Life Is Cells
snigdha |
People like to say, as if it were obvious, that life is hard to define.
This is misleading. Life has properties that clearly distinguish it from
everything else. First, every living thing is cellular. In other words,
it is either a single-celled creature or a creature composed of many
cells. Every cell is bounded by its own outer membrane and contains a
full set of instructions necessary for its operation and reproduction.
Furthermore, every cell uses the same operating system: "DNA makes RNA
makes protein." DNA is a long complex molecule that contains the cell's
instructions. It is transcribed into RNA, another long complex molecule
similar to DNA; and then the RNA transcript is translated into protein.
There are hundreds of billions of different proteins used by living
things (3), but all of them are made from the same twenty amino acids, the "building blocks of life."
Other Properties of Life
Living things reproduce themselves. Either individually or in sexual
pairs, they have both the encoded instructions and the machinery
necessary for self-reproduction. (Some creatures cannot reproduce, but
every creature comes from reproduction.) Periodic crystals like sodium
chloride (table salt) also undergo a kind of self-reproduction. In
crystals however, the "instructions" are much simpler, they are not
encoded, and they are not different from the "machinery."
Life uses processes collectively called metabolism to convert materials
and energy for its needs. Metabolism creates waste products. When
metabolism ceases with no prospect of starting again, we call it death.
Machines also convert materials and energy for their needs, create
waste, and could be said to die.
Life undergoes evolution. Notably, simpler forms are succeeded by forms
with greater organization. Cars evolve also, in their way. Computers
do, too. And computers even contain their own encoded instruction sets.
What Is Motor Vehicle Traffic?
It
is tempting to say that motor vehicle traffic is simply the things that
move along the streets and highways — cars and trucks. Of course buses
and motorcycles should be included, although they are absent or
prohibited on some streets. But what about wheelchairs, bicycles and
skateboards — sometimes these are motorized. What about a trailer that
is merely towed behind a tractor? What about a tire that happens to come
off and roll a tenth of a mile? What about rocks that fall out of a
dump truck and bounce and skid along the highway?As it turns out,
motor vehicle traffic is quite difficult to define. But naturally it
would be hard to draw a line between cars and trucks, and the bouncing
and skidding rocks from which they must have evolved. |
These latter properties of life are sometimes used to make the point that life is hard to define. But nothing else has all
of these latter properties except cellular life using life's
DNA—RNA—protein operating system. Another kind of life, entirely
different from ours, is conceivable, yes. But the only kind we have ever
seen is the one we are part of here on Earth. As biologist and
philosopher Harold J. Morowitz says, "The only life we know for certain
is cellular..." (4).
Viruses and prions are not alive; they lie on the fringe of life.
Viruses contain instructions encoded in DNA or RNA. (Prions don't.)
Both are reproduced. Viruses certainly and prions probably can evolve.
But neither can reproduce itself; each needs the machinery of a living
cell to carry out its reproduction. Without a cell, viruses and prions
are merely inert, complicated particles which do nothing. Do they make
it hard to define life? No, just as trailers don't make it hard to
define motor vehicle traffic. We know what motor vehicle traffic is. And
we know what life is.
A Cell Is Like a Computer
All the regularities of biology strike me as being exactly like the regularities of engineering — Daniel C. Dennett (4.5)
One analogy for a cell is a computer. Computers have coded
instructions inside them called programs. The programs in computers are
analogous to the genetic programming in the DNA within cells. DNA is
subdivided into functional units called genes; these would correspond to
files in the computer. A computer even has a metabolism: it consumes
electrical energy and discharges heat.
The programs in cells and those in computers can both be 1)
copied and 2) executed. Some of the proteins made when a genetic program
is executed would loosely correspond to the computer's paper printout.
But other proteins are more analogous to the computer's cabinetry or
wiring. Of course, computers don't make their own cabinetry or wiring;
the analogy is not perfect.
In fact, nothing about the computer is analogous to a cell's
reproduction. A cell can make a complete copy of itself; it contains the
complete instructions (programs) and the cellular machinery (hardware)
necessary to reproduce itself. A computer cannot make a copy of itself.
It lacks the necssary machinery (but it may be able to reproduce its
instruction set by "automatic full backup".) A computer that could
reproduce itself would be more properly described as a self-reproducing
robot. Such a thing is conceivable, but none exists on Earth today.
A multicelled creature is like a network of computers. It
requires parallel computer architecture on a huge scale to operate
multicelled creatures such as mammals with billions or trillions of
cells, all working in harmony, each doing its task. The nervous system
and the hormonal system are two important networking systems used by
mammals.
Changing the way a computer works requires new programs.
Sometimes one can simply insert a disc into a slot: the computer
recognizes the disc, accepts its new code, and uses it. Other times,
reprogramming a computer is more trouble. The new software may have
"bugs"; it may not be compatible with the existing software; additional
software patches may be needed; it may introduce a computer virus; or it
may cause everything to crash without explanation.
Biological evolution happens when cells are reprogrammed.
Somehow, new genetic programs are installed and activated. How does new
genetic software get installed and activated? And where does it come
from? These are some of the questions that Cosmic Ancestry attempts to answer.
The Two Kinds of Cells
There are two kinds of cells. You might guess the two are plant and
animal cells. This distinction, however, is even more profound. The two
kinds are prokaryotes and eukaryotes. (All plant and animal cells are
eukaryotic.)
bacteria / Susan M. Barns |
Prokaryotes are smaller and simpler than eukaryotic cells. They have no
cell nucleus. They can multiply faster than eukaryotic cells, mainly for
two reasons: 1) They have shorter genetic instructions to be
replicated; and 2) The replication process goes about ten times as fast.
Prokaryotes don't combine and specialize to form multicelled creatures.
Prokaryotes are also called bacteria. They come in a wide variety of
types; their diversity is much greater than that of eukaryotes.
Prokaryotes were here first, appearing very soon after Earth had
cooled enough for life to survive. The oldest rocks that could contain
recognizable fossils contain evidence of domelike structures left by
colonies of cyanobacteria and other bacteria. Even older rocks contain
chemical evidence that the metabolism of these bacteria was under way (5).
Prokaryotes are divided into two major subkingdoms: eubacteria
and archaebacteria. Eubacteria, or "true bacteria", are more familiar
and ubiquitous, thriving in soil, water, our own mouths, etc.
Archaebacteria differ from eubacteria in some basic ways. For example,
their ribosomes (nanoscale protein factories) have a different shape. In
fact, archaebacteria are in some ways more similar to eukaryotes than
to eubacteria. Biologists now think, based on the reconstruction of
genetic "trees," that archaebacteria are the oldest kind of cell. Today
some biologists maintain that archaebacteria constitute a third domain
of life which could be called simply archaea (6-8).
There are four types of archaea. Two are known for their ability
to inhabit extremely hostile environments such as very salty brines, and
boiling springs or ocean thermal vents. The third group of can
metabolize some very unappetizing chemicals to make methane. A fourth
type, the sulfate-reducers, were recently distinguished from the others (9).
eukaryote / The ESG Biology Hypertextbook |
Eukaryotic
cells are much more complicated than prokaryotic cells. The eukaryotic
cell has a differentiated nucleus enclosed in a nuclear membrane. It
usually has two whole copies of the genome, so in computer terms the
eukaryotic cell has a backup copy of its programs. Outside of its
nucleus, the eukaryotic cell has an array of complex subunits that are
essential to it. Two of the subunits, mitochondria and plastids, have
their own DNA. These two subunits enable eukaryotic cells that contain
them to conduct respiration and photosynthesis, respectively. Eukaryotic
cells are able to constitute multicelled animals and plants. Eukaryotes
are able to acquire much more complex features than prokaryotes. If
life has existed on Earth for almost four billion years, the consensus
is that eukaryotes first appeared just after the halfway point, maybe
1.7 billion years ago.
Returning to the computer analogy, the relationship between
prokaryotes and eukaryotes is like the relationship between handheld
calculators and desktop personal computers. Both kinds of cells come in a
broad range of sizes. Prokaryotes are, on average, about an order of
magnitude smaller, like handheld calculators. And they come in a wide
variety, each with a narrow special purpose. Consider scientific
calculators, inventory scanners, GPS units, cellphones, cordless phones,
pagers, beepers, walkie-talkies, PDAs, TV remote controllers, keyless
entry buttons, Gameboys, Walkmans, iPods, guitar tuners, electronic or
medical diagnostic kits, digital cameras, smoke detectors, portable
radios, digital thermometers and cordless shavers. Like eukaryotes,
personal computers have greater memory capacity, have more complicated
structure, and can be networked (eukaryotes form multicelled creatures).
The size of a cell's genome can be compared to the amount of
programming stored in a computer, using the equation, 4 nucleotides = 8
bits = 1 byte. The simplest prokaryotic cell would correspond to a
handheld calculator with about 200 kilobytes of stored programs; the E.
coli bacterium would correspond to a handheld calculator with about 1.2
megabytes of stored programs. Among eukaryotic cells, counting the
backup copy of the genome and the "silent" DNA, a yeast cell would
correspond to a personal computer with 12 megabytes of program storage
capacity; a human cell corresponds to a personal computer with 1.5
gigabytes of program storage capacity. And the human body would
correspond to a computer network of a hundred trillion (10^14) or more
such units.
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