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What’s happened since Icons of Evolution (2002)?

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Icons of Evolution (Jonathan Wells, Regnery, 2002) is 13 years old.

A friend, forensic engineer Stephen Batzer, summarizes,

I think that there are three “show stoppers” since then.

1. That Darwin’s finches are simply races of the same bird. There has been no speciation.

2. That the tree of life is not viable. “It’s a bush!” they respond. Well, then Darwin was wrong, and the model is wrong. If it’s a *bush* it isn’t a *tree*. The Darwinian model is common descent and gradual differentiation. That has been shown to be false, because of #3.

3. ORFAN (Orphan) genes. Where do novel genes come from? If common genes mean common descent, then novel genes mean intervention and an innovator.

The entire rigor of Darwinism is genetic, and it is now known that distinct species (or kinds, or what have you) do not share a common ancestor in the way that individuals within a species share a common ancestor.

Not only that, but long-exploded Icons were still in 22 taxpayer-funded textbooks in 2011. Probably still are.

Rumour has it that author Jonathan Wells is updating Icons for a 2016 edition.

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25 Replies to “What’s happened since Icons of Evolution (2002)?

  1. 1
    daveS says:

    2. That the tree of life is not viable. “It’s a bush!” they respond. Well, then Darwin was wrong, and the model is wrong. If it’s a *bush* it isn’t a *tree*. The Darwinian model is common descent and gradual differentiation. That has been shown to be false, because of #3.

    What’s the sharp distinction between trees and bushes referred to here? Does this mean the tree of life just has more branches than it was formerly believed to have? Does it mean that it’s not a binary tree? Something else?

  2. 2
    bornagain77 says:

    Icons of Evolution – video
    https://www.youtube.com/watch?v=AZh-VJ20uC8

    “Icons of Evolution” – video playlist – video
    https://www.youtube.com/watch?v=jPKkxaZwXJ0&list=PL3E68C794E1D66A08

    ‘Icons Of Evolution’ – Tenth Anniversary
    http://www.iconsofevolution.com/index.php3
    video clip playlist:
    https://www.youtube.com/playlist?list=PLR8eQzfCOiS2RPQAPifs6t__mIAqITpYy

    Dr. Wells wrote an article defending his criticism against the Ten Icons of Evolution in detail here:

    Inherit the Spin: The NCSE Answers “Ten Questions to Ask Your Biology Teacher About Evolution”
    http://www.evolutionnews.org/2....._answ.html

    (Not) Making the Grade: Recent Textbooks & Their Treatment of Evolution (Icons of Evolution update) podcast and paper – October 2011
    http://www.idthefuture.com/201.....nt_te.html

    A Solid 10: Concluding My Review of Massimo Pigliucci’s Treatment of Jonathan Wells’s Icons of Evolution – June 6, 2014
    http://www.evolutionnews.org/2.....86281.html

  3. 3
    bornagain77 says:

    The appearance of major forms of life on Earth does not take the form of a gradually branching tree, or a bush, or a lawn, or any other metaphor of that type. The appearance of major forms of life on Earth is best characterized as a top-down ‘disparity preceding diversity’ pattern where distinct kinds of life forms appear suddenly in the fossil record then rapid diversity from that distinct kind follows. And then long term stability follows that.
    Make up whatever metaphor you need to to reflect that pattern, but don’t say the pattern reflects a tree, bush, lawn, or anything of that sort because the fossil record, (nor the genetic evidence), doesn’t really closely reflect any of those patterns!

    Here are a few notes to that effect:

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.””From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.”
    http://www.terradaily.com/repo.....s_999.html
    University of Chicago paleontologist Mark Webster; article on the “surprising and unexplained” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    Cambrian Explosion Ruins Darwin’s Tree of Life (2 minutes in 24 hour day) – video (2:55 minute mark)
    https://www.youtube.com/watch?v=vA2LDiWeWb4

    , as Dr. Wells points out in the preceding video, Darwin predicted that minor differences (diversity) between species would gradually appear first and then the differences would grow larger (disparity) between species as time went on. i.e. universal common descent as depicted in Darwin’s tree of life. What Darwin predicted should be familiar to everyone and is easily represented in the following graph.,,,

    The Theory – Diversity precedes Disparity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/F.gif

    But that ‘tree pattern’ that Darwin predicted is not what is found in the fossil record. The fossil record reveals that disparity (the greatest differences) precedes diversity (the smaller differences), which is the exact opposite pattern for what Darwin’s theory predicted.

    The Actual Fossil Evidence- Disparity precedes Diversity – graph
    http://www.veritas-ucsb.org/JOURNEY/IMAGES/G.gif

    Jerry Coyne’s Chapter on the Fossil Record Fails to Show “Why Evolution is True” – Jonathan M. – December 4, 2012
    Excerpt: Taxonomists classify organisms into categories: species are the very lowest taxonomic category. Species are classified into different genera. Genera are classified into different families. Families are classified into different orders. Orders are classified into different classes. And classes are classified into different phyla. Phyla are among the very highest taxonomic categories (only kingdom and domain are higher), and correspond to the high level of morphological disparity that exists between different animal body plans. Phyla include such groupings as chordates, arthropods, mollusks, and echinoderms.
    Darwin’s theory would predict a cone of diversity whereby the major body-plan differences (morphological disparity) would only appear in the fossil record following numerous lower-level speciation events. What is interesting about the fossil record is that it shows the appearance of the higher taxonomic categories first (virtually all of the major skeletonized phyla appear in the Cambrian, with no obvious fossil transitional precursors, within a relatively small span of geological time). As Roger Lewin (1988) explains in Science,
    “Several possible patterns exist for the establishment of higher taxa, the two most obvious of which are the bottom-up and the top-down approaches. In the first, evolutionary novelties emerge, bit by bit. The Cambrian explosion appears to conform to the second pattern, the top-down effect.”
    Erwin et al. (1987), in their study of marine invertebrates, similarly conclude that,
    “The fossil record suggests that the major pulse of diversification of phyla occurs before that of classes, classes before that of orders, orders before that of families. The higher taxa do not seem to have diverged through an accumulation of lower taxa.”
    Indeed, the existence of numerous small and soft-bodied animals in the Precambrian strata undermines one of the most popular responses that these missing transitions can be accounted for by them being too small and too-soft bodied to be preserved.
    http://www.evolutionnews.org/2.....67021.html

    Investigating Evolution: The Cambrian Explosion Part 1 – (4:45 minute mark – upside-down fossil record) video
    http://www.youtube.com/watch?v=4DkbmuRhXRY
    Part 2 – video
    http://www.youtube.com/watch?v=iZFM48XIXnk

    Challenging Fossil of a Little Fish
    Excerpt: “In Chen’s view, his evidence supports a history of life that runs opposite to the standard evolutionary tree diagrams, a progression he calls top-down evolution.”
    Jun-Yuan Chen is professor at the Nanjing Institute of Paleontology and Geology
    http://www.fredheeren.com/boston.htm

  4. 4
    daveS says:

    Ah, reading the linked helps. The diagram on this page is useful, although I’m still having trouble with the bush metaphor.

  5. 5
    bornagain77 says:

    Timeline graphic on Cambrian Explosion – ‘Darwin’s Doubt’ (Disparity preceding Diversity) – infographic
    http://www.evolutionnews.org/2.....74341.html

    Evolutionists Are Losing Ground Badly: Both Pattern and Process Contradict the Aging Theory – Cornelius Hunter – July 2012
    Excerpt: Contradictory patterns in biology include the abrupt appearance of so many forms and the diversity explosions followed by a winnowing of diversity in the fossil record. It looks more like the inverse of an evolutionary tree with bursts of new species which then die off over time.
    http://darwins-god.blogspot.co.....badly.html

    “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas.”
    James W. Valentine – as quoted from “On the Origin of Phyla: Interviews with James W. Valentine” – (as stated at 1:16:36 mark of video)
    https://www.youtube.com/watch?v=xtdFJXfvlm8&feature=player_detailpage#t=4595

    Erwin and Valentine’s The Cambrian Explosion Affirms Major Points in Darwin’s Doubt: The Cambrian Enigma Is “Unresolved” – June 26, 2013
    Excerpt: “In other words, the morphological distances — gaps — between body plans of crown phyla were present when body fossils first appeared during the explosion and have been with us ever since. The morphological disparity is so great between most phyla that the homologous reference points or landmarks required for quantitative studies of morphology are absent.”
    Erwin and Valentine (p. 340)
    http://www.evolutionnews.org/2.....73671.html

    Moreover, there are ‘yawning chasms’ in the ‘morphological space’ between the phyla which suddenly appeared in the Cambrian Explosion,,,

    “Over the past 150 years or so, paleontologists have found many representatives of the phyla that were well-known in Darwin’s time (by analogy, the equivalent of the three primary colors) and a few completely new forms altogether (by analogy, some other distinct colors such as green and orange, perhaps). And, of course, within these phyla, there is a great deal of variety. Nevertheless, the analogy holds at least insofar as the differences in form between any member of one phylum and any member of another phylum are vast, and paleontologists have utterly failed to find forms that would fill these yawning chasms in what biotechnologists call “morphological space.” In other words, they have failed to find the paleolontogical equivalent of the numerous finely graded intermediate colors (Oedleton blue, dusty rose, gun barrel gray, magenta, etc.) that interior designers covet. Instead, extensive sampling of the fossil record has confirmed a strikingly discontinuous pattern in which representatives of the major phyla stand in stark isolation from members of other phyla, without intermediate forms filling the intervening morphological space.”
    Stephen Meyer – Darwin’s Doubt (p. 70)

    Moreover, this top down pattern in the fossil record, which is the complete opposite pattern as Darwin predicted for the fossil record, is not only found in the Cambrian Explosion, but this ‘top down’, disparity preceding diversity, pattern is found in the fossil record subsequent to the Cambrian explosion as well.

    Scientific study turns understanding about evolution on its head – July 30, 2013
    Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form.
    Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories.
    ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,,
    Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on.
    Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,,
    http://phys.org/news/2013-07-s.....ution.html

    “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.”
    TS Kemp – Fossils and Evolution,– Curator of Zoological Collections, Oxford University, Oxford Uni Press, p246, 1999

    “What is missing are the many intermediate forms hypothesized by Darwin, and the continual divergence of major lineages into the morphospace between distinct adaptive types.”
    Robert L Carroll (born 1938) – vertebrate paleontologist who specialises in Paleozoic and Mesozoic amphibians

  6. 6
    Robert Byers says:

    ICONS is a seminal book in modern biological science. its loved and hated and thats proof it matters. Things that don’t matter don’t matter.
    Evolutionism for too long was allowed a free ride in assuming it had explained the wonderful and complicated world of biology.
    It was all gibberish and an embarrassment to Anglo- american civilization. Which is top dog in mans history.
    These are small circles that seriously think about these things and smaller, as usual, in criticisms of establishment conclusions.
    Icons should be a read for serious biology students if dealing with bio origins.

  7. 7
    daveS says:

    Robert,

    Your post #6 would make a great blurb for the rumored 2016 edition.

  8. 8
    Dr JDD says:

    ORFAN genes per se don’t cause a problem for Darwinian evolution as of course new genes have to arise somehow and somewhere. So the concept of a functional gene that does not show ancestry and is restricted to a species or kind is not unexpected by the evolutionary model. As clearly genes had to arise from no genes in the simplest organism if the account is to be believed.

    Where the problem really lies is in observations about specific ORFANs:

    – Rapid appearance in short evolutionary space with little to no homology to existing genes or frame shifts
    – Appearance across distantly related species
    – Essential function of such genes for the organism’s survival

    Those aspects of ORFANs are the real problem and some of these are being observed far more frequently than certain people would have us believe.

  9. 9
    forexhr says:

    The question of where do novel genes come from is the most important from the scientific point of view. The reason lies in the fundamental evolutionary premise by which evolutionary processes created every level of biological organisation. Since biological organization is represented in genes, from the scientific point of view evolution is nothing but the process by which new genes are produced. So, the real scientific question is as follows: is there a knowledge in biology, based on facts learned through experiments and observation which shows that processes of evolution(RV+NS) can create new genes?

    Why are new genes important? Because the hypothetical first self-replicator did not contain genes for three-dimensional cellular structures and arrangements like lungs, heart, blood vessels, stomach, kidneys, muscles, brain, bones, ligaments, etc. All these arrangements are significantly different in their three-dimensional shape, and function, so the information written in genes that represent them also have to be significantly different. Ear is different than eye, heart is different than kidneys, DNA polymerase is different ATP synthase, mechanical gears in jumping insects are diferent then bacterial flagellum, etc. So, you can’t just randomly duplicate existing genetic code for a particular organ or part of the organ, add few hundred random mutations and voilà, new organ or molecular machine will emerge. Hundred years of experimentation and millions of lab-induced random mutation in various organisms have shown that this is not possible.

    Due to this reason the only real scientific test for the idea od evolution is the answer to a question of evolution’s ability to create novel or de novo genes? De novo genes are genes without homologues in genomes of other organisms. This question is especially important because comparative genome analyses indicate that every taxonomic group so far studied contains 10–20% of genes that lack recognizable homologs in other species. These genes are also called orphan genes.

    For example this research identified a total of 60 protein-coding genes that originated de novo on the human lineage since divergence from chimpanzee:

    http://journals.plos.org/plosg.....en.1002379

    Since the chimpanzees and humans shared a common ancestor 240,000 generations ago, this indicates that the rate of origin of de novo genes is 1 gen per 4,000 generations. Of course, this rate will grow with the future discovery of new unique genes.

    So, what can empirical science say about the power of evolution to create novel genes?
    Well, the biggest scientific observations of evolution in action is E. coli evolution experiment. On February 24, 1988. Richard Lenski and his team at Michigan State University embarked on an ongoing long-term evolution experiment. He started 12 genetically identical lines from a single strain of E. coli. The bacteria reproduced every few hours. The populations reached the milestone of 50,000 generations in February 2010 and 60,000 in in April 2014. What did Lenski experiment show? How many new genes evolutionary processes created after 60,000 generations? Well, the answer is 0 – ZERO. Most of the changes in this experiment involved streamlining the genome, deleting genes no longer needed, or reducing protein expression.

    One of the changes in this experiment involved something that proponents of evolution refers to as evidence for bacteria evolving a “key innovation”, a “new function” and a “fascinating case of evolution in action.” A New Scientist writer proclaims: “A major innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait”. In September of 2012 the well-known science journal Nature published an article about Lenski’s experiment entitled, “Evolution: How the unicorn got its horn”. One evolutionary biologist said that Richard Lenski’s published research is: “another poke in the eye for anti-evolutionists”. So, te question is: what all the fuss was about?

    Well, Lenski’s lab discovered that at generation 31,500, one line of E. coli could utilize citrate – something they weren’t able to do before. And, they achieved this novel function via evolutionary processes – random mutations and natural selection. As is generally the case, the devil is in the details. And, when one looks a bit more closely at the details of the Lenski experiment, it loses quite a bit of its luster.

    What Dr. Lenski did was to grow E. coli under oxic conditions in citrate-rich media. E. coli bacteria are generally unable to use citrate under oxic conditions as a source of energy. However, they can use it under anoxic conditions. In other words, they already have the gene for citrase in their genome. It is just that it is normally turned off under oxic conditions. How is it turned off? Well, the promoter for the gene that transports citrate into the bacterium (citT) is not active under oxic conditions. So, all that needs to happen is to move the citrate transport gene close to a promoter that is actually active under oxic conditions. Once this is done, citrate will enter the bacterium and be used for energy.
    And, this is exactly what happened. Nothing structurally new needed to be evolved. After about 31,000 generations, in a large population of bacteria, there was a single genetic mutation in a bacterium that ended up moving the citT gene and placing it under the control of a promoter that is active under oxic conditions. The protein product, however, remained the same with no required amino acid changes to achieve a selectable effect. All that was required was to move a pre-existing gene close to a promoter to turn it on during oxic conditions. That’s it.

    Now, imagine how many new, different coding and noncoding genes, you need to be able to construct every observable level of biological organisation, all three-dimensional cellular structures and arrangements, organs, organ systems, tisues, signaling and regulatory networks, control mechanisms, molecular machines, metabolic pathways, etc. And all that evololution can do in 60.000 generation is to move one pre-existing gene from one location to another. That is all. And this is what proponents of evolution all aroud the globe refers to as “fascinating case of evolution in action.” Hm…, isn’t that interesting?

    Why empirical science demonstrates the complete impotence of evolution in the creation of new genes? Well, to create a new gene it is not sufficiently to randomly add variation(mutations) throughout the genome. A coordinated mutations at specific location of the DNA are needed. Also, for the completion of evolution it is not enough that certain variation enters the population (gene pool). Completion of evolution requires that such variation avoid stochastic loss and ultimately become established (fixed) in the population. What result do we get when we create mathematical models of evolution with this realistic requirements for gene production?

    Well, this study showed that the appearance of only two coordinated mutations in humans would have an expected time of appearance of 216 million years:

    Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution, http://www.genetics.org/content/180/3/1501.full

    If these calculations are put alongside the research which identified a total of 60 protein-coding genes that originated de novo on the human lineage since divergence from chimpanzee, failure of evolutionary ideas is even more obvious. If absurd assumption is made, that only two coordinated mutation are nedded to create one protein coding gene from junk DNA, the appearance of this gene in humans would have an expected time of appearance of 216 million years. Since ancestors of humans and chimps diverged 5-7 million years ago, it is obvious that evolutionary hypothesis are in complete contradiction with empirical science.

    But that’s not all. Besides mentioned, Lenski experiment with asexual species(bacteria), in September 2010, Molly K. Burke report results of a second largest evolution experiment, this time with sexual populations – fruit flies, which were selected in the lab for more than 600 generations to develop rapidly from egg to adult. For decades, most researchers have assumed that sexual species evolve the same way single-cell bacteria do – a genetic mutation sweeps through a population and quickly becomes “fixated” on a particular portion of DNA. But the fruit flies experiment shows that when sex is involved, it’s far more complicated.

    The authors of the experiment conclude: “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 is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for 600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case.”

    So, the scientific answer to the question mentioned at the beginning is: no. There is no knowledge in biology, based on facts learned through experiments and observation which shows that process of evolution can create new genes. And since all features of living organisms are written on genes, scientific fact is that living organisms are not the product of evolution.

    I am genuinely stunned that seemingly intelligent people like Lenski, despite a clear empirical demonstration of total inability of evolution to create even the simplest level of biological organisation – a new gene, still believe in evolution’s ability to produce myriad of highly interconnected genes containing all the information necessary to build every observable level of biological organisation that exist or has ever existed on Earth.
    Many people hold unscientific beliefs for many reasons, but in this case maybe the reason lies within these words said by George Wald, who was an American scientist and 1967 Nobel Prize winner:

    “When it comes to the origin of life, we have only two possibilities as to how life arose. One is spontaneous generation arising to evolution; the other is a supernatural creative act of God. There is no third possibility…Spontaneous generation was scientifically disproved one hundred years ago by Louis Pasteur, Spellanzani, Reddy and others. That leads us scientifically to only one possible conclusion — that life arose as a supernatural creative act of God…I will not accept that philosophically because I do not want to believe in God. Therefore, I choose to believe in that which I know is scientifically impossible, spontaneous generation arising to evolution.” – Scientific American, August, 1954.

    So here’s the reason why evolutionists choose to believe in that which they know is in contradiction with empirical science – they do not want to believe in God.

  10. 10
    Dr JDD says:

    Great post Forexhr. I completely agree and many here will.

    However, I have learned when debating with evolutionists that they will pick up on one small abberant statement that they can poke a hole in, and beat that to death whilst failing to address the bigger overall picture that was merely a part of. It’s like trying to convince someone there is not an elephant in the room by telling them to look the opposite way from where the elephant is. Hence my post.

    Likewise with what you state I agree however the standard answers no doubt will consist of:
    – the orphan genes tend to code for very small proteins,
    – they are not playing essential roles and are often dispensing
    – e coli has a much tighter control on its genome and lower mutation rates than humans
    – the citrate mutations was a complex set of mutations that should be considered as gain in novel function mutations
    – etc. Etc.

    Of course I agree with you, but this is what our Darwinist friends will pick up on here. It’s a common detraction tactic. Great post though.

  11. 11
    forexhr says:

    Thanks Dr JDD.

    The manner and means by which evolutionist chooses to respond to the scientific knowledge which shows that process of evolution are not able to create novel genes will not cause this knowledge cease to exist. So, standard answers that you mentioned are nothing but empty mental constructs, ad hoc rationalizations and excuses for ignorance of science.

    Appeal to size of orphan genes rests on the implicit assumption that production of small genes is not a problem for evolution. But this assumption is clearly false, as demonstrated by Lenski experiment and mathematical model of evolution mentioned above. Scientifically, evolution is not able to create neither small nor large genes.

    Second statement, which states that orphan genes are not playing essential roles is non sequitur because evolution is a set of ideas that tries to explain how X originated and not whether X plays an essential role or not.

    Finally, novel function is an abstract term that can include every random variation that is of selective advantage to the organism. It also can include a loss of genetic information from the genetic code. So, this has nothing to do with the evolution’s ability to create new genes containing information necessary to build every observable level of biological organisation.

  12. 12
    Cabal says:

    forexhr said:

    So here’s the reason why evolutionists choose to believe in that which they know is in contradiction with empirical science – they do not want to believe in God.

    I strongly beg to differ. There isn’t any such thing as “that which they know is in contradiction with empirical science.” (“Because they don’t want to believe in God.”)

    As far as they – and me as well – accept as strong evidence based on the facts, taking into account that there is no positive evidence of divine intervention in mundane matters. No miracles, nothing at all, except the universe’s mother nature doing her work, silently without much ado. But when we bend down and look closer, we know she’s been there. And sometimes she does it before our very eyes.

    It is fair enough to have opinions about scientists and science, but I view statements like the quoted one in line with “bearing false witness.” It is not a question of not wanting to believe in God; it is the fundamental problem that we don’t see any signs of divine intervention. Until that happens, the only reasonable attitude is to leave claims about divine intervention out of matters of science. Maybe the solution is to realize – as it seems to me the Bible tries to say – that the Kingdom of Heaven is not of this (material) world, it is a matter of the spiritual world.

    The only world of spirit that I know of is in ourselves, in our soul. “The kingdom of Heaven is within (the soul of all of us).”

  13. 13
    REW says:

    forexhr,

    I think you’re right about the importance of this topic. I’ve often thought that all of the other topics of discussion- the Cambrian explosion, the flagellum etc – could be dispensed with and only this topic debated because both ID and evolution will either sink or swim depending on its outcome. If de novo genes can come into existence through natural causes then there is absolutely no need to invoke a designer. If on the other hand they can’t come into existence that way we pretty much have proof of the designer.
    This is not a philosophical question. The 2 proposed mechanisms are about as polar opposites as you can get so its reasonable to assume that we could gather evidence from the natural world that would point in one direction or the other. We can ask the question: “if de novo genes arose by natural processes what observations would support that” Even making minimal assumptions about the Intelligent Designer- just the most basal assumptions that go with any designer- we could ask what patterns, structure we might or might not see when we look at de novo genes.

    So……does anyone have any ideas on what to look for?

  14. 14
    bFast says:

    I remember blogging with a biologist on this topic some years ago. He basically said that humans should show maybe one or two functional orphan genes, that these genes should be small, and play a very secondary role. He said that more than that “would be a problem.” At this point, I think that either we have very false data or there is a “problem”.

  15. 15
    forexhr says:

    Cabal,

    Divine intervention or natural creation(evolution) has never been a matter of science but of logic. Science provides insight into cause-and-effect structure of natural world by demonstrating what outcome occurs when a particular set of natural phenomena is manipulated.
    On the other hand, divine intervention and natural creation are nothing but mental constructs of a human mind. In order to refute or verify this mental constructs, an orderly procedure is carried out – experiment. In my examples of evolution in action, it is experimentally demonstrated that a long term change in the genetic composition of a population from one generation to the next(cause) does not result in a new genes(effect). This is science. Now logic: since all features of living organisms are written on genes and since we know from direct scientific observation that natural processes cannot create them, it l o g i c a l l y follows that organisms are the products of supernatural creation. If someone wants to believe otherwise I don’t have any problem with that, but this belief falls into the category of logical fallacies and pseudoscience because it presupposes something that is in contradiction with knowledge based on facts learned through experiments and observation.

  16. 16
    bFast says:

    REW (13), in general I agree with you. This is a big, HUGE, topic! I am concerned, however, that the threshold of proof by the evos will be set very low. I think that de novo or orphan genes can be classed into three categories:

    1 – Useless. I think it perfectly clear that a “read frame” (the marker for the beginning/end of a gene) can show up in DNA with no challenge. The resultant gene may happily translate, but would offer no value.

    2 – “Functional”. Ie, it does something. Please understand what a protein is. It is a “tool”. Just like the tools in my toolbox, there are a gazillion different kinds. Further, I often need to solve a problem, and find a tool (usually a simple one like string or tape) that was not particularly designed to solve my problem, but that does the job anyway. The key here being that some tools (string) are pretty simple things, other tools are very precise and nonstandard.

    3 – “Provisional”. Provisional (in this context): provides the correct solution to the specific problem. (I am intrigued by the concept of “providence”, the sense that our needs are provided for.) I was particularly struck by the “polar cod” that has an orphan gene “antifreeze” (https://youtu.be/1Zz6vio_LhY?t=2m20s) This is my kind of example of a provisional gene.

    So it is one thing for the evos to say “the orphan was functional”, its very much another to say “the orphan provided a contextually relevant function.”

  17. 17
    bFast says:

    A story is in order to clarify what I mean by “provisional” above.

    A friend of mine reports driving on a relatively remote road in Alaska. He blew a heater hose. While his family stayed in the vehicle and prayed, he walked up the road to see if he could find a farm house or something, and prayed.

    He didn’t go very far, when he noticed something laying beside the road. Yes, it was a replacement heater hose. It was the correct diameter and length (he didn’t need to trim it, though that would have been easy). It even came with stainless steel hose clamps.

    He, being rather mechanical, had the vehicle permanently repaired in no time.

    Now, had he walked up the road and found a bolt, it would have meant nothing to him. Had he found a roll of duct tape, it would have meant nothing to him. He found the “provisional” part. Of the thousands of parts that make up a vehicle, of the tens of thousands of parts that make up all of the vehicles that drive the roads, he found the part that was provisional for him.

    In the same way, there are a gazillion “functional” proteins out there. But for a cod that lives near icy waters, the discovery of a protein that functions as an antifreeze, well that’s special. ‘Not much use to a marlin, but pretty handy for a cod in northern climates.

  18. 18
    REW says:

    bFAST,

    Thanks but here is what I was getting at: Biologists assume that a non-coding segment of DNA was ‘accidentally’ transcribed and translated and that the resulting protein acquired a function. That seems astronomically unlikely but lets consider it for the moment. IDers assume that an intelligent designer created this one protein and inserted? it into a particular species ( all species seem to have a few) for a specific function. Are there any differences we can expect from those 2 very different mechanisms that we can go check…any ideas?

  19. 19
    bFast says:

    “IDers assume that an intelligent designer created this one protein and inserted? it into a particular species”
    I, as an IDer, do not make this assumption. I suspect that if you could watch the events unfold, you would see the code for the desired protein slowly appear in the “junk”, only to be switched on by a mutation creating a read frame.

    What do you presume happened surrounding my friend’s discovery of the right part at the side of the road? One of three things must have happened:

    > The part just appeared, like a Star Trek transporter put it there.

    > Someone felt compelled to go to the store, buy the part, and throw it out the window at the right spot. Having heard stories of miracles, I don’t find this possibility that far fetched.

    > Someone needed the same part, went to the store, bought the part. In this scenario he probably placed the part in the back of his pickup truck, hit a bump, and had the part fly out.

    Each method gets the part there. Each method leaves your mouth drop-open to find the right part. Each is well into the category I call “miracle”.

    By the same token, the question of how the DNA got “just right” to be providential for the organism is a statistical challenge. Does this happen at a statistically reasonable rate, or is somebody messin’ with the mutations? That is the question.

  20. 20
    Zachriel says:

    forexhr: After about 31,000 generations, in a large population of bacteria, there was a single genetic mutation in a bacterium that ended up moving the citT gene and placing it under the control of a promoter that is active under oxic conditions.

    That is incorrect. It took at least one potentiating mutation, as well as a tandem duplication. This was followed by optimizing mutations. Because not all strains had the potentiating mutation, it means that evolution of the trait is contingent. See Blount et al., Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 2008.

  21. 21
    Virgil Cain says:

    Thank you, Zachriel, for showing us the process is too complex for undirected evolution to happen upon.

  22. 22
    bFast says:

    Virgil Cain, “Thank you, Zachriel, for showing us … ”
    What the heck you talkin ’bout?
    A potentiating mutation happened. It wasn’t deleterious. Ie, drift happened. A duplication happened. It was not deleterious. Duplications happen. Some “optimizing mutations” happened — these happen all the time. If a single point mutation is advantageous, the natural process is quite capable of taking the advantage.

    Zachriel makes this thing sound really big. Its actually pretty small, especially in an organism colony larger than all of humanity, during a reproduction period equivalent to 1/2 million years of human evolution. Evolution needs to be much more potent than this study shows, but the natural processes are not without some power.

  23. 23
    Zachriel says:

    bFast: makes this thing sound really big

    If you and your children could utilize a new food source, while your neighbors starved, you would think it a really big thing. It’s a matter of perspective.

    As for the science, it’s considered an important finding, not because it confirms evolution — which is a foregone conclusion in biology —, but because it demonstrates evolutionary contingency.

  24. 24
    Virgil Cain says:

    bFast:

    What the heck you talkin ’bout?

    If you didn’t chop my sentence you would read what I was talking ’bout.

    A potentiating mutation happened. It wasn’t deleterious. Ie, drift happened. A duplication happened. It was not deleterious. Duplications happen. Some “optimizing mutations” happened — these happen all the time. If a single point mutation is advantageous, the natural process is quite capable of taking the advantage.

    A gene duplication that just happened to put the gene under the control of a proper promoter. This is evidence for directed evolution. See Spetner 1997.

  25. 25
    Virgil Cain says:

    Zachriel:

    If you and your children could utilize a new food source, while your neighbors starved, you would think it a really big thing.

    Except the bacteria that didn’t have this modification were not starving as evidenced by the other colonies that are doing just fine without it.

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