The Theory of Evolution

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  • vicsinad
    Senior Member
    • May 2011
    • 2337

    #16
    Originally posted by Vangelovski View Post
    Maybe you can actually try to provide a few answers to some burning questions.

    For evolution to be true, it would require the continuous creation of new genetic information. How is that even possible? How is it possible for new information to just appear?

    Let me clarify here, I'm not talking about jumbling up existing information, for example, ABC = ACB = BCA etc, or the loss of information, for example, ABC = AC. I'm talking about the addition of new information, such as ABC + D. This is what is required for evolution - the addition of new information. For example, without the addition of new genetic information, a creature would not be able to grow an eye where that genetic information did not previously exist.
    You could start by reading and understanding the following articles:


    Origins of New Genes and Pseudogenes


    By: Chitra Chandrasekaran, Ph.D. (Texas Wesleyan University) & Esther Betrán, Ph.D. (Department of Biology, University of Texas, Arlington, TX) © 2008 Nature Education

    The formation of new genes is a primary driving force of evolution in all organisms. How exactly do these new genes crop up in an organism’s genome and what must occur in order for them to be passed on.


    New gene origination is a driving force of evolutionary innovation in all organisms. Recent research has focused on identifying the mechanisms that generate new genes, and scientists have found that these mechanisms involve a variety of molecular events, all of which must occur in the germ line to be inherited by the next generation. After the germ-line mutational event, the new gene (e.g., a new gene duplicate located on human chromosome 2) will be polymorphic in the population; in other words, not all second chromosomes in the population will carry the duplication. Subsequently, the two most likely outcomes for the new gene are fixation (i.e., the new gene will reach a frequency of 100%) or extinction (i.e., the new gene will be lost).


    Current knowledge of the origin of new genes encompasses information regarding both protein-coding genes and RNA genes. All of these genes are transcribed, but only protein-coding genes are translated into proteins. The study of pseudogenes, originally defined as sequences that resemble known genes but cannot produce a functional protein, has revealed not only how often genes degenerate, but also that many sequences once believed to be degenerating protein-coding genes are in fact functional RNA genes.


    Mechanisms of New Gene Generation


    Over the years, scientists have proposed several mechanisms by which new genes are generated. These include gene duplication, transposable element protein domestication, lateral gene transfer, gene fusion, gene fission, and de novo origination.




    Gene Duplication


    Gene duplication was the first mechanism of gene generation to be suggested (Ohno, 1970), and this process does indeed appear to be the most common way of creating new genes. Duplications are typically classified according to the size of the portion of the genome that is duplicated; thus, a duplication may be described as involving an entire genome, large segments of a genome, individual genes, individual exons, or even specific parts of exons (Betrán & Long, 2002). The mechanisms that generate duplicate genes are diverse, and more details about these mechanisms are continually being discovered. These mechanisms include whole-genome duplications originating through nondisjunction, tandem duplications originating through unequal crossover, retropositions originating through the retrotranscription of an RNA intermediate, transpositions involving transposable elements (Jiang et al., 2004; Morgante et al., 2005), and duplications occurring after rearrangements and subsequent repair of staggered breaks (Ranz et al., 2007). Such duplications involve not only protein-coding genes, but also noncoding RNA genes. For example, a novel class of retroduplicates includes snoRNAs, which are a class of RNA genes that are involved in ribosomal RNA processing (Weber, 2006).


    Much of the current excitement about gene duplication stems from the fact that with the number of sequenced genomes now available, researchers have more accurate estimates of how often genes duplicate, and these rates are extremely high. For example, more than 100 genes duplicate in the human genome per 1 million years (Hahn et al., 2007a). This means that the percentage of the genome affected by gene number differences (estimated to be 6%) contributes more to the differences between humans and chimpanzees than do single nucleotide differences between orthologous sequences (estimated to be 1.5% [Demuth et al., 2006]). High rates (17 genes per 1 million years) have also been estimated in flies (Hahn et al., 2007b). Additional excitement comes from the realization that duplications occur so often that individuals of the same species differ greatly in DNA content and gene number (i.e., many duplications are polymorphic and contribute to individual differences [Sebat et al., 2004]). It is estimated that, on average, two humans will differ by approximately 5 megabases of information.


    Unexpectedly, several duplication trends have been described in genomes with respect to sex chromosome evolution. Many new male genes originate in species' Y chromosomes. Some of these male genes are organized in families that undergo gene conversion to avoid Y-chromosome degeneration. Male germ-line genes can also duplicate out of the X chromosome through retroposition (Betrán et al., 2002; Emerson et al., 2004; Lahn et al., 2001; Rozen et al., 2003). These findings reveal that genomic location and organization matter for gene origination and function.


    Transposable Element Protein Domestication

    Transposable elements (TEs) are so-called "selfish" segments of DNA that encode proteins that allow these segments to copy or move themselves within a genome. There are two types of TEs: DNA transposons and retrotransposons. DNA transposons are able to excise themselves out of the genome and be inserted somewhere else, whereas retrotransposons copy themselves through an RNA intermediate. Similar to viral insertions in the genome, TE insertions cause mutations and contribute to increased genome size, but they usually do not encode cellular proteins.


    Interestingly, one way for a genome to acquire new genes is by recruiting transposable element proteins and using them as cellular proteins. Such events are called domestications of TE proteins. A recent review by Fechotte and Pritham (2007) compiled many examples of these events, and it revealed that some of the unexpected functions in which TE domesticated proteins play a role include functioning of the vertebrate immune system and light sensing in plants. Several examples of domestication have also been described in Drosophila (Casola et al., 2007). In one case, codomestication of the two proteins encoded by the PIF/Harbinger transposable element was observed. In this fascinating example, the two genes that the original TE contained were domesticated simultaneously; one of these genes encoded a transposase that binds and cuts DNA, while the other encoded a protein that contains a Myb/SANT domain believed to function in transcription, chromatin remodeling, and protein-protein interactions. More data are needed to reveal whether both of these proteins were domesticated to function in the same biological process.


    Lateral Gene Transfer


    Scientists use the term "lateral gene transfer" to refer to the case in which a gene does not have a vertical origin (i.e., direct inheritance from parent to offspring) but instead comes from an unrelated genome. It is well known that this sort of transfer occurs between bacteria, and that it also has taken place between the genomes of the cellular organelles (mitochondria and chloroplasts) and the nuclear genomes (Roger, 1999). However, more recent transfer events between organelles and/or endosymbiont bacteria continue to occur (Bergthorsson et al., 2003; Hotopp et al., 2007). For example, large-scale sequencing efforts have revealed that much of the genome of the intracellular endosymbiont Wolbachia pipentis was integrated into Drosophila species (Hotopp et al., 2007). However, the mechanism for these transfers remains largely unknown, and the functional consequences of some of these transfers have yet to be explored.


    Gene Fusion and Fission


    Existing genes can also fuse (i.e., two or more genes can become part of the same transcript) or undergo fission (i.e., a single transcript can break into two or more separate transcripts), thereby forming new genes. Interestingly, it has been observed that chimeric fusion genes sometimes involve two copies of the same gene (e.g., the alcohol dehydrogenase gene in Drosophila), and when that happens, the resulting genes undergo parallel evolution (Jones & Begun, 2005), in which they shift away from the functions of their parental genes.


    De Novo Gene Origination


    New genes can additionally originate de novo from noncoding regions of DNA. Indeed, several novel genes derived from noncoding DNA have recently been described in Drosophila (Begun et al., 2007; Levine et al., 2006). For these recently originated Drosophila genes with likely protein-coding abilities, there are no homologues in any other species. Note, however, that the de novo genes described in various species thus far include both protein-coding and noncoding genes. These new genes sometimes originate in the X chromosome, and they often have male germ-line functions.


    The action of all the mechanisms described in the previous sections leads to exon shuffling (i.e., the observation that many genes share exons) (Gilbert et al., 1997; Li et al., 2001). In addition, analyses of "young" genes (genes that originated only a few million years ago) allow investigators to document all of the events that gave rise to these genes, because time has not eroded the footprints of these events. Using this approach, it has been inferred that combinations of several mechanisms and several events are often responsible for the generation of new genes (Betrán & Long, 2002). Two good examples of this are the jingwei gene (Long & Langley, 1993) and the SETMAR gene (Cordaux et al., 2006; Figure 1).


    What Happens to New Genes?


    All these new sequences add to the complexity and diversity of genomes. As with any mutation, when new genes become fixed in a genome, they add to the differences between species and serve as the raw material for evolution (Ohno, 1970). This is easy to see in the case of gene duplication. Gene duplication results in two or more copies of a gene: one that can maintain its original function in the organism, and other(s) that can be "played with" to take on new functions. As a consequence, new duplicates are a main source of genome innovation and often evolve under positive selection, in which rapid changes in the protein encoded by the new gene occur to gain a new function (Presgraves, 2005). This process is referred to as neofunctionalization of the new gene.


    Other possible outcomes after duplication include gene loss or pseudogenization; maintenance of both genes as a way to increase expression or to maintain multiple variants within individuals (essentially "fixing" heterozygosity); or the occurrence of subfunctionalization (i.e., the occurrence of mutually complementing neutral disabling mutations such that both genes need to be kept in the genome [Lynch & Force, 2000]). Subfunctionalization is an interesting phenomenon because it begins with a partition of function but can set the grounds for specialization (Torgerson & Singh, 2004). Some mixed outcomes (such as subfunctionalization followed by neofunctionalization and subneofunctionalization) are also possible (He & Zhang, 2005).


    One unanticipated consequence of gene duplication and gene loss is that these events can become the basis for some incompatibilities between species. Duplications and losses have been shown to play a role in hybrid breakdown and in the reduced fitness of the descendants of matings between genetically differentiated populations. Thus, these processes might contribute to the process of speciation (Masly et al., 2006).


    The Origin and Fate of Pseudogenes


    This schematic illustration depicts two mechanisms by which siRNA can be produced. A horizontal curved line separates the diagram into an upper and lower half. The upper half represents the nucleus, and the lower half represents the cytoplasm. In the nucleus, process A shows a parent gene undergoing two alternative pathways: a duplication and a retroposition. Both pathways result in the production of a pseudogene. The pseudogene has two potential fates: it can exit the nucleus and exist as an antisense transcript in the cytoplasm, or undergo a duplication and inversion inside the nucleus. If it exits the nucleus as an antisense transcript, it can base pair with normal mRNA sequences, and the protein Dicer can cut it into 21-base pair pieces that act as siRNA. If the pseudogene instead undergoes duplication and inversion, it forms a long strand of DNA with complementary sequences on each end. This can form a hairpin RNA, which is a target for the Dicer enzyme. The Dicer products then interact with the RISC complex to degrade target mRNA sequences.

    As previously mentioned, pseudogenes are commonly defined as sequences that resemble known genes but cannot produce functional proteins. Pseudogenes originate through the same mechanisms as protein-coding genes, followed by the subsequent accumulation of disabling mutations (e.g., nucleotide insertions, deletions, and/or substitutions) that disrupt the reading frame or lead to the insertion of a premature stop codon. Pseudogenes can be broadly classified into two categories: processed and nonprocessed. Nonprocessed pseudogenes usually contain introns, and they are often located next to their paralogous parent gene. Processed pseudogenes are thought to originate through retrotransposition; accordingly, they lack introns and a promoter region, but they often contain a polyadenylation signal and are flanked by direct repeats. Errors in reverse transcription and the lack of an appropriate regulatory environment often lead to the degeneration of processed copies of genes (D'Errico et al., 2004).


    The abundance of pseudogenes in a given genome usually depends on rates of gene duplication and loss. Mammals appear to have a high number of processed pseudogenes—approximately 8,000 (Zhang et al., 2003; Zhang et al., 2004). On the other hand, most other organisms have many fewer; for instance, in Drosophila, only 20 retropseudogenes are detectable (Harrison et al., 2003). This pattern has been explained by the deletion bias that exists in Drosophila; indeed, after studying the size distribution of deletions in Drosophila and mammals, researchers concluded that deletions in Drosophila are much bigger (Petrov & Hartl, 2000).


    The most interesting pseudogene finding to date is that degenerated protein-coding genes have been proven to "live on" as RNA genes (Sasidharan & Gerstein, 2008). Although researchers had previously proven that pseudogenes could be transcribed (Harrison et al., 2005), they only recently realized that these sequences can regulate parental genes through siRNAs; evidence of this phenomenon has been found in both flies and mammals (Figure 2; Sasidharan & Gerstein, 2008). In addition, some processed pseudogenes seem to have evolved into primate microRNA genes (Devor, 2006).


    Of course, genomes remain full of surprises. Additional work will continue to reveal even more about the functional potential of many new DNA sequences.


    New genes arise quickly


    What role does the appearance of new genes, versus simple changes in old ones, play in evolution? There are two reasons why this question has recently become important.

    The first involves a scientific controversy. Some researchers—the most prominent being evo-devotee Sean Carroll—maintain that most important evolutionary change, at least in body form, involves changes in regulatory sequences rather than simple changes in genes themselves, or the appearance of new genes. This question hasn’t yet been answered, since we don’t know a great deal about those mutations that have been important in creating new body plans.

    The second controversy is religious. Some advocates of intelligent design (ID)—most notably Michael Behe in a recent paper—have implied not only that evolved new genes or new genetic “elements” (e.g., regulatory sequences) aren’t important in evolution, but that they play almost no role at all, especially compared to mutations that simply inactivate genes or make small changes, like single nucleotide substitutions, in existing genes. This is based on the religiously-motivated “theory” of ID, which maintains that new genetic information cannot arise by natural selection, but must installed in our genome by a magic poof from Jebus.

    I’ve criticized Behe’s conclusions, which are based on laboratory studies of bacteria and viruses that virtually eliminated the possibility of seeing new genes arise, but I don’t want to reiterate my arguments here. What I want to do is point out a new paper by some Chicago colleagues that suggests that new genes, at least in the genus Drosophila (fruit fly), not only arise pretty quickly, but also diverge very quickly to become essential parts of the genome.

    The paper, by Sidi Chen, Yong Zhang, and my friend Manyuan Long, appears in this week’s Science: “New genes in Drosophila quickly become essential.” It’s a clever piece of work. What the authors did was compare whole-genome sequences between various species of Drosophila (there are now many of these) to see how often new genes appeared in one lineage: the lineage that diverged from the ancestors of D. willistoni to become D. melanogaster. The divergence between these two lineages is 35 million years, but by comparing the genomes of other species that branched off these two branches, they could estimate how often new genes arise over the entire period from 3 million to 35 million years ago.

    What do they mean by “new genes”? These are genes in D. melanogaster that aren’t found in D. willistoni, but have arisen since their divergence by several processes—most often the duplication of an ancestral gene or its RNA followed by extensive genetic divergence, so that the gene acquires a brand new function. (This process accounts for about 90% of the new genes. Some genes, however, are so different between the species that how they arose is a mystery.) These “new genes,” then, would qualify as what Behe calls “gain-of-FCT” adaptive mutations (“FCT” = functional coded element): the kind of mutations that Behe did not see arising in short-term lab experiments on bacteria and viruses.

    Chen et al. found that a surprisingly large number of genes had arisen in the D. melanogaster lineage over this 35-myr period. Here’s a summary of their results:
    ◾ The authors identified 566 new genes that arose over this period. That’s about 4% of the total genes in the D. melanogaster genome. And that’s quite a few given that the divergence is only 35 myr. The genus Drosophila itself (including the scaptomyzids) diverged from its sister group about 63 million years ago, so we can estimate that, in the genus as a whole, at least 7% of the genome comprises brand new genes.
    ◾The authors were able to take a sample of these genes (195 of them) and knockdown their transcripts using novel RNAi technology (this involves inserting transposable genetic elements in those genes and then using those elements to kill the genes). They found that about 30% of these new genes are essential for viability—that is, the fly dies if it has no active copies. This proportion didn’t vary depending on how long ago the “new” gene had arisen. Nor did it differ much from the proportion of “old” genes (those present in both lineages) that are essential for viability, which is about 35%. It seems, then, that even if these genes arise as duplicates from pre-existing genes, they quickly assume new functions that make the fly unable to survive without them.
    ◾The “new function” conclusion is supported by two other pieces of data. First, the average difference in DNA sequence between the “new” genes in the D. melanogaster lineage and their parental copies (that is, the genes from which they originated, usually by duplication) is 47.3%. That’s a big difference—a change in nearly every other nucleotide. Second, there are new ways to determine what the new genes do: by estimating which proteins in the genome each new gene’s protein product interacts with. Chen et al. found that many of the products of new genes interact with proteins completely different from the ancestral genes. This implies that the new genes have evolved completely different functions. And, as theory suggests, that’s the way these genes become essential: at first they do the same thing as their ancestral genes (they’re duplicates, after all), but as they diverge they assume new functions (usually impelled by natural selection) that fit them into new developmental pathways. In this way a gene that is at first “gratuitious” can become essential. It’s nice that we can actually see this happening with protein-protein interaction data.
    ◾In further support of the above scenario for the evolution of new genetic information, the authors found that in young and new “essential” genes, there was a strong signature of natural selection having acted, as suggested by the high rates of DNA substitution. As the “new” essential genes become older, and assume new functions, these rates slow down. This again supports the theory of how new genes originate: when they’re formed by duplication, they are quickly eliminated from the genome (see below) unless they diverge quickly to do something new. Thus the duplicates that do survive are usually those that have diverged quickly. Once the new function has been assumed, and the gene is essential, selection then acts to preserve its new function by eliminating new mutations (“purifying selection”).
    ◾These results, which show that new genetic information (“FCT”s) arises quickly, don’t imply that every new gene duplication becomes a brand-new gene with a new function. That’s far from the case. We don’t know the figure in Drosophila, but in the human lineage it’s estimated that only about 5% of new duplications diverge to become new genes that do something novel. The rest are inactivated, becoming dead “pseudogenes” that don’t do anything. In Drosophila these are quickly removed from the genome, but in our own lineage many of them linger, so we can estimate the proportion of duplicated genes that don’t go on to do something new.
    ◾Nevertheless, genes duplicate frequently enough that they can provide sufficient raw material for genetic novelty. Estimates of how often a given gene duplicates in evolution run about one duplication event per 100 million gene copies. That seems low, but remember that there are thousands of genes in the genome, and, in many species (including Drosophila and now ours), there are hundreds of millions of individuals. That means that, in the species, there are many genes that duplicate each generation. Even if only a few percent of these survive inactivation, that’s a lot of raw material for evolutionary change.
    ◾The presence of frequent gene duplications is supported by an independent study: Emerson et al. (2008) found that in only fifteen lines of D. melanogaster from nature there were several hundred duplicate genes segregating as polymorphisms (that is, some individuals had one copy of a gene, some had two or more). They estimated that 2% of the genome was tied up in this copy-number variation. Clearly, there are a lot of duplicate genes variants floating around in nature.

    The data of Chen et al., then, show that new genetic information can arise quickly, at least on an evolutionary timescale, and that the new genes rapidly assume new functions. (Note: I am using Behe’s characterization of “new genetic information” as involving only new FCTs. I don’t agree with this, since new genetic information can also arise when a single gene copy changes sufficiently to do something new.)

    Although this doesn’t answer the question of what proportion of new evolutionary traits involve changes in gene sequence versus changes in gene regulation, it does show that a substantial part of the genome in one group of eukaryotes arises by the evolution of new FCTs that become involved in new developmental networks. In other words, Behe’s conclusion from short-term lab studies of bacteria and viruses doesn’t apply to this well-studied group of organisms—and probably not to other eukaryotes, either. All the evidence tells us that a rapid and important way to create new genetic information is through the duplication of genes and then their divergence by natural selection.


    Poems are made by fools like me
    But only selection makes an FCT

    Now ID advocates like Behe could—and do—suggest that maybe the successfully duplicated-and-diverged genes didn’t arise by natural selection, but appeared by the instantaneous intervention of the designer (aka God/Jebus). But that idea is nixed by at least two observations. The first is the appearance in many groups of dead, nonfunctional pseudogenes that were unsuccessful duplicates. If the Great Designer made gene duplications to create genetic novelty, he surely failed in the majority of cases, and left his failures sitting around in the genome.

    The second is the correlation between the age of a new gene and the type of selection acting on it. If a Great Designer created these duplicates de novo to have a new function—presumably because natural selection couldn’t take a gene to a new function by gradual stepwise evolution—they would show instantaneous changes of DNA sequence that looked like selection, and then an instantaneous cessation of that selection right after the gene got its newly created function. But that’s not what we see. What we see is not instantaneous but gradual change: the younger a gene is (as estimated by the position on the evolutionary tree where it arose), the more rapid natural selection acts. That directional selection continues to act as the gene gets older, but then slows down and finally becomes purifying selection, so that new DNA changes are eliminated. This pattern is precisely what’s predicted if duplicates arise by accident and then quickly change by selection to assume new functions.

    I suppose Behe and his minions will find a way to explain these two patterns by intelligent design, but that’s because ID theory isn’t science: there is no conceivable observation that can prove it wrong. Every bit of data, no matter what it is, can always be fitted into the ID scheme, especially since its advocates allow a little bit of Darwinian evolution and posit an unpredictable and unknowable Designer. But let us not tarnish the nice results of Chen et al. by using them to cast aspersions on ID. They are a valuable contribution to the real science of evolutionary biology, showing how fast new genetic information can arise by gene duplication.
    What role does the appearance of new genes, versus simple changes in old ones, play in evolution? There are two reasons why this question has recently become important. The first involves a scienti…


    It has been argued that the small, simple, everyday examples of evolution do not involve new information. This argument is sometimes correct. For example, the famous black moths did not contain new genetic information.

    In order to make room for new information, there have to be types of mutation which make a genome larger. It turns out that several kinds of mutation do this, notably duplication and polyploidy.

    If a bacteria becomes penicillin-resistant, it really does contain new information. We know this because researchers have now got to the point where they have read out (sequenced) every last bit of the DNA in some bacteria. This means that it's possible to do before-and-after measurements.

    Here's an example. Take a nice fresh culture dish, and place a single bacteria on it. A colony will grow. This is "before".

    Take one bacteria from "before", and start a new culture with it. After the culture is well-started, add some antibiotic. Somewhere in the culture, there may be a mutant who is resistant to the antibiotic. If there isn't such a mutant, they all die. In that case, start over. If necessary, you can encourage mutation, maybe with some radioactivity.

    Eventually, you will find such a mutant. You will know it's there because it reproduces, and your culture dish will contain a living colony instead of a dead one. This is "after".

    Now get the DNA sequences of "before" and "after". Several researchers have done just this, and the DNA sequences have been published. It is definitely the case that "after" can have new genetic information, which is not present in "before".

    In the above example, a beneficial mutation allowed the bacteria to survive a negative thing. It is equally easy to get a mutation that allows a positive thing. For example, give your colony a huge supply of some food which they cannot eat. Eventually some mutant will be able to eat the food, and will have a great many descendants. Then wipe out the normals (by withdrawing the normal food) and you have an "after" colony. As one researcher said:

    Here's a tested recipe for isolating successful mutations... Grow a batch culture of Salmonella typhimurium strain SK2979 at 37 deg. C on Neidhardt's MOPS-based minimal medium with 0.4% glycerol as the carbon source and 10 mM L-aspartate as the nitrogen source. Dilute and subculture for several days. L-aspartate fast growing mutants will take over the culture in something under 3 days. These typically have a doubling time of 60 minutes on asparate, compared to about 120 minutes for the parental, wild-type strain.
    Even better, starting with the fast-growing strain, one can easily isolate secondary mutation(s) which permit growth on aspartate as the sole carbon and nitrogen source -- which the parental strain simply cannot do. This demonstrates how cumulative mutations can arise.

    Basically, techniques involving the natural occurrence of spontaneous, beneficial mutations are commonly used by bacterial geneticists.

    The above is from a 1995 Usenet posting by Tim Ikeda ([email protected]), UC-Berkeley Plant Biology.

    Some Creationists have argued that these beneficial mutations involve simplification of the bacteria, so that some aspect attacked by the antibiotic is no longer present. That idea would rarely explain the ability to consume a new food, since that usually requires new chemical pathways. Before-and-after genetic analysis says that the "simplification" idea is just not always the case. For example, the malaria parasite has become resistant to chloroquine, by learning to make a new protein. Other examples are known from studies of pesticide resistant insects.

    It is also illogical that "simplification" always be the case. A mutation is due to a completely random malfunction of the genetic mechanisms. There is simply nothing to prevent a bacteria from occasionally acquiring increased complexity. If the more complex genetic material happens to be useful, then the bacteria has by definition acquired information. It has "learned" what works. As one scientist put it, "evolution is a transfer of information from the environment to the genome."

    You might wonder how a change could fail to be damaging. If all of a bacteria's genetic information is useful, then any change must have removed something useful. This is half-true, because bacteria do indeed run a tight ship. ("Higher" creatures are different, and carry around lots of genetic junk.) However, the chemical mechanisms which use genes do not really understand the idea of dosage. That is, if a creature needs twice as much of one chemical as another, there is no way to tell the mechanism "make twice as much". (I'm simplifying. Actually, hemoglobin has "enhancers" and "promoters".) The obvious trick for solving this problem is to simply have two copies of the gene. Therefore, creatures carry around two or more copies of some genes. If one copy is changed by a mutation, the creature can get along fairly well on the other one(s).

    Gene duplication is a fairly common mutation. Having an extra copy doesn't "cost" much, so a creature with such a mutation isn't at any great disadvantage. Extra copies are actually fairly common in the genetic material of "higher" creatures. And of course a mutation that changes an extra copy is not the same problem as a mutation that changes an only copy.

    Comment

    • Philosopher
      Senior Member
      • Sep 2008
      • 1003

      #17
      Originally posted by Vicsinad
      "At least hundreds, possibly thousands, of transitional fossils have been found so far by researchers. The exact count is unclear because some lineages of organisms are continuously evolving."

      http://www.livescience.com/3306-foss...in-theory.html
      False.

      Anyone reading creationist literature for a few years soon becomes aware that we often use quotes by evolutionists which discredit their own belief system. This raises the ire of many in the evolutionary establishment, and often they will accuse creationists of ‘taking their remarks out of context’. This is rarely the case. However, one can imagine that the spectre of condemnation from fellow evolutionists would these days tend to limit any careless remarks from the pro-evolutionary camp.

      One of the most famous and widely circulated quotes was made a couple of decades ago by the late Dr Colin Patterson, who was at the time the senior paleontologist (fossil expert) at the prestigious British Museum of Natural History.

      So damning was the quote—about the scarcity of transitional forms (the ‘in-between kinds’ anticipated by evolution) in the fossil record—that one anticreationist took it upon himself to ‘right the creationists’ wrongs’. He wrote what was intended to be a major essay showing how we had ‘misquoted’ Dr Patterson.1 This accusation still appears occasionally in anticreationist circles, so it is worth revisiting in some detail.

      Dr Patterson had written a book for the British Museum simply called Evolution.2 Creationist Luther Sunderland wrote to Dr Patterson inquiring why he had not shown one single photograph of a transitional fossil in his book. Patterson then wrote back with the following amazing confession which was reproduced, in its entirety, in Sunderland’s book Darwin’s Enigma:

      ‘I fully agree with your comments on the lack of direct illustration of evolutionary transitions in my book. If I knew of any, fossil or living, I would certainly have included them. You suggest that an artist should be used to visualise such transformations, but where would he get the information from? I could not, honestly, provide it, and if I were to leave it to artistic licence, would that not mislead the reader?’

      He went on to say:

      ‘Yet Gould [Stephen J. Gould—the now deceased professor of paleontology from Harvard University] and the American Museum people are hard to contradict when they say there are no transitional fossils. … You say that I should at least “show a photo of the fossil from which each type of organism was derived.” I will lay it on the line—there is not one such fossil for which one could make a watertight argument.’3 [Emphasis added].
      Creation or evolution? It makes a big difference! Over 10,000 trustworthy articles. Evidence for biblical creation.


      And

      The fossil record reflects the original diversity of life, not an evolving tree of increasing complexity. There are many examples of "living fossils," where the species is alive today and found deep in the fossil record as well.

      According to evolution models for the fossil record, there are three predictions:

      1. wholesale change of organisms through time
      2. primitive organisms gave rise to complex organisms
      3. gradual derivation of new organisms produced transitional forms.

      However, these predictions are not borne out by the data from the fossil record.

      Trilobites, for instance, appear suddenly in the fossil record without any transitions. There are no fossils between simple single-cell organisms, such as bacteria, and complex invertebrates, such as trilobites.

      Extinct trilobites had as much organized complexity as any of today’s invertebrates. In addition to trilobites, billions of other fossils have been found that suddenly appear, fully formed, such as clams, snails, sponges, and jellyfish. Over 300 different body plans are found without any fossil transitions between them and single-cell organisms.

      Fish have no ancestors or transitional forms to show how invertebrates, with their skeletons on the outside, became vertebrates with their skeletons inside.

      Fossils of a wide variety of flying and crawling insects appear without any transitions. Dragonflies, for example, appear suddenly in the fossil record. The highly complex systems that enable the dragonfly's aerodynamic abilities have no ancestors in the fossil record.

      In the entire fossil record, there is not a single unequivocal transition form proving a causal relationship between any two species. From the billions of fossils we have discovered, there should be thousands of clear examples if they existed.

      The lack of transitions between species in the fossil record is what would be expected if life was created.


      But then a new question arises. How complete is the fossil record? Can we legitimately expect to find these transitions?

      Dr. Michael Denton, an agnostic but a decided non-evolutionist compiled a chart on "The Adequacy of the Fossil Record" in his book, Evolution: A Theory In Crisis, by comparing the number of living types to fossil types, gleaning information from Romer's classic book, Vertebrate Paleontology. He found that 97.7% of living orders of terrestrial vertebrates are found as fossils. (Orders are larger groupings of families which are larger than genera which are larger then species.) Many creationists consider the groupings family or genus to best approximates the Genesis kind. Of living families of terrestrial vertebrates, 79.1% are represented, a number which jumps to 87.8% if birds (hardly ever preserved) are excluded. Thus, the fossil record of even terrestrial vertebrates is seen to be remarkably complete.

      But far less than 1% of all fossils are terrestrial vertebrates. Approximately 95% are marine invertebrates, with the rest being mostly plants, fish, and insects. Land fossils are notoriously scarce, and when found are usually fragmentary. With partial evidence an evolutionary story can sometimes be told.

      When we look at the invertebrates, we see separate and distinct categories (i.e., clams, corals, trilobites, etc.) existing in the earliest strata with no hint of ancestors or of intermediates. We find clams by the trillions, with a lot of variety among them, but no evolution. Furthermore, we have no idea how vertebrate fish could have arisen from any invertebrate. Where there are good data, we see no evolution. Where the data are scanty, evolutionists can tell a story. The fossil record is voluminous and apparently substantially complete. Yet no evolution is seen.

      Speaking of this issue, Darwin wrote in an 1881 letter that "the case at present must remain inexplicable and may be truly argued as a valid argument against the views here entertained." Evolution—a theory of change without any evidence of change.
      A favorite argument of creationists has always been the lack of transitional organisms preserved in the fossil record. The argument goes like this: If one basic type of animal evolved into another basic type, it must have passed through "in between" stages, or transitional forms. Whether or not these transitions were ever preserved as fossils, they must have existed. In fact, they must have existed by the trillions. Consider an evolutionary favorite—the evolution of a four-legged land a

      Comment

      • vicsinad
        Senior Member
        • May 2011
        • 2337

        #18
        You should check out this museum in Kentucky. I hear they have humans riding dinosaurs. They don't quite explain how humans and dinosaurs manage to coexist 10,000 years ago, but it fits in nicely with your religion!

        The state-of-the-art 75,000-square-foot Creation Museum brings the Bible to life, casting its characters and animals in dynamic form. Prepare to believe.

        Comment

        • Vangelovski
          Senior Member
          • Sep 2008
          • 8531

          #19
          Originally posted by vicsinad View Post
          You could start by reading and understanding the following articles:
          lots of interesting stuff there about combining, re-configuring and losing existing information, but I missed the bit about the creation of new information. Seeing as you have a degree in evolution, can you dumb it down for me?
          If my people who are called by my name will humble themselves and pray and seek my face and turn from their wicked ways, I will hear from heaven and will forgive their sins and restore their land. 2 Chronicles 7:14

          The Revolution was in the minds and hearts of the people; a change in their religious sentiments, of their duties and obligations...This radical change in the principles, opinions, sentiments, and affections of the people was the real American Revolution. John Adams

          Comment

          • vicsinad
            Senior Member
            • May 2011
            • 2337

            #20
            You didn't read them or bother to understand them.

            Comment

            • Phoenix
              Senior Member
              • Dec 2008
              • 4671

              #21
              I have some questions regarding this argument based on the 'fossil record' or lack thereof as proof against evolutionary processes...

              Do we understand enough about the processes and conditions of fossil creation?

              The 'fossil record' defense of creationism is somewhat flawed in my opinion because clearly the mechanics of fossil generation won't necessarily exist for every living thing on planet Earth to be 'recorded' at such and for there to be an uninterrupted 'fossil record' for us to compare over millennia.

              Comment

              • Philosopher
                Senior Member
                • Sep 2008
                • 1003

                #22
                Originally posted by vicsinad View Post
                You should check out this museum in Kentucky. I hear they have humans riding dinosaurs. They don't quite explain how humans and dinosaurs manage to coexist 10,000 years ago, but it fits in nicely with your religion!

                http://creationmuseum.org/
                Maybe you explain this.


                A recent discovery in the field of paleontology has sent shockwaves through the scientific community. Evolutionist Mary H. Schweitzer of North Carolina State University has discovered flexible blood vessels inside the fossilized thighbone of a "68-70 million year old" Tyrannosaurus rex1 from the Hell Creek formation in eastern Montana. Further investigation revealed round microscopic structures that look to be cells inside the hollow vessels. Even to the untrained eye, the tissue samples look as if the animal died recently. Fibrous protein material was dissolved with an enzyme called collegenase, indicating that amino acid sequencing could probably be done (amino acids are the building blocks of protein).

                Although it is too early to make definite statements regarding this stunning and wholly unexpected find, the evidence seems to indicate the T. rex fossil is -- well, young. Young as in just centuries-old, certainly not an age of millions of years. Indeed, Dr. Schweitzer said, "I am quite aware that according to conventional wisdom and models of fossilization, these structures aren't supposed to be there, but there they are. I was pretty shocked."2

                Would evolutionary theory have predicted such an amazing discovery? Absolutely not, soft tissue would have degraded completely many millions of years ago no matter how fortuitous the preservation process. Will evolutionary theory now state -- due to this clear physical evidence -- that it is possible dinosaurs roamed the earth until relatively recent times? No, for evolutionary theory will not allow dinosaurs to exist beyond a certain philosophical/evolutionary period.

                This is not the first time that puzzling soft tissue has been unearthed. Nucleic acid (DNA) taken from wet "fossil" magnolia leaves allegedly 17-20 million years old have been discovered.3 Fragments of genetic material up to 800 base pairs long were recovered -- amazing considering it does not take long for water to degrade DNA. A microbiologist in California dissected a 25-to-40-million-year-old Dominican stingless bee from amber.4 Spores of bacteria were found inside the insect and actually grew when placed in the proper medium. Dr. Cano, the discoverer, took careful measures to avoid contamination. Analysis of the DNA extracted showed it was very much like the DNA found in bacteria growing in bees today. Just as the creation model predicts, bees have always been bees and bacteria have always been bacteria.

                If this is in fact what these various scientific evidences indicate -- soft tissue, bacteria, and DNA ensconced in fossils and amber allegedly millions of years old -- then there needs to be a complete re-evaluation of these evolutionary time spans, especially in light of the advances of the ICR RATE project.

                As the great English author Charles Dickens said over a century ago, "these are the best of times" -- for creation science!
                A recent discovery in the field of paleontology has sent shockwaves through the scientific community. Evolutionist Mary H. Schweitzer of North Carolina State University has discovered flexible blood vessels inside the fossilized thighbone of a "68-70 million year old" Tyrannosaurus rex1 from the Hell Creek formation in eastern Montana. Further investigation revealed round microscopic structures that look to be cells inside the hollow vessels. Even to the untrained eye, the tissue samples look as

                Comment

                • Vangelovski
                  Senior Member
                  • Sep 2008
                  • 8531

                  #23
                  Originally posted by vicsinad View Post
                  You didn't read them or bother to understand them.
                  I did, in fact, I've read two of them previously. Can you please respond to my question about the creation of new information?
                  If my people who are called by my name will humble themselves and pray and seek my face and turn from their wicked ways, I will hear from heaven and will forgive their sins and restore their land. 2 Chronicles 7:14

                  The Revolution was in the minds and hearts of the people; a change in their religious sentiments, of their duties and obligations...This radical change in the principles, opinions, sentiments, and affections of the people was the real American Revolution. John Adams

                  Comment

                  • vicsinad
                    Senior Member
                    • May 2011
                    • 2337

                    #24
                    I did respond with my post in the article. Pick which segments you disagree with and I'll answer in kind.

                    Comment

                    • Vangelovski
                      Senior Member
                      • Sep 2008
                      • 8531

                      #25
                      Originally posted by vicsinad View Post
                      I did respond with my post in the article. Pick which segments you disagree with and I'll answer in kind.
                      I did not understand from your articles how new information is created. Can you dumb down the process, seeing as you have a degree in evolution.
                      If my people who are called by my name will humble themselves and pray and seek my face and turn from their wicked ways, I will hear from heaven and will forgive their sins and restore their land. 2 Chronicles 7:14

                      The Revolution was in the minds and hearts of the people; a change in their religious sentiments, of their duties and obligations...This radical change in the principles, opinions, sentiments, and affections of the people was the real American Revolution. John Adams

                      Comment

                      • Redsun
                        Member
                        • Jul 2013
                        • 409

                        #26
                        P - This is another hot topic. What are your thoughts on the science of evolution?

                        How hot can this topic be, it has been debated for decades.

                        I believe in the science of evolution.

                        Comment

                        • vicsinad
                          Senior Member
                          • May 2011
                          • 2337

                          #27
                          If you don't understand them, it's probably because you don't understand what the basic of genetics is about, and I'm afraid I can't really dumb it down enough for you to understand, because it's not easily dumbed down.

                          Comment

                          • vicsinad
                            Senior Member
                            • May 2011
                            • 2337

                            #28
                            And by the above I mean explain it to you without using much of the same terminology that they use.

                            Comment

                            • Vangelovski
                              Senior Member
                              • Sep 2008
                              • 8531

                              #29
                              Originally posted by vicsinad View Post
                              If you don't understand them, it's probably because you don't understand what the basic of genetics is about, and I'm afraid I can't really dumb it down enough for you to understand, because it's not easily dumbed down.
                              Or is it that you just can't explain it?
                              If my people who are called by my name will humble themselves and pray and seek my face and turn from their wicked ways, I will hear from heaven and will forgive their sins and restore their land. 2 Chronicles 7:14

                              The Revolution was in the minds and hearts of the people; a change in their religious sentiments, of their duties and obligations...This radical change in the principles, opinions, sentiments, and affections of the people was the real American Revolution. John Adams

                              Comment

                              • vicsinad
                                Senior Member
                                • May 2011
                                • 2337

                                #30
                                Originally posted by Vangelovski View Post
                                Or is it that you just can't explain it?
                                No, I can. Just not as well as many articles. So is this about me being able to explain it to you rather than that it is explained to you? Because if it isn't, there's better explanations than I can give, and I gave them to you. And I can give you more:

                                This one is quite technical, but the conclusion should provide you with a starting place.




                                This one is dumbed down, but you'll say it doesn't do the job for you, and then I'll point you to the more technical studies, and you'll say you need it dumbed down...thus we'll go in a cycle, but here goes:

                                In biology, everything has a history. Creationists love to try to calculate the probability of a new gene spontaneously coming into existence, but that's not how genes are born.


                                This one gives a dumbed-down specific example about what came first regarding the benefits and genes, but I'll refer to my above comment as to why you'll refute this one.

                                Researchers have observed in an experiment the exact steps bacterial genes take to evolve a new ability, unexpectedly adding a new twist on an old model

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