Web of C-lief: conjectures vs. model assumptions vs. scientific beliefs

Web of C-lief with the non-contradiction spider

A sketch of the theoretical computer science Web of C-lief weaved by the non-contradiction spider.

In his 1951 paper on the “Two Dogmas of Empiricism”, W.V.O Quine introduced the Web of Belief as a metaphor for his holistic epistemology of scientific knowledge. With this metaphor, Quine aimed to give an alternative to the reductive atomising epistemology of the logical empiricists. For Quine, no “fact” is an island and no experiment can be focused in to resole just one hypothesis. Instead, each of our beliefs forms part of an interconnected web and when a new belief conflicts with an existing one then this is a signal for us to refine some belief. But this signal does not unambiguously single out a specific belief that we should refine. Just a set of beliefs that are incompatible with out new one, or that if refined could bring our belief system back into coherence. We then use alternative mechanisms like simplicity or minimality (or some aesthetic consideration) to choose which belief to update. Usually, we are more willing to give up beliefs that are peripheral to the web — that are connected to or change fewer other beliefs — than the beliefs that are central to our web.

In this post, I want to play with Quine’s web of belief metaphor in the context of science. This will force us to restrict it to specific domains instead of the grand theory that Quine intended. From this, I can then adapt the metaphor from belief in science to c-liefs in mathematics. This will let me discuss how complexity class seperation conjectures are structured in theoretical computer science and why this is fundamentally different from model assumptions in natural science.

So let’s start with a return to the relevant philosophy.

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Idealization vs abstraction for mathematical models of evolution

This week I was in Turku, Finland for the annual congress of the European Society for Evolutionary Biology. I presented in the symposium on mathematical models in evolutionary biology organized by Guy Cooper, Matishalin Patel, Tom Scott, and Asher Leeks. It was a fun. It was also a big challenge given the short ten minute format. I decided to use my ten minutes to try to convince the audience that we should consider not just idealized models but also abstractions. So after my typical introduction of computational vs algorithmic biology, I switched to talking about triangles. If you would like, dear reader, then you can watch the whole session online (or grab my slides as pdf). In this post, I just want to focus on the distinction between idealized vs. abstract models.

Just as in my ESEB talk, I’ll use triangles to explain the distinction between idealized vs. abstract models.

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Allegory of the replication crisis in algorithmic trading

One of the most interesting ongoing problems in metascience right now is the replication crisis. This a methodological crisis around the difficulty of reproducing or replicating past studies. If we cannot repeat or recreate the results of a previous study then it casts doubt on if those ‘results’ were real or just artefacts of flawed methodology, bad statistics, or publication bias. If we view science as a collection of facts or empirical truths than this can shake the foundations of science.

The replication crisis is most often associated with psychology — a field that seems to be having the most active and self-reflective engagement with the replication crisis — but also extends to fields like general medicine (Ioannidis, 2005a,b; 2016), oncology (Begley & Ellis, 2012), marketing (Hunter, 2001), economics (Camerer et al., 2016), and even hydrology (Stagge et al., 2019).

When I last wrote about the replication crisis back in 2013, I asked what science can learn from the humanities: specifically, what we can learn from memorable characters and fanfiction. From this perspective, a lack of replication was not the disease but the symptom of the deeper malady of poor theoretical foundations. When theories, models, and experiments are individual isolated silos, there is no inherent drive to replicate because the knowledge is not directly cumulative. Instead of forcing replication, we should aim to unify theories, make them more precise and cumulative and thus create a setting where there is an inherent drive to replicate.

More importantly, in a field with well-developed theory and large deductive components, a study can advance the field even if its observed outcome turns out to be incorrect. With a cumulative theory, it is more likely that we will develop new techniques or motivate new challenges or extensions to theory independent of the details of the empirical results. In a field where theory and experiment go hand-in-hand, a single paper can advance both our empirical grounding and our theoretical techniques.

I am certainly not the only one to suggest that a lack of unifying, common, and cumulative theory as the cause for the replication crisis. But how do we act on this?

Can we just start mathematical modelling? In the case of the replicator crisis in cancer research, will mathematical oncology help?

Not necessarily. But I’ll come back to this at the end. First, a story.

Let us look at a case study: algorithmic trading in quantitative finance. This is a field that is heavy in math and light on controlled experiments. In some ways, its methodology is the opposite of the dominant methodology of psychology or cancer research. It is all about doing math and writing code to predict the markets.

Yesterday on /r/algotrading, /u/chiefkul reported on his effort to reproduce 130+ papers about “predicting the stock market”. He coded them from scratch and found that “every single paper was either p-hacked, overfit [or] subsample[d] …OR… had a smidge of Alpha [that disappears with transaction costs]”.

There’s a replication crisis for you. Even the most pessimistic readings of the literature in psychology or medicine produce significantly higher levels of successful replication. So let’s dig in a bit.

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Process over state: Math is about proofs, not theorems.

A couple of days ago, Maylin and I went to pick blackberries along some trails near our house. We spent a number of hours doing it and eventually I turned all those berries into one half-litre jar of jam.

On the way to the blackberry trails, we passed a perfectly fine Waitrose — a supermarket that sells (among countless other things) jam. A supermarket I had to go to later anyways to get jamming sugar. Why didn’t we just buy the blackberries or the jam itself? It wasn’t a matter of money: several hours of our time picking berries and cooking them cost much more than a half-litre of jam, even from Waitrose.

I think that we spent time picking the berries and making the jam for the same reason that mathematicians prove theorems.

Imagine that you had a machine where you put in a statement and it replied with perfect accuracy if that statement was true or false (or maybe ill-posed). Would mathematicians welcome such a machine? It seems that Hilbert and the other formalists at the start of the 20th century certainly did. They wanted a process that could resolve any mathematical statement.

Such a hypothetical machine would be a Waitrose for theorems.

But is math just about establishing the truth of mathematical statements? More importantly, is the math that is written for other mathematicians just about establishing the truth of mathematical statements?

I don’t think so.

Math is about ideas. About techniques for thinking and proving things. Not just about the outcome of those techniques.

This is true of much of science and philosophy, as well. So although I will focus this post on the importance of process over state/outcome in pure math, I think it can also be read from the perspective of process over state in science or philosophy more broadly.

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Twitter vs blogs and science advertising vs discussion

I read and write a lot of science outside the traditional medium of papers. Most often on blogs, twitter, and Reddit. And these alternative media are colliding more and more with the ‘mainstream media’ of academic publishing. A particularly visible trend has been the twitter paper thread: a collection of tweets that advertise a new paper and summarize its results. I’ve even written such a thread (5-6 March) for my recent paper on how to use cstheory to think about evolution.

Recently, David Basanta stumbled across an old (19 March) twitter thread by Dan Quintana for why people should use such twitter threads, instead of blog posts, to announce their papers. Given my passion for blogging, I think that David expected me to defend blogs against this assault. But instead of siding with David, I sided with Dan Quintana.

If you are going to be ‘announcing’ a paper via a thread then I think you should use a twitter thread, not a blog. At least, that is what I will try to stick to on TheEGG.

Yesterday, David wrote a blog post to elaborate on his position. So I thought that I would follow suit and write one to elaborate mine. Unlike David’s blog, TheEGG has comments — so I encourage you, dear reader, to use those to disagree with me.

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Description before prediction: evolutionary games in oncology

As I discussed towards the end of an old post on cross-validation and prediction: we don’t always want to have prediction as our primary goal, or metric of success. In fact, I think that if a discipline has not found a vocabulary for its basic terms, a grammar for combining those terms, and a framework for collecting, interpreting, and/or translating experimental practice into those terms then focusing on prediction can actually slow us down or push us in the wrong direction. To adapt Knuth: I suspect that premature optimization of predictive potential is the root of all evil.

We need to first have a good framework for describing and summarizing phenomena before we set out to build theories within that framework for predicting phenomena.

In this brief post, I want to ask if evolutionary games in oncology are ready for building predictive models. Or if they are still in need of establishing themselves as a good descriptive framework.

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Fighting about frequency and randomly generating fitness landscapes

A couple of months ago, I was in Cambridge for the Evolution Evolving conference. It was a lot of fun, and it was nice to catch up with some familiar faces and meet some new ones. My favourite talk was Karen Kovaka‘s “Fighting about frequency”. It was an extremely well-delivered talk on the philosophy of science. And it engaged with a topic that has been very important to discussions of my own recent work. Although in my case it is on a much smaller scale than the general phenomenon that Kovaka was concerned with,

Let me first set up my own teacup, before discussing the more general storm.

Recently, I’ve had a number of chances to present my work on computational complexity as an ultimate constraint on evolution. And some questions have repeated again and again after several of the presentations. I want to address one of these persistent questions in this post.

How common are hard fitness landscapes?

This question has come up during review, presentations, and emails (most recently from Jianzhi Zhang’s reading group). I’ve spent some time addressing it in the paper. But it is not a question with a clear answer. So unsurprisingly, my comments have not been clear. Hence, I want to use this post to add some clarity.

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Hiding behind chaos and error in the double pendulum

If you want a visual intuition for just how unpredictable chaotic dynamics can be then the go-to toy model is the double pendulum. There are lots of great simulations (and some physical implementations) of the double pendulum online. Recently, /u/abraxasknister posted such a simulation on the /r/physics subreddit and quickly attracted a lot of attention.

In their simulation, /u/abraxasknister has a fixed center (block dot) that the first mass (red dot) is attached to (by an invisible rigid massless bar). The second mass (blue dot) is then attached to the first mass (also by an invisible rigid massless bar). They then release these two masses from rest at some initial height and watch what happens.

The resulting dynamics are at right.

It is certainly unpredictable and complicated. Chaotic? Most importantly, it is obviously wrong.

But because the double pendulum is a famous chaotic system, some people did not want to acknowledge that there is an obvious mistake. They wanted to hide behind chaos: they claimed that for a complex system, we cannot possibly have intuitions about how the system should behave.

In this post, I want to discuss the error of hiding behind chaos, and how the distinction between microdynamics and global properties lets us catch /u/abraxasknister’s mistake.
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Introduction to Algorithmic Biology: Evolution as Algorithm

As Aaron Roth wrote on Twitter — and as I bet with my career: “Rigorously understanding evolution as a computational process will be one of the most important problems in theoretical biology in the next century. The basics of evolution are many students’ first exposure to “computational thinking” — but we need to finish the thought!”

Last week, I tried to continue this thought for Oxford students at a joint meeting of the Computational Society and Biological Society. On May 22, I gave a talk on algorithmic biology. I want to use this post to share my (shortened) slides as a pdf file and give a brief overview of the talk.

Winding path in a hard semi-smooth landscape

If you didn’t get a chance to attend, maybe the title and abstract will get you reading further:

Algorithmic Biology: Evolution is an algorithm; let us analyze it like one.

Evolutionary biology and theoretical computer science are fundamentally interconnected. In the work of Charles Darwin and Alfred Russel Wallace, we can see the emergence of concepts that theoretical computer scientists would later hold as central to their discipline. Ideas like asymptotic analysis, the role of algorithms in nature, distributed computation, and analogy from man-made to natural control processes. By recognizing evolution as an algorithm, we can continue to apply the mathematical tools of computer science to solve biological puzzles – to build an algorithmic biology.

One of these puzzles is open-ended evolution: why do populations continue to adapt instead of getting stuck at local fitness optima? Or alternatively: what constraint prevents evolution from finding a local fitness peak? Many solutions have been proposed to this puzzle, with most being proximal – i.e. depending on the details of the particular population structure. But computational complexity provides an ultimate constraint on evolution. I will discuss this constraint, and the positive aspects of the resultant perpetual maladaptive disequilibrium. In particular, I will explain how we can use this to understand both on-going long-term evolution experiments in bacteria; and the evolution of costly learning and cooperation in populations of complex organisms like humans.

Unsurprisingly, I’ve writen about all these topics already on TheEGG, and so my overview of the talk will involve a lot of links back to previous posts. In this way. this can serve as an analytic linkdex on algorithmic biology.
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Four stages in the relationship of computer science to other fields

This weekend, Oliver Schneider — an old high-school friend — is visiting me in the UK. He is a computer scientist working on human-computer interaction and was recently appointed as an assistant professor at the Department of Management Sciences, University of Waterloo. Back in high-school, Oliver and I would occasionally sneak out of class and head to the University of Saskatchewan to play counter strike in the campus internet cafe. Now, Oliver builds haptic interfaces that can represent virtually worlds physically so vividly that a blind person can now play a first-person shooter like counter strike. Take a look:

Now, dear reader, can you draw a connecting link between this and the algorithmic biology that I typically blog about on TheEGG?

I would not be able to find such a link. And that is what makes computer science so wonderful. It is an extremely broad discipline that encompasses many areas. I might be reading a paper on evolutionary biology or fixed-point theorems, while Oliver reads a paper on i/o-psychology or how to cut 150 micron-thick glass. Yet we still bring a computational flavour to the fields that we interface with.

A few years ago, Karp’s (2011; Xu & Tu, 2011) wrote a nice piece about the myriad ways in which computer science can interact with other disciplines. He was coming at it from a theorist’s perspective — that is compatible with TheEGG but maybe not as much with Oliver’s work — and the bias shows. But I think that the stages he identified in the relationship between computer science and others fields is still enlightening.

In this post, I want to share how Xu & Tu (2011) summarize Karp’s (2011) four phases of the relationship between computer science and other fields: (1) numerical analysis, (2) computational science, (3) e-Science, and the (4) algorithmic lens. I’ll try to motivate and prototype these stages with some of my own examples.
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