Home » Darwinism, Intelligent Design » Recent papers confirm that genetic entropy decreases fitness

Recent papers confirm that genetic entropy decreases fitness

File:First law open system.svg

entropy illustrated

Over at Creation-Evolution Headlines, Dave Coppedge reports that two recent journal article’s have confirmed Cornell’s John Sanford’s “genetic entropy”: An accumulation of mutations always decreases fitness (contrary to neo-Darwinists’ hopes):

For mutations under epistasis to produce innovation, there must be a way for them to work together (synergistic epistasis). This is often assumed but has not been observed. Most experiments have shown beneficial mutations working against each other (antagonistic epistasis; see 12/14/2006), or causing even less fitness than if they acted alone (decompensatory epistasis; see 10/19/2004). In a new paper in Science,3 Khan et al, working with Richard Lenski [Michigan State], leader of the longest-running experiment on evolution of E. coli, found a law of diminishing returns with beneficial mutations due to negative epistasis.

Diminishing returns?

Like this, for example?: An increased number of spelling errors in a letter retyped in series by a number of different people does not add up to a new, better letter over time?

Coppedge also notes the way the science media handled the news, for example:

“The more mutations the researchers added, the more they interfered with each other,” was one of the “surprising” results.

Surprising to whom? Not to Dembski and other members of the No Free Lunch club.

Follow UD News for breaking news on the design controversy.

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199 Responses to Recent papers confirm that genetic entropy decreases fitness

  1. 1
    Elizabeth Liddle

    Yes, accumulation of mutations during a period where few mutations result in reduced probability of reproduction will tend to decrease fitness in the long term when that period comes to an end, but as they can only accumulate when those selection pressures are relaxed, they are likely to be purged when the very conditions in which they actually reduce fitness come to pass.

    Which may not happen.

    Darwinian evolution does not predict that most mutations will be beneficial; it predicts that only neutral and beneficial mutations will persist. But the system can’t look ahead, so periods of relaxed selection can be followed by periods of drastic selection.

    Which is the problem faced by Giant Pandas right now.

  2. Elizabeth, basically you are saying, No matter what the evidence says, I will make up any ‘just so’ I can story so that I can maintain my blind faith in neo-Darwinism.

  3. 3
    Elizabeth Liddle

    No, I’m not saying that at all :)

    I agree that the evidence shows that most mutations are harmful, and that in a period of “relaxed selection” mutations that would be harmful in a period of more stringent selection will tend to build up, and that this can be a problem (e.g. Giant Pandas).

    It’s especially a problem with very small populations, or once a population gets very small. Indeed it’s part of the process of extinction, which we know occurs with great frequency.

    So I’m not clear what evidence you think I’m ignoring :)

    All I’m saying is that it’s not “contrary to neo-Darwinists’ hopes”.

    Buildup of mutations without selection isn’t the same as buildup of those mutations that survive selection.

    Anyway, gotta love you and leave you for a bit :)

    Cheers

    Lizzie

  4. Elizabeth as to this statement of yours:

    ‘it predicts that only neutral and beneficial mutations will persist.’

    AHH, the elusive, shy and docile, beneficial mutation. Have you, by chance :) , located an unambiguous ‘beneficial mutation’, so that we might know if they really and truly exist?

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net ‘fitness gain’ within a ‘stressed’ environment i.e. remove the stress from the environment and the parent strain is always more ‘fit’)
    http://behe.uncommondescent.co.....evolution/

    Michael Behe’s Amazon Blog – October 2007
    Excerpt: As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene. Since there are so many ways to break or degrade a gene, those sorts of beneficial mutations can happen relatively quickly. For example, there are hundreds of different mutations that degrade an enzyme abbreviated G6PD, which actually confers some resistance to malaria. Those certainly are beneficial in the circumstances. The big problem for evolution, however, is not to degrade genes (Darwinian random mutations can do that very well!) but to make the coherent, constructive changes needed to build new systems.
    http://behe.uncommondescent.com/page/6/

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

    Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010
    Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator.
    http://www.arn.org/blogs/index.....ruit_flies

    Moreover Elizabeth, Genetic Entropy, besides being based on the fact that all known mutations are detrimental, is also primarily based on the fact that the vast majority of mutations are ‘slightly detrimental’ and are thus far below the power of natural selection to remove from a genome before they spread throughout the entire population:

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

  5. further note:

    The evidence for the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.

    Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57 By John C. Avise
    Excerpt: “Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.”

    I went to the mutation database website cited by John Avise and found:

    HGMD®: Now celebrating our 100,000 mutation milestone!
    http://www.biobase-internation.....mddatabase

    I really question their use of the word ‘celebrating’.

    This following study confirmed the detrimental mutation rate for humans, of 100 to 300 per generation, estimated by John Sanford in his book ‘Genetic Entropy’ in 2005:

    Human mutation rate revealed: August 2009
    Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome. (Of note: this number is derived after “compensatory mutations”)
    http://www.nature.com/news/200.....9.864.html

    This ‘slightly detrimental’ mutation rate of 100 to 200 per generation is far greater than even what evolutionists agree is an acceptable mutation rate for an organism:

    Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction
    Excerpt: Shakhnovich’s group found that for most organisms, including viruses and bacteria, an organism’s rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material.
    http://www.sciencedaily.com/re.....172753.htm

    Contamination of the genome by very slightly deleterious mutations:
    why have we not died 100 times over? Kondrashov A.S.
    http://www.ingentaconnect.com/.....4/art00167

    The Frailty of the Darwinian Hypothesis
    “The net effect of genetic drift in such (vertebrate) populations is “to encourage the fixation of mildly deleterious mutations and discourage the promotion of beneficial mutations,”
    http://www.evolutionnews.org/2......html#more

    High genomic deleterious mutation rates in hominids
    Excerpt: Furthermore, the level of selective constraint in hominid protein-coding sequences is atypically (unusually) low. A large number of slightly deleterious mutations may therefore have become fixed in hominid lineages.
    http://www.nature.com/nature/j.....344a0.html

    High Frequency of Cryptic Deleterious Mutations in Caenorhabditis elegans ( Esther K. Davies, Andrew D. Peters, Peter D. Keightley)
    “In fitness assays, only about 4 percent of the deleterious mutations fixed in each line were detectable. The remaining 96 percent, though cryptic, are significant for mutation load…the presence of a large class of mildly deleterious mutations can never be ruled out.”
    http://www.sciencemag.org/cgi/...../5434/1748

    All life eventually succumbs to the effects of Genetic Entropy, but humans are especially vulnerable. As This following study reveals:

    Sanford’s pro-ID thesis supported by PNAS paper, read it and weep, literally – September 2010
    Excerpt: Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).
    http://www.uncommondescent.com.....literally/

    As well, the slow accumulation of ‘slightly detrimental mutations’ in humans, that is ‘slightly
    detrimental mutations’ which are far below the power of natural selection to remove from our genomes, is revealed by this following fact:

    “When first cousins marry, their children have a reduction of life expectancy of nearly 10 years. Why is this? It is because inbreeding exposes the genetic mistakes within the genome (slightly detrimental recessive mutations) that have not yet had time to “come to the surface”. Inbreeding is like a sneak preview, or foreshadowing, of where we are going to be genetically as a whole as a species in the future. The reduced life expectancy of inbred children reflects the overall aging of the genome that has accumulated thus far, and reveals the hidden reservoir of genetic damage that have been accumulating in our genomes.”
    Sanford; Genetic Entropy; page 147

  6. I don’t think it’s correct to say that it decreases fitness. It’s the rate of fitness increase that is slowed. Which contrasts with work doing this sort of study of interactions for mutations all in the same protein – there they interact violently, sometimes being good or bad, and there have been no apparent trends between benefit of a mutation and how good you were before it arrived.

  7. There still isn’t any evidence that any amount of accumulated mutations can do what the theory of evolution requires for universal common descent.

    Accumulated mutations gets you an albino dwarf with sickle-cell anemia.

    Just sayin’…

  8. 8
    Elizabeth Liddle

    ba77: it’s very difficult to know whether a new allele is beneficial or deleterious, especially if the effect is slight. They can usually only be detected statistically.

    And remember that “beneficial” and “deleterious”, in the population genetics sense, are only meaningful in relation to the current environment. What is beneficial in one environment may be neutral or deleterious in the next, and vice versa.

    But, since you ask:

    http://www.lbl.gov/Science-Art.....licki.html

    The vast majority of mutations are near-neutral in any given environment. This is an unusual one in conferring a clear benefit to the individual. Whether it will actually “be selected” or not, remains unclear, though. That will depend on whether it confers a reproductive advantage. It may not.

    On the other hand there is some evidence that women’s access to fertility control may be resulting in extended fertility, which would make sense; as women postpone child-bearing, women bearing alleles (whether new or existing) that tend to result in later menopause are more likely to have children than those bearing alleles that promote earlier menopause earlier. The former will therefore tend to increase in prevalence, and there is some evidence that they are doing so.

    It may be a good example of alleles that were slightly deleterious becoming advantageous, and vice versa. I’ll try to look out the source (can’t find it right now).

  9. Elizabeth, ignoring your blatant ‘excuse mongering’ in the main of your post, let’s just look at your cited claim for a beneficial mutation:

    Site #1)The Milano Mutation: A Rare Protein Mutation Offers New Hope for Heart Disease Patients1
    Site #2)‘Defective’ but beneficial gene may bring about novel ways to clear arterial plaque buildup2

    I have checked these, and they work as of Feb 04, 2003.
    Thanks for the good communication.
    In Christ,
    J.R.

    It would appear that the questioner is under the mistaken impression that beneficial mutations are a problem for creationists. Some creationists make this unfortunate error. The mutations Q&A section of our Web site clearly teaches that the issue is not whether the mutation is beneficial but if it adds new genetic information (specified complexity). So it would have been clear that the A-I Milano mutation is not evidence for microbe-to-man evolution.

    What has happened? One amino acid has been replaced with a cysteine residue in a protein that normally assembles high density lipoproteins (HDLs), which are involved in removing ‘bad’ cholesterol from arteries. The mutant form of the protein is less effective at what it is supposed to do, but it does act as an antioxidant, which seems to prevent atherosclerosis (hardening of arteries). In fact, because of the added -SH on the cysteine, 70% of the proteins manufactured bind together in pairs (called dimers), restricting their usefulness. The 30% remaining do the job as an antioxidant. Because the protein is cleverly designed to target ‘hot spots’ in arteries and this targeting is preserved in the mutant form, the antioxidant activity is delivered to the same sites as the cholesterol-transporting HDLs. In other words, specificity of the antioxidant activity (for lipids) does not lie with the mutation itself, but with the protein structure, which already existed, in which the mutation occurred. The specificity already existed in the wild-type A-I protein before the mutation occurred.

    Now in gaining an anti-oxidant activity, the protein has lost a lot of activity for making HDLs. So the mutant protein has sacrificed specificity. Since antioxidant activity is not a very specific activity (a great variety of simple chemicals will act as antioxidants), it would seem that the result of this mutation has been a net loss of specificity, or, in other words, information. This is exactly as we would expect with a random change.
    http://creation.com/a-i-milano.....-evolution

    Elizabeth, perhaps you would like to look for another ‘beneficial’ mutation???

  10. Elizabeth,

    First, let me say that I appreciate your attitude and tone, a refreshing change from most of what you hear in this debate. Second, let me say that I’m an engineer, not a biologist; I just happened to become interested when I was most of the way through engineering school. So correct me if I’m wrong about something that is a scientific fact

    From comment #1

    Darwinian evolution does not predict that most mutations will be beneficial; it predicts that only neutral and beneficial mutations will persist. But the system can’t look ahead, so periods of relaxed selection can be followed by periods of drastic selection.

    That sounds great and makes perfect sense, except that there is a staggering lack of observed “beneficial” (i.e. complex-system-building) mutations. Also, I thought Darwinian evolution predicts that the most “fit” genomes will persist, regardless of whether they are better or worse than their predecessors, just as long as they’re better than their current competitors?

    From comment #3

    Buildup of mutations without selection isn’t the same as buildup of those mutations that survive selection.

    So if random mutation and natural selection is all that occurs in nature, and the vast majority of mutations are at least slightly harmful, aren’t most selected mutations going to be at least slightly harmful, even during periods of “drastic selection”? And so even if there are system-building mutations (not yet verified?) that are then selected, these are tremendously out-numbered by the most-fit “slightly harmful” mutations. How does this eventually result in perfectly tuned, extremely complex systems? If I had to “evolve” a book using random mutation and selection with these mechanisms, starting with a coherent book, it seems like maybe I could change a few words, if I focused on them, but most of the book would go to pot. The other image that comes to mind is trying to solve a 10,000 x 10,000 x 10,000 Rubik’s cube. You might be able to mutate/select and accumulate a few small patches of like-color squares, but to get the whole thing, or most of it, solved would take a heck of a lot of intelligence.

    Also from comment #3

    I agree that the evidence shows that most mutations are harmful, and that in a period of “relaxed selection” mutations that would be harmful in a period of more stringent selection will tend to build up, and that this can be a problem (e.g. Giant Pandas).

    It’s especially a problem with very small populations, or once a population gets very small. Indeed it’s part of the process of extinction, which we know occurs with great frequency.

    That seems to beg the question of what happened at the beginning of life or maybe also the beginning of “branches” when populations were very small. How did these flourish when small populations that we observe struggle tremendously?

  11. 11
    Elizabeth Liddle

    Joseph: I think there might be some confusion over the word “mutation”.

    Many human genes have many polymorphisms, all of which function pretty well, but have slightly different phenotypic effects.

    The question is: where did those polymorphisms come from? Well, we have good ideas as to where some of them came from, because we know the kind of copying mechanisms that produce those variants, from repeated sections of code, to single nucleotide replacements, to recombination processes by which two parent alleles recombine to produce a new “child” allele.

    Are you suggesting that all but two of each set of human alleles are deleterious mutations? Because there is no reason to think so – they are just the variance that make us different from each other.

    Or are you suggesting that mutation is a specific, damaging process that can only result in deleterious alleles, and some other, perhaps Intelligent, process is responsible for the non-deleterious alleles?

    Because that isn’t what the evidence suggests. The evidence suggests that most of what seem to be perfectly functional alleles have resulted from specific copying mechanisms that do not always result in the child allele being identical to either parent allele.

    It’s possible of course that the kind of flexibility in the copying mechanisms was a deliberate design feature!

    But that wouldn’t alter the fact that they are “mutations”. Indeed, a better ID hypothesis, it seems to me, would be to posit that mutations are a deliberate design feature that enable populations to adapt (I think Behe’s position may be near this one).

    But polymorphisms have to be explained somehow, and they seem, on the whole, to be pretty cool things.

  12. 12
    Elizabeth Liddle

    ba77: there was no “excuse mongering” in my post!

    And you might like to re-read the part where I mentioned the Milano mutation.

  13. 13
    Elizabeth Liddle

    @ uoflcard

    Thank you for your kind words :)

    You wrote:

    That sounds great and makes perfect sense, except that there is a staggering lack of observed “beneficial” (i.e. complex-system-building) mutations.

    Well, we need to get terminology a bit straighted here. In population genetic terms, a “beneficial” mutation is simply one that confers on the phenotype (i.e. the critter that bears it) a enhanced probability of reproductive success, usually considered relative to the allele it mutated from, although that gets complicated once an allele has been around for a while.

    So “beneficial” is not, in fact, defined as “complex-system-building”. In fact, Darwin did not propose (and most biologists do not posit) that any single mutation was/is “complex-system-building”, but rather, that complex systems must have been built up, incrementally, from new alleles that each conferred only a slight advantage (or perhaps neutral, or even slightly deleterious alleles that had only propagated through drift the population by drift).

    This is viewed, in some quarters, of course, as the Achilles heel of Darwinism. I don’t think it is, but I think it’s important to be clear what evolutionary theory is saying and what it is not. No evolutionary biologist would expect that any complex system appeared in a single mutation. Thus complex-systems, under evolutionary theory, have to be explained by incremental changes, not “hopeful monsters”.

    Also, I thought Darwinian evolution predicts that the most “fit” genomes will persist, regardless of whether they are better or worse than their predecessors, just as long as they’re better than their current competitors?

    Yes, and this is a very important point (although, to nitpick, it’s not that Darwinian evolution “predicts” this, so much as this is what the theory actually is – namely that adaptataion occurs because the alleles that persist will be those best at persisting!).

    However, you are absolutely right that under certain circumstances (for instance in small populations with very high mutation rates) the rate of deleterious allele production may be so high that although the most fit of each generation are those that pass on their alleles to the next generation, each generation also supplies its own new, bad alleles, and so the net fitness of the population still goes down.

    This is relatively easy to model, in fact, and there are even equations around that give the thresholds at which “mutational meltdown” becomes a problem. Only, sometimes it doesn’t seem to when it should, which is an interesting puzzle :)

    I think my comments above also address your subsequent point, but I will make an additional point, which is that yes, again you are right, and because you are right, we can infer, that IF Darwinian evolution is broadly correct, then at least three things must be true: mutation rates cannot be so high as to swamp each new generation (effectively drowning out selection); at least some mutations must confer actual increased probability of reproduction; the system cannot be “brittle” – there must be a reasonable number of variants around any given allele that are more or less functional.

    In addition, there is an issue horizontal gene transfer, which is important (and achieved in sexually reproducing species by sexual reproduction) and helps to guard against genetic meltdown.

    oops gotta run, be back in a bit :)

    Cheers

    Lizzie

  14. Elizabeth, and you might like to reread the part where the mutation, you cited as ‘beneficial’, was actually found to be deleterious as far as the overall functional complexity of the protein was concerned.,,, But then being fair to the evidence was not your primary concern in the first place was it???

    “The neo-Darwinians would like us to believe that large evolutionary changes can result from a series of small events if there are enough of them. But if these events all lose information they can’t be the steps in the kind of evolution the neo-Darwin theory is supposed to explain, no matter how many mutations there are. Whoever thinks macroevolution can be made by mutations that lose information is like the merchant who lost a little money on every sale but thought he could make it up on volume.” Lee Spetner (Ph.D. Physics – MIT – Not By Chance)

    “The opportune appearance of mutations permitting animals and plants to meet their needs seems hard to believe. Yet the Darwinian theory is even more demanding: a single plant, a single animal would require thousands and thousands of lucky, appropriate events. Thus, miracles would become the rule: events with an infinitesimal probability could not fail to occur,,, There is no law against day dreaming, but science must not indulge in it.” Pierre P. Grasse – past President of the French Academie des Sciences

    =============

    Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? (Thomas Bataillon)
    Abstract……It is argued that, although most if not all mutations detected in mutation accumulation experiments are deleterious, the question of the rate of favourable mutations (and their effects) is still a matter for debate.
    http://www.nature.com/hdy/jour.....7270a.html

    Distribution of fitness effects caused by random insertion mutations in Escherichia coli
    Excerpt: At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect.
    http://www.springerlink.com/co.....q5l0q3832/

    “But in all the reading I’ve done in the life-sciences literature, I’ve never found a mutation that added information… All point mutations that have been studied on the molecular level turn out to reduce the genetic information and not increase it.”
    Lee Spetner – Ph.D. Physics – MIT – Not By Chance

    “Bergman (2004) has studied the topic of beneficial mutations. Among other things, he did a simple literature search via Biological Abstracts and Medline. He found 453,732 “mutation” hits, but among these only 186 mentioned the word “beneficial” (about 4 in 10,000). When those 186 references were reviewed, almost all the presumed “beneficial mutations” were only beneficial in a very narrow sense- but each mutation consistently involved loss of function changes-hence loss of information.” Sanford: Genetic Entropy

  15. Whoever posted this might have benefitted from reading the original papers. The conclusions are quite the opposite of this post.

    Post: “An accumulation of mutations always decreases fitness”

    Paper: “Adaptation……resulted in an average fitness increase after 600 generations of 66.8% ”
    “These mutations together produced a fitness increase of ~30% relative to the ancestor…..”

    So, wrong on that point. Beneficial mutations accumulated.

    What was observed is an increase in fitness that is less that that of the individual beneficial mutations summed (they don’t totally work synergistically and independently). So, the ‘net’ fitness isn’t equal to the ‘gross’. The authors say: “In other words, epistasis acts as a drag that reduces the contribution of later beneficial mutations.”

    Think of it this way-if you get a raise doubling your pay, your net income increases, but probably doesn’t actually double due to increased taxes, etc. This is not to say your income didn’t increase! Would you turn down the raise because gross doesn’t equal net?

    Also, the negative epistasis wasn’t universal!

    Summarizing the studies:
    “Thus, across these two distinct model systems 7 of 10 alleles consistently showed antagonism, whereas only 2 exhibited synergy.”

    So all we can say is that adaptation more frequently shows negative epistasis than synergy.

    Which was predicted:
    “This tendency toward diminishing returns between beneficial mutations was predicted from trajectories of fitness increase and substitution rate (12) but had never been tested directly.”

  16. Elizabeth,

    My point is there isn’t any evidence that mutations can accumulate in such a way- that is take all the polymorphisms you like and you still won’t have anything resembling universal common ancestry.

    But you can get an albino dwarf with SCA.

    Also Dr Lee Spetner wrote “Not By Chance”- published in 1997- which explains the telic approach to mutations.

  17. DrREC, of course what you fail to mention, is that the ‘beneficial’ adaptations, taken from the Lenski study, were only ‘more fit’ in the sense of a ‘stressed environment’ that was different from the original ‘normal’ wild type environment, yet when the ‘evolved’ strain was compared to the parent wild type in the original ‘normal’ environment we find;

    Lenski’s e-coli – Analysis of Genetic Entropy
    Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.
    http://www.answersingenesis.or.....n-bacteria

    DrREC, why would you leave out this most important piece of the equation???

    ==================

    Michael Behe’s Quarterly Review of Biology Paper Critiques Richard Lenski’s E. Coli Evolution Experiments – December 2010
    Excerpt: After reviewing the results of Lenski’s research, Behe concludes that the observed adaptive mutations all entail either loss or modification–but not gain–of Functional Coding ElemenTs (FCTs)
    http://www.evolutionnews.org/2.....41221.html

  18. So, wrong on that point. Beneficial mutations accumulated.

    from the article in science daily:

    The more mutations the researchers added, the more they interfered with each other. It was as if the mutations got in each other’s way as they all tried to accomplish the same thing.

    It was found that the beneficial mutations allowing the bacteria to increase in fitness didn’t have a constant effect. The effect of their interactions depended on the presence of other mutations, which turned out to be overwhelmingly negative.

    “These results point us toward expecting to see the rate of a population’s fitness declining over time even with the continual addition of new beneficial mutations,”
    </strong

    since the more complex the new function/feature the more mutations it takes, how can these complex functions/features evolve at all?

  19. 19
    Elizabeth Liddle

    Joseph: beneficial mutations are more likely to accumulate than deleterious once. If dwarfism doesn’t impair your probability of successful reproduction, than it isn’t deleterious, but if it is, you are less likely to have descendents than your non-dwarf friend. So when an albino mutation comes along, it is more likely to happen in one of your friends descendents than in one of your own.

    However, if you have an allele that does enhance your probability of successful reproduction (makes you tall dark and handsome, perhaps) you are more likely to have descendents that your nerdy-looking friend. So when a smartness enhancing mutation comes along, it is more likely to happen in one of your descendents than in one of your nerdy-looking friend’s descendents.

    That is why beneficial mutations tend to build, and deleterious mutations tend not to.

    However, if mutations are very frequent, and are mostly slightly, but not disastrously, deleterious, in a small population they may well build up, just by force of numbers.

  20. “Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. …. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment.”

    So, E. coli grown at 37 lose ability to grow at cold or hot temperatures. E. coli grown on glucose lose other pathways.

    No kidding. Animals living on land have lost the ability to breath underwater, too.

    Natural selection selects for fitness only in the environment that the selection occurred in.

    Organisms growing in a yellowstone hot spring are poorly adapted to your refrigerator. Fish are poorly adapted to life on land.

    Now, if that environment changes frequently, the organism might appear robust and adaptable. If it is constant, that organism will lose adaptability to other environments. This is likely why wild organisms deal with differing conditions better than ones grown in a lab under a single condition.

    You’re actually making an interesting anti-design argument. ‘Front-loading’ would fail, because the ‘front-loaded’ information would be lost if not used and selected for.

  21. tsmith @ 18:

    The key phrase is : “the rate of a population’s fitness declining over time”

    The rate, not overall fitness.

    Fitness is improving, that rate just slows over time.

  22. DrREC, your whole problem is that you have to show a GAIN in functional complexity/information over what is already present yet,,,

    Michael Behe’s Quarterly Review of Biology Paper Critiques Richard Lenski’s E. Coli Evolution Experiments – December 2010
    Excerpt: After reviewing the results of Lenski’s research, Behe concludes that the observed adaptive mutations all entail either loss or modification–but not gain–of Functional Coding ElemenTs (FCTs)

    ,,, you ain’t got ANY evidence for mutations that build functional complexity/information!!! So, even though you make lame excuses as to why we ALWAYS observe loss of function/information mutations, and how that consistent loss is compatible with neo-Darwinian evolution, the plain fact is that you are blatantly ignoring the fact that you DON”T have the types of complexity building ‘beneficial’ mutations that you absolutely need to make evolution work!!!

  23. bornagain77 @22

    Citing Behe’s review without reading it might not be the best idea.

    Where you claim “you ain’t got ANY evidence for mutations that build functional complexity/information”

    Behe lists a number of ‘gain-of-FCT’ mutations.

    “An interesting variation on this pattern is reported in Chapter 5 by Lin and Wu (1984). Mutants of E. coli and S. typhimurium (S. enterica var Typhimurium) gain the ability to metabolize the unusual substrate d-arabinose by altering the specificity of a regulatory protein. …because the protein has apparently gained an additional binding site for the novel substrate, the mutation is classed as gain-of-FCT.”

    “Both the 6-nucleotide deletion and the 14-nucleotide duplication are gain-of-FCT mutations since they both produced new coded molecular features in the virus that did not exist in the immediate precursor….”

    So, even Behe (with his odd definition, where what look like totally novel functions still get lumped in as ‘modifications of function’) has to acknowledge the direct observation of gain-of-FCT mutations that increase fitness!

    Several of Lenski’s have the potential to fall in this class as well-that appeared as unknowns in Behe’s review.

    Now, this is a pretty tough definition, with Behe selecting very carefully. But even he can’t deny the novel functional information emerging from these evolution experiments.

  24. The rate, not overall fitness.

    Fitness is improving, that rate just slows over time.

    the question still stands…ever hear of Haldane’s dilemma?

    It takes a great many mutations to produce sight, for example, (although no one has any clue how many or what mutations produced sight) and with the rarity of beneficial mutations to begin with, coupled with the negative epistatic effect, how does anything evolve?

  25. a few earlier studies produced rather interesting results…

    The tendency for genetic architectures to exhibit epistasis among mutations plays a central role in the modern synthesis of evolutionary biology and in theoretical descriptions of many evolutionary processes. Nevertheless, few studies unquestionably show whether, and how, mutations typically interact. Beneficial mutations are especially difficult to identify because of their scarcity. Consequently, epistasis among pairs of this important class of mutations has, to our knowledge, never before been explored. Interactions among genome components should be of special relevance in compacted genomes such as those of RNA viruses. To tackle these issues, we first generated 47 genotypes of vesicular stomatitis virus carrying pairs of nucleotide substitution mutations whose separated and combined deleterious effects on fitness were determined. Several pairs exhibited significant interactions for fitness, including antagonistic and synergistic epistasis. Synthetic lethals represented 50% of the latter. In a second set of experiments, 15 genotypes carrying pairs of beneficial mutations were also created. In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components.

    http://www.pnas.org/content/101/43/15376.abstract

  26. Subjecting TEM-1 to random mutational drift and purifying selection (to purge deleterious mutations) produced changes in its fitness landscape indicative of negative epistasis; that is, the combined deleterious effects of mutations were, on average, larger than expected from the multiplication of their individual effects. As observed in computational systems, negative epistasis was tightly associated with higher tolerance to mutations (robustness). Thus, under a low selection pressure, a large fraction of mutations was initially tolerated (high robustness), but as mutations accumulated, their fitness toll increased, resulting in the observed negative epistasis. These findings, supported by FoldX stability computations of the mutational effects, prompt a new model in which the mutational robustness (or neutrality) observed in proteins, and other biological systems, is due primarily to a stability margin, or threshold, that buffers the deleterious physico-chemical effects of mutations on fitness. Threshold robustness is inherently epistatic—once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.

    rshtein et al, “Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein,” Nature 444, 929-932 (14 December 2006) | doi:10.1038/nature05385.

  27. The rate, not overall fitness.

    Fitness is improving, that rate just slows over time.

    I do think you missed this part of the quote…


    “These results point us toward expecting to see the rate of a population’s fitness declining over time even with the continual addition of new beneficial mutations,”

  28. 28
    Elizabeth Liddle

    I assume that means: “…the rate of a population’s fitness increase declining over time…”

    Or conceivably “decrease”. But it doesn’t parse as written, so there must be a word missing.

    But if a rate-of-increase declines, that doesn’t mean it decreases, unless the rate goes negative.

    In fact a decline in rate-of-increase makes sense; at some point a ceiling must be reached, certainly if resources are finite.

  29. BA77:

    I think you could be a little more polite (1 Peter 3:15)…

    “Elizabeth, ignoring your blatant ‘excuse mongering’ in the main of your post, let’s just look at your cited claim for a beneficial mutation:”

    Such flamboyant language actually detracts from your argument — imo at least…

  30. tsmith,

    I don’t know where that quote came from. It is not in the papers. There, it is abundantly clear the authors would mean: …the rate at which a population’s fitness increases declining over time even with the continual addition of new beneficial mutations.

    As the papers say:
    “These data support models in which negative epistasis contributes to declining rates of adaptation over time. ”

    “diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation.”

    I’m not sure what the other references are for. I’m not denying epistasis.

  31. I don’t know where that quote came from. It is not in the papers.

    its from:

    http://www.sciencedaily.com/re.....143202.htm

    I think it means just what it says…

  32. It is perhaps ambiguous, but if you are interpreting that overall fitness is declining, you are wrong.

    The original papers, not Science Daily are the authority on this. The wording and context in them is 100% unambiguous.

    “These data support models in which negative epistasis contributes to declining rates of adaptation over time. ”

    “diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation.”

  33. 33
    Elizabeth Liddle

    It’s a direct quote from an interview apparently:

    “These results point us toward expecting to see the rate of a population’s fitness declining over time even with the continual addition of new beneficial mutations,” he said. “As we sometimes see in sports, a group of individual stars doesn’t necessarily make a great team.”

    But either interview missed out a word (easily done), or the transcriber missed it.

    “rate..of fitness” doesn’t make sense. Fitness is a scalar, it doesn’t have a rate.

    It must be a rate of change of fitness, and in the context, only rate of increase makes sense.

  34. 34
    Elizabeth Liddle

    interview=interviewee. oops.

  35. I’m not sure what the other references are for. I’m not denying epistasis.

    just more support to genetic entropy…

    I find the one from nature interesting because it seems there is a certain amount of mutations that are tolerated…until a certain point is crossed.

    the other one is interesting because of the following:

    Synthetic lethals represented 50% of the latter. In a second set of experiments, 15 genotypes carrying pairs of beneficial mutations were also created. In this case, all significant interactions were antagonistic

    these are just pairs of beneficial mutations…and such poor results…

  36. DrREC, if you honestly think that this variation (which is questionable as to its ‘randomness),,,

    “An interesting variation on this pattern is reported in Chapter 5 by Lin and Wu (1984). Mutants of E. coli and S. typhimurium (S. enterica var Typhimurium) gain the ability to metabolize the unusual substrate d-arabinose by altering the specificity of a regulatory protein. …because the protein has apparently gained an additional binding site for the novel substrate, the mutation is classed as gain-of-FCT.”

    (put more simply- alteration or ‘alternative splicing’ of a preexisting protein which allows the digestion of a ‘simple sugar’),

    ,,, DrREC if you think this actually added functional complexity/information over and above what was already present in the e-coli,,,, then in order to validate your claim that this is the type of proof that you need in order to make your case for neo-Darwinian evolution, then what you are claiming is happening should look something like this:

    ,,,parent e-coli plus evolved ability to digest a novel ‘simple sugar’ is greater than the ability that was originally present in parent e-coli alone,,,

    Is this or is this not what you are claiming for neo-Darwinian abilities???

    If you agree that you are claiming that simple should ‘evolve’ into more complex, then DrREC, why is it whenever we test any of these ‘beneficial adaptations’, that should read parent strain plus evolved ability is greater than parent strain alone, according to your neo-Darwinian reasoning, why do we find, after literally millions upon millions of tests, that parent strain plus evolved ability is LESS THAN parent strain alone???,,, thus completely contradicting neo-Darwinian reasoning!!!

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    http://www.answersingenesis.or.....-drugstore

    Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
    Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
    http://www.evolutionnews.org/2.....s_wro.html

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    http://www.trueorigin.org/bacteria01.asp

    further note as to the severe limit of neo-Darwinian processes ever generating protein-protein binding sites;

    A review of The Edge of Evolution: The Search for the Limits of Darwinism
    The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
    http://creation.com/review-mic.....-evolution

    Dr. Behe states in The Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....est_s.html

    An Atheist Interviews Michael Behe About “The Edge Of Evolution” – video
    http://www.in.com/videos/watch.....34623.html

    Thus, the actual rate for ‘truly’ beneficial mutations, which would account for the staggering machine-like complexity we see in life, is far in excess of one-hundred-billion-billion mutational events. So this one in a thousand, to one in a million, number for ‘truly’ beneficial mutations is actually far, far, too generous for an estimate for evolutionists to use as an estimate for beneficial mutations.

    In fact, from consistent findings such as these, it is increasingly apparent the principle of Genetic Entropy is the overriding foundational rule for all of biology, with no exceptions at all, and belief in ‘truly’ beneficial mutations is nothing more than wishful speculation on the materialist part which has no foundation in empirical science whatsoever.

    Evolution vs. Genetic Entropy – video
    http://www.metacafe.com/watch/4028086

    The foundational rule for explaining the diversification of all life on earth, of Genetic Entropy, a rule which draws its foundation in science from the twin pillars of the Second Law of Thermodynamics and from the Law of Conservation of Information (Dembski, Marks, Abel), can be stated something like this:

    “All beneficial adaptations away from a parent species for a sub-species, which increase fitness to a particular environment, will always come at a loss of the optimal functional information that was originally created in the parent species genome.”

  37. The original papers, not Science Daily are the authority on this. The wording and context in them is 100% unambiguous.

    oh please…this is a direct quote from cooper.

    the transcriber missed it

    again its not transcribed…its a direct quote from cooper himself.

  38. “These results point us toward expecting to see the rate of a population’s fitness declining over time even with the continual addition of new beneficial mutations,” he said. “As we sometimes see in sports, a group of individual stars doesn’t necessarily make a great team.”

    notice the quotes…and HE SAID…

  39. of course Cooper’s statement of the fitness declining over time fits in well with the following from the article I posted earlier…

    Threshold robustness is inherently epistatic— once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.

  40. DrRec wrote:

    “No kidding, animals living on land have lost the ability to breathe underwater, too”

    Soooo….if a pop of bacteria keeps losing functional elements the”ll gain the ability to walk like us?

  41. tsmith-are you just dispensing with the words “the rate of”? How can you conclude fitness is decreasing given the context of the news article, and the original publications?

    Maybe you can’t get the publications free, but at least read the abstracts, or at the very least, the quotes I’ve provided you!

  42. DrREC, falsely states:

    ‘It is perhaps ambiguous, but if you are interpreting that overall fitness is declining, you are wrong.’

    Slowly but surely Lenski’s ‘cuddled’ e-coli, which Lenski dare not let compete with wild parent strain for they would be eliminated, are getting less and less fit than the parent strain.

    Even more crushing evidence can be gleaned from Lenski’s long term evolution experiment on E-coli. Upon even closer inspection, it seems Lenski’s ‘cuddled’ E. coli are actually headed for genetic meltdown instead of evolving into something, anything, better.

    New Work by Richard Lenski:
    Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal.
    http://www.evolutionnews.org/2.....enski.html

  43. are you just dispensing with the words “the rate of”? How can you conclude fitness is decreasing given the context of the news article, and the original publications?

    apparently Dr. Cooper the author of those papers is too…

  44. “(put more simply- alteration or ‘alternative splicing’ of a preexisting protein which allows the digestion of a ‘simple sugar’),”

    Bacteria are incapable of alternative splicing. Behe doesn’t see a ‘modification’, he sees a novel binding site.

    “,,, DrREC if you think this actually added functional complexity/information over and above what was already present in the e-coli,,,, ”

    That is Dr. Behe’s conclusion. He calls it a gain-of-fct
    I agree with him.

    ” that should read parent strain plus evolved ability is greater than parent strain alone, ”

    In all cases, Behe is discussing gain-of-phenotype, where the parental has either no or very little function that is evolved by the progenitor.

    “Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video”

    Again, fitness refers to fitness in the environment of selection. You are not naturally fit underwater. Fish are not fit on land. These are not arguments against evolution.

    Some antibiotic resistant bacteria show no fitness cost in the absence of antibiotic.

    “we demonstrate that prolonged patient treatment can result in multidrug-resistant strains with no fitness defect and that strains with low- or no-cost resistance mutations are also the most frequent among clinical isolates.”

    http://www.sciencemag.org/cont...../1944.full

    So I’ve passed your test. Happy?

  45. Science daily is not the scientific literature.

    From the Science papers:

    “These data support models in which negative epistasis contributes to declining rates of adaptation over time. ”

    “diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation.”

    declining rates of adaptation
    decelerating fitness gains

  46. DrRec wrote:

    “Again, fitness refers to fitness in the environment of selection. You are not naturally fit underwater. Fish are not fit on land. These are not arguments against evolution.”

    Wouldn’t we expect to find a really weak bacteria instead?

  47. Science daily is not the scientific literature.

    who cares? do you not understand a direct quote???

  48. diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation

    and my previous answer to that was:

    the question still stands…ever hear of Haldane’s dilemma?

    It takes a great many mutations to produce sight, for example, (although no one has any clue how many or what mutations produced sight) and with the rarity of beneficial mutations to begin with, coupled with the negative epistatic effect, how does anything evolve?

  49. DrREC you state:

    ‘So I’ve passed your test. Happy?’

    Actually no you haven’t passed the test; When the sensitivity of the test is cranked up, genetic entropy holds!!!

    Testing the Biological Fitness of Antibiotic Resistant Bacteria – 2008
    Initially, it was difficult to demonstrate differences between wild-type and clinical strains in a rich media (Nutrient or Typticase-soy agar). There were no differences in growth rate or colony size. However, after switching to minimal media and observing hourly, the differences were readily observed.
    http://www.answersingenesis.or.....-drugstore

    Also of interest DrREC, is that this ‘law of diminishing returns with beneficial mutations due to negative epistasis’ of Lenski’s, is exactly the ‘diminishing returns’ we expect from a poly-functional constraint perspective!!!

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

    “Whatever we may try to do within a given species, we soon reach limits which we cannot break through. A wall exists on every side of each species. That wall is the DNA coding, which permits wide variety within it (within the gene pool, or the genotype of a species)-but no exit through that wall. Darwin’s gradualism is bounded by internal constraints, beyond which selection is useless.”
    R. Milner, Encyclopedia of Evolution (1990)

    Simplest Microbes More Complex than Thought – Dec. 2009
    Excerpt: PhysOrg reported that a species of Mycoplasma,, “The bacteria appeared to be assembled in a far more complex way than had been thought.” Many molecules were found to have multiple functions: for instance, some enzymes could catalyze unrelated reactions, and some proteins were involved in multiple protein complexes.”
    http://www.creationsafaris.com.....#20091229a

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

  50. tsmith,

    This is getting silly. The context of the science daily article-referring to beneficial mutations and fitness increases over ancestral populations should be enough to indicate your interpretation is flawed.

    You’ve also been presented with direct quotes of the science paper by the same author.

    Persisting in hanging on to your interpretation of this quote, which itself doesn’t particularly make sense, is silly.

  51. and then we have Nachman’s U paradox…

    Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common.

    http://www.genetics.org/content/156/1/297.full

    which sanford refers to.

    To evolve the population, one needs to add new mutations and either fix some mutations and remove (purify away) others. Haldane’s dilemma deals with the difficulty of fixation. Nachman U-Paradox problem deals with the difficulty of purification. Even if the mutations were neutral, Nachman’s paper still poses the problem of how to purify away neutral mutations such that the genomes between each member of the species remains relatively similar (humans are about 99.5% similar to each other).

    http://www.uncommondescent.com.....u-paradox/

  52. 52
    Elizabeth Liddle

    tsmith: Cooper could well have said what is reported, or it could have been mistranscribed.

    Either way, it doesn’t actually make sense. “Fitness” is a scalar quantity, it doesn’t have a “rate”. As reported, it’s the equivalent of saying “the rate of height declined”.

    So there must be a missing word.

    Somebody made an error, possibly Cooper. It happens, especially in oral interviews.

    But as it stands it doesn’t actually mean anything at all. It has a deleterious mutation!

    Fortunately we can infer the missing word from the context, and check it against the paper itself.

  53. DrREC,, I find it extremely strange that you are so enamored to make a case that this is proof of neo-Darwinian evolution, when clearly all evidence, that is all evidence that is not tortured by your severe prejudice, points to deterioration as well as to limits of the e-coli genome!!! It is only by severe disregard of reason that you can maintain any of this evidence supports your position. ,,,, But my question is of a more personal nature DrREC, exactly what would you lose if you accepted the truth that neo-Darwinism was false??? Would finding that life actually has a purpose be such a terrible thing to find out to be true??? Why do you fight so hard against such a wonderful truth???

  54. This is getting silly. The context of the science daily article-referring to beneficial mutations and fitness increases over ancestral populations should be enough to indicate your interpretation is flawed

    yes you are being silly…this is NOT *my interpretation* this is a quote from COPPER HIMSELF….how hard is this?

  55. Fortunately we can infer the missing word from the context, and check it against the paper itself.

    thats a huge assumption…with really nothing to support it. do you think Cooper himself read that article in science daily? bet he did…and he could have easily corrected it.

  56. Is that what fitness is? So if I am bedridden with illness am I more fit in an environment with a lot of car accidents?

  57. I also see other paradox tsmith http://www.benthamscience.com/.....OEVOLJ.pdf

  58. Moreover, DrREC and Elizabeth, please do tell (weave a tale) of this ‘anomaly’:

    Static evolution: is pond scum the same now as billions of years ago?
    Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial microbial. “They surprisingly looked exactly like modern species,” Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. “This similarity in morphology is widespread among fossils of [varying] times,” says Schopf. As evidence, he cites the 3,000 such fossils found;
    http://www.thefreelibrary.com/.....a014909330

    Now DrREC and Elizabeth, that is pretty bad in itself for neo-Darwinism, but check this out:

    The Paradox of the “Ancient” (250 million year old) Bacterium Which Contains “Modern” Protein-Coding Genes:
    “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ;
    http://mbe.oxfordjournals.org/...../19/9/1637

    These following studies, by Dr. Cano on ancient bacteria, preceded Dr. Vreeland’s work:

    “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.”
    http://www.physicsforums.com/s.....p?t=281961

    In reply to a personal e-mail from myself, Dr. Cano commented on the ‘Fitness Test’ I had asked him about:
    Dr. Cano stated: “We performed such a test, a long time ago, using a panel of substrates (the old gram positive biolog panel) on B. sphaericus. From the results we surmised that the putative “ancient” B. sphaericus isolate was capable of utilizing a broader scope of substrates. Additionally, we looked at the fatty acid profile and here, again, the profiles were similar but more diverse in the amber isolate.”:
    Fitness test which compared ancient bacteria to its modern day descendants, RJ Cano and MK Borucki

    Thus, the most solid evidence available for the most ancient DNA scientists are able to find does not support evolution happening on the molecular level of bacteria. In fact, according to the fitness test of Dr. Cano, the change witnessed in bacteria conforms to the exact opposite, Genetic Entropy; a loss of functional information/complexity, since fewer substrates and fatty acids are utilized by the modern strains. Considering the intricate level of protein machinery it takes to utilize individual molecules within a substrate, we are talking an impressive loss of protein complexity, and thus loss of functional information, from the ancient amber sealed bacteria. Here is a revisit to the video of the ‘Fitness Test’ that evolutionary processes have NEVER passed as for a demonstration of the generation of functional complexity/information above what was already present in a parent species bacteria:

    Is Antibiotic Resistance evidence for evolution? – ‘Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    According to prevailing evolutionary dogma, there ‘HAS’ to be ‘major genetic drift’ to the DNA of modern bacteria from 250 million years ago, even though the morphology (shape) of the bacteria can be expected to remain exactly the same. In spite of their preconceived materialistic bias, scientists find there is no significant genetic drift from the ancient DNA. In fact recent research, with bacteria which are alive right now, has also severely weakened the ‘genetic drift’ argument of evolutionists:

    The consequences of genetic drift for bacterial genome complexity – Howard Ochman – 2009
    Excerpt: The increased availability of sequenced bacterial genomes allows application of an alternative estimator of drift, the genome-wide ratio of replacement to silent substitutions in protein-coding sequences. This ratio, which reflects the action of purifying selection across the entire genome, shows a strong inverse relationship with genome size, indicating that drift promotes genome reduction in bacteria.
    http://genome.cshlp.org/conten.....091785.109

    I find it interesting that the materialistic theory of evolution expects there to be a significant amount of genetic drift from the DNA of ancient bacteria to its modern descendants, while the morphology can be allowed to remain exactly the same with its descendants. Alas for the materialist once again, the hard evidence of ancient DNA has fell in line with the anthropic hypothesis.

    Many times a materialist will offer what he considers conclusive proof for evolution by showing bacteria that have become resistant to a certain antibiotic such as penicillin. Yet upon close inspection, once again this ‘conclusive proof’ dissolves away. All observed instances of ‘beneficial’ adaptations of bacteria to new antibiotics have been shown to be the result of degradation of preexisting molecular abilities:

    List Of Degraded Molecular Abilities Of Antibiotic Resistant Bacteria:
    http://www.trueorigin.org/bacteria01.asp

    The following is a reflection on the true implications of the ‘evolution’ of bacteria becoming resistant to multiple antibiotics that has so many people concerned as to their danger:

    Superbugs not super after all
    Excerpt: It is precisely because the mutations which give rise to resistance are in some form or another defects, that so-called supergerms are not really ‘super’ at all—they are actually rather ‘wimpy’ compared to their close cousins.
    http://creation.com/superbugs-not-super-after-all

    MRSA – Supergerms Do they prove evolution?
    In places that are exposed to dirt from the street—such as your house—the supergerms are kept in their place not by powerful drugs and poisons but by competition with other germs. And their resistance genes are diluted by genes of the susceptible or non-resistant germs of the same species rather than being concentrated by selective breeding. That is why most non-hospital infections respond readily to antibiotics—the drug kills most of the germs, the body takes care of the rest. If it were not so, the so called supergerms would escape from hospitals and sweep the world.

    Are You Too Clean? – New Studies Suggest Getting A Little Dirty May Be Just What The Doctor Ordered – December 2010
    http://www.creationsafaris.com.....#20101208a

    For materialists to conclusively prove evolution they would have to violate the principle of Genetic Entropy by clearly demonstrating a gain of functional information bits (Fits) over the parent species (Abel – Null-Hypothesis) in the fitness test which I’ve listed previously. Materialists have not done so, nor will they ever. The interrelated complexity for the integrated whole of a life-form simply will not allow the generation of complex functional information above the parent species to happen in its genome by chance alone. (Sanford, Genetic Entropy 2005)

    This following site highlights the problem that the integrated complexity of a genome presents for Neo-Darwinism mechanism of random mutation:

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

    This following quote reiterates the principle that material processes cannot generate functional information:

    “There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology) His challenge to scientifically falsify this statement has remained unanswered since first published.

  59. 59
    Elizabeth Liddle

    Well, Science Daily is off the hook – the mistake is in the press release as well:

    http://www.uh.edu/news-events/.....stasis.php

    However,the second abstract makes it crystal clear:

    These results provide the first evidence that patterns of epistasis may differ for within- and between-gene interactions during adaptation and that diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation.

    So it is that the rate of fitness increase that is declining, not fitness itself. It reaches a ceiling, in other words. From the body of the paper (to which I am fortunate enough to have access):

    A conspicuous feature of the mean-fitness trajectory for this population—and indeed for most experimental populations evolving in a constant environment—is that the rate of adaptation declined over time. Mechanisms that may explain this deceleration include reductions in the number and effect-size of beneficial mutations as a population becomes better adapted to its environment.

  60. In response to a query from BA77, I present a paper where antibiotic resistant bacteria show no decrease in fitness over non-resistant strains. This should pass his fitness test.

    He presents a creationist article. It has a nice warning for him:

    “Creation biologists should be careful about making dogmatic statements like, “Wild-type bacteria always outcompete antibiotic resistant mutants in nature.”

    That made my day.
    LOL. Read the articles first.

    Context:

    “Our experience with competition studies reveals that demonstrating fitness costs in the laboratory is tricky and creation biologists should be careful about making dogmatic statements like, “Wild-type bacteria always outcompete antibiotic resistant mutants in nature.” Some bacteria that have an antibiotic resistance gene integrated into their chromosome can make compensatory mutations, over multiple, successive generations. These resistant bacteria compete favorably with wild-type bacteria in nature given certain environmental conditions (Criswell, 2004; 2007, personal communication).”

    There are many cases where antibiotic gain of resistance is without fitness cost, or that cost has been compensated for.

  61. “integrated into their chromosome can make compensatory mutations, over multiple, successive generations”

    Hmmm seems like backup system with original information there. Can we use that to see what original organism is like?

  62. 62
    Elizabeth Liddle

    tsmith:

    Fortunately we can infer the missing word from the context, and check it against the paper itself.

    thats a huge assumption…with really nothing to support it. do you think Cooper himself read that article in science daily? bet he did…and he could have easily corrected it.

    Well, no, it’s not a huge assumption. The sentence doesn’t actually make sense as it stands, so there’s definitely a mistake. So candidate errors are, as you suggest, that the words “the rate of” are extraneous, or, alternatively that the word “increase” is missing.

    And to know which we simply need to turn to the abstract of the paper, or indeed, as I was able to do, to the paper itself, which says, unambiguously, that it was the rate of increase in fitness that declined, not fitness.

    And if Tom Cooper read the press release, he probably didn’t notice the error. Not sure I would have done :)

    And it’s not as though it matters, because it’s clear in the papers.

    They found several beneficial mutations (i.e. mutations that increased fitness) but that as they accumulated, there were “diminishing returns”, i.e. 5 beneficial mutations weren’t 5 times as good as one. This makes sense. Either a lifebelt or a life jacket can make the difference between life or death, but once you’ve got one, the other doesn’t make a huge deal of difference to your survival chances :)

    Although, interestingly, one of the mutations was neutral in the ancestral population, but beneficial in combination with the other mutations – suggesting that unlike the lifebelt/lifejacket scenario, this mutation was like the whistle you get to attract attention – not much good if you are sinking because you have neither lifebelt nor lifejacket, but a lot of use if you have at least one of those latter two :)

    Hope this clears things up.

    Cheers

    Lizzie

  63. “There is no known law of nature, no known process and no known sequence of events which can cause information to originate by itself in matter.” Werner Gitt, “In the Beginning was Information”, 1997, p. 106. (Dr. Gitt was the Director at the German Federal Institute of Physics and Technology) His challenge to scientifically falsify this statement has remained unanswered since first published.

    I read his work a few years ago and I’m not surprised by this – Gitt defines information as having to have a ‘mental source’ so he is creating his own definition for the word information that explicitly requires it to have a non material source.

    If I define ‘information’ as something that requires a non-material (mental) source” then by definition it cannot be of material origin.

    What if I define ‘airplane’ as ‘a machine incapable of flight’ and then say “There is no known law of nature, no known process and no known sequence of events which can cause airplanes to fly.

  64. DrREC, please do quote the rest of the article DrREC:

    but as to the part you quoted:

    Some bacteria that have an antibiotic resistance gene integrated into their chromosome can make compensatory mutations, over multiple, successive generations. These resistant bacteria compete favorably with wild-type bacteria in nature given certain environmental conditions,

    Thus DrREC, due to ‘compensatory mutations’ bringing the bacteria up to par, (which I hold is negligible due to ‘sensitivity of test) this is ‘PASSING” the fitness test for you???? EXCUSE me DrREC, but your claim is that parent strain plus evolved ability is MORE FIT than the parent strain alone. You MUST DEMONSTRATE a gain in fitness. But Alas DrREC, billion year bacteria that looks the same as bacteria of today are no problem to you because??? because??? well because by-golly you have decided to believe whatever lie you must and ignore whatever truth you must so as to maintain your atheism???

  65. of note:

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

  66. DrBot;

    perhaps you would care to show material processes creating a code??? There’s a million dollars in it for you!!!

    “The Origin-of-Life Prize” ® (hereafter called “the Prize”) will be awarded for proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. The explanation must be consistent with empirical biochemical, kinetic, and thermodynamic concepts as further delineated herein, and be published in a well-respected, peer-reviewed science journal(s).
    http://www.us.net/life/index.htm

    The DNA Code – Solid Scientific Proof Of Intelligent Design – Perry Marshall – video
    http://www.metacafe.com/watch/4060532

    Moreover the first DNA code of life on earth had to be at least as complex as the current DNA code found in life:

    Shannon Information – Channel Capacity – Perry Marshall – video
    http://www.metacafe.com/watch/5457552/

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    Deciphering Design in the Genetic Code
    Excerpt: When researchers calculated the error-minimization capacity of one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution where the naturally occurring genetic code’s capacity occurred outside the distribution. Researchers estimate the existence of 10 possible genetic codes possessing the same type and degree of redundancy as the universal genetic code. All of these codes fall within the error-minimization distribution. This finding means that of the 10 possible genetic codes, few, if any, have an error-minimization capacity that approaches the code found universally in nature.
    http://www.reasons.org/biology.....netic-code

    ====================

    Codes and Axioms are always the result of mental intention, not material processes
    https://docs.google.com/document/pub?id=1PrE2Syt5SJUxeh2YBBBWrrPailC3uTFMdqPMFrzvwDY

  67. Well, no, it’s not a huge assumption. The sentence doesn’t actually make sense as it stands, so there’s definitely a mistake. So candidate errors are, as you suggest, that the words “the rate of” are extraneous, or, alternatively that the word “increase” is missing.

    it makes a great deal of sense…but apparently you don’t like to let facts get in the way of your faith in evolution.

    no it doesn’t ‘clear things up’ at all…you present what you want to believe…not what truly is…

    as those other papers I posted demonstrate.


    Threshold robustness is inherently epistatic—once the stability threshold is exhausted, the deleterious effects of mutations become fully pronounced, thereby making proteins far less robust than generally assumed.

  68. Well, Science Daily is off the hook – the mistake is in the press release as well:

    http://www.uh.edu/news-events/…..stasis.php

    uh its obviously not a mistake.

    you just can’t handle the truth.

  69. 69
    Elizabeth Liddle

    tsmith, I won’t belabour this point much more, but I am really bemused.

    First of all we have a sentence that doesn’t make logical sense (you can’t have a “rate” of “fitness” right?)

    And so we assume that either “rate” shouldn’t be there or “fitness” should be “fitness increase”.

    You decide that the first is the most likely parsing.

    However, the person quoted is actually the author of the paper, and is describing the findings.

    So we check the findings, and find, in an actual proof-read paper (not a press-release), supported by data and graphs, that it was indeed the increase in fitness that declined, not fitness.

    Moreover, this was only true of four out of the five mutations studied – in the fifth, the opposite was the case: alone, that mutation was neutral, but in combination with the others it was beneficial.

    How can you possibly continue to maintain that the quote from Tom Cooper in the press release meant that “fitness declined”? The paper says the opposite, and even the quote doesn’t say that (it says “the rate of fitness declined” which makes no sense anyway, because fitness doesn’t have a rate!)

    Seriously, it’s not I who is refusing to let facts get in the way! I’ve actually read the paper!

    And unless the authors lied in the paper, and inadvertently let slip a garbled version of the truth to the university PR person writing the press release, the facts say that fitness increase declined with successive mutations!

    And do you really think that is a more likely scenario?

    Which would you generally have most faith in – a newspaper article about something, reporting an informal oral statement that contains a logical inconsistency, or a published proof-read scholarly paper about it?

    Anyway, let’s leave it there.

    I will continue to assume that the authors meant what they report in the papers, and you can continue to assume that they meant what you think one of the authors said in a press release, but which contradicts the papers.

    Peace :)

    Lizzie

  70. Fascinating to witness the evolution of an ID paradigm.

  71. First of all we have a sentence that doesn’t make logical sense (you can’t have a “rate” of “fitness” right?)

    why not? what is your measure for fitness? if you can’t quantify it then its not science…just a tautology….if its fit, it survives…how do you know its fit? it survives.

    So we check the findings, and find, in an actual proof-read paper (not a press-release), supported by data and graphs, that it was indeed the increase in fitness that declined, not fitness.

    the author of the paper was taking his finding to their logical conclusion….which is ‘fitness’ hits a tipping point…and you get a mutational meltdown. which is genetic entropy.

    How can you possibly continue to maintain that the quote from Tom Cooper in the press release meant that “fitness declined”? The paper says the opposite, and even the quote doesn’t say that (it says “the rate of fitness declined” which makes no sense anyway, because fitness doesn’t have a rate!)

    because thats what he said…how hard is this? I find it amusing to see how far you can twist and turn to avoid what the author of that study said!

    you just prove that evolution is a matter of faith…and nothing can be said or shown to shake your faith.

  72. And unless the authors lied in the paper, and inadvertently let slip a garbled version of the truth to the university PR person writing the press release, the facts say that fitness increase declined with successive mutations!

    the facts say that the fitness keeps declining…until it crosses the line and the fitness gains become losses…this is perfectly logical…to any who are not blinded by their faith in evolution.

  73. I will give a simple analogy:

    bigger heavier people are stronger than smaller lighter people…

    thats true, up to a point…a lightweight can lift a higher percentage of their bodyweight than a superheavyweight….

    then of course you get to the point where a very heavy person cannot get out of bed…and even lift their own body…much less any additional weight.

  74. tsmith,

    Did you read the Science Daily article?

  75. no I just wrote a few words down and they happened to match exactly what dr. cooper said in that article…

    just more proof of evolution.

  76. DrREC as to this statement of yours:

    ‘He presents a creationist article.’

    Now DrREC, apparently ‘creationist article’ is suppose to make the article not as legitimate as a atheistic article,,, Yet, despite your intended slur, it would seem that since the universe is now shown to be Theistic in its foundation,,,

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007
    http://henry.pha.jhu.edu/aspect.html

    ,,,that at least you, DrREC, would be a little more sober minded as to your derogatory comments towards ‘creationists articles’. :) I don’t know about you DrREC, but as for me, the prospect that I may ultimately have to face the Creator of this universe when I die, to give an account of myself, rightly inspires reverential fear as to the thought of the proposition, and indeed makes me greatly appreciate the dire need I have for the perfect atoning sacrifice of Jesus Christ so that I may stand worthy before such unimaginable glory as must belong to the Creator of this universe!!!

    I don’t know DrREC, perhaps you feel that man has no soul and that you will not have to God when you die?!? If so, there is now strong evidence to show that you are wrong in this reasoning of yours as well:

    Quantum mind–body problem
    Parallels between quantum mechanics and mind/body dualism were first drawn by the founders of quantum mechanics including Erwin Schrödinger, Werner Heisenberg, Wolfgang Pauli, Niels Bohr, and Eugene Wigner

    The ‘Fourth Dimension’ Of Living Systems
    https://docs.google.com/document/pub?id=1Gs_qvlM8-7bFwl9rZUB9vS6SZgLH17eOZdT4UbPoy0Y

    ,,, DrREC,,,besides life having a ‘higher dimensional’ component to it, there is also now shown to be a higher ‘eternal dimension’ above this temporal material reality:

    notes:

    ….To grasp the whole ‘time coming to a complete stop at the speed of light’ concept a little more easily, imagine moving away from the face of a clock at the speed of light. Would not the hands on the clock stay stationary as you moved away from the face of the clock at the speed of light? Moving away from the face of a clock at the speed of light happens to be the same ‘thought experiment’ that gave Einstein his breakthrough insight into e=mc2.

    Albert Einstein – Special Relativity – Insight Into Eternity – video
    http://www.metacafe.com/w/6545941/

    Experimental confirmation of Time Dilation
    http://en.wikipedia.org/wiki/T.....nfirmation

    It is very interesting to note that this strange higher dimensional, eternal, framework for time, found in special relativity, finds corroboration in Near Death Experience testimonies:

    ‘In the ‘spirit world,,, instantly, there was no sense of time. See, everything on earth is related to time. You got up this morning, you are going to go to bed tonight. Something is new, it will get old. Something is born, it’s going to die. Everything on the physical plane is relative to time, but everything in the spiritual plane is relative to eternity. Instantly I was in total consciousness and awareness of eternity, and you and I as we live in this earth cannot even comprehend it, because everything that we have here is filled within the veil of the temporal life. In the spirit life that is more real than anything else and it is awesome. Eternity as a concept is awesome. There is no such thing as time. I knew that whatever happened was going to go on and on.’
    Mickey Robinson – Near Death Experience testimony

    ‘When you die, you enter eternity. It feels like you were always there, and you will always be there. You realize that existence on Earth is only just a brief instant.’
    Dr. Ken Ring – has extensively studied Near Death Experiences

    It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in very many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as an observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences:

    Traveling At The Speed Of Light – Optical Effects – video
    http://www.metacafe.com/watch/5733303/

    The NDE and the Tunnel – Kevin Williams’ research conclusions
    Excerpt: I started to move toward the light. The way I moved, the physics, was completely different than it is here on Earth. It was something I had never felt before and never felt since. It was a whole different sensation of motion. I obviously wasn’t walking or skipping or crawling. I was not floating. I was flowing. I was flowing toward the light. I was accelerating and I knew I was accelerating, but then again, I didn’t really feel the acceleration. I just knew I was accelerating toward the light. Again, the physics was different – the physics of motion of time, space, travel. It was completely different in that tunnel, than it is here on Earth. I came out into the light and when I came out into the light, I realized that I was in heaven.(Barbara Springer)

    Near Death Experience – The Tunnel, The Light, The Life Review – video
    http://www.metacafe.com/watch/4200200/

    ,,, DrREC, I’ve seen you go to extraordinary extremes to deny the overwhelming evidence of design in life, but I would hope in this instance that you at least pause, and know that God REALLY DID create this universe and all life in it, and then soberly consider what MAY be truly unimaginable consequences for you in denying God and choosing to be separate from Him in your thoughts.

  77. So what did the article say about the fitness of the bacterial population?

  78. 78
    Elizabeth Liddle

    tsmith:

    OK, thanks for the more detailed response:

    First of all we have a sentence that doesn’t make logical sense (you can’t have a “rate” of “fitness” right?)

    why not? what is your measure for fitness? if you can’t quantify it then its not science…just a tautology….if its fit, it survives…how do you know its fit? it survives.

    Yes, you can quantify it, and the math is in the paper. But you are right, “fitness” in population genetics is a measure of breeding (rather than survival) probability. “Increase in fitness” means, by definition, that “the probability of breeding is increased”. And empirically, it is measured by the change in frequency of the allele in question. If the frequency increases, then the allele is deemed beneficial; if it decreases, then it is deemed “deleterious”. You can also directly measure it by breeding rate, compared with the ancestral population.

    So we check the findings, and find, in an actual proof-read paper (not a press-release), supported by data and graphs, that it was indeed the increase in fitness that declined, not fitness.

    the author of the paper was taking his finding to their logical conclusion….which is ‘fitness’ hits a tipping point…and you get a mutational meltdown. which is genetic entropy.

    Well, no, that is not what the paper reports. What the paper reports (at least the second one, Khan et al, I haven’t read the other) is five mutations, each of which increased in frequency (indeed went to “fixation” in their respective populations, i.e. propagated through the entire population), hence were deemed beneficial. Then they transferred each mutation into clones of the ancestral population in all possible combinations, and compared the fitness of each new population (32 populations, i.e. 2^5) Of the five, one was not beneficial (did not increase in frequency) unless it was accompanied by the others. Of the rest, being in company with the others did not confer much additional fitness.

    So their conclusion was that five times a good thing isn’t five times better than one thing, only a little better, except in one case where one mutation only conferred a benefit when in combination with the others.

    I’m summarising – there are more details about each mutation. But they do not report “genetic meltdown” – indeed the populations with all five mutations were fitter than the populations without any, just not hugely better than those with three or four. And it’s probably worth pointing out that these five mutations were artificially transferred to clones of the ancestral population – this was not a case of natural “mutational build up”. Indeed, the mutations were transferred into clones of the ancestral “originals”.

    How can you possibly continue to maintain that the quote from Tom Cooper in the press release meant that “fitness declined”? The paper says the opposite, and even the quote doesn’t say that (it says “the rate of fitness declined” which makes no sense anyway, because fitness doesn’t have a rate!)

    because thats what he said…how hard is this? I find it amusing to see how far you can twist and turn to avoid what the author of that study said!

    I’m going by what the author of the study said in the paper!

    you just prove that evolution is a matter of faith…and nothing can be said or shown to shake your faith.

    Ah well.

  79. why don’t you tell me, since only you know the secret code and can decipher what he really said…not what was actually reported, which we all know is part of the *conspiracy*

  80. And empirically, it is measured by the change in frequency of the allele in question. If the frequency increases, then the allele is deemed beneficial; if it decreases, then it is deemed “deleterious”

    so in other words its a tautology…it its fit it survives…how do we know its fit? it survives.

    Well, no, that is not what the paper reports.

    now you’re telling me the author is lying…either in the paper, or in the press release or the science daily article….

    please.

    I’m summarising – there are more details about each mutation. But they do not report “genetic meltdown” – indeed the populations with all five mutations were fitter than the populations without any, just not hugely better than those with three or four

    so why not with 8 or 10, the rate would tip from being beneficial to harmful?

    that is what the author is saying in that quote.

  81. 81
    Elizabeth Liddle

    It’s not that I “know the secret code” tsmith, it’s because I read the abstracts (which are open access) and also one of the papers (which unfortunately isn’t).

    driver:

    So what did the article say about the fitness of the bacterial population?

    There are two sets of populations: a set of five, bred from a single ancestral population, members of which were frozen IIRC for later use. In each of those five, a different beneficial mutation appeared.

    Then, the authors transferred each of those five mutations, in all combinations, into clones of the frozen ancestral population, giving them a second set of 32 populations, each with a different combination of the five mutations.

    And they compared the fitness of those 32 populations. All were fitter than the ancestral population (bred better) but those with all five mutations were not five times fitter than those with only one.

  82. Why don’t you tell me

    “Cooper and his team focused on a bacterial population that had been evolved for thousands of generations such that its fitness had increased by approximately 35 percent over its ancestor.”

    only you know the secret code and can decipher what he really said

    If he’s not too busy to reply, that’s true, since I just emailed him. :-)

  83. here’s the quote again..


    It was found that the beneficial mutations allowing the bacteria to increase in fitness didn’t have a constant effect. The effect of their interactions depended on the presence of other mutations, which turned out to be overwhelmingly negative.

    “These results point us toward expecting to see the rate of a population’s fitness declining over time even with the continual addition of new beneficial mutations,” he said. “As we sometimes see in sports, a group of individual stars doesn’t necessarily make a great team.”

  84. It’s not that I “know the secret code” tsmith, it’s because I read the abstracts (which are open access) and also one of the papers (which unfortunately isn’t).

    I wasn’t talking to you with that..but replying to the snotty post by driver.

  85. thousands of generations such that its fitness had increased by approximately 35 percent over its ancestor.”

    35 percent…in thousands of generations…back to my previous observation which has been studiously ignored by darwinists…

    the question still stands…ever hear of Haldane’s dilemma?

    It takes a great many mutations to produce sight, for example, (although no one has any clue how many or what mutations produced sight) and with the rarity of beneficial mutations to begin with, coupled with the negative epistatic effect, how does anything evolve?

  86. If he’s not too busy to reply, that’s true, since I just emailed him

    thats nice…I doubt he cares about some people arguing on a message board….did you ask him if he was quoted correctly?

    if not, what did you email him about?

  87. 87
    Elizabeth Liddle

    Well, tsmith, either the author is wrong in the press release (I wouldn’t assume lying), or wrong in the paper (again, I wouldn’t assume lying). He can’t be right in both.

    So I’m assuming he’s right in the paper, seeing as he has several coauthors to check, and actually makes logical sense, which he doesn’t in the press release.

    As for your point about tautology – it’s fair one, as this is always a problem in discussing evolutionary theory, because it does sound tautological. It isn’t though, it’s just so simple that it sounds that way. Darwin’s theory can be summed up by something like:

    When things replicate with variance, things that replicate better will be replicated more often.

    It’s so obviously true, it’s almost not worth saying!

    But that’s really all it is. And it does have powerful implications.

    So “fitter” simply means “replicates better” – but it’s not a static quantity. It depends on the environment. A trait that can make you fitter (breed better) in a cold climate (fur, for instance) can make you breed worse if the climate warms up.

    But keeping the environment constant, as Lenski’s team did, mutations that promote breeding will result in faster breeding, and this can be measured.

    And that’s all that “fitness” means in a Darwinian sense, unfortunately. We may enjoy traits that enhance the kick we get out of life, but unless they also improve our chances of passing those traits to our offspring, they don’t make us “fitter” in an evolutionary sense. And won’t therefore be preferentially passed on.

  88. Thanks for the explanation of the paper, Elizabeth.

  89. I emailed him to let him know that his paper was being used to support the theory of genetic entropy. I thought he might be amused. I also asked him if his quote supported the theory of genetic entropy.

  90. 90
    Elizabeth Liddle

    I wasn’t talking to you with that..but replying to the snotty post by driver.

    OK, no problem :)

  91. Well, tsmith, either the author is wrong in the press release (I wouldn’t assume lying), or wrong in the paper (again, I wouldn’t assume lying). He can’t be right in both.

    I think he can..he only presents his findings in the paper…and then his quote is the logical result of those findings…

    he’s not lying..he’s not misquoted…he’s just taking the results to their logical conclusion.

    you are SO threatened by that statement you just have to dismiss it. which indicates that your belief in evolution has crossed the line to faith.

    it’s fair one, as this is always a problem in discussing evolutionary theory, because it does sound tautological. It isn’t though, it’s just so simple that it sounds that way. Darwin’s theory can be summed up by something like:

    usually things sound or appear the way they really are.

    the whole ‘survival of the fittest’ is a tautology. your posts are proving that evolution is a faith.

    When things replicate with variance, things that replicate better will be replicated more often.

    yeah so…a creationist would say the same thing. the only difference is evolutionists think evolution can create new forms and functions…did you notice with this experiment with all the thousands of generations…and lenski’s experiment with his 20,000 or so generations…and its still a bacteria? or a recent study about fruit flies…with 600 generations…

    Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.

    Burke, Dunham et al, “Genome-wide analysis of a long-term evolution experiment with Drosophila,” Nature 467, 587-590 (30 September 2010); doi:10.1038/nature09352.

  92. I emailed him to let him know that his paper was being used to support the theory of genetic entropy. I thought he might be amused. I also asked him if his quote supported the theory of genetic entropy.

    oh good…did you remind him of the consequences to his career if he dares goes against the high priests of darwinism?

  93. I also asked him if his quote supported the theory of genetic entropy.

    oh and the quote obviously does….but don’t worry, you won’t let anything get in the way of your faith in the racist eugenicist theory of evolution….

  94. 94
    Elizabeth Liddle

    BTW, just a technicality:

    A “positive” interaction means that one factor enhances the other.

    A “negative” interaction” means that one factor tends to cancel out the effect of the other. An “overwhelmingly negative interaction” doesn’t mean that the effect on fitness was negative, it means that the interaction between the two meant they tended to cancel each other out, meaning that both isn’t much better, if at all, than only one. It could mean that both is worse than one (for instance two drugs that help you could interact negatively if used together and make you iller), but the paper says not.

    And you can’t extrapolate that to predict that even more will be worse than one. It’s more like there being a ceiling beyond which you can’t go, no matter how much you continue to gild the lily.

  95. It’s more like there being a ceiling beyond which you can’t go, no matter how much you continue to gild the lily.

    bingo. thats the crux of the debate…things only ‘evolve’ so far. then they hit the wall.

    I hope you’re not professionally employed in the field of biology….that quote may cost you your job….

  96. Of course, what really matters is the scientific paper, not his quote, but if he replies to my email then we’ll know what he meant for sure.

    the racist eugenicist theory of evolution

    It’s very post-modern to posit that scientific theories present political opinions.

  97. Well let’s see,,,

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution
    Excerpt: The research paper published out of the Cooper lab (with Richard Lenski as a co-author), by Khan et al., is titled “Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population.” It found that “Epistasis depended on the effects of the combined mutations–the larger the expected benefit, the more negative the epistatic effect. Epistasis thus tended to produce diminishing returns with genotype fitness, although interactions involving one particular mutation had the opposite effect. These data support models in which negative epistasis contributes to declining rates of adaptation over time.”

    The other paper from the Marx lab, by Chou et al., is titled “Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation.” The article’s abstract likewise explains that: “patterns of epistasis may differ for within- and between-gene interactions during adaptation and that diminishing returns epistasis contributes to the consistent observation of decelerating fitness gains during adaptation.”

    The title of a summary piece in Science tells the whole story: “In Evolution, the Sum Is Less than Its Parts.” It notes that these studies encountered “antagonistic epistasis,” where negative effects arise from epistatic interactions:

    Both studies found a predominance of antagonistic epistasis, which impeded the rate of ongoing adaptation relative to a null model of independent mutational effects.

    In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

    Thus, Elizabeth and DrREC, this inability of ‘beneficial mutations’ to add to one another, indeed their propensity to severely interfere with each other, supports your atheistic delusions of neo-Darwinism how???

    Whereas, ID readily expects this limit to ‘evolvability’ with poly-functional constraint!!

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

  98. Of course, what really matters is the scientific paper, not his quote, but if he replies to my email then we’ll know what he meant for sure.

    oh of course…we can’t rely on our lying eyes now can we? just keep repeating ‘it evolved’ ‘it evolved’ ‘it evolved’

    It’s very post-modern to posit that scientific theories present political opinions.

    oh I knew you’d say something so ‘chic’

    tell ya what…why don’t you list for me the ‘lower races’ your savior refers to:

    “The more civilized so-called Caucasian races have beaten the Turkish hollow in the struggle for existence. Looking to the world at no very distant date, what an endless number of the lower races will have been eliminated by the higher civilised races throughout the world.” (Darwin, Charles R. [English naturalist and founder of the modern theory of evolution], “The Life of Charles Darwin”, [1902], Senate: London, 1995, reprint, p.64).

    now go ahead and accuse of quote mining…I can always use a few laughs…

  99. 99

    Liz, I recommend retracting this:

    “It’s more like there being a ceiling beyond which you can’t go, no matter how much you continue to gild the lily.”

    Or you will end up being interviewed by Ben Stein shortly.

  100. , but if he replies to my email then we’ll know what he meant for sure.

    and OF COURSE we will rely upon the word of an anonymous internet poster to tell us what the good dr. said…

    hey I have a large some of money that needs to be moved out of africa, can you help me?

  101. Elizabeth this quote gives me hope for you yet;

    ‘It’s more like there being a ceiling beyond which you can’t go, no matter how much you continue to gild the lily.’

    :) In fact, you can’t go up past the ‘ceiling’ of fitness already present in parent strain!,,, and As DrREC pointed out previously, the best Darwinists have done so far is demonstrate ‘comparable fitness’ to parent strain after ‘several rounds’ of compensatory mutations (Though I hold sensitivity can be tweaked to show decline even in that instance):

  102. 102
    Elizabeth Liddle

    Well, we got sidetracked about what the paper was actually reporting, but now I think (I hope!) that is clear, yes, ba77, you are right, negative epistasis of beneficial mutations is a potential “drag” on adaptation, as the authors make clear (although it is mutation-pair specific – in one case, epistasis was positive).

    However, it works the other way as well – negative epistasis of deleterious mutations is one of the reason “genetic entropy” isn’t as disastrous as simple calculations would suggest.

  103. 103
    Elizabeth Liddle

    Ah, ba77 I do find your concern touching, seriously :)

    Bless you.

    But I still disagree :)

  104. Elizabeth…I was the first one to show concern…especially if you are beautiful and rich…

    if not, nevermind…LOL

  105. Darwin’s Victorian political opinions are irrelevant to the science of evolution. Einstein was a pacifist, but that doesn’t make the theory of relativity more friendly.

    Scientific theories are attempts to explain facts about the world. If I have a theory that my cat knocked over my drink to explain the fact that my tea is on the floor, it really doesn’t matter what I think of cats. Either it’s true that the cat knocked over my drink or it isn’t.

    As for the email, I am not going to gain any money from making up email replies. I wouldn’t be surprised if Dr Cooper doesn’t reply to me, but you are free to email him yourself. It’s irrelevant though really – what matters is what the paper says.

  106. Darwin’s Victorian political opinions are irrelevant to the science of evolution.

    Darwin’s views are driven by his theory of evolution…just like Waton’s views are….

    Watson is credited with discovering the double helix along with Maurice Wilkins and Francis Crick in 1962.
    In the newspaper interview, he said there was no reason to think that races which had grown up in separate geographical locations should have evolved identically. He went on to say that although he hoped everyone was equal, “people who have to deal with black employees find this not true”.

    even Gould admitted the truth, why can’t you?

    “Biological arguments for racism may have been common before 1859, but they increased by orders of magnitude following the acceptance of evolutionary theory.” Stephen Jay Gould,

    Stephen Jay Gould, Ontogeny and Phylogeny (Cambridge, Mass: Harvard University Press, 1977), p. 127.

    As for the email, I am not going to gain any money from making up email replies. I wouldn’t be surprised if Dr Cooper doesn’t reply to me, but you are free to email him yourself. It’s irrelevant though really – what matters is what the paper says.

    and why would anyone believe what you report that he says? please the quote stands…you just can’t handle the truth. OBVIOUSLY.

  107. tsmith LOL!!!

    Elizabeth:
    But I still disagree;

    But not so quick Elizabeth, even if you are ugly and poor, (I’m not near as picky, or handsome, as tsmith :) ,, let’s look to where we agree, you said:

    ‘It’s more like there being a ceiling beyond which you can’t go, no matter how much you continue to gild the lily.’

    ,,, I’m saying Elizabeth, we can this work, give me a ballpark ceiling!!!

  108. oh and lets not forget the entire title of Darwin’s book…


    On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

    struggle…where have I heard that word used in the title of a book….let me think…..oh yeah….my struggle…mein kempf….

  109. mein kampf…sorry….

    BA77: go for the money…looks fade….

  110. Darwin’s views are driven by his theory of evolution…just like Waton’s views are

    After Watson made his infamous comments, DNA didn’t cease to exist. A theory either explains facts about the world or it does not.

    On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.

    struggle…where have I heard that word used in the title of a book….let me think…..oh yeah….my struggle…mein kempf….

    Consider a lunatic who has a book
    called “When water boils at 100 degrees I do something evil.” If he kills a billion people, what is the boiling point of water?

    Hitler wasn’t into Darwinism at all (He had Origin of the Species burnt), as it happens, but it would make no difference to the facts if he had called his book “I love evolution”. Evolution either explains the facts or it doesn’t.

  111. 111

    tsmith:

    “Biological arguments for racism may have been common before 1859, but they increased by orders of magnitude following the acceptance of evolutionary theory.” Stephen Jay Gould”

    You mean like this gem:

    Evolutionary psychologist Satoshi Kanazawa posted a piece on the Psychology Today website (originally titled Black Women Are Ugly) that was retitled a few times before deletion.

    http://www.whatsonchengdu.com/.....trage.html

    Black girls: 0
    Darwin: 1

  112. Driver exactly how do you derive objective morality from materialism? i.e. an ought from an is?

    The Knock-Down Argument Against Atheist Sam Harris – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

    Driver sadly, and I can only hope innocently for you, you are severely misinformed as to Darwin’s ‘sufficient condition’ that was provided towards the holocaust in his book:

    From Darwin to Hitler – Richard Weikart – video
    http://www.youtube.com/watch?v=w_5EwYpLD6A

    A expanded look at Hitler’s ethic, by Weikart, is now out in paperback:

    New in Paperback: Hitler’s Ethic by Richard Weikart
    Excerpt: In this work Weikart helps unlock the mystery of Hitler’s evil by vividly demonstrating the surprising conclusion that Hitler’s immorality flowed from a coherent ethic. Hitler was inspired by evolutionary ethics to pursue the utopian project of biologically improving the human race. Hitler’s evolutionary ethic underlay or influenced almost every major feature of Nazi policy: eugenics (i.e., measures to improve human heredity, including compulsory sterilization), euthanasia, racism, population expansion, offensive warfare, and racial extermination. Hitler also believed that morality was biologically innate, so he thought that eliminating the “evil” Jews would bring moral progress.
    http://www.evolutionnews.org/2.....47311.html

    The Dark Legacy Of Charles Darwin – 150 Years Later – video
    http://www.metacafe.com/watch/4060594/

    How Darwin’s Theory Changed the World – Rejection of Judeo-Christian values
    Excerpt: Weikart explains how accepting Darwinist dogma shifted society’s thinking on human life: “Before Darwinism burst onto the scene in the mid-nineteenth century, the idea of the sanctity of human life was dominant in European thought and law (though, as with all ethical principles, not always followed in practice). Judeo-Christian ethics proscribed the killing of innocent human life, and the Christian churches explicitly forbade murder, infanticide, abortion, and even suicide.
    “The sanctity of human life became enshrined in classical liberal human rights ideology as ‘the right to life,’ which according to John Locke and the United States Declaration of Independence, was one of the supreme rights of every individual” (p. 75).
    Only in the late nineteenth and especially the early twentieth century did significant debate erupt over issues relating to the sanctity of human life, especially infanticide, euthanasia, abortion, and suicide. It was no mere coincidence that these contentious issues emerged at the same time that Darwinism was gaining in influence. Darwinism played an important role in this debate, for it altered many people’s conceptions of the importance and value of human life, as well as the significance of death” (ibid.).
    http://www.gnmagazine.org/issu.....-world.htm

    And Driver, the war against basic human worth and dignity, by neo-Darwinian materialism, continues unabated,,, for the body count for abortion is now over 50 million in America since it was legalized in 1973:

    Born Alive – Abortion Survivor Gianna Jessen
    http://www.faithandfacts.com/a.....na-jessen/

    further notes:

    Stalin’s Brutal Faith
    http://www.icr.org/index.php?m.....038;ID=276

    The Black Book of Communism: Crimes, Terror, Repression:
    Excerpt: Essentially a body count of communism’s victims in the 20th century, the book draws heavily from recently opened Soviet archives. The verdict: communism was responsible for between 85 million and 100 million, non-war related, deaths in the century. (of note: this estimate is viewed as very conservative by many, with some more realistic estimates passing 200 million dead) (Of Note: Atheistic Communism is defined as Dialectic Materialism)
    http://www.amazon.com/Black-Bo.....0674076087

    The unmitigated horror visited upon man, by state sponsored atheism, would be hard to exaggerate,,,

    Chairman MAO: Genocide Master
    “…Many scholars and commentators have referenced my total of 174,000,000 for the democide (genocide and mass murder) of the last century. I’m now trying to get word out that I’ve had to make a major revision in my total due to two books. I’m now convinced that that Stalin exceeded Hitler in monstrous evil, and Mao beat out Stalin….”
    http://wadias.in/site/arzan/bl.....de-master/

    Lives Saved By Christianity
    Excerpt: here is an article, detailing how Christianity improved the status of women and saved millions of people in ancient Rome from death by female infanticide and from the plagues which periodically swept the Roman Empire:
    http://www.uncommondescent.com.....ent-337994

    From Josh McDowell, Evidence for Christianity, in giving examples of the influence of Jesus Christ cites many examples. Here are just a few:

    1. Hospitals
    2. Universities
    3. Literacy and education for the masses
    4. Representative government
    5. Separation of political powers
    6. Civil liberties
    7. Abolition of slavery
    8. Modern science
    9. The elevation of the common man
    10. High regard for human life

    Driver, beliefs have consequences, if you ultimately believe the lie that life is the result of a purposeless process, well then life has no purpose for you and you will act more or less accordingly!!!

  113. Driver exactly how do you derive objective morality from materialism? i.e. an ought from an is?

    The Knock-Down Argument Against Atheist Sam Harris – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

    Driver sadly, and I can only hope innocently for you, you are severely misinformed as to Darwin’s ‘sufficient condition’ that was provided towards the holocaust in his book:

    From Darwin to Hitler – Richard Weikart – video
    http://www.youtube.com/watch?v=w_5EwYpLD6A

    A expanded look at Hitler’s ethic, by Weikart, is now out in paperback:

    New in Paperback: Hitler’s Ethic by Richard Weikart
    Excerpt: In this work Weikart helps unlock the mystery of Hitler’s evil by vividly demonstrating the surprising conclusion that Hitler’s immorality flowed from a coherent ethic. Hitler was inspired by evolutionary ethics to pursue the utopian project of biologically improving the human race. Hitler’s evolutionary ethic underlay or influenced almost every major feature of Nazi policy: eugenics (i.e., measures to improve human heredity, including compulsory sterilization), euthanasia, racism, population expansion, offensive warfare, and racial extermination. Hitler also believed that morality was biologically innate, so he thought that eliminating the “evil” Jews would bring moral progress.
    http://www.evolutionnews.org/2.....47311.html

    The Dark Legacy Of Charles Darwin – 150 Years Later – video
    http://www.metacafe.com/watch/4060594/

    How Darwin’s Theory Changed the World – Rejection of Judeo-Christian values
    Excerpt: Weikart explains how accepting Darwinist dogma shifted society’s thinking on human life: “Before Darwinism burst onto the scene in the mid-nineteenth century, the idea of the sanctity of human life was dominant in European thought and law (though, as with all ethical principles, not always followed in practice). Judeo-Christian ethics proscribed the killing of innocent human life, and the Christian churches explicitly forbade murder, infanticide, abortion, and even suicide.
    “The sanctity of human life became enshrined in classical liberal human rights ideology as ‘the right to life,’ which according to John Locke and the United States Declaration of Independence, was one of the supreme rights of every individual” (p. 75).
    Only in the late nineteenth and especially the early twentieth century did significant debate erupt over issues relating to the sanctity of human life, especially infanticide, euthanasia, abortion, and suicide. It was no mere coincidence that these contentious issues emerged at the same time that Darwinism was gaining in influence. Darwinism played an important role in this debate, for it altered many people’s conceptions of the importance and value of human life, as well as the significance of death” (ibid.).

    ,,,And Driver, the war against basic human worth and dignity, by neo-Darwinian materialism, continues unabated,,, for the body count for abortion is now over 50 million in America since it was legalized in 1973:

    Born Alive – Abortion Survivor Gianna Jessen
    http://www.faithandfacts.com/a.....na-jessen/

    further notes:

    Stalin’s Brutal Faith
    http://www.icr.org/index.php?m.....038;ID=276

    The Black Book of Communism: Crimes, Terror, Repression:
    Excerpt: Essentially a body count of communism’s victims in the 20th century, the book draws heavily from recently opened Soviet archives. The verdict: communism was responsible for between 85 million and 100 million, non-war related, deaths in the century. (of note: this estimate is viewed as very conservative by many, with some more realistic estimates passing 200 million dead) (Of Note: Atheistic Communism is defined as Dialectic Materialism)
    http://www.amazon.com/Black-Bo.....0674076087

    The unmitigated horror visited upon man, by state sponsored atheism, would be hard to exaggerate,,,

    Chairman MAO: Genocide Master
    “…Many scholars and commentators have referenced my total of 174,000,000 for the democide (genocide and mass murder) of the last century. I’m now trying to get word out that I’ve had to make a major revision in my total due to two books. I’m now convinced that that Stalin exceeded Hitler in monstrous evil, and Mao beat out Stalin….”
    http://wadias.in/site/arzan/bl.....de-master/

    Lives Saved By Christianity
    Excerpt: here is an article, detailing how Christianity improved the status of women and saved millions of people in ancient Rome from death by female infanticide and from the plagues which periodically swept the Roman Empire:
    http://www.uncommondescent.com.....ent-337994

    From Josh McDowell, Evidence for Christianity, in giving examples of the influence of Jesus Christ cites many examples. Here are just a few:

    1. Hospitals
    2. Universities
    3. Literacy and education for the masses
    4. Representative government
    5. Separation of political powers
    6. Civil liberties
    7. Abolition of slavery
    8. Modern science
    9. The elevation of the common man
    10. High regard for human life

    Driver, beliefs have consequences, if you ultimately believe the lie that life is the result of a purposeless process, well then life has no purpose for you and you will act more or less accordingly!!!

  114. Elizabeth,

    I apologize for going so far back in the message list, but in your second response I found this:

    “On the other hand there is some evidence that women’s access to fertility control may be resulting in extended fertility, which would make sense; as women postpone child-bearing, women bearing alleles (whether new or existing) that tend to result in later menopause are more likely to have children than those bearing alleles that promote earlier menopause earlier. The former will therefore tend to increase in prevalence, and there is some evidence that they are doing so.”

    I understand how natural selection may be selecting for women bearing alleles (whether new or existing) that tend to result in later menopause, but there is a limit to the extent that menopause can be delayed. This is not evolution. It is just like the finch beak example. In a certain environment, the long beaks are selected for and in a different environment, the shorter beaks are selected for and it goes back and forth depending on the environment. Result, no net change. Natural selection is good at doing that, but it cannot come up with new genetic information, genes, etc that would allow new organs to be formed. This example just shows to support Mendel’s laws of genetics. If the information is not there to begin with, it cannot be selected. Natural selection can play with what it finds in the genome pool already, but it cannot create any new information.

  115. Scientific theories are not falsified by association with Nazis.

    “evolutionary ethics”, or any kind of ethics, has nothing to do with scientific theories. If I have a theory that my cat knocked over my tea, it is either true or false that my cat knocked over my tea. If I hate cats or my cat is called Hitler, or someone says me or my cat are Nazis, or Hitler liked cats, it doesn’t change the fact of how my tea got knocked over.

    Similarly, evolution either explains the facts of the world or it doesn’t.

    Again, consider a lunatic who has a book called “When water boils at 100 degrees I do something evil.” If he kills a billion people, what is the boiling point of water?

    I think it is a dangerous road to go down if you want to start believing or not believing things based on whether Hitler believed them.

    if you ultimately believe the lie that life is the result of a purposeless process, well then life has no purpose for you

    This is simply false.

    Anyway, I thought we were discussing the scientific theory of ID, not religion.

  116. After Watson made his infamous comments, DNA didn’t cease to exist. A theory either explains facts about the world or it does not.

    evolutionary racism didn’t cease to exist either.

    your precious theory sure explains racism.

    Hitler wasn’t into Darwinism at all (He had Origin of the Species burnt), as it happens, but it would make no difference to the facts if he had called his book “I love evolution”. Evolution either explains the facts or it doesn’t.

    oh of course nothing makes a difference to the faithful darwiniac…praise darwin.

    here ya go…all these historians are closet CREATIONISTS…I’m sure thats what you will tell yourself…

    The Darwin-Hitler connection is no recent discovery. In her classic 1951 work The Origins of Totalitarianism, Hannah Arendt wrote: “Underlying the Nazis’ belief in race laws as the expression of the law of nature in man, is Darwin’s idea of man as the product of a natural development which does not necessarily stop with the present species of human being.”

    The standard biographies of Hitler almost all point to the influence of Darwinism on their subject. In Hitler: A Study in Tyranny, Alan Bullock writes: “The basis of Hitler’s political beliefs was a crude Darwinism.” What Hitler found objectionable about Christianity was its rejection of Darwin’s theory: “Its teaching, he declared, was a rebellion against the natural law of selection by struggle and the survival of the fittest.”

    John Toland’s Adolf Hitler: The Definitive Biography says this of Hitler’s Second Book published in 1928: “An essential of Hitler’s conclusions in this book was the conviction drawn from Darwin that might makes right.”

    In his biography, Hitler: 1889-1936: Hubris, Ian Kershaw explains that “crude social-Darwinism” gave Hitler “his entire political ‘world-view.’ ” Hitler, like lots of other Europeans and Americans of his day, saw Darwinism as offering a total picture of social reality. This view called “social Darwinism” is a logical extension of Darwinian evolutionary theory and was articulated by Darwin himself.

    http://article.nationalreview......Q2NGE1Mjc=

    oh did the good doctor get back to you? I’m sure he’d drop everything to respond to such an august person as yourself……

  117. Scientific theories are not falsified by association with Nazis.

    its much more than a scientific theory, obviously…

    “‘Social Darwinism’ is often taken to be something extraneous, an ugly concretion added to the pure Darwinian corpus after the event, tarnishing Darwin’s image. But his notebooks make plain that competition, free trade, imperialism, racial extermination, and sexual inequality were written into the equation from the start- ‘Darwinism’ was always intended to explain human society.” (Desmond, Adrian [Science historian, University College, London] & Moore, James [Science historian, The Open University, UK], “Darwin,” [1991], Penguin: London, 1992, reprint, pp.xix).

    but evolution has been falsified by the lack of support in the fossil record, in the lab, by the many false prediction such a ‘vestigial organs’ (no such thing) junk dna…no junk, sorry…the tree of life…no tree…sorry.

    Anyway, I thought we were discussing the scientific theory of ID, not religion.

    people like you prove evolution is a faith…you never let facts get in the way of your faith in evolution.

  118. tjguy,

    Evolution is the change over time in inherited traits found in populations of organisms. A finch’s beak is an inherited trait; a finch is an organism. In some populations of finches (on one island), the finches have shorter beaks (on average); in another population (on another island), the finches have longer beaks. Both populations of finches descended from one ancestral population, which was (and looked) slightly different to both. The populations of finches we find now have changed their traits (e.g beaks) over time.

    This is evolution.

  119. Social Darwinism is indeed an ugly ideology, which has nothing to do with whether the scientific theory of evolution is true or false.

    You can bring up Hitler or Social Darwinism as much as you like, it isn’t going to convince any rational person that the scientific theory of evolution is false. Nor would it convince them that it was true. It is simply irrelevant to the scientific facts. Either all life is descended from a common ancestor or it isn’t. This is a fact that is immune to argumentum ad Hitlerum. Populations change traits over time or they don’t. This is a *factual matter* that cares not if you call it a Nazi or not.

  120. but evolution has been falsified

    The scientists haven’t noticed. They are still doing evolutionary biology. How do you explain it?

  121. of interest; new podcast

    “Hitler’s Ethic and the Pursuit of Evolutionary Progress in Nazi Policy”
    http://intelligentdesign.podom.....3_16-07_00

  122. as to the falsification of materialistic neo-Darwinism:

    Here is the falsification of local realism (materialism).

    Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of materialism, to explain reality:

    The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    The falsification for local realism (materialism) was recently greatly strengthened:

    Physicists close two loopholes while violating local realism – November 2010
    Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview.
    http://www.physorg.com/news/20.....alism.html

    Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009
    Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables.
    http://www.sciencedaily.com/re.....142824.htm

    (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.)

    And yet, quantum entanglement, which rigorously falsified local realism (materialism) as the true description of reality, is now found in molecular biology!

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    Quantum entanglement holds together life’s blueprint – 2010
    Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford.
    http://neshealthblog.wordpress.....blueprint/

    Untangling the Quantum Entanglement Behind Photosynthesis – May 11 2010
    Excerpt: “This is the first study to show that entanglement, perhaps the most distinctive property of quantum mechanical systems, is present across an entire light harvesting complex,” says Mohan Sarovar, a post-doctoral researcher under UC Berkeley chemistry professor Birgitta Whaley at the Berkeley Center for Quantum Information and Computation. “While there have been prior investigations of entanglement in toy systems that were motivated by biology, this is the first instance in which entanglement has been examined and quantified in a real biological system.”
    http://www.sciencedaily.com/re.....151356.htm

    i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put
    more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘special’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place!
    ,,,To refute this falsification of neo-Darwinism, one must show local realism to be sufficient to explain the quantum non-locality we find within molecular biology!

    ,,, As well, appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology, or anything else for that matter, destroys the very possibility of doing science rationally;

    Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.

    “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.
    http://www.washingtontimes.com.....arguments/

    =================

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

  123. Here is the basic outline of the falsification criteria for Intelligent Design

    For a broad outline of the ‘Fitness test’, required to be passed to show a violation of the principle of Genetic Entropy, please see the following video and articles:

    Is Antibiotic Resistance evidence for evolution? – ‘The Fitness Test’ – video
    http://www.metacafe.com/watch/3995248

    i.e.,, the fitness test must be passed by the sub-species against the parent species. If the fitness test is shown to be passed then the new molecular function, which provides the more robust survivability for the sub-species, must be calculated to its additional Functional Information Bits (Fits) it has gained in the beneficial adaptation, and then be found to be greater than 140 Fits. 140 Fits is what has now been generously set by Kirk Durston as the maximum limit of Functional Information which can reasonably be expected to be generated by the natural processes of the universe over the entire age of the universe (The actual limit is most likely to be around 40 Fits)(Of note: I have not seen any evidence to suggest that purely material processes can exceed the much more constrained ’2 protein-protein binding site limit’, for functional information/complexity generation, found by Michael Behe in his book “The Edge Of Evolution”).

    Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
    http://www.metacafe.com/watch/3995236

    Functional information and the emergence of bio-complexity:
    Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
    Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
    http://genetics.mgh.harvard.ed.....S_2007.pdf

    Measuring the functional sequence complexity of proteins – Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors – 2007
    Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,,
    http://www.tbiomed.com/content/4/1/47

    The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf

    further notes:

    Dr. Behe states in The Edge of Evolution on page 135:

    “Generating a single new cellular protein-protein binding site (in other words, generating a truly beneficial mutational event that would actually explain the generation of the complex molecular machinery we see in life) is of the same order of difficulty or worse than the development of chloroquine resistance in the malarial parasite.”

    That order of difficulty is put at 10^20 replications of the malarial parasite by Dr. Behe. This number comes from direct empirical observation.

    Richard Dawkins’ The Greatest Show on Earth Shies Away from Intelligent Design but Unwittingly Vindicates Michael Behe – Oct. 2009
    Excerpt: The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10^20 cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.
    http://www.evolutionnews.org/2.....26651.html

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....26281.html

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain – Michael Behe – December 2010
    Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.

    etc..etc..

  124. of note to avoid confusion; the basic falsification criteria of ID grants the unreasonable presupposition that materialism may be true.

  125. Elizabeth Liddle:

    But polymorphisms have to be explained somehow, and they seem, on the whole, to be pretty cool things.

    And the explanation is?

    Non-Darwinian

  126. Elizabeth Liddle:

    …beneficial mutations are more likely to accumulate than deleterious once.

    By the very fact alone that deleterious mutations vastly outnumber beneficial mutations, deleterious mutations will be more likely to increase. By force of numbers alone.

    Add to that the additional fact that the vast number of even beneficial mutations are lost due to chance alone and again deleterious mutations will be more likely to increase.

    So you’re not just wrong, but doubly wrong. Egregiously wrong.

  127. Elizabeth Liddle @87:

    As for your point about tautology – it’s fair one, as this is always a problem in discussing evolutionary theory, because it does sound tautological. It isn’t though, it’s just so simple that it sounds that way.

    This is false. It’s not tautological because it’s simple. It’s tautological because it is tautological. Now there’s a tautology for you!

    When things replicate with variance, things that replicate better will be replicated more often.

    It’s so obviously true, it’s almost not worth saying!

    Then stop saying it.

    Nice try Lizzie. Have you not figured out that we’re on to you and your little game with the meaning of natural selection?

    Time to stop now.

    So “fitter” simply means “replicates better”

    Hand waving. Watch the shell. Find the pea.

    It’s not what does fitness mean, since no one was talking about fitness. It’s what does “replicates better” mean and what does “will be replicated more often mean”?

    Let me guess. It means LEAVES MORE OFFSPRING.

    So what you meant to say was:

    When things replicate with variance, things that LEAVE MORE OFFSPRING will LEAVE MORE OFFSPRING.

    No wonder it sounds so simple. It is. Tautologically simple.

  128. ba77,

    on what basis do you equate local realism and materialism?

  129. kf,

    where are your calls for civility now that the ID proponents are dishing out rude remarks to people honestly trying to engage them? or do you also question those people’s honesty and integrity?

  130. 130
    Elizabeth Liddle

    Mung:

    When things replicate with variance, things that LEAVE MORE OFFSPRING will LEAVE MORE OFFSPRING.

    Yes. Now, think about the implications of that obviously true statement.

    Which is: variants of traits which, for whatever reason, increase the probability with which the phenotype will produce offspring will become more prevalent in the population.

    Again, it’s obviously true. But has profound implications.

    And, btw, there is no “game”. I hope eventually you will come to see that I am, in fact, honest.

  131. When things replicate with variance, things that LEAVE MORE OFFSPRING will LEAVE MORE OFFSPRING.

    The tautology is in the semantics, not the process. Its a type of feedback cycle.

    If I get an amp, speaker and mic, and stick the mic in the speaker I can say ‘an increase in sound level will cause an increase in sound level’

  132. Elizabeth:

    Aren’t these finding consistent with what breeders encounter? That is, you can only breed so many types of a cat or dog, e.g., before they become sickly.

    Now, you want to say that “fitness” is relative to the environment. Fine. But in the case of breeders, how has the environment changed? It hasn’t.

    The breeds just get more sickly.

    There’s a “limit” to evolution (Oops! Breeding one type of a cat to get another kind of a cat isn’t evolution is it?).

    The articles being analyzed here show that, in a mathematical sense, mutations “converge” onto a certain level of “fitness” increase.

    This is a “limit” to evolution, it it not?

    And, what does this mean for neo-Darwinian evolution?

    Directed selection would seem to ‘peter out’. And, with neutral drift, since any “new beneficial mutation” will have increasingly slight advantage, there’s all those “deleterious mutations” that can become fixed as well.

    None of this bodes well for neo-Darwinism, does it, EL?

    And, I bet you were “surprised” by their findings, right?

  133. paragwinn, you ask;

    ‘on what basis do you equate local realism and materialism?’

    Actually local realism is equated with ‘reductive materialism’ on the basis of the work of A. Aspect and company.

    The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    etc.. etc…

    Paragwinn, you are free to postulate a ‘non-reductive material’ cause for finding quantum non-locality (quantum entanglement/information) on a massive scale within molecular biology, since only the reductive material framework, which is constrained by space-time, is falsified by the failure of local realism to explain reality, but remember in appealing to the non-reductive material framework, such as the many worlds and multiverses conjectures, you are destroying your ability to do science rationally.

    Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever.

    “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook

    BRUCE GORDON: Hawking’s irrational arguments – October 2010
    Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science.

    ,,,, But alas paragwinn, how come most neo-Darwinian atheists will choose a world of absurd irrationality over God???

  134. Mutations can alter traits- however being a human is not a trait. Blue eyes are a trait.

    That said there still isn’t any evidence that mutations can accumulate in such a way as to give rise to new, useful and functional multi-part systems. And seeing that living organisms are full of them you would think that would count against the theory of evolution.

    Strange how evolutionists ignore all of that…

  135. 135
    Elizabeth Liddle

    OK, perhaps this formulation will make the thing clear:
    Heritable traits that tend to promote successful reproduction in one generation will be preferentially represented in the next.
    Again, it’s self-evidently true, but that doesn’t make it tautological.

  136. you are free to postulate a ‘non-reductive material’ cause for finding quantum non-locality

    The rational conclusion is that the world on the small scale does not conform to our large (human) scale expectations. The rational conclusion is not “Therefore God.”

    Again, why the religion? I thought ID was science.

  137. Elizabh,

    What happens when there are a dozen or more competing traits- each beneficial to the individals who have them?

    And then what happens when a flash flood comes along and wipes out the entire population?

  138. Social Darwinism is indeed an ugly ideology, which has nothing to do with whether the scientific theory of evolution is true or false.

    social darwinism is applied evolution. truth hurts…you should try it sometimes.

    You can bring up Hitler or Social Darwinism as much as you like, it isn’t going to convince any rational person that the scientific theory of evolution is false. Nor would it convince them that it was true. It is simply irrelevant to the scientific facts

    Ideas have consequences.

    A direct line runs from Darwin, through the founder of the eugenics movement-Darwin’s cousin, Francis Galton-to the extermination camps of Nazi Europe.” (Brookes, Martin.,”Ripe old age,” Review of “Of Flies, Mice and Men,” by Francois Jacob, Harvard University Press, 1999. New Scientist, Vol. 161, No. 2171, 30 January 1999, p.41).

    Populations change traits over time or they don’t. This is a *factual matter* that cares not if you call it a Nazi or not.

    and I already listed a number of falsifications of evolution….you of course chose to ignore them….no surprise you have a great deal of difficulty dealing with things that challenge your faith in that racist theory you love so much.

  139. The scientists haven’t noticed. They are still doing evolutionary biology. How do you explain it?

    which scientists? you mean dogmatic athiests like PZ Meyers?

    ok then, prove your theory…list the exact mutations that led to the eye, in order.

    oh you say you can’t? yet you beleive the eye evolved….yea its called faith…not science.

  140. Dr Liddle:

    Nope:

    Heritable traits that tend to promote successful reproduction in one generation will be preferentially represented in the next.

    Again, it’s self-evidently true, but that doesn’t make it tautological.

    There is indeed a sharp difference between a self evident truth and a tautology, but the claim is simply not self evident.

    For simple instance, if a trait would otherwise have been advantageous but a devastating wild fire or volcanic eruption reduces an island to starvation and extinciton of life, there is no reproduction to speak about.

    A self evident truth is true, and on reflection on our understanding of the world, is necessarily so, on pain of patent absurdity.

    There are simply too many gaps between traits in members of a population and the patterns of reproduction that will prevail for such an assertion to be self-evident.

    However, there is a major problem that many forms of the survival of the fittest theme are indeed circular and in that sense empty tautologies. (There are key mathematical tautologies that are highly useful as baseline axioms or definitions.)

    GEM of TKI

    PS: In the other thread I have pointed to the importance of ostensive definition [underscoring the limitations of operational de3finitions], and have used this in outlining the rationale for the Chi metric, in the context of Shannon’s own work as clipped a couple of days back.

  141. tsmith,

    Re the evolution of the eye: We know that mutations take place that change organisms.

    Can you prove that the eye was designed? Until ID has more than faith in that respect, evolution is the only science in town.

  142. TS:

    Sorry, but the relevant history of ideas and of evolutionary “science” cannot be so easily brushed aside by trying to wedge apart Social Darwinism from Darwinism, as the connexion was there almost from the beginning, starting with Darwin himself in Chs 5 – 7 of his Descent of Man.

    There is a major moral hazard that has been historically important and which must be squarely faced, not ducked.

    If you doubt me, look carefully at the logo for the 2nd international conference on Eugenics, and the surrounding discussion here. Notice the definition in the logo: “Eugenics is the self-direction of human evolution.” Notice the roots of the eugenics tree, including: biology, anthropology, statistics, geology, anatomy, phsyiology, psychology and mental testing.

    There is absolutely no doubt that this was viewed — at highest levels in science and culture, and for many decades over the span of coming on a century — as an applied science to improve the breed so to speak.

    It is only when the horrors of what was done not only by Hitler but by so called advanced democratic countries — what was done to Amerindians, Blacks and others deemed unfit is appalling — was exposed, especially in the civil rights era that the tree was cut down, and in fact it is still pushing up shoots.

    GEM of TKI

  143. Re the evolution of the eye: We know that mutations take place that change organisms.

    we also know that the vast majorities of mutations are harmful.

    Can you prove that the eye was designed? Until ID has more than faith in that respect, evolution is the only science in town.

    so in other words, ya got nothing…except faith in evolution. no surprise.

    you can’t answer the question…all you can do is punt!! LOL

    sure I can prove the eye is designed…ever hear of the PAX-6? interesting how all animals with eyes use the same gene…even though they are widely divergent…let me guess…you’ll just say ‘common ancestry’

    but its also found in animals without eyes…

  144. which scientists?

    Well there’s 1162 Steves.

    Every department of biology at every university

    The two papers mentioned in the article are examples of evolutionary biology.

  145. Drver:

    Re the evolution of the eye: We know that mutations take place that change organisms.

    Yet there still isn’t any vidence that they cn accumulate in such a way as to give rise to new, useful and functional multi-part systems.

    Can you prove that the eye was designed?

    Science isn’t about proof. The evidence says it was desiged.

    Until ID has more than faith in that respect, evolution is the only science in town.

    ID is not anti-evolution.

  146. you can’t answer the question

    It is naive to think that because a scientific discipline cannot answer a particular complex question the entire scientific discipline is then somehow invalid.

    Even most ID proponents admit that evolution has taken place. The party line is usually that there are limits on evolution (“micro-evolution occurs, but macro-evolution is not possible”). If someone could provide evidence for those limits, I would convert to the ID side.

  147. All those scientists doing evolutionary biology and yet not one piece of evidence that demonstrates mutations can accumulate in such a way as to construct new, useful and functional multi-part systems.

    Just what are they doing?

  148. Gem: very true. racism and eugenics were part of the theory of evolution from the beginning.

    like this exceprt from ‘a civic biology’ which was the textbook at the heart of the ‘scopes monkey trial’

    At the present time there exist upon the earth five races or varieties of man, each very different from the other in instincts, social customs, and, to an extent, in structure. These are the Ethiopian or negro type, originating in Africa; the Malay or brown race, from the islands of the Pacific; the American Indian; the Mongolian or yellow race, including the natives of China, Japan, and the Eskimos; and finally, the highest type of all, the Caucasians, represented by the civilized white inhabitants of Europe and America.

    evolution is racist to its core..since the races evolved separately some must be superior to others…and Watson admitted in an earlier quote I posted from him…

  149. Driver,

    ID is OK with universal common descent- meaning ID does not argue against it.

    ID argues against the claim that all mutations are genetic accidents/ errors/ mistakes- meaning organisms were designed to evolve.

    That said there isn’t any genetic data that can be linked to the physiological and anatomical transformations required for UCD.

    THAT is the issue- what we observe as “microevolution” cannot be extrapolated to the grand changes required.

  150. It is naive to think that because a scientific discipline cannot answer a particular complex question the entire scientific discipline is then somehow invalid.

    what complex questions has evolution EVER answered? hmm?? how about any simple ones?

    evolution is useless for science, as coyne admits:

    To some extent these excesses are not Mindell’s fault, for, if truth be told, evolution hasn’t yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn’t evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of `like begets like’. Even now, as its practitioners admit, the field of quantitative genetics has been of little value in helping improve varieties. Future advances will almost certainly come from transgenics, which is not based on evolution at all.

    http://www.nature.com/nature/j.....2983a.html

    Even most ID proponents admit that evolution has taken place. The party line is usually that there are limits on evolution (“micro-evolution occurs, but macro-evolution is not possible”). If someone could provide evidence for those limits, I would convert to the ID side.

    lets see since there is no macro evolution shown in the lab or the fossil record, then evolution is nothing more than faith.

  151. Joseph,

    Are not Lenski’s E Coli experiment and nylonase sufficient examples?

    If you are wondering why scientists haven’t yet observed a mouse evolving from a bacteria then I can give you a clue why, if you like.

  152. re not Lenski’s E Coli experiment and nylonase sufficient examples?

    as Behe says:

    Despite his understandable desire to spin the results his way, Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems. So much for the power of random mutation and natural selection.

    http://behe.uncommondescent.co.....rd-lenski/

  153. evolution is useless for science

    No, Coyne is talking about practical benefits, not whether it is science.

  154. Driver unbeknownst to you when you state:

    ‘Again, why the religion? I thought ID was science.’

    and stuff like this:

    Until ID has more than faith in that respect, evolution is the only science in town.

    ,, is that science is impossible from a materialistic framework; i.e. Only Theism guarantees our investigation within ‘science’ to lead to true conclusions:

    THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodical.....27241.html

    This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    Stephen Meyer – Morality Presupposes Theism (1 of 4) – video
    http://www.youtube.com/watch?v=uSpdh1b0X_M

    Nuclear Strength Apologetics – Presuppositional Apologetics – video
    http://www.answersingenesis.or.....pologetics

    John Lennox – Science Is Impossible Without God – Quotes – video remix
    http://www.metacafe.com/watch/6287271/

    Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video
    http://www.youtube.com/watch?v=5yNg4MJgTFw

    Can atheists trust their own minds? – William Lane Craig On Alvin Plantinga’s Evolutionary Argument Against Naturalism – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality;

    The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” Creation-Evolution Headlines
    http://creationsafaris.com/cre.....#20110227a

  155. no comment about the pax-6 gene…no surprise…oh and Lenski took 20,000 generations for this one small change…ever hear of Haldane’s dilemma???

    (I’ve mentioned this several times…crickets chirping)

  156. evolution is racist to its core

    This is evolution:

    The change over time in one or more inherited traits found in populations of organisms.

    What is racist about that?

    As I already said, everyone sensible admits that evolution occurs. Are you saying that reality is racist?

  157. THE GOD OF THE MATHEMATICIANS – DAVID P. GOLDMAN – August 2010
    Excerpt: we cannot construct an ontology that makes God dispensable. Secularists can dismiss this as a mere exercise within predefined rules of the game of mathematical logic, but that is sour grapes, for it was the secular side that hoped to substitute logic for God in the first place. Gödel’s critique of the continuum hypothesis has the same implication as his incompleteness theorems: Mathematics never will create the sort of closed system that sorts reality into neat boxes.
    http://www.faqs.org/periodical.....27241.html

    This following site is a easy to use, and understand, interactive website that takes the user through what is termed ‘Presuppositional apologetics’. The website clearly shows that our use of the laws of logic, mathematics, science and morality cannot be accounted for unless we believe in a God who guarantees our perceptions and reasoning are trustworthy in the first place.

    Proof That God Exists – easy to use interactive website
    http://www.proofthatgodexists.org/index.php

    Stephen Meyer – Morality Presupposes Theism (1 of 4) – video
    http://www.youtube.com/watch?v=uSpdh1b0X_M

    Nuclear Strength Apologetics – Presuppositional Apologetics – video
    http://www.answersingenesis.or.....pologetics

    John Lennox – Science Is Impossible Without God – Quotes – video remix
    http://www.metacafe.com/watch/6287271/

    Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:

    Dr. Bruce Gordon – The Absurdity Of The Multiverse & Materialism in General – video
    http://www.metacafe.com/watch/5318486/

    What is the Evolutionary Argument Against Naturalism? (‘inconsistent identity’ of cause leads to failure of absolute truth claims for materialists) (Alvin Plantinga) – video
    http://www.youtube.com/watch?v=5yNg4MJgTFw

    Can atheists trust their own minds? – William Lane Craig On Alvin Plantinga’s Evolutionary Argument Against Naturalism – video
    http://www.youtube.com/watch?v=byN38dyZb-k

    “But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?” – Charles Darwin – Letter To William Graham – July 3, 1881

    It is also interesting to point out that this ‘inconsistent identity’, pointed out by Plantinga, which leads to the failure of neo-Darwinists to make absolute truth claims for their beliefs, is what also leads to the failure of neo-Darwinists to be able to account for objective morality, in that neo-Darwinists cannot maintain a consistent identity towards a cause for objective morality;

    The Knock-Down Argument Against Atheist Sam Harris – William Lane Craig – video
    http://www.youtube.com/watch?v=tvDyLs_cReE

    “Atheists may do science, but they cannot justify what they do. When they assume the world is rational, approachable, and understandable, they plagiarize Judeo-Christian presuppositions about the nature of reality and the moral need to seek the truth.
    As an exercise, try generating a philosophy of science from hydrogen coming out of the big bang. It cannot be done. It’s impossible even in principle, because philosophy and science presuppose concepts that are not composed of particles and forces. They refer to ideas that must be true, universal, necessary and certain.” Creation-Evolution Headlines

  158. No, Coyne is talking about practical benefits, not whether it is science.

    how can it be science, when you don’t know how it evolved, you don’t have a clue actually, yet you believe the eye evolved?

    sounds like faith to me.

    can you tell me another branch of science that has no practical benefits and IS science?

  159. Haldane’s dilemma is based on faulty calculations. No-one takes it seriously any more.

  160. This is evolution:

    The change over time in one or more inherited traits found in populations of organisms.

    What is racist about that?

    this is evolution….

    Watson is credited with discovering the double helix along with Maurice Wilkins and Francis Crick in 1962.
    In the newspaper interview, he said there was no reason to think that races which had grown up in separate geographical locations should have evolved identically. He went on to say that although he hoped everyone was equal, “people who have to deal with black employees find this not true”.

  161. Haldane’s dilemma is based on faulty calculations. No-one takes it seriously any more.

    of course they don’t take it seriously…best to ignore what they cannot explain…’faulty calculations’ LOL

  162. Driver:

    Pardon, but you are indulging in burden of proof shifting.

    We know on massive evidence that intelligence is capable of creating functionally specific, complex organised entities. The eye is a member of this class of entity.

    What we have yet to see shown is that chance plus necessity, starting from a still warm pond can spontaneously originate a metabolising, self-replicating automaton that uses — notice the additionality — the code based von Neumann kinematic self replicator to do that. Then, it needs to be shown that such an entity can and does spontaneously originate further complex body plans and associated organs including the eye.

    A priori imposition of materialism through the backdoor of so called methodological naturalism, backed up by just so stories that do not address specifically and on specific observational evidence relevant to origin how irreducibly complex organisation of parts into wholes came about or come about incrementally or by co-option — have you ever had to get the specific part of a general type to match your particular car? — do not hack it.

    Philip Johnson’s rebuke to Lewontin is apt:

    For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    GEM of TKI

  163. you don’t have a clue actually, yet you believe the eye evolved?

    There is more than a clue.

    A clue or two

    If there is any positive evidence from the science of ID that the eye was designed, I would be interested to see it.

  164. evolution is racist to its core

    Gravity is deeply predjucided against obese people and the sun tends to be kinder to those with dark skin (and a lack of ginger hair;) )

  165. 165
    Elizabeth Liddle

    Joseph asks:

    What happens when there are a dozen or more competing traits- each beneficial to the individals who have them?

    Well, it’s an interesting question, and partly depends what you mean by “competing traits”. In a sexually reproducing population, it may well be that some combinations of traits have a positive effect on phenotypic fitness and some a negative. I’ll assume that’s what you mean. If the alleles are on very different parts of genome, don’t tend to be inherited together, then we will tend to have a normalish distribution of the combined phenotypic effects, where individuals with the “good” cocktail will be the lucky ones, whereas those at the “bad” end of the spectrum will be less fit. Traits that tend to concentrate at the “bad” end will tend to go down in frequency, but those that tend to concentrate at the “good” end will tend to go up. However, if traits that are towards the “bad” end nonetheless have positive effects at the “good” end, the “bad” effects will persist in the population, even though those individuals will tend to have few, if any, children.

    This is one possible explanation for highly heritable disorders that seem to have very small but significant association with a large number “risk” alleles. Those “risk” alleles may persist in the population because in most individuals they are neutral, and may even be positive (the “risk” alleles for schizophrenia, for example, may be beneficial if not found in a cocktail with other “risk” alleles”.

    So the answer is complicated! In a non-sexually reproducing species (unless artificially manipulated like Lenski’s) a beneficial mutation that is then succeeded by a mutation that, if, alone, would have been beneficial but which, in combination with the earlier one, adds no (or little) more benefit, then its chances of propagating through the population is much reduced.

    And then what happens when a flash flood comes along and wipes out the entire population?

    All those precious new alleles are lost!

    (Unless Noah comes along, I guess :))

  166. A clue or two

    LOL…more ‘just so’ stories…

    Development of the vertebrate eye cup. a | The neural plate is the starting point for the development of the vertebrate eye cup. b | The neural plate folds upwards and inwards. c | The optic grooves evaginate. d | The lips of the neural folds approach each other and the optic vesicles bulge outwards. e | After the lips have sealed the neural tube is pinched off. At this stage the forebrain grows upwards and the optic vesicles continue to balloon outwards: they contact the surface ectoderm and induce the lens placode.

    shazam…amazing how that just happens isn’t it?

  167. KF,

    The burden is on ID to oust evolutionary science as the mainstream paradigm.

    As you surely know, the theory of evolution does not depend on abiogenesis. Abiogenesis either results from natural processes or by divine fiat. Either will do for the theory of evolution.

  168. F/N: A different view on the “slam dunk” case for eye evolution.

  169. If there is any positive evidence from the science of ID that the eye was designed, I would be interested to see it.

    uh I just gave it to you…the same gene produces widely divergent types of eyes in widely divergent animals.

  170. LOL…more ‘just so’ stories…

    No, that bit you quoted is a description of the actual development the eye in vertebrates. That is, how the eye develops in embryos.

  171. the same gene produces widely divergent types of eyes in widely divergent animals.

    It’s a bit more complicated than that, but how is that scientific evidence of design?

  172. 172
    Elizabeth Liddle

    Back to the OP: I have read both papers now, and the headline of the OP is incorrect.

    Neither paper shows that genetic entropy decreases fitness. It may do, but the papers aren’t about that.

    Both papers concern the Lenski E-coli lineage, in which the ancestral lineage was stored so that it can be compared with populations bred separately from that common ancestral lineage.

    Both papers show that beneficial mutations (which occured in different lineages) did not have an additive effect, but rather a “law of diminishing returns”, when artificially inserted into already-fit genomes.

    No decrease of fitness was observed, just a reduced increase.

    The papers have nothing to do with “genetic entropy” which is to do with the gradual buildup of mostly Very Slightly Deleterious Mutations (VSDMs) in a population over time.

    This was nothing to do with buildup over time (the “buildup” was an experiment manipulation); the mutations were beneficial alone, not deleterious; there was no decrease in fitness (just a decrease in rate of fitness increase).

    Interesting papers, but not what it says on the OP tin :)

    If you want a take-home anti-Darwinian message from the papers, it isn’t that genetic entropy decreases fitness, but that beneficial mutations tend not to be additive. Although at least one was actually multiplicative.

  173. No, that bit you quoted is a description of the actual development the eye in vertebrates. That is, how the eye develops in embryos.

    yes and it assumes evolution…but no list of the mutations that led to all of these wonderful things happening…oh and how did some of these mutations…which by themselves provide no benefit, hang around until the rest of the pieces evolved?

    its kind of like the ‘evolution’ of male and female…it sho is clever of evolution to evolve em at the same time isn’t it? shazam!

    It’s a bit more complicated than that, but how is that scientific evidence of design?

    its rather obvious isn’t it?

  174. oh yeah driver, did Dr. Cooper ever get back to you?

    I’m sure he droppedd everything when you wrote him….

  175. Driver:

    Nope, since the dominance of the institutions and the public sphere was usurped by back-door a priori imposition of evolutionary materialism, the first thing is to expose that.

    The evolutionary materialism will then fall of its own weight, but if one tries to “prove” something to an institution locked into an ideology, then one cannot disprove what is built in as a controlling assumption and censor on thought.

    The real task is to expose Lewontinian-Saganian a priori materialism and how this warps origins science and origins science eduction.

    Let’s give three key clips:

    ______________

    Lewontin: >> To Sagan, as to all but a few other scientists, it is self-evident [a total misunderstanding of self-evidence BTW . . . what is happening is that they are caught up in an ideological circle of question-begging . . . ] the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test . . . .

    It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door.

    [[From: “Billions and Billions of Demons,” NYRB, January 9, 1997.] >>

    US NAS: >> In science, explanations must be based on naturally occurring phenomena. Natural causes are, in principle, reproducible and therefore can be checked independently by others. If explanations are based on purported forces that are outside of nature [notice the loaded language, marking a strawman distortion: the real issue is the empirical markers of natural [chance plus necessity] vs ART-ificial causes, as was laid on the table since Plato in The Laws Bk X, 360 BC], scientists have no way of either confirming or disproving those explanations. Any scientific explanation has to be testable — there must be possible observational consequences that could support the idea but also ones that could refute it. Unless a proposed explanation is framed in a way that some observational evidence could potentially count against it, that explanation cannot be subjected to scientific testing. [The artificial is eminently suitable for empirical testing on characteristic signs] [[Science, Evolution and Creationism, 2008, p. 10 ] >>

    US NSTA: >> The principal product of science is knowledge in the form of naturalistic [note the question-begging] concepts and the laws and theories related to those concepts . . . .

    Although no single universal step-by-step scientific method captures the complexity of doing science, a number of shared values and perspectives characterize a scientific approach to understanding nature. Among these are a demand for naturalistic explanations supported by empirical evidence that are, at least in principle [note the question-begging, naturalism is a worldview, one aka evolutionary materialism, aka scientific atheism etc], testable against the natural world. Other shared elements include observations, rational argument, inference, skepticism, peer review and replicability of work . . . .

    Science, by definition, is limited to naturalistic methods and explanations and, as such, is precluded from using supernatural elements in the production of scientific knowledge. [NSTA, Board of Directors, July 2000.] >>

    _______________

    The effect of such ideologisation of science, especially on origins, is to warp results by censoring out the possibility for science to follow the evidence freely where it leads.

    A better approach is to restore a more historically and philosophically well warranted understanding of what science should seek to be and do, e.g.:

    science, at its best, is the unfettered — but ethically and intellectually responsible — progressive, observational evidence-led pursuit of the truth about our world (i.e. an accurate and reliable description and explanation of it), based on:

    a: collecting, recording, indexing, collating and reporting accurate, reliable (and where feasible, repeatable) empirical — real-world, on the ground — observations and measurements,

    b: inference to best current — thus, always provisional — abductive explanation of the observed facts,

    c: thus producing hypotheses, laws, theories and models, using logical-mathematical analysis, intuition and creative, rational imagination [[including Einstein's favourite gedankenexperiment, i.e thought experiments],

    d: continual empirical testing through further experiments, observations and measurement; and,

    e: uncensored but mutually respectful discussion on the merits of fact, alternative assumptions and logic among the informed. (And, especially in wide-ranging areas that cut across traditional dividing lines between fields of study, or on controversial subjects, “the informed” is not to be confused with the eminent members of the guild of scholars and their publicists or popularisers who dominate a particular field at any given time.)

    As a result, science enables us to ever more effectively (albeit provisionally) describe, explain, understand, predict and influence or control objects, phenomena and processes in our world.

    GEM of TKI

    PS: I am very aware of how Darwin artfully cut off his public discussion at the point of the root of the tree of life.

    He knew he had no evidence and he knew that the trend of thought would be followed to the logical conclusion by others. He did make sure to put something into a letter [that warm little pond quote], knowing that it would be the subject of writing of biographies and onward investigations.

    Darwin was first and foremost a clever and patient rhetor of what he termed Free Thought, a synonym of skeptical agnositcism or atheism.

    The logic of the case is that absent the root, there is no basis for the tree of life. And, if there is good reason to infer to the origin of a metabolising self replicating automaton on the only known cause of the required FSCI, design, then there is a fortiori good reason to infer to the same cause as the main cause of the much larger increments of FSCI to account for novel body plans.

    For first life we are looking at 100 – 100+ k bits of functionally specific complex digital info, and for body plans credibly 10 – 100+ million bits. Just 1,000 bits of FSCI specifies 10^150 times the number of Planck time quantum states that the atoms of our observed cosmos will go through across the effective — heat death — lifespan of our cosmos. In short, something that, per specificity, is isolated in that scope of a space of possibilities will be maximally unreachable apart from by intelligent design.

  176. can you tell me another branch of science that has no practical benefits and IS science?

    Most of cosmology. Much of particle physics.

  177. Nope, since the dominance of the institutions and the public sphere was usurped by back-door a priori imposition of evolutionary materialism, the first thing is to expose that.

    Well, if by “usurped” you mean that evolutionary theory became a mainstream scientific paradigm and replaced the philosophical musings of Paley and the theological assumptions of the time, then I accept that evolutionary theory was a usurper.

    To show that evolution usurped science (a serious charge), all that needs to be shown is that the emperor is naked. A well written paper or two should take care of this, if the emperor is indeed naked.

  178. Most of cosmology. Much of particle physics.

    and all of evolution…

    In 1942, Nobel Laureate Ernst Chain wrote that his discovery of penicillin (with Howard Florey and Alexander Fleming) and the development of bacterial resistance to that antibiotic owed nothing to Darwin’s and Alfred Russel Wallace’s evolutionary theories.

    The same can be said about a variety of other 20th-century findings: the discovery of the structure of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; new surgeries; and other developments.

    Additionally, I have queried biologists working in areas where one might have thought the Darwinian paradigm could guide research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I learned that evolutionary theory provides no guidance when it comes to choosing the experimental designs. Rather, after the breakthrough discoveries, it is brought in as a narrative gloss.

    The essence of the theory of evolution is the hypothesis that historical diversity is the consequence of natural selection acting on variations. Regardless of the verity it holds for explaining biohistory, it offers no help to the experimenter–who is concerned, for example, with the goal of finding or synthesizing a new antibiotic, or how it can disable a disease-producing organism, what dosages are required and which individuals will not tolerate it. Studying biohistory is, at best, an entertaining distraction from the goals of a working biologist.

    It is noteworthy that Darwin’s and Wallace’s theories of evolution have been enormously aggrandized since the 1850s. Through the writings of neo-Darwinian biologists, they have subsumed many of the biological experimental discoveries of the 20th century. This is so despite the fact that those discoveries were neither predicted nor heuristically guided by evolutionary theory.

    The overselling of the theory of evolution, because of the incorporation of these later discoveries, may have done a grave disservice both to those two 19th-century scientists and to modern biology.

    http://www.forbes.com/2009/02/.....arwin.html

  179. A better approach is to restore a more historically and philosophically well warranted understanding of what science should seek to be and do

    A scientific paper on ID that makes positive predictions should do the trick. Then those predictions can be tested and voila! – ID usurps evolution.

    I must say I find it difficult to reconcile the almost universal acceptance of (micro)evolution (including in ID circles) with the idea that evolution is an unwarranted usurper.

  180. I am very aware of how Darwin artfully cut off his public discussion at the point of the root of the tree of life.

    He knew he had no evidence

    Do you accept microevolution or don’t you? Surely you don’t accept it on no evidence?

  181. The logic of the case is that absent the root, there is no basis for the tree of life.

    You are surely too intelligent to think abiogenesis is necessary for the theory of evolution, since you are learned enough to be aware that the theory of evolution would still be valid whether life arose by natural processes or divine fiat.

    There is nothing in the theory of evolution that says that the first life, the common ancestors (the root), couldn’t have been created by an intelligent designer.

  182. Elizabeth, it is very interesting to note, in your trying to distance this paper from the principle of Genetic Entropy, is not what in you do mention, as in regards to the buildup of slightly detrimental mutations (the paper is not focused on that), but is in what you fail to mention. You fail to mention that Genetic Entropy was not violated over and above ‘the fitness’ that which was already present in parent lineage in the parent lineage’s native environment. This is a glaring lack of ‘evolution’ of functional complexity/information over and above the parent lineage!!! Especially given the fact that the 50,000 generations of Lenski’s e-coli are equivalent to 2,000,000 years of supposed human evolution!!! In fact here’s exactly what they did:

    Mutations : when benefits level off – June 2011
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    So Elizabeth whether you admit it or not this is crushing to evolution!!! For it nails you from two different directions. 1. you can’t evolve up above the parent species!!! 2. You can’t evolve past the wall that negative epistasis presents!!! So Elizabeth what do you do instead OF HONESTLY FACING THE TRUTH??? You ‘interpret’ the findings to mean what you want!!! This is sheer personal bias on your part, and I’m calling you on your intellectually dishonesty to it!!! ,,, Also of interest is that this ‘severe limit’ to ‘evolvability’, is exactly what has been noticed in previous ID research, that was ignored by neo-Darwinists;

    Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009
    Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own.
    http://www.discovery.org/a/9951

    Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness – Ann K. Gauger, Stephanie Ebnet, Pamela F. Fahey, and Ralph Seelke – 2010
    Excerpt: When all of these possibilities are left open by the experimental design, the populations consistently take paths that reduce expression of trpAE49V,D60N, making the path to new (restored) function virtually inaccessible. This demonstrates that the cost of expressing genes that provide weak new functions is a significant constraint on the emergence of new functions. In particular, populations with multiple adaptive paths open to them may be much less likely to take an adaptive path to high fitness if that path requires over-expression.
    http://bio-complexity.org/ojs/.....O-C.2010.2

  183. Elizabeth:

    Heritable traits that tend to promote successful reproduction in one generation will be preferentially represented in the next.

    Is this true?

    In Hoyle’s “Mathematics of Evolution”, the very first thing he demonstrates is that if you compensate the power law that is supposed to define evolution, things slow down very quickly.

    If you have populations in which pairs of adults produce four offspring, then the likelihood of any of the offspring surviving to reproductive age is roughly 1/2. Why? Because most populations of species are stable populations, with stable population size.

    And if a “beneficial” mutation occurs, there’s at least (putting stochastic effects to the one side) a 50% chance it will be eliminated in the first generation.

    So, I guess it’s true that there is ‘tendency’ to promote successful reproduction, but it is an extremely slight tendency

  184. no comment about the pax-6 gene…no surprise…oh and Lenski took 20,000 generations for this one small change…ever hear of Haldane’s dilemma???

    Did Lenski’s populations have a deteriorating environment? That’s a hidden assumption in Haldane’s calculations, which makes it faulty.

  185. 185
    Elizabeth Liddle

    ba77: you are reading far too much into my posts!

    All I’m saying is that I’ve read the papers, and they don’t say what the headline says – they aren’t even on that topic.

  186. Elizabeth you stated:

    ‘The papers have nothing to do with “genetic entropy” which is to do with the gradual buildup of mostly Very Slightly Deleterious Mutations (VSDMs) in a population over time.’

    That is simply false. Not only does Genetic Entropy hold that genomes will deteriorate over very long periods of time (as is witnessed by Dollo’s law) Genetic Entropy also holds speciation is a ‘top down’ affair. i.e. Genetic Entropy holds parent species to be ‘optimal’ and that evolutionary processes will NEVER increase the optimal functional information that was originally designed in the parent species genome!,,,

  187. Elizabeth Liddle:

    No decrease of fitness was observed, just a reduced increase.

    So how was it determined that these bacteria were originally becoming increasingly fit over time?

    Because that would have to be the case, would it not, for there to then follow a decreased increase?

    The study seems to be about the effects of

    beneficial

    mutations.

    This is relevant to the “genetic entropy” debate because “synergistic epistasis” is supposed to be a way out of the genetic entropy dilemma.

  188. 188
    Elizabeth Liddle

    Mung:

    Elizabeth Liddle:

    No decrease of fitness was observed, just a reduced increase.

    So how was it determined that these bacteria were originally becoming increasingly fit over time?

    It’s a long term experiment, so I’d have to dig back among several papers, but IIRC, the original population was cloned and divided, and a sample was frozen.

    Relative fitness of any two lineages from the original population was assayed by direct comparison, and fitness relative to the original population by comparison with a defrosted sample, I think!

    Details of the fitness assays and computations are given in this paper:

    http://isites.harvard.edu/fs/d.....l-1991.pdf

    Because that would have to be the case, would it not, for there to then follow a decreased increase?

    Yes. They isolated five mutations (in separate lineages) that conferred increased fitness relative to the ancestral population, and then artificially combined those mutations, in all possible combinations, in a clone from the ancestral population. They found that the effects were not additive, but obeyed a “law of diminishing returns” (except in the case of one mutation where the epistasis was positive).

    The study seems to be about the effects of

    beneficial

    mutations.

    This is relevant to the “genetic entropy” debate because “synergistic epistasis” is supposed to be a way out of the genetic entropy dilemma.

    Well, it’s one of the hypothesed reasons we have not “died 100 times over”:

    http://www.sciencedirect.com/s.....9385701671

    There are others.

    The Kondrashov paper is interesting though, if you can get hold of it.

  189. I want to respond to the specific point raised in the initial post that our work supports a view that the fitness of the population that we studied will decline over time.

    It doesn’t.

    Our work describes evidence that the rate of fitness *increase* will decline over time. That is, the rate of fitness improvement slows, but does not become negative.

    For anyone interested, a link to the actual article is now live on my lab website: web.mac.com/tim_f_cooper/Cooper_lab/Publications.html

  190. Tim Cooper emailed me back. He said he will make one post here to clarify what he meant.

    Hopefully it will get through moderation quickly.

  191. 191
    Elizabeth Liddle

    Thanks for confirming that, Tim Cooper!

    Lovely papers, btw.

  192. *crickets*

    In the future, could everyone at least read the abstracts?

  193. And yet the ‘fitness’ (functional complexity) never increased over the parent species in the parent species native environment!!! Thus genetic entropy holds which has been my point all along!!!

    Thus, to break it down, we have fast adaptation to ‘niche’ environments, all coming, according to Behe, at a loss of Functional Elements,

    Michael Behe’s Quarterly Review of Biology Paper Critiques Richard Lenski’s E. Coli Evolution Experiments – December 2010
    Excerpt: After reviewing the results of Lenski’s research, Behe concludes that the observed adaptive mutations all entail either loss or modification–but not gain–of Functional Coding ElemenTs (FCTs)
    http://www.evolutionnews.org/2.....41221.html

    and then these fast adaptations are shown to peter out dramatically, but not come to a complete stop,,,

    ,,,and yet after 50,000 generations (equivalent to 2,000,000 years of hypothesized human evolution), they scrutinize through billions of detrimental mutations and find just 5 ‘beneficial’ mutations, (mutations that ‘burnt bridges’ to allow adaptations), moreover when they put these 5 beneficial together they produce ‘negative epistasis’ instead of the incremental step by step improvement that is presupposed neo-Darwinian evolution…

    And all this helps a neo-Darwinists sleep better at night how???

  194. Thanks Coop.

  195. ba77:”,,,and yet after 50,000 generations (equivalent to 2,000,000 years of hypothesized human evolution)”

    have people always waited until they were 40 years old to reproduce?

  196. 196
    Elizabeth Liddle

    I take it we are all clear now that the papers do not support the headline claim in the OP?

  197. Actually, the result is expected from a genetic entropy perspective and is very antagonistic to what is expected from a neo-Darwinian framework.

  198. note:

    Poly-Functional Complexity equals Poly-Constrained Complexity
    http://docs.google.com/Doc?doc.....Zmd2emZncQ

    DNA – Evolution Vs. Polyfuctionality – video
    http://www.metacafe.com/watch/4614519

    K´necting The Dots: Modeling Functional Integration In Biological Systems
    Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream”
    http://www.uncommondescent.com.....l-systems/

    Insight into cells could lead to new approach to medicines
    Excerpt: Scientists expected to find simple links between individual proteins but were surprised to find that proteins were inter-connected in a complex web. Dr Victor Neduva, of the University of Edinburgh, who took part in the study, said: “Our studies have revealed an intricate network of proteins within cells that is much more complex than we previously thought.
    http://www.physorg.com/news196402353.html

  199. paragwinn correct on the math my man,,, perhaps a million would be more reasonable???!!! Now let’s see if you are willing to look at some more math, to see if you can spot the problems here???

    God by the Numbers – Charles Edward White
    Excerpt: “Even if we limit the number of necessary mutations to 1,000 and argue that half of these mutations are beneficial, the odds against getting 1,000 beneficial mutations in the proper order is 2^1000. Expressed in decimal form, this number is about 10^301. 10^301 mutations is a number far beyond the capacity of the universe to generate. Even if every particle in the universe mutated at the fastest possible rate and had done so since the Big Bang, there still would not be enough mutations.”
    http://www.christianitytoday.c.....ml?start=2

    Indeed, math is not kind to Darwinism in the least when considering the probability of humans ‘randomly’ evolving:

    In Barrow and Tippler’s book The Anthropic Cosmological Principle, they list ten steps necessary in the course of human evolution, each of which, is so improbable that if left to happen by chance alone, the sun would have ceased to be a main sequence star and would have incinerated the earth. They estimate that the odds of the evolution (by chance) of the human genome is somewhere between 4 to the negative 180th power, to the 110,000th power, and 4 to the negative 360th power, to the 110,000th power. Therefore, if evolution did occur, it literally would have been a miracle and evidence for the existence of God. William Lane Craig

    William Lane Craig – If Human Evolution Did Occur It Was A Miracle – video
    http://www.youtube.com/watch?v=GUxm8dXLRpA

    Along that same line:

    Darwin and the Mathematicians – David Berlinski
    “The formation within geological time of a human body by the laws of physics (or any other laws of similar nature), starting from a random distribution of elementary particles and the field, is as unlikely as the separation by chance of the atmosphere into its components.”
    Kurt Gödel, was a preeminent mathematician who is considered one of the greatest to have ever lived. Of Note: Godel was a Theist!
    http://www.evolutionnews.org/2.....cians.html

    “Darwin’s theory is easily the dumbest idea ever taken seriously by science.”
    Granville Sewell – Professor Of Mathematics – University Of Texas – El Paso

    Waiting Longer for Two Mutations – Michael J. Behe
    Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model.
    http://www.discovery.org/a/9461

    Can Darwin’s enemy, math, rescue him? – May 2011
    http://www.uncommondescent.com.....escue-him/

    This following calculation by geneticist John Sanford for ‘fixing’ a beneficial mutation, or for creating a new gene, in humans, gives equally absurd numbers:

    Dr. Sanford calculates it would take 12 million years to “fix” a single base pair mutation into a population. He further calculates that to create a gene with 1000 base pairs, it would take 12 million x 1000 or 12 billion years. This is obviously too slow to support the creation of the human genome containing 3 billion base pairs.
    http://www.detectingtruth.com/?p=66

    Oxford University Admits Darwinism’s Shaky Math Foundation – May 2011
    Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. – On a 2011 Job Description for a Mathematician, at Oxford, to ‘fix’ the persistent mathematical problems with neo-Darwinism within two years.
    http://www.evolutionnews.org/2.....46351.html

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