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“The arrow of time”, as it was first introduced by Eddington [Eddington, 1928], is one of the mysteries of the physical world. While all fundamental physical processes are described as reversible (time-symmetric), unidirectional time obviously “appears somewhere” in the world [Prigogine, 1997] and needs to be understood. The puzzle of this origin-of-irreversibility occupied great scientists for more than a century [Boltzmann, 1896; Poincare, 1921], and became (modernly) understandable only in XX century [Prigogine, 1997]. Another mystery is the contradiction between the “arrows of time” in physics (as given by the II law of thermodynamics) and embryology. The “physical arrow of time” is directed “from complex to simple”, “from order to chaos”. The “embryological arrow of time” is associated with emergence of amazing structures (morphogenesis) and gene expression patterns (determination and differentiation). Thus it is directed from relatively “simple” zygote to a stunningly complex organism. What is the nature of this contradiction? According to the present-day physics, the time-asymmetry appears in systems with unstable dynamics, and can thus point both to “chaotization” and to emergence of new structures depending on the remoteness from equilibrium and the feedback system. The actual “web of life” [Capra, 1997] – the system of molecular and mechanical interactions lying behind the embryo development – is becoming more and more understandable right these years. Here we summarize the present data on mammalian embryo self-organization: emergence of the first differences between blastomeres [Bruce et al., 2010; Wennekamp, 2013], “cell fate decisions” and plasticity [Bedzhov et al., 2014; Artus, 2014], formation of amnion and yolk sack [Deglincerti, 2016; Shahbazi, 2016]. We then discuss all this in the context of the symmetry theory and the self-organization theory [Beloussov, 2015]. The “dual role” of the II law of thermodynamics [Prigogine, Stengers, 1993] – “chaotization” on the one hand and self-organization on the other hand, manifests in two types of biological processes: structurally-stable developmental paths (chreods) [Waddington, 1957] and variable quazi-stochastic patterns in the time of the “cell-fate decisions” [Dietrich, Hieragi, 2007; Plusa et al., 2008] and key morphodynamical processes [Beloussov, 2015; Maitre, 2016].