Essay/Term paper: Evolution from a molecular perspective

Essay, term paper, research paper:  Science Reports

Evolution From A Molecular Perspective


Introduction: Why globular evolution?

Evolution has been a heavily debated issue since Charles Darwin first
documented the theory in 1859. However, until just recently, adaptation at a
molecular level has been overlooked except by the scientific world. Now with
the help of modern technology, the protein sequences of nearly every known
living thing have either been established or are in the process of establishment,
and are widely accessible via the internet. With the knowledge of these
sequences, one can actually look at several organisms genetic codes and point
out the similarities. Entire genomes of creatures have been sequenced, and the
human genome project is well underway and ahead of schedule. With this new
knowledge comes worries, for humans, however. What if the information stored in
our genes was available to the public? Would insurance companies and employers
base their selections on these traits? Also, with the total knowledge of every
sequence of every amino acid chain in a person's genome, couldn't a laboratory
perceivably reconstruct an exact copy of, or clone, that person? These are all
issues that will have to be dealt with in the near future, but for now we need
only concern ourselves with the objective observation of these proteins in our
attempt to explain our ever mysterious origin. As humans, we are the first
creatures to question exactly where we came from and how we got here. Some
cling to religious creationism as a means, while others embrace the evolutionary
theory. As of now, and possibly forever, neither can be proven to be absolute
truth with hard facts, and both have their opposing arguments. The point of
this paper being composed is not to attempt to abolish the creationist view, a
feat that at this point seems impossible, but merely to educate those seeking to
unravel the mystery of our forthcoming by pointing out facts that exist in the
modern world and that can be quite easily and independently researched. It is
conceivable that the two ideas, creationism and evolutionism, can exist
symbiotica lly due to the fact that both views have very good points.

Hemoglobin: Comparisons between species

Of all the proteins in living things, hemoglobin is "the second most
interesting substance in the world," as American biochemist L. J. Henderson once
stated (Hemoglobin, 4). However bold this statement seems, it must be realized
that hemoglobin is, at least in the scientific world, by far the most studied
and most discussed substance in the human body, as well as in other living
organisms. Hemoglobin is the carrier in blood that transports oxygen to our
tissues and carbon dioxide out of our body, changing colors as it does so.
Hence, hemoglobin has long been termed the pigment of our blood. Hemoglobin was
one of the first proteins to be purified to the point where its molecular weight
and amino acid composition could be accurately measured. This finding was very
important in that it eventually lead to the understanding that a protein is a
definite compound and not a colloidal mixture of polymers. Each molecule was
built from exactly the same amino acid subunits connected in the same order
alonga chain, and had exactly the same weight. Most organisms have their own
unique, individual chain of proteins to make up their hemoglobin, but all
organisms share certain similarities, so striking that they are unable to be
ignored. Let's take, for example, the first twenty-five amino acids in the
alpha hemoglobin chains of 7 different animals: a human man, rhesus monkey, cow,
platypus, chicken, carp (bony fish), and shark (cartilaginous fish) (See Table
1.1.) As is shown, the variations increase the further apart the organisms are
on the proposed evolutionary scale. A human man differs from a rhesus monkey
only twice in the first twenty-five amino acids of their alpha hemoglobin chains,
whereas a man and a cow differ in three areas. This is the product of many
thousands of years of natural fine tuning, if you will, through the slow but
precise processes of natural selection and adaptation. The fact of natural
selection shows us that while most genetic mutations usually prove fatal, a slim
few are ac tually beneficial, and assist the mutant in living and procreating
offspring. This assistance helps the mutant-gene's frequency grow in the gene
pool and remain there since all progeny possessing this certain trait are going
to have an advantage over the other organisms lacking this quality. This is the
basis for evolution. The higher a certain species is on the evolutionary scale,
the more advanced that organism is due to a slight change in the amino acid
sequences of certain genes. An example would be that of the human man, the
rhesus monkey, and the cow. There is a smaller difference in the amino acid
sequences between a man and a monkey than between a man and a cow, and,
respectively, a monkey is more advanced than a cow, genetically (monkeys and
humans have far advanced apposable thumbs.) Also, where the amino acids have
been conserved between all the studied organisms, such as in columns 27, 31, and
39, indicates that in order for the species to survive, that certain amino acid
must be there. it is changed in any way, the organism can not survive. There
are thirty-four conserved positions in the first 141 amino acids in the seven
studied organisms. After just these few demonstrations, how could anyone doubt
the theory of evolution? This question leads me into a short interlude where I
will discuss the arguments on both sides, and show just how endless this debate
could be.

Evolution -vs- Creation: Which Is Truth?

When evolution is mentioned to many people, the first thing that enters
their mind is the completely incorrect thought that man evolved from monkeys.
Man did not, in fact, evolve from monkeys, this is a known and agreed upon fact.
The only connection between modern day men and modern day chimpanzees, for
example, is the fact that they must have shared a common ancestor. The "common
ancestor" theory, as I have chosen to name it, states that all life living, or
ever to have lived on this planet can be traced back to a single, common
ancestor. At some point in time, between 3.5 and 4.1 billion years ago, a
certain grouping of chemicals came together at just the right time and life
began. From this single life-form, the slow process of natural selection began.
First came the proteinoid microsphere, the first organisms on the planet to
carry on all life functions. Eventually, then, came viruses, parasites,
saprophytes, holotrophs, chemosynthesizers, and photosynthesizers, all mutants
of the very first cell. Some have tried to use thermodynamics to disprove
evolution, especially the second law. The second law of thermodynamics states
that "all energy transfers or transformations make the universe more
disordered." These speculatives claim that since man is more advanced than any
other creature, we are more ordered. This is wrong. Man is more advanced due
to the mutations in his genes. Compared to the very first life-form's genes, a
human man's amino acid sequences are very dissimilar, or more disordered. Also,
the first law of thermodynamics can be used for either argument. The first law
of thermodynamics states that energy cannot be created or destroyed--in other
words it has always been here. Using this law, the matter in the universe can
either be thought of as always being here, or that the creator, with his
infinite power, simply transformed the energy that he possessed into the matter
of the universe. Both sides have an arguable point that agrees with the laws of
thermodynamics. Anot her arguable point that is worthy of mention is the
discrepancies in the fossil record. The Earth's crust, and all the fossils
contained therein, can also be utilized as arguments for both sides. The "Pre-
Cambrian Void" (Creation-Evolution: The Controversy, 362) shows very little sign
of fossilization. Then, suddenly, massive amounts of fossilization can be found
during the Cambrian times, pointing to some sort of catastrophe, like a flood.
The Bible mentions a flood sent by God to destroy every living thing on Earth.
The fact that a flood could have happened, in that sense, strengthens the
creationists' views. The evolutionist theory can use these facts in two ways.
One, when the selection pressure on a species is constant for a long time, a
species could become so specialized that any slight change in their environment
could lead to extinction, this is called a climax group. Around the time that
the large amounts of fossilization was occurring, the Earth had cooled down
enough to allow the immense ly dense atmosphere to condense, thus causing many
years of rain. Would not this rain cause almost any climax group's entire
population to become extinct? Also, before the rains came, the great majority
of the organisms inhabiting the Earth were land creatures. Once the rains came,
the Earth was covered in water, killing thousands of populations, and
effectively burying them in the water. The water preserved their parts for
fossilization. These have been just a few double sided arguments demonstrating
that either side can turn any facts around to fit their own hypothesis.

Leghemoglobin, Protein Relations Between Species, and the Evolution of the
Globin Family

Like animals, plants also carry a sort of hemoglobin, leghemoglobin.
Leghemoglobin is a globin which is less evolved than that of hemoglobin or
myoglobin. The whole globin family, itself, has undergone much evolution and
mutation. At one time, animals had no globin at all. As life evolved, a
single-chain oxygen-binding substance formed--we will call this the basic globin.
Then life branched into two parts: animals carrying the basic globin, such as
annelid worms, insects, and mollusks, and creatures (manly plants) carrying
leghemoglobin, a mutation of the basic globin. The animal kingdom's globin
eventually split into myoglobin (Mb) and hemoglobin (Hb). Since then, myoglobin
has basically stayed the same in many organisms (See Table 1.3.) Hemoglobin, on
the other hand, has undergone some major mutations. After the basic globin
bifurcated into Mb and Hb, Hb split into alpha (a) and beta (b) chains. The a-
chain eventually split into two parts, and has remained this way up to present
times. The b-cha in split into many more parts. Everything that has been said
up until now about the evolution of the globins from a common single-chained
oxygen-binding ancestor has been summarized in Table 2. If one would compare
sequences of globin between species, one would notice that the less amino acids
that are different the more closely related two species are. If we used this
theory on the vertebrates that were studied it would give us a "schematic family
tree of globin containing vertebrates" (Hemoglobin, 78) (See Table 3). This
same tree is obtained by comparing sequences of myoglobin, or the a or b chains
of hemoglobin. This tree tells us that all organisms alive today are just as
evolved as any other living organism. Different species evolve in different
ways, that is the basis of evolution. Man is just as evolved as a chimpanzee,
or a carp, or a rose bush. Different organisms simply evolved differently.
Another excellent way of showing the relationships between organisms is the mean
amino acid differenc es. The more amino acids that are different between two
species, the further apart they are genetically. For instance, of the entire b-
chain of human and rhesus monkey hemoglobin, there are, on the average, eight
places where the amino acids are different. However, when comparing b-chains of
man and platypus, there are thirty four average differences. A chart and a
graph can help us better understand these points (See Table 4.) The amino acids
that have changed are a result of mutated DNA that has proven beneficial to the
carrier mutant. This process, as stated before, is the basis of evolution.
Speaking solely of hemoglobin, the variances between species can be
shown through greater or less affinity for oxygen. "H. F. Bunn has shown that
mammalian hemoglobin can be divided broadly into two groups: the great majority
have intrinsically high oxygen affinity, which is lowered in the red cell by
DPG," (D-2,3-biphosphoglycerate) "while those of ruminants and cats (Cervidae,
Bovidae, Felidae) and of one primate, the lemur, have an intrinsically low
oxygen affinity that is little, or not at all, lowered by DPG ("Species
Adaptation in a Protein Molecule", 16). DPG is one of the ligands that "reduces
the oxygen affinity of hemoglobin in a physiologically advantageous manner by
combining preferentially with the T structure." ("Species Adaptation in a
Protein Molecule", 3) For instance, the mole (Talpa europaea) lives in its
burrows under conditions lacking a rich oxygen supply. This creatures
hemoglobin has adapted to having a high oxygen affinity, a high concentration
per unit volume of blood, and a lo w body temperature. This high affinity is
due to the mole's hemoglobin's low affinity for DPG. So as you can see, DPG
asks as a type of buffer. The more DPG the creature's hemoglobin can hold, the
less space it has for oxygen. Since the environment has low amounts of oxygen,
the blood needs to hold as much oxygen as possible, so the mole has adapted.

Which Came First?

One final point that should be mentioned is the question of which change
came first. Did a mutation occur that adapted a species to a new environment
take place before the species occupied that environment, or did the genetic
change occur after the environment changed in order to assist the creature with
living in its new surroundings? "W. Bodmer suggested that once a large change
in chemical affinities produced by one mutation had enabled a species to occupy
a new environment, its effect might have been refined by later adaptive
mutations, each contributing minor shifts, over a long period of time."
("Species Adaptation in a Protein Molecule", 22.) For example, did a llama's
hemoglobin adapt to a higher grazing altitude by increasing the oxygen affinity,
or did the oxygen affinity increase and the llama then realize that it could
graze higher than some other animals. This could show the "punctuated
equilibria" (Biology, 296) in the evolution of a species.

What Does It All Mean?

After seeing all of these demonstrations of adaptation at a molecular
level, you may ask what it adds to the betterment of the world. The truth is,
merely knowledge. It is doubtful that the evolution-creation controversy will
ever be settled, but without interest, research, and work by people in all
corners of the debate, be it theological, or scientific, the answer will never
be discovered. It is quite possible that neither hypothesis is correct--perhaps
the truth lies in a combination of the two, or something completely different.
I believe that the truth, at least a partial truth, can be found somewhere at
the molecular level. If the genes, and amino acid sequences are examined, I
believe that the actual evolutionary time table can be reconstructed. The human
species, however, must be the last "stem" on this branch of the evolutionary
tree, due to our personal views of mutations. We all see mutations as negative,
when some may actually be positive. If a child is born with twelve fingers
instead of ten, two are surgically removed, and the child becomes less
attractive to the opposite sex, and may not get his mutated genes back into the
gene pool. This process has almost always worked in the opposite way in every
species up until now--the mutant with the beneficial, but different, genotype
and (perhaps) phenotype has had an advantage that makes him more attractive to
the opposite sex, and his genes are passed on to his offspring. One of the only
mutations that could, and has, gone unnoticed is the expansion of the control of
the mind. Over the hundreds of years of human existence, especially in the past
few decades, the knowledge of the modern man has expanded dramatically, and now,
with the ease of the internet, anyone can learn about anything imaginable.
People are tired of mind-numbing thoughtless hours spent in front of the
television, and are now expanding their minds in their free time. I can only
hope that this paper has inspired some thought about the subject, and has
brought us a small step closer to the conclusion of the debate.

Works Utilized

Dickerson, Richard E. and Geis, Irving. Hemoglobin: Structure, Function, and
Pathology.
California: The Benjamin/Cummings Publishing Company Inc., 1983. Perutz,
Max. "Species Adaptation in a Protein Molecule", Molecular Biology and
Evolution Chicago: University of Chicago, 1983 Mammrack, Mark.
Biology 112 Lecture Notes. Ohio: Wright State, 1996 Wysong, Randy. The
Creation-Evolution Controversy. Michigan: Inquiry Press, 1978 Lasker, Gabriel.
Human Evolution. New York: Holt, Rinehart, and Winston, Inc., 1963 Campbell,
Neil. Biology Second Edition. California: The Benjamin/Cummings Publishing
Company Inc., 1990 Solomon, Eldra; Berg, Linda; Martin, Diana; Villee,
Claude. Biology Fourth Edition. New York: Saunders College Publishing,
1996 Genbank. National Center for Biotechnology Information, 1996
Available www: http://www2.ncbi.nlm.nih.gov/cgi-bin/genbank


--Tables!-- (tables 2-4 were scanned in from the
Hemoglobin book in the Bibliography GET IT!)

Table 1.1 Sequence comparisons of globin (information gathered from Hemoglobin
and from "Genbank")

1 25
50 67
ALPHA HEMOGLOBIN CHAIN

1. VLSPADKTNVKAAWGKVGAHAGEYG--AEALERMFLSFPTTKTYFPHF-DLSH--GSAQVKGHGKKVA-
DALT 2. VLSPADKSNVKAAWGKVGGHAGEYG--AEALERMFLSFPTTKTYFPHF-DLSH--
GSAQVKGHGKKVA-DALT 3. VLSAADKGNVKAAWGKVGGHAAEYG--AEALERMFLSFPTTKTYFPHF-DLSH--
GSAQVKGHGAKVA-AALT 4. MLTDAEKKEVTALWGKAAGHGEEYG--AEALERLFQAFPTTKTYFSHF-DLSH--
GSAQIKAHGKKVA-DALS 5. VLSNADKNNVKGIFTKIAGHAEEYG--AETLERMFIGFPTTKTYFPHF-DLSH--
GSAQIKGHGKKVA-LAIT 6. SLSDKDKAAVKIAWAKISPKADDIG--AEALGRMLTVYPQTKTYFAHWADLSP--
GSGPVK-HGKKVIMGAVG 7. DYSAADRAELAALSKVLAQNAEAFG--AEALARMFTVYAATKSYFKDYKDFTA--
AAPSIKAHGAKVV-TALA

1. Human Man 2. Rhesus Monkey 3. Cow 4. Platypus
5. Chicken 6. Carp 7. Shark

Table 1.2 Sequence comparisons of globin (information gathered from Hemoglobin
and from "Genbank")
68 75
100 125
141
ALPHA HEMOGLOBIN CHAIN (Part two)

1. NAVAHVDD--MPNALSALSNLHAHKLRVDPVNFKL--LSHCLLVTLAAHLPAEFTPAVHASL--
DKFLASVSTVLTSKYR 2. LAVGHVDD--MPNALSALSDLHAHKLRVDPVNFKL--
LSHCLLVTLAAHLPAEFTPAVHASL--DKFLASVSTVLTSKYR 3. KAVEHLDD--
LPGALSELSDLHAHKLRVDPVNFKL--LSHSLLVTLASHLPSDFTPAVHASL--DKFLANVSTVLTSKYR 4.
TAAGHFDD--MDSALSALSDLHAHKLRVDPVNFKL--LAHCILVVLARHCPGEFTPSAHAAM--DKFLSKVATVLTSKYR
5. NAIEHADD--ISGALSKLSDLHAHKLRVDPVNFKL--LGQCFLVVLVAHLPAELAPKVHASL--
DKFLCAVGTVLTAKYR 6. DAVSKIDD--LVGGLASLSELHASKLRVDPANFKI--
LANHIVVGIMFYLPGDFPPEVHMSV--DKFFQNLALALSEKYR 7. KACDHLDD--
LKTHLHKLATFHGSELKVDPANFQY--LSYCLEVALAVHL-TEFSPETHCAL--DKFLTNVCHELSSRYR

1. Human Man 2. Rhesus Monkey 3. Cow 4. Platypus
5. Chicken 6. Carp 7. Shark

Table 1.3 Sequence comparisons of globin (information gathered from Hemoglobin
and from "Genbank")

1 25 50
75 80
MYOGLOBIN

1. GLSDGEWQLVLNVWGKVEADIPGHG--QEVLIPLFKGHPETLEKFDKFKHLK--
SEDEMKASEDLKKHGATVLTALGGI--LKKKG 2. GLSDGEWQAVLNAWGKVEADVAGHG--
QEVLIRLFTGHPETLEKFDKFKHLK--TEAEMKASEDLKKHGNTVLTALGGI--LKKKG 3.
VLSEGEWQLVLHVWAKVEADVAGHG--QDILIRLFKSHPETLEKFDRFKHLK--TEAEMKASEDLKKHGVTVLTALGAI-
-LKKKG 4. GLSDGEWQLVLKVWGKVEGDLPGHG--QEVLIRLFKTHPETLEKFDKFKGLK--
TEDEMKASADLKKHGGTVLTALGNI--LKKKG 5. GLSDQEWQQVLTIWGKVEADIAGHG--
-HEVLMRLFHDHPETLDRFDKFKGLK--TEPDMKGSEDLKKHGQTVLTALGAQ--LKKKG 6. ----
TEWEHVNKVWAVVEPDIPAVG--LAILLRLFKEHKETKDLFPKFKEI---PVQQLGNNEDLRKHGVTVLRALGNI--
LKQKG

1. Human Man 2. Cow 3. Sperm Whale 4. Platypus 5.
Chicken 6. Shark

Table 1.3 Sequence comparisons of globin (information gathered from Hemoglobin
and from "Genbank")

1 25 50
75 80
MYOGLOBIN (part two)

1. HHEAEIKPLAQSHATKHKIP--VKYLEFISECIIQVLQSKHPGDFGA--DAQGAMNKALELFRKDMASNYKELG--
FQG 2. HHEAEVKHLAESHANKHKVP--IKYLEFISDAIIHVLHAKHPSNFAA--
DAQGAMNKALELFRKDMASNYKELG--FQG 3. HHEAELKPLAQSHATKHKIP--
IKYLEFISEAIIKVLHSRHPGDFGA--DAQGAMNKALELFRKDIAAKYKELG--YQG 4.
QHEAELKPLAQSHATKHKIS--IKFLEYISEAIIHVLQSKHSADFGA--DAQAAMGKALELFRNDMAAKYKEFG--FQG
5. HHEADLKPLAQTHATKHKIP--VKYLEFISEVIIKVIAEKHAADFGA--DSQAAMKKALELFRDDMASKYKEFG--
FQG 6. KHSTNVKELADTHINKHKIP--PKNFVLITNIAVKVLTEMYPSDMIG--
PMQESFSKVFTVICSDLETLYKEAD--FQG

1. Human Man 2. Cow 3. Sperm Whale 4. Platypus 5.
Chicken 6. Shark