M i c r o b e s . n l

Go Mendel!

2011-07-20T05:44:00.000-07:00

Today’s Google Doodle celebrates what would have been the 189th birthday of Gregor Mendel. Mendel is known as the founder of the science of genetics for his works with pea plants.

Although, inheritance of traits in most microorganisms is mostly remarkably non-Mendelian, Mendel's concept of transmissible genes has been the starting point that led to the identification of DNA as the primary genetic information carier. It allowed for the discovery of the biochemical structure of genes, an understanding of how DNA stores and regulates the flow of genetic material, and ultimately the development of techniques that allow for the manipulation of DNA.

EHEC

2011-05-31T12:28:00.000-07:00

Enterohaemorrhagic E. coli (EHEC), can cause severe foodborne disease. Symptoms of an infection include abdominal cramps and diarrhoea that may progress to bloody diarrhoea (haemorrhagic colitis). In a small proportion of patients (particularly young children and the elderly), the infection may lead to a life-threatening disease, such as haemolytic uraemic syndrome (HUS). HUS is characterized by acute renal failure, haemolytic anaemia and thrombocytopenia.

EHEC is transmitted to humans primarily through consumption of contaminated foods, such as raw or undercooked ground meat products and raw milk. Its significance as a public health problem was recognized in the early eighties, following an outbreak in the USA. Since early May 2011, an increased incidence of EHEC infections has been observed in North Germany. Cases reported from other European countries had traveled to this area. This particular E. coli O104:H4 strain seems to be particularly virulent and is resistant to most β-Lactam antibiotics. Unfortunately, as of 31 May 2011, more than 30 patients in Germany have died of EHEC induced HUS. There seems to be an association between the outbreak the consumption of ~~raw cucumbers, tomatoes, and leaf~~ ~~salad~~ vegetable sprouts. I am not sure what the Google Insights graph below exactly tells us... but it is kind of interesting to see that for a while the "web search interest" of EHEC approached Lady Gaga's.

Evidence of "extra" terrestrial life?

2010-11-30T14:40:00.000-08:00

NASA will hold a news conference at 11 a.m. PST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life. Astrobiology is the study of the origin, evolution, distribution and future of life in the universe.

Very exciting stuff! I have a gut feeling that this story involves Arsenic.

If it turns out that Felisa Wolfe was right after all she will have to grow a large beard ASAP.... because she will be a f**$#!? new Darwin.

UPDATE:

Now most of the media dust has settled, some of us might have actually read the Science paper. I admire the "progressive" attitude of this team of scientist. I think they have found a cool bug that is unusually resistant to As, but I am both a bit disappointed and alarmed by some of the presented evidence.

One of the things that struck me was how the Felisa and her team aim to show that the genomic DNA contains As in place of P.

Their mass spectrometry analysis seems to reveal only very little As relative to carbon. The study lacks some controls (e.g. other genomic DNA incubated with As medium) to rule out that the small amounts of As result from carry over during DNA extraction and purification.

UPDATE II:

A good but slightly virulent post by Rosie Redfield. Rosie shares (and does a good job explaining) my doubts about the As being covalently bound into nucleotides and describes a few other potential weaknesses of this paper.

Robert Krulwich: Why Can't We Walk Straight?

2010-11-28T10:56:00.000-08:00

Try as you might, you can't walk in a straight line without a visible guide point, like the Sun or a star.

In this cool animation, Robert Krulwich, a correspondent for NPR's Science Desk shows that while you might think you're walking straight, a map of your route would reveal you are doomed to walk in circles.

Random Blog Post

2010-09-03T00:45:00.000-07:00

"Any one who considers arithmetical methods of producing random digits is, of course, in a state of sin. For, as has been pointed out several times, there is no such thing as a random number — there are only methods to produce random numbers, and a strict arithmetic procedure of course is not such a method". (John von Neumann [1951] Various techniques used in connection with random digits. National Bureau of Standards, Applied Math Series, 11:36-38. )

Nevertheless, I added a "Random Blog Post" button.

Tree time!

2010-08-27T06:58:00.000-07:00

My favorite dendrograms (randomly ordered)

The first-known sketch by Charles Darwin of an evolutionary tree describing the relationships among groups of organisms (Notebook B: Transmutation of species, 1837-1838). This tree figure, with the most ancestral species at the bottom and their descendants branching off, reveals that Darwin understood all plants and animals are related. Above this tree Darwin wrote firmly, "I think."

Lentebloesem (Spring Blossom) 1987; the Dutch painter René Daniels depicts his own oeuvre as a branched tree, which leaves are formed by the titles of his previous paintings.

Ribosomal RNA gene based phylogenetic tree by Carl Woese (1987) illustrating the three-domain classification system.

W. Ford Doolittle’s reticulated tree, or net, stresses the importance of horizontal gene transfer in archaeal and bacterial evolution.

NDM-1

2010-08-14T15:45:00.000-07:00

Louis-Ferdinand Célin once said “Even diseases have lost their prestige, there aren't so many of them left. Think it over... no more syphilis, no more clap, no more typhoid... antibiotics have taken half the tragedy out of medicine.”

He didn’t anticipate carbapenem resistant Enterobacteriaceae coming into existence.

Bacterial genome size & base composition

2010-08-10T05:08:00.000-07:00

Browsing through the currently available microbial genomes in Genbank I noticed that it is remarkably easy to make some highly illustrative graphs. E.g. plotting the G+C percentage of a complete genome against the total size of the genome reveals a remarkable trend.

In the early sixties it was first noted that “Among bacteria the mean G+C content of DNA varies approximately from 25 to 75%, and this range extends over the range of the mean G+C content of DNA of higher organisms” (Sueoka, 1962).
Currently, the mean G+C content for sequenced bacterial genomes deposited in Genbank is 48.3% and ranges from 74.9% (Anaeromyxobacter dehalogenans 2CP-C) to 16.6 % (Candidatus Carsonella ruddii PV).
The figure above shows the “linear” correlation between bacterial genome size and base composition.
An adaptive explanation for this apparent correlation could be the fact that synthesis of GTP and CTP is energetically more expensive than ATP and TTP (Rocha & Danchin, 2002). In addition, the central role of ATP in cellular metabolism results in a greater availability relative to other nucleotides. Under resource limiting conditions, this could drive microbial genomes to drift towards AT-richness.
Another possible explanation is DNA repair. Small (reduced) genomes often lack genes involved in DNA repair machineries (Moran, 2002) allowing accumulation of point mutations. Experiments have shown that the most frequent random mutation occurring in cells is C to T (or G to A), due to the deamination of Cytosine to form Uracil, which is subsequently replicated as Thymidine (Glass et al., 2000). Thus in the absence of DNA repair mechanisms, genomes might become more AT-rich.

References
Glass JI, Lefkowitz EJ, Glass JS, Heiner CR, Chen EY, Cassell GH. 2000. The complete sequence of the mucosal pathogen Ureaplasma urealyticum. Nature 407:757-762.
Moran NA. 2002. Microbial minimalism: Genome reduction in bacterial pathogens. Cell 108:583-586.
Rocha EPC, Danchin A. 2002. Base composition bias might result from competition for metabolic resources. Trends Genet 18:291–294.
Sueoka N. 1962. On genetic basis of variation and heterogeneity of DNA base composition. PNAS 48:582-592.

Fallible Design

2010-07-19T02:52:00.000-07:00

The basic concept of intelligent design comes in two parts and is as simple as it is satisfying for those unwilling to think deeply about the natural world, science, or the nature of religion. 1) Nature is so perfectly integrated that it must have been designed just as we see it. 2) While some aspects of nature might have changed (evolved) over time, others are so complex that they must always have existed in the form we find them in today, and must have been created by an "intelligent designer".

This part can be largely attributed to Michael Behe (Lehigh University), who claims that certain biochemical processes are "irreducibly complex". They involve multiple proteins, and without any one of them the overall pathway would not work. Like the good old ... eye.
It is quite needless to say that both parts of ID are spectacularly wrong, but it is not a bad thing to preach to the choir every now and then. The choir can enjoy reading about the wonders of biology and human stupidity. Enfin. A notably elegant ID rebuttal appeared recently in PNAS. In “Footprints of nonsentient design inside the human genome” John Avise (University of California) provides entertaining examples of the human genomes incredible imperfection.

2010-07-12T13:43:00.000-07:00

Lies, Damn Lies and Medical Research

7th Annual Microbial Sciences Symposium; open to all

2010-04-13T06:37:00.000-07:00

The Microbial Sciences Initiative (MSI) at Harvard is an interdisciplinary science program aimed at a comprehensive understanding of the richest biological reservoir of the planet, the microbial world. On Saturday, April 17, 2010 MSI will host the 7th Annual Microbial Sciences Symposium, free and open to all. Eight prominent microbial scientists haling from a wide variety of disciplines are invited to talk about their research:

Ruth Ley - The human gut microbiome and obesity-related diseases
Michael Gilmore - Multidrug resistant enterococci: Evolution of leading hospital pathogens from commensals
Susan Golden - A circadian checkpoint on cell division in cyanobacteria
Christopher Marx - Microbial evolution and mobile genetic elements: adaptation and exchange
David Rudner - Cell-cell signaling through regulated proteolysis
Joanna Aizenberg - Bacteria in nanoforests
Susan Lindquist - Protein folding and environmental stress redraw the relationship between genotype and phenotype
Rob Knight - Diversity of the human microbiome across spatial and temporal scales

April 17, 2010
Radcliffe Gym - Radcliffe Institute for Advanced Studies
Harvard University
Cambridge, MA

Life beneath your beard

2010-04-01T09:56:00.000-07:00

Automated Methods

2010-03-18T12:15:00.000-07:00

Flipping through a bound volume of Annual Reviews of Microbiology (volume 1976, my year of birth) I came across an interesting review by Henry D. Isenberg and James D. Maclowry. Considering the current state of molecular (micro)biology this review is quit visionary and very off the mark at the same time. The problems and tasks they identify for "those who would automate bacteriological procedures" are still valid. Nevertheless, DNA is not mentioned once in the whole review.

back to our concestor

2010-02-17T08:03:00.000-08:00

The Swedish Meindbender Studios made this cool leader for Cartoon Network. What looks like a stop motion-like clay animation is in fact completely digitally rendered.

Dutch universities go OPEN ACCESS

2010-02-02T09:03:00.000-08:00

Dutch universities have made a big step in their effort to make research results publicly accessible (Open Access). Authors are thought to be more ‘visible’ if their work is freely available on the Internet, and they will have a wider audience than if they publish in the traditional journals only. The greatly increased cost of subscriptions to the traditional journals means that university libraries can afford fewer and fewer of them.
The VNSU (Association of Universities in the Netherlands) announced an agreement with the Berlin-based Springer Group, the world's second-largest science publisher, that all articles which are published by Dutch university researchers are made publicly accessible. This agreement runs initially up to 2011. With Elsevier, the VNSU has agreed to start a pilot to examine how open access can be broadened further.
These are remarkable steps indeed because the rules of the “open access game” are changing a bit. In this model authors will be able to publish open access without paying those pesky page charges (not a trivial amount of money...). I imagine that in this model the universities will probably pay a huge flat fee. In order to fully bypass the traditional publishers one would have to transfer funds destined to pay for journal subscriptions into “publication funds” and have scientists pay for their own open access publications. Having a limited publication fund sounds horrible but on a bright side it might counter the wide spread “least publishable unit” (LPU) syndrome.

大全

2010-01-13T19:39:00.000-08:00

After recent attacks by Chinese hackers, apparently seeking information on Chinese human rights activists, Google announced their new approach to China in a post on their official blog. Although Google did not explicitly accuse the Chinese government of the breach, it said it was no longer willing to censor search results on google.cn. I don't read Chinese very well but it seems that their new aproach is in effect.

update:
Using a free online translation tool "据当地法律法规和政策，部分搜索结果未予显示" turned out to mean something like "According to the local legislation laws, regulations and the policy, part of the search results are not shown".

"pro-inflammatory anaerobes" ?

2010-01-06T12:56:00.000-08:00

A team of American and Ugandan scientist described the penis microbiome using 16S rRNA gene amplicon pyrosequencing (PLOS One [2010] 5: e8422). They show that circumcision is associated with significant shifts in the penis microbiome. It is not surprising, but nevertheless interesting, that they observed a decrease in anaerobic Bacteria.

Boldly they conclude: "The anoxic microenvironment of the subpreputial space may support pro-inflammatory anaerobes that can activate Langerhans cells to present HIV to CD4 cells in draining lymph nodes. Thus, the reduction in putative anaerobic bacteria after circumcision may play a role in protection from HIV and other sexually transmitted diseases."

...unfortunately this is merely a causation hypothesis that was not experimentally addressed in this study.

Mimicry

2010-01-04T10:48:00.000-08:00

I have always wondered about the function of blue camouflage gear often worn by riot police and paramilitary units. To me these uniforms seem to be more like a form of aposematism, the intent to become noticeable, which is the antithesis of natural camouflage. To be specific, this coloration could be a case of Müllerian mimicry. Instead of concealing the animal, this coloration pattern conveys a clear message “I’m not just a cop... I’m totally badass”. A brief literature search shows that constraints on camouflage may also have favored the evolution of antipredator warning signals on Lepidoptera (Merilaita & Tullberg, 2005, Evolution 59:38-45).

cherry-picking

2009-12-06T07:40:00.000-08:00

Now the "hoax screamers" have blown off their steam, one more post about those hacked emails…before we finally all agree that the burning of fossil fuels has NOTHING to do with CO2 emission, which is NOT a greenhouse gas, and a global temperature increase has NEVER been empirically measured. In addition, 97% of climate scientists actively publishing on this topic do NOT endorse the concept of anthropogenic climate change. etc.

Thanksgiving special

2009-12-04T18:52:00.000-08:00

It's time for some Old School microbiology!

This 1976 paper, completely based on good old colony counts, comes with the following smashing conclusion:
"Comminuted turkey meat purchased fresh at the retail level is a product with a high degree of bacterial contamination, limited keeping quality, and the ability to convey salmonellae and other enteric bacilli, staphylococci, and clostridia to the surfaces of equipment and the hands of kitchen workers in homes, hospitals, and factories."

Carnage

2009-12-04T17:40:00.000-08:00

On a sunny afternoon, I walk through the Yard, on my way to the Square, desperate for lunch. Then there is a sudden flash out of the clear blue sky, like feathered lightning. A red-tailed hawk, an alluring resident of Harvard Yard's urban nature, swiftly turns an oblivious sparrow into a late afternoon snack. Having witnessed this little carnage for a couple of minutes, I continue my quest for a Reuben sandwich.

Comics

2009-11-28T12:34:00.000-08:00

Technologies that assess characteristics of large families of genes, proteins, or small metabolites, have been named by appending with "-omics". Omics refers to the collective technologies used to explore the roles, relationships, and actions of the various types of molecules that make up the cells of an organism. These technologies include: Genomics, "the study of genes and their function", Proteomics (proteins), Transcriptomics (mRNA). "Omics" words are somewhat useful as they provide easy short-hands to encapsulate a field. However, as scientists are rapidly taking up omes and omics, shown by the explosion of omics-terms in PubMed since the mid '90s, the spread of omics words is getting a bit lame. Some recent tragic examples: fermentomics, interactomics, and museomics (for more see: Jonathan Eisen's Worst Omics Word Awards). The above picture of a mold covered X-men issue inspired me to coin the word "Comics"; the study that is all about the microbial diversity associated with comic books.

Solemya velum

2009-11-12T07:48:00.000-08:00

Solemyidae is a family of bivalves in the order Solemyoida, its members are known as Solemyids. They are remarkable in that their digestive tract is either extremely small or non-existent, and their feeding appendages are too short to reach outside the shell. It has been shown that these clams harbour sulphur-oxidizing Bacteria intracellularly within their gill filaments. As chemoautotrophs, these bacterial symbionts synthesize organic matter from CO2 and are the primary source of nutrition for the whole organism. In turn, the animal host provides its symbionts a habitat in which they have access to the substrates of chemoautotrophy (O2, CO2, and reduced inorganic compounds such as H2S). Together, these partners create "animals" with novel metabolic capabilities.

Laboratory Safety

2009-11-11T06:27:00.000-08:00

The Sounds of Science made this musical extravaganza on the importance and execution of laboratory safety.
The Sounds of Science (not to be mistaken with the Beastie Boys classic) is a group of graduate students and alumni of UC Berkeley that "share a common love of science and music". Their aim is to promote awareness of science to the community through fun music videos available free on the internet. Here are a bunch of other great songs that show how hard science rocks.

The 5-Second Rule

2009-10-29T07:55:00.000-07:00

Although it has received little scholarly attention, the five-second rule has been studied as both a public health recommendation and as a sociological effect. In 2003, Jillian Clarke, then a high school senior, decided to do some experiments. During an internship at the University of Illinois at Urbana-Champaign, she and PhD candidate, Meredith Agle, took swab samples from floors all over the campus, including labs, hallways, and bathrooms, and found that the amount of bacteria on the floors was very low. When she published her research, she concluded that if a piece of food falls on a relatively clean floor, the five-second rule is, in fact, applicable. According to Clarke, the 5-second rule dates back to the time of Genghis Khan, who first determined how long it was safe for food to remain on a floor when dropped there. However, the founder of the Mongol Empire had slightly lower standards, he specified 12 hours, more or less. In 2004 Clarke received the Ig Nobel Prize in public health for this study. The five-second rule was also featured in an episode of the Discovery Channel series MythBusters (episode 39). They found that moisture, surface geometry and the location the food item was dropped on did affect the transfer of bacteria more than "exposure time".

David Attenborough about Hydrothermal Vents

2009-10-27T13:37:00.000-07:00

Deep-sea hydrothermal vents, ventilating heat and reduced chemical compounds from the interior of the Earth, support ecosystems completely independent of sunlight. Chemoautotrophic bacteria and marine invertebrates living at hydrothermal vents function as autotrophic symbioses by oxidizing hydrogen sulfide as an energy source and fixing carbon dioxide into organic compounds.

These peculiar environments on and beneath the seafloor may represent a model for the origin of life on Earth and on other planets.

Just as islands on the surface of our planet revealed the mechanisms of speciation to Charles Darwin 150 years ago, deep-sea vent communities offer biologists a way of understanding the origin of species.

Gas fields of joy

2009-07-27T08:37:00.000-07:00

Fifty years ago, huge natural gas field was discovered in Slochteren (Groningen, the Netherlands). The Netherlands became the second-greatest natural gas producer in the European Union and the ninth-greatest in the world, accounting for more than 30% of EU total annual gas production and about 2.7% of the annual world total. The total revenue from the Groningen gas fields has been more than 211 billion euros. Most of this unexpected "free money" went straight to the treasury and allowed the Netherlands to live beyond its means for half a century.

In fact, it was the natural gas that allowed Dutch politicians to build the generous welfare state the Netherlands is famous for. The gas revenues shielded the Netherlands from the effect of the 1973 oil crisis and one could argue that natural gas paid for the so-called "poldermodel", the famous Dutch consensus-based system of cooperation between government, unions and employers organizations

Now the report Focus on Dutch Gas 2009 (PDF), published by the Dutch energy management agency (EBN), estimates there are an additional 500,000 billion cubic metres of unconventional gas hidden under Dutch territory that could be exploited with new technologies.

In the last 50 years the Dutch petroleum corporation NAM produced ~50 billion cubic meters gas a year. Hence, this discovery would be good for another 10.000 years of good old "free money".

Unfortunately, burning 500,000 billion cubic meters natural gas (primarily methane) will result in 500,000 billion cubic meters CO2. The Netherlands has an annual CO2 emission of ~142 million tons (71 billion m3). Taking sea level rising due to anthropogenic climate change into account, the Netherlands—most of which lies beneath sea level, hence the name- will be well of on it's way becoming Europe's Bangladesh.

Time flies

2009-07-18T10:33:00.000-07:00

For no apparent reason, the Social Cultural Planning Office of the Netherlands developed a tool that reflects what US citizens do at different days of the week and at different times of the day.

This entertaining flash-animated piechar t shows the percentages of participation in different activities during 96 different 15 minute time intervals, for each of the 7 days of the week. There is actually a lot of interesting human behavior hidden in this figure. E.g. note how people in the US tend to got to sleep at the whole hour.

It's not clear if this graph includes children but the amount of time spend on education seems somewhat low considering that ~20% of the population is younger than 14.

Voyage of the Beagle

2009-06-24T09:19:00.000-07:00

To celebrate Charles Darwin’s 200th birth year, and the 150th anniversary of his publication of “On the Origin of Species”, the Dutch public broadcasting organization VPRO is preparing a 40-part documentary series called Beagle: On the future of species. With the three mast sailing ship “Clipper Stad Amsterdam” the crew aims to reconstruct Darwin’s 5-year long voyage on the HMS Beagle in the course of one year, and attempt to answer ambitious questions as “where the world stands today in light of Darwin’s evolution theory”, “Is there reason to worry about the future?” and “Can science offer us sufficient answers to some of our most compelling questions? In addition, the TV makers will try to add some actual science to the show by letting scientists from various disciplines perform experiments on board and at the various destinations along the route. The accompanying website has some beautiful footage and updates on a daily basis about the project.

A life in germ free islolation

2009-05-30T05:06:00.000-07:00

Today I visited the Gnotobiotic Animal Models Core at Harvard Digestive Disease Center for a pottential collaboration. The mice living in positive pressure isolators reminded me of the bizarre and heartbreaking story of David Phillip Vetter, a boy living virtually his whole life inside a germ free isolator. Suffering from rare genetic disease now known as severe combined immune deficiency syndrome (SCIDS), he was forced to live in an isolated environment. Because his older brother had died shortly after birth from complications of the same disease, his parents were prepared for David's birth and arranged for a an aseptic delivery on September 21, 1971, at Texas Children's Hospital in Houston. Once it was determined that David was also afflicted with SCID, he stayed in plastic isolator environments while waiting for a matching bone marrow donor or a cure for his ailment. Known as “the bubble boy” he became a famous medical case. As a captivated public watched, the child grew up isolated from both pathogenic microbes and human touch before finally dying, at age 12, after the failure of a pioneering bone-marrow transplantation.
It is remarkable that despite the large numbers of microbiota and their protective value they do not appear to be essential to life, or at least not life in a sterile environment, as demonstrated by our animal models and rare cases of humans reared in germ free conditions.

Colony collapse disorder

2009-05-05T07:48:00.000-07:00

The European honey bee or western honey bee (Apis mellifera) may be the only insect ever obtaining the "charismatic megafauna status".

Albert Einstein is supposed to have once said:

“If the bee disappeared off the surface of the globe then man would only have four years of life left. No more bees, no more pollination, no more plants, no more animals, no more man.”

Colony collapse disorder (or CCD) is a phenomenon in which worker bees from a honey bee colony abruptly disappear. While such disappearances have occurred throughout the history of apiculture, the term colony collapse disorder was first applied to a drastic rise in the number of disappearances of Western honey bee colonies in North America in late 2006.

The cause of the observed massive abandonment of beehives is, officially, a mystery. Among the possible causes are drought, fungal parasites, the insecticides beekeepers use to control mites and the stress of trucking bees around the country in a race for high pollination fees. More speculative possibilities range from cell phone radiation and genetically modified crops to chemtrails, aliens, and population control conspiracies.

Now an increasingly prevalent class of insecticides called neonicotinoids have become the prime suspect. Neonicotinoids are artificial forms of nicotine that act as neurotoxins to insects (Iwasa et al. 2004). That may account for worker bees neglecting to provide food for eggs and larvae, and for a breakdown of the bees' navigational abilities. The use of neonicotinoids has spread rapidly in recent years as the hives began collapsing.

Neonicotinoids are less toxic to humans than most conventional pesticides and, because they are absorbed by the plants, can be narrowly focused to the pests that feed on the treated crop. But because the chemicals are taken up by the plants, they are likely to appear in nectar and pollen of crops that cover vast areas.

Swine influenza virus

2009-05-04T08:33:00.000-07:00

The swine influenza virus (SIV) is a RNA virus of the family Orthomyxoviridae, which commonly affect birds and mammals. The current "swine flu" or "Mexican flu" outbreak is due to a new strain of influenza, an apparent fusion of at least four strains of influenza A virus subtype H1N1, including one strain endemic in humans, one endemic in birds, and two endemic in swine. The symptoms are relatively mild, including fever, cough, sore throat, body aches, headache, chills and fatigue.
Nevertheless, influenza kills 36,000 Americans every year, on average, but that is from what experts call the "regular" or seasonal flu.
The problem is that SIV appeared "off season" and caught health organizations off guard, prompting them to take appropriate action. People panicked!
Believe it or not, in Egypt, officials have begun slaughtering an estimated 300,000 pigs - despite there is absolutely no evidence that the disease spreads by eating pork and there have been no reported cases of SIV in Egypt.

Violent by nature?

2009-04-08T06:58:00.000-07:00

"The Guardian obtained this footage of Ian Tomlinson at a G20 protest in London shortly before he died. It shows Tomlinson, who was not part of the demonstration, being assaulted (from behind!) by baton-wielding police."
Seeing these highly disturbing images reminded me of an important theoretical idea in classical ethology: Lorenz's Hydraulic Model. Lorenz' model describes the relationship between behaviour (fixed action patterns), motivation (action specific energy), and external stimuli (sign or releasing stimuli).
the Hydraulic Theory predicts:
1. Aggression is inevitable - accumulating energy must find an outlet.
2. Humans & animals will actively 'look for fights'.
3. After an attack an animal / human will become less aggressive.
4. Animals & humans reared in isolation will show aggressive behaviour.
Wether the origin of human aggressive behaviour lies mostly in nature or nurture may remain unanswered, but some basic knowledge about primate behaviour can increase your chances of survival when dealing with riot police. I.o.w. don't turn your back on an angry ape.

Arxula adeninivorans

2009-04-06T13:18:00.000-07:00

The non-pathogenic, dimorphic, haploid, ascomycetous yeast Arxula adeninivorans is a very attractive organism for biotechnological applications. This yeast species is able to assimilate and ferment a range of compounds as sole carbon, nitrogen, or phophorus source. A. adeninivorans is able to grow at cultivation temperatures of up to 48 °C, even surviving cultivation at 55 °C for some hours. On one hand it is a source for many interesting enzymes, for instance glucoamylase, tannase, lipase, phytase etc. On the other hand it is a very robust and safe organism that can be genetically engineered to express foreign genes with attractive properties.

Microbial Monet

2009-02-18T10:28:00.000-08:00

Michel Blazy is a French artist who works with organic matter. At the International Design Biennial at Saint Étienne, Blazy showed his work titled Jus de Nymphea; giant ponds filled with fermenting tea. The tea ponds harbored vibrantly colored gelatinous lily-pads, floating kombucha colonies, that gave the ponds their antioxidants and a spark of CO2. Kombucha is actualy a floating biofilm formed by a rather poorly defined consortium of yeasts and acetic acid bacteria. Presumed to be beneficial to human health, kombucha kolonies may also make an interesting model for the study of biofilms, microbial mats and other complex microbial associations. (photo by Debra Solomon)

The Hygiene Hypothesis

2009-02-17T14:29:00.000-08:00

The prevalence of allergic diseases such as asthma has increased markedly over the past few decades. It has been suggested that people in developing countries suffer less from allergic diseases than people who live in industrialized countries because the former are frequently exposed to parasitic worms (helminth) associated with lack of basic sanitary conditions. Helminth infections and allergic diseases are both associated with cytokines produced by Type 2 helper T cells (Th2) and high levels of IgE and eosinophilia. Though they appear to have similar immune responses, a negative correlation between helminth infection and allergic disease has been observed. Epidemiological studies have shown that some parasites are associated with reduced risk of atopy (allergic hypersensitivity) in children. Medeiros et al. (2003) found decreased prevalence and severity of asthma in individuals living in areas where schistosomiasis is endemic. The current hypothesis is that parasite-induced regulatory T cells can downregulate Th2 allergic inflammation (Pacifico et. 2009).

Over thousands of years the human immune system has adapted to cope with widespread parasite infections (and the subsequent modulation of the immune system). Now that helminth infections have been virtually wiped-out in the West, our immune systems are unbalanced.

Perhaps infecting patients with worms could facilitate the treatment of asthma....or maybe we should just stop cleaning.

Harvard Museum of Natural History

2009-02-13T08:16:00.000-08:00

The Harvard Museum of Natural History is on my favorite places in Cambridge (since I work at the department of OEB, I am actually affiliated to the museum). A visit to the HMNH is like journey back in time. A time when the equipment of a good naturalist included a small handgun. The aging but still spectacular collection of mounted animals says as much about how we once thought about the natural world as it shows us that world.

Go Google Go!

2009-02-12T20:52:00.000-08:00

Google logo in honor of Charles Darwin, whose 200th birthday is today (February 12, 2009). The watercolour-like logo includes Galapagos Island finches that prompted Darwin to contemplate his theory of evolution by natural selection.

Enlightenment

2009-02-12T10:54:00.000-08:00

Barack Obama is serious about science and technology.

He has appointed Carol Browner, the former EPA Administrator under President Clinton, as the Assistant to the President for Energy and Climate Change. He nominated Nobel-prize winning physicist and strong proponent of "carbon-neutral" energy technology, Steve Chu, to head the Department of Energy. Harvard physicist John Holdren is confirmed as the next Assistant to the President for Science and Technology. But just as important as the team is the philosophy behind it. In today’s address (12/20/2008), Obama emphasized the importance of science and evidence-based decision-making in society. Is this the end of a decade of endarkenment?

2009-02-12T07:43:00.001-08:00

Atheist Bus Campaign

Nadat in Groot-Brittanië de Atheist Bus Campaign een groot succes werd, namen meer landen het initiatief over (Spanje, Italië en zelfs de VS).
Het lijkt er echter op dat bussen in Nederland nooit zullen rijden. CBS Outdoor (monopolist voor reclame in en rond NS stations) heeft laten weten de reclame niet toe te staan omdat het om een religieuze, levensbeschouwelijke uiting gaat. Vreemd...

2009-02-12T07:28:00.000-08:00

In The News

Wat is genomics? (Educatieve website van het Netherlands Genomics Initiative in Den Haag)

Groene biofilmen zuiveren water

2009-02-12T07:25:00.000-08:00

In The News

Hoe?Zo! Radio, Teleac
Afvalwaterzuivering met blauwalg (podcast)

'Hagens op de middag', Avro, Radio 1

De oorsprong van het leven (podcast)

2009-02-10T21:36:00.000-08:00

NOS Journaal FAIL!

Dat is heel geen bever...