at the post-transcriptional level. Stem cells express specific pro-
files of miRNAs that, in turn, can alter the cells’ differentiation
potential. As for epigenetics, the stemness state of a cell appears
to be correlated with its chromatin organization state and
epigenetic modifications.References
- Morange M (1998) A history of molecular
biology. Harvard University Press, Cambridge,
MA - Rheinberger H-J (2007) What happened to
molecular biology? BIF Futura 22:218–223 - Weinberg RA (2014) Coming full circle-from
endless complexity to simplicity and back
again. Cell 157(1):267–271.https://doi.org/
10.1016/j.cell.2014.03.004 - Darden L (2006) Reasoning in biological dis-
coveries. Cambridge University Press, Cam-
bridge, UK - Bechtel W, Richardson R (2010) Discovering
complexity - decomposition and localization as
strategies in scientific research. The MIT Press,
Cambridge, MA - Nicholson DJ (2010) Biological atomism and
cell theory. Stud Hist Philos Biol Biomed Sci
41(3):202–211. https://doi.org/10.1016/j.
shpsc.2010.07.009 - Garraway LA, Lander ES (2013) Lessons from
the cancer genome. Cell 153(1):17–37.
https://doi.org/10.1016/j.cell.2013.03.002 - Vogelstein B, Papadopoulos N, Velculescu VE,
Zhou S, Diaz LA, Kinzler KW (2013) Cancer
genome landscapes. Science (New York, NY)
339(6127):1546–1558. https://doi.org/10.
1126/science.1235122 - Bizzarri M, Cucina A (2016) SMT and TOFT:
why and how they are opposite and incompati-
ble paradigms. Acta Biotheor 64(3):221–239.
https://doi.org/10.1007/s10441-016-9281-
4 - Nicholson DJ (2012) The concept of mecha-
nism in biology. Stud Hist Philos Biol Biomed
Sci 43(1):152–163. https://doi.org/10.
1016/j.shpsc.2011.05.014 - Bizzarri M, Palombo A, Cucina A (2013) The-
oretical aspects of systems biology. Prog Bio-
phys Mol Biol 112(1–2):33–43.https://doi.
org/10.1016/j.pbiomolbio.2013.03.019 - Bertolaso M (2016) Philosophy of cancer: a
dynamic and relational view. Springer,
New York - Esfeld M (2003) Do relations require underly-
ing intrinsic properties?—a physical argument
for a metaphysics of relations. Metaphysica 4
(1):5–25- Boem F, Ratti E, Andreoletti M, Boniolo G
(2016) Why genes are like lemons. Stud Hist
Philos Biol Biomed Sci 57:88–95.https://doi.
org/10.1016/j.shpsc.2016.04.005 - Baraba ́si A-L, Oltvai ZN (2004) Network biol-
ogy: understanding the cell’s functional orga-
nization. Nat Rev Genetics 5(2):101–113.
https://doi.org/10.1038/nrg1272 - Wolff J (2011) Do objects depend on struc-
tures? Br J Philos Sci 63(3):607–625.https://
doi.org/10.1093/bjps/axr041 - Craver CF (2016) The explanatory power of
network models. Philos Sci 83(5):698–709 - Palumbo MC et al (2005) Functional essenti-
ality from topology features in metabolic net-
works: a case study in yeast. FEBS Lett 579
(21):4642–4646 - Palumbo MC et al (2007) Essentiality is an
emergent property of metabolic network
wiring. FEBS Lett 581(13):2485–2489 - Bertolaso M, Giuliani A, Filippi S (2013) The
mesoscopic level and its epistemological rele-
vance in systems biology, Recent advances in
systems biology. Nova Science Publishers, Inc.,
New York, pp 19–36 - Giuliani A (2010) Collective motions and spe-
cific effectors: a statistical mechanics perspec-
tive on biological regulation. BMC Genomics
11(Suppl 1):S2 - Bissell MJ, Hall HG, Parry G (1982) How does
the extracellular matrix direct gene expression?
J Theor Biol 99(1):31–68 - Bissell MJ et al (2002) The organizing princi-
ple: microenvironmental influences in the nor-
mal and malignant breast. Differentiation 70
(9–10):537–546 - Correia AL, Bissell MJ (2012) The tumor
microenvironment is a dominant force in mul-
tidrug resistance. Drug Resist Updat 15
(1–2):39–49 - Boogerd FC et al (2005) Emergence and its
place in nature: a case study of biochemical
networks. Synthese 145(1):131–164
12 Marta Bertolaso and Emanuele Ratti