Review of Prokaryotes, Eukaryotes, & Viruses Tutorial

First, it was inspirational to me too see that the Prokaryotic cells had diversity also. It was the kind of awe and inspiration you get when you visit an Aquarium and see that the underwater world has so many diverse creatures. Diversity is the key characteristic of nature. It would be so unnatural to have all the same looking human beings in everywhere we are. It seems to me strange but true that we are more comfortable among strangers, and we make the strangers our friends through humanity. I believe that is the beauty of our lives that we live in this way - in harmony among differently shaped , coloured creatures. It was a pleasant discovery to find even at the Prokaryotic cell level this diversity existed such as colored ones as the cyanobacteria, multiped shaped ones as cocci, baccilli, and spirilla and helical and ones with functional options like flagella or pili

It was also interesting that bacteria lives in a medium that has the similar viscosity as asphalt. Then is a more evolved biological self one that has a lighter out side? Like the skin we have? I do think having a lighter outside shield can have merits and also downfalls but overall I believe that there is more plus than minus to have skin rather than living in a medium with a viscosity like asphalt. Thank God ! :)

It was impressive to me that the Metanococcus jannaschii is found 3 km down, at 85 deg C
has 1738 genes, 56% of which are new to science has bacteria-like genes and operons
but with eukaryotic-like information processing and secretion systems and eukaryotic protein synthesis and that these findings represent the scientific equivalent of opening a new porthole on Earth and discovering a wholly new view of the universe. In decoding the genetic structure of archaea that the two-thirds of the genes do not look like anything we've ever seen in biology before. The fact that this brings to closure the question of whether archaea are separate and distinct life forms may be a prood of an old saying ...... the world we can't see is bigger than we think.

Even though 99.4 % of the most critical DNA sites are identical in human and chimp genes

Even though 99.4 % of the most critical DNA sites are identical in human and chimp genes, I would not justify reclassifying Homo Sapiens as Pan Sapiens. Below is an article about how human differ from Chimpanzees, and I consider it more right to have a different name if there is a difference between the two.

Most Human-Chimp Differences Due To Gene Regulation -- Not Genes

ScienceDaily (Mar. 10, 2006) — The vast differences between humans and chimpanzees are due more to changes in gene regulation than differences in individual genes themselves, researchers from Yale, the University of Chicago, and the Hall Institute in Parkville, Victoria, Australia, argue in the 9 March 2006 issue of the journal Nature.

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The scientists provide powerful new evidence for a 30-year-old theory, proposed in a classic paper from Mary-Claire King and Allan Wilson of Berkeley. That 1975 paper documented the 99-percent similarity of genes from humans and chimps and suggested that altered gene regulation, rather than changes in coding, might explain how so few genetic changes could produce the wide anatomic and behavioral differences between the two.

Using novel gene-array technology to measure the extent of gene expression in thousands of genes simultaneously, this study shows that as humans diverged from their ape ancestors in the last five million years, genes for transcription factors -- which control the expression of other genes -- were four times as likely to have changed their own expression patterns as the genes they regulate.

Because they influence the activity of many "downstream" genetic targets, small changes in the expression of these regulatory genes can have an enormous impact.

"When we looked at gene expression, we found fairly small changes in 65 million years of the macaque, orangutan, and chimpanzee evolution," said study author Yoav Gilad, Ph.D., assistant professor of human genetics at the University of Chicago, "followed by rapid change, along the five million years of the human lineage, that was concentrated on these specific groups of genes. This rapid evolution in transcription factors occurred only in humans."

"For 30 years scientists have suspected that gene regulation has played a central role in human evolution," said Kevin White, Ph.D., associate professor of genetics and ecology and evolution at Yale and senior author of the study. "In addition to lending support to the idea that changes in gene regulation are a key part of our evolutionary history, these new results help to define exactly which regulatory factors may be important, at least in certain tissues. This helps open the door to a functional dissection of the role of gene regulation during the evolution of modern humans."

To measure changes in gene expression from different species, White and Gilad developed the first multi-species gene array. This allowed them to compare the level of expression of more than 1,000 genes between humans, chimps, orangutans and rhesus macaques -- representing about 70 million years of evolution. To make the samples comparable, the researchers studied tissue from the liver -- one of the most homogeneous sources -- from five adult males from each of the four species.

They focused their search on expression levels of two sets of genes, those that remained largely unchanged across all four species, suggesting that there was little room -- or need -- for improvement, and those that changed most dramatically, usually in the human lineage -- an indication of powerful incentives to adapt to a changing environment.

Of the 1,056 genes from all four species, 60 percent had fairly consistent expression levels across all four species. "The expression levels of these genes seem to have remained constant for about 70 million years," the authors wrote, "suggesting that their regulation is under evolutionary constraint."

Many of these genes are involved in basic cellular processes. The authors suggest that altering the regulation of these fundamental and ancient genes may be harmful. In fact, five of the 100 most stable genes have altered expression levels in liver cancer.

When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased expression in humans were. None of those with lower expression were transcription factors. This pattern, the authors note, is consistent with "directional selection."

Previous studies have found that many of these same genes have also evolved rapidly in humans, accumulating changes in their coding sequence as well as in expression rates. "Together," they add, "these findings raise the possibility that the function and regulation of transcription factors have been substantially modified in the human lineage."

This is a very efficient way to make big changes with very little effort, according to Gilad. By altering transcription factors, the entire regulatory network can change with very few mutations, increasing the impact and minimizing the risk.

"The big question," he said, "is why are humans so different? What sort of changes in the environment or lifestyle would drive such a rapid shift in the expression of genes -- in this case in the liver -- in humans and in no other primate?"

Part of the answer, he suspects, is rapid alterations in diet, probably related to the acquisition of fire and the emerging preference for cooked food. "No other animal relies on cooked food," he said. "Perhaps something in the cooking process altered the biochemical requirements for maximal access to nutrients as well as the need to process the natural toxins found in plant and animal foods."

This is just the first of a series of similar studies, said Gilad, that will look at changes in gene expression over evolutionary time. The next steps are to look at larger arrays of genes and to focus on other tissue types.

Additional authors include Alicia Oshlack, Gordon Smyth and Terence Speed from the Hall Institute in Parkville, Victoria, Australia. This study was supported grants from the Keck Foundation, the Beckman Foundation and the National Human Genome Research Institute to Professor White.

How does Darwinism matter to me ?

I think Darwinism worked a lot as a way to encourage people to develop themselves, to become a more fit being to survive through the everyday challenges and competition we face. Living a lot of my life in South Korea which is a highly competitive society I guess I always had that idea that I should be more diligent or efficient and should not be lazy work hard and strive towards excellence and be a better being to ultimately be able to fit in and survive successfully in the world we live in. Especially as a developing country, Korea is always talking about this sleeping less and dong more work efficiently. It occurred to me? In what sense does it mean to be more fit in order to survive? Is it being competitive and refraining from what we want from life ? Is the ultimate ideal of the Darwinism in our society be a person who can be less human ? I guess this is a state of mind but does portrait a concept than underlies in every area we live in. Being the better one. Have to better than the other in order to avoid falling back and in order to survive successfully. I always think that people are infinitely precious and valuable because they are human being but at the same time we live in the society that always would present the concept of Darwinism ' Survival of the fittest ' .

Evo-Devo , Wagyu Mammoth and the ethical issues we discussed in class

My thoughts about Evo-Devo is inevitably full of concerns. What if everything goes haywire and Evo-Devo develops nothing more that potential threats and chaos to the world? Therefore, I talked with my friend that enlightened me with a little more positive view than I had. I talked about evo-devo with my friend and the article about could cloned mammoths be in our future as an example. My friend said why it could actually work in a good way maybe a solution for the food industry and brought up an example which I thought was rather interesting. My friend said people would love to have another source of meat - especially the curious adventurous people would and if people could have an option they could try Mammoth meat, some would like it, and some could make it into Wagyu Mammoth. :) Who knew ? This story led me a little to looking at the brighter side of Evo-Devo that as long as we are in control this could be an evolutionary development that would work in a benefit to us in various areas of our life. However, then again I think we should always come back to the ethical issues discussed in class. So is bringing back and mutating creatures ethical ? I think it has not been long before we became comfortable with In Vitro Fertilization but people do it and are getting use to it. I think the more people get familiar with Evo-Devo the more people would be using it at their benefits without raising the question of " Is this really ethical ? ". However, in my point of view, ethical issues should be raised in every occasion and be discussed throughout the society and should be able to prove that it is ethical in various ways before the significant changes it would inevitably bring to people's lives.

Thought about the Mystery of three-year hiccup ordeal solved

Our Biological selves are connected to everything. In an Oriental medicine perspective, our body is an all connected organism and cannot consider our body and the symptoms the body is showing as a separate thing. Therefore, in an Oriental medicine point of view, the brain tumor, and the hiccups in the article The Mystery of three-year hiccup ordeal solved cannot be treated separately. Moreover, treatments have to benefit the whole body not only the symptom in order to be a right treatment. A treatment that ignores the fact that our biological self is an organism cannot be considered as a proper treatment. A treatment that stops the symptom but damages the whole body is not considered as a proper treatment. Simple as it sounds, many treatments and drugs and surgeries often ignore the fact that our body is a organism and whatever is done to a part of the body or to a symptom the body is showing, the whole body is effected. Actually a vast majority of the treatments neglect that our biological selves are an organism and mainly focuses on treating just the symptom itself. In Eastern medicine our biological selves are al l connected. All of the organs in our body is connected and interacts with each other. All of the symptoms our body manifests are connected to our body. Our body interacts and are affected and are connected with the thoughts that go through our mind. In other words, our body and mind are also connected. How stress can damage our health could be a great example for that. Our body is not only connected internally but also connected externally. That is, our body is connected with what is going on outside our body and with the whole earth and universe. How pollution can be so bad for our health would be a good example for this. In traditional Eastern medicine health is achieved through harmony with what is connected to the body, everything, the earth, the everyday life the person is going through, the relationship the person is sharing. To put it in other words, those would be out physical, environmental, social health. Eastern medicine lies on the basis of the concept that health is achieved by having all these health and if the person lives in harmony and is healthy, the body doesn't have symptoms that bothers the person.