Keep time to music: also Bonobos stay on beat!

Some animals, like humans, can sense and respond to a musical beat, a finding that has implications for understanding how the skill evolved.
A study of bonobos (Species P. paniscus), closely related to chimpanzees, shows they have an innate ability to match tempo and synchronise a beat with human experimenters. Bonobos are very attuned to sound. They hear above our range of hearing.

For the study, researchers designed a highly resonate, bonobo-friendly drum able to withstand 500 pounds of jumping pressure, chewing, and other ape-like behaviours.
Scientists suspect that the musical and rhythmic abilities of humans evolved to strengthen social bonds, "so, one might think that a common ancestor to humans and the bonobo would have some of these capabilities," said Patricia Gray a biomusic program director at University of North Carolina in Greensboro.

Working with a group of language-competent bonobos at the Great Ape of Trust of Iowa, several whom have recorded with Peter Gabriel and Paul McCartney, and compose melodies using synthesizers, and in collaboration with renowned scientist, Dr. Savage-Rumbaugh, the research focuses on both empirical and theoretical inquiries in music cognition and perception, origins of culture, and theory of mind.
Experimenters beat a drum at a tempo favored by bonobos roughly 280 beats per minute, or the cadence that humans speak syllables.
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Microbial Bebop: Creating Music from Complex Dynamics in Microbial Ecology

Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, Peter Larsen  and Jack Gilbert, generated Microbial Bebop  (described in this paper), a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. They used a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented in their work can be applied to a wide variety of complex biological datasets.

For implementation of rectifying melody to harmony, they used the freely available jazz improvisation program ‘ImproVisor’ a free open-source software from Harvey Mudd College Computer Science Department.

Those are the songs:

• Blues for Elle: This composition highlights seasonal patterns in marine physical parameters at the L4 Station. The chords are generated from seasonal changes in photosynthetically active radiation. The melody of each measure is comprised of eight notes, each mapped to a physical environmental parameter, in the following order: temperature, soluble reactive phosphate, nitrate, nitrite, saline, silicate, and chlorophyll A concentrations.
• Bloom: Some marine microbial taxa are most often present in the L4 Station community at very low abundance, but occasionally become highly dominant community members. To link these microbial blooms to relevant physical parameters, the chords in this composition are derived from changes in chlorophyll A concentrations and salinity. The melody for each measure is derived from the relative abundances of typically rare taxa that were observed to occasionally bloom to higher abundance in the following order: Cyanobacteria, Vibrionales, Opitulates, Pseudomondales, Rhizobiales, Bacillales, Oceanospirallales, and Sphingomonadales.
• Far and Wide: Microbial species of the Order Rickettsiales, such as the highly abundant, free-living planktonic species Pelagibacter ubique, are typically, highly abundant taxa in L4 Station data. Its relative abundance in the microbial community at L4 Station follows a distinctive seasonal pattern. In this composition, there are two chords per measure, generated from photosynthetically active radiation measurements and temperature. The melody of each measure is six notes that describe the relative abundance of the Order Rickettsiales  The first note of each measure is from the relative abundance at a time point. The next five notes of a measure follow one of the following patterns: a continuous rise in pitch, a continuous drop in pitch, a rise then drop in pitch, or a drop then rise in pitch. These patterns are matched to the relative abundance of Rickettsiales at the given time point, relative to the previous and subsequent time points. The pattern of notes in a measure is mapped to the relative abundance of Rickettsiales with fewer rests per measure indicating higher abundance. For time points at which Rickettsiales was the most abundant microbial taxa, the corresponding measure is highlighted with a cymbal crash.
• Fifty Degrees North, Four Degrees West: All of the data in this composition derives from twelve observed time points collected at monthly intervals at the L4 Station during 2007. The composition is composed of seven choruses. Each chorus has the same chord progression of 12 measures each in which chords are derived from monthly measures of temperature and chlorophyll A concentrations. The first and last chorus melodies are environmental parameter data as in ‘Blues for Elle’. The melody in each of the second through sixth chorus is generated from the relative abundances of one of the five most common microbial taxa: Rickettsiales  Rhodobacterales, Flavobacteriales, Cyanobacteria, and Pseudomonadales. A different ‘instrument’ is used to represent each microbial taxon. Melodies for microbial taxa were generated as in ‘Far and Wide’.

 
Enjoy the sound of nature!

The Genoma Music Project

Both genetic and musical sequences are ordered structures composed of combinations of a small number of elements, of nucleotides and musical notes. In the case of the genome, the emergence of cellular functions makes the order meaningful; in the case of musical sequences, the consequence of order is the pro- duction of mysterious esthetical effects in the human mind. Can any musical significance be found in DNA sequence? In this work Aurora Sánchez Sousa, Fernando Baquero and Cesar Nombela present the technique used to convert DNA sequences into musical sequences. The musical equivalent of the sequence of a number of genes, either of fungal origin, such as Candida albicans or Sacharomyces cerevisiae, or belonging to the human genome (genes involved in Alzheimer syndrome, blindness, and deafness such as Connexine 26 gene) has been obtained. Non-coding sequences are also important in life and music. The non-coding alphoid sequence has also been translated into a musical sequence, in this case using Fibonacci ́s golden number basic series as structural helper. The elementary musical sequence derived from DNA sequence has served as an imposing frame in which rhythms, sounds, and melodies have been harmonically inserted. The “Genoma Music” Project is essentially a creative metaphor of the basic unity between the human mind and the natural ordered structure of life. (Read the PDF)

On the way to Synthetic Life

Less than two years ago at the Craig J Venter Institute, the homonymus founder of the Center, announced to the World that Synthia, the first synthetic organism, was created into their labs.

Of course, this event got a lot of visibility from the mass media all around the World, since the humankind has never achieved this big step that put it in a market until now just businnes of one actor: God.

But let's analyze with more attention what the Craig Venter's band really performed and, for doing this, we just begin with the initial part of the press conference he gave in the june of the 2010:

"We're here today to announce the first synthetic cell, a cell made by starting with the digital code in the computer, building the chromosome from four bottles of chemicals, assembling that chromosome in yeast, transplanting it into a recipient bacterial cell and transforming that cell into a new bacterial species. So this is the first self-replicating species that we've had on the planet whose parent is a computer. It also is the first species to have its own website encoded in its genetic code."

Hence, they have started to design the primary sequence of the future Synthia genome in the computer and in this step there is a very important key of reading of the overall procedure. In fact the researchers at the Venter Institute for their synthetic organism have mimed the genetic information of one natural bacterium M. mycoides. This is the blueprint of Synthia is always a natural-one and it was shaped from natural selection since millions of years.  So its real parent is not a computer at all and to avoid any kind of mislead we should talk of semi-synthetic life...

By the way the Venter's group performed a minimization of the M. mycoides genome by the knock-out of dispensable genes (about 100 over 485 genes) in order to obtain a bacterial with the smallest set of genes of any known organism capable of indipendent grow in lab (Wow!).

 The second challenging step was to assembly the (semi-)synthetic chromosome in yeast and without any doubts in the semantic field this  rapresents a very innovative and elegant procedure

They than performed the biggest cloning ever made  assembling a very huge DNA string (1.08 Mkb!!!) by combination of in vitro enzymatic methods and in vivo recombination in Saccharomyces cerevisiae.

Schematic experimental procedure

Once accomplished the production of the (semi-)synthetic chromosome of M. mycoides JCVI-syn1.0,  the construct was transfered in another bacterium,  M. capricolum, which acted as recipient. 

What does it mean? From a technical point if view it means that the assembled new chromosome were moved into the membrane-boundary of another bacterium deprived of own-genome, in order to get  M. mycoides JCVI-syn1.0 in the condition to start to be alive. But at the same time this means, again, that maybe could be much more intellectually correct talking about semi-synthetic...

Anyway the achivements of this controversial biologist and his group is a millestone in the road toward the real synthetic era (thanks to the people as Craig Venter not so far from now), when we will able to program in front of a computer the desiderable traits of an organism and gain from their inimaginable potential.

Follow the Chain Reaction

Before the PCR (Polymerase Chain Reaction) the life for a biologist was so hard.

We can just imagine the way of dealing of a resercher before start an experiment with the few picomoles of DNA (10 to minus 12 mole of DNA)...scare and anxiety of loosing the precious sample maybe fruit of the previous weeks of work.

But fortunatly, one evening in the spring 1983, the breakthrough appeared.

Kary Mullis, a chemist working at that time for a private company, was driving his Honda from San Francisco to Mendocino, with his girlfriend and collegue, in order to enjoy a cabin week-end. In the meanwhile he is completely immersed in his thoughts about some experimental tricks that always tormented the lame life of a researchers, when... .

"But... wait a moment... not it is no possible... maybe someone already tried something similar... but I have never heard something about it before..."

Suddenly his mind was involved in the flux of brain that will revolutionized the way to do molecular biology,  biochemistry and medicine. And of course which will bring him to Stockholm.

In fact in this car, Kary Mullis started to figure out the PCR, a molecular reaction inspired to what happen normally in Nature, that allows to the todays researcher to count on a major amount of DNA for their lab routine and to start to perform all of series of different researches (Genomic Sequencing, DNA Cloning, Synthetic Biology, ecc.) inaccesible before the introduction of PCR.

The key aspect of the PCR reaction is the simplicity and the rapidity for the production of consistent quantity of DNA. It is based on cycles of temperatures alternation and on the use of an enzyme able to retain an activity in those temperature sudden jumps.  And of course Nature already knew a good guy for this job: the DNA Polymerase of Thermophilus aquaticus.  In fact this bacterium can live at high temperature and consequently also its molecular machine retains activity at such temperatures.

So, after performing  twenty or more cycles of PCR you can achieve the exponential amplification of your initial DNA sample with the possibility of carry out a series of investigations inimmaginable before!

Ok, everything sounds like a weird discovery made by a weird lab rat.

But the whole image of Kary Mullis get in another frame when we consider his biography-like best seller, Dancing naked in the mind fild.

The Nobel Prize Kary Mullis ready to surf some nice waves

In this book, Mullis explores all the Science panorama, from the climatic change to the AIDS, from the neurobiology to the biotechnology until dealing with some borderline scientific issues, as the extraterrestrial life and the telephaty. Everything dressed with some LSD experiences and surf session that make the all story much more catchy and intriguer.

Hence,  the first post of this new scientific blog by Bamboo Prodution is dedicated to Kary Mullis, a scientist which made possible the last shift of paradigm, at least from a technical point of view, in the Life Science and which with his extravagance deserves one of the honorous citizenship of ScientiaBilly community!

And at the same time such post is in honour of PCR it-self, which makes our everydays lab life not so shitty as it could have been without this  mix of oligos, nucleotides , salt and enzyme!

P.S.: Enjoy, but could be very hard, our music playlist about Chain Reaction!