Nicholas Wade gets schooled, briefly

A few weeks ago, Nicholas Wade wrote a terrible review of Dawkins’ latest book (it wasn’t a negative review, but it just weirdly spun off into some half-baked philosophy of science).

Now the poor guy has been publicly spanked. The NY Times published short letters of rebuttal from Dan Dennett and Philip Kitcher, and then published online another dozen letters. That last link is more of a mixed bag, with some good replies and some strangely skewed ones…but it’s all fun anyway.

Unfortunately, all the letters are necessarily short. This kind of corrective actually needs some longer discussion.

How badly can a paper summary be botched?

Perhaps you are a scientist. And perhaps you have wondered how badly the popular press could possibly mangle your research. Wonder no more: we have discovered a new maximum.

Behold this research summary in The Daily Galaxy, and be amazed!

It’s about a paper in the ACS Journal of Physical Chemistry B. It’s straightforward physical chemistry using some cool tools to image the formation of double helices of DNA: it’s simply addressing the question of how complementary strands align themselves in solution. It’s physical chemistry, OK? It’s about tiny molecular interactions…until the Daily Galaxy gets ahold of it. Now it’s about how DNA uses telepathy.

DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to. Explanation: None, at least not yet.

Scientists are reporting evidence that contrary to our current beliefs about what is possible, intact double-stranded DNA has the “amazing” ability to recognize similarities in other DNA strands from a distance. Somehow they are able to identify one another, and the tiny bits of genetic material tend to congregate with similar DNA. The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.

…

In the study, scientists observed the behavior of fluorescently tagged DNA strands placed in water that contained no proteins or other material that could interfere with the experiment. Strands with identical nucleotide sequences were about twice as likely to gather together as DNA strands with different sequences. No one knows how individual DNA strands could possibly be communicating in this way, yet somehow they do. The “telepathic” effect is a source of wonder and amazement for scientists.

Cue the theremins, everyone, and bring on the reanimated corpse of Rod Serling to narrate this sucker. Audience, say “OOOOOoooooOOOOOOOOooOOH!”

Oh, wait. Read the actual paper, first. It turns out that not only are the scientists not mystified, but they provide a reasonable explanation for the phenomenon, and go on to give some alternatives, even. None of them involve molecular telepathy. They actually are amazed at the ability of these molecules to align…at distances of one whole nanometer!

Pay especially careful to the first sentence of the following paragraph. If you are a journalist writing a summary of a paper, claiming that it says no one knows how the two molecules recognize each other, you should probably read more closely a paragraph that begins, “We hypothesize that the origin of this recognition may be as follows.” It’s a clue that an explanation will follow.

We hypothesize that the origin of this recognition may be as follows. In-register alignment of phosphate strands with grooves on opposing DNA minimizes unfavorable electrostatic interactions between the negatively charged phosphates and maximizes favorable interactions of phosphates with bound counterions. DNAs with identical sequences will have the same structure and will stay in register over any juxtaposition length. Nonhomologous DNAs will have uncorrelated sequence-dependent variations in the local pitch that will disrupt the register over large juxtaposition length. The register may be restored at the expense of torsional deformation, but the deformation cost will still make juxtaposition of nonhomologous DNAs unfavorable. The sequence recognition energy, calculated from the corresponding theory is consistent with the observed segregation within the existing uncertainties in the theoretical and experimental parameters. This energy is ˜1 kT under the conditions utilized for the present study, but it is predicted to be significantly amplified, for example, at closer separations, at lower ionic strength, and in the presence of DNA condensing counterions.

So, their preferred explanation is that there are electrostatic interactions between the molecules that favor pairs that fit together well. Not telepathy. As cautious investigators, they also suggest some alternative explanations; perhaps telepathy will appear here? Or maybe elves?

Presently, we cannot exclude other mechanisms for the observed segregation. For instance, sequence-dependent bending of double helices may also lead to homology recognition by affecting the strand-groove register of two DNA molecules in juxtaposition. The juxtaposition of bent, nonhomologous DNAs may also be less energetically favorable under osmotic stress, since it may reduce the packing density of spherulites. In addition, formation of local single-stranded bubbles and base flipping may cause transient cross-hybridization between the molecules, as proposed to explain Mg2+ induced self-assembly of DNA fragments with the same sequence and length. We consider it to be rather unlikely in this instance, since the probability of bubble formation in unstressed linear DNA of the studied length is very small in contrast to the case where topological strain is relieved by bubble formation in small circular DNA molecules. Furthermore, bubble formation would distort the cholesteric order of spherulites and we see no evidence of this in spherulites composed of a single type of DNA molecule.

I’m so disappointed. Telepathy isn’t mentioned once in the whole danged paper, and there aren’t even tiny diaphanous fairies tugging at the molecules. And no, the Intelligent Designer doesn’t appear, either.

Baldwin GS, Brooks NJ, Robson RE, Wynveen A, Goldar A, Leikin S, Seddon JM, Kornyshev AA (2008) DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment. J. Phys. Chem. B 112(4):1060-1064.

Dogs can be good without god

This clip is from a traffic camera in Chile — it shows a dog hit by a car, and then another dog risking the heavy traffic to pull the injured animal to the side, out of danger.

I wonder what church the heroic dog attends?

Keep this in mind when you encounter people — yeah, I’m looking at you, Francis Collins — try to argue that morality and altruism and empathy are unique markers of a divine hand in our origin.

Discovering Ardi

The Discovery Channel is having a documentary about Ardipithecus ramidus at 8pm Central time (in about half an hour). I’m planning to set my work aside for a while and fix a bowl of hot soup — it’s cold here, with a snow storm on the way — and see if they actually do it right.

First half hour wasn’t bad: nice overview of the practice of finding old bones, and a good illustration of the fragmentary nature of the fossil. At the same time, though, it’s also doing a good job of showing how they know the pieces of Ardi are from a single individual.

S l o w i n g   d o w n. So far this program is taking longer to watch than it took me to read the original papers. It’s got some nicely done bits, but it sure is taking it’s time, and it’s annoyingly repetitive. It’s also got commercials, and the frequency of commercial breaks is steadily increasing.

I thought we Americans were supposed to have short attention spans. How is this sort of drawn out programming supposed to appeal to the average person with a general interest in evolution?

The worst article on Ardipithecus yet

The dishonor goes to ABC News, which put together an appalling mess of an article that gives credibility to creationist denialists. Right from the beginning, you know this article is bunk.

But despite the excitement from the paleontology community, another group of researchers, many of them with advanced degrees in science, are unimpressed by Ardi, who they believe is just another ape — an ape of indeterminate age, they add, and an ape who cannot be an ancestor of modern man for a range of reasons, including one of singular importance: God created man in one day, and evolution is a fallacy.

The whole article is like that: they cite Creation Ministries International, the Institute for Creation Research, and Answers in Genesis, puffing up the credentials of these loons and credulously reporting their dissent. None of these fellows is any kind of researcher, all are looked upon as utterly crazy, and there is no reason to consult any of them on a science story, let alone dedicating a long article solely to their batty position (they quote one of the real researchers just once, saying that the discovery was an important find — but it is more to lend weight to the parade of nutcases declaring it trivial.)

They give a lot of space to Answers in Genesis, especially to one of their pet frauds-with-a-degree, David Menton.

“What creationists believe about human origins we get from the Bible,” said David Menton an acclaimed anatomist and also a creationist. “The creation of the world takes place on page one of the Bible. If you throw out the first page of the Bible you might as well throw out the whole thing. If you can’t live with the first page then pitch out the remaining thousand pages.”

Menton is not an acclaimed anatomist. His sole claim to fame is his weird belief that the earth is only 6000 years old. Although, I must say, I agree with his sentiment here: the first page is metaphorical, poetical nonsense and should be thrown out, and the rest should be tossed right after it. But what really annoys me is the patent disrespect for knowledge in these people. Ardipithecus is a genus that lived over 4 million years ago. Shouldn’t there be a little bit of awe at that? Not from the ICR.

“This is a meaningless discovery of another ape. As far as the creationist community is concerned, this is a big yawn. There is nothing about Ardi that has anything to do with the evolution of man,” said John Morris, president of the Institute for Creation Research in Dallas.

Menton just keeps on bringing the dementia.

Menton believes scientists sat on the Ardi discovery for over a decade just to roll it out during the Darwin anniversary. He questions the ability to accurately date any fossils more than a few thousand years old, let alone millions, and he said the condition of the skeleton was so incomplete and fragile that serious research was almost impossible.

Menton said Ardi’s skull and feet are exactly the kind of skull and feet you would expect an ape to have and have none of the features of modern humans.

“Evolutionists want to call Ardi ‘ape-like.’ This creature is ape-like, because she is an ape. Just call it an ape,” he said.

The biggest problem Menton has with Ardi is her estimated age. The Earth, he says, is no more around 5,000 years old, a number creationists have estimated by counting the generations of man named in the Bible from Adam to Jesus.

“Evolution is supposedly based on science, but the science does not prove what they want it to. Creationism is not based on scientific observation but on God’s word. God created everything in six days, and that’s it.”

Errm, the scientists all agree: Ardi was an ape. They say it right out. They’ll also tell ‘acclaimed’ anatomist Menton that, based on the anatomy, we humans are also apes. We also regard the even older last common ancestor of chimps (which are apes) and humans (also apes) to have been an ape. Therefore, any transitional form between an ancient ape and a modern ape is expected to be an ape.

What did Menton expect? A frickin’ giraffe?

As for the rest…anyone in the 21st century who rants about the earth being 6000 years old and unthinkingly accepts the scientific authority of an ancient book cobbled together by tribes of sheepherders really needs to be shuffled off to a rubber room.

So what is ABC News doing getting a story on a serious scientific issue from a series of lunatic asylums? I don’t know. Who is this ‘journalist,’ Russel Goldman, who scribbled up this gullible slop? I don’t know and I don’t care, except that I’ll know to throw anything else he writes in the rubbish.

Nice psalm

Here are the lyrics:

Don’t need no god.
Don’t need no eternal paternal god.
Don’t need no reassuringly protective
good and evil in perspective god.
Don’t need no imported distorted,
inflated updated,
holy roller, save your soul, or
anaesthetisingly opiate gods.
Don’t need no “all creatures that on Earth do dwell”
be good or you go to Hell god.
Don’t need no Hare Krishna Hare Krishna,
Hail Mary, Hail Mary god.
Got no yen for zen, Baghavad-Gita or Gurdjieff.
No Mormon, Methodist, Seventh Day Adventist god,
no absolutes beyond refute,
no reverential preferential Judaic Messianic god.
No Bibles, no Mahayanas, Delai Lhama
instant dharma gods.
Don’t need no spiritual suicide or
prefrontal lobotomising god.
Don’t need no stoic sexless
anticeptic god.
Don’t need no neon crucifix,
no jade Buddhas, no Vedas or Upanishads,
no camels or needles or Papal decrees,
no mail-order ikons, Koran’s or Mandala’s,
no Sri Chimnoys, Meha Baba’s, or Ayatollah’s,
no Guatama’s, no Manitou, Ouspensky or Marx,
no yin/yang, no tao, no tarot or incense,
no sacred mushrooms
no dianetics,
no Tibetan prayer mats
no “Immortal invisible gods only wise”.
Don’t need no televised circumcised
incessant incandescent god.
Don’t need no god.
I need human beings.
I need some kind
of love.
I need
you.