Freecell

 

Andrew Brown over at Helmintholog points us to Freecell fanatic about a man who has played all 32,000 games three times, and is working his way through the fourth round. You probably don't want to know which games can be won by never using the free cells, but I bet you want to know the one and only game that can't be won at all!

Here it is!!!

Dissection of larval CNS in Drosophila melanogaster

Have you ever wanted to know how to remove the central nervous system (CNS) from a fruit fly larva? Of course you have.

Now you can see an expert in action thanks to The Journal of Visualized Experiments. Nathaniel Hafer in Paul Schedl's lab at Princeton shows you how to do it.

Watch the CNS form during development of the embryo in this video from YouTube. (The CNS is the black thing at the bottom.)

Calico Cats

There's been a discussion on talk.origins about calico cats—do they have to be female? The color pattern is an interesting combination of sex-linked genetics and epigenetics. Epigenetics is the inheritance of characteristics other than nuleotide sequence. In this case, it's inheritance of an inactivated X-chromosome.I used calico cats as an example in the Moran/Scrimgeour et al. textbook (1994) published by Neil Patterson/Prentice Hall. Here's an excerpt from that book.

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One X Chromosome Is Inactivated in Mammalian Females by Condensation into Heterochromatin
The DNA within polytene chromosome bands is condensed but nevertheless accessible to transcription factors. However, there are forms of chromatin known as heterochromatin, that are much more highly condensed. Constitutive heterochromatin refers to chromosomes or parts of chromosomes that are heterochromatic in all cells of a given species. Examples of constitutive heterochromatin can be found in every multicellular eukaryote and can take the form of entire chromosomes or parts of chromosomes. For example, some maize cells contain multiple copies of a small, heterochromatic chromosome called chromosome B. In addition, between one-fourth and one-third of all DNA in Drosophila is found in heterochromatic regions near the centromeres.
Condensation of chromatin is an effective mechanism of repressing eukaryotic gene expression and is best exemplified by the process of X-chromosome inactivation in mammalian females. The sex of a mammal is determined by the presence or absence of the male-specific Y chromosome. In humans, males normally have one X and one Y chromosome per somatic cell, whereas females normally have two X chromosomes per somatic cell. The X chromosome is quite large and contains a number of genes, most of which play no role in sex differences. Proper human development requires that only one X chromosome be fully active in each somatic cell of an adult. Thus, one of the X chromosomes in females is inactivated by condensation into heterochromatin (Figure 27.53). Such condensed chromosomes are known as sex-chromosome bodies or Barr bodies. X-chromosome inactivation is one example of the genetic phenomenon known as dosage compensation because it involves regulating the dosage of genes.

In human females, X-chromsome inactivation occurs very early in embryonic development, at about the 20-cell stage. Condensation of an X chromosome into heterochromatin appears to begin at a unique point, the xist gene, and proceed bidirectionally along the DNA. Inactivation is associated with extensive methylation of DNA. Once a specific X chromosome has been inactivated in a particular cell of the 20-cell embryo, the same X chromosome remains inactivated in all daughter cells descended from that presursor cell (Figure 27_54). In each human cell, either the maternal of paternal X chromosome can be inactivated.

The frequencies of maternal and paternal X chromosome inactivation vary among mammals. In female marsupials, for example, the paternal X chromosome appears to be preferentially inactivated. This observation indicates that the maternal and paternal chromosomes are not identical and can be distinguished in the developing embryo. However, in most other mammals, including humans, the X chromosome that is condensed appears to be selected more or less at random. As a result, some of the cells in the mature organism contain an active maternal X chromsome, and some contain an active paternal chromosome. Consequently, the organism is a mosaic composed of cells expressing different genetic information.
Sometime cells containing an active maternal X chromosome can be physically distinguished from those containing an active paternal X chromosome. An example of such a visible mosaic is the calico cat, which has patches of orange and black fur. Calico cats are always female if they have normal X chromosomes. The patchiness results from random inactivation of X chromosomes in female cats in which the X chromosome inherited from one parent carries the gene [allele] for orange fur and the X chromosome inherited from the other parent carries the gene [allele] for black fur. (The white fur on the underside is due to expression of an autosomal gene.)
Genetic mosaicism due to X-chromosome inactivation also occurs in human females. For example, the gene for glucose-6-phosphate dehydrogenease is located on the X chromosome. If each chromosome carries a different allele, patches of cells will contain either one isoform or the other, depending on which X chromosome is inactivated. The theory of X-chromosome inactivation was developed in large part by Mary Lyon, and the process is sometimes known as Lyonization.

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[Calico_cat_Phoebe is from Free Software Foundation.]

Go, Leafs, Go!!!

Tonight is hockey night in Canada. We get to watch Don Cherry on TV.

Last night, the Leafs punished the Washington Capitals 7-1. This puts them solidly in third place in the Northeast Division of the Eastern Conference. They're only 8 points behind the division leader (Buffalo) with over 55 games left!

Tonight, the Leafs play Boston at the Air Canada Centre. Some of you might recall that Boston barely squeaked out an overtime victory last time they played. Boston is home to Boston University, MIT, and some other schools.

This is the year the Leafs are going to win the Stanley Cup. Yes Siree, Bob, you can count on it! There'll be dancing in the streets next June.

Poking with Needles, Running with Scissors

noctiluca has posted an interesting article on talk.origins, "The Humpty Dumpty argument - the wit and wisdom of Jonathan Wells." noctiluca quotes Jonathan Wells from a Lee Strobel DVD called"The Case for the Creator." (If you go to the site you can actually watch clips showing the IDiots in action!)

It comes down to this: no matter how many molecules you can produce with early earth conditions, plausible conditions, you're still nowhere near producing a living cell.

And here's how I know: If I take a sterile test tube and I put in it a little bit of fluid with just the right salts, just the right balance of acidity and alkalinity, just the right temperature - the perfect solution for a living cell, and I put in it one living cell, this cell is alive, it has everything it needs for life. Now I take a sterile needle and I poke that cell, and all its stuff leaks out into this test tube, you have in this nice little test tube all the molecules you need for a living cell, not just the pieces of the molecules but the molecules themselves, and you can't make a living cell out of them.

You can't put Humpty Dumpty back together again. So what makes you think that a few amino acids dissolved in the ocean are going to give you a living cell? It's totally unrealistic.

You can't make this stuff up. And you wonder why we call them IDiots?

The talk.origins article closes with, "My wife didn't know if I was laughing or crying." Thanks noctilura, for sharing that with us. :-)

We tell little children not to run with scissors. We should not forget to warn them against poking at things with needles.

Biochemistry Major

How many universities have a biochemistry major? My students want to know if most universites have such a program. We know that it's common in Canadian universities. What about the rest of the world?

Teaching the Science of Evolution under the Threat of Alternative Views

I posted a version of this over at Stranger Fruit but after doing so I thought it might be of interest to others ...

After years of keeping quiet, I was prompted to enter this debate after attending a meeting organized by the American Society for Biochemistry and Molecular Biology [ASBMB]. The title of the symposium was "Teaching the Science of Evolution under the Threat of Alternative Views". You can see the video by following the link.

Now, it seemed to me entirely inappropriate to emphasize Miller's religion when introducing him at a scientific conference. It seemed inappropriate to invite Rev. Ted Peters to give one of the talks. It seemed inappropriate for Eugenie Scott to praise Miller but take a swipe at Dawkins.

For me that was the tipping point. Now, I know it sounds childish to say "they started it" but it's important to keep it in mind. Atheists have kept their mouths shut for years but the attack on atheistic views—and the praise of religious scientists—have escalated in recent years.

I was getting tired of being told that atheists were not welcome but religious scientists were.

The important talk is the one by Rev. Ted Peters, an ordained pastor of the Evangelical Lutheran church. He makes the case for Theistic Evolution. Keep in mind that this talk was given at a scientific meeting and most of the audience were scientists. A good many of them were atheists.

Listen to Eugenie Scott's talk as well. I like the bit about "We are not Darwinists." At the end of her talk she presents the case for appeasement: Dawkins bad, Peters good.

Undefended Borders

This is a pretty picture. That's Canada on the right. The border isn't very well protected—I think it's way too easy for terrorists to swim across the river from the other side. We need to build a fence.

Mythbusters

The New York Times asks whether Mythbusters is The Best Science Show on Television. Who cares? It's lots of fun even if it doesn't teach very much science. Gets my vote.

The Neville Chamberlain School of Evolutionists

Richard Dawkins writes about the "Neville Chamberlain 'appeasement' school" of evolutionists. These are scientists who are willing to compromise science in order to form an alliance with some religious groups who oppose Christian fundamentalism. Do you believe in miracles? That's okay, it's part of science. Do you believe that God guides evolution in order to produce beings who worship him? That's fine too; it's all part of the Neville Chamberlain version of intelligent design. Souls, moral law, life after death, a fine-tuned universe, angels, the efficacy of prayer, transubstantiation ... all these things are part of the new age science according to the appeasement school. There's no conflict with real science. We mustn't question these things for fear of alienating our potential allies in the fight against the IDiots. Welcome to the big tent.

Ed Brayton has declared himself one of the leading members of the Neville Chamberlain School. And now, John Lynch and Pat Hayes have joined the Ed Brayton team.

Me and PZ are on the side of science and rationalism.

Young Earth Creationsts (YEC's) and Intelligent Design Creationists (IDiots) are anti-science because they propose explanations of the natural world that conflict with science. But they're not alone in doing that. Many of the so-called Theistic Evolutionists also promote a version of evolution that Darwin wouldn't recognize. They are more "theist" than "evolutionist."

For some reason the Neville Chamberlain team is willing to attack the bad science of a Michael Denton or a Michael Behe but not the equally—and mostly indistinguishable—bad science of leading Theistic Evolutionists. Isn't that strange?

Public understanding of science will not be advanced by people like Francis Collins, Simon Conway Morris, and Ken Miller. They are subverting science in order to make it conform to their personal religious beliefs. (Which, by the way, conflict.) They are doing more harm to science than those who oppose it directly from the outside because the Theistic Evolutionists are subverting from within. It is sad that they are being supported by people who should know the difference between rationalism and superstition.

Is the appeasement strategy working? Of course not, but the most amazing thing is happening. The Neville Chamberlain School thinks it is winning in spite of the fact that leading politicians oppose evolution; most schools don't teach evolution; and the general public doesn't accept evolution. Talk about delusion. The appeasers think we should continue down the same path that led us to this situation. They think we should continue to compromise science in order to accommodate the religious moderates.

PZ Myers is only the most recent in a long list of people who have noticed that the good guys are not winning ...

Now, what is this winning strategy that Ed's Team is pushing? It seems to be more of the same, the stuff that we've been doing for 80 years, accommodating the watering down of science teaching to avoid conflict with religious superstition…the strategy that has led to a United States where a slim majority opposes the idea of evolution, and we're left with nothing but a struggle in the courts to maintain the status quo.

I don't know why this is so hard to understand. We are not winning. We are clinging to tactics that rely on legal fiat to keep nonsense out of the science classroom, while a rising tide of uninformed, idiotic anti-science opinion, tugged upwards by fundamentalist religious fervor, cripples science education. Treading water is not a winning strategy. I'm glad we're not sinking, and I applaud the deserving legal efforts that have kept us afloat, but come on, people, this isn't winning.

Hallelujah! Right on, brother.

Peer Marking

Today's Toronto Star has an interesting article on Peer Marking Gets a Negative Grade.

Students in one of our first year psychology classes were asked to submit a short writing assignment to an online evaluation program called "peerScholar." The site, which was developed by teachers at our Scarborough campus, is set up to allow papers to be graded anonomously by fellow students.

University of Toronto Teaching Assistants, represented by their union (CUPE local 3902), objected. They say this is a blatent attempt to do away with TA's in favor of a computer program. The students in the class also expressed some concern, according to the newspaper article. Apparently, students see the peer evaluation system as "inaccurate" and "unfair."

I first heard about this experiment last year when I went to a presentation by one of the authors. What impressed me was the possibility of teaching students how to critically evaluate the work of their fellow students. I was also interested in giving students some direct experience in how their grades are determined. There's no better way to learn how the system works than grading a fellow student. We did it when I was in school. As a matter of fact, I took a university course where our entire grade was based on a group discussion at the end of term where we assigned grades for each other, by consensus. But that was the 60's.

The peerScholar project seemed like a good way of introducing more participation into a course and I was/am seriously thinking of using it in my course. Here's a desrciption of how it works in the PSYA01 class. There's more information on the peerScholar discussion page. I think it's unifortunate that the authors put so much emphasis on saving money by avoiding TA's. While I recognize that's a legitimate concern, I think that peer evaluation is an important goal by itself.

I've seen the data on fairness and accuracy and it's very impressive. Students tend to be a little too hard on their colleagues but that's easy to compensate for. By the second evaluation they've become much better. If the practice were more common, the students would get much better at it. As it is, the grade assigned by the students is at least as good as that assigned by a TA. It tends to deviate more from the grade assigned by the Professors, but then so do the TA's grades.

Bill Dembski Needs Help, Again

Bill Dembski asks, ...

I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.

Fortunately, there are some smart people who post comments on Uncommon Descent. They have told Bill that the concept of junk DNA is explicitly non-Darwinian. It was proposed by scientists who didn't feel the need to explain everything as an adaptation.

I don't know how many times we've explained to Bill that not all evolutionary biologists are "Darwinists." I know I first told him four years ago but I'm sure there were others before me. He seems to be a very slow learner.

One of these years he'll realize that there's more to evolution than just natural selection.

Iraqi Children Throwing Rocks

This video from YouTube is poignant in so many ways ... It's the same situation that Canadian forces face in Afghanistan. If the children hate us then why are we there?

        

A Simple Act of Kindness

This morning I drove over to my local Tim Horton's to get a coffee. There was a lineup in the drive-through, as usual. The woman in front of me stopped by the garbage bin and tossed out an empty cup. She missed, and the cup bounced off the receptacle and rolled under her car. She opened the door a crack, peered out, saw nothing, and drove on.

I have to admit I'm really annoyed at this kind of behavior. I hate it when people throw garbage on the street, especially when there are garbage bins everywhere. I've been known to pick up litter and hand it back to the owner. Rather than drive over her discarded cup, I stopped, picked it up, and put it in the bin. I was not thinking nice thoughts when I did this and I made sure that she saw me do it.

Back in the car, I drove up to the window to get my coffee. Imagine my surprise when the server told me my coffee was free today! She informed me that the woman ahead of me had paid for my coffee.

Thanks, whoever you are. You made my day. In fact, you made my week.

City of Toronto

Here's a 360° view of Toronto.

Click here to see a larger image.