Archive for the 'Molecular biology' Category

December 28, 2016

“Algorithmic thinking as a novel and productive point of view for understanding and transforming the sciences, started probably with Turing. Natural phenomena in many scientific fields (including mathematics, statistics, physics, astronomy, biology and economics) are intrinsically computational in nature: examples include chemical processes in living cells, the self-organizing behavior of complex systems consisting of many interacting particles, mechanisms governing human evolution, and the collective behavior of competing agents in an economy. These natural science areas should be explored through a computational lens.”

December 28, 2016


“Life is not governed by will or intention. Life is a question of nerves, and fibres, and slowly built-up cells in which thought hides itself and passion has its dreams.” ~ Wilde

December 26, 2016

[…] “compared by Baudelaire to a “deep and dark mirror”, Leonardo seduces us by his hermeticism, his strangeness.”

“This Leda no more appeals to the delirium of the senses than the Mona Lisa does; it speaks of the obscure mechanism of childbirth, of genetic aberration, of the imperious and primitive surge of life in the depths of the body and the entrails of the earth. Some critics admit to finding the contents of this work terrifying. Looking at it, one senses only too well the transcendence of science: one feels how the painter, in conceiving his picture, had studied the relentless growth of plants, whirlpools of water, and abdomens dissected by flickering candlelight: One grasps above all the fascination, unease, and irrational anguish aroused by the “hideous” idea of procreation and the “great mystery” of woman. … With its idolatrous and tormented naturalism, the painting outraged not so much virtue as Christian reason.”

“His figures are not smiling the smile of inner peace. They are smiling in order to bewitch. … Leonardo sets out to disturb and trouble the emotions. … His subject has ceased to be “a voice crying in the wilderness”. He has reached the ultimate limits of human knowledge; he smiles and points at the source of everything, which amazes him but which is unfathomable.”

~ “Leonardo. The artist and the man”, Serge Bramly.

December 26, 2016
“Von Neumann e Wiener condividevano un interesse appassionato per la biologia. Entrambi vedevano in una comprensione piu’ approfondita della biologia il fine ultimo delle loro esplorazioni della scienza del computer e dell’informazione.”
~ “Lo scienziato come ribelle”, Dyson.

October 18, 2012

Yeast has only around 200–300 transcription factors to regulate its complex regulatory function — from budding to the cell cycle to selectively metabolizing dozens of different energy sources. This relatively small number of TFs orchestrates the regulation of thousands of genes to achieve innumerable phenotypic responses.

September 22, 2012

« Some suggestions for people in the “complex” living systems field. Think of the forgotten dimensions of the cell (all of them related to structure), which are beyond the world of nucleic acids, which have their own code, and whose information content is orders of magnitude greater than nucleic acids. A single cell can drive cancer to the very last step on the road to the death of a person, in three days, solely by the admirable organization of such dimensions. The main question must be: how is the cell organized? The answer will not come from a molecule, nor from a sequence, but from a vision. »
~ Walter Schubert

January 4, 2012

« Besides being a tight place, a cell is also a crowdy environment whose participants are for the most part invisible at the sequence level. Often they are not even known or are only partially understood. »
~ “On motifs in biological sequences”, M-F Sagot.


November 27, 2011

« The endosymbiont hypothesis has been refined in two major ways. First, as it became increasingly apparent (especially for mitochondria) that many organellar functions are encoded in the nucleus, it was assumed that these nuclear genes had been relocated to the nucleus by lateral transfer from the organellar genome (a reason why some genes have remained in the organelle is then needed). Second, 16S rRNA phylogenies also required that, at least for chloroplasts, existing organelles are descended not from one endosymbiont but from several which invaded different lineages at different times. A central unresolved problem concerns whether mitochondrial evolution is monophyletic or polyphyletic. Moreover, there is substantial evidence for secondary loss of the mitochondrion from various protists, in which several well identified mitochondrial genes are found in the nuclear chromosomes. Multiple independent losses and gains of genes (and of full mitochondria and chloroplasts) is probably the norm. »

« The dinucleotide relative abundance values of temperate double-stranded DNA phages are very close to their hosts, filamentous and single-stranded DNA phages are moderately to distantly related to their hosts, and lytic double-stranded DNA phages are generally distant from their hosts, with phage T7 being substantially farther than phage T4. This gradient in similarity to the host parallels the extent to which the phage uses the complete replication and repair machinery of the host and the duration of such use. »

~ “Compositional biases of bacterial genomes and evolutionary implications”. S. Karlin, J. Mrazek, A.M. Campbell. Journal of Bacteriology, Vol. 179, No. 12, 1997.

November 12, 2011

« Many who draw a distinction between bioinformatics and computational biology portray the former as a tool kit and the latter as science. All would allow that the science informs the tools and the tools enable the science; in any case, bioinformatics and computational biology are near enough cousins that their origins and early influences are likely to be commingled as well. Therefore […] [we] will construe bioinformatics broadly, bearing in mind it can thus be expected to have a dual nature. This duality echoes another that goes back to Aristotle, between “episteme” (knowledge, especially scientific) and “techne” (know-how, in the sense of craft or technology). The power of bioinformatics might be seen as arising from their harmonious combination, in the Greek tradition, lending it emergent capabilities beyond the simple intersection of computers and biology, or indeed of science and engineering. »

« Gamow’s remarkable letter [to Watson and Crick] reimagined the DNA in each chromosome as a long number written in base four, so as to open up its analysis to number theory. He was soon calling this “the number of the beast”, suggesting that it varied only slightly among individuals, “whereas the numbers representing the members of two different species must show larger differences”. Not only did Gamow thus neatly frame the future of sequence bioinformatics, but he went on to pose the question of the genetic code for the first time in purely formal terms — that is, in Crick’s words, “not cluttered up with a lot of unnecessary chemical details”. »

« […] Theoretical computer scientists who first encountered biology sometimes seemed less interested in nature than in citing motivating examples for string algorithms or combinatoric problems with little regard for their practical application. »

~ “The roots of bioinformatics”, D.B. Searls. PLOS Computational Biology, 2010.

October 30, 2011

The PA protein in the anthrax toxin changes 3D structure 3 times during its normal function.