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History, Philosophy, and Biology
Teaching Lab (LEHFBio)
Gene: The evasive concept
Charbel Niño El-Hani
(Institute of Biology, Federal University of Bahia, Brazil.
Coordinator of INCT IN-TREE. Productivity in Research Grantee
1-B CNPQ)
• The gene concept in the 20th century
• The “crisis” of the classical molecular concept
• Reactions to the “gene problem”
• Reasons for concern: discourse about genes in
society and genetics education
• Implications for teaching about genes and their
functions in living systems
The gene concept in the 20th century
• The gene concept as a hallmark of the history of
science in the 20th century.
• The birth of the gene (Johannsen, 1909).
• The “Mendelian” concept: Gene as unit of
inheritance  Instrumental concept, inferred
from the phenotype.
W. Johannsen
• Classical concept: Linkage maps and “beads in
necklace”  Deterministic relation to
phenotype, from which they are instrumentally
inferred (despite increasing realism).
T. H. Morgan
The gene concept in the 20th century
• Biochemical-classical concept: In the road to the
realist, material gene.
• Gene as enzyme  Producer of enzymes.
• From one gene-one enzyme to one gene-one
polypeptide (or RNA).
The gene concept in the 20th century
• The double helix model, the classical molecular concept
(Neumann-Held, 1999) , and the central dogma.
• Informational conception: Gene as matter and information.
• Classical molecular concept and updating of the gene as unit.
• Unit of structure  DNA sequence with well specified localization
and boundaries.
• Unit of function  responsible for the production of polypeptide
or RNA with a single function.
• Unit of information  containing a single genetic message.
• Classical molecular concept explained:
 Nature of the linear sequence of nucleotides in the gene and its
relation to amino acid sequence (Crick, 1958)  Elucidation of the
genetic code;
 Mechanism of gene replication and RNA synthesis;
 Separation of mutation, recombination and function at the
molecular level.
• Responsible for large acceptance of a realist
view about the gene.
The gene concept in the 20th century
• The success of molecular biology research program (Stent,
1968)  Now we need only to iron out the details.
• Discovery of restriction enzymes, genetic engineering,
increasing research on eukaryote genomes  Anomalies in
relation to the classical molecular concept.
• The gene concept in the 20th century
• The “crisis” of the classical molecular concept
• Reactions to the “gene problem”
• Reasons for concern: discourse about genes in
society and genetics education
• Implications for teaching about genes and their
functions in living systems
The “crisis” of the classical
molecular concept
• Several anomalies faced by this gene concept (El-Hani, 2007):
 Correspondence between one DNA segment and many
RNAs⁄polypeptides (e.g., alternative splicing).
 Correspondence between many DNA segments and one
RNA⁄polypeptide (e.g., genomic rearrangements).
El-Hani, C. N. (2007). Between the cross and the sword: the crisis of the gene concept.
Genetics and Molecular Biology, 30(2), 297-307.
 No correspondence between DNA segments and
RNAs⁄polypeptides (e.g., mRNA editing).
El-Hani, C. N. (2007). Between the cross and the sword: the crisis of the gene concept.
Genetics and Molecular Biology, 30(2), 297-307.
But is there really a “crisis” of the gene concept?
• Since the end of the 20th century, persistent doubts about the
gene.
• First, in the literature on philosophy of biology (1980s).
• At the turn of the millenium, in the empirical literature.
• In mid-2000s, editorials of high-impact journals.
But is there really a “crisis” of the gene concept?
• In a sense, YES  Important difficulties in teaching about genes
based on a concept under siege by several anomalies.
• In a sense, YES  Important difficulties in properly communicating
about genes within society based on a deterministic language
marked by confusion and incompatibility with what we know about
the roles of genes.
• In a sense, YES  Research fields affected by the gene concept, e.
g., estimates of quantities of genes per species in comparative
genomics.
But is there really a “crisis” of the gene concept?
• In a sense, NOT  In most research fields dealing with genes,
hardly any effect on inquiry practices.
• Genes as epistemic objects, defined as targets for research
questions.
• The gene concept in the 20th century
• The “crisis” of the classical molecular concept
• Reactions to the “gene problem”
• Reasons for concern: discourse about genes in
society and genetics education
• Implications for teaching about genes and their
functions in living systems
Reactions to the “gene problem”
• Time to frame new concepts and words,
and abandon the gene?
• New language to genetics,
without “gene”
Reactions to the “gene problem”
• Survival of the gene concept, more or less radically
reconceptualized.
• Systemic and dynamical views  Genetic systems and hierarchical
models of biological systems. Genes as dynamical entities.
• Gene should be properly situated in the cell, as fundamental
morphogenetic unit (Hall, 2001).
• It is not the gene that makes things to the cell; it is the cell that
makes things with the gene.
• Critique of discourse situating cell agency only at the DNA level
(Santos et al., 2012).
Reactions to the “problem”: Rethinking the
gene
• Genes as processes leading to the
expression of particular polypeptides
• Genes as sets of domains in DNA
• Abandon of gene as unit  Gene as
collection of components that, together,
define its structure and influence
phenotype.
• Components are domains distinguished
by structural properties or activities (exons,
promoters, enhancers etc.).
Reactions to the “problem”: Rethinking the
gene
• Genes are not found in DNA, only domains.
• A domain can be part of more than one gene  Without unit in
DNA corresponding to the gene  Accommodate anomalies
affecting classical molecular concept.
• Fogle has realist view about domains, but what about genes?
• Where can we find them in the cell?  It is tempting to think:
“at mature RNA”  But Fogle doesn’t say so.
Reactions to the “problem”: Rethinking the
gene
• A new definition of gene coming from the
ENCODE Project.
• The gene as union of genomic sequences
encoding coherent set of potentially
overlapping functional products.
• It avoids anomalies by breaking with one-to-one relation
between DNA sequences and gene products.
• But it is conceptually shallow  It doesn’t do much more than
accommodating anomalies…
Reactions to the “problem”: Rethinking the
gene
• New language to Genetics, with
“gene”.
• Distinction between two aspects involved in polypeptide
production synthesis: coding and regulation.
• From coding to gene expression  Further distinction between
gene function and mechanisms for storage and expression of
genetic information.
• Gene concept related to functional aspect.
Reactions to the “problem”: Rethinking the
gene
• New language to Genetics, with
“gene”.
• Where do we find unit related to gene function?
• Not at the DNA level!
• Gene emerges at the level of mature mRNAs .
• In protein-coding genes  Gene = uninterrupted sequence in
mature mRNA that serves as unit of function. (?)
Reactions to the “problem”: Rethinking the
gene
• Gene expression  process of creating genes in RNA from
genomic domains in DNA, followed by translation to corresponding
amino acid sequence.
• Similarities with Fogle’s proposal, but more explicit concerning
gene location.
Reactions to the “problem”: Rethinking the
gene
• Transcript contains program in cis for gene expression in the right
time and space  Genon: set of binding sites for regulatory
molecules, added to or superimposed onto the gene.
• Genon build
along with the
gene, unique to
each mRNA and
polypeptide.
• Genon  Set of signals for Transgenon.
• Transgenon: set of regulatory molecules codified in trans.
• mRNA genon is immersed into pool of regulatory molecules 
Specific transgenon selected by each genon.
• Genontransgenon
interaction 
Regulation of gene
expression.
• Unit of function
is system genegenon-transgenon
(El-Hani et al.,
2016)
Reactions to the “problem”: Rethinking the
gene
• Location of gene as structural unit in mRNA solves a large part of
the anomalies challenging the classical molecular concept.
• Gene as unit of structure, not unit of inheritance.
• Units of inheritance can be chromosomes or, at least,
chromosomal regions rarely separated by recombination events.
Reactions to the “problem”: Rethinking the
gene
• Conceptual analysis and distinction between gene-P
and gene-D.
• Gene-P: determinant of phenotypes without reference
to specific sequence.
• Instrumental preformationism, distal view.
• “Gene for”  Some deviation from normal sequence
results with some predictability in phenotypic difference
 Genome-Wide Association Studies (GWAS).
• Shorthand for “locus in which sequence variation
causes a difference in phenotype, all other things being
equal” (difference maker).
Reactions to the “problem”: Rethinking the
gene
• Conceptual analysis and distinction between gene-P
and gene-D.
• Gene-D: developmental resource indeterminate with
respect to phenotype.
• Realist gene, proximal view.
• Matching genes and phenotypes  GWAS as
population study partitioning phenotypic variation in
explanatory components, not as individual study about
phenotype development.
• Delicate terrain: conflation between gene-P and geneD as a powerful source of genetic deterministic thinking.
Reactions to the “problem”: Rethinking the
gene
• Current situation:
• Classical molecular concept under fierce questioning.
• Meaning of gene in flux.
• At the same time, research goes on with few problems in
several fields, due to use of gene as epistemic object.
• The gene concept in the 20th century
• The “crisis” of the classical molecular concept
• Reactions to the “gene problem”
• Reasons for concern: discourse about genes in
society and genetics education
• Implications for teaching about genes and their
functions in living systems
Reasons for concern: discourse about
genes in society and genetics education
• Despite knowledge about the complexity of genetic
systems and their interactions with epigenetic and
environmental factors, genetic determinist beliefs still
prevail.
• People face difficulty in understanding idea that
genetic and environmental factors interact.
• Genetic determinist discourse predominates in the
media.
• Determinist views have deep roots, including religious
backgrounds.
• Genetics education don’t put into question but even
promotes determinism.
• Studies on high school and higher education textbooks show
prevalence of classical molecular and gene-P (“gene for”) concepts,
with informational conception being especially important in high
school.
• They also show high level of hybridization between molecular
gene (≈ gene-D) and gene-P, favoring determinism.
• Indiscriminate mixture of features ascribed to genes by different
historical models is quite common.
• Teachers and students have slight chance of grasping that books
are talking about models and concepts (naïve realism)  A
seamless discourse about genes throughout the books, leading to
amalgamation of historically separate ideas.
• Students learn about classical molecular concept as if there were
no problems, despite the coverage of the very anomalies
challenging this concept.
• Gene-phenotype association addressed without stressing
populational and instrumental nature of studies.
• Other studies found correlation between students’ views and textbook
contents.
• Given all these problems, genetics education tend to favor simplistic and
erroneous views about genetic systems, far from what we currently know
about them and their interactions with epigenetic factors, environment,
experience.
• Impairment of students’ capacity to make decisions and act in an informed
and critical manner in societies increasingly marked by genetic determinist
discourse and growing use of genetic technologies.
• (Usually) silenced aspects in genetics education:
Conceptual consequences of challenges to our
understanding of genes (HS, HE).
 Nature of scientific knowledge as composed by theories and
models, not mere descriptions of reality (HS, HE).
Non-determinist views about the role of genes in biological
systems, in particular, in development and phenotype
construction (HS, HE).
 Population nature of gene-phenotype association and limits
of extrapolation to individual level rarely addressed (HE).
How genes are treated is a key problem for
genetics education!
• The gene concept in the 20th century
• The “crisis” of the classical molecular concept
• Reactions to the “gene problem”
• Reasons for concern: discourse about genes in
society and genetics education
• Implications for teaching about genes and their
functions in living systems
Implications for teaching about genes and their
functions in living systems
 Create conditions for teachers’ and students’ learning about
and with models concerning genes and their functions in living
systems.
 A single term, “gene”, binds discourse about different models of
genes and their functions; thus, it is important to be explicit
about which model or concept is being considered at each
moment.
 It is especially important to distinguish between instrumental
(like gene-P, “gene for”) and realist gene concepts (like the
molecular gene).
Implications for teaching about genes and their
functions in living systems
 It is important to connect phenomena challenging the classical
molecular concept with their conceptual consequences, making
it clear for teachers and students that there are doubts about
the gene nowadays.
 Explicit consideration of research practices in Genetics,
Molecular Biology and related fields can help teachers and
students understand how investigation can proceed despite
conceptual problems (genes as epistemic objects) (authentic
science approach).
 It is important to explain to teachers and students how
Association Studies are made and what does it mean to
associate a genetic explanatory component to phenotypic
diversity in a population.
Implications for teaching about genes and their
functions in living systems
 It is important to present complex models of development and
cellular function, which avoid gene-centric perspectives,
recognizing that complex networks of interactions between
genetic, epigenetic, and environmental (including social,
experiential) factors are the rule.
 It is important to progress from simpler models (e.g.,
continuous genes, complete dominance, monogenic diseases,
etc.) to more complex models (e.g., split genes, epistasis,
incomplete penetrance, epigenetic inheritance, etc.), creating
conditions for a deeper understanding of the complexity of
biological systems and their relations to genetic memory.
Ongoing work
• What are the relations between modern genetics/genomics
knowledge, genetic determinism, and attitudes towards
genetics-based technologies? (PUGGS Project) - w/ Rebecca
Carver, Niklas Gericke, Jérémy Castéra, Neima Alice M.
Evangelista.
• How does discourse about GWAS circulate from scientific
literature to the media? Where do things go wrong with “gene
for” discourse? – w/ Diogo Meyer, Neima Alice M. Evangelista.
• Design and testing of teaching approaches about genephenotype association studies for teacher education and high
school biology teaching – w/ Diogo Meyer, Neima Alice M.
Evangelista, Ana Maria R. de Almeida, Andreia Oliveira, Andrea
Grieco, Alessandra Bizerra.
Ongoing work
• Do views about genes change with increasing knowledge? – w/
Ana Maria R. de Almeida e Leonardo Celin Patiño.
• Why do textbooks make use of irrelevant examples of
monogenic human traits that are not diseases? – w/ Ana Maria
R. de Almeida .
• Development of models for gene function using biosemiotics
and an organizational approach to function – w/ João Queiroz,
Vanessa Carvalho dos Santos and Nei Nunes-Neto.
• Epistemological Foundations for Genetics Education - Addressing
Conceptual Variation and Genetic Determinism - w/ Niklas
Gericke – book for series edited by K. Kampourakis in Springer:
Science: Philosophy, History and Education.
Work to be done
• Do views about genes change with increasing knowledge? – w/
Ana Maria R. de Almeida e Leonardo Celin Patiño.
• Is there a correlation among views about genes in textbooks, in
classroom interactions, and in student understanding? – w/ Ana
Maria R. de Almeida, Leonardo Celin Patiño and looking for
more students and colleagues…
• Development and investigation of teaching sequences about
genes and their functions in higher education and high school –
Looking for students and colleagues…
THANK YOU!!!