The Genetic Landscape of a Cell
Networks
The living things of the world are extremely varied and intricately made, yet the theory of evolution has always been about simplicity: once upon a time, some chemicals assembled, began to make copies of themselves, and little by little changed into all life forms. Evolutionists like to use the words "simply" and "merely" when telling their stories to the public. There is certainly nothing complicated about the idea of mutation-natural selection. However, by the year 2000, research had reached a point where a new branch of biology was needed: Systems Biology. Discoveries in this field are the exact opposite of merely simple. Biological systems are vastly more complex than anyone could imagine. Some wonder if we will ever fully understand them.
"To make sense of the genome, systems biologists think in terms of networks. If two kinds of proteins or other biological molecules interact, they are connected on the network." "These network diagrams... show how individual pathways crisscross to form a tangled web. Each protein in a pathway can interact with molecules in other pathways, sometimes dozens of them." Additionally, "systems biologists produce complex maps of how genes and proteins interact, and these maps help scientists analyze results from drug screening." "Cells 'talk' to each other by passing chemical signals back and forth. They also sense their physical surroundings through proteins on their surfaces called integrins. All these cues serve to orient the cells in the body and inform them about how to behave so that they cooperate with the rest of the cells in the tissue." "The cells are not complete by themselves. They need signals from outside," says Mina J. Bissell of Lawrence Berkeley National Laboratory. "The unit of function literally is the tissue."-- Patrick Barry. April 5, 2008. You, in a dish: cultured human cells could put lab animals out of work for chemical and drug testing. Science News, Vol. 173, No. 14, pp. 218-220.
"The interesting point coming out of all these studies is how complex these systems are; the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent. The simple pathway models are a gross oversimplification of what is actually happening", says Mike Tyers, a systems biologist at the University of Edinburgh, UK.-- Blow, Nathan. 16 July 2009. Untangling the protein web. Nature, Vol. 460, pp. 415-418.
"The life of every organism depends crucially on networks of interacting proteins that detect signals and generate appropriate responses. Examples include chemotaxis, heat shock response, sporulation, hormone secretion, and cell-cycle checkpoints."
"When the information in molecular mechanisms that underlie the adaptive behaviour of living cells is laid out in graphical form, the molecular network looks strikingly similar to the wiring diagram of a modern electronic gadget. Instead of resistors, capacitors and transistors hooked together by wires, one sees genes, proteins and metabolites hooked together by chemical reactions and intermolecular interactions."
"Certain feedback and feedforward signals can create diverse types of responses: sigmoidal switches (buzzers), transient responses (sniffers), hysteretic switches (toggles), and oscillators (blinkers). From these components, nature has constructed regulatory networks of great complexity. With accurate mathematical representations of the individual components, we can assemble a computational model of any such network" using "differential equations, limit cycles and bifurcation diagrams."
"Complex molecular networks, like electrical circuits, seem to be constructed from simpler modules: sets of interacting genes and proteins that carry out specific tasks and can be hooked together by standard linkages."--Tyson, John J., Katherine C. Chen, Bela Novak. 2003. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology, Vol. 15, No. 2, pp. 221–231.
This is a map of how the genes in a cell of the budding yeast Saccharomyces cerevisiae interact with one another. Each color shows what a group of genes does. Genes in these functional networks interact with other genes throughout the cell; a cell of yeast.
By 2010, real biologists had determined that gene regulatory networks (GRNs) build and operate all living things. There are gene regulatory networks for everything that happens in them, and some networks control other networks in a chain of command. Each species has a body plan, and it is encoded in the DNA. "Development of the body plan is caused by the operation of GRNs". "Embryonic development is an enormous informational transaction, in which DNA sequence data generate and guide the system-wide spatial deployment of specific cellular functions." That is, an embryo grows because GRNs tell other GRNs what to do at the right time and place and in the right order; it is tremendously complex. GRNs then guide the development of different types of cells, organs, and growth of the embryo into an adult. They also control each creature's abilities and the way it responds to changes around it. Among the most studied are sea urchins, which are low on the evolutionist's "tree of life".
An embryo has a particular growth program for the type of creature it will develop into. Yet it is likely that all the different programs are constructed from just a few types of sub-circuits. "Structurally similar sub-circuits, but composed of different regulatory genes" do "similar developmental jobs in different GRNs." This discovery gives researchers hope that they can use these "modules of developmental logic function" to decipher the "enormous mazes of interconnections in system level GRNs". You can tell what a sub-circuit does by its shape or structure. There is a sub-circuit for each task, and GRNs are made up of sub-circuits. The same control processes are used "throughout embryonic development because the problems that have to be solved are general: the initial spatial inputs have to be interpreted, the regulatory state then has to be locked down (the initial inputs are always transient), signals have then to be generated, other states have to be excluded, and differentiation drivers have to be activated. It is not surprising that all this requires a lot of sequential circuitry."
GRNs in embryos "are hierarchical in their overall structure. Their depth reflects the long sequence of regulatory steps required to complete any component of embryonic development." A GRN might have many layers of sub-circuits or very few, depending on its job. The last step in the chain of command is the signal for "batteries" (groups) of genes to change stem cells into specific types of cells (such as muscle, blood, nerve, etc.) at the right place.-- Davidson, Eric H. 16 December 2010. Emerging properties of animal gene regulatory networks. Nature, Vol. 468, pp. 911-920.
Some evolutionists have publicly welcomed GRNs because a change in one controller can affect many genes, and we are back to simplicity. That is like saying a child can use Windows operating system on a computer. Just point and click with a mouse, and the computer does many complicated things. It is simplicity itself. So why are GRNs the death blow to evolution theory? It took computer and software engineers decades of intelligent design to build the computer and operating system. GRNs are the operating system of living things. The theory of evolution cannot explain how gene regulatory networks came to be. As with other insurmountable problems with the theory, this one remains in their pile marked "needs further study".
Today there is an explosion of knowledge going on in the study of gene regulatory networks. But it is not led, assisted, or even inspired by the theory of evolution. "We have little empirical knowledge on the evolutionary history of such networks."-- Dean, Antony M., Joseph W. Thornton. September 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics, Vol. 8, pp. 675-688.
Some of the things GRNs have been found to do:
-- Erwin, Douglas H., Eric H. Davidson. February 2009. The evolution of hierarchical gene regulatory networks. Nature Reviews Genetics, Vol. 10, pp. 141-148.
Mutation-natural selection could no more build the vast, intricate networks in living creatures than a beaver could build the Hoover dam.
To the next level
At this point we are light-years beyond the simplistic notions of Darwinism. Now even systems biology is being overwhelmed.
"Increasingly, leaders in the fields of systems biology realise that it is our inability to understand and model the true underlying complexity of whole biological systems (as opposed to their reduced parts) that is holding back deep physiological understanding of organisms: truly understanding biology involves getting to grips with unimaginable complexity".-- Moore, Andrew. 2012. Bringing systems biology to the clinic: An acute case. Bioessays Vol. 35, No. 1, pg. 1.
"The protein p53, for example, was discovered in 1979." "It soon gained notoriety as a tumor suppressor - a 'guardian of the genome' that stifles cancer growth by condemning genetically damaged cells to death. Few proteins have been studied more than p53."
"Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death, structure and DNA repair. It also binds to numerous other proteins." "Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development."
Research "has dismantled old ideas about signaling 'pathways', in which proteins such as p53 would trigger a defined set of downstream consequences. 'When we started out, the idea was that signaling pathways were fairly simple and linear,' says Tony Pawson, a cell biologist at the University of Toronto in Ontario. 'Now, we appreciate that the signaling information in cells is organized through networks of information rather than simple discrete pathways. It's infinitely more complex.' "
"Systems biology was supposed to help scientists make sense of the complexity. The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved."
Unfortunately, "there is no way to gather all the relevant data about each interaction". "In many cases, the models themselves quickly become so complex that they are unlikely to reveal insights about the system, degenerating instead into mazes of interactions". "Many of the mechanisms and principles governing inter- and intracellular behavior are still a mystery."-- Hayden, Erika Check. 1 April 2010. Life is Complicated. Nature, Vol. 464, pp. 664-667.
When cells repair damaged DNA using so-called "replicate DNA" (for making copies) or "transcribe DNA" (the first step in making a protein), the parts are rapidly assembled from a pool of parts floating in the nucleus of a cell to form "factories". The size of a repair center is according to the amount of damage it has to repair. "A replication factory persists for a few minutes before it disassembles. A new factory is then assembled... immediately adjacent to the previous one". Whether it is repair, replication, or transcription, once the job is done the "factories" disassemble and the parts float back into the pool.32
Chromatin is DNA packaged into chromosomes. Chromatin is in constant motion.3 Different sections along DNA are apparently guided to each other directly and rapidly, forming loops.11 Chromatin loops are very common. Loops range in size from thousands to hundreds-of-thousands of bases long. Loops bring together genes and their regulators to form "transcription hubs" where transcription can occur.32 "Long-range interactions can occur over very large genomic distances, up to tens of megabases". "Interactions occur not only along chromosomes, but also between them." "Chromosomes extensively interact with each other"42, and neighboring chromosomes intermingle.32
There is a "bewildering complexity in long-range communication among a variety of genomic elements across chromosomes and the genome."42
The Bottom Line
Evolutionists assume evolution is true, then write endlessly about when and where it happened, rates and lineages, etc. But if macroevolution is physically impossible in the real world, and it is, then all the rest is fantasy. There are only two possibilities. Either every part of every living thing arose by random chance, or an intelligence designed them.
In spite of overwhelming evidence that the theory of evolution is dead wrong, many are not ready to throw in the towel. They desperately hope that some natural process will be found that causes things to fall together into organized complexity. These are people of great faith. And they are so afraid of connecting God with science that, like the Japanese Army of World War II, they would rather die than surrender. Unfortunately, the staunchest defenders sit in places of esteem and authority as professors, scientists, and editors, and have the full faith of the news media. The public is naturally in awe of their prestige. But once the facts are understood it becomes obvious that the theory of evolution is long overdue for the trash can, and to perpetuate it is fraud. Perhaps it made sense for what was known when On the Origin of Species was published in 1859, but not today.
1) http://www.newgeology.us/presentation32.html
Networks
The living things of the world are extremely varied and intricately made, yet the theory of evolution has always been about simplicity: once upon a time, some chemicals assembled, began to make copies of themselves, and little by little changed into all life forms. Evolutionists like to use the words "simply" and "merely" when telling their stories to the public. There is certainly nothing complicated about the idea of mutation-natural selection. However, by the year 2000, research had reached a point where a new branch of biology was needed: Systems Biology. Discoveries in this field are the exact opposite of merely simple. Biological systems are vastly more complex than anyone could imagine. Some wonder if we will ever fully understand them.
A small section of a biological system in an organism, displayed as a 3D network
"The interesting point coming out of all these studies is how complex these systems are; the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent. The simple pathway models are a gross oversimplification of what is actually happening", says Mike Tyers, a systems biologist at the University of Edinburgh, UK.-- Blow, Nathan. 16 July 2009. Untangling the protein web. Nature, Vol. 460, pp. 415-418.
"The life of every organism depends crucially on networks of interacting proteins that detect signals and generate appropriate responses. Examples include chemotaxis, heat shock response, sporulation, hormone secretion, and cell-cycle checkpoints."
"When the information in molecular mechanisms that underlie the adaptive behaviour of living cells is laid out in graphical form, the molecular network looks strikingly similar to the wiring diagram of a modern electronic gadget. Instead of resistors, capacitors and transistors hooked together by wires, one sees genes, proteins and metabolites hooked together by chemical reactions and intermolecular interactions."
"Certain feedback and feedforward signals can create diverse types of responses: sigmoidal switches (buzzers), transient responses (sniffers), hysteretic switches (toggles), and oscillators (blinkers). From these components, nature has constructed regulatory networks of great complexity. With accurate mathematical representations of the individual components, we can assemble a computational model of any such network" using "differential equations, limit cycles and bifurcation diagrams."
"Complex molecular networks, like electrical circuits, seem to be constructed from simpler modules: sets of interacting genes and proteins that carry out specific tasks and can be hooked together by standard linkages."--Tyson, John J., Katherine C. Chen, Bela Novak. 2003. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology, Vol. 15, No. 2, pp. 221–231.
This is a map of how the genes in a cell of the budding yeast Saccharomyces cerevisiae interact with one another. Each color shows what a group of genes does. Genes in these functional networks interact with other genes throughout the cell; a cell of yeast.
Costanzo, Michael, et al. 22 January 2010. The Genetic Landscape of a Cell.
Science, Vol. 327, No. 5964, pp. 425-431
An embryo has a particular growth program for the type of creature it will develop into. Yet it is likely that all the different programs are constructed from just a few types of sub-circuits. "Structurally similar sub-circuits, but composed of different regulatory genes" do "similar developmental jobs in different GRNs." This discovery gives researchers hope that they can use these "modules of developmental logic function" to decipher the "enormous mazes of interconnections in system level GRNs". You can tell what a sub-circuit does by its shape or structure. There is a sub-circuit for each task, and GRNs are made up of sub-circuits. The same control processes are used "throughout embryonic development because the problems that have to be solved are general: the initial spatial inputs have to be interpreted, the regulatory state then has to be locked down (the initial inputs are always transient), signals have then to be generated, other states have to be excluded, and differentiation drivers have to be activated. It is not surprising that all this requires a lot of sequential circuitry."
GRNs in embryos "are hierarchical in their overall structure. Their depth reflects the long sequence of regulatory steps required to complete any component of embryonic development." A GRN might have many layers of sub-circuits or very few, depending on its job. The last step in the chain of command is the signal for "batteries" (groups) of genes to change stem cells into specific types of cells (such as muscle, blood, nerve, etc.) at the right place.-- Davidson, Eric H. 16 December 2010. Emerging properties of animal gene regulatory networks. Nature, Vol. 468, pp. 911-920.
Some evolutionists have publicly welcomed GRNs because a change in one controller can affect many genes, and we are back to simplicity. That is like saying a child can use Windows operating system on a computer. Just point and click with a mouse, and the computer does many complicated things. It is simplicity itself. So why are GRNs the death blow to evolution theory? It took computer and software engineers decades of intelligent design to build the computer and operating system. GRNs are the operating system of living things. The theory of evolution cannot explain how gene regulatory networks came to be. As with other insurmountable problems with the theory, this one remains in their pile marked "needs further study".
Today there is an explosion of knowledge going on in the study of gene regulatory networks. But it is not led, assisted, or even inspired by the theory of evolution. "We have little empirical knowledge on the evolutionary history of such networks."-- Dean, Antony M., Joseph W. Thornton. September 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics, Vol. 8, pp. 675-688.
Some of the things GRNs have been found to do:
- Specialized GRNs determine which genes are active or inactive in each part of a developing creature
- GRN sub-circuits, usually consisting of 3 to 8 regulatory genes plus the elements they regulate, perform specific functions
- Switches permit or forbid the activity of whole sub-circuits
- Gene batteries are groups of genes required for particular cell functions; they are controlled by a small set of transcriptional drivers
- Segments of DNA a few hundred base pairs long, called cis-regulatory elements, control expression of the genes near them
- Signals are deployed between one cell and another using cis-regulatory elements
-- Erwin, Douglas H., Eric H. Davidson. February 2009. The evolution of hierarchical gene regulatory networks. Nature Reviews Genetics, Vol. 10, pp. 141-148.
Mutation-natural selection could no more build the vast, intricate networks in living creatures than a beaver could build the Hoover dam.
To the next level
At this point we are light-years beyond the simplistic notions of Darwinism. Now even systems biology is being overwhelmed.
"Increasingly, leaders in the fields of systems biology realise that it is our inability to understand and model the true underlying complexity of whole biological systems (as opposed to their reduced parts) that is holding back deep physiological understanding of organisms: truly understanding biology involves getting to grips with unimaginable complexity".-- Moore, Andrew. 2012. Bringing systems biology to the clinic: An acute case. Bioessays Vol. 35, No. 1, pg. 1.
"The protein p53, for example, was discovered in 1979." "It soon gained notoriety as a tumor suppressor - a 'guardian of the genome' that stifles cancer growth by condemning genetically damaged cells to death. Few proteins have been studied more than p53."
"Researchers now know that p53 binds to thousands of sites in DNA, and some of these sites are thousands of base pairs away from any genes. It influences cell growth, death, structure and DNA repair. It also binds to numerous other proteins." "Through a process known as alternative splicing, p53 can take nine different forms, each of which has its own activities and chemical modifiers. Biologists are now realizing that p53 is also involved in processes beyond cancer, such as fertility and very early embryonic development."
Research "has dismantled old ideas about signaling 'pathways', in which proteins such as p53 would trigger a defined set of downstream consequences. 'When we started out, the idea was that signaling pathways were fairly simple and linear,' says Tony Pawson, a cell biologist at the University of Toronto in Ontario. 'Now, we appreciate that the signaling information in cells is organized through networks of information rather than simple discrete pathways. It's infinitely more complex.' "
"Systems biology was supposed to help scientists make sense of the complexity. The hope was that by cataloguing all the interactions in the p53 network, or in a cell, or between a group of cells, then plugging them into a computational model, biologists would glean insights about how biological systems behaved."
Unfortunately, "there is no way to gather all the relevant data about each interaction". "In many cases, the models themselves quickly become so complex that they are unlikely to reveal insights about the system, degenerating instead into mazes of interactions". "Many of the mechanisms and principles governing inter- and intracellular behavior are still a mystery."-- Hayden, Erika Check. 1 April 2010. Life is Complicated. Nature, Vol. 464, pp. 664-667.
When cells repair damaged DNA using so-called "replicate DNA" (for making copies) or "transcribe DNA" (the first step in making a protein), the parts are rapidly assembled from a pool of parts floating in the nucleus of a cell to form "factories". The size of a repair center is according to the amount of damage it has to repair. "A replication factory persists for a few minutes before it disassembles. A new factory is then assembled... immediately adjacent to the previous one". Whether it is repair, replication, or transcription, once the job is done the "factories" disassemble and the parts float back into the pool.32
Chromatin is DNA packaged into chromosomes. Chromatin is in constant motion.3 Different sections along DNA are apparently guided to each other directly and rapidly, forming loops.11 Chromatin loops are very common. Loops range in size from thousands to hundreds-of-thousands of bases long. Loops bring together genes and their regulators to form "transcription hubs" where transcription can occur.32 "Long-range interactions can occur over very large genomic distances, up to tens of megabases". "Interactions occur not only along chromosomes, but also between them." "Chromosomes extensively interact with each other"42, and neighboring chromosomes intermingle.32
There is a "bewildering complexity in long-range communication among a variety of genomic elements across chromosomes and the genome."42
The Bottom Line
Evolutionists assume evolution is true, then write endlessly about when and where it happened, rates and lineages, etc. But if macroevolution is physically impossible in the real world, and it is, then all the rest is fantasy. There are only two possibilities. Either every part of every living thing arose by random chance, or an intelligence designed them.
 | It is now clear that the theory of evolution's only mechanism for building new parts and creatures, mutation-natural selection, is totally, utterly, pathetically inadequate. |
1) http://www.newgeology.us/presentation32.html
