Opinion Piece: The Sun Microsystems website is ugly now that Oracle run it

Emblazoned across every page on the Sun Microsystems website you now see the Oracle logo.  They have basically modified the style sheets to display gray beams here and there and the logo shows up on every page. If you visit http://www.sun.com now, it automatically redirects to the Oracle site. Some of the java.sun.com pages that used to have more content are now trimmed down and thus less useful. The good old calm blueness of the Java site is forever gone and the new industrial, corporate grey and red has replaced it. It is now an unbearably ugly website and frankly, it fills me with grief.. I hate the Oracle logo and the redness. Oracle are branding Sun with a red hot iron and man it hurts. /bitch

Thankfully, the MySQL website has not been violated... yet.

Dolphins have diabetes off switch

Dolphins appear to be resistant to insulin, say researchers

A study in dolphins has revealed genetic clues that could help medical researchers to treat type 2 diabetes.

Scientists from the US National Marine Mammal Foundation said that bottlenose dolphins are resistant to insulin - just like people with diabetes.
But in dolphins, they say, this resistance is switched on and off.
The researchers presented the findings at the annual meeting of the American Association for the Advancement of Science (AAAS) in San Diego.
They hope to collaborate with diabetes researchers to see if they can find and possibly even control an equivalent human "off switch".
The team, based in San Diego, took blood samples from trained dolphins that "snack" continuously during the day and fast overnight.
"The overnight changes in their blood chemistry match the changes in diabetic humans," explained Stephanie Venn-Watson, director of veterinary medicine at the foundation.
This means that insulin - the hormone that reduces the level of glucose in the blood - has no effect on the dolphins when they fast.
Big brains
In the morning, when they have their breakfast, they simply switch back into a non-fasting state, said Dr Venn-Watson. In diabetic people, chronic insulin resistance means having to carefully control blood glucose, usually with a diet low in sugar, to avoid a variety of medical complications.
But in dolphins, the resistance appears to be advantageous. Dr Venn-Watson explained that the mammals may have evolved this fasting-feeding switch to cope with a high-protein, low-carbohydrate diet of fish.
"Bottlenose dolphins have large brains that need sugar," Dr Venn-Watson explained. Since their diet is very low in sugar, "it works to their advantage to have a condition that keeps blood sugar in the body… to keep the brain well fed".
But other marine mammals, such as seals, do not have this switch, and Dr Venn-Watson thinks that the "big brain factor" could be what connects human and dolphin blood chemistry.

There are several interesting diseases that you only see in humans and dolphins Lori Schwacke NOAA

"We're really looking at two species that have big brains with high demands for blood glucose," she said.
"And we have found changes in dolphins that suggest that [this insulin resistance] could get pushed into a disease state. "If we started feeding dolphins Twinkies, they would have diabetes."
Genetic link
Since both the human genome and the dolphin genome have been sequenced, Dr Venn-Watson hopes to work with medical researchers to turn the discovery in dolphins into an eventual treatment for humans.
"There is no desire to make a dolphin a lab animal," she said. "But the genome has been mapped - so we can compare those genes with human genes."
Scientists at the Salk Institute in San Diego have already discovered a "fasting gene" that is abnormally turned on in people with diabetes, "so maybe this is a smoking gun for a key point to control human diabetes", Dr Venn-Watson said.
If scientists can find out what switches the fasting gene on and off in dolphins, they may be able to do the same thing in people.
Lori Schwacke, a scientist from the National Oceanic and Atmospheric Administration (NOAA) in Charleston, South Carolina, said that the work demonstrated that there are interesting similarities between dolphins and humans.
Dr Schwacke, who is studying the effect of pollution on dolphins along the coast of the US state of Georgia, is also interested in the links between dolphin and human health.
"There are several interesting diseases that you only see in humans and dolphins," she told BBC News. In this case, Dr Venn-Watson said, "the fundamental difference is that dolphins can switch it off and humans can't".

http://news.bbc.co.uk/1/hi/sci/tech/8523412.stm

The future of medicine: Gene Testing

Gene test to see which diet is best for you: http://news.bbc.co.uk/1/hi/health/8550091.stm
Gene test to identify best chemotherapy drugs for cancer patients: http://news.bbc.co.uk/1/hi/health/8539502.stm
Studying cancer genomes: http://www.guardian.co.uk/science/2009/dec/16/cancer-genome-sequences-genetic-mutations

Human gut microbes hold 'second genome'

Clostridium difficile bacteria, a normal inhabitant of the human gut

The human gut holds microbes containing millions of genes, say scientists.

In fact, there are more genes in the flora in the intestinal system than the rest of our bodies. So many that they are being dubbed our "second genome".
A study published in the journal Nature details the analysis of the genes, carried out to better understand how the gut flora is affected by disease.
"Basically, we are a walking bacterial colony," said Professor Jeroen Raes, one of the researchers involved.
"There is a huge diversity. We have about 100 times more microbial genes than human genes in the body. We also have 10 times more bacterial cells in our body than human cells," he told BBC News. Most of the microbes present in our bodies live in the gut.

We're basically living in symbiosis with these microbes Professor Jeroen Raes

The study was led by Professor Jun Wang from the Beijing Genomics Institute-Shenzhen.
Scientists from Germany, Belgium, Denmark, Spain, France and the UK also took part in the international effort, named the European MetaHIT consortium, which has been co-ordinated by Dr Stanislav Dusko Ehrlich.
"Everyone was so motivated," said Dr Dusko Ehrlich. "To have such an exciting project to run - it's a piece of cake. The work went much faster than we expected."
Professor Raes, who works at Vrike Universiteit Brussel, explained why the microbes warranted such an intensive study: "Gut flora is crucial for our health. We're basically living in symbiosis with these microbes.
"The bacteria help digest food, provide vitamins, protect us from invading pathogens. If there's a disturbance, people get all sorts of diseases such as Crohn's disease, Ulcerative colitis, and a link has also been made to obesity."
Untangling a mess
The researchers have developed what is called a metagenome, a combined genome of all the bacteria sequenced at once.
"This creates a huge dataset that has to be disentangled," explained Professor Raes. "The untangling of this mess is what I do; it's my role in the study."
The team analysed faecal matter from 124 Europeans and found each person had about 160 bacterial species. The samples were more alike than they had expected and a significant fraction of the bacteria was shared between all the people who took part.

We already have very exciting results in terms of differences between healthy and sick people Dr Stanislav Dusko Ehrlich

By mapping the genes, the scientists have found a way around the problem of having to culture bacteria in order to study them.
Many bacteria are very difficult to grow in cultures in the lab. From looking at the genes, the researchers hope to be able to investigate how the flora changes when a person has a disease.
"It will allow us to understand diseases better," said Professor Raes. "We know there is a microbial component but we don't know exactly how [it works]. We will use it for prognostic and diagnostic markers so we can predict disease severity or sensitivity to these diseases."
Dr Dusko Ehrlich said the work was showing promising results: "We have extremely interesting findings based on the results of this gene catalogue. We already have very exciting results in terms of differences between healthy and sick people."
Professor Elaine Holmes from Imperial College, London, who was not involved in the research, said it was a welcome advance on previous studies.
"The article is extremely timely given the escalating interest in the influence of the gut microbiota in many aspects of health ranging from Irritable Bowel Disease, sepsis and obesity to autism," she told BBC News.
"It uses a large number of participants and therefore one assumes it is more representative of the 'real' microbial composition than previous studies. Also, it is an amazing feat of data processing."

http://news.bbc.co.uk/1/hi/sci/tech/8547454.stm

Neural Networks in PHP

PHPclasses.org recently published an article about a PHP implementation of Neural Networks by neuralmesh.com. The great thing about this is you don't really need to understand the inner workings of NNs but you can just use their framework to get things done. This might come in very handy in the future: http://www.phpclasses.org/blog/post/119-Neural-Networks-in-PHP.html

Just one thing I noticed, their Connect 4 NN doesn't learn very well at all.

Ancient DNA

I can't believe this is something I missed all these years. I was always under the impression that biological molecules break down very quickly upon death but apparently they have been discovering fragments (<1kb) of ancient DNA for over 30 years. Basically, they find ultra small DNA samples in fossils and inside amber (like Jurassic Park), make a whole load of copies using PCR and then analyse it. Recently they managed to extract DNA from the eggshells of the "Elephant bird" (a bit like a huge emu).

http://scienceblogs.com/notrocketscience/2010/03/dna_from_the_largest_bird_ever_sequenced_from_fossil_eggshel.php
http://www.newscientist.com/article/mg14119104.600-fact-fiction-and-fossil-dna-analysis-of-ancient-dna-should-give-clues-about-the-origin-of-species-and-how-they-evolved-over-time-but-only-if-the-dna-really-is-ancient.html?full=true
http://findarticles.com/p/articles/mi_m1200/is_n21_v146/ai_15951710/
http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html

PHP anonymous function (closure) serialization

Serialization is the conversion of object states, arrays and simple variables into a String type to allow transmission and storage for later use or by another script. PHP provides the serialize() and unserialize() functions to deal with this but after experimenting with anonymous functions (also called closures) which I blogged about earlier, I found out that trying to serialize a closure threw an exception because anonymous functions are actually internal PHP Closure objects that have serialization disabled.

I thought - "there's a gap that needs to be filled", and set out to write my second class for phpclasses.org but after a quick google search I found this (Extending PHP 5.3 Closures with Serialization and Reflection), and I must say, I'm glad I'm not the one who wrote the code for this class. The code is complex and brilliant, check it out!