Evolution basically means the change in the characteristics of living organisms over a number of generations. The processes of evolution are the ones that give rise to the diversity of living organisms. The occurrence of evolution basically leads to the diverse population of the components of the living organisms. This means that diversity is usually witnessed in the species, in the individual organisms, and even at the molecular level.
At the molecular level, the diversity that people usually talk of is DNA diversity. The change in the structure of the DNA is an important indication of the evolution taking place. The process of evolution has been of major concern to many scholars who have always struggled to understand the factors that contribute to it.
This is due to many questions that arise in conjunction with evolution. People air many questions, for example, there are many people who have great doubts that the human being has originated from the evolution of the primates as it is put in the stories of creation. Due to the fact that the immediate component of the cell that is involved with diversity is the DNA, scientists have thence been involved in a lot of studies that concern the DNA structure.
This has been done through the separation of the DNA of different organisms to check the similarity in these separated molecules, which then act as a source of information on the similarity of different DNA molecules. The similarity then indicates that the organisms from which the DNA molecules have been separated have a common ancestry origin.
In the study of diversity and heredity, the DNA structure has been represented as the core area of the idea basement (Tattersall, DeSalle, Wynne 89). This is because DNA as the component for the heredity is involved in the transfer of the genetic materials from an organism to the offspring. This then is the origin of the inheritance of the traits such as height, eye color, and skin color. DNA is a long double-stranded molecule that is composed of the bases that are joined together by hydrogen bonds.
In the study of genetics using the DNA molecules, the bonds are first broken using the denaturing agents. The single-stranded DNA is the one that is exposed to other experimental procedures so that it can be studied in details that are required. One of the methods that are used to separate the DNA is polyacrylamide gel electrophoresis.
When this is used, the DNA fragments travel to different distances of the gel, depending on the size of the molecule and also the charge of the same molecule. Then, the distance that is covered by each fragment is estimated and the phylogenetic tree can be constructed, which in turn shows the closeness in the ancestral origin of various organisms.
The main concern of this work is to understand the evolution process on the basis of DNA diversity. This coincides with the core purpose to understand the issue of common ancestry. Many people have argued about the origin of human beings: some belief in the bible stories of the creation while others believe in evolution as the origin of human beings. The latter aspect has then led to the arguments by many scientists and also many attempts to seek the truth. The following questions are the ones that this work struggles to answer:
- Is there a piece of good evidence to show a common ancestry between the apes and humans?
- If there is, which ape is more closely related to humans?
- What caused the big difference in various aspects between the apes and humans as the evolution took place?
The father of evolution, Charles Darwin, clearly put it that human beings originated from the apes. In the search for this truth, scientists began the study of the DNA molecule. In April 1953, two scientists, namely James Watson and Francis Crick, were on the front line in the study of the DNA molecule. They then presented the DNA molecule as a double helix structure responsible for the transfer of the hereditary materials.
According to these scientists, the two strands are anti-parallel and they run in the opposite directions. The sugar-phosphate backbone is always on the outer side of the helix while the bases are on the inside. The joining of the DNA strands actually follows the criterion that is the Adenine-Thymine pair that is joined together and this forms the hydrogen bond.
During the separation of the DNA molecule for study, these bonds are the ones that are broken (Tattersall et al. 88). During the breaking of these bonds, a good denaturing agent is required because the hydrogen bonding is usually very strong. As the quest for these studies went on, many scientists came with methods of DNA separation in order to compare different DNAs and hence come up with the correct comparison, for example, the DNA of human beings and Apes so as to check their similarity.
According to Jonathan Brody who was a Ph.D. assistant colleague of medicine and surgery at the Hopkins University of Baltimore, these scientists have developed among others one technique of DNA separation that is electrophoresis. This was the first model of electrophoresis and the separation was not that efficient. Later on, the same fellows identified the electrophoresis that was a bit faster. In this method, the electric current was used in the separation of different DNA molecules.
After some years of research, these researchers realized that the lithium boric acid would serve as a catalyst in this kind of separation and that the speed would be more than while using the 30-year-old methods that had been used by then. The research by these scientists has been a key step in the study of molecular biology and more specifically in the study of the DNA structure. From these discoveries, a lot has been done in the field of DNA functions and also in the making of genomic libraries.
Moreover, this has been used by many scientists even in the splicing of DNA molecules. This would also help in the determination of the closeness in the ancestral origin, hence being able to explain the story of diversity. As earlier discussed, the gel electrophoresis method has been used for a long time in the separation of the DNA molecules, yet it has served a very important role in explaining evolution details.
One of the methods that are used in the separation of macro and micro molecules, for example, the DNA, RNA, and other kinds of protein molecules that are basically separated on the basis of the size and the charge is electrophoresis (Dutta 23). It is basically used in hospital chemistry for proteins separation by charge and also used in the biochemistry in the separation of the mixed RNA and DNA fragments by their length.
This is usually possible because the molecules of the DNA are usually longer than those of RNA. This method is also used in the separation of the nucleic acids by the nature of their charges. In this case, the electric field is introduced and as such the molecules, which are negatively charged, are moved along the agarose matrix.
When this happens, the molecules, which are shorter, will move faster due to the less weight while the heavier molecules move slower, and hence different sizes of the molecules are easily separated. All this is possible because the smaller molecules diffuse easily in the gel pores. Such a phenomenon in the field of separation is known as the act of sieving. In this separation, the separation of the proteins is by charge differentiation as the proteins are too big in size for their sieving to be possible.
This then means that the protein molecules during the separation remain on the upper side of the matrix. Gel electrophoresis is also used in the separation of the nanoparticles. This method uses gel as sieving or anticonvective media during the separation. The gel electrophoresis for DNA separation is mostly used for the sole purpose of the analysis. It is mostly used after the DNA is amplified using the PCR method and also in the PRLP, in mass spectrometry, in cloning practice, in DNA sequencing, and finally in southern blotting. The figure below shows the machine that is used to perform the gel electrophoresis method.
Gel electrophoresis apparatus is prepared by the following components:
- The slab holder for the vertical or horizontal gels, which are the thin flat sheet made of many lanes.
- There is also the polyacrylamide or agarose gel, which is poured for each analysis. The gel is always amended with the particles to dissociate and charge it.
- There is also a very high voltage power supply of about 0.1-6 Kv. In the setup, there is also the detection technique, which can be dye staining, fluorescence, or even an autoradiography for imaging the separated bands.
The prepared samples of the SDS are carefully pipetted in each of the wells of the gel/slab. When this is being done, the electrodes are already in the holder above and also below to contact the gel via the liquid buffer (Dutta 23). The connectors are separated electrically from each other, but they usually contact the opposite edges of the gel.
The running of the gel electrodes are connected to the power (Dutta 23). During this process, heat is usually generated and it is dissipated via the cooling chambers, which are held in between and against the gel. In this preparation, there is a tracking dye that is usually incorporated so as to stain the fragments, hence making them visible.
During the separation period, the materials that are to be sorted are usually dispensed on the gel, and then the gel is placed in the electrophoresis chamber. After this is done, the power is put on and the gel separation starts. In this separation, the matrix is the material that is used to separate the target molecules (Bandelt, Macaulay, Richards 23).
This operates in the sense that it holds some molecules inside and outside. The term electrophoresis means the electromotive force that is used to move the molecules along the slab. When the molecules are correctly put on the correct wells, the molecules practically move through the matrix at different rates of the fragments, which is determined by the molecule size. Hence, this means that the molecules will move at different speeds altogether. When the separation is made, then the bands are keenly studied.
The most common types of gel include agarose and polyacrylamide. The agarose gel is used fresh, but after a certain separation is over, the gel is packed carefully for another usage. This type of gel is the one that is used to separate the DNA fragments the range of which is 50 base pairs into several megabases using the specialized apparatus. In this case, the distance between the bands of the DNA of different types is given by the agarose gel percentage.
In this method, there is always the disadvantage with the higher concentrations because there will be long-running times. In this case, the agarose of high percentage is run using the pulse-field electrophoresis or the FIE electrophoresis (Jurgen et al. 23). The current agarose gels are mostly made within the 0.7% agarose that is usually dissolved in the electrophoresis buffer. The one that is made of 3% is used to separate fragments, which are tiny. However, the one that is most appropriate in separating such fragments is the polyacrylamide gel. The gels of low percentage are very weak and as such, they can break when one lifts them.
This gel is used for the separation of large protein molecules of about 5 to 2000kda (Jurgen et al. 23). The traditional way of sequencing DNA is the sanger method and also the likes of the Maxam-Gilbert. In this separation, polyacrylamide gel is used.
It is partially hydrolyzed so as to create a non-toxic environment for the electrophoresis. These gels are basically slightly more opaque as compared to the polyacrylamide or even the agarose. In most cases, the starch is always concentrated at 5% to 10%.
In the electrophoresis procedures, there are many types of gel conditions that are required for the best results of the experiments. These include:
This is a step of electrophoresis where the native structure of the macromolecules is broken down by the use of denaturing agents.
These are the kind of gels that are mostly used in proteomics and also the metallomics department of molecular biology. The detergents that are used in this case are the only ones that are required to lyse the membranes of lipid in the cell. One of the disadvantages of this kind of separation is that there are remains of compounds in most of the folded part. Another disadvantage is that the complexes can fail to separate to the level that is needed to be clear. In this type of detergent, the denaturing agent is not used (Jurgen et al. 25).
The molecules that are separated are the proteins and the nuclei and differ by the mass and the internal charge. They also differ in the actual cross-section area, hence they experience the overall electrophoretic force, which depends on the overall structural shape. Since proteins are always found in a situation, which is native, they are visualized using the reagents that generally stain protein and the specific enzyme-linked with the method of staining.
These are very important in the biological experiment. This is because they carry the ions that are able to make the environment of the experiment neutral, hence maintaining the overall reaction stable. In simple terms, the work of the buffers is pH maintenance of the medium in which the reaction is taking place. There are many buffers used in these kinds of experiments with the most used being made from nucleic acids. Some of the commonest buffers include the Tris /Acetate buffer and the tris/Borate buffer among others.
In this kind of operation, there are specific buffers that are used as the science recommends. This is then very important to be considered because if a wrong buffer is used, it even means the whole process will be affected and most of the time the expected results all go in vain.
After the procedures of the gel electrophoresis are over, the gel content is stained so as to ensure visibility. For instance, the visualization of the DNA is made possible by the use of ethidium bromide, which is very poisonous, and so people should take care when using it. When this chemical is intercalated with the DNA, it produces ultraviolet fluorescent, which is very visible, and hence one is able to see the fragments.
In the case of the protein, another dye known as the coomassie blue is used. Apart from these stated methods, there are other methods that may be used in the visualization of the fragments. These include the use of an autoradiogram in the case when t-DNA sequencing is done. Other methods involve taking photos of the gels, which is mostly done using the Gel Doc.
In the cases of the DNAs, as said earlier, the dye that is mostly used is the ethidium bromide the abbreviation of which is commonly seen as EtBr. This shines in the presence of the DNA molecules and hence it can be able to identify the presence of the DNA molecule. SYBR is another chemical that is used to stain the dsDNA. This chemical is produced by Invitrogen and it is the most expensive of all other mentioned methods.
It is also much more sensitive than the counterpart by being 25 times more sensitive. The earlier mentioned ethidium bromide is poisonous to human health. SYBR has low levels of mutagenicity and is non-hazardous. It has equal or more sensitivity than the ethidium bromide, hence it is most preferred.
The only drawback is that this chemical is very expensive, which makes it difficult for people to afford it (Sivarajan, Robson 46). Since ethidium bromide when mixed with the DNA is invisible in the natural light, it is then mixed with the natural loading buffer and this makes it more visible. The importance of the loading buffers is that they are visible in the natural light; hence, they make other chemicals visible. The most common chemicals used as loading buffers include the Xylene cyanol and the Bromophenol blue. These chemicals actually run the same speed as the DNA fragments that are about 5000bp and 300bp in length.
However, the exact position varies with the percentage of the gel. Another method to accomplish visualization is through the transfer of the DNA to the nitrocellulose membrane and then exposing it to the Hybridization probe in a process known as Western blotting. This is shown below.
The analysis is carried out after the electrophoresis when the gel is actually illuminated using the ultraviolet lamp. The apparatus that serves as the illuminator also contains an imaging apparatus the purpose of which is to take the image of the gel after the illumination of the UV light. The ethidium bromide in this case will flourish reddish-orange in the presence of the DNA since the ethidium bromide was intercalated with the DNA (Sivarajan, Robson 46).
One can also cut a DNA band out of the gel and then dissolve it so as to retrieve the purified DNA. The gel can also be photographed using a digital camera and the picture can be kept for observation and also for reference. Even though the DNA will florescence reddish-orange, the pictures are always given in the form of the black color.
Caution must be taken so as not to expose the nucleic acids to UV light since it would cause a lot of damage to the nucleic acid. The damage of the UV light to the sample then reduces the extent of the manipulation. These manipulations include cloning of the sample and ligation, which are very important in learning the properties of the nucleic acids. Due to these reasons, it means that if the DNA is extracted for the purpose of utilization, then it should not be exposed to UV light. Then, the light that should be used on this type of DNA is, for example, the blue light excitation source. This chemical is of importance because it is not harmful to human beings.
Application of your problem to the problem you are interested in.
The application of the electrophoretic technique in the world of science is important as the knowledge has been adopted in the solution of many scientific questions and also in the clarification of scientific dilemmas (Sivarajan, Robson 46). As earlier discussed, the main aim of this paper is to answer the question of genetic similarity that exists between human beings and primates and other outlaid questions. Depending on the extent of the similarity, a conclusion can be drawn concerning the big question of whether a human being has evolved from the primates or not.
The practical aspect of this technique involves withdrawing the DNA of both human beings and primates. One can use the chimpanzee as a sample because of all the existing primates it is seen as being more close to humans in physical appearance. However, for perfect research work, the working samples also include gorillas’ and world monkeys’ DNAs.
Samples are taken into consideration of many factors so as to avoid the biases of the results. The factors that are considered in the sampling procedure include:
- geographical location;
- population amongst others (Sivarajan, Robson 46).
In the human beings’ DNA selection, one can take samples from international DNA banks, which include:
- NIAS DNA Bank.
- RBG Kew DNA Bank.
- DNA Bank Network.
- DNA banking.
The choice of the DNA should consider the geographical regions that the individuals originate from, for example, one can consider sample from Africa, Asia, Europe, and other continents so that there are enough samples for the analysis. One can also consider the races such as the Negroes population, the Mongloids, and the White amongst others. In the collection of the primates’ DNA, one can consider the habitats of these primates, for example, some primates live in the bushes while others live in the parks. Another consideration should be the geographical areas of these primates, so that one picks the primates from Africa, America, etc.
For a good analysis in scientific research, the number of samples that are valued is not less than 30 for each category. The samples should then be preserved in the molecular laboratories waiting for the laboratory tests.
The gel electrophoresis is prepared prior to separation procedures. The running of the gel electrodes is connected to the power (Sivarajan, Robson 46). During this process, heat is usually generated and dissipated via the cooling chambers, which are held in between and against the gel. In this preparation, there is a tracking dye that is usually incorporated so as to stain the fragments, hence making them visible.
During the separation period, the DNAs from the primates and the human beings are dispensed on the gel. The dispensation involves the actual placement of each DNA in the wells of the gel using the micropipettes. Many gels should be prepared to ensure that each sample of the DNA is accommodated so as to perfect the analysis of the result.
After the placement of the DNAs on the gel, it is placed in the electrophoresis chamber, which has the negative and positive terminals and is connected to the power supply. After the whole set up is ready, the power is put on and the gel separation starts. In this separation, the matrix is the kind of material that is used to separate the target molecules. In its operation, the matrix holds some molecules inside and outside.
The term electrophoresis means the electromotive force that is used to move the molecules along the slab (Sivarajan, Robson 46). When the molecules that are applied are correctly put on the correct wells, the molecules will actually move through the matrix at different rates of the fragments, which depends on the size of the molecule. Hence, this means that the molecules, as explained earlier, will move at different speeds altogether.
When the separation is made, the bands are keenly studied. After the separation process, the bands of different DNAs travel at different distances on the gel. The explanation for this is that the larger is the size of the DNA, the shorter is the distance of the travel, and the smaller is the molecule, the longer is the distance.
For the purpose of broad comparison, the DNAs of other animals, which do not belong to the primates’ family, are also put to test. This is for the purpose of comparison. so that one may testify the ancestral similarity in case the primates’ DNA and that of the human beings move to almost the same distance contrary to the DNAs from the human beings and the ones from other animals. The distance moved by the human DNA and the primate DNA on the gel is almost the same and this gives a clue of the similarity of the two species. The distance traveled by DNA from other primates can also be checked out.
The separated DNA is then stored for further molecular analysis, such as sequencing and splicing. The research that has been done before indicated some insights for the similarity between the human DNA and the primate DNA as follows: Different genomic parts indicate a divergence in the hominoids. The research also shows that there is a great variation between the two DNAs, for example, the divergence has been observed to be 0% to 2.66% between the non-coding and non-repetitive genomic regions of the chimpanzees and humans.
Additionally, the phylogenetic trees that are generated by the comparative analysis of the DNA do not fit the tree of the species. All in all, for most of the DNA sequences, chimpanzees and humans appear to be the closest members of the ancestry origin. In this observation, some scientists point to the chimpanzee-gorilla pair while others to the human-gorilla one. In this sequencing, it has also been found that humans have 23 chromosomes while chimpanzees have 24.
The time that has elapsed in the divergence of human beings from other apes is of great interest (Sivarajan, Robson 45). In the world of research, a lot of work has been done to approximate this time. Amongst various studies that have been done, there are the first molecular studies, which were published in 1967 and measured the immunological distances between different primates. The study was based on the immunological response strength that an antigen existing in one species (human albumin) induced in the immunological system of another typical species (humans, chimpanzees, and gorillas).
The species that are closely related should have the same antigens and therefore should show weaker immunological responses to each other’s antigens. In that study, the immunology distance between human beings and the gorillas was determined to be about 1.09 and the one between the chimpanzee and human beings were found to be 1.14.
On the other hand, the immunological distance between human beings and the world monkeys was found to be about 2.46. The research then indicated that the African apes were more closely related to humans than to the monkeys. This study also concluded the divergence period of humans and the African apes to be about 5 million years ago. This was contrary to the thoughts of many scientists that humans-African Apes diverged more than 15 million years ago. Though the immunological distance between humans and gorillas is less than the one between human beings and chimpanzees, the solution of the trichotomy indicated that chimpanzees were phylogenetically closer to humans than to gorillas.
In recent times, DNA analysis has served a key role in the estimation of the genetic distances between humans and primates. In this case, the analytical methods of DNA separation and sequencing have played a majors part in the final determination (Sivarajan, Robson 54). This is because through electrophoresis DNAs of humans, chimpanzees, and gorillas have been separated and sequenced, hence giving the genetic closeness, as mentioned above.
Other methods that have been added in the research to support analytical procedures are the molecular clocks. According to one of the studies (Takahata et al. 95), 15 DNA sequences were used from different regions of the genome from humans and chimpanzees and 7 other DNA sequences from humans, chimpanzees, and gorillas. In the research, it was determined that the chimpanzees are closer to human beings than the gorillas. With the use of various statistical methods, it was determined that the estimated time divergence for the human-chimp pair is 4.7 million years while the one for the gorillas-humans (and chimps) group is 7.2 million years.
The study also estimated the effective population of the common chimpanzees and human beings to be about 100,000. If this is true, it then means that the human lineage had an experience of an immense decrease in its effective population size during evolution, which also means less diversity. In another study (Chen & Li 200), 53 non-repetitive intergenic segments of DNA from a human, a chimpanzee, and a gorilla were sequenced and the DNA was concatenated to one long sequence.
The generated neighbor-joining tree has supported the idea that humans and chimpanzees are the closest in relation amongst all the primates. All these studies have greatly confirmed that human beings are closely related to primates and specifically the chimpanzee. This information can then be used to support the evolution theory and withdraw the dilemma about what is closer to human beings when the chimps and the gorillas are studied.
Surely, according to the studies outlined above, human beings originated from the apes, but the question that arises is about the cause of all the difference that is seen today between the human beings and the apes. The advancement of human beings structurally, in terms of minds capacity and the population tends to invite a serious debate whenever the issues of evolution are mentioned. Through the same analytical technique of electrophoresis, scientists have been able to study the DNA more and hence give a concrete response to this. The following has been explained as the cause of this difference in the course of evolution.
Gene loss could be one of the evolutionary mechanisms. This is because the inactivation mutations can be a good cause for the selection in action. According to the studies that are discussed above, 80 genes were lost in the human lineage after humans separated from the last common ancestor with the chimpanzee. The genes that were lost for the olfactory receptors were 36 and in this process genes involved in the chemoreception and the immunology were over presented. Some of the specific genes that were lost from the human lineage include the hair keratin gene KRTHAP1.
It is believed that though humans still have 9 functional types 1 gene, the loss of the specific named gene may have resulted in the thinning of the human hair. It is also believed that the loss of this gene occurred recently in the human evolution, i.e. about 240,000 years ago. The other gene that is said to have been lost by human beings is the Myosin gene MYH16. According to (Steadman et al. 78), the loss of this gene has led to the reduction in the size of the masticatory muscles.
The mutation that led to this loss is estimated to have occurred around 2.4 million years ago. After this, the period that followed was marked with an increase in cranial capacity, which put speculation that the loss of this gene might have removed evolutional constricts on the size of the brain in the genus Homo. Another gene that is mentioned to have been lost by the human being is the CASPASE12 the consequence of which has been predicted to cause the reduction in the lethality of infections of bacteria to human beings.
Apart from the gene deletion, other possible reasons for the difference between the apes and humans include the genetic drift over time as the two shared one common ancestor. The drift is explained by the areas of the genome that differ between chimps and human beings. The example of these areas includes the HARIF, which is believed to relate to brain development, and HAR2, which is believed to have a role in opposable thumb development (Durrett 18). The above can then serve as a good explanation of the differences that arose in the evolution of human beings. This can also explain to people that evolution occurred and that evolution included many changes, which then created the difference between the apes and human beings.
In conclusion, human beings can be explained to have originated from the apes and undergone evolution for many years. This then supports the evolution theory by Charles Darwin and also removes the dilemma concerning whether the chimps or gorillas are closer to human beings. Most of this research is supported by electrophoresis and hence a conclusion can be drawn that analytic methods are important tools in the clarification of the evolution questions.
It can also be concluded that various factors, as stated above, have led to the difference between the apes and human beings throughout the evolution period. For these findings to be fully supported, more research needs to be conducted with the use of more DNA samples and modern sequencing.