Genetics and Evolution through the Ages
My reflection when I first made myself master of the
central idea of the Origin was, "How extremely stupid
not to have thought of that."
— Thomas Huxley, on reading Charles Darwin's seminal book
on Evolution, On the Origin of Species
Genes: the units of heredity
One of the key things we see in the living world all around us is
the principle of heredity: the rule that like begets like. A seed from
an apple gives rise to another apple tree, not an orange tree or a
beanstalk. Children invariably resemble their parents, both in looks
and in personality. How does this come about? How does the tiny seed
'know' that it has to grow into an apple tree and not anything else?
Clearly, there must be some medium for the transmission of information
from plant to seed, or parent to child. The concept of a gene as
the basic unit of this medium was first proposed by an Austrian priest
who enjoyed experimenting with pea plants in his backyard — Gregor Mendel.
In his most famous experiments, done between 1856–63, Mendel took two
different varieties of the plant, a tall one and a short one, and
produced offspring by hybridising them (i.e., using pollen from one to
fertilise the other). According to the blending inheritance theory
popular at that time, the progeny should have been of medium height,
intermediate between the characteristics of the parents. However,
Mendel found that the progeny in the first generation, known as the F1
(first filial) generation, were always tall. When these hybrids were
further interbred, to produce second generation or F2 progeny, the
short variety reappeared, but only 1 in 4 (or 25%) of the F2 plants
were short and the rest were tall.
Based on his experiments, Mendel proposed the idea that biological
traits were inherited discretely — for instance, the height of the
pea plant would take on one of only two values, 'tall' or 'short',
rather than being able to vary continuously over a range of values.
The term 'gene' was coined for a unit of heredity that determined
a single biological trait; at that time people had no idea what
genes were actually made of or where they were located, but we now know
that they are composed of a molecule called deoxy-ribonucleic acid (DNA),
and are found inside the cell nucleus. According to Mendel's theory, a
gene could have several types, known as alleles: the gene for
height in pea plants would have two types, tall and short. Also, each
individual would have two copies of a given gene, since one would be
inherited (at random) from each parent. What if the two copies were of
different types? Mendel's results suggested that in such cases only one type
would actually be expressed biologically — meaning the effects of only
one would be observed in the individual's physical characteristics,
whilst the other would remain hidden. The former type is known as the
dominant allele, and the latter as the recessive allele.
In the above diagram, the dominant type for the height gene is 'tall',
denoted by 'T', whilst the recessive type is 'short', denoted by 's'.
We use the terms genotype and phenotype to distinguish
between what genes an individual has and what its physical
characteristics are. Genotype simply means the types of the two
copies for any gene: in the above figure, for example, all the F1
plants have genotype 'Ts'. Phenotype means the actual properties
seen for that trait: the F1 plants above all have the phenotype 'Tall'.
Inferrring allele dominance
In the example of Mendel's experiment above, he could infer that the
tall type is dominant because he knew that the original plants used by
him were purebred, meaning that both their gene copies were of the
same type. However, in general a single inheritance event may not
provide enough information to infer which of two types of a given trait
is dominant. For instance, if we find that a tall plant hybridised with
a short plant to produce a tall offspring, both of these scenarios are
possible:
On the other hand, if two short plants produce a tall offspring, then
we can be sure the short type must be dominant. Consider the
alternative: supposing the tall type is dominant. Then both parents
must have the genotype 'ss', as even a single copy of 'T' would have
made them tall. This means the child must inherit 's' from both
parents, and therefore also have genotype 'ss' and phenotype 'Short'.
So if we observe the child to be tall, this possibility is ruled out
and short must be dominant. Similarly, two tall plants producing
a short child would imply that tall is dominant.
So far we have been talking about single instances, but what if we
have an entire population of individuals with different
characteristics, and based on our observations we want to find out
which trait types are dominant? Well, the first thing to keep in mind
is that in the real world, the rules of Mendelian inheritance we have
been talking about do not always work perfectly. This is because our
bodies, and those of all other animals are plants, are ultimately
machines of a sort, and like any other machine they make errors
sometimes. So when a gene is being copied from parent to child,
it may get altered, perhaps changing its type or even becoming a new
type altogether. This means that in a large population, it is unlikely
that what we see will be 100% consistent with the dominance of any one
type of trait.
Nevertheless, the error rate is generally very small: it has to be, or
heredity wouldn't work. Our bodies may not be perfect at copying genes,
but they are very, very good. So if we see a particular pattern of
inheritance in a large number of cases, we can be quite confident
that it is not due to error but reflects actual relationships between
trait types. Let us take an example: supposing there is a population
of people in which we observe two eye colours, blue and brown. We also
see that children with brown eyes are likely to have brown-eyed
parents. What does this tell us about which eye colour might be the
dominant trait? In order to see this, let us consider both
possibilites: brown may be dominant (we denote the gene types in this
case by 'Br'/'bl') or blue may be dominant (we denote the gene types by
'Bl'/'br'). In the first case, brown-eyed children could have genotype
'BrBr' or 'Brbl'; in the second case, they must have the genotype
'brbr'. A given child genotype determines the type of one gene copy
for both mother and father; the other copy for both parents can be of
either one of the two types. So for a given child genotype, there are
2x2=4 possibilities for the parent genotypes. The table below
show all the possible parent genotypes that could give rise to
brown-eyed children for each case:
From this picture, we can see immediately that if brown is dominant,
the parents are much more likely to be brown-eyed than blue-eyed: 14
out of 16 parent possibilities have brown eyes. On the other hand, if
blue is dominant, the chances of having a parent of either eye colour
are equal for a brown-eyed child. So, since for our population
we have observed that brown-eyed children most often have brown-eyed
parents, we can infer that most probably brown is the dominant type.
Another way of thinking about this is to consider the converse of what
we observe. The converse of our population would be one where many
brown-eyed children had blue-eyed parents. According to what we noted
above with the plants example, if two blue-eyed parents give birth
to a brown-eyed child, then as per Mendelian rules we can be
sure that blue is dominant. A few such instances may happen even in our
population: we only know that brown-eyed parents are likely, not
necessary. However, whilst a small number of such instances can be
accounted for by copying error and other anomalies, the large numbers
that would be there in the converse population would strongly imply
that blue is dominant. So in our population, the relative absence of
such instances means that blue is likely to be recessive.
The creation of variation
Thus far, we have seen how information can be transmitted from parent
to child by means of genes. However, if this genetic copying were
always perfect, children would be exactly like their parents, and
we would not see the tremendous amount of variety that we do in
populations in the real world. So along with a mechanism for heredity,
there must also be some procedures that allow for small changes to
happen in order to create variation. One such procedure is the
'copying error' we talked about above; these errors, known as
mutations, are in fact crucial, as they are needed to generate
variation, and as we will see below, variation is necessary for
evolution. So the tremendous diversity of life on earth could not
have come about without these errors!
Another means of creating variation is a procedure called
crossover, which happens during sexual reproduction. This
essentially involves random mixing of the two copies of every gene
that each parent has, so that the child may sometimes inherit a gene
that is not identical to either copy, but a combination of parts of
the two. This can happen because a gene is actually a large molecule
that consists of many smaller parts:
So we see that these processes ensure that each child tends to be
slightly different from its parents, and thus they lead to the creation
of a lot of variation. However, there are also certain crucial things
that must be conserved: supposing there is a gene that is necessary
for the heart to work properly, then any changes in that gene will
probably mean the child will be unable to survive. In general, the
traits that are more conserved (i.e., they occur in a larger
percentage of the population) are older. This is easy to see if we
consider a tree of descendants from an individual of some species (for
simplicity, let us assume it reproduces asexually by binary fission):
Here trait changes are represented by changes in colour; variation
builds up as we go down the tree. The oldest traits are all blue,
and we can see that they are generally the most common. For instance,
8/15 = 53% of the population has blue squares. The next oldest kind
of square is red, arising in the second generation, and we see that
6/15 = 40% of individuals have red squares. The newest kind of square
is yellow, arising in the fourth generation, and its occurrence is
only 1/15 = 7%. The reason more conserved traits are likely to be older
is simply that the lower we come down the tree, the smaller the area
of the tree affected by a change at that level. However, there can
sometimes be exceptions due to older traits getting diminished by
multiple changes: for instance, the above tree has only 5 individuals
with blue ovals but 6 with red ovals. Such exceptions are rare,
and traits with high occurrence are invariably older than traits with
low occurrence.
Evolution: A Very Simple Idea
To the British naturalist Charles Darwin
goes the credit for coming up with what is arguably simultaneously
the most important, most successful, and most controversial theory in
the history of science: evolution by natural selection. And yet, as
the quote at the top of this article indicates, Darwin's basic insight
was very simple. The inspiration for his ideas came from a journey
he made aboard the ship HMS Beagle to various locations
in and around South America, most notably the Galápagos
Islands. Here he observed subtle variations in the
characteristics of the species found on different islands. For
instance, he saw that the finches
(a kind of bird) on each island had beaks with slightly different
shapes and sizes to those on all the other islands. He also
realised that in each case, the beak was adapted to the main food
sources available on that island — where the main source was small
seeds, the beaks were smaller, and for larger seeds or nuts the beaks
were larger.
Darwin concluded that it was extremely unlikely that all these types
of finches, with their high degree of similarity, had arisen (or been
created, if one believed in God) independently. A much better
explanation was that they had all originally been a single species,
which had spread to various islands. Over time, as the
population on each island grew via reproduction, it developed variations
due to random mutation and crossover events of the type we saw above.
However, not all the variants were equally successful: some had
characteristics that enabled them to survive better and longer
than others, such as beaks better adapted to the available food.
Since these survived more, they also reproduced more and gave rise to
more offspring with the same characteristics. So, eventually, birds
that were best adapted to the conditions came to dominate the population
on each island. This, in a nutshell, is the idea of
natural selection, also often described as "survival of the
fittest".
Darwin's great leap of faith was to the say that the same idea could
be used to explain all of the enormous variety of species
on the planet: over a sufficiently long time period, all of these
could have arisen by the same processess of variation and
natural selection, starting from a single common ancestor. Of course,
the theory does not say anything about how that common
ancestor first came about — it does not solve the problem of the
origin of life, which remains one of the great mysteries
of science.
Why Diversity is Important
The mechanisms for creating variation lead to diverse populations
of individuals; over time, accumulating changes may even lead to the
creation of new species, often aided by factors such as geographical
isolation. Diversity, both across species and within species, is
very important from the point of view of genetic robustness. This
is because changing environmental conditions can make it difficult
for some individuals to survive, and may even threaten the existence
of entire species or groups of species. The greater the variety
of existing individuals and species, the more the likelihood that at
least some will be able to survive even a catastrophic event,
environmental or otherwise. A good example is provided by the mass
extinction of the dinosaurs 65 million years ago. This is believed to
have been caused by a meteorite hitting the earth, and led to a
complete wipeout of dinosaurs, who were at that time the dominant form
of life on our planet. However, because there were many other
species, in particular mammals, who managed to survive, life on earth
did not end altogether. Despite the extinction of a large number of
species, many of the genes necessary for the success of advanced forms
of life, which had been discovered via evolution over billions of
years, managed to survive in other species. So evolution did not have
to start from scratch again, and over just(!!) 65 million years since
then, has led to the creation of the wondrous diversity and
complexity of life we see today.
Sadly, we are now faced with a situation where human activity
has already lead to the extinction of many species, and many more
are endangered. With the possibility of global warming and drastic
climate change looming over us, things could get much worse. So it
is crucial for us to change our ways of living and take better
care of our precious environment, not only for our own sake, but also
for the sake of the very future of life on our planet.