2.5 – The fitness of the Aqueous Environment for Living Organisms
Organisms have effectively adapted to their aqueous environment and, in the course of
evolution, have developed means of exploiting the unusual properties of water.
The high specific heat of water (the heat energy required to raise the temperature of 1 g of
water by 1 °C) is useful to cells and organisms because it allows water to act as a “heat
buffer,” keeping the temperature of an organism relatively constant as the temperature of
the surroundings fluctuates and as heat is generated as a byproduct of metabolism.
Furthermore, some vertebrates exploit the high heat of vaporization of water (Table 2-1) by
using (thus losing) excess body heat to evaporate sweat. The high degree of internal
cohesion of liquid water, due to hydrogen bonding, is exploited by plants as a means of
transporting dissolved nutrients from the roots to the leaves during the process of
transpiration. Even the density of ice, lower than that of liquid water, has important
biological consequences in the life cycles of aquatic organisms.
Ponds freeze from the top down, and the layer of ice at the top insulates the water below
from frigid air, preventing the pond (and the organisms in it) from freezing solid.
Most fundamental to all living organisms is the fact that many physical and biological
properties of cell macromolecules, particularly the proteins and nucleic acids, derive from
their interactions with water molecules in the surrounding medium.
The influence of water on the course of biological evolution has been profound and
determinative. If life forms have evolved elsewhere in the universe, they are unlikely to
resemble those of Earth unless liquid water is plentiful in their planet of origin.
Science is both a way of thinking about the natural world and the sum of the information
and theory that result from such thinking. The power and success of science flow directly
from its reliance on ideas that can be tested: information on natural phenomena that can be
observed, measured, and reproduced and theories that have predictive value. The progress
of science rests on a foundational assumption that is often unstated but crucial to the
enterprise: that the laws governing forces and phenomena existing in the universe are not
subject to change. The Nobel laureate Jacques Monod referred to this underlying assumption
as the “postulate of objectivity.” The natural world can therefore be understood by applying
a process of inquiry— the scientific method. Science could not succeed in a universe that
played tricks on us. Other than the postulate of objectivity, science makes no inviolate
assumptions about the natural world. A useful scientific idea is one that (1) has been or can
be reproducibly substantiated, (2) can be used to accurately predict new phenomena, and
(3) focuses on the natural world or universe.
Scientific ideas take many forms. The terms that scientists use to describe these forms have
meanings quite different from those applied by nonscientists. A hypothesis is an idea or
assumption that provides a reasonable and testable explanation for one or more
observations, but it may lack extensive experimental substantiation. A scientific theory is
much more than a hunch. It is an idea that has been substantiated to some extent and
provides an explanation for a body of experimental observations. A theory can be tested and
built upon and is thus a basis for further advance and innovation. When a scientific theory
has been repeatedly tested and validated on many fronts, it can be accepted as a fact.
, In one important sense, what constitutes science or a scientific idea is defined by whether or
not it is published in the scientific literature after peer review by other working scientists. As
of late 2014, about 34,500 peer- reviewed scientific journals worldwide were publishing
some 2.5 million articles each year, a continuing rich harvest of information that is the
birthright of every human being.
Scientists are individuals who rigorously apply the scientific method to understand the
natural world. Merely having an advanced degree in a scientific discipline does not make
one a scientist, nor does the lack of such a degree prevent one from making important
scientific contributions. A scientist must be willing to challenge any idea when new findings
demand it. The ideas that a scientist accepts must be based on measurable, reproducible
observations, and the scientist must report these observations with complete honesty.
The scientific method is a collection of paths, all of which may lead to scientific discovery.
In the hypothesis and experiment path, a scientist poses a hypothesis, then subjects it to
experimental test. Many of the processes that biochemists work with every day were
discovered in this manner. The DNA structure elucidated by James Watson and Francis Crick
led to the hypothesis that base pairing is the basis for information transfer in polynucleotide
synthesis. This hypothesis helped inspire the discovery of DNA and RNA polymerases.
Watson and Crick produced their DNA structure through a process of model building and
calculation. No actual experiments were involved, although the model building and
calculations used data collected by other scientists. Many adventurous scientists have
applied the process of exploration and observation as a path to discovery. Historical voyages
of discovery (Charles Darwin’s 1831 voyage on H.M.S. Beagle among them) helped to map
the planet, catalog its living occupants, and change the way we view the world. Modern
scientists follow a similar path when they explore the ocean depths or launch probes to
other planets. An analog of hypothesis and experiment is hypothesis and deduction. Crick
reasoned that there must be an adaptor molecule that facilitated translation of the
information in
messenger RNA into protein. This adaptor hypothesis led to the discovery of transfer RNA by
Mahlon Hoagland and Paul Zamecnik.
Not all paths to discovery involve planning. Serendipity often plays a role. The discovery of
penicillin by Alexander Fleming in 1928 and of RNA catalysts by Thomas Cech in the early
1980s were both chance discoveries, albeit by scientists well prepared to exploit them.
Inspiration can also lead to important advances. The polymerase chain reaction (PCR), now a
central part of biotechnology, was developed by Kary Mullis after a flash of inspiration during
a road trip in northern California in 1983.
These many paths to scientific discovery can seem quite different, but they have some
important things in common. They are focused on the natural world. They rely on
reproducible observation and/or experiment. All of the ideas, insights, and experimental
facts that arise from these endeavors can be tested and reproduced by scientists anywhere
in the world. All can be used by other scientists to build new hypotheses and make new
discoveries. All lead to information that is properly included in the realm of science.
Understanding our universe requires hard work. At the same time, no human endeavor is
more exciting and potentially rewarding than trying, with occasional success, to understand
some part of the natural world.
With the advent of increasingly robust technologies that provide cellular and organismal
views of molecular processes, progress in biochemistry continues apace, providing both new
wonders and new challenges. The image on our cover depicts an active spliceosome, one of
Organisms have effectively adapted to their aqueous environment and, in the course of
evolution, have developed means of exploiting the unusual properties of water.
The high specific heat of water (the heat energy required to raise the temperature of 1 g of
water by 1 °C) is useful to cells and organisms because it allows water to act as a “heat
buffer,” keeping the temperature of an organism relatively constant as the temperature of
the surroundings fluctuates and as heat is generated as a byproduct of metabolism.
Furthermore, some vertebrates exploit the high heat of vaporization of water (Table 2-1) by
using (thus losing) excess body heat to evaporate sweat. The high degree of internal
cohesion of liquid water, due to hydrogen bonding, is exploited by plants as a means of
transporting dissolved nutrients from the roots to the leaves during the process of
transpiration. Even the density of ice, lower than that of liquid water, has important
biological consequences in the life cycles of aquatic organisms.
Ponds freeze from the top down, and the layer of ice at the top insulates the water below
from frigid air, preventing the pond (and the organisms in it) from freezing solid.
Most fundamental to all living organisms is the fact that many physical and biological
properties of cell macromolecules, particularly the proteins and nucleic acids, derive from
their interactions with water molecules in the surrounding medium.
The influence of water on the course of biological evolution has been profound and
determinative. If life forms have evolved elsewhere in the universe, they are unlikely to
resemble those of Earth unless liquid water is plentiful in their planet of origin.
Science is both a way of thinking about the natural world and the sum of the information
and theory that result from such thinking. The power and success of science flow directly
from its reliance on ideas that can be tested: information on natural phenomena that can be
observed, measured, and reproduced and theories that have predictive value. The progress
of science rests on a foundational assumption that is often unstated but crucial to the
enterprise: that the laws governing forces and phenomena existing in the universe are not
subject to change. The Nobel laureate Jacques Monod referred to this underlying assumption
as the “postulate of objectivity.” The natural world can therefore be understood by applying
a process of inquiry— the scientific method. Science could not succeed in a universe that
played tricks on us. Other than the postulate of objectivity, science makes no inviolate
assumptions about the natural world. A useful scientific idea is one that (1) has been or can
be reproducibly substantiated, (2) can be used to accurately predict new phenomena, and
(3) focuses on the natural world or universe.
Scientific ideas take many forms. The terms that scientists use to describe these forms have
meanings quite different from those applied by nonscientists. A hypothesis is an idea or
assumption that provides a reasonable and testable explanation for one or more
observations, but it may lack extensive experimental substantiation. A scientific theory is
much more than a hunch. It is an idea that has been substantiated to some extent and
provides an explanation for a body of experimental observations. A theory can be tested and
built upon and is thus a basis for further advance and innovation. When a scientific theory
has been repeatedly tested and validated on many fronts, it can be accepted as a fact.
, In one important sense, what constitutes science or a scientific idea is defined by whether or
not it is published in the scientific literature after peer review by other working scientists. As
of late 2014, about 34,500 peer- reviewed scientific journals worldwide were publishing
some 2.5 million articles each year, a continuing rich harvest of information that is the
birthright of every human being.
Scientists are individuals who rigorously apply the scientific method to understand the
natural world. Merely having an advanced degree in a scientific discipline does not make
one a scientist, nor does the lack of such a degree prevent one from making important
scientific contributions. A scientist must be willing to challenge any idea when new findings
demand it. The ideas that a scientist accepts must be based on measurable, reproducible
observations, and the scientist must report these observations with complete honesty.
The scientific method is a collection of paths, all of which may lead to scientific discovery.
In the hypothesis and experiment path, a scientist poses a hypothesis, then subjects it to
experimental test. Many of the processes that biochemists work with every day were
discovered in this manner. The DNA structure elucidated by James Watson and Francis Crick
led to the hypothesis that base pairing is the basis for information transfer in polynucleotide
synthesis. This hypothesis helped inspire the discovery of DNA and RNA polymerases.
Watson and Crick produced their DNA structure through a process of model building and
calculation. No actual experiments were involved, although the model building and
calculations used data collected by other scientists. Many adventurous scientists have
applied the process of exploration and observation as a path to discovery. Historical voyages
of discovery (Charles Darwin’s 1831 voyage on H.M.S. Beagle among them) helped to map
the planet, catalog its living occupants, and change the way we view the world. Modern
scientists follow a similar path when they explore the ocean depths or launch probes to
other planets. An analog of hypothesis and experiment is hypothesis and deduction. Crick
reasoned that there must be an adaptor molecule that facilitated translation of the
information in
messenger RNA into protein. This adaptor hypothesis led to the discovery of transfer RNA by
Mahlon Hoagland and Paul Zamecnik.
Not all paths to discovery involve planning. Serendipity often plays a role. The discovery of
penicillin by Alexander Fleming in 1928 and of RNA catalysts by Thomas Cech in the early
1980s were both chance discoveries, albeit by scientists well prepared to exploit them.
Inspiration can also lead to important advances. The polymerase chain reaction (PCR), now a
central part of biotechnology, was developed by Kary Mullis after a flash of inspiration during
a road trip in northern California in 1983.
These many paths to scientific discovery can seem quite different, but they have some
important things in common. They are focused on the natural world. They rely on
reproducible observation and/or experiment. All of the ideas, insights, and experimental
facts that arise from these endeavors can be tested and reproduced by scientists anywhere
in the world. All can be used by other scientists to build new hypotheses and make new
discoveries. All lead to information that is properly included in the realm of science.
Understanding our universe requires hard work. At the same time, no human endeavor is
more exciting and potentially rewarding than trying, with occasional success, to understand
some part of the natural world.
With the advent of increasingly robust technologies that provide cellular and organismal
views of molecular processes, progress in biochemistry continues apace, providing both new
wonders and new challenges. The image on our cover depicts an active spliceosome, one of
