Links

[jack]

"A proof of the Riemann hypothesis"

Linked from God plays dice blog, a putative paper on the Riemann hypothesis. I can't read it, I never was plugged into the mathematical grapevine. But it would feel remiss in the extreme not to pass on the comment.

For non-mathematicians, the Riemann hypothesis refers to a simple formula f(z), where z is a complex number. It is zero at z=-2, z=-4, z=-6, etc. It is also zero for many complex numbers z=0.5+it, ie. with real part 1/2, and some imaginary part. The hypothesis is that these are the only complex numbers with f(z)=0.

This is explained in more detail in the comments below, directly after "unnecessarily confusing, you should have..." and before "not entirely accurate because...".

The Riemann hypothesis is interesting because it ties into all sorts of different maths (eg. primes), and everyone's sure it's true, and people have had computers checking millions of solutions and seeing that they do conform, and there's lots of maths proved on the assumption that it's true. If it were proved, it would be the most famous result in maths in the last, um, ten years :)

ETA: The result is from a stable that does work on the Riemann Hypothesis, but has had several flawed proofs published before. This was flawed, and maybe patched already.

Bacteria make major evolutionary shift in the lab

Evolution , with the magic of stop-motion fridges. (Also: Dumbasses put hands over their ears and say "la la la, can't hear you". Original scientist sends long, thoughtful reply saying "Pull your fucking heads out of your asses, already. Duh.") Disclaimer: people who believe in the absence of any sort of evolution are not automatically dumbasses. Really.

God hates FAQs

A friend recently linked to a service which, when you're raptured, can send a last message to a loved one. There are two basic approaches. You've been left behind .com is run by Christians, and employs an ingenious dead-man's-handle.

Post Rapture Post .com is run by atheists. Post Rapture Post is a lot funnier.

Q. How Do We Know that You Will Not Ascend To Heaven with Us?
A. The Bible says that only those that repent of their sins and accept Jesus as the True Son of God will be saved. We do neither. Some of our personal sins include: drunkenness, heresy, sacrilige/blasphemy, gluttony, laciviousness, and sloth. There is no way we are going to disappear into Heaven any time soon.

Q. Aren't You Afraid of God's Wrath?
A. We don't believe in God, remember? In the event that the Rapture actually occurs, we will go to Plan B: "Lifetime of Sin Followed by Deathbed Repentance."

FWIW, I think both sites, whatever their personal beliefs, genuinely offer the service, but don't hold me to that.

Comments

[liv]

Wow, the dumbasses are really depressing, somehow. I mean, you've got all these non-scientists who are really excited about science, who are reading the latest results and commenting on New Scientist articles, and instead of discussing the intricacies of a rather clever experiment, they're arguing about whether God exists and calling eachother names. The stop-motion fridges thing (is that your term? it's rather a good one) is really clever, and a bit related to some of the stuff that the rest of my lab work on.

I wonder what has led to the conjunction in recent years of finally slaying all the big mathematical problems which are easy to state but really hard to solve. It may be just a coincidence, of course, but I wonder if it isn't some analogous process to the bacteria: there was some advance made a few generations ago which means that mathematicians now have the possibility of solving a whole swathe of stuff that was inaccessible before.

[simont]

I wonder what has led to the conjunction in recent years of finally slaying all the big mathematical problems which are easy to state but really hard to solve.

I haven't tried reading the actual paper in this instance, but the abstract suggested that this research is along structurally similar lines to the proof of Fermat's Last Theorem: the paper claims to be proving a more modern and more general conjecture of which the original problem is a corollary or a special case.

(I say "claims" only because of automatic scepticism after many other failed proof attempts, not because I have any specific reason to think this one is definitely faulty. I imagine in a few months' time we'll know if it stood up to scrutiny or not.)

So perhaps this is something to do with the coincidence: perhaps this is the way old problems will tend to fall, by first expanding the terms of reference into a larger arena in which the problem becomes bigger but so do the available means of solution, and then solving that and having the original problem drop out as a special case.

I note, incidentally, that André Weil was involved in formulating both the STW conjecture of which FLT was a special case and this one of which RH is a special case. Perhaps he should get a lot of the overall credit!

[cartesiandaemon.livejournal.com]

perhaps this is the way old problems will tend to fall, by first expanding the terms of reference into a larger arena in which the problem becomes bigger but so do the available means of solution, and then solving that and having the original problem drop out as a special case.

I'd almost assume that's just automatically the case.

Whether there's anything special now I don't know, I'd guess that there is an awful lot bigger body of knowledge than a hundred (or at least, two hundred) years ago, but within that time, breakthroughs occur randomly and it's just coincidence there seem to have been several recently.

[cartesiandaemon.livejournal.com]

The stop-motion fridges thing (is that your term? it's rather a good one) is really clever

*hugs* Thanks; yes, it just came to me as the simplest and funniest way of describing what was going on. I assumed it was just standard when I read it, it seemed retrospectively so obvious, but I guess not necessarily?

[arnhem.livejournal.com]

[ disclaimer - my instinct is that the evolution experiment is valid; however, it's much more important to try to look for the potential flaws in things you'd like to be right ].

My assumption would be that they're pretty confident that none of the samples have become contaminated with other bacteria during any of the re-sampling operations. However, it's less clear to me that they can rule out a viral or prion or dna-fragment contamination occurring.

[innocencest.livejournal.com]

I'm not sure if that's a problem. An extra bit of DNA floating about causing all this new mischief might mean the experiment has less evidence in favour of tiny-point-mutations-causing-drastic-results, but there's no reason to suspect a lot of evolution didn't happen this other way instead. It's still an organism and it has still mutated, and with these principles in place the different strands are now free to go an naturally-selectively duke it out and see if either become dominant.

Woo for run on sentences.

Possibly it counts as a problem if the extra DNA doesn't reproduce with regular mitosis, but I don't think that can be the case if the behaviour persists through generations.

[arnhem.livejournal.com]

Disclaimer: I'm typing this in the boring gaps between tending a shagged windows machine; I'm not thinking as clearly as I'd like to be; nevertheless:

I think it's substantially less interesting to have a behaviour acquired from acquisition of genetic material from elsewhere that already had evolved or otherwise acquired that behaviour, than to have a behaviour that spontaneously develops.

I don't think there's much debate about whether there are small changes in the genetic code from generation to generation; the dangerous argument to deal with is the "but you can't get significant large-scale change out of lots of very small changes" one, and in the absence of contamination, this experiment is very important on that front. If contamination could have occurred (and I can't see a way of ruling it out), the experiment is interesting but weak.

It's going to be fascinating (but I sadly suspect inconclusive) to see what the differences are between the first generation that will exhibit the change and the last generation that won't.

Of course, even if it turns out that the difference consists of a very small point change (which makes available a previously unavailable section of material that's present in both), then the annoying creationist argument will still be that all the interesting code sequences had to always have been there all the time.

[robhu.livejournal.com]

Hopefully they'll get sequenced and we can work this stuff out.

Slightly relevant information: I work for the Macromolecular Structures Database group - who are the repository of protein crystal structure files.

[robhu.livejournal.com]

If there was some extra bit of DNA that got hoovered up and incorporated in to the E.coli then that would give the creationists a field day, as their present model is to say that evolution cannot produce 'new' 'information' (where information is defined in a non standard, i.e. creationist way).

The current attempt at a get out seems to be that the creator intentionally put this capability in to E.coli, but for some unknown reason it hasn't been active anymore. ha

Disclaimer: I am a Christian, but not a stupid one or a creationist (which certainly overlaps with stupid), and I work at a premier bioinformatics institute but I am not a biologist.

[cartesiandaemon.livejournal.com]

that would give the creationists a field day

Literally, if people run off and run experiments on it :)

Although they'd surely be wrong: it'd be disappointing that this experiment wasn't an interesting example of evolution, but there's things that aren't interesting examples of evolution all over the place, the claim is that species evolve sometimes :)

the creator intentionally put this capability in to E.coli, but for some unknown reason it hasn't been active anymore. ha

That would make more sense for the evolution of antibiotic resistant bacteria: Here are the species of the world, but when you invent antibiotic, you'll discover you haven't solved biblical plagues after all...

Disclaimer: I am a Christian, but not a stupid one or a creationist (which certainly overlaps with stupid), and I work at a premier bioinformatics institute but I am not a biologist.

:)

[robhu.livejournal.com]

I'm quite quite sure the creationists are wrong (in general).

The problem is (if we want to point out to them that they're wrong) that the average creationists (which I used to be!) have swallowed various ideas that are pseudo-scientific like information theory... but not actual information theory, the creationist versions that are suitably redefined so that they think certain things are impossible.

It's also important to point out that modern creationists would say something like this "We believe in micro-evolution, but not macro-evolution. Micro-evolution is change within a kind while macro-evolution is change from one kind to another kind". When they say kind they're referring to a word used in Genesis.

Generally they mean that a dog can micro-evolve in to another type of dog, but that it can't gain any new properties that dogs didn't have (like wings or something). Of course 'kind' isn't the same as species, it's defined so poorly it's hard to argue against when using their language.

Their other idea is that 'no new information can be created, it can only be lost through evolution'. So they see that everything started perfect - so all modern dogs are derivatives of some earlier 'super dog' that was in some sense genetically perfect. It fits in to various theological ideas to see the universe (and genetics) to be in a downward state of decay, so they assume that when something evolves say anti-bacterial resistance it's because some bit of the bacterium stopped working. While their general idea is wrong AFAIUT the common case for anti-bacterial resistance (which is the most common example people throw back at them) does work like that. Some anti-bacterial stuff sticks to some binding site on the bacteria, but bacteria that don't have that binding site (due to some copying error or mutation) can't be bound to by the agent, and so it has resistance - but generally the bit that is missing off the bacteria did something so compared to the non-resistant strain it isn't as fit (if for the moment we compare their fitness in an environment without the anti-bacterial agent). I don't doubt that there are other ways in which resistance evolves, but AFAIK that is by far the most common way.

A similar example at the moment is HIV resistance in humans. Humans with a mutated CCR5 gene have CCR5 less expressed on the surface of their T cell proteins. HIV needs a working CCR5 receptor to infect the T-cells. So people who have a mutated CCR5 gene have immunity to HIV (which is clearly very good), but AFAIUI CCR5 does actually do something, so there is some negative side effect of it not being expressed properly (which may be better than getting HIV of course). Interestingly some researchers have just discovered a way to modify the expression of CCR5 in people who do not have this mutation (and so do not have immunity), which if it works safely in humans (of which there is a reasonably high chance given that people with CCR5 mutations already exist in the population) then we'll have another powerful weapon in our armory against HIV.

[robhu.livejournal.com]

So ... errr... in case I didn't make it clear.

They don't think that anti-biotic resistance falsifies creationism because they think is it an example of 'information being lost'.

If it is proven that 'information is gained' they'll either argue that the capability was hidden in there somewhere but is only now expressed, or they'll fall back to the next line of sandbags where they say "aha, but it's still bacteria, it hasn't become multicellular or anything like that, it's still of the same kind".

I feel sorry for creationists, and I'm not sure what can be done about reeducating them. I don't think they're completely lost though (although no doubt some are - the ones at the top), some of the smarter ones can be persuaded with actual science (this could have happened to me in the past, but I didn't know any smart biologists at the time), others may be persuaded by those of us inside the church using theological arguments. In the long term getting rid of creationism is going to require a concerted theological push from inside the church, and good science education of kids (which is why all this 'teach the controversy in science classes' stuff must be stopped at all costs), then in a few generations there'll be far fewer creationists (which is what happened in the UK AFAICT).

[cartesiandaemon.livejournal.com]

Thanks, that's really interesting; I hadn't heard the "running down" way of thinking before. It does indeed make some sort of sense.

[robhu.livejournal.com]

It seems to be true that the universe is 'in decay' in the sense of the second law of thermodynamics. At one point creationists argued that this meant that evolution was impossible because things should tend towards less complexity, but someone realised that is only within a closed system, and the earth isn't a closed system (it receives energy from the Sun). So while overall the universe is 'decaying' that doesn't mean you won't get localised examples of increased order.

[cartesiandaemon.livejournal.com]

Yeah.

There's generally a conversation like:

A: But... that'd only be possible if some external source was pouring energy into the system!
B: LOOK UP! IT'S THE SUN! IT'S A BALL OF NUCLEAR FLAMING GAS 300,000 TIMES BIGGER THAN THE EARTH, HOW HAVE YOU NOT NOTICES THIS?

:)

[robhu.livejournal.com]

Heh.

See also: http://www.answersingenesis.org/home/area/faq/dont_use.asp

[robhu.livejournal.com]

After going through the AiG site it's interesting that they look a lot more professional than they did back in my day. I guess they've got a lot more money now, and having faced fresh opposition they've got smarter people on their side.

It's also nice to see them state that Einstein did not believe in God. It really annoys me when people claim that he did.

[robhu.livejournal.com]

One could almost say they've evolved...

[robhu.livejournal.com]

That would make more sense for the evolution of antibiotic resistant bacteria: Here are the species of the world, but when you invent antibiotic, you'll discover you haven't solved biblical plagues after all...
I think a more serious question is why the creator (in their 6,000 year old world model) would intentionally put such features in to viruses and bacteria at all. They assume that these things originally served some useful purpose, but that a consequence of the fall was that as the world was corrupted by sin, all these things that had a good purpose before now do bad things.

I can kind of see how that would work for some things, but not everything, and it's a very hand wavy explanation that works if you already believe in creationism and have no scientific background, but if you understand something of biology it's a lot harder to swallow. Of course it could be that the world is like that, I just don't see that the empirical evidence really supports statements like that, and I don't see that the Bible requires one to believe them either.

[cartesiandaemon.livejournal.com]

Roughly what innocencest said. Or, actually, I didn't think this was such a big deal with respect to if evolution actually happens: that seemed conclusive before, so I just thought this was interesting.

So, what they have, is a bacterium A, and a descendant B, and if you grow B, it evolves into a citrate-eating version, and if you grow A, it doesn't? So something happened. But that could, in theory, either be an unusual mutation, or some DNA being spliced in by something else from some other species which can already eat citrate?

And if the second, it wouldn't really be evidence that species evolved by evolution, because possibly they can just share traits and evolve in small ways. (I don't think that point of view is very convincing, but that this wouldn't be extra evidence against it.)

Presumably the lab are now going to put A and B through the ringer and find the difference: if there's a tiny change, then it almost certainly was an unusual mutation (from whatever cause); if a whole bunch of DNA appeared, then maybe not.

(Or, in theory, there could be latent DNA which is turned on by mutations. So human DNA is all hidden away in bacteria, waiting to be switched on. But this is so blatantly stupid not even creationists propose it, only Startrek :))

[robhu.livejournal.com]

The interesting bit is if you read the talk page - or look at the history of the talk page. You find that there are pro-conservapaedia people on there arguing that although they don't want to agree, they're trained biologists, and his data does strongly support his argument. There has been a banning frenzy and a delete and purge policy for such people and comments.

Or, in theory, there could be latent DNA which is turned on by mutations. So human DNA is all hidden away in bacteria, waiting to be switched on. But this is so blatantly stupid not even creationists propose it, only Startrek
I don't know how crazy that is (remember I'm not a biologist). We don't properly understand how DNA / RNA is expressed at the moment. It used to be that everyone thought DNA was the big thing, then they thought the RNA was the important thing. There was the idea that 'simpler' life would have far fewer megabases of DNA than more complex life, but that isn't that clear cut either. There was also this idea that most DNA was 'junk', but they don't think that anymore. I can believe there may be ancestral stuff hiding in the DNA but not expressed. However, remember I am not a biologist although I play one on Livejournal.

[simont]

Dumbasses put hands over their ears and say "la la la, can't hear you"

It's actually worse than that. They've certainly got their hands over their ears and they certainly can't hear him, but then they keep insisting that he speak up!

[cartesiandaemon.livejournal.com]

ROFL. Good point.

[robhu.livejournal.com]

FWIW: The rapture stuff seems to be based on a particular reading of visions / prophecies in Daniel and Revelation. I don't think Christians are meant to infer direct stuff like this from those visions, so all this "we're going to be raptured away" stuff might sell a nice line of fantasy books, but I wouldn't try it's weight for anything else.

[cartesiandaemon.livejournal.com]

I heartily endorse this theological interpretation and/or service.

(I've not examined it myself, but I've heard well-put critiques objecting vociferously to mainstream media repeating claims that beliefs about the rapture are a literal interpretation of the bible: even if you do choose to take those parts literally, I don't think you could give the bible to someone else and have them come to the same conclusions, you have to "interpret" a lot. Which can be correct, but is disingenuous to claim "is a literal interpretation.")

[robhu.livejournal.com]

Claiming a literal interpretation of a vision seems particularly stupid. It talks about cities made of glass, dragons, bowls of wrath being poured out, and all that kind of stuff which is all clearly metaphoric.

[cartesiandaemon.livejournal.com]

Yes, very much so.

[leonerd.livejournal.com]

Hehe.. Amazing. Loads of companies all over the world try very hard to keep their systems working for a fee. Yet, here is someone who's invented a way to charge a fee for their systems specifically -no- working, until they stop looking after them.

I almost wish I'd thought of that...

[cartesiandaemon.livejournal.com]

Exactly :)

Although, to be fair, creating a fraudulent such service would be ever so easy, creating a legitimate such service is reasonably difficult: imagine testing it! :)