Showing posts with label genes. Show all posts
Showing posts with label genes. Show all posts

Sep 19, 2015

What Genetics Is, and How the Field Got Its Name

Genetics is the study of genes, genetic variation, and heredity in living things. That is three subjects in one sentence, and all three matter. Heredity is the part everyone knows: traits arrive from parents. Variation is the part that makes genetics interesting: why no two people are the same. Genes are the part that turned both from a description into something you can measure.

The earlier version of this post ran to a single paragraph. It defined heredity, credited Bateson with naming the field, and called it the study of traits passing from parent to offspring. That is a fair description of animal breeding. It is not a description of the discipline.

It also left out what a reader most needs. Genes are written in DNA, in a sequence of four chemical letters, long enough to be read.

This version fills that in. It also puts Bateson and Mendel in their correct order, which the original did not.

What genetics actually covers

The field is usually divided by what kind of question it asks.

  • Classical genetics asks how a single trait is passed on. It works by following crosses and counting offspring.
  • Molecular genetics asks what a gene is made of and how the cell reads it. This is where DNA became the subject rather than the tool.
  • Population genetics asks why a variant is common in one place and rare in another. It is where genetics joins up with evolution.
  • Genomics asks what an entire genome contains, rather than one gene at a time. It is the youngest branch and the one growing fastest.
  • Medical genetics asks what a variant does when it goes wrong in a person. It is the branch most people meet.

Those five come out of the field itself. A sixth, epigenetics, studies changes in how genes are switched on and off that do not change the DNA sequence at all.

How the information is carried

DNA is a chain of nucleotides. Each nucleotide is a sugar, a phosphate, and one of four bases: adenine, cytosine, guanine, or thymine. The four are the alphabet.

Two of them pair with each other, always: adenine with thymine, cytosine with guanine. DNA is normally two such chains wound around each other in a double helix, with the bases meeting in the middle like the rungs of a ladder.

Molecular model of the DNA double helix
The structure Watson and Crick proposed in 1953. Each strand can be read on its own and used to build a matching partner, which is the whole reason the molecule can be copied. Jerome Walker and Dennis Myts, public domain, via Wikimedia Commons

That pairing is what makes inheritance possible rather than merely likely. Before the strands are pulled apart to be copied, each one already specifies the other. The sequence is a written record, and copying it needs no instruction beyond the complementarity already built into the chemistry.

A gene is a stretch of that sequence. Its information is copied into RNA, and the RNA is read to build a protein. The chain runs DNA to RNA to protein, and most of what a gene ultimately does in a cell is through that protein.

How much of it there is

The human genome holds about 3.2 billion base pairs. Roughly 20,000 of its genes code for proteins. More than 98 percent of the genome does not, which is the single most counter-intuitive fact about it.

The noncoding part is not all padding. Some of it switches genes on and off, and some of it protects the ends of chromosomes from damage during copying. Researchers are still working out what a good deal of the rest does.

Karyotype of a human male, showing 46 chromosomes in 23 pairs
Twenty-two pairs plus one. The chromosomes are cut out of one microscope image and arranged by size, which is the only way to see that a person is carrying exactly as many as they should. National Human Genome Research Institute, public domain, via Wikimedia Commons

How the field got its name

The word was needed before it was written down. People had been selecting plants and animals for breeding for thousands of years, but they had no name for the thing they were doing.

The word "genetic" appeared first. Imre Festetics, a Hungarian noble writing in 1819, used it about inheritance in a work called The Genetic Laws of Nature. He also argued from farm practice that organisms inherit their characteristics rather than acquire them, and he described recessive traits reappearing after generations. That is Mendel's central insight, arrived at by breeding animals, some eighty years earlier.

The field then had a name for the adjective and no name for the subject.

Mendel, and thirty-five years of silence

Between 1856 and 1865 Gregor Mendel, an Augustinian friar at the monastery in Brno, crossed pea plants and counted the results. He chose seven traits, each of which came in two sharply different forms with nothing in between: tall or dwarf, round or wrinkled, purple or white.

The seven characteristics of pea plants used by Mendel
The seven character pairs, one for each part of the plant. Each was chosen to be sharply two-valued, so that counting offspring gave a clean number. LadyofHats und ich, CC0, via Wikimedia Commons

He presented the results to a local natural history society in 1865 and published them the following year. He had worked through somewhere near 28,000 plants.

The paper appeared in the proceedings of a local society. Almost nobody read it, and nothing was built on it for thirty-five years. Mendel died in 1884.

When it was picked up, it was picked up three times over, by three scientists who found it while searching the literature for their own results. Hugo de Vries, Carl Correns, and Erich von Tschermak each published in 1900, each describing ratios that Mendel had already described.

De Vries published first without mentioning Mendel. Correns found the earlier paper and accused him of taking Mendel's terminology without crediting him. The dispute settled into the accepted account: all three rediscovered the result, and Mendel had it first.

Tall and dwarf pea plants growing at the Mendelianum in Brno
The dwarf plants are not diseased or stunted. They are healthy pea plants that make less of a growth hormone, and that one difference is inherited cleanly. Daniel J. Fairbanks, CC BY 4.0, via Wikimedia Commons

Bateson, who named it

William Bateson was born in 1861 and read Mendel's work with enthusiasm. He did not discover it, and he was not among the 1900 rediscovers. His contribution was to champion it, and then to give the subject its name.

He used the word "genetics" in 1905, in a letter to his colleague Adam Sedgwick at Cambridge. He made it public at the Third International Conference on Plant Hybridization in London in 1906. The word comes from the Greek genetikos, meaning generative, and genetikon, from genesis, origin.

He was so committed to defending Mendel that he picked up the nickname "Mendel's bulldog". He also coined most of the vocabulary the field still runs on, including "allele", "zygote", "heterozygote" and "homozygote".

Two details about how that work happened are worth knowing. First, Bateson's research group at Cambridge between 1900 and 1910 was largely made up of women from Newnham College, including his wife Beatrice and her sister Florence Durham.

They ran the breeding experiments while Mendelism was still not accepted as a subject worth studying.

Second, Bateson had already been thinking about the problem for a decade before Mendel came back into view. In his 1894 book Materials for the Study of Variation he argued that a theory of heredity could only come out of systematic breeding experiments. He also recorded that his results were discordant: some crosses did not behave the way Mendel's would predict. He spent the rest of his life insisting those exceptions were real.

He was right about that. The explanation began emerging in 1910, with Morgan's work on fruit flies. Most of what looked like a failure of Mendel's rules turned out to be genes sitting close together on one chromosome. That is a fact about chromosomes, not about inheritance itself.

Where the molecular half came from

For the first fifty years after 1900, genetics was a science of counts. Geneticists knew reliably what traits were passed on and in what ratios, and had no idea what any of it was made of.

That changed in stages, each one ruling out the obvious alternative.

  • In 1902, Thomas Hunt Morgan found a white-eyed fly among red-eyed ones in Drosophila, and the white eye turned up only in males. That put a gene somewhere it had to travel with sex.
  • In 1910, Morgan argued that genes are carried on chromosomes. Chromosomes had been known since the 1870s and had no known job.
  • In 1913, Alfred Sturtevant, working in Morgan's group, put the first genes in order on a map. He used the fact that genes close together on a chromosome are inherited together.
  • In 1928, Frederick Griffith found that material from dead bacteria could transform living ones, showing that a chemical substance carried the hereditary information.
  • In 1944, Oswald Avery and his colleagues showed that the transforming substance in Griffith's experiment was DNA, not protein.
  • In 1952, Alfred Hershey and Martha Chase confirmed it for viruses, which removed protein as a candidate.
  • In 1953, James Watson and Francis Crick worked out the double helix from Rosalind Franklin's and Maurice Wilkins' X-ray work, and the copying mechanism followed from the base pairing.

Two later inventions made genetics a practical science rather than a slow one. Frederick Sanger's chain-termination method in 1977 allowed DNA to be read one base at a time. Kary Mullis developed the polymerase chain reaction in 1983, which copies a chosen stretch of DNA from a vanishingly small starting sample.

Gel electrophoresis image from DNA sequencing
A sequencing gel read as rows of bands. Every band is a base called at one position. Sequencing on this scale is what took the Human Genome Project from a concept to a measurement. Qi-Liang Ding, CC BY-SA 3.0, via Wikimedia Commons

The Human Genome Project ran from October 1990 to April 2003 and published a first complete human sequence. A last gap remained in the Y chromosome until 2023.

What a gene does in practice

Take one gene with two versions of it, called alleles. Write the uppercase letter for one and the lowercase for the other.

An organism carrying two of the same letter is homozygous at that gene. One of each is heterozygous. Every cell in a human body carries two copies of almost every gene, one from each parent.

Cross two heterozygotes and each parent hands over one allele at random. Four equally likely combinations come out.

Bb
ABABAb
aBaBab

A Punnett square. Reading down and across gives four cells, and one of them carries a different allele twice.

Punnett square for a cross between two carriers of a recessive condition
The same square drawn for a human condition. One cell in four carries two copies of the recessive allele, which is why such conditions can skip a generation entirely. KatieAnn127, CC BY-SA 4.0, via Wikimedia Commons

One cell in four carries two copies of the recessive allele. That is the whole reason a recessive condition can run through a family for generations without appearing. Then it appears in a child whose parents both carry it, and neither parent shows it.

This is also why dominance is a description of what you can see rather than a claim about strength. An allele that is dominant is not stronger or more common. It is simply the one whose effect shows up in the presence of the other. Some genes do not behave that way at all: with incomplete dominance you get something in between, and with codominance both effects show at once.

Genes do not act alone

Mendel worked with traits controlled by a single gene, which is why his ratios came out clean. Most traits are not like that.

Height is one of the hardest. It depends on many genes, each making a small contribution, and on nutrition and health on top of them.

The share of the variation in a trait attributable to genes is called heritability. It is a property of a population in a particular environment, not a property of a person.

Human height is a useful illustration. Measured in the United States, its heritability is about 89 percent. Measured in Nigeria, where nutrition and health care vary far more widely, the same trait comes out at about 62 percent. The genes did not change between the two measurements. The environment did, and it took up more of the difference.

Genes also interact with each other. When two genes both affect the same trait, and one masks the other outright, the relationship is called epistasis. That is common enough that Bateson spent years arguing Mendel's ratios must be broken, and he was looking at epistasis without being able to see it.

Inheritance is also not always from both parents. Mitochondria carry their own small set of 37 genes and are inherited from the mother only, which is what makes mitochondrial DNA useful for tracing maternal ancestry.

The numbers worth remembering

FigureWhat it is
3.2 billionbase pairs in the human genome
about 20,000genes that code for proteins
over 98%of the genome does not code for protein
46chromosomes, in 23 pairs, in most cells
37genes in mitochondrial DNA
99.9%how much of your DNA matches anyone else's
3.2 millionbase pairs that differ between two people

Human genetics in figures, from the NIGMS figures published in 2024.

The 99.9 percent figure is the one that surprises people, and it is worth taking slowly.

The DNA of any two people on Earth is about 99.9 percent identical. That remaining tenth of one percent is roughly 3.2 million base pairs. Each gene differs between people by only about one to three base pairs on average.

That is where everything that makes you individually you is written. Eye color, height, blood type, the hundreds of diseases that run in families. A very small amount of sequence is doing a very large amount of work here.

It also sets the limit on what genetics can explain about a person. A genome is not a blueprint for the person it describes. Environment does the rest, and the heritability figures above are a direct measurement of how much.

Key Terms in Plain English

These are the words in this article that would send you to a dictionary. Each one is given here the way it is actually used above.

TermWhat it means
GeneA stretch of DNA sequence. Its information is copied into RNA and read to build a protein, and the protein does most of the work.
AlleleOne version of a gene. Two copies per cell, one from each parent.
GenotypeThe alleles an organism carries. The part you cannot see.
PhenotypeThe trait you observe. What the genotype produces, which is not always all of it.
HomozygousCarrying two of the same allele at a gene.
HeterozygousCarrying two different alleles at a gene.
DominantThe allele whose effect shows in the presence of the other. Not the stronger one.
RecessiveAn allele masked when a dominant one is present, and visible in the phenotype only when homozygous.
ChromosomeA long DNA molecule with proteins, carrying many genes in line. Humans have 46.
HeritabilityHow much of the variation in a trait within a population is attributable to genes. A property of the population and its environment, not of a person.
EpistasisOne gene masking the effect of another, so the ratio a simple cross should give never appears.
VariationGenetic differences between people. The reason no two people are identical, and a large part of what genetics studies.

Terms used above, in roughly the order they first appear.

Key Takeaways

  • Genetics studies three things: genes, genetic variation, and heredity. Heredity alone is the oldest of the three and the least surprising.
  • DNA carries the information in a four-letter alphabet, held as two complementary strands so that each one specifies the other.
  • The human genome is about 3.2 billion base pairs, of which under 2 percent codes for protein.
  • William Bateson coined "genetics" in 1905 and popularized it in 1906, more than thirty-five years after Mendel had died.
  • Mendel's work was found independently three times in 1900 by de Vries, Correns, and von Tschermak.
  • Any two people share about 99.9 percent of their DNA. The 3.2 million base pairs that differ are where individual difference lives.
  • Most traits are not controlled by one gene, and heritability depends on the environment it was measured in.

Frequently Asked Questions

If only 0.1 percent of my DNA differs from everyone else's, why do we look so different?

Because 3.2 million base pairs is a large number of building instructions, and the ones that matter sit in genes and in the regions that switch them on. The rest of the sequence carries no visible consequence.

Two people differ at about three base pairs per gene on average. Which genes those differences fall in, and what the changes do, matters far more than the total count.

Are traits inherited from the father and the mother equally?

For the nuclear genes, yes. Each parent supplies one copy of each chromosome, and so one allele at each gene.

Mitochondria are the exception. They come from the egg, so their 37 genes are inherited from the mother alone.

If a condition is recessive, can it disappear from a family?

Yes, and it regularly does. Carriers show no symptoms, so a recessive allele can be carried silently through any number of generations.

It reappears when two carriers have a child, with a one in four chance each time. This is the single most useful thing to know about family trees and genetic counseling.

Does having a high heritability mean an outcome is fixed?

No. Heritability describes variation within a population, not the determination of one individual.

It is also relative. The 89 percent figure for height in the United States becomes about 62 percent in Nigeria, from the same genes, because the environment is less uniform. Neither number says anything about what any particular person will grow to.

Why is almost all DNA noncoding if genes are the point?

Part of it is regulatory. Noncoding regions switch genes on and off, and they protect chromosome ends during copying.

The rest is doing something we have not fully worked out. It is also not inert simply because it does not code for protein. "Junk DNA" was a useful complaint against a model that turned out to be wrong, not a description of the DNA.

Did Bateson discover Mendel's work?

No. He did not find the 1866 paper in 1900; the three rediscovers did, and each found it while checking the literature for their own results.

Bateson read Mendel, believed him, and spent his career defending him to a scientific establishment that did not accept him. That is why he is called Mendel's bulldog, and why naming the field is the part of his work that lasted.

Key references
• Genetics: genes, heredity and variation
• The history of genetics
• William Bateson, 1861-1926
• NIGMS, genetics by the numbers
• Khan Academy, Mendel and his peas

Images: Wikimedia Commons, with the author and license named in each caption. Figures follow the sources above.