The genome of the bee: like and unlike the human

The Loom has a terrific post on the recently sequenced bee genome. Emphases mine. A must read for everyone. Bees are sometimes like flies, sometimes like us  …

The Loom : To Bee

... The honeybee genome is the product of billions of years of evolution, as is the genome of every other living species. Humans and honeybees share a common ancestor that has been estimated to have lived 600 million years ago. While our ancestors evolved into fish and then moved on land, the honeybee's ancestors evolved into crustacean-like ocean-dwelling animals, some of which moved ashore and became insects. Early lineages of flying insects had fixed wings, represented today by dragonflies. The ancestors of honeybees evolved folded wings, and one lineage of the folded-wing insects evolved larvae about 300 million years ago. This lineage gave rise to many of the most common insects today, including beetles, ants, flies, mosquitoes, wasps, and bees. ...

… One of the biggest surprises of the honeybee genome project is how much like humans they are--at least compared to other insects. Fruit flies and mosquitoes have undergone a much faster rate of evolution than honeybees. In addition, they have also lost many genes that honeybees and other animals--including humans--have preserved. The genome team identified that 762 genes in the honeybee that are also found in mammals but have been lost in flies. (This is the nice thing about studying genomes: there's nowhere for missing genes to hide. If they're gone, they're gone.)

The similarities between honeybees and humans go beyond retained genes, however. Many of their genes work much like ours. The honeybee's body clock, for example, uses the same system of genes we do, while fruit flies use a different set. It appears that the common ancestor of insects and humans had two systems of genes for telling time. Fruit flies lost one system, while honeybees and vertebrates lost the other….

I want to know how their immune system works. There’s intense interest in how bees fight bacteria, viruses and other parasites.

Recommended: Hawks essay on human evolution

John Hawks has written a short and interesting essay around an older work:

John Hawks Anthropology Weblog : 2006 10

On a bit of a writing junket for his book, Mankind Evolving, in 1963 Theodosius Dobzhansky put an essay in Current Anthropology titled 'Anthropology and the Natural Sciences -- The Problem of Human Evolution'...

I hope this will become a full article. It's an interesting insight into modern thinking on human evolution and it's another illustration of how the work of great minds ages well. Worth reading.

KIBRA and the feeble memories of euros

People with the T allele of the KIBRA gene have better memories. The distribution of this allele breaks down by ethnic ancestry:

John Hawks Anthropology Weblog : 2006 10:

.... In populations of European ancestry, the T allele is the minor one with a frequency of 25%, as also shown in this study. In contrast, in Asian populations the T allele is most frequent (75%) and in African-American populations, the T and C alleles are almost equally frequent (54% and 46%, respectively). Therefore, it would be interesting for subsequent studies to assess KIBRA's relation to memory in populations of non-European ancestry.

I struggled memorizing my med school anatomy. Now I know I'm a disadvantaged paleface with a crappy memory subsystem. Maybe this explains why China has been able to bear the burden of a rather challenging system of writing.

Hawks explains that the KIBRA gene also plays a role in estrogen receptor activity, so KIBRA variations probably have a wide range of phenotype results. Evolution is going to be balancing conflicting optimizations. There's probably a way to use the math developed for microeconomics to model those optimizations ...

iPods and hearing loss: A misleading report

The reporting on a recent study of iPods and hearing loss is incomplete if not misleading ....

Hazards: A Study Gauges the Risks for Ears With iPods - New York Times:

... The researchers, who are audiologists, concluded that the average young person could listen to a player at 70 percent of full volume for four and a half hours without much risk. They also said that if people used the earphones that come with the devices they could listen to music at an 80 percent level for 90 minutes a day without great risk.

But listening to the music full blast for just five minutes can affect hearing, they said...

iPod output depends partly on volume settings and partly on the music's intrinsic "recording/encoding levels". So device volume setting is only a part of what determines energy output. They might have done better to recommend both electronic level equalization and volume limitation together.

Geriatric iPod users (age > 40, younger folk don't tolerate the dorky look) may wish to use noise canceling headphones. With noise canceling headphones a volume setting of 40-50% produces a good listening experience, with the default ear buds a comparable experience requires a volume setting of 70-80% in a standard office environment. Users who can tolerate them may use occlusive earphones to get a similar effect -- but beware otitis externa! Also, you won't hear the fire alarm ...

Closed ear phones are helpful, but probably don't deliver enough value to offset the associated bulk and inconvenience.

How to referee a paper

Aeons ago I used to referee papers. I dimly recall enough to say that this is a very useful guide: Marginal Revolution: How to be a good referee

Fallacies: I'll have more time in a few months

I recently posted about 42 errors in reasoning. I'm wonder how this fallacy fits in: "I'll have more time in a few months".

Sometime in the past six months I read that many busy people expect that their lives will be less busy sometime in the "near future". It turns out that this rarely happens; at a given phase of one's life all randomly sampled times are approximately equally busy. In terms of task management, if there's a project one is to busy for right now, it is fair to assume that one will not have time for it in the near to medium future.

Clearly this cannot always be true. I recall some relatively quiet periods in my life only ... ummm ... 20 or 30 years ago. Ok, so the rule holds.

I'd like to find a reference on this, if anyone knows of it please tell me in the comments.

Fallacies: 42 errors in reasoning

Nizkor, a holocaust memorial site, has republished Michael Loabossiere, author of the 'Fallacy Tutorial Pro 3.0'. The result is a list of 42 types of reasoning errors, known as logical Fallacies. This is an excellent reference the next time you have to deconstruct an extremely annoying chunk of illogic. Among my favorites are 'Middle Ground', 'Begging the Question', 'False Dilemma', and 'Poisoning the Well'.

Virtualization and DRM are mortal enemies: Vista Licensing

Microsoft's Vista licensing will make use of Parallels (OS X) and other non-Microsoft virtualization solutions prohibitively expensive.

Other than enriching Microsoft's virtualization solutions and breaking all the competition, why would a convicted monpolist do this? Isn't Microsoft risking a return trip to the courts? (True, they found a way around those pesky American courts, but there's still Europe.)

Virtualization breaks Microsoft's Digital-rights-management and licensing models. If you authenticate your XP license in a virtual enviroment, then it will be authenticated in that virtual environment no matter the underlying hardware. So, one license, many machines. It's the same problem with their software license, their DRM copy protection etc. You can have one machine run a dozen instances of Word, and as far as each instance knows it's the only copy running.

Virtualization is a terrible threat to Microsoft's basic business. This will be war.

Iraq is not Vietnam. It's much worse.

Kaplan, who supported the invasion of Iraq, says Iraq isn't Vietman, it's much worse. Also, "civil war" is too optimistic a phrase. Anarchic collapse is a better name.

So all those who raised the specter of Vietnam owe Bush an apology. We should have been raising the specter of Rwanda.

Personally, I have only a limited mental model of what's going on in Iraq. I obviously have no trust at all in our GOP government and there appear to be no reliable and uncensored information streams left in Iraq.

In the very unlikely event that the GOP loses control of the Senate, we might get some data I'd have some confidence in -- primarily senate testimony of US military command based in Iraq. In the meantime American citizenry is flying blind. All we can say is that we need to get the GOP out of the Senate and ideally out of government. If we can't do that, we can't do anything.

The startup library: Graham, Spolsky and more

Y Combinator: Startup Library. They didn't include anything from Kawasaki. All worth reading; of course one will need to ignore some of it ...

Assertive atheism: a 21st century cult

The Nov 2006 (14.11) issue of Wired headlines the assertive atheism movement most closely identified with Richard Dawkins. I've seen aspects of this over the past few months, especially in blogs like Pharyngula. The Wired article clarifies something that had puzzled me -- the aggressive attitude of the Dawkinites towards rationalists who are respectful of religious sentiment. To the Dawkinites, such sympathy is heresy.

The journalist ends up deciding heresy is an odd partner to rationalism, and that the Dawkinites have more than a few aspects of the religions they abhore. I agree. To be quick about it, I part company in many respects from this 21st century cult:

1. I've not seen any persuasive evidence that the nastiness in humanity is particularly related to religion. Sure many theists are nasty, but the simplest explanation is that humans are nasty. Our nervous systems are an evolutionary kludge that barely holds together, we have a lot of chimpiness to us, we're just nasty, brutish and of variable height.
   
   
2. We don't have a robust theory yet of the early history of the universe (quantum gravity and more), so there's still room for at least a designed universe. There's also those pesky theories that our "world" is a simulation, these speculations might yet be testable. There's not really any difference between an entity outside of a simulation and a supreme being. Lastly, there's the Fermi Paradox - the last, best, argument for design.
   
   
3. There does not appear to be any rational derivation of ethics, rather we create ethical systems as a post hoc explanatory framework for our actions. We don't really know how well the bulk of humanity (not just the "brights") would do when all "ethical" systems are equally valid and arbitrary.
   
   
4. It's a tough universe. Hellish for many. Really, the truth is overvalued. A comforting story is nothing to sniff at; denial is not just the proverbial river. Sure Dawkins claims he's fine staring reality in the face (I wonder how clear his vision is?), but most of us do not do so well.
   
   
5. I like studying human religious systems -- from cult to traditional doctrine. That gives me some sympathy for the practice as well as theory of religion.
   
   
6. Many of my favorite people are theists. I don't like to cause them suffering.
   
   
7. Dawkins is mean. Rude too. Not nice. Nice is good, especially given our fundamental natures.
   

Zimmer on complexity: and evolution - National Geographic

The exceptional Mr. Zimmer has a publicly available NG article on complexity and natural selection: From Fins to Wings @ National Geographic Magazine.

The bigger the palette, the more colors can be painted ...

How closely does Vista track OS X?

David Pogue is writing a book about Vista:

Pogue’s Posts - Technology - New York Times Blog:

.... I copy and pasted the ENTIRE discussion on iCal from my Mac OS X book into the Vista book. After only about 15 minutes of editing, it was an incredibly complete, witty writeup of the new Windows Calendar.

Now that's flattery.

Business method patents will make heroes of hackers

In 1998 a US appeals court made a terrible mistake. They ruled business methods could be patented ...

Patent law is getting tax crazy - Business - International Herald Tribune

As the American tax law gets more and more complicated, lawyers have come up with one more way to make life difficult for taxpayers: Now you may face a patent infringement suit if you use a tax strategy that someone else thought of first.

"I can't even imagine what it will be like in 5 or 10 years," said Dennis Drabkin, a tax lawyer with Jones Day in Dallas, "if anytime a lawyer or accountant gives tax advice, they have to find out if there is a patent on this." He notes that researching patents, and then licensing them, would just make tax compliance more costly.

Drabkin is chairman of an American Bar Association task force on the issue. He said that at one conference where tax strategies were discussed, participants later got a letter warning that using one idea mentioned would be in violation of a patent.

Why would Congress pass a law allowing such a thing? The answer is that it did not. But a U.S. appeals court ruled in 1998 that business methods could be patented, and since then the U.S. Patent and Trademark Office has issued 50 tax- strategy patents, with many more pending.

Congress should reverse the court's mistake -- no matter how loud the screaming. Alas, there's about zero chance of that happening, our polity is far too corrupt.

The combination of the Digital Millenium Copyright Act (DMCA), business process patents, and digital-rights management is going to make us all either miserable or criminal. Hackers will be heroes yet.

Our senator, Norm "Coal" Coleman: serving his future employers

Clearly, Minnesota's GOP senator, Norm Coleman, does not expect to be re-elected. He's already planning for his next job with the coal industry:

Coleman is knee-deep in global-warming fray:

... Sen. Norm Coleman is suggesting that Congress strip California and all other states, along with the federal Environmental Protection Agency, of much of their authority to control carbon dioxide emissions...

For decades California has given America a cleaner environment. It's too big a market to ignore, and it rarely makes business sense to produce one product for California and another for Nebraska. California rules become de facto national rules.

Some folks don't like that. Norm Coleman, a relatively smart member of the amoral wing of the GOP, is likely doing their bidding.

If the GOP retains its lock on power, Coleman will earn his next job, and retain his title as the 'shame of Minnesota'.