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In keeping with the concept that people of earlier
ages were not stupid, it was long understood that most
reproduction produced offspring that somehow displayed combinations of
the traits of the parents. If you bred individuals
with some particular trait in common, you increased the chance that such a
trait would be prominent in the offspring, but it didn't always
work that way. You could make plant cuttings and pretty much
get a duplicate plant, traitwise, but pollination produced the
same sort of mixtures that animal reproduction gave. How did
it all work? Were there hidden rules that could be discovered and
applied?
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Gregor Mendel was fascinated with science and Nature, but in
order to get enough training he had to enter a monastery in what was
then Austria (now Brno of Czechia). In a classic
example of using the materials at hand, Mendel took advantage of
the monastery's production of peas: for years he bred peas
in special separate plots, focusing on a few one-or-the-other features
(such as Tall / Short, or Wrinkly Pea / Smooth Pea) that he could
isolate in a "pure" form. After hundreds of
tests,
with new plots of hybrid plants and plots of hybrid-hybrid
crosses, Mendel developed the first basic
rules of what would come
to be called genetics. |
Mendel mini-biography.
More on Mendel's tests.
Mendel's
rules. |
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Mendel decided that traits were determined by
some sort of internal code pieces which he called genes.
For any particular trait, there might be code variations
of a trait, like leaf color, or degree of the trait, such as a
variation in the Height Gene for Tall and one for Short.
These variations he called alleles, which, he realized, are
carried in each individual in pairs (although there may be way
more than two allele variations in a whole population, each individual
generally just gets two, one from each parent), of which only one is passed on to
each offspring.
For each trait that is determined by a single gene, an individual's
particular version of that trait is a product
of their two alleles. Mendel thought
that every single allele pair was sorted separately for
reproduction, which turned out later to not be true, but many of
them do sort independently. |
More on Mendel.
Mendel's Laws and terms.
Mendel "tells you" his work (animation). |
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As a side effect of Mendel's choice of pea
traits, he also discovered a
genetic feature called dominance,
where the presence of a dominant allele can completely hide
the presence of a recessive allele. This either-or
condition was necessary to his working out genetic rules, but it
has since been found (and he almost certainly realized) that many traits
don't follow such a simple pattern. Many allele effects are not
that strong or weak, but rather blend to produce the
trait. (In human eye color, very dark alleles can be
dominant over very light alleles - brown can dominate blue - but
middle-strength alleles blend, such as when green and light brown
produce hazel) It also turns out that many traits, in fact
most traits, are a product of at least two genes working together,
two alleles per gene; these multiple-gene traits
(also called polygenic) do follow rules based upon Mendel's discoveries, but the complex
mixing of many alleles makes predictions of offspring traits a
matter of complex probability. With all that we know of genetics,
breeding racehorses is still a matter of mating parents with
desired traits and hoping everything mixes properly in the offspring
(racing ability is a multiple-gene trait), which is what they have been doing
since before Mendel was born. |
Dominant
/ recessive human traits (most probably not that strongly).
How gene patterns (genotypes) affect visible features (phenotypes).
A few
types of inheritance.
Human height - a multiple-gene trait
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Mendel wrote and
published several papers on his discoveries, but no one in the
scientific community noticed, possibly because no one had taken such
a mathematical approach to biology before. When he died, as
far as he knew his research and findings would make no difference to
the world. However, in the very early 1900's, three scientists
investigating the same sorts of processes discovered Mendel's
papers, and those papers became the foundations of what is now
called genetics.
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Following Mendel. |
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We know a bit more about genes today. The
researchers who followed up on Mendel's work through the 20th
century discovered some additional details: |
A genetics timeline. |
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Groups of genes are linked together.
Researchers in Britain and the Netherlands, building upon Mendel's rules,
found that seemingly unrelated alleles sometimes follow inheritance patterns
that suggests they were connected to each other in some way. It turns out that our cells do not carry thousands of separate
codes floating about; genes are bound together along
the lengths of chromosomes. This is called linkage:
for example, genes that are found on sex chromosomes (many of which
have no direct effect on gender) exhibit what's called sex
linkage.
One feature of any
species is its characteristic chromosome number, usually an
even number in sexually-reproducing species because of the
pairs (humans have a chromosome number of 46, for 23
pairs). There are advantages and disadvantages to both low
and high chromosome numbers: with low numbers, the
distribution of copies that must happen whenever new cells are
made is easier - there are fewer chromosomes to copy and fewer copies
to distribute properly; but with higher numbers, the sorting becomes
more complicated, increasing variability in
offspring, which increases evolutionary flexibility. The numbers
vary widely, including some plants
with amazingly high numbers. |
Linkage.
How linkage is used.
Sex linkage.
Some chromosome numbers.
Extreme chromosome numbers. |
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For each chromosome gotten from one parent, there''s one
from the other that "matches" it, with spots for all of the same
genes even if the alleles differ. These pairs are called homologous
chromosomes.
About twenty years later, as
it became obvious that linkages could occasionally be broken, it was
discovered that pieces of homologous chromosomes could be swapped
during certain cell events. This process, called crossing
over, supplied yet another way that alleles could be recombined.
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Homologous chromosomes.
Crossing over. |
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One weakness of Darwin's original theory is that
it could not explain where "new" features (which turn out to be old features,
dramatically changed) came from - natural variations
couldn't really explain how feathers evolved from scales, for
instance. But many years later, in work mostly with fruit flies, mutations were
discovered: spontaneous changes in genetic material,
producing new alleles that produced new variations on traits, sometimes
distinctly new traits. Soon
it was found that x-rays could induce mutations, with greater doses making
more changes. We now consider any change in
DNA, whether it is in genes or not, to be a mutation, and it is known that mutations
to a gene will usually have no effect on the coded
trait, will tend to have a bad effect if an effect exists, but
occasionally will produce a valuable change. And a
particular type of mutation from crossing over can produce duplicate genes
in offspring, allowing for the mutational change of an existing trait (say,
snake saliva to venom through changes of the "extra"
saliva gene) while preserving the original action (not losing the
original saliva protein). This might also explain why more
"advanced" organisms seem to have more genes than more
"primitive" ones. Genetic redundancy works
these two ways - coding is redundant (for reasons covered when the details
of code-to-protein are covered) and is hard to effectively alter, and
"extra" or redundant genes may be produced by duplication. The extra
genes, according to
recent research, have at least 4 functions if they are not shut off or
deleted: they can help produce more of the coded protein; they
can be available to perform if the "original" fails; they can become involved in differential expression, allowing fine-tuned
regulation of production (especially in multi-step chemical pathways);
and they can develop a new function, possibly dramatically different from
the original, which was mentioned above as important to evolutionary
"jumps."
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Discovery of mutations.
One way
that redundancy can work (abstract).
Redundancy
in plants.
Code redundancy.
Recent
redundancy research. |
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Work with a
bread mold,
Neurospora,
in the 1940's, led to the discovery that allele mutations were producing changed traits
by affecting single enzymes (which are proteins) in the mold's metabolic pathways, leading to a
clear idea of
what exactly a gene
is: a code that is used to make particular proteins.
Cells then use those proteins to create the "traits"
that Mendel connected to genes. Mendel's height gene, for
instance, codes for a type of plant growth hormone protein. What makes
alleles different is that they produce proteins that have slight (or major) molecular
differences, changing how they work. The definition of "gene"
itself has
continued to evolve; this simple one works at the introduction
level.
As mentioned, the
Neurospora mutations affected single enzymes in a pathway that
used several. The fact is that many if not most traits are the result
of pathway processes; even what seems like single-gene traits are
actually multiple-gene traits.
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Images of
Neurospora.
All about
Neurospora.
How discoveries of functional RNAs is changing the term "gene."
A glossary
of genetics terms.
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DNA
had long been suspected of being the coding material in cells, but when
broken down to its handful of components, it seemed too simple to be able
to carry such complex information. However,
during the late 1940's, work done with
phages, viruses that
use bacterial cells as sources to produce more viruses, showed that in many
circumstances the only viral material getting into the host cell
was DNA, and that supplied all that was necessary for the cell to make and
assemble the next generation of viruses. DNA, it was confirmed, could act as a code,
and it could carry all necessary information all by itself. |
Intro to phages (on a site suggesting they
should replace antibiotics, a
real thing but maybe not from this place). |
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During the 1950's, work done
by James Watson, Francis Crick, Maurice Wilkin, and Rosalind Franklin led
to an understanding of how DNA can hold complex information on a molecular
level. They found that the molecule was a two-stranded,
cross-connected spiral, called a double
helix, and
that a type of component called a nitrogenous base, in only
4 varieties, produced the code from their sequential order along one strand.
Since each base type will only connect to one other type across the way, the two
strands could be separated and a new strand added on that would exactly
duplicate the old complement. Most mutations arise when some aspect
of the sequence is changed. |
A page from the Nobel Prize people on this discovery.
Image of the double helix. |
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The four nitrogenous bases
(there is a fifth, used in RNA) are
Adenine, which cross-connects
only to
Thymine (and vice versa), and
Cytosine,
which only connects to
Guanine. In RNA,
Uracil
replaces Thymine and cross-connects to Adenine. Inside an
actual gene sequence, each 3-base sequence on the DNA strand is a
codon
(actually, its a codon once its transcribed to RNA)
that will be translated into one amino acid of the protein coded for. Often
a single base-change in a codon will translate to exactly the same amino
acid (or one very similar), which is the molecular basis of that one type
of genetic redundancy. More detail on how this all
works appears in the next chapter. |
Adenine.
Thymine.
Cytosine.
Guanine.
Uracil.
Codon. |
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Since Mendel, it has been discovered that in
some circumstances for an individual, having two different alleles for a
trait can be better than
a matched pair of the same alleles, a condition called hybrid vigor
(also heterozygote advantage or heterosis).
This often is the reason that human genetic diseases have spread
through a population. For example, the gene for the oxygen
carrier hemoglobin has a allele that makes a nonround version of
the protein when oxygen is not attached; if you get a pair of these alleles, it gives
you sickle-cell anemia, a dangerous disease that affects the shape of
entire red
blood cells and impairs
circulation. In areas where malaria, a disease caused by a
blood parasite, is common, people carrying one regular hemoglobin
allele and one sickle-cell allele have more resistance to malaria
than those with two regular alleles, giving them an advantage that
passes sickle-cell alleles to their offspring. Other genetic
diseases may have similar effects: cystic fibrosis alleles
might make single-carriers resistant to diarrheal diseases (which
kill huge numbers across the world), Tay-Sachs seems to produce a
tuberculosis resistance, and schizophrenia (which is a
multiple-gene trait and harder to sort out) may in some
combinations increase creativity and the willingness to take risks,
important features for some individuals in human societies.
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More on hybrid vigor.
How this applies to cystic fibrosis.
And sickle-cell anemia.
And Tay-Sachs disease.
And schizophrenia-? |
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Over recent decades, the role of
genetics in traits of all kinds has become a major focus of
research. As a bridge to answering those questions, lots of
high-profile work has been done in the analysis of genomes,
or the total DNA carried by particular species of
organisms (or, really, by an individual selected as a representative).
Genomes have been determined for many disease organisms and popular
research organisms, as well as through the Human Genome
Project.
Of course, knowing the sequence of all of human DNA doesn't tell you which
gene does what, or even what all of the non-gene DNA does, but it's a
useful step. |
The Human Genome Project.
The mouse
genome.
Even E. coli! |
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Very recent work has led to the hypothesis that changes in
parts of the DNA involved in regulating gene expression,
especially a type called a
cis-regulatory element, may be even more important to
evolutionary changes than gene mutations. It may not be so much
what we have as how we use it. The idea that development, with
its environmental-response gene expression, is a major player in
evolution is called evo-devo. |
Research on cis-regulatory elements (abstract). |
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