Will Santa be Affected by Solar Flares?

An article posted on the Natural Sciences and Engineering Research Council of Canada (NSERC) website has the answer [Santa Claus and Solar Flares]. Learn the size of Santa's sled and how he manages to deliver all the presents.

The Hypocrisy of Scientific American

 
The editors of Scientific American are worried about PLoS ONE, the new online journal of science [Peer Review Is Sooooo Old School. They claim this is a big step backwards since the PLoS ONE articles reportedly circumvent peer review. Scientific American set itself up as the protector of scientific integrity and they vow to uphold these high standards in spite of the fact that the scientific community is letting them down.

This is wrong on so many levels that I hardly know where to begin. The real problem with science education is Scientific American, not PLoS ONE.


Here's what the Scientific American editors say,

With the burden of proof off of the reviewers, we in the science press will have to be more vigilant than ever. We can't rush to put stories out until we've focus- grouped findings with a number of experts in a study's particular field. It will force us to become better reporters and to resist the urge to sensationalize and invoke hyperbole--which, while it may not move magazine units or generate hits, will make our service more noble. We'll put in contingencies in order to avoid situations like the false alarm that plagued Lehigh mathematician Penny Smith--the poor woman who posted a flawed proof of the Navier-Stokes equations this fall on arXiv.

SciAm has already started on this path, by the way, as evidenced by JR Minkel's write-up of this morsel from the journal's inaugural issue: Rest easy, creationists, turns out we're a little less like chimps than we previously thought.

PLoS ONE is opening a possible Pandora's box into a brave new world of publishing that's as terrifying as it is exciting. From this point forth, information going from the lab to the journalist's wire (and then onto the public) will be less and less scrutinized and fact-checked. It's the dissemination of scientific information sped up to the breakneck velocity of the 21st century. Here we go...

Bullshit! This is not the end of peer review. The review of PLoS ONE articles is no different than that of many other scientific journals. I will be very surprised if the quality of papers ends up being any different than those published in Cell, Journal of Biological Chemistry, or Nature. All of these journals publish unadulterated rubbish from time to time and brilliant papers as well. The quality of papers in the leading "peer-reviewed" journals ranges from embarrassing to excellent.

PLoS ONE won't be any different.

I'm very upset by the fact that Scientific American editors see themselves as the guardians of scientific integrity, and I'm flabbergasted that they think they can recognize good science from bad science. Their record over the past few years proves them wrong. They have published all kinds of trash in my field, and probably other fields as well. They have hyped stories that don't deserve to be featured in Scientific American proving that their editors are suckers for press releases and self-promotion [The Alternative Genome, Why Are Some Animals So Smart?, The Real Life of Pseudogenes].

In the recent past, the "vigilance" of Scientific American editors and staff writers has left a great deal to be desired. If this crazy false alarm over PLoS ONE makes them pull up their socks and consult more widely before publishing then that's going to be good for science education.

I'm not holding my breath.

(RPM at Evolgen is also upset with Scientific American: Science Reporters Lament the Advent of PLoS ONE.)

E-Z Answer Squirrel

The E-Z Answer Squirrel will answer your most profound questions about religion, like "Does God hate me because I'm gay?"

Brought to you by the United Church of Canada, a church that understands sarcasm.

You Can Call Me Pope Larry !

Which Historical Lunatic Are You?
From the fecund loins of Rum and Monkey.

In the UK, 63% Are Not Religious

According to a Guardian/ICM poll 63% of the people in Briton are non-religious compared to 33% who describe themselves as religious. The non-religious group includes many who call themselves Christian but presumably don't practice the religion. Most people think that Religion does more harm than good - poll.

It's important for North Americans to understand the differences between us and Europeans. While religion still seems to be a powerful force in America, it is on the wane in most other western industrialized nations. That's a reason for optimism. It's possible that North America will soon abandon religion as well.

Breaking News: the IDiots Don't Understand Neutral Theory

 
DaveScot reveals his ignorance in: The Sound of The Neutral Theory Exploding.

Poor Dave, he doesn't know that there are many examples of synonymous mutations having an effect on protein expression. They've been known for decades. Look up "codon bias" for one such example.

As usual, the IDiots get confused about the difference between exceptions and generalities. They think that every little exception to a general rule invalidates the rule and overturns all of biology. This is why we call them IDiots.

Jason Rosenhouse Reviews Orr's Review of Dawkins

Read it at Orr on Dawkins. Good job, Jason. Orr looks like one of them appeaser scientists who have to bend over backwards to defend religion against atheism. I especially like the argument that it's okay to believe in magic and superstition as long as you couch it in sophisticated, intellectual language.

Don't Forget Somalia

As we ponder what to do in Iraq and Afghanistan we do well to remember our failed attempt to impose democray in Somalia. The fighting is still going on and the United Nations is still making noises about it [UN urges end to Somalia fighting].

Would it have been any better if 50,000 western troops have tried to establish law and order? Was cut-and-run a good strategy for Somalia? I think so, and I think it might be the best strategy for Afghanistan and Iraq as well. Let them sort out their own problems and stop complicating things by giving the people a reason to unite against a common enemy (foreign invaders).

They Closed My Timmy's!

It was three weeks ago today and it was only for one day, but it's taken me this long to get over it.

I got up one Saturday morning and went off to my local Tim Horton's to get coffee and a donut. The store was closed and there were strange looking trucks parked on the road. What was going on? Timmy's are supposed to be open 24/7—they're not allowed to close Tim Horton's, are they?

There were famous-looking people living in the white trailers. Cameras were everywhere. There was even a hearse parked in the drive-through. (Look closely in the photo on the left.

The manager (below right) needed a police escort because of the rioting customers. He gave us all gift certificates but that was small compensation for our tragic loss. They opened up the next day but the damage had been done. I'm told we can see what they were up to by going to the movie theatre next summer. As if I'm going to believe that!

Excellent!

My Peculiar Aristocratic Title is: His Excellency Laurence the Incomplete of Midhoop St Giggleswich Get your Peculiar Aristocratic Title

The White House

 
Friday's Urban Legend

The Canadians soundly trounced the Americans in the War of 1812. One of the goals of the campaign was to demonstrate the ability of the mighty British Empire to deliver shock and awe to the enemy capital. To this end, Washington was invaded and looted in 1814 and the White House was set on fire. The Americans were so intimidated that President Monroe soon surrendered.

This is all well-known historical fact. Something that Canadian and British schoolchildren learn in history classes when they are 10 years old.

The name "White House" is thought to be derived from the whitewash that Americans put on the house when the fire damage was repaired. It seemed to have been part of a larger campaign to whitewash everything that had to do with losing of the War of 1812.

That part is urban myth according to snopes.com [White House Wash]. The President's house was known as the White House before the War of 1812 and the original house, built in 1798, was whitewashed.

Skeptical Climatologists

 
Kevin Vranes of No Se Nada writes about impressions he got from a recent meeting of geophysicists [So what happened at AGU last week?]. Apparently, some climatologists are worried that they may have oversold climate change and supressed legtimate skepticism over some of the details.

This is a very important issue in science. It does not mean that warnings about climate change are totally wrong or misguided. What it means is that contrary opinions within the scientific community aren't getting attention for fear of diluting the important message that the public needs to hear.

It's an issue in other disciplines as well, such as evolutionary biology. Skepticism, which is the essence of science, doesn't play very well in the public arena. Scientists who are skeptical about some aspects of evolutionary biology are sometimes considered to be traitors to the cause of defeating creationism. I imagine that the same sort of thing might be happening in the field of climate change.

Varsity Centre Bubble Now Inflated

 
The new Varsity Centre bubble has now been inflated over the University of Toronto football field on Bloor Street. Students have been looking forward to this event for some time: it means they can now play Ultimate Frisbee all winter.

The press release talks exclusively about athletics but we all know the real reason for creating such a large, heated enclosure. In Canada, the gyms and arenas are stuffed with desks and chairs at this time of year and used for exams.

Rumor has it that the bubble is energy efficient. It recycles a lot of the hot air generated on campus.

Mammalian Gene Families: Humans and Chimps Differ by 6%

The first issue of PLoS ONE has just been published. PloS ONE publishes peer-reviewed, open-access, articles that are freely available on the internet. The journal is supported by the Public Library of Science (PloS), a non-profit organization.

The article that I've been waiting to see is,

Demuth, J.P., De Bie, T., Stajich, J.E., Cristianini, N., and Hahn, M.W. (2006) The Evolution of Mammalian Gene Families

Demuth et al. examined gene families in five species whose genomes have been sequenced (human, chimpanzee, mouse, rat, dog). Gene families are normally defined as groups of related genes having more than one copy in a genome. For example, the globin gene family consists of multiple copies of related globin genes such as myoglobin, α-globin, β-globin, and others. The authors appear to use a different definition, which counts orthologous genes in different species as a gene family. Thus, their paper discusses "gene families" that have single genes in different species.

By scanning the available genome sequences, Demuth et al. were able to cluster all genes into 15,389 groups called "gene families." Of these, 3,114 were single genes confined to a single species. These were presumed to be annotation artifacts and were discarded. Not all of the remaining groups were present in all five species. A total of 2,285 additional groups were confined to distinct lineages on the mammalian tree indicating that they had been "created" after divergence from the common ancestor. This leaves 9,990 groups that were probably present in the ancestor of dog, human, chimp, mouse, and rat.

The question is, how many of these gene families show gain or loss of numbers during mammalian evolution? The answer is 5,622 or 56.3% (5622/9,990). The data is shown in Figure 1 (below). The red section of the pie chart represents groups that have experienced a reduction in the number of members of a gene family (or loss of the entire group) in a particular lineage. The green section represents a gain in the number of genes in a family.

Figure 1. Distribution of gene gain and loss among mammalian lineages.

Creative Commons Attribution License

If we focus on the human/chimp comparison, it turns out that the human genome contains 1,418 genes that do not have orthologs in the chimpanzee genome. What this means is that if we look at the identical sections of human and chimp chromosomes one of them will have a gene that the other one does not have at that position. It turns out that the human genome has 689 genes not present in the chimp and the chimp has 729 genes not present in humans. If there are 22,000 genes in the genome, then this total of 1,418 differences represents 6.4% of the genes.

It's important to note that this does not mean that entirely new genes are created or destroyed. What it means is that there have been duplication events such that a gene has been duplicated in one of the lineages. For example, let's say that the region of the chromosome containing the α-globin genes was duplicated in the chimpanzee lineage. This would count as a gain in chimps relative to humans.

There are several problems with the analysis. One of the most severe is the lack of complete coverage of the chimp genome and the relatively poor annotation compared to the human genome. Only 94% of the chimp genome is available while the human genome is about 99% complete and much more accurate. This means that there will be a number of genes in humans that won't appear in chimps. It's unlikely that these problems lead to errors of more than 2-fold.

The authors are clearly aware of the fact that most of these changes in gene number have no effect on the organism. They are accidental changes due to random genetic drift. They are also aware of the fact that some of the duplications and losses are variants that are segregating in the human and chimp populations. In other words, they are not fixed differences.

Nevertheless, Demuth et al. point out that some of the gains and losses of genes could be responsible for the phenotypic differences between chimpanzees and humans. They caution us that the traditional 1% difference in the sequences of orthologous genes may not be the whole story.

An Example of High School Biochemistry

 
I don't know exactly what to make of this. It is not exactly correct, but it's not exactly wrong, either. I wonder what grade produced it?