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I was talking to someone about this subject when it dawned on me that it shares some of the problems of the "germ theory." Basically, the underlying claim is that species evolve due to natural selection. However, you probably have never heard anybody ask the obvious question, "is our notion of species imprecise and at least somewhat arbitrary?"
"Complex organisms" are basically cell colonies. Cellsa re |
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This is the kind of research I think is more important in the context of "evolutionary theory." There is just not that much difference between the cells that make up a human than make up a dog, or even worms. I'm not suggesting that nobody should study the differences, but the evolution of the cell, "objectively," is at least as significant.
http://www.sciencedaily.com/releases/2007/07/070711105750.htm |
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On www.amazon.com, there was an interesting review of a book entitled, "Darwin's Black Box," by Michael J. Behe:
QUOTE: I am a PhD student in microbiology that has recently become interested in the ID/evolution debate. In his book, Michael Behe presents some common examples of biological structures/cascades as they are presented in any upperlevel undergraduate molecular biology text. The remainder of the book is spent dismissing evolutionary theory because scientists have not answered questions such as "How did the photosynthetic reaction center develop? How did intramolecular transport start? How did cholesterol biosynthesis begin? How did retinal become involved in vision? etc. (pg 176)." As a graduate student involved in biomedical research I can tell you that these questions are rigged. If Mike Behe knows of a way they could be tested I sure haven't seen him present this. Behe is claiming that evolutionary theory is inadequate and must be replaced by ID because we haven't shown the evolution of a photocenter in the lab (nor will we)!!!! That's like reasoning that the laws of physics must be discarded because no one has ever reproduced the big bang singularity in a beaker. The fact is that Dr. Behe's attack on evolutionary theory is based largely on either ignorance or deceit. As a biochemist who must have a good handle on evolutionary theory to present his case against it, Dr. Behe must surely be aware that science does not contend that the only mechanism of evolution is by natural selection acting on single point mutations. This is why I say deceit or ignorance. Either he isn't aware of it which is unlikely, or he has a clear agenda he wishes to push in order to neglect to mention horizontal and lateral gene transfer, chromosomal rearrangements, regulatory genes, gene duplication, transposable elements, and transduction in bacteria as evolutionary mechanisms (See Microbial Evolution: Gene Establishment, Survival, and Exchange edited by Robert V. Miller and Martin J. Day for a technical account). This is not the main thing that concerns me about his book. He uses poor analogies to illustrate what he believes are flaws in evolutionary theory. The bike evolving into a motorcycle is a perfect example (pg 43-44). "To be a precursor in Darwin's sense we must show that a motorcycle can be built from "numerous, successive, slight modifications" to a bicycle." "If we are to keep our analogy relevant to biology, however, each change can only be a slight modification, duplication, or rearrangement of a preexisting component, and the change must improve the function of the bicycle." Not true Dr. Behe. Bacteria evolve rapidly both through modification, duplication or rearrangement of existing structures in their genome as well as by acquiring DNA from other bacterial cells, viruses or the environment. Think I'm kidding. I'll use the most familiar example...antibiotic resistance in bacteria. It turns out that bacteria can have a form of sexual reproduction with one another through a tubular rod known as a pillus. Some bacteria contain small self replicating circular pieces of DNA which are called plasmids. Plasmids contain genes that are not necessarily required for growth normally, though can have selective advantage in some environments, such as a patient taking antibiotics. Bacteria can become resistant to an antibiotic through acquiring a plasmid containing an antibiotic resistance gene from another bacterium! THIS IS EVOLUTION!!!! So his bike analogy falls apart because biology does not exist in a vacuum as Mike Behe would have you believe. Instead, genes encoding functional proteins are exchanged routinely in the case of microorganisms. Dr. Behe's "evidence" for an intelligent designer is in what he calls irreducible complexity, i.e. if you take away one component the system fails to work...so how could complex biochemical pathways/structures have evolved by natural selection. Dr. Behe's first example of an irreducibly complex structure is the bacterial flagellum. Dr. Behe states, "Yet here again, the evolutionary literature (on the evolution of the bacterial flagellum) is totally missing. Even though we are told that all biology must be seen through the lens of evolution, no scientist has ever published a model to account for the gradual evolution of this extraordinary molecular machine." Actually, it's in the second edition of a textbook called Cellular Microbiology by Cosart P. et al. by ASM Press on pg 369 so it is in fact in the literature. What I am referring to is the bacterial Type III secretion system (TTSS) which functions to inject toxins into eukaryotic cells. Both the bacterial flagellum and the TTSS are put together in the cell by the same mechanism, and proteins in each system are homologous (meaning derived from common components). This system is not irreducibly complex, when you take away the flagellar whip and replace it with the needle like structure encoded by the PrgJ and InvG genes you have a functional syringe. It turns out that numerous genes involved in this process can be transferred from one bacterium to another in toto and not through "stepwise modifications of existing structures" as ID "theorists" would have you believe. Sure, many complex pathways seem to be irreducibly complex if the reader has no background in biochemistry or molecular biology and the author restricts natures means to produce such structures to slight, gradual processes..." UNQUOTE.
Source: http://www.amazon.com/Darwins-Black-Box-Biochemical-Challenge
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QUOTE: ...Lidia Perfeito, Isabel Gordo and colleagues from the Institute Gulbenkian of Science in Lisbon, Portugal... measured the mutation rate of Escherichia coli in many different sized populations, including some small enough to avoid clonal interference although big enough to avoid disadvantageous mutations to spread too easily and kill the population.
Through the comparison of these different size populations, which ranged from to 20,000 cells to 10 million, Perfeito, Gordo and colleagues reached an amazing conclusion: that Escherichia coli mutation rate was a thousand times bigger than previously predicted and that thousand of mutations were going overseen because “better�?ones overtook them in the population...
The importance of Perfeito, Gordo and colleagues�?results resides in two facts: first the fact that they show that beneficial mutations in bacteria are much more common than previously predicted suggesting that bacteria can adapt both to anti-bacterial medication, but also to their host, much quicker than previously thought and second the fact many more bacterial genes are mutating than those seen in the population what can have implications for the way evolution is understood... UNQUOTE.
Source: http://www.sciencedaily.com/releases/2007/08/070818112338.htm |
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Now here's an interesting passage from a report on the "river blindness parasite," but while it's obviously evidence for "evolution," it is not discussed in that framework:
QUOTE: ...Recent reports of patients failing to respond to ivermectin treatment have suggested the emergence of drug-resistant Onchocerca volvulus (the parasite that causes river blindness), and recent studies have associated ivermectin resistance with certain genetic markers, particularly the â-tubulin gene. In Prichard and colleagues' study, genetic changes in â-tubulin were seen in parasites obtained from patients exposed to repeated ivermectin treatment when compared with parasites obtained from the same patients before any exposure to ivermectin... UNQUOTE.
Source: http://www.sciencedaily.com/releases/2007/08/070829212815.htm |
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Here are some interesting finding from a new report:
QUOTE: ...in the system of Prochlorococcus and virus P-SSP7, an unprecedented 41 of the bacteria's 1,717 genes were upregulated. That is, the researchers detected increased quantities of the messenger RNA encoded by these genes in the cell during the infection process. The upregulation of so many host genes during infection is a phenomenon unseen before in the world of bacteriology.
Moreover, many of the host genes upregulated during infection are among those that are found in genomic islands in the host, variable regions that appear to be hot-spots for genetic exchange between bacterial hosts and viruses. In this case, some of the genes that have been transferred back and forth encode for proteins that affect the bacteria's ability to adapt to changes in environmental factors, such as nutrient deprivation and light stress. The scientists hypothesize that modifications made to the bacterial genes when they were in the virus led to new versions of the proteins that may provide the bacteria with an increased ability to withstand environmental changes. It is also possible that multiple copies of a gene provide some benefit.
Another unusual occurrence is that the viral genome contains genes transferred from bacterial hosts that encode energy-producing proteins, including photosynthesis genes that cyanobacteria need for metabolism and DNA replication. Although these genes are positioned far apart in the viral genome, they are transcribed at the same time during infection rather than in the usual left-to-right order. This leads the researchers to surmise that the virus is trying to keep its host alive longer so that the host continues to provide the energy needed for the virus's own DNA replication.
Lindell and Chisholm believe the most plausible scenario to explain the gene upregulation and gene trading is that the bacterium activates certain genes in response to infection as a means of self-protection. The virus has "learned" to use those genes to its own advantage and so incorporates them into its own genome. Later, when infecting another bacterium, the virus upregulates those genes itself to facilitate its own reproduction within the host bacterium. When a bacterium survives an infection, those viral modified genes are incorporated back into the bacterial DNA in genome islands, making that bacterium and its descendants more likely to survive in the harsh ocean environment.
"These viral parasites cooperate with their hosts during infection, providing proteins that probably function within host metabolic pathways, to squeeze every bit of energy out them before killing them off," said Lindell. "Yet on evolutionary scales, such host-pathogen interactions are influencing the evolution of gene content in both host and virus, which in turn is likely impacting their ability to colonize new niches." UNQUOTE.
Source: http://www.sciencedaily.com/releases/2007/09/070905134534.htm |
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QUOTE: "...Generally, there are two schools of thought about what affects evolution," said Andrew P. Allen, Ph.D., a researcher with the National Center for Ecological Analysis and Synthesis in Santa Barbara, Calif. "One says the environment dictates changes that occur in the genome and phenotype of a species, and the other says the DNA mutation rate drives these changes. Our findings suggest physiological processes that drive mutation rates are important..." UNQUOTE.
Source: http://www.sciencedaily.com/releases/2007/10/071004100013.htm |
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The human evolution is speeding up. Does it mean that we may have adapted to using the fire for cooking and thus oxidized cholesterol is not dangerous to humans?
SOURCE: REUTERS Mon Dec 10, 2007 5:43pm EST
Rapid acceleration in human evolution described
By Will Dunham
WASHINGTON (Reuters) - Human evolution has been moving at breakneck speed in the past several thousand years, far from plodding along as some scientists had thought, researchers said on Monday.
In fact, people today are genetically more different from people living 5,000 years ago than those humans were different from the Neanderthals who vanished 30,000 years ago, according to anthropologist John Hawks of the University of Wisconsin.
The genetic changes have related to numerous different human characteristics, the researchers said.
Many of the recent genetic changes reflect differences in the human diet brought on by agriculture, as well as resistance to epidemic diseases that became mass killers following the growth of human civilizations, the researchers said.
For example, Africans have new genes providing resistance to malaria. In Europeans, there is a gene that makes them better able to digest milk as adults. In Asians, there is a gene that makes ear wax more dry.
The changes have been driven by the colossal growth in the human population -- from a few million to 6.5 billion in the past 10,000 years -- with people moving into new environments to which they needed to adapt, added Henry Harpending, a University of Utah anthropologist.
"The central finding is that human evolution is happening very fast -- faster than any of us thought," Harpending said in a telephone interview.
"Most of the acceleration is in the last 10,000 years, basically corresponding to population growth after agriculture is invented," Hawks said in a telephone interview.
The research appears in the journal Proceedings of the National Academy of Sciences.
FAVORABLE GENE MUTATIONS
The researchers looked for the appearance of favorable gene mutations over the past 80,000 years of human history by analyzing voluminous DNA information on 270 people from different populations worldwide.
Data from this International HapMap Project, short for haplotype mapping, offered essentially a catalogue of genetic differences and similarities in people alive today.
Looking at such data, scientists can ascertain how recently a given genetic change appeared in the genome and then can plot the pace of such change into the distant past.
Beneficial genetic changes have appeared at a rate roughly 100 times higher in the past 5,000 years than at any previous period of human evolution, the researchers determined. They added that about 7 percent of human genes are undergoing rapid, relatively recent evolution.
Even with these changes, however, human DNA remains more than 99 percent identical, the researchers noted.
Harpending said the genetic evidence shows that people worldwide have been getting less similar rather than more similar due to the relatively recent genetic changes.
Genes have evolved relatively quickly in Africa, Asia and Europe but almost all of the changes have been unique to their corner of the world. This is the case, he said, because since humans dispersed from Africa to other parts of the world about 40,000 years ago, there has not been much flow of genes between the regions.
See also: http://johnhawks.net/weblog/topics/evolution/selection/acceleration_embargo_ends_2007.html |
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Hans, There is nothing erroneous with "Evolution by means of Natural Selection" being described as a scientific theory. It fits the criteria of a theory in that it provides an explanation for observations of the physical world. This particular theory predicts that the frequency in alleles within a species will be determined by the conditions that species finds itself in ( a species is simply a group of organisms that can interbreed and produce fertile offspring). Our "notion" of a species is certainly not impercise nor is it arbitrary. Evolution by means of Natural Selection is one of the most ground-breaking ideas of this or any other time. To discount it because it doesn't encompass the entirety of biologic study is surely an insult to the great scientists who contributed to this theory. |
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I really don't care who perceives scholarly pursuits as an "insult," and I'll add that it demonstrates an anti-scientific attitude.
First, you will need to describe, in detail, what a "scientific theory" is then we can proceed from there. The problem is that if you go to a dictionary, you will find a short, vague definition that is not very useful for complex phenomena such as "evolution." Moreover, in a similar way, it is up to those who put forth the claim to define it precisely. Otherwise, it's an obligation of people such as myself to criticize. What is a "species?" For example, suppose that fertile offspring can sometimes be produced, but not always, depending upon environmental conditions?
I suggest "evolutionary theory" focus on cellular and molecular-level phenomena rather than trying to fit the square peg in the round hole with human linguistic constructs, such as "species." The "species" level may some day be amenable to the scientific method (and it may be today if research was redirected), but as of today, it is best described as "natural history," and there is nothing wrong with it on this level. Elevating phenomena that is not yet amenable (even if it is due to political reasons) to the level of "scientific theory" when it simply is not only damages science, not the critics of science who want to place theology on the same level of science, for instance. "Friends" often do more harm to their "cause" than their "enemies" do. |
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In biology, organisms are classified thusly: Kingdom, Phyla, Order, Class, Family, Genus and Species. The organisms in the final category can mate and produce fertile offspring.This has been the standard method of classifying organisms (cell clusters) for quite some time. There is nothing arbitrary about it. Either two organisms can mate and produce fertile offspring or not. The scientific method can be applied quite readily to this system of classification. Firstly, gather the following organisms: cow, chicken, frog, kangaroo, squid, bear, bull, panda, fern, elephant, deer and human.Secondly, spend the next 14 years trying to mate each organism with the other. Once you have gone through all the permutations, you will discover that the cow mates with the bull in a very repeated and provable way (veal anyone?). Once it has been proven that a cow can indeed mate with a bull and produce fertile offspring, we then scientifically classify the two organisms as the same species. Furthermore, evolutionary theory has branched out into many different disciplines of study, molecular biology being just one of many. Your backhanded attack at Charles Darwin, Thalmus et al. is akin to attacking Newton for not beginning the race to the moon directly after publishing Principia Mathematica. It does not make sense to me to do so. Perhaps I am not quite understanding exactly what it is you're trying to articulate here. I don't think anyone discounts the importance of cellular understanding (Monsanto sure doesn't). |
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| The problem is that in science, the exception negates the rule. There can be no "exceptions" to a scientific theory. You provided an example which may indeed be correct, but I have no doubt that I can find two organisms of different "species" that can produce fertile offspring under certain circumstances. If I had the funding, I would attempt to find such an exception, by doing things like feeding different diets. However, the point is that what can maintain scientific rigor is the molecular-level mechanism (s) of usual exclusion. The notion of "species" is a great aid to those doing practical research, but you don't realize that you are arguing tautologically. For example, if I did my experiment, you would then claim that the two organisms really were the same species, somehow. And this is what leads to "bad science," and allows critics of science to say ridiculous things like, "see, scientists have been proven to be wrong about things they thought were undeniably factual." In reality, this situation occurs because scientists don't follow the scientific method. |
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A new report supports my view that the "theory of evolution" should be reconsidered conceptually (I'm not arguing that it's "wrong," but that it's presented too abstractly):
QUOTE: Scientists at Scripps Institution of Oceanography at UC San Diego have shown for the first time that a genetic malfunction found in marine crustaceans called copepods likely explains why populations of animals that diverge and eventually reconnect produce weak "hybrid" offspring...
For the past several years, Ellison and Burton have been studying copepods of the species Tigriopus californicus, animals about one millimeter in length that live in coastal intertidal habitats. The researchers produced hybrid specimens in the laboratory by mating animals from San Diego, Los Angeles and Santa Cruz, Calif. At their home between high and low tides, these copepods experience rapid changes in their environment, such as when rainwater dilutes tide pools and the animals are forced to "up-regulate," or activate, specific genes to produce the energy required to manage the stress caused by the rapid change in salinity levels.
Ellison and Burton found that hybrids were incapable of turning on the required genes, and traced this "gene regulation" malfunction to mitochondria, the location inside cells where energy is generated. They further pinned the problem area to a single enzyme, called "RNA polymerase," for the failed trigger.
"In hybrids we found that these genes don't turn on in response to stress, which means the animals don't have enough energy, and that leads to low survivorship," said Burton.
Burton said the study demonstrates how evolution continually molds the interactions of genes in animal populations.
"When populations are hybridized, genes that normally work well within populations are forced to interact with genes from other populations, sometimes leading to dramatic incompatibilities," said Burton. "When the incompatibility affects something as central as cellular energy production, as in Tigriopus, it is not surprising that hybrids show slower growth and reduced reproduction and survivorship..." UNQUOTE.
Source: http://www.sciencedaily.com/releases/2008/10/081013132625.htm
Here, we see that there is an actual mechanism involved, that is, energy production. However, as the scientists point out, while there may be reduced reproduction and survivorship, but that doesn't mean there is none at all. Moreover, they demonstrate the problem with how "experts" articulate this concept by saying that "evolution" is doing something, though the reality is whatever it is, exactly. There are mechanisms at work, so why not just talk about them, rather than talk in abstractions (and notice they assume you know what they mean when they use this term)? They've become prisoners of textbook notions, and when that happens, scientific "progress" can grind to a halt, as has occurred in so many areas of various biomedical fields. |
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QUOTE: ...Standard evolutionary theory offered no clues. Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems, the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car's cruise control or a home's thermostat, allowing them to fine-tune and control their subsequent evolution. The scientists are working on formulating a new general theory based on this finding they are calling "evolutionary control."
The work is likely to provoke a considerable amount of thinking, according to Charles Smith, a historian of science at Western Kentucky University. "Systems thinking in evolutionary studies perhaps began with Alfred Wallace's likening of the action of natural selection to the governor on a steam engine --- that is, as a mechanism for removing the unfit and thereby keeping populations 'up to snuff' as environmental actors," Smith said. "Wallace never really came to grips with the positive feedback part of the cycle, however, and it is instructive that through optimal control theory Chakrabarti et al. can now suggest a coupling of causalities at the molecular level that extends Wallace's systems-oriented approach to this arena."
Evolution, the central theory of modern biology, is regarded as a gradual change in the genetic makeup of a population over time. It is a continuing process of change, forced by what Wallace and Darwin, his more famous colleague, called "natural selection." In this process, species evolve because of random mutations and selection by environmental stresses. Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking... UNQUOTE.
Source: http://www.sciencedaily.com/releases/2008/11/081111183039.htm |
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