get another single cell, then at least enough single cells to handle every possible solution. All of these single cells have a value associated with them, so that “person” cell might give the image 0.7 “person”s. Having cataloged what’s in the image already, you know there’s actually 1.0 “person” there, and so you propagate that information back down the chain. Prior cell weights which were pro-person are increased, while the anti-person ones are decreased. Do this right to the bottom, and for every input cell, then repeat the process for a new image.

It’s loosely patterned after how our own neurons are laid out. Biology is a bit more liberal with how it connects, but this structure has the virtue of being easy to calculate and massively parallel, quite convenient for a company which manufactures processors that specialize in massively parallel computations. NVidia’s farm-betting comes from the fact that it’s wildly successful; all of the best image recognition algorithms follow the deep-learning pattern, and their success rates are not only impressive but also resemble our own.[2]

Heard of the AI that could play Atari games? Emphasis mine:

Our [Deep action-value Network or DQN] method outperforms the best existing reinforcement learning methods on 43 games without incorporating any of the additional prior knowledge about Atari 2600 games used by other approaches … . Furthermore, our DQN agent performed at a level that was comparable to that of a professional human games tester across the set of 49 games, achieving more than 75% of the human score on more than half of the games […]

Indeed, in certain games DQN is able to discover a relatively long-term strategy (for example, Breakout: the agent learns the optimal strategy, which is to first dig a tunnel around the side of the wall allowing the ball to be sent around the back to destroy a large number of blocks; …). […]

In this work, we demonstrate that a single architecture can successfully learn control policies in a range different environments with only very minimal prior knowledge, receiving only the pixels and the game score as inputs, and using the same algorithm, network architecture and hyperparameters each game, privy only to the inputs a human player would have.[3]

This deep learning network has no idea what a video game is, nor is it permitted to peek at the innards of the game itself, yet can not only learn to play these games at the same level as human beings, it can develop non-trivial solutions to them. You can’t get more “blank slate” than that.

This basic pattern has repeated multiple times over the decades. Neural nets aren’t as zippy as the new kid on the “bottom-up” block, yet they too have had great success where the modular top-down approach has failed miserably. I haven’t worked with either technology, but I’ve worked with something that’s related: genetic algorithms. Represent your solutions in a sort of genome, come up with a fitness metric for them, then mutate or randomly construct those genomes and keep the fittest ones in the pool until you’ve tried every possibility, or you get bored. Two separate runs might converge to the same solution, or they might not. A lot depends on the “fitness landscape” they occupy, which you can visualize as a 3D terrain map with height representing how “fit” something is.

A visualization of three "evolutionary fitness landscapes," ranging from simple to complex to SUPER complex.That landscape has probably got more than three dimensions, but those aren’t as easy to visualize and they behave very similarily to the 3D case. The terrain might be a Mount Fiji with a single solution at the top of a fitness peak, or a Himalayas with many peak solutions scattered about but a single tallest standing above them, or a foothills where solutions are aplenty but the best solution is tough to find.

All of these take the “bottom-up” approach, the opposite of the “top-down” one, and work up from very small components towards a high-level goal. The path to there is rarely known in advance, so the system “feels” its way there via evolutionary algorithms.

That path may not go the way you expect, however. Take the case of a researcher, Dr. Adrian Thompson, who used an evolutionary algorithm to find the smallest computer processor that could sense the difference between two tones.

Finally, after just over 4,000 generations, the test system settled upon the best program. When Dr. Thompson played the 1kHz tone, the microchip unfailingly reacted by decreasing its power output to zero volts. When he played the 10kHz tone, the output jumped up to five volts. He pushed the chip even farther by requiring it to react to vocal “stop” and “go” commands, a task it met with a few hundred more generations of evolution. As predicted, the principle of natural selection could successfully produce specialized circuits using a fraction of the resources a human would have required. And no one had the foggiest notion how it worked.

Dr. Thompson peered inside his perfect offspring to gain insight into its methods, but what he found inside was baffling. The plucky chip was utilizing only thirty-seven of its one hundred logic gates, and most of them were arranged in a curious collection of feedback loops. Five individual logic cells were functionally disconnected from the rest— with no pathways that would allow them to influence the output— yet when the researcher disabled any one of them the chip lost its ability to discriminate the tones. Furthermore, the final program did not work reliably when it was loaded onto other FPGAs of the same type.

It seems that evolution had not merely selected the best code for the task, it had also advocated those programs which took advantage of the electromagnetic quirks of that specific microchip environment. The five separate logic cells were clearly crucial to the chip’s operation, but they were interacting with the main circuitry through some unorthodox method— most likely via the subtle magnetic fields that are created when electrons flow through circuitry, an effect known as magnetic flux. There was also evidence that the circuit was not relying solely on the transistors’ absolute ON and OFF positions like a typical chip; it was capitalizing upon analogue shades of gray along with the digital black and white.[4]

Evolutionary approaches are very simple and require no understanding or insight into the problem you’re solving, but they usually requires ridiculous amounts of computation or training merely to keep pace with the top-down “modular” approach. The fitness function may lead to a solution much too complicated for you to understand or much too fragile to operate anywhere but where it was generated. But the bottom-up approach may be your only choice for certain problems.

The moral of the story: the ability to do complex calculation can be built up from a blank slate, in principle and practice. When we follow the bottom-up approach we tend to get results that more closely mirror biology than when we work from the top-down and modularize, though this is less insightful than it first appears. Nearly all bottom-up approaches take direct inspiration from biology, whereas top-down approaches owe more to Plato then Aristotle.

Biology prefers the blank slate.

[Part 3]


[1] Tooby, John, and Leda Cosmides. “Conceptual Foundations of Evolutionary Psychology.The Handbook of Evolutionary Psychology (2005): 5-67.

[2] Kheradpisheh, Saeed Reza, et al. “Deep Networks Resemble Human Feed-forward Vision in Invariant Object Recognition.” arXiv preprint arXiv:1508.03929 (2015).

[3] Mnih, Volodymyr, et al. “Human-level control through deep reinforcement learning.” Nature 518.7540 (2015): 529-533.

[4] Bellows, Alan. “On the Origin of Circuits • Damn Interesting.” Accessed May 4, 2016.

A Computer Scientist Reads EvoPsych, Part 1

Computer Science is weird. Most of the papers published in my field look like this:

We describe the architecture of a novel system for precomputing sparse directional occlusion caches. These caches are used for accelerating a fast cinematic lighting pipeline that works in the spherical harmonics domain. The system was used as a primary lighting technology in the movie Avatar, and is able to efficiently handle massive scenes of unprecedented complexity through the use of a flexible, stream-based geometry processing architecture, a novel out-of-core algorithm for creating efficient ray tracing acceleration structures, and a novel out-of-core GPU ray tracing algorithm for the computation of directional occlusion and spherical integrals at arbitrary points.[1]

A speed improvement of two orders of magnitude is pretty sweet, but this paper really isn’t about computers per se; it’s about applying existing concepts in computer graphics in a novel combination to solve a practical problem. Most papers are all about the application of computers, and not computing itself. You can dig up examples of the latter, like if you try searching for concurrency theory,[2] but even then you’ll run across a lot of applied work, like articles on sorting algorithms designed for graphics cards.[3]

In sum, computer scientists spend most of their time working in other people’s fields, solving other people’s problems. So you can imagine my joy when I stumbled on people in other fields invoking computer science.

Because the evolved function of a psychological mechanism is computational—to regulate behavior and the body adaptively in response to informational inputs—such a model consists of a description of the functional circuit logic or information processing architecture of a mechanism (Cosmides & Tooby, 1987; Tooby & Cosmides, 1992). Eventually, these models should include the neural, developmental, and genetic bases of these mechanisms, and encompass the designs of other species as well.[4]

Hot diggity! How well does that non-computer-scientist understand the field, though? Let’s put my degree to work.

The second building block of evolutionary psychology was the rise of the computational sciences and the recognition of the true character of mental phenomena. Boole (1848) and Frege (1879) formalized logic in such a way that it became possible to see how logical operations could be carried out mechanically, automatically, and hence through purely physical causation, without the need for an animate interpretive intelligence to carry out the steps. This raised the irresistible theoretical possibility that not only logic but other mental phenomena such as goals and learning also consisted of formal relationships embodied nonvitalistically in physical processes (Weiner, 1948). With the rise of information theory, the development of the first computers, and advances in neuroscience, it became widely understood that mental events consisted of transformations of structured informational relationships embodied as aspects of organized physical systems in the brain. This spreading appreciation constituted the cognitive revolution. The mental world was no longer a mysterious, indefinable realm, but locatable in the physical world in terms of precisely describable, highly organized causal relations.[4]

Yes! I’m right with you here. One of the more remarkable findings of computer science is that every computation or algorithm can be executed on a Turing machine. That includes all of Quantum Field Theory, even those Quant-y bits. While QFT isn’t a complete theory, we’re extremely confident in the subset we need to simulate neural activity. Those simulations have long since been run and matched against real-world data, the current problem is scaling up from faking a million neurons at a time to faking 100 billion, about as many as you have locked in your skull.

Our brains can be perfectly simulated by a computational device, and our brain’s ability to do math proves they are computational. I can quibble a bit on the wording (“precisely describable” suggests we’ve faked those 100 billion), but we’re off to a great start here.

After all, if the human mind consists primarily of a general capacity to learn, then the particulars of the ancestral hunter-gatherer world and our prehuman history as Miocene apes left no interesting imprint on our design. In contrast, if our minds are collections of mechanisms designed to solve the adaptive problems posed by the ancestral world, then hunter-gatherer studies and primatology become indispensable sources of knowledge about modern human nature.[4]

Wait, what happened to the whole “our brains are computers” thing? Look, here’s a diagram of a Turing machine.

An annotated diagram of a Turing machine. Copyright HJ Hornbeck 2016, CC-BY-SA 4.0.

A read/write head sits somewhere along an infinite ribbon of tape. It reads what’s under the head, writes back a value to that location, and moves either left or right, all based on that value. How does it know what to do? Sometimes that’s hard-wired into the machine, but more commonly it reads instructions right off the tape. These machines don’t ship with much of anything, just the bare minimum necessary to do every possible computation.

This carries over into physical computers as well; when the CPU of your computer boots up, it does the following:

  1. Read the instruction at memory location 4,294,967,280.
  2. Execute it.

Your CPU does have “programs” of a sort, instructions such as ADD (addition) or MULT (multiply), but removing them doesn’t remove its ability to compute. All of those extras can be duplicated by grouping together simpler operations, they’re only there to make programmers’ lives easier.

There’s no programmer for the human brain, though. Despite what The Matrix told you, no-one can fiddle around with your microcode and add new programs. There is no need for helper instructions. So if human brains are like computers, and computers are blank slates for the most part, we have a decent reason to think humans are blank slates too, infinitely flexible and fungible.

[Part 2]


[1] Pantaleoni, Jacopo, et al. “PantaRay: fast ray-traced occlusion caching of massive scenes.” ACM Transactions on Graphics (TOG). Vol. 29. No. 4. ACM, 2010.

[2] Roscoe, Bill. “The theory and practice of concurrency.” (1998).

[3] Ye, Xiaochun, et al. “High performance comparison-based sorting algorithm on many-core GPUs.” Parallel & Distributed Processing (IPDPS), 2010 IEEE International Symposium on. IEEE, 2010.

[4] Tooby, John, and Leda Cosmides. “Conceptual Foundations of Evolutionary Psychology.The Handbook of Evolutionary Psychology (2005): 5-67.

Index Post: P-values

Over the months, I’ve managed to accumulate a LOT of papers discussing p-values and their application. Rather than have them rot on my hard drive, I figured it was time for another index post.

Full disclosure: I’m not in favour of them. But I came to that by reading these papers, and seeing no effective counter-argument. So while this collection is biased against p-values, that’s no more a problem than a bias against the luminiferous aether or humour theory. And don’t worry, I’ll include a few defenders of p-values as well.

What’s a p-value?

It’s frequently used in “null hypothesis significance testing,” or NHST to its friends. A null hypothesis is one you hope to refute, preferably a fairly established one that other people accept as true. That hypothesis will predict a range of observations, some more likely than others. A p-value is simply the odds of some observed event happening, plus the odds of all events more extreme, assuming the null hypothesis is true. You can then plug that value into the following logic:

  1. Event E, or an event more extreme, is unlikely to occur under the null hypothesis.
  2. Event E occurred.
  3. Ergo, the null hypothesis is false.

They seem like a weird thing to get worked up about.

Significance testing is a cornerstone of modern science, and NHST is the most common form of it. A quick check of Google Scholar shows “p-value” shows up 3.8 million times, while its primary competitor, “Bayes Factor,” shows up 250,000. At the same time, it’s poorly understood.

The P value is probably the most ubiquitous and at the same time, misunderstood, misinterpreted, and occasionally miscalculated index in all of biomedical research. In a recent survey of medical residents published in JAMA, 88% expressed fair to complete confidence in interpreting P values, yet only 62% of these could answer an elementary P-value interpretation question correctly. However, it is not just those statistics that testify to the difficulty in interpreting P values. In an exquisite irony, none of the answers offered for the P-value question was correct, as is explained later in this chapter.

Goodman, Steven. “A Dirty Dozen: Twelve P-Value Misconceptions.” In Seminars in Hematology, 45:135–40. Elsevier, 2008. http://www.sciencedirect.com/science/article/pii/S0037196308000620.

The consequence is an abundance of false positives in the scientific literature, leading to many failed replications and wasted resources.

Gotcha. So what do scientists think is wrong with them?

Well, th-

And make it quick, I don’t have a lot of time.

Right right, here’s the top three papers I can recommend:

Null hypothesis significance testing (NHST) is arguably the mosl widely used approach to hypothesis evaluation among behavioral and social scientists. It is also very controversial. A major concern expressed by critics is that such testing is misunderstood by many of those who use it. Several other objections to its use have also been raised. In this article the author reviews and comments on the claimed misunderstandings as well as on other criticisms of the approach, and he notes arguments that have been advanced in support of NHST. Alternatives and supplements to NHST are considered, as are several related recommendations regarding the interpretation of experimental data. The concluding opinion is that NHST is easily misunderstood and misused but that when applied with good judgment it can be an effective aid to the interpretation of experimental data.

Nickerson, Raymond S. “Null Hypothesis Significance Testing: A Review of an Old and Continuing Controversy.” Psychological Methods 5, no. 2 (2000): 241.

After 4 decades of severe criticism, the ritual of null hypothesis significance testing (mechanical dichotomous decisions around a sacred .05 criterion) still persists. This article reviews the problems with this practice, including near universal misinterpretation of p as the probability that H₀ is false, the misinterpretation that its complement is the probability of successful replication, and the mistaken assumption that if one rejects H₀ one thereby affirms the theory that led to the test.

Cohen, Jacob. “The Earth Is Round (p < .05).” American Psychologist 49, no. 12 (1994): 997–1003. doi:10.1037/0003-066X.49.12.997.

This chapter examines eight of the most commonly voiced objections to reform of data analysis practices and shows each of them to be erroneous. The objections are: (a) Without significance tests we would not know whether a finding is real or just due to chance; (b) hypothesis testing would not be possible without significance tests; (c) the problem is not significance tests but failure to develop a tradition of replicating studies; (d) when studies have a large number of relationships, we need significance tests to identify those that are real and not just due to chance; (e) confidence intervals are themselves significance tests; (f) significance testing ensure objectivity in the interpretation of research data; (g) it is the misuse, not the use, of significance testing that is the problem; and (h) it is futile to reform data analysis methods, so why try?

Schmidt, Frank L., and J. E. Hunter. “Eight Common but False Objections to the Discontinuation of Significance Testing in the Analysis of Research Data.” What If There Were No Significance Tests, 1997, 37–64.

OK, I have a bit more time now. What else do you have?

Using a Bayesian significance test for a normal mean, James Berger and Thomas Sellke (1987, pp. 112–113) showed that for p values of .05, .01, and .001, respectively, the posterior probabilities of the null, Pr(H₀ | x), for n = 50 are .52, .22, and .034. For n = 100 the corresponding figures are .60, .27, and .045. Clearly these discrepancies between p and Pr(H₀ | x) are pronounced, and cast serious doubt on the use of p values as reasonable measures of evidence. In fact, Berger and Sellke (1987) demonstrated that data yielding a p value of .05 in testing a normal mean nevertheless resulted in a posterior probability of the null hypothesis of at least .30 for any objective (symmetric priors with equal prior weight given to H₀ and HA ) prior distribution.

Hubbard, R., and R. M. Lindsay. “Why P Values Are Not a Useful Measure of Evidence in Statistical Significance Testing.” Theory & Psychology 18, no. 1 (February 1, 2008): 69–88. doi:10.1177/0959354307086923.

Because p-values dominate statistical analysis in psychology, it is important to ask what p says about replication. The answer to this question is ‘‘Surprisingly little.’’ In one simulation of 25 repetitions of a typical experiment, p varied from .44. Remarkably, the interval—termed a p interval —is this wide however large the sample size. p is so unreliable and gives such dramatically vague information that it is a poor basis for inference.

Cumming, Geoff. “Replication and p Intervals: p Values Predict the Future Only Vaguely, but Confidence Intervals Do Much Better.Perspectives on Psychological Science 3, no. 4 (July 2008): 286–300. doi:10.1111/j.1745-6924.2008.00079.x.

Simulations of repeated t-tests also illustrate the tendency of small samples to exaggerate effects. This can be shown by adding an additional dimension to the presentation of the data. It is clear how small samples are less likely to be sufficiently representative of the two tested populations to genuinely reflect the small but real difference between them. Those samples that are less representative may, by chance, result in a low P value. When a test has low power, a low P value will occur only when the sample drawn is relatively extreme. Drawing such a sample is unlikely, and such extreme values give an exaggerated impression of the difference between the original populations. This phenomenon, known as the ‘winner’s curse’, has been emphasized by others. If statistical power is augmented by taking more observations, the estimate of the difference between the populations becomes closer to, and centered on, the theoretical value of the effect size.

is G., Douglas Curran-Everett, Sarah L. Vowler, and Gordon B. Drummond. “The Fickle P Value Generates Irreproducible Results.” Nature Methods 12, no. 3 (March 2015): 179–85. doi:10.1038/nmeth.3288.

If you use p=0.05 to suggest that you have made a discovery, you will be wrong at least 30% of the time. If, as is often the case, experiments are underpowered, you will be wrong most of the time. This conclusion is demonstrated from several points of view. First, tree diagrams which show the close analogy with the screening test problem. Similar conclusions are drawn by repeated simulations of t-tests. These mimic what is done in real life, which makes the results more persuasive. The simulation method is used also to evaluate the extent to which effect sizes are over-estimated, especially in underpowered experiments. A script is supplied to allow the reader to do simulations themselves, with numbers appropriate for their own work. It is concluded that if you wish to keep your false discovery rate below 5%, you need to use a three-sigma rule, or to insist on p≤0.001. And never use the word ‘significant’.

Colquhoun, David. “An Investigation of the False Discovery Rate and the Misinterpretation of P-Values.” Royal Society Open Science 1, no. 3 (November 1, 2014): 140216. doi:10.1098/rsos.140216.

I was hoping for something more philosophical.

The idea that the P value can play both of these roles is based on a fallacy: that an event can be viewed simultaneously both from a long-run and a short-run perspective. In the long-run perspective, which is error-based and deductive, we group the observed result together with other outcomes that might have occurred in hypothetical repetitions of the experiment. In the “short run” perspective, which is evidential and inductive, we try to evaluate the meaning of the observed result from a single experiment. If we could combine these perspectives, it would mean that inductive ends (drawing scientific conclusions) could be served with purely deductive methods (objective probability calculations).

Goodman, Steven N. “Toward Evidence-Based Medical Statistics. 1: The P Value Fallacy.” Annals of Internal Medicine 130, no. 12 (1999): 995–1004.

Overemphasis on hypothesis testing–and the use of P values to dichotomise significant or non-significant results–has detracted from more useful approaches to interpreting study results, such as estimation and confidence intervals. In medical studies investigators are usually interested in determining the size of difference of a measured outcome between groups, rather than a simple indication of whether or not it is statistically significant. Confidence intervals present a range of values, on the basis of the sample data, in which the population value for such a difference may lie. Some methods of calculating confidence intervals for means and differences between means are given, with similar information for proportions. The paper also gives suggestions for graphical display. Confidence intervals, if appropriate to the type of study, should be used for major findings in both the main text of a paper and its abstract.

Gardner, Martin J., and Douglas G. Altman. “Confidence Intervals rather than P Values: Estimation rather than Hypothesis Testing.” BMJ 292, no. 6522 (1986): 746–50.

What’s this “Neyman-Pearson” thing?

P-values were part of a method proposed by Ronald Fisher, as a means of assessing evidence. Even as the ink was barely dry on it, other people started poking holes in his work. Jerzy Neyman and Egon Pearson took some of Fisher’s ideas and came up with a new method, based on long-term prediction. Their method is superior, IMO, but rather than replacing Fisher’s approach it instead wound up being blended with it, ditching all the advantages to preserve the faults. This citation covers the historical background:

Huberty, Carl J. “Historical Origins of Statistical Testing Practices: The Treatment of Fisher versus Neyman-Pearson Views in Textbooks.” The Journal of Experimental Education 61, no. 4 (1993): 317–33.

While the remainder help describe the differences between the two methods, and possible ways to “fix” their shortcomings.

The distinction between evidence (p’s) and error (a’s) is not trivial. Instead, it reflects the fundamental differences between Fisher’s ideas on significance testing and inductive inference, and Neyman-Pearson’s views on hypothesis testing and inductive behavior. The emphasis of the article is to expose this incompatibility, but we also briefly note a possible reconciliation.

Hubbard, Raymond, and M. J Bayarri. “Confusion Over Measures of Evidence ( p ’S) Versus Errors ( α ’S) in Classical Statistical Testing.” The American Statistician 57, no. 3 (August 2003): 171–78. doi:10.1198/0003130031856.

The basic differences are these: Fisher attached an epistemic interpretation to a significant result, which referred to a particular experiment. Neyman rejected this view as inconsistent and attached a behavioral meaning to a significant result that did not refer to a particular experiment, but to repeated experiments. (Pearson found himself somewhere in between.)

Gigerenzer, Gerd. “The Superego, the Ego, and the Id in Statistical Reasoning.” A Handbook for Data Analysis in the Behavioral Sciences: Methodological Issues, 1993, 311–39.

This article presents a simple example designed to clarify many of the issues in these controversies. Along the way many of the fundamental ideas of testing from all three perspectives are illustrated. The conclusion is that Fisherian testing is not a competitor to Neyman-Pearson (NP) or Bayesian testing because it examines a different problem. As with Berger and Wolpert (1984), I conclude that Bayesian testing is preferable to NP testing as a procedure for deciding between alternative hypotheses.

Christensen, Ronald. “Testing Fisher, Neyman, Pearson, and Bayes.” The American Statistician 59, no. 2 (2005): 121–26.

C’mon, there aren’t any people defending the p-value?

Sure there are. They fall into two camps: “deniers,” a small group that insists there’s nothing wrong with p-values, and the much more common “fixers,” who propose making up for the shortcomings by augmenting NHST. Since a number of fixers have already been cited, I’ll just focus on the deniers here.

On the other hand, the propensity to misuse or misunderstand a tool should not necessarily lead us to prohibit its use. The theory of estimation is also often misunderstood. How many epidemiologists can explain the meaning of their 95% confidence interval? There are other simple concepts susceptible to fuzzy thinking. I once quizzed a class of epidemiology students and discovered that most had only a foggy notion of what is meant by the word “bias.” Should we then abandon all discussion of bias, and dumb down the field to the point where no subtleties need trouble us?

Weinberg, Clarice R. “It’s Time to Rehabilitate the P-Value.” Epidemiology 12, no. 3 (2001): 288–90.

The solution is simple and practiced quietly by many researchers—use P values descriptively, as one of many considerations to assess the meaning and value of epidemiologic research findings. We consider the full range of information provided by P values, from 0 to 1, recognizing that 0.04 and 0.06 are essentially the same, but that 0.20 and 0.80 are not. There are no discontinuities in the evidence at 0.05 or 0.01 or 0.001 and no good reason to dichotomize a continuous measure. We recognize that in the majority of reasonably large observational studies, systematic biases are of greater concern than random error as the leading obstacle to causal interpretation.

Savitz, David A. “Commentary: Reconciling Theory and Practice.” Epidemiology 24, no. 2 (March 2013): 212–14. doi:10.1097/EDE.0b013e318281e856.

The null hypothesis can be true because it is the hypothesis that errors are randomly distributed in data. Moreover, the null hypothesis is never used as a categorical proposition. Statistical significance means only that chance influences can be excluded as an explanation of data; it does not identify the nonchance factor responsible. The experimental conclusion is drawn with the inductive principle underlying the experimental design. A chain of deductive arguments gives rise to the theoretical conclusion via the experimental conclusion. The anomalous relationship between statistical significance and the effect size often used to criticize NHSTP is more apparent than real.

Hunter, John E. “Testing Significance Testing: A Flawed Defense.” Behavioral and Brain Sciences 21, no. 02 (April 1998): 204–204. doi:10.1017/S0140525X98331167.