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\DOI{10.5802/crbiol.173}
\datereceived{2024-10-08}
\daterevised{2024-11-29}
\dateaccepted{2024-12-20}
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\title{Use and dual use of synthetic biology}

\alttitle{Usage et double usage de la biologie synth\'{e}tique}

\author{\firstname{Antoine} \lastname{Danchin}\CDRorcid{0000-0002-6350-5001}}
\address{School of Biomedical Sciences, Li KaShing Faculty of Medicine,
Hong Kong University, 21 Sassoon Road, Pokfulam, SAR Hong Kong, China}
\email{antoine.danchin@academie-sciences.fr}
\email{adanchin@hku.hk}

\keywords{\kwd{Information}\kwd{Nature and artifice}\kwd{Flexizymes}\kwd{James Danielli}\kwd{Xenobiology}}

\altkeywords{\kwd{Information}\kwd{Nature et artifice}\kwd{Flexizymes}\kwd{James Danielli}\kwd{X\'{e}nobiologie}}

\begin{abstract} 
A brief history of the field shows that the impression of novelty we
have today when we talk about synthetic biology is merely the sign of a
rapid loss of memory of the events surrounding its creation. The
dangers of misuse were identified even before the first experiments,
but this has not led to a shared awareness. Building a cell {ab initio}
involves combining a machine (called a chassis by specialists in the
field) and a program in the form of synthetic DNA. Only the
latter---the program---is the subject of the vast majority of work in
the field, and it is there that the risks of misuse appear. Combined
with knowledge of the genomic sequence of pathogens, DNA synthesis
makes it possible to reconstitute dangerous organisms or even to
develop new ways of propagating malicious software. Finally, the lack
of thought given to the risk of accidents when laboratories develop
gain-of-function experiments that increase the virulence of a pathogen
makes a world where this type of experiments is developed particularly
dangerous.
\end{abstract} 

\begin{altabstract} 
Une br\`{e}ve histoire du domaine montre que l'impression de
nouveaut\'{e} que nous avons aujourd'hui lorsque nous \'{e}voquons la
biologie synth\'{e}tique n'est que le signe d'une perte rapide de la
m\'{e}moire des \'{e}v\'{e}nements qui ont entour\'{e} sa cr\'{e}ation.
Les dangers d'un usage malveillant ont \'{e}t\'{e} identifi\'{e}s avant
m\^{e}me les premi\`{e}res exp\'{e}riences, mais cela n'a pas conduit
\`{a} une prise de conscience partag\'{e}e par tous. Construire une
cellule \textit{ab initio} n\'{e}cessite de combiner une machine (appel\'{e}e
ch\^{a}ssis par les sp\'{e}cialistes du domaine) et un programme sous
la forme d'un ADN synth\'{e}tique. Seul ce dernier est l'objet de la
tr\`{e}s grande majorit\'{e} des travaux du domaine, et c'est l\`{a}
qu'apparaissent les risques d'un mauvais usage. Combin\'{e}e \`{a} la
connaissance de la s\'{e}quence g\'{e}nomique des pathog\`{e}nes, la
synth\`{e}se d'ADN permet de reconstituer des organismes dangereux ou
m\^{e}me de d\'{e}velopper de nouveaux moyens de propager des logiciels
malveillants. Enfin, l'absence de r\'{e}flexion sur les risques
d'accidents associ\'{e}s aux exp\'{e}riences gain de fonction,
augmentant la virulence d'un pathog\`{e}ne, rend particuli\`{e}rement
dangereux un monde o\`{u} ces exp\'{e}riences sont d\'{e}velopp\'{e}es.
\end{altabstract} 

\maketitle
\vspace*{.9pc}

\twocolumngrid

\end{noXML}

\section{Introduction}

Biology embodies two very different conceptions of what life is. In its
most commonly understood form, it exploits what we know of chemistry.
On the other hand, under the name of genetics, it conjures up an
abstract world, more difficult for most people to grasp, that of the
rules of heredity. Either one of these approaches, biochemistry or
genetics, provides a conceptual and experimental framework for
validating, or not, the hypotheses that seek to explain what life is.
The consensus---usually not made explicit---is that
for a biological demonstration to be acceptable, it must involve an
analytical approach using biochemical experiments in which all the
elements are identified and understood. For more than half a century,
this consensus has been illustrated by the development of a new field
of life sciences, molecular biology, which implies that a purely
genetic demonstration---where the modification of a
hereditary trait within an organism is used to establish proof of what
is sought to be shown---is not \mbox{accepted} as sufficiently
convincing by the majority of experimenters. It is in this context that
a new discipline, \textit{synthetic biology}, has emerged. The
underlying idea is to transpose to the entire living organism the
necessary requirement of a biochemical demonstration, by going beyond
the simple analytical method. To do this, it would be sufficient to
combine the two entities that define the living cell, defined by its
biochemical characteristics, namely a nucleic acid that plays the role
of the genetic program and a ``chassis'' made up of all the machinery
that enables this program to be expressed within a semi-permeable
envelope that allows the cell to interact with its environment, into a
functional whole.

Because of the spectacular successes of molecular biology and the
central role played by nucleic acids, most researchers have limited
their vision of synthetic biology to the design and synthesis of
nucleic acids or analogues acting as genetic programs. This restrictive
view is based on the generalization of transfer by conjugation of
chromosome pieces, and even whole chromosomes from one species to
\mbox{another}, known since the beginnings of molecular
biology~\cite{1}. Since the late 2000s, we have been able to construct
and transplant synthetic genes or genomes directly into model
cells~\cite{2}. This experimental subset accounts for the vast majority
of experiments labeled as synthetic biology. This is where the
construction of entities for malicious use is most critical.

To date, the majority of efforts to design chassis for synthetic
biology have been focused on simplifying the genome of existing species
to make them compatible with the implementation of synthetic genetic
networks (see for example~\cite{3,4,5,6}). However, focusing solely on
the genetic program and its artificial synthesis ignores that, within
the cellular chassis, ubiquitous agents that cause the apparent
``animation'' of biological chemistry make a central contribution,
resulting in highly variable outcomes~\cite{7}. This is understood by
only a very small minority of investigators. The scientific and
technical challenges involved in synthesizing a functional chassis
{de novo} are such that only a few laboratories have attempted
to achieve this feat~\cite{8}, and they are still a long way from
succeeding. This is mainly due to the fact that it is not enough to
assemble all the known components of a model chassis to make it
functional~\cite{9}. Fortunately, an analysis of the properties
required for this creation shows that this domain is ill-suited to a
use that can be controlled by malicious operators. We will therefore
limit our discussion to gene and genome synthesis, which is a
particularly worrying area when considering possibly harmful
\mbox{applications}.

\section{What synthetic biology is} \label{sec2}

Unfortunately, fashion often dominates the onset of research trends. In
order to have a reasonable chance of developing work, which is always
expensive, we have to act like advertising agencies and show that we
are part of a vibrant trend. This pervasive constraint, which has
replaced the curiosity that was once at the root of the most important
discoveries, leads us to use terms that attract funders. ``Synthetic
biology'' is one such term. To understand what is covered by the field,
we need to understand what naming means.

\subsection{Naming is not without consequences} \label{sec2.1}

Umberto Eco underlined this in his book \textit{The Name of the Rose}:
we are nominalists, and for us, the essence of a thing lies in the
purity of its name: \textit{Stat rosa pristina nomine, nomina nuda
tenemus}. This is not without consequences, as naming directs our
thinking towards a whole context, that of the use of the name in
question. The true advocates of the scientific approach are well aware
of this, and use Greek roots to name what belongs to science~\cite{10},
reminding us all of its origins. However, the discipline we call
synthetic biology encompasses two distinct fields, each of which
involves practices covering both academic expertise and the
applications of this knowledge. These practices involve creating
processes that are either,
\begin{itemize}
\item unnatural with natural components (in this case, it is simply an
extension of genetic engineering, which explains why, for many people,
synthetic biology is not at all original); 
\end{itemize}
or,
\begin{itemize}
\item natural with unnatural components.
{\vspace*{.2pc}}
\end{itemize}

This dichotomy vanishes when these processes are combined into
heterogeneous assemblies. This obscures the image of synthetic biology,
which then evolves in parallel with a very blurred field, that of
``systems biology''. This situation amplifies the ambiguity of the term
``system'', which is widely used by those who make immoderate use of
the term ``complex'', meaning both ``so complicated that it is
impossible to understand'' and ``which implies a particularly elaborate
and therefore mysterious order''. The physicist Murray Gell-Mann tried
to remedy this deleterious ambiguity by replacing the Latin ``complex''
with the Greek ``plectics'' to avoid the confusion caused by overuse of
the term~\cite{11}. In a parallel effort Victor de~Lorenzo and I
attempted to bring the two fields together under the name of
``symplectic biology''. We had no better success than Gell-Mann's
attempt, whose article, curiously, did not appear online until long
after it had been written, just as we were advancing the same
idea~\cite{12}. This point of history underscores the ambivalence that
affects all discussions questioning the uses, good or bad, of synthetic
biology.\looseness=-1

\subsection{A brief history of the domain} \label{sec2.2}

What is fashionable today is the result of a sometimes ancient history
that is often ignored by fashion designers or users.\ Ignorance, which
is becoming \mbox{increasingly} widespread, leads us not only to
reinvent the wheel, but also, because we have lost our memory, to
construct fashions based on the accretion of mutually incompatible
entities. This conceptual flaw makes the consequences of the
development of synthetic biology, whether good or bad, not only
difficult to assess, but also difficult to control{\break} properly.

Because it is the title of a work that was quite successful in its day,
reference is sometimes made to the book by Leduc (1853--1939),
\textit{La Biologie Synth\'{e}tique}, published in 1912~\cite{13}, to
introduce this new field. Its content deserves to be analyzed in depth,
as it provides a remarkable illustration of the abusive use of analogy,
which is very much in fashion, particularly when it comes to the
analogy of forms. What is presented as new today was, in fact, already
explicit in 1970 in a commentary by Danielli \mbox{(1911--1984)} \cite{14},
detailed in a journal concerned with the negative consequences of the
applications of science, the \textit{Bulletin of the Atomic
Scientists}~\cite{15}:\vspace*{.75pc}
\begin{quote}
\fontsize{8.65}{10.2}\selectfont
We can now readily discern three ages in the science of modern biology:
Age of Observation $\sim$ Age of Analysis $\sim$ Age of Synthesis.
[\ldots] The age of synthesis is in its infancy, but is clearly
discernable. In the last decade (1960--70), we have seen the first
syntheses of a protein, a gene, a virus, a cell, and of allophenic
mice. Nothing with such dramatic implications has ever been seen in
biology before. Previously, plant and animal breeders have been able to
create what are virtually new species, and have been able to do so at a
rate which is of the order of $10^{4}$ times that of average
evolutionary processes. A further increase in rate is now on the
horizon. We need a few additional ``firsts'' before this will occur:
(1)~to be able to synthesize a chromosome from genes and other
appropriate macromolecules; (2)~to be able to insert a chromosome into
a cell; or, alternatively to~(1) and~(2), to be able (3)~to insert
genes into a cell in some other way; (4)~we must also learn how to
bring the set of genes, which is introduced into a cell, within the
domain of cellular control mechanisms, so that they do not run wild in
the cell. None of these problems appear to be of exceptional
difficulty.\vspace*{.65pc}
\end{quote}

In this 1972 article, Danielli warns us, as we do again half a century
later:
\begin{quote}
\fontsize{8.65}{10.2}\selectfont
As this evolution takes place, it may well become necessary to ensure
that such \mbox{organisms} cannot live outside their particular
required industrial environment, and even include self-destruct
mechanisms to reduce their viability in the natural biosphere.\ However,
self-destruct mechanisms, and all other mechanisms which are pathogenic
to one species, can only be introduced after the most rigorous
theoretical and experimental study because of the possibility, always
present with genetic systems, that the pathogenic process may pass from
species to species and so generate new fulminating pathogens. 
\end{quote}
\vspace*{.55pc}

Shortly afterwards, in 1974, the English name ``synthetic biology'' was
proposed by Szybalski~\cite{16}, to define what was to become genetic
engineering, based on the recent access to experimental determination
of the sequence of genes. But, as a result of this fashion that ignores
history, the year 2004 is often considered to be the start of the
discipline, with Drew Endy's construction of an artificial genome of
bacteriophage T7, in which the signals controlling the expression of
viral genes were rewritten in a way that could be understood by human
beings~\cite{17}. And in 2005, these purely academic experiments were
followed by the reconstruction of the genome of the 1918 pandemic
influenza virus, a thoughtless experiment that opened up an innovative
space for malicious applications~\cite{18}. The chemical synthesis of
genes and genomes then became widespread. This gave rise to serious
reservations because of the obvious danger of pathogens being
reconstructed by malicious actors, but no restrictive measures were put
in place to set limits~\cite{19}. Europe was not been left behind. In
April 2006, the first joint Europe--US workshop was held in Airlie,
Virginia, to identify current research and its consequences for
society, including in terms of biosafety: ``Synthetic Biology and
Synthetic Genomes'' (see the summary of the event in the box). However,
no constraints were imposed to regulate the possible use of synthetic
biology techniques leading to dual-use applications.

\subsection{Principles of synthetic biology} \label{sec2.3}

To distinguish it from simple genetic engineering, the creators of this
new field, specific to the life sciences, imposed four approaches:
\onecolumngrid

\mbox{}\unskip\noindent\begin{frtextbox}{\textbf{Summary of the US-EC
Workshop on Synthetic Biology, Airlie House, 24--25 April 2006}}
\enlabel{box1}
\mbox{}\fontsize{9}{11}\selectfont

Co-chairs: Maurice Lex (EU) and Marvin Stodolsky (DOE)

\medskip
\textbf{Sessions:}
\begin{enumerate}[(1)]
\item Biological research, empowerment by Synthetic Biology tools. 
\item The novel R\&amp;D arenas empowered by Synthetic Biology
\item Lessons already learned in the ELSI sector, with broad discussion
on the novelties posed by Synthetic Biology.
\item Novel gene constructs, genomes and their resource base.
\item Discussions on issues of guarding against the misuse of broadly
available Synthetic Biology resources. 
\end{enumerate}
\vspace*{.5pc}

Synthetic biology means a range of things to different people,
including molecular biologists engaged in science that may fall under
the rubric of ``synthetic'' biology. 

\medskip
\textbf{In session~1}, the works presented included discussions of
analyses of codon usage in bacterial genomes as a way to describe the
``domain structure'' of their chromosomes (Danchin, Pasteur, France);
the role (and use) of transcription factors, both native and artificial
(single chain antibody fragments, scFvs, which can mimic regulatory
factors) to downregulate \textit{lacZ} expression (de Lorenzo, CSIC,
Madrid); the synthesis, from chemically synthesized oligonucleotides,
of the minimal chromosome of \textit{Mycoplasma genitalium} (H.~Smith,
Venter Institute); and the use of Human Artificial Chromosomes (HACs)
generated using a special cloning method building on human centromeric
alphoid regions, to introduce protein-coding genes of choice into human
cells (Larionov, NCI).\unskip

\medskip
\textbf{In session~2}, Drew Endy, MIT, one of the principals in the
synthetic biology field, discussed the Registry of Biological Parts
(\url{http://parts.mit.edu}) and how early attempts were underway to
build functionalities using them. Stelling (ICS, Zurich, Switzerland)
discussed the challenges facing synthetic biology (and the differences
from electrical engineering), among them the lack of robustness, the
(so far) poorly characterized biological ``parts'', the noisy cellular
background in which they must perform, the lack of isolation from other
(cytoplasmic) influences, and the lack of understanding of integration
into systems. Panke (IPE, Zurich) discussed experiments attempting to
build artificial protein pathways that can exist and function
independently of the cellular environment, starting with the glycolysis
pathway from \textit{E.~coli}. Other talks covered the {de novo}
design of proteins and the alteration of the function of bacterial
catalysts.

\medskip
\textbf{Session~3} focused on societal implications. Joyce Tait
(Innogen Center, Edinburgh, Scotland) discussed international issues
related to the governance of synthetic biology, including processes of
scientific discovery and innovation, policy and regulatory aspects and
concerns being expressed by public groups. Perspectives are
internationally affected by long-running controversies surrounding
Genetically Modified Organisms (GMOs) and there exists a public
apprehension that is not being mollified by current educational and
outreach efforts, and could be exacerbated by over-enthusiastic claims
of research benefits and timescales of delivery, along with arguments
against the need for regulation. Shannon Nesby-Odell (CDC, Atlanta)
discussed biosafety in the US, focusing principally on facility
construction, safety equipment, and good laboratory practices as ways
to reduce the likelihood of an accidental release. She also discussed
the need for clear concise messages giving equal emphasis to the
benefits of the technology, the need to promote technology advocates
(e.g. in Congress), and to promote a balanced approach to politicy.
Oversight policies should be proactive rather than reactive, and should
involve the research community. There should be a tiered approach
involving legal instruments and also engaging the community to minimize
unjustified adverse perceptions. She emphasized the need for an
enforcement authority, including harmonized international oversight, to
provide a defence against claims of vested interest and noted that the
actions of industry can unwittingly hinder progress. Dan Drell (DOE, a
last-minute substitute for Mildred Cho of Stanford) discussed past
Ethical, Legal and Social Implications (ELSI) programs, noting that
integrating societal implications with cutting-edge science has always
been challenging, especially when those carrying out social
implications investigations don't continuously work to justify why such
studies are important to the success of the science. The benefits have
to be explained with great candor and without overselling. Many issues
will arise (and are already arising) that go beyond immediate safety
and health concerns. It must also be recognized that larger decisions
about what is to be done (and not done) with new technologies are made
by society at large, not by the scientists acting alone.

The subsequent open discussion of the issues raised in Session~3
indicated nervousness in the scientific community about regulatory
oversight and the possibility that poor regulatory choices could reduce
our ability, both to respond rapidly to natural or man-made infectious
agents, and to take up new opportunities to develop products of public
benefit. European scientists felt that regulatory oversight in the EU
was already adequate to cover the issues being included in the Berkeley
Agreement. However, at other points in the discussion, the need for an
enforcement capability was emphasized, along with the need to identify
experiments of concern as they occur. In this complex arena,
legislation, agency oversight and professional codes of practice are
all needed. This is not just a challenge for biologists---numerous
academic disciplines are involved. Also, the question of standard
setting is at least as important as regulation in governing innovation
processes for synthetic biology and it will be easier to set rules for
standards when, as now, there are relatively few players involved.

\bigskip
\textbf{Session~4}, the second day, began with George Church (Harvard)
talking about his work on micron-scale oligonucleotide synthesis and
dealing with polymerase-generated errors that can compromise success.
Santi (UCSF) discussed his work constructing altered polyketide
synthase genes for the purpose of engineering novel polyketide
synthases by assembling them from smaller modules. Overall, he used
more than 2.5~million bp of novel PKS gene sequences to validate his
approach of identifying novel, productive multi-module sets, resulting
in a combinatorial approach for the production of polyketides to order.
Mulligan (Blue Heron Technologies) talked about his company's attempts
to industrialize gene synthesis. Given the rapid expansion of this
technology into many hands, the feasibility of regulation outside of
centralized facilities may be a vain hope.

\bigskip

While synthetic biology is not yet a cleanly defined activity, ranging
from DNA synthesis to protein reengineering, the workshop dramatized
the increasing potential for synthesizing the working ``parts'' of
living systems and thus reconfiguring them, both to study how they work
and to try to engineer new capabilities. \textbf{This work shows
considerable promise for the development of numerous benefits to human
health and society, but also raises some concerns about how it could be
used and misused}. Impressive work is underway on both sides of the
Atlantic and continued conversations and information exchanges will be
necessary and beneficial.
\end{frtextbox}

\vspace*{15pt}

\twocolumngrid

\noindent
---Firstly, a principle of \textit{abstraction} applies the known laws
of life to the canonical entities of cells in order to design analogues
but of a different nature, whether this concerns the elements used in
the constructions or their interrelationships (architectures or
regulatory controls).

This idea, illustrated in 1957 by Fred Hoyle in his book \textit{The
Black Cloud}, enabled him to imagine life based on a physics completely
different from that witnessed in biology~\cite{20}. Beyond this
romanticized view, the REPRAP (REPlicating RApid Prototyper,
\url{https://reprap.org}) project aims to create a 3D laser printer
that reproduces itself. The machine produces most of its own
components, but it lacks crucial elements: a program (information
management), an assembly line (time and space management), and specific
functions such as lubrication. So it is not a real illustration of what
we expect from synthetic biology. It should be noted here that this
project aims to synthesize a counterpart to the chassis, forgetting the
program, whereas the dominant efforts in synthetic biology do the
opposite.\ The \mbox{ultimate} goal, of course, would be to synthesize
both the chassis and the \mbox{program}.

For our purposes, the interest of approaches that use elementary
building blocks different from those based on the chemistry of living
matter is that they can be seen as a means of avoiding the harmful
consequences of accidents or even of the malicious use of synthetic
biology, called \textit{xenobiology} in this context~\cite{21}.
However, as access to basic materials and equipment becomes easier, it
becomes increasingly difficult to control their use. This increases the
risk of accidents and the dangers of misuse. By way of example, the
situation can be compared to that of 3D printers, which can easily be
used to illegally produce weapons for criminal purposes~\cite{22}. As
gene synthesis and expression processes become increasingly accessible
to a wide range of players, the possibility of effective control is
illusory, and their use for malicious purposes cannot be ruled out.

\noindent
---A second principle is based on the \textit{standardization} of
processes and components. It sees synthetic biology as belonging to the
field of engineering.{\break} This~means respecting standards in which
the building of artificial constructs harmonizes and organizes the
materials and basic principles of molecular biology in a rational way,
in the form of programs expressed in a chassis. As a common starting
point, the chassis is derived from existing organisms that we naively
imagine to be fully characterized (which presupposes knowledge that, in
reality, is neither complete nor universally accessible). We can see
here that making standardized elements available to the general public
makes the construction of synthetic circuits very easy. Once again,
this is a feature that can be misused.

\noindent
---The third principle concerns the main goal of synthetic biology. In
particular, it aims to use engineering reasoning to reconstitute a
living organism in order to \textit{understand} what life is and
discover the missing entities.\ Those involved in this field like to
quote Feynman: ``What I cannot create, I do not \mbox{understand}'' 
(Figure~\ref{fig1}).

\begin{figure}
{\vspace*{.25pc}}
\includegraphics{fig01}
\caption{\label{fig1}On Feynman's blackboard at the time of his
death. \url{https://digital.archives.caltech.edu/collections/Images/1.10-29/}.}
{\vspace*{-.5pc}}
\end{figure}

\noindent
---Finally, the fourth principle takes account of Dobzhansky's maxim:
``nothing in biology makes sense except in the light of
evolution''~\cite{23}. Synthetic organisms will evolve, and natural
selection must be used rationally to produce variants of functions that
are considered important, combining design and evolution to guide their
adaptation to the conditions of interest~\cite{24}.

One constant consequence of the use of evolution of synthetic
organisms, whether chosen or undergone, must be emphasized: evolution
has no a priori reason to go in the direction desired by human.\ This
is an essential feature to understand when considering the applications
of synthetic biology, which, although harmless in principle, can evolve
into a dangerous form.\ Any organism, even one far removed from existing
forms, that is capable of surviving in a natural environment without
human help will evolve on its own, escaping its creators and
\mbox{turning} them into sorcerer's apprentices.\ This risk is well
\mbox{understood} and taken into account by academic, governmental and
even industrial governance structures. However, it is likely to be
overlooked due to ignorance by a number of players, especially if they
are ill-intentioned.

\subsection{Chemical synthesis of genes and genomes} \label{sec2.4}

Originally time-consuming and difficult, and for a long time limited to
the synthesis of oligonucleotides, gene synthesis has been commercially
possible for many years. Synthesizing a few kilobases of DNA is now
commonplace, and this technology is constantly improving. These
technical advances are crucial for the development of the ``natural''
area of synthetic biology. In a nutshell, strings of elementary
building blocks (``biobricks'') are designed for industrial use: new
metabolic pathways or improved modes of regulating gene expression for
a particular application, or for introducing variants of canonical
nucleotides into genomes~\cite{25}. Synthetic sequences can also be
used to re-create entire genomes, particularly, alas, those of
dangerous pathogenic organisms, as was the case with the influenza of
1918, and also poxviruses \cite{26,27}. These techniques can even be
used to increase their virulence~\cite{28}. Moreover, for the genomes
of natural pathogens, a small quantity of an initial construct is
easily amplified. A new player, artificial intelligence (AI), which has
long remained in the shadows, has added to the power of malicious
invention based on the vast amount of genome data~\cite{29}. Especially
in its generative form, AI can manipulate and rewrite the text of
genetic programs, incorporating the possible harmful expression of
genes involved in the pathogenic power of bacteria or
viruses~\cite{30}. This danger must be emphasized at a time when the
evolution of one of these viruses, mPox, is causing a worldwide
epidemic~\cite{31}. This is all the more worrying, as these nucleic
acid syntheses can now be reproduced in home laboratories.\looseness=-1

In the military field, however, one should note that biological warfare
has little strategic value on the battlefield. This was demonstrated
during Japan's invasion of China with the Unit~731 programme, which
began in 1932 and ended in 1945~\cite{32}: the biological weapons used
against the Chinese population (\textit{Yersinia pestis},
\textit{Bacillus anthracis}, \textit{Vibrio cholerae}, typhus agents,
etc.) caused casualties in the \mbox{Japanese} army. For example, the
use of \textit{V.~cholerae} spread in 1942 in wells south of Shanghai
killed hundreds of Japanese soldiers and thwarted their attacks on the
ground. However, for human societies, the spread of disease has many
effects other than a direct impact on health. This was clearly seen
once more in the recent analysis of the economic and social
consequences of the SARS-CoV-2 pandemic~\cite{33}. They are
considerable. There is no doubt that an intentional biological attack,
whether in a military or terrorist context, would have the same
effects, which would probably be amplified by a climate of panic linked
to the strategic or political context.

All this makes not only the chemical synthesis of long nucleic acid
molecules critical, but also genome transplantation
techniques~\cite{34}. DNA replication in selected hosts is
straightforward as long as it does not lead to its expression (for
example, YAC artificial chromosomes in yeast for the human genome
sequencing program~\cite{35}, \textit{Mycoplasma mycoides} in
yeast~\cite{36}, the genome of cyanobacteria in
\textit{B.~subtilis}~\cite{37}, etc.). This makes it possible to obtain
all sorts of new constructs and then transplant them into chassis where
they will be active. However, the transplantation process remains
challenging, particularly for large genomes. This is not the case for
viruses, for which transfection techniques are commonplace~\cite{38}.
The use of genomic synthesis based on self-splicing ribozymes used by
Liang et~al.~\cite{39} for the generation of viruses that are difficult
to multiply is now commonplace in virology~\cite{40}, certainly without
the slightest control. There is indeed a warning issued by the mass
media~\cite{41}, which gives ideas for controlling synthesis
laboratories or the equipment used for this synthesis. Unfortunately,
its implementation worldwide seems illusory~\cite{42}.

\subsection{Unconventional uses of synthetic nucleic{\hfill\break}
acids for synthetic biology} \label{sec2.5}

It is not uncommon for a technical invention intended for a specific
use to be used, or even misappropriated, for other purposes. This is
the case with DNA synthesis, an essential technique for synthetic
biology. Its success has given rise to a multitude of uses, the
potential harmful effects of which have not yet been fully explored.
Some of the currents developments in synthetic biology are completely
unconventional and original. Here are a few examples.

\subsubsection{Highly parallel miniaturized computing} \label{sec2.5.1}

Provided they are in water, nucleic acids form structures consisting of
double helix sections made up of strands whose sequence is
complementary. In fact, the increase in entropy of the solution due to
the constraint imposed on the structure of water when the nucleotide
bases are accessible to this solvent with its unique physical
characteristics leads to this remarkable property. The kinetics of
double helix formation is fast because the process very quickly
re-equilibrates the network of protons in water over a long distance.
This property, which is strictly linked to the nucleotide sequence, has
aroused great interest for performing highly parallel
calculations~\cite{43}. For example, the classic NP-complete problem of
finding subsets (cliques) of vertices all adjacent to each other in a
graph, often formulated as the search for a ``maximum clique'', has
been solved using techniques requiring the synthesis of a group of
oligonucleotides corresponding to the set of six-vertex cliques, and
then implementing the selection process involving the formation of
double helices specifically associating them with each
other~\cite{44}.

More recently, DNA has been used to create analogues of neuromimetic
computation using enzymes active on DNA, whose activities and biases
are adjustable, and which are assembled in multilayer
architectures~\cite{45}. These logic assemblies are formed in
cell-sized droplets. This computing power and extreme miniaturization
pave the way for interrogating and managing molecular systems with
complex content. Using DNA rather than a computer for a malicious
purpose may be a way to conceal it. However, it is important to bear in
mind the errors introduced during the construction of oligonucleotides,
as well as the time required to build them, which have hindered the
widespread use of DNA for computing. This impact can be reduced through
redundancy, by multiplying constructions that are in principle
identical. This is not suitable for computing, but it is perfect for
archiving.

\subsubsection{A new type of writing and the archiving of big data}
\label{sec2.5.2}

Many archives, sometimes housed in huge buildings, bear witness to past
history. Their purpose is to preserve the memory of a very large number
of facts that may one day be of interest, but that do not require
immediate access. Made up of text or images, they can easily be encoded
in binary form. Rather than keeping the originals, a variety of \mbox{media,}
such as magnetic tapes or optical discs, were very quickly used to
reduce their storage space. However, the lifespan of these media is
very short, often much less than a century. This is much shorter than
what is expected of important archives. In contrast, DNA is remarkably
stable, as demonstrated by the successful reconstruction of the genomes
of long-extinct species~\cite{46}. As DNA behaves like the material
support for a text written in a four-letter alphabet, it is easy to
imagine encoding any sequence of symbols in the form of a sequence of
nucleotides, which can be stored in an extremely small volume. It is
also possible to make several independent copies of the same text,
which reduces the negative consequences of errors or ageing, and
enables the initial text to be reconstituted even after a very long
time. The French National Archives have preserved the digitized text of
the 1789 Rights of Man and the Citizen and the 1791 Rights of Woman and
the Citizen in the form of double-stranded DNA~\cite{47}. We shall see
later that, in addition to creating a new means of communicating
messages or images, this use of DNA to transmit useful information can
unfortunately be misused for harmful purposes.

\subsubsection{Origami and DNA nanoboxes} \label{sec2.5.3}

The rational use of the subunits of DNA polymerase and other enzymes
that manipulate the molecule makes it possible to assemble DNA into a
variety of shapes, in a process similar to the construction of origami,
a traditional Japanese craft~\cite{48}. To build an origami, a long
single strand of DNA is folded using multiple smaller complementary
strands chosen by the experimenter and acting as staples, where they
pair up as a double strand with a region of the main strand.\ This
folding creates predictable biocompatible static nano-architectures or
dynamic nanodevices whose geometry is rationally designed, with precise
spatial addressability.\ Peptides, proteins, aptamers, fluorescent
probes, nanoparticles, etc. can be easily integrated with nanometric
precision.\ Triggered by chemical or physical stimuli, dynamic
nanodevices can, controlled by different molecular components or
external stimuli, switch from one
\mbox{conformation} to another or move autonomously, providing powerful
tools for intelligent biosensing and drug delivery~\cite{49}.
DNA analogues such as peptide nucleic acids (PNAs) have also been
proposed for the fabrication of origami-forming
\mbox{nanostructures}~\cite{50}. As with the majority of nanotechnology
approaches, it is not easy to avoid the possibilities of dual use (see,
for \mbox{example},~\cite{51}).

These approaches are summarized in Table~\ref{tab1}, where a few
examples of the constructs mentioned are given. Some of these are
described in the following paragraphs.

\begin{table*}%tab1
\caption{\label{tab1}Some examples of the use of genetic program
synthesis}
\fontsize{9.3}{10.7}\selectfont\tabcolsep=3pt
\begin{tabular}{llc}
\thead
Theme &amp; Examples &amp; References\\
\endthead
\morerows{3}{Genome streamlining} &amp; \textit{Mycoplasma mycoides} JCVI-syn 3.0 &amp; \cite{69}\\
&amp; \textit{Escherichia coli} &amp; \cite{70}\\
&amp; \textit{Bacillus subtilis} &amp; \cite{71}\\
&amp; \textit{Pseudomonas putida} &amp; \cite{72}{\vspace*{4pt}}\\
\morerows{2}{Rebuilding what is known} &amp; Bacteriophage phiX174 &amp; \cite{73}\\
&amp; Influenza H1N1 1918 &amp; \cite{18}\\
&amp; \textit{Mycoplasma genitalium} &amp; \cite{74}{\vspace*{4pt}}\\
\morerows{3}{Rewriting while simplifying} &amp; Bacteriophage T7 &amp; \cite{17}\\
&amp; Synthetic yeast genome (Sc2.0) &amp; \cite{75,76}\\
&amp; \textit{Mycoplasma mycoides} JCVI-syn 1.0 &amp; \cite{36}\\
&amp; \textit{Escherichia coli} &amp; \cite{77}{\vspace*{4pt}}\\
\morerows{3}{\parbox[t]{6.3cm}{\raggedright Rewriting the genetic program or metabolism through innovation}} &amp; HCV &amp; \cite{39}\\
&amp; Optimized carbon flow &amp; \cite{78}\\
&amp; Artemisic acid &amp; \cite{79}\\
&amp; Biobricks &amp; \cite{80}{\vspace*{4pt}}\\
\morerows{3}{Building ancestral genes} &amp; Carbonic anhydrase &amp; \cite{81}\\
&amp; Diterpene cyclase &amp; \cite{82}\\
&amp; Thermostable proteins &amp; \cite{83}\\
&amp; Polyphosphate kinase &amp; \cite{84}{\vspace*{4pt}}\\
\morerows{3}{Changing the skeleton of the heredity support} &amp; l-threofuranosyl nucleic acid (TNA) &amp; \cite{85}\\
&amp; Peptide nucleic acids (PNA) &amp; \cite{86}\\
&amp; Glycol nucleic acids (GNA) &amp; \cite{87}\\
&amp; Xeno nucleic acids (XNAs) &amp; \cite{88}{\vspace*{4pt}}\\
\morerows{3}{Changing nucleic acid bases} &amp; 2-aminoad\'{e}nine (Z-genomes) &amp; \cite{89}\\
&amp; \textit{N}1-m\'{e}thyl-pseudouridine &amp; \cite{60}\\
&amp; 5-chlorouracil, 7-deazaad\'{e}nine, etc. &amp; \cite{90}\\
&amp; Unnatural hydrophobic base pairs (UBPs) &amp; \cite{91}{\vspace*{4pt}}\\
\morerows{2}{Creating new application} &amp; Functional synthetic biology &amp; \cite{92}\\
&amp; Explosives detector &amp; \cite{93}\\
&amp; International Genetically Engineered Machine (iGEM) &amp; \cite{94}{\vspace*{4pt}}\\
\morerows{1}{Changing the genetic code} &amp; Translation with noncanonical amino acids &amp; \cite{95}\\
&amp; Refactored \textit{Escherichia coli} genome &amp; \cite{96}{\vspace*{4pt}}\\
\morerows{1}{Changing amino acids in vivo} &amp; Norleucine, selenomethionine &amp; \cite{97}\\
&amp; 4-fluorotryptophane &amp; \cite{98}{\vspace*{4pt}}\\
\morerows{1}{Synthetic pseudomessenger RNA} &amp; Non-immunogenic RNA for vaccination &amp; \cite{99}\\
&amp; Synthetic RNA for high-level protein expression &amp; \cite{100,101}{\vspace*{4pt}}\\
\parbox[t]{6.3cm}{\raggedright Synthesizing non-peptide polymers with defined sequences}\vspace*{3pt} &amp; Flexizymes &amp; \cite{68}
\botline
\end{tabular}
\end{table*}

\subsection{Non-canonical synthetic RNAs can mimic{\hfill\break}
messenger RNAs} \label{sec2.6}

The ongoing episode of the COVID-19 pandemic has brought to light a
remarkable application of synthetic nucleic acids. In this application,
vaccination with synthetic RNA stimulates mammalian adaptive immunity,
usually directed against directly administered antigens, in a two-step
process. First, the expression of a synthetic RNA that mimicks
messenger RNA in the cytoplasm of immune system cells directs the
synthesis of an antigen, the action of which then triggers the immune
response.

Why is this not possible with natural RNA? To rapidly defend against
infections, especially viral ones, the immune response evolved
{via} the emergence of an innate immunity capable of recognizing
a certain number of signatures universally present in pathogens, such
as the presence of a genome. This led to the emergence of specific
receptors that recognize free nucleic acids, especially RNA in its form
of the four canonical ribonucleotides. As soon as a natural RNA binds
to one of these receptors, such as the cytoplasmic RIG-I-like receptors
or one of the Toll-like receptors involved in this
recognition~\cite{52}, the genes that code for cytokines, which ensure
an antiviral response, are activated~\cite{53}.\ It was therefore
observed very early on that this type of RNA is recognized and
eliminated by the natural defence, but that this is not the case for
cellular RNAs.

One of the mechanisms recently identified \mbox{enables} the cell to
discriminate between natural cellular RNA and viral RNA~\cite{54} by
dissipating energy {via} ATPase activity, the triggering factors
of which are gradually becoming better
understood~\cite{55}.\ It~has also been observed that the
extremities of nucleic acids in the cell are specifically modified
(most often, for messenger RNAs, a cap at the $5'$ end and a poly-A at
the $3'$ end) and that these modifications are different in viruses.
All this means that the genomic RNA of viruses can be recognized by the
immune system, but we still do not know enough about them to be able to
synthesize canonical nucleotide RNAs that can be used as vaccines.
Another reason why these RNAs have been excluded from medical
approaches is that they are particularly fragile molecules, sensitive
to the activity of ribonucleases, which are omnipresent. Finally, they
can be used by enzymes such as reverse transcriptases to produce DNA
copies capable of integrating into the host cell's genome, as in the
case of HIV. For these reasons, although attempts have long been made
to use natural RNA to produce interfering RNA or messenger RNA for
vaccine, this approach has not been as successful as hoped.

\looseness=-1
In the absence of sufficient knowledge for their routine use, research
has turned to the synthesis of nucleic acids comprising modified
nucleosides \cite{56}, especially pseudouridine ($\Psi$) or
\textit{N}1-methyl-{\ubreak}pseudouridine (\textit{N}1Me$\Psi$), which alters
the general structure of the molecule very little~\cite{57}.

These natural analogues of canonical nucleosides have long been known
to occur in certain stable RNAs, transfer RNAs, and ribosomal
RNAs~\cite{58,59}. When they replace uridine in messenger RNAs,
experience shows that they are translated, opening up a new field for
the use of synthetic RNA as a template for the synthesis of vaccine
proteins~\cite{25}. As they escape innate immunity~\cite{60}, they are
excellent candidates for use {via} expression in immunocompetent
cells~\cite{61}. Indeed, this application of synthetic biology had a
considerable impact when it emerged that a synthetic RNA molecule
containing these modified nucleosides yielded a highly effective
vaccine against the coronavirus responsible for the COVID-19
\mbox{pandemic}~\cite{62} (Figure~\ref{fig2}).\looseness=-1

\begin{figure*}
{\vspace*{-.2pc}}
\includegraphics{fig02}
\caption{\label{fig2}Pseudouridine and methyl-pseudouridine are very
similar in shape. However, the canonical bond between nitrogen~1 of the
base and carbon~$1'$ of ribose is shorter than the bond between the
same carbon and what is then base carbon~5. This affects the speed and
fidelity of decoding during translation of synthetic RNA.}
{\vspace*{-.5pc}}
\end{figure*}

\looseness=-1
Knowing that the details of molecular events during the expression of
synthetic RNA in animals could not be known, the generalization of this
vaccination can be seen as a full-scale experiment involving hundreds
of millions of people. Thus, today we know considerably more. The
movement of an RNA in the ribosome during translation is sensitive to
the sequence of nucleotides translated in groups of three (codons),
which follow one another without overlap, establishing a well-defined
reading frame. Depending on the context, the RNA molecule will slide
and modulate the adjustment of its reading frame forwards or backwards.
This property allows viruses to direct the synthesis of several
proteins encoded by the same nucleotide sequence, but in different
reading frames. This is how SARS-CoV-2 produces two different proteins
essential for its replication, Orf1a(Nsp11) and Orf1b(Nsp12). The
second proteins results from the viral genome sliding back one
nucleotide in the $5'$-UUUAAAC-$3'$ nucleotide sequence, which amounts
to reading the last nucleotide, C, twice (shift~${-}1$)~\cite{63}. This
is therefore a ``programmed frameshift''~\cite{64}, a common process in
gene expression.

However, when substituted for canonical messenger RNAs, synthetic RNAs
alter the accuracy and speed of their decoding by the ribosome. Recent
experience has shown that this affects the reading frame of their
translation, depending on the sequence in which the non-canonical
nucleotides are located. We are beginning to understand the
consequences of this discovery. Incorporation of \textit{N}1Me$\Psi$
into mRNA causes the ribosomal reading frame to shift forward by one
nucleotide at certain points in the sequence. This has been observed
{in vitro} and {in vivo} after vaccination, as seen in mice and in
humans with the presence of antibodies against products translated from
a ${+}$1-shifted sequence during translation of the synthetic RNA
encoding the vaccinating viral spike protein~\cite{65}. It is therefore
an accidental ``vaccination'' against an antigen that is involuntarily
present. This could have had an adjuvant effect, i.e. a positive
one~\cite{66}, and had no negative effect, as far as we know. It should
also be noted that a similar process, but in different parts of the
genome, occurs during the normal translation of the viral genome. To
control this process during vaccination, the consequences of which are
unknown, it would seem useful to replace codons containing certain
\textit{N}1Me$\Psi$ residues responsible for these shifts by synonyms,
so as to reduce the production of coded products in the shifted
phase~\cite{67}. On the other hand, this observation leads us to think
that this phenomenon could be used to produce toxic variants based on
this principle. This must be taken into account in future regulations
authorizing these{\break} vaccine families.

\subsection{Beyond the synthesis of non-canonical{\hfill\break}
proteins, synthesis of polymers with{\hfill\break} programmable motifs}
\label{sec2.7}

\looseness=-1
Synthesizing polymers with programmable sequences from a variety of
elementary building blocks is of considerable industrial interest.
Beyond the {in vivo} introduction of analogues of canonical
amino acids into a synthetic construct mimicking protein synthesis
(Table~\ref{tab1}), this approach is most promising {in vitro},
especially with basic motifs chemically distant from amino acids. This
has been achieved by the remarkable invention of ``flexizymes'' in
\mbox{Hiroaki} Suga's Tokyo laboratory for the synthesis of
non-repetitive polymers~\cite{68}, a revolution already proposed by
Danielli half a century ago in the article cited above: 
\begin{quote}
\fontsize{8.65}{10.2}\selectfont
A field of enormous potential in the biological industry is the
manufacture of sequence-determined polymers.\ There is little hope that
the present-day polymer industry can develop its existing techniques to
give a wide range of sequence-determined polymers.\ But cells have been
producing sequence-determined polypeptides and polynucleotides in a
vast variety for two billion years. Even limited access to such
versatility at the industrial level would extend our horizons beyond
what we can now comprehend~\cite{15}.
\end{quote}

\looseness=-1
Flexizymes are synthetic ribozymes designed to load a wide variety of
unnatural amino acids or other polymer precursors onto transfer RNAs.
This makes it possible to reprogram the genetic code {in vitro}
by reassigning codons corresponding to natural amino acids to unnatural
residues, and thus to achieve the synthesis of unnatural polypeptides
or even polymers far removed from polypeptides whose sequence may be
aperiodic. These polymers, whose sequence is defined by the
experimenter, are of academic or industrial interest~\cite{102}. Of
course, these techniques can be used for the expression of synthetic
genetic programs enabling, for example, the production of toxins or
chemical precursors of dangerous compounds that would be difficult to
obtain otherwise. These are therefore technologies that can be
``dual-used'' depending on the scientific or industrial context. The
use of these techniques is subject to a prior ``risk analysis'', which
should be carried out on a case-by-case basis.

\section{A future to explore, the chassis, with at the{\hfill\break}
heart of synthetic biology a neglected{\hfill\break} currency of
physics: information} \label{sec3}

To conclude this brief analysis of the most common status of synthetic
biology and its applications, we need to consider the often-overlooked
machine. This ``chassis'' defines an inside and an outside, produces a
copy similar to itself, and enables the expression of a program (a
``recipe book'') that directs the synthesis of a replica (an exact
copy) of itself. During this process, metabolism recursively transfers
information from the program and manages the flow of matter and energy.
However, it is important to stress an original feature that is often
overlooked, as evidenced by the omnipresent use of the word
``reproduction'', which is certainly not replication. This is
demonstrated by the experiment of transplanting the genome of one
species into another~\cite{103}. The program replicates (produces an
exact copy), whereas the chassis reproduces (produces an approximate
copy)~\cite{104}. This implies a set of properties that deviate sharply
from the logic of standardization and may account for the lack of
interest of researchers in the creation of synthetic chassis.

\subsection{Information management in the cell} \label{sec3.1}

For example, the chassis inevitably includes time-sensitive, aged
entities whose age is constrained by their physico-chemical properties
in the cell's environment. As with human machines, managing this
phenomenon presupposes the existence of a maintenance process. However,
this process, seldom taken into account in synthetic biology, has the
unique characteristic of being necessarily endogenous, unlike
industrial maintenance, which, in the vast majority of cases, requires
external action. In the case of proteins, aging is intrinsically
dependent on their sequence and folding. Two amino acids play a central
role in this inevitable aging process: Aspartate and asparagine. They
spontaneously cyclize into succinimide (with deamidation in the case of
asparagine), then form an analogous residue, iso-aspartate, which
locally deforms the polypeptide skeleton~\cite{105}. This universal
phenomenon, long known but curiously neglected, imposes that all cells
contain simultaneously a set of young and aged proteins, the latter
having lost or altered their function~\cite{106}. Therefore, a set of
agents must exist within them that are capable of managing this
information and ensuring that when the cell produces offspring, it is,
preferably or only, young offspring~\cite{107}. These discriminating
agents, which are an integral part of the cell's setup, identify
classes of objects---for example, what is young and what is old---and
lead them to a \mbox{different} fate according to their age class. In
general, when thinking about the chassis required for the total
synthesis of a cell that can be recognized as alive, the importance of
these classifying agents, which are nevertheless present even within
cells with the smallest genomes has not yet been understood~\cite{108}.

We emphasize here that information is a necessary concept for
understanding life. It must be taken into account in experiments or
applications aimed at synthesizing living cells, in particular through
the identification of these discriminating agents and their role.
Unfortunately, the use of the term is particularly vague, and is not
well formalized except in a restricted field of statistical physics.
And yet the idea that information, more than a figure of speech, is a
genuine currency of nature is a very old one. It has long been
illustrated by the image of Theseus' ship, recounted in Plutarch's
\textit{Lives of Illustrious Men}:
\begin{quote}
\fontsize{8.65}{10.2}\selectfont
The thirty-oared ship on which Theseus embarked with the young men
offered to the Minotaur, and which brought him victorious back to
Athens, was preserved by the Athenians until the time of Demetrius of
Phalerus. They changed the boards as they aged, replacing them with
new, sturdier pieces. Philosophers, in their discussions on the nature
of change, chose this ship as an example, some arguing that it remains
the same, others that it is different from Theseus' ship.
\end{quote}

This is because information as a fundamental currency of physics has so
far only really been discussed to account for the quality of the
transmission of messages made up of sequences of symbols, without
having to consider the meaning of the message. Shannon and Brillouin
thus proposed a theory of communication that is abusively referred to
as ``information theory''~\cite{109}. However, the use of this concept
in biology shows that there is much more to it than Shannon's model, as
soon as we are concerned with the meaning of the message rather than
its integrity: a synthetic DNA molecule does not produce the same
result at all, depending on the context in which it is placed. This is
a crucial observation when it comes to synthesizing life. Yet the dream
of the synthetic biology engineer is that artificial cells should not
be innovative (who would fly in an airplane that would innovate during
the flight?). The consequence is that, like factories, cell factories
will age and need to be systematically rebuilt. This poses a problem
for the large-scale use of synthetic cells, and the uncertainty about
their future makes it difficult to make malicious use of this original
feature of all life forms.

\subsection{Synthetic biology and information{\hfill\break} contagion}
\label{sec3.2}

To conclude with the importance of taking it into account, there is
still a completely different role for information when exploring
potential misuses of synthetic biology. Information itself is
contagious, and therefore easily subject to dual use, as we can easily
illustrate in various fields. The WHO is attempting to eradicate
contagious diseases specific to humans, especially viral diseases. This
eradication is based on vaccination, and assumes that the majority of
the world's population is vaccinated. Alas, the spread of fear, which
is useful for limiting contact and disease contagion~\cite{110}, runs
counter to this objective, particularly {via} social networks
where it spreads misinformation~\cite{111}. Another negative aspect of
information is the symbolic nature of a simple, explicit description of
the genome of a pathogenic organism, in the form of a text written
using a four-letter alphabet. Knowledge of the genome of the smallpox
virus made its eradication ineffective. Since the virus sequence itself
is not pathogenic, it can be propagated unhindered over the Internet,
for example~\cite{112}, while we now know how to synthesize poxviruses
completely, as shown for horsepox~\cite{113}.

There are other, more refined forms of back-and-forth between the text
of a genetic sequence and its malicious concrete realization. Computers
can be infected with malware encoded in DNA sequences, and biological
threats can be generated from publicly accessible data, making
databases of pathogenic organisms particularly dangerous~\cite{29,114}.
These databases may contain fictitious sequences that hide malicious
programs that begin to run when the corresponding file is opened. To
understand this, it is useful to remember that computer attacks are
based on inevitable flaws in the implementation of a program in a
machine~\cite{115}. In biology, these flaws are particularly numerous
when it comes to exchanging material between laboratories. Just as
opening an email attachment can trigger a malicious process, so can
sending material made of nucleic acid. Good laboratory practice
requires verifying the sequence of any received material. However,
this practice is decisive in the case of hostile actions, as an
apparently innocuous object may in reality be harmful or simply
intended, by being different from expected, to delay or derail costly
experiments~\cite{116}. Moreover, the verification process itself can
be the source of malice, if a DNA segment is sent for sequencing and
encodes hostile programs designed to contaminate computer equipment
during sequencing~\cite{117}. As synthetic biology approaches,
particularly industrial ones, combine all experimental levels, from {in
silico} design, to {in vivo} evolution and {in vitro} production, all
computer-dependent, the entry points for hacking are very numerous
(Figure~\ref{fig3}).

\begin{figure*}
{\vspace*{-3pt}}
\includegraphics{fig03}
{\vspace*{-3pt}}
\caption{\label{fig3}Back and forth between the design and synthesis of
synthetic nucleic acids and the piloting of an integrated industrial
process. In an integrated industrial process, synthetic biology
combines the synthesis of selected genes, produced after {in
silico} (computer-mediated) exploration, with their expression
{in vivo} within chassis that are multiplied in fermentors, or
{in vitro}, where they are used to develop new metabolic
pathways or to synthesize novel polymers difficult to obtain with
sufficient yield. The introduction of corrupted sequences can make it
possible to conceal programs designed not only to enslave the control
computer, but also to infect the telecommunications network linking
this computer to the Internet, for example. Blue arrows: flow of
information associated with nucleic sequences, either real or in text
form. Red arrows: flow of commands.}
{\vspace*{-3pt}}
\end{figure*}

\section{By way of conclusion, we need to raise{\hfill\break}
awareness} \label{sec4}

When a new scientific and technical field emerges, we cannot anticipate
its political, economic, societal, or behavioral impact. When driven by
curiosity and inventiveness, scientific research is seen as a positive
quest to advance knowledge that can lead to applications for the
benefit of humanity and its environment. Unfortunately, history teaches
us that this hope has often been hijacked by the quest for power. To
avoid this pitfall and to define a responsible objective for scientific
research, we must try to avoid misuse and unacceptable risk-taking. The
\textit{raison d'\^{e}tre} of synthetic biology is to seek to
understand what life is. Along the way, this leads to the emergence of
new techniques and important applications in legitimate economic
sectors, such as health and quality of life, whether human, animal or
plant. An analysis of the spectrum of possibilities, through the
examples cited here, shows that the future of this field remains wide
open and that many other uses are yet to be discovered or invented. The
increasing ease of access to synthetic biology techniques means that it
is becoming increasingly difficult to effectively control the flow of
materials and associated resources. However, we must not ignore the
fact that they can be misused for malicious purposes, or that
accidents, particularly those linked to the evolutionary nature of
living organisms, are always possible. So, because of its highly
innovative nature, synthetic biology is an area of ``dual use and
risk''. And this applies to all forms of ``advanced technology'': those
involved in innovation and the acquisition of new knowledge need to be
aware of the consequences of {disclosing}~it. For the scientific
community, this means developing a culture of responsibility that takes
into account the acceptable level of risks in research and innovation,
as well as the ethical implications. All~too \mbox{often,} the danger comes
not from hostile actors but from people who are reluctant to set limits
on their activities, which they present as being in the general
interest. This is because the pursuit of notoriety is encouraged by the
current system of evaluating a researcher's activity through their
publications, based on an economic model akin to advertising. This
contributes to this reprehensible behavior, which, in the absence of
collective awareness, will result in the multiplication of avoidable
accidents, epidemics and, ultimately, to the development of an
obscurantism that rejects scientific exploration of the world.
Fortunately, the scientific community has become aware of this with the
San Francisco Declaration on Research Assessment (DORA
\url{https://sfdora.org/read/read-the-declaration-french/}). It~is
\mbox{essential} to \mbox{introduce} the notion of ``dual-use and risky
research'' into the training of researchers and engineers at a very
early stage, and to know how to detect it and prevent it from
developing, in particular through in-depth reflection on the ways in
which research and the people who carry it out are evaluated.

\section*{Declaration of interests}

The author does not work for, advise, own shares in, or receive funds
from any organization that could benefit from this article, and has
declared no affiliations other than their research organizations.

\section*{Acknowledgements}

This work, which received no funding, benefited from discussions
sparked by the I2Cell programme of the Fondation Fourmentin-Guilbert,
which is recognized as being in the public interest.

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