Thursday, August 20, 2009

Prions, Viroids, Transposons and Strange Things that go bump in the night

If you haven't heard of prions, they are bits of misfolded protein that have the capacity to replicate themselves. Mad cow disease is one well known disease resulting from eating the brains and nervous tissue of cows. However under certain circumstances these proteins can be found in the organs of animals in significant quantities as a result of viral infection. Viral infection can also cause prions to spread to the milk and muscle, however even in such conditions, they are only found in rather small amounts, and should not cause mad cow disease. The naturally forming variation of this protein is also known to cause Alzheimer's disease and gene therapy in rats has been shown to cure the disease by essentially preventing the production of the protein. The prion protein is known to survive cooking and digestion. The mad cow disease in cows is known to have been caused by feeding the brain and nervous tissue of cows to other cows. We then eat these cannibalistic cows. Prions are also known to exist in fungi, but are not currently associated with a disease, well kinda. Some prions of fungus are known to protect one group of genetically similar fungus from another group of non genetically similar fungus by killing the non prion fungus. Kuru disease is a prion disease caused by cannibalism. The logical conclusion for prions is they are a part of the immune system, which is likely shared by all organisms from plant life to animal life. Basically prions protect an organism from foreign proteins.

Viroids are implicated in a number of plant diseases and are known to spread via a number of vectors. Aphids and seed spreading are common methods. Viroids are bits of circular, single-stranded, complementary RNA lacking the protein commonly associated with viruses. They also contain a shorter number of bases than viruses and are smaller in size. They do not code for protein. One such viroid is the potato spindle tuber viroid. It causes stunted growth, altered color, and leaf deformation. You can see the viroids in an electron microscope, however you are unable to see how it works because electron microscopes only take still pictures. A viroid like molecule is also implicated in hepatitis D, however it requires a preexisting infection, Hepatitis B.

Transposons are mobile genetic elements of dna, implicated in evolution. Sometimes they are cut and paste but in other cases they simply replicate. They make a significant portions of eukaryotic organisms. They can also be involved in horizontal gene transfer between different species. One class of transposons is involved in retroviruses. Some diseases that are attributed to transposons are haemophilia, sever combined immunodeficiency, porphyrias, and duchenne muscular dystrophy. Transposons can cause color changes in corn. Mariner construct transposons horizontal gene transfers are known to occur between tapeworms and humans.

Satellite genetic material can also be found in the cell. Satellite genetic material, whether rna or dna, can interfere in the replication machinery.

Thus I am brought to the point of this whole tirade. Infectious agents exist that are very difficult to detect. Increasingly these 3 elements and potentially variations of these will found to be increasingly found to be involved in disease and likely with aging as well. Also in spite of the common propaganda you find with forensics shows, the genome is not static. It changes in the course of an organism's lifetime. This applies to humans. Reproduction is also very active in the use of transposable elements, resulting in the slight variations from parent to child. The effect of a gene depends on where it is located in the genome. Genes are sometimes referenced as exons and code for protein. Introns are considered the non coding portion of the genome. However they code for specialization. They are the instructions for when a certain gene should be turned on or off and in what circumstances. Without introns there would be no cell types, no organs, etc. Also when they say a plant shares 50% of its genes with humans(or 95% with apes) they are referencing a limited set of base pairs and exclude certain genetic material based mainly on base pair substitutions, so contrary to what people have been lead to believe the similarity between humans and other species is not as large. At one time they only looked at the exons for genetic comparison. Currently the effect of introns is only barely understand and was initially considered to be junk dna. That idea is slowly being eroded. The mitochondria also has its own dna and is inherited from the mother. If I were to point to a cause of aging, transposable elements likely result in the genes in the mitochondria becoming dysfunctional until eventually one can do nothing but die.

Gene therapy in the future will likely be used to combat aging. However the human genome will need to be better understand. All species that people eat will increasingly have to be modified to combat the subtle diseases they cause in humans. Researchers in various places are already working on mad cow disease resistant cows. Also animals and plants will need to be modified and immunized against infectious agents. Also humans will also need to be genetically modified. This may not be an idea many like, but once the human genome is understood, a government sponsored human genome modification program should be implemented. The reduction in cost of both healthcare and education would be enormous as well as the huge increase in productive. No good reason exists against it once the technology exists that is both safe and well understood.

I tried to find base pair lengths for different animal species but was unable to find the data online for any except humans and that value was only a rough value. Humans are supposed to have around 3 billion base pairs(seen it listed as 2.9 billion, 3 billion, and 3.2 billion) and chimps have approximately the same. Humans have 46 chromosomes, while the ape species have 48. This is due to chromosome merging. Chimps and humans may have the exact number of base pairs or they may not. If there is a variation, how large is that variation? Chimps are considered to be humans' closest relatives based on genetic and molecular analysis, however orangutans display higher intelligence than chimps and more similar morphological features to humans than chimps. Eventually a greater understanding of genetics will reveal that orangutans possess at least some genetic traits that are closer to humans than chimps. Some genetic length variation(base pairs) may exist among the non-human primate species, however I could not find any data to confer or deny. C-values online(see http://www.genomesize.com/) were unreliable. The methods of gene deactivation logically have an effect on measured weight of dna. C-value among different cell types likely varies. Large variations also were reported for the same species, so I had to discharge that avenue. At least in eukaryotic life, cells divide by the process of mitosis, which involves the chromosomes breaking up and you end up with one extra pair of chromosomes. In meiosis, the number of chromosomes is halved, which then allows the male and female to each contribute genetic material. Various methods exist to alter the genetic code. Transposons, viral infection and plasmid gene swapping are a few. Geneticists have also come up with a few synthetic methods as well like use of zinc finger nuclease.

Basically to the point, potentially small base pair length alterations could exist on individual chromosomes which can give rise to an increase or decrease of the genome length. So potentially two people can have kids even though they don't necessarily possess the same genome length or contribute the same length for their haploids. http://www3.interscience.wiley.com/journal/120159615/abstract illustrates that y chromosome length can vary among males. It is also possible that these small genetic length variations (coming from chromosome length variations) could result in birth defects even though they don't have an abnormal number of chromosomes. Accumulative genetic length variations could also result in speciation and maybe cause a chromosome to merge with another or to divide itself in two. The method of reproduction could effect this genetic length variation drift rate. Likely organisms that reproduce asexually can experience large drift rates. Maybe amoebas reproducing asexually can help to explain their large genome size. One chromosome could also lose some base pairs to another chromosomes, thus if one chromosome has a high mutation rate it could help to contribute to the changes in the other chromosomes.

Though the other primate species, like gorillas, monkeys, chimps, orangutans, etc. maybe classified as a different species than human, perhaps they should in fact be considered human or a variation of such(subspecies, another race maybe?). With the right challenging environment and selective breeding these non-human primate species could become even more human-like until their intellectual abilities nearly match our own. The main attribute that makes us humans is not necessarily what we eat or how we look, but the intellectual abilities that our brains possess. If such a day happens when other primates can talk like us(learning language), socialize with us, write poetry, participate in science, wonder over religion to the point where the only difference between us and them is our appearance and the fact we couldn't sexually reproduce, should they not appropriately be given the title human and thus afforded the same rights as other humans. As long as we continue to interact with other primates and manage not to kill all its members we will eventually see the day where other primates may be called brothers.

Random prophetic predictions: In the future some people will be born without having a father or a mother.

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