Week #13 - Social and Ethical Issues (due 4/23)

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Watch the documentary film "The New Biology".
http://www.pacificbiosciences.com/aboutus/video-gallery?videoImage=The%2...

Propose to address a question with a systems biology approach and be prepared to discuss this further.

Comments

The new biology

Will the new biology be able to map a complete human genome in real time? The video has shown a number of different future possibilities for biology. The real time mapping of all genes in the body will require huge amounts of information to be transferred at incredibly fast speeds. In order to do this, a serious evolution of technology and our understanding of the human genome will need to occur.

The new biology

Will the new biology be able to map a complete human genome in real time? The video has shown a number of different future possibilities for biology. The real time mapping of all genes in the body will require huge amounts of information to be transferred at incredibly fast speeds. In order to do this, a serious evolution of technology and our understanding of the human genome will need to occur.

week 13 response

Some researchers in the video demonstrate that we can use a systems biology approach to genotype vast numbers of corn kernels, to identify the perfect combination of crossbreeds that will generate an agriculturally superior plant. Can we use this same genotyping technology to restore genetic diversity in various crop species? Through thousands of years of agriculture, humans have generated narrow genetic bottlenecks in many plants, and it may be necessary to restore the natural genetic diversity of these species to avoid potential extinctions in the future.

Week 13

Will new biology actually be able to cure cancer? It was stated in the video that we have actually already cured cancer, we just don’t know which medications or treatments to give to which people because the effectiveness of our current treatments can vary 5% to 50% from person to person. Our increasing technological advances and our knowledge of cancer may be the key to finding a cure for cancer for all patients and that is what this new biology approach will hopefully be able to achieve for us; integrating computer and biological systems.

Week 13 - Alice Trei

I propose to use a systems biology approach to investigate epigenetic changes within individuals and populations over time and in response to environmental influences. If information on epigenetic effects such as methylation states for individual genes could be recorded in individuals as they aged and compared across subjects or populations, it might lead to a lot on insight on what might become a valuable, malleable system we could predict or even alter the effects of, over time.

  • Alice trei

With the systems biology

With the systems biology approach it is possible to sequence DNA at a much faster rate. This has a lot application in potentially locating genes that contribute to disease. As is mentioned in the film, this may be useful in finding genes responsible for different forms of cancer.

Week 13

Will the new biology be the key to finding susceptibility regions and causes for disease within in the human genome? The SMRT transcription abilities and DNA banks like the one in Tokyo Japan can be used to compare thousands of individual's genomes. If we can inexpensively sequence massive numbers of individual genomes with a specific disease and compare them, we can look for genetic mutation. The SMRT detection provides the ability to directly observe in real time the regulation of transcription of a gene into an RNA message and the first phase of protein expression. This technology can enable transcription analysis on a whole genome scale rather than in shorter fragments.

Week #13 - Social and Ethical Issues (due 4/23)

Based on the "New Biology" would a cancer idetification and diagnosis database be more viable? What I mean by this is that initially all known cancers would need to be identified through the method used by Gary Noland. This data would then need to be input into a database. Additionally the information of what drugs up or downr egulate that particular cancer and in what dose they should be used should also be taken from the work of the Broad Institute. This information would need to be correlated with the different cancers and the information on the protien composition of the cancer cells. With this information propperly assembled it should be possible for a lab in a hospital to either enter the name of the cancer and pull up its protien composition and what treatment is recommended. With the information on the protien it would be possible to double check if the cancer is indeed the cancer that it is thought to be.

Week 13 Response

The systems biology approach emphasizes the study of interactions across tissues rather than individual and seemingly isolated pathways. As a result, we could greatly advance our understanding of diseases that have numerous effects throughout the body, including endocrine disorders. Hormonal imbalances can cause abnormalities in tissue formation, growth, and even neural networks that control behavior. We already have an understanding of the negative feedback mechanisms that regulate hormone secretion, but we may be missing other components that also play a major role in regulating the activity of hormones. For example, we could examine transcription factors that are commonly activated by hormones in addition to looking at hormone levels themselves. Consequently, we would obtain a more complete picture of endocrine disorders.

Systems Biology

I think the systems biology approach would be helpful in the area of Heart disease. Though the term heart disease is vague because of the subtopics of it (cardiovascular disease, cardiomyopathy, coronary heart disease, etc) protocol in heart disease research is to determine gene/protein functions but there is no cure for heart disease because the information of that gene/proteins function tells nothing about the whole system. Systems biology approach would place an emphasis on gathering information on all genes and proteins and see how they work together rather than gathering information on the individual protein and its individual functions.

blog 13

The systems biology approach could help learn more about recognition systems in cell-cell interactions and cell-pathogen interactions. It could be used to visuals the real time immediate interactions of cells to the stimulus of other cells or pathogens as well as trace the interactions that occur following the initial recognition. This information can be used to study immune system responses response and give a better whole picture view of the interactions that occur during cell-cell relations as well as cell-pathogen relations. From the initial molecular pathway responses to the regulation of genes that are used in longer term immune response we could learn how the entire system works together.

Week 13 Response

The systems biology approach I would like to see researched is that with stem cells. If stem cells were to be researched more in depth from a systems approach we may be better able to harness them and help them to differentiate in the appropriate pathways. If these cells are able to be differentiated in the appropriate pathways it may be able to be a break through that allows for the creation of synthetic organs helping to save the lives of people who have defects and are in need of transplants.

Week 13 Response

I remember hearing Neil deGrasse Tyson once say that scientific innovations often come from fields of study that are completely unrelated to where they end up being used. He gave the example of the MRI (which has just done so much awesome) and how it was invented by a physicist who didn't give two damns about medicine while inventing it, yet resulted in arguably the most valuable diagnostic tool we currently have.
I think that in order to expand our knowledge of biology, and especially in the face of this "New Biology" we should invest in computing technologies. The sheer scale at which we can now collect data depicted in the documentary will need to be interpreted, and we're not only going to need raw computing power (which is accelerating at an astonishing rate anyway) but also new methods in computing.
This leads into my proposal: Could we use this new biology to examine neural networks and maybe 'reverse engineer' a computer or piece of software from nature's own supercomputer? Perhaps use systems biology to create a computer that is more efficient at recognizing patterns than we are. Using systems biology to construct a tool, that would then furthermore expand our understanding of systems biology. I admit it does sound far-fetched, and it may be completely stupid, but it's worth considering at least.

New Biology

I have always been interested in the ways in which crops can be engineered to supply the growing population (growth of 100% in the coming years) with adequate food. I was interested in the documentaries discussion on corn and how they are able to test which seeds will produce the better crops without even growing them. I want to know with what yield monsanto is able to increase the production of corn year by year. I can see that it is good to search out corn kernels that will provide the best yield, but this seems to be a rather slow process. If year to year we are increasing yield just slowly, how long will it take to have a seventy percent increase in corn production?

The New biology says that 70% of food in the future will have to come from their modifications, such as the modifications they are making on super rice, by modifying it to survive harsher conditions with more yield. Is this selection of better seeds, but not actually genetically inserting new sequences the best way to fix the impending food crisis? Its certainly less controversial but will it be enough?

Week #13 Response

If it is possible to create a computing system which is able to assemble all the genomic information into a usable and understandable form, how will this advancement in medicine or food be passed to enough parts of the world to be able to keep up with our growing population? Cancer is causing the most recorded deaths in well-developed areas which are more likely to have the finances to purchase these new medicines. These areas also seem to be more than capable of feeding themselves, while less-developed places are starving to death from simple nutrient deprivation. How would it be possible to distribute this newly found high yield of food at a cost that less-developed areas can afford when we are unable to evenly do this now?

week 13 response

The question I want to address is, will this "new biology" approach help us quicker find alternative energy for the future? We are in need of more energy resources that are also more efficient. Can the microbial world help us achieve this. Well, in order to look into this researcher from different fields of biological studies will need to work together. And organism needs to be found- one that produces some sort of collectible and usable energy. Next we need someone to understand the biological network of the product; how does the product come to be? Then we need someone to be able to identify the product and isolate it. Then we need somebody to sequence the product and pcr it so that it can further be tested and analyzed. Once the ingredients, the genetic code, is identified for this product, there needs to be a way to mass produce it. Doing all of this requires all sorts knowledge from genomics, proteonomics, to probably even bio-engineering.

Week 13 Blog Entry

A researcher from the video tested the effects of multiple drugs on gene expression for cancerous macrophages. A similar approach could be used to map the epigenetic effects of various substances on various cells types. For example, one could expand upon the cancer researcher's work and test gene expression in macrophages of various stages of cancer against one or several drugs. This could provide insight into both oncogene expression and drug effectiveness in relation to cancer progression. This method could also be a powerful tool for analyzing phenomena that aren't pathological. For instance, how does the presence of cocaine change genome-wide gene expression in brain neurons? In cardiac muscle cells? How does gene expression change in every human cell type in response to a narcotic? How does the gene expression of a single cell type differ across a range of narcotics? Exploring these questions would provide a massive amount of data that could be used to solve some of the problems that plague humankind today.

Week 13

If I had to pick one topic to apply systems biology, though unoriginal, it would have to be food production because I believe in doing the most good. The trait networks I would be targeting would involve increasing nutrient uptake and retention to allow sowing of marginal farm land, increasing water uptake and retention for example by limiting water loss by respiration, deeper root penetration rather than greater spread so fields can be more densely planted limited only by foliage coverage, increasing number of ovaries, just to name a few. But I would like to take this a step further using the "systems" paradigm. I hear the statement "there will be 9 billion people by 2050 and we will have to increas food production by 100%". This is unsatifyingly narrow statement because they exclude what going to happen towards 3000 and beyond. Since population increase is exponential, we may be looking at 200% of today's population. Food production just like the genes themselves is a just a piece of the picture, we would need to make changes at every part of the "system" in order to sustain life.

Week 13 Blog

The question I am interested in from "The New Biology" is how can the systems approach work the the maize species. Since they determine the best corn without planting the kernels and look at a few markers, how can they look for more traits and better ones. By looking at only the genome, don't they miss important factors in the growth and development of maize?