How molecular techniques are developed from natural systems

Abstract A striking characteristic of the molecular techniques of genetics is that they are derived from natural occurring systems. RNA interference, for example, utilizes a mechanism that evolved in eukaryotes to destroy foreign nucleic acid. Other case studies I highlight are restriction enzymes, DNA sequencing, polymerase chain reaction, gene targeting, fluorescent proteins (such as, green fluorescent protein), induced pluripotent stem cells, and clustered regularly interspaced short palindromic repeats-CRISPR associated 9. The natural systems’ strategy for technique development means that biologists utilize the activity of a mechanism's effector (protein or RNA) and exploit biological specificity (protein or nucleic acid can cause precise reactions). I also argue that the developmental trajectory of novel molecular techniques, such as RNA interference, has 4 characteristic phases. The first phase is discovery of a biological phenomenon. The second phase is identification of the biological mechanism's trigger(s): the effector and biological specificity. The third phase is the application of the trigger(s) as a technique. The final phase is the maturation and refinement of the technique. Developing new molecular techniques from nature is crucial for future genetic research.


Introduction
Biologists can explain the complex phenomena underlying living processes by identifying the genetic mechanisms that produce such processes (Schaffner 1996;Darden 2006;Tabery et al. 2015). To access the causal structure of genetic mechanisms, biologists use sophisticated molecular techniques to manipulate the components of the mechanism and observe the resulting effects. Scientific knowledge in genetics therefore progresses in a distinctive way; progress is driven by the introduction and use of novel techniques (Vance 1996;Waters 2008). In contrast, ecology is an area of biology that has progressed through theoretical developments and model building (Sarkar and Elliott-Graves 2016). What drives the development of molecular techniques in genetics?

From natural systems to techniques
A striking feature of the development of molecular techniques, which biologists themselves often highlight (for example, Mello and Conte 2004;Lander 2016), is that they are derived from naturally occurring systems. These techniques are not developed through "rational design" using engineering principles (discussed in O'Malley 2009), do not utilize physiochemical properties (such as microscopy and gel electrophoresis), nor do they mimic nature (Ahn et al. 2015).
I will highlight 8 contemporary molecular techniques that are derived from natural systems, as highly successful and prominent examples. These techniques have been patented, led to landmark scientific articles, and been the subject of a Nobel Prize (Ronai and Griffiths 2019). Therefore, the scientific community sees these 8 techniques as significant advances. In chronological order, these techniques are restriction enzymes, DNA sequencing, polymerase chain reaction (PCR), gene targeting, fluorescent proteins (such as, green fluorescent protein), RNA interference (RNAi), induced pluripotent stem cells (iPS), and clustered regularly interspaced short palindromic repeats-CRISPR associated 9 (CRISPR-Cas9) (see Table 1 for a description of the techniques). These 8 molecular techniques are so ubiquitous that they are regarded as common knowledge by geneticists, and when these techniques are mentioned in the Methods section of a scientific article, a citation for the technique is not required (see for example RNAi in Ronai et al. 2016).
The 8 highly successful molecular techniques examined are derived from mechanisms that each evolved for a particular biological function in a natural system (see Table 1). The biological function of the RNAi mechanism, for example, is a eukaryotic defense system for the destruction of foreign nucleic acid and mobile elements (Waterhouse et al. 1998(Waterhouse et al. , 2001van Rij and Andino 2006). In addition, the RNAi mechanism is thought to have been repurposed (Cerutti and Casas-Mollano 2006) for the precise regulation of endogenous gene expression, in particular for the regulation of developmental genes (Carrington and Ambros 2003). The same biological function, to destroy foreign nucleic acid in an organism, underlies the techniques of RNAi (derived from eukaryotes) and CRISPR-Cas9 (derived from prokaryotes) (Bhaya et al. 2011;Wright et al. 2016), but the 2 techniques involve different molecular mechanisms (Table 1). Therefore, the "arms race" that occurs between viruses and their organismal hosts has provided biologists with the basis of 2 techniques. Natural systems show biologists what is mechanistically possible and natural mechanisms have been selected by evolution so are likely to have a high level of effectiveness (Arnold 2018). However, the components of these natural mechanisms are contingent on historical, iterative events rather than being at an optimal state. Biologists can alter these components to reach an optimal state but are constrained by their possibility space (Arnold 2015).
Biologists use molecular techniques developed from preexisting, natural mechanisms because they are compatible with living processes (Weber 2017) and do not create artificial phenomena. Furthermore, the use of a natural mechanism may allow the continuing function of the biological process (for example, fluorescent proteins), and cellular-based techniques can be stably inherited in designed constructs with transgenerational effects (Chalfie et al. 1994). These techniques can therefore be used to observe or intervene in active, complex biological processes even when no comprehensive understanding of these processes exists.

The importance of natural systems for the development of molecular techniques
I propose that molecular techniques are developed by exploiting 2 key components of natural mechanisms: an effector molecule's (such as, proteins or RNAs) activity and the use of biological specificity (protein or nucleic acid can cause precise reactions). The importance of an effector's activity and the use of biological specificity for molecular techniques are often implicitly recognized by geneticists. For example, many studies on RNAi highlight the technique's effector, which is the RNA-induced silencing complex (RISC) (see Vaucheret et al. 1998;Filipowicz et al. 2005;Li et al. 2006;Rana 2007;Siomi and Siomi 2009;Fellmann and Lowe 2014), and that specificity is derived from double-stranded RNA (dsRNA) (see Fire et al. 1998;Kennerdell and Carthew 1998;Waterhouse et al. 1998;Hamilton and Baulcombe 1999;Hammond et al. 2000;Parrish et al. 2000;Hammond et al. 2001;Waterhouse et al. 2001;Elbashir et al. 2001b;Bartel 2004;Rana 2007;Siomi and Siomi 2009;Fellmann and Lowe 2014).

Effector activity
Living systems use effector molecules to generate a particular activity within a mechanism (Bich and Bechtel 2022). I have identified the protein effector, all from a natural system, for each of the 8 highly successful molecular techniques ( Table 1). The majority of the techniques utilize proteins that are catalytic enzymes, and the techniques leverage the efficiency of the enzymatic activity (Table 1). The 2 exceptions are the techniques of fluorescent proteins and iPS which utilize a protein's stereochemistry, a fluorophore or structural motif, respectively (Table 1).
A technique's effector is either endogenous or exogenous to the experimental system (Table 1). Endogenous effector techniques use the effector for its original purpose but appropriate the overall mechanism. For example, the effector of RNAi is the RISC, which is an endogenous component of a molecular mechanism present in all eukaryotes (Cerutti and Casas-Mollano 2006). Exogenous effector techniques use the effector for its original biological function, but in another biological context. For example, the effector of a restriction enzyme experiment is a restriction endonuclease, which is a component that must be added to the experiment. As the exogenous effector is introduced into the experimental system (either permanently or transiently), it is more tractable than an endogenous effector.

Biological specificity
Living systems need biological specificity to achieve precise control over their molecular mechanisms (Woodward 2010;Griffiths et al. 2015). In the 8 highly successful molecular techniques examined, geneticists introduce biological specificity into their experimental systems to precisely access the target mechanism with fine-grained control (Waters 2007). Geneticists need interventions with minimal off-target events. Also, high specificity means that the technique can be "multiplexed," as multiple nucleic acid sites can be targeted at the same time. I have identified that the majority of the 8 molecular techniques use nucleic acid sequence informational specificity (Griffiths and Stotz 2013); nucleic acid is the substrate of the mechanism (Table 1). For example, RNAi provides fine-grained control of gene expression because it uses nucleic acid sequence informational specificity. Before RNAi, such modulation of gene expression was not possible (Bellés 2010). One molecular technique, fluorescent proteins, uses what I term "engineered informational specificity," where the geneticist creates the specificity by placing the effector in a highly specific location. The last 2 molecular techniques, iPS and restriction enzymes (Table 1), use protein stereochemical specificity (Griffiths and Stotz 2013). For techniques that have stereochemical specificity (Table 1), the effector provides the specificity.

The importance of an effector's activity and biological specificity
If there are multiple techniques available to achieve the same experimental purpose, then the technique with the greatest efficiency or superior type of specificity is preferred by the scientific community. For example, 3 recent techniques used for the purpose of DNA editing are zinc finger nucleases (ZFNs), a technique that uses 2 protein domains coupled together (Kim et al. 1996); transcription activator-like effector nucleases (TALENs), a technique derived from the bacteria Xanthomonas (Boch et al. 2009;Moscou and Bogdanove 2009); and CRISPR-Cas9 (Table 1). A ZFNs' and TALENs' specificity is stereochemical, so they require proteins to be reengineered for every experiment. These 2 techniques are therefore not as easily programmable for a wide range of targets when compared with CRISPR-Cas9, which uses a guide RNA (informational specificity). The superior specificity of CRISPR-Cas9 has meant that it has been commercially viable and has replaced ZFNs and TALENs as the premier genome-editing technique (Doudna and Charpentier 2014;Corbyn 2015). The effector activity and specificity of a technique are critical to its success.

Molecular technique development has 4 phases
I propose that molecular techniques derived from natural systems have a specific pattern of historical development, with 4 critical phases. These phases are the discovery of a biological phenomenon, identification of the biological mechanism's trigger(s) (the specificity and effector components), application of the technique, and maturation of the technique. Each of the 8 highly successful molecular techniques shows the 4 phases of technique development (see Table 2). I use RNAi as a detailed case study due to its contemporary history. This technique introduces molecules of RNA into an organism or cell to reduce the expression of a gene of interest (reviewed in Mello and Conte 2004).  Luria and Human (1952) Discovered that bacteriophage (T1, T2, T3, T4, T5,  T6, and T7) vary in their ability to grow in different bacterial (Escherichia coli and Shigella dysenteriae) strains. Dussoix and Arber (1962) Discovered that bacteriophage λ DNA degrades in E. coli strains.

Identification of triggers (effector/specificity)
Kelly Jr and , Smith and Welcox (1970) (study in 2 parts) Identified the nucleotide recognition sequence that causes restriction enzymes (in particular, a type II which recognizes DNA and cuts sites at the same place, endonuclease R from Haemophilus influenzae) to cut DNA. Danna and Nathans (1971) Applied restriction enzyme (endonuclease R from H. influenzae) to cut up DNA. Feinberg and Vogelstein (1983) Developed restriction enzymes using radiolabeling to efficiently recover DNA fragments. DNA sequencing 1. Discovery Watson and Crick (1953) Discovered the complementary DNA structure in calf thymus (possibly) and proposed a mechanism for DNA replication. Also, predicted the existence of DNA polymerase. Matthaei et al. (1962) Discovered that 3 nucleotides code for a specific amino acid in a cell-free system of E. coli. Also, predicted the code was universal. Kornberg et al. (1956b) Identified DNA polymerase in E. coli. Atkinson et al. (1969) Identified that dideoxynucleotides cause DNA polymerase to terminate synthesis of DNA. Sanger et al. (1977) Applied dideoxynucleotides with DNA polymerase from E. coli to determine the DNA sequence of bacteriophage φX174.

Maturation
The C. elegans Sequencing Consortium (1998) Developed DNA (Sanger) sequencing to sequence the first multicellular organism (Caenorhabditis elegans) genome. International Human Genome Sequencing Consortium (2001) Developed DNA (Sanger) sequencing to sequence the human genome. PCR 1. Discovery Watson and Crick (1953) Discovered the complementary DNA structure in calf thymus (possibly) and proposed a mechanism for DNA replication. Also, predicted the existence of DNA polymerase. Meselson and Stahl (1958) Discovered that DNA replicates semi-conservatively in E. coli. Kornberg et al. (1956b) Identified DNA polymerase in E. coli. Kornberg et al. (1956a) Identified that a primer causes DNA polymerase to initiate synthesis of DNA. Saiki et al. (1985) Applied primers with DNA polymerase from E. coli to amplify DNA region. Saiki et al. (1988) Developed PCR to be thermostable using DNA polymerase from Thermus aquaticus. Gene targeting 1. Discovery Gluzman et al. (1977); Vogel et al. (1977) (study in 2 parts)

Maturation
Discovered that a mutant phenotype can be rescued in a simian virus 40 (SV40) temperature-sensitive mutant (tsD202) when added to monkey CV1 cells (containing endogenous integrated SV40). Also, discovered that the rescue is due to recombination.

Identification of trigger
(specificity) Hinnen et al. (1978) Identified that exogenous DNA of LEU2 causes site-specific recombination with homologous chromosomal DNA in Saccharomyces cerevisiae.

Identification of trigger (effector)
A single study cannot be identified because the biological mechanism underlying gene targeting has multiple effectors Identified that an endogenous endonucleases create a double-stranded break and this initiates repair pathway. For example, SPO11. Smithies et al. (1985) Applied exogenous DNA to modify only the target gene (β-globin) in human cells. Thomas and Capecchi (1987) Developed gene targeting to inactivate an endogenous gene (hptr) in mouse embryonic stem cells. Doetschman et al. (1987) Developed gene targeting to correct mutant hptr in mouse embryonic stem cells. Mansour et al. (1988) Developed gene targeting selection (positive for cells that have incorporated exogenous DNA (continued)

The first phase: discovery of a biological phenomenon
In the first phase of technique development, biologists identify and describe an unusual phenomenon in a natural system. At this stage, the underlying mechanism is not well characterized, and the biological function of the mechanism is typically unknown. These studies can be identified by examining the studies that the later phases build upon.  Davenport and Nicol (1955) Discovered the green fluorescence in Aequorea victoria.

Identification of trigger
(specificity) Prasher et al. (1992) Identified the genomic DNA and cDNA sequence of GFP that causes fluorescence in Aequorea victoria. Chalfie et al. (1994) Applied GFP cDNA to generate fluorescence in E. coli and Caenorhabditis elegans cells.

Maturation
Heim et al. (1995) Developed GFP spectral characteristics using a point mutation in E. coli. Cormack et al. (1996) Developed GFP variants that fluoresce at higher intensity in E. coli. RNAi 1. Discovery Napoli et al. (1990) Discovered the knockdown of chalcone synthase in P. hybrida. Fire et al. (1998) Identified that dsRNA causes sequence specific regulation of mRNA in Caenorhabditis elegans. Applied dsRNA to knockdown gene expression in Caenorhabditis elegans.

Identification of trigger
(specificity processed component) Hamilton and Baulcombe (1999) Identified that siRNA (processed product of dsRNA) causes sequence specific regulation of mRNA in plants.

Identification of trigger (effector)
Hammond et al. (2000) Identified the endogenous RISC complex which contains an endonuclease that cleaves target mRNA in Drosophila cells. Elbashir et al. (2001a) Developed RNAi to knockdown gene expression in mammalian and Drosophila cells. iPS 1. Discovery Gurdon (1962) Discovered that cell differentiation is reversible, as the nucleus of a somatic cell can successfully replace the nucleus of an egg cell in Xenopus laevis.

& 3. Identification of trigger (effector/specificity) & application of trigger
Takahashi and Yamanaka (2006) Identified the genome and transcriptome changes that cause 4 transcription factors (Oct3/4, Sox2, c-Myc, and Klf4 in mice) to make somatic cells become pluripotent stem cells. Applied the 4 transcription factors cDNA to reprogram embryonic and adult fibroblast mice cells. Takahashi et al. (2007) Developed iPS in human cells. CRISPR-Cas9 1. Discovery Ishino et al. (1987) Discovered the CRISPR motif (repeated sequence with spacers) in the DNA sequence of E. coli. Makarova et al. (2002) Identified the CRISPR-associated (cas) genes in the genome sequences of Bacteria and Archaea. In particular, the class 2, Type II (recognizes DNA and cleavage results in double-stranded break) Cas9 (COG3513) in Streptococcus pyogenes, Campylobacter jejuni, Neisseria meningitidis, and Pasteurella multocida. Brouns et al. (2008) Identified that CRISPR RNAs (crRNAs) cause Cas9 to sequence specifically cleave DNA in E. coli.

& 3. Identification of trigger (specificity component B) & application of triggers
Jinek et al. (2012) Identified that crRNA and transactivating CRISPR RNA (tracrRNA) must complementary base pair to cause Cas9 to site-specifically cleave DNA. Applied a tracrRNA-crRNA complex (the "single-guide RNA") with Cas9 from S. pyogenes to cleave DNA. Gasiunas et al. (2012) Applied crRNA with Cas9 from Streptococcus thermophilus to cleave DNA. Cong et al. (2013) Developed CRISPR-Cas9 to edit the genome of mammalian (human and mouse) cells. Mali et al. (2013) For each technique, I highlight the published papers, in chronological order, for each of the 4 phases: discovery of the biological phenomenon, identification of the biological mechanism's triggers, application of the trigger(s) as a technique, and examples of highly cited papers that demonstrate the maturation of the technique. For example, in the early 1990s, the RNAi phenomenon was first identified in plants (Table 2). Napoli et al. (1990) and van der Krol et al. (1990) aimed to increase color intensity in the Petunia hybrida flower and introduced synthetic sense RNA into the plant in order to overexpress a gene in the pathway that controls formation of the flower pigment. Contrary to expectation, these flowers had reduced pigment, rather than more. Therefore, the sense RNA had reduced the mRNA of the endogenous gene. During the 1990s, multiple studies were conducted on how different organisms actively respond to the introduction of RNA (Fire et al. 1991;Romano and Macino 1992;Guo and Kemphues 1995;Lin et al. 1995;Mello et al. 1996;Powell-Coffman et al. 1996;Guedes and Priess 1997). At this time, the RNAi phenomenon was described using many different terms: the initial study by Napoli et al. (1990) termed this phenomenon "co-suppression," but a follow-up study (Van Blokland et al. 1994) demonstrated that silencing occurred posttranscriptionally, so the phenomenon was then referred to as "posttranscriptional gene silencing." Another study identified the RNAi phenomenon in a fungus, Neurospora crassa, and termed it "quelling" (Romano and Macino 1992). While the term "RNA-mediated interference" was coined in an early Caenorhabditis elegans RNAi study (Rocheleau et al. 1997). These early studies on RNA produced knowledge that was critical to the development of RNAi.

The second phase: identification of the trigger(s) of a biological mechanism
In the second phase of technique development, biologists identify the specificity and effector component of the mechanism (see Table 3a and b). I term the specificity and effector components of a mechanism as trigger(s) because they are the key causative agents and are the "causally specific actual difference maker" under typical conditions (Carrier 2004;Waters 2007;Woodward 2010). Once biologists identify the trigger(s), they can use it to precisely manipulate the mechanism. If the effector is endogenous to the experimental system (Table 1), then it does not need to be added to the experiment and its identification is not essential for the development of the technique. However, effectors that are exogenous to the experimental system are identified before the specificity trigger (Table 1).
For example, in the late 1990s, dsRNA was found to be causally specific for the RNAi mechanism ( Table 2). The dsRNA was investigated due to it being accidently produced in earlier experiments, as it was found that: … polymerases, although highly specific, produce some random or ectopic transcripts. DNA transgene arrays also produce a fraction of aberrant RNA products 3 … we surmised that the interfering RNA populations might include some molecules with double-stranded character. , p. 807) Fire et al. (1998 tested the specificity of RNA molecules to control the RNAi mechanism in C. elegans (Table 3a). The dsRNA was identified as the cause of sequence-specific regulation of mRNA, as they: … investigate[d] the requirements for structure and delivery of the interfering RNA. To our surprise, we found that doublestranded RNA was substantially more effective at producing interference than was either strand individually. Fire et al. (1998, p. 806) Therefore, the study was a conclusive demonstration of how dsRNA can be used to control the RNAi mechanism.
After dsRNA was identified as a trigger, biologists wondered how it could bind and sequence specifically cleave mRNA. They found that dsRNA is processed into small RNA fragments (antisense and sense) in multiple organisms and suggested that these were necessary for RNAi (Hamilton and Baulcombe 1999;Hammond et al. 2000;Parrish et al. 2000;Zamore et al. 2000). These small interfering RNAs (siRNAs), 21-23 nucleotides in length, were shown to sequence specifically guide the cleavage of the mRNA (Elbashir et al. 2001b) (Table 2).
Two years after the RNAi technique was developed, the endogenous effector component that degrades the target mRNA was identified as the RISC ( Table 2). The endonuclease that cuts the target mRNA sequence specifically was identified in Drosophila melanogaster cells as Argonaute, which is part of the RISC (Hammond et al. 2000;Martinez et al. 2002). The effector that cleaves dsRNA into siRNAs was identified as a ribonuclease type III named Dicer (Bernstein et al. 2001). Biologists then pursued further mechanistic details, such as the functions of different forms of the Argonaute protein (Rana 2007).

The third phase: application of the trigger(s) as a technique
In the third phase of technique development, biologists conclusively determine that when the trigger is introduced into the experimental system, it achieves some intended effect on the target of the specificity. The trigger is exploited in 3 types of investigative strategies: to intervene on a cellular experimental system (for example, RNAi); to manipulate an effector's activity in a noncellular experimental system (for example, restriction enzymes); or as a tracer, to follow a biological process (see Griesemer 2007; for example, fluorescent proteins) (Table 1). At this stage, a deep understanding of the mechanism underlying the technique is not necessary for the technique to work.
For example, the RNAi technique was first applied in the Fire et al.'s (1998) paper "Potent and specific genetic interference by dsRNA in Caenorhabditis elegans" ( Table 2). The study was a conclusive demonstration of how dsRNA can be applied as a molecular technique to manipulate gene expression in C. elegans. Fire et al. (1998, p. 810) concluded that RNAi: … adds to the tools available for studying gene function in C. elegans. In particular, it should now be possible functionally to analyse many interesting coding regions 21 for which no specific function has been defined.
Interestingly, Fire et al. (1998, p. 810) explicitly stated that they did not understand the biological function of the RNAi mechanism: Whatever their target, the mechanisms underlying RNA interference probably exist for a biological purpose.
It is important to note that when a molecular technique is developed for an organismal experimental context (Table 1), it is typically tested in a genetic model organism system. For example, RNAi was first developed using the model organism C. elegans . A model organism provides standardized experimental systems that are relatively well characterized at the molecular level, which therefore act as a prototype for technique development (Ankeny 2000;Leonelli and Ankeny 2013). When a technique has been validated in a model organism, there is the expectation that due to the fundamental unity of living systems, the technique will be able to be applied to other organisms. The use of model organisms in this phase is particularly important given the complexity and cost of molecular experiments.

The fourth phase: maturation of the technique
In the fourth phase of technique development, the technique has been established, and biologists improve and expand its performance. The scientific community invests considerable research activity into characterizing, both spatially and temporally, the mechanism in natural systems. Therefore, the technique generates further research on the biological mechanism that underlies Table 3. Key experiments for the RNAi technique conducted by Fire et al. (1998  Experiments that (a) identified the triggers in the RNAi mechanism and (b) identified the target of the specificity in the RNAi mechanism.
it. The new knowledge acquired may improve access to the mechanism or allow the technique to be better controlled, enabling the technique to continue to be refined and standardized. Immediately following the seminal RNAi study of Fire et al. (1998), the technique was shown to work in multiple organisms (Table 2): C. elegans (Fitzgerald and Schwarzbauer 1998;Montgomery et al. 1998;Ogg and Ruvkun 1998;Page and Winter 1998;Skop and White 1998;Tabuse et al. 1998;Timmons and Fire 1998); 2 species of plants, Nicotiana tabaccum and Oryza sativa (Waterhouse et al. 1998); and D. melanogaster (Kennerdell and Carthew 1998). In mammals, RNAi using dsRNA initially failed due to the immune response elicited; however, when siRNAs were used, gene expression could be altered (Elbashir et al. 2001a). RNAi has become a highly selective molecular technique for reducing expression of a target gene, and today it is widely used for both fundamental and applied research (Mello and Conte 2004;Deng et al. 2014;Fellmann and Lowe 2014). To this day, the biological mechanism of RNAi is still being investigated.

Molecular technique development
The 4 phases I have identified are necessary features of technique development when derived from a natural system. I have shown that 8 highly successful molecular techniques have these 4 phases of development (Table 2). Additional techniques that likely follow this phased development from natural systems, include reverse transcription, transposable elements, molecular cloning (utilizing a plasmid vector), monoclonal antibodies, site directed mutagenesis, recombinases, optogenetics, and immunotherapy (utilizing endogenous immune system components).
The development of new molecular techniques helps accelerate research in genetics and generates new scientific knowledge that would otherwise not exist. A new technique can also help uncover previously undetected biological phenomena, in turn leading to the development of yet another technique. For example, restriction enzymes were instrumental to the initial detection of the RNAi phenomena (Napoli et al. 1990;van der Krol et al. 1990), and during the application phase of development for RNAi, green fluorescent protein was used to visualize that the RNAi mechanism occurs within cells (Table 3b; Fire et al. 1998). Therefore, the molecular techniques used in genetics build upon one another and are cumulative.

Scientific values and the success of biological techniques
Three scientific values (Kuhn 1977;Darden 1991;Douglas 2013) are important for the genetics community's adoption of a molecular technique. First, a technique should be fruitful for further research. Techniques generate knowledge and open up new areas of research. For example, RNAi has helped geneticists manipulate RNA thus leading to a more sophisticated understanding of the function of RNA (Mello and Conte 2004) and has allowed geneticists to manipulate genes that are lethal in development in order to investigate their functions (for example, Fitzgerald and Schwarzbauer 1998). Second, a technique should allow expansion of its scope of application far beyond its original biological context. A technique that has applications in many experimental contexts means that a larger scientific community can use the technique. In addition, a technique that can be used in mammals is particularly desired due to the value placed on medical and therapeutic research. For example, the RNAi effector, RISC, is present in all eukaryotes (Cerutti and Casas-Mollano 2006) and RNAi can be used in human cell lines (Elbashir et al. 2001a). Third, a technique should have "extendability." A technique should accommodate modifications so that it can be used for different capabilities to its original purpose. A technique can therefore become the progenitor for a family of related techniques. For example, a form of RNAi has been developed that used RNA molecules targeted at promoters to increase rather than decrease gene expression (Li et al. 2006). These 3 scientific values have helped establish the success of the 8 biological techniques in the scientific community.

Concluding remarks
I have highlighted 8 highly successful techniques of contemporary genetics that are derived from natural systems. The history of these techniques, I have shown, falls into 4 distinctive phases. It is an open question whether genetics will continue to progress through the development of molecular techniques derived from natural systems. Perhaps knowledge construction in biology requires a natural systems strategy. Alternatively, there is some evidence that geneticists working on synthetic biology have started to use rational design in organisms (Hutchison et al. 2016); for example, the high profile "Human Genome Project-Write" aims to artificially synthesize the whole human genome to improve medical research and therapeutics (Boeke et al. 2016). However, geneticists often find that rational design is laborious and that selection methods on natural systems lead to improved technique development and outcomes (Silverman 2003). Furthermore, a rational design strategy cannot be used to access the causal structure of molecular mechanisms when no comprehensive understanding of these mechanisms exists.
Genetics has a historically accumulated set of molecular techniques to manipulate, intervene on, and trace molecular processes. Progress in genetics is greatly dependent on its powerful techniques-the cycle between discovery of biological phenomenon, mechanistic understanding, and application as a technique will continue.

Data availability
The author affirms that all data necessary for confirming the conclusions of the article are present within the article and tables.

Acknowledgments
I am most grateful to my PhD co-supervisor Paul Griffiths, who told me that this was the worthwhile project I should pursue for my PhD and helped me develop this project. Thank you also to the Theory and Method in Biosciences group at the University of Sydney who supported me while I researched this project and provided feedback while writing the manuscript. Lastly, thank you to my undergraduate biology teachers, as this project was inspired by their lectures on revolutionary molecular techniques being developed from the intricacies of the natural world.
Funding IR was financially supported by an APA from the Australian Government.

Conflicts of interest statement
The author(s) declare no conflict of interest.