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Comment: Re:What is life? What is a virus? (Score 5, Insightful) 157

by radtea (#47428331) Attached to: Hints of Life's Start Found In a Giant Virus

Then, in that case, what separates pithovius from the prokaryotes?

Structure, from the sound of it, although mostly this is people committing various fallacies of reification and making false claims of "natural kinds".

Everything is a continuum. Humans divide the continuum up using acts of selective attention. The only infinitely sharp edge is the edge of our attention (because we scale the edge to match the scale we are attending to, so whatever scale we are attending to seems to have a sharp division between the things we are selecting out.)

"Species" do not have particularly crisp boundaries in the general case: they fade into each other, and we draw edges around them in more-or-less arbitrary ways. When we find new varieties we can either create new categories (by drawing new edges) or lump them into old categories (by moving old edges). Which move is to be preferred depends on the purposes of the knowing subject.

Comment: Re:quelle surprise (Score 1) 713

by radtea (#47397485) Attached to: When Beliefs and Facts Collide

Yes, but climate change is scientific fact.

Insofar as that statement isn't gibberish (that is: not very far) it's anti-science.

Here's a question for you: is it a "scientific fact" that the impact of an extraterrestrial body occurred at the KT boundary and cause the mass extinction associated with that world-wide discontinuity in the geological record?

A fair majority of scientists concerned with the question certainly think so. But there are some notable hold-outs:

People whose area of expertise is directly relevant to the question at hand, who bring up cogent if not compelling counter-arguments, alternative interpretations of the evidence, facts that appear to be in contradiction to the impact theory, and so on.

Yet they don't have a crowd of anti-scientific loud-mouths calling them "Denialists" or accusing them of being shills for "Big Paleontology."

They sometimes get into heated discussions at scientific meetings, but that's the way science works: there is no limit on the questions we can ask and if we have evidence and Bayesian argument we get a seat at the table, no matter how wigged out the ideas might seem ab initio.

Only in the area of AGW has the arena become a completely political one, where anti-scientific loudmouths compete with shills for Big Hydrocarbon, and everyone ignores the serious question, which is: given its almost certain human activity is adding about 0.25% to the Earth's energy budget (1.6 W/m**2) and we have almost no idea how the climate will respond to that (despite what climatologists sometimes claim about their unphysical models) how do we best respond?

There is a loud and well-funded contingent who believe in "abstinence only" solutions, despite those having failed in every other case they have been applied to (drugs, alcohol, contraception...)

There are green-energy people promoting solar, wind, algal biodeisel, biomass, and other carbon-neutral forms of energy generation and storage.

There are people working on better battery tech (Heinlein's "shipstones").

There are people saying we should seriously consider nuclear power as the only currently known working alternative to base-load coal.

There are people saying we should investigate geo-engineering to stablize CO2 levels.

And there are people saying that since we don't know what is going to happen we should do nothing (see: Shills for Big Hydrocarbon, above)

All of that important stuff in the middle gets drowned out by the anti-scientific loud-mouths and bullies allied with the first and last of those groups, who do nothing but spew gibberish like "climate change is a scientific fact" as if that added something to the debate rather than helped to quell the debate we should be having.

"Scientific literacy" is not or should not be knowledge of discoveries, but a willingness to practice the discipline (not method) that is science: the discipline of testing ideas by systematic observation, controlled experiment and Bayesian inference. If you aren't practicing that discipline, you are almost certainly an enemy of science, because that is the natural state of the human mind.

Comment: Re: "The real problem..." he explained (Score 5, Interesting) 131

by radtea (#47384969) Attached to: Damian Conway On Perl 6 and the Philosophy of Programming

Fragmentation and stagnation, despite some assurances to the contrary

I use Python both professionally and for fun (and C and C++ professionally) and don't get this impression at all. Major upgrades to shipped languages take time. The willingness to impose one-time incompatible changes for the sake of long-term improvements takes guts, and can certainly go wrong, but can very well be worth it.

As someone who worked in C and C++ pre-standardization, I recall (perhaps erroneously) that the new standards broke a fair bit of existing code, albeit in minor ways. And of course Microsoft's broken C++ compiler in Visual Studio 6 resulted in a vast amount of borken code when they finally caught up to the rest of the world.

That said, I haven't moved to Python 3 yet, although I believe all the libraries I really care about have now migrated. I tend toward late-adoption, though, and my sense of the Python community is that everyone accepts we are eventually going to move to 3. Big changes take years, so it's no surprise that lots of developers are still on 2.x. The real watershed will be when a few major libs (wxPython, say) drops 2.x support.

In contrast, my impression of Perl 6 is that it's the language of the future, and always will be. It appears so different from Perl 5 that it's a little weird the same name is being used, and it has mostly resulted in sucking the oxygen out of Perl 5 development.

Comment: Re:Confusing article (Score 2) 37

by radtea (#47384877) Attached to: Polymer-Based Graphene Substitute Is Easy To Mass-Produce

What exactly is a "substitute carbon nanosheet"

Reading between the lines, it looks like it is a thin layer of mixed carbon and hydrogen with a structure that they have not yet properly characterized but which they have shown has the properties required for transparent electrodes in solar cells.

Specifically, they say the properties of the layer can be controlled by the properties of the polymer they start with, which suggests that it partakes in the polymer's nature, which would mean it is more than just a single layer of carbon atoms.

They may be being cautious and simply saying it is "graphene-like-enough" for this application, but having not fully characterized it may not want to claim it is "truly" graphene, which is a fairly vague term for a variety of single-sheet carbon materials that may have a variety of defects, in just the same was as "paper" is also fairly vague (from tissue to construction.)

Comment: Re:R... (Score 4, Interesting) 143

So can Python do everything that R can?

No, but Rpy can.

I've used R, and it really has a lot of strong points, but I prefer to access it these days via Rpy, which gives me all the power of R along with everything else I get from Python (other libraries, better application development frameworks, etc.)

Both R and Python are real programming languages that are going to be completely useless to non-programmers, so neither of them is a SAS replacement, but of the two, I'd choose Python+Rpy over R for flexibility, power and ease of use (the latter is of course a strongly personal preference... if you really think like a traditional stats geek R will likely seem nicer, as it is clearly created for and by such people.)

Comment: Re:Were Denisovans really a DIFFERENT SPECIES? (Score 2) 133

by radtea (#47378259) Attached to: Tibetans Inherited High-Altitude Gene From Ancient Human

Why are Denisovans considered different species, rather than simply a different race (or breed?) of the same Homo Sapiens?

"Variety" is probably a better word than "race" or "species". The "biological species concept" is extremely poorly defined, which is a bit of an embarrassment for a field largely based on a book called "The Origin of Species".

Like all concepts, the boundaries of a "species" are fuzzy, and the only really precise dividing line is the attention of the knowing subject. In many cases this is unprobelmatic: almost any knowing subject looking at the same population would draw the edges between species in the same way. There are, however, many cases where different people will draw different edges for different purposes.

Again: this is no different from any other concept, although people who don't get out much will often insist that the edges they choose to draw by an act of selective attention are "real" and everyone else's are "wrong".

In the extreme case, in the plant world, ubiquitous hybridization results in populations that are practically all genetically unique individuals, and the species concept breaks down entirely.

Comment: Re:Disagree with first sentiment (Score 2) 105

by radtea (#47335537) Attached to: Fixing Faulty Genes On the Cheap

There is a whole swath of biological research under the banner of "basic science"...

Absolutely. I've worked both with pure biologists and physicians (and biologists in a medical context) and they have dramatically different outlooks and mindsets. Many, many biologists are deeply interested in understanding what is going on, while physicians and medical-focused biologists are much more interested in finding stuff that works to solve this problem.

The divide is very similar to that between pure and applied physicists, although for some reason we don't talk about "applied biologists" (perhaps we should.) Pure physicists are simply trying to find answers to questions; applied physicists are trying to find solutions to problems. The same is true in biology.

Comment: Re:How long before... (Score 1) 105

by radtea (#47335461) Attached to: Fixing Faulty Genes On the Cheap

In places where people have to worry about starvation I wonder if IQ might even be a liability.

Brain size and IQ are not particularly correlated, and I've seen at least some research suggesting that people with high IQs or more education are actually more efficient at using their brains, to the extent that there is some thinning of the grey matter in such individuals in their late teens or early 20's.

Thinking does take more energy than not, but this isn't a big effect compared to brain size: http://www.scientificamerican....

Comment: Re:How long before... (Score 1) 105

by radtea (#47335357) Attached to: Fixing Faulty Genes On the Cheap

I suggest you ask evolutionary biologists.

And evolutionary biologists will ask, "What is the evolutionary advantage of intelligence?"

What we think of as "intelligence"--the specifically human abilities to build complex machines and to use anything to represent anything else and to create unbounded chains of logical inference--is almost certainly an epiphenomenon of having a brain big enough to engage in the kind of complex social and cultural behaviour that developed due to sexual selection in our evolutionary history.

The human brain is like the peacock's tail: men with big brains were more likely to get laid, probably because we could be more entertaining and interesting to women with big brains. Once the process started it ran away with itself, until both men and women ended up with these enormous brains that happen to be able to think deep thoughts.

Evolution does this kind of thing, like flight-feathers evolving from modified scales that were selected for thermal rather than aerodynamic properties.

Comment: Re:How long before... (Score 3, Interesting) 105

by radtea (#47335207) Attached to: Fixing Faulty Genes On the Cheap

Why is there a whole raft of genetic diseases in the human population now? Shouldn't they have been "selected out" a long time ago?

Many genetic diseases are the result of optimizations for other things (anemia is related to malaria resistance, there is some problematic gene in a Jewish sub-population that is related to plague resistance, etc.)

Evolution is continuously running an extremely complex multi-dimensional optimization problem with a time-varying objective function. Local minima abound, and it's easy for organisms to get trapped in them.

Furthermore, kin selection and possibly group selection play a role in human evolution, which makes the whole thing even more complex and non-linear. So looking at specific genes and saying, "That doesn't make sense!" as if there was some obligation for the universe to "make sense" to our naive pre-scientific intuition is fairly silly.

The human genome is a Rube Goldberg apparatus that manages to make hundreds of thousands of products out of 40,000 strongly interacting templates plus a bunch of ridiculously inefficient secondary control mechanisms like micro-RNAs (which in some typically degrade already-transcribed mRNA). Pointing to one step as if it can be considered in isolation from everything else is not a good move.

Loss of vitamin C manufacture could well have to do with the development of some other pathway that was more important at the time, and may well continue to be more important today. The only way to really find out is to either a) understand the genetic trade-offs in detail or b) ask some volunteer to have their vitamin C production turned back on by a technique like this. Personally, I'd recommend the former.

Given how weird humans are developmentally, some things like this may be important when we're young and not so much when we're older, so in the fullness of time we may find we can turn on vitamin C production only after people mature, for example. The possible range of futures, given how little we know now, is large.

In the meantime, we have plenty of people with genetic diseases that we know the cure will not significantly disrupt their cellular machinery, because we have lots of examples of people without those diseases who are just fine.

Comment: Re:That's not what I took away from this... (Score 2) 347

by radtea (#47311083) Attached to: Evidence of a Correction To the Speed of Light

Photons in the visible light range are not sufficiently energetic to create an electron-positron pair. I do not know if the photons in question were in the visible light range or not.

The photons were in the visible, but the e+/e- pair exists "off the mass shell", which is an obscure way of saying that the normal conservation laws don't apply. There is an uncertainty relation that goes dE*dt >~ h/2Pi, which is to say: you can violate the law of conservation of energy by any amount so long as you do it for a short enough time. That's what's happening here.

That said, this whole thing is pure speculation, and somewhat problematic speculation at that. If you take the first neutrino detection seriously, the real question becomes not the difference between the first neutrinos and the light, but why the one neutrino detector has such a different arrival time. Conventional wisdom is that it is an instrumental artifact, and that's a pretty good bet.

If it is not--and this slowing-down-light is real--then we need even more new physics to explain why the Mont Blanc neutrino detector saw such different arrival time from three other detectors: Kamiokande II, Baskan and IMB, all of which detected events that are consistent in time of arrival.

Their energy sensitivities are not that different, and there's no very obvious explanation of why some neutrinos would happen to make it out earlier than others, particularly when segregated by detection technology.

Comment: Re:How does this not violate the 5th and/or 14th.. (Score 2) 371

by radtea (#47301487) Attached to: Court Releases DOJ Memo Justifying Drone Strike On US Citizen

The memo cites case law to justify the suppression of 4th and 5th amendment rights. For example:

at least where high-level government officials have determined that a capture operation overseas is infeasible and that the targeted person is part of a dangerous enemy force and is engaged in activities that pose a continued and imminent threat to U.S. persons or interests the use of lethal force would not violate the Fourth Amendment. and thus that the intrusion on any Fourth Amendment interests would be outweighed by "the importance of the governmental interests [that] justify the intrusion," Garner, 4 71 U.S. at 8, based on the facts that have been represented to us.


In Hamdi, a plurality of the Supreme Court used the Mathews v. Eldridge balancing test to analyze the Fifth Amendment due process rights of a U.S. citizen captured on the battlefield in Afghanistan and detained in the United States who wished to challenge the government's assertion that he was a part of enemy forces, explaining rbat "the process due in any given instance is determined by weighing 'the private interest that will be affected by the official action' against the Government's asserted interest, 'including the function involved' and the burdens the Government would face in providing greater process." 542 U.S. at 529 (plurality opinion) (quoting Mathews v. Eldridge, 424 U.S. 319, 335 (1976)).

So if I'm reading this correctly, 4th amendment rights don't apply if the government deems that its interests outweigh yours, and 5th amendment rights don't apply if the the government deems that its interests outweigh yours or the government asserts that it would be excessively burdensome to give you due process.

The only reasonable interpretation of this is that the government of the United States has become exactly what the Framers feared: an utterly autocratic organization that asserts its own interests over and above the interests of citizens who may come into conflict with it.

Comment: Re:More than one Higgs Boson? (Score 3, Informative) 42

by radtea (#47301249) Attached to: Fresh Evidence Supports Higgs Boson Discovery

So, how can there be more than one Higgs boson?

Physicists have a funny way of talking about theoretical entities, particularly these days when theory almost always leads experiment. We have years or decades to talk about theoretical entities, and that leads to a strange nomenclature.

"The Higgs" is actually a class of particles. In the "bare" electro-weak theory none of the particles have masses. The only way to give them mass is to break one of the internal symmetries of the theory, and one "natural" way of doing that was invented by Peter Higgs and others in the form of a massive scalar field that takes on a non-zero vacuum expectation value as energy decreases (this is the famous "Mexican hat" potential.)

Suppose we arrived on Earth from Mars and were observing the inhabitants, and we wondered how emergency vehicles would get through busy traffic. One of our number--call it Sggih--theorizes that humans, being visually-oriented, might use a flashing light to warn motorists of an emergency vehicle. Others might elaborate on this and suggest that both a flashing light and a loud noise would be use. All of these types of local warning mechanisms might go under the name of Sggih, with the original one being the "minimal Sggih mechanism" and the other ones going under different names.

In the meantime, there are those who think that humans are telepathic, or use radios, or some other non-local signalling mechanism.

Then one day in the course of observation a Martian--and let's say Martians are deaf, the air being so thin there--sees an emergency vehicle with a flashing light on top zipping through traffic. Horray! The Sggih mechanism is correct! At least probably... it may be that wasn't an emergency vehicle but some kind of advertising stunt. And if it is the Sggih, which one is it? Further research is required to determine if humans use the minimal Sggih mechanism or one of the more complex elaborations...

This work is in the vein of that further research, and the outcome strongly suggests that of the various theoretical possibilities, nature is actually using the minimal Higgs and that is what has been seen, rather than some unexpected but similar exotic particle.

All of this is good news for those of us who are unenthused by supersymmetry and other more-or-less exotic extensions to the Standard Model.

Comment: Re:Two things (Score 1) 85

by radtea (#47275213) Attached to: The Game Theory of Life

Mathematics is a language. As such, it is created.

The interesting thing about math is that it is a language that reveals underlying isomorophisms, like the one described in TFA. This feature is one of the things that leads to naive people thinking that the math somehow "precedes" the things it describes.

But we see similar isomorphisms in all languages. Consider the "ballad" form of poem. It occurs in incredibly diverse contexts, but the underlying structure is always the same, which means you can sing "Amazing Grace" to the tune of the theme from "Gilligan's Island". So claiming that "pi" shows up in a variety of contexts doesn't prove anything except that it reflects those parts of the universe we find it interesting as humans to describe.

Furthermore, mathematical descriptions include extraneous bits. Wave equations have both advanced and retarded solutions, for example. If the math truly "preceded" the reality you'd expect that this would never happen, or that there would be some mathematical (rather than empirical) principle that let us get rid of the parts that don't describe reality.

The role of mathematics in biology is an, err, evolving one. The possibility of a law-like mathematical description underlying biological and evolutionary processes is at least worth speculating about:

Comment: Re:As someone with autism, (Score 3, Informative) 207

by radtea (#47257587) Attached to: Century-Old Drug Reverses Signs of Autism In Mice

From TFA: "Second, suramin is a poor drug choice for chronic use because of potentially toxic side effects that can occur with prolonged treatment."

And from the Wikipedia page on the drug (

The most frequent adverse reactions are nausea and vomiting. About 90% of patients will get an urticarial rash that disappears in a few days without needing to stop treatment. There is a greater than 50% chance of adrenal cortical damage, but only a smaller proportion will require lifelong corticosteroid replacement. It is common for patients to get a tingling or crawling sensation of the skin with suramin. Suramin will cause clouding of the urine which is harmless: patients should be warned of this to avoid them becoming alarmed.

Kidney damage and exfoliative dermatitis occur less commonly.

Suramin has been applied clinically to HIV/AIDS patients resulting in a significant number of fatal occurrences and as a result the application of this molecule was abandoned for this condition.

So while this is an important piece of work that identifies purine metabolism as a critical set of pathways related to ASD, it should be viewed primarily as a starting point for a more precisely targeted drug that will have the same effect on the pathways that matter without also messing up the ones that cause the side-effects.

"No problem is so formidable that you can't walk away from it." -- C. Schulz