First draft of The Deal.

bib/dealb.bib

@@ -296,3 +296,51 @@ keywords = {Boolean P systems, Boolean networks, Reachability, Complexity},
   bibsource =	 {dblp computer science bibliography,
                   https://dblp.org}
 }
+
+@article{BjornbergKGH2017,
+  title =	 {Climate and environmental science denial: A review
+                  of the scientific literature published in 1990–2015},
+  journal =	 {Journal of Cleaner Production},
+  volume =	 167,
+  pages =	 {229--241},
+  year =	 2017,
+  issn =	 {0959-6526},
+  doi =		 {https://doi.org/10.1016/j.jclepro.2017.08.066},
+  url =
+                  {https://www.sciencedirect.com/science/article/pii/S0959652617317821},
+  author =	 {Karin Edvardsson Björnberg and Mikael Karlsson and
+                  Michael Gilek and Sven Ove Hansson}
+}
+
+@article{ONeillB2010,
+  author =	 {Saffron J. O’Neill and Max Boykoffb},
+  title =	 {Climate denier, skeptic, or contrarian?},
+  journal =	 {Proceedings of the National Academy of Sciences of
+                  the United States of America},
+  volume =	 {107(39):E151},
+  doi =		 {doi:10.1073/pnas.1010507107},
+  year =	 {2010}
+}
+
+@misc{wikiClimate,
+  author =	 "{Wikipedia contributors}",
+  title =	 "Climate change --- {Wikipedia}{,} The Free
+                  Encyclopedia",
+  year =	 "2024",
+  howpublished =
+                  "\url{https://en.wikipedia.org/w/index.php?title=Climate_change&oldid=1210314463}",
+  note =	 "[Online; accessed 26-February-2024]"
+}
+
+@book{DryzekNS2011,
+  author =	 {Dryzek, John S. and Norgaard, Richard B. and
+                  Schlosberg, David},
+  title =	 "{The Oxford Handbook of Climate Change and Society}",
+  publisher =	 {Oxford University Press},
+  year =	 {2011},
+  month =	 {08},
+  isbn =	 {9780199566600},
+  doi =		 {10.1093/oxfordhb/9780199566600.001.0001},
+  url =
+                  {https://doi.org/10.1093/oxfordhb/9780199566600.001.0001},
+}

deal.tex

@@ -326,7 +326,7 @@ the cytoskeletal track it is attached to
   \label{fig:ratchet-motor}
 \end{figure}
 
-\section{A Deal: Mutually beneficial interactions}
+\section{The Deal: Mutually beneficial interactions}
 \label{sec:deals}
 
 Seeing Life as an ensemble of machines biases how we expect to collect
@@ -347,12 +347,119 @@ asymmetric relationship between the controller and the controlled,
 which is unnatural biological context because both the controller and
 the controlled are made out of the same kind of matter, and are
 ultimately embedded in the same environment.
-of a Deal with Life is to render the interactions \emph{mutually
+
-  beneficial}: ideally, both systems engaging in the interaction
+This chapter outlines a conceptual framework putting symmetry back
-should benefit from it.  In practice, this should be translated into
+into the picture, \emph{the Deal with Life}: instead of
-joint maximization of a pair of functions measuring the utility of the
+surreptitiously lifting the human above and out of the living matter
-interaction for both parties, possibly with one of the two functions
+by self-designating ourselves as superior Engineers, I propose to
-being prioritized over the other.
+account for the fact that we act \emph{within} Life and its complex
+feedback loops by looking to organize \emph{mutually beneficial
+  interactions} with the living systems, as opposed to trying to
+control, hack, or engineer them.  Since we are talking about the
+general mindset, the choice of words in not contingent: controlling,
+hacking, and engineering impose a vertical power relationship, while
+thinking in terms of mutual benefit admits that our target system has
+a trajectory of its own, which we would like to preserve it to some
+degree.  Playing with words and summarizing the control-hack-engineer
+mindset as ``We control, Life obeys'' makes the power imbalance even
+more striking.
+
+Today, the most obvious inspiration for considering mutual benefit
+comes from the climate crisis: for centuries, we have acted on the
+environment expecting it to behave like a heat bath, i.e., to absorb
+whatever we throw at it without essentially changing its state.
+Besides brandishing a certain naïveté, this point of view is so
+difficult to abandon that is has become the epitome of science denial
+according to certain studies,
+e.g.~\cite{BjornbergKGH2017,ONeillB2010,wikiClimate}, as well
+as~\cite[page~155]{DryzekNS2011}.  As these references and multiple
+others show, refusing to admit human cause as central to the climate
+crisis has been invariably and strongly supported by the fossil fuel
+industry. I suspect nevertheless that one of the reasons for the
+resilience of the denialist mindset is the deeply anchored feeling
+that we are engineers and the environment a mere tool.  My own
+inspiration for the Deal with Life comes from theoretical biology
+discussions with Nicolas \textsc{Glade} at the TIMC lab in
+Grenoble\footnote{\url{https://www.timc.fr/}}, and specifically from
+the remarks outlined in Section~\ref{sec:mechanicism} above concerning
+the dominance of the engineering mindset in modern biology, especially
+in molecular biology, and the ruts it forces our thinking in.
+
+Thinking about mutual benefit in dealing with Life unpacks multiple
+different levels of caring about the destiny of the system of
+interest:
+\begin{itemize}
+\item \emph{Level 0}: This is the Engineer's mindset: fundamental
+  reductionism and mechanicism---we control, Life obeys.  At this
+  level, we do not conceive of any kind of benefit to the
+  target system.
+\item \emph{Level 1}: We aim to preserve the destiny of the target
+  system to a certain degree.  If it is a yeast population, we may
+  want to not allow its size below a certain threshold, or if it is
+  a farm animal, we may want to ensure a certain quality of life
+  according to a set of measures.
+\item \emph{Level 2}: We aim to benefit the target system to a certain
+  degree, while also extracting our own profit from the interaction.
+  In the case of a farm animal, we may want to ensure that its the
+  state of well-being be \emph{improved} in the context of its
+  interaction with respect to a life without any human intervention.
+\end{itemize}
+
+All three levels of this hierarchy of mutual benefit are in fact
+already present in our interactions with living organisms.
+Respecting Level 1 is almost ubiquitously needed, since otherwise we
+may kill the system of interest before it is capable of producing the
+deliverable we are after.  Level~2 manifests itself to different
+degrees in interactions with domesticated animals, especially in the
+context of increased awareness of the conditions to which livestock
+are typically treated in modern agriculture.  Levels 1 and 2 are also
+progressively making their way to prominence in dealing with
+ecosystems: cutting down forests brings about various kinds of
+catastrophes, so it is now laudable to curb deforestation, and even to
+conduct reforestation campaigns.
+
+It would seem on the other hand that biomedical research is stubbornly
+fond of ignoring Levels~1 and 2, and instead focuses on proudly
+brandishing the Engineer's Level 0, claiming that if something does
+not work out today, it will certainly work out tomorrow, provided that
+tomorrow brings around more energy, more computing power, more
+workforce, more data.  Yet again, in no way do I aim to deny or
+minimize the benefits of mechanicism and reductionism in
+biology---which has been instrumental in multiple groundbreaking
+achievements over the 20th century and beyond.  I insist nevertheless
+that exclusively sticking to Level 0 of the hierarchy of mutual
+benefit is a fundamental limitation of thought.  Lifting this
+limitation will undoubtedly open up a multitude of new approaches and
+solutions, as this chapter attempts to outline.
+
+A final argument for taking into consideration the destiny of the
+system of interest which has been lurking around the corner the whole
+time is that we as humans do not often have a choice on this matter:
+the living system serving as a target is often required to survive our
+intervention, and sometimes to maintain the majority of the functions
+it had before the intervention.  That biomedical research is reluctant
+to go from accepting this obvious constraint to taking more holistic
+approaches including mutual benefit is possibly due to the complexity
+that awaits us on the very threshold of the comfortable Engineer's
+mindset.  In other words, it is much easier to see the disease as
+separate from the carrying organism, and imagine curative strategies
+tightly focused on a well defined set of diseased structures than to
+admit that the onset of the disease is a consequence of a complex
+interplay of multiple factors.  Indeed, conceiving of diseases from
+this more holistic viewpoint is often prohibitively complex with the
+currently available data and knowledge, all while the reductionist
+approach gives at least some solutions.  I claim however that this is
+no way should hinder our motivation to tackle the complexity of the
+more holistic approach.
+
+Finally, the way I employ the terms ``deal'' and ``mutual benefit''
+corroborates no particular social ideology.  The Deal with Life simply
+calls for including the potential benefit of the target system into
+the picture by establishing a measure of it.  It is up to the
+protagonists of the concrete context, problem, or practical
+application to decide whether, how much, and in which way to
+prioritize this benefit over the profit we humans are expecting
+to extract.
 
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