Hop Hop Hop the Slime Mold Said!
- Posted: 28.Mar.2006.
The slime mold Physarum polycephalum has been grown on non-uniform substrates, where nutrients were confined in separated drops of agar medium. Spatial and temporal aspects of the resulting growth structures were studied by time-lapse video techniques and analyzed using image processing software.
- Posted: 28.Mar.2006.
The slime mold Physarum polycephalum has been grown on non-uniform substrates, where nutrients were confined in separated drops of agar medium. Spatial and temporal aspects of the resulting growth structures were studied by time-lapse video techniques and analyzed using image processing software.
BacterioPhage
- Posted: 03.Jun.2009.
A Bacterium under attack by BacteriaPhages, bacterial viruses.
- Posted: 03.Jun.2009.
A Bacterium under attack by BacteriaPhages, bacterial viruses.
Bacteriophages (viruses that infect bacteria) are fascinating organisms that have played and continue to play a key role in bacterial genetics and molecular biology. Phage can confer key phenotypes on their host, for example converting a non-pathogenic strain into a pathogen, and they play a key role in regulating bacterial populations in all sorts of environments. The phage-bacterium relationship varies enormously: from the simple predator-prey model to a complex, almost symbiotic relationship that promotes the survival and evolutionary success of both. While infection of bacteria used in the fermentation industry can be very problematic and result in financial losses, in other scenarios phage infection of bacteria can be exploited for industrial and/or medical applications. In fact interest in phage and phage gene products as potential therapeutic agents is increasing rapidly and is likely to have a profound impact on the pharmaceutical industry and biotechnology in general over the coming years. One potential application is the use of phage to combat the growing menace of antibiotic-resistant infections.
Inhibition of E. coli biofilm swarming
- Posted: 03.Feb.2006.
(Click for full size)
"Inhibition of E. coli biofilm swarming (quorum sensing phenomenon) using furanone"
Quorum sensing is the means which bacteria use to communicate.
VIA
- Posted: 03.Feb.2006.
(Click for full size)
"Inhibition of E. coli biofilm swarming (quorum sensing phenomenon) using furanone"
Quorum sensing is the means which bacteria use to communicate.
VIA
ToothScraping
- Posted: 02.Feb.2006.
(Click for full size)
and more reasons to visit the dentist regularly.
- Posted: 02.Feb.2006.
(Click for full size)
and more reasons to visit the dentist regularly.
Anthrax on Blood
- Posted: 30.Jan.2006.
Typical appearance of Bacillus anthracis on blood agar. Art it could be!
- Posted: 30.Jan.2006.
Typical appearance of Bacillus anthracis on blood agar. Art it could be!
Stress turns the bacteria into a Crystalpunk
- Posted: 30.Jan.2006.
Trees and ferns often grow in fractal forms. Bacteria colonies can, too. But how?
Are these patterns the result of simple physical processes, or do they represent self-organization and communication on many levels?
Certainly, different causes can produce the same effect: the existence of fractal bacteria colonies does not favor one mechanism over another.
But note 3 billion years of evolution have given Nature ample opportunity to discover and exploit purely physical processes.
VIA
- Posted: 30.Jan.2006.
Trees and ferns often grow in fractal forms. Bacteria colonies can, too. But how?
Are these patterns the result of simple physical processes, or do they represent self-organization and communication on many levels?
Certainly, different causes can produce the same effect: the existence of fractal bacteria colonies does not favor one mechanism over another.
But note 3 billion years of evolution have given Nature ample opportunity to discover and exploit purely physical processes.
VIA
Non-living Dissipative Systems
- Posted: 30.Jan.2006.
The investigation of such self-organizing chemical systems is still going on. All these chemical systems, mainly variants of the BZ-reaction, strongly point in the direction of corresponding biochemical processes in Organisms, for example the aggregation patterns of the Slime Mold. This mold consists of amoebae (unicellular animals) living on the forest floor. When starved (i.e. finding themselves in unfavorable conditions) they aggregate into a multicellular body which can then move in search of a more favorable habitat. The aggregation is triggered by the release of the compound cyclic adenosine monophosphate (cAMP) from some of the amoebae
These patterns are created when the mold forms aggregates in response to some external 'stress', such as a lack of moisture or nutrients.
- Posted: 30.Jan.2006.
The investigation of such self-organizing chemical systems is still going on. All these chemical systems, mainly variants of the BZ-reaction, strongly point in the direction of corresponding biochemical processes in Organisms, for example the aggregation patterns of the Slime Mold. This mold consists of amoebae (unicellular animals) living on the forest floor. When starved (i.e. finding themselves in unfavorable conditions) they aggregate into a multicellular body which can then move in search of a more favorable habitat. The aggregation is triggered by the release of the compound cyclic adenosine monophosphate (cAMP) from some of the amoebae
These patterns are created when the mold forms aggregates in response to some external 'stress', such as a lack of moisture or nutrients.
AGAR for Literature
- Posted: 30.Jan.2006.
"However, in one class Thompson was surprised. She told the students to think of inoculation of agar as "invisible writing" that would be visualized in a day or so. The students interpreted her literally and actually wrote on the agar with bacteria stock that grew into a readable message."
VIA
- Posted: 30.Jan.2006.
"However, in one class Thompson was surprised. She told the students to think of inoculation of agar as "invisible writing" that would be visualized in a day or so. The students interpreted her literally and actually wrote on the agar with bacteria stock that grew into a readable message."
VIA
Germs are Us
- Posted: 07.Aug.2006.
"In a peculiar sense, it is okay to refer to our individual selves as “we” without belonging to royalty, yet be scientifically precise since our bodies which have a thousand billion cells harbor ten thousand billion bacteria. Germs are Us."
VIA
- Posted: 07.Aug.2006.
"In a peculiar sense, it is okay to refer to our individual selves as “we” without belonging to royalty, yet be scientifically precise since our bodies which have a thousand billion cells harbor ten thousand billion bacteria. Germs are Us."
VIA
The Bacteria in your Ass-Hole
- Posted: 02.Aug.2006.
(Click for full size)
The adult human intestine is home to an almost inconceivable number of microorganisms. The size of the population—up to 100 trillion—far exceeds that of all other microbial communities associated with the body's surfaces and is ~10 times greater than the total number of our somatic and germ cells. Thus, it seems appropriate to view ourselves as a composite of many species and our genetic landscape as an amalgam of genes embedded in our Homo sapiens genome and in the genomes of our affiliated microbial partners (the microbiome).
VIA
- Posted: 02.Aug.2006.
(Click for full size)
The adult human intestine is home to an almost inconceivable number of microorganisms. The size of the population—up to 100 trillion—far exceeds that of all other microbial communities associated with the body's surfaces and is ~10 times greater than the total number of our somatic and germ cells. Thus, it seems appropriate to view ourselves as a composite of many species and our genetic landscape as an amalgam of genes embedded in our Homo sapiens genome and in the genomes of our affiliated microbial partners (the microbiome).
VIA
Synchronised Swimming
- Posted: 05.Jul.2006.
(Click for full size)
"If cultures of E. coli are grown in a medium containing chemicals evolved in the cell's biochemistry, they will swim together in predictable patterns. Compounds like succinate and fumarate will stimulate them to seek each other out and swim in coordinated arrays. This truly is synchronised swimming on a microscopic scale."
Brian J. Ford - the secret language of life
Picture VIA
- Posted: 05.Jul.2006.
(Click for full size)
"If cultures of E. coli are grown in a medium containing chemicals evolved in the cell's biochemistry, they will swim together in predictable patterns. Compounds like succinate and fumarate will stimulate them to seek each other out and swim in coordinated arrays. This truly is synchronised swimming on a microscopic scale."
Brian J. Ford - the secret language of life
Picture VIA
2 Peter Medawar Quotes
- Posted: 30.Jun.2006.
1:) On Teilhard de Chardin
The Phenomenon of Man stands square in the tradition of Naturphilosophie, a philosophical indoor pastime of German origin which does not seem even by accident (though there is a great deal of it) to have contributed anything of permanent value to the storehouse of human thought. French is not a language that lends itself naturally to the opaque and ponderous idiom of nature-philosophy, and Teilhard has according resorted to the use of that tipsy, euphoristic prose-poetry which is one of the more tiresome manifestations of the French spirit.
2:) On Learning in Bacteria
bacteriologists have known for years that if bacteria are forced to live upon some new unfamiliar kind of foodstuff or are exposed to the actions of an anti-bacterial drug, they acquire the ability to make use of that new food, or to make the drug harmless to them by breaking it down. The treatment was at one time referred to as the training of bacteria --- with the clear implication that the new food or drug taught the bacteria how to manufacture the new ferments upon which their new behavior depends. But it turns out that the process of training belies its name: it is not instructive. A bacterium can synthesize only those ferments it is genetically entitled to synthesize. The process of training merely brings out or exploits or develops an innate potentiality of the bacterial population, a potentiality underwritten or subsidized by the particular genetic make-up of one or another of its members.
VIA
- Posted: 30.Jun.2006.
1:) On Teilhard de Chardin
The Phenomenon of Man stands square in the tradition of Naturphilosophie, a philosophical indoor pastime of German origin which does not seem even by accident (though there is a great deal of it) to have contributed anything of permanent value to the storehouse of human thought. French is not a language that lends itself naturally to the opaque and ponderous idiom of nature-philosophy, and Teilhard has according resorted to the use of that tipsy, euphoristic prose-poetry which is one of the more tiresome manifestations of the French spirit.
2:) On Learning in Bacteria
bacteriologists have known for years that if bacteria are forced to live upon some new unfamiliar kind of foodstuff or are exposed to the actions of an anti-bacterial drug, they acquire the ability to make use of that new food, or to make the drug harmless to them by breaking it down. The treatment was at one time referred to as the training of bacteria --- with the clear implication that the new food or drug taught the bacteria how to manufacture the new ferments upon which their new behavior depends. But it turns out that the process of training belies its name: it is not instructive. A bacterium can synthesize only those ferments it is genetically entitled to synthesize. The process of training merely brings out or exploits or develops an innate potentiality of the bacterial population, a potentiality underwritten or subsidized by the particular genetic make-up of one or another of its members.
VIA
Quasispecies
- Posted: 19.Jun.2006.
(Click for full size)
"A quasipecies is in effect a cloud of genomes, clustering around a 'wild-type' coordinate (that is, genome) that may or may not actually have an extant or extinct instance."
Hardcore non-pop stuff, but leading some to deny the existence of species in bacteria.
VIA_1
VIA_2
VIA_3
- Posted: 19.Jun.2006.
(Click for full size)
"A quasipecies is in effect a cloud of genomes, clustering around a 'wild-type' coordinate (that is, genome) that may or may not actually have an extant or extinct instance."
Hardcore non-pop stuff, but leading some to deny the existence of species in bacteria.
VIA_1
VIA_2
VIA_3
Biofilm = the BacterioPoetic Movement
- Posted: 08.Jun.2006.
Excerpts from a 2003 review by Matthew R. Parsek and Clay Fuqua
http://jb.asm.org/cgi/content/short/186/14/4427
"For over a century microbiologists have studied liquid cultures of bacteria. In fact, a common criterion for choosing a microorganism to study has been its ability to grow in a suspended, homogeneous culture format, thereby simplifying examination of microbial physiology and genetics. Although these studies have been tremendously informative, they neglect the observation that many bacteria in the natural environment grow aggregated with each other, with solid surfaces, and at gas-liquid interfaces. There is a growing appreciation that, although clearly worthwhile, studies of standard planktonic cultures provide us with a biased view of microbial life."
"Outside of certain types of infections or symbioses, most biofilms consist of multiple species of both eukaryotic and prokaryotic organisms. There are obvious consequences to different organisms in a biofilm being present in high density and close proximity. The potential for interspecies communication, competition, and cooperation is high. How different species perceive and respond to one another is a key feature of any multispecies system. Although this fact is widely appreciated, most of the biofilm research being conducted in the field today involves pure-culture systems. This is not surprising—trying to study the complexity present in simple, pure-culture biofilms is daunting enough. Microbiologists studying complex environmental systems have developed wonderful, sophisticated tools to determine what organisms are present, where they are, and their metabolic disposition. However, the tractability of natural, complex communities is limited. Important questions such as the physiological response of one population to another and how this impacts community structure and function are usually difficult to answer. Researchers have taken an alternative route by developing closed, artificial multispecies systems, where the composition of the community and environmental parameters can be carefully controlled. The downside to this approach is that the system is artificial and may not accurately represent the complex community being modeled. The advantages are that the researcher can ask basic reductionist questions and take advantage of technologies such as genomics/DNA microarrays and proteomics."
"The general features and three-dimensional complexity achieved in some biofilms has led to the idea that biofilm formation is a developmental process, with true differentiation of at least some of the cells within a biofilm into a new, nonplanktonic state. Given the definition of development and differentiation, this would require that cells within the biofilm enter into a rigid path towards the sessile, biofilm-specific state, including the successful transit of checkpoints along the way (see reference 10 for such a definition). The differentiation of these cells should at some point be independent of additional environmental inputs. While there are certainly some examples of such fixed, metazoan-type development in prokaryotes, biofilm formation in most systems does not appear to meet all of the criteria described above. In most cases, the process is still strongly influenced by prevailing environmental conditions (flow properties, nutrient conditions, etc.) and is reversible at many steps along the way. Individual cells can dissociate from the biofilm apparently at any time. Likewise, biofilms are readily colonized by planktonic cells virtually at any point. Given such observations, it seems that the consideration of microbial biofilms in terms of metazoan development may miss the target. Defining experimental approaches and evaluative criteria based on metazoan-type development may ignore or miss some of the important features and emergent properties of biofilm communities. Furthermore, restricting our studies and conceptual framework in terms of development is probably selling biofilms short."
Image: Biofilms associated with microbially assisted corrosion. Quorum sensing as a mechanism of cell-to-cell communication appears to be ubiquitous in microbial communities such as these biofilms.
http://jb.asm.org/content/vol184/issue10/cover.shtml
- Posted: 08.Jun.2006.
Excerpts from a 2003 review by Matthew R. Parsek and Clay Fuqua
http://jb.asm.org/cgi/content/short/186/14/4427
"For over a century microbiologists have studied liquid cultures of bacteria. In fact, a common criterion for choosing a microorganism to study has been its ability to grow in a suspended, homogeneous culture format, thereby simplifying examination of microbial physiology and genetics. Although these studies have been tremendously informative, they neglect the observation that many bacteria in the natural environment grow aggregated with each other, with solid surfaces, and at gas-liquid interfaces. There is a growing appreciation that, although clearly worthwhile, studies of standard planktonic cultures provide us with a biased view of microbial life."
"Outside of certain types of infections or symbioses, most biofilms consist of multiple species of both eukaryotic and prokaryotic organisms. There are obvious consequences to different organisms in a biofilm being present in high density and close proximity. The potential for interspecies communication, competition, and cooperation is high. How different species perceive and respond to one another is a key feature of any multispecies system. Although this fact is widely appreciated, most of the biofilm research being conducted in the field today involves pure-culture systems. This is not surprising—trying to study the complexity present in simple, pure-culture biofilms is daunting enough. Microbiologists studying complex environmental systems have developed wonderful, sophisticated tools to determine what organisms are present, where they are, and their metabolic disposition. However, the tractability of natural, complex communities is limited. Important questions such as the physiological response of one population to another and how this impacts community structure and function are usually difficult to answer. Researchers have taken an alternative route by developing closed, artificial multispecies systems, where the composition of the community and environmental parameters can be carefully controlled. The downside to this approach is that the system is artificial and may not accurately represent the complex community being modeled. The advantages are that the researcher can ask basic reductionist questions and take advantage of technologies such as genomics/DNA microarrays and proteomics."
"The general features and three-dimensional complexity achieved in some biofilms has led to the idea that biofilm formation is a developmental process, with true differentiation of at least some of the cells within a biofilm into a new, nonplanktonic state. Given the definition of development and differentiation, this would require that cells within the biofilm enter into a rigid path towards the sessile, biofilm-specific state, including the successful transit of checkpoints along the way (see reference 10 for such a definition). The differentiation of these cells should at some point be independent of additional environmental inputs. While there are certainly some examples of such fixed, metazoan-type development in prokaryotes, biofilm formation in most systems does not appear to meet all of the criteria described above. In most cases, the process is still strongly influenced by prevailing environmental conditions (flow properties, nutrient conditions, etc.) and is reversible at many steps along the way. Individual cells can dissociate from the biofilm apparently at any time. Likewise, biofilms are readily colonized by planktonic cells virtually at any point. Given such observations, it seems that the consideration of microbial biofilms in terms of metazoan development may miss the target. Defining experimental approaches and evaluative criteria based on metazoan-type development may ignore or miss some of the important features and emergent properties of biofilm communities. Furthermore, restricting our studies and conceptual framework in terms of development is probably selling biofilms short."
Image: Biofilms associated with microbially assisted corrosion. Quorum sensing as a mechanism of cell-to-cell communication appears to be ubiquitous in microbial communities such as these biofilms.
http://jb.asm.org/content/vol184/issue10/cover.shtml
BioFilm Shapes in E. Coli
- Posted: 08.Jun.2006.
Cell distribution pattern during biofilm formation. Escherichia coli (MG1655) cells were allowed to attach to a microscope coverslip, and a digital image of the cells was subjected to fast Fourier transform (FFT) analysis. The doughnut-shaped two-dimensional FFT spectrum is indicative of a nonrandom distribution of cells on the glass surface, which is shown to be genetically determined.
VIA
- Posted: 08.Jun.2006.
Cell distribution pattern during biofilm formation. Escherichia coli (MG1655) cells were allowed to attach to a microscope coverslip, and a digital image of the cells was subjected to fast Fourier transform (FFT) analysis. The doughnut-shaped two-dimensional FFT spectrum is indicative of a nonrandom distribution of cells on the glass surface, which is shown to be genetically determined.
VIA
Tendril Patterns
- Posted: 08.Jun.2006.
Rhamnolipid surfactants modulate the distinct tendril patterns formed by Pseudomonas aeruginosa swarming across semisolid medium. The image shows the outline of the swarming pattern formed by the wild-type P. aeruginosa strain PA14 against a false-color background.
/> VIA
[nobody is saying science is poetic; only the bacteria]
- Posted: 08.Jun.2006.
Rhamnolipid surfactants modulate the distinct tendril patterns formed by Pseudomonas aeruginosa swarming across semisolid medium. The image shows the outline of the swarming pattern formed by the wild-type P. aeruginosa strain PA14 against a false-color background.
/> VIA
[nobody is saying science is poetic; only the bacteria]
Explosive-Contaminated
- Posted: 06.Jun.2006.
Abstract image of 2,4-dinitrotoluene (2,4-DNT) generated with RasMol and Adobe Photoshop. Metabolic pathways for synthetic compounds like 2,4-DNT evolve readily within bacterial populations in explosives-contaminated environments.
VIA
- Posted: 06.Jun.2006.
Abstract image of 2,4-dinitrotoluene (2,4-DNT) generated with RasMol and Adobe Photoshop. Metabolic pathways for synthetic compounds like 2,4-DNT evolve readily within bacterial populations in explosives-contaminated environments.
VIA
gliding motility by Mycoplasma mobile
- Posted: 06.Jun.2006.
Time series of photomicrographs showing gliding motility by Mycoplasma mobile on glass, annotated with computationally detected gliding paths. Images proceed from left to right and in successive rows at intervals of 1 s. The cells always glide in the direction of the tapered end by an unknown mechanism. The length of a single cell is about 1 μm.
VIA
- Posted: 06.Jun.2006.
Time series of photomicrographs showing gliding motility by Mycoplasma mobile on glass, annotated with computationally detected gliding paths. Images proceed from left to right and in successive rows at intervals of 1 s. The cells always glide in the direction of the tapered end by an unknown mechanism. The length of a single cell is about 1 μm.
VIA
Escherichia coli comparative genomics
- Posted: 06.Jun.2006.
Schematic diagrams representing the similarities and differences in the genomes of three E. coli strains.
VIA
- Posted: 06.Jun.2006.
Schematic diagrams representing the similarities and differences in the genomes of three E. coli strains.
VIA
Les Maladies Contagieuses
- Posted: 28.Jan.2008.
Bacteria and Illness, the George W. Bush approach to Bacteriopoetics.
- Posted: 28.Jan.2008.
Bacteria and Illness, the George W. Bush approach to Bacteriopoetics.
They Like their Oats
- Posted: 16.Jan.2008.
Another Slime Mold on the the move. Great sense of purpose.
- Posted: 16.Jan.2008.
Another Slime Mold on the the move. Great sense of purpose.
MicroPsycho
- Posted: 11.Jan.2008.
Let Crystalpunk introduce you to a classic in speculative comparative psychology by a psychologists who also wrote about chess. "The Psychic Life of Microorganisms" by Alfred Binet (1894) endeavors "to show that psychological phenomena begin among the very lowest classes of beings; they are met with in every form of life from the simplest cellule to the most complicated organism. It is they that are the essential phenomena of life, inherent in all protoplasm." The title alone makes it a BacterioPoetic classic.
- Posted: 11.Jan.2008.
Let Crystalpunk introduce you to a classic in speculative comparative psychology by a psychologists who also wrote about chess. "The Psychic Life of Microorganisms" by Alfred Binet (1894) endeavors "to show that psychological phenomena begin among the very lowest classes of beings; they are met with in every form of life from the simplest cellule to the most complicated organism. It is they that are the essential phenomena of life, inherent in all protoplasm." The title alone makes it a BacterioPoetic classic.
An Affectionate Machine-Tickling Aphid?
- Posted: 07.Jan.2010.
From "The Book of the Machines" , in Erewhon. Samuel Butler 1872.
- Posted: 07.Jan.2010.
From "The Book of the Machines" , in Erewhon. Samuel Butler 1872.
“But who can say that the vapour engine has not a kind of consciousness? Where does consciousness begin, and where end? Who can draw the line? Who can draw any line? Is not everything interwoven with everything? Is not machinery linked with animal life in an infinite variety of ways? The shell of a hen’s egg is made of a delicate white ware and is a machine as much as an egg-cup is: the shell is a device for holding the egg, as much as the egg-cup for holding the shell: both are phases of the same function; the hen makes the shell in her inside, but it is pure pottery. She makes her nest outside of herself for convenience’ sake, but the nest is not more of a machine than the egg-shell is. A ‘machine’ is only a ‘device.’”
“Shall we say that the plant does not know what it is doing merely because it has no eyes, or ears, or brains? If we say that it acts mechanically, and mechanically only, shall we not be forced to admit that sundry other and apparently very deliberate actions are also mechanical? If it seems to us that the plant kills and eats a fly mechanically, may it not seem to the plant that a man must kill and eat a sheep mechanically?
“But it may be said that the plant is void of reason, because the growth of a plant is an involuntary growth. Given earth, air, and due temperature, the plant must grow: it is like a clock, which being once wound up will go till it is stopped or run down: it is like the wind blowing on the sails of a ship — the ship must go when the wind blows it. But can a healthy boy help growing if he have good meat and drink and clothing? can anything help going as long as it is wound up, or go on after it is run down? Is there not a winding up process everywhere?
“Who shall say that a man does see or hear? He is such a hive and swarm of parasites that it is doubtful whether his body is not more theirs than his, and whether he is anything but another kind of ant-heap after all. May not man himself become a sort of parasite upon the machines? An affectionate machine-tickling aphid?
Rock-Scissors-Paper as a Model for E. coli
- Posted: 22.Sep.2006.
A growing colony of bacteria faces fierce competition for space and resources. To keep the lead, Escheria coli produces a toxin to efficiently reduce the number of competitors. Concurrently, the bacteria obviously have to produce an antidote that makes them immune themselves. After some time the vicious toxic strain may have eliminated all competitors and this renders the toxin production utterly useless. Consequentially, a mutant strain that only produces the antidote but not the toxin saves energy that can be dedicated to reproduction and hence it will eventually replace the toxic strain. But now that no toxins are around, the production of the antidote becomes equally useless and another mutant strain can take over that dedicates all ressources to reproduction. This leads to a population bacteria that is again vulnerable to toxins and the cycle may repeat itself endlessly: Rock beats Scissors beats Paper beats Rock... Actually this is not exactly what occurs in nature. For bacteria in solution, the amplitude of the frequency oscillations of the three types keeps increasing such that eventually one bacterial strain dies out and another follows shut. However, in spatially extended settings, this Rock-Scissors-Paper-type dominance can lead to traveling waves and was suggested to promote biodiversity
VIA
- Posted: 22.Sep.2006.
A growing colony of bacteria faces fierce competition for space and resources. To keep the lead, Escheria coli produces a toxin to efficiently reduce the number of competitors. Concurrently, the bacteria obviously have to produce an antidote that makes them immune themselves. After some time the vicious toxic strain may have eliminated all competitors and this renders the toxin production utterly useless. Consequentially, a mutant strain that only produces the antidote but not the toxin saves energy that can be dedicated to reproduction and hence it will eventually replace the toxic strain. But now that no toxins are around, the production of the antidote becomes equally useless and another mutant strain can take over that dedicates all ressources to reproduction. This leads to a population bacteria that is again vulnerable to toxins and the cycle may repeat itself endlessly: Rock beats Scissors beats Paper beats Rock... Actually this is not exactly what occurs in nature. For bacteria in solution, the amplitude of the frequency oscillations of the three types keeps increasing such that eventually one bacterial strain dies out and another follows shut. However, in spatially extended settings, this Rock-Scissors-Paper-type dominance can lead to traveling waves and was suggested to promote biodiversity
VIA
Digital Interfaces for the Exploration of Genetic Networks
- Posted: 14.Sep.2006.
(Click for full size)
The E. coli [that humble soul in your intestines] is the favorite pet of those merging biology, genetics and an information-overload fetish. Santiago Ortiz emailed some images of work done in visualising the genetic network of the E.coli, presumably because he is involved with it.
Have a Look at the site
- Posted: 14.Sep.2006.
(Click for full size)
The E. coli [that humble soul in your intestines] is the favorite pet of those merging biology, genetics and an information-overload fetish. Santiago Ortiz emailed some images of work done in visualising the genetic network of the E.coli, presumably because he is involved with it.
Have a Look at the site
Bacteria generate Electricity
- Posted: 19.May.2006.
The Science :
Electricity can be produced in different types of power plant systems, batteries, or fuel cells. A biofuel cell is a device that directly converts microbial metabolic or enzyme catalytic energy into electricity by using conventional electrochemical technology. Chemical energy can be converted to electric energy by coupling the biocatalytic oxidation of organic or inorganic compounds to the chemical reduction of an oxidant at the interface between the anode and cathode. It has been shown that direct electron transfer from microbial cells to electrodes occurs only at very low efficiency. In microbial fuel cells, two redox couples are required, one for coupling reduction of an electron mediator to bacterial oxidative metabolism and the other for coupling oxidation of the electron mediator to the reduction of the electron acceptor on the cathode surface (where the electron acceptor is regenerated with atmospheric oxygen.
The Popular View:
Bacteria battery may be powered by poo
- Posted: 19.May.2006.
The Science :
Electricity can be produced in different types of power plant systems, batteries, or fuel cells. A biofuel cell is a device that directly converts microbial metabolic or enzyme catalytic energy into electricity by using conventional electrochemical technology. Chemical energy can be converted to electric energy by coupling the biocatalytic oxidation of organic or inorganic compounds to the chemical reduction of an oxidant at the interface between the anode and cathode. It has been shown that direct electron transfer from microbial cells to electrodes occurs only at very low efficiency. In microbial fuel cells, two redox couples are required, one for coupling reduction of an electron mediator to bacterial oxidative metabolism and the other for coupling oxidation of the electron mediator to the reduction of the electron acceptor on the cathode surface (where the electron acceptor is regenerated with atmospheric oxygen.
The Popular View:
Bacteria battery may be powered by poo
BacterioPoetics is a Chain Reaction
- Posted: 17.May.2006.
A [part of the] schematic of all pathways of E. coli metabolism. Bacteria are a circuit.
VIA
- Posted: 17.May.2006.
A [part of the] schematic of all pathways of E. coli metabolism. Bacteria are a circuit.
VIA
BacteriophagePoetics
- Posted: 23.Apr.2006.
(Click for full size)
Bacteriophage ”X-174 DNA molecules on mica substrate (2D).
- Posted: 23.Apr.2006.
(Click for full size)
Bacteriophage ”X-174 DNA molecules on mica substrate (2D).
Bacteria as Camera
- Posted: 09.Jan.2006.
A dense bed of light-sensitive bacteria has been developed as a unique kind of photographic film. Although it takes 4 hours to take a picture and only works in red light, it also delivers extremely high resolution.
- Posted: 09.Jan.2006.
A dense bed of light-sensitive bacteria has been developed as a unique kind of photographic film. Although it takes 4 hours to take a picture and only works in red light, it also delivers extremely high resolution.
Bacteria are Us
- Posted: 02.Jan.2006.
"We would have to accept that bacteria, touted to be our enemies, are not merely neutral or friendly but that they are us. They are direct ancestors of our most sensitive body parts. Our culture's terminology about bacteria is that of warfare: they are germs to be destroyed and forever vanquished, bacterial enemies make toxins that poison us. We load our soaps with antibacterials that kill on contact, stomach ulcers are now agreed to be caused by bacterial infection. Even if some admit the existence of "good" bacteria in soil or probiotic food like yogurt few of us tolerate the dangerous notion that human sperm tails and sensitive cells of nasal passages lined with waving cilia, are former bacteria. If this dangerous idea becomes widespread it follows that we humans must agree that even before our evolution as animals we have hated and tried to kill our own ancestors. Again, we have seen the enemy, indeed, and, as usual, it is us. Social interactions of sensitive bacteria, then, not God, made us who were are today."
- Posted: 02.Jan.2006.
"We would have to accept that bacteria, touted to be our enemies, are not merely neutral or friendly but that they are us. They are direct ancestors of our most sensitive body parts. Our culture's terminology about bacteria is that of warfare: they are germs to be destroyed and forever vanquished, bacterial enemies make toxins that poison us. We load our soaps with antibacterials that kill on contact, stomach ulcers are now agreed to be caused by bacterial infection. Even if some admit the existence of "good" bacteria in soil or probiotic food like yogurt few of us tolerate the dangerous notion that human sperm tails and sensitive cells of nasal passages lined with waving cilia, are former bacteria. If this dangerous idea becomes widespread it follows that we humans must agree that even before our evolution as animals we have hated and tried to kill our own ancestors. Again, we have seen the enemy, indeed, and, as usual, it is us. Social interactions of sensitive bacteria, then, not God, made us who were are today."
Lynn Margulis
Chemotaxis in E.coli
- Posted: 05.Dec.2006.
(Click for full size)
Eski diagram from hardcore_science_paper on how E.coli deals with noise in the environment. Or better put, how evolution evolved its critter to deal with uncertainty. One of the reasons for reading this is that I want to find out how to use the Chain_Reaction CA to control object in a real environment.
- Posted: 05.Dec.2006.
(Click for full size)
Eski diagram from hardcore_science_paper on how E.coli deals with noise in the environment. Or better put, how evolution evolved its critter to deal with uncertainty. One of the reasons for reading this is that I want to find out how to use the Chain_Reaction CA to control object in a real environment.
Seed mag on Bacteria
- Posted: 06.Nov.2006.
(Click for full size)
Scientists had previously hypothesized that an organism couldn't have a genome with fewer than 400,000 nucleotides, the units that compose a strand of DNA. But Carsonella's genome has evolved right past that theoretical limit, weighing in at a mere 160,000 bases. In fact, it is the smallest genome ever sequenced.
LINK
There are many scholarly papers documenting the collective motion of bacteria in suspension. Even more people have seen swarms of bacteria beneath a cover-slip or in a droplet of fluid moving together like nose-plugged synchronized-swimmers creating whirling patterns. But, what choreographs this complex dance?
LINK
Satellites, aerial photography, and computerized geographic imaging systems have enabled us to map the Earth with unprecedented accuracy. Planes now feature screens that let passengers monitor the flight's path, while real-time websites map highway traffic flow with stunning precision. But when it comes to mapping another travel pattern—that of bacteria within the human body—scientists have only a vague idea of what is going on.
LINK
PICTURE
- Posted: 06.Nov.2006.
(Click for full size)
Scientists had previously hypothesized that an organism couldn't have a genome with fewer than 400,000 nucleotides, the units that compose a strand of DNA. But Carsonella's genome has evolved right past that theoretical limit, weighing in at a mere 160,000 bases. In fact, it is the smallest genome ever sequenced.
LINK
There are many scholarly papers documenting the collective motion of bacteria in suspension. Even more people have seen swarms of bacteria beneath a cover-slip or in a droplet of fluid moving together like nose-plugged synchronized-swimmers creating whirling patterns. But, what choreographs this complex dance?
LINK
Satellites, aerial photography, and computerized geographic imaging systems have enabled us to map the Earth with unprecedented accuracy. Planes now feature screens that let passengers monitor the flight's path, while real-time websites map highway traffic flow with stunning precision. But when it comes to mapping another travel pattern—that of bacteria within the human body—scientists have only a vague idea of what is going on.
LINK
PICTURE
Large Interesting Vertebrates
- Posted: 30.Apr.2010.
Life is not just a diurnal property of large interesting vertebrates; it is also nocturnal, anaerobic, cannibalistic, microscopic, digestive, fermentative: cooking away in the warm dark. Life is well-maintained at four-mile ocean depth, is waiting and sustained on a frozen rock wall, is clinging and nourished in hundred-degree temperatures. - Gary Snyder
- Posted: 30.Apr.2010.
Life is not just a diurnal property of large interesting vertebrates; it is also nocturnal, anaerobic, cannibalistic, microscopic, digestive, fermentative: cooking away in the warm dark. Life is well-maintained at four-mile ocean depth, is waiting and sustained on a frozen rock wall, is clinging and nourished in hundred-degree temperatures. - Gary Snyder
DADA DOES NOT MEAN ANYTHING
- Posted: 28.Mar.2008.
What an eye-opener: Tristan Tzara's 1918 DaDa manifesto explains the nonsense word DaDa in terms that we now call Bacteriopoetics and Ethnopoetics!
- Posted: 28.Mar.2008.
What an eye-opener: Tristan Tzara's 1918 DaDa manifesto explains the nonsense word DaDa in terms that we now call Bacteriopoetics and Ethnopoetics!
If we consider it futile, and if we don't waste our time over a word that doesn't mean anything... The first thought that comes to these minds is of a bacteriological order: at least to discover its etymological, historical or psychological meaning. We read in the papers that the negroes of the Kroo race call the tail of a sacred cow: DADA. A cube, and a mother, in a certain region of Italy, are called: DADA. The word for a hobby horse, a children's nurse, a double affirmative in Russian and Romanian, is also: DADA. Some learned journalists see it as an art for babies, other Jesuscallingthelittlechildrenuntohim saints see it as a return to an unemotional and noisy primitivism - noise and monotonous. A sensitivity cannot be built on the basis of a word; every sort of construction converges into a boring sort of perfection, a stagnant idea of a golden swamp, a relative human product. A work of art shouldn't be beauty per se, because it is dead; neither gay nor sad, neither light nor dark; it is to rejoice or maltreat individualities to serve them up the cakes of sainted haloes or the sweat of a meandering chase through the atmosphere. A work of art is never beautiful, by decree, objectively, for everyone. Criticism is, therefore, useless; it only exists subjectively, for every individual, and without the slightest general characteristic.
E. coli Growing
- Posted: 24.Feb.2008.
(Click for full size)
Is it just me or is there some form of (quasi-)crystalgrowth going on with this colony of. E coli.
- Posted: 24.Feb.2008.
(Click for full size)
Is it just me or is there some form of (quasi-)crystalgrowth going on with this colony of. E coli.
The Woesian Revolution
- Posted: 23.Feb.2008.
(Click for full size)
Carl Woese is the great historian of the Bacteria. Before him, they did not have a past, they just were, undifferentiated, unchanging, stupid and primitive; after him they turned out to be much more complex and new. The result was that the three domain system of classifying life in archaea, bacteria, and eukaryote domains. The differences between the archaea and the bacteria larger than those between us and the dinosaur.
David W. Wolfe's 'Tales from the Underground, a Natural History of Subterranean Life' (which is a great book) devotes a (biographical) chapter to tell us how Woese's stubbornly achieved his result and why it was so important. This picture is perhaps one of the best pictures ever made of the lone scientific genius in his lab. Does he not look like Christopher Walken?
- Posted: 23.Feb.2008.
(Click for full size)
Carl Woese is the great historian of the Bacteria. Before him, they did not have a past, they just were, undifferentiated, unchanging, stupid and primitive; after him they turned out to be much more complex and new. The result was that the three domain system of classifying life in archaea, bacteria, and eukaryote domains. The differences between the archaea and the bacteria larger than those between us and the dinosaur.
David W. Wolfe's 'Tales from the Underground, a Natural History of Subterranean Life' (which is a great book) devotes a (biographical) chapter to tell us how Woese's stubbornly achieved his result and why it was so important. This picture is perhaps one of the best pictures ever made of the lone scientific genius in his lab. Does he not look like Christopher Walken?
The Tree of Life is a Joke
- Posted: 22.Feb.2008.
Wrap your BacterioPoetics around Horizontal Gene Transfer: the origin of life was not a cell but a community. Quote: "organisms that don’t exchange genes appear more primitive from a comparative standpoint. They fall out of the rich ongoing genetic exchange that is occurring among the other organisms, and thus they do not incorporate the latest inventions shared among the others. Thus, one hypothesis about the deep branching lineages in the tree of life is that these organisms stopped participating in HGT and therefore started to appear older on the evolutionary scale, when in fact they just had stopped sharing genes."
Carl Woese's "A New Biology for a New Century (PDF-Link) is the best scientific introduction for the layperson to the idea of evolution as (? in?) a network.
Most compelling ideas:
- Posted: 22.Feb.2008.
Wrap your BacterioPoetics around Horizontal Gene Transfer: the origin of life was not a cell but a community. Quote: "organisms that don’t exchange genes appear more primitive from a comparative standpoint. They fall out of the rich ongoing genetic exchange that is occurring among the other organisms, and thus they do not incorporate the latest inventions shared among the others. Thus, one hypothesis about the deep branching lineages in the tree of life is that these organisms stopped participating in HGT and therefore started to appear older on the evolutionary scale, when in fact they just had stopped sharing genes."
Carl Woese's "A New Biology for a New Century (PDF-Link) is the best scientific introduction for the layperson to the idea of evolution as (? in?) a network.
Most compelling ideas:
The ancestor cannot have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in their turn became the three primary lines of descent (bacteria, archaea and eukaryotes)' In other words, early cells, each having relatively few genes, differed in many ways. By swapping genes freely, they shared various of their talents with their contemporaries. Eventually this collection of eclectic and changeable cells coalesced into the three basic domains known today. These domains become recognisable because much (though by no means all) of the gene transfer that occurs these days goes on within domains.
That compelling tree image resides deep in our representation of biology. But the tree is no more than a graphical device; it is not some a priori form that nature imposes upon the evolutionary process. It is not a matter of whether your data are consistent with a tree, but whether tree topology is a useful way to represent your data. Ordinarily it is, of course, but the universal tree is no ordinary tree, and its root no ordinary root. Under conditions of extreme HGT, there is no (organismal) "tree." Evolution is basically reticulate.
The minimounds
- Posted: 13.Mar.2006.
(Click for full size)
needle-cloned plaques of a bacteriophage that produces satellite plaques around each of its primary plaques.
VIA
- Posted: 13.Mar.2006.
(Click for full size)
needle-cloned plaques of a bacteriophage that produces satellite plaques around each of its primary plaques.
VIA
Dynamics of self-propagating fronts of motile bacteria
- Posted: 13.Mar.2006.
(Click for full size)
"Self-propagating reaction fronts occur in many chemical and physical systems including flames, free-radical initiated polymerization processes and some aqueous reactions. All of these systems are characterized by two key features: a reactive medium (for example a fuel-air mixture in the case of flames) and an autocatalyst that is a product of the reaction which also accelerates the reaction (for example thermal energy in the case of flames). Self-propagation occurs when the autocatalyst diffuses into the reactive medium, initiating reaction and creating more autocatalyst. This enables reaction-diffusion fronts to propagate at steady rates far from any initiation site."
VIA
- Posted: 13.Mar.2006.
(Click for full size)
"Self-propagating reaction fronts occur in many chemical and physical systems including flames, free-radical initiated polymerization processes and some aqueous reactions. All of these systems are characterized by two key features: a reactive medium (for example a fuel-air mixture in the case of flames) and an autocatalyst that is a product of the reaction which also accelerates the reaction (for example thermal energy in the case of flames). Self-propagation occurs when the autocatalyst diffuses into the reactive medium, initiating reaction and creating more autocatalyst. This enables reaction-diffusion fronts to propagate at steady rates far from any initiation site."
VIA
Siberian Peat
- Posted: 13.Mar.2006.
(Click for full size)
The Mighty PRUNED picked up on BacterioPoetics and added some more dishes to the meme. In the mean while this all is just preparation for the SyllaboTaxis I am working on, when time permits.
- Posted: 13.Mar.2006.
(Click for full size)
The Mighty PRUNED picked up on BacterioPoetics and added some more dishes to the meme. In the mean while this all is just preparation for the SyllaboTaxis I am working on, when time permits.
Essential genes of a minimal bacterium
- Posted: 09.Mar.2006.
Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life.
VIA
- Posted: 09.Mar.2006.
Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism and little genomic redundancy. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life.
VIA
The Bacterial I Ching
- Posted: 18.Jun.2008.
Evolution in Variable Environment! That is the new buzz word!!
Bacteria anticipate coming changes in their environment: the first evidence that bacteria can use sensed cues from their environment to infer future events. Lacking a brain or even a primitive nervous system, how is a single-celled bacterium able to pull off this feat? While higher animals can learn new behavior within a single lifetime, bacterial learning takes place over many generations and on an evolutionary time scale. To gain a deeper understanding there was developed a virtual microbial ecosystem, called "Evolution in Variable Environment." Each microbe in this novel computational framework is represented as a network of interacting genes and proteins. An evolving population of these virtual bugs competes for limited resources within a changing environment, mimicking the behavior of bacteria in the real world. When the researchers examined a number of fit virtual bugs, they could at first make little sense out of them. "Their biochemical networks were filled with seemingly unnecessary components. That is not how an engineer would design logic-solving networks." Pared down to their essential elements, however, the networks revealed a simple and elegant structure.
To implement this framework, the researchers had to deal with the sheer scale and complexity of simulating any realistic biological system. They had to keep track of hundreds of genes, proteins and other biological factors in the microbial population, and observe them as they varied over millions of time points. "Simulations at this scale and complexity would have been impossible in the past," said Tagkopoulos. Even with the vast number crunching power the supercomputers provided by the University's computational science and engineering support group, their experiments took nearly 18 months to run, said Tagkopoulos.
Original paper (PDF-link)
- Posted: 18.Jun.2008.
Evolution in Variable Environment! That is the new buzz word!!
Bacteria anticipate coming changes in their environment: the first evidence that bacteria can use sensed cues from their environment to infer future events. Lacking a brain or even a primitive nervous system, how is a single-celled bacterium able to pull off this feat? While higher animals can learn new behavior within a single lifetime, bacterial learning takes place over many generations and on an evolutionary time scale. To gain a deeper understanding there was developed a virtual microbial ecosystem, called "Evolution in Variable Environment." Each microbe in this novel computational framework is represented as a network of interacting genes and proteins. An evolving population of these virtual bugs competes for limited resources within a changing environment, mimicking the behavior of bacteria in the real world. When the researchers examined a number of fit virtual bugs, they could at first make little sense out of them. "Their biochemical networks were filled with seemingly unnecessary components. That is not how an engineer would design logic-solving networks." Pared down to their essential elements, however, the networks revealed a simple and elegant structure.
To implement this framework, the researchers had to deal with the sheer scale and complexity of simulating any realistic biological system. They had to keep track of hundreds of genes, proteins and other biological factors in the microbial population, and observe them as they varied over millions of time points. "Simulations at this scale and complexity would have been impossible in the past," said Tagkopoulos. Even with the vast number crunching power the supercomputers provided by the University's computational science and engineering support group, their experiments took nearly 18 months to run, said Tagkopoulos.
Original paper (PDF-link)
The SlimeMold Gospel
- Posted: 13.Jun.2008.
(Click for full size)
Simon Park, a microbiologist with a heart for the BacterioPoetic, has been releasing Slime Molds into his library, as you can see below. Today I received the following message from him with the above image.
- Posted: 13.Jun.2008.
(Click for full size)
Simon Park, a microbiologist with a heart for the BacterioPoetic, has been releasing Slime Molds into his library, as you can see below. Today I received the following message from him with the above image.
Following its escape into my library (see below), I eventually retrieved the slime mold from a copy of an old school bible that I happen to own and placed it back into confinement.
Back in containment the slime mold now seems to be expressing itself in ways that it hadn't before its escape (cross). It seems to be assessing the information it has inadvertently been exposed to and responding by reorganising itself into to new forms (see above). I am what Dawkins would call a "temporary agnostic" so I guess this is just coincidence.
To Imagine a Form of Language is to Imagine a Form of Life
- Posted: 08.Jun.2008.
"To Imagine a Form of Language is to Imagine a Form of Life" - Cy Twombly
Straight to my PrimatePoetic and BacterioPoetic and EthnoPoetic heart this one, found at the excellent 83Russel
- Posted: 08.Jun.2008.
"To Imagine a Form of Language is to Imagine a Form of Life" - Cy Twombly
Straight to my PrimatePoetic and BacterioPoetic and EthnoPoetic heart this one, found at the excellent 83Russel
Artificial Evolution
- Posted: 04.Jun.2008.
Richard Lenski's long term E. coli experiment is a BacterioPoetics classic. PZ Myers explains it as a historical contingency; as not as caused by one random mutation but of a sequence of little events. Carl Zimmer at Scienceblogs has posted his explanation of this breakthrough:
- Posted: 04.Jun.2008.
Richard Lenski's long term E. coli experiment is a BacterioPoetics classic. PZ Myers explains it as a historical contingency; as not as caused by one random mutation but of a sequence of little events. Carl Zimmer at Scienceblogs has posted his explanation of this breakthrough:
Lenski started 12 colonies. He kept each of these 12 lines in its own flask. Each day he and his colleagues provided the bacteria with a little glucose, which was gobbled up by the afternoon. The next morning, the scientists took a small sample from each flask and put it in a new one with fresh glucose. And on and on and on, for 20 years and running.
Over the generations, in fits and starts, the bacteria did indeed evolve into faster breeders. The bacteria in the flasks today breed 75% faster on average than their original ancestor. Lenski and his colleagues have pinpointed some of the genes that have evolved along the way; in some cases, for example, the same gene has changed in almost every line, but it has mutated in a different spot in each case. Lenski and his colleagues have also shown how natural selection has demanded trade-offs from the bacteria; while they grow faster on a meager diet of glucose, they've gotten worse at feeding on some other kinds of sugars.
After 33,127 generations Lenski and his students noticed something strange in one of the colonies. The flask started to turn cloudy. This happens sometimes when contaminating bacteria slip into a flask and start feeding on a compound in the broth known as citrate. Citrate is made up of carbon, hydrogen, and oxygen; it's essentially the same as the citric acid that makes lemons tart. Our own cells produce citrate in the long chain of chemical reactions that lets us draw energy from food. Many species of bacteria can eat citrate, but in an oxygen-rich environment like Lenski's lab, E. coli can't. The problem is that the bacteria can't pull the molecule in through their membranes. In fact, their failure has long been one of the defining hallmarks of E. coli as a species.
But in one remarkable case, however, they discovered that a flask had turned cloudy without any contamination. It was E. coli chowing down on the citrate. The researchers found that when they put the bacteria in pure citrate, the microbes could thrive on it as their sole source of carbon.
To gauge the flukiness of the citrate-eaters, Blount and Lenski replayed evolution. They grew new populations from 12 time points in the 33,000-generations of pre-citrate-eating bacteria. They let the bacteria evolve for thousands of generations, monitoring them for any signs of citrate-eating. They then transferred the bacteria to Petri dishes with nothing but citrate to eat. All told, they tested 40 trillion cells.
The BacterioSphere
- Posted: 28.Dec.2008.
"So in a single drop of water the microscope discovers, what motions, what tumult, what wars, what pursuits, what stratagems, what a circle-dance of Death & Life, Death hunting Life & Life renewed and invigorated by Death … a many meaning cypher."
Bacteria are cults of interpretation not endless reprints of a few domesticated strands as if they were best-selling paperbacks. In the wild only a fraction of bacterial species can be cultured and the smallest working unit is the individual only in artificial situations of abundance. The biofilm, animalcule phalanxes immersed in self-brewed Bella Donna, is what the naturalist catalogues as the keystone organizational form of bacterial survival. The BacterioSphere is the microbial equivalent of the weather, a provisional collection of recognized formations to name by analogy what is mostly beyond direct observation. Shotgun sequencing reveals the diverse make-up of the biofilm, hints at its existence as an assortment of adaptive feedback loops but it leaves to the imagination the fierness of their independence and the intelligence of their strategies. When the bacteria are united they can never be divided: in their fight against death, bactericide by antibiotics or otherwise, the collective sculpts the bodies and programmes the behaviour of its constituent by direct excitation. Souls are rewritten by accepting and ejecting genetic shrapnel, this happens with such speed and with such variety of means and mechanisms that they change faster than our notion of a specie can accommodate for.
A bacterium is a system within a system, a wheel within a wheel. Hindu mythology in its effort to set a deity against every essential quality of the universe is a minor work in comparison to the pandemonium of niches inhabited by bacteria, from deep-sea thermal vents to magnetic fields to human probes orbiting outer space. Mutations are the background radiation of biology, a slow invisible random hand pushing species apart. This is in the textbooks and it means to say that an organism can only learn what it already knows, that the thinker/seer/hearer has no direct control over what it thinks/sees/hears. The bacteria jaywalk their way out of this fatalist dilemma by working magic. "They even..." are the bacteriologists most frequently overheard colloquial prefix. Yes: the applause thunders from the benches when 1) a colony under attack makes a heroic comeback by stealing the right bit of DNA from the poisonous other to synthesize the antidote 2) a bacterium targets specific regions of its structure to mutate with accelerated pace to provide creative solutions when they are needed most. 3) dished-in bacteria generate electricity, oil and insulin 4) a biofilm solves chess problems, performs logical operations and predicts future states of its environment. By holding on to its open-ended relationship with the world, by remaining a process instead of becoming a finished beast, by resisting purity, bacteria are able to create their own relevance by colonizing esoteric realities.
The savage simplicity of the bacteria is not a sign of its stupidity but a token of its long term commitment to survival. When looking at the tree of life in terms of creative ability it is clear that it is not the bacteria that are primitive; it are the branches 'above' them that are caged in an ancient, conservative, over-elaborate and fragile textual heritage. The lichen, that many-coloured plant-like coat of nothingness, that centrifugal furry Mandelbrot cloak spreading-out in search for a minimal splash of sunlight across otherwise lifeless mineral surfaces underscores the point that the vortex may be the ideal but that the bacterial condition is above strict obedience to even its own principles.
The chattering classes are fond of quoting big bacterial numbers like the following on their blogs: 500 different species of bacteria are to be found in any single human body, 100 trillion cells in all equalling 10% of our dry bodyweight, one kilogram of bacterial matter is in our gut alone, etc. etc. The numbers reiterate a position defended by one prominent student of the bug: "They are Us". Without the unacknowledged legislation of the bacteria, inside and outside us, there is no us. The animal kingdom, is a pareidoliac catastrophe, a by-product of the BacterioSphere. Let it be noted.
With the bacteria life has put its foot down: what the life force has woven into the bacteria, with the finest threads of gold it could find, is a complete disregard for superfluous possessions. Bacteria are an anarchic reticulating bulk of slime. They are composed out of bits of everything, as if the most talented Jura watchmaker found himself scratching an itch on an intergalactic nanotech scrapyard. They are as self-reliant as a mob of freshly ashore Russian sailors looking for a drink: they will get what they want in one way or another. Bacteria have past nor future. They are always brand new and forever close to their roots. As a superorganism they are obedient to the metaphor of the magic carpet only, and of course the starry-eyed have proposed sentience, speculating on the possibility of human-bacteria communication through an interface of chemico-poetic matrices. Cherish these thoughts with agnostic sympathy. Like Chinese is its own classic language, bacteria are their own ur-species. But while Chinese caved in to the flaky concessions of Pinyin and the foreign logic of the Qwerty-keyboard, the bacteria have remained high-spirited literati, loyal to the allusive rococo of Classic Mandarin. By taking life as it comes, by making sense of what is available, bacteria are able to arrive at bewildering solutions to the ever pressing problem of how to make the best of a hopeless situation on a beggars budget: every white coat has at least one story of bacteria thriving under conditions meant to kill them.
Bacterial ingenuity has written a new chapter to the book of the death: even on the brink of whispering last words the final call does not always come. The rock-hand-scissors motive stands as a parallel for those self-mummifying bacteria who outmanoeuvre death by transforming themselves into a metabolically suspended quasi-crystal: the endospore is the downward spiral that goes upwards, a tautological emergency exit into blissful oblivion or oblivious bliss or blissful obliviousness, an paradoxical ark that only prolonged boiling can sink. The formation of an endospore is the most monumental coup of evolution, a transformation of life into non-life. According to any meaningful definition or theory of life the endospore is death, but, of course, it is death with the snag of resurrection. Once environmental conditions favour normal living again the endospore return to life as if the last 6000 years never happened. Religions have been founded on less.
In short. Bacteria are vivid shorthand pictures of nature, the psychedelic spectrum analysis of what life can be, the Gordian knot that ties everything together, the near-immortal ideograms through which life creates its floating record of extreme imagination. Bacteria are a jubilant never-ending free verse without punch line.
Images: Screenshots of a self-written Mickey Mouse ecosystem.
- Posted: 28.Dec.2008.
"So in a single drop of water the microscope discovers, what motions, what tumult, what wars, what pursuits, what stratagems, what a circle-dance of Death & Life, Death hunting Life & Life renewed and invigorated by Death … a many meaning cypher."
- Samuel Taylor Coleridge
“It was as if Botany should reason from the leaf-patterns woven into our table-cloths ... Thought deals with no bloodless concepts but watches things move under its microscope”
- Ernest Fenollosa
We do not see things as they are,
we see them as we are.
- Anais Nin
Bacteria are cults of interpretation not endless reprints of a few domesticated strands as if they were best-selling paperbacks. In the wild only a fraction of bacterial species can be cultured and the smallest working unit is the individual only in artificial situations of abundance. The biofilm, animalcule phalanxes immersed in self-brewed Bella Donna, is what the naturalist catalogues as the keystone organizational form of bacterial survival. The BacterioSphere is the microbial equivalent of the weather, a provisional collection of recognized formations to name by analogy what is mostly beyond direct observation. Shotgun sequencing reveals the diverse make-up of the biofilm, hints at its existence as an assortment of adaptive feedback loops but it leaves to the imagination the fierness of their independence and the intelligence of their strategies. When the bacteria are united they can never be divided: in their fight against death, bactericide by antibiotics or otherwise, the collective sculpts the bodies and programmes the behaviour of its constituent by direct excitation. Souls are rewritten by accepting and ejecting genetic shrapnel, this happens with such speed and with such variety of means and mechanisms that they change faster than our notion of a specie can accommodate for.
A bacterium is a system within a system, a wheel within a wheel. Hindu mythology in its effort to set a deity against every essential quality of the universe is a minor work in comparison to the pandemonium of niches inhabited by bacteria, from deep-sea thermal vents to magnetic fields to human probes orbiting outer space. Mutations are the background radiation of biology, a slow invisible random hand pushing species apart. This is in the textbooks and it means to say that an organism can only learn what it already knows, that the thinker/seer/hearer has no direct control over what it thinks/sees/hears. The bacteria jaywalk their way out of this fatalist dilemma by working magic. "They even..." are the bacteriologists most frequently overheard colloquial prefix. Yes: the applause thunders from the benches when 1) a colony under attack makes a heroic comeback by stealing the right bit of DNA from the poisonous other to synthesize the antidote 2) a bacterium targets specific regions of its structure to mutate with accelerated pace to provide creative solutions when they are needed most. 3) dished-in bacteria generate electricity, oil and insulin 4) a biofilm solves chess problems, performs logical operations and predicts future states of its environment. By holding on to its open-ended relationship with the world, by remaining a process instead of becoming a finished beast, by resisting purity, bacteria are able to create their own relevance by colonizing esoteric realities.
The savage simplicity of the bacteria is not a sign of its stupidity but a token of its long term commitment to survival. When looking at the tree of life in terms of creative ability it is clear that it is not the bacteria that are primitive; it are the branches 'above' them that are caged in an ancient, conservative, over-elaborate and fragile textual heritage. The lichen, that many-coloured plant-like coat of nothingness, that centrifugal furry Mandelbrot cloak spreading-out in search for a minimal splash of sunlight across otherwise lifeless mineral surfaces underscores the point that the vortex may be the ideal but that the bacterial condition is above strict obedience to even its own principles.
The chattering classes are fond of quoting big bacterial numbers like the following on their blogs: 500 different species of bacteria are to be found in any single human body, 100 trillion cells in all equalling 10% of our dry bodyweight, one kilogram of bacterial matter is in our gut alone, etc. etc. The numbers reiterate a position defended by one prominent student of the bug: "They are Us". Without the unacknowledged legislation of the bacteria, inside and outside us, there is no us. The animal kingdom, is a pareidoliac catastrophe, a by-product of the BacterioSphere. Let it be noted.
With the bacteria life has put its foot down: what the life force has woven into the bacteria, with the finest threads of gold it could find, is a complete disregard for superfluous possessions. Bacteria are an anarchic reticulating bulk of slime. They are composed out of bits of everything, as if the most talented Jura watchmaker found himself scratching an itch on an intergalactic nanotech scrapyard. They are as self-reliant as a mob of freshly ashore Russian sailors looking for a drink: they will get what they want in one way or another. Bacteria have past nor future. They are always brand new and forever close to their roots. As a superorganism they are obedient to the metaphor of the magic carpet only, and of course the starry-eyed have proposed sentience, speculating on the possibility of human-bacteria communication through an interface of chemico-poetic matrices. Cherish these thoughts with agnostic sympathy. Like Chinese is its own classic language, bacteria are their own ur-species. But while Chinese caved in to the flaky concessions of Pinyin and the foreign logic of the Qwerty-keyboard, the bacteria have remained high-spirited literati, loyal to the allusive rococo of Classic Mandarin. By taking life as it comes, by making sense of what is available, bacteria are able to arrive at bewildering solutions to the ever pressing problem of how to make the best of a hopeless situation on a beggars budget: every white coat has at least one story of bacteria thriving under conditions meant to kill them.
Bacterial ingenuity has written a new chapter to the book of the death: even on the brink of whispering last words the final call does not always come. The rock-hand-scissors motive stands as a parallel for those self-mummifying bacteria who outmanoeuvre death by transforming themselves into a metabolically suspended quasi-crystal: the endospore is the downward spiral that goes upwards, a tautological emergency exit into blissful oblivion or oblivious bliss or blissful obliviousness, an paradoxical ark that only prolonged boiling can sink. The formation of an endospore is the most monumental coup of evolution, a transformation of life into non-life. According to any meaningful definition or theory of life the endospore is death, but, of course, it is death with the snag of resurrection. Once environmental conditions favour normal living again the endospore return to life as if the last 6000 years never happened. Religions have been founded on less.
In short. Bacteria are vivid shorthand pictures of nature, the psychedelic spectrum analysis of what life can be, the Gordian knot that ties everything together, the near-immortal ideograms through which life creates its floating record of extreme imagination. Bacteria are a jubilant never-ending free verse without punch line.
Images: Screenshots of a self-written Mickey Mouse ecosystem.
Crystal Evolution
- Posted: 02.Dec.2008.
Rocks Evolve!!
- Posted: 02.Dec.2008.
Rocks Evolve!!
Over 1,500 minerals are thought to have formed on Earth before the beginnings of life some four billion years ago. Obviously, minerals do not have genes and thus cannot mutate as living things do. Nevertheless, when life appeared, the evolution of minerals and the diversity of life became entwined.
Microscopic algae, the earliest living organisms, drew carbon dioxide from the atmosphere and expelled oxygen. Over millions of years this created an oxygen-rich atmosphere that rapidly removed electrons from minerals near the surface, creating rust out of iron and forming thousands of new minerals from other metals like nickel, copper and uranium.
Living Stones:
In the oceans, as animals with hard parts evolved, their bodies mineralised shells and skeletons for protection and support. Corals too started combining the calcium and carbonate that was floating freely in the water to construct reefs. All of the materials that animals made started to litter the sea floor and this vast accumulation of bone, shell and coral got pressed together into a mineral known as calcite.
On the land, plants produced acids around their roots that converted minerals of volcanic origin, like mica, feldspar and pyroxene, into clay minerals that ultimately formed intensely rich soils. This explains why volcanic islands like Hawaii are so lush.
New minerals created by living things continue to turn up. One of the most recent discoveries was by Hexiong Yang, who named it Hazenite as a tribute to Dr Hazen, his former teacher. Hazenite is a mineral formed by microbes in the highly alkaline Mono Lake in California.
Bacterial Mats
- Posted: 10.Nov.2008.
(Click for full size)
A bacterial mat is a layer of bacteria that may form in environments where other organisms are unable to thrive. Their fossilized forms are works of art.
- Posted: 10.Nov.2008.
(Click for full size)
A bacterial mat is a layer of bacteria that may form in environments where other organisms are unable to thrive. Their fossilized forms are works of art.
We do not see
- Posted: 19.Sep.2008.
We do not see things as they are,
we see them as we are.
Anais Nin
- Posted: 19.Sep.2008.
We do not see things as they are,
we see them as we are.
Anais Nin
Subcultured Mycelium
- Posted: 13.Jul.2009.
Paul Stamets, author of Mycelium Running in an interview with Derrick Jensen:
- Posted: 13.Jul.2009.
Paul Stamets, author of Mycelium Running in an interview with Derrick Jensen:
Jensen: In your book you say that animals are more closely related to fungi than they are to plants or protozoa or bacteria.
Stamets: Yes. For example, we inhale oxygen and exhale carbon dioxide; so do fungi. One of the big differences between animals and fungi is that animals have their stomachs on the inside. About 600 million years ago, the branch of fungi leading to animals evolved to capture nutrients by surrounding their food with cellular sacs — essentially primitive stomachs. As these organisms evolved, they developed outer layers of cells — skins, basically — to prevent moisture loss and as a barrier against infection. Their stomachs were confined within the skin. These were the earliest animals.
Mycelia took a different evolutionary path, going underground and forming a network of interwoven chains of cells, a vast food web upon which life flourished. These fungi paved the way for plants and animals. They munched rocks, producing enzymes and acids that could pull out calcium, magnesium, iron, and other minerals. In the process they converted rocks into usable foods for other species. And they still do this, of course.
Fungi are fundamental to life on earth. They are ancient, they are widespread, and they have formed partnerships with many other species. We know from the fossil record that evolution on this planet has largely been steered by two cataclysmic asteroid impacts. The first was 250 million years ago. The earth became shrouded in dust. Sunlight was cut off, and in the darkness, massive plant communities died. More than 90 percent of species disappeared. And fungi inherited the earth. Organisms that paired with fungi through natural selection were rewarded. Then the skies cleared, and light came back, and evolution continued on its course until 65 million years ago, bam! It happened again. We were hit by another asteroid, and there were more massive extinctions. That’s when the dinosaurs died out. Again, organisms that paired with fungi were rewarded. So these asteroid impacts steered life toward symbiosis with fungi: not just plants and animals, but bacteria and viruses, as well.
Jensen: Can you give some examples of these partnerships?
Stamets: A familiar one is lichens, which are actually a fungus and an alga growing symbiotically together. Another is “sleepy grass”: Mesoamerican ranchers realized that when their horses ate a certain type of grass, the horses basically got stoned. When scientists studied sleepy grass, they found that it wasn’t the grass at all that was causing the horses to get stoned, but an endophytic fungus, meaning one that grows within a plant, in the stems and leaves.
Nano Wires
- Posted: 20.Jun.2009.
See this bacterial colony engineering gossamer filaments of nanowire as a power-grid protruding outwards.
- Posted: 20.Jun.2009.
See this bacterial colony engineering gossamer filaments of nanowire as a power-grid protruding outwards.
Microbial Art Climatology
- Posted: 21.May.2007.
Wim van Egmond is a fellow countrymen and a fellow surveyer of the BacterioPoetic. One of his projects is the 'microbial art climatological analysis' :
Excellent!
- Posted: 21.May.2007.
Wim van Egmond is a fellow countrymen and a fellow surveyer of the BacterioPoetic. One of his projects is the 'microbial art climatological analysis' :
The practice of microbial art climatology starts with immersing (a sample of) the art works (submergence) in an environment with a lot of micro-organisms (ditchwater). Micro-organisms will settle in and on the art works in great numbers and by doing so provide the key to the microbial art climatological analysis. In the end, the quality of the art work is determined by the type of organism that it attracts [...] Determination is the most essential part of the microbial art climatology. It needs to be carried out with the utmost precision. If you cannot distinguish a Ciliate from a Gastrotrich you will certainly not be able to tell a good 'hard edge' from a mediocre 'colourfield painting'. An incorrect determination can cause a lot of damage to both museum and- private collections. Eventually, it might disrupt our overall view of the course of art history. The art climatologist should assume full responsibility for his determination. [...]
Excellent!
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