Till 2015-Some unresolved questions in genomics research?
Here are opinions of some experts:
1. Michael Wendell from Washington University in St. Louis says "A very broad goal of "genomics" and its companion "bioinformatics" is to transition us beyond the purely empirical state of knowing gene (and pathway) lists, their basic functions and interactions, etc. to a state where we understand the (almost certainly non-linear) set of control laws that govern the cellular and larger-scale biological machinery of an organism. As Eric Lander said many times regarding the first human genome sequence: it's a list of parts. At the moment, one might say that genomics is now figuring how they fit together and what types of problems "broken parts" can cause. Ultimately, we need to know how these parts *work as a system* (at all scales), so that predictive models can be constructed. As a corollary, I think genomics will see an increasing influx of workers who specialize in these types of problems, especially from the engineering and mathematical realms."
2. Alex Ignatov of Research Center of Phytoengineering says most important stuff to consider is:
1) What is the mechanism of genome dynamics
2) What is the mechanism of information transfer from gene to phenotypic trait?
3) Is there any general rules ant purposes or evolution? "
3. Mark M. Abitol of Necker University Hospital and INSERM CENTER UMR says "The most immediate questions to solve seem to me the following ones :
1) Identifying and clarifying the different families of Non Coding RNAs and the role of each non Coding RNA
2) There are many genes encoding small peptides apparently and it is likely that most of them have not yet be identified. For Those identified, the role of these peptides are still unknown in many instances
3) the links between energy expenditure and the occurence of biological events or processes are in most instances unknown
4) The energetic cost of alternative splicing is still unknown and the same holds true for translation
5) Energy homeostasis is still an enormous conundrum without a crystal clear overwiew and modelization
6) The dynamics of genomes remains largely a mystery
7) DNA DAMAGE RESPONSE and DNA repair remain a huge fields of mysteries even though a lot of work has provided many answers
8) The RNA world remains largely unexplored
9) The mathematic modelization of biological pathways and of life is in its infancy."
4. Miguel Andarde of Johannes Gutenberg-Universität Mainz says "The 3D structure of genomes, their dynamic changes and their control."
5. Y. Tom Yang from First Dimension Biosciences (Suzhou) LTD says "Seeking "The Main Program"
I like to watch kids playing an orchestra. "An orchestra is a large instrumental ensemble that contains sections of string, brass, woodwind, and percussion instruments." There is a single person, you may or may not notice his existence. Yet, his hand moves, with a baton or not, drive the entire orchestra to make the fantastic music we enjoy. Is a "life" like an orchestra? Are there many instruments that work seamlessly together? If yes, who is "The Conductor"?
Here is another comparison:
To program with modern languages (C++, Java, Python, etc), we would have basic modules (i.e. classes), and objects for these classes; and then these modules would be linked together by a "Main" program. The "Main Program" usually takes some input arguments, and then call upon these objects to achieve a function. The Main operates essentially in the time domain and its working logic is determined by the status reported back from those objects. "The Main Program" is the system integrator and decision maker. It is part of the system, but in the mean time it is kind of beyond the system.
In genetic programs (i.e. all life forms), the architect should be similar to concerts and to computer programming. For simplicity, I will just use the case of programming. The genes are "classes". Each transcription of a gene is an "instance" of the "class", hence, an "object". The collection of genes are the working parts. They are the classes for programming. That said, how can we make the genes to work together? By comparing it to programming, we know we need a drive, i.e. "the Main Program".
Where "The Main Program" is located in the genome? How "the Main" was written? Nobody knows yet. Presumably it is a COMMON part that is within every genome for all life forms, being it be bacteria, eukaryotes, fungi, plants, but excluding virus. It should be mostly composed of genes in the class of "Transcription Factors", as it needs to call upon many genes, and to conduct a symphony.
So if we study some model systems, from the time of "fertilization" in diploid genomes, or from the time of budding in a yeast, the "Main" is kicked off. Through an evolutionary study of the pathways, we should be able to pinpoint to this Main. It should contain some massive genes (large in size) which acts as integrators of the system states, ie. the switch board protein, which then makes a decision and turns on a group of other genes through cascades.
Let's we join hand to find this "The Main Program". It is the "Conductor of Life". From there, the genetic logic will become clear. "
1. Michael Wendell from Washington University in St. Louis says "A very broad goal of "genomics" and its companion "bioinformatics" is to transition us beyond the purely empirical state of knowing gene (and pathway) lists, their basic functions and interactions, etc. to a state where we understand the (almost certainly non-linear) set of control laws that govern the cellular and larger-scale biological machinery of an organism. As Eric Lander said many times regarding the first human genome sequence: it's a list of parts. At the moment, one might say that genomics is now figuring how they fit together and what types of problems "broken parts" can cause. Ultimately, we need to know how these parts *work as a system* (at all scales), so that predictive models can be constructed. As a corollary, I think genomics will see an increasing influx of workers who specialize in these types of problems, especially from the engineering and mathematical realms."
2. Alex Ignatov of Research Center of Phytoengineering says most important stuff to consider is:
1) What is the mechanism of genome dynamics
2) What is the mechanism of information transfer from gene to phenotypic trait?
3) Is there any general rules ant purposes or evolution? "
3. Mark M. Abitol of Necker University Hospital and INSERM CENTER UMR says "The most immediate questions to solve seem to me the following ones :
1) Identifying and clarifying the different families of Non Coding RNAs and the role of each non Coding RNA
2) There are many genes encoding small peptides apparently and it is likely that most of them have not yet be identified. For Those identified, the role of these peptides are still unknown in many instances
3) the links between energy expenditure and the occurence of biological events or processes are in most instances unknown
4) The energetic cost of alternative splicing is still unknown and the same holds true for translation
5) Energy homeostasis is still an enormous conundrum without a crystal clear overwiew and modelization
6) The dynamics of genomes remains largely a mystery
7) DNA DAMAGE RESPONSE and DNA repair remain a huge fields of mysteries even though a lot of work has provided many answers
8) The RNA world remains largely unexplored
9) The mathematic modelization of biological pathways and of life is in its infancy."
4. Miguel Andarde of Johannes Gutenberg-Universität Mainz says "The 3D structure of genomes, their dynamic changes and their control."
5. Y. Tom Yang from First Dimension Biosciences (Suzhou) LTD says "Seeking "The Main Program"
I like to watch kids playing an orchestra. "An orchestra is a large instrumental ensemble that contains sections of string, brass, woodwind, and percussion instruments." There is a single person, you may or may not notice his existence. Yet, his hand moves, with a baton or not, drive the entire orchestra to make the fantastic music we enjoy. Is a "life" like an orchestra? Are there many instruments that work seamlessly together? If yes, who is "The Conductor"?
Here is another comparison:
To program with modern languages (C++, Java, Python, etc), we would have basic modules (i.e. classes), and objects for these classes; and then these modules would be linked together by a "Main" program. The "Main Program" usually takes some input arguments, and then call upon these objects to achieve a function. The Main operates essentially in the time domain and its working logic is determined by the status reported back from those objects. "The Main Program" is the system integrator and decision maker. It is part of the system, but in the mean time it is kind of beyond the system.
In genetic programs (i.e. all life forms), the architect should be similar to concerts and to computer programming. For simplicity, I will just use the case of programming. The genes are "classes". Each transcription of a gene is an "instance" of the "class", hence, an "object". The collection of genes are the working parts. They are the classes for programming. That said, how can we make the genes to work together? By comparing it to programming, we know we need a drive, i.e. "the Main Program".
Where "The Main Program" is located in the genome? How "the Main" was written? Nobody knows yet. Presumably it is a COMMON part that is within every genome for all life forms, being it be bacteria, eukaryotes, fungi, plants, but excluding virus. It should be mostly composed of genes in the class of "Transcription Factors", as it needs to call upon many genes, and to conduct a symphony.
So if we study some model systems, from the time of "fertilization" in diploid genomes, or from the time of budding in a yeast, the "Main" is kicked off. Through an evolutionary study of the pathways, we should be able to pinpoint to this Main. It should contain some massive genes (large in size) which acts as integrators of the system states, ie. the switch board protein, which then makes a decision and turns on a group of other genes through cascades.
Let's we join hand to find this "The Main Program". It is the "Conductor of Life". From there, the genetic logic will become clear. "
Labels:
bioengineering,
bioinformatics,
biotechnology
