Evolution1
A central organizing concept in biology is that life changes and develops through evolution and that all lifeforms known have a common origin (see Common descent). This has led to the striking similarity of units and processes discussed in the previous section. Introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809,Charles Darwin established evolution fifty years later as a viable theory by articulating its driving force, natural selection (Alfred Russel Wallace is recognized as the co-discoverer of this concept as he helped research and experiment with the concept of evolution). Darwin theorized that species and breeds developed through the processes of natural selection as well as by artificial selection or selective breeding. Genetic drift was embraced as an additional mechanism of evolutionary development in the modern synthesis of the theory.
The evolutionary history of the species— which describes the characteristics of the various species from which it descended— together with its genealogical relationship to every other species is called its phylogeny. Widely varied approaches to biology generate information about phylogeny. These include the comparisons of DNA sequences conducted within molecular biology or genomics, and comparisons of fossils or other records of ancient organisms in paleontology. Biologists organize and analyze evolutionary relationships through various methods, including phylogenetics, phenetics, and cladistics. For a summary of major events in the evolution of life as currently understood by biologists, see evolutionary timeline.
Up into the 19th century, it was commonly believed that life forms could appear spontaneously under certain conditions (see spontaneous generation). This misconception was challenged by William Harvey's diction that "all life [is] from [an] egg" (from the Latin "Omne vivum ex ovo"), a foundational concept of modern biology. It simply means that there is an unbroken continuity of life from its initial origin to the present time.
A group of organisms share a common descent if they share a common ancestor. All organisms on the Earth both living and extinct have been or are descended from a common ancestor or an ancestral gene pool. This last universal common ancestor of all organisms is believed to have appeared about 3.5 billion years ago. Biologists generally regard the universality of the genetic code as definitive evidence in favor of the theory of universal common descent (UCD) for all bacteria, archaea, and eukaryotes (see: origin of life).
Evolution does not always give rise to progressively more complex organisms. For example, the process of dysgenics has been observed among the human population.
Monday, June 30, 2008
Saturday, June 28, 2008
DNA molecules are complex molecules which contain the assembly instructions for every living creature. Certain aspects of DNA have been interpreted as evidence for Darwinian evolution. DNA evidence for evolution includes mutations, genetic similarities among species, so-called “Junk DNA” and “Pseudogenes.” Here we will look at these evidences and briefly make note of some of the criticism levied against them by opponents of Darwin’s theory.
The fact that mutations can corrupt DNA is important for the Darwinian paradigm because in order for an organism to eventually evolve into an entirely different organism, changes must be made to the creature’s genome over time. But Darwinian evolution needs more than just change. It needs an increase in genetic information. Critics point out that genetic mutation does not appear to provide a mechanism for that increase. In fact, there appear to be genetic limitations to the potential for biological change. As biophysicist Dr. Lee Spetner explains, “. . .Reptiles and birds are very different. Reptiles have no genetic information for wings or feathers. To change a reptile into a bird would require the addition of. . .complex information. . . . I really do not believe that the neo-Darwinian model can account for large scale evolution. What they really can’t account for is the build up of information. . . .And not only is it improbable on the mathematical level, that is theoretically, but experimentally one has not found a single mutation that one can point at that actually adds information. In fact, every beneficial mutation that I have seen reduces the information, it loses information”1
Genetic similarities between species are also interpreted as DNA evidence for evolution. The fact that human and chimp DNA are more than 96% the same is taken to mean that humans are genetically related to chimps and therefore descended from a common ancestor. Opponents of Darwin’s theory point out that there is a certain degree of genetic similarity to all living systems and that the more similar two species are, the more similar their DNA should appear. “The DNA of a cow and a whale, two mammals, should be more alike than the DNA of a cow and a bacterium. If it were not so, then the whole idea of DNA being the information carrier in living things would have to be questioned. Likewise, humans and apes have a lot of morphological similarities, so we would expect there would be similarities in their DNA. Of all the animals, chimps are most like humans, so we would expect that their DNA would be most like human DNA.”2
The final category of DNA evidence for evolution which we will look at concerns Junk DNA and Pseudogenes. Junk DNA are segments of DNA whose function remains a mystery. We do not know what they do. Darwinists believe that Junk DNA are similar to vestigial organs in that they are useless vestiges from our evolutionary past. Opponents of the theory point out that just because we do not know what something does, that does not mean that it does not serve an important function. Consider vestigial organs. Back in the 19th Century there were dozens of organs which were designated “vestigial” because scientists could not figure out what they did. These, like Junk DNA, were interpreted as evidence for Darwin’s theory. Of a list of 86 put together by Robert Wiedersheim, one of Darwin’s disciples, only a handful remain ambiguous at the present time. Scientists have discovered important functions for all of the rest.
Similarly, we do not know much about Pseudogenes. Scientists believe that they are genes which have lost their function through mutation. As John Woodmorappe explains, “Arguments for shared evolutionary ancestry have been advanced based on the similarities in perceived disablements found in orthologous pseudogenes (counterpart pseudogenes in other primates).” Woodmorappe goes on to say however, “. . .A close examination shows that this presumed evidence is equivocal. Dissimilarities between the pseudogenes of presumably related organisms are at least as prominent as the similarities, and similarities in orthologous pseudogenes can arise independently of shared evolutionary ancestry.”3
The debate over DNA evidence for evolution rages on. Too much remains unknown at this current stage. Hopefully, as time goes on and we learn more about DNA we will be in a better position to know whether or not DNA truly supports Darwin’s theory of evolution.
Tuesday, June 24, 2008
- What is the DNA evidence for evolution?
DNA molecules are complex molecules which contain the assembly instructions for every living creature. Certain aspects of DNA have been interpreted as evidence for Darwinian evolution. DNA evidence for evolution includes mutations, genetic similarities among species, so-called “Junk DNA” and “Pseudogenes.” Here we will look at these evidences and briefly make note of some of the criticism levied against them by opponents of Darwin’s theory.
The fact that mutations can corrupt DNA is important for the Darwinian paradigm because in order for an organism to eventually evolve into an entirely different organism, changes must be made to the creature’s genome over time. But Darwinian evolution needs more than just change. It needs an increase in genetic information. Critics point out that genetic mutation does not appear to provide a mechanism for that increase. In fact, there appear to be genetic limitations to the potential for biological change. As biophysicist Dr. Lee Spetner explains, “. . .Reptiles and birds are very different. Reptiles have no genetic information for wings or feathers. To change a reptile into a bird would require the addition of. . .complex information. . . . I really do not believe that the neo-Darwinian model can account for large scale evolution. What they really can’t account for is the build up of information. . . .And not only is it improbable on the mathematical level, that is theoretically, but experimentally one has not found a single mutation that one can point at that actually adds information. In fact, every beneficial mutation that I have seen reduces the information, it loses information”1
Genetic similarities between species are also interpreted as DNA evidence for evolution. The fact that human and chimp DNA are more than 96% the same is taken to mean that humans are genetically related to chimps and therefore descended from a common ancestor. Opponents of Darwin’s theory point out that there is a certain degree of genetic similarity to all living systems and that the more similar two species are, the more similar their DNA should appear. “The DNA of a cow and a whale, two mammals, should be more alike than the DNA of a cow and a bacterium. If it were not so, then the whole idea of DNA being the information carrier in living things would have to be questioned. Likewise, humans and apes have a lot of morphological similarities, so we would expect there would be similarities in their DNA. Of all the animals, chimps are most like humans, so we would expect that their DNA would be most like human DNA.”2
The final category of DNA evidence for evolution which we will look at concerns Junk DNA and Pseudogenes. Junk DNA are segments of DNA whose function remains a mystery. We do not know what they do. Darwinists believe that Junk DNA are similar to vestigial organs in that they are useless vestiges from our evolutionary past. Opponents of the theory point out that just because we do not know what something does, that does not mean that it does not serve an important function. Consider vestigial organs. Back in the 19th Century there were dozens of organs which were designated “vestigial” because scientists could not figure out what they did. These, like Junk DNA, were interpreted as evidence for Darwin’s theory. Of a list of 86 put together by Robert Wiedersheim, one of Darwin’s disciples, only a handful remain ambiguous at the present time. Scientists have discovered important functions for all of the rest.
Similarly, we do not know much about Pseudogenes. Scientists believe that they are genes which have lost their function through mutation. As John Woodmorappe explains, “Arguments for shared evolutionary ancestry have been advanced based on the similarities in perceived disablements found in orthologous pseudogenes (counterpart pseudogenes in other primates).” Woodmorappe goes on to say however, “. . .A close examination shows that this presumed evidence is equivocal. Dissimilarities between the pseudogenes of presumably related organisms are at least as prominent as the similarities, and similarities in orthologous pseudogenes can arise independently of shared evolutionary ancestry.”3
The debate over DNA evidence for evolution rages on. Too much remains unknown at this current stage. Hopefully, as time goes on and we learn more about DNA we will be in a better position to know whether or not DNA truly supports Darwin’s theory of evolution.
The evolution solution revolution
Good scientific theories are predictive. They don't just describe the way the world is as we know it but suggest experiments or other investigation that we don't know the answer to. If the theory is correct then the predictions should turn out to be true. The theory should also be able to explain future observations. That's why Darwin's theory of evolution by natural selection is accepted by scientists. It's sometimes argued that evolutionary theory can't be good science because you can't do experiments about the past. There's more to scientific investigation than test tube science though. There have been vastly many correct predictions based on the theory of natural selection (see "Evolutionary Predictions" for a couple of recent ones). The most profound is that it predicted the need for a biological way for passing information between generations. That ultimately led to the discovery of the DNA molecule and within half a century the mapping of the human genome as well as that of other animals.
Computer science naturally
Where does computer science come in? Well it works both ways. Computer simulations can be used to explore whether things might be possible. For example, some people find it hard to believe that complex biological features like an eyeball could possibly come about step by step as predicted by natural selection. Computer simulations have shown that such things are feasible: for example an early such computer experiment showed it is possible to construct sequences of partial eyeballs from single light detecting cells to complete eyeballs that each work in a way that would help a creature survive. This compares well in fact with the range of similar "eyes" found in real creatures.
Evolving answers
In the other direction the ideas of evolution have given computer scientists ideas for new ways to program - the notion of genetic algorithms. Computer science is about coming up with solutions to problems and that is exactly what nature does over time - adapt animal species via natural selection to allow them to survive better in their changing environments. The idea is that to solve a problem you turn it into "digital DNA" and evolve a solution.
Instructive DNA
DNA is the biological molecule that codes the instructions for creating all living things on earth. It's a sequence of instructions, data, that cells use to build new cells, and it's also the key to evolution. When species mate, part of the mother's and part of the father's DNA combine to give the new instructions for the child. That's why you look a bit like your mum and dad. Parts of their data were used to build you. That DNA has been crossed over. When a species is under environmental threat often only particular types of offspring survive: those that can run fastest, or climb highest or blend into the background best. Inspired by Darwin, this is what english philosopher Herbert Spencer pithily called "survival of the fittest": the new set of instructions in an offspring, combined from parents, can give that offspring a survival advantage. Survival means this creature can go on to breed itself and will pass those useful instructions to its offspring and so on. Very occasionally due to the effects of cosmic rays or other factors the DNA can be changed, the chemical sequences are mutated. Normally this causes death. The instructions are corrupted and the offspring dies, but from time to time a non-lethal mutation occurs, and this can lead to offspring with a new survival trick. If it's advantageous it will let the offspring and its descendants thrive. In effect the process of evolution keeps the species and the environment matched to one another. You could say the species solves the problem of survival in the environment.
Visiting with a Genetic Algorithm
So computer scientists can now take a problem, code it up as a sort of digital DNA and use the evolutionary model, crossover between parents to create offspring and mutation, to find a good solution. A classic example is the Travelling Salesperson problem. In this problem you have to visit say twenty towns, and do the least travelling (you need to keep the travelling expenses down). We start by randomly creating a population of 'creatures' whose digital DNA is simply a list of the twenty towns (say numbered 1-20) initially in random order. We then test how fit each of these 'creatures' is by calculating the amount of travel expenses each of them requires (how expensive that route would be to follow). From our initial population of possible solutions we choose the best solutions, those with the lowest travel expenses, and let these bred together: making a new route with parts from each parent. Those solutions with high costs don't survive in this low cost financial environment, and are simply killed off, removed from the program. The next generation, made by swapping (crossover) the digital DNA of the original best solutions, are then tested, again the best solutions survive and we breed them to create a new generation and so on. Many thousands of generations later we have really good solutions, which have survived because they are a good solution to the problem.
Mutate and explore
We always have a small random mutation rate in the background, as this parent offspring breeding can often result in you only exploring a good solution, they are breeding in only one isolated part of all the possible good solutions, and possibly missing the best solution, which may require something very different. After running a genetic algorithm on your problem you simply turn the digital DNA back into, in this case the list of towns in order, and you're done. Problem solved.
Genetic Programming - growing the solution
A variation of this is called genetic programming. Here the digital DNA are bits of program code that if executed solve the problem. They are linked together through something called a tree structure. One part of the program (the root) calls another bit of code in the program (the leaf). This leaf can then be a root for another couple of leaves, and so on. The whole program, if you wrote it out, looks like a tree, with the links between code as branches. To breed a genetic program you swap branches of this tree around. Most of the programs don't work of course, but some will and if you chop and change (and do the occasional mutate where you remove bits completely for example), and keep working on the best over many generations you can create computer programs that actually work, and work very well.
Better or best?
You can use a genetic algorithm, as long as you can take your problem and turn it into digital DNA: a list of elements called a representation (numbers in DNA = towns in the example, or trees of bits of code in Genetic Programming), and define a way to calculate your creature's 'fitness' (for example the travelling expenses needed to go round the towns in the order given). There are many different variants on the basic genetic algorithm which try to ensure that they find the best solution possible rather than just a good solution. This ability to find the very best, or global solution, cannot yet be guaranteed mathematically - nature doesn't guarantee perfection either. However Genetic Algorithms are useful and powerful and have been used to solve problems in water distribution and computer networks, robotic learning, school timetabling and even back into biology and chemistry to calculate the shapes of folded proteins or atomic forces.
Friday, June 13, 2008
WHAT IS EVOLUTION
This is a never ending process from a single cell organism to higher level one (Human in animal and Angiosperms in plant kingdom )