Home » Biology, Darwinism » Another windy day in the junkyard …

Another windy day in the junkyard …

From Jason Palmer at BBC News (19 May 2011), we learn, “Protein flaws responsible for complex life, study says.” This time mistakes produce more functional proteins:

Tiny structural errors in proteins may have been responsible for changes that sparked complex life, researchers say.A comparison of proteins across 36 modern species suggests that protein flaws called “dehydrons” may have made proteins less stable in water.

This would have made them more adhesive and more likely to end up working together, building up complex function.

Remarkably, we read,

Natural selection is a theory with no equal in terms of its power to explain how organisms and populations survive through the ages; random mutations that are helpful to an organism are maintained while harmful ones are bred out.But the study provides evidence that the “adaptive” nature of the changes it wreaks may not be the only way that complexity grew.

Natural selection is a theory with no equal – in terms of much belief and little evidence. But it can be supplemented by tiny structural errors that somehow produce co-operation.

The authors suggest then that other adaptations occur that “undo” the deleterious effects of the sticky proteins.

Convenient, that.

Fred Hoyle, wherever you are, check your mail: Your Boeing 747 is ready.

Isn’t this the sort of mess that Steve Fuller says “floored astrology”?

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104 Responses to Another windy day in the junkyard …

  1. A simple, single question.

    What makes this a ‘flaw’?

  2. Natural selection is a theory with no equal in terms of its power to explain …

    As an “explanation,” natural selection is, at best, a tautology — those which survive, survive. Well, yes, they would, wouldn’t they?

    On the other hand, when one tries to make of natural selection something more than a mere minor tautology, one gets one of those “explanations” which “explains” everything and its opposite.

  3. What makes this a ‘flaw’?

    Bad design?

  4. Bad design?

    Sure, but what’s the bad design here? The flaws are said to have been possibly important for causing complex life. If that was the goal, then this flaw was a feature, assuming the scenario is true.

  5. I’m scratching my head like you.

    We introduce a quantifiable structural motif, called dehydron, that is shown to be central to protein-protein interactions. A dehydron is a defectively packed backbone hydrogen bond suggesting preformed monomeric structure whose Coulomb energy is highly sensitive to binding-induced water exclusion.

    http://www.ncbi.nlm.nih.gov/pm.....MC1303363/

    In the past decade, research has demonstrated that defectively packed hydrogen bonds, or “dehydrons,” play an important role in protein-ligand interactions and a host of other biochemical phenomena. These results are due in large part to the development of computational techniques to identify and analyze the hydrophobic microenvironments surrounding hydrogen bonds in protein structures. Here, we provide an introduction to the dehydron and the computational techniques that have been used to uncover its biological and biomedical significance.

    http://www.ncbi.nlm.nih.gov/pubmed/20865532

  6. 6
    Elizabeth Liddle

    “flaw” makes no more sense from a Darwinian perspective than an ID one. Less, probably.

    The only “flaws” from a Darwinian point of view or features that bias against successful reproduction, and even then, a flaw in one generation can become a feature in the next.

    I don’t know if it’s sloppy journalism or a sloppy attempt by scientists to write a “lay” press release, but it’s highly misleading.

    Unless they are using it a highly technical sense, like a “flaw” in a regular lattice.

    Still, careless writing, whatever.

  7. The only “flaws” from a Darwinian point of view or features that bias against successful reproduction, and even then, a flaw in one generation can become a feature in the next.

    Is it therefore tautological to say that flaws are never selected for, given the “Darwinian point of view”? I realize that ‘a flaw can become a feature’ of course, but if something is being selected for, then by the DPOV it cannot be a flaw. Yes?

  8. 8
    Elizabeth Liddle

    Yes, I would say so :)

    There are complications in that story, because of drift effects, but, yes.

  9. There are complications in that story, because of drift effects, but, yes.

    Fair enough, that’s what I expected.

    Let’s think about a case like this: We have a single organism, let’s say a flower. The only thing we know for certain is that the flower was bred purposefully by a flower breeder. Given that, would it be the case that we could not therefore say whether the traits were flaws or features without getting input from the flower breeder?

  10. Natural selection is a theory with no equal – in terms of much belief and little evidence. But it can be supplemented by tiny structural errors that somehow produce co-operation.

    The ‘somehow’ is more readily understood from the original paper than its popular summary:
    Non-adaptive origins of interactome complexity.

  11. 11
    Elizabeth Liddle

    Hi there, nullasalus

    Let’s think about a case like this: We have a single organism, let’s say a flower. The only thing we know for certain is that the flower was bred purposefully by a flower breeder. Given that, would it be the case that we could not therefore say whether the traits were flaws or features without getting input from the flower breeder?

    A subtle question! But I’m going to give a subtle answer:

    No, the flower breeder is irrelevant unless the flower is in the flower breeder’s greenhouse.

    While in the breeder’s greenhouse, “flaws” are whatever will cause the breeder to discard the flowers seeds.

    Once the flower is in your garden, “flaws” are whatever causes you to neglect it or kill it.

    So if the breeder bred a pink daisy, but you had a rabbit that liked eating pink daisies, then what was a beneficial trait while the flower was being bred, has now become a flaw because it increases the probability that the flower will be eaten by the bunny.

    In short: a flaw is something that decreases breeding chances in the current environment. When the environment changes, what was a bug can become a feature, and what was a feature can become a bug.

  12. Elizabeth Liddle,

    In short: a flaw is something that decreases breeding chances in the current environment. When the environment changes, what was a bug can become a feature, and what was a feature can become a bug.

    Naturally. Let’s go back.

    No, the flower breeder is irrelevant unless the flower is in the flower breeder’s greenhouse.

    While in the breeder’s greenhouse, “flaws” are whatever will cause the breeder to discard the flowers seeds.

    Alright. And if we don’t know whether the flower is in the breeder’s greenhouse?

  13. 13
    Elizabeth Liddle

    Then we’d have to record allele frequencies in the population over time, and see which alleles became more frequent and which less.

    Even then we may not actually be able tell the difference between an actual flaw and neutral or slightly beneficial variant that fell foul of stochastic processes and decreased in frequency (i.e. due to sheer bad luck) and vice versa.

    Although being good scientists, we would run parallel experiments with random samples of the original population, and determine whether a particular allele increased in frequency more often than would be expected under the null hypothesis of neutrality.

    But clearly very small effects (i.e. the effects of Very Slightly Beneficial Mutations) would take very great statistical power to detect.

    The smaller the “real” effect, the more drift effects will dominate the picture.

  14. 14
    Elizabeth Liddle

    Oh, and our results even then would only generalise to the environment we provide.

    If we then sell the seeds to someone else, our feature may prove to be their bug, all over again :)

    The point being, of course, that in a Darwinian context, selection simply means: this allele tends to breeds more successfully in this environment.

  15. Then we’d have to record allele frequencies in the population over time, and see which alleles became more frequent and which less.

    Right, but at that point you wouldn’t be determining the features and flaws of the flower, but of successive generations. And the simulations you’d run would have to make assumptions about the environments, among other things. Do you run simulations with the ‘this was done by a breeder’ environment in mind?

    I have no doubt you can tell a good story about the flower, if the sky’s the limit as far as hypothetical environments and histories and who-knows-what is involved, to overlay over any actual data gathered.

  16. 16
    Elizabeth Liddle

    Exactly. In a Darwinian context, the only quality criterion for a trait is: does it increase or reduce the probability that, in this environment,I will reproduce successfully?

    Of course that criterion is completely orthogonal to the subjective effects, in a sentient organism, of that trait. For example, not being able to reproduce, may, conceivably, improve the quality of my life. But from a Darwinian perspective, it’s a flaw.

    Of course nothing is quite as simple as that (although that’s the basic Darwinian principle, I would say); for example there are some alleles that increase the probability of reproduction when heterozygous, but reduce it when homozygous. In a sexually reproducing population, there will tend to be a few homozygous individuals that get the rough end of the deal, but the allele still propagates through the population because heterozygous individuals reproduce better (although there will be an optimal level of frequency in the population, clearly).

    In that sense, from the individuals point of view, heterozygosity is a benefit, but homozygosity, probably a flaw (unless it confers something fun as well).

    But what is inherited, will be the allele, not the homozygosity!

    To take your last point:

    You don’t have to tell a story at all. I’m just giving a more precise definition of the concept of a “flaw” in Darwinian terms. It’s probably a bad word to use, in fact, because it has absolutist baggage.

    The value of an allele is a function of its phenotypic effects and the current environment. It’s not a static quantity. And in many cases its only inferable statistically anyway, as the vast majority of gene variants are near-neutral in effect.

  17. as to: as the vast majority of gene variants are near-neutral in effect.

    ,,,but not quite neutral; the vast majority of mutations are shown to be ‘slightly detrimental’;

    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

    ,,, the vast majority of mutations being “Slightly Detrimental” means that the vast majority of mutations are far below the power of natural selection to remove from a genome until it is too late, i.e. long before the effects of ‘slightly detrimental mutations’ are noticed by natural selection they will spread throughout the entire population.

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

  18. as to; ‘The value of an allele is a function of its phenotypic effects’

    There is no evidence that mutations to DNA will effect body-plan morphogenesis in a significant novel, and positive, way;

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells
    http://www.evolutionnews.org/2.....footnote19

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    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

    further notes:

    Getting Over the Code Delusion (Epigenetics) – Talbot – November 2010 – Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism:
    http://www.thenewatlantis.com/.....e-delusion

    The Origin of Biological Information and the Higher Taxonomic Categories – Stephen Meyer
    “Neo-Darwinism seeks to explain the origin of new information, form, and structure as a result of selection acting on randomly arising variation at a very low level within the biological hierarchy, mainly, within the genetic text. Yet the major morphological innovations depend on a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. Yet if DNA is not wholly responsible for body plan morphogenesis, then DNA sequences can mutate indefinitely, without regard to realistic probabilistic limits, and still not produce a new body plan. Thus, the mechanism of natural selection acting on random mutations in DNA cannot in principle generate novel body plans, including those that first arose in the Cambrian explosion.”
    http://eyedesignbook.com/ch6/eyech6-append-d.html

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    The Gene Myth, Part II – August 2010
    Excerpt: So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous influence over their functions.,,, So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used.,,, Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent.
    http://darwins-god.blogspot.co.....rt-ii.html

    etc.. etc..

  19. 19
    Elizabeth Liddle

    It is true, bornagain77, that in a population that is already at near-optimum, most changes will be deleterious. When things are pretty good, there is nowhere to go but down :)

    But that doesn’t mean that during the climb to that optimal peak, a much greater proportion of changes would have been beneficial. In fact, that is the heart of the theory – that where genotypic variation results in variance in reproductive success, the most successful variants will become the most prevalent.

  20. 20
    Elizabeth Liddle

    @ nullasalus:

    Further to my point above, I would make the additional point that “the environment” should probably be taken to include the context of the rest of the genotype.

    Just as homozygosity for one allele might reduce the probability of breeding, while heterozygosity increases it, so an allele in one genetic context may increase reproductive success, but reduce it in another.

    For example, we know that both schizophrenia and ADHD are highly heritable (estimates are over 50%) and yet Genome Wide Association Studies (GWAS) show that while individual alleles have a statistically significant odds ratio (over 1, which would indicate no association)), they rarely hit even hit two.

    In other words, while “risk alleles” exist, the vast majority of bearers of those alleles will not develop the disorder, and indeed, the alleles in a different genetic context may confer some benefit.

    I also thought of a (totally hypothetical example) of the homozygosity thing that might make my point clearer:

    Let’s say that a particular allele slightly increased testosterone expression in women, and in so doing greater enthusiasm for sex. And let’s say that when heterozygous for that allele, there is no measurable effect on fertility, but where homozygous, fertility is impaired (but sexual enjoyment increased).

    That allele would tend to reach homeostasis, because heterozygous individuals would tend to have more babies (more sex) but homozygous individuals fewer (even more sex, but fewer babies).

    Do we call that allele a “flaw” or not? Is it a bug or a feature?

    From the PoV of evolution, it’s a net feature, but the cost of the feature is a proportion of the population for which it is a bug; the allele prevalence will stabilise at a level at which the number extra fecund heterozygous individuals is balanced by the number of less fecund homozygous individuals.

    However, for the individual homozygous woman, however, it might be either bug or feature, depending on how great their desire for babies was. For some, great sex without worry of pregnancy might be win-win! For others, a mixed blessing.

    And for the individual heterozygous woman it might be great nuisance, certainly in a pre-contraceptive era.

    So I think it’s important to distinguish between the value of the allele to the individual (and we can probably usefully use words like “flaw” in that context), and the “value” (in deliberate scare quotes) of the allele from an evolutionary PoV. “Selection coefficient less than 1) is probably a better term, if a bit technical, but you still have to remember that selection coefficient remains a function of context, where context includes both the external and internal environment, including the rest of the genome.

  21. Lizzie-

    There isn’t any evidence that genetic accidents can accumulate in such a way as to give rise to useful, functional multi-part systems. That means there couldn’t have been any climbing.

  22. Also “natural selection” is an oxymoron as mature does not select. Natural selection is a result, ie differential reproduction due to heritable variation.

  23. 23
    Elizabeth Liddle

    Joseph @ #22
    Actually I sort of agree with you that it’s a bad term, although I understand entirely why Darwin chose it – he was making the fairly simple point that just as farmers and breeders deliberately select desirable traits, traits that “naturally” confer greater fecundity will be automatically “selected”.

    But it tends to result in tautologies like “selection selects”, so I try to avoid it where I can.

    The Darwinian principle is simply this:

    When things replicate with variance, variants that replicate better will become more prevalent.

    Which isn’t even a theory really, its more like a syllogism.

  24. Elizabeth Liddle you state;

    ‘in a population that is already at near-optimum,’

    And exactly why do you say that bacteria are near optimum complexity, and cannot improve any further over their current ‘optimal’ state (as the evidence now demands you say), when you in fact hold, according to your own neo-Darwinian worldview, the completely contrary view that bacteria are not of optimum complexity and that all life evolved from bacteria??? You can’t have it both ways Elizabeth, either bacteria are of the optimal complexity allowable for any particular bacterium, because they were designed that way, or bacteria are not of optimum functional complexity and can evolve by neo-Darwinian means, ‘naturally’, to greater and greater heights of integrated functional complexity.

    ,,, But to further highlight the sheer absurdity of your position, even if we grant that you must always ‘descend’ from the optimal function complexity of a bacterium before you can ascend to anything more functionally complex than a bacterium, and test for that extremely charitable allowance to the almighty power of evolution to succeed in such a convoluted, circuitous, manner, this is what we find:

    These following articles refute Richard E. Lenski’s ‘supposed evolution’ of the citrate ability for the E-Coli bacteria after 20,000 generations of the E-Coli from his ‘Long Term Evolution Experiment’ (LTEE) which has been going on since 1988:

    Multiple Mutations Needed for E. Coli – Michael Behe
    Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we’ve seen evolution do, then there’s no reason to believe evolution could produce many of the complex biological features we see in the cell.
    http://behe.uncommondescent.co.....or-e-coli/

    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

    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

    Lenski’s work actually did do something useful in that it proved that ‘convergent evolution’ is impossible because it showed that evolution is ‘historically contingent’. This following video and article make this point clear:

    Lenski’s Citrate E-Coli – Disproof of Convergent Evolution – Fazale Rana – video (the disproof of convergence starts at the 2:45 minute mark of the video)
    http://www.metacafe.com/watch/4564682

    The Long Term Evolution Experiment – Analysis
    Excerpt: The experiment just goes to show that even with historical contingency and extreme selection pressure, the probability of random mutations causing even a tiny evolutionary improvement in digestion is, in the words of the researchers who did the experiment, “extremely low.” Therefore, it can’t be the explanation for the origin and varieity of all the forms of life on Earth.
    http://www.scienceagainstevolution.org/v12i11f.htm

    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

    The following shows that we can actually watch the ‘final act’ of Genetic Entropy, ‘mutational meltdown’, in the laboratory for small asexual populations (bacteria, yeast, etc.):

    The Mutational Meltdown in Asexual Populations – Lynch
    Excerpt: Loss of fitness due to the accumulation of deleterious mutations appears to be inevitable in small, obligately asexual populations, as these are incapable of reconstituting highly fit genotypes by recombination or back mutation. The cumulative buildup of such mutations is expected to lead to an eventual reduction in population size, and this facilitates the chance accumulation of future mutations. This synergistic interaction between population size reduction and mutation accumulation leads to an extinction process known as the mutational meltdown,,,
    http://www.oxfordjournals.org/.....84-339.pdf

    and of course no matter what convoluted route you want to take for bacteria, the bottom line is that no bacteria has EVER passed the fitness test against its parent strain!!

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

    further note:

    Again I would like to emphasize, I’m not arguing Darwinism cannot make complex functional systems, the data on malaria, and the other examples, are a observation that it does not. In science observation beats theory all the time. So Professor (Richard) Dawkins can speculate about what he thinks Darwinian processes could do, but in nature Darwinian processes have not been shown to do anything in particular.
    Michael Behe – 46 minute mark of video lecture on ‘The Edge of Evolution’ for C-SPAN
    http://www.uncommondescent.com.....ent-361037

  25. Lizzie,

    Darwin chose it to cause confusion. And he was corrected in his own time. Unfortunately that has been lost and “natural selection”still remains.

    However we now know that it is but a minor player in the scheme of life.

  26. 26
    Elizabeth Liddle

    Joseph @ #21:

    Lizzie-

    There isn’t any evidence that genetic accidents can accumulate in such a way as to give rise to useful, functional multi-part systems. That means there couldn’t have been any climbing.

    Well, I would have to disagree with you! Certainly genetic accidents can “accumulate” as I’m sure you would agree, and you would probably agree that genetic “accidents” that confer reproductive advantage will tend to accumulate at the expense of those that do not.

    So the question is: can those accumulations result in “useful, multipart systems”, and I’d say there is abundant evidence that they, and indeed, for the way that the accumulation happens.

    You probably know about “hox” genes, that specify, extremely simply, such matters as which end of the developing embryo is front and which the back, given chemical inputs from neighbouring cells. There are also fairly basic genes that determine, again, given chemical inputs from neighbouring cells, whether the dividing embryo will have radial or bilateral symmetry.

    This is so simple that it’s directly analogous to the features that determine whether a growing snowflake will be columnar or flat. And once it’s started growing in a particular manner, the growth pattern itself is a determining factor in what happens next.

    Now obviously I accept that you do not think such evidence is valid, but I would have to disagree. We know a lot about the genes that specify whether a forelimb becomes a flipper, a wing, or an arm, or whether a skin cell becomes a tooth, a scale, a hair, or a feather.

    I think the best way to conceive of the developmental process is as a nested “decision tree” where the initial “decisions” (Head or tail? four segments or five?) are very simple, but once down one of the branches of the tree, what has already developed interacts with what may be slight variants of regulatory genes and others to determine which of a subset of possibilities is executed.

  27. further notes;

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.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/

  28. Elizabeth states:

    ‘So the question is: can those accumulations result in “useful, multipart systems”, and I’d say there is abundant evidence that they, and indeed, for the way that the accumulation happens.’

    see post 27!!!

  29. 29
    Elizabeth Liddle

    Joseph:

    Lizzie,

    Darwin chose it to cause confusion. And he was corrected in his own time. Unfortunately that has been lost and “natural selection”still remains.

    Oh I have to disagree, there, Joseph. I think it was a very apt analogy in its day. I just think it has acquired a misleading life of its own since.

    I presume you agree that, for example, a modern poodle, say, has the characteristics it has because those characteristics were consistently bred for by breeders?

    In other words, those dogs with the desired characteristics were selectively bred from?

    In other words, certain naturally occurring variants increased the probability that the individual would be chosen by the breeder as a breeding animal, i.e. would increase the animal’s chances of reproductive success (within the context of the breeding farm).

    Yes?

    So all Darwin did was to extrapolate this particular example to what happens naturally – characteristics that increase an individuals chance of reproductive success will tend to be propagated through the population.

    The only difference is that in the wild, the probability of a characteristic leading reproductive success doesn’t depend on whether a dog-breeder likes that characteristic, but on whether it increases the organism’s chance of surviving, finding a mate, or rearing its offspring successfully to maturity.

    Hence “natural” selection by analogy to the “artificial” selection by breeders.

  30. 30
    Elizabeth Liddle

    Bornagain77: well I did read your post, but I don’t find your sources very convincing!

    Did you read the rest of mine?

  31. Elizabeth you ask;

    ‘well I did read your post, but I don’t find your sources very convincing!

    Did you read the rest of mine?’

    Well Elizabeth, I did not think you find it ‘convincing’ since it does not sit well with your neo-Darwinian worldview. But alas for you Elizabeth, my post are the actual empirical results, whereas your posts are merely conjecture. You keep alluding to the fact that your materialistic conjectures are ‘demonstrated’,,, Yet I never find any citation from you so as to counter Behe and Axe’s work. ,,, You know Elizabeth, you can believe whatever you want, as you clearly demonstrate that you are intent on doing, but that is not science, and the blunt truth is, when the rubber meets the road, that you have ZERO empirical evidence to back up all your 25 cent word rhetoric!!!

  32. 32
    Elizabeth Liddle

    @bornagain, #25

    Elizabeth Liddle you state;

    ‘in a population that is already at near-optimum,’

    And exactly why do you say that bacteria are near optimum complexity, and cannot improve any further over their current ‘optimal’ state (as the evidence now demands you say), when you in fact hold, according to your own neo-Darwinian worldview, the completely contrary view that bacteria are not of optimum complexity and that all life evolved from bacteria??? You can’t have it both ways Elizabeth, either bacteria are of the optimal complexity allowable for any particular bacterium, because they were designed that way, or bacteria are not of optimum functional complexity and can evolve by neo-Darwinian means, ‘naturally’, to greater and greater heights of integrated functional complexity.

    Good question, bornagain77, but one with a good answer :)

    In fact, several.

    Biologists do not hold that all life descended from bacteria. In fact, only modern bacteria descended from ancient bacteria. What biologists hold is that both bacteria and all other living things descended from a common ancestor that was probably simpler than either.

    Second: fitness is multidimensional, and while it is convenient to talk about a 2 or 3 dimensional “fitness landscape” because that is easy to visualise, in fact there are countless dimensions along which a population can “move”. However, there will also be local “maxima” occupied by particular populations, and populations of populations, and these include bacteria.

    But my fundamental point is related to Gould’s point about “punctuated equilibrium”. Once a population is at equilibrium, most “directions” will be down, and so “selective pressures” will tend to be conservative (sharks are a good example).

    But if that equilibrium is broken, by an environmental change of some kind, populations will tend to “move” to a new optimum. At that point, a much larger proportion of what would otherwise have been either neutral or “Very Slightly Deleterious” mutations will be “Very Slightly Beneficial”.

    So the fact that in a population at equibrium, most mutations are VSDMs or neutral doesn’t extrapolate to populations in flux.

  33. 33
    Elizabeth Liddle

    bornagain77, #31

    No, my posts relate to empirical results, bornagain77. But you are very good at citing your sources, and I will try to cite some of mine.

    One source worth referring to, and it contains a lot of references to primary empirical sources, is Sean Carroll’s book, “Endless forms most beautiful”.

    Another is Neil Shubin’s “Your Inner Fish”.

    http://www.amazon.com/Your-Inn.....0375424474

    http://www.amazon.com/Endless-.....=1-1-spell

  34. Well Elizabeth let’s take a closer look:

    For a clear instance of your inability to honestly face the truth Elizabeth, you hold that simpler life gradually changes, by purely ‘natural’ processes, into more and more complex life, but when we look as far back as we can, through the wildly changing environment of the earth’s deep past, we find that bacteria look exactly the same as they did hundreds of millions of years ago;

    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

    ,,, i.e. if neo-Darwinism were true, this extreme stasis should not be present, and to make excuses for why there is no change is certainly not facing the evidence honestly Elizabeth!!!

    further notes;

    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

    Dr. Cano’s work on ancient bacteria came in for intense scrutiny since it did not conform to Darwinian predictions, and since people found it hard to believe you could revive something that was millions of years old. Yet Dr. Cano has been vindicated:

    “After the onslaught of publicity and worldwide attention (and scrutiny) after the publication of our discovery in Science, there have been, as expected, a considerable number of challenges to our claims, but in this case, the scientific method has smiled on us. There have been at least three independent verifications of the isolation of a living microorganism from amber.”
    http://www.uncommondescent.com.....ent-357693

    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

    Thus Elizabeth, your conjectures fail on all fronts they are tested!!!

  35. 35
    Elizabeth Liddle

    bornagain77: I’d be grateful if you wouldn’t impugn my honesty. Wrong, I may well be (I am frequently wrong), and biased I may be too, but I am not dishonest, and I am far more interested in finding a model that fits the data than in defending an a priori view, or even my own ego.

    Still, no problem – I often encounter the same accusations of dishonesty levelled at IDists, and I get just as cross. It seems to me we get nowhere by assuming the other “side” is posting in bad faith. So please can we agree to at least make that assumption, for the time being?

    Yes, there is good evidence that bacteria reached an optimal peak several hundred million years ago, around which they continue to move between adjacent sub-peaks. That doesn’t mean their ancestors were at that peak two or three billion years ago. Nor does it mean that we are descended from bacteria of any kind (we aren’t).

  36. Elizabeth, the problem for you is that you want to have your cake and eat it to. You have no evidence, thus you make up any excuse you can, and push your problem back, under the rug to a former age of ‘miracles’ if you will, but this is not science Elizabeth, what you are doing is rationalization in the face of all contrary evidence. You get upset that I call you on not honestly facing the evidence, but that is in fact what you are doing!!!,,, Moreover, if you really cared to follow the evidence where it leads, instead of making up more and more extremely far fetched excuses for your ‘preferred’ worldview, you would find that the problem traces back to the inability of material processes to generate ANY amount of non-trivial functional information/complexity! And once you see that “information’ is the insurmountable problem, then you can then follow the evidence deeper, to try to answer the question, ‘Where does the information come from?”, and you will find that all of reality itself reduces to information, of a ‘infinite’ (mind of God) Theistic order, and thus indeed, all of reality (the entire material universe) must originate from the ‘infinite information’ that originates from the purposeful intent of the infinite Mind Of God.

    notes:

    It is also very interesting to note that the quantum state of a photon is actually defined as ‘infinite information’:

    Explaining Information Transfer in Quantum Teleportation: Armond Duwell †‡ University of Pittsburgh
    Excerpt: In contrast to a classical bit, the description of a (photon) qubit requires an infinite amount of information. The amount of information is infinite because two real numbers are required in the expansion of the state vector of a two state quantum system (Jozsa 1997, 1) — Concept 2. is used by Bennett, et al. Recall that they infer that since an infinite amount of information is required to specify a (photon) qubit, an infinite amount of information must be transferred to teleport.
    http://www.cas.umt.edu/phil/fa.....lPSA2K.pdf

    The following articles show that even atoms (Ions) are subject to teleportation:

    Of note: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge.

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,
    http://www.rsc.org/chemistrywo.....ammeup.asp

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.
    http://www.freerepublic.com/fo.....1769/posts

    Moreover Elizabeth, from the preceding experiments, and other experiments, ‘information’ is shown to be ‘conserved’ to a greater degree than energy;

    Quantum no-hiding theorem experimentally confirmed for first time
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. (This experiment provides experimental proof that the teleportation of quantum information in this universe must be complete and instantaneous.)
    http://www.physorg.com/news/20.....tally.html

    ,,, thus Elizabeth, since we have no reason to believe that purely material processes, according to the first law of thermodynamics, will ever create energy, then thus how much more so shall we not expect purely material processes to create ‘information’ which exceeds energy in its rank of conservation???

    etc.. etc.. etc..

  37. 37
    Elizabeth Liddle

    oops, I meant “make the assumption that the other is posting in good faith”?

    cheers

    Lizzie

  38. 38
    Elizabeth Liddle

    bornagain77: no I’m not upset, don’t worry! It’s just that by assuming that I’m being dishonest you are consistently missing the points I’m trying to make.

    Obviously we are in deep disagreement, but I suggest that this is not because either of us are dishonestly looking at (or failing to look at) the evidence. It’s that we each seem to be referring to very different bodies of evidence, and, indeed, have very different ways of even evaluating what is “admissible” evidence.

    So by making the assumption of good faith, perhaps we can drill down to what that evidence is, and why you think it supports your position, and why I think it supports mine.

    I am, as I think you know, a scientist, and so I have, I guess, a particular slant on evaluating evidence. I would contend it is a rigorous one. And, using the evaluation tools at my disposal, I think the evidence for evolutionary theory is extremely strong. I simply disagree with you that there is “no evidence” and I’ve given you a couple of books that cite a lot of the primary findings.

    Let’s try to move on from the question as to who is the blinkered one here to what the arguments and evidence for each case actually are.

    OK?

    Cheers

    Lizzie

  39. Elizabeth, if you are looking for me to cosign your rationalizations, you ain’t going to find it. The evidence is clear and unmistakeable, indeed goes to the core of how reality is actually constructed in the first place!!!

  40. 40
    Elizabeth Liddle

    No, indeed, bornagain77, I am not looking to you to “cosign [my] rationalizations”, as should be very clear from my posts.

    I am simply putting it to you that what you are attributing to my apparent inability to accept what you consider lack of evidence may instead be my view that there is a great deal of evidence.

    However, one problem we seem to have between us, is that I notice that a lot of your posts, which you present, it seems as evidence that infirms the Darwinian model of evolution, are in fact posts about physics and cosmology.

    I simply do not see these as counter arguments to evolutionary theory. Why should the weirdness of existence be an argument against the processes by which existence unfolds?

    I am not arguing against an some transcendental reality that we might call God. I’m simply arguing for Darwinian processes as an account of biological diversity, as I would argue for chemical processes as an account of chemical reactions. There is simply no conflict between a transcendental view of reality and modern biology.

    Your other sources have been to writers who claim there is no evidence for various evolutionary hypotheses. I dispute the claims made by those writers, because I am aware of the work of many scientists, including Neil Shubin and Sean Carroll, who cite, and indeed provide, direct empirical evidence that I consider strongly support evolutionary theory.

    So when you say that “there is no evidence”, can you explain why you discount this evidence? Neil Shubin gives a detailed, empirically supported account of the evolution of “novel body plans” including the very important (for our ancestry) evolution of the four limb patterns.

    And Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.

    Again, by what reasoning do you dismiss this empirical evidence?

    Far from asking you to “cosign [my] rationalizations” I am asking you to defend your own position, namely, that there is “no evidence”.

    In what sense is the above “no evidence”?

    Cheers

    Lizzie

  41. Elizabeth you equate story telling for evidence; for instance you state:

    ‘Neil Shubin gives a detailed, empirically supported account of the evolution of “novel body plans” including the very important (for our ancestry) evolution of the four limb patterns.’

    So you are saying that Shubin provided undeniable evidence that a four limbed creature evolved from some creature that did not have four limbs, yet clearly Shubin did not do this, he only ‘told a story’ that you happily believed.,,, As well, Shubin seems to have some serious, serious, issues with rampant ‘just so’ story telling, instead of solid science, as is clearly noted here:

    Evolutionary biologist Neil Shubin claims that the human breast evolved from fish teeth. (5:08) – Colbert Report
    http://www.colbertnation.com/t.....eil-shubin

    Yet even though he clearly did not demonstrate anything he conjectured, you have ‘dishonestly’ implied that he did have undeniable evidence, what you should have ‘truthfully’ said, but forgot to do, was that Shubin traced a convoluted pathway using pre-chosen genetic similarity to arrive at his predetermined conclusion!!! But alas, when I cut out all the story telling and show you decades of work trying to change a fruit fly into anything other than a fruit fly, all to no avail, this is of no import to you… because??? because??? Well because by golly, Shubin, and company, have told you such wonderful stories that confirms your predetermined conclusion!! This is EXACTLY how you ARE NOT suppose to practice science!!!

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

    There is no evidence that mutations to DNA will effect body-plan morphogenesis in a significant novel, and positive, way;

    …Advantageous anatomical mutations are never observed. The four-winged fruit fly is a case in point: The second set of wings lacks flight muscles, so the useless appendages interfere with flying and mating, and the mutant fly cannot survive long outside the laboratory. Similar mutations in other genes also produce various anatomical deformations, but they are harmful, too. In 1963, Harvard evolutionary biologist Ernst Mayr wrote that the resulting mutants “are such evident freaks that these monsters can be designated only as ‘hopeless.’ They are so utterly unbalanced that they would not have the slightest chance of escaping elimination through natural selection.” – Jonathan Wells

    Darwin’s Theory – Fruit Flies and Morphology – video
    http://www.youtube.com/watch?v=hZJTIwRY0bs

    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.

  42. 42
    Elizabeth Liddle

    OK, bornagain77, perhaps we are homing in on our real difference here.

    Science, you might be surprised to hear me say, is all about telling stories. In other words it’s about devising a causal narrative that explains what we see.

    However, unlike novelists, whose critics are their readers, the ultimate critic of scientific stories are is evidence.

    And the procedure has two parts: First, scientists tell a story that could explain the data they have. Then they use that story to predict data that they do not yet have.

    Then they go out and try to find the data that should exist if their story is true. If they don’t find it, their story remains a story, and, if they find data that is inconsistent with their original story then they have to change the story.

    However, if they do find it, then they can claim support for their story as a viable account of the evidence.

    And, famously, this exactly what Shubin and his colleagues did. They made a story about tetrapod evolution that fit the facts as they had them. And then they used that story to predict that there should be, at a particular level in the geological column, and in a particular kind of habitat, creatures with certain intermediate characteristics, including the beginnings of what would eventually become a “wrist”.

    So they went off to Greenland, where they knew that strata corresponding to the predicted time period and habitat was close to the earth’s surface. And they found fossils of the predicted tetrapod.

    That is the kind of evidence that scientists regard as evidence for their hypothesis – their hypothesis starts as an explanatory “story” that fits the existing data. But that hypothesis must be tested by making a prediction that is subsequently confirmed by new evidence.

    That’s the hard part, and that’s the rigorous part. A hypothesis can be a beautiful story, but unless it predicts new evidence, and that new evidence is found, it remains, at best, unsupported, and at worst, infirmed, and must be changed or discarded completely.

    So that a piece of evidence that I count as evidence.

    Let’s look at what you regard as contrary evidence – the negative evidence of the lack of evidence that a fruit-fly can evolve into anything other than a fruit-fly.

    It may surprise you to know that evolutionary theory not only does not predict that fruitflies will turn into anything other than fruitflies, it predicts that all their descendents will be fruitflies!

    That’s why biological nomenclature is arranged in a nested hierarchy. What may be a species, at one time point, may subdivide into sub-species at another level, and sub-subspecies at yet another level. But the sub-sub-species is still a member of the original species, which we might now re-term a “genus” or some other term.

    So a dog’s descendents will always be dogs, just as the descendants of the carnivora ancestor of both dogs and cats will always be carnivora, and the descendents of the mammalian ancestors of carnivora will always be mammals.

    As for the experiment that involved irradiating fruitfly – why on earth would anyone expect that inflicting gross damage to the genome would result in viable organisms? This is simply not the mechanisms by which novel evolutionary features are proposed to evolve. On the other hand, much more slight mutations to an existing genome can result in some wonderfully adaptive novelties. Look at these extraordinary, closely related, insects:

    http://www.google.co.uk/search.....=&oq=

    (I just discovered them recently).

    And here is a paper on the genetics of these extraordinary features:

    http://www.nature.com/nature/j.....09977.html

    This is an excellent example of what I would consider positive evidence for standard evolutionary theory. I would be interested to know why you think it is not.

  43. Elizabeth, you state:

    ‘Science, you might be surprised to hear me say, is all about telling stories.’

    No Elizabeth, science is about actually proving, by rigorous experimentation, that your narrative is true. On that count you fail miserably. As your ‘story telling’ citations abundantly testify!!!

  44. 44
    Elizabeth Liddle

    Well, nothing is “proven” in science (all conclusions must be provisional), but apart from that niggle, yes, of course, and that’s exactly what I am saying. In science, we create narratives (“tell stories”) but the critics, in the end, are not our readers but the data that either does, or does not, support those narratives.

    So we seem to be agreed on that :)

    Where we disagree on is whether I have failed or succeeded! (well not me personally, although I guess I’ve made the odd small contribution in a very different domain). Shubin’s finding of Tiktaalik was a superb demonstration of a scientific narrative predicting something, in a particular place, and that thing being found!

    That’s as good as it gets in science!

    For what reason do you discount this finding as evidence for Shubin’s narrative?

  45. Elizabeth you state:

    ‘Shubin’s finding of Tiktaalik was a superb demonstration of a scientific narrative predicting something, in a particular place, and that thing being found!’

    And yet once again your evidence falls completely apart upon scrutiny;

    The supposed ‘evidence’ for the evolution of fish to land dwelling creatures is not even close to the conclusive evidence evolutionists pretend that it is:

    Tiktaalik- Out Of Order
    Excerpt: One of the problems with an evolutionary interpretation of the fishapods is that these creatures appear to be out of order.
    http://www.reasons.org/OutofOrder

    Tiktaalik Blown “Out of the Water” by Earlier Tetrapod Fossil Footprints – January 2010
    Excerpt: The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr.
    http://www.evolutionnews.org/2.....e_wat.html

    This following article has a excellent summary of the ‘less than forthright’ manner in which Darwinists handle anyone who dares to tell of falsifications to their paltry evidence for ‘transitional’ fossils:

    Evolutionary Biologists Are Unaware of Their Own Arguments: Reappraising Nature’s Prized “Gem,” Tiktaalik – Casey Luskin – September 2010
    http://www.evolutionnews.org/2.....38261.html

    But alas Elizabeth, you are left with nothing but story telling once again!!!

  46. There isn’t any evidence that genetic accidents can accumulate in such a way as to give rise to useful, functional multi-part systems. That means there couldn’t have been any climbing.

    You’ve never heard of climbing downhill?

  47. For a clear instance of your inability to honestly face the truth Elizabeth…

    That’s right Elizabeth. You are a WONDERFUL person, and the sooner you come to accept that fact the better off we’ll all be. You simply MUST honestly face the truth.

    Cheers.

  48. Elizabeth, you alluded to a ‘prediction’, which you unwittingly was falsified a few years back, as quote, ‘That’s as good as it gets in science!’

    Now Elizabeth verified, and falsified, predictions are indeed ‘about as good as it gets in science!’ and are a very, very strong indication of a hypothesis veracity towards the truth.,, So Elizabeth please note that earlier in this post I presented this evidence;

    The following articles show that even atoms (Ions) are subject to teleportation:

    Ions have been teleported successfully for the first time by two independent research groups
    Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,,

    Atom takes a quantum leap – 2009
    Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,,
    “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second.

    So Elizabeth materialism, which is the basis of neo-Darwinian thought, predicted, for thousands of years, that the foundational basis of reality was a solid indestructible particle that has always existed. Whereas Theism, particularly Christian Theism, in John 1:1-3, predicted that The Word (Logos) was/is the foundational basis of reality; i.e. Theism predicted ‘information’ as the foundational basis of reality and moreover that prediction was confirmed at the expense of falsifying the very foundation of reality that neo-Darwinism affirms!!! As you said Elizabeth ‘That’s as good as it gets in science!’!!!

    But Elizabeth, though that ought to severely shake your belief in anything based on materialism in the first place, it gets far worse if we dig just a bit deeper into the predictive power of theism compared to materialism;

    ,,,The materialistic and Theistic philosophy make, and have made, several natural contradictory predictions about what evidence we will find. These predictions, and the evidence we have found, can be tested against one another within the scientific method.

    Steps of the Scientific Method
    http://www.sciencebuddies.org/.....thod.shtml

    For a quick overview, here are a few:

    1. Materialism predicted an eternal universe, Theism predicted a created universe. – Big Bang points to a creation event. -

    2. Materialism predicted time had an infinite past, Theism predicted time had a creation. – Time was created in the Big Bang. -

    3. Materialism predicted space has always existed, Theism predicted space had a creation (Psalm 89:12) – Space was created in the Big Bang. -

    4. Materialism predicted that material has always existed, Theism predicted ‘material’ was created. – ‘Material’ was created in the Big Bang.

    5. Materialism predicted at the base of physical reality would be a solid indestructible material particle which rigidly obeyed the rules of time and space, Theism predicted the basis of this reality was created by a infinitely powerful and transcendent Being who is not limited by time and space – Quantum mechanics reveals a wave/particle duality for the basis of our reality which blatantly defies our concepts of time and space. -

    6. Materialism predicted the rate at which time passed was constant everywhere in the universe, Theism predicted God is eternal and is outside of time – Special Relativity has shown that time, as we understand it, is relative and comes to a complete stop at the speed of light. (Psalm 90:4 – 2 Timothy 1:9)-

    7. Materialism predicted the universe did not have life in mind and life was ultimately an accident of time and chance. Theism predicted this universe was purposely created by God with man in mind – Every transcendent universal constant scientists can measure is exquisitely fine-tuned for carbon-based life to exist in this universe. -

    8. Materialism predicted complex life in this universe should be fairly common. Theism predicted the earth is extremely unique in this universe – Statistical analysis of the hundreds of required parameters which enable complex life to be possible on earth gives strong indication the earth is extremely unique in this universe. -

    9. Materialism predicted much of the DNA code was junk. Theism predicted we are fearfully and wonderfully made – ENCODE research into the DNA has revealed a “biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.”. -

    10. Materialism predicted a extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. Theism predicted only God created life on earth – The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial mutations whatsoever. (M. Behe; JC Sanford) -

    11. Materialism predicted a very simple first life form which accidentally came from “a warm little pond”. Theism predicted God created life – The simplest life ever found on Earth is far more complex than any machine man has made through concerted effort. (Michael Denton PhD) -

    12. Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11) – We find evidence for complex photo-synthetic life in the oldest sedimentary rocks ever found on earth -

    13. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God’s fifth day of creation. – The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short “geologic resolution time” in the Cambrian seas. -

    14. Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record – Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. -

    15. Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth – Man himself is the last generally accepted major fossil form to have suddenly appeared in the fossil record. -

    references:
    https://docs.google.com/document/pub?id=1ubha8aFKlJiljnuCa98QqLihFWFwZ_nnUNhEC6m6Cys

    As you can see when we remove the artificial imposition of the materialistic philosophy, from the scientific method, and look carefully at the predictions of both the materialistic philosophy and the Theistic philosophy, side by side, we find the scientific method is very good at pointing us in the direction of Theism as the true explanation. – In fact it is even very good at pointing us to Christianity:

    General Relativity, Quantum Mechanics, Entropy & the Shroud Of Turin – video
    http://www.metacafe.com/watch/5070355

  49. correction; which unwittingly, to you, was falsified a few years back,

  50. Elizabeth @40:

    And Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.

    Honest question.

    Does he show how small changes to existing genes can specify radically different body plans, or does he show how it came to be the case that small changes to genes came to specify radically different body plans?

    Do you see the distinction and do you agree it’s a valid one?

    Don’t you think it’s the latter question that needs to be answered, rather than the former?

  51. 51
    Elizabeth Liddle

    No, bornagain77, the evidence does NOT “fall apart on scrutiny”. Shubin et al predicted that a creature like Tiktaalik would be found in a particular place in Greenland, it it was. This is a spectactular example of new data supporting a prior
    hypothesis.

    The hypothesis was not that no other tetrapods would be found, nor that Tiktaalik was the earliest tetrapod.

    And virtually no fossil is likely to be in a direct line of descent to modern species. There are likely to be no living descendents of Tiktaaliks.

  52. Elizabeth you say Shubin’s fossil is an amazing ‘predicted’ find. Well lets look at a couple of falsified predictions that call into question the severe import that you want to place on this one fossil;

    notes;

    ,,,,13. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God’s fifth day of creation. – The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short “geologic resolution time” in the Cambrian seas. -

    Materialistic Basis of the Cambrian Explosion is Elusive: BioEssays Vol. 31 (7):736 – 747 – July 2009

    Excerpt: “going from an essentially static system billions of years in existence to the one we find today, a dynamic and awesomely complex system whose origin seems to defy explanation. Part of the intrigue with the Cambrian explosion is that numerous animal phyla with very distinct body plans arrive on the scene in a geological blink of the eye, with little or no warning of what is to come in rocks that predate this interval of time.” —”Thus, elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists.”

    http://www.evolutionnews.org/2.....mater.html

    Deepening Darwin’s Dilemma – Jonathan Wells – Sept. 2009

    Excerpt: “The truth is that (finding) “exceptionally preserved microbes” from the late Precambrian actually deepen Darwin’s dilemma, because they suggest that if there had been ancestors to the Cambrian phyla they would have been preserved.”

    http://www.discovery.org/a/12471

    Deepening Darwin’s Dilemma – Jonathan Wells – The Cambrian Explosion – video

    http://www.metacafe.com/watch/4154263

    14. Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record – Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. -

    Here is a page of quotes by leading paleontologists on the true state of the fossil record:

    https://docs.google.com/document/pub?id=15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg

    Here are four more pages of quotes, by leading experts, on the fossil record here:

    Creation/Evolution Quotes: Fossil Record #1 – Stephen E. Jones

    http://members.iinet.net.au/~sejones/fsslrc01.html

  53. 53
    Elizabeth Liddle

    Mung:

    Honest question.

    Does he show how small changes to existing genes can specify radically different body plans, or does he show how it came to be the case that small changes to genes came to specify radically different body plans?

    Do you see the distinction and do you agree it’s a valid one?

    Don’t you think it’s the latter question that needs to be answered, rather than the former?

    Well, I think answers to the first shed light on the second. Obviously we can’t, in most cases, do genetic analyses of long extinct species. We can however do experiments with extant species and observe the effects of tampering with genes that are implicated in the embryological time table that determines body plans, as well as examine genetic phylogenies.

    There’s a paper relevant to your second point here:

    http://icb.oxfordjournals.org/.....9.abstract

    The developmental perspective on genetics is fascinating, and of course extremely relevant to practical research into developmental disorders.

  54. 54
    Elizabeth Liddle

    Well, bornagain77, I don’t think the evidence you cite in anyway calls into question the import of Shubin’s find. It’s perfectly true that Darwin envisaged a very slow and steady process, and that what we see instead is a process that is far more rapid than Darwin foresaw (remember that Darwin had no idea about the mechanics of inheritance). But we now know from both genetics and mathematical models much more about the dynamics of fitness landscapes, and that “punctuated equilibrium” is a common pattern, as observed in the fossil record. Sudden extinction events and periods of comparatively rapid radiation turn out to be consistent with the dynamics of adaptive evolution, especially now that we know what we know about the role of drift (something that Darwin did not consider).

    And I’m afraid I simply disagree with the interpretations expressed in your cited sources.

  55. Elizabeth, as to your citation, here is another citation that directly parallels it;

    I like this following paper for though it is materialistic in its outlook at least Dr. Eugene Koonin, unlike many materialists, is brutally honest with the genetic evidence we now have.

    The Biological Big Bang model for the major transitions in evolution – Eugene V Koonin – Background:
    “Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin’s original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life’s history, the principal “types” seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate “grades” or intermediate forms between different types are detectable;
    http://www.biology-direct.com/content/2/1/21

    Biological Big Bangs – Origin Of Life and Cambrian – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4284466

    It should be noted that Dr. Koonin tries to account for the origination of the massive amounts of functional information, required for the Cambrian Explosion, and other ‘explosions’, by trying to access an ‘unelucidated and undirected’ mechanism of Quantum Mechanics called ‘Many Worlds’. Besides Dr. Koonin ignoring the fact that Quantum Events, on a whole, are strictly restricted to the transcendent universal laws/constants of the universe, including and especially the second law of thermodynamics, for as far back in time in the universe as we can ‘observe’, it is also fair to note, in criticism to Dr. Koonin’s scenario, that appealing to the undirected infinite probabilistic resource, of the quantum mechanics of the Many Worlds scenario, actually greatly increases the amount of totally chaotic information one would expect to see generated ‘randomly’ in the fossil record. In fact the Many Worlds scenario actually greatly increases the likelihood we would witness total chaos surrounding us as the following points out:

    The Many Worlds interpretation of Quantum Mechanics, that Koonin has used in his paper, is in fact derived because of the inability of ‘materialistic scientists to find adequate causation for quantum wave collapse (adequate causation that did not involve God!):

    Quantum mechanics
    Excerpt: The Everett many-worlds interpretation, formulated in 1956, holds that all the possibilities described by quantum theory simultaneously occur in a multiverse composed of mostly independent parallel universes.[39] This is not accomplished by introducing some new axiom to quantum mechanics, but on the contrary by removing the axiom of the collapse of the wave packet:
    http://en.wikipedia.org/wiki/Quantum_mechanics

    Perhaps some may say Everett’s Many Worlds in not absurd, if so,, then in some other parallel universe, where Elvis happens to now be president of the United states, they actually do think that the Many Worlds conjecture is absurd,, and that type of ‘flexible thinking’ I find to be completely absurd!!! And that one ‘Elvis’ example from Many Worlds is just small potatoes to the levels of absurdity that we could draw out if Many Worlds were actually true.

    The Absurdity Of The Many Worlds Hypothesis – William Lane Craig – Last 5 minutes of this video
    http://www.metacafe.com/watch/4784630

    Though Eugene Koonin is correct to recognize that the infinite probabilistic resource found in ‘Quantum Mechanics’ does not absolutely preclude the sudden appearance of massive amounts of functional information in the fossil record, he is very incorrect to disregard the ‘Logos’ of John 1:1 needed to correctly specify the ‘precisely controlled mechanism of implementation’ for the massive amounts of complex functional and specified information witnessed abruptly and mysteriously appearing in the ancient genomes of these ancient fossils. i.e. He must sufficiently account for the ’cause’ for the ‘effect’ he wants to explain. And as I have noted previously, Stephen Meyer clearly points out that the only known cause now in operation, sufficient to explain the generation of massive amounts of functional ‘digital’ information, is intelligence:

    Stephen C. Meyer – What is the origin of the digital information found in DNA? – August 2010 – video
    http://www.evolutionnews.org/2.....37271.html

    This following paper corroborates Koonin’s observation of irreconcilable differences being found in the genetic evidence with Darwinian evolution:

    Why Darwin was wrong about the (genetic) tree of life: – 21 January 2009
    Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts – also known as tunicates – are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says. .”We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely,” says Syvanen. “What would Darwin have made of that?”
    http://www.newscientist.com/ar.....-life.html

    I would like to point out that this, ‘annihilation’ of Darwin’s genetic tree of life, article came out on the very day that Dr. Hillis, a self-proclaimed ‘world leading expert’ on the genetic tree of life, testified before the Texas State Board Of Education that the genetic tree of life overwhelmingly confirmed gradual Darwinian evolution. One could almost argue it was ‘Intelligently Designed’ for him to exposed as a fraud on that particular day of his testimony instead of just any other day of the year.

  56. So Elizabeth, basically, by refusing to honestly address the evidence, you are saying that nothing can falsify your worldview. i.e. You hold one very, very, shaky ‘verified prediction’ for materialism, in the face of many more directly. and concretely ‘verified predictions’ for Theism.,,, Well I don’t know exactly what your thinking, but what you are doing certainly IS NOT science!, perhaps God, who does know exactly what you are thinking, will help you sort it all out when you die and meet Him:

    It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in 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)

    coast to coast – Blind since birth – Vicki’s NDE
    http://www.youtube.com/watch?v=e65KhcCS5-Y

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

  57. 57
    Elizabeth Liddle

    bornagain77: yes, Koonin is an interesting guy. Nice link!

    Note though that he makes it absolutely clear in his paper, and in the interesting discussion below,that he is drawing an analogy.

    I think it’s a bit strained myself, but his “Biological Big Bang” model seems to stand on its own merits.

    It is, however, an evolutionary model:

    I propose that most or all major evolutionary transitions that show the “explosive” pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements.

    (my bold)

    It makes a fair bit of sense to me, and should generate testable hypotheses.

  58. Such as this testable hypothesis Elizabeth???

    This following study is very interesting for the researcher surveyed 130 DNA-based evolutionary trees to see if the results matched what ‘natural selection’ predicted for speciation and found:

    Accidental origins: Where species come from – March 2010
    Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel’s team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation – but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: “It isn’t the accumulation of events that causes a speciation, it’s single, rare events falling out of the sky, so to speak.”
    http://www.newscientist.com/ar.....tml?page=2

    So Elizabeth how do you like that ‘falling out of the sky’ bit???

  59. Another busy day in the junkyard!

    Elizabeth Liddle @53:

    Well, I think answers to the first shed light on the second. Obviously we can’t, in most cases, do genetic analyses of long extinct species.

    So your answer then is the former, correct? Not that I had any doubt.

    Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.

    Existing genes, existing body plans. So what does this tell us about how such genes and body plans came about in the first place?

    Does Carroll address that question?

    Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.

    Cite time. If you can. Please cite an example of Sean Carroll showing how a small change in a gene specifies a radically different body plan.

    I have the book, so you don’t have to type it up unless you want to. Just give me a reference.

    And please address the question, if you can, how does changing an existing gene and watching how it affects body plan development actually tell us how such genes and body plans came about in the first place?

    THAT is the $64,000 question.

  60. Elizabeth, I noticed that you highlighted the word ‘evolution’ in post 57; That reminded me of this observation by Phil Skell:

    ‘I also examined the outstanding biodiscoveries of the past century: the discovery 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; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin’s theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.’
    (Phil Skell, “Why Do We Invoke Darwin?,” The Scientist, 2005, Vol. 19(16):10 (2005) (emphasis added).)

    And in this following video, at the 7:00 minute mark, Dr. Behe demonstrates the mere ‘narrative gloss’ characteristic of the word ‘evolution’, by removing the word ‘evolution’ from a piece of peer-reviewed literature, and showing that it had no effect on the core finding of the research!:

    Michael Behe – Life Reeks Of Design – video
    http://www.youtube.com/watch?v=Hdh-YcNYThY

    So Elizabeth, how much was ‘narrative gloss’, in Koonin’s paper, and how much was actual evidence that neo-Darwinism can actually create functional information. Once you see the fact that there is ZERO empirical evidence that purely material processes can create integrated functional information, then you may perhaps start to see how bankrupt neo-Darwinism is of true explanatory power!!!

  61. 61
    Elizabeth Liddle

    Mung, if it can be shown that a small change in a gene results in a large change in body plan, the objection that changes in body plan cannot have evolved by means of incremental changes to DNA ceases to have force, no?

    So the two questions are intimately connected.

  62. Mung, if it can be shown that a small change in a gene results in a large change in body plan, the objection that changes in body plan cannot have evolved by means of incremental changes to DNA ceases to have force, no?

    No, it does not cease to have force. That’s why am trying to take you along this path, so that you will be able to understand why.

    I’m just asking that we take this and look at it in depth. You use it as a somewhat flippant response to BA77, but it does not carry the force you think it does.

    Using it in an argument might work against people who don’t know better, but to others it looks like you’re just spouting talking points.

    Sean Carroll explains, at a detailed genetic level, just how small changes to genes can specify radically different body plans.

    Your biggest mistake is in thinking that these genes act as a specification for a body plan. But isn’t it the case that really they just act as a switch and the specification is somewhere else?

    Maybe you were just using sloppy language to describe a complex subject. It happens.

    But you really seam to think that a small tweak to one or two genes here and there can specify radically different body plans, and you seem to think that this is demonstrated by Carroll in Endless Forms.

    I just want to find out of this is what Carroll actually demonstrates in the book you cite, or if you’re just winging it.

    I have the book, let’s take a look.

    Can you provide an example?

  63. 63
    Elizabeth Liddle

    No, Mung, I don’t think that a small tweak to a gene in an existing organism can make it, for example, become an arthropod rather than a vertebrate.

    It’s not what I’m claiming, and I apologise if you misread me.

    What I am claiming is that findings in “evo-devo” show us that genes are hierarchical, and that the same genes, in creatures with radically different body-plans, are nonetheless key to those body plans, and how they develop depends, as you say, on “switches”.

    And no, I’m not “just spouting talking points”. Why on earth would I? If something I say doesn’t make sense to you, I’m only too happy to try to clarify.

    I can’t actually find my copy of Endless Forms right now (I think it is buried in my son’s bedroom somewhere) so I can’t give you a citation that I can guarantee comes from there. I can cite some primary literature however (and did so above). Here are a three more:

    http://www.imbb.forth.gr/peopl.....Nature.pdf

    http://www.sciencemag.org/cont...../796.short (paywall, unfortunately)

    http://blogimages.bloggen.be/t...../16147.pdf (found a pdf posted somewhere for this one).

  64. Elizabeth, with respect, I try not to play the “here, read all these links and maybe you’ll find something in them that makes the point I’m trying to make” game.

    Do you have something specific in mind from one of these? Make it one that I can access for free, please.

    And like I said, I have a copy of the book. If you can just tell me what to look for. Perhaps something specific that you remember that stuck out in your mind.

    I’ve told you that I think it does not cease to have force, perhaps you can explain why you think it does for you.

  65. 65
    Elizabeth Liddle

    Mung, me too, but you asked me for some examples from Carroll, which I didn’t have to hand, so I gave you some papers instead, all of which give examples of genes, or gene regulatory network implicated in the evolution of diverse body plans by means of regulation of hox genes.

    Two of the citations I gave you are full text. I couldn’t find an open access source for the other.

    As for the book – well, the whole book is about the role of hox genes and regulatory gene networks in specifying body plans.

    And right now, I’m not clear why you don’t think the evidence that small incremental changes can have a large effect on body plans has no force.

    It seems to me it is the major message of Carroll’s book, and I have given you three references in support.

    But then we seem to disagree with the message of Sanford’s book too, so perhaps that is telling :)

    (I wrote to him, btw, but I haven’t heard back).

    Anyway, the Averof 1995 Nature paper references an earlier paper in Current Biology, which is behind a firewall, unfortunately, but continues the story of investigating divergence in hox genes that led to crustaceans and arthropods.

    The Science paper (Davidson and Erwin 2006) is about the role of Gene Regulatory Networks, and reports evidence suggesting that these were laid down prior to the diversification and placed strong constraints on evolution of new body plans down that lineage (hence their bilateral ground plan).

    The other Nature paper (Ronshaugen et al, 2002) reports evidence for “that links naturally selected alterations of a specific protein sequence to a major morphological transition in evolution”, again the divergence of insects from the line that would become crustaceans.

  66. Elizabeth Liddle:

    I’m not clear why you don’t think the evidence that small incremental changes can have a large effect on body plans has no force.

    Ok, let’s start with that.

    It was not my contention that changes to existing genes cannot have a “large” effect on existing body plans.

    I’d willingly grant that’s what Carroll shows. I just don’t see how it’s relevant.

    So to understand each other better we obviously need to concentrate on the latter half of that statement.

    I understand the context to be the question of the origination of body plans themselves.

    I don’t see how changing an existing gene, and showing how it effects an existing body plan, tells us anything at all about how body plans themselves came to be, nor how genes which have a large effect on body plans came to be.

    That’s what I mean when I say these arguments have little or no force.

    IOW, we can explain B, but what we can’t explain is A, where A is required for there even to be a need for an explanation for B.

    Does that help?

    Would you like me to attempt to develop an analogy?

    In summary:

    What needs to be explained is:

    A. The origination of body plans

    B. The origination of gene regulatory networks

    C. The origination of genes which when changed have a large effect on A and B.

    How can C effect A or B unless A or B exist before C?

    But if A or B exist before C, what need is there of C?

    Now I will say this. I am willing to drop this entire line. Personally I prefer to concentrate on unicellular organisms.

    If you’re not willing to accept the modern cell as the starting point then you need to explain how we got from something else to where we are today.

    My own personal area of interest is the cell membrane.

    If that interests you perhaps you could point me to some sources that explain how it evolved. If not, that’s ok too.

  67. I wrote to him, btw,
    but I haven’t heard back.

    Hey, that’s great! I hope he’ll respond.

    I am really interested in hearing what he has to say. I need to know if I need to stop claiming he meant one thing if he says he meant another!

    I would be immensely ashamed if BA77 turned out to be right and I was wrong, lol.

    Will you share which question(s) you posed?

  68. 68
    Elizabeth Liddle

    I’ll wait until Sanford replies, I think, before I post the text of the email, I sent. But I did invite him to comment on the thread, so I’ll keep checking there too!

  69. 69
    Elizabeth Liddle

    Mung @ #66

    Elizabeth Liddle:

    I’m not clear why you don’t think the evidence that small incremental changes can have a large effect on body plans has no force.

    Ok, let’s start with that.

    It was not my contention that changes to existing genes cannot have a “large” effect on existing body plans.

    I’d willingly grant that’s what Carroll shows. I just don’t see how it’s relevant.

    So to understand each other better we obviously need to concentrate on the latter half of that statement.

    Cool.

    I understand the context to be the question of the origination of body plans themselves.

    I don’t see how changing an existing gene, and showing how it effects an existing body plan, tells us anything at all about how body plans themselves came to be, nor how genes which have a large effect on body plans came to be.

    That’s what I mean when I say these arguments have little or no force.

    IOW, we can explain B, but what we can’t explain is A, where A is required for there even to be a need for an explanation for B.

    Does that help?

    Yes indeed.

    I guess I was taking an example of a genetic account of a fairly radical change in body plan (and that research does contribute a response to a fairly frequently made challenge that Darwinian evolution can’t account for major new features, which is the point I thought you were making). However, as you say, the research I cited does not address the whole issue of how multicellular organisms came into being (in a Darwinian framework), although there is research that does (or at least looks promising).

    None of this is my area of course, although I would argue, not a hundred miles away, neither, which is why I am an interested consumer of the research, being about systems biology, which is much closer to what I do.

    So I’ve read a number of interesting papers about it,and I’m trying to find some that aren’t behind a paywall (having university access to journals is a huge boon, and I do hope that the trend for open access continues).

    The general approach seems to be that multicellularity evolved from populations of single-celled organisms that had evolved to live in colonies, which would have necessitated some kind of signalling. That in itself needs an evolutionary account of course (in evolutionary biology, all questions lead further back, of course!) but the idea is that once you have some kind of chemical signalling process i.e. a cell develops differentially depending on chemical inputs from either other organisms or the environment, you have the beginnings of the kind of cell differentiation we see in multicellular organisms. The earliest may have been no more than mats of floating cells, in which the outer organisms developed in a way that gave greater protection from the environment, leaving the inner cells to do something else.

    Anyway, there is one open access review paper here that you might like:

    http://people.vanderbilt.edu/~.....as_ARG.pdf

    I hadn’t actually read it, but it cites some papers I have read, which is how I found it.

    In summary:

    What needs to be explained is:

    A. The origination of body plans

    B. The origination of gene regulatory networks

    C. The origination of genes which when changed have a large effect on A and B.

    How can C effect A or B unless A or B exist before C?

    But if A or B exist before C, what need is there of C?

    I think a key concept here is “co-evolution”. But, to be specific, gene-regulatory networks are likely to have evolved from the kind of signalling processes that enhance the survival chances of unicellular organisms – the kind of simple chemical signals that emanate from food or threat, and to which a particular physiological response is protective. Once you have that kind of system, you have the potential for incremental tuning of responses to signals that can potentially extend to between-organism signalling. So my hypothesis would be that the beginnings of B preceded A. However, B would also have had to have an effect on the development of the unicellular organism (by definition) in other words must have been some kind of switch mechanism that modulated gene expression. So there’s a touch of C in there too. And once you have inter-organism signalling processes (the proximity of another organism modulates gene expression) then you have the potential for A. And once you have A, B’s effects can affect both A and C.

    But, as I say, it’s not my field. However, such a system would be easy enough to model, and would make testable predictions.

    Now I will say this. I am willing to drop this entire line. Personally I prefer to concentrate on unicellular organisms.

    Cool :) Yes, let’s keep drilling backwards.

    If you’re not willing to accept the modern cell as the starting point then you need to explain how we got from something else to where we are today.

    Absolutely. Well, I’d be “willing” in principle to accept the “modern cell as the starting point” if it became impossible to explain how we got from “something else” to the modern cell. But that’s a good reason to attempt to explain it!

    My own personal area of interest is the cell membrane.

    If that interests you perhaps you could point me to some sources that explain how it evolved. If not, that’s ok too.

    Yes indeed. The most promising approaches as far as I can see right now posit both a “self-replicating” spherical membrane (which is relatively easy to do, given the properties of lipids and their hydrophilic/hydrophobic poles) within a marine environment that is rich in polymers and other compounds.

    The most prominent researcher in this field, as you probably know, is Joe Szostak

    http://genetics.mgh.harvard.edu/szostakweb/

    The core of his idea seems to be that self-replicating polymers trapped within lipid vesicles might differentially affect the rate of subdivision of the vesicle, leading to “selection” (i.e. greater prevalence) of those vesicles that “inherited” a particular configuration of polymer.

    But there are also other approaches.

    (Hey, I’ve just discovered that the editing marquee window here can enlarged! That might improve my proof-reading!)

  70. Elizabeth, whatever you may think of Sanford’s YEC position, the fact is that you cannot produce evidence that Genomes are not Deteriorating. Moreover it is very suspect that you would choose to ignore the extreme poverty of evidence for your very own worldview, while dismissing his solid empirical evidence for genetic deterioration. If you want to look at worldviews by all means let’s put all cards on the table and see your materialistic worldview for the absurdity it really is!!!

  71. 71
    Elizabeth Liddle

    ba77:

    Obviously our starting points are very different, so I do understand that it must be difficult to see my position as anything other than “suspect”. That’s OK, though – it just means that we have to be very careful to ensure that we are not comparing apples and oranges – that we are talking about the same thing when we each use certain words.

    In a Darwinian framework, as I tried to explain elsewhere, a “deleterious” allele/mutation is simply one that reduces your chances of reproducing successfully in the current environment.

    So, by definition, in a Darwinian framework, our Genome is, by definition, not deterioriating, because the human population, far from shrinking, is exploding! So in terms of reproductive success, our genomes have never been better.

    However, that doesn’t mean we necessarily live as long (although I don’t share Sanford’s view of the validity of biblical data wrt to past life-spans), nor even that we have as many children (we don’t), but that the net effect on the population, of our current genome, in this environment, is “advantageous”. We are populating the world as never before.

    Nor does it mean that we are not more prone to genetic diseases (we may be) nor more resistant to infection (we may not be). Because of modern medical care, it is actually quite likely that those traits are increasing in our population, and from a certain point of view,that could be described as “degeneration”. However, modern medical care is our current environment, and just as a broken vitamin C gene is not “deleterious” in an environment full of fruit, so decreased resistance to disease is not “deleterious” in an environment full of vaccines.

    I would note, of course, that mutations are extremely common. You and I possess a large number of de novo mutations in our genome. Most of these are harmless. Some may even benefit us. Rather more may be potentially harmful.

    But the emphasis must be on the “potentially”. In the absence of the kind of life-threats our species faced even in the recent past (think how perinatal mortality has come down), any mutation that confers vulnerability to past threats will no longer tend to be “weeded out” by premature death.

    So in that sense, it is likely that our human genome is “deteriorating” i.e. in the sense that it is no longer well suited to, say, Victorian urban life.

    But we aren’t Victorian urban dwellers! All that matters, in judging the “degeneracy” of a genome is whether, in the current environment, our population is shrinking or not.

    And sadly, for some populations, it is. Very small populations are at serious risk of extinction because of buildup of mutations that really do reduce the probability of successful reproduction in the current environment.

    But with the human population standing at 6.92 billion and climbing – well, that’s my evidence that Genomes are not Deteriorating!

  72. Elizabeth, you cannot appeal to evidence that fits just as easily within the theistic worldview to support your own materialistic worldview. You must use direct empirical evidence to make your case for neo-Darwinism, So thus once again I remind you that you simply have ZERO empirical evidence to support your worldview!!

    notes:

    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

    Even if a truly beneficial random mutation/variation event to the DNA ever did occur, ignoring the fact that that the DNA doesn’t solely control encoding for body plans, the ‘beneficial mutation’ would still be of absolutely no use for a Darwinian scenario because the mutation would be swallowed in the vast ocean of slightly detrimental mutations which are far below the culling power of natural selection to remove from a genome. these following studies make this point clear:

    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/

  73. 73
    Elizabeth Liddle

    Well, if we are talking about my worldview, ba77, I’m not really sure what to offer.

    I’m not sure what aspect of it you think I have zero evidence for.

    In fact, I’m not even sure what you think my worldview is!

    But as I said, the evidence that the human genome is not deteriorating is the simple evidence that the human population is rapidly increasing!

  74. Elizabeth you stated:

    ‘Obviously our starting points are very different, so I do understand that it must be difficult to see my position as anything other than “suspect”.’

    Elizabeth, besides materialism being shown to be false by science, you can’t even justify doing science, in the first place, with your materialistic ‘starting point’, so why in blue blazes should I see your ‘starting point’ as anything other than ‘suspect’???

    “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

    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

    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/

    Can atheists trust their own minds? – William Lane Craig on 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

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

    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

    ———————
    etc.. etc.. etc..

  75. 75
    Elizabeth Liddle

    Oh, and yes, I do know the literature cited by Sanford. As I think I said elsewhere, I read his book extremely thoroughly, and also read most of the papers he cited.

    I don’t agree with the inferences he draws from them.

    The papers themselves are good.

  76. Elizabeth, your ‘empirical’ proof for neo-Darwinism is that human populations are increasing??? Shoot by your standards I’ve just proved Theism as true!!!!

    Genesis 1:28
    And God blessed them. And God said to them, “Be fruitful and multiply and fill the earth and subdue it and have dominion over the fish of the sea and over the birds of the heavens and over every living thing that moves on the earth.”

    ,,,Shoot Elizabeth, using your standard of human populations increasing as solid proof for my worldview, I can even prove that Christian Theism is true:

    Sometimes it is honestly asked, “Why did God wait so many billions of years to send Jesus to this earth to reconcile God with man?” Yet from the perspective of human race itself it is found:

    What happened 5000 years ago? – Dinesh D’Souza

    Excerpt: The Population Reference Bureau estimates that the number of people who have ever been born is approximately 105 billion. Of this number, about 2 percent were born before Christ came to earth. “So in a sense,” Kreps notes, “God’s timing couldn’t have been more perfect. If He’d come earlier in human history, how reliable would the records of his relationship with man be? But He showed up just before the exponential explosion in the world’s population, so even though 98 percent of humanity’s timeline had passed, only 2 percent of humanity had previously been born, so 98 percent of us have walked the earth since the Redemption.”

    http://www.estatevaults.com/bo.....ned_5.html

    World Population Growth Through History – Graph

    http://cdn.physorg.com/newman/.....opulat.gif

    Galatians 4:4

    But when the fullness of the time was come, God sent forth his Son, made of a woman, made under the law,

  77. 77
    Elizabeth Liddle

    Bornagain77:

    Elizabeth you stated:

    ‘Obviously our starting points are very different, so I do understand that it must be difficult to see my position as anything other than “suspect”.’

    Elizabeth, besides materialism being shown to be false by science, you can’t even justify doing science, in the first place, with your materialistic ‘starting point’, so why in blue blazes should I see your ‘starting point’ as anything other than ‘suspect’???

    The thing is, ba77, I don’t actually accept that “materialism [has been] shown to be false by science”! At least, I’m not persuaded that it has, but then I don’t exactly know what you are referring to as “materialism” nor in what sense it has been “shown to be false”. So it’s difficult for me to even evaluate your links to see whether they do show materialism to be false, because I’m not at all sure what showing materialism to be false would even look like.

    Perhaps you could explain what you think my “materialistic starting” point is? And why it means that I can’t “justify doing science”?

  78. Well Elizabeth, since Sanford actually provides solid empirical support for his position, and you have merely ‘disagreed’ with his ‘interpretation, exactly whose opinion do you think I should pay heed to??? And whose opinion should I regard as merely a philosophical presupposition trumping science???

  79. 79
    Elizabeth Liddle

    ba77:

    Elizabeth, your ‘empirical’ proof for neo-Darwinism is that human populations are increasing??? Shoot by your standards I’ve just proved Theism as true!!!!

    No, ba77, I didn’t offer it as “proof” of anything, and certainly not as “proof for neo-Darwinism” whatever that is.

    I offered it as evidence that the Genome is not Deterioriating.

    Which it is, as long as we consider “deterioriating” as meaning “rendering successful reproduction less likely.

    On other definitions it may well be deteriorating, but on those definitions we wouldn’t be heading for extinction, as Sanford claims.

  80. Elizabeth you state;

    ‘I don’t actually accept that “materialism [has been] shown to be false by science”!’

    Of COURSE YOU DON”T!!!

    ,,,Transcendent origin of universe, No Prob,,, Infinite multiverse,,,,

    Quantum wave collapse, No Prob,,,, Infinite parallel universes,,,

    Quantum teleportation of atoms, No prob,,, let me get back to you on that,, :)

    Yes indeed a materialistic funhouse of where Alice in wonderland rules the day!!!

  81. 81
    Elizabeth Liddle

    ba77:

    Well Elizabeth, since Sanford actually provides solid empirical support for his position, and you have merely ‘disagreed’ with his ‘interpretation, exactly whose opinion do you think I should pay heed to??? And whose opinion should I regard as merely a philosophical presupposition trumping science???

    No, in fact, he doesn’t provide “solid empirical support” for his position. Three of his main references are to the work of Crow, Kondrashov and Kimura, all of whom are population geneticists working with theoretical models. Indeed, Kondrashov’s paper (the one you cited) actually asks, in effect: this is what the theory shows, and it is at odds with the data, so what is wrong with the theory? (“Why have we not died 100 times over?”)

    There is certainly empirical data showing that in small populations “genetic meltdown” is a problem. There is also empirical data showing that many populations cycle between periods of relaxed selection, in which potentially deleterous mutations accumulate, followed by more stringent selection, in which those mutations are purged.

    Sanford also makes a few actual errors,though I’d have to go back to my notes to see what they were – one was to do with his extrapolation from a graph derived from Kimura, IIRC.

    I’m not asking you to regard me as authority, of course, ba77, so of course you are entitled to reference people who view Sanford’s work differently, but I would certainly strongly dispute the claim that Sanford’s work has empirical support.

  82. 82
    Elizabeth Liddle

    ba77: what do you mean by “materialism”? I’ve asked this on another thread, but I still don’t know the answer.

    So I don’t even know whether I’m a “materialist” or not!

  83. Elizabeth,,,, and all you got to do, to support your position, is show ‘evolution’;

    The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy:

    “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 talks about the preceding paper on this podcast:

    Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time – December 2010
    http://intelligentdesign.podom.....3_46-08_00

  84. Elizabeth, if you are an Atheist, you are a materialist.

  85. 85
    Elizabeth Liddle

    That doesn’t really help, ba77.

    Can you be more precise?

  86. 86
    Elizabeth Liddle

    So, do I take it that by “genetic entropy” you mean that any new function always destroys an old one?

    What about instances of mutations with new functions in duplicate genes?

  87. Elizabeth you ask;

    ‘What about instances of mutations with new functions in duplicate genes?’

    Evolution by Gene Duplication Falsified – December 2010
    Excerpt: The various postduplication mechanisms entailing random mutations and recombinations considered were observed to tweak, tinker, copy, cut, divide, and shuffle existing genetic information around, but fell short of generating genuinely distinct and entirely novel functionality. Contrary to Darwin’s view of the plasticity of biological features, successive modification and selection in genes does indeed appear to have real and inherent limits: it can serve to alter the sequence, size, and function of a gene to an extent, but this almost always amounts to a variation on the same theme—as with RNASE1B in colobine monkeys. The conservation of all-important motifs within gene families, such as the homeobox or the MADS-box motif, attests to the fact that gene duplication results in the copying and preservation of biological information, and not its transformation as something original.
    http://www.creationsafaris.com.....#20110103a

    Is gene duplication a viable explanation for the origination of biological information and complexity? – December 2010 – Excerpt: The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case. Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. © 2010 Wiley Periodicals, Inc. Complexity, 2011 http://onlinelibrary.wiley.com.....5/abstract

    The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations Douglas D. Axe*
    Excerpt: In particular, I use an explicit model of a structured bacterial population, similar to the island model of Maruyama and Kimura, to examine the limits on complex adaptations during the evolution of paralogous genes—genes related by duplication of an ancestral gene. Although substantial functional innovation is thought to be possible within paralogous families, the tight limits on the value of d found here (d ? 2 for the maladaptive case, and d ? 6 for the neutral case) mean that the mutational jumps in this process cannot have been very large.
    http://bio-complexity.org/ojs/.....O-C.2010.4

    An Insurmountable Problem for Darwinian Evolution – Gene Duplication – And Minor Transformation of Protein Function – May 2011
    http://intelligentdesign.podom.....1_43-07_00

  88. 88
    Elizabeth Liddle

    Well, again, I have to dispute your sources.

    There’s a nice review of the origins of new genes here:

    http://www.nature.com/nrg/jour.....g1204.html

    Unfortunately, being Nature, the full paper is behind a paywall.

    Turning to your own citations: only two are to scientific journals, and I know both those papers.

    Both are theoretical papers, and the Axe paper is inconclusive.

    The Bozorghmeyer paper simply concludes (IIRC) that there can be positive selection for intact duplicates (in other words there is fitness benefit to having two copies, even if the individual only benefits from one).

    This does not preclude evolution of a secondary function for the duplicate, and IMO it would be a stretch to say that loss of the original potential function of the duplicate is a “loss of function” since the duplicate has no actual function in the individual.

    In contrast, the Nature paper cites actual empirical findings.

  89. Elizabeth you state;

    ‘In contrast, the Nature paper cites actual empirical findings.’

    And yet the abstract states:

    ‘The study of ancient genes has highlighted the antiquity and general importance of some mechanisms of gene origination, and recent observations of young genes at early stages in their evolution have unveiled unexpected molecular and evolutionary processes.’

    So they did not actually ‘empirically’ evolve anything in the lab. They just studied genetic similarity and inferred relationship. How special!!!

    Not that I doubt your unbiased ‘interpretation’, but what does the largest real world ‘empirical’ test, that can be performed on the claims of neo-Darwinism, show us???

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2....._edge.html

    further note:

    This following paper clearly reveals that there is a ‘cost’ to duplicate genes that further precludes the scenario from being plausible:

    Experimental Evolution of Gene Duplicates in a Bacterial Plasmid Model
    Excerpt: In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. This study highlights the importance of the cost of duplicate genes and the quantitative nature of the tradeoff in the evolution of gene duplication through functional divergence. http://www.springerlink.com/co.....4014664w8/

    This recent paper also found the gene duplication scenario to be highly implausible:

    The Extinction Dynamics of Bacterial Pseudogenes – Kuo and Ochman – August 2010
    Excerpt: “Because all bacterial groups, as well as those Archaea examined, display a mutational pattern that is biased towards deletions and their haploid genomes would be more susceptible to dominant-negative effects that pseudogenes might impart, it is likely that the process of adaptive removal of pseudogenes is pervasive among prokaryotes.”
    http://www.evolutionnews.org/2.....37581.html

    A Fishy Story About AntiFreeze Gene Evolution – Casey Luskin – January 2011
    Excerpt: In his 2005 textbook Evolution, Douglas Futuyma states that a high estimate of the gene duplication rate is “about 0.01 duplication per gene per million years.” (p. 470) A given gene will thus be duplicated about once every 100 million years. The present paper speculates that the antifreeze gene evolved in response to cooling temperatures in the Antarctic deep ocean water over the past 50 million years. What are we to make, then, of the fact that Antarctic eelpouts have over 30 AFPIII genes, all of which are said to have resulted from a duplication of a single AFPIII gene which evolved at some point in the past 50 million years in response to changing ocean temperatures? http://www.evolutionnews.org/2.....43141.html

  90. 90
    Elizabeth Liddle

    Well, it’s a review of a large number of empirical studies.

    But no, the authors cited didn’t “‘empirically’ evolve anything in the lab.” They did, however, empirically test predictive hypotheses derived from their theories, which is how science works. There are vast domains of science where we can’t actually replicate what we infer must have happened. That doesn’t mean we can make no inferences about what did.

    They just studied genetic similarity and inferred relationship. How special!!!

    Well, not especially special, it’s just how science works. Often a research program starts with the kind of theoretical mathematical studies of the kind you cited by Axe and Bozorghmeyer, then, from that, testable predictions are made, and new data is collected and analysed for consistency with the predictions.

    It seems odd to me that you can cite (as Sanford does) theoretical computational models quite happily, yet reject evidence derived from actual data.

    Not that there is anything wrong with theoretical models – they are important (though sometimes they contain simple errors).

    It’s just that you seem to have what strike me as odd criteria for evaluating what is valid evidence for what.

    And I’d still like to know what “materialism” is :)

    Cheers

    Lizzie

  91. Elizabeth, though you have falsely accused me of doing exactly what you are doing, ignoring ‘real world’ evidence, here is the gold standard of a empirical test for you to pass;

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

    pass that test, then calculate the gain in functional information for the bacteria;

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

    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

    Intelligent Design: Required by Biological Life? K.D. Kalinsky – Pg. 10 – 11
    Case Three: an average 300 amino acid protein:
    Excerpt: It is reasonable, therefore, to estimate the functional information required for the average 300 amino acid protein to be around 700 bits of information. I(Ex) > Inat and ID (Intelligent Design) is 10^155 times more probable than mindless natural processes to produce the average protein.
    http://www.newscholars.com/pap.....rticle.pdf

    And see if you have exceeded what is plausible for ‘material’ processes;

    The Universal Plausibility Metric (UPM) & Principle (UPP) – Abel – Dec. 2009
    Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.”,,,

    c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108

    c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96

    c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85

    c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70

    http://www.tbiomed.com/content/6/1/27

    New Peer-Reviewed Paper Demolishes Fallacious Objection: “Aren’t There Vast Eons of Time for Evolution?” – Dec. 2009
    http://www.evolutionnews.org/2.....molis.html

    i.e Elizabeth, 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”).

    further note:

    Premise One: No materialistic cause of specified complex information is known.
    Conclusion: Therefore, it must arise from some unknown materialistic cause

    On the other hand, Stephen Meyer describes the intelligent design argument as follows:

    “Premise One: Despite a thorough search, no material causes have been discovered that demonstrate the power to produce large amounts of specified information.
    “Premise Two: Intelligent causes have demonstrated the power to produce large amounts of specified information.
    “Conclusion: Intelligent design constitutes the best, most causally adequate, explanation for the information in the cell.”

    There remains one and only one type of cause that has shown itself able to create functional information like we find in cells, books and software programs — intelligent design. We know this from our uniform experience and from the design filter — a mathematically rigorous method of detecting design. Both yield the same answer. (William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 90 (InterVarsity Press, 2010).)

    Stephen C. Meyer – The Scientific Basis For the Intelligent Design Inference – video
    http://www.metacafe.com/watch/4104651

  92. 92
    Elizabeth Liddle

    Goodness me, bornagain77, I haven’t accused you of anything, let alone falsely!

    We do seem to be having trouble communicating!

    Maybe we should take a break.

    Cheers

    Lizzie

  93. Elizabeth, and the fitness test will be waiting for you when you return!!!

  94. 94
    Elizabeth Liddle

    Well, the thing is, ba77, I have a fundamental issue with the validity of that fitness test in the first place!

    And this is the problem really. Still, maybe a break will clarify things a little. See you soon :)

    Cheers

    Lizzie

  95. Elizabeth, you state;

    ‘I have a fundamental issue with the validity of that fitness test in the first place!’

    You have a fundamental issue with anything that so clearly points out the bankruptcy of neo-Darwinism. Why, because atheism has become your religion!!!

  96. 96
    Elizabeth Liddle

    Just as a matter of interest, though, why do you think that the senior author of the PNAS paper cited in your second video, Jack Szostak (sorry I called him Joe, earlier) is at the forefront of abiogenesis research, if the evidence in his paper indicates that it is impossible?

    Does not that, at the very least, indicate that the evidence of that paper can be interpreted as supporting evolutionary theory? And is interpreted so by the actual authors?

  97. 97
    Elizabeth Liddle

    Elizabeth, you state;

    ‘I have a fundamental issue with the validity of that fitness test in the first place!’

    You have a fundamental issue with anything that so clearly points out the bankruptcy of neo-Darwinism. Why, because atheism has become your religion!!!

    No, that simply isn’t the case, bornagain77.

    It really is not.

  98. Jack Szostak and abiogenesis??? Let’s check out his ‘forefront research’ on the probability of functional proteins being generated randomly.,,, Since nature does not form proteins naturally, and indeed has a severe aversion for generating proteins ‘naturally’,,,,

    ,,,,water is considered a ‘universal solvent’ which is a very thermodynamic obeying and thus origin of life defying fact.

    Abiogenic Origin of Life: A Theory in Crisis – Arthur V. Chadwick, Ph.D.
    Excerpt: The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment. A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.
    http://origins.swau.edu/papers.....fault.html

    Professor Arthur E. Wilder-Smith “Any amounts of polypeptide which might be formed will be broken down into their initial components (amino acids) by the excess of water. The ocean is thus practically the last place on this or any other planet where the proteins of life could be formed spontaneously from amino acids. Yet nearly all text-books of biology teach this nonsense to support evolutionary theory and spontaneous biogenesis … Has materialistic Neo-Darwinian philosophy overwhelmed us to such an extent that we forget or overlook the well-known facts of science and of chemistry in order to support this philosophy? … Without exception all Miller’s amino acids are completely unsuitable for any type of spontaneous biogenesis. And the same applies to all and any randomly formed substances and amino acids which form racemates. This statement is categorical and absolute and cannot be affected by special conditions.”
    http://theevolutioncrisis.org.uk/testimony3.php

    Sea Salt only adds to this thermodynamic problem:

    …even at concentrations seven times weaker than in today’s oceans. The ingredients of sea salt are very effective at dismembering membranes and preventing RNA units (monomers) from forming polymers any longer than two links (dimers). Creation Evolution News – Sept. 2002

    The following article and videos have a fairly good overview of the major problems facing any naturalistic Origin Of Life scenario:

    On the Origin of Life – The Insurmountable Problems Of Chemistry – Charles Thaxton PhD. – video
    http://www.youtube.com/watch?v=6Ye3oDDAxeE

    Also of interest is that even though water is a very thermodynamic obeying medium that prevents bio-molecules from forming in the first place, there is a seeming ‘miraculous’ transformation that takes place in water once proteins are constructed by the ribosome,,,,

    Protein Folding: One Picture Per Millisecond Illuminates The Process – 2008
    Excerpt: The RUB-chemists initiated the folding process and then monitored the course of events. It turned out that within less than ten milliseconds, the motions of the water network were altered as well as the protein itself being restructured. “These two processes practically take place simultaneously“, Prof. Havenith-Newen states, “they are strongly correlated.“ These observations support the yet controversial suggestion that water plays a fundamental role in protein folding, and thus in protein function, and does not stay passive.
    http://www.sciencedaily.com/re.....075610.htm

    Water Is ‘Designer Fluid’ That Helps Proteins Change Shape – 2008
    Excerpt: “When bound to proteins, water molecules participate in a carefully choreographed ballet that permits the proteins to fold into their functional, native states. This delicate dance is essential to life.”
    http://www.sciencedaily.com/re.....113314.htm

    indeed water is ‘full to the brim’ (pun intended) of seemingly miraculous attributes:

    Water’s remarkable capabilities – December 2010 – Peer Reviewed
    Excerpt: All these traits are contained in a simple molecule of only three atoms. One of the most difficult tasks for an engineer is to design for multiple criteria at once. … Satisfying all these criteria in one simple design is an engineering marvel. Also, the design process goes very deep since many characteristics would necessarily be changed if one were to alter fundamental physical properties such as the strong nuclear force or the size of the electron.
    http://www.evolutionnews.org/2.....42211.html

    Anomalous life enabling properties of water
    http://www.lsbu.ac.uk/water/anmlies.html

  99. anyway back to Szostak:

    The entire episode of Szostak’s failed attempt to establish the legitimacy of the 1 in 10^12 functional protein number from a randomly generated library of proteins can be read here::
    http://www.uncommondescent.com.....ent-358394

    This following paper was the paper that put the final nail in the coffin for Szostak’s work:

    A Man-Made ATP-Binding Protein Evolved Independent of Nature Causes Abnormal Growth in Bacterial Cells
    Excerpt: “Recent advances in de novo protein evolution have made it possible to create synthetic proteins from unbiased libraries that fold into stable tertiary structures with predefined functions. However, it is not known whether such proteins will be functional when expressed inside living cells or how a host organism would respond to an encounter with a non-biological protein. Here, we examine the physiology and morphology of Escherichia coli cells engineered to express a synthetic ATP-binding protein evolved entirely from non-biological origins. We show that this man-made protein disrupts the normal energetic balance of the cell by altering the levels of intracellular ATP. This disruption cascades into a series of events that ultimately limit reproductive competency by inhibiting cell division.”
    http://www.plosone.org/article.....ne.0007385

    How Proteins Evolved – Cornelius Hunter – December 2010
    Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a
    potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.
    http://darwins-god.blogspot.co.....olved.html

  100. However, as you say, the research I cited does not address the whole issue of how multicellular organisms came into being (in a Darwinian framework), although there is research that does (or at least looks promising).

    I never asked how multi-cellular organisms came into being.

    I’m happy to grant you a multi-cellular organism.

    I guess I was taking an example of a genetic account of a fairly radical change in body plan (and that research does contribute a response to a fairly frequently made challenge that Darwinian evolution can’t account for major new features, which is the point I thought you were making).

    You still don’t seem to understand the point.

    Here’s what you should have written:

    I guess I was taking an example of a genetic account of a fairly radical change in AN EXISTING BODY PLAN (and that research does contribute a response to a fairly frequently made challenge that Darwinian evolution can’t account for MAJOR NEW BODY PLANS, which is the point I thought you were making).

    You don’t see the difference between changing something that already exists and claiming this shows how things like that come into being in the first place.

    I claim there is a difference and that the former does not explain the latter.

    You apparently thought I was saying little changes cannot not have a large effect. But that’s an absurd thing for anyone to believe.

    How you came away with that from what I have written is a bit of a mystery to me.

  101. Elizabeth Liddle @69:

    The most promising approaches as far as I can see right now posit both a “self-replicating” spherical membrane (which is relatively easy to do, given the properties of lipids and their hydrophilic/hydrophobic poles) within a marine environment that is rich in polymers and other compounds.

    I’m trying to parse this.

    You said BOTH a “self-replicating” sperical membrane…

    But never seemed to complete the thought. BOTH … AND … what?

    Also, how do you know that these membranes are “self-replicationg” and how do you know it’s an easy thing to do?

    What is the need for a marine environment that is rich in polymers and other compounds?

    …self-replicating polymers trapped within lipid vesicles might differentially affect the rate of subdivision of the vesicle, leading to “selection” (i.e. greater prevalence) of those vesicles that “inherited” a particular configuration of polymer.

    So is this a different hypothesis from the one expressed in the first quote? Is this different from self-replicating membranes?

    So what is the wall of the “lipid vesicle” composed of? That’s pretty vague.

    So this vesicale somehow divides, with no known mechanism?

    And the rate of division is affected by some unknown mechanism?

    And these self-replicating polymers which are trapped within these membranes obtain energy through some as yet unknown mechanism?

    And these self-replicating polymers which are trapped within these membranes obtain the material needed for additional copies of themselves also through some as yet unknown mechanism?

  102. Elizabeth Liddle @73:

    …the evidence that the human genome is not deteriorating is the simple evidence that the human population is rapidly increasing!

    This is just silly. Do you really believe this argument or do you think we’re just too stupid to spot it and call you on it?

    What is the rate of increase. To put it another way, what is the current average number of offspring per couple.

  103. 103
    Elizabeth Liddle

    Mung, I don’t assume other people are “too stupid to spot” my errors, and I certainly do not deliberately make errors on the foolish assumption that I won’t be called on them.

    If I make an error I’m delighted to be called on it. I certainly make errors, and I’d far rather they were corrected than not.

    And if I express something badly, I’m always pleased to clarify.

    I am not actually sure, now you mention it,what the current average number of offspring (we need to count fertile adult offspring) per couple is – and it occurs to me that it might have finally dropped to two, and that the ongoing population increase is just the bulge going through (the human population is certainly still rapidly increasing) so I’ll try and check.

    So, I’ll modify my claim at least until I’ve done so: the evidence that the human genome has not been deterioriating for many generations, as Sanford claims, is that the human population has been growing for many generations.

  104. 104
    Elizabeth Liddle

    Mung @ 101: sorry about the incomplete thought – the other part was supposed to be self-replicating polymers.

    And specific mechanisms are postulated, and have been produced in the lab.

    I’ll try to dig out the paper I’m thinking of (though the Szostak lab page has some details of the program).

    Will be a bit busy for the next few days but will try to drop by.

    Cheers

    Lizzie

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