New DNA Sequencing Technologies
Topic: Biology
All I have to say is - brilliant!

Two new awesome DNA sequencing technologies were reported this week in Nature and Science (as mentioned in a previous post).

So how do these work?

Well both techniques start by linking the genomic DNA fragments to a short DNA sequence (aka a primer or oligonucleotide) that has a biotin on the end. Biotin sticks very strongly to avidin and beads coated with avidin are used to trap the genomic DNA fragments - the ratio of DNA fragments to beads are fixed so that there is one fragment per bead. Now excess DNA primers (linked to biotin) are then added in excess to the bead. These primers are used to amplify the genomic fragment by PCR.

So now we have a population of beads each with many copies of a single stretch of DNA sequence. The beads can be immobilized to a sticky surface or inside microwells. These two techniques allow the monitoring of many beads in a conventional microscope.

OK for non-biologists - the following will be very technical ...

In method number one, "anchor primers" that are complementary to the linkage primer are annealed to the DNA-bead preparations. Then degenerate 9mers are mixed in - if the 9mer can bind to the genomic fragment that lies adjacent to the anchor primer the ligase will link the two ligated to the anchor primers. Depending on the identity of the query base (lets say base #4 of the degenerate sequence), the primer is conjugated to one of four fluorophores, each correlating with the identity of the query base (so blue for primers with base #4 being an A, Green for T, Red for C, Infrared for G). Conditions are tweaked until only perfect matches can base pair. After ligating the sequences with DNA ligase, the color of each bead is monitored by microscope. Thus identity of base #4 is revealed. Depending on how many beads you can visualize (potentially up to 500 000 per image) you will know the identity of base #4 for all those DNA fragments. Now you can wash off the anchor primer-query primer ligation product and use new anchor primer to ligate a different 9mer probe (but to querry a different base). Using some tricks the researchers inserted multiple primers into each sequence so that with this "ligation based sequencing" you can figure out the identity of potentially 20 to 100 nucleotides on every visualized bead. (500 000 beads X 100 nucleotides = half a billion nucleotides sequenced!) The authors claim that this sequencing method utilizes reagents off the shelf.

In the second paper, the authors annealed their anchor, then added DNA polymerase, pyrophosphatase and one type of nucleotide to their beads. If the primer can be extended with the given nuclerotide, DNA polymerase will utilize the nucleotide and release pyrophosphate that can be further processed into free phosphate by pyrophosphatase. This last reaction can be monitored on a microscope. So if the researchers add "T", every bead (this time in a microwell) whose first base has an A (thus needing a T to form the base pair) will catalyze the reaction ... and light up. Everything is then washed off the beads and the next nucleotide (say "C") is added. By monitoring which bead lights up during each round the authors can figure out each individual sequence simultaneously. Incredible!

Shendure et al., Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome. Science. (2005) Published online 4 August

Margulies et al., Genome sequencing in microfabricated high-density picolitre reactors. Nature (2005) Published online 31st July

Wedding Accomplished
Finally got married.

Everything worked out ... even the weather was great ... heading in to Sunday, the forecast predicted "isolated thunderstorms", but not a drop fell.

So what's been happening while I was gone from the www?

I could comment on the recent series in the NY Times, which they call "the Evolution Debate", but I might as well comment on other idiotic debates such as how Einstein led to the down fall of culture.

Speaking of pre-conceived notions that lead to unfounded attacks against scientific theories, listen to this episode of This American Life about regular people dealing with or rebelling against ideas and modern scientific theories. It's incredible how the small steps initiated by misconceptions, can lead people to perform incredible leaps into the realm of bizarre beliefs!

Upsidedown Catfish
Topic: Biology
Got into an interesting conversation with "P" about upside-down catfish and the how evolution may (or may not) have selected this trait.

Here's an email that P sent to me ... enjoy:

"This Catfish IS Upside Down!"

"...why they swim upside down. The reason is quite simple: it's easier to eat that way!" "Food on top of the water or under logs is much easier acquired by a fish floating upside down with it's mouth fully directed toward the food!" "...it is speculated that when food became scarce on the bottom (where most catfish eat), some species inverted (swam upside down) to take advantage of a food supply that was available at the surface. As the catfish acquired neutral buoyancy, it became more difficult to resist that upside down force. In order to save energy, the catfish gave in to the upside down swimming!"

"Some scientists believe the upside down catfish took up inverted swimming as a means of protection. The theory is that because mid-water predators usually attack from below, the upside down catfish is better able to see the imminent attack, enhancing their chance of survival."

"Another oddity, which is attributed to the inverted swimming, is the fact that the upside down catfish's belly is darker than the rest of the fish. Most fish have a lighter underside, a feature developed by them in order to escape detection from predators lurking beneath them. The lighter underside against the light water makes for a less obvious target. However, the upside down catfish has a reversal of the normal shading."

"In the wild, upside down catfish are found in huge shoals of several thousand fish."

"... "If they die, do they float right side up?" The answer: surprisingly not! Belly up like other fish, like they have spent their entire lives!"

Upside-down Catfish Site
http://www.aquafriend.com/modules.php?op=modload&name=News&file=article&sid=41&mode=thread&order=0&thold=0

Good Spoof in The Onion
Topic: Science and Culture
Gravity? How secular!

Thing do fall but it's due to a process called Intelligent Falling.

The Fall of Advanced Civilizations
Topic: Science and Culture
Is this entry about the eventual fall of the west?

Perhaps not directly.

Although wedding plans loom large, the people and places from our last trip to Iberia keep coming back to haunt me.

No this entry is about the demise of the Andalus Caliphate. From an article in today's NY times about Medina Azahara, the summer home of the Andalus Caliphate, whose capital was in the nearby Cordoba:

Medina Azahara, also known as Madinat al-Zahra, was an Islamic metropolis built in the 10th century as a testament to Spain's proclamation in 929 that it was the true caliphate of the Muslim world.

The construction of the city, which began around 940, was a singular moment in history, when the most vibrant intellectual and cultural force in Europe was rooted in Islam, and when the heart of Islam was in many ways rooted in Europe.

And how could the Moors of Spain build this city?

Maria Rosa Menocal, a professor of Spanish at Yale and author of "Ornament of the World," a book about Muslim Spain, said that Al Andalus and its capital, Cordoba, were probably justified in considering themselves the center of the known universe when Medina Azahara was built. "There was no comparison between Cordoba and anything else in Europe in the 10th century - like New York versus well, a rural village in Mexico," she said in an e-mail interview.

Many think of Islam as technologically backwards, but in those days it was the Islamic countries that were tolerant, and technologically advanced.

Cordoba had running water, paved and lighted streets, and, when large collections of books were scarce in Europe, some 70 libraries, the biggest containing 400,000 volumes, according to some accounts.

Al Andalus introduced Western Europe to paper, algebra, advanced irrigation techniques and Latin translations of many of the classic works of Greek philosophy.

But Cordoba, and eventually Granada fell. But was this solely due to the foreign, uneducated, barbarian Christian invaders from the North?

...around 1010, Medina Azahara was sacked by Islamic purists from North Africa who considered the Muslim culture it represented far too liberal in its interpretation of the Koran. The raid effectively wiped the city off the map for a millennium.

Hmm. So the fall of this advanced empire, was due to foreign and inner foes - many uneducated and moved by religious zealotry. What was ironic was that the Umayyad Dynasty that conquered the Arabian Peninsula, North Africa and Iberia (and eventually used Cordoba then Granada as their Capitol) used religion as a political tool rather than a life guiding philosophy.

Once the Umayyad dynasty was over, religious ideology took over in Spain (in the form of fanatical Christianity) and spread through out the Muslim world (in the form of fanatical Islam). In both places these forces squashed tolerance, education and technology. Spain (despite it's American "empire") became a backwater where prosperity from the New World was funneled out to enrich the other more technological neighbors (such as France and theHapsburgs) ... and the once advanced Islamic world became the technological backwater it is today.

How Marriage Can Change You
Topic: Science and Culture
Well as the wedding day approaches (Aug 21st) I'll be blogging less and less (as I'm being swamped with wedding errands).

So how will marriage change us (that is Jenni and I)?

Well on the personal front - not much. We've been living together for almost seven years and we've been planing our lives together for almost that same amount of time.

So demographically how will we change?

Good question!

-Married people live longer.

-Atheists are less likely to get divorced - than any other religious (or non-religious) group.

-North easterners are less likely to get divorced than any other regional group in the US.

Now why is this?

Note that the original stats are from the BARNA group, a pro-religion "think-tank". The stats are now no longer available from their website, as their conclusions are ...

If you want to see how perplexed they are about these stats read this press release and see how they twist the numbers so that atheists have an apparent divorce rate as high as religious and born again Christians!

Here are the original stats:

Religion, % have been divorced

Jews 30%
Born-again Christians 27%
Other Christians 24%
Atheists, Agnostics 21%

Perhaps Atheists are just more likely to be open, tolerant and less rigid in their world views than other groups. The same can be said about cosmopolitan (and population dense) Northeast (19% divorce rate). Also Atheists and agnostics are more likely to sample potential mates. In addition many partners actually live together before marriage hence they get to know their marriage partners and better assess compatibility. Atheists also tend to be more educated, and studies (although not listed here) have shown that divorce goes down with education level.

[Update 8/25/05]

I came across the work of Steve P. Martin from the Department of Sociology at the University of Maryland, College Park.

He has an interesting power point presentation on how college level education decreases the divorce rate among women. I've copied one figure from his presentation displaying the 10 year divorce rate of women (the % of married woman that get divorce in 10 years), with and without a 4 year college education.

[end of update]

In the end, real world experience, education and tolerance do more to predict happy marriages than religion.

So getting back to Jenni and I, looks like we'll be together for a long happy life.

Refs for stats:
http://www.religioustolerance.org/chr_dira.htm
http://www.cdc.gov/nchs/about/major/dvs/mortdata.htm

http://www.infoplease.com/ipa/A0923080.html

ID & Dawkins On WBUR
Topic: Science and Culture
I was alerted to this radio program yesterday. Now I had heard of the awesome debating skills of the ID people such as those from that pseudo-academic Discovery Institute (talk about Orwellian!) So I went online and listened to this set of interviews and ..?

Well the ID guy (George Guilder) was horrible - basically he sat there and gave an unintelligible ramble about "information" and how evolution was Lamarck-ism. I could have made a better case for Intelligent Design (ID) than this guy! 20 mins of garbled ideas. What a disappointment. To the credit of the host, Tom Ashbrook, he got George Guilder to admit that ID implies the existence of God. Thus it follows that ID is nothing but creationism (with some advocates of ID throwing a little evolution in the mix).

Then Richard Dawkins came on. I basically agreed with everything he said, but I must say that he could have done a better job of it. Dawkins made the mistake of criticizing ID because it's foundations are based on a creator (i.e. God) and then advocated that ID couldn't be because there was no creator. Richard you are not going to convince the faithful (I not being one of them) using this line of reasoning. It is enough to say that the existence of God is untestable but in any case God does not have to be invoked to understand how diversity and complexity are generated in Nature. I also thought that Dawkins should have glossed over the main axioms, which underpins evolution. Overall, Steven Pinker gave a better critique of religion in this Time Mag. article.

Well if you are still interested follow this link to hear the episode "Debate Over Intelligent Design" on WBUR's (Boston's NPR) show OnPoint.

Wizard Genomics?
No this entry is not about the latest developements in reducing the cost of genomic sequencing but about a letter that appeared in the latest issue of Nature ... Harry Potter and the recessive allele.

According to the authors:

Wizards or witches can be of any race, and may be the offspring of a wizard and a witch, the offspring of two muggles ('muggle-born'), or of mixed ancestry ('half-blood').

This suggests that wizarding ability is inherited in a mendelian fashion, with the wizard allele (W) being recessive to the muggle allele (M).

I wonder if these guys could get a grant from the budget-slashed NIH?

4th Nuclear RNA Polymerase Identified
Topic: Biology
Well remember central dogma of Biology (DNA => RNA => protein)?

There were 3 known polymerases in mammalian nuclei that copied DNA into RNA (this copying process is known as transcription).

Pol I: responsible for transcribing rRNAs (the RNAs that form the catalytic portion of the ribosome, the machine responsible for translating mRNA into protein - see this entry on why RNA can support catalytic reactions)

Pol II: responsible for transcribing mRNA (the common messenger RNA that is translated into proteins) and snRNA (small nuclear RNAs that are part of the RNA splicing machinery, see entry on mRNA splicing).

Pol III: responsible for transcribing one rRNA (the 5s rRNA) one snRNA (called U6) and the tRNAs (tiny t-shaped RNAs that plug into the ribosome and bind both to the mRNA sequence and to the appropriate amino acid - remember amino acids are the lego blocks of proteins).

But wait there is more! Eukaryotic cells are the result of a symbiotic relation ship between a large primordial cell and mitochondria (see organelle C). These "mitos" (as some researchers affectionately call them) are thought to be descendants of oxidative alpha-proteobacteria bacteria that could oxidize sugars to water and CO2, as proposed by Lynn Margulis (click here for a brief summary of her ideas). Mitochondria have their own DNA that encodes for their own mRNA - and thus they have their own RNA polymerases. The translation of mRNA into protein is slightly different in mitos than in the nucleus, so mitos also have their own tRNA.

OK now you are ready ...

In the latest issue of Nature, a fourth RNA polymerase has been discovered - named spRNAP-IV, for single-polypeptide RNA Polymerase IV ... or Pol IV. This protein is actually encoded by a mitochondrial gene! The gene is alternatively spliced into spRNAP-IV, that is transported to the nucleus and mtRNAP, an RNA polymerase responsible for translating mitochondrial genes. Like Pol II, spRNAP-IV seems to translate genes that encode mRNAs. An interesting side note is that many putative proteins required for mito function are encoded by nuclear genes ... it is thought that these genes once resided in the mitos but then were transfered to the nucleus. Perhaps when the mito genes were "transfered", the nucleus also had to import mito specific RNA polymerases to copy these mito derived genes into mRNA ... and Pol IV is a remnant of that event?

In anycase this study demonstrates that many basic cellular functions are yet to be discovered and it leaves open the question of what other basic machinery is out there to be found?

Ref: Kravchenko et al., Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature 436:735-739

Autism and Hormones
Topic: Biology
Fascinating piece in today's NY Times about Autism and Testosterone by the researcher Simon Baron-Cohen.

From the article:

On average, males finish faster and score higher than females on a test that requires the taker to visualize an object's appearance after it is rotated in three dimensions. The same is true for map-reading tests, and for embedded-figures tests, which ask subjects to find a component shape hidden within a larger design. Males are over-represented in the top percentiles on college-level math tests and tend to score higher on mechanics tests than females do. Females, on the other hand, average higher scores than males on tests of emotion recognition, social sensitivity and language ability.

Many of these sex differences are seen in adults, which might lead to the conclusion that all they reflect are differences in socialization and experience. But some differences are also seen extremely early in development, which may suggest that biology also plays a role. For example, girls tend to talk earlier than boys, and in the second year of life their vocabularies grow at a faster rate. One-year-old girls also make more eye contact than boys of their age.

In my work I have summarized these differences by saying that males on average have a stronger drive to systemize, and females to empathize. Systemizing involves identifying the laws that govern how a system works. Once you know the laws, you can control the system or predict its behavior. Empathizing, on the other hand, involves recognizing what another person may be feeling or thinking, and responding to those feelings with an appropriate emotion of one's own.


His research has found that men tend to be systhemizers (type S) and women empoathizers (type E). He points out some studies that suggest that exposure of prenatal infants to testosterone in amnionic fluid influences their ability to display S-type and E-type behaviors. Testosterone exposure levels correlates with S-type behavior and inversely correlates with E-type behavior. Hmm, is Larry reading this? Although I warn you all not to make simplistic judgements based on these studies.


What does all this have to do with autism? According to what I have called the "extreme male brain" theory of autism, people with autism simply match an extreme of the male profile, with a particularly intense drive to systemize and an unusually low drive to empathize. When adults with Asperger's syndrome (a subgroup on the autistic spectrum) took the same questionnaires we gave to non-autistic adults, they exhibited extreme Type S brains. Psychological tests reveal a similar pattern.


Very interesting! Instead of a little Einsteins, testosterone exposure can produce a Rain Man.


FIRST, both mothers and fathers of children with autism complete the embedded figures test faster than men and women in the general population.

Second, both mothers and fathers of children with autism are more likely to have fathers who are talented systemizers (engineers, for example).

Third, when we look at brain activity with magnetic resonance imaging, males and females on average show different patterns while performing empathizing or systemizing tasks. But both mothers and fathers of children with autism show strong male patterns of brain activity.

Fourth, both mothers and fathers of children with autism score above average on a questionnaire that measures how many autistic traits an individual has. These results suggest a genetic cause of autism, with both parents contributing genes that ultimately relate to a similar kind of mind: one with an affinity for thinking systematically.

Tangled Bank
Topic: Science and Culture
Well I'm back. Had a nice time in Iberia, and from a friend at the Pasteur Institute I learned a lot about South Korean research ... (the next day I'm reading about how they cloned a dog for the first time.) I'll have more to say about science in S. Korea on a future post.

As I have nothing further to add (I'm massively jet lagged) here is an alternative morning read. To browse over a large collection of blog entries from various scientifically minded bloggers visit Tangled Bank, a repository for interesting science blogs.



To read the 33rd edition of Tangled Bank click here.

Drunk in Porto
So after 4 days of roving around Andalusia, we returned to Portugal. We spent time in Lisboa, Setubal and now we just finished our Marathon Port tasting tour ... tonight we see the musical Amalia about the queen of Fado, Amalia Rodrigues (pronouced Rod-ree-gsh).

The difference between Andalusia and Portugal is stark. In Washington Irving's Tales of the Alhambra, he described Andalusia as a desolate place where the barren hills (now filled with olive groves) are uninhabited and the towns are few and far between but also dense. People clustered in cities for protection from warring nations (Christians vs Moors, then Spanish civil wars). And much of this can be said about the landscape today.

In contrast, the inhabitants are more scatered in Portugal and the hills are lush. It is easy to szee how history has shaped these two places.

More than Spain, Portugal has modrernized quite a bit in the last few years, and almost everyone there speaks either English or French. Portigal is doing a good job, it would seem, of catching up with other western countries in terms of technology and education. If only the leaders of our country could be foward thinking. With the current crop it may take a while.

News from Granada
Traveling in the desolate landscape of Iberia is truly eye opening. Instead of lush green, you find dry harsh environments, desolate of inhabitants. The cities are dense, crowded full of life - late into the night. The culture here is a big mix ... not the usual cosmopolitan mix of New York, London or Paris but a mix of European, Arab, Jewish and of course Gypsy who have all lived together and mixed for a thousand years (well the Gypsies are still a bit distinct). Cordoba, while lacking in the many tourist attractions of Granada (except the fabulous Mezquita), feels more authentic than the big Granada. Cordoba was also the largest city in Europe 1000 years ago and at the time was the center of knowledge in this part of the world. Some great thinkers and scientists originated from Cordoba (e.g. the Roman philosopher Seneca, the Islamic Philosopher Averroes and the Jewish Philosopher Maimonides). Funny how things change. To read more on Cordoba's history, click here.

One amazing feature of Granada is the Alhambra ...

I will update later with more info and photos.

[Update 8/8/05]

Here are my travel companions in the Plaza de la Corredera in the center of Cordoba's old city. Later we visited la Mezquita (see pics below), it was first a Visigothic Cathedral that was destroyed by the Moors, then a giant Mosque (3rd biggest in the world). Where Cordoba was reconquered by the Christians in the 1200s, a giant Cathedral (see pic #4) was built in the center of the Mosque.

After the Muslims fled Cordoba, they installed their new capital in the fortress on a hill overlooking Granada. Here are pictures from this fortress, the Alhambra.

And if you think that Moorish influence was restricted to Spain, there are plenty of examples in Portugal, such as the fantastic photo seen bellow of a fountain in Sintra Portugal (summer residence of the Portuguese Royal family - when Portugal had a Royal Family). Also the use of ceramic tiles to decorate the outside of buildings is much more prominent in Portugal than in Spain, as you can see from this fantastic city-scape painting (on ceramic tiles) from the Alfama neighborhood of Lisbon (see bellow).

Off to Europe
So today, we're getting ready to leave for Portugal and southern Spain, to visit and to attend a good friend's wedding.

Last night another at another friend's place we had an intense discussion of recent events. We are living in trying times. I've also gobbled up Thomas Frank's What's the Matter with Kansas in a couple of days. Scary stuff.

So what do all these events have in common? From the WTC to the underground in London, to the resorts in Egypt ... from the small towns in Kansas to the madrasas in Peshawar - I feel that free western society (or is it moderation) is under siege. From all sides, the knives of ideologiocal conflict are being sharpened. Each group is pointing towards its leopard - and often they are pointing at us.

We're not there yet, but it would seem that we are heading down the path to ... I don't know what. What can we do? I guess we need to stand up - not to fight, but to try to bring reason - but how do you reason with individuals that are full of irrational ideas? We need to fight paranoia in others and ourselves.

There is no "Zionist Conspiracy" and there is no "Liberal Conspiracy".

I think that this vacation is well needed - I've been working too hard ... and thinking and worrying too much about where western society, and the world in general are headed.

The Descent of Woman
Last week I picked up Elaine Morgan's The Descent of Woman. Morgan has an entertaining conversational style that makes her book not only informative, but quite a pleasure to read. She makes quite a good case for the Aquatic Ape Theory (see previous post), and how evolutionary logic should explain how unique human traits in men and women, developed.

Also she has a great passage I'd like to share with you:

[explaining baboon behavior] As soon as an outside enemy appears, hostile encounters between members of the male cohort cease. All aggression is directed outward, against the enemy. And the rewarding sensation of hostile arousal against the enemy is deepened and enriched by the warmer and more rewarding sensation of love for, and solidarity with, the brother in arms.

... Because the most disturbing thing about the primate male bond is that it works only when the leopard [or enemy] comes. And if it is rewarding for all the male cohort, it is especially so for the leader, who knows that the leopard's arrival is the signal for all rivals to cease challenging, for unruly subordinates to step into line, for all the strength of the pack to be subservient to his will. An alpha-male baboon only tastes this heady sensation at the approach of a real enemy, but an alpha Homo sapiens with enough ingenuity can invent his own leopard.

... The whole business of politics and government as conducted by males hinges around the process of identifying or inventing the kind of leopard that will unite the greatest possible number of men in the tightest possible bond.

In wartime it is easy: they have territorialism and xenophobia on their side, and the other tribe, or the other nation, constitutes the leopard. But as nation states grow larger and administration more complex, men have to be given the drive to exert themselves, and cooperate, and carry out orders, for long periods when there is no war. They subdivide into factions and cliques: the Whigs are the leopard, or the Republicans, or the abolitionists; and if bond shows sign of weakening they bring on a sabre-tooth tiger: Popish Plot, International Jewry, Yellow Peril, Bolsevik Conspiracy, capitalist lackeys. It is a curious way to run a society, but this is the way men are built, and this is the psychological mechanism that powers most of their political systems.

Eye Candy & Quiz
Topic: Biology
Well I was taking some phase pictures of hepatocytes (liver cells) that we plated on a collagen coated coverslip - nice cells, if I do say so myself. To the left is an image of a hepathocyte (or part of a hepathocyte), all those lines and squiggles being organelles ... compartments where specialized cellular functions take place.

So here is your quiz ...

What is organelle A (the big round slightly out-of-focus thing)?
What is organelle B (the dark dots)?
What is organelle C (the long squiggles)?

And finally, which of these organelles contains DNA?

Funny thing is that I just noticed the question mark in side of organelle A ...

Good luck!

Global Warming Witch Hunt
Topic: Science and Culture
On July 6th President Bush declared:

I recognize the surface of the earth is warmer and that an increase in greenhouse gases caused by humans is contributing to the problem ...

So why is a certain member of congress on a witch hunt after climatologists?

From the Houston Chronicle:

Late last month, Barton requested mounds of documents from three scientists known for studying global warming. As chairman of the House Committee on Energy and Commerce, Barton demanded detailed documentation of almost every aspect of hundreds of studies the scientists had penned.

He made a similar request to the head of the National Science Foundation, writing, "The term 'records' is to be construed in the broadest sense ... whether printed or recorded electronically or magnetically or stored in any type of data bank, including, but not limited to ... summaries of personal conversations or interviews ... diaries ... checks and canceled checks ... bank statements."

Barton gave the scientists 18 days to comply with the request, which he has the power to convert into a subpoena.

And why would this Texas Republican try to discredit scientific research that points to a drastic increase in the global temperature? I wonder.

Even the house Science Committee chair, Republican Sherwood Boehlert is calling for an end to this idiotic crusade, stating to Barton:

My primary concern about your investigation is that its purpose seems to be to intimidate scientists rather than to learn from them.

The way science is evaluated is not through politics, but through peer review. I guess we live in a time when people believe only convenient facts, while anything that does not justify our prejudices (or our wishes) is simply thrown out the window.

Flying Snakes!
Topic: Biology
(Well maybe they just glide.)

I saw an interesting article in the current issue of Science on these curious serpents.

Apparently there are five related species (of the genus Chrysopelea) that jump out of trees and glide. To find out more visit http://www.flyingsnake.org, a website maintained by Jake Soka who studies these snakes at the University of Chicago.

Paperless Notebooks?
Topic: Science Workplace
As a scientist I spend a large chunk of time putting to paper all the things that happen in the lab everyday. But in the lab of the future, instead of notebooks, perhaps scientists will be keeping electronic notebooks ... OK confession, I've been keeping an electronic notebook for a year and a half using Microsoft Word.

But I just read in the July edition of Nature that spurred on by pharmaceutical companies, the time of electronic notebooks is at hand!

So are there any e-notebook programs, beside typical word processing programs? There are a couple of commercially available programs and at least one free one.

From a personal experience, I can tell you that the biggest plus is that my enotebook is neat, easy to search and is flexible enough to readily incorporate data straight into my notes (as long as it's digital data). Also the cut and paste feature allows one to easily incorporate info from the web or often used protocols.

I'll experiment with the freeware (see above) and update you on how it compares to MS Word.

Bug Tampers with Fly Sex
Topic: Biology
I was just alerted about an interesting "News item" in the July 7th edition of Nature that describes how a small bacterial parasite, Wolbachia, drastically alters how flies respond to genetic changes. This bacterium seems to be able switch the sex of infected embryos. In certain cases, the parasite actually rescued the viability of flies harboring lethal genetic mutations.

When looking at a large collections of mutant fly colonies housed at the Bloomington Stock Center at Indiana University, researchers identified that about 30% of the strains were infected with the bug!

This bug could cause problems for fly geneticists ... and others who read their papers!

So how many published results are just wrong? Well labs that study sex determination must be extra vigilant, and this field may be the most affected. I also wonder how many other unknown parasites exist out there that can drastically affect how our biological subjects respond to our experimental protocols?