Rants, Mutations, and Loony Stuff

Workout notes
This afternoon, I walked 3 miles on my own (Michael Bridge course) and then 2 with the group. That gives me 8 miles for the day, to go along with 2000 yards of swimming and 10 minutes of cool down on the bike.

Race schedule: The projected fall line up looks something like this (provided I can avoid flus, colds, etc.):

August 30′th (my 49′th birthday): Badgerland Striders F/X. My goal will be 49 miles; not sure if I’ll sign up for the 12 hour and just go like crazy or sign up for the 24 and take my time. Probably the latter. Last year it was hot as hell.

September: Quad Cities Marathon. Yep, last year was a disaster for me. This year: no cold water at mile 23.

October: Farmdale 33 miler (trail). I hope to do better this time than last year.

November: Chicago Ultra 50K. I’ve done this in the past (spring: north course, fall: southern course) and have had some modest success.

Science and mathematics

Recursivity posts an “easy to understand, hard to do” open problem.

I added a a problem about discrete iterations, which I’ll repeat here because it is so easy to state, yet frustratingly difficult to solve.

Start with two integers, a and b, with a > b > 0. Now repeatedly replace b with a mod b, counting the number of steps it takes to get to 0, and call this P(a,b). For example, if we start with a = 35 and b = 22, we get

35 mod 22 = 13
35 mod 13 = 9
35 mod 9 = 8
35 mod 8 = 3
35 mod 3 = 2
35 mod 2 = 1
35 mod 1 = 0

It took 7 steps to get down to 0, so P(35,22) = 7.

The question is, at what rate does P(a,b) grow? [...]

Follow the link to see some known partial results and to see the cash award.

I’ll go ahead and give another example: a = 41, b = 19
41 mod 19 = 3
41 mod 3 = 2
41 mod 2 = 1
41 mod 1 = 0. So, P(41, 19) = 4.

More mathematics: here is a brief article on chaos theory. It is this principle that makes certain things (such as weather) difficult, if not impossible, to predict (other than general trends). Example: if I wanted to say what the weather in Austin, TX would be one week from now, I could guess that the temperature range would be from 75-100 (highs and lows) and be reasonably accurate on that, but I couldn’t say with any confidence what the exact highs and lows would be, or whether it would rain or not.

Cosmology: there is a lack of symmetry in the background microwave radiation from the big bang; this provides clues about the “edge of spacetime”.

Evolution: directly observed in the laboratory (in bacteria).

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait.

And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.

Profound change

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

“It’s the most profound change we have seen during the experiment. This was clearly something quite different for them, and it’s outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting,” says Lenski.

Rare mutation?

By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the “citrate-plus” trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

To find out which, Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution “replay” again.

Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?

Evidence of evolution

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.

Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events,” he says. “That’s just what creationists say can’t happen.”

By the way, here is an excellent resource on evolution and its deniers.

Scientists get closer to constructing a living cell. Yep, right in the laboratory:

n an attempt to duplicate an early cell, scientists put fatty acids (that were likely membrane candidates) and a strip of DNA into a test tube of water. While in there, the fatty acids formed into a ring, or membrane, around the genetic segment. The researchers then added nucleotides—units of genetic material—to the test tube to determine whether they would penetrate the membrane and copy the DNA inside it. Their findings: the nucleotides did enter the cell, latch onto and replicate the DNA over 24 hours.

Of course, these last two discoveries won’t phase the creationists one bit; they admit that “small” changes can take place via evolution; they might argue that we haven’t seen a colony of bacteria change into, say, a fly. When one believes something that can’t be falsified, well, you can’t ever show them that their beliefs are false!

Social/Political Issues:

A good rant by postsimian. Republicans, right wing nut jobs and SUV drivers take it on the chin!

Religion and society: Friendly Atheist reports that Fox News is outraged over an atheist billboard. What does it say?

“Don’t believe in God? You’re not alone.”

Video here.

Yep, that’s it! I’m sorry, but they will just have to be outraged, given that many churches openly advertise.

By the way, here is Friendly Atheist on the news.

Political
This fits in well with the above topic: right wing nutjob Cal Thomas says that Barack Obama isn’t a Christian. Hmmm, normally I’d say “thank you” but for most people, being a Christian is considered to be a good thing. So I’d say that Mr. Thomas being a bit presumptuous here; evidently the fact that BHO is doing better than normal (for a Democrat) among evangelicals is scaring him.

Oh yes, Mr. Thomas is a creationist. So, I challenge him to do without the benefits of modern science (including medicine and the like).

Now for a different kind of wingnut reaction to Barack Obama: Some white supremacists and some white separatists aren’t unhappy that he is doing well; in fact they see his political success as the event that will drive many white people over to them. Example:

Even David Duke, the neo-Nazi and former Klan boss who is the closest thing the movement has to a real intellectual these days, sees clear advantages in an Obama victory in the fall. “Obama will be a signal, a clear signal for millions of our people,” Duke wrote in an essay entitled “A Black Flag for White America” last week. “Obama is like that new big dark spot on your arm that finally sends you to the doctor for some real medicine. … Obama is the pain that let’s [sic] your body know that something is dreadfully wrong. Obama will let the American people know that there is a real cancer eating away at the heart of our country and Republican aspirin will not only not cure it, but only masks the pain and makes you think you don’t need radical surgery. … My bet is that whether Obama wins or loses in November, millions of European Americans will inevitably react with new awareness of their heritage and the need for them to defend and advance it.”

Don’t get me wrong: not all religious right wing woos are bigots; some are simply delusional. So, I am NOT comparing the religious right to the racists; not even close. The former is just nutty and may or may not be evil; the latter is both nutty and inherently evil.

Barack Obama: who is on his short list for VP? Some of the names that I had floated aren’t being floated in this article.

John “more of the same” McCain

The problem is that our presence in Iraq will lead to continued violence; this isn’t the case of occupying a defeated nation that had is relatively homogeneous (Japan, Germany) or a nation that we saved from being overrun (Korea). Iraq has long standing historical tensions between its main factions.