Evolutionary Tinkering
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Evolutionary tinkering is an explanation of how
evolution Evolution is the change in the heritable Phenotypic trait, characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, re ...
happens in nature. It explains that evolution works as a tinkerer who experiments with miscellaneous items, unsure of the outcome, and utilizes whatever is available to craft functional objects whose utility may only become evident later. None of the materials serve a defined purpose initially, and each can be employed in multiple ways. According to the tinkering concept, “evolution does not produce novelties from scratch". It comes from previously unseen associations of old materials to modify an existing system to give a new function or combine systems together to enhance the functions. The transformation from
unicellular A unicellular organism, also known as a single-celled organism, is an organism that consists of a single cell, unlike a multicellular organism that consists of multiple cells. Organisms fall into two general categories: prokaryotic organisms and ...
to
multicellular A multicellular organism is an organism that consists of more than one cell (biology), cell, unlike unicellular organisms. All species of animals, Embryophyte, land plants and most fungi are multicellular, as are many algae, whereas a few organism ...
during evolution is such an event which has elaborated the existing function. The process of evolutionary tinkering takes quite a long time. As a meticulous tinkerer who continuously refines its creations, making adjustments, trimming and extending here and there, seizing every chance to gradually tailor them to their evolving purposes, this process happens over countless eons. Most of the time, traits in nature are barely favorable enough for
organism An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...
s to survive. For instance,
RuBisCO Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the light-independent (or "dark") part of photosynthesis, including the carbon fixation by wh ...
is profoundly inefficient, despite the fact that it catalyzes one of the most important reactions on the planet:
carbon fixation Biological carbon fixation, or сarbon assimilation, is the Biological process, process by which living organisms convert Total inorganic carbon, inorganic carbon (particularly carbon dioxide, ) to Organic compound, organic compounds. These o ...
. This is likely due to the
enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
originating in the
common ancestor Common descent is a concept in evolutionary biology applicable when one species is the ancestor of two or more species later in time. According to modern evolutionary biology, all living beings could be descendants of a unique ancestor commonl ...
of all
plastid A plastid is a membrane-bound organelle found in the Cell (biology), cells of plants, algae, and some other eukaryotic organisms. Plastids are considered to be intracellular endosymbiotic cyanobacteria. Examples of plastids include chloroplasts ...
s when the atmospheric conditions were drastically different than they are today.


François Jacob

In his seminal article 'Evolution and Tinkering',
François Jacob François Jacob (; 17 June 1920 – 19 April 2013) was a French biologist who, together with Jacques Monod, originated the idea that control of enzyme levels in all cells occurs through regulation of transcription. He shared the 1965 Nobel ...
first introduced the idea of tinkering to a broad audience of scientists, drawing from diverse fields such as molecular biology, evolutionary biology, and cultural anthropology. The concept of tinkering, or more precisely, the notion of ''bricolage'', serves as a theoretical framework for analyzing various phenomena characterized by a common underlying process: the opportunistic rearrangement and recombination of existing elements. Jacob and Monod also won the
Nobel Prize The Nobel Prizes ( ; ; ) are awards administered by the Nobel Foundation and granted in accordance with the principle of "for the greatest benefit to humankind". The prizes were first awarded in 1901, marking the fifth anniversary of Alfred N ...
in 1965 for his work on the ''lac'' operon.


Engineering versus tinkering

Natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the Heredity, heritable traits characteristic of a population over generation ...
is frequently likened to the work of an engineer, yet this analogy falls short. Unlike the engineer who operates based on meticulous planning and a clear vision of the end product, evolution lacks such deliberate intent. Additionally, while the engineer has access to carefully selected materials and specialized equipment tailored for their tasks,
evolution Evolution is the change in the heritable Phenotypic trait, characteristics of biological populations over successive generations. It occurs when evolutionary processes such as natural selection and genetic drift act on genetic variation, re ...
relies on the resources available in its surroundings. Moreover, the engineer's creations tend to approach a level of perfection achievable with current technology, whereas evolution does not strive for perfection but rather resembles a tinkerer. This tinkerer, akin to evolution, lacks a precise blueprint of the outcome and instead utilizes whatever materials are at hand to fashion something functional. While the engineer depends on specific materials and tools precisely suited to their project, the tinkerer makes do with miscellaneous scraps and remnants. The resulting creations of the tinkerer emerge from a series of opportunistic events, enriching their repertoire with each encounter. The development of
lung The lungs are the primary Organ (biology), organs of the respiratory system in many animals, including humans. In mammals and most other tetrapods, two lungs are located near the Vertebral column, backbone on either side of the heart. Their ...
s in terrestrial
vertebrate Vertebrates () are animals with a vertebral column (backbone or spine), and a cranium, or skull. The vertebral column surrounds and protects the spinal cord, while the cranium protects the brain. The vertebrates make up the subphylum Vertebra ...
s illustrates a process akin to tinkering rather than deliberate engineering. It originated in certain freshwater fish faced with oxygen deficient environments, leading them to ingest air and absorb oxygen through their esophageal walls. Over time, this behavior favored the enlargement of the esophageal surface area, eventually giving rise to lung-like structures through the emergence and enlargement of esophageal diverticula. The
brain The brain is an organ (biology), organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It consists of nervous tissue and is typically located in the head (cephalization), usually near organs for ...
is the key adaptive feature of humans, yet still holds mysteries regarding its precise purpose. The brain has also evolved through natural selection over millions of years, like other body parts, primarily to serve our reproductive needs. However, the human brain's development was more complex unlike straightforward evolutionary changes such as a leg into a wing. It involved adding new structures, particularly the
neocortex The neocortex, also called the neopallium, isocortex, or the six-layered cortex, is a set of layers of the mammalian cerebral cortex involved in higher-order brain functions such as sensory perception, cognition, generation of motor commands, ...
, onto older ones. This rapid evolution led to a division between the neocortex, responsible for intellectual functions, and the older structures, controlling
emotion Emotions are physical and mental states brought on by neurophysiology, neurophysiological changes, variously associated with thoughts, feelings, behavior, behavioral responses, and a degree of pleasure or suffering, displeasure. There is ...
al and
visceral In a multicellular organism, an organ is a collection of Tissue (biology), tissues joined in a structural unit to serve a common function. In the biological organization, hierarchy of life, an organ lies between Tissue (biology), tissue and an o ...
activities. These older structures lack the discriminative and symbolic abilities of the neocortex and are primarily associated with emotions. Despite the dominance of the neocortex in intellectual processes, the older structures maintain strong connections with automatic centers, ensuring vital functions like obtaining food and responding to threats. This evolutionary process, characterized by the emergence of a dominant neocortex alongside the persistence of older systems, resembles a tinkering process, where new elements are added onto existing ones without fully replacing them.


Evolution by molecular tinkering

Jacob was convinced that although morphological analysis supports his notion of ''bricolage'', one would find more evidence of tinkering at the
molecular A molecule is a group of two or more atoms that are held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry, ...
level. The tinkering model suggests that the
gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...
s of the earliest organisms were very short, and all subsequent genes were formed by duplication, combination, and reassorting these original sequences. It is well established that gene duplication has produced a great deal of diversity throughout evolutionary history. One example of molecular tinkering can be found in
mitochondrial A mitochondrion () is an organelle found in the cells of most eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is used ...
nucleoprotein Nucleoproteins are proteins conjugated with nucleic acids (either DNA or RNA). Typical nucleoproteins include ribosomes, nucleosomes and viral nucleocapsid proteins. Structures Nucleoproteins tend to be positively charged, facilitating inte ...
s, some of which originate from
eukaryote The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...
s; in this case, the tinkerer used whatever tools were at her disposal, including materials from an entirely different taxonomic domain. To understand molecular tinkering, it is important to grasp the concept of a
protein domain In molecular biology, a protein domain is a region of a protein's Peptide, polypeptide chain that is self-stabilizing and that Protein folding, folds independently from the rest. Each domain forms a compact folded Protein tertiary structure, thre ...
, which is a distinct region of a
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
that has a defined shape, which determines the function of the protein. Some have used the analogy of Lego blocks to explain: the domains can be taken apart and put together again in unique ways, thus changing the shape and function of the protein. There are many different means by which tinkering can result in molecular and
phenotypic In genetics, the phenotype () is the set of observable characteristics or traits of an organism. The term covers the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological propert ...
novelty, primarily by taking apart the Lego blocks of proteins and putting them together again in unique patterns. Generally, these processes add to the organizational complexity of the
genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...
, the
proteome A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. P ...
, or both.


Internal gene duplication

There are several forms of gene duplication. The product of whole-gene duplication is two copies of the gene, whereas that of diploid-type gene duplication is one gene that has doubled in length. Internal gene duplication results in repeated
nucleotide Nucleotides are Organic compound, organic molecules composed of a nitrogenous base, a pentose sugar and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both o ...
sequences within a gene, and less than 100% of the gene is replicated. Because adding nucleotides to a sequence could impact splicing, this process may result in changing the identity of
intron An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e., a region inside a gene."The notion of the cistron .e., gen ...
s and
exon An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence ...
s; alternatively, the sequence may retain its original identity as an exon or intron, respectively. If an exon that encodes for one or more domains is duplicated, this could directly result in a more complex protein via domain accretion. Eukaryotic genes have undergone frequent internal gene duplication throughout evolutionary history. One example is seen in the dinucleotide-binding regions of glyceraldehyde 3-phosphate dehydrogenase and alcohol dehydrogenase: the duplicated domain is capable of binding with more molecules than the unduplicated. Another is the ovomucoid gene, which is the product of two internal duplications.


Mosaic proteins

Mosaic proteins are encoded by
chimeric gene Chimeric genes (literally, made of parts from different sources) form through the combination of portions of two or more coding sequences to produce new genes. These mutations are distinct from fusion genes which merge whole gene sequences into ...
s (or mosaic genes). These genes result from domain shuffling, which is accomplished via exon shuffling, gene fusion, or gene fission. Domain shuffling has been found to be at least partially responsible for some traits in modern vertebrates. Most domains only have a small number of uses, while very few domains are used as Lego blocks over and over again in multidomain proteins. Phenotypic innovation does not arise solely from the creation of new proteins, but also from changing gene expression and protein-protein interactions. One example of novelty associated with domain shuffling is multicellularity. Gene fusion (the creation of a fusion gene by joining two genes together) and gene fission or fragmentation, which results in splitting one gene with many domains into multiple smaller genes, are the other two molecular mechanisms by which mosaic proteins can be formed.


Alternative splicing

Alternative splicing Alternative splicing, alternative RNA splicing, or differential splicing, is an alternative RNA splicing, splicing process during gene expression that allows a single gene to produce different splice variants. For example, some exons of a gene ma ...
is another mechanism of molecular tinkering that may be responsible for increasing diversity in the proteome. One special kind of alternative splicing is nested genes, which produce intron-encoded proteins. It has been proposed that nested gene structures could be maintained via neutral processes according to the neutral theory of evolution.


De novo evolution of protein-coding genes from non-coding DNA

De novo gene birth is very rare. The most probable path from noncoding DNA to a protein-coding gene is to first become a protogene, similar to how functional genes first become
pseudogene Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Pseudogenes can be formed from both protein-coding genes and non-coding genes. In the case of protein-coding genes, most pseudogenes arise as superfluous copies of fun ...
s before becoming completely nongenic. Although they are too rare to notably increase the number of proteins in a given lineage, the tinkering model posits that adding just a few Lego blocks to the collection allows for many new possible combinations of domains, i.e., proteins with new shapes and functions.


Exonization of introns and pseudoexonization of exons

Exonization is a very rare phenomenon in which an intron becomes an exon. In pseudoexonization, an exon becomes nonfunctional; this in turn changes the shape and function of the protein.


Gene loss and unitary pseudogenes

When selective constraints disappear, it is possible for genes to be lost via one of two mechanisms. The first is deleting a single-copy gene. The second is nonfunctionalization of a single-copy gene; this produces a unitary
pseudogene Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Pseudogenes can be formed from both protein-coding genes and non-coding genes. In the case of protein-coding genes, most pseudogenes arise as superfluous copies of fun ...
, which has no functional paralogs, is comparable to
vestigial Vestigiality is the retention, during the process of evolution, of genetically determined structures or attributes that have lost some or all of the ancestral function in a given species. Assessment of the vestigiality must generally rely on co ...
anatomical structures, and is uncommon due to its often deleterious nature. In the rare case that gene loss becomes fixed in a
population Population is a set of humans or other organisms in a given region or area. Governments conduct a census to quantify the resident population size within a given jurisdiction. The term is also applied to non-human animals, microorganisms, and pl ...
, it is difficult to definitively say what was the cause.


References

{{genarch Biological evolution Biology theories