Molecular genetics

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Molecular_genetics

Molecular genetics is a branch of biology that addresses how differences in the structures or expression of DNA molecules manifests as variation among organisms. Molecular genetics often applies an "investigative approach" to determine the structure and/or function of genes in an organism's genome using genetic screens.

The field of study is based on the merging of several sub-fields in biology: classical Mendelian inheritance, cellular biology, molecular biology, biochemistry, and biotechnology. It integrates these disciplines to explore things like genetic inheritance, gene regulation and expression, and the molecular mechanism behind various life processes.

A key goal of molecular genetics is to identify and study genetic mutations. Researchers search for mutations in a gene or induce mutations in a gene to link a gene sequence to a specific phenotype. Therefore molecular genetics is a powerful methodology for linking mutations to genetic conditions that may aid the search for treatments of various genetics diseases.

History

For a detailled timeline, see Timeline of the history of genetics.

The discovery of DNA as the blueprint for life and breakthroughs in molecular genetics research came from the combined works of many scientists. In 1869, chemist Johann Friedrich Miescher, who was researching the composition of white blood cells, discovered and isolated a new molecule that he named nuclein from the cell nucleus, which would ultimately be the first discovery of the molecule DNA that was later determined to be the molecular basis of life. He determined it was composed of hydrogen, oxygen, nitrogen and phosphorus. Biochemist Albrecht Kossel identified nuclein as a nucleic acid and provided its name deoxyribonucleic acid (DNA). He continued to build on that by isolating the basic building blocks of DNA and RNA; made up of the nucleotides: adenine, guanine, thymine, cytosine, and uracil. His work on nucleotides earned him a Nobel Prize in Physiology.

In the early 1800s, Gregor Mendel, who became known as one of the fathers of genetics, made great contributions to the field of genetics through his various experiments with pea plants where he was able to discover the principles of inheritance such as recessive and dominant traits, without knowing what genes where composed of. In the mid 19th century, anatomist Walther Flemming discovered what we now know as chromosomes and the separation process they undergo through mitosis. His work along with Theodor Boveri first came up with the chromosomal theory of inheritance, which helped explain some of the patterns Mendel had observed much earlier.

For molecular genetics to develop as a discipline, several scientific discoveries were necessary.  The discovery of DNA as a means to transfer the genetic code of life from one cell to another and between generations was essential for identifying the molecule responsible for heredity. Molecular genetics arose initially from studies involving genetic transformation in bacteria. In 1944 Avery, McLeod and McCarthy^[8] isolated DNA from a virulent strain of S. pneumoniae, and using just this DNA were able to convert a harmless strain to virulence. They called the uptake, incorporation and expression of DNA by bacteria "transformation". This finding suggested that DNA is the genetic material of bacteria.^[9] Bacterial transformation is often induced by conditions of stress, and the function of transformation appears to be repair of genomic damage.

In 1950, Erwin Chargaff derived rules that offered evidence of DNA being the genetic material of life. These were "1) that the base composition of DNA varies between species and 2) in natural DNA molecules, the amount of adenine (A) is equal to the amount of thymine (T), and the amount of guanine (G) is equal to the amount of cytosine (C)." These rules, known as Chargaff's rules, helped to understand of molecular genetics. In 1953 Francis Crick and James Watson, building upon the X-ray crystallography work done by Rosalind Franklin and Maurice Wilkins, were able to derive the 3-D double helix structure of DNA.

The phage group was an informal network of biologists centered on Max Delbrück that contributed substantially to molecular genetics and the origins of molecular biology during the period from about 1945 to 1970. The phage group took its name from bacteriophages, the bacteria-infecting viruses that the group used as experimental model organisms. Studies by molecular geneticists affiliated with this group contributed to understanding how gene-encoded proteins function in DNA replication, DNA repair and DNA recombination, and on how viruses are assembled from protein and nucleic acid components (molecular morphogenesis). Furthermore, the role of chain terminating codons was elucidated. One noteworthy study was performed by Sydney Brenner and collaborators using "amber" mutants defective in the gene encoding the major head protein of bacteriophage T4. This study demonstrated the co-linearity of the gene with its encoded polypeptide, thus providing strong evidence for the "sequence hypothesis" that the amino acid sequence of a protein is specified by the nucleotide sequence of the gene determining the protein. 

The isolation of a restriction endonuclease in E. coli by Arber and Linn in 1969 opened the field of genetic engineering. Restriction enzymes were used to linearize DNA for separation by electrophoresis and Southern blotting allowed for the identification of specific DNA segments via hybridization probes. In 1971, Berg utilized restriction enzymes to create the first recombinant DNA molecule and first recombinant DNA plasmid.  In 1972, Cohen and Boyer created the first recombinant DNA organism by inserting recombinant DNA plasmids into E. coli, now known as bacterial transformation, and paved the way for molecular cloning.  The development of DNA sequencing techniques in the late 1970s, first by Maxam and Gilbert, and then by Frederick Sanger, was pivotal to molecular genetic research and enabled scientists to begin conducting genetic screens to relate genotypic sequences to phenotypes. Polymerase chain reaction (PCR) using Taq polymerase, invented by Mullis in 1985, enabled scientists to create millions of copies of a specific DNA sequence that could be used for transformation or manipulated using agarose gel separation. A decade later, the first whole genome was sequenced (Haemophilus influenzae), followed by the eventual sequencing of the human genome via the Human Genome Project in 2001. The culmination of all of those discoveries was a new field called genomics that links the molecular structure of a gene to the protein or RNA encoded by that segment of DNA and the functional expression of that protein within an organism. Today, through the application of molecular genetic techniques, genomics is being studied in many model organisms and data is being collected in computer databases like NCBI and Ensembl. The computer analysis and comparison of genes within and between different species is called bioinformatics, and links genetic mutations on an evolutionary scale.

Central dogma

This image shows an example of the central dogma using a DNA strand being transcribed then translated and showing important enzymes used in the processes.

The central dogma plays a key role in the study of molecular genetics. The central dogma states that DNA replicates itself, DNA is transcribed into RNA, and RNA is translated into proteins. Along with the central dogma, the genetic code is used in understanding how RNA is translated into proteins. Replication of DNA and transcription from DNA to mRNA occurs in the nucleus while translation from RNA to proteins occurs in the ribosome. The genetic code is made of four interchangeable parts of DNA molecules, called "bases": adenine, cytosine, thymine (uracil in RNA), and guanine and is redundant, meaning multiple combinations of these base pairs (which are read in triplicate) produce the same amino acid. Proteomics and genomics are fields in biology that come out of the study of molecular genetics and the central dogma.

Structure of DNA

An organism's genome is made up by its entire set of DNA and is responsible for its genetic traits, function and development. The composition of DNA itself is an essential component to the field of molecular genetics; it is the basis of how DNA is able to store genetic information, pass it on, and be in a format that can be read and translated.

DNA is a double stranded molecule, with each strand oriented in an antiparallel fashion. Nucleotides are the building blocks of DNA, each composed of a sugar molecule, a phosphate group and one of four nitrogenous bases: adenine, guanine, cytosine, and thymine. A single strand of DNA is held together by covalent bonds, while the two antiparallel strands are held together by hydrogen bonds between the nucleotide bases. Adenine binds with thymine and cytosine binds with guanine. It is these four base sequences that form the genetic code for all biological life and contains the information for all the proteins the organism will be able to synthesize.

Its unique structure allows DNA to store and pass on biological information across generations during cell division. At cell division, cells must be able to copy its genome and pass it on to daughter cells. This is possible due to the double-stranded structure of DNA because one strand is complementary to its partner strand, and therefore each of these strands can act as a template strand for the formation of a new complementary strand. This is why the process of DNA replication is known as a semiconservative process.

Techniques

Forward genetics

Forward genetics is a molecular genetics technique used to identify genes or genetic mutations that produce a certain phenotype. In a genetic screen, random mutations are generated with mutagens (chemicals or radiation) or transposons and individuals are screened for the specific phenotype. Often, a secondary assay in the form of a selection may follow mutagenesis where the desired phenotype is difficult to observe, for example in bacteria or cell cultures. The cells may be transformed using a gene for antibiotic resistance or a fluorescent reporter so that the mutants with the desired phenotype are selected from the non-mutants.

Mutants exhibiting the phenotype of interest are isolated and a complementation test may be performed to determine if the phenotype results from more than one gene. The mutant genes are then characterized as dominant (resulting in a gain of function), recessive (showing a loss of function), or epistatic (the mutant gene masks the phenotype of another gene). Finally, the location and specific nature of the mutation is mapped via sequencing. Forward genetics is an unbiased approach and often leads to many unanticipated discoveries, but may be costly and time consuming. Model organisms like the nematode worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the zebrafish Danio rerio have been used successfully to study phenotypes resulting from gene mutations.

An example of forward genetics in C. elegans (a nematode) using mutagenesis

Reverse genetics

Diagram illustrating the development process of avian flu vaccine by reverse genetics techniques

Reverse genetics is the term for molecular genetics techniques used to determine the phenotype resulting from an intentional mutation in a gene of interest. The phenotype is used to deduce the function of the un-mutated version of the gene. Mutations may be random or intentional changes to the gene of interest. Mutations may be a missense mutation caused by nucleotide substitution, a nucleotide addition or deletion to induce a frameshift mutation, or a complete addition/deletion of a gene or gene segment. The deletion of a particular gene creates a gene knockout where the gene is not expressed and a loss of function results (e.g. knockout mice). Missense mutations may cause total loss of function or result in partial loss of function, known as a knockdown. Knockdown may also be achieved by RNA interference (RNAi). Alternatively, genes may be substituted into an organism's genome (also known as a transgene) to create a gene knock-in and result in a gain of function by the host. Although these techniques have some inherent bias regarding the decision to link a phenotype to a particular function, it is much faster in terms of production than forward genetics because the gene of interest is already known.

Molecular genetic tools

Molecular genetics is a scientific approach that utilizes the fundamentals of genetics as a tool to better understand the molecular basis of a disease and biological processes in organisms. Below are some tools readily employed by researchers in the field.

Microsatellites

Microsatellites or single sequence repeats (SSRS) are short repeating segment of DNA composed to 6 nucleotides at a particular location on the genome that are used as genetic marker. Researchers can analyze these microsatellites in techniques such DNA fingerprinting and paternity testing since these repeats are highly unique to individuals/families. a can also be used in constructing genetic maps and to studying genetic linkage to locate the gene or mutation responsible for specific trait or disease. Microsatellites can also be applied to population genetics to study comparisons between groups.

Genome-wide association studies

Genome-wide association studies (GWAS) are a technique that relies on single nucleotide polymorphisms (SNPs) to study genetic variations in populations that can be associated with a particular disease. The Human Genome Project mapped the entire human genome and has made this approach more readily available and cost effective for researchers to implement. In order to conduct a GWAS researchers use two groups, one group that has the disease researchers are studying and another that acts as the control that does not have that particular disease. DNA samples are obtained from participants and their genome can then be derived through lab machinery and quickly surveyed to compare participants and look for SNPs that can potentially be associated with the disease. This technique allows researchers to pinpoint genes and locations of interest in the human genome that they can then further study to identify that cause of the disease.

Karyotyping

Karyotyping allows researchers to analyze chromosomes during metaphase of mitosis, when they are in a condensed state. Chromosomes are stained and visualized through a microscope to look for any chromosomal abnormalities. This technique can be used to detect congenital genetic disorder such as Down syndrome, identify gender in embryos, and diagnose some cancers that are caused by chromosome mutations such as translocations.

Modern applications

Genetic engineering

Genetic engineering is an emerging field of science, and researcher are able to leverage molecular genetic technology to modify the DNA of organisms and create genetically modified and enhanced organisms for industrial, agricultural and medical purposes. This can be done through genome editing techniques, which can involve modifying base pairings in a DNA sequence, or adding and deleting certain regions of DNA.

Gene editing

Gene editing allows scientists to alter/edit an organism's DNA. One way to due this is through the technique Crispr/Cas9, which was adapted from the genome immune defense that is naturally occurring in bacteria. This technique relies on the protein Cas9 which allows scientists to make a cut in strands of DNA at a specific location, and it uses a specialized RNA guide sequence to ensure the cut is made in the proper location in the genome. Then scientists use DNAs repair pathways to induce changes in the genome; this technique has wide implications for disease treatment.

Personalized medicine

Molecular genetics has wide implications in medical advancement and understanding the molecular basis of a disease allows the opportunity for more effective diagnostic and therapies. One of the goals of the field is personalized medicine, where an individual's genetics can help determine the cause and tailor the cure for a disease they are afflicted with and potentially allow for more individualized treatment approaches which could be more effective. For example, certain genetic variations in individuals could make them more receptive to a particular drug while other could have a higher risk of adverse reaction to treatments. So this information would allow researchers and clinicals to make the most informed decisions about treatment efficacy for patients rather than the standard trial and error approach.

Forensic genetics

Forensic genetics plays an essential role for criminal investigations through that use of various molecular genetic techniques. One common technique is DNA fingerprinting which is done using a combination of molecular genetic techniques like polymerase chain reaction (PCR) and gel electrophoresis. PCR is a technique that allows a target DNA sequence to be amplified, meaning even a tiny quantity of DNA from a crime scene can be extracted and replicated many times to provide a sufficient amount of material for analysis. Gel electrophoresis allows the DNA sequence to be separated based on size, and the pattern that is derived is known as DNA fingerprinting and is unique to each individual. This combination of molecular genetic techniques allows a simple DNA sequence to be extracted, amplified, analyzed and compared with others and is a standard technique used in forensics.

Biology in fiction

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Biology_in_fiction 

Boris Karloff in James Whale's 1931 film Frankenstein, based on Mary Shelley's 1818 novel. The monster is created by an unorthodox biology experiment.

Biology appears in fiction, especially but not only in science fiction, both in the shape of real aspects of the science, used as themes or plot devices, and in the form of fictional elements, whether fictional extensions or applications of biological theory, or through the invention of fictional organisms. Major aspects of biology found in fiction include evolution, disease, genetics, physiology, parasitism and symbiosis (mutualism), ethology, and ecology.

Speculative evolution enables authors with sufficient skill to create what the critic Helen N. Parker calls biological parables, illuminating the human condition from an alien viewpoint. Fictional alien animals and plants, especially humanoids, have frequently been created simply to provide entertaining monsters. Zoologists such as Sam Levin have argued that, driven by natural selection on other planets, aliens might indeed tend to resemble humans to some extent.

Major themes of science fiction include messages of optimism or pessimism; Helen N. Parker has noted that in biological fiction, pessimism is by far the dominant outlook. Early works such as H. G. Wells's novels explored the grim consequences of Darwinian evolution, ruthless competition, and the dark side of human nature; Aldous Huxley's Brave New World was similarly gloomy about the effects of genetic engineering.

Fictional biology, too, has enabled major science fiction authors like Stanley Weinbaum, Isaac Asimov, John Brunner, and Ursula Le Guin to create what Parker called biological parables, with convincing portrayals of alien worlds able to support deep analogies with Earth and humanity.

Aspects of biology

Aspects of biology found in fiction include evolution, disease, ecology, ethology, genetics, physiology, parasitism, and mutualism (symbiosis).

Evolution

Main article: Evolution in fiction

Evolution, including speculative evolution, has been an important theme in fiction since the late 19th century. It began, however, before Charles Darwin's time, and reflects progressionist and Lamarckist views (as in Camille Flammarion's 1887 Lumen) as well as Darwin's. Darwinian evolution is pervasive in literature, whether taken optimistically in terms of how humanity may evolve towards perfection, or pessimistically in terms of the dire consequences of the interaction of human nature and the struggle for survival. Other themes include the replacement of humanity, either by other species or by intelligent machines.

Disease

Main article: Disease in fiction

See also: Tuberculosis in human culture

Jack London's 1912 The Scarlet Plague (reprinted in 1949) takes place after an uncontrollable epidemic.

Diseases, both real and fictional, play a significant role in both literary and science fiction, some like Huntington's disease and tuberculosis appearing in many books and films. Pandemic plagues threatening all human life, such as The Andromeda Strain, are among the many fictional diseases described in literature and film. Science fiction takes an interest, too, in imagined advances in medicine. The Economist suggests that the abundance of apocalyptic fiction describing the "near annihilation or total extinction of the human race" by threats including deadly viruses rises when general "fear and unease", as measured by the Doomsday Clock, increase.

Disease in science fiction is often an allegory for societal issues, highlighting the phenomena of othering. Plague metaphors allow authors to consider the role of "us versus them" mentalities and break down dichotomies between humans and "others." Disease is also used as a metaphor for fear of globalization, highlighting the impulse to separate and surveil in order to define borders and control the "contamination" of intermingling.

Tuberculosis was a common disease in the 19th century. In Russian literature, it appeared in several major works. Fyodor Dostoevsky used the theme of the consumptive nihilist repeatedly, with Katerina Ivanovna in Crime and Punishment; Kirillov in The Possessed, and both Ippolit and Marie in The Idiot. Turgenev did the same with Bazarov in Father and Sons. In English literature of the Victorian era, major tuberculosis novels include Charles Dickens's 1848 Dombey and Son, Elizabeth Gaskell's 1855 North and South, and Mrs. Humphry Ward's 1900 Eleanor.

Genetics

Main article: Genetics in fiction

Further information: Reproduction and pregnancy in speculative fiction

Aspects of genetics including mutation or hybridisation, cloning (as in Brave New World), genetic engineering, and eugenics have appeared in fiction since the 19th century. Genetics is a young science, having started in 1900 with the rediscovery of Gregor Mendel's study on the inheritance of traits in pea plants. During the 20th century it developed to create new sciences and technologies including molecular biology, DNA sequencing, cloning, and genetic engineering. The ethical implications of modifying humans (and all their descendants) were brought into focus with the eugenics movement. Since then, many science fiction novels and films have used aspects of genetics as plot devices, often taking one of two routes: a genetic accident with disastrous consequences; or, the feasibility and desirability of a planned genetic alteration. The treatment of science in these stories has been uneven and often unrealistic. The 1997 film Gattaca attempted to portray science accurately but was criticised by scientists. Michael Crichton's 1990 novel Jurassic Park portrayed the cloning of whole dinosaur genomes from fossil remains of species extinct for millions of years, and their use to recreate living animals, using what was then known of genetics and molecular biology to create an "entertaining" and "thought-provoking" story.

Naomi Alderman's 2016 novel The Power imagines that women have electric organs like those of the electric eel, Electrophorus electricus, creating powerful electric fields with modified muscles. The pits along the electric eel's body are lateral line organs, used to detect prey by sensing small vibrations.

The lack of scientific understanding of genetics in the 19th century did not prevent science fiction works such as Mary Shelley's 1818 novel Frankenstein; or, The Modern Prometheus and H. G. Wells's 1896 The Island of Dr Moreau from exploring themes of biological experiment, mutation, and hybridisation, with their disastrous consequences, asking serious questions about the nature of humanity and responsibility for science.

Physiology

The creation scene in James Whale's 1931 film Frankenstein makes use of electricity to bring the monster to life. Shelley's idea of reanimation through electric shock was based on the physiology experiments of Luigi Galvani, who noted that a shock made the leg of a dead frog twitch. Electric shock is now routinely used in pacemakers, maintaining heart rhythm, and defibrillators, restoring heart rhythm.

The ability to produce electricity is central to Naomi Alderman's 2016 science fiction novel The Power. In the book, women develop the ability to release electrical jolts from their fingers, powerful enough to stun or kill. Fish such as the electric eel, Electrophorus electricus, create powerful electric fields with modified muscles, stacked end-to-end as cells in a battery in their electric organs, and the novel indeed references such fish and the electricity generated in striated muscle.

Parasitism

Main article: Parasites in fiction

A 1990s gargoyle at Paisley Abbey resembling a Xenomorph parasitoid from Alien

Parasites appear frequently in fiction, from ancient times onwards as seen in mythical figures like the blood-drinking Lilith, with a flowering in the nineteenth century. These include intentionally disgusting alien monsters in science fiction films, though these are sometimes less "horrible" than real examples in nature. Authors and scriptwriters have to some extent exploited parasite biology: lifestyles including parasitoid, behaviour-altering parasite, brood parasite, parasitic castrator, and many forms of vampire are found in books and films. Some fictional parasites, like the deadly parasitoid Xenomorphs in Alien, have become well known in their own right. Terrifying monsters are clearly alluring: writer Matt Kaplan notes that they induce signs of stress including raised heart rate and sweating, but people continue indulging in such works. Kaplan compares this to the "masochism" of liking very hot spicy foods, which induce mouth burns, sweating, and tears. The psychologist Paul Rozin suggests that there is a pleasure in seeing one's own body react as if to stress while knowing that no real harm will result. Some parasitic organisms in fictional works often have a Hive mind that they associate with. An example of this would be The Flood, from the Halo franchise.

Symbiosis

Main article: Symbiosis in fiction

Symbiosis (mutualism) appears in fiction, especially science fiction, as a plot device. It is distinguished from parasitism in fiction, a similar theme, by the mutual benefit to the organisms involved, whereas the parasite inflicts harm on its host. Fictional symbionts often confer special powers on their hosts. After the Second World War, science fiction moved towards more mutualistic relationships, as in Ted White's 1970 By Furies Possessed, which viewed aliens positively. In The Phantom Menace, Qui-Gon Jinn says microscopic lifeforms called midi-chlorians, inside all living cells, allow characters with enough of these symbionts in their cells to feel and use the Force.

Ethology

Delia Owens's 2018 novel Where the Crawdads Sing is set in a North Carolina swamp, where the "marsh girl" protagonist compares her wayward boyfriends to the "Sneaky Fuckers" she reads about in an ethology article.

Ethology, the study of animal behaviour, appears in the wildlife scientist Delia Owens's 2018 novel Where the Crawdads Sing. The protagonist, Kya, is abandoned by her parents at age six, and grows up alone in a North Carolina swamp, learning camouflage and how to hunt from the animals there. The local townspeople call her "the marsh girl". She reads about ethology including an article entitled "Sneaky Fuckers", using her knowledge to navigate the tricks and dating rituals of the local boys; and she compares herself to a female firefly, who uses her coded flashing light signal to lure a male of another species to his death, or a female mantis, who starts eating her mate's head and thorax while his abdomen is still copulating with her. "Female insects, Kya thought, know how to deal with their lovers."

Ecology

Main article: Ecofiction

Ecology, the study of the relationships between organisms and their environment, appears in fiction in novels such as Frank Herbert's 1965 Dune, Kim Stanley Robinson's 1992 Red Mars, and Margaret Atwood's 2013 MaddAddam. Dune brought ecology centre stage, with a whole planet struggling with its environment. Its lifeforms included giant sandworms for whom water is fatal and mouse-like animals able to survive in the planet's desert conditions. The book was influential on the environmental movement of the time.

In the 1970s, the impact of human activity on the environment stimulated a new kind of writing, ecofiction. It has two branches: stories about human impact on nature; and stories about nature (rather than humans). It encompasses books written in styles from modernism to magical realism, and in genres from mainstream to romance and speculative fiction. A 1978 anthology of ecofiction includes 19th and 20th century works by authors as diverse as Ray Bradbury, John Steinbeck, Edgar Allan Poe, Daphne du Maurier, E. B. White, Kurt Vonnegut Jr., Frank Herbert, H. H. Munro, J. G. Ballard, and Isaac Asimov.

Fictional organisms

A mock taxidermy specimen of a fictional rhinograde invented by the German zoologist Gerolf Steiner

Further information: Lists of fictional species and Speculative evolution

Fiction, especially science fiction, has created large numbers of fictional species, both alien and terrestrial. One branch of fiction, speculative evolution or speculative biology, consists specifically of the design of imaginary organisms in particular scenarios; this is sometimes informed by precise science.

Functions

Fictional biology serves a variety of function in film and literature, including the supply of suitably terrifying monsters, the communication of an author's worldview, and the creation of aliens for biological parables to illuminate what it is to be human. Real biology, such as of infectious diseases, equally provides a variety of contexts, from personal to highly dystopian, that can be exploited in fiction.

Monsters and aliens

Further information: Extraterrestrials in fiction and Humanoid

A common use of fictional biology in science fiction is to provide plausible alien species, sometimes simply as terrifying subjects, but sometimes for more reflective purposes. Alien species include H. G. Wells's Martians in his 1898 novel The War of the Worlds, the bug-eyed monsters of early 20th century science fiction, fearsome parasitoids, and a variety of giant insects, especially in early 20th century big bug movies.

Humanoid (roughly human-shaped) aliens are common in science fiction. One reason is that authors use the only example of intelligent life that they know: humans. The zoologist Sam Levin points out that aliens might indeed tend to resemble humans, driven by natural selection. Luis Villazon points out that animals that move necessarily have a front and a back; as with bilaterian animals on Earth, sense organs tend to gather at the front as they encounter stimuli there, forming a head. Legs reduce friction, and with legs, bilateral symmetry makes coordination easier. Sentient organisms will, Villazon argues, likely use tools, in which case they need hands and at least two other limbs to stand on. In short, a generally humanoid shape is likely, though octopus- or starfish-like bodies are also possible.

Many fictional plants were created in the 20th century, including John Wyndham's venomous, walking, carnivorous triffids. in his 1951 novel The Day of the Triffids, The idea of plants that could attack an incautious traveller began in the late 19th century; the potatoes in Samuel Butler's Erewhon had "low cunning". Early tales included Phil Robinson's 1881 The Man-Eating Tree with its gigantic flytraps, Frank Aubrey's 1897 The Devil Tree of El Dorado, and Fred White's 1899 Purple Terror. Algernon Blackwood's 1907 story "The Willows" powerfully tells of malevolent trees that manipulate people's minds.

• Types of monster in science fiction
• 
  Cephalopod-like sea monster in Jules Verne's Twenty Thousand Leagues Under the Seas drawn by Alphonse de Neuville, 1871
   
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  A bug-eyed monster, a trope of early science fiction. Illustration shows Stanley G. Weinbaum's 1951 story "A Man, A Maid, and Saturn's Temptation".
   
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  Big bug movie: Reynold Brown's poster for Nathan H. Juran's 1957 The Deadly Mantis
   
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  Man-eating plant: 1962 poster by Steve Sekely for a film adaptation of John Wyndham's 1951 novel The Day of the Triffids

Optimism and pessimism

Further information: Evolution in fiction

H. G. Wells's 1898 The War of the Worlds struck a pessimistic note about human evolution.

A major theme of science fiction and of speculative biology is to convey a message of optimism or pessimism according to the author's worldview. Whereas optimistic visions of technological progress are common enough in hard science fiction, pessimistic views of the future of humanity are far more usual in fiction based on biology.

A rare optimistic note is struck by the evolutionary biologist J. B. S. Haldane in his tale, The Last Judgement, in the 1927 collection Possible Worlds. Both Arthur C. Clarke's 1953 Childhood's End and Brian Aldiss's 1959 Galaxies Like Grains of Sand, too, optimistically imagine that humans will evolve godlike mental capacities.

The grim possibilities of Darwinian evolution with its ruthless "survival of the fittest" has been explored repeatedly from the beginnings of science fiction, as in H. G. Wells's novels The Time Machine (1895), The Island of Dr Moreau (1896), and The War of the Worlds (1898); these all pessimistically explore the possible dire consequences of the darker sides of human nature in the struggle for survival. Aldous Huxley's 1931 novel Brave New World is similarly gloomy about the oppressive consequences of advances in genetic engineering applied to human reproduction.

Biological parables

The protagonist's journey across Mars in Stanley Weinbaum's 1934 A Martian Odyssey

The literary critic Helen N. Parker suggested in 1977 that speculative biology could serve as biological parables which throw light on the human condition. Such a parable brings aliens and humans into contact, allowing the author to view humanity from an alien perspective. She noted that the difficulty of doing this at length meant that only a few major authors had attempted it, naming Stanley Weinbaum, Isaac Asimov, John Brunner, and Ursula Le Guin. In her view, all four had impressively full characterizations of alien beings. Weinbaum had created a "bizarre assortment" of intelligent beings, unlike Brunner's crablike but extinct Draconians. What united all four writers, she argued, was that the novels centred on the interactions between aliens and humans, creating deep analogies between the two kinds of life and from there commenting on humanity now and in the future. Weinbaum's 1934 A Martian Odyssey explored the question of how aliens and humans could communicate, given that their thought processes were utterly different. Asimov's 1972 The Gods Themselves both makes the aliens major characters, and explores parallel universes. Brunner's 1974 Total Eclipse creates a whole alien world, extrapolated from terrestrial threats.

In her 1969 The Left Hand of Darkness, Le Guin presents her vision of a universe of planets all inhabited by "men", descendants from the planet Hain. In the book, the ambassador Genly Ai from the civilised Ekumen worlds visits the "backward- and inward-looking" people of Gethen, only to end up in danger, from which he escapes by crossing the polar ice cap on a desperate but well-planned expedition with an exiled Gethenian Lord Chancellor, Estraven. They are ambisexual with no fixed gender, and go through periods of oestrus, called "kemmer", at which point an individual comes temporarily to function as either a male or a female, depending on whether they first encounter a male- or female-functioning partner during their period of kemmer. The invented biology reflects and exemplifies, according to Parker, the opposing but united dualities of Taoism such as light and darkness, maleness and femaleness, yin and yang. So too do the opposed characters of Genly Ai with his carefully objective reports, and of Estraven with his or her highly personal diary, as the story unfolds, illuminating humanity through adventure and science fiction strangeness.

Structure and themes

"The leafy sea dragon" (actually weedy seadragon) from William Buelow Gould's Sketchbook of fishes, c. 1832, used by Richard Flanagan in his 2001 novel Gould's Book of Fish

Modern novels sometimes make use of biology to provide structure and themes. Thomas Mann's 1912 Death in Venice relates the feelings of the protagonist to the progress of an epidemic of cholera, which eventually kills him. Richard Flanagan's 2001 novel Gould's Book of Fish makes use of the illustrations from artist and convict William Buelow Gould's book of 26 paintings of fish for chapter headings and as the inspiration for the various characters in the novel.

Realism

The geneticist Dan Koboldt observes that the science in science fiction is often oversimplified, reinforcing popular myths to the point of "pure fiction". In his own field, he gives as examples the idea that first-degree relatives have the same hair, eyes and nose as each other, and that a person's future is predicted by their genetic code, as (he states) in Gattaca. Koboldt points out that eye colour changes as children grow up: adults with green or brown eyes often had blue eyes as babies; that brown-eyed parents can have children with blue eyes, "and vice versa"; and that the brown pigment melanin is controlled by around 10 different genes, so inheritance is along a spectrum rather than being a blue/brown switch. Other authors in his edited collection Putting the Science in Fiction point out a wide variety of errors in the portrayal of other biological sciences.