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2.4  Cell Processes

pair depending on the cell type and organism. If these errors occur within a gene, then they

can be manifested as a mutation in the phenotype due to a change resulting from the phys­

ical, chemical, or structural properties of the resulting peptide or protein that is expressed

from that particular gene.

Such a change could affect one or more biological processes in the cell, which utilize

this particular protein, resulting in an ultimate distribution of related biological properties,

depending on the particular nature of the mutated protein. If this mutated DNA nucleo­

tide sequence is propagated into another cellular generation, then this biological variation

will also be propagated, and if this cell happens to be a so-​called germ cell of a multicellular

organism, then this mutation may subsequently be propagated into offspring through sexual

reproduction. Hence, selective pressures can bias the distribution of the genetic makeup in

a population of cells and organisms of subsequent generations resulting, over many, many

generations, in the evolution of that species of organism.

However, there is increasing evidence for some traits, which can be propagated to subse­

quent cellular generations not through alteration of the DNA sequence of the genetic code

itself but manifested as functional changes to the genome. For example, modification of his­

tone proteins that help to package DNA in eukaryotes can result in changes to the expression

of the associated gene in the region of the DNA packaged by these histones. Similarly, the

addition of methyl chemical groups to the DNA itself are known to affect gene expression,

but without changing the underlying nucleotide sequence. The study of such mechanisms is

called “epigenetics.” An important factor with many such epigenetic changes is that they can

be influenced by external environmental factors.

This concept, on the surface, appears to be an intriguing reversion back to redundant the­

ories exemplified by the so-​called Lamarckism, which essentially suggested erroneously that,

for example, if a giraffe stretched its neck to reach leaves in a very tall tree, then the offspring

from that giraffe in subsequent generations would have slightly longer necks. Although epi­

genetics does not make such claims, it does open the door to the idea that what an organism

experiences in its environment may affect the level of expression of genes in subsequent

generations of cells, which can affect the behavior of those cells in sometimes very dra­

matic ways.

This is most prominently seen in cellular differentiation. The term “differentiation” used

by biologists means “changing into something different” and is not to be confused with the

term used in calculus. This is the process by which nongerm cells (i.e., cells not directly

involved in sexual reproduction, also known as somatic cells) turn into different cell types;

these cells all have the same DNA sequence, but there are significant differences in the timing

and levels of gene expressions between different cell types, now known to be largely due to

epigenetics modifications. This process is first initiated from the so-​called stem cells, which

are cells that have not yet differentiated into different cell types. The reason why stem cells

have such current interest in biomedical applications is that if environmental external phys­

ical and chemical triggers can be designed to cause stem cells to controllably and predictably

change into specific cell types, then these can be used to replace cells in damaged areas of the

body to repair specific physiological functions in humans, for example.

The exact mechanisms of natural selection, and ultimately species evolution, are not

clear. Although at one level, natural selection appears to occur at the level of the whole

organism, on closer inspection, a similar argument could be made at both larger and smaller

length scales. For example, at larger length scales, there is natural selection at the level of

populations of organisms, as exhibited in the selfless behavior of certain insects in appearing

to sacrifice their own individual lives to improve the survival of the colony as a whole. At a

smaller length scale, there are good arguments to individual cells in the same tissue com­

peting with each other for nutrients and oxygen, and at a smaller length scale, still an argu­

ment for completion occurring at the level of single genes (for a good background to the

debate, see Sterelny, 2007).

An interesting general mechanism is one involving the so-​called emergent structures, a

phenomenon familiar to physicists. Although the rules of small length and time scale inter­

action, for example, at the level of gene expression and the interactions between proteins, can

be reduced to relatively simple forces, these interactions can lead to higher-​order structures