Generation of Animals  consists of five books, which are themselves split into varying numbers of chapters. Most editions of this work categorise it with  Bekker numbers . In general, each book covers a range of related topics, however there is also a significant amount of overlap in the content of the books. For example, while one of the two principal topics covered in book I is the function of  semen  ( gone ,  sperma ), this account is not finalised until partway through book II.


Book I (715a – 731b)


Chapter 1 begins with Aristotle claiming to have already addressed the parts of animals, referencing the author's work  of the same name . While this and possibly his other  biological works , have addressed three of the  four causes  pertaining to animals, the  final ,  formal , and  material , the  efficient cause  has yet to be spoken of. He argues that the efficient cause, or "that from which the source of movement comes" [ 1 ]  can be addressed with an inquiry into the generation of animals. Aristotle then provides a general overview of the processes of reproduction adopted by the various genera, for instance most ' blooded ' animals reproduce by  coition  of a male and female of the same  species , but cases vary for 'bloodless' animals.


The  reproductive organs  of males and females are also investigated. Through chapters 2–5 Aristotle successively describes the general reproductive features common to each sex, the differences in  reproductive parts  among blooded animals, the causes of differences of  testes  in particular, and why some animals do not have external reproductive organs. The latter provides clear examples of Aristotle's  teleological  approach to causation, as it is applied to  biology . He argues that the male  hedgehog  has its testes near its  loin , unlike the majority of vivipara, because due to their spines hedgehogs mate standing upright. The hedgehog's form is that of an animal able to use its spines for self-defence, and so its reproductive organs are situated in such a way as to complement this.


Chapter 6 describes why  fish  and  serpents  copulate in a short space of time, and chapter 7 provides an explanation for why serpents intertwine during coition. Chapters 8–11 focus on female reproductive organs, and in particular the differences in viviparous and  oviparous  production of young, and the differing states of the  eggs  produced by ovipara. This is continued in chapters 12 and 13, where Aristotle discusses the reasons the  uterus  is internal and the testes external, and their locations among various species. Concluding this section on the reproductive parts of animals is an overview from chapters 14–16 of the generative faculties of  crustacea ,   cephalopods , and  insects . This section contains an admission of an observational uncertainty, with Aristote stating that observations of insect coition are not yet detailed enough to classify into types. [ 2 ]


The remainder of Book I (chapters 17 – 23) is concerned with providing an account of semen and its contribution to the generative process. The primary conclusions reached in this section are, firstly, that semen is not a bodily waste product, but "a residue of useful nutriment", [ 3 ]  and that because the bodily emissions produced by females during copulation are not of a similar nutritive character, semen must be the efficient cause of offspring.


Book II (731b – 749a)


Chapters 1–3 of Book II continue the discussion of semen from the end of Book I. As a result of questioning potential ways in which the particular parts of animals might come to be formed, such as semen containing small versions of the bodily organs, [ 4 ]  before settling on the idea that semen contributes the potential ( dunamis ) for the parts to come into being as they are. This is the basis for the imparting of the  soul  upon the material substratum present in the egg, as the female reproductive residue itself contains no active principle for the motion required to form an  embryo . Aristotle's conception of the soul should not be mistaken for one which takes the soul to be a non-physical substance separate to the body. It instead comprises the ability for some function to be performed, which in the case of bodily development means the ability for organs to perform their bodily functions. Scholar Devin Henry describes Aristotle's view as follows:


"Aristotelian souls are not the sorts of things that are capable of being implanted in bodily organs from without (except perhaps intellectual soul). Soul is not an extra ingredient added to the organ over-and-above its structure. Once there is a properly constructed organ it straightaway possess the corresponding soul-function in virtue of its structure." [ 5 ]


The generative capacity of semen in imparting the soul is its heat, with semen itself being "a compound of breath and water". [ 6 ]  It is the component of breath ( pneuma ) that shapes the material provided by the female into the correct form.


The mechanics of the development of the embryo take up much of chapters 4–7, with Aristotle addressing first the different stages of development at which vivipara and ovipara expel their young. In chapter 5 the theory of soul-imparting is amended slightly, as observations of  wind-eggs  show that the female, unassisted, is able to impart the nutritive aspect of the soul, which Aristotle claims is its lowest portion .  Chapter 6 addresses the order in which the parts of an embryo come about, and in chapter 7 Aristotle argues that, contrary to what  Democritus  apparently thought, that "children are nourished in the uterus by sucking some lump of flesh", [ 7 ]  in actuality unborn vivipara are nourished by the  umbilical cord . Chapter 8 discusses cross-breeding of species, and the  sterility  of  mules .


Book III (749a – 763b)


Book III covers non-viviparous embryonic development. The first four chapters provide a description and explanation of eggs, while in chapters 5–7 Aristotle responds to other ideas about eggs and some observational difficulties in providing an empirical account of all eggs. The final chapters cover the development of hitherto unmentioned animals.


Chapter 1 is on the subject of bird eggs, with Aristotle providing explanations for why different birds produce different amounts of eggs, why some birds produce wind-eggs, and why bird eggs are sometimes of two colours. Following an explication of the formation of eggs and how they provide nutrition for the embryo in chapter 2, in chapter 3 Aristotle compares the eggs of  birds  against those of fish. The descriptive account of eggs is completed in chapter 4, which describes the growth of some eggs after they have been laid.


Chapters 5 and 6 are a response to what Aristotle takes to be falsely-held beliefs of other  scientists  concerning the process of procreation. For example,  Anaxagoras  apparently held that  weasels  give birth from their mouths because "the young of the weasel are very small like those of the other fissipeds, of which we shall speak later, and because they often carry the young about in their mouths. [ 8 ]  Aristotle states instead that weasels have the same uteruses as other  quadrupeds , and there is nothing to connect the uterus to the mouth, so such a claim as Anaxagoras' must be unfounded.


Chapters 7–10 cover the generative processes of  selachians , cephalopods, crustacea, insects and  bees , in successive order. Chapter 11 concerns the generation of  testacea , which are said to generate spontaneously. While it is possible for some of the Testacea, such as mussels, to emit a  liquid  slime which can form others of the same kind, they are also formed "in connexion with putrefaction and admixture of rain-water." [ 9 ]


Book IV (763b – 778a)


Book IV is primarily on the topic of biological inheritance. Aristotle is concerned with both the similarities between the offspring and parents and the differences that can arise within a particular species as a result of the generative process. Chapters 1 is an account of the origin of the sexes. Aristotle considers the sexes to be "the first principles of all living things". [ 10 ]  Given this, the sex of an embryo is determined entirely by the potency of the fertilising semen, which contains the male principle. If this semen lacks heat in fashioning the material present in the female then the male principle cannot take hold, and therefore its opposite principle must take hold. In chapter two Aristotle provides pieces of observational evidence for this, including the following:


"Again, more males are born if copulation takes place when north than when south winds are blowing; for animals' bodies are more liquid when the wind is in the south, so that they produce more residue – and more residue is harder to concoct; hence the semen of the males is more liquid and so is the discharge of the menstrual fluids in women." [ 11 ]


In chapter 3 Aristotle provides the primary elements of his theory of inheritance and resemblances. Utilising the account of the function of semen from Book II Aristotle describes how the movement of semen upon the proto-embryonic material gives rise to particular traits inherited from one's ancestors. Semen contains the general male principle, and contains in addition that of the  particular  male whose semen it is, so  Socrates ' semen will contain his particular genetic traits. In fashioning the material the semen imparts, or does not impart, genetic traits in the same way as the determination of sex, where a resemblance to the father will be imparted onto the material if the semen is of a suitable temperature, provided the male principle has established the sex as male. If instead the male principle was hot enough to be imparted but not that of the particular male, Socrates, was not then the movement may either put forth a resemblance to the mother, or it could relapse into that of the father of the father or some other non-immediate ancestor.


Chapter 4 develops this theory for the cases of  deformities , and why different animals produce different amounts of  offspring . The former is due to malformed reproductive material present in the female, and for the latter it is particular relations of the size of the animal, the moisture of reproductive materials, and the heat of semen. Chapter 5 presents the causes of  superfetation , which is an inadequate separation of multiple young during gestation. Chapters 6 and 7 focus on the causes of other birth defects, and why males are allegedly more likely to suffer from  defects . Chapters 8–10 concern the production of  milk , why animals are born headfirst, and on the length of gestation being proportional to the length of life, respectively.


Book V (778a – 789b)


Aristotle takes Book V to be an investigation of  "the qualities by which the parts of animals differ." [ 12 ]  The subjects addressed by this book are a miscellaneous range of animal parts, such as  eye colour  (chapter 1),  body hair  (chapter 3) and the  pitch of the voice  (chapter 7). The apparent lack of a single causal scheme or subject matter for these discrete topics has led to disagreement in how this book relates to the rest of the  Generation of Animals . Some scholars [ 13 ] [ 14 ]  take the Book only to be concerned only with  material causes  of intra-species differences that arise later in development, in contrast with the earlier books' systematic use of teleology. Others [ 15 ]  have suggested that Book V does utilise causation other than material to a considerable extent.


Works Cited


Genetic architecture  is the underlying genetic basis of a  phenotypic   trait  and its variational properties. [ 1 ]  Phenotypic variation for  quantitative traits  is, at the most basic level, the result of the  segregation of alleles  at  quantitative trait loci (QTL) . [ 2 ]  Environmental factors and other external influences can also play a role in phenotypic variation. Genetic architecture is a broad term that can be described for any given individual based on information regarding gene and allele number, the distribution of allelic and mutational effects, and patterns of  pleiotropy ,  dominance , and  epistasis . [ 1 ]


There are several different experimental views of genetic architecture. Some researchers recognize that the interplay of various genetic mechanisms is incredibly complex, but believe that these mechanisms can be averaged and treated, more or less, like statistical noise. [ 3 ]  Other researchers claim that each and every gene interaction is significant and that it is necessary to measure and model these individual systemic influences on evolutionary genetics. [ 1 ]


Genetic architecture can be studied and applied at many different levels. At the most basic, individual level, genetic architecture describes the genetic basis for differences between individuals, species, and populations. This can include, among other details, how many genes are involved in a specific phenotype and how gene interactions, such as epistasis, influence that phenotype. [ 1 ]   Line-cross analyses  and  QTL analyses  can be used to study these differences. [ 2 ]  This is perhaps the most common way that genetic architecture is studied, and though it is useful for supplying pieces of information, it does not generally provide a complete picture of the genetic architecture as a whole.


Genetic architecture can also be used to discuss the evolution of populations. [ 1 ]  Classical quantitative genetics models, such as that developed by  R.A. Fisher , are based on analyses of phenotype in terms of the contributions from different genes and their interactions. [ 3 ]  Genetic architecture is sometimes studied using a  genotype–phenotype map , which graphically depicts the relationship between the genotype and the phenotype. [ 4 ]


Genetic architecture is incredibly important for understanding  evolutionary theory  because it describes phenotypic variation in its underlying genetic terms, and thus it gives us clues about the evolutionary potential of these variations. Therefore, genetic architecture can help us to answer biological questions about speciation, the evolution of sex and recombination, the survival of small populations, inbreeding, understanding diseases, animal and plant breeding, and more. [ 1 ]


Evolvability  is literally defined as the ability to evolve. In terms of genetics, evolvability is the ability of a genetic system to produce and maintain potentially adaptive genetic variants. There are several aspects of genetic architecture that contribute strongly to the evolvability of a system, including autonomy, mutability, coordination, epistasis, pleiotropy, polygeny, and robustness. [ 1 ] [ 2 ]


A study published in 2006 used phylogeny to compare the genetic architecture of differing human skin color. In this study, researchers were able to suggest a speculative framework for the evolutionary history underlying current-day phenotypic variation in human skin pigmentation based on the similarities and differences they found in the genotype. [ 7 ]  Evolutionary history is an important consideration in understanding the genetic basis of any trait, and this study was among the first to utilize these concepts in a paired fashion to determine information about the underlying genetics of a phenotypic trait.


In 2013, a group of researchers used  genome-wide association studies (GWAS)  and genome-wide interaction studies (GWIS) to determine the risk of  congenital heart defects  in patients with  Down Syndrome . [ 8 ]  Down Syndrome is a genetic disorder caused by trisomy of human chromosome 21. The current hypothesis regarding congenital heart defect phenotypes in Down Syndrome individuals is that three copies of functional genomic elements on chromosome 21 and genetic variation of chromosome 21 and non-chromosome 21 loci predispose patients to abnormal heart development. This study identified several congenital heart defect risk loci in Down Syndrome individuals, as well as three  copy number variation (CNV)  regions that may contribute to congenital heart defects in Down Syndrome individuals.


Another study, which was published in 2014, sought to identify the genetic architecture of psychiatric disorders. The researchers in this study suggested that there are a large number of contributing loci that are related to various psychiatric disorders. [ 9 ]  Additionally, they, like many others, suggested that the genetic risk of psychiatric disorders involves the combined effects of many common variants with small effects - in other words, the small effects of a wide number of variants at specific loci add together to produce a large, combined effect on the overall phenotype of the individual. They also acknowledged the presence of large but rare mutations that have a large effect on phenotype. This study showcases the intricacy of genetic architecture by providing an example of many different SNPs and mutations working together, each with a varying effect, to generate a given phenotype.


Other studies regarding genetic architecture are many and varied, but most use similar types of analyses to provide specific information regarding loci involved in producing a phenotype. A study of the human immune system in 2015 [ 10 ]  uses the same general concepts to identify several loci involved in the development of the immune system, but, like the other studies outlined here, failed to consider other aspects of genetic architecture, such as environmental influences. Unfortunately, many other aspects of genetic architecture remain difficult to quantify.


Although there are a few studies that seek to explore the other aspects of genetic architecture, there is little ability with current technologies to link all of the pieces together to build a truly comprehensive model of genetic architecture. For example, in 2003, a study of genetic architecture and the environment was able to show an association of social environment with variation in body size in  Drosophila melanogaster . [ 11 ]  However, this study was not able to tie a direct link to specific genes involved in this variation.


The  genetic code  is the set of rules used by living  cells  to  translate  information encoded within genetic material ( DNA  or  RNA  sequences of nucleotide triplets or  codons ) into  proteins . Translation is accomplished by the  ribosome , which links  proteinogenic amino acids  in an order specified by  messenger RNA  (mRNA), using  transfer RNA  (tRNA) molecules to carry amino acids and to read the mRNA three  nucleotides  at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.


The codons specify which amino acid will be added next during  protein biosynthesis . With some exceptions, [ 1 ]  a three-nucleotide codon in a nucleic acid sequence specifies a single amino acid. The vast majority of  genes  are encoded with a single scheme (see the  RNA codon table ). That scheme is often called the canonical or standard genetic code, or simply  the  genetic code, though  variant codes  (such as in  mitochondria ) exist.


Efforts to understand how proteins are encoded began after  DNA's structure  was discovered in 1953. The key discoverers, English biophysicist  Francis Crick  and American biologist  James Watson , working together at the  Cavendish Laboratory  of the University of Cambridge, hypothesied that information flows from DNA and that there is a link between DNA and proteins. [ 2 ]  Soviet-American physicist  George Gamow  was the first to give a workable scheme for protein synthesis from DNA. [ 3 ]  He postulated that sets of three bases (triplets) must be employed to encode the 20 standard amino acids used by living cells to build proteins, which would allow a maximum of  4 3  = 64  amino acids. [ 4 ]  He named this DNA–protein interaction (the original genetic code) as the "diamond code". [ 5 ]


In 1954, Gamow created an informal scientific organisation the  RNA Tie Club , as suggested by Watson, for scientists of different persuasions who were interested in how  proteins were synthesised  from genes. However, the club could have only 20 permanent members to represent each of the 20 amino acids; and four additional honorary members to represent the four nucleotides of DNA. [ 6 ]


The first scientific contribution of the club, later recorded as "one of the most important unpublished articles in the history of science" [ 7 ]  and "the most famous unpublished paper in the annals of molecular biology", [ 8 ]  was made by Crick. Crick presented a type-written paper titled  "On Degenerate Templates and the Adaptor Hypothesis: A Note for the RNA Tie Club" [ 9 ]  to the members of the club in January 1955, which "totally changed the way we thought about protein synthesis", as Watson recalled. [ 10 ]  The hypothesis states that the triplet code was not passed on to amino acids as Gamow thought, but carried by a different molecule, an adaptor, that interacts with amino acids. [ 8 ]  The adaptor was later identified as tRNA. [ 11 ]


The  Crick, Brenner, Barnett and Watts-Tobin experiment  first demonstrated that  codons  consist of three DNA bases.


Marshall Nirenberg  and  J. Heinrich Matthaei  were the first to reveal the nature of a codon in 1961. [ 12 ]  They used a  cell-free system  to  translate  a poly- uracil  RNA sequence (i.e., UUUUU...) and discovered that the  polypeptide  that they had synthesized consisted of only the amino acid  phenylalanine . [ 13 ]  They thereby deduced that the codon UUU specified the amino acid phenylalanine.


This was followed by experiments in  Severo Ochoa 's laboratory that demonstrated that the poly- adenine  RNA sequence (AAAAA...) coded for the polypeptide poly- lysine [ 14 ]  and that the poly- cytosine  RNA sequence (CCCCC...) coded for the polypeptide poly- proline . [ 15 ]  Therefore, the codon AAA specified the amino acid  lysine , and the codon CCC specified the amino acid  proline . Using various  copolymers  most of the remaining codons were then determined.


Subsequent work by  Har Gobind Khorana  identified the rest of the genetic code. Shortly thereafter,  Robert W. Holley  determined the structure of  transfer RNA  (tRNA), the adapter molecule that facilitates the process of translating RNA into protein. This work was based upon Ochoa's earlier studies, yielding the latter the  Nobel Prize in Physiology or Medicine  in 1959 for work on the  enzymology  of RNA synthesis. [ 16 ]


Extending this work, Nirenberg and  Philip Leder  revealed the code's triplet nature and deciphered its codons. In these experiments, various combinations of  mRNA  were passed through a filter that contained  ribosomes , the components of cells that  translate  RNA into protein. Unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments. [ 17 ]  Khorana, Holley and Nirenberg received the Nobel Prize (1968) for their work. [ 18 ]


The three stop codons were named by discoverers Richard Epstein and Charles Steinberg. "Amber" was named after their friend Harris Bernstein, whose last name means "amber" in German. [ 19 ]  The other two stop codons were named "ochre" and "opal" in order to keep the "color names" theme.


In a broad academic audience, the concept of the evolution of the genetic code from the original and ambiguous genetic code to a well-defined ("frozen") code with the repertoire of 20 (+2) canonical amino acids is widely accepted. [ 20 ]
However, there are different opinions, concepts, approaches and ideas, which is the best way to change it experimentally. Even models are proposed that predict "entry points" for synthetic amino acid invasion of the genetic code. [ 21 ]


Since 2001, 40 non-natural amino acids have been added into proteins by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring  protein structure  and function or to create novel or enhanced proteins. [ 22 ] [ 23 ]


H. Murakami and M. Sisido extended some codons to have four and five bases.  Steven A. Benner  constructed a functional 65th ( in vivo ) codon. [ 24 ]


In 2015  N. Budisa ,  D. Söll  and co-workers reported the full substitution of all 20,899  tryptophan  residues (UGG codons) with unnatural thienopyrrole-alanine in the genetic code of the bacterium  Escherichia coli . [ 25 ]


In 2016 the first stable semisynthetic organism was created. It was a (single cell) bacterium with two synthetic bases (called X and Y). The bases survived cell division. [ 26 ] [ 27 ]


In 2017, researchers in South Korea reported that they had engineered a mouse with an extended genetic code that can produce proteins with unnatural amino acids. [ 28 ]


In May 2019, researchers reported the creation of a new "Syn61" strain of the  bacterium   Escherichia coli . This strain has a fully  synthetic  genome that is refactored (all overlaps expanded), recoded (removing the use of three out of 64 codons completely), and further modified to remove the now unnecessary tRNAs and release factors. It is fully viable and grows 1.6× slower than its wild-type counterpart "MDS42". [ 29 ] [ 30 ]


A reading frame is defined by the initial triplet of nucleotides from which translation starts. It sets the frame for a run of successive, non-overlapping codons, which is known as an " open reading frame " (ORF). For example, the string 5'-AAATGAACG-3' (see figure), if read from the first position, contains the codons AAA, TGA, and ACG ; if read from the second position, it contains the codons AAT and GAA ; and if read from the third position, it contains the codons ATG and AAC. Every sequence can, thus, be read in its  5' → 3' direction  in three  reading frames , each producing a possibly distinct amino acid sequence: in the given example, Lys (K)-Trp (W)-Thr (T), Asn (N)-Glu (E), or Met (M)-Asn (N), respectively (when translating with the vertebrate mitochondrial code). When DNA is double-stranded, six possible  reading frames  are defined, three in the forward orientation on one strand and three reverse on the opposite strand. [ 32 ] : 330   Protein-coding frames are defined by a  start codon , usually the first AUG (ATG) codon in the RNA (DNA) sequence.


In  eukaryotes , ORFs in  exons  are often interrupted by  introns .


Translation starts with a chain-initiation codon or  start codon . The start  codon alone is not sufficient to begin the process. Nearby sequences such as the  Shine-Dalgarno  sequence in  E. coli  and  initiation factors  are also required to start translation. The most common start codon is AUG, which is read as  methionine  or as  formylmethionine  (in bacteria, mitochondria, and plastids). Alternative start codons depending on the organism include "GUG" or "UUG"; these codons normally represent  valine  and  leucine , respectively, but as start codons they are translated as methionine or formylmethionine. [ 33 ]


The three  stop codons  have names: UAG is  amber , UGA is  opal  (sometimes also called  umber ), and UAA is  ochre . Stop codons are also called "termination" or "nonsense" codons. They signal release of the nascent polypeptide from the ribosome because no cognate tRNA has anticodons complementary to these stop signals, allowing a  release factor  to bind to the ribosome instead. [ 34 ]


During the process of  DNA replication , errors occasionally occur in the  polymerization  of the second strand. These errors,  mutations , can affect an organism's  phenotype , especially if they occur within the protein coding sequence of a gene. Error rates are typically 1 error in every 10–100 million bases—due to the "proofreading" ability of  DNA polymerases . [ 36 ] [ 37 ]


Missense mutations  and  nonsense mutations  are examples of  point mutations  that  can cause genetic diseases such as  sickle-cell disease  and  thalassemia  respectively. [ 38 ] [ 39 ] [ 40 ]  Clinically important missense mutations generally change the properties of the coded amino acid residue among basic, acidic, polar or non-polar states, whereas nonsense mutations result in a  stop codon . [ 32 ]


Mutations that disrupt the reading frame sequence by  indels  ( insertions  or  deletions ) of a non-multiple of 3 nucleotide bases are known as  frameshift mutations . These mutations usually result in a completely different translation from the original, and likely cause a  stop codon  to be read, which truncates the protein. [ 41 ]  These mutations may impair the protein's function and are thus rare in  in vivo  protein-coding sequences. One reason inheritance of frameshift mutations is rare is that, if the protein being translated is essential for growth under the selective pressures the organism faces, absence of a functional protein may cause death before the organism becomes viable. [ 42 ]  Frameshift mutations may result in severe genetic diseases such as  Tay–Sachs disease . [ 43 ]


Although most mutations that change protein sequences are harmful or neutral, some mutations have benefits. [ 44 ]  These mutations may enable the mutant organism to withstand particular environmental stresses better than  wild type  organisms, or reproduce more quickly. In these cases a mutation will tend to become more common in a population through  natural selection . [ 45 ]   Viruses  that use  RNA  as their genetic material have rapid mutation rates, [ 46 ]  which can be an advantage, since these viruses thereby evolve rapidly, and thus evade the  immune system  defensive responses. [ 47 ]  In large populations of asexually reproducing organisms, for example,  E. coli , multiple beneficial mutations may co-occur. This phenomenon is called  clonal interference  and causes competition among the mutations. [ 48 ]


Degeneracy is the redundancy of the genetic code. This term was given by Bernfield and Nirenberg. The genetic code has redundancy but no ambiguity (see the  codon tables  below for the full correlation). For example, although codons GAA and GAG both specify  glutamic acid  (redundancy), neither specifies another amino acid (no ambiguity). The codons encoding one amino acid may differ in any of their three positions. For example, the amino acid leucine is specified by  Y U R  or CU N  (UUA, UUG, CUU, CUC, CUA, or CUG) codons (difference in the first or third position indicated using  IUPAC notation ), while the amino acid  serine  is specified by UC N  or AG Y  (UCA, UCG, UCC, UCU, AGU, or AGC) codons (difference in the first, second, or third position). [ 49 ]  A practical consequence of redundancy is that errors in the third position of the triplet codon cause only a silent mutation or an error that would not affect the protein because the  hydrophilicity  or  hydrophobicity  is maintained by equivalent substitution of amino acids; for example, a codon of NUN (where N = any nucleotide) tends to code for hydrophobic amino acids. NCN yields amino acid residues that are small in size and moderate in  hydropathicity ; NAN encodes average size hydrophilic residues. The genetic code is so well-structured for hydropathicity that a mathematical analysis ( Singular Value Decomposition ) of 12 variables (4 nucleotides x 3 positions) yields a remarkable correlation (C = 0.95) for predicting the hydropathicity of the encoded amino acid directly from the triplet nucleotide sequence,  without translation. [ 50 ] [ 51 ]   Note in the table, below, eight amino acids are not affected at all by mutations at the third position of the codon, whereas in the figure above, a mutation at the second position is likely to cause a radical change in the physicochemical properties of the encoded amino acid.
Nevertheless, changes in the first position of the codons are more important than changes in the second position on a global scale. [ 52 ]   The reason may be that charge reversal (from a positive to a negative charge or vice versa) can only occur upon mutations in the first position of certain codons, but not upon changes in the second position of any codon. Such charge reversal may have dramatic consequences for the structure or function of a protein. This aspect may have been largely underestimated by previous studies. [ 52 ]


The frequency of codons, also known as  codon usage bias , can vary from species to species with functional implications for the control of  translation . The codon varies by organism; for example, most common proline codon in E. coli is CCG, whereas in humans this is the least used proline codon. [ 53 ]


In some proteins, non-standard amino acids are substituted for standard stop codons, depending on associated signal sequences in the messenger RNA. For example, UGA can code for  selenocysteine  and UAG can code for  pyrrolysine . Selenocysteine came to be seen as the 21st amino acid, and pyrrolysine as the 22nd. [ 55 ]  Both selenocysteine and pyrrolysine may be present in the same organism. [ 55 ]  Although the genetic code is normally fixed in an organism, the achaeal prokaryote  Acetohalobium arabaticum  can expand its genetic code from 20 to 21 amino acids (by including pyrrolysine) under different conditions of growth. [ 56 ]


There was originally a simple and widely accepted argument that the genetic code should be universal: namely, that any variation in the genetic code would be lethal to the organism (although Crick had stated that viruses were an exception). This is known as the "frozen accident" argument for the universality of the genetic code. However, in his seminal paper on the origins of the genetic code in 1968, Francis Crick still stated that the universality of the genetic code in all organisms was an unproven assumption, and was probably not true in some instances. He predicted that "The code is universal (the same in all organisms) or nearly so". [ 58 ]  The first variation was discovered in 1979, by researchers studying  human mitochondrial genes . [ 59 ]  Many slight variants were discovered thereafter, [ 60 ]  including various alternative mitochondrial codes. [ 61 ]  These minor variants for example involve translation of the codon UGA as  tryptophan  in  Mycoplasma  species, and translation of CUG as a serine rather than leucine in yeasts of the "CTG clade" (such as  Candida albicans ). [ 62 ] [ 63 ] [ 64 ]  Because viruses must use the same genetic code as their hosts, modifications to the standard genetic code could interfere with viral protein synthesis or functioning. However, viruses such as  totiviruses  have adapted to the host's genetic code modification. [ 65 ]  In  bacteria  and  archaea , GUG and UUG are common start codons. In rare cases, certain proteins may use alternative start codons. [ 60 ]
Surprisingly, variations in the interpretation of the genetic code exist also in human nuclear-encoded genes: In 2016, researchers studying the translation of malate dehydrogenase found that in about 4% of the mRNAs encoding this enzyme the stop codon is naturally used to encode the amino acids tryptophan and arginine. [ 66 ]  This type of recoding is induced by a high-readthrough stop codon context [ 67 ]  and it is referred to as  functional translational readthrough . [ 68 ]


Despite these differences, all known naturally occurring codes are very similar. The coding mechanism is the same for all organisms: three-base codons,  tRNA , ribosomes, single direction reading and translating single codons into single amino acids. [ 69 ]  The most extreme variations occur in certain ciliates where the meaning of stop codons depends on their position within mRNA. When close to the 3' end they act as terminators while in internal positions they either code for amino acids as in  Condylostoma  magnum [ 70 ]  or trigger  ribosomal frameshifting  as in  Euplotes . [ 71 ]


The origins and variation of the genetic code, including the mechanisms behind the evolvability of the genetic code, have been widely studied, [ 72 ] [ 73 ]  and some studies have been done experimentally evolving the genetic code of some organisms. [ 74 ] [ 75 ] [ 76 ] [ 77 ]


Variant genetic codes used by an organism can be inferred by identifying highly conserved genes encoded in that genome, and comparing its codon usage to the amino acids in homologous proteins of other organisms. For example, the program FACIL infers a genetic code by searching which amino acids in homologous protein domains are most often aligned to every codon. The resulting amino acid (or stop codon) probabilities for each codon are displayed in a genetic code logo. [ 57 ]


As of January 2022, the most complete survey of genetic codes is done by Shulgina and Eddy, who screened 250,000 prokaryotic genomes using their Codetta tool. This tool uses a similar approach to FACIL with a larger  Pfam  database. Despite the NCBI already providing 27 translation tables, the authors were able to find new 5 genetic code variations (corroborated by tRNA mutations) and correct several misattributions. [ 78 ]  Codetta was later used to analyze genetic code change in  ciliates . [ 79 ]


The genetic code is a key part of the  history of life , according to one version of which self-replicating RNA molecules preceded life as we know it. This is the  RNA world hypothesis . Under this hypothesis, any model for the emergence of the genetic code is intimately related to a model of the transfer from  ribozymes  (RNA enzymes) to proteins as the principal enzymes in cells. In line with the RNA world hypothesis, transfer RNA molecules appear to have evolved before modern  aminoacyl-tRNA synthetases , so the latter cannot be part of the explanation of its patterns. [ 80 ]


A hypothetical randomly evolved genetic code further motivates a biochemical or evolutionary model for its origin. If amino acids were randomly assigned to triplet codons, there would be 1.5 × 10 84  possible genetic codes. [ 81 ] :  163    This number is found by calculating the number of ways that  21 items (20 amino acids plus one stop) can be placed in 64 bins, wherein each item is used at least once. [ 82 ]  However, the distribution of codon assignments in the genetic code is nonrandom. [ 83 ]  In particular, the genetic code clusters certain amino acid assignments.


Amino acids that share the same biosynthetic pathway tend to have the same first base in their codons. This could be an evolutionary relic of an early, simpler genetic code with fewer amino acids that later evolved to code a larger set of amino acids. [ 84 ]  It could also reflect steric and chemical properties that had another effect on the codon during its evolution. Amino acids with similar physical properties also tend to have similar codons, [ 85 ] [ 86 ]  reducing the problems caused by point mutations and mistranslations. [ 83 ]


Given the non-random genetic triplet coding scheme, a tenable hypothesis for the origin of genetic code could address multiple aspects of the codon table, such as absence of codons for D-amino acids, secondary codon patterns for some amino acids, confinement of synonymous positions to third position, the small set of only 20 amino acids (instead of a number approaching 64), and the relation of stop codon patterns to amino acid coding patterns. [ 87 ]


Three main hypotheses address the origin of the genetic code. Many models belong to one of them or to a hybrid: [ 88 ]


Hypotheses have addressed a variety of scenarios: [ 93 ]


Genetic ecology  is the study of the stability and expression of varying genetic material within abiotic mediums. [ 1 ]  Typically, genetic data is not thought of outside of any organism save for criminal forensics. However, genetic material has the ability to be taken up by various organisms that exist within an abiotic medium through natural transformations that may occur. [ 2 ]  Thus, this field of study focuses on interaction, exchange, and expression of genetic material that may not be shared by species had they not been in the same environment.


E.B. Ford was the first geneticist to begin work in this field of study. E.B. Ford worked mostly during the 1950s and is most noted for his work with  Maniola jurtina  and published a book entitled  Ecological Genetics  in 1975. [ 3 ] [ 4 ]  This type of evolutionary biological study was only possible after gel electrophoresis had been designed in 1937. [ 5 ]  Prior to this, a high throughput method for DNA analysis did not exist. This field of study began to become more popular following the 1980s with the development of polymerase chain reaction (PCR 1985) and poly- acrylamide  gel electrophoresis  (p. 1967). [ 6 ] [ 7 ]  With this technology, segments of DNA could be sequenced, amplified, and proteins produced using bacterial transformations. The genetic material along with the proteins could be analyzed and more correct phylogenetic trees could be created.


Since E.B. Ford's research, multiple other genetic ecologists have continued study within the field of genetic ecology such as PT Hanford [ 8 ]  Alina von Thaden, [ 9 ]  and many others. [ 10 ] [ 11 ] [ 12 ] [ 13 ] [ 14 ]


Genetic information may transfer throughout an ecosystem in multiple ways. The first of which, on the smallest scale, being bacterial gene transfer (see  bacterial transformation ). Bacteria have the ability to exchange DNA. This DNA exchange, or  horizontal gene transfer , may provide various species of bacteria with the genetic information they need to survive in an environment. [ 15 ]  This can help many bacterial species survive within an environment.


A similar event has the ability to happen between plants and bacteria. For example,  Agrobacterium tumefaciens  has the ability to introduce genes into plants to cause the development of Gall disease. This occurs through genetic transfer between the  A. tumefaciens  and between the plant in question. [ 16 ]


In fact, a similar event occurs each time viral infections occur within living organisms. The  viruses , whether positive or negative sense viruses, require a living organism to replicate their genes and produce more viruses. Once a virus is inside a living organism, it utilizes polymerases, ribosomes, and other biomolecules to replicate its own genetic material and to produce more virus genetic material similar to the original virus. [ 17 ]  Thus, gene transfer may occur through many varying means. Thus, the study of this gene transfer throughout each ecosystem, whether it be through a bacterial ecosystem or through the ecosystem of an organism, genetic ecology is the study of this gene transfer and its causes.


Genetic exceptionalism  is the belief that  genetic information  is special and so must be treated differently from other types of medical data or other  personally identifiable information .


For example, patients are able to obtain information about their  blood pressure  without involving any medical professionals, but to obtain information about their genetic profile might require an order from a physician and expensive counseling sessions. Disclosure of an individual's genetic information or its meaning, such as telling a woman with red hair that she has a higher risk of skin cancer, has been legally restricted in some places, as providing  medical advice . [ 1 ]


That policy approach has been taken by state legislatures to safeguard individuals' genetic information in the  United States  from individuals, their families, their employers, and the government. The approach builds upon the existing protection required of general health information provided by such laws as the  Health Insurance Portability and Accountability Act .


There is ongoing debate over whether or when certain genetic information should be considered exceptional. [ 2 ]  In some cases, the predictive power of genetic information (such as a risk for a disease like  Huntington's disease , which is highly penetrant) may justify special considerations for genetic exceptionalism, in that individuals with a high risk for developing this condition may face a certain amount of discrimination. However, for most common human health conditions, a specific genetic variant only plays a partial role, interacting with other genetic variants and environmental and lifestyle influences to contribute to disease development. In these cases, genetic information is often considered similarly to other medical and lifestyle data, such as smoking status, age, or  biomarkers .


Genetic  imbalance  is to describe situation when the  genome  of a cell or organism has more copies of some genes than other genes due to  chromosomal   rearrangements  or  aneuploidy .
Changes in  gene dosage , the number of times a given gene is present in the  cell nucleus , can create a genetic imbalance.


This imbalance in gene dosage alters the amount of a particular  protein  relative to all other proteins, and this alternation in the relative amounts of protein can have a variety of  phenotypic  effects. These effects are depending on how the proteins function and how critical the maintenance of a precise ratio of proteins is to the  survival  of the organism.


Diminishing the dosage of most genes produces no obvious change in  phenotype . For some genes the phenotypic consequences of a decrease in gene dosage are noticeable but not catastrophic. For example,  Drosophila  containing only one copy of the  wild type  Notch gene has visible wing abnormalities but otherwise seems to function normally. For some rare genes, the normal  diploid  level of  gene expression  is essential to individual survival; fewer than two copies of such a gene results in  lethality . In  Drosophila , a single dose of the locus known as Triplolethal is in an otherwise diploid individual.


Although a single dose of any gene may not cause substantial harm to the individual, the genetic imbalance resulting from a single dose of many genes at the same time can be lethal. Humans, for example, cannot survive, even as  heterozygotes , with  deletions  that remove more than about 3% of any part of their  haploid   genome .


Genetic interaction  networks  represent the  functional interactions  between pairs of  genes  in an  organism  and are useful for understanding the relation between  genotype  and  phenotype . The majority of genes do not code for particular phenotypes. Instead, phenotypes often result from the interaction between several genes. In  humans , "Each individual carries ~4 million  genetic variants  and  polymorphisms , the overwhelming majority of which cannot be pinpointed as the single cause for a given phenotype. Instead, the effects of genetic variants may combine with one another both additively and synergistically, and each variant's contribution to a quantitative trait or disease risk could depend on the genotypes of dozens of other variants. Interactions between genetic variants, along with the  environmental conditions , are likely to play a major role in determining the phenotype that arises from a given genotype. [ 1 ] "  Genetic interaction networks help to understand genetic interactions by identifying such interactions between pairs of genes. [ 1 ]


Because genetic interactions provide insight into how genotype connects to phenotype in an organism, improved knowledge of genetic interactions in humans could provide crucial insight into complex diseases. Unfortunately, due to the impossibility of isolating subjects with single genetic variants, it is not possible to directly map the genetic interaction networks in humans. Researchers hope that learning about the characteristics of genetic interaction networks in suitable organisms will provide tools for constructing the genetic interaction network of humans. [ 1 ]


A genetic interaction occurs when the interactions between two or more genes results in a phenotype that differs from the phenotype expected if the genes were independent of each other. In the context of genetic interaction networks, a genetic interaction is defined as "the difference between an experimentally measured double- mutant  phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the  mutations  act independently. [ 1 ] " In this context, a commonly studied phenotype is  fitness  which measures the relative reproduction rate of a mutant. A strong phenotype refers to a low level of fitness while a weak phenotype refers to a level of fitness close to that of the non-mutant  strain . [ 1 ]


A negative genetic interaction occurs when the phenotype of the double mutant is stronger than expected. A special case is a  synthetic lethal  interaction which occurs when the removal of individual genes does not significantly harm an organism but the removal of both genes results in an inviable organism. A positive genetic interaction occurs when the phenotype of the double mutant is weaker than expected. A special case is  genetic suppression  which occurs when the phenotype of the double mutant is weaker than that of the least-fit single mutant. [ 1 ] [ 2 ]


In order to measure the interaction between two genes, one must have some standard for the expected phenotype if the genes do not interact. Some common models for how the phenotypes of independent genes combine include the min, additive, and multiplicative models. [ 1 ] [ 3 ]  In the min model, the expected fitness resulting from the mutation of two independent genes is the same as the fitness of the least-fit single mutant. [ 3 ]  In the additive model, the expected phenotype resulting from the mutation of two independent genes is the sum of the phenotypes due to the individual mutations. In the multiplicative model, the expected phenotype resulting from the mutation of two independent genes is the product of the phenotypes due to the individual mutations. Which model is best depends on the situation. [ 1 ] [ 3 ]  It turns out in the case that fitness is used as the phenotype, the multiplicative model is best option.


Methods exist to measure genetic interactions even when one of the genes is  essential  to an organism. [ 2 ]


Genetic interaction networks have been studied extensively in several organisms including  Saccharomyces cerevisiae ,  Schizosaccharomyces pombe ,  Escherichia coli ,  Caenorhabditis elegans , and  Drosophila melanogaster . [ 1 ] [ 2 ] [ 4 ]  These studies have given insight into properties of genetic interaction networks, including the topology of genetic interaction networks, how genetic interaction networks provide information about gene function, and what characteristics of genetic interaction networks are conserved by evolution. Researchers hope that an understanding of the general properties of genetic interaction networks as well as how they relate to other biological information such as  protein-protein interaction networks  will make it possible to infer the  genetic interaction networks in organisms such as humans for which it is not possible to determine genetic interaction networks directly. [ 1 ] [ 3 ]


The  hubs  of genetic interaction networks tend to be essential proteins. [ 3 ] [ 2 ]


When two genes interact with a similar set of neighbors, this, along with the particular nature of those interactions, provides information about how the functions of the two genes are related. For example, genes that share a common set of synthetic lethal interactions tend to be involved in the same  biological pathway . The set of genes with which a gene interacts and the type of those interactions (i.e. synthetic lethal) make up that gene's interaction profile. This information allows the creation of a genetic profile similarity network from a genetic interaction network. In a genetic profile similarity network, edges connect genes with similar interaction profiles. The result is a network consisting of clusters of genes that tend to be involved in the same biological process and where the connections between these clusters provide information about the interdependencies of these biological processes. This can provide a powerful tool for predicting the function of uncharacterized genes. [ 1 ] [ 3 ] [ 2 ] [ 4 ]


Some studies have looked into how genetic networks are conserved across evolutionary distance. [ 1 ] [ 3 ] [ 5 ]  While it is not clear the degree to which individual gene-gene interactions are conserved, the general properties of genetic interaction networks appear to be conserved such as the network hubs and the ability of genetic interaction profiles to predict biological function. [ 1 ] [ 3 ]


Genetic interactions have important implications for the connection between genotype and phenotype. [ 3 ] [ 2 ] [ 6 ]  For example, they have been proposed as an explanation for  missing heritability . Missing heritability refers to the fact that the genetic sources of many heritable phenotypes are yet to be discovered. While a variety of explanations have been proposed, genetic interactions could majorly decrease the amount of missing heritability by increasing the explanatory power of known genetic sources. Such genetic interactions would most likely go beyond the pairwise interactions considered in genetic interaction networks. [ 1 ] [ 2 ] [ 6 ]


In  genetics ,  mapping functions  are used to model the relationship between  map  distances (measured in map units or  centimorgans ) and  recombination  frequencies, particularly as these measurements relate to regions encompassed between  genetic markers . One utility of this approach is that it allows one to obtain values for distances in genetic mapping units directly from recombination fractions, as map distances cannot typically be obtained from empirical experiments. [ 1 ]


The simplest mapping function is the  Morgan Mapping Function , eponymously devised by  Thomas Hunt Morgan . Other well-known mapping functions include the  Haldane Mapping Function  introduced by  J. B. S. Haldane  in 1919, [ 2 ]  and the  Kosambi Mapping Function  introduced by  Damodar Dharmananda Kosambi  in 1944. [ 3 ] [ 4 ]  Few mapping functions are used in practice other than Haldane and Kosambi. [ 5 ]  The main difference between them is in how  crossover interference  is incorporated. [ 6 ]


Where  d  is the distance in map units, the Morgan Mapping Function states that the recombination frequency  r  can be expressed as

 r
 =
 d

 {\displaystyle \ r=d}

  . This assumes that one crossover occurs, at most, in an interval between two loci, and that the probability of the occurrence of this crossover is proportional to the map length of the interval.


Where  d  is the distance in map units, the recombination frequency  r  can be expressed as:


r
 =

 1
 2

 [
 1
 −
 (
 1
 −
 2
 d
 )
 ]
 =
 d

 {\displaystyle \ r={\frac {1}{2}}[1-(1-2d)]=d}


The equation only holds when

 1
 2

 ≥
 d
 ≥
 0

 {\displaystyle {\frac {1}{2}}\geq d\geq 0}

  as, otherwise, recombination frequency would exceed 50%. Therefore, the function cannot approximate recombination frequencies beyond short distances. [ 4 ]


Two properties of the Haldane Mapping Function is that it limits recombination frequency up to, but not beyond 50%, and that it represents a linear relationship between the frequency of recombination and map distance up to recombination frequencies of 10%. [ 7 ]  It also assumes that crossovers occur at random positions and that they do so independent of one another. This assumption therefore also assumes no  crossover interference  takes place; [ 5 ]  but using this assumption allows Haldane to model the mapping function using a  Poisson distribution . [ 4 ]


r
 =

 1
 2

 (
 1
 −

 e

 −
 2
 d

 )

 {\displaystyle \ r={\frac {1}{2}}(1-e^{-2d})}


d
 =
 −

 1
 2

 ln

 (
 1
 −
 2
 r
 )

 {\displaystyle \ d=-{\frac {1}{2}}\ln(1-2r)}


The Kosambi mapping function was introduced to account for the impact played by  crossover interference  on recombination frequency. It introduces a parameter C, representing the  coefficient of coincidence , and sets it equal to 2r. For loci which are strongly  linked , interference is strong; otherwise, interference decreases towards zero. [ 5 ]  Interference declines according to the linear function i = 1 - 2r. [ 8 ]


r
 =

 1
 2

 tanh

 (
 2
 d
 )
 =

 1
 2

 e

 4
 d

 −
 1

 e

 4
 d

 +
 1

 {\displaystyle \ r={\frac {1}{2}}\tanh(2d)={\frac {1}{2}}{\frac {e^{4d}-1}{e^{4d}+1}}}


d
 =

 1
 2

 tanh

 −
 1

 (
 2
 r
 )
 =

 1
 4

 ln

 (

 1
 +
 2
 r

 1
 −
 2
 r

 )

 {\displaystyle \ d={\frac {1}{2}}\tanh ^{-1}(2r)={\frac {1}{4}}\ln({\frac {1+2r}{1-2r}})}


Below 10% recombination frequency, there is little mathematical difference between different mapping functions and the relationship between map distance and recombination frequency is linear (that is, 1 map unit = 1% recombination frequency). [ 8 ]  When genome-wide SNP sampling and mapping data is present, the difference between the functions is negligible outside of regions of high recombination, such as recombination hotspots or ends of chromosomes. [ 6 ]


While many mapping functions now exist, [ 9 ] [ 10 ] [ 11 ]  in practice functions other than Haldane and Kosambi are rarely used. [ 5 ]  More specifically, the Haldane function is preferred when distance between markers is relatively small, whereas the Kosambi function is preferred when distances between markers is larger and crossovers need to be accounted for. [ 12 ]


Genetic matchmaking  is the idea of matching couples for romantic relationships based on their biological compatibility.  The initial idea was conceptualized by  Claus Wedekind  through his "sweaty t-shirt" experiment. [ 1 ]   Males were asked to wear T-shirts for two consecutive nights, and then females were asked to smell the T-shirts and rate the body odors for attractiveness.  Human body odor has been associated with the   human leukocyte antigens (HLA)  genomic region.  They discovered that females were attracted to men who had dissimilar HLA alleles from them.  Furthermore, these females reported that the body odors of HLA-dissimilar males reminded them of their current partners or ex-partners providing further evidence of biological compatibility.


Following research done by Dr. Wedekind, [ 1 ]  several studies found corroborating evidence for biological compatibility.  Garver-Apgar  et al. [ 2 ]  presented evidence for HLA-dissimilar alleles playing a factor in the healthiness of romantic relationships.  They discovered that as the proportion of HLA-similar alleles increased between couples, females reported being less sexually responsive to their partners, less satisfaction from being aroused by their partners, and having additional sexual partners (while with their current partner).  Additionally, Ober  et al. [ 3 ]  conducted an independent study on a population of American  Hutterites  by comparing the HLA alleles of married couples.  They discovered that married couples were less likely to share HLA alleles than expected from random chance; thus their results were consistent with tendencies for same-HLA alleled partners to avoid mating. Further evidence of the importance of genetic compatibility can be found in the finding that couples sharing a higher proportion of HLA alleles tend to have recurring spontaneous abortions, [ 4 ]  reduced body mass in babies, [ 4 ]  and longer intervals between successive births. [ 5 ]


The application of this research to find romantic partners via  genetic testing  has been described as "dubious". [ 6 ]  Analyses of data from the  International HapMap Project  has not found a consistent relationship between marital partners and genes related to the immune system. [ 7 ]


There are several biological reasons why women would be attracted to and mate with men with dissimilar HLA alleles: [ 8 ]


A  genetic predisposition  is a  genetic  characteristic which influences the possible  phenotypic  development of an individual organism within a species or population under the influence of  environmental  conditions. In medicine,  genetic susceptibility  to a  disease  refers to a genetic predisposition to a health problem, [ 1 ]  which may eventually be triggered by particular environmental or lifestyle factors, such as  tobacco smoking  or  diet .   Genetic testing  is able to identify individuals who are genetically predisposed to certain diseases.


Predisposition  is the capacity humans are born with to learn things such as language and concept of self. Negative  environmental influences  may block the predisposition (ability) one has to do some things.   Behaviors  displayed by animals can be influenced by genetic predispositions. Genetic predisposition towards certain human behaviors is  scientifically investigated  by attempts to identify patterns of human behavior that seem to be invariant over long periods of time and in very different cultures.


For example, philosopher  Daniel Dennett  has proposed that humans are genetically predisposed to have a  theory of mind  because there has been  evolutionary  selection for the human ability to adopt the  intentional stance . [1]  The  intentional stance  is a useful behavioral strategy by which humans assume that others have  minds  like their own. This assumption allows one to predict the behavior of others based on personal knowledge.


In 1951,  Hans Eysenck  and  Donald Prell  published an experiment in which  identical (monozygotic) and fraternal (dizygotic) twins , ages 11 and 12, were tested for neuroticism.  It is described in detail in an article published in the  Journal of Mental Science  in which Eysenck and Prell concluded that, "The factor of neuroticism is not a statistical artifact, but constitutes a biological unit which is inherited as a whole....neurotic Genetic predisposition is to a large extent hereditarily determined." [ 2 ]


E. O. Wilson's   book on sociobiology  and his book  Consilience  discuss the idea of genetic predisposition of behaviors.


The field of  evolutionary psychology  explores the idea that certain behaviors have been selected for during the course of evolution.


In the  United States , the  Genetic Information Nondiscrimination Act , which was signed into law by President  George W. Bush  on May 21, 2008, [ 3 ]  prohibits discrimination in employment and health insurance based on genetic information.


Genetic resources  are genetic material of actual or potential value, where genetic material means any material of plant, animal,  microbial  or other origin containing functional units of  heredity . [ 1 ]
Genetic resources is one of the three levels of  biodiversity  defined by the  Convention on Biological Diversity  in Rio, 1992.


Genetic resources  means  genetic material  of actual or potential value where genetic material means any material of plant, animal, microbial or other origin containing functional units of heredity... [ 1 ]  Genetic resources thus refer to the part of  genetic diversity  that has or could have practical use, such as in plant breeding. The term was introduced by  Otto Frankel  and  Erna Bennett  for a technical conference on the exploration, utilization and conservation of plant genetic resources, organized by the  Food and Agriculture Organisation (FAO)  and the  International Biological Program  (IBP), held in Rome, Italy, 18–26 September 1967. [ 2 ]


Genetic resources is one of the three levels of  biodiversity  defined by Article 2 of the  Convention on Biological Diversity  (CBD) in Rio, 1992 [ 3 ]


Under the CBD, discussions and negotiations regarding genetic resources are organized by the FAO  Commission of Genetic Resources for Food and Agriculture . This commission distinguishes the following domains of genetic resources:


Genetic resources are threatened by  genetic erosion  and conservation activities are undertaken to prevent loss of diversity.


Before the introduction of the term, the Russian scientist  Nikolai Vavilov  initiated comprehensive studies on plant genetic resources and conservation work in the 1920’s. The American botanist  Jack Harlan  stressed the tight link between  plant genetic resources  and man in a seminal publication "Crops and Man". [ 5 ]


There are two complementary ways to conserve genetics resources:


Policies are key to ensure the fair and equitable sharing of benefits derived from the use of genetic resources, for present and future generations. The main international policy framework that regulates genetic resources exchange and use is the  Nagoya Protocol  which entered into force in 2014. It defines and protects the owners of genetic resources and it sets the rules for  Access and Benefit Sharing  (ABS) [ 9 ]


The following scientific journals are dedicated to the topic of genetic resources conservation and sustainable use:


Genetic viability  is the ability of the genes present to allow a cell, organism or population to survive and reproduce. [ 1 ] [ 2 ]   The term is generally used to mean the chance or ability of a  population  to avoid the problems of  inbreeding . [ 1 ]  Less commonly genetic viability can also be used in respect to a single cell or on an individual level. [ 1 ]


Inbreeding depletes  heterozygosity  of the genome, meaning there is a greater chance of identical alleles at a locus. [ 1 ]  When these alleles are non-beneficial, homozygosity could cause problems for genetic viability. [ 1 ]  These problems could include effects on the individual  fitness  (higher mortality, slower growth, more frequent developmental defects, reduced mating ability, lower fecundity, greater susceptibility to disease, lowered ability to withstand stress, reduced intra- and inter-specific competitive ability) or effects on the entire population fitness (depressed population growth rate, reduced regrowth ability, reduced ability to adapt to environmental change). [ 3 ]   See  Inbreeding depression . When a population of plants or animals loses their genetic viability, their chance of going extinct increases. [ 4 ]


To be genetically viable, a population of plants or animals requires a certain amount of  genetic diversity  and a certain  population size . [ 5 ]  For long-term genetic viability, the population size should consist of enough breeding pairs to maintain genetic diversity. [ 6 ]  The precise  effective population size  can be calculated using a  minimum viable population  analysis. [ 7 ]   Higher genetic diversity and a larger population size will decrease the negative effects of  genetic drift  and inbreeding in a population. [ 3 ]  When adequate measures have been met, the genetic viability of a population will increase. [ 8 ]


The main cause of a decrease in genetic viability is loss of  habitat . [ 4 ] [ 9 ] [ 10 ]  This loss can occur because of, for example  urbanization  or deforestation causing  habitat fragmentation . [ 4 ]  Natural events like earthquakes, floods or fires can also cause loss of habitat. [ 4 ]  Eventually, loss of habitat could lead to a  population bottleneck . [ 3 ]  In a small population, the risk of inbreeding will increase drastically which could lead to a decrease in genetic viability. [ 3 ] [ 4 ] [ 11 ]  If they are specific in their diets, this can also lead to habitat isolation and reproductive constraints, leading to greater population bottleneck, and decrease in genetic viability. [ 8 ]  Traditional  artificial propagation  can also lead to decreases in genetic viability in some species. [ 12 ] [ 13 ]


A small highly  inbred  population of gray wolves ( Canis lupus ) residing in  Isle Royale National Park , Michigan, USA has been undergoing population decline and is nearing extinction. [ 14 ]   These gray wolves have been experiencing severe  inbreeding depression  primarily determined by the  homozygous  expression of strongly deleterious recessive  mutations  leading to decreased genetic viability. [ 14 ] [ 15 ]   Reduced genetic viability due to severe inbreeding was expressed as reduced reproduction and survival as well as specific defects such as malformed vertebrae, probable cataracts, syndactyly, an unusual “rope tail,” and anomalous fur phenotypes.  A separate inbred Scandinavian population of gray wolves ( Canis lupus ), also suffering from loss of genetic viability, is experiencing inbreeding depression likely due to the homozygous expression of deleterious recessive mutations. [ 14 ]


Habitat protection is associated with more allelic richness and heterozygosity than in unprotected habitats. [ 16 ]  Reduced habitat fragmentation and increased landscape permeability can promote allelic richness by facilitating gene flow between populations that are isolated or smaller. [ 16 ]


The minimum viable population needed to maintain genetic viability is where the loss of genetic variation because of small population size ( genetic drift ) is equal to genetic variation gained through  mutation . [ 17 ]  When the numbers of one sex is too low, there may be a need for crossbreeding to maintain viability. [ 18 ]


When genetic viability seems to be decreasing within a population, a  population viability analysis  (PVA) can be done to assess the risk of extinction of this species. [ 19 ] [ 20 ] [ 21 ]  The result of a PVA could determine whether further action is needed regarding the preservation of a species. [ 19 ]


Genetic viability is applied by wildlife management staff in zoos, aquariums or other such ex situ habitats. [ 22 ]   They use the knowledge of the animals' genetics, usually through their pedigrees, to calculate the PVA and manage the population viability. [ 22 ]


Genetics  is the study of  genes ,  genetic variation , and  heredity  in  organisms . [ 1 ] [ 2 ] [ 3 ]  It is an important branch in  biology  because heredity is vital to organisms'  evolution .  Gregor Mendel , a  Moravian   Augustinian  friar working in the 19th century in  Brno , was the first to study genetics scientifically. Mendel studied "trait inheritance", patterns in the way traits are handed down from parents to offspring over time. He observed that organisms (pea plants) inherit traits by way of discrete "units of inheritance". This term, still used today, is a somewhat ambiguous definition of what is referred to as a gene.


Trait  inheritance and  molecular  inheritance mechanisms of genes are still primary principles of genetics in the 21st century, but modern genetics has expanded to study the function and behavior of genes. Gene structure and function, variation, and distribution are studied within the context of the  cell , the organism (e.g.  dominance ), and within the context of a population. Genetics has given rise to a number of subfields, including  molecular genetics ,  epigenetics , and  population genetics . Organisms studied within the broad field span the domains of life ( archaea ,  bacteria , and  eukarya ).


Genetic processes work in combination with an organism's environment and experiences to influence development and  behavior , often referred to as  nature versus nurture . The  intracellular  or  extracellular  environment of a living cell or organism may increase or decrease gene transcription. A classic example is two seeds of genetically identical corn, one placed in a  temperate climate  and one in an  arid climate  (lacking sufficient waterfall or rain). While the average height the two corn stalks could grow to is genetically determined, the one in the arid climate only grows to half the height of the one in the temperate climate due to lack of water and nutrients in its environment.


The word  genetics  stems from the  ancient Greek   γενετικός   genetikos  meaning "genitive"/"generative", which in turn derives from  γένεσις   genesis  meaning "origin". [ 4 ] [ 5 ] [ 6 ]


The observation that living things inherit  traits  from their parents has been used since prehistoric times to improve crop plants and animals through  selective breeding . [ 7 ] [ 8 ]  The modern science of genetics, seeking to understand this process, began with the work of the  Augustinian  friar  Gregor Mendel  in the mid-19th century. [ 9 ]


Prior to Mendel,  Imre Festetics , a  Hungarian  noble, who lived in Kőszeg before Mendel, was the first who used the word "genetic" in hereditarian context, and is considered the first geneticist. He described several rules of biological inheritance in his work  The genetic laws of nature  (Die genetischen Gesetze der Natur, 1819). [ 10 ]  His second law is the same as that which Mendel published. [ 11 ]  In his third law, he developed the basic principles of mutation (he can be considered a forerunner of  Hugo de Vries ). [ 12 ]  Festetics argued that changes observed in the generation of farm animals, plants, and humans are the result of scientific laws. [ 13 ]  Festetics empirically deduced that organisms inherit their characteristics, not acquire them. He recognized recessive traits and inherent variation by postulating that traits of past generations could reappear later, and organisms could produce progeny with different attributes. [ 14 ]  These observations represent an important prelude to Mendel's theory of particulate inheritance insofar as it features a transition of heredity from its status as myth to that of a scientific discipline, by providing a fundamental theoretical basis for genetics in the twentieth century. [ 10 ] [ 15 ]


Other theories of inheritance preceded Mendel's work. A popular theory during the 19th century, and implied by  Charles Darwin 's 1859  On the Origin of Species , was  blending inheritance : the idea that individuals inherit a smooth blend of traits from their parents. [ 16 ]  Mendel's work provided examples where traits were definitely not blended after hybridization, showing that traits are produced by combinations of distinct genes rather than a continuous blend. Blending of traits in the progeny is now explained by the action of multiple genes with  quantitative effects . Another theory that had some support at that time was the  inheritance of acquired characteristics : the belief that individuals inherit traits strengthened by their parents. This theory (commonly associated with  Jean-Baptiste Lamarck ) is now known to be wrong—the experiences of individuals do not affect the genes they pass to their children. [ 17 ]  Other theories included Darwin's  pangenesis  (which had both acquired and inherited aspects) and  Francis Galton 's reformulation of pangenesis as both particulate and inherited. [ 18 ]


Modern genetics started with Mendel's studies of the nature of inheritance in plants. In his paper " Versuche über Pflanzenhybriden " (" Experiments on Plant Hybridization "), presented in 1865 to the  Naturforschender Verein  (Society for Research in Nature) in  Brno , Mendel traced the inheritance patterns of certain traits in pea plants and described them mathematically. Although this pattern of inheritance could only be observed for a few traits, Mendel's work suggested that heredity was particulate, not acquired, and that the inheritance patterns of many traits could be explained through simple rules and ratios. [ 19 ]


The importance of Mendel's work did not gain wide understanding until 1900, after his death, when  Hugo de Vries  and other scientists rediscovered his research.  William Bateson , a proponent of Mendel's work, coined the word  genetics  in 1905. [ 20 ] [ 21 ]  The adjective  genetic , derived from the Greek word  genesis —γένεσις, "origin", predates the noun and was first used in a biological sense in 1860. [ 22 ]  Bateson both acted as a mentor and was aided significantly by the work of other scientists from Newnham College at Cambridge, specifically the work of  Becky Saunders ,  Nora Darwin Barlow , and  Muriel Wheldale Onslow . [ 23 ]  Bateson popularized the usage of the word  genetics  to describe the study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in  London  in 1906. [ 24 ]


After the rediscovery of Mendel's work, scientists tried to determine which molecules in the cell were responsible for inheritance. In 1900, Nettie Stevens began studying the mealworm. [ 25 ]  Over the next 11 years, she discovered that females only had the X chromosome and males had both X and Y chromosomes. [ 25 ]  She was able to conclude that sex is a chromosomal factor and is determined by the male. [ 25 ]  In 1911,  Thomas Hunt Morgan  argued that genes are on  chromosomes , based on observations of a sex-linked  white eye  mutation in  fruit flies . [ 26 ]  In 1913, his student  Alfred Sturtevant  used the phenomenon of  genetic linkage  to show that genes are arranged linearly on the chromosome. [ 27 ]


Although genes were known to exist on chromosomes, chromosomes are composed of both  protein  and DNA, and scientists did not know which of the two is responsible for inheritance.  In 1928 ,  Frederick Griffith  discovered the phenomenon of  transformation : dead bacteria could transfer  genetic material  to "transform" other still-living bacteria. Sixteen years later, in 1944, the  Avery–MacLeod–McCarty experiment  identified DNA as the molecule responsible for transformation. [ 28 ]  The role of the nucleus as the repository of genetic information in eukaryotes had been established by  Hämmerling  in 1943 in his work on the single celled alga  Acetabularia . [ 29 ]  The  Hershey–Chase experiment  in 1952 confirmed that DNA (rather than protein) is the genetic material of the viruses that infect bacteria, providing further evidence that DNA is the molecule responsible for inheritance. [ 30 ]


James Watson  and  Francis Crick  determined the structure of DNA in 1953, using the  X-ray crystallography  work of  Rosalind Franklin  and  Maurice Wilkins  that indicated DNA has a  helical  structure (i.e., shaped like a corkscrew). [ 31 ] [ 32 ]  Their double-helix model had two strands of DNA with the nucleotides pointing inward, each matching a complementary nucleotide on the other strand to form what look like rungs on a twisted ladder. [ 33 ]  This structure showed that genetic information exists in the sequence of nucleotides on each strand of DNA. The structure also suggested a simple method for  replication : if the strands are separated, new partner strands can be reconstructed for each based on the sequence of the old strand. This property is what gives DNA its semi-conservative nature where one strand of new DNA is from an original parent strand. [ 34 ]


Although the structure of DNA showed how inheritance works, it was still not known how DNA influences the behavior of cells. In the following years, scientists tried to understand how DNA controls the process of  protein production . [ 35 ]  It was discovered that the cell uses DNA as a template to create matching  messenger RNA , molecules with  nucleotides  very similar to DNA. The nucleotide sequence of a messenger RNA is used to create an  amino acid  sequence in protein; this translation between nucleotide sequences and amino acid sequences is known as the  genetic code . [ 36 ]


With the newfound molecular understanding of inheritance came an explosion of research. [ 37 ]  A notable theory arose from  Tomoko Ohta  in 1973 with her amendment to the  neutral theory of molecular evolution  through publishing the  nearly neutral theory of molecular evolution . In this theory, Ohta stressed the importance of natural selection and the environment to the rate at which genetic  evolution  occurs. [ 38 ]  One important development was chain-termination  DNA sequencing  in 1977 by  Frederick Sanger . This technology allows scientists to read the nucleotide sequence of a DNA molecule. [ 39 ]  In 1983,  Kary Banks Mullis  developed the  polymerase chain reaction , providing a quick way to isolate and amplify a specific section of DNA from a mixture. [ 40 ]  The efforts of the  Human Genome Project , Department of Energy, NIH, and parallel private efforts by  Celera Genomics  led to the sequencing of the  human genome  in 2003. [ 41 ] [ 42 ]


At its most fundamental level, inheritance in organisms occurs by passing discrete heritable units, called  genes , from parents to offspring. [ 43 ]  This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in  pea  plants, showing for example that flowers on a single plant were either purple or white—but never an intermediate between the two colors. The discrete versions of the same gene controlling the inherited appearance (phenotypes) are called  alleles . [ 19 ] [ 44 ]


In the case of the pea, which is a  diploid  species, each individual plant has two copies of each gene, one copy inherited from each parent. [ 45 ]  Many species, including humans, have this pattern of inheritance. Diploid organisms with two copies of the same allele of a given gene are called  homozygous  at that  gene locus , while organisms with two different alleles of a given gene are called  heterozygous . The set of alleles for a given organism is called its  genotype , while the observable traits of the organism are called its  phenotype . When organisms are heterozygous at a gene, often one allele is called  dominant  as its qualities dominate the phenotype of the organism, while the other allele is called  recessive  as its qualities recede and are not observed. Some alleles do not have complete dominance and instead have  incomplete dominance  by expressing an intermediate phenotype, or  codominance  by expressing both alleles at once. [ 46 ]


When a pair of organisms  reproduce sexually , their offspring randomly inherit one of the two alleles from each parent. These observations of discrete inheritance and the segregation of alleles are collectively known as  Mendel's first law  or the Law of Segregation. However, the probability of getting one gene over the other can change due to dominant, recessive, homozygous, or heterozygous genes. For example, Mendel found that if you cross heterozygous organisms your odds of getting the dominant trait is 3:1. Real geneticist study and calculate probabilities by using theoretical probabilities, empirical probabilities, the product rule, the sum rule, and more. [ 47 ]


Geneticists use diagrams and symbols to describe inheritance. A gene is represented by one or a few letters. Often a "+" symbol is used to mark the usual,  non-mutant allele  for a gene. [ 48 ]


In fertilization and breeding experiments (and especially when discussing Mendel's laws) the parents are referred to as the "P" generation and the offspring as the "F1" (first filial) generation. When the F1 offspring mate with each other, the offspring are called the "F2" (second filial) generation. One of the common diagrams used to predict the result of cross-breeding is the  Punnett square . [ 49 ]


When studying human genetic diseases, geneticists often use  pedigree charts  to represent the inheritance of traits. [ 50 ]  These charts map the inheritance of a trait in a family tree.


Organisms have thousands of genes, and in sexually reproducing organisms these genes generally assort independently of each other. This means that the inheritance of an allele for yellow or green pea color is unrelated to the inheritance of alleles for white or purple flowers. This phenomenon, known as " Mendel's second law " or the "law of independent assortment," means that the alleles of different genes get shuffled between parents to form offspring with many different combinations. Different genes often interact to influence the same trait. In the  Blue-eyed Mary  ( Omphalodes verna ), for example, there exists a gene with alleles that determine the color of flowers: blue or magenta. Another gene, however, controls whether the flowers have color at all or are white. When a plant has two copies of this white allele, its flowers are white—regardless of whether the first gene has blue or magenta alleles. This interaction between genes is called  epistasis , with the second gene epistatic to the first. [ 51 ]


Many traits are not discrete features (e.g. purple or white flowers) but are instead continuous features (e.g. human height and  skin color ). These  complex traits  are products of many genes. [ 52 ]  The influence of these genes is mediated, to varying degrees, by the environment an organism has experienced. The degree to which an organism's genes contribute to a complex trait is called  heritability . [ 53 ]  Measurement of the heritability of a trait is relative—in a more variable environment, the environment has a bigger influence on the total variation of the trait. For example, human height is a trait with complex causes. It has a heritability of 89% in the United States. In Nigeria, however, where people experience a more variable access to good nutrition and  health care , height has a heritability of only 62%. [ 54 ]


The  molecular  basis for genes is  deoxyribonucleic acid  (DNA). DNA is composed of  deoxyribose  (sugar molecule), a phosphate group, and a base (amine group). There are four types of bases:  adenine  (A),  cytosine  (C),  guanine  (G), and  thymine  (T). The phosphates make phosphodiester bonds with the sugars to make long phosphate-sugar backbones. Bases specifically pair together (T&A, C&G) between two backbones and make like rungs on a ladder. The bases, phosphates, and sugars together make a  nucleotide  that connects to make long chains of DNA. [ 55 ]  Genetic information exists in the sequence of these nucleotides, and genes exist as stretches of sequence along the DNA chain. [ 56 ]  These chains coil into a double a-helix structure and wrap around proteins called  Histones  which provide the structural support. DNA wrapped around these histones are called chromosomes. [ 57 ]   Viruses  sometimes use the similar molecule  RNA  instead of DNA as their genetic material. [ 58 ]


DNA normally exists as a double-stranded molecule, coiled into the shape of a  double helix . Each nucleotide in DNA preferentially pairs with its partner nucleotide on the opposite strand: A pairs with T, and C pairs with G. Thus, in its two-stranded form, each strand effectively contains all necessary information, redundant with its partner strand. This structure of DNA is the physical basis for inheritance: DNA replication duplicates the genetic information by splitting the strands and using each strand as a template for synthesis of a new partner strand. [ 59 ]


Genes are arranged linearly along long chains of DNA base-pair sequences. In  bacteria , each cell usually contains a single circular  genophore , while  eukaryotic  organisms (such as plants and animals) have their DNA arranged in multiple linear chromosomes. These DNA strands are often extremely long; the largest human chromosome, for example, is about 247 million  base pairs  in length. [ 60 ]  The DNA of a chromosome is associated with structural proteins that organize, compact, and control access to the DNA, forming a material called  chromatin ; in eukaryotes, chromatin is usually composed of  nucleosomes , segments of DNA wound around cores of  histone  proteins. [ 61 ]  The full set of hereditary material in an organism (usually the combined DNA sequences of all chromosomes) is called the  genome .


DNA is most often found in the nucleus of cells, but Ruth Sager helped in the discovery of nonchromosomal genes found outside of the nucleus. [ 62 ]  In plants, these are often found in the chloroplasts and in other organisms, in the mitochondria. [ 62 ]  These nonchromosomal genes can still be passed on by either partner in sexual reproduction and they control a variety of hereditary characteristics that replicate and remain active throughout generations. [ 62 ]


While  haploid  organisms have only one copy of each chromosome, most animals and many plants are  diploid , containing two of each chromosome and thus two copies of every gene. The two alleles for a gene are located on identical  loci  of the two  homologous chromosomes , each allele inherited from a different parent. [ 45 ]


Many species have so-called  sex chromosomes  that determine the sex of each organism. [ 63 ]  In humans and many other animals, the  Y chromosome  contains the gene that triggers the development of the specifically male characteristics. In evolution, this chromosome has lost most of its content and also most of its genes, while the  X chromosome  is similar to the other chromosomes and contains many genes. This being said, Mary Frances Lyon discovered that there is X-chromosome inactivation during reproduction to avoid passing on twice as many genes to the offspring. [ 64 ]  Lyon's discovery led to the discovery of X-linked diseases. [ 64 ]


When cells divide, their full genome is copied and each  daughter cell  inherits one copy. This process, called  mitosis , is the simplest form of reproduction and is the basis for asexual reproduction. Asexual reproduction can also occur in multicellular organisms, producing offspring that inherit their genome from a single parent. Offspring that are genetically identical to their parents are called  clones . [ 65 ]


Eukaryotic  organisms often use sexual reproduction to generate offspring that contain a mixture of genetic material inherited from two different parents. The process of sexual reproduction alternates between forms that contain single copies of the genome ( haploid ) and double copies ( diploid ). [ 45 ]  Haploid cells fuse and combine genetic material to create a diploid cell with paired chromosomes. Diploid organisms form haploids by dividing, without replicating their DNA, to create daughter cells that randomly inherit one of each pair of chromosomes. Most animals and many plants are diploid for most of their lifespan, with the haploid form reduced to single cell  gametes  such as  sperm  or  eggs . [ 66 ]


Although they do not use the haploid/diploid method of sexual reproduction,  bacteria  have many methods of acquiring new genetic information. Some bacteria can undergo  conjugation , transferring a small circular piece of DNA to another bacterium. [ 67 ]  Bacteria can also take up raw DNA fragments found in the environment and integrate them into their genomes, a phenomenon known as  transformation . [ 68 ]  These processes result in  horizontal gene transfer , transmitting fragments of genetic information between organisms that would be otherwise unrelated.  Natural bacterial transformation  occurs in many  bacterial  species, and can be regarded as a  sexual process  for transferring DNA from one cell to another cell (usually of the same species). [ 69 ]  Transformation requires the action of numerous bacterial  gene products , and its primary adaptive function appears to be  repair  of  DNA damages  in the recipient cell. [ 69 ]


The diploid nature of chromosomes allows for genes on different chromosomes to  assort independently  or be separated from their homologous pair during sexual reproduction wherein haploid gametes are formed. In this way new combinations of genes can occur in the offspring of a mating pair. Genes on the same chromosome would theoretically never recombine. However, they do, via the cellular process of  chromosomal crossover . During crossover, chromosomes exchange stretches of DNA, effectively shuffling the gene alleles between the chromosomes. [ 70 ]  This process of chromosomal crossover generally occurs during  meiosis , a series of cell divisions that creates haploid cells.  Meiotic recombination , particularly in microbial  eukaryotes , appears to serve the adaptive function of repair of DNA damages. [ 69 ]


The first cytological demonstration of crossing over was performed by Harriet Creighton and  Barbara McClintock  in 1931. Their research and experiments on corn provided cytological evidence for the genetic theory that linked genes on paired chromosomes do in fact exchange places from one homolog to the other. [ 71 ]


The probability of chromosomal crossover occurring between two given points on the chromosome is related to the distance between the points. For an arbitrarily long distance, the probability of crossover is high enough that the inheritance of the genes is effectively uncorrelated. [ 72 ]  For genes that are closer together, however, the lower probability of crossover means that the genes demonstrate genetic linkage; alleles for the two genes tend to be inherited together. The amounts of linkage between a series of genes can be combined to form a linear  linkage map  that roughly describes the arrangement of the genes along the chromosome. [ 73 ]


Genes  express  their functional effect through the production of proteins, which are molecules responsible for most functions in the cell. Proteins are made up of one or more polypeptide chains, each composed of a sequence of  amino acids . The DNA sequence of a gene is used to produce a specific  amino acid sequence . This process begins with the production of an RNA molecule with a sequence matching the gene's DNA sequence, a process called  transcription .


This  messenger RNA  molecule then serves to produce a corresponding amino acid sequence through a process called  translation . Each group of three nucleotides in the sequence, called a  codon , corresponds either to one of the twenty possible amino acids in a protein or an  instruction to end the amino acid sequence ; this correspondence is called the  genetic code . [ 74 ]  The flow of information is unidirectional: information is transferred from nucleotide sequences into the amino acid sequence of proteins, but it never transfers from protein back into the sequence of DNA—a phenomenon  Francis Crick  called the  central dogma of molecular biology . [ 75 ]


The specific sequence of amino acids  results  in a unique three-dimensional structure for that protein, and the three-dimensional structures of proteins are related to their functions. [ 76 ] [ 77 ]  Some are simple structural molecules, like the fibers formed by the protein  collagen . Proteins can bind to other proteins and simple molecules, sometimes acting as  enzymes  by facilitating  chemical reactions  within the bound molecules (without changing the structure of the protein itself). Protein structure is dynamic; the protein  hemoglobin  bends into slightly different forms as it facilitates the capture, transport, and release of oxygen molecules within mammalian blood. [ citation needed ]


A  single nucleotide difference  within DNA can cause a change in the amino acid sequence of a protein. Because protein structures are the result of their amino acid sequences, some changes can dramatically change the properties of a protein by destabilizing the structure or changing the surface of the protein in a way that changes its interaction with other proteins and molecules. For example,  sickle-cell anemia  is a human  genetic disease  that results from a single base difference within the  coding region  for the β-globin section of hemoglobin, causing a single amino acid change that changes hemoglobin's physical properties. [ 78 ]
Sickle-cell versions of hemoglobin stick to themselves, stacking to form fibers that distort the shape of  red blood cells  carrying the protein. These sickle-shaped cells no longer flow smoothly through  blood vessels , having a tendency to clog or degrade, causing the medical problems associated with this disease. [ citation needed ]


Some DNA sequences are transcribed into RNA but are not translated into protein products—such RNA molecules are called  non-coding RNA . In some cases, these products fold into structures which are involved in critical cell functions (e.g.  ribosomal RNA  and  transfer RNA ). RNA can also have regulatory effects through hybridization interactions with other RNA molecules (such as  microRNA ). [ citation needed ]


Although genes contain all the information an organism uses to function, the environment plays an important role in determining the ultimate phenotypes an organism displays. The phrase " nature and nurture " refers to this complementary relationship. The phenotype of an organism depends on the interaction of genes and the environment. An interesting example is the coat coloration of the  Siamese cat . In this case, the body temperature of the cat plays the role of the environment. The cat's genes code for dark hair, thus the hair-producing cells in the cat make cellular proteins resulting in dark hair. But these dark hair-producing proteins are sensitive to temperature (i.e. have a mutation causing temperature-sensitivity) and  denature  in higher-temperature environments, failing to produce dark-hair pigment in areas where the cat has a higher body temperature. In a low-temperature environment, however, the protein's structure is stable and produces dark-hair pigment normally. The protein remains functional in areas of skin that are colder—such as its legs, ears, tail, and face—so the cat has dark hair at its extremities. [ 79 ]


Environment plays a major role in effects of the human genetic disease  phenylketonuria . The mutation that causes phenylketonuria disrupts the ability of the body to break down the amino acid  phenylalanine , causing a toxic build-up of an intermediate molecule that, in turn, causes severe symptoms of progressive intellectual disability and seizures. However, if someone with the phenylketonuria mutation follows a strict diet that avoids this amino acid, they remain normal and healthy. [ 80 ]


A common method for determining how genes and environment ("nature and nurture") contribute to a phenotype involves  studying identical and fraternal twins , or other siblings of  multiple births . [ 81 ]  Identical siblings are genetically the same since they come from the same zygote. Meanwhile, fraternal twins are as genetically different from one another as normal siblings. By comparing how often a certain disorder occurs in a pair of identical twins to how often it occurs in a pair of fraternal twins, scientists can determine whether that disorder is caused by genetic or postnatal environmental factors. One famous example involved the study of the  Genain quadruplets , who were  identical quadruplets  all diagnosed with  schizophrenia . [ 82 ]


The genome of a given organism contains thousands of genes, but not all these genes need to be active at any given moment. A gene is expressed when it is being transcribed into mRNA and there exist many cellular methods of controlling the expression of genes such that proteins are produced only when needed by the cell.  Transcription factors  are regulatory proteins that bind to DNA, either promoting or inhibiting the transcription of a gene. [ 83 ]  Within the genome of  Escherichia coli  bacteria, for example, there exists a series of genes necessary for the synthesis of the amino acid  tryptophan . However, when tryptophan is already available to the cell, these genes for tryptophan synthesis are no longer needed. The presence of tryptophan directly affects the activity of the genes—tryptophan molecules bind to the  tryptophan repressor  (a transcription factor), changing the repressor's structure such that the repressor binds to the genes. The tryptophan repressor blocks the transcription and expression of the genes, thereby creating  negative feedback  regulation of the tryptophan synthesis process. [ 84 ]