In the Hunt

Workout notes Last night, 2 miles with the group. This morning: 2000 yard swim (100 free, 100 pull, alternating), yoga, then 5 miles in West Peoria, which included 5 laps on the W. Peoria track where I did about a 2:15 pick up (not quite half a lap) then another 1 minute pick up each lap; 25:15 was the total.

I stayed up too late watching Wednesday Night Fights; in each case, the winner deserved to win, but the loser put up a good battle and got in licks of their own. Let’s just say that I wouldn’t pick a fight with either man.

Photo by Scott Foster at FightNews.com

Edner Cherry won a unanimous (but hard fought) decision over a tough Wes Furguson during these fights.

Rotten Red Winged Blackbirds
they have caused havoc:

un 13, 2007 – With one sudden swoop…runners training for the Steamboat Classic get that extra push in training that might just get them to the finish line quicker.

And for them and the unsuspecting pedestrian, it’s also a peck of unwanted pain.

Runners Tuesday evening were out training for the Steamboat Classic, minding their own business.

But there’s one thing that stands between them and the finish line, a nesting red winged blackbird. The city has posted signs on the sidewalk warning people about how the birds are protecting their nest and to take an alternate route.

Some pedestrians have taken caution…others have not. “I feel something sharp hit the back of my head and I didn’t know what it was and then I see everyone laughing and then I turn around and he’s getting attacked by a bird,” said Brandon Frye.

“It was like a sharp needle hits the back of your head and it startles you. It won’t change the way I feel about birds, but it’s something new,” said Evan Hocker.

Taking it to the streets doesn’t guarantee safety either. But for the birds and even passersby, it’s a family affair. “My dad got attacked by a bird last week too. He did. The same thing happened. He got hit in the back of the head too,” said Hocker. [So, it's running in the family now?] “I guess so, yeah.”

Video here.

This story also made the front page of the Journal Star:

It’s the week of Father’s Day. Don’t mess with Dad – at least, not the one patrolling the 200 block of Hamilton Boulevard in Peoria, and especially if you’re ornithophobic.

That means you’re afraid of birds. Legendary movie director Alfred Hitchcock created a classic on the subject in 1963.

And, just like the characters in “The Birds,” local attorney John Faletto learned Wednesday our feathered friends will attack.

“Holy . . .! Did you see that?” Faletto said after a red-winged blackbird, punctuating his loudly chirped warning with action, fluttered from a tree branch and struck the back of his head with its claws – twice.

Faletto, just as three other noon-hour walkers did within a mere 15 minutes, became the target of a species known for aggressive protection of its nesting territory, and of one particular blackbird with both powerful instincts and incentives.

“It’s been nesting there for several weeks, but it didn’t get defensive until its babies fell out of the nest” in a tree in the middle of the block, said an employee from the Caterpillar Inc. headquarters watching the action from the building’s rear lot.

Harold Church, who for 71 years has owned and still operates Kelly Seed & Hardware on the block, has a sage perspective of the phenomenon.

“It’s been going on for about two weeks,” he said. “People would go by” the tree “and that bird would whack ‘em.”

But, he added, “This goes on every year; it’s happened before.” [...]

“Momma’s feeding the baby in the bush,” she said, pointing to an evergreen shrub beneath the tree where the brown-colored female of the species hovered over one of her newborns. Above them, dad hopped from branch to branch, chirping like a referee’s whistle and, when occasion arose, attacking those who approached from behind.

While protected under the U.S. Migratory Bird Act, the red-winged blackbird is one of the nation’s most abundant species, at about 190 million. An amendment to the law allows poisoning, trapping, shooting or noise harassment to keep huge flocks from stripping farm fields of seeds.

“If I had my gun, I’d shoot it,” said a man as he watched the Hamilton marauder in action.

Church advised patience. “Another week or so and it’ll be over with.”

Until then, “Your best bet is to wear a hard hat,” said the Cat employee.

Thumbnails link to the Journal Star photos.

Photos of one of these little b@stards attacking a blue heron here.

This is funny; which fictional “make believe fairy tale nonsense with no basis in reality” character do they want to discuss: the Loch Ness Monster or Ron Paul’s campaign?

Barack Obama wants to talk to us too.

Creationist tatics

Whoa, they stumped Dr. Dawkins with this question, right? Well….wrong…

(hat tip to Dr. Montague)

Here Dawkins tells what happened:

n September 1997, I allowed an Australian film crew into my house in Oxford without realising that their purpose was creationist propaganda. In the course of a suspiciously amateurish interview, they issued a truculent challenge to me to “give an example of a genetic mutation or an evolutionary process which can be seen to increase the information in the genome.” It is the kind of question only a creationist would ask in that way, and it was at this point I tumbled to the fact that I had been duped into granting an interview to creationists – a thing I normally don’t do, for good reasons. In my anger I refused to discuss the question further, and told them to stop the camera. However, I eventually withdrew my peremptory termination of the interview as a whole. This was solely because they pleaded with me that they had come all the way from Australia specifically in order to interview me. Even if this was a considerable exaggeration, it seemed, on reflection, ungenerous to tear up the legal release form and throw them out. I therefore relented.

My generosity was rewarded in a fashion that anyone familiar with fundamentalist tactics might have predicted. When I eventually saw the film a year later 1, I found that it had been edited to give the false impression that I was incapable of answering the question about information content 2. In fairness, this may not have been quite as intentionally deceitful as it sounds. You have to understand that these people really believe that their question cannot be answered! Pathetic as it sounds, their entire journey from Australia seems to have been a quest to film an evolutionist failing to answer it.

With hindsight – given that I had been suckered into admitting them into my house in the first place – it might have been wiser simply to answer the question. But I like to be understood whenever I open my mouth – I have a horror of blinding people with science – and this was not a question that could be answered in a soundbite. First you first have to explain the technical meaning of “information”. Then the relevance to evolution, too, is complicated – not really difficult but it takes time. Rather than engage now in further recriminations and disputes about exactly what happened at the time of the interview (for, to be fair, I should say that the Australian producer’s memory of events seems to differ from mine), I shall try to redress the matter now in constructive fashion by answering the original question, the “Information Challenge”, at adequate length – the sort of length you can achieve in a proper article.

And tells what happened with the video:

At the end of the long pause, they cut to a scene of me talking about something completely different (presumably the answer to another question which was cut), to make it look as though I was evading the question by changing the subject.

In the original film, ‘From a Frog to a Prince’, the ‘information content’ question is put to me by a MAN. We see him in a bare room, very obviously not the well-furnished room in which I am shown (not) answering the question. The new version on YouTube is different in at least two respects. First, the question is put to me by a WOMAN (we don’t see her). And while she is speaking I am obviously not listening to anybody asking questions (I would be looking straight at the questioner if so) but I am clearly lost in thought, the same long train of thought that persists for a long time after the question ends (intended to look embarrassingly long, as if I am incapable of answering the question).

There is another difference. In this new version of the film, I ask them to stop the camera (and this really happened, for the reason given above). Then there is the cut to me answering the completely different question, as if trying to change the subject. In the original film, my request to stop the camera is missing.

And here Dawkins answers the question:

[...]
DNA carries information in a very computer-like way, and we can measure the genome’s capacity in bits too, if we wish. DNA doesn’t use a binary code, but a quaternary one. Whereas the unit of information in the computer is a 1 or a 0, the unit in DNA can be T, A, C or G. If I tell you that a particular location in a DNA sequence is a T, how much information is conveyed from me to you? Begin by measuring the prior uncertainty. How many possibilities are open before the message “T” arrives? Four. How many possibilities remain after it has arrived? One. So you might think the information transferred is four bits, but actually it is two. Here’s why (assuming that the four letters are equally probable, like the four suits in a pack of cards). Remember that Shannon’s metric is concerned with the most economical way of conveying the message. Think of it as the number of yes/no questions that you’d have to ask in order to narrow down to certainty, from an initial uncertainty of four possibilities, assuming that you planned your questions in the most economical way. “Is the mystery letter before D in the alphabet?” No. That narrows it down to T or G, and now we need only one more question to clinch it. So, by this method of measuring, each “letter” of the DNA has an information capacity of 2 bits.

Whenever prior uncertainty of recipient can be expressed as a number of equiprobable alternatives N, the information content of a message which narrows those alternatives down to one is log2N (the power to which 2 must be raised in order to yield the number of alternatives N). If you pick a card, any card, from a normal pack, a statement of the identity of the card carries log252, or 5.7 bits of information. In other words, given a large number of guessing games, it would take 5.7 yes/no questions on average to guess the card, provided the questions are asked in the most economical way. The first two questions might establish the suit. (Is it red? Is it a diamond?) the remaining three or four questions would successively divide and conquer the suit (is it a 7 or higher? etc.), finally homing in on the chosen card. When the prior uncertainty is some mixture of alternatives that are not equiprobable, Shannon’s formula becomes a slightly more elaborate weighted average, but it is essentially similar. By the way, Shannon’s weighted average is the same formula as physicists have used, since the nineteenth century, for entropy. The point has interesting implications but I shall not pursue them here. [...]

The total information capacity of the human genome is measured in gigabits. That of the common gut bacterium Escherichia coli is measured in megabits. We, like all other animals, are descended from an ancestor which, were it available for our study today, we’d classify as a bacterium. So perhaps, during the billions of years of evolution since that ancestor lived, the information capacity of our genome has gone up about three orders of magnitude (powers of ten) – about a thousandfold. This is satisfyingly plausible and comforting to human dignity. Should human dignity feel wounded, then, by the fact that the crested newt, Triturus cristatus, has a genome capacity estimated at 40 gigabits, an order of magnitude larger than the human genome? No, because, in any case, most of the capacity of the genome of any animal is not used to store useful information. There are many nonfunctional pseudogenes (see below) and lots of repetitive nonsense, useful for forensic detectives but not translated into protein in the living cells. The crested newt has a bigger “hard disc” than we have, but since the great bulk of both our hard discs is unused, we needn’t feel insulted. Related species of newt have much smaller genomes. Why the Creator should have played fast and loose with the genome sizes of newts in such a capricious way is a problem that creationists might like to ponder. From an evolutionary point of view the explanation is simple (see The Selfish Gene pp 44-45 and p 275 in the Second Edition). [...]

Human adult haemoglobin is actually a composite of four protein chains called globins, knotted around each other. Their detailed sequences show that the four globin chains are closely related to each other, but they are not identical. Two of them are called alpha globins (each a chain of 141 amino acids), and two are beta globins (each a chain of 146 amino acids). The genes coding for the alpha globins are on chromosome 11; those coding for the beta globins are on chromosome 16. On each of these chromosomes, there is a cluster of globin genes in a row, interspersed with some junk DNA. The alpha cluster, on Chromosome 11, contains seven globin genes. Four of these are pseudogenes, versions of alpha disabled by faults in their sequence and not translated into proteins. Two are true alpha globins, used in the adult. The final one is called zeta and is used only in embryos. Similarly the beta cluster, on chromosome 16, has six genes, some of which are disabled, and one of which is used only in the embryo. Adult haemoglobin, as we’ve seen contains two alpha and two beta chains.

Never mind all this complexity. Here’s the fascinating point. Careful letter-by-letter analysis shows that these different kinds of globin genes are literally cousins of each other, literally members of a family. But these distant cousins still coexist inside our own genome, and that of all vertebrates. On a the scale of whole organism, the vertebrates are our cousins too. The tree of vertebrate evolution is the family tree we are all familiar with, its branch-points representing speciation events – the splitting of species into pairs of daughter species. But there is another family tree occupying the same timescale, whose branches represent not speciation events but gene duplication events within genomes.

The dozen or so different globins inside you are descended from an ancient globin gene which, in a remote ancestor who lived about half a billion years ago, duplicated, after which both copies stayed in the genome. There were then two copies of it, in different parts of the genome of all descendant animals. One copy was destined to give rise to the alpha cluster (on what would eventually become Chromosome 11 in our genome), the other to the beta cluster (on Chromosome 16). As the aeons passed, there were further duplications (and doubtless some deletions as well). Around 400 million years ago the ancestral alpha gene duplicated again, but this time the two copies remained near neighbours of each other, in a cluster on the same chromosome. One of them was destined to become the zeta of our embryos, the other became the alpha globin genes of adult humans (other branches gave rise to the nonfunctional pseudogenes I mentioned). It was a similar story along the beta branch of the family, but with duplications at other moments in geological history.

Now here’s an equally fascinating point. Given that the split between the alpha cluster and the beta cluster took place 500 million years ago, it will of course not be just our human genomes that show the split – possess alpha genes in a different part of the genome from beta genes. We should see the same within-genome split if we look at any other mammals, at birds, reptiles, amphibians and bony fish, for our common ancestor with all of them lived less than 500 million years ago. Wherever it has been investigated, this expectation has proved correct. Our greatest hope of finding a vertebrate that does not share with us the ancient alpha/beta split would be a jawless fish like a lamprey, for they are our most remote cousins among surviving vertebrates; they are the only surviving vertebrates whose common ancestor with the rest of the vertebrates is sufficiently ancient that it could have predated the alpha/beta split. Sure enough, these jawless fishes are the only known vertebrates that lack the alpha/beta divide.

Gene duplication, within the genome, has a similar historic impact to species duplication (“speciation”) in phylogeny. It is responsible for gene diversity, in the same way as speciation is responsible for phyletic diversity. Beginning with a single universal ancestor, the magnificent diversity of life has come about through a series of branchings of new species, which eventually gave rise to the major branches of the living kingdoms and the hundreds of millions of separate species that have graced the earth. A similar series of branchings, but this time within genomes – gene duplications – has spawned the large and diverse population of clusters of genes that constitutes the modern genome.

The story of the globins is just one among many. Gene duplications and deletions have occurred from time to time throughout genomes. [...]

Read the whole article; it takes some time and effort, but is worth it.

Yoga Perhaps this is a practical application of yoga???
Hat tip to Watertiger at Dependable Renegade.

Quit Picking on my Harriet!

Guess who got issued a subpoena by that mean old congress? That’s right.

The chairmen of two congressional committees issued subpoenas Monday for testimony from former White House counsel Harriet Miers and former political director Sara Taylor on their roles in the firings of eight federal prosecutors.

Democrats probing whether the White House improperly dictated which prosecutors the Justice Department should fire also are subpoenaing the White House for all relevant documents.

Senate Judiciary Committee Chairman Patrick Leahy of Vermont issued Taylor’s subpoena for her testimony July 11. His counterpart in the House, Judiciary Committee Chairman John Conyers of Michigan, issued a subpoena for Miers’ testimony the next day.

The White House has repeatedly refused to make current and former officials involved in the firings available except in private interviews, without transcripts. Congressional investigators have refused that offer.
[...]

The House and Senate chairmen implicitly threatened a constitutional showdown if the White House does not comply — or strike a deal.

“The breadcrumbs in this investigation have always led to 1600 Pennsylvania,” said Conyers, D-Mich. “This investigation will not end until the White House complies with the demands of this subpoena in a timely and reasonable manner so that we may get to the bottom of this.”

“The White House cannot have it both ways — it cannot stonewall congressional investigations by refusing to provide documents and witnesses, while claiming nothing improper occurred,” Leahy added.

Technically, if the showdown between the White House and Congress is not resolved, the matter could end up with House and Senate contempt citations and a session in federal court.

Congressional officials knowledgeable about the probe painted a dark picture of what the Democratic-led committees might do if the White House refuses to comply.

One option, these officials said, are votes in committee and on the House and Senate floors on contempt citations against any subjects of the subpoenas who don’t comply. Another, according to one aide, is a subpoena for White House Counsel Fred Fielding, compelling him to testify publicly about the Bush administration’s reasons if the subpoenas are ignored. The officials spoke on condition of anonymity because the White House, Miers and Taylor had not yet responded to the subpoenas.

How unfair; asking my Harriet to be held accountable by mean old transcripts. Seesh, when will they stop picking on her!