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cbkeller

1,804 karma · joined October 22, 2018

geologist - brenhinkeller.github.io
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cbkeller··on Macrostrat: A Global Geological Map
Geologist here! I'm a fan of this project. The maps are only part of it; they're trying to build a three-dimensional scaffolding (based on drill cores, etc.).

Almost all normal geologic maps are maps of the rocks at the surface, since that's what we can see most easily -- but the rocks are no less complicated with depth, and in principle with enough data you could make the same sorts of map at any depth within the crust.

The same team is also working on data-mining from (academic paper) PDFs - some of the information from which may eventually be tied into the Macrostrat framework: https://geodeepdive.org/

cbkeller··on A New Golden Age for Computer Architecture
Interesting article with a lot of great historical context. I think a significant part of the tl;dr is that the end of Dennard Scaling and trouble with Moore's law may mean that the best architecture will finally win out, rather than just the one with the best semiconductor design team behind it.

I'm a bit skeptical of the promise of DSAs, though it does seem we're already going that way. Curious what others think on that point.

cbkeller··on Confirmationist and falsificationist paradigms of science (2014)
Well, we like to say science is deductive, because induction doesn't give you perfect certainty -- but in practice induction and parsimony are and have been absolutely critical to scientific progress..

I think QED provides a nice example. I don't know if there are any formal mathematical constraints on the size of theoryspace, but for practical purposes we can probably agree that one may conceive of arbitrarily many hypotheses that fail to be falsified by a given set of observations. If deduction is all we have at our disposal, how do we choose among all these options? And should we really not have any more confidence in a theory like QED which as been tested many times and "failed to be falsified" to nine significant digits, versus one that has only "failed to be falsified" at 5% relative?

In practice, I would also claim that parsimony is (and has been historically) absolutely critical in culling away the dross of theoryspace, yet this can hardly be presented as a deductive method?

I think induction has been given an unnecessarily bad name lately. The falsification-centric paradigm that is popular today was proposed by Karl Popper as a solution to Hume's "problem of induction" [1] -- but Hume, and the rest of the Empiricists that laid the foundation for the scientific method, would have considered this entirely backwards. While Hume did claim that induction could not be justified by reason alone, Hume's conclusion was not to reject induction, but rather to prefer induction over deduction!

> It is far better, Hume concludes, to rely on “the ordinary wisdom of nature”, which ensures that we form beliefs “by some instinct or mechanical tendency”, rather than trusting it to “the fallacious deductions of our reason” [2]

[1] https://en.wikipedia.org/wiki/Hume%27s_problem_of_induction

[2] https://plato.stanford.edu/entries/hume/

cbkeller··on Confirmationist and falsificationist paradigms of science (2014)
Thanks, I hadn't seen that one before - some really interesting historical context. That's about the clearest articulation I've ever seen of the contrast between the idealized purely-deductive hypothesis-falsification paradigm and the way science has actually progressed.
cbkeller··on Response to the ASA’s Statement on p-Values
I'll have to check it out!
cbkeller··on Response to the ASA’s Statement on p-Values
Sounds fair enough.

I do wish that physical scientists, including myself, had more philosophical training though, even if its not science per se, such that we could reliably have original, educated opinions on empiricism, rationalism, etc.

cbkeller··on Response to the ASA’s Statement on p-Values
Without having looked into it, my impression is that the popularity of astrology (and psychics, etc.) is down to the fact that they tend to make broad, vague predictions with a relatively high P(E) that people (emotionally) tend to underestimate. For instance "something bad will happen to you this month" -> "OMG, I stubbed my toe the other day, they were totally right". If we're accurate at assigning P(E), however, then we'll probably end up with a low P(H|E).

The prior P(H) is also arguably trouble. What's a good prior likelihood for the hypothesis that magic sky gods affect your fortune? I don't know, but I'd probably have to start somewhere pretty low.

cbkeller··on Response to the ASA’s Statement on p-Values
Great points. It's one thing to say that a scientific theory should be falsifiable (as a necessary but not sufficient condition), but the Popperians lose me when they claim either (1) that the only valid scientific study is an attempt at falsification, (2) that corroboration (or in Popperian terms, a failed attempt at falsification) has no significance. Both of these tropes come up in this "response", where Ionides et al. use them to throw some pretty serious shade at the ASA:

> This approach to the logic of scientific progress, that data can serve to falsify scientific hypotheses but not to demonstrate their truth, was developed by Popper (1959) and has broad acceptance within the scientific community. In the words of Popper (1963), “It is easy to obtain confirmations, or verifications, for nearly every theory,” while, “Every genuine test of a theory is an attempt to falsify it, or to refute it. Testability is falsifiability.” The ASA’s statement appears to be contradicting the scientific method described by Einstein and Popper.

However, (1) completely ignores discovery science (something I have ranted about here previously), and implies fully accepting Popper's claim to have solved the centuries-old "problem of induction" [1]. Meanwhile, (2) seems to pop up pretty frequently even though I'm not sure Popper himself would have agreed, considering [2]:

> It is easy, [Popper] argues, to obtain evidence in favour of virtually any theory, and he consequently holds that such ‘corroboration’, as he terms it, should count scientifically only if it is the positive result of a genuinely ‘risky’ prediction

Ionides et al. conveniently left out the second half of that context. Hmm, if only there were some sort of way to quantify that "riskiness". Like some sort of theorem... maybe of the form P(H|E) = P(E|H)*P(H)/P(E)

[1] https://en.wikipedia.org/wiki/Problem_of_induction

[2] https://plato.stanford.edu/entries/popper/

cbkeller··on Response to the ASA’s Statement on p-Values
Obligatory xckd: https://xkcd.com/2078/
cbkeller··on Response to the ASA’s Statement on p-Values
Yeah, or Francis Bacon, or any of the original Empiricists.

I find a lot more to like in the ASA's statement [1] than in any of these responses, which seem to act as if Karl Popper were the only one to ever have a worthwhile philosophy of science.

This paragraph of the response was particularly telling to me:

> A judgment against the validity of inductive reasoning for generating scientific knowledge does not rule out its utility for other purposes. For example, the demonstrated utility of standard inductive Bayesian reasoning for some engineering applications is outside the scope of our current discussion.

Translation: Ok, so maybe induction works fine when you're going to build a bridge where someone's life is on the line, but it still has no place in science. Falsification or bust!

[1] https://www.tandfonline.com/doi/full/10.1080/00031305.2016.1...

cbkeller··on GNU Octave: A high-level interactive language for numerical computations [pdf]
I assume they're referring to cases like this [1].

A few years ago I think there were some performance regressions in Julia relative to JIT'd Python (which, using LLVM like Julia, is way faster than normal Python). This seems to be mostly fixed now.

In the example above, the OP was getting 2ms in Numba vs 8ms in Julia three years ago, and recommendations from Julia folks were able to get the latter down to parity with an equivalent algorithm or 386us with an improved algorithm.

On my laptop today, I seem to get 2.0ms in Numba, 2.7ms with Julia 1.0, and 80us using the improved algorithm in Julia 1.0 (and, just to drive home the importance of compilation, 780ms in Python without Numba).

[1] https://old.reddit.com/r/Julia/comments/3x6tg9/why_is_this_l...

cbkeller··on GNU Octave: A high-level interactive language for numerical computations [pdf]
This is what held me back for a long while too, but Juno (the Atom plug-in) seems to finally have all the features I was missing in Julia compared to the Matlab IDE, including a decent variable inspector.
cbkeller··on GNU Octave: A high-level interactive language for numerical computations [pdf]
> Julia is even slower

Huh? This has definitely not been my experience -- most of the things I've ported over seem to run about twice as fast in Julia as in the original vectorized Matlab (and probably more like 10x faster than naive non-vectorized Matlab)..

cbkeller··on GNU Octave: A high-level interactive language for numerical computations [pdf]
I've been porting over a bunch of my old academic Matlab to Julia. It's obviously nowhere as close to Matlab syntax as Octave is, but it's a lot closer than Python. YMMV of course, but there are enough similarities that a decent proportion of my code has worked after pretty easy find/replace changes like switching array indexing from parentheses to square brackets. And I usually end up with something that runs about 2x faster than the original Matlab, which is always nice.
cbkeller··on Cancer Progress: Much More Than You Wanted To Know (2018)
> We can't conclude "O is true, therefore H"

Definitely, but if O had been false we might have learned something. More interestingly though:

> another thing to consider is fallout incorporated into tobacco and then smoked

That's an interesting thought, I'd never considered that.

My expectation for beta and gamma emitters is that they would be unlikely to cause cancer specifically in the lungs, because lungs aren't very dense and would have a pretty low interaction cross section for such penetrating radiation. For comparison, I-131 -- a beta emitter common in fallout -- is a significant risk for thyroid cancer only because iodine is biologically concentrated in the thyroid.

However, if there were significant fallout of alpha emitters, which were deposited in tobacco, this could conceivably deliver a significant localized dose to the lungs. Alpha emitters are more or less only dangerous internally, but smoke particulates that become lodged in the lungs could do the job. There appears to be a fair amount of literature on this -- Naturally occurring Po-210 is apparently still considered a danger today [1], and has been known to the cigarette companies since the 60s [2]. Some apparently comes from decay of natural U (via a few intermediaries) in phosphate fertilizer.

A figure in one paper I was able to find [3] suggests up to 100 pCi/kg Pu-239 and Pu-240 (both alpha) in leaves and grass in Finland circa 1963, declining to less than 5 pCi by 1967. The modern Po-210 alpha activity in tobacco appears to be much higher than either of these values (perhaps several hundred pCi/kg in dry tobacco, if not more), but I couldn't find good data on variation over time. For Pb-210 (beta) there is more data, but seems to be a lot of scatter and not so much of a clear trend through time [4].

[1] https://scienceblog.cancerresearchuk.org/2008/08/29/radioact... [2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2509609/ [3] https://www.osti.gov/biblio/5271041 [4] https://doi.org/10.1016/j.jenvrad.2011.01.005

cbkeller··on How we achieve growth by ignoring conventional startup advice
Might be a sign that we're not in an epistemic bubble, which would be good!
cbkeller··on Cancer Progress: Much More Than You Wanted To Know (2018)
That's interesting -- doesn't seem to have a graph, but states a significant increase between 1914 and 1967 in nonsmokers. There doesn't appear to be any control for secondhand smoke, however, which could also be a significant factor over that time period.
cbkeller··on Cancer Progress: Much More Than You Wanted To Know (2018)
This is missing their point: you can distinguish the two potential causes by comparing lung cancer incidence rate through time for smokers versus non-smokers.

If nuclear tests are a significant factor in lung cancer rate, we should still see a correlation between lung cancer incidence and nuclear test frequency when looking at people with no exposure to cigarette smoke. If the correlation in the general population just a coincidence, we should not.

cbkeller··on Algorithms, by Jeff Erickson
There appears to be some evidence to suggest that traditional (grade-school style) "graded homework" at the advanced undergrad and higher level may just not be particularly good pedagogy though [1]. If possible, it may be better to assign ungraded homework with complete guided solutions provided, plus regular in-class quizzes (the latter to motivate students to actually spend time on that assigned homework every week) [2].

[1] https://scholarlycommons.pacific.edu/soecs-facpres/16/ [2] https://www.tandfonline.com/doi/full/10.1080/00091383.2011.5...

cbkeller··on Chicago’s Deep Tunnel: The solution to urban flooding, or a cautionary tale?
Yeah, I never noticed them mention that possibility, even to dismiss it.
cbkeller··on A fifth of Earth’s geologic history might have vanished because of glaciers
NOVA's always been my favorite science documentary series. I don't know if they've ever covered snowball earth, but they have a somewhat recent series on geological history of North America: https://www.pbs.org/wgbh/nova/series/making-north-america/
cbkeller··on A fifth of Earth’s geologic history might have vanished because of glaciers
Oh, and regarding the survival of life through a Snowball Earth state, there's been some interesting discussion of potential refugia such as polynyas [1] and cryoconite ponds [2,3], though for context the most advanced multicellular organism I've seen anyone propose prior to the last snowball is still only a sort of sponge [4]

[1] https://en.wikipedia.org/wiki/Polynya

[2] https://en.wikipedia.org/wiki/Cryoconite

[3] https://onlinelibrary.wiley.com/doi/abs/10.1111/gbi.12191

[4] https://www.nature.com/articles/ngeo934

cbkeller··on A fifth of Earth’s geologic history might have vanished because of glaciers
Yeah, I think the vastness of geologic time has been aptly described as "geology’s signal contribution to human thought" -- the same way astronomy showed us we weren't the literal center of the universe. I think about Myr and Gyr timescales every day at work, but it's still hard to really intuitively grasp.

Obligatory John McPhee:

> Numbers do not seem to work well with regard to deep time. Any number above a couple of thousand years—fifty thousand, fifty million—will with nearly equal effect awe the imagination.

> Consider the earth’s history as the old measure of the English yard, the distance from the king’s nose to the tip of his outstretched hand. One stroke of a nail file on his middle finger erases human history.

cbkeller··on A fifth of Earth’s geologic history might have vanished because of glaciers
> So does this imply that we'll never know if the Cambrian Explosion is actually an explosion or just a continuation from a previously unrecoverable geological record? Is it even possible to have complex multicellular life under snowball earth conditions?

That's a good question. I'm the first author of the new PNAS article discussed here (open access at https://doi.org/10.1073/pnas.1804350116). This does raise some questions about preservation bias and taphonomy, but there are areas we know escaped Neoproterozoic erosion (mostly at actively rifting continental margins) and we can find continuous sedimentary sections from the Cryogenian to the Cambrian -- and in these sections we still see a pretty rapid rise in complex shelly fossils in the early Cambrian. That said, when people first started talking about the "Cambrian Explosion", we didn't know much anything about the Ediacaran biota [1], the Ediacaran extension of the "Small Shelly Fauna" [2], or the Doushantuo Formation [3] -- so the evolutionary problem's not quite as bad as when Darwin first worried about it.

One new point to add is that erosion and comminution of this much crust may be expected to free up a lot of phosphorus stored in the igneous crust -- arguably the key limiting nutrient on geological timescales. This seems to be be consistent with previous observations of an increase in phosphorus abundance in sediments around Cryogenian times [4].

[1] https://en.wikipedia.org/wiki/Ediacaran_biota

[2] https://en.wikipedia.org/wiki/Small_shelly_fauna

[3] https://en.wikipedia.org/wiki/Doushantuo_Formation

[4] https://www.nature.com/articles/nature20772

cbkeller··on Earth is missing a huge part of its crust. Now we may know why
Ah yeah. That crater is about 30 km wide, which is pretty big. Most craters follow roughly a 1:10 scaling between depth and diameter [1], so we can approximate a 3 km initial depth for this new new Hiawatha Crater. This crater is quite young (12 ka to 3 Ma est.), but if it had existed 720 Myr ago, then our estimates suggest it would have been borderline -- probably erased unless it got lucky and landed in one of the regions with little or no Neoproterozoic glacial erosion

The number one condition for fast glacial erosion is what's called "wet-based ice": if pressure and temperature at the base of the ice sheet (warmed by geothermal heat flow) is near the melting point, then ice tends to slip against the rock and erode rapidly; if it's too cold, then the ice will flow internally instead and not erode very well. Coupled climate-icesheet models so far [2] suggest it's possible to get wet-based ice even in a "hard snowball" state with limited precipitation from sublimation alone (though not under all parts of the icesheet at once).

[1] https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/JB07... [2] https://www.sciencedirect.com/science/article/pii/S0012821X0...

cbkeller··on Earth is missing a huge part of its crust. Now we may know why
Good questions!

1) Perhaps counter-intuitively, it's generally thought to be easier to enter a Snowball state when most of the continents are at the equator, the reasons being (A) silicate weathering of the continents consumes CO2 and is faster at low latitudes and (B) the albedo (reflectivity) contrast between ice and water is greater than the albedo contrast between ice and land. Ice is very reflective, water is not, and land is in between. In other words, if you grow sea ice at the poles, you make Earth more reflective, and the change in light (and heat) reflected per unit area of ice cover is greater for ice grown over oceans than ice grown over land. There is some background on the history of the Snowball Earth hypothesis, including the above points about albedo, here: https://en.wikipedia.org/wiki/Snowball_Earth

2) Definitely. I don't know the right answer yet, but here's a relatively recent (and relatively accessible) Scientific American article on the topic: https://www.scientificamerican.com/article/a-new-idea-on-how...

cbkeller··on Earth is missing a huge part of its crust. Now we may know why
I'm the first author of the relevant study [1] (open-access) so I'm biased to think this is cool. The unconformity certainly isn't everywhere (in some places there is no missing crust or time at all), but it can be found on just about every continent, and there has been surprisingly little previous quantification of this. Happy to answer any questions if anyone's interested.

[1] https://www.pnas.org/content/early/2018/12/26/1804350116

cbkeller··on Spain will soon overtake Japan in life expectancy rankings
That is apparently also a significant problem in Japan [1], so I'm not really sure what to think as far as which region should take the prize for longevity.

[1] https://www.nytimes.com/2010/08/15/world/asia/15japan.html

cbkeller··on Magdeburg Hemispheres
I think there's a few digits missing here even. 1 mol = 6.022E23 particles = 22.4 L at STP for an ideal gas, and 1 m^3 = 1000 L

Of course real air isn't quite an ideal gas, but some reasonable approximations [1] come out to 2.53E25 molecules (N2 and O2) per cubic meter at 15 C and 1 atm.

[1] https://www.quora.com/How-many-air-molecules-are-present-in-...

cbkeller··on A EULA in FOSS clothing?
You're certainly right that "EULA" is ambiguous -- but Bryan provided a more specific definition which was pretty clearly concerned with the "contract law in addition to copyright law" part:

> EULAs are an attempt to get out of copyright law — where the copyright owner is quite limited in the rights afforded to them as to how the content is consumed — and into contract law, where there are many fewer such limits. And EULAs have accordingly historically restricted (or tried to restrict) all sorts of uses like benchmarking, reverse engineering, running with competitive products (or, say, being used by a competitor to make competitive products), and so on.

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