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Common descent: Ann Gauger’s response to Vincent Torley

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Well, I must say I didn’t expect to be honored by a 7500 word broadside by philosopher Dr. Vincent Torley, assisted by Dr. Josh Swamidass, Assistant Professor at Washington University. I guess they must have a lot of spare time. The reason for the post at Uncommon Descent? Both hold common descent to be absolutely, incontrovertibly, obviously true, and they apparently wish I would fall into line and stop embarrassing them by doubting common descent. They wish I would give up my “peculiar kind of intellectual obstinacy.”

The argument is in the end all about common descent. (There are a few accusations of poor reasoning, obscuring the issue, and even a little bad faith along the way.) Look, intelligent design is not wedded to common descent. Neither is it wedded to a denial of common descent. Intelligent design states that there is evidence of design in the universe. I think we are in agreement on this point. In terms of biology, how the designer instantiated that design is still subject to debate, based on the strength of the evidence for each position.

As a biologist, I see evidence on both sides of the debate. The evidence is equivocal — hence the fact that ID advocates take different positions on the subject. Yet common descent — the idea that organisms descend from one or a few common ancestors — is treated like a sacred cow by many scientists, and even, it appears, by some philosophers. Indignation arises that anyone would doubt it, would even have questions. Scientists take common descent as axiomatic, and accept evidence that is itself interpreted through a lens of common descent as proof of common descent. As a consequence, any evidence against common descent meets opposition and is explained away.More.

Background: Vincent Torley: Evidence for common descent: here

249 Replies to “Common descent: Ann Gauger’s response to Vincent Torley

  1. 1
    vjtorley says:

    Hi News,

    Thanks for this post. Here’s a quick quote from Professor Michael Behe (The Edge of Evolution, Free Press, New York, 2007, pp. 71-72):

    The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now. It’s hard to imagine how there could be stronger evidence for the common ancestry of chimps and humans.

    That strong evidence from the pseudogene points well beyond the ancestry of humans. Despite some remaining puzzles, there’s no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.

    He goes on to say that common descent is true but trivial, and that it does not, by itself, explain how the differences between humans and chimps originated: “Something that is nonrandom must account for the common descent of life” (p. 72, italics Behe’s).

  2. 2
    Mung says:

    VJT does seem to be a bit long-winded at times.

    The post @1 shows remarkable constraint.

    🙂

  3. 3
    bornagain77 says:

    As to the Torley’s reference of Behe in regards to the beta-globin pseudogene

    Beta-Globin Pseudogene Is Functional After All
    by Jeffrey P. Tomkins, Ph.D. * – April 2013
    One of the key arguments of human evolution has now suffered the same fate as many other debunked icons of the errant paradigm of “junk DNA.” In this case, it is new research related to the beta-globin pseudogene—which now shows it to be functional and important to hemoglobin gene regulation.

    Hemoglobin is a protein in human red blood cells that transports oxygen throughout the body’s circulatory system. The human hemoglobin protein is actually a cluster of two chains of different sub proteins. One of these chains is called the “alpha-globin” which remains the same from embryo development to adulthood. The second set is called the “beta-hemoglobin” chain which specifically changes at the embryo-to-fetal transition and again at the fetal-to-adult transition. This amazing bio-engineering allows the developing embryo-baby to receive oxygen at the correct levels throughout its critical growth processes.

    The human beta-globin proteins are encoded in a cluster of six genes that extends over 80,000 bases on chromosome 11. The embryo-to-adult growth stage expression of each gene in the cluster depends on that specific gene’s interaction with a control region preceding the whole cluster called the “locus control region” or LCR.

    While five out of the six genes in the beta-globin cluster encode functional proteins, one of the genes called HBBP1 does not, because of several stop sequences in its code that were once thought to be mutations. This gene was classified as a pseudogene (a broken defunct remnant) because of its assumed non-functionality. Because the gene, along with its presumed errors, is also found in chimpanzees, evolutionists claimed it as proof that humans inherited their version of the gene from a common ancestor with chimps.

    One of the main problems with this idea is the actual evidence for the claim. Molecular evolutionist’s who study DNA sequence, have wondered why, if the HBBP1 gene is non-functional, its DNA has not mutated over the past 3 to 6 million years of assumed human evolution (compared to chimps) if there has been no selection restraint imposed on it. In other words, the so-called evidence for common ancestry with this sequence actually argues against it. It also indicates that the HBBP1 gene may actually be functional and serving a common purpose in both humans and chimps.

    A recent paper published in the journal Genome Biology and Evolution now confirms the fact that the HBBP1 gene is highly resilient to change and is in fact functional.1 Researchers compared the beta-globin gene clusters in many different individuals in both humans and chimpanzees. Out of the six genes in the beta-globin cluster, the HBD gene and its companion (the next gene in the cluster), the HBBP1 pseudogene, are highly non-variable compared to the other beta-globin genes. These results indicate that virtually no mutation is tolerated in the so-called pseudogene area, implying that it is functionally important.

    The researchers then analyzed the HBBP1 pseudogene region for gene-function data, related to the ENCODE project,2, 3 and found that it is actively associated with transcriptional (gene control) regulation in conjunction with the LCR region that controls the whole beta-globin gene cluster.

    In addition, new information in the PseudoMap database4 shows that the HBBP1 pseudogene encodes two different regulatory RNAs that are thought to control the first gene in the beta-globin cluster (HBE) that is involved in early embryogenesis. These regions in the HBBP1 pseudogene also have the classic biochemical genetic marks of functionally active DNA—just like regular genes.

    This new functional data meshes well with another recent study showing that a single base mutation in the HBBP1 pseudogene is associated with a blood disease called beta-thalasemia.5

    Instead of being a useless mutated remnant according to failed evolutionary predictions, the HBBP1 beta-globin pseudogene appears to be genetically active and plays a key functional role as a cleverly engineered feature programmed by God the Creator.

    References

    Moleirinho, A., et al. 2013. Evolutionary Constraints in the ?-Globin Cluster: The Signature of Purifying Selection at the ?-Globin (HBD) Locus and its Role in Developmental Gene Regulation. Genome Biology and Evolution. 5 (3): 559–571.
    Tomkins, J. 2012. Junk DNA Myth Continues Its Demise. Acts & Facts. 41 (11): 11-13.
    The ENCODE Project Consortium. 2012. An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature. 489 (7414): 57-74.
    PseudoMap – A resource of exploring esiRNA-mediated mechanism of pseudogenes. Posted on pseudomap.mbc.edu.tw, accessed March 25, 2013.
    Giannopoulou, E. et al. 2012. A Single Nucleotide Polymorphism in the HBBP1 Gene in the Human ?-Globin Locus is Associated with a Mild ?-Thalassemia Disease Phenotype. Hemoglobin. 36 (5): 433-445.
    https://www.icr.org/article/7405/

  4. 4
    bFast says:

    I honestly find this dialog to be, well, infighting. I personally am compelled by the case for common descent. That said, I recently watched Dr. Hunter put out a compelling case against common descent. I think that we the ID community need to demonstrate to the rest of science that we are an evidence driven people, not a position driven people. Let us hold our conclusions loosely, allow our opinions to be our personal synthesis of the evidence, and attempt to sway other peoples’ perspectives solely by making an evidentiary case.

  5. 5
    bill cole says:

    bFast

    I honestly find this dialog to be, well, infighting. I personally am compelled by the case for common descent. That said, I recently watched Dr. Hunter put out a compelling case against common descent. I think that we the ID community need to demonstrate to the rest of science that we are an evidence driven people, not a position driven people. Let us hold our conclusions loosely, allow our opinions to be our personal synthesis of the evidence, and attempt to sway other peoples’ perspectives solely by making an evidentiary case.

    I agree. A healthy exchange is good. Lets discover together what the evidence is really telling us. I thought Ann did a very good job defending her position and agree Dr Hunter has surfaced some very good points.

  6. 6
    mahuna says:

    I lean more in the direction of there being a “shared design”.

    “Common descent” goes with the Evolutionary idea that the reason there are today both chimps and humans (and marsupial wombats) is that some Common Ancestor produced offspring with different mutations. And these related but different offspring then fathered (and mothered) separate strings of increasingly mutated offspring until here in the super whizz bang, Buck Rogers 21st century it is no longer obvious that (especially if we examine the skeletons) that chimps and humans are related at all.

    Share design on the other hand suggests that the design teams for the various projects made use of bits and pieces that already worked in older designs while laying out the distinctly new systems and subsystems for Project CHIMP and Project HUMAN.

    If we and our chimp friends actually shared a “common descent”, then we would have already found fossils of the intermediate ancestors.

    But more challenging are bats. Bats share common descent from WHAT? Modern bats are virtually identical to the oldest known bat fossils, and the pre-historic sabre-toothed cave bats appeared POOF! with the ability to fly and navigate and hunt prey using echo location.

    Bats of course share COMMON DESIGNS with many other mammals, again suggesting that the design team only changed the parts they knew wouldn’t work on Project BAT.

  7. 7
    buffalo says:

    @mahuna 6
    I too fall in the common design camp. Creative intelligence can use basic building blocks, even those that have mutations in common to achieve an end result. The programming is the key to dealing with the imperfect copy.

    IDvolution.org – – God “breathed” the super language of DNA into the “kinds” in the creative act.

    This accounts for the diversity of life we see. The core makeup shared by all living things have the necessary complex information built in that facilitates rapid and responsive adaptation of features and variation while being able to preserve the “kind” that they began as. Life has been created with the creativity built in ready to respond to triggering events.
    Since it has been demonstrated that all living organisms on Earth have the same core, it is virtually certain that living organisms have been thought of AT ONCE by the One and the same Creator endowed with the super language we know as DNA that switched on the formation of the various kinds, the cattle, the swimming creatures, the flying creatures, etc.. in a pristine harmonious state and superb adaptability and responsiveness to their environment for the purpose of populating the earth that became subject to the ravages of corruption by the sin of one man (deleterious mutations).
    IDvolution considers the latest science

  8. 8
    Robert Byers says:

    Amen to the statement in the thread.
    is common descxent based on biological evidence or is it based on comparative evidence.
    Is this a high intellectual investigation or just people comparing separate biological entities and reasoning that like equals like parents??
    Is comparative evidence, standing alone on its comparativeness, actually biological evidence for common descent.
    If there was no other option for likeness in biology WOULD this still mean comparing things is bio evidence.
    No one saw men/apes origins. So common descent folks must simply conclude this by like parts.
    In short eyeballs everywhere proves a eyeball common origin for eyeballs. If not proves at least evidence.
    I say its not bio evidence but only a line of reasoning someone could of thought up thousands oy years ago before a pretence to be scientists.

    Everyone is just comparing parts and not doing anymore then that.
    Another option would instantly nullify likeness as evidence.
    Other options or not its not based on bio sci.
    its trivial lines of reasoning.

  9. 9
    jimmontg says:

    Me? I’ve always thought that common plans simply mean a common Planner. You are welcome to refute if you want. Here is the catch, you cannot prove your hypothesis without your philosophical presuppositions or assumptions.
    “Wisdom is justified by her children.” A thought to consider for all and let’s not fight amongst ourselves. Nonessentials are just that.

  10. 10
    Mung says:

    bill cole @5:

    Lets discover together what the evidence is really telling us.

    The scientific evidence? Because I’d really like to know the Biblical evidence against the proposition that chickens and porcupines share a common ancestor.

    Were both chickens and porcupines on the ark? How do you decide what “kind” a chicken belongs to and what “kind” a porcupine belongs to? How do you decide which “kinds” survived the flood?

  11. 11
    ThickPython says:

    Hi Ann,

    Here are the alignments you were questioning in the original article:

    https://roohif.wordpress.com/2016/06/11/where-did-that-guy-get-his-data-from/

  12. 12
    Mung says:

    ThickPyton:

    Here are the alignments you were questioning in the original article:

    The question is about the evidence for synteny. You’ve offered none. What evidence for synteny do you have to offer that does not beg the question?

    Do your best. Please.

  13. 13
    bFast says:

    There is still such a dichotomy in this discussion. Design or descent. One or the other. Let me demonstrate that descent does stand in opposition to design.

    Let me just say that I come at this from the framework of a software developer. One tool that we use in the software industry are update patches. You see these things all the time, you know, “Windows needs to install important security updates”.

    Sometimes these “security updates” will be new versions of whole executable programs. These programs will be merely edits from the original, and a recompile. But the entire program is transmitted in the “patch”. This is an example of common design. A whole new fresh program, even if the underlying “source code” was a modification of the original.

    Sometimes, however, rather than send a whole new executable, the patching program will be given instructions like: At offset 123 in executable xyz.exe replace 100 bytes with this sequence: ft8iullwe8y sglvshe
    This is common descent. The original executable persists, but it was changed in situ.

    It is quite difficult to tell the difference between these two methods. If you can see the stream of data, it may be easy. But analyzing after the fact, it can be very difficult. (Not impossible in the real world, as the new .exe will have a different location on the hard drive, etc., but not easy.)

    So the question is, are there any clues left in the data of the DNA that indicate whether the designer is using a patch method (at this offset, insert this data) or a recompile method to implement modifications.

  14. 14
    Andre says:

    Dr Gauger

    Thank you for articulating this in a manner I could not. I agree with your position and have come to my own conclusions on the matter after analysis of the data.

    The evidence, while there is some, is not strong enough to indicate common descent is the real deal.

    Thank you.

  15. 15
    bornagain77 says:

    bfast as I’m not familiar with programming, I’ll just have to lay out the evidence that I have. But first let’s examine the competing hypothesis.

    Both Atheistic Darwinists and Theistic Evolutionists both hold that life came from preexisting simpler life in a gradual manner. i.e. universal common ancestry. They both hold that it happened in a, ‘bottom up’, simple to complex manner.
    The Theistic Evolutionists hold varying positions. Positions ranging from being completely in line with Darwinian presuppositions to those of Torley and others in the ID camp who hold that Intelligence was necessary for every novel protein fold and molecular machine to be brought into existence. Pinning them down on exactly when they think God implemented this design in life is a bit of a tricky affair. It is reminiscent of the ‘and then a miracle occurs’ cartoon with the punch line being ‘can you be a little more specific here’. I would greatly appreciate the Theistic Evolutionists of the ID camp to ‘be a little more specific here’.

    But regardless of the haziness in their thinking as to exactly when and how they think God implemented design in life, none-the-less, as I said before, they hold to the general outline of a gradual, from simple to complex, ‘bottom up’ scenario.

    Whereas the classical Theist’s position is more clear and pronounced, and easier to discern. Theists hold that God uniquely created man, and each ‘kind’ of life, uniquely, in a top down manner.

    The fossil, and even the genetic evidence, supports the ‘top down’ position of classical Theism:

    As mentioned on the other thread, the Cambrian explosion, and the fossil record in general, reveal an undeniable pattern of ‘top down’ sudden appearance and then overall stasis, and certainly does NOT reveal a pattern of God gradually morphing one creature into another creature in a ‘bottom up’ fashion as Theistic evolutionists hold. I could produce dozens of quotes from leading paleontologists testifying to this ‘top down’ pattern, but let these two suffice for now:

    “The record of the first appearance of living phyla, classes, and orders can best be described in Wright’s (1) term as ‘from the top down’.”
    (James W. Valentine, “Late Precambrian bilaterians: Grades and clades,” Proceedings of the National Academy of Sciences USA, 91: 6751-6757 (July 1994).)

    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

    The only place one really encounters any real stiff resistance to this fact that the fossil record is completely antagonistic to Darwinian claims is with the human fossil record itself. Here, besides the many fraudulent fossils that Darwinists have proffered over the last century, fossils contending to be the missing link between apes and humans are a dime a dozen. Each contender has been shot down when cooler heads prevail over the media hype. Yet, despite the media hype on fossils purporting to be ‘the missing link’, and the fraudulent cartoon drawings and sculptures showing a chimp morphing into a human, (one misleading drawing of a ‘ape/man which Torley displayed on his other post), the missing link between humans/neanderthals and apes is still missing. Let these few quotes suffice for now to get this point across.

    Skull “Rewrites” Story of Human Evolution — Again – Casey Luskin – October 22, 2013
    Excerpt: “There is a big gap in the fossil record,” Zollikofer told NBC News. “I would put a question mark there. Of course it would be nice to say this was the last common ancestor of Neanderthals and us, but we simply don’t know.” –
    http://www.evolutionnews.org/2.....78221.html

    “A number of hominid crania are known from sites in eastern and southern Africa in the 400- to 200-thousand-year range, but none of them looks like a close antecedent of the anatomically distinctive Homo sapiens…Even allowing for the poor record we have of our close extinct kin, Homo sapiens appears as distinctive and unprecedented…there is certainly no evidence to support the notion that we gradually became who we inherently are over an extended period, in either the physical or the intellectual sense.”
    Dr. Ian Tattersall: – paleoanthropologist – emeritus curator of the American Museum of Natural History – (Masters of the Planet, 2012)

    When we consider the remote past, before the origin of the actual species Homo sapiens, we are faced with a fragmentary and disconnected fossil record. Despite the excited and optimistic claims that have been made by some paleontologists, no fossil hominid species can be established as our direct ancestor.
    Richard Lewontin – “Human Diversity”, pg.163 (Scientific American Library, 1995) – Harvard Zoologist

    Moreover, where the fossil record is clearest to read for humans and not so fragmentary, over the last 30,000 years or so, we find that humans are ‘devolving’ instead of evolving:

    If Modern Humans Are So Smart, Why Are Our Brains Shrinking? – January 20, 2011
    Excerpt: John Hawks is in the middle of explaining his research on human evolution when he drops a bombshell. Running down a list of changes that have occurred in our skeleton and skull since the Stone Age, the University of Wisconsin anthropologist nonchalantly adds, “And it’s also clear the brain has been shrinking.”
    “Shrinking?” I ask. “I thought it was getting larger.” The whole ascent-of-man thing.,,,
    He rattles off some dismaying numbers: Over the past 20,000 years, the average volume of the human male brain has decreased from 1,500 cubic centimeters to 1,350 cc, losing a chunk the size of a tennis ball. The female brain has shrunk by about the same proportion. “I’d call that major downsizing in an evolutionary eyeblink,” he says. “This happened in China, Europe, Africa—everywhere we look.”
    http://discovermagazine.com/20.....-shrinking

    Cro Magnon skull shows that our brains have shrunk – Mar 15, 2010 by Lisa Zyga
    Excerpt: Using new technology, researchers have produced a replica of the 28,000-year-old brain and found that it is about 15-20% larger than our brains.
    http://phys.org/news187877156.html

    Moreover, the genetic evidence supports the ‘devolving’ fossil record:

    Human Genetic Variation Recent, Varies Among Populations – (Nov. 28, 2012)
    Excerpt: Nearly three-quarters of mutations in genes that code for proteins — the workhorses of the cell — occurred within the past 5,000 to 10,000 years,,,
    “One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,”,,,
    “Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older.” (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,,
    The report shows that “recent” events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers.
    The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,,
    http://www.sciencedaily.com/re.....132259.htm

    Thus the classical Theist has a very strong case that God created all the different kinds of life, including man, unique and distinct, in a ‘top down’ fashion and that He did not create in a gradual bottom up fashion as is held by both Theistic Evolutionists and Darwinists.

    The place where the Theistic evolutionist and Darwinist try to make their strongest case for common ancestry, since the fossil record does not support them, is with the genetic evidence. But as with the overall fossil record, the overall pattern in genetic evidence does not support common ancestry. Let this paper suffice for now:

    Logged Out – Scientists Can’t Find Darwin’s “Tree of Life” Anywhere in Nature by Casey Luskin – Winter 2013
    Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.
    Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,,
    Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:
    • A 1998 paper in Genome Research observed that “different proteins generate different phylogenetic tree[s].”6
    • A 2009 paper in Trends in Ecology and Evolution acknowledged that “evolutionary trees from different genes often have conflicting branching patterns.”7
    • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”8
    Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.”9 The author quoted researcher Eric Bapteste explaining that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “many biologists now argue that the tree concept is obsolete and needs to be discarded.”,,,
    Syvanen succinctly summarized the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” ,,,
    “battles between molecules and morphology are being fought across the entire tree of life,” leaving readers with a stark assessment: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”10,,,
    A 2012 paper noted that “phylogenetic conflict is common, and [is] frequently the norm rather than the exception,” since “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.”12,,,
    http://www.salvomag.com/new/ar.....ed-out.php

    And, as with the fossil record, the only place you will get any real stiff resistance to the overall pattern of genetic evidence is when you come to the human/chimp genetic evidence.

    But as heavily as ‘common descenters’ rely on this one piece of genetic evidence to try to make their case for common ancestry between chimps and humans, the evidence is not nearly as robust as they imagine it to be. For starters, several ‘unrelated’ species have been found to have ‘great chunks of the human genome’. For instance, this one example:

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

    Moreover, it has recently been found that alternative splicing patterns are ‘species specific’

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Besides ‘species specific’ alternative splicing, here is another exciting recent finding:

    Unexpected features of the dark proteome – Oct. 2015
    We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ~14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions,
    http://www.pnas.org/content/ea.....1508380112

    Thus all in all, the classical Theist is sitting pretty well as far as the overall pattern of evidence is concerned, and those who hold to common ancestry have the far weaker hand as far as the overall pattern of evidence in concerned.

    i.e. The only place common ancestry is confirmed is in their imagination!

  16. 16
    ThickPython says:

    @Mung, #12:

    The question is about the evidence for synteny.

    I posted the alignments because Ann Gauger intimated in her article that they did not exist. If you’d bothered to look at the results, you’d see that there are six alignments and they are syntenic in the sense that they maintain their order between the two species.

  17. 17
    ThickPython says:

    @Ann, from the original article:

    The 50 percent identity that is so disputed was simply calculated based on the percent identical positions for this 150 base alignment.

    The 150 base alignment shown in figure S2, with its 50 percent identity …

    It’s probably disputed because it doesn’t make sense to count the identical positions from an alignment with four species. If you keep adding species, you’ll increase the chances of seeing a new SNP/mutation at a particular position, and that reduces the identity.

    I could go and do an alignment for a thousand mammals against the chicken, and claim a 0% identity, but I won’t because I’m not an idiot.

  18. 18
    bill cole says:

    Mung@10

    The scientific evidence? Because I’d really like to know the Biblical evidence against the proposition that chickens and porcupines share a common ancestor.

    Were both chickens and porcupines on the ark? How do you decide what “kind” a chicken belongs to and what “kind” a porcupine belongs to? How do you decide which “kinds” survived the flood?

    Is there biblical evidence for the chicken and porcupine? Biochemically two different sequences that required very precise and intentional arrangement.

  19. 19
    vjtorley says:

    Hi everyone,

    I’d like to second bFast’s observation that common descent and common design are not mutually exclusive.

    I might add that Glenn Williamson has written a couple of excellent posts in response to Dr. Jeffrey Tomkins, regarding chromosome 2:

    https://roohif.wordpress.com/2016/05/14/chromosome-2-fusion-the-low-hanging-fruit/

    https://roohif.wordpress.com/2016/05/29/chromosome-2-fusion-dead-in-a-day/

  20. 20
    PaV says:

    vjt:

    You quote Behe as:

    It’s hard to imagine how there could be stronger evidence for the common ancestry of chimps and humans.

    I had no recall of this quote, but you see that he uses the very term I prefer–“common ancestry”–though I maintain that common descent is too strong a statement, while Behe is comfortable with it.

    No one is now—nor do I think ever will be—able to confirm, or disprove, a ‘discontinuous’ line of inheritance.

    You also say that Michael Behe considers CD trivial. I suspect everyone here at UD does so also. As they say, “There are bigger fish to fry.”

    Lastly, you’ll notice that Dr. Swamidrass never responded to my question about the ‘bird feather.’ If you want to “prove” that CD doesn’t exist, and that it should rather be replace by ‘common ancestry’, implying a discontinuous form of inheritance, then that is the candidate. It continues to be problematic for evolutionary biologists.

    Las

  21. 21
    mw says:

    Hi vjt, # 1; citing Professor Michael Behe:

    ————————
    “He goes on to say that common descent is true but trivial, and that it does not, by itself, explain how the differences between humans and chimps originated: “Something that is nonrandom must account for the common descent of life” (p. 72, italics Behe’s).”
    ————————

    As for the “truth,” in terms of similarities, and based on never seen imperceptible increments according to the common descent terminology of Darwinism; that’s when alarm bells should ring for what constitutes ‘certainty’ in terms of common descent.

    The ID movement, in strict terms, does not identify any higher intelligent designer.

    To my understanding, ID science has also grounded itself mainly on a landscape of theology, or in a “trivial” or jovial manner (to some), Martians in some form or another. Consequences there must be.

    Darwin used theology as a starting pistol to blast the brains out of his version of natural selection.

    In my opinion, Christians are gravely in danger of following Darwin, who no sooner out of the starting blocks of “Origin,” ‘masterly’ concluded the Judaeo-Christian God of Sinai was “erroneous” p 6, by dismissing recorded evidence, hence becoming an honoured expert as recognised by fallible humans.

    When Christians’ use starting pistols to blow the brains out of the Judaeo-Christian scripture and belief, to favour an interpretation based on an alternative historic bound scientific belief, we blow the brains out of Christ, and our own life force!

    However, for ID Judaeo-Christians, a little light reflection on what Jesus said may not go amiss:

    ———————————–
    “The one who rejects me and does not receive my word has a judge; on the last day the word that I have spoken will serve as judge, for I have not spoken on my own, but the Father who sent me has himself given me a commandment about what to say and what to speak. And I know that his commandment is eternal life. What I speak, therefore, I speak just as the Father has told me.” (Jn 12:48-50).
    ————————————

    For a Christian, surely, as the supreme intelligence; of whom Jesus is one in essence with Yahweh; said He spoke: “face to face–clearly;” not in riddles” with “my servant Moses” (Num 12:7-8).

    Jesus confirmed the law of Sinai (Matt 5:17-18). He said it was hypocrisy to elasticate divine law (Matt 15:3-9). His words are relevant today in terms of the ‘tradition’ of Darwinism.

    Vjt’s scholarly and philosophical version of the “truth” — common descent is true — again, needed may be further stocktaking. Jesus said he is the “truth” (Jn 14:6) and he said the Father was also the “truth” (Jn 17:17).

    As for the cited comment by vjt, “common descent is true but trivial,” such may need further exploration as it may seem ambiguous, loaded, and misleading.

    Common descent exists from one parent to the next, and via some hiccups, from the beginning. Also, common descent exists in the imagination that is a fact and by consensus science. However, it is impossible for such science to prove humans have ascended from worm and fish parents; or from sterile lifeless dust ‘parentage.’ And beyond that, believing in gaseous ‘parents’ created in outer space; out of no space and nowhere. All that is from the thought beans of agnostic Darwin bringing forth his magic tree of life.

    Of course, theistic evolutionist, including ID theistic evolutionism, claims God did it to their way of thinking when the God of Sinai said totally the opposite and placed his command as a divine law. Yet:

    ——————————–
    Dr Vincent Torley and Dr Josh Swamidass, Assistant Professor; “both hold common descent to be absolutely, incontrovertibly, obviously true,” Dr Ann Gauger states.
    ——————————–

    However, there is room for the interpretation that common similarity may be rooted in a common designer based on God’s intelligent words at Sinai.

    Is there an afterglow from the believed big bang of miracles at origins: similar building blocks and method used, but laid down at divine speed, and at such a speed that it is humanly impossible to see where one life form ends and another starts, that is in the three separate appearing kingdoms of; mineral; vegetable; animal, and the super animal that is both human and divine forever.

    Jesus never went to any formal set of learning: he just had the Father the Almighty. He just created the universe in six days, so he said, and among other things, biologically speaking, kick-started Lazarus back to life after his life functions were stinking with rotten system decay.

    Every recorded miracle in the Judaeo-Christian scriptures was instant in some way. The one continuous origin miracle spread out to suit humans, not God, as he could have instantly created the earth and all life on it perfectly fit, including then the cosmos. God is not deceiving us; we are deceiving ourselves by drinking Darwinian moonshine. As Christians, surely, therefore, better science must follow from following his “way” (Jn 14:6).

    We surely cannot end up in greater fragmentation to suit common consensus science bogged down in a system of thought generated from a person who denied Judaeo-Christianity as being a divinely revealed religion!

    However, then the theological generator spins; surely, the ‘higher intelligence’ confirmed as divine law, origin miracles at Sinai. Every miracle in scripture so recorded, has been done speedily by unknown means.

    In that context, we also do well to remember, concerning miracles, no scientific interpretation of miraculous data is possible. They are beyond our understanding. Otherwise, we — fallen humanity in Judaeo-Christian scriptural terms, would be able to profess to examine God, and by implication, be equal to, or greater than God through science. Now where have we heard similar before?

    Judaeo-Christians are not justified by science, but by faith in what God said and wrote. And the Ten Commandments are the only scripture historically recorded as written by the finger of God, and hence deserving the utmost respect and learning from.

    When will humans be allowed to integrate miracles into origin theory, as a valid means to intelligent understanding?

    Before that event, needed is a second exodus; out of bondage to the house of Darwin.

    However, I look forward to Dr A Gauger’s further additions to her comment:
    ———————–
    “My dispute with Torley (and Venema) is at bottom a dispute about the scientific interpretation of data, or should be.”
    ———–——————
    We do well to remember that.

  22. 22
    gpuccio says:

    PaV:

    Could you please clarify what is the difference in your opinion between “common descent” and “common ancestry”? I must admit that I am not sure I understand. 🙂

  23. 23
    Querius says:

    bFast,

    So the question is, are there any clues left in the data of the DNA that indicate whether the designer is using a patch method (at this offset, insert this data) or a recompile method to implement modifications.

    I’ve sometimes wondered whether viruses were originally intended for this purpose.

    -Q

  24. 24
    Eric Anderson says:

    While we’re at it, let’s make an effort to be clear about what we mean by common descent. Common descent, as understood by some ID proponents is radically different from the common descent that adorns our textbooks and popular claims about the veracity of the materialistic evolution story.

    As with so very many things in the debate, once we get past the popular terminology and understand what people really mean, we find that there is quite a bit of agreement among ID proponents on this issue, even, I should add, Mike Behe, as quoted at the top.

  25. 25
    Dr JDD says:

    vjtorley @1:

    How does Behe know this is a mutation? Defining the observed pattern or sequence in the alleged “pseudogene” depends on the assumption of common descent itself.

  26. 26
    caleb says:

    @ Glenn

    I have looked at the alignments you posted and i agree, they are good alignments. But if I read your BLAST specifications right, they are not for the same regions as reported in the Brawand paper. I could be wrong, but the coordinates used in their paper appear to be written along each graph. Are your alignments a demonstration of synteny? It would appear so–but not in the VIT gene regions.

    You are correct about not using all four species for comparison–it probably reduces the percent identity. My mistake.

    Ann

  27. 27
    bFast says:

    Querius (33), “I’ve sometimes wondered whether viruses were originally intended for this purpose.” Viruses as agents whose job it is to provide DNA patches. An interesting hypothesis.

  28. 28
    bFast says:

    My challenge to the common designers.

    There is one case, and one case alone that has me hold to common descent (at least common between chimps and humans.)

    That case is the approximately 80 disease causing point mutations that are shared between humans and chimps. (Unfortunately I do not have source material for this claim, as I read it in a magazine while waiting for the hair dresser.)

    If I understand correctly, there are about 80 identified genetic alleles that are different from their healthy sibling at a single point — alleles that exist both in chimp and human. If I understand correctly, if a person or chimp has one of these alleles expressed, he is diseased. (Usually these alleles are recessive, hence a person needs two matching alleles to get the disease.) My understanding is that some of these alleles also exist in other great apes.

    Now, if you are a common design advocate, please explain this to me. Optionally, please find the source material and show me that the source material is wrong. The common descent position sees this kind of thing as totally natural. (Please understand, however, that this evidence, as seen through a common descent filter, abolishes the concept of a literal Adam and Eve. There must have been a minimum of hundreds of individuals in the species at any given time so that 80 recessive dysfunctional alleles could be carried around.)

  29. 29
    Dr JDD says:

    bFast:
    I don’t understand your point. Do all humans have these and all chimps?

    Well surely not. As all don’t have said “disease”.

    A valid alternative then is mutational susceptibility or “hot-spots”.

    I’m wiling to bet there’s a lot more of that than most people realise.

    common design and specifically the Judeo-Christian paradigm would be in line with this interpretation.

    However evolutionists like to assume all sequences are equally mutable. Except when it suits….

  30. 30
    ThickPython says:

    @caleb, #26:

    But if I read your BLAST specifications right, they are not for the same regions as reported in the Brawand paper. I could be wrong, but the coordinates used in their paper appear to be written along each graph. Are your alignments a demonstration of synteny? It would appear so–but not in the VIT gene regions.

    The Brawand paper uses an older version of the human genome – NCBI36 (also known as hg18), Dr Tomkins uses GRCh37/hg19, while the current version is GRCh38. The coordinates differ between versions, but luckily Ensembl have a translation facility. So, for example, when Dr Tomkins describes the locus of the 150bp fragment as chr1:79254632-79254781, I can convert that to GRCh38 coordinates like so:

    http://rest.ensembl.org/map/hu.....ation/json

    … you’ll see that in GRCh38 coordinates are 78,789,096 to 78,788,947 which correspond to my BLAST results.

    You are correct about not using all four species for comparison–it probably reduces the percent identity. My mistake.

    Thank you.

  31. 31
    caleb says:

    @ thickpython
    then why not report this data in their paper?

    Ann

  32. 32
    ThickPython says:

    @Ann, #31:

    then why not report this data in their paper?

    Full disclosure: I haven’t actually read the Brawand paper from start to finish, and don’t intend to. I’m here merely to show that the synteny is much greater than the 150bp claimed by Tomkins.

    So you will have to take your question to the authors. My suspicion is that they were only concerned with the exons … ?

  33. 33
    bill cole says:

    VJT

    https://roohif.wordpress.com/2016/05/29/chromosome-2-fusion-dead-in-a-day/

    How would you propose the gene arrived in this location from fused telomeres?

  34. 34
    ThickPython says:

    @bill cole, #33:

    How would you propose the gene arrived in this location from fused telomeres?

    Hello, and welcome to the misinformation that is spread by Jeff Tomkins.

    If the chromosome were to be split at the fusion point, the DDX11L2 pseudogene would still exist. It is NOT the case that before the fusion there was no gene, and after the fusion there was a gene.

    The fusion made a binding site available on the other side, and this allowed an additional transcript.

  35. 35
    vjtorley says:

    Hi everyone,

    I would like to thank Dr. Ann Gauger for her participation in this discussion over at Uncommon Descent. For the record, although my recent article on UD contained some criticisms of her work, I have the highest respect for her accomplishments and her integrity.

  36. 36
    vjtorley says:

    Hi everyone,

    In other news: Professor Swamidass has sent me the results of some BLAST tests which he performed recently, and they accord well with Glenn’s results. I’m off to work now, but I’d be happy to supply more details in about 14 hours.

  37. 37
    bill cole says:

    ThickPython

    http://www.icr.org/i/articles/.....on_pic.jpg

    This image is from Dr Tompkins article. Is this image wrong? If two chromosomes fuse at the telomeres how does a gene or a transcription site appear?

    The fusion made a binding site available on the other side, and this allowed an additional transcript.

    How would a telomere fusion create a binding site?

  38. 38
    ThickPython says:

    @bill cole, #37:

    This image is from Dr Tompkins article. Is this image wrong? If two chromosomes fuse at the telomeres how does a gene or a transcription site appear?

    No, the image looks about right to me.

    But again, you’re using language that suggests that a new (pseudo-)gene was created by the fusion when that is not the case. There are two transcripts to this pseudogene – the shorter, canonical transcript (wholly on one side of the fusion site) which is expressed about 4 times as frequently as the longer transcript that spans the fusion site.

    Transcription factor binding sites are a lot more common than people realise. The binding site on the other side of the fusion didn’t “appear” in the sense that it just popped into existence, it was just on the other chromosome. And then we have the binding site in the fusion sequence itself, to which I say whoopty-frikkin-doo.

    My third post on the fusion model (which is in the works) is on this topic.

  39. 39
    bFast says:

    Dr. JDD (29)
    First, most humans don’t have any of these alleles. However the population does.

    The mutational hot spot theory would only be a reasonable explanation if “hot spots” didn’t mean “hot zones”, but it would require specific hot mutational points. If not, then the fact that the alignment of these mutations (relative to the gene’s start) would rarely match.

  40. 40
    bornagain77 says:

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    The genetic similarity argument for common ancestry highlights the unfalsifiable nature of Darwinian theory. If genetic similarity between supposedly closely related species, as their reasoning goes, is suppose to be undeniable proof for the hypothesis of common ancestry, then finding highly similar sequences in widely divergent species should serve as a falsification for that hypothesis. Yet highly similar sequences in widely divergent species are not allowed to falsify the common ancestry hypothesis. Darwinists and Theistic Evolutionists, whether intentionally or not, invoke ‘convergent evolution’ to ‘explain away’ highly similar sequences in widely divergent species.

    Darwinism Versus the Octopus: An Evolutionary Dilemma – Eric Metaxas – September 08, 2015
    Excerpt: What’s the difference between evolutionary theory and an octopus? Well, one is a slippery, color-changing escape artist that can get out of any tough situation and the other is an aquatic invertebrate.,,,
    The key to this uncanny intelligence is the octopus’ so-called “alien” nervous system, brain, and eyes. But these features are not alien to the animal kingdom at all. In fact, they’re quite common in higher vertebrates. The octopus genome shares key similarities with ours, including the development of high-powered brains and “camera eyes” with a cornea, lens, and retina.
    Now here’s the problem for evolution: according to Neo-Darwinists, we’re not related to octopi—at least not within the last several hundred million years. That means all of these genes, complex structures, and incredible capabilities came about twice.
    The researchers who sequenced the octopus genome call this “a striking example of convergent evolution,” or the supposed tendency of unrelated creatures to develop the same traits in response to environmental pressures. Isn’t that just a fancy way of saying a miracle happened twice?
    But the octopus isn’t the only such miracle. “Convergent evolution” is all over nature, from powered flight evolving three times to each continent having its own version of the anteater. Think about that. As one delightfully un-self-conscious “Science Today” cover put it, convergent evolution is “nature discover[ing] the same design over and over.” Well, good for nature!
    But as Luskin argues, there’s a better explanation for a tentacled mollusk having a mammal’s brain and human eyes. And that explanation is common design by an intelligent Engineer. And like all good engineers, this this one reused some of His best designs.
    Now that explanation isn’t going to satisfy Darwinian naturalists. And they’ll probably keep on invoking “convergent evolution” when faced with impossible coincidences in nature.
    But hopefully knowing a more straightforward explanation leaves you forearmed—or should I said “eight-armed”?
    http://www.christianheadlines......lemma.html

    Here are a few more examples of ‘convergent evolution’:

    Newly Discovered Convergent Genetic Evolution Between Bird and Human Vocalization Poses a Severe Challenge to Common Ancestry – Casey Luskin – December 15, 2014
    Excerpt: “We’ve known for many years that the singing behavior of birds is similar to speech in humans — not identical, but similar -,,, “But we didn’t know whether or not those features were the same because the genes were also the same.”
    “Now scientists do know, and the answer is yes — birds and humans use essentially the same genes to speak.”,,,
    “there is a consistent set of just over 50 genes,,,”
    “These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak,”
    So certain birds and humans use the same genes for vocalization — but those genetic abilities are absent in non-human primates and birds without vocal learning? If not derived from a common ancestor, as they clearly were not, how did the genes get there? This kind of extreme convergent genetic evolution points strongly to intelligent design.
    http://www.evolutionnews.org/2.....92041.html

    First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007
    Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,,
    The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.
    http://news.nationalgeographic.....m-dna.html

    When both the supporting evidence and the falsifying evidence count as evidential support for your hypothesis, it is a sure sign you are dealing with a pseudo-science instead of a proper science.

    Although examples of Darwinists adding ‘epicycles’ to their theory in order to protect it from falsification abound (Cornelius Hunter: 2015), the primary reason why Darwinian evolution is more properly thought of as a pseudo-science instead of a proper science is because Darwinian evolution has no rigid mathematical basis like other overarching physical theories of science do. A rigid mathematical basis to test against in order to potentially falsify it (in fact, in so far as math can be applied to Darwinian claims, mathematics constantly shows us that Darwinian evolution is astronomically unlikely),,

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    – Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003

    Darwinian Evolution is a Unfalsifiable Pseudo-Science – Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

    Moreover, in all of this talk about genetic similarity, there is one VERY important point that seems to be completely lost on Darwinists (and apparently completely lost on Theistic Evolutionists too)!

    That very important point is that to say that organism A and B are similar and that you have a theory that can explain the similarities is to say nothing at all. Because similarities don’t need an explanation. What needs an explanation are the differences that produced the changes not the similarities that tell us nothing.

    “If the overall biology of the animals tells you that they are very different, and the genetics tells you that they are nearly identical, it follows that the genetic comparison is telling you something relatively trivial about the overall biology.”
    Jonathan Marks – evolutionary biologist/anthropologist at the University of North Carolina – 1993
    http://www.evolutionnews.org/2.....89441.html

    Doug Axe on What Seduces Us in the “Darwinian Story” – video
    Quote: “I’ve recognized that people find something seductive about the evolutionary story. And that is, if you can point out similarities between things then people find it at least intriguing the idea that there can be transitions that go from A to B, because you see the similarities. And the similarities are certainly suggestive. A key take home for me that I would like people to get from reading the book, (Human Origins), is that Darwinists really need to confront not the similarities, but the differences. To say that A and B are similar and that you have a theory that can explain the similarities is to say nothing at all. Because similarities don’t really need an explanation.
    What needs explanation is the differences in all these transitions of going from A to B. So that is the key focus for us. In all of these substantial transitions of form, there are not only similarities , they are there, but there are differences. Can Darwinism explain the differences? If I can get people to think about that, to realize how hard it is for Darwinism to explain even really, really modest differences”,,,
    https://www.youtube.com/watch?v=pnFs5D-vvnI

    And when one tries to explain the differences that produced the changes, instead of just focusing on the similarities which tell us next to nothing important scientifically as to how transformation of form is even remotely possible, then one soon realizes that Darwinian explanations are grossly inadequate:

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time. Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be. That’s just not what scientists should be doing.
    Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.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/

  41. 41
    bornagain77 says:

    “Shared Evolutionary History or Shared Design?” – Ann Gauger – January 1, 2015
    Excerpt: The waiting time required to achieve four mutations is 10^15 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    http://www.evolutionnews.org/2.....92291.html

    Is There Enough Time For Humans to have Evolved from Apes? Dr. Ann Gauger Answers – video
    http://www.youtube.com/watch?v=KN7NwKYUXOs

    Dr. Sanford’s work agrees with Gauger and Axe’s empirical work, as this paper from BioMed shows:

    The waiting time problem in a model hominin population – 2015 Sep 17
    John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner
    Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,,
    Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information.
    While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man.
    It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years.
    http://www.ncbi.nlm.nih.gov/pm.....MC4573302/

    Here are several more peer reviewed papers by Dr. Sanford and company, on population genetics, falsifying Darwinian evolution from numerous different angles:

    Genetic Entropy – peer reviewed references
    http://www.geneticentropy.org/#!properties/ctzx

    Moreover, even as bad as the preceding is for ‘bottom up’ Darwinian explanations, it was still falsely presumed in the preceding papers by Drs. Gauger, Axe, and Sanford, that changes to DNA can explain transformations in form, or ‘body-plan morphogenesis’ as Dr. Stephen Meyer calls it. Yet, Darwinists and Theistic Evolutionists have no hard evidence whatsoever that changes to DNA will lead to fundamentally new transformations in form:

    “Any transition of form is pure fantasy. There is no demonstration of it.”
    Douglas Axe – co-author of Science & Human Origins – video
    http://www.youtube.com/watch?v=XxMmLakH2LQ

    Response to John Wise – October 2010
    Excerpt: A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

    Dr. Stephen Meyer puts the insurmountable problem for Darwinian explanations of ‘form’ like this:

    ‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body-plan. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’
    Stephen Meyer – Functional Proteins and Information for Body Plans – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1140536289292636/?type=2&theater

    That the ‘form’ of a organism is not reducible to material particulars, as is presupposed by both Darwinists and Theistic Evolutionists, is made clear by the two following examples:

    What Do Organisms Mean? Stephen L. Talbott – Winter 2011
    Excerpt: Harvard biologist Richard Lewontin once described how you can excise the developing limb bud from an amphibian embryo, shake the cells loose from each other, allow them to reaggregate into a random lump, and then replace the lump in the embryo. A normal leg develops. Somehow the form of the limb as a whole is the ruling factor, redefining the parts according to the larger pattern. Lewontin went on to remark: “Unlike a machine whose totality is created by the juxtaposition of bits and pieces with different functions and properties, the bits and pieces of a developing organism seem to come into existence as a consequence of their spatial position at critical moments in the embryo’s development. Such an object is less like a machine than it is like a language whose elements… take unique meaning from their context.[3]”,,,
    http://www.thenewatlantis.com/.....nisms-mean

    “Last year I had a fair chunk of my nose removed in skin cancer surgery (Mohs). The surgeon took flesh from a nearby area to fill in the large hole he’d made. The pictures of it were scary. But in the healing process the replanted cells somehow ‘knew’ how to take a different shape appropriate for the new location so that the nose now looks remarkably natural. The doctor said he could take only half the credit because the cells somehow know how to change form for a different location (though they presumably still follow the same DNA code) . — I’m getting the feeling that we’ve been nearly as reductionist in the 20-21st century as Darwin and his peers were when they viewed cells as little blobs of jelly.”
    leodp – UD blogger

  42. 42
    bornagain77 says:

    And as should be needless to say, if your materialistic theory cannot explain the ‘form’ of an organism in the first place, then any materialistic theory that purports to explain the transformation of form in all organisms on earth is, to put it mildly, severely misguided in its theoretical foundation.

    Moreover, this failure of materialistic explanations to explain ‘form’ happens at a very foundational level. “Random” Darwinian explanations cannot even explain how a protein finds it final folded form, much less how an entire organism achieves its final form:

    Physicists Discover Quantum Law of Protein Folding – February 22, 2011
    Quantum mechanics finally explains why protein folding depends on temperature in such a strange way.
    Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from.
    To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,,
    Today, Luo and Lo say these curves can be easily explained if the process of folding is a quantum affair. By conventional thinking, a chain of amino acids can only change from one shape to another by mechanically passing though various shapes in between.
    But Luo and Lo say that if this process were a quantum one, the shape could change by quantum transition, meaning that the protein could ‘jump’ from one shape to another without necessarily forming the shapes in between.,,,
    Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins.
    That’s a significant breakthrough. Luo and Lo’s equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics.
    http://www.technologyreview.co.....f-protein/

    Of related note to ‘quantum’ proteins: Quantum Mechanics is completely antagonistic to the ‘bottom up’ materialistic foundation that Darwinian evolution is built upon:

    Jim Al-Khalili, at the 2:30 minute mark of the following video states,
    “,,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can’t build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn’t really require much in the way of quantum mechanics in the way to explain it.”
    At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
    “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
    Jim Al-Khalili – Quantum biology – video
    https://www.youtube.com/watch?v=zOzCkeTPR3Q

    Here is a bit closer look at the falsification of Darwinian evolution by Quantum Mechanics:

    Molecular Biology – 19th Century Materialism meets 21st Century Quantum Mechanics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1141908409155424/?type=2&theater

    Looking beyond space and time to cope with quantum theory – 29 October 2012
    Excerpt: “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,”
    http://www.quantumlah.org/high.....uences.php

    Physicists find extreme violation of local realism in quantum hypergraph states – Lisa Zyga – March 4, 2016
    Excerpt: Many quantum technologies rely on quantum states that violate local realism, which means that they either violate locality (such as when entangled particles influence each other from far away) or realism (the assumption that quantum states have well-defined properties, independent of measurement), or possibly both. Violation of local realism is one of the many counterintuitive, yet experimentally supported, characteristics of the quantum world.
    Determining whether or not multiparticle quantum states violate local realism can be challenging. Now in a new paper, physicists have shown that a large family of multiparticle quantum states called hypergraph states violates local realism in many ways. The results suggest that these states may serve as useful resources for quantum technologies, such as quantum computers and detecting gravitational waves.,,,
    The physicists also showed that the greater the number of particles in a quantum hypergraph state, the more strongly it violates local realism, with the strength increasing exponentially with the number of particles. In addition, even if a quantum hypergraph state loses one of its particles, it continues to violate local realism. This robustness to particle loss is in stark contrast to other types of quantum states, which no longer violate local realism if they lose a particle. This property is particularly appealing for applications, since it might allow for more noise in experiments.
    Per physorg

    Moreover, it is important to learn that ‘non-local’, beyond space and time, quantum entanglement (A. Aspect, A. Zeilinger, etc..) can be used as a ‘quantum information channel’,,,

    Quantum Entanglement and Information
    Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory.
    http://plato.stanford.edu/entries/qt-entangle/

    Besides providing direct empirical falsification of neo-Darwinian claims that say information is emergent from a material basis, the implication of finding ‘non-local’, beyond space and time, and ‘conserved’ quantum information/entaglement in molecular biology on such a massive scale, in every DNA and protein molecule, is fairly, and pleasantly, obvious.
    That pleasant implication, or course, being the fact that we now have direct physical evidence of a transcendent component to our being that is strongly suggestive to the fact that we do indeed have an eternal soul that lives beyond the death of our material bodies.

    Scientific (physical) evidence that we do indeed have an eternal soul – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1116313858381546/?type=2&theater

    Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff – video
    https://www.youtube.com/watch?v=iIyEjh6ef_8

    Verse and Music:

    Mark 8:36
    What good is it for someone to gain the whole world, yet forfeit their soul?

    Metallica & San Francisco Symphony Orchestra – Nothing Else Matters
    http://www.youtube.com/watch?v=ziThYl6B2vw

  43. 43
    HeKS says:

    bFast @39

    Dr. JDD (29)
    First, most humans don’t have any of these alleles. However the population does.

    The mutational hot spot theory would only be a reasonable explanation if “hot spots” didn’t mean “hot zones”, but it would require specific hot mutational points. If not, then the fact that the alignment of these mutations (relative to the gene’s start) would rarely match.

    Not necessarily. For example, what if you had functional elements in both chimps and humans that relied on dependencies that were prone to degradation or wholesale loss? If that were the case, all of the similarities would be due to function but the current disease outcome in both species would be a result of malfunction of a shared system due to breakage in dependencies that are prone to failure.

    I’m a web UI programmer and I’ve been talking recently in the ‘consider the opossum’ thread about how programming design patterns should impact on assumptions about junk DNA and common descent. I think that in order to make sense of DNA from a design standpoint, one needs to consider DNA from the dual perspective of software programming and structural engineering. I have no expertise whatsoever in the latter, but I know from personal experience that physical systems tend to have consistent break points, or pathways of least resistance to system failure. This system over here tends to have this element fail after X amount of time. That system over there tends to have another element fail after a certain amount of time. In programming you don’t typically have blocks of code that are prone to breaking down in the sense of the language somehow getting corrupted, but you can sometimes have blocks of code that are prone to failing because they rely on external resources that might be unreliable.

    Take care,
    HeKS

  44. 44
    Querius says:

    bornagain77,

    The genetic similarity argument for common ancestry highlights the unfalsifiable nature of Darwinian theory. If genetic similarity between supposedly closely related species, as their reasoning goes, is suppose to be undeniable proof for the hypothesis of common ancestry, then finding highly similar sequences in widely divergent species should serve as a falsification for that hypothesis. Yet highly similar sequences in widely divergent species are not allowed to falsify the common ancestry hypothesis. Darwinists and Theistic Evolutionists, whether intentionally or not, invoke ‘convergent evolution’ to ‘explain away’ highly similar sequences in widely divergent species.

    Great point! The theory of evolution can explain everything, but successfully predicts nothing.

    HeKS,
    Considering the similarity between software and DNA, another problem is that not only does one need an effective mechanism for the program to be able to evolve, but the programming language and the operating system must also have evolved somehow before there was any survival advantage. This leaves massively improbable “luck” as the mechanism, for which the age of the universe is a ridiculously insufficient amount of time.

    But don’t worry.

    Some scientists can draw on the limitless probabilities available from the Multiverse, each one of which also needs to be able to instantly spawn trillions of the Many Worlds needed to avoid the interpretation problems materialists have with the demonstrated ability for human observation being able to collapse the wave functions in quantum mechanics.

    All we need is an infinity of infinities, more properly called “a miracle.” Parsimony need not apply.

    And when this Miraculous Mutation (TM) finally appears in an organism, all that needs to happen is for the *identical* Miraculous Mutation to appear within thousands of other organisms at the same time to ensure that this amazing trait is able to survive within the genome. But, hey. We have plenty of time.

    No wonder Thick Python and Professor Swamidrass don’t seem to be eager to accept the challenge of demonstrating their assertions using a huge, rapidly reproducing population of non-motile bacteria subjected to enough ionizing radiation to simulate millions of years of mutagenic impact to finally produce a mutated bacteria with flagella, cilia, legs, propellers, teensy jet engines, or whatever to make them motile!

    This is called “science” in contrast to imaginative extrapolation, interpretation, and speculation.

    -Q

  45. 45
    mw says:

    Dr Hunter is mentioned a few times in this thread, who, in relation to the “truth” of common descent (which Dr Torley appears to hold as scientifically dogmatic), disagrees with Professor Dennis Venema, and to whom Dr Ann Gauger also refers to, as “weak evidence for common descent.”

    Dr Hunter writes:
    ———————————————–

    “In spite of these problems with his argument, Venema is enthusiastic about this evidence. In fact his enthusiasm leads to the fallacy of affirming the consequent, as he equates shared synteny (genes with similar positioning in the genomes of different species) with common descent”:

    ‘This evidence increases our confidence that we are indeed looking at regions with shared synteny: in other words, a region in two present-day species that was once a region in the genome of their common ancestral population.’

    “That is a fallacy. Ignoring the problems discussed above for the moment, even if evolution did make a hard prediction of shared synteny, and even if it was universally observed, that would not prove evolution. In that case, you would have a confirmed prediction. That is good, but it is not equivalent to a finding of evolution. Venema violates this scientific fundamental when he defines shared synteny as ‘a region in two present-day species that was once a region in the genome of their common ancestral population.’ Unfortunately, affirming the consequent is not uncommon in the evolution literature.”
    http://darwins-god.blogspot.co.....s.html?m=1
    ————————————————–

    “I am the way, and the truth and the life” (Jn 14:6). Not in this case when it comes to common descent, Lord!

  46. 46
    tjguy says:

    Mung @10

    The scientific evidence? Because I’d really like to know the Biblical evidence against the proposition that chickens and porcupines share a common ancestor.

    The biblical evidence against said idea is that chickens would have been created on day 5 according to their kind while porcupines would have been created on day 6 according to their kind.

    Were both chickens and porcupines on the ark? How do you decide what “kind” a chicken belongs to and what “kind” a porcupine belongs to? How do you decide which “kinds” survived the flood?

    Since the Bible doesn’t tell us what the original kinds were, we have to try and figure that out using genetics. This necessarily involves a lot of assumptions and interpretation, so nothing is for certain. Research in baraminology is ongoing.

    All of the “kinds” would have survived the flood unless some of them had already gone extinct before the flood and therefore would not have been on the ark.

    Of course, most IDers do not believe in a global flood so I’m not sure why you would bring this up here.

  47. 47

    Hello All,

    VJ asked me to contribute a few comments. I have a small break today, and decided to use it to participate. I do have one request. Please be kind and respectful. Disagree with me, of course, but please give me reason to gladly spend my time with you.

    I’ll post a few comments. First regarding infighting and terminology.

    @6 terminology

    Some have expressed concern with the term “common descent”. This has come up before. I will say, as a scientist, that there are several nearly equivalent terms that are acceptable in this conversation:

    common descent
    common ancestry
    common descent with designed modification
    common ancestry with designed modification

    To be clear, this conversation does not even concern “universal” common descent. We are talking, usually, in the more restricted sense of common ancestry of man, mammals, or vertebrates. If you don’t like one term, and feel the use to another from this list, that is entirely fine by me.

    I will also point out (at some risk) that this notion of “common ancestry” is the historically most consistent definition of evolution. This is why Behe considers himself, correctly, a theistic evolutionist. I know that “evolution” is a bad word for many in the ID community, so I understand if you reject evolution but accept CD.

    @5 @4 about infighting

    “I think that we the ID community need to demonstrate to the rest of science that we are an evidence driven people, not a position driven people.”

    “I agree. A healthy exchange is good. Lets discover together what the evidence is really telling us. I thought Ann did a very good job defending her position and agree Dr Hunter has surfaced some very good points.”

    This is significant and important. I want to affirm it. Right now, there is a perception that ID is only concerned with attacking people outside the ID camp, without really grappling with evidence internally. This is why internal debate (even with me as an outside observer) is healthy and valuable. If you demonstrate to the scientific world you can come to and evidence based consensus about things like, for example. common descent, it enables to take you more seriously about other things.

    @4 @5 about Hunter

    “That said, I recently watched Dr. Hunter put out a compelling case against common descent.”

    I disagree with this strongly. Every point that Hunter has raised is clearly wrong on an evidentiary basis. Dead wrong, often accusatory, and also what appears to be deceptive. The only reason his specific arguments are not being answered by me is because (1) he has refused to publicly conceded a point in where was clearly demonstrated to be wrong, and (2) he has not even attempted to answer VJ’s 13 questions.

    If you think Hunter has made a solid case, ask him why he is unwilling to answer VJ’s questions. Why is he is unable/unwilling to answer an careful and honest critique from a member of the ID community? Instead of engaging, he moved on to another long list of inaccurate and false claims about the evidence.

    In particular, I find it galling that he seems to argue that there is “absolutely no evidence” for common descent. This is a truly absurd claim. Even Ann acknowledges that at least some evidence exists for CD, even though she ultimately seems to reject it. I would love to entertain a real conversation with Hunter, but until he answers VJ and can acknowledge the clear evidence for CD that he himself uncovered, I dispute the notion that he has made a compelling case against CD.

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

    For those that just do not like CD, despite the evidence.

    I will point out too, that I have said repeatedly that there are good reasons for rejecting CD. In particular, there are good and dignified reasons for rejecting CD for theological reasons. This is what Todd Woods does, and I respect that. On the scientific front, looking at evidence, I (and the rest of the mainstream scientific community) contend that the case for CD is rock solid. So I am doing too things here. Scientifically, “recent” evolutionary history (e.g. the last 50M years of mammalian evolution) the evidence points in one direction unambiguously to CD. More remote evolutionary history (e.g. microbial evolution) is less clear, primarily because the genomic signature degrades substantially past about 100mya.

  48. 48

    @44 “Great point! The theory of evolution can explain everything, but successfully predicts nothing.”

    I had to smile when I read this. You are in the middle of a case study in a successful prediction of evolution. It absolutely does make predictions.

    Let’s recap…

    1. A paper was published claiming that VTG1 has homology to DNA in humans in the exact right place in Chr1. The exact p-values were not reported.

    2. Ann Gauger doubts CD, and disputed the statistical quality of that match. She asserted that perhaps the match was not really there, and just a statistical illusion.

    3. I, however, trust that CD is a helpful framework in biology, that has a very good track record of PREDICTING patterns in biology. I supposed that the statistical match between VTG1 and this region was probably high.

    So now, we have two hypothesis: there (#3) is or (#2) is not a good statistical match between VTG1 and the correct region in the human genome. Now we can ALL test this for ourselves to see what hypothesis the data indicates is justified. Of course, this is not “proof.” Science, rather is about making rigorous explanations, and CD explains this data.

    An independent party has done just this, demonstrating that I was right and that Ann was wrong.

    https://roohif.wordpress.com/2016/06/11/where-did-that-guy-get-his-data-from/

    HERE IS THE RECIPE FOR YOU TO TRY TOO…

    a) Get the VTG1 sequence from here:
    http://www.ncbi.nlm.nih.gov/gene/424547
    http://www.ncbi.nlm.nih.gov/nu.....o=18737086

    b) Paste sequence into blastn website (default parameters, https://blast.ncbi.nlm.nih.gov/Blast.cgi). Choose to search against human…and you get this top hit..

    Homo sapiens chromosome 1, alternate assembly CHM1_1.1 291 1.613e+06 9% 5e-74 75% NC_018912.2

    To be clear, you might get a slightly different result if you use different parameters. The e-value of 5e-74 is not exactly a p-value, but has some close correspondence to it, close enough to be interpreted in a “similar” way.

    c) Now, we can also visualize this using the UCSC genome browser BLAT search. Just paste the VTG1 sequence into BLAT (https://genome.ucsc.edu/cgi-bin/hgBlat?command=start). Click the first hit, then zoom out far enough to see ETLD1 and check the tracts as required. I did this to get this image here:

    https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr1%3A78659897-78919796&hgsid=497817261_89LABjkhtaZ9Vn8cDAIDVganAACJ
    http://swami.wustl.edu/hgt_genome_680f_62a4d0 (if the first one doesn’t work use this).

    A couple things to note. (1) the sequence is right where we expect it to be, (2) in my image, I plotted the match alongside transcript levels. The VTG1 match is not expressed nearly at all (because it is not likely functional) while the two flanking genes (see bar graphs) are expressed in a large number of tissues at a high level.

    THE SAME PROCESS CAN BE REPEATED (minus blat) USING THE WHOLE INTERGENEC REGION.

    Gotta go now, but I will post this recipe later.

    Depending on the exact parameters, I get 8 to 24 matches accross the region. Here is the summary of the matches in one run…

    Length 278bp, identity 71%
    Length 248bp, identity 73%
    Length 288bp, identity 70%
    Length 278bp, identity 75%
    Length 483bp, identity 74%
    Length 390bp, identity 74%
    Length 321bp, identity 68%

    So this gives us an overall alignment of 2286 base pairs with an overall similarity (weighted) of about 72.3%. Much better than 150bp with 50% similarity that Ann reports. Also, all with very very high statistical significance.

    Now, for those of you that now want to claim that this is all a lncRNA. A few points. From a CD point of view, “exaptation” allows this to be functional. It does not to be non-functional to be evidence for CD. That is just a red herring.

    Moreover, this is little (no?) evidence that this actually is a lncRNA. I reread the Tomkins paper that claims this and see no strong evidence (just wild speculation) that the original vtg fragment actually is a lncRNA. As for the whole region? He does not even try to claim it is all a lncRNA. So, for two reasons, that lncRNA theory really is entirely irrelevant here.

    Now, if you really do care about evidence as you claim, do the experiment yourself, and see if CD makes predictions. It does, and they are usually correct.

    ===EXTRA CREDIT: SYNTENY===

    @26 Ann..

    We can also ask, does the VTG1 sequence match to the right place in the human genome with the highest similarity? Does it match next to the ETLD1 gene?

    HINT: Just as we would predict with CD, it does match there. And it does so in the right direction too.

    This becomes obvious when you use the BLAT search in the UCSC browser, and zoom out to see the surrounding genes: PGTFR and ETLD1. You can also just click the link I gave you there to see it.

    Btw, Ann, I give you credit for acknowledging publicly that this is a good match. I respect your willingness to change your mind, especially in public like that.

  49. 49

    A word about exapation and homology.

    Exaptation is the use of one structure (e.g. a stretch of DNA) for different purpose than it was used in evolutionary history. Just proving that the remnants of a pseudogene (e.g. b-hemoglobin or VTG1) might have a new function (in gene regulation or as a non-functional lncRNA) does not in any way invalidate CD.

    Asserting function in the pseudogenes does not validate design either. In addition to showing function you have to demonstrate that the POSITION (the synteny) in the genome right there is necessary. That is the specific signature here we are focusing on. Not just homology, but also synteny.

    Now, regarding exaptation and homology for distantly related sequences, there is a relationship. It turns out for very distantly related sequences (like VTG1 and the human DNA match), homology is more likely to be preserved where there is some evolutionary history of function (e.g. exaptation). This is an explicit part of some mathematical models. The more function, the more exaptation, the more preservation of the original sequence.

    This is important, because (in these distantly related sequence) we do expect to occasionally encounter new functions and for this to be where they homology is strongest. This is exactly predicted by CD and neutral theory.

    While this is consistent with design, the POSITION in the genome is not precisely predicted by design, unless we include some form of common ancestry too.

    This is why scientists think the evidence for CD is so solid. This (of course) is just one line of evidence. The correlation between de novo mutation and divergence is also predicted by CD, and not explained by design. That should be the next type of evidence to look closely at.

  50. 50
    bornagain77 says:

    As to this claim:

    “You are in the middle of a case study in a successful prediction of evolution. It absolutely does make predictions.”

    Except when Darwinian evolution does not make successful predictions, then it is merely ‘explained away’ as ‘a striking example of convergent evolution between these clades at the molecular level.”

    The octopus genome and the evolution of cephalopod neural and morphological novelties – August 13, 2015
    Excerpt: the independent expansions and nervous system enrichment of protocadherins in coleoid cephalopods and vertebrates offers a striking example of convergent evolution between these clades at the molecular level.
    http://www.nature.com/nature/j.....14668.html

    Contrary to what Prof. S. Joshua Swamidass prefers to believe, and besides Darwinian evolution being a unfalsifiable pseudo-science (posts 40-43), the list of fundamentally failed predictions of Darwinian evolution is rather long:

    First a little background as to ‘predictive power’s’ rank in science. Predictive power, although impressive, actually ranks below falsifiability as to determining whether a theory is ‘scientific’ or not.

    “In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.”
    Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge

    Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution By John Horgan on July 6, 2010
    Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table.
    http://blogs.scientificamerica.....evolution/

    Unlike Popper, philosopher of science Imre Lakatos tipped toed around the fact that Darwinism does not have rigid mathematical falsification criteria to test against, as other overarching theories of science have, in order to potentially falsify it,,,

    A Philosophical Question…Does Evolution have a Hard Core ?
    Some Concluding Food for Thought
    In my research on the demarcation problem, I have noticed philosophers of science attempting to balance (usually unconsciously) a consistent demarcation criteria against the disruptive effects that its application might have with regard to the academic status quo (and evolution in particular)… Few philosophers of science will even touch such matters, but (perhaps unintentionally) Imre Lakatos does offer us a peek at how one might go about balancing these schizophrenic demands (in Motterlini1999: 24)

    “Let us call the first school militant positivism; you will understand why later on. The problem of this school was to find certain demarcation criteria similar to those I have outlined, but these also had to satisfy certain boundary conditions, as a mathematician would say. I am referring to a definite set of people to which most scientists as well as Popper and Carnap would belong. These people think that there are goodies and baddies among scientific theories, and once you have defined a demarcation criterion. you should divide all your theories between the two groups. You would end up. for example, with a goodies list including Copernicus’s (Theory1), Galileo’s (T2), Kepler’s (T3), Newton’s (T4) … and Einstein’s (T5), along with (but this is just my supposition) Darwin’s (T6). Let me just anticipate that nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific, but this is exactly what we are looking for.”

    So basically, the demarcation problem is a fun game philosophers enjoy playing, but when they realize the implications regarding the theory of evolution, they quickly back off…
    http://www.samizdat.qc.ca/cosm.....ore_pg.htm

    Lakatos, although he tipped toed around the failure of Darwinism to have a rigid demarcation criteria, he was brave enough to state that a good scientific theory will make successful predictions in science and a bad scientific theory will generate ‘epicycle theories’ to cover up embarrassing failed predictions:

    “In degenerating programmes, however, theories are fabricated only in order to accommodate known facts”
    – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture

    And that is exactly what we find with Darwinian evolution. Dr. Hunter comments,,

    “When their expectations turn out to be false, evolutionists respond by adding more epicycles to their theory that the species arose spontaneously from chance events. But that doesn’t mean the science has confirmed evolution as Velasco suggests. True, evolutionists have remained steadfast in their certainty, but that says more about evolutionists than about the empirical science.”
    ~ Cornelius Hunter

    Here’s That Algae Study That Decouples Phylogeny and Competition – June 17, 2014
    Excerpt: “With each new absurdity another new complicated just-so story is woven into evolutionary theory. As Lakatos explained, some theories simply are not falsifiable. But as a result they sacrifice realism and parsimony.”
    – Cornelius Hunter
    http://darwins-god.blogspot.co.....uples.html

    And following in Lakatos footsteps, Dr. Hunter has compiled a list of some of the major false predictions generated by evolutionary theory. False predictions that are fundamental to evolutionary theory, i.e. go to the ‘core’ of the theory, and falsify it from the inside out as it were.

    Darwin’s (failed) Predictions – Cornelius G. Hunter – 2015
    This paper evaluates 23 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena, and how they bear on evolutionist’s claims about their theory.

    *Introduction
    Why investigate evolution’s false predictions?
    Responses to common objections

    *Early evolution predictions
    The DNA code is not unique
    The cell’s fundamental molecules are universal

    *Evolutionary causes predictions
    Mutations are not adaptive
    Embryology and common descent
    Competition is greatest between neighbors

    *Molecular evolution predictions
    Protein evolution
    Histone proteins cannot tolerate much change
    The molecular clock keeps evolutionary time

    *Common descent predictions
    The pentadactyl pattern and common descent
    Serological tests reveal evolutionary relationships
    Biology is not lineage specific
    Similar species share similar genes
    MicroRNA

    *Evolutionary phylogenies predictions
    Genomic features are not sporadically distributed
    Gene and host phylogenies are congruent
    Gene phylogenies are congruent
    The species should form an evolutionary tree

    *Evolutionary pathways predictions
    Complex structures evolved from simpler structures
    Structures do not evolve before there is a need for them
    Functionally unconstrained DNA is not conserved
    Nature does not make leaps

    *Behavior
    Altruism
    Cell death

    *Conclusions
    What false predictions tell us about evolution
    https://sites.google.com/site/darwinspredictions/home

    Why investigate evolution’s false predictions?
    Excerpt: The predictions examined in this paper were selected according to several criteria. They cover a wide spectrum of evolutionary theory and are fundamental to the theory, reflecting major tenets of evolutionary thought. They were widely held by the consensus rather than reflecting one viewpoint of several competing viewpoints. Each prediction was a natural and fundamental expectation of the theory of evolution, and constituted mainstream evolutionary science. Furthermore, the selected predictions are not vague but rather are specific and can be objectively evaluated. They have been tested and evaluated and the outcome is not controversial or in question. And finally the predictions have implications for evolution’s (in)capacity to explain phenomena, as discussed in the conclusions.
    https://sites.google.com/site/darwinspredictions/why-investigate-evolution-s-false-predictions

    of supplemental note to the Darwinian prediction that genes are supposedly not suppose to be that similar or even in the same order in supposedly widely divergent species:

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

  51. 51

    @50 BornAgain77

    With all sincerity and fondness, I must complement you in your suberb ability to Gish Gallop (http://rationalwiki.org/wiki/Gish_Gallop). Your posts are great examples of “Proof by Verbosity,” and you are at a master at this. You repeat several false and misleading arguments in quick sequence, quoting others rather than explaining actual data.

    You, sir, are amazingly effective at your intended goal: blowing so much smoke that casual readers are effectively blinded from the truth. Congratulations.

    To be clear, every argument you raise is false, and is easily demonstrated to be false using the evidence. In fact, many of the papers you quote actually expose the your arguments as false. I have a history of demonstrating that I am not BSing when I say there is evidence that proves a bad arguments false (look at my comments on prior VJ posts). I just refuse to do so when people are GIsh Galloping, even when one does so as expertly as do you.

    Those of us that care about evidence, I am sure, will just ignore you from here out. I hope you consider learning science some day. It is really amazing, and much more beautiful than an awkward gallop.

  52. 52
    bornagain77 says:

    I consider your post a compliment. Despite your blatant ad hominem, my posts stand on their own merit. And I will leave it to the unbiased reader to decide who is being ‘scientific’ and who is ‘blowing smoke’.

  53. 53
    Origenes says:

    Swamidass: I have a history of demonstrating that I am not BSing when I say there is evidence that proves a bad arguments false …

    Yes, you have a history indeed.

    Swamidass: (on SETI vs. ID methodology):

    Of the top of my head, I can come up with about five material differences.

    &

    Swamidass: So let me start with the ID work I found highest quality in this genre. This is is a paper published by Behe in 2004 (…) As a trained computational biologist, I spent 15 minutes reading the paper, about 2 hours thinking about it, and identified two clear errors.

    In both cases you are simply BSing. You don’t point out those “five material differences”, nor do you point out those “two clear errors” by Behe. It’s all just part of your attempt to blow smoke.

  54. 54
    Andre says:

    BA

    When someone tells you you’re Gish Galloping you can absolutely consider it a compliment. Dwayne Gish has never lost a debate against a Darwinist…

    Keep it coming…

  55. 55
    Querius says:

    Prof. S. Joshua Swamidass @48,

    Thank you. I always prefer to make people smile.

    Nevertheless, it seems that most evolutionary predictions that I’ve seen over time are abandoned when “surprising” evidence to the contrary emerges.

    I have no ideological or theological qualms with the concept of evolution. The primary problem is that mutation is an inadequate mechanism within the time frame given (not to mention that a mutation in only one organism won’t persist as I’m sure you know), and that TOE has pushed out other paradigms by incorporating or rationalizing any other approach to the data.

    While your statistical analysis is commendable, perhaps even irrefutable, I think there are a lot of assumptions built into your approach. Let me explain.

    Let’s consider the genome of dogs. Imagine every variety from Chihuahuas to Great Danes. Now let’s say that dogs are sadly hit with some deadly virus that leaves only a tiny percentage of their varieties alive: Chihuahuas, Poodles, Greyhounds, and Great Danes.

    Not knowing about this event, what would your statistical analysis tell you about the evolution of these four (what would be subsequently be considered different) species? What if the genomes of all animals at one time had as much diversity as that of dogs? Would your statistical analysis be able to detect this?

    Let’s consider bacteria, specifically the wide variety of gut bacteria. As you know, bacteria are the most adapted (or evolved) organisms on the planet, and that the prevalence of the varieties of gut bacteria vary depending on their location within their host’s gut, and their host’s diet. Let’s assume that there’s an efficient method for these bacteria to transfer certain genes to their hosts, helping their hosts adapt to changing environmental conditions. How would your statistical analysis be able to detect the source of these genes to gut bacteria?

    Finally, the most important factor is scientific validation by direct observation. This is why I wonder whether you’ve ever tried to validate the similarities (and differences!) in DNA by simulating evolution. The easiest way that I can think of is through using proportionately high levels of ionizing radiation on bacterial populations, although I’ve just read that there might be an alternative:

    https://www.sciencedaily.com/releases/2016/06/160609134243.htm

    Although evolutionary biologists were (once again) surprised at what they found, what unpublished predictions would you be willing to make regarding these bacteria?

    Regards,

    -Q

  56. 56
    Dr JDD says:

    Let’s look at the b-hemoglobin pseudogene then, or hbbp1. You say that this is a generic “remnant of evolution” but again as per my previous post this is completely circular.

    1) why is it a genetic remnant?
    2) how do you know it is a genetic remnant?
    3) how do you know any assigned function is the result of exaltation?

    I’m genuinely interested to know the answers to these questions.

  57. 57
    PaV says:

    gpuccio:

    If you take a Chevy truck chasis used for their large sized trucks, and then turn it into a Suburban, which is basically a SUV, they share “common ancestry,” but not “common descent.”

    The axles will be the same. Much of the electrical system will be the same. The engine may be the same. But the exterior and interior design will be entirely different.

  58. 58
    PaV says:

    Prof. Swamidass:

    You wrote:

    Let’s recap…

    1. A paper was published claiming that VTG1 has homology to DNA in humans in the exact right place in Chr1. The exact p-values were not reported.

    2. Ann Gauger doubts CD, and disputed the statistical quality of that match. She asserted that perhaps the match was not really there, and just a statistical illusion.

    3. I, however, trust that CD is a helpful framework in biology, that has a very good track record of PREDICTING patterns in biology. I supposed that the statistical match between VTG1 and this region was probably high.

    So now, we have two hypothesis: there (#3) is or (#2) is not a good statistical match between VTG1 and the correct region in the human genome. Now we can ALL test this for ourselves to see what hypothesis the data indicates is justified. Of course, this is not “proof.” Science, rather is about making rigorous explanations, and CD explains this data.

    An independent party has done just this, demonstrating that I was right and that Ann was wrong.

    Point-by-point:

    (1) Entirely correct.

    (2) Ann Gauger doesn’t “doubt” CD; rather, she is an agnostic. In her latest post at EvolNews she demonstrates that supposed match, and doesn’t feel it matches the “claims” the authors make. I tend to agree with her. (More on this later) Now, I haven’t followed the entirety of this conversation, but, I don’t think Ann was “predicting” anything.

    (3) You again, and again, fail to distinguish between “common ancestry” and “common descent.” It would be silly for someone to claim that new “types” are mad entirely “de novo.” The entire idea, actually, is silly. Why would a designer ‘design’ that way if various organisms were meant to interact with one another. (Philosophically, more could be said about this; but we leave it to the one side). Naturally, there will be similarities. These similarities, however, do NOT prove “common descent,” but, rather, only “common ancestry.” The entire revolution in modern physics revolves around moving away from the continuous fields of classical theory, and embracing the discrete fields of quantum theory. Common descent implies a continuous, gradual evolution of sorts. We don’t know this to have happened. We ONLY see “discrete” differences. The human and chicken versions of this gene are only slightly similar. There are huge differences between the two of them–at least as far as I can see based on Gauger’s latest post.

    Your whole point in all of this is trivial. It has no bearing on any kind of discussion of Darwinian evolution versus Intelligent Design. The fact that most of those who take the ID position accept common descent as you seem to understand it makes this point exactly.

    Finally, who is this “independent party”? Are you referring to vjtorley? He is entitled to his opinion; but it is no more than opinion.

    Years ago, I had a go-round with an “expert” in BLAST searches. I told him that the vpu protein of HIV reminded me quite a bit of the influenza A (or was it B, matters not really). He did one BLAST sequence match after another, and told me I didn’t know anything, and that there was no way that the two were related. I said that if you replaced the hydrophobic (or was it hydrophilic) portion of the vpu with the Influenza A virus, that the HIV would likely reproduce. He said again, no way. However, it turned out that experimenters had performed this exact experiment, and that, indeed, the Influenza A virus worked just fine.

    IOW, so much for BLAST matching, and experts who do it.

  59. 59
    vjtorley says:

    Andre writes:

    When someone tells you you’re Gish Galloping you can absolutely consider it a compliment. Dwayne Gish has never lost a debate against a Darwinist…

    Sorry, but that’s just not true. First of all, it’s Duane Gish, and second, he died in 2013. Third, Gish did indeed lose spectacularly to Darwinist Kenneth Miller in a debate that took place in Tampa, Florida, on March 21, 1982. The following is an excerpt from the article, “Creation-Evolution Debates: Who’s Winning Them Now?” by Frederick Edwords, in the Creation Evolution Journal, Issue 8 (Spring 1982), pp. 35-36:

    But now Miller was facing Gish (whom he had faced only once before). Gish used the usual creationist debate arguments, particularly those linking the gaps in the fossil record and the absence of transitional fossils. Miller focused again on the theories of the worldwide flood and the young earth. He also predicted that Gish would not defend his model, and this prediction came true. Miller presented quotes from Henry Morris’s writings that declared creationism to be a science and quotes from Gish’s writing that said creationism was not science. After this he suggested that maybe the next debate should feature Morris arguing with Gish on this point until it is settled.

    After attacking creationism, Miller defended evolution. He answered Gish’s arguments against Archaeopteryx and Ichthyostega being transitional fossils. He then quoted from Gish’s paper on the mammal-like reptiles and showed how it contained rudimentary errors (such as misrepresenting the position of the middle-ear bones in reptiles and in saying that the columella connects the eardrum to the tympanum when actually the eardrum is the tympanum). Finally, he showed how the probability calculations against evolution used by Gish were based on faulty premises. The audience appeared surprised that Gish had made so many mistakes in his speaking and writing.

    Since Miller had presented a slide series on Triceratops, showing how it evolved from Monoclonius which evolved from Protoceratops, Dr. Gish argued that Monoclonius did not show any incipient horns that were precursors to the horns on Triceratops. He declared that Dr. Miller’s slide was in error. But Miller rebutted by reading word-for-word from a leading text on the evolution of this dinosaur. The text even used Gish’s words, “incipient horns,” declaring their existence, complete with illustrations. Miller then handed this material to Gish and suggested that he study up before the next debate, causing the audience to roar with laughter.

    Dr. Gish used a humorous caricature drawing of a cow evolving from a whale; Dr. Miller came back with solid data supporting the evolution of whales from land mammals. There were other thrusts and parries, but, by the time the question-and-answer period came, Gish was rather quiet. He even made a stab at supporting “progressive creation,” the position that the creator “created” on a number of occasions over billions of years. But Miller quoted Henry Morris on the evils of “progressive creation” and jokingly told Gish that he would inform Dr. Morris of this compromise and get Gish into trouble when he went home.

  60. 60
    Andre says:

    Dr Torley

    On The evidence Duane Gish won… we know today what Kenneth Miller cited as transitional fossils were in fact not. Duane has never lost a debate on Darwinian evolution against any Darwinist.

  61. 61
    Andre says:

    We also know today that whale evolution is nonsense and Dr. Warner exposed that Dr. Grinirich added artistic license to his fossil finds. So it is Kenneth Miller who was being ignorant.

  62. 62
    HeKS says:

    Dr JDD @56

    Let’s look at the b-hemoglobin pseudogene then, or hbbp1. You say that this is a generic “remnant of evolution” but again as per my previous post this is completely circular.

    1) why is it a genetic remnant?
    2) how do you know it is a genetic remnant?
    3) how do you know any assigned function is the result of exaltation?

    I’m genuinely interested to know the answers to these questions.

    These are the same kinds of questions I’ve been trying to get some kind of answer to for the past few days (week?)… Well, answers apart from the obvious, which is that Methodological Naturalism is used as a guiding principle and so purposelessness is assumed until definitively proven otherwise.

    I don’t mean to annoyingly keep referencing my background as a programmer (among other things), but that is the perspective that I look at this issue from, and I think quite rightly, since DNA is widely recognized as software by people on both sides of this issue. Also, the fact that I’m specifically a UI programmer, for the most part, may give me a particularly applicable perspective, since my work requires me to split my attention between the underlying functional requirements in the code and the constraints presented by the various physical media on which it will display.

    The reason I bring up this background yet again is because, over the last several days, I’ve repeatedly seen smug declarations about the presence of copious amounts of evidence that only make sense on the hypothesis of naturalistic common descent and are not explicable on a pure design hypothesis. And what is the nature of this evidence? Well, it seems to be things like the presence of similar or identical code in sections of DNA that are not observed to execute and which are, for this reason, assumed to be purposeless junk, and the presence of different function from similar DNA sequences at the same or similar locations, or the fact that greater amounts of sequence divergence is observed in organisms believed to be more distantly related than in ones believed to be more closely related.

    When I see claims that these sorts of things don’t make sense on a pure design hypothesis, the first thing that occurs to me is that either the people making such claims have no experience with software development, or else they are so trained to assume the truth of natural explanations over artificial ones that they completely fail to realize that these types of things are not only consistent with a software design hypothesis, but they are actually expected on it. In my opinion, all one needs to do to make sense of all of this data is conceive of life, in its entirety, as one big software application instantiated in 3D.

    On an only slightly different note, here’s a question I’d like to know the answer to. Someone on another thread (can’t remember who) said it was believed that carrying around a whole bunch of DNA that is currently assumed to be junk has little or no fitness cost on an organism. Does anyone know if that’s correct?

  63. 63
    aap says:

    Dr. Joshua Swamidass #47
    “I will point out too, that I have said repeatedly that there are good reasons for rejecting CD. In particular, there are good and dignified reasons for rejecting CD for theological reasons. This is what Todd Woods does, and I respect that.”
    TE would fit in well with most philosophical theology in which an individual is free to create and make the image of a god according to their own personal, scientific or philosophical perspective. Deism is a perfectly legitimate TE theology. One of humanities obsessions is to attempt to create a god in our own image, after our likeness or preference. This has been the source of religions down through history. Most today prefer the absentee father kind of god which TE certainly provides. If there has to be a god, that is the kind of god they prefer over a god who would actually interfere with their life or hold them accountable, or, bring his judgement. The theistic god of evolution is certainly comfortable enough to fit in pretty well with most religious, mystic views of a god: native religion, Hinduism, Buddhism, Bahai, humanism, liberal theology in many churches, etc. TE is a new gnostic version of god conjured up from the “superior” insights of the great theological and philosophical minds of the past 100 years who know god better than those simple early Christians.
    To put it mildly, TE really doesn’t fit in with the GOD of the Bible, with JESUS and His FATHER and HOLY SPIRIT of Truth. Christian theology isn’t a philosophical theology that springs from human imagination or reason, but a Word – Logos based, CHRIST centered, HOLY SPIRIT revealed faith. Through faith in CHRIST and through the ministry of GOD’S SPIRIT alone an individual can receive and grow in their understanding of the grace and truth of GOD and His Word, but cannot approach GOD and His Word by human reason alone. It is a faith that little children can perceive, but learned theologians and philosophers stumble over, even in the institutional church (1 Corinthians 1: 18-31).
    The Apostle Peter wrote: “Above all, you must understand that no prophecy of Scripture came about by the prophet’s own interpretation. For prophecy never had its origin in the will of man, but men spoke from GOD as they carried along by the HOLY SPIRIT.” 2 Peter 1:20,21
    The Apostle Paul through the same HOLY SPIRIT stated: “The Church is built on the foundation of the apostles and prophets, with CHRIST JESUS Himself as the chief cornerstone.” Ephesians 2:20
    TE fails as a Christian theology because it isn’t based on CHRIST or the testimony of the HOLY SPIRIT through the prophets and apostles. It is a theology based on faith in the assured results of methodological naturalism; faith in human reason alone. As JESUS said to the Sadducees of His generation: “You are in error because you do not know the Scriptures or the power of GOD.” (Matthew 22:29)
    The heart and center of the Christian faith is the profession that JESUS, Was, Is, and Always will be GOD’S SON, One with the FATHER and the SPIRIT. JESUS is the Word- Logos (information) through which all things have been created, and brought into being (John 1, Colossians 1). To hold to TE, and some forms of ID, would be to believe that their Jesus is the Creator of all diseases, mutational deformities, violence, pain, and death. They further believe that he has pronounced that all of these realities in our world today are very good; that he was and is pleased with his evolutionary common descent world. The one who confronted the religious leaders of his generation for being hypocritical would be the master hypocrite. He shows up on the scene for a few brief years, claims to be compassionate and heals a few people of their suffering, while for at least a few hundred million years he has enjoyed the spectacle of all of the suffering caused by his deadly process. Contrary to the lavish praise that most TE’s heap on evolution for its ability to produce the incredible marvels of life today, the truth is evolutionary common descent is a death cult. It only progresses through the immeasurable pain and death of trillions of creatures and this continues today. The TE god is a god of death, not life. Their Jesus is a mild mannered compassionate philosopher doctor during office hours and a sadistic torturous murderer the rest of the day and night who loves to invent new diseases to inflict on his disposable creatures. Is that a JESUS you can worship?
    The real JESUS, weeps over this fallen world of ours, and His true followers weep with Him. Anyone who has come to know JESUS, through the testimony of His HOLY SPIRIT in His Word given through His prophets and apostles, will understand that JESUS is not the god of TE.
    TE: a theology “yes”, Christian “no”.
    Dr. Swamidass #47
    “On the scientific front, looking at evidence, I (and the rest of the mainstream scientific community) contend that the case for CD is rock solid. So I am doing too things here. Scientifically, “recent” evolutionary history (e.g. the last 50M years of mammalian evolution) the evidence points in one direction unambiguously to CD.”
    Within the definition of science that the mainstream scientific community operates under, his statement here is a true statement. If you hold to methodological naturalism, that everything in our world has to have its cause and origin in material alone, then the case for CD is rock solid. There is simply no other materialistic explanation for life on earth besides CD. All data has to be forced into a CD mold because it is the only possible naturalistic explanation. The reality that:
    1) CD is mathematically impossible,
    2) they cannot demonstrate the creation of any new life form or organ through genetic mutations,
    3) all of observable science bears testimony that life only comes from life, and that kinds of life only reproduce after their kind,
    4) many aspects of life are irreducibly complex, not only in their function but in the genetic computerized specified information that is involved, etc.
    These observable and experimental realities are all irrelevant to them, because they don’t fit in with their assumptions. Life exists and there is some morphological or genetic commonality amongst different kinds of life and therefore CD is true. Within their closed naturalistic circle there is nothing else that can account for life. They are very close minded when it comes to GOD having anything to do with reality or life. Creationists and IDers are often accused of implying that scientists are hiding some massive conspiracy about the truth about evolution. There is absolutely no need for a conspiracy of scientists because their naturalistic presuppositions have limited their options to evolutionary CD. Human reason based on belief in nature alone, which isn’t the conclusion of modern science but their starting premise, has predetermined that CD has to be true, and, therefore all of the evidence has to fit in. Any scientist that suggests otherwise deserves to be tar and feathered and run out of town, or at least the university. For all of you ID advocates out there, don’t ever expect that the mainstream scientific community will ever tolerate the possibility of an intelligent designer having anything to do with either the cosmos or life, that is not a possibility that their assumptions allow for. To allow for an ID alternative they would have to change their basic understanding of science to a pursuit of truth, instead of the pursuit of a naturalistic explanation.
    What if there is no naturalistic explanation for life on earth? That is the testimony of the HOLY SPIRIT: “In the beginning GOD”! He is the Beginning and the End, and I believe we are much closer to the end than the beginning. Amen, come LORD JESUS!
    “It’s a battlefield brother, not a recreation room. It’s fighten, not a game.””

  64. 64
    bornagain77 says:

    If virtually unlimited ‘plasticity of form’ for an entire organism that is built with over a billion-trillion protein molecules total is supposedly undeniably true, (as is currently held by Atheistic Darwinists and by Theistic Evolutionists such as Prof Swamidass who toe the Darwinian line), then virtually unlimited ‘plasticity of form’ should be that much more undeniably true for single proteins themselves.

    Yet proteins themselves are severely constrained in their ‘plasticity of form’.

    In trying to get an enzyme to switch functions, Dr. Ann Gauger and Dr. Axe found severe constraints with the Darwinian scenario:

    “Shared Evolutionary History or Shared Design?”
    Ann Gauger January 1, 2015
    Excerpt: In an evolutionary scenario, to get an enzyme to switch functions the first step is to make a spare copy that can be mutated without destroying a function the cell needs. Second, the cell has to overproduce the mutating enzyme, because any newly emerging enzyme will be very bad at the job at first. To compensate there will need to be lots of enzyme around. Third, there is the problem of finding the right combination of mutations by random search.
    Taken together, since we found no enzyme that was within one mutation of cooption, the total number of mutations needed is at least four: one for duplication, one for over-production, and two or more single base changes. The waiting time required to achieve four mutations is 1015 years. That’s longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations.
    http://www.evolutionnews.org/2.....92291.html

    Along that same line, Dr. Gauger also comments that to the extent that proteins do evolve then ‘the enzyme already has to be arranged to carry out the innovative function’.

    New Article in BIO-Complexity Addresses the Problem of Biological Innovation – Ann Gauger – January 4, 2016
    Excerpt: Next he, (Doug Axe), tested whether an already existing character with some weak similarity to the target could be evolved by mutation and selection to a proficient version of the target character. Once again, the answer was no. However, if the starting character was only six mutations away from optimization, it improved rapidly upon mutation and selection.,,,
    Our conclusion? Unless the starting protein already exists as a functional fold of the right design, the protein’s activity cannot be optimized to wild-type levels. In other words, you’ll never get an innovation optimized, even with a pre-existing low level of the desired activity if the innovation is not already present in substantial form. By that I mean that the enzyme already has to be arranged to carry out the innovative function — its structure has to be of the right kind. Natural selection cannot create innovation, and it can’t even optimize pre-existing weak functions that are not of the right design to begin with.
    http://www.evolutionnews.org/2.....02051.html

    You don’t have to take Dr. Gauger’s word for it, you can also look at the excellent experimental work of Dan S. Tawfik’s Group.

    Dan S. Tawfik Group – The New View of Proteins – Tyler Hampton – 2016
    Excerpt: To the extent that Tawfik’s selection experiments were successful, it is because mutations were localized and contextualized. Mutation had a key but confined role. If evolution proceeded, the prevailing architecture of the active sites and protein shapes nonetheless remains intact. Changes were not to central structures, but to peripheral loops. A great deal of flexibility was discovered. Still, it is hard to see how any of this could build proteins—that is, in the sense of building their fundamental shapes, or scaffolds; and build proteins in terms of explaining the key catalytic strategies of each active site. Even in the impressive demonstration of a transition through nine orders of magnitude, in which a full exchange of a promiscuous activity for the primary activity was seen, the overall geometry of the protein was unchanged, and, although substrates had changed, the fundamental active site strategy stayed the same. ,,,
    “Modern neo-Darwinism and neutral evolutionary treatments,” remark Leonard Bogarad and Michael Deem, “fail to explain satisfactorily the generation of the diversity of life found on our planet.” It is not that they did not evolve, they say, but that “… most theoretical treatments of evolution consider only the limited point-mutation events that form the basis of these theories.” Their sober conclusion is that “point mutation alone is incapable of evolving systems with substantially new protein folds.”60,,,
    “In fact, to our knowledge,” Tawfik and Tóth-Petróczy write, “no macromutations … that gave birth to novel proteins have yet been identified.”69
    The emerging picture, once luminous, has settled to gray. It is not clear how natural selection can operate in the origin of folds or active site architecture (of proteins). It is equally unclear how either micromutations or macromutations could repeatedly and reliably lead to large evolutionary transitions. What remains is a deep, tantalizing, perhaps immovable mystery.
    http://inference-review.com/ar.....f-proteins

    Thus, since proteins themselves are severely constrained in their ability to evolve a new ‘form’, then why in blue blazes should anyone believe that an entire organism consisting of over a billion-trillion protein molecules should be any less constrained in its plasticity than the protein molecule itself is?

    Here is a supplemental quote from Dr. Gauger on the often overlooked, but crucially important, issue of ‘context dependency’:

    “Why Proteins Aren’t Easily Recombined, Part 2” – Ann Gauger – May 2012
    Excerpt: “So we have context-dependent effects on protein function at the level of primary sequence, secondary structure, and tertiary (domain-level) structure. This does not bode well for successful, random recombination of bits of sequence into functional, stable protein folds, or even for domain-level recombinations where significant interaction is required.”
    http://www.biologicinstitute.o.....ned-part-2

  65. 65
    Dr JDD says:

    Hi HeKs,

    Thanks for your reply. Please do not apologise for referencing your background as a programmer as DNA is a code (and that is very clear now to anyone who studies it) that is far more complex than any code any human has designed. So understanding DNA as a code from that perspective is entirely relevant. Completely agree with what you say and the analogy.

    The reason those 3 questions are important is because they speak to what I think you are trying to ask yourself. I expect the commonly given answers would be something like:

    1) Why is it a genetic remnant? Ans: it is non-functional, and, see (2)
    2) How do you know it is a genetic remnant? Ans: it is non-functional, and a duplication of a functional gene (high sequence homology but “broken”)
    3) How do you know any assigned function is the result of [corrected word] exaptation? Ans: because anything that differs from the original gene (see 2) is an adapted function and not original.

    There are multiple problems with such answers:

    1)Not currently knowing a function does not equal non-functional. Second to this, the evidence is growing that a number of alleged “pseudogenes” are in fact sequences with different function than traditionally thought. E.g. do not have traditional promotor sites, stop codon usage, usual flanking sequences etc so we have decided they must not be functional and have used CD as evidence (!) to assume they must have originated from functional genes first
    2) See flaw with (1); again, how do you know it is a duplication of a working gene? Homology does not mean that it is, only it must be under methodological naturalism. Now imagine a scenario where a designer is making increasingly complex organisms. The more complex ones require greater regulation of genes than the more simple ones, perhaps. Therefore you need more complex code and new regulatory information to control the other genes. Pseudogenes in the literature and constant new research keeps identifying regulatory roles for pseudogenes. I could cite many examples but the trend is that actually these are not traditional genes but encode RNA regulatory molecules with function. There is a chance that these are therefore not duplications but intentional. Now this statement only applies under the design paradigm – under the naturalistic paradigm the only way they could arise would be through a duplication of a similar sequence and then RM into a regulatory RNA role. But that is self-propelling the naturalistic viewpoint and not therefore proof of CD. Further to this, we know that a Toyota Yaris hybrid looks more similar to a Toyota Yaris than it does to a Toyota Avensis. We would expect more similarities between those. Similarly, a human looks phenotypically (not just outward appearance but on anatomy and physiology settings) more like a chimp than a chicken therefore is it any surprise that if they shared a common designer that designer would use the same type of regulation between the two organisms and therefore these two organisms are more likely to share these apparent pseudogenes?
    3) Again this is where the “evidence” presented is self-fulfilling and circular. To arrive to exaptation you must assume a role that once existed (assume CD to do this) but now no longer exists. This is because it “looks like” another gene that is functional. If a designer decides to use similar sequences in regulatory function (rather than as a protein-encoding gene) to existing genes, how do you know that is a duplication event?

    Of course this is just one example of b-hemoglobin and I am making my own assumptions here. But it demonstrates the circular thinking and reasoning and self-fulfilment of CD (CD in the sense of chimps share a CA with humans). It also highlights the inability for many people who hold to this to view the simple explanation of how design can explain some of these phenomenon. Granted, other observations are harder to explain by design than perhaps such an example as discussed in this post, but the point remains that design can explain quite rationally many of these observations. It is merely a choice to ignore this explanation as it relies on design rather than naturalistic means – which is ultimately what this argument boils down to. Not evidence nor even conception; rather your starting assumptions on supernatural designers or everything must fall into the naturalistic category.

    With regards to your slightly different note this was on the Opossum thread and in response to a point I made about so much junk. Given that ~80% of the genome is transcribed, and that 100% of the genome is copied in mitosis, I find it difficult to believe that if an organism could get away with less of a genome (10-fold less if junk figures are to be believed) that this would not be of an advantage. That is a lot of transcription and copying that is required for no gain. I am not sure where this evidence about fitness cost comes from.

  66. 66
    bornagain77 says:

    In further reflection of the inability of Darwinian processes to create new protein folds:

    Estimating the prevalence of protein sequences adopting functional enzyme folds: Doug Axe:
    Excerpt: The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain. Combined with the estimated prevalence of plausible hydropathic patterns (for any fold) and of relevant folds for particular functions, this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.
    http://www.toriah.org/articles/axe-2004.pdf

    Dan S. Tawfik Group – The New View of Proteins – Tyler Hampton – 2016
    Excerpt: Their sober conclusion is that “point mutation alone is incapable of evolving systems with substantially new protein folds.”
    http://inference-review.com/ar.....f-proteins

    Although new protein folds are extremely prohibitive for Darwinian processes to account for, (optimistic low end of 1 in 10^12), most all Darwinists and Theistic Evolutionists (such as Prof Swamidass, Torley, and gpuccio), hold that there are really no new protein folds, or exceeding few protein folds, required for the supposed transition from an ape-like create to a human.

    This recent paper calls that Darwinian presumption into question.

    Unexpected features of the dark proteome – Oct. 2015
    Excerpt: We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ~14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions,
    http://www.pnas.org/content/ea.....1508380112

    methods of tertiary protein structure determination
    http://www.proteinstructures.c.....thods.html

    ter·ti·ar·y struc·ture
    the overall three-dimensional structure resulting from folding and covalent cross-linking of a protein or polynucleotide molecule.

    and this:

    Orphan enzymes could be an unexplored reservoir of new drug targets. – 2006
    Excerpt: Despite the immense progress of genomics, and the current availability of several hundreds of thousands of amino acid sequences, >39% of well-defined enzyme activities (as represented by enzyme commission, EC, numbers) are not associated with any sequence.
    http://www.ncbi.nlm.nih.gov/pubmed/16580971

    As well, although Darwinists and Theistic evolutionists have tried to ‘explain away’ the large percentage of ORFan genes being found in all genomes that are being sequenced by appealing to supposedly ‘junk’ DNA sequences that are similar to the ORFan sequence, (with no actual demonstration of how a supposedly non-functional ‘junk’ sequence can suddenly become functional),

    Mechanisms and dynamics of orphan gene emergence in insect genomes – January 2013
    Excerpt: Orphans are an enigmatic portion of the genome since their origin and function are mostly unknown and they typically make up 10 to 30% of all genes in a genome.
    http://gbe.oxfordjournals.org/.....l.pdf+html

    Is the Origin of New Genes “Basically a Solved Problem”? – Cornelius Hunter – Sept. 11, 2014
    Excerpt: If you read the headlines, you would have the impression that the problem is well in hand. For instance, super-star science writer Carl Zimmer wrote in the New York Times earlier this year that “researchers have documented the step-by-step process by which a new gene can come into existence.”
    Case closed right?
    Well not quite. In fact, not even close. What Zimmer tells his readers is a “step-by-step process” is what scientists affectionately refer to as a cartoon. In fact, here it is:,,,
    ,,,This evolutionary narrative is certainly not “basically a solved problem.” In fact, what evolutionists have are high claims of the spontaneous evolution of incredibly complex structures, not because of the evidence, but in spite of the evidence. So what gives evolutionist’s their confidence? It is not that they understand how such genes could have evolved, but that the genes must have evolved because solo genes are observed over and over:
    “Several studies have by now also shown that de novo emerged transcripts and proteins can assume a function within the organism. All of this provided solid evidence that de novo gene birth was indeed possible.”,,,
    Does any of this mean that the de novo genes evolved from random mutations as the evolutionists claim? Of course not.,,,
    Only a few years ago they agreed that such evolution of new genes would be impossible. Now they have been forced to adopt it because the evidence unambiguously reveals solo genes, and evolutionists dogmatically insist that everything must have spontaneously evolved.,,
    http://darwins-god.blogspot.co.....olved.html

    Although Darwinists (and theistic evolutionists) unsuccessfully tried to sweep this huge problem under the rug, this ORFan gene problem simply is not so easily dismissed by Darwinists as this recent paper by Tomkins highlights

    Genetic Gap Widens Between Humans and Chimps by Jeffrey P. Tomkins, Ph.D. – January 21, 2016
    Excerpt: In yet another recent research report, scientists describe 634 orphan genes in humans and 780 in chimpanzees.1 In other words, we now have a new set of 1,307 genes that are completely different between humans and chimpanzees. In fact, the chimp-specific genes are not found in any other supposed chimp ancestor—like macaque, an extant monkey. They are unique to the chimps just like the human orphan genes are unique to humans. Darwinian evolution did not predict this remarkable discovery.
    Essentially exposing evolution’s weakness in explaining orphan genes, the researchers say, “For the past 20 years scientists have puzzled over a strange-yet-ubiquitous genomic phenomenon; in every genome there are sets of genes which are unique to that particular species i.e. lacking homologues [similar counterparts] in any other species.”1
    Another interesting fact about these newly discovered orphan genes is that they represent just a subset of the genes unique to chimp or human. The researchers only analyzed genes expressed in liver, heart, brain, and testes. Many other bodily tissues still need to be examined. In addition, the team only analyzed genes that were spliced, meaning complex genes that have coding and non-coding regions, with the coding regions being snipped out of the RNA transcript after they are copied from the DNA. Many other genes in the genome are not spliced and were not included in this study. Needless to say, the numerous gene differences that scientists discovered between humans and chimps cannot be accounted for by Darwin’s theory of common ancestry.
    http://www.icr.org/article/gen.....ans-chimps

    Needless to say, Darwinian evolution did not ‘predict’ any of this.

  67. 67
    vjtorley says:

    aap’s arguments against theistic evolution are based on emotion rather than reason:

    …[T]he truth is evolutionary common descent is a death cult. It only progresses through the immeasurable pain and death of trillions of creatures and this continues today. The TE god is a god of death, not life. Their Jesus is a mild mannered compassionate philosopher doctor during office hours and a sadistic torturous murderer the rest of the day and night who loves to invent new diseases to inflict on his disposable creatures. Is that a JESUS you can worship?

    1. Dembski’s book, The End of Christianity, has shown how belief in common descent is perfectly compatible with the belief (held by many Christians) that animal suffering was caused by the Fall, provided you are willing to accept the possibility of retrospective causation.

    2. In any case, we don’t know how much animals suffer, and how many (if any) have a sense of “self.” Without an “I” who suffers, there is no-one whom suffering can be ascribed to.

    3. Nor do we know whether God has, in His goodness, prepared an after-life (not Heaven, but some kind of happy hereafter) for sentient creatures. If He has, then the transient sufferings of this world are unimportant by comparison.

  68. 68
    vjtorley says:

    bornagain77,

    In response to your post #66 about ORFan genes, you might like to have a look at Glenn Williamson’s latest post, demolishing Dr. Tomkins’ claims about these genes:

    https://roohif.wordpress.com/2016/06/13/jeff-tomkins-orphan-genes-mind-the-gap/

    “Drum Roll, Please.
    Who would have thunk it? These human genes which supposedly had no evolutionary history have corresponding sequence in the chimpanzee genome which is – on average – about 95.41% identical.”

    I’d say Dr. Tomkins has some explaining to do.

  69. 69
    bornagain77 says:

    Torley you do know those sequences are not protein coding don’t you? And you do know that is why I commented on that fact and why I also referenced Dr. Hunter’s paper refuting the just so story from Darwinists and Theistic evolutionists of how those sequences supposedly magically and ‘randomly’ became functional don’t you?

    Moreover, It is disingenuous of you to ignore my main observation which focused on the extreme rarity of protein folds and yet the recent finding of a huge percentage of ‘Dark’ proteins with no known structural homologs.

    That finding, regardless of what I consider to be hoodwinked gene sequence comparisons that overlook several problems, is devastating to the gradualistic scenario.

    re-reference:

    Unexpected features of the dark proteome – Oct. 2015
    Excerpt: We surveyed the “dark” proteome–that is, regions of proteins never observed by experimental structure determination and inaccessible to homology modeling. For 546,000 Swiss-Prot proteins, we found that 44–54% of the proteome in eukaryotes and viruses was dark, compared with only ~14% in archaea and bacteria. Surprisingly, most of the dark proteome could not be accounted for by conventional explanations, such as intrinsic disorder or transmembrane regions. Nearly half of the dark proteome comprised dark proteins, in which the entire sequence lacked similarity to any known structure. Dark proteins fulfill a wide variety of functions,
    http://www.pnas.org/content/ea.....1508380112

    Orphan enzymes could be an unexplored reservoir of new drug targets. – 2006
    Excerpt: Despite the immense progress of genomics, and the current availability of several hundreds of thousands of amino acid sequences, >39% of well-defined enzyme activities (as represented by enzyme commission, EC, numbers) are not associated with any sequence.
    http://www.ncbi.nlm.nih.gov/pubmed/16580971

  70. 70
    vjtorley says:

    Andre,

    You write that “we know today what Kenneth Miller cited as transitional fossils were in fact not” and that “whale evolution is nonsense.”

    The Wikipedia article on Archaeopteryx makes it clear that the bird is still viewed by scientists as transitional: “Archaeopteryx, sometimes referred to by its German name Urvogel (“original bird” or “first bird”), is a genus of bird-like dinosaurs that is transitional between non-avian feathered dinosaurs and modern birds.” Controversy continues as to whether another fossil, Xiaotingia, is more closely related to modern birds than Archaeopteryx is.

    If Ichthyostega was not itself a transitional form, it was certainly related to other animals that were:

    https://en.wikipedia.org/wiki/Ichthyostega#Relationships

    These animals had not yet been discovered when Gish debated Miller, in 1982.

    Finally, we have a large number of transitional fossils between land animals and whales, none of which were known to Gish:

    https://en.wikipedia.org/wiki/Evolution_of_cetaceans

    You might argue that intelligent guidance was required to effect the transition, and I would agree. But the fact remains: there is a transition in the fossil record.

  71. 71
    vjtorley says:

    HeKS, PaV and Dr. JDD,

    Re the case for common descent as opposed to common design, you might like to have a look at these comments by gpuccio over on my “Consider the Opossum” thread, which are particularly well-argued:

    http://www.uncommondescent.com.....ent-610082

    http://www.uncommondescent.com.....ent-610140

    Gpuccio makes an excellent case, in my opinion, and he writes very clearly and persuasively.

  72. 72
    bornagain77 says:

    “Gpuccio makes an excellent case”

    Gpuccio. like you, refuses to consider evidence that falsifies his CD hypothesis and only focuses on evidence that supports his hypothesis. It is simply bad science since it does not submit to the criteria of falsification (Much like everything else in Darwinian theory).

    “Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought.”
    ~ Cornelius Hunter

  73. 73
    bornagain77 says:

    as to whale evolution:

    Whale Evolution vs. Population Genetics – Richard Sternberg and Paul Nelson – (excerpted from ‘Living Waters’ video) (2015)
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1161131450566453/?type=2&theater

    Papa Giorgio took it upon himself to organize some of my notes falsifying whale evolution into a much more aesthetically pleasing blog post

    Whale of a Tale ~ Debating Evolution – June 5, 2016 by Papa Giorgio (fraudulent fossils revealed)
    http://religiopoliticaltalk.co.....evolution/
    excerpt: Philip Gingerich, the paleontologist who discovered and reconstructed Rhohocetus, which has been called by evolutionists, ‘the most spectacular intermediary fossil in whale evolution’, states this about that, “most spectacular intermediary fossil”….

    “Well, I told you we don’t have the tail in Rodhocetus. We don’t know for sure whether it had a ball vertebrate indicating a (tail) fluke or not. So I speculated (that) it might have had a (tail) fluke…. Since then we found the forelimbs, the hands, and the front arms, the arms in other words of Rodhocetus, and we understand that it doesn’t have the kind of arms that can be spread out like flippers are on a whale.,, If you don’t have flippers, I don’t think you can have a fluke tail and really powered swimming. And so I now doubt that Rodhocetus would have had a fluke tail.”

    also of note;

    Explosive Evolution of Whales Followed by Little Change – June 1, 2010
    Excerpt: We could have found that the main whale lineages over time each experimented with being large, small and medium-sized and that all the dietary forms appeared throughout their evolution, or that whales started out medium-sized and the largest and smallest ones appeared more recently—but the data show none of that. Instead, we find that the differences today were apparent very early on.
    http://darwins-god.blogspot.co.....lowed.html

  74. 74
    Andre says:

    Dr Torley…..

    This is important….

    Here is the guy that made whale evolution famous….

    http://www-personal.umich.edu/.....Whales.htm

    He even gets an honourable mention at Talk Origins!

    http://www.talkorigins.org/features/whales/

    Here is Dr Gingerich admitting his fraud.

    https://youtu.be/R7e6C6yUqck

    It’s a scam!

  75. 75
    Andre says:

    Dr Torley

    I’ll let Dr Werner speak

    Since only two closely linked scientists had found nearly all of the “fossil” evidence of walking whales, Dr. Werner began to wonder if the other walking whales were created in this same way. In 2013, he interviewed the second scientist, Dr. Hans Thewissen, (a former student of Dr. Gingerich), who found the walking whale called Ambulocetus. Dr. Werner said, “It was like Déjà vu. I walked in for the interview and saw the skeleton lying there on the table and I was again stunned. The most spectacular part of the fossil, a partially evolved blowhole, was missing on the fossil. It appeared that Thewissen had added whale parts (in this case a blowhole) to the areas where he had no fossil evidence, just as his former professor had done.” When Dr. Werner began questioning Dr. Thewissen about the shape of the skull and missing fossil parts, Thewissen retracted the entire blowhole idea even though he had supplied the world’s top museums with skeletons having blowholes.

    https://www.youtube.com/watch?v=tkwhd_gIR7c

  76. 76
    vjtorley says:

    bornagain77,

    You mention dark proteins. You might like to have a look at this post by Larry Moran, who wasn’t too impressed with the paper you cited:

    http://sandwalk.blogspot.jp/20.....human.html

    By the way, I don’t believe new proteins can arise out of junk. But I have a simple question for you: how many proteins do you think are unique to human beings, and what is your evidence for that figure?

  77. 77
    vjtorley says:

    bornagain77 and Andre,

    Your claims of fraud with regard to whale evolution are mistaken. Please see here:

    http://marmotism.blogspot.jp/2.....onist.html

  78. 78
    PaV says:

    vjtorley:

    HeKS, PaV and Dr. JDD,

    Re the case for common descent as opposed to common design, you might like to have a look at these comments by gpuccio over on my “Consider the Opossum” thread, which are particularly well-argued:

    In both of those posts, gpuccio is arguing against “special creation.” On a number of occasions, I have already made it perfectly clear that I do not believe in “special creation,” so why do you think that I do?

    The important difference between “common descent” and “common ancestry” is not one of “special creation,” rather, it is simply about “design,” and how that might take place.

    I would think this would be rather apparent to everyone. So, since it is not, then let me be a bit more specific:

    So, let me ask: How did the various types of animal eggs come about?

    We’re talking about chicken eggs, aren’t we? Well, how did the ‘bird egg’ come about? Does anyone know?

    Did it come about gradual step by step? If so, then how? Where are the “intermediaries”? When you talk about different body-types, then you’re talking about different egg cells. There can be NO development of the body-type if the intelligence stored in the cell is not already present. This stored knowledge must properly interact with the nuclear DNA for the animal to form. Thus, part of the “design” principle strongly suggests that not only is the nuclear DNA reconfigured, but also the egg itself. If this is true, then the whole notion of “common descent” makes no sense. Why? Because, and I use this phrase simply to illustrate, “mitochondrial Eve” is not just a plain succession of egg cells, but changes when the overall body-plan is significantly changed.

    Hence my question (that Professor Swamidass apparently doesn’t want to touch with a ‘ten-foot pole’) about where the ‘bird feather’ came about is completely caught up in what I have just stated.

    So, e.g., referencing the Wikipedia page, how did the bird egg come about from the reptilian one? Did feathers appear slowly? Did one reptile show the beginnings of a feather, and then later on, its descendants showed a little bit more, and so on? The fossil record doesn’t indicate this. So, the “egg” changed, and changed dramatically, and changed in a “discrete,” not a “continuous” fashion.

    All of this should be patently clear to everyone. And it is the fossil record, not the DNA comparison, that tells us how we should think about all of this. Q.E.D.

  79. 79
    HeKS says:

    vjtorley,

    I have a few questions I’d like to ask you but I don’t the time right now. Can you please check back a bit later and respond?

    Take care,
    HeKS

  80. 80
    bornagain77 says:

    Torley, the same Moran who was not impressed with the ENCODE findings?

    So, You have an dogmatic atheist running sequence comparisons for you, and another dogmatic atheist who is not impressed with ANYTHING whatsoever that might point to ID. Hmmm Torley, since you clearly are more of a biologos type now than an ID type, exactly why do you even bother to post on UD anymore Torley? You use to give Darwinists fits with your posts, but lately it seems you are completely in bed with Darwinists. Perhaps it is time for you to move on?

    Moreover, How much junk DNA do you think is in the human genome Torley?

    As to your question about unique proteins, besides the dark proteome study I listed, it is now found that the alternative splicing patterns are very different between species,, even very different chimps and humans. And since alternative splicing can produce variant proteins and expression patterns as different as the products of different genes, then I expect humans to contain a healthy percentage of human specific proteins that are different from chimps since the alternative splicing patterns are very different between chimps and humans.

    It is a prediction I am very comfortable with.

    Alternative Splicing Codes are Species Specific
    Excerpt: On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    https://docs.google.com/document/d/1UMbNM8V2b7mRzPJt05mlev3UO4SG1bMTV5wkNunezjY/edit

    Frequent Alternative Splicing of Human Genes – 1999
    Excerpt: Alternative splicing can produce variant proteins and expression patterns as different as the products of different genes.
    http://www.ncbi.nlm.nih.gov/pm.....PMC310997/

  81. 81
    vjtorley says:

    bornagain77,

    You write:

    If genetic similarity between supposedly closely related species, as their reasoning goes, is supposed to be undeniable proof for the hypothesis of common ancestry, then finding highly similar sequences in widely divergent species should serve as a falsification for that hypothesis.

    Tell you what. Let’s consider your claim that birds and humans use essentially the same genes to speak. If you can find these genes in humans and birds but not in chimps and gorillas, then I’ll agree that would constitute a sever difficulty for the hypothesis of common descent. Name your genes, please.

  82. 82
    bill cole says:

    Hi VJt

    By the way, I don’t believe new proteins can arise out of junk. But I have a simple question for you: how many proteins do you think are unique to human beings, and what is your evidence for that figure?

    http://www.ncbi.nlm.nih.gov/pubmed/15716009#….80% different
    We should over time figure out how much is due to alternative splicing
    Abstract
    The chimpanzee is our closest living relative. The morphological differences between the two species are so large that there is no problem in distinguishing between them. However, the nucleotide difference between the two species is surprisingly small. The early genome comparison by DNA hybridization techniques suggested a nucleotide difference of 1-2%. Recently, direct nucleotide sequencing confirmed this estimate. These findings generated the common belief that the human is extremely close to the chimpanzee at the genetic level. HOWEVER, IF ONE LOOKS AT PROTEINS, WHICH ARE MAINLY RESPONSIBLE FOR PHENOTYPIC DIFFERENCES, THE PICTURE IS QUITE DIFFERENT, AND ABOUT 80% OF PROTEINS ARE DIFFERENT BETWEEN THE TWO SPECIES. Still, the number of proteins responsible for the phenotypic differences may be smaller since not all genes are directly responsible for phenotypic characters.

  83. 83
    bornagain77 says:

    ‘Name your genes, please.’

    Why not the genes that were claimed in the study Luskin referenced

    Let me guess, if you can find matches in non-coding sequences that give a high percentage match you will claim victory for Darwinian evolution?

  84. 84
    bill cole says:

    Bornagain77

    So, You have an dogmatic atheist running sequence comparisons for you, and another dogmatic atheist who is not impressed with ANYTHING whatsoever that might point to ID. Hmmm Torley, since you clearly are more of a biologos type now than an ID type, exactly why do you even bother to post on UD anymore Torley? You use to give Darwinists fits with your posts, but lately it seems you are completely in bed with Darwinists. Perhaps it is time for you to move on?

    Vincent is facilitating debate on this website which is healthy. We all want the truth to surface. If it does after strong debate vs strong agreement it will be more valuable.

  85. 85
    vjtorley says:

    Hi PaV,

    Thank you for pointing out to me your views on common ancestry. I’m sorry I mistook you for a special creationist. I’ve been very busy answering emails during the past few days, so I haven’t had the chance to read all comments on this thread.

    You seem to believe in radical re-design during the course of evolution. Fine. I have no quarrel with that. That may well have happened with the origin of different kinds of eggs.

    Regarding feathers, it appears that they passed through eight stages during their evolution:

    https://en.wikipedia.org/wiki/Feather#Evolutionary_stages

    I’m quite happy to agree with you that some of these stages were most likely intelligently guided, but judging from the fossil record, there was no overnight radical re-design, of the sort you seem to be envisioning. Intermediate forms have been found. Make of that what you will.

    https://en.wikipedia.org/wiki/Feather#Feathered_dinosaurs
    https://en.wikipedia.org/wiki/Feathered_dinosaur

  86. 86
    PaV says:

    Here’s a NCBI “aceview” on “worm” genes.

    WormBase ID:
    WBGene00006925
    vit-1 is predicted to have lipid transporter activity, based on protein domain information

    What should we infer from the fact that worms have this “yolk” gene?
    That this discussion is a complete waste of time.

  87. 87
    bornagain77 says:

    Torley, Gingerich himself admitted on the video that he was mistaken on his supposed transitional whale fossil and yet the fraudulent misrepresentations (plaster reconstructions) are still in museums.

    I am NOT mistaken!

  88. 88
    vjtorley says:

    bornagain77,

    My original challenge was: “Let’s consider your claim that birds and humans use essentially the same genes to speak. If you can find these genes in humans and birds but not in chimps and gorillas, then I’ll agree that would constitute a sever difficulty for the hypothesis of common descent. Name your genes, please.”

    I’ve located the original paper:

    http://science.sciencemag.org/.....6.full.pdf

    As far as I can tell, it says that 50 or so genes are expressed in humans and in birds that vocalize, but it does not say that these genes are absent in non-human primates. They simply aren’t expressed, that’s all.

    By the way, I believe about 10% of our DNA is functional – maybe 20% at a stretch. I used to think otherwise, but Moran’s posts on junk DNA have convinced me otherwise. He always manages to trounce his critics.

  89. 89
    PaV says:

    vjt:

    What you’re not aware of is that the “establishment” is behind these “eight stages.” This work is highly contested to this day.

    But what is the point you’re trying to make? Are you trying to say to those who believe in “special creation” that they’re making the rest of ID look bad? Do you want them to change their “scientific views”?

    All of that is a side-issue. There is enough evidence for them to let loose of this view. Unfortunately, it usually comes when they go to college, and there the youth lose their faith, which is regrettable. But, here at ID, I don’t see how that’s an issue at all.

  90. 90
    bornagain77 says:

    bill cole, I hope you are right, but I don’t see Torley being reasonable thus far, so that hope is faint.

  91. 91
    vjtorley says:

    Hi bill cole,

    You appear to believe that 80% of human proteins are unique. The paper you cite doesn’t say that 80% of our proteins are unique; it says that 80% of our proteins are different in humans and chimpanzees.

    http://www.evolutionarymodel.c.....oteins.htm

  92. 92
    PaV says:

    vjt:

    By the way, I believe about 10% of our DNA is functional – maybe 20% at a stretch. I used to think otherwise, but Moran’s posts on junk DNA have convinced me otherwise. He always manages to trounce his critics.

    This is the problem. You shouldn’t listen to Larry Moran. He’ll be proven to be immensely wrong. In fact, the ENCODE project has already done that. It’s the beginning of the end for Larry and his fellow sojourners.

  93. 93
    vjtorley says:

    Hi PaV,

    I have no quarrel with ID proponents believing in special creation. But if they are going to believe it, then all I ask is that they don’t base their belief on faulty arguments, that’s all.

    If someone wants to develop an alternative model to common descent, then they are welcome to do so – and who knows? They may be right. But they’re going to have to adduce a lot of evidence before they can overthrow the common descent model, in a scientific forum.

  94. 94
    bornagain77 says:

    “By the way, I believe about 10% of our DNA is functional – maybe 20% at a stretch. I used to think otherwise, but Moran’s posts on junk DNA have convinced me otherwise. He always manages to trounce his critics.”

    So you really believe that your DNA is 80% junk? And you believe this because of Moran of all people? Simply amazing!

    IMHO, Anyone who thinks their genome is 80 percent junk is delusional!

    For example

    Information Storage in DNA by Wyss Institute – video
    https://vimeo.com/47615970
    Quote from preceding video:
    “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.”
    Sriram Kosuri PhD. – Wyss Institute

    Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA – January 29, 2013
    Excerpt: researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they’ve improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,,
    http://www.evolutionnews.org/2.....68641.html

    Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    Scientists achieve critical steps to building first practical quantum computer – April 30, 2015
    Excerpt: If a quantum computer could be built with just 50 quantum bits (qubits), no combination of today’s TOP500 supercomputers could successfully outperform it (for certain tasks).
    http://phys.org/news/2015-04-s.....antum.html

    Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010
    Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” Dr. Bennett Van Houten – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot.
    http://www.sciencedaily.com/re.....123522.htm

    So the entire DNA molecule utilizing quantum computation is 80% junk in your book Torley?

  95. 95
    bill cole says:

    VJT

    You appear to believe that 80% of human proteins are unique. The paper you cite doesn’t say that 80% of our proteins are unique; it says that 80% of our proteins are different in humans and chimpanzees.

    That is right but 80% with different sequences is an extraordinary difference especially if you consider splicing and DNA timing differences.
    http://www.sciencemag.org
    Science 21 December 2012:
    Vol. 338 no. 6114 pp. 1587-1593 DOI: 10.1126/science.1230612
    RESEARCH ARTICLE
    All Science Journals
    ADVANCED
    Enter Search Term
    ???????My Science
    About the Journal
    Prev | Table of Contents | Next Read Full Text to Comment (0)
    ?????????????????????????The Evolutionary Landscape of Alternative Splicing in Vertebrate Species
    Nuno L. Barbosa-Morais1,2, Manuel Irimia1,*, Qun Pan1,*, Hui Y. Xiong3,*, Serge Gueroussov1,4,*,
    Leo J. Lee3, Valentina Slobodeniuc1, Claudia Kutter5, Stephen Watt5, Recep Çolak1,6, TaeHyung Kim1,7, Christine M. Misquitta-Ali1, Michael D. Wilson4,5,7, Philip M. Kim1,4,6, Duncan T. Odom5,8,
    Brendan J. Frey1,3, Benjamin J. Blencowe1,4,†
    Author Affiliations
    ?†To whom correspondence should be addressed. E-mail: b.blencowe@utoronto.ca ?* These authors contributed equally to this work.
    ?????????????????????????????????????????????????+
    ??????
    ABSTRACT
    How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning ~350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species- specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.

  96. 96
    PaV says:

    vjt:

    This is from your citation:

    However, Foth (2011) showed that some of these purported stages (stages 2 and 5 in particular) are likely simply artifacts of preservation caused by the way fossil feathers are crushed and the feather remains or imprints are preserved. Foth re-interpreted stage 2 feathers as crushed or misidentified feathers of at least stage 3, and stage 5 feathers as crushed stage 6 feathers.[82]

    From a blog:

    As concluded by Foth (2012, pg.100),

    examples of simple and aberrant feather morphologies can be taphonomic in origin, and thus not represent intermediate steps of feather evolution (see Benton et al. 2008). The overlapping nature of feather plumage, the two-dimensional state in which the feathers are usually preserved and other taphonomic conditions make identification of feather type difficult, and misinterpretations cannot be ruled out. To avoid or at least minimize such mistakes, it is necessary to expand current knowledge of the diverse morphology of recent bird feathers, and further investigate the changes which integumental structures undergo during decomposition and the fossilization process in similar experimental approaches. Fossil feathers and plumage should additionally be investigated under ultraviolet (UV) light, because of the higher contrast that can be achieved in photographic documentation [but see Hone et al. (2010) for application and limitations of this method]. The discovery of feathered non-avian dinosaur fossils, the clarification of their phylogeny and the identification of different feather types in the fossil record are essential to our understanding of feather evolution in particular, and bird evolution in general.”

    As I said, this is still a controverted area. Let’s not jump to conclusions.

    If you look at the putative “stages,” stage 1 is just a filament of sorts and hardly represents anything like a feather. According to Foth, then, we jump from “nothing” to Stage 7. This supports my thesis.

    Now, over here, we show crocodiles on one side of a tree stemming from “archeosaur”, and “feathered” dinosaurs on the other. Where is the “intermediate”?

    Will you cede my point?

    Here’s a paper that is titled: A gigantic feathered dinosaur from the Lower
    Cretaceous of China
    . Well, take a look at Figures 1 and 2 and tell me if you would conclude it was “feathered.” Dramatic claims require dramatic evidence, as they say in physics.

  97. 97
    bill cole says:

    VJT all
    I also think the existence of the intron that has a binding site inside the fused chromosome 2 telomere that python agreed is real, is very problematic. I would like to see this debated aggressively. Does anyone know Dr Tompkins? Would he join the debate?http://www.icr.org/i/articles/.....on_pic.jpg

  98. 98
    Andre says:

    Dr Torley

    Dr Gingerich admitted that he personally added the fluke and flippers to Rodocetus…

    It is on record!

  99. 99

    @86

    C. elegans lays eggs with yolk using their own version of VTG1. Cool how surprising things like this happen in biology. It is not intuitive.

    http://www.ncbi.nlm.nih.gov/pm.....PMC366982/

    What are we to inferrer from this? Take gene predictors with a grain of salt. Learn biology instead of arguing it.

  100. 100
    PaV says:

    From Foth’s 2011 paper abstract:

    To simulate the preservation process, a cadaver of recent Carduelis spinus European siskin) was flattened in a printing press. Afterwards, the structure of the plumage was compared with the morphology of a single body feather from the same specimen. In comparison with the single feather, the body plumage of the flattened bird looked rather filamentous. It was almost impossible to identify single structures, and in their place, various artefacts were produced. The investigation of plumage in a specimen of the Mesozoic bird Confuciusornis sanctus reveals similar structures. This indicates that flattening of specimens during fossilization amplifies the effect of overlapping among feathers and also causes a loss of morphological detain which can lead to misinterpretations. The results are discussed in connection with some dubious feather morphologies in recently described therapods and basal birds. Based on recent feather morphology, the structure of so-called proximal ribbon-like pennaceous feathers (PRPFs) found in many basal birds in reinterpreted. [pav: Here, he likely means what Wikipedia has as “Stage 1”] Furthermore, the morphology of a very similar looking feather type found in the forelimb and tail of an early juvenile oviraptorosaur is discussed and diagnosed as the first feather generation growing out of the feather sheath. Thus, the whole plumage of this therapod might represent neoptile plumage. [pav: more-or-less, “down feathers”]

    From a March 2011 paper:

    Neoptile body feathers from over 22 bird species were investigated using light microscopy, SEM, and MicroCT. Characters such as an anterior-posterior axis, a central rhachis, medullary cells, and structure of the calamus wall were defined and mapped onto recent phylogenetic hypotheses for extant birds. It can be shown that bilaterally symmetric neoptile feathers (with a solid calamus wall) were already present in the stem lineage of crown-group birds (Neornithes). In contrast, simple radially symmetric neoptile feathers (with a fragile calamus wall) are an apomorphic character complex for the clade Neoaves.

    “Apomorphic”: “apomorphy (derived trait) A novel evolutionary trait that is unique to a particular species and all its descendants and which can be used as a defining character for a species or group in phylogenetic terms. Hence, the possession of feathers is unique to birds and defines all members of the class Aves.

    This is exactly why Prof. Swamidass avoids the discussion.

  101. 101
    gpuccio says:

    PaV:

    OK, then what you call common ancestry is exactly what I call descent with designed modifications. My only point is that some things are the same, and are physically conveyed from one species to the other.

    In biology, the simple way to do that is to implement modifications on some existing being, but there could be other ways.

  102. 102
    bornagain77 says:

    “In biology, the simple way to do that is to implement modifications on some existing being, but there could be other ways.”

    Since no one has ever changed even one bacterium into another bacterium, much, much, less has anyone ever changed a multicellular organism into another one, how in blue blazes do you know if it is ‘easier’?

    that is simply you stating your philosophical druthers to support your own position. I could just as well maintain, and produce evidence to support it, that it is easier to build a new type of creature de-novo instead of going to all the trouble of morphing an old one into a new one

  103. 103
    bornagain77 says:

    Torley you stated somewhere that those who not hold to the Darwinian theory of common descent had to produce much scientific evidence that common descent was not true so as to be ‘accepted’ by the scientific community at large.

    Well, as someone who believes in Intelligent Design, I’m fairly use to not being accepted by the scientific community at large. But anyways, I hold that there is more than enough scientific evidence that calls common descent into question. The problem as I see it is that no matter how much scientific evidence is presented against Darwinian claims it will never be enough because, (since it has no rigid falsification criteria), Darwinian evolution is not even a testable science in a first place, but is more properly classified as a pseudo-science. In other words, like astrology and tea leaf reading, scientific evidence is useless to dissuade true believers, such as yourself, from believing it is true.

    comment 40
    http://www.uncommondescent.com.....ent-610029

    and comment 50

    Dubitable Darwin? Why Some Smart, Nonreligious People Doubt the Theory of Evolution By John Horgan on July 6, 2010
    Excerpt: Early in his career, the philosopher Karl Popper ,, called evolution via natural selection “almost a tautology” and “not a testable scientific theory but a metaphysical research program.” Attacked for these criticisms, Popper took them back (in approx 1978). But when I interviewed him in 1992, he blurted out that he still found Darwin’s theory dissatisfying. “One ought to look for alternatives!” Popper exclaimed, banging his kitchen table.
    http://www.uncommondescent.com.....ent-610075

    “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?”
    – Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003

    Darwinian Evolution is a Unfalsifiable Pseudo-Science – Mathematics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1132659110080354/?type=2&theater

  104. 104
    PaV says:

    Prof. Swamidass:

    C. elegans lays eggs with yolk. Cool how surprising things like this happen in biology. It is not intuitive.

    Yes, it’s not intuitive that humans share “yolk” genes with worms. BTW, are we more similar to worms, or chickens?

    And would you like to address the issue that the suspect the function of VIT1 in worms is that of “lipid” transport?

  105. 105
    PaV says:

    vjt:

    You’re pushing too hard with something that is weak. That’s my point. CD is not definitely established. It is a convenient presupposition; yet, it remains a presupposition.

    Do all animals, in some ways, share a common set of tools? Yes. Does this make us related? Yes. Does this mean that there is such a thing as CD? Well, it all depends on exactly what you mean by that.

    It serves little purpose to push this point with those who believe otherwise. It is at most peripheral to ID.

    There is no need to “clean up” people’s thinking here. That, I’m afraid, is the impression I have: that we must all think as you do. Such orthodoxy is exactly what ID and UD oppose. So, I simply suggest that you go with the flow. There’s lots of room for different ways of thinking here. It’s not the “ivory tower” of academics—and, thankfully so.

  106. 106
    PaV says:

    gpuccio:

    We see things the same way. It is a matter of degree. I think that in certain instances, the amount of modification is so great that CD becomes misnomer. When cell structure and DNA both change substantially, then it’s hard to call this “common descent.” There’s really nothing common about it. Common ancestry I think is sufficient. “Special creation” is something altogether different, and, personally, I don’t see how you can justify this position.

    In fact, this is what Darwin railed against in the Origins. However, then, as now, this was an entirely minority position. IOW, it was a strawman argument.

  107. 107
    bornagain77 says:

    “Special creation” is something altogether different, and, personally, I don’t see how you can justify this position.”

    And the Cambrian explosion is what exactly, chopped liver?

    What Types of Evolution Does the Cambrian Explosion Challenge? – Stephen Meyer – video – (The Cambrian Explosion challenges Universal Common Descent and the Mechanism of Random Variation/Natural Selection)
    https://www.youtube.com/watch?v=AaF7t5wRFtA&list=UUUMhP2x7_7psVO-H4MJFpAQ

    Dr. Stephen C. Meyer, PhD talks about the Case for Intelligent Design – video (excellent lecture on the Cambrian Explosion – Oct. 2015)
    https://www.youtube.com/watch?v=vl802lHAk5Y
    Oct 18, 2015 – Trinity Classical Academy’s Speaker Series welcomes Dr. Stephen C. Meyer, PhD, author of the New York Times® Bestseller Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, and Signature in the Cell: DNA and the Evidence for Intelligent Design, which won “Book of the Year” by The Times of London Literary Supplement.

  108. 108
    bill cole says:

    Hi PaV
    Do you think the theory that chimps and man share a common ancestor 6 million years ago can be reconciled biochemically through known natural mechanisms such as neutral theory and RMNS? Do you think an unknown mechanism such as one that has design capability was required?

    Does anyone on this site think that this transition can be biochemically reconciled through known mechanisms other than design?

  109. 109
    bornagain77 says:

    “Does anyone on this site think that this transition can be biochemically reconciled through known mechanisms other than design?”

    Bill, not to be flippant, but I don’t even think ‘known’ materialistic mechanisms can account for how one cell turns into tens of trillions of cells, that function as a single cohesive whole for precisely a life-time and not a moment a longer. Much less the transition you mention. Talbott puts that elephant in the living room question like this:

    HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE – Stephen L. Talbott – May 2012
    Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,,
    Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling… and so on without end. Yet the coherence of the whole is maintained.
    The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?”
    The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary.
    Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way:
    “The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)”,,,
    And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,,
    http://www.netfuture.org/2012/May1012_184.html#2

    Talbott also asks this penetrating question:

    The Unbearable Wholeness of Beings – Stephen L. Talbott – 2010
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?
    Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity.
    http://www.thenewatlantis.com/.....-of-beings

    Scientific evidence that we do indeed have an eternal soul (Elaboration on Talbott’s question “What power holds off that moment — precisely for a lifetime, and not a moment longer?”)– video 2016
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1116313858381546/?type=2&theater

    Supplemental note, Darwinian evolution, since it it based on reductive materialism, is not even on the proper scientific framework in order to coherently explain how living organisms operate

    Jim Al-Khalili, at the 2:30 minute mark of the following video states,
    “,,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can’t build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn’t really require much in the way of quantum mechanics in the way to explain it.”
    At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
    “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
    Jim Al-Khalili – Quantum biology – video
    https://www.youtube.com/watch?v=zOzCkeTPR3Q

    Molecular Biology – 19th Century Materialism meets 21st Century Quantum Mechanics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1141908409155424/?type=2&theater

  110. 110
    ThickPython says:

    @bill cole,  #97:

    “I also think the existence of the intron that has a binding site inside the fused chromosome 2 telomere that python agreed is real, is very problematic. I would like to see this debated aggressively.”

    Me too! Well, the “debated aggressively” part at least.

    “Does anyone know Dr Tompkins?”

    It’s Tomkins. No “P”. He is jtomkins at the ICR ORGanisation.

    “Would he join the debate?”

    I doubt it. From my experience, his vitellogenin gene is a little more functional than mine, if you catch my drift.

  111. 111
    HeKS says:

    vjtorley,

    Here’s what I would like to know…

    1) You seem to agree that design is a necessary part of the explanation for the evolution and diversification of life, and that this fact is discernible on the evidence.

    Am I correct?

    2) Presumably you are aware of the fact that highly qualified people in the computer sciences and the biological sciences, including people who do not support ID, say that DNA, for all intents and purposes, is software (i.e. they don’t use ‘software’ as a mere analogy).

    For a small sampling:

    “DNA is like a computer program but far, far more advanced than any software ever created.” – Bill Gates [SOMEONE WHO DESIGNS SOFTWARE]

    “Life is a DNA software system” – Craig Venter [SOMEONE WHO DESIGNS DNA]

    Steve Meyer has recounted a story about a former Microsoft engineer who he was working with [SOMEONE WHO DESIGNS SOFTWARE FOR A LIVING AND IS NOW STUDYING DNA]. Of this software engineer he says:

    He walks into my office one day, throws a book down on the table. It’s called Design Patterns — standard textbook for computer design engineers — and he says, ‘I get the eerie feeling, when I’m looking at what’s going on in the cell, that’s somebody’s figured this out before us.’ And I said, ‘What do you mean?’ And he says, ‘Well, it’s the design patterns,’ and then he points to the book. . . . ‘We’ve got design logic for processing information, for doing error correction, for doing distributed data retrieval and reassembly, and for hierarchical organization — we’ve got files within folders, like on your desktop, you know, in the hierarchical filing system.’ And he says, ‘All those design patterns are inside the cell, except they’re using a design logic that’s like an 8.0, 9.0, 10.0 version of ours. It’s the same basic logic, but it’s more elegantly executed,’ and he says, ‘It gives me an eerie feeling.

    Here’s another comment from Venter:

    “All living cells run on DNA software, which directs hundreds to thousands of protein robots. We have been digitizing life for decades, since we first figured out how to read the software of life by sequencing DNA.” – Craig Venter, DNA, the Software of Life

    Notice that in these quotes, only Bill Gates says that DNA is “like” computer software, but the rest of his sentence shows that what he means by “like” is that it is far more advanced that what humans have been able to produce. Venter, in both cases, says that DNA is software.

    Can I assume that you agree with these people, at least with regard to the 10-20% of DNA that you think is functional?

    Take care,
    HeKS

  112. 112
    Origenes says:

    VJTorley: By the way, I believe about 10% of our DNA is functional – maybe 20% at a stretch. I used to think otherwise, but Moran’s posts on junk DNA have convinced me otherwise. He always manages to trounce his critics.

    If there is so much junk DNA, then where is the information stored for the (adult) body plan? Where is the information stored for e.g. the brain? And where is the information stored for how to build all this? What is Moran’s position on this?

    I’m just asking.

  113. 113
    PaV says:

    bill cole:

    Hi PaV
    Do you think the theory that chimps and man share a common ancestor 6 million years ago can be reconciled biochemically through known natural mechanisms such as neutral theory and RMNS? Do you think an unknown mechanism such as one that has design capability was required?

    Well, first of all, it “must” be reconciled biochemically, but these correlations exist. As to the question of whether known natural mechanisms such as NT or RMNS can account for it, I guess it’s obvious that if I thought that, I wouldn’t have much to say in favor of ID.

    However, ask yourself this question: if a “Designer” modified the DNA of one creature so as to ‘form’ another creature, what would that ‘look’ like? It would ‘look’ exactly like if RMNS or NT brought it about. You cannot tell the difference between the two. So, that leaves us with improbabilities, doesn’t it? And, of course, nothing in the universe is that improbable, not even a “camel passing through the eye of a needle.”

  114. 114
    Eric Anderson says:

    Origenes @112:

    Good questions.

    The claims that the vast majority of our DNA is junk are based on terrible assumptions, poor logic, a paucity of evidence, a nearly complete lack of engineering analysis, and are contrary to the trend and trajectory of evidence.

  115. 115
    PaV says:

    BA77:

    PaV: Special creation” is something altogether different, and, personally, I don’t see how you can justify this position.

    And the Cambrian explosion is what exactly, chopped liver?

    First, BA77, I have the utmost respect for you. I in no way want to quash or diminish your sincerely held religious belief. Now, I’m not saying this because of your comment, but simply so you know how I feel about things.

    As to your comment, no, I think the Cambrian Explosion is a big thing. But what I understand as “special creation” is where almost every “type” is formed by the “hand of God,” and, further, that it is accomplished in no time at all.

    If you feel that the age of the earth is of short duration, I don’t know how you arrive there scientifically. Could God do things in such a way that the universe appears older than it actually is? Yes, of course. But what purpose would that serve? How does that make things ‘better’ than if the world was actually 14 billion years old, or whatever the latest estimate says it is? It seems like a needless complication. God is Simple.

    But, do I think that unguided natural mechanisms can explain the complexity of life as we know it? No possible way.

    Of course, Michael Denton would hold this position, not from a “Darwinian” point of view, but from the point of view of 19th Century “structuralists.” I respect him greatly; but, I disagree. Yet, maybe something will be discovered that will change that. But, as of right now, that ‘something’ isn’t even on the ‘radar screen’ as far as I’m concerned.

    Again, I very much respect your heartfelt position on all of this. Hope I didn’t offend you in any way.

  116. 116
    Origenes says:

    Eric Anderson @114,

    My questions seem relevant to your interaction with Torley on another thread:

    Eric Anderson: Do you seriously think 340 beneficial mutations in DNA could turn an ape-like creature into a human, and 3000 beneficial mutations in DNA could turn a land animal into a whale?

    VJTorley: I have to say (reluctantly) that I haven’t seen any rigorous quantitative argument yet as to why this could not be the case.

    I cannot speak for Vincent Torley of course, but it seems quite obvious that he doesn’t hold that the information for body plans (and how to build a body) is stored in the DNA.

  117. 117
    bornagain77 says:

    PaV,

    I’m not a YEC, never have been, never even intimated it on UD and have actually defended OEC a time or two on UD against YECers such as Sal. My Faith in God is doing just fine by the way because of the science not in spite of it:

    Theism compared to Materialism/Naturalism – a comparative overview of the major predictions of each philosophy – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1139512636061668/?type=2&theater

    But let me get this straight, instead of you believing God creating ‘after their kinds’ in the Cambrian, you instead feel that God perhaps took a bacteria, or took a jellyfish and/or took some sponges and then made all the different phyla out of it/them instead of creating them at their proper time from scratch? Perhaps you think God ‘frontloaded’ bacteria and/or the laws of nature? And now He is just off somewhere watching it all unfold? Faced with any of those alternatives, my faith is doing just fine PaV.

    Especially considering the fact that God, in his infinite power, upholds this universe in its continued existence and He is not off somewhere in management, as most people conceptualize Him, but is everywhere present at every moment of time and space, and infinitely so at that!:

    Lecture 11: Decoherence and Hidden Variables – Scott Aaronson – MIT associate Professor
    Excerpt: “Look, we all have fun ridiculing the creationists who think the world sprang into existence on October 23, 4004 BC at 9AM (presumably Babylonian time), with the fossils already in the ground, light from distant stars heading toward us, etc. But if we accept the usual picture of quantum mechanics, then in a certain sense the situation is far worse: the world (as you experience it) might as well not have existed 10^-43 seconds ago!”
    http://www.scottaaronson.com/democritus/lec11.html

    New Mind-blowing Experiment Confirms That Reality Doesn’t Exist If You Are Not Looking at It – June 3, 2015
    Excerpt: The results of the Australian scientists’ experiment, which were published in the journal Nature Physics, show that this choice is determined by the way the object is measured, which is in accordance with what quantum theory predicts.
    “It proves that measurement is everything. At the quantum level, reality does not exist if you are not looking at it,” said lead researcher Dr. Andrew Truscott in a press release.,,,
    “The atoms did not travel from A to B. It was only when they were measured at the end of the journey that their wave-like or particle-like behavior was brought into existence,” he said.
    Thus, this experiment adds to the validity of the quantum theory and provides new evidence to the idea that reality doesn’t exist without an observer.
    http://themindunleashed.org/20.....at-it.html

    “We know what the particle is doing at the source when it is created. We know what it is doing at the detector when it is registered. But we do not know what it is doing in-between.”
    Anton Zeilinger
    Double Slit, Quantum-Electrodynamics, and Christian Theism – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1127450170601248/?type=2&theater

    Acts 17:28
    For in Him we live, and move, and have our being; as also certain of your own poets have said, ‘For we are also His offspring.’

  118. 118
    wd400 says:

    Origines,

    The puffer fish, Fugu, has a genome that’s about 10% of the size of the human genome. Doesn’t seem to prevent it from having a body plan, making a brain, doing biochemistry.

  119. 119
    ThickPython says:

    @Bornagain77, #69:

    Glenn: “These human genes which supposedly had no evolutionary history have corresponding sequence in the chimpanzee genome which is – on average – about 95.41% identical.

    Bornagain77: “Torley you do know those sequences are not protein coding don’t you?”

    Hold up. Were you under the impression that these “634 human-specific genes” were protein coding? In the 13 minutes between Vincent’s post at #68, and your response at #69, how much of that was spent reading the actual paper?

    I’d be guessing zero.

    Would you like to know how many of those 634 genes are protein-coding?

    One. They found one protein. It was a paltry 49 amino acids long. There are five other transcripts that might be translated, but obviously not frequently enough for a peptide to actually be detected.

  120. 120
    ThickPython says:

    @Bornagain77, #80:

    “So, You have an dogmatic atheist running sequence comparisons for you …”

    Wow. I didn’t know the BLAST algorithm took my religious views into account. Oh, wait, hang on – there it is, how could I have missed it!

    USAGE
    blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-atheist_mode int_value] [-template_type type]
    [-template_length int_value] [-dust DUST_options]
    [-filtering_db filtering_database]

  121. 121
    bornagain77 says:

    ThickPython,

    Discussion
    Excerpts from discussion:

    We performed a large-scale transcriptomics-based investigation on the emergence of new genes in hominoids. Our strategy was annotation-independent, which allowed us to recover many novel (non-annotated) genes and compare species for which the level of annotation varies greatly. The approach was entirely different from that employed in previous studies in which the initial datasets were composed of annotated protein coding genes in humans that lacked homologous proteins in other species [12,19–21]. We instead focused on new transcriptional events and subsequently analyzed the properties of the transcripts including coding potential and purifying selection signatures. We assembled the transcriptomes from different species to account for differences in the level of annotation, being able to recover a large number of genes likely to have originated very recently.

    We employed a polyadenylated RNA sequencing strategy that was based on a combination of high sequencing depth and strand-specific sequencing, with an average of 115 Million mapped reads per sample. After performing exhaustive sequence similarity searches, we identified 2,714 genes which were specific of human, chimpanzee, or their hominoid ancestor. This is more than one order of magnitude greater than the number of human or primate-specific genes reported in previous studies [12,19–21]

    Most de novo genes were not annotated in the databases and their coding status was unclear. We analyzed two coding properties in de novo genes as well as in other sequences: ORF length and ORF coding score. The latter score was based on hexanucleotide frequencies in bona fide sets of coding and non-coding sequences (see Methods). The median length of the longest ORF of each de novo gene was 52 amino acids. De novo predicted proteins were shorter than proteins encoded by annotated coding RNAs (codRNA) with the same transcript length distribution as the set of de novo genes, and comparable to ORFs from similarly sampled intronic sequences (Fig 4a and 4b). In contrast, the coding score of the longest ORF was higher in de novo genes than in intronic ORFs (Wilcoxon test, p-value < 10?10) and comparable to the score for proteins shorter than 100 amino acids in the set of annotated protein-coding genes.

    Next we searched for experimental evidence of proteins produced by de novo genes. We employed mass-spectrometry data from a recent study [64], limiting the searches to the same tissues we used for transcript assembly to increase specificity (testis, brain, heart, and liver), and also searched in Proteomics DB [65]. We identified uniquely mapping peptides in 6 de novo genes; 1 human and 5 hominoid-specific genes (Table 1). All 6 were expressed in testis; one was preferentially expressed in heart. In addition, we detected signatures of translation in 5 human and 10 hominoid-specific de novo genes using available ribosome profiling sequencing data from human brain [66]. Overall, 21 de novo genes had evidence of translation

    Here we detected 20 putative new human proteins using ribosome profiling from brain tissue [66]. Considering that the expression of most de novo genes was restricted to testis for which no ribosome profiling data has yet been published, we expect this number to increase substantially in the future.
    http://journals.plos.org/plosg.....en.1005721

    also note ‘non-random’

  122. 122
    bornagain77 says:

    Moreover, you are also wrong to imply that ORFan genes are trivial in the functional roles they play

    This following study, in which the functional role of ORFan genes was analyzed, the (Darwinian) researchers were ‘very shocked’ and ‘taken aback’ by what they found;

    New Genes, New Brain – October 2011
    Excerpt: “This is one of the first studies to look at the role of completely novel genes” in primate brain development,,, A bevy of genes known to be active during human fetal and infant development first appeared at the same time that the prefrontal cortex,,, Finally, 54 of the 280 genes found to be unique to humans were also highly expressed in the developing prefrontal cortex,,,, “We were very shocked that there were that many new genes that were upregulated in this part of the brain,” said Long, who added that he was also taken aback by synchronicity of the origin of the genes and the development of novel brain structures.,,,
    http://the-scientist.com/2011/.....new-brain/

    This study states that they are not ‘dispensable’

    New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation – Aoife McLysaght, Daniele Guerzoni 31 August 2015
    Excerpt: From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease.
    http://rstb.royalsocietypublis.....8/20140332

    Can new genes arise from junk DNA? – August 2015
    Excerpt: Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.,,,
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....-junk-dna/

    Same here:

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    http://www.sciencedaily.com/re.....142523.htm

    New genes in Drosophila quickly become essential. – December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.sciencemag.org/cont.....2.abstract

    A few more notes:

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    http://ccsb.dfci.harvard.edu/w.....n_2013.pdf

    Darwin’s (Failed Predictions) – Similar species share similar genes – Cornelius Hunter PhD.
    Excerpt: As much as a third of the genes in a given species may be unique, and even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. (Daubin and Ochman)
    Significant genetic differences were also found between different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. (Levine et. al.) As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” (Le Page) These novel genes must have evolved over a few million years, a time period previously considered to allow only for minor genetic changes. (Begun et. al.; Chen et. al., 2007)
    Initially some evolutionists thought these surprising results would be resolved when more genomes were analyzed. They predicted that similar copies of these genes would be found in other species. But instead each new genome has revealed yet more novel genes. (Curtis et. al.; Marsden et. al.; Pilcher)
    Next evolutionists thought that these rapidly-evolving unique genes must not code for functional or important proteins. But again, many of the unique proteins were in fact found to play essential roles. (Chen, Zhang and Long 1010; Daubin and Ochman; Pilcher) As one researcher explained, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.” (Pilcher)
    https://sites.google.com/site/darwinspredictions/similar-species-share-similar-genes

  123. 123
    bornagain77 says:

    of note from discussion

    “An interesting observation was that the coding score of de novo genes was clearly non-random.”

    Better throw a just so story at that finding! 🙂

  124. 124
    ThickPython says:

    @Bornagain77, #121:

    Here we detected 20 putative new human proteins using ribosome profiling from brain tissue [66]. Considering that the expression of most de novo genes was restricted to testis for which no ribosome profiling data has yet been published, we expect this number to increase substantially in the future.

    While I have to give you partial credit for your link-clicking and copy-pasting abilities, you get a fail for emphasising completely the wrong paragraph.

    The question was not “how many new human proteins were detected overall?” (for which the answer is indeed 20), it was “how many of the human-specific genes code for a protein?”

    Just so I know you understand the paper – please state how many of these 634 human-specific genes were found to be protein-coding genes. It’s a very simple question, you even copy-pasted the relevant paragraph.

  125. 125
    bornagain77 says:

    go soak your head troll, your overall point is refuted regardless of what you want to drag up. ORFans have already, and very unexpectedly on Darwinian presuppositions, been found to be just as essential as old genes.

    If you were the least bit concerned with honesty and finding the truth, you would readily admit that falsifying point to your Darwinian position rather than trying to play stupid troll games with irrelevant details!

  126. 126
    ThickPython says:

    @Bornagain77:

    Your refusal to answer a simple question has been duly noted.

    Again.

  127. 127
    Eric Anderson says:

    Origenes @116:

    OK, that is probably a more charitable way of reading his comment. The context of the discussion and the way he approached it made it seem that he actually thought a few mutations here and there in DNA was adequate to the task.

  128. 128
    Andre says:

    Thickpython…..

    Well as you know by now there are varying results…..

    Some say less than 10%

    https://www.geneticliteracyproject.org/2014/08/05/how-much-of-human-dna-is-doing-something/

    Some say 2% – 15%

    http://www.ncbi.nlm.nih.gov/pm.....MC3622293/

    Larry Moran says less than 10%

    http://sandwalk.blogspot.co.za.....enome.html

    Encode says perhaps 80%

    https://www.genome.gov/10005107/encode-project/

    Prokaryote’s apparently have 20%

    https://en.wikipedia.org/wiki/Prokaryote

    This paper does not give a figure but it explains the possible importance of the non-coding regions….

    https://genomebiology.biomedcentral.com/articles/10.1186/gb4140

    What is the lesson here? Nobody is actually sure, except, you of course…

  129. 129
    Andre says:

    My youngest son is 8, and like any other kid he loves Dinosaurs, last week he came home and told me that Birds evolved from Dinosaurs, when I asked him if he think’s it is true he said of course it is his teacher told him all about Dino fluff evolving into feathers, and the hollow bones of a dinosaur made it very easy for them to start flying.

    I’m gutted because how do I explain to my son the difficulties of such a transition when it comes to morphological changes required? He is uncritical of any contradictory evidence and only because his teacher told him so……

    They sure are indoctrination these kids at a young age.

    In addition my 10 year old last night at the dinner table told me about the importance of governments having to create more laws to keep people in check and that this is a good thing………

    Like I said I’m gutted…….

  130. 130
    PaV says:

    BA77:

    For some reason I assumed that the objection you were making was grounded on a YEC conception. Sorry for the mix-up.

    As to the bacteria/multicellular/Cambrian divide, I don’t presume to know how this happened, but I would say that the prokaryote and eukaryote cell are very much different. And certainly RMNS or Random Drift or Neutral Theory is not going to explain this difference. What is required is some kind of intervention by an intelligent agent.

    But if you, like me, see the Cambrian Explosion as that time when true “types,” or BauPlans, came about—which is my stated view here, as you know—then I don’t see how this connects up with the whole question of “special creation.” I’ve used this term consistently (I hope) with quotation marks. I associate it with YEC, and use the quotation marks to set it to the one side since it represents a very specific view of how life came about.

    If by “special creation” you believe that God constituted each being in a very distinct way, then fine: that’s your belief. But from a scientific point of view, I would say that such a view cannot now be supported by what we know.

    So, perhaps I need to ask you what “special creation” means to you. We don’t seem to understand it in the same way.

  131. 131
    ThickPython says:

    @Andre, #128:

    Some say less than 10% … Some say 2% – 15% … Larry Moran says less than 10% … Encode says perhaps 80% … Prokaryote’s apparently have 20% … This paper does not give a figure but it explains the possible importance of the non-coding regions

    What is the lesson here? Nobody is actually sure, except, you of course

    Are you sure this comment is meant for me? I think it was Vincent in post #88 that said “I believe about 10% of our DNA is functional – maybe 20% at a stretch.” I don’t recall putting a number out there.

  132. 132
    Origenes says:

    WD400:

    Origenes: If there is so much junk DNA, then where is the information stored for the (adult) body plan? Where is the information stored for e.g. the brain? And where is the information stored for how to build all this?

    The puffer fish, Fugu, has a genome that’s about 10% of the size of the human genome. Doesn’t seem to prevent it from having a body plan, making a brain, doing biochemistry.

    So you are saying that somehow a huge amount of information (body plan & instructions for building the body) is stored in the DNA, despite the high percentage of junk DNA?
    If so, in which areas of the DNA do you expect this information to be found? Non-coding areas perhaps?

    – – –

    Eric @127,

    🙂

  133. 133
    evnfrdrcksn says:

    andre

    Sounds like your sons are well on their way to being informed, intelligent citizens. You’ve done well!

  134. 134
    Dr JDD says:

    Vjtorley @71:

    Thanks for your reply. I think however, that as with many of these discussions I have with others, that you and others are missing my point here.

    So let me try to be clear: my comments in this (and the other) thread are not an attempt to provide a general refutation of CD. I will repeat that in other way – I am not saying that the argument I am making disproves CD.

    So what am I doing? I am trying to argue against and expose the illogical nature of some poor arguments used in this debate. I am not pretending that in doing so that will cause the whole and complete argument of CD to crumble, however, when someone centres their argument for a belief system on a flawed premise, they have every right to expect that flawed argument to be challenged.

    So again, your response to my post is irrelevant because you are essentially saying that you will disregard the questions I have about specific “evidence” presented in favour of a belief system and instead just tell me to look at another piece of evidence or logical argument for that belief system. But that is not addressing the problem at hand.

    Which is why I come back to the whole issue of certain sequences and pseudogenes like the HBBP1 “pseudogene”. These are being claimed as strong evidence for CD, and that CD is the only way to rationally explain these. As I have pointed out above, there are some key questions to be answered, with evidence, rather than circular arguments that depend on CD in the first place to allow these observations to be used as evidence for CD. That is what I am challenging here.

    Yet this is typical in these debates quite frankly. Those who suppose mainstream evolution seem incapable of seeing the flaws in many of these arguments, or at least incapable of discussing these points in a fair manner. Another example is in the opossum thread where I questioned the statement by Prof Swamidass that “the vast majority of lncRNAs have no function.” I challenged this, citing several mainstream papers and I used the example of mainstream biology once stating that 99% of the genome is junk but then changing that to 10% as being akin to even recently lncRNAs were considered largely non-functional, but the evidence is changing in one direction.

    As a result of that discussion, you (vjtorley) and others use the classic “bait and switch” (not even bait – just latching onto a word that I used as an example, i.e. “junk”) and try to shut down that discussion with quotes and references that state the majority of the genome is junk, and also it was harped on about how lncRNAs make up a very low %age of the genome so my argument was irrelevant.

    But you missed the point!! My point was not about if lncRNAs were all functional than junk DNA has lost and there is no junk. That was emphatically not my point at all. My point was that if you make a statement, such as “the vast majority of lncRNAs are non-functional” then you must expect to defend that in light of opposing evidence. Yet intelligent people seem to completely miss that point or just disregard and refuse to engage in a sensible discussion about it, which I think is a shame.

    The same is true of using circular arguments with CD, or using pseudogenes as supporting evidence for CD. If people are to present these specific examples, then expect the flaws to be pointed out and the evidence to be questioned. That’s what science is! It’s not ignoring the challenge of the data and reverting to “well its already proven elsewhere anyway” otherwise what is the point in discussion?!?

    I think this is why many of us here feel like we are banging our heads against the wall. HeKs, PaV, Querius, others. We sound like broken records – pseudogenes, feathers, simulating evolution on bacteria, software code analogies. But why do we sound like broken records? Because no one is taking these discussions and arguments presented to them seriously. They just skirt the issue and defer to the mainstream position that “it [CD] is all proven anyway”.

    Yet as already said on this thread, UD is the very first place that should welcome sound challenging of the mainstream position and not just defer to that as is done in academic circles with the silencing or putting down of those who challenge this.

  135. 135
    bornagain77 says:

    Python, in case you ever decide to be honest towards the evidence instead of playing ‘gotcha’ games (which would be a miracle in its own right), and for the unbiased readers who are interested in a closer look, Paul Giem has a video on one of the ORFan papers that falsified the Darwinian position

    New Genes Are Essential 6-13-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6qgGPV1AO1E

    Darwinian explanations for essential ORFan genes are un-parsimonious to put it mildly

    Can new genes arise from junk DNA? – August 24, 2015
    Excerpt: Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said.
    BA77: Moreover, the essential genes were somehow incorporated into the ‘bicycle’ while the bicycle was being peddled, i.e. while the cell was busy being alive.
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....ent-577484

    This entire episode with ORFans has highlighted the unfalsifiable nature of Darwinian Theory as a science. No matter how contrary a finding is to Darwinian explanations, that finding is simply never really allowed a real chance to falsify Darwinian theory. The contrary finding is simply ‘explained away’ with another ‘epicycle’ (Lakatos & Hunter).

    As Dr. Hunter would say, when it comes to Darwinian evolution, ‘religion drives science and it matters’!

  136. 136
    bornagain77 says:

    PaV, not to be funny, but if you don’t believe God creating the body plans of the Cambrian explosion in a ‘top down’ manner can be supported ‘scientifically’, (please note that in order to do science in the first place Theism must be true), do you then think that the most ‘scientific’ explanation is that He took a jelly fish, or some other creature, and morphed it into all the different creatures of the Cambrian explosion?

    Since Theism must be true in order to rationally practice science in the first place, exactly what constitutes the most ‘scientific’ explanation for you for the Cambrian explosion or even what constitutes the most ‘scientific’ explanation for you for the Big Bang?

    The Great Debate: Does God Exist? – Justin Holcomb – audio of the 1985 Greg Bahnsen debate available at the bottom of the site
    Excerpt: The transcendental proof for God’s existence is that without Him it is impossible to prove anything. The atheist worldview is irrational and cannot consistently provide the preconditions of intelligible experience, science, logic, or morality. The atheist worldview cannot allow for laws of logic, the uniformity of nature, the ability for the mind to understand the world, and moral absolutes. In that sense the atheist worldview cannot account for our debate tonight.,,,
    http://justinholcomb.com/2012/.....god-exist/

    supplemental note for unbiased readers as to ‘natural’ causality vs. agent causality

    “to say that a stone falls to earth because it’s obeying a law, makes it a man and even a citizen”
    – CS Lewis

    “The dazzlingly obvious conclusion now arose, in my mind: in the whole history of the universe the laws of Nature have never produced a single event… Up till now I had had a vague idea that the laws of Nature could make things happen. I now saw that this was exactly like thinking that you could increase your income by doing sums about it. The laws are the pattern to which events conform: the source of events must be sought elsewhere.
    “This may be put in the form that the laws of Nature explain everything except the source of events. But this is rather a formidable exception. The laws, in one sense, cover the whole of reality except–well, except that continuous cataract of real events which makes up the actual universe. They explain everything except what we should ordinarily call ‘everything’. The only thing they omit is — the whole universe.”
    – C.S. Lewis, God in the Dock

    A Professor’s Journey out of Nihilism: Why I am not an Atheist – University of Wyoming – J. Budziszewski
    Excerpt page12: “There were two great holes in the argument about the irrelevance of God. The first is that in order to attack free will, I supposed that I understood cause and effect; I supposed causation to be less mysterious than volition.
    If anything, it is the other way around. I can perceive a logical connection between premises and valid conclusions. I can perceive at least a rational connection between my willing to do something and my doing it. But between the apple and the earth, I can perceive no connection at all. Why does the apple fall? We don’t know. “But there is gravity,” you say. No, “gravity” is merely the name of the phenomenon, not its explanation. “But there are laws of gravity,” you say. No, the “laws” are not its explanation either; they are merely a more precise description of the thing to be explained, which remains as mysterious as before. For just this reason, philosophers of science are shy of the term “laws”; they prefer “lawlike regularities.” To call the equations of gravity “laws” and speak of the apple as “obeying” them is to speak as though, like the traffic laws, the “laws” of gravity are addressed to rational agents capable of conforming their wills to the command. This is cheating, because it makes mechanical causality (the more opaque of the two phenomena) seem like volition (the less). In my own way of thinking the cheating was even graver, because I attacked the less opaque in the name of the more.
    The other hole in my reasoning was cruder. If my imprisonment in a blind causality made my reasoning so unreliable that I couldn’t trust my beliefs, then by the same token I shouldn’t have trusted my beliefs about imprisonment in a blind causality. But in that case I had no business denying free will in the first place.”
    http://www.undergroundthomist......theist.pdf

    Agent Causality (of Theists) vs. The self refuting Blind Causality (of Atheists) – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1118356054843993/?type=2&theater

    The ‘Mental Cell’: Let’s Loosen Up Biological Thinking! – Stephen L. Talbott – September 9, 2014
    Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”.
    Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness1.
    One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself.
    http://natureinstitute.org/txt.....ell_23.htm

  137. 137
    Dr JDD says:

    Regarding special creation:

    Personally I completely accept, from an anthropological view that there is non-acceptance of special creation. Just like I accept atheism is inevitable. Special creation (depending on what that even is defined as, which I think is unclear to be honest) is “unscientific” as there is no known or describable mechanism nor can one be determined. It is supernatural. So I expect the unacceptance of this.

    However, here is my challenge to those who hold to ID but do not accept special creation, or let us say creation ex nihilo: How then did the designer design the first life (abiogenesis)? Modification of what? Design from what? What about pre-life? Do you believe in a designer so detached from the natural world that we still have the problem of the origin of material?

    My second challenge to those who claim to be Christian but do not hold to any “special creation”: Do you believe that Jesus performed miracles? How did he produce a few 10,000 loaves of bread and fish form just 5 loaves and 2 fish? How did he regenerate a human who had died several days prior? How did he restore sight? How did he heal a shrivelled arm? Modification of design? What do you say to “by faith we understand the worlds were formed at God’s command so that which is visible came from that which is invisible”? This is not “special creation”?

  138. 138
    bornagain77 says:

    Dr. JDD

    “(SC) is “unscientific” as there is no known or describable mechanism nor can one be determined”

    Really?, and exactly what was the scientific ‘mechanism’ by which you just created the information in your own post?

    re-reference:

    A Professor’s Journey out of Nihilism: Why I am not an Atheist – University of Wyoming – J. Budziszewski
    Excerpt page12: “There were two great holes in the argument about the irrelevance of God. The first is that in order to attack free will, I supposed that I understood cause and effect; I supposed causation to be less mysterious than volition.
    If anything, it is the other way around. I can perceive a logical connection between premises and valid conclusions. I can perceive at least a rational connection between my willing to do something and my doing it. But between the apple and the earth, I can perceive no connection at all. Why does the apple fall? We don’t know. “But there is gravity,” you say. No, “gravity” is merely the name of the phenomenon, not its explanation. “But there are laws of gravity,” you say. No, the “laws” are not its explanation either; they are merely a more precise description of the thing to be explained, which remains as mysterious as before. For just this reason, philosophers of science are shy of the term “laws”; they prefer “lawlike regularities.” To call the equations of gravity “laws” and speak of the apple as “obeying” them is to speak as though, like the traffic laws, the “laws” of gravity are addressed to rational agents capable of conforming their wills to the command. This is cheating, because it makes mechanical causality (the more opaque of the two phenomena) seem like volition (the less). In my own way of thinking the cheating was even graver, because I attacked the less opaque in the name of the more.
    The other hole in my reasoning was cruder. If my imprisonment in a blind causality made my reasoning so unreliable that I couldn’t trust my beliefs, then by the same token I shouldn’t have trusted my beliefs about imprisonment in a blind causality. But in that case I had no business denying free will in the first place.”
    http://www.undergroundthomist......theist.pdf

    Agent Causality (of Theists) vs. The self refuting Blind Causality (of Atheists) – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1118356054843993/?type=2&theater

    Moreover, if you are absolutely committed to explaining everything in the universe ‘scientifically’ solely by reference to chance and necessity, and never invoking ‘unscientific’ agent causality, then ‘you’ yourself become an illusion and all rationality is lost for you:

    The Confidence of Jerry Coyne – Ross Douthat – January 6, 2014
    Excerpt: then halfway through this peroration, we have as an aside the confession that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant:,,) Read more here:
    http://douthat.blogs.nytimes.c.....oyne/?_r=0

    “One absolutely central inconsistency ruins [the popular scientific philosophy]. The whole picture professes to depend on inferences from observed facts. Unless inference is valid, the whole picture disappears… unless Reason is an absolute, all is in ruins. Yet those who ask me to believe this world picture also ask me to believe that Reason is simply the unforeseen and unintended by-product of mindless matter at one stage of its endless and aimless becoming. Here is flat contradiction. They ask me at the same moment to accept a conclusion and to discredit the only testimony on which that conclusion can be based.”
    —C.S. Lewis, Is Theology Poetry (aka the Argument from Reason)

  139. 139
    Origenes says:

    Naturalism is difficult to debate not because of its coherency, but because of its incoherency. The first obstacle is that naturalism utterly fails to ground freedom, personhood, rationality in general and science in particular. That’s an incredibly poor start for any meaningful rational discussion between persons and maybe things should end right there. Stopping right there may very well be the appropriate course of action. One thing is for sure, the only way to get a discussion going is to ignore those perplexing shortcomings.
    ”Okay, let’s assume that you guys are rational free responsible agents that can be reasoned with, even though your philosophy insists that such things cannot exist.”

    WRT biology, the ‘scientific’ (read: naturalistic) concept of an organism as a bag of chemicals obfusticates just about every discussion on this forum.

    “How can living systems be so robust (dynamically stable), when they consist of thousands of chemical interactions that must all be coordinated precisely in time and space? From the point of view of physics, cells (not to speak of more complex organisms) should not exist, and yet they do. How is that possible?” [J.A.Barham]

    The great strength of ID is that it is able to accommodate this erroneous naturalistic view on the organism — to connect with naturalism, if you will — and still provide arguments for non-physicality (intelligent cause).
    However, for me personally, ID arguments for intelligent design are merely tools in the debate with naturalism. I do not hold the naturalistic view that organisms are bags of chemicals. Nor do I hold that organisms are machines.

    S.L.Talbott — reviewing ‘Darwin’s Doubt’ by Stephen Meyer):

    In addition to this, both Meyer and the neo-Darwinist accept a machine-like understanding of the organism. This goes without saying for the conventional biologist. But Meyer, too, refers freely to “molecular machines” and “protein machines”; he talks about “instructions”, “switches”, and “circuits”; and he imagines “digital” elements of DNA functioning like “computer code”. Part Two of his book is entitled “How to Build an Animal”.

    … Where Meyer wants to differ from the neo-Darwinist is in his belief that this world of mindless stuff is by itself inadequate to explain the rise of complex, meaningful (“informational”) order over the course of evolution.

    … Meyer’s solution — since he assumes throughout that nature really is, in its own right, a strictly materialistic affair — is to posit a designing intelligence acting upon the evolutionary process somehow from without, rather as a human engineer contrives to build various devices with the materials at hand.

    … I had hoped that Meyer would avoid making machines out of his organisms, for two reasons. First, the usage simply doesn’t work. As I have tried to show elsewhere, the organism is not machine-like and it also is far from being, in any part, a computer. Second, and more important for present purposes: the machine metaphor invites — almost demands — that we inquire about the designer of the machine. By appealing to such an external agency, one ignores the living agency of the organism itself.

    How much accommodation of the ‘scientific’ view is acceptable — even for debating purposes? Why do we have to agree with a concept like ‘common descent’, which is based on naturalistic warped views on the organism?
    I wonder what percentage of ID-ists share my view that ID is a valuable tool in the larger debate with naturalists, but that it is primarily based on the erroneous naturalistic view on the organism.

  140. 140
    wd400 says:

    So you are saying that somehow a huge amount of information (body plan & instructions for building the body) is stored in the DNA, despite the high percentage of junk DNA?
    If so, in which areas of the DNA do you expect this information to be found? Non-coding areas perhaps?

    Sure. The “plan” is in both coding and non-coding regions. If you want to get an idea of how it works read up on, say, the role of Sonic Hedgehog in the developing limb and neural tube.

  141. 141
    bornagain77 says:

    Origenes, while I agree that many in the ID camp are nearly as reductionist in their thinking as Darwinists are, I don’t necessarily agree with Talbott in putting the focal point solely on the living organism itself. As much as revealed about the inadequacy of the Darwinian explanation from looking at the organism as a whole, as Talbott so eloquently does in his writings, that focal point still does not address or solve the main enigma of where the information is coming from in the first place.

  142. 142
    Gordon Cunningham says:

    BA77: “(please note that in order to do science in the first place Theism must be true)”

    That is not only wrong, it has to be one of the most absurd things I have ever heard. Science can be done regardless of the truth of theism. And what theism are you talking about? Because they can’t all be true.

  143. 143
    bornagain77 says:

    podcast – Dr. Jonathan Wells discusses a popular claim, which he describes as “DNA makes RNA makes protein makes us”—or, every organism contains a program for itself in its DNA. Though this view fits neatly with the perspective of Darwinian evolution, it has been shown to be incorrect at every step. Listen in as Dr. Wells explains.
    http://www.discovery.org/multi.....evolution/

    podcast – Dr. Jonathan Wells explains the concept of codes in living things, and how they affect the debate over neo-Darwinism and intelligent design. (at least 5 different codes outside DNA are discussed) – Oct. 2015
    http://www.discovery.org/multi.....more-31141

  144. 144
    Origenes says:

    WD400: Sure. The “plan” is in both coding and non-coding regions.

    A certain amount of storage space in DNA is required for the information of the body plan & instructions for building the body. Has anyone attempted to come up with an estimation of the size of this storage space?
    To be frank, the information mapping the human brain and its building process seem to require more storage space than DNA has to offer.

  145. 145
    wd400 says:

    A certain amount of storage space in DNA is required for the information of the body plan & instructions for building the body.

    I don’t know what this means, to be honest. Organisms aren’t computers, analogies like this don’t usually work very well.

    Biologists have studied development a lot though. I you want to understand the basis of development start there, not with a poor analogy. The Fugu case is illustrative though, as it appears to have reduced it’s genome size over evolutionary time, but does exactly as much development as related fish with much larger genomes.

  146. 146
    Dr JDD says:

    Hi BA77 @138.

    I do appreciate your posts and I think we probably agree on a lot, but you often run the risk of coming across aggressively on single statements made out of context. Your last post seems quite accusatory against me and even suggests I do not believe in special creation. I think quite frankly a full reading of my post suggests I do.

    However, I put “unscientific” in quotation marks because like it or not, there is a definition of science. That definition is generally that you can deduce something based on observations or analysis of said thing or phenomenon. Or even better, the process of verifying a hypothesis by experimental repetition.

    So when I say SC is “unscientific” I stand by that. Please do enlighten me how you can verify a miracle, apart from witness testimony? Please do tell me, how you would expect to analyze a piece of bread created in a miraculous fashion at the feeding of the 5000 if you had a sample? What do you think you would find that would allow you to determine it was created ex nihilo, in a miraculous event? I sincerely think you would never be able to tell that apart from testimony. You could not take that piece of bread and using the scientific method (“science”) determine it came to that form through SC. Unless you have an alternative theory or insight into what the scientific method would reveal something such a miraculous event would have produced?

    The problem with trying to shoe-horn EVERYTHING theological and to do with your faith into a human classification of “science” is that you negate half the point of the Christian faith. It is not meant to be a 100% scientifically verifiable belief system, otherwise, you as I say negate FAITH.

    I am a YEC of sorts, a believer in a literal 6-day creation week and a global flood not primarily because the evidence demands that and is overwhelming in support of it, but because of faith and the evidence around Biblical veracity.

    However I do sincerely believe that evolution is pseudoscience itself and a faith based system as it is not verifiable and reproducible. Ultimately, whatever you believe about origins requires some form of faith.

    Best Wishes,

    JDD

  147. 147
    Origenes says:

    WD400:

    Origenes: A certain amount of storage space in DNA is required for the information of the body plan & instructions for building the body.

    I don’t know what this means, to be honest.

    It means exactly what it says. DNA has a limited amount of coding space. If a huge amount of information (body plan & instructions for building the body) is somehow encoded in the DNA, then it requires a certain amount of coding/storage space. Agree?

    WD400: Organisms aren’t computers ….

    I don’t know what that means, to be honest. Do you mean that the information we are discussing is not stored?

  148. 148
    wd400 says:

    It means exactly what it says. DNA has a limited amount of coding space. If a huge amount of information (body plan & instructions for building the body) is somehow encoded in the DNA, then it requires a certain amount of coding/storage space. Agree?

    Sure I guess. It’s not a very useful way of thinking about biology though. The “encoding” is in a set of proteins and regulatory elements that that react with the environment to produce chemical reactions. Talking about how many bytes of storage such a process needs doesn’t seem very important.

    If you are asking can 300 million base pairs encode that information, then the field of genetics is telling you ‘yes’. If you want to understand development then focus on the biology, and not on inapt comparisons.

  149. 149
    bornagain77 says:

    Dr JDD, apologize for picking on this one point, but it is an important point.

    I hold that the post you just wrote is repeatable evidence of a miracle.

    I personally witnessed it miraculously appear on the screen after you hit ‘post comment’!

    Bet you did not know you were a miracle worker did you! 🙂

    In fact, if you can point to just one instance of non-trivial information coming into existence by purely within space-time material processes, without conscious intelligence, that would falsify ID.

    This repeatable miracle that you just performed of bringing information into existence is all reasonable, repeatable, and perfectly ‘scientific’.

    And since we only know of one cause that can produce information, i.e. mind, then we are more than justified to reason that a superior mind ‘miraculously’ created the highly sophisticated information we see in life.

    In fact, it is the exact same method of science Charles Darwin himself used. i.e. presently acting cause known to produce the effect in question.

    Stephen Meyer: Charles Darwin’s Methods, Different Conclusion
    https://www.youtube.com/watch?v=iqq6JP5gE0E

  150. 150
    Origenes says:

    WD400: Talking about how many bytes of storage such a process needs doesn’t seem very important.

    “Doesn’t seem very important” is wishful thinking on your part, because there is no way for your position to provide such storage.

    WD400: If you are asking can 300 million base pairs encode that information, then the field of genetics is telling you ‘yes’.

    You are referring to the 10% of the human DNA that is supposedly functional. However a lot of that 10% encodes for functions that are utterly unhelpful wrt human body plan and instructions for building the human body. Information for building blocks does not tell you how to build a house.
    So, contrary to your suggestion, not all 300 million base pairs are available.
    Moreover the brain alone consists of 86 billion neurons and each neuron has 5,000 – 10,000 synapses connecting to other neurons and cells. Assuming that this is all produced with some precision a few million base pairs doesn’t seem enough.
    And let’s not forget about all the other parts of the body — all the information for the ultra-complex system of blood clothing, the mind bottling complexities involved in vision, to name but a few.

  151. 151
    wd400 says:

    Moreover the brain alone consists of 86 billion neurons and each neuron has 5,000 – 10,000 synapses connecting to other neurons and cells. Assuming that this is all produced with some precision a few million base pairs doesn’t seem enough.

    This is what I mean about learning about development. The position of synapses is not specified as some map of synapse 10001 connecting to 10002 at position x,y,z. Development is regulated such that synpases grow, interact with each other through morphogens and form connections. The “encoding” only sets up the environment in which development plays out, not a explicit map of what an organism will end up like.

    Again, I encourage your to try and understand development before you try to shoe horn in analogies from other fields.

  152. 152
    PaV says:

    BA77:

    PaV, not to be funny, but if you don’t believe God creating the body plans of the Cambrian explosion in a ‘top down’ manner can be supported ‘scientifically’, (please note that in order to do science in the first place Theism must be true), do you then think that the most ‘scientific’ explanation is that He took a jelly fish, or some other creature, and morphed it into all the different creatures of the Cambrian explosion?

    I had asked if you could explain what you mean by “special creation.” You haven’t done that exactly, but when you write of body plans coming out of “the Cambrian Explosion in a ‘top-down’ manner,” I suspect that is your view.

    No, I’m not of the opinion that, let’s say, in an Aristotlean way you can say that God is always using “prime matter.” I have two reasons for this. The first is simply the Law of Parsimony—IOW, why reinvent the wheel. The second is theological.

    In Christ, St. Paul tells us, the whole cosmos is to be recapitulated. God has place everything under his feet.” So, as I see it—and the first creation account lends itself to this view—creation ‘shares’ life with all the rest of creation. Man is at the pinnacle of this creation. Then Jesus, who is head of the Body, the Church, is the summit of the created order, which begins with the Big Bang, shifts to ‘nucleosynthesis,’ at then shifts to the Earth, where creation is brought about. Man sums up that creative activity, and has a ‘share’ in the entire created order: the Cosmos we see about us. So, I see God’s Plan as bringing all things into unity, with Christ at the Head.

    “Special creation,” OTOH, would make living things “separate,” not “united,” from one another.

    But this quibble over “special creation” risks being something which might “divide” us; yet, it is so much smaller than that which “unites” us. So let’s focus on what we agree on.

    Pace.

    P.S. Reflecting a little bit further, I want to add this.

    Plato and Aristotle differed, as you know, as to where the “form” might be found. I have, I guess, a more Platonic view, where I see the “matter”—but not “prime matter”—being molded whilst the “form” is placed within it. Just think of DNA and the ‘cell’ itself. So, technically, this is NOT creatio ex nihilo, but something very much like it; in fact, so much like it that the term itself applies.

    Hope this helps.

  153. 153
    bornagain77 says:

    GC: you claim you can practice science perfectly well without belief in God. If you truly believe this, might I suggest that you stop stealing from God in order to practice science?

    How Atheists Steal Science From God | Frank Turek, PhD – video
    https://www.youtube.com/watch?v=gurMfV5Pmus

    Contrary to what you believe, you are absolutely dependent on presuppositions about the rationality of the world, and our ability our mind to comprehend that rational world, that can only be firmly grounded in Theistic metaphysics.

    The truth about science and religion By Terry Scambray – August 14, 2014
    Excerpt: In 1925 the renowned philosopher and mathematician, Alfred North Whitehead speaking to scholars at Harvard said that science originated in Christian Europe in the 13th century. Whitehead pointed out that science arose from “the medieval insistence on the rationality of God, conceived as with the personal energy of Jehovah and with the rationality of a Greek philosopher”, from which it follows that human minds created in that image are capable of understanding nature.
    The audience, assuming that science and Christianity are enemies, was astonished.
    http://www.americanthinker.com.....igion.html

    The Great Debate: Does God Exist? – Justin Holcomb – audio of the 1985 Greg Bahnsen debate available at the bottom of the site
    Excerpt: When we go to look at the different world views that atheists and theists have, I suggest we can prove the existence of God from the impossibility of the contrary.
    The transcendental proof for God’s existence is that without Him it is impossible to prove anything. The atheist worldview is irrational and cannot consistently provide the preconditions of intelligible experience, science, logic, or morality. The atheist worldview cannot allow for laws of logic, the uniformity of nature, the ability for the mind to understand the world, and moral absolutes. In that sense the atheist worldview cannot account for our debate tonight.,,,
    http://justinholcomb.com/2012/.....god-exist/

    Science and Theism: Concord, not Conflict* – Robert C. Koons
    IV. The Dependency of Science Upon Theism (Page 21)
    Excerpt: Far from undermining the credibility of theism, the remarkable success of science in modern times is a remarkable confirmation of the truth of theism. It was from the perspective of Judeo-Christian theism—and from the perspective alone—that it was predictable that science would have succeeded as it has. Without the faith in the rational intelligibility of the world and the divine vocation of human beings to master it, modern science would never have been possible, and, even today, the continued rationality of the enterprise of science depends on convictions that can be reasonably grounded only in theistic metaphysics.
    http://www.robkoons.net/media/.....ffd524.pdf

    Moreover, since atheism denies that a rational Mind is behind the universe, and even denies that we have rational minds ourselves, then Darwinian evolution and atheism in general both collapse into a heap of worthless fantasies and imagination.

    First off, in regards to Intelligent Design, atheists hold that the design that we pervasively see throughout life is merely an illusion, i.e. merely an ‘appearance of design’,

    “Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning.”
    Richard Dawkins – “The Blind Watchmaker” – 1986 – page 21
    quoted from this video – Michael Behe – Life Reeks Of Design – 2010 – video
    https://www.youtube.com/watch?v=Hdh-YcNYThY

    Can Darwinian Evolutionary Theory Be Taken Seriously? – Stephen L. Talbott – May 17, 2016
    Excerpt: Julian Huxley, who coined the phrase “Modern Synthesis” to describe the now canonical, twentieth-century formulation of what is also called “neo-Darwinism”, wrote in 1942:
    “It was one of the great merits of Darwin himself to show that the purposiveness of organic structure and function was apparent only. The teleology of adaptation is a pseudo-teleology, capable of being accounted for on good mechanistic principles, without the intervention of purpose, conscious or subconscious, either on the part of the organism or of any outside power”.11
    Here, again, we are said to be saved from the “intervention” of an alien force, as if real purpose and intelligence would be an offense against the natural world.
    And, several decades later, the author who gave us the “selfish gene” warned us how hard it can be to escape illusion: “So overwhelming is the appearance of purposeful design that, even in this Darwinian era when we know ‘better’, we still find it difficult, indeed boringly pedantic, to refrain from teleological language when discussing adaptation”. And yet, Richard Dawkins is ever ready to remind us, “the theory of natural selection provides a mechanistic, causal account of how living things came to look as if they had been designed for a purpose”12
    http://natureinstitute.org/txt.....ogy_30.htm

    Julian Huxley and Richards Dawkins are far from the only prominent atheists who seem to be afflicted with the mental illness of seeing the ‘illusion of design’ pervasively throughout life. The well known atheist Francis Crick, co-discoverer of DNA, seems to have been particularly haunted by this illusion of seeing design everywhere he looked in molecular biology:

    “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”
    Francis Crick – What Mad Pursuit
    “Organisms appear as if they had been designed to perform in an astonishingly efficient way, and the human mind therefore finds it hard to accept that there need be no Designer to achieve this”
    Francis Crick – What Mad Pursuit – p. 30

    Yet, despite the fact that, according to atheists themselves, life gives the overwhelming ‘appearance’ of having been designed for a purpose, all the supposed evidence, that is suppose to explain how this overwhelming appearance of design in life came to be, turns out, itself, to be ‘illusory’.
    In fact, one of the main themes of many of Michael Behe’s talks is that all ‘grand Darwinian claims rest on undisciplined imagination’:

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe – 29:24 mark of following video
    http://www.youtube.com/watch?f.....fM#t=1762s

    As well, Franklin M. Harold, whom I believe is an atheist, calls all Darwinian explanations ‘a variety of wishful speculations’.

    “,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.”
    Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205.
    *Professor Emeritus of Biochemistry, Colorado State University, USA

    Thus, since atheists themselves are self admittedly seeing the ‘illusion of design’ in life, and yet they have no experimental evidence whatsoever that unguided material processes can produce this ‘illusion of design’ that they themselves are seeing, then of course the ID advocate would be well justified in saying that the design they are seeing in life is real and that these atheists are not really suffering from some sort of a mental illness after all but they are in fact ‘naturally detecting design’ because of the inherent ‘image of God’ that they have within themselves.

  154. 154
    bornagain77 says:

    Moreover, although reliable ‘observation’ of reality is a necessary cornerstone of the scientific method itself,,,

    Steps of the Scientific Method
    Observation/Research
    Hypothesis
    Prediction
    Experimentation
    Conclusion
    http://www.sciencemadesimple.c.....ethod.html

    ,,, Although reliable ‘observation’ of reality is a necessary cornerstone of the scientific method, materialism undermines this cornerstone. Given materialistic/atheistic premises, not only are our interpretations of reality held to be somewhat flawed, but even our perceptions/observations of reality itself held to be untrustworthy and thus ‘illusory’ given the materialistic premises of atheism.

    Why Atheism is Nonsense Pt.5 – “Naturalism is a Self-defeating Idea”video
    Excerpt: “Since we are creatures of natural selection, we cannot totally trust our senses. Evolution only passes on traits that help a species survive, and not concerned with preserving traits that tell a species what is actually true about life.”
    Richard Dawkins – quoted from “The God Delusion”
    https://www.youtube.com/watch?v=ff-5rsrDRGM

    Donald Hoffman: Do we see reality as it is? – Video – 9:59 minute mark
    Quote: “fitness does depend on reality as it is, yes.,,, Fitness is not the same thing as reality as it is, and it is fitness, and not reality as it is, that figures centrally in the equations of evolution. So, in my lab, we have run hundreds of thousands of evolutionary game simulations with lots of different randomly chosen worlds and organisms that compete for resources in those worlds. Some of the organisms see all of the reality. Others see just part of the reality. And some see none of the reality. Only fitness. Who wins? Well I hate to break it to you but perception of reality goes extinct. In almost every simulation, organisms that see none of reality, but are just tuned to fitness, drive to extinction that perceive reality as it is. So the bottom line is, evolution does not favor veridical, or accurate perceptions. Those (accurate) perceptions of reality go extinct. Now this is a bit stunning. How can it be that not seeing the world accurately gives us a survival advantage?”
    https://youtu.be/oYp5XuGYqqY?t=601

    Why Evolutionary Theory Cannot Survive Itself – Nancy Pearcey – March 8, 2015
    Excerpt: Steven Pinker writes, “Our brains were shaped for fitness, not for truth. Sometimes the truth is adaptive, but sometimes it is not.” The upshot is that survival is no guarantee of truth. If survival is the only standard, we can never know which ideas are true and which are adaptive but false.
    To make the dilemma even more puzzling, evolutionists tell us that natural selection has produced all sorts of false concepts in the human mind. Many evolutionary materialists maintain that free will is an illusion, consciousness is an illusion, even our sense of self is an illusion — and that all these false ideas were selected for their survival value.
    So how can we know whether the theory of evolution itself is one of those false ideas? The theory undercuts itself.,,,
    Of course, the atheist pursuing his research has no choice but to rely on rationality, just as everyone else does. The point is that he has no philosophical basis for doing so. Only those who affirm a rational Creator have a basis for trusting human rationality.
    The reason so few atheists and materialists seem to recognize the problem is that, like Darwin, they apply their skepticism selectively. They apply it to undercut only ideas they reject, especially ideas about God. They make a tacit exception for their own worldview commitments.
    http://www.evolutionnews.org/2.....94171.html

    also see Plantinga’s ‘evolutionary argument against naturalism’

    Needless to say, a worldview that undermines the scientific method itself by holding all our observations could be illusory is NOT a worldview that can firmly ground the practice of science!

    Here is an important side-note to ‘reliable observation’: Completely contrary to materialistic premises, conscious observation, far from being illusory, is experimentally found to be far more integral to reality, i.e. far more reliable, than materialism had ever predicted.

    New Mind-blowing Experiment Confirms That Reality Doesn’t Exist If You Are Not Looking at It – June 3, 2015
    Excerpt: The results of the Australian scientists’ experiment, which were published in the journal Nature Physics, show that this choice is determined by the way the object is measured, which is in accordance with what quantum theory predicts.
    “It proves that measurement is everything. At the quantum level, reality does not exist if you are not looking at it,” said lead researcher Dr. Andrew Truscott in a press release.,,,
    “The atoms did not travel from A to B. It was only when they were measured at the end of the journey that their wave-like or particle-like behavior was brought into existence,” he said.
    Thus, this experiment adds to the validity of the quantum theory and provides new evidence to the idea that reality doesn’t exist without an observer.
    http://themindunleashed.org/20.....at-it.html

    Apparently science itself could care less if atheists believe their observations are illusory!

    Moreover, as Nancy Pearcey alluded to in her ‘Why Evolutionary Theory Cannot Survive Itself’ article, given the materialistic/atheistic premises of Darwinian evolution, not only are our observations of reality itself held to be illusory, but even our sense of self, i.e. the belief that we really exist as real persons, which is the most sure thing we can know about reality, becomes illusory too.
    In what I consider to be a shining example of poetic justice, in their claim that God is not really a real person but is merely an illusion, the naturalist also ends up claiming that he himself is not really a real person but is merely an illusion.,,,

    “that “You”, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased: “You’re nothing but a pack of neurons.” This hypothesis is so alien to the ideas of most people today that it can truly be called astonishing.”
    Francis Crick – “The Astonishing Hypothesis” 1994

    “We have so much confidence in our materialist assumptions (which are assumptions, not facts) that something like free will is denied in principle. Maybe it doesn’t exist, but I don’t really know that. Either way, it doesn’t matter because if free will and consciousness are just an illusion, they are the most seamless illusions ever created. Film maker James Cameron wishes he had special effects that good.”
    Matthew D. Lieberman – neuroscientist – materialist – UCLA professor

    The Confidence of Jerry Coyne – Ross Douthat – January 6, 2014
    Excerpt: But then halfway through this peroration, we have as an aside the confession (by Coyne) that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant: But more on that below.) Prometheus cannot be at once unbound and unreal; the human will cannot be simultaneously triumphant and imaginary.
    Per NY Times

    Atheistic Materialism – Does Richard Dawkins Exist? – video 37:51 minute mark
    Quote: “You can spout a philosophy that says scientific materialism, but there aren’t any scientific materialists to pronounce it.,,, That’s why I think they find it kind of embarrassing to talk that way. Nobody wants to stand up there and say, “You know, I’m not really here”.
    https://www.youtube.com/watch?v=rVCnzq2yTCg&t=37m51s

    At the 23:33 minute mark of the following video, Richard Dawkins agrees with materialistic philosophers who say that:
    “consciousness is an illusion”
    A few minutes later Rowan Williams asks Dawkins
    ”If consciousness is an illusion… what isn’t?”.
    https://www.youtube.com/watch?v=HWN4cfh1Fac&t=22m57s

    Thus, given materialistic premises, people become illusions whose observations of reality are illusory.
    And why in blue blazes should anyone trust what illusions having illusions say about reality?

  155. 155
    bornagain77 says:

    Finally, this unconstrained ‘illusory’ nature inherent to naturalism/materialism becomes even more acute when atheists try to explain the origin and sustaining of the universe, i.e. try to explain the origin, fine-tuning, and quantum wave collapse of the universe.

    WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Infinity – Max Tegmark – January 2014 and Feb. 2015
    Excerpt: Physics is all about predicting the future from the past, but inflation seems to sabotage this: when we try to predict the probability that something particular will happen, inflation always gives the same useless answer: infinity divided by infinity. The problem is that whatever experiment you make, inflation predicts that there will be infinitely many copies of you far away in our infinite space, obtaining each physically possible outcome, and despite years of tooth-grinding in the cosmology community, no consensus has emerged on how to extract sensible answers from these infinities. So strictly speaking, we physicists are no longer able to predict anything at all!
    http://blogs.discovermagazine......OsRyS7cBCA

    Why Most Atheists Believe in Pink Unicorns – May 2014
    Excerpt: Given an infinite amount of time, anything that is logically possible(11) will eventually happen. So, given an infinite number of universes being created in (presumably) an infinite amount of time, you are not only guaranteed to get your universe but every other possible universe. This means that every conceivable universe exists, from ones that consist of nothing but a giant black hole, to ones that are just like ours and where someone just like you is reading a blog post just like this, except it’s titled: “Why most atheists believe in blue unicorns.”
    By now I’m sure you know where I’m going with this, but I’ll say it anyway. Since we know that horses are possible, and that pink animals are possible, and that horned animals are possible, then there is no logical reason why pink unicorns are not possible entities. Ergo, if infinite universes exist, then pink unicorns must necessarily exist. For an atheist to appeal to multiverse theory to deny the need of a designer infers that he believes in that theory more than a theistically suggestive single universe. And to believe in the multiverse means that one is saddled with everything that goes with it, like pink unicorns. In fact, they not only believe in pink unicorns, but that someone just like them is riding on one at this very moment, and who believes that elephants, giraffes, and zebra are merely childish fairytales.
    Postscript
    While it may be amusing to imagine atheists riding pink unicorns, it should be noted that the belief in them does not logically invalidate atheism. There theoretically could be multiple universes and there theoretically could be pink unicorns. However, there is a more substantial problem for the atheist if he wants to believe in them and he wants to remain an atheist. Since, as I said, anything can happen in the realm of infinities, one of those possibilities is the production of a being of vast intelligence and power. Such a being would be as a god to those like us, and could perhaps breach the boundaries of the multiverse to, in fact, be a “god” to this universe. This being might even have the means to create its own universe and embody the very description of the God of Christianity (or any other religion that the atheist otherwise rejects). It seems the atheist, in affirming the multiverse in order to avoid the problem of fine-tuning, finds himself on the horns of a dilemma. The further irony is that somewhere, in the great wide world of infinities, the atheist’s doppelganger is going to war against an army of theists riding on the horns of a great pink beast known to his tribesman as “The Saddlehorn Dilemma.”
    https://pspruett.wordpress.com/2014/05/12/why-most-atheists-believe-in-pink-unicorns/

    Fine Tuning, Pink Unicorns, and The Triune God – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1145151962164402/?type=2&theater

    Too many worlds – Philip Ball – Feb. 17, 2015
    Excerpt:,,, You measure the path of an electron, and in this world it seems to go this way, but in another world it went that way.
    That requires a parallel, identical apparatus for the electron to traverse. More – it requires a parallel you to measure it. Once begun, this process of fabrication has no end: you have to build an entire parallel universe around that one electron, identical in all respects except where the electron went. You avoid the complication of wavefunction collapse, but at the expense of making another universe (and another you).,,,
    http://aeon.co/magazine/scienc.....a-fantasy/

    Thus, basically, without God, everything within the atheistic/naturalistic worldview, (i.e. sense of self. observation of reality, even reality itself), collapses into self refuting, unrestrained, flights of fantasies and imagination.

    Verse, Video and Music:

    2 Corinthians 10:5
    Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ;

    The Resurrection of Jesus Christ from Death as the “Theory of Everything” – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1143437869002478/?type=2&theater

    Hillsong United – Taya Smith – Touch The Sky – Acoustic Cover – Live – HD
    https://www.youtube.com/watch?v=pyl34fHQi3U

  156. 156
    bornagain77 says:

    PaV, sorry but I still don’t really understand your position exactly. I’m guessing you are something of a ‘front-loader’? Semi-Deistic?

    update, I re-read your post, and I ‘think’ our positions might be a bit more like trying to split hairs?

    To clarify, ‘special creation’ to me does not mean completely disjointed but means God introducing new information ‘top down’ into creation, which is what I believe He did in the Cambrian and even with man.

  157. 157
    Origenes says:

    WD400,

    WD400: The position of synapses is not specified as some map of synapse 10001 connecting to 10002 at position x,y,z.

    So a body plan doesn’t require a huge amount of information, because things are not that specified. Are you suggesting that synapses just improvise as they grow?

    WD400: Development is regulated such that synpases grow, interact with each other through morphogens and form connections.

    What directs the process? What tells synapses where to grow, when to stop growing, which connections to form and when to stop forming connections? Just a few easy questions for which there is absolutely no bottom-up explanation.

    WD400: The “encoding” only sets up the environment in which development plays out, not a explicit map of what an organism will end up like.

    “Development plays out” and doesn’t need instructions? Okay, good luck with that.
    After noticing that your position cannot offer the required storage, you seem to resort to arguing that not much information is necessary to build a human body. I think we are done talking.

  158. 158
    wd400 says:

    What directs the process? What tells synapses where to grow, when to stop growing, which connections to form and when to stop forming connections?

    Proteins mostly, from the surrounding tissues and and expressed in a given cell. The most extreme examples of neural connections, long axons and the like, are still just organised by gradients of signalling molecules.

    So I’ll repeat it again. If you want to understand biology, then study biology.

  159. 159
    Origenes says:

    WD400:

    What directs the process? What tells synapses where to grow, when to stop growing, which connections to form and when to stop forming connections?

    Proteins mostly, from the surrounding tissues and and expressed in a given cell.

    Non-responsive. What directs the correct proteins to the proper place at the proper time?

    WD400: So I’ll repeat it again. If you want to understand biology, then study biology.

    Your position offers nothing but non-explanations wrt to biology.

  160. 160
    wd400 says:

    I’m probably not going to explain all of developmental biology in the comment box at UD.

    If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on. To the extend that a body plan is “stored” in DNA, it’s stored in these genes and their regulator elements.

    If you want a small example of how this works then read about about something like Sonic Hedgehog in neural (or limb) development.

  161. 161
    Origenes says:

    WD400: If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on.

    What you say simply doesn’t make sense. You suggest something like a cascade of chemical reactions without system-wide coordination. In biology things are too contingent and unpredictable to lend any plausibility to such views.

  162. 162
    Phinehas says:

    Origenes:

    Don’t you get it? It’s a black box. You just need to have more faith and not sweat all those pesky details.

  163. 163
    wd400 says:

    If you say so.

  164. 164
    PaV says:

    BA77:

    To clarify, ‘special creation’ to me does not mean completely disjointed but means God introducing new information ‘top down’ into creation, which is what I believe He did in the Cambrian and even with man.

    I agree. Further, and what I’ve been alluding to along the way, I believe that God has had to change the “matter,” that is, the “cell.” But this change to the cell is not made whole hog, something along the lines of what happens to DNA.

    So, “I see you; and raise you one.” 🙂

  165. 165
    PaV says:

    wd400:

    I saw this (certainly out of context for me) and couldn’t resist:

    You say:

    If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on. To the extend that a body plan is “stored” in DNA, it’s stored in these genes and their regulator elements.

    To which I respond: In a corvette, no one sees a “plan.” All you see are various metallic parts linked together, and which work in a particular sequence. One also sees, related to these metal parts, wires of all sorts. Now, if you follow these wires, you actually see how they’re connected to other parts of the car that regulate the flow of electricity within the wires. As long as it has enough energy, it can move you from place A to place B.

    I hope you see what I’m saying.

  166. 166
    Eric Anderson says:

    Sure I guess. It’s not a very useful way of thinking about biology though. The “encoding” is in a set of proteins and regulatory elements that that react with the environment to produce chemical reactions. Talking about how many bytes of storage such a process needs doesn’t seem very important.

    Ah, yes, the old refuge argument of the materialist creation myth when someone points out that the story doesn’t seem to make sense: “Biology is different. You can’t think about biology in terms of computers and storage and machines. Biology isn’t intuitive.”

    Yep, it is just a kind of magic. No need to specify structures or precise interactions. Just all kind of happens by interactions with the environment.

    Sheesh. Can we please get more people to start thinking about building an organism for what it really is — an engineering problem. Let’s start considering organisms from a standpoint of integrated systems engineering, instead of handwaving stories about stuff just happening, unsupported claims about mistakes turning organism A into organism B, requests to set aside our intuition and our understanding of what is required to build a digitally-coded, functionally-integrated system and just believe . . .

  167. 167
    wd400 says:

    Ans where in the corvette is this plan stored PaV?

  168. 168
    Mung says:

    ThickPython:

    If you’d bothered to look at the results, you’d see that there are six alignments and they are syntenic in the sense that they maintain their order between the two species.

    I can appreciate the gratuitous insult, but before slinging it perhaps you should have looked up the meaning of synteny.

    How do you know they are on the same chromosome? Try to not beg the question.

  169. 169
    wd400 says:

    Yep, it is just a kind of magic. No need to specify structures or precise interactions. Just all kind of happens by interactions with the environment.

    I am certainly saying that biolgy is different, and that someone who wants to challange mainstream biological science might want to start by undertandign it. But this quote doesn’t reflect what I’ve said here at all — I’ve given several examples of well-understood systems that readers could follow up on. I encourage you to do so too.

  170. 170
    wd400 says:

    Mung,

    If they can be ordered they have to be one the same chromosome, no?

  171. 171
    ThickPython says:

    @Mung, #168:

    I can appreciate the gratuitous insult, but before slinging it perhaps you should have looked up the meaning of synteny.

    How do you know they are on the same chromosome? Try to not beg the question.

    The term “synteny” isn’t precisely defined – take the very first paragraph from Wikipedia:

    In classical genetics, synteny describes the physical co-localization of genetic loci on the same chromosome within an individual or species. Today, however, biologists usually refer to synteny as the conservation of blocks of order within two sets of chromosomes that are being compared with each other. This concept can also be referred to as shared synteny.

    You’re taking the narrow definition, and I’m taking the broader definition. I don’t care for an argument about semantics – my comment was clear enough in the first place.

  172. 172
    bill cole says:

    WD400

    WD400: If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on.

    What do you consider the result of the fusion of a sperm and egg? No plan? We can very well predict the result and yes the sonic pathway is part of this and also the WNT beta catenin pathway. The stem cells get converted to differentiated cells and form all the parts of the human body with great precision from the genetic information(DNA sequences) passed along by the mother and father. Is DNA coded information? Hard to imagine how this process works so repeatably if it isn’t.

  173. 173
    wd400 says:

    You can call it a plan if you like, the point in making if that all comes about from gene products interacting with the environment (including other gene products). To the extent there is a plan, it is in these genes, their regulatory elements and the environment.

  174. 174
    bornagain77 says:

    You tell em wd400, however it happens, evolution did it! Although, evolution hasn’t ever been seen creating anything, it is a undeniable fact that it created all things. (snark off) 🙂

    “Evolution by natural selection, for instance, which Charles Darwin originally conceived as a great theory, has lately come to function more as an antitheory, called upon to cover up embarrassing experimental shortcomings and legitimize findings that are at best questionable and at worst not even wrong. Your protein defies the laws of mass action? Evolution did it! Your complicated mess of chemical reactions turns into a chicken? Evolution! The human brain works on logical principles no computer can emulate? Evolution is the cause!” –
    Robert B. Laughlin, Nobel laureate – Physics – A Different Universe: Reinventing Physics from the Bottom Down (New York: Basic Books, 2005), 168-69)

  175. 175
    ThickPython says:

    @Bornagain77, #135:

    Python, in case you ever decide to be honest towards the evidence instead of playing ‘gotcha’ games …

    In the Opossum thread:

    1. At post #24, you posted 8 links, one of which was the shark-zebrafish-human paper.

    2. In post #28, I addressed this shark-zebrafish-human paper, explaining why this does not contradict common descent; it’s a statistical coin flip.

    3. In posts #38, #39 and #42 you do not address my explanation.

    4. In post #125, you accuse me of running away. You posted 8 links, I addressed one of them. But instead of responding to my rebuttal, you just say “well, what about this one?”

    Also in the Opossum thread:

    1. At post #74, you posted a video of yours that made mention of some of Jeff Tomkins work.

    2. I responded at post #112, pointing you towards two of my recent posts addressing Tomkins’ work.

    3. In post #113, you feigned insult, and did not address the content of my posts.

    In this current thread:

    1. In posts #64 and #66 you post several links regarding proteins, one of which was Jeff Tomkins’ article about orphan genes.

    2. In post #68, Vincent points out a post of mine that I had coincidentally finished the night before addressing that very article.

    3. In post #69 you seem to imply that these 634 human-specific genes are protein-coding genes while the DNA matches in the chimpanzee genome are not protein-coding (“you do know those sequences are not protein coding don’t you?”)

    4. In post #119 I ask whether that is indeed your belief (which you have yet to confirm, by the way) and point out that only ONE of these genes is confirmed as protein-coding (while five others are possible).

    5. In post #121 you emphasise a paragraph saying that 20 new human proteins were detected.

    6. In post #123 I explain why this is incorrect, and ask you to confirm the number of protein-coding genes that are human-specific.

    7. In post #125 you refuse to answer a simple question, and instead accuse me of being a troll.

    You’re not fooling anyone – the record is there for everyone to see.

  176. 176
    Mung says:

    wd400:

    If they can be ordered they have to be one the same chromosome, no?

    I’m asking if you have evidence to support this assertion that does not beg the question.

    Stuff can be ordered therefore they are on the same chromosome.
    They are on the same chromosome because they can be ordered.
    If they could not be ordered, they would not be on the same chromosome.
    Therefore, synteny.

    Make an argument for synteny that does not beg the question. That’s all I’m asking for.

  177. 177
    bornagain77 says:

    ThickPython, rest assured, you are a atheistic troll who is not dealing with the evidence forthrightly. It is NOT an accusation but a fact. I certainly stand by my posts and, as you say, the record is there for all to see.

    for instance, here is a repost of the video you did not watch that goes through a paper that refuted your position on ORFans, which you will not ever honestly admit

    Python, in case you ever decide to be honest towards the evidence instead of playing ‘gotcha’ games (which would be a miracle in its own right), and for the unbiased readers who are interested in a closer look, Paul Giem has a video on one of the ORFan papers that falsified the Darwinian position

    New Genes Are Essential 6-13-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6qgGPV1AO1E

    Darwinian explanations for essential ORFan genes are un-parsimonious to put it mildly

    Can new genes arise from junk DNA? – August 24, 2015
    Excerpt: Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said.
    BA77: Moreover, the essential genes were somehow incorporated into the ‘bicycle’ while the bicycle was being peddled, i.e. while the cell was busy being alive.
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....ent-577484

    This entire episode with ORFans has highlighted the unfalsifiable nature of Darwinian Theory as a science. No matter how contrary a finding is to Darwinian explanations, that finding is simply never really allowed a real chance to falsify Darwinian theory. The contrary finding is simply ‘explained away’ with another ‘epicycle’ (Lakatos & Hunter).

    As Dr. Hunter would say, when it comes to Darwinian evolution, ‘religion drives science and it matters’!

  178. 178
    Mung says:

    ThickPython:

    I don’t care for an argument about semantics – my comment was clear enough in the first place.

    Sadly, your “argument” depends on the semantics. So, “semantically speaking,” I am correct.

  179. 179
    bornagain77 says:

    Darwin’s (Failed Predictions) – Similar species share similar genes – Cornelius Hunter PhD.
    Excerpt: As much as a third of the genes in a given species may be unique, and even different variants within the same species have large numbers of genes unique to each variant. Different variants of the Escherichia coli bacteria, for instance, each have hundreds of unique genes. (Daubin and Ochman)

    Significant genetic differences were also found between different fruit fly species. Thousands of genes showed up missing in many of the species, and some genes showed up in only a single species. (Levine et. al.) As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” (Le Page) These novel genes must have evolved over a few million years, a time period previously considered to allow only for minor genetic changes. (Begun et. al.; Chen et. al., 2007)

    Initially some evolutionists thought these surprising results would be resolved when more genomes were analyzed. They predicted that similar copies of these genes would be found in other species. But instead each new genome has revealed yet more novel genes. (Curtis et. al.; Marsden et. al.; Pilcher)

    Next evolutionists thought that these rapidly-evolving unique genes must not code for functional or important proteins. But again, many of the unique proteins were in fact found to play essential roles. (Chen, Zhang and Long 1010; Daubin and Ochman; Pilcher) As one researcher explained, “This goes against the textbooks, which say the genes encoding essential functions were created in ancient times.” (Pilcher)
    https://sites.google.com/site/darwinspredictions/similar-species-share-similar-genes

  180. 180
    wd400 says:

    Mung,

    What do you think “beg the question” means? What do you think synteny means?

    It’s not possibly for genes to be in synteny (order sense) and not on the same chromosome. So if you establish they are are in synteny you establish they are on the same chromosome.

  181. 181
    bornagain77 says:

    mung:

    “Sadly, your “argument” depends on the semantics. So, “semantically speaking,” I am correct.”

    Touche
    http://vignette1.wikia.nocooki.....0423114652

  182. 182
    Mung says:

    wd400:

    It’s not possibly for genes to be in synteny (order sense) and not on the same chromosome. So if you establish they are are in synteny you establish they are on the same chromosome.

    So what is the “broader definition” of synteny that ThickPython appeals to?

    It’s not possibly for genes to be in synteny (order sense) and not on the same chromosome. So if you establish they are are in synteny you establish they are on the same chromosome.

    So if you establish that they are on the same chromosome you establish that they are on the same chromosome, because it’s not possible for genes to be in synteny (order sense) and not on the same chromosome. Which begs the question.

    It’s not possibly for genes to be in synteny (order sense) and not on the same chromosome.

    Why is it not possible?

    Because by definition…

    Which begs the question.

    How do you know the genes are on the same chromosome?

  183. 183
    Mung says:

    It seems to be a matter of substantial importance that the genes under question can be shown to be on the same chromosome. Why is that a matter of such importance?

  184. 184
    wd400 says:

    I hope this is some sort of elaborate troll, but in case it’s not: genes can only be said to have an order reletive to each other if they are on the same chromosome. In what sense could a gene on the X be between one on chromosomes 2 and 5? Now read what you said in 168…

  185. 185
    ThickPython says:

    @Bornagain77, #177:

    for instance, here is a repost of the video you did not watch that goes through a paper that refuted your position on ORFans, which you will not ever honestly admit

    Please tell me what my “position” is on ORFans, because I don’t recall putting my “position” out there.

    What I do recall, is responding to a claim you have made – via Jeff Tomkins – that there are “634 human-specific genes” that have “no evolutionary history” and are “completely different between humans and chimpanzees”. My results show that these genes have corresponding sequence in the chimpanzee genome with at least 95% similarity.

    So you can either engage with that, or call me a troll. Entirely up to you.

    Maybe you’d like to suggest that 95% still qualifies as “completely different”? Maybe you’d like to suggest that my result is just plain wrong, and Tomkins is right? Maybe you can show some integrity and withdraw your endorsement of the article?

    But no, you want me to watch an hour-long video that supposedly refutes a position I haven’t stated. And let’s say I went ahead and watched it. Then what? You’ll ignore my response again?

    For someone that has posted roughly half of the content in this thread, you have surprisingly little substance behind it. Consider yourself on “Ignore” until you have the courage to address direct responses to your claims.

  186. 186
    ThickPython says:

    @Mung, #182:

    So what is the “broader definition” of synteny that ThickPython appeals to?

    It’s the second definition in that first paragraph on Wikipedia:

    Today, however, biologists usually refer to synteny as the conservation of blocks of order within two sets of chromosomes that are being compared with each other.

    while yours refers to the first definition:

    synteny describes the physical co-localization of genetic loci on the same chromosome within an individual or species

    My definition refers to just “two sets of chromosomes that are being compared with each other”. Your definition applies to only one individual or species; your definition is a vague measure of recombination during meiosis.

    You’ll notice that your definition uses the phrase “same chromosome” while mine does not.

    This is why you’re getting into this circular argument.

    I feel dirty for even having to explain this.

  187. 187
    bornagain77 says:

    Python,

    “Please tell me what my “position” is on ORFans, because I don’t recall putting my “position” out there.”

    Sorry, besides a troll, I thought you were a Darwinist. My mistake, you are only a troll.

  188. 188
    Querius says:

    Dr JDD,

    I think this is why many of us here feel like we are banging our heads against the wall. HeKs, PaV, Querius, others. We sound like broken records – pseudogenes, feathers, simulating evolution on bacteria, software code analogies. But why do we sound like broken records? Because no one is taking these discussions and arguments presented to them seriously. They just skirt the issue and defer to the mainstream position that “it [CD] is all proven anyway”.

    Yes, exactly.

    The debate seems to be so much fun that science gets trampled in the process.

    – Why create an experiment using proportionally increased levels of ionizing radiation on rapidly reproducing populations of bacteria, when one can huff and puff over circumstantial interpretations like cranky old philosophers.

    – Why think of new possibilities and perspectives, when one can enslave data fragments to nail into arguments to prop up a rotten old 19th century speculation.

    If physics took the same route, we’d be arguing vehemently about Newtonian mechanics, ignoring all outlying evidence.

    Not only is it not science, it’s . . . boring.

    -Q

  189. 189
    bornagain77 says:

    Querius, although I like your point very much, please don’t sully Newtonian mechanics with Darwinian evolution. Although Newtonian mechanics was only an approximation, it was at least good enough to get us to the moon. There is nothing comparable to that stunning success for man in the pseudo-science of Darwinian evolution.

    “Truth be told, evolution hasn’t yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn’t evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of ‘like begets like’. Even now, as its practitioners admit, the field of quantitative genetics has been of little value in helping improve varieties. Future advances will almost certainly come from transgenics, which is not based on evolution at all.”
    (Jerry Coyne, “Selling Darwin: Does it matter whether evolution has any commercial applications?,” reviewing The Evolving World: Evolution in Everyday Life by David P. Mindell, in Nature, 442:983-984 (August 31, 2006).)

    “In fact, over the last 100 years, almost all of biology has proceeded independent of evolution, except evolutionary biology itself. Molecular biology, biochemistry, and physiology, have not taken evolution into account at all.”
    Marc Kirschner, Boston Globe, Oct. 23, 2005

    “While the great majority of biologists would probably agree with Theodosius Dobzhansky’s dictum that “Nothing in biology makes sense except in the light of evolution”, most can conduct their work quite happily without particular reference to evolutionary ideas. Evolution would appear to be the indispensable unifying idea and, at the same time, a highly superflous one.”
    A.S. Wilkins, editor of the journal BioEssays, Introduction to “Evolutionary Processes” – (2000).

    NASA website
    Excerpt: The motion of a rocket from the surface of the Earth to a landing on the Moon can be explained and described by physical principals discovered over 300 years ago by Sir Isaac Newton. Newton worked in many areas of mathematics and physics. He developed the theories of gravitation in 1666, when he was only 23 years old. Some twenty years later, in 1686, he presented his three laws of motion in the “Principia Mathematica Philosophiae Naturalis.” The laws are shown above, and the application of these laws to rockets is given on separate slides.
    https://spaceflightsystems.grc.nasa.gov/education/rocket/newton.html

    This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent and powerful Being.,,,
    This Being governs all things, not as the soul of the world, but as Lord over all; and on account of his dominion he is wont to be called Lord God pantokrator, or Universal Ruler;,,, The Supreme God is a Being eternal, infinite, absolutely perfect;,,, from his true dominion it follows that the true God is a living, intelligent, and powerful Being; and, from his other perfections, that he is supreme, or most perfect. He is eternal and infinite, omnipotent and omniscient; that is, his duration reaches from eternity to eternity; his presence from infinity to infinity; he governs all things, and knows all things that are or can be done. He is not eternity or infinity, but eternal and infinite; he is not duration or space, but he endures and is present. He endures for ever, and is every where present:
    Sir Isaac Newton – Quoted from what many consider the greatest science masterpiece of all time, his book “Principia”

    NEWTON’S REJECTION OF THE “NEWTONIAN WORLD VIEW”: THE ROLE OF DIVINE WILL IN NEWTON’S NATURAL PHILOSOPHY
    Abstract: The significance of Isaac Newton for the history of Christianity and science is undeniable: his professional work culminated the Scientific Revolution that saw the birth of modern science, while his private writings evidence a lifelong interest in the relationship between God and the world. Yet the typical picture of Newton as a paragon of Enlightenment deism, endorsing the idea of a remote divine clockmaker and the separation of science from religion, is badly mistaken. In fact Newton rejected both the clockwork metaphor itself and the cold mechanical universe upon which it is based. His conception of the world reflects rather a deep commitment to the constant activity of the divine will, unencumbered by the “rational” restrictions that Descartes and Leibniz placed on God, the very sorts of restrictions that later appealed to the deists of the 18th century.
    http://home.messiah.edu/~tdavis/newton.htm

  190. 190
    Eric Anderson says:

    Ans where in the corvette is this plan stored PaV?

    The plan is stored in the blueprints, the schematics, the engineering diagrams. Implemented with sensors, feedbacks, production machines, assembly processes, manufacturing facilities.

    Those things are required for any complex functionally-integrated system. And in the case of a self-reproducing organism they must, by neo-Darwinian logic, be contained in the DNA.

    So where are they?

    We cannot say, we must not say, if we are to have any intellectual integrity or if we are to propose a theory that has a chance of mapping to the real world — we must not say that such things don’t matter, that the rest of the stuff we don’t yet understand (constituting the majority of the storage system) is just junk, that things simply come together by dint of some chemical interaction in the environment.

    A moment’s reflection about what is required to actually build such a system in the real world should be sufficient to convince any objective observer that much, much more is required than a few sequences for a few proteins contained in a small portion of one part of the organism is sufficient to explain it all.

  191. 191
    Querius says:

    Point taken, bornagain77.

    Discovery and progress in science is not achieved by self-congratulatory confirmation of what seems to agree with a theory, but rather the observing and investigating of precisely what doesn’t agree.

    With Darwinism, such observing and subsequent investigating is not tolerated.

    -Q

  192. 192
    Origenes says:

    WD400,

    Since the 1980s, developmental and cell biologists such as Brian Goodwin, Wallace Arthur, Stuart Newman, Fred Nijhout, and Harold Franklin have discovered or analyzed many sources of epigenetic information.
    Even molecular biologists such as Sidney Brenner, who pioneered the idea that genetic programs direct animal development, now insist that the information needed to code for complex biological systems vastly outstrips the information in DNA.
    DNA helps direct protein synthesis. Parts of the DNA molecule also help to regulate the timing and expression of genetic information and the synthesis of various proteins within cells. Yet once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures. Genes and proteins are made from simple building blocks—nucleotide bases and amino acids, respectively—arranged in specific ways. Similarly, distinctive cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet the properties of individual proteins do not fully determine the organization of these higher-level structures and patterns. Other sources of information must help arrange individual proteins into systems of proteins, systems of proteins into distinctive cell types, cell types into tissues, and different tissues into organs. And different organs and tissues must be arranged to form body plans.

    [S.Meyer, ‘Darwin’s Doubt’, Ch.14]

    The hierarchical layering or arrangement of different sources of information.

    WD400: If it is not clear enough, there is no over-arching “plan” in the genome. There are genes, that have regulatory elements, which produce gene produces respond to environments and influence other genes and so on and so on.

    This neo-darwinistic concept boils down to circular reasoning and therefor fails to make sense. Regulatory capacity is assigned to a level which is itself in need of regulation.

    Again Stephen Meyer:

    Note that the information necessary to build the lower-level electronic components does not determine the arrangement of those components on the circuit board or the arrangement of the circuit board and the other parts necessary to make a computer. That requires additional informational inputs.

    Two analogies may help clarify the point. At a construction site, builders will make use of many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood. Similarly, electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But such lower-level components do not determine their own arrangement in an integrated circuit (see Fig. 14.2).
    In a similar way, DNA does not by itself direct how individual proteins are assembled into these larger systems or structures—cell types, tissues, organs, and body plans—during animal development. Instead, the three-dimensional structure or spatial architecture of embryonic cells plays important roles in determining body-plan formation during embryogenesis. Developmental biologists have identified several sources of epigenetic information in these cells.

    [S.Meyer, ‘Darwin’s Doubt’, Ch.14]

  193. 193
    bornagain77 says:

    Excellent quotes Origenes:

    They are going right below this video:

    Functional Proteins and Information for Body Plans – Stephen Meyer – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1140536289292636/?type=2&theater

  194. 194
    wd400 says:

    Don’t suppose Meyer gives any examples? The “three-dimensional structure or spatial architecture” of cells in determined in part by cytoskeletal proteins. But these are gene products themselves, and their growth and structure is regulated by others. A new embryo inherits cytosol from the egg, but again these structures are the result of genetic programs in the mother.

  195. 195
    bornagain77 says:

    a few notes undermining the central dogma

    In Embryo Development, Non-DNA Information Is at Least as Important as DNA – Jonathan Wells – May 2012
    Excerpt: Evidence shows that non-DNA developmental information can be inherited in several ways. For example, it can be inherited through chromatin modifications, which affect gene expression without altering underlying DNA sequences. Another example is cytoplasmic inheritance, which involves cytoskeletal patterns and localization of intracellular molecules. Still another example is cortical inheritance, which involves membrane patterns.
    http://www.evolutionnews.org/2.....60031.html

    Peer-Reviewed Paper: Development Needs Ontogenetic Information that Cannot Arise from Neo-Darwinian Mechanisms – Casey Luskin – June 2, 2014
    Excerpt: Jonathan Wells has published a new peer-reviewed scientific paper in the journal BIO-Complexity, “Membrane Patterns Carry Ontogenetic Information That Is Specified Independently of DNA.” With over 400 citations to the technical literature, this well-researched and well-documented article shows that embryogenesis depends on crucial sources of information that exist outside of the DNA.
    This ontogenetic information guides the development of an organism, but because it is derived from sources outside of the DNA, it cannot be produced by mutations in DNA. Wells concludes that because the neo-Darwinian model of evolution claims that variation is produced by DNA mutations, neo-Darwinism cannot account for the origin of epigenetic and ontogenetic information that exists outside of DNA. (Read more here:)
    http://www.evolutionnews.org/2.....86201.html

    Not Junk After All—Conclusion – August 29, 2013
    Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]
    http://www.uncommondescent.com.....onclusion/

    “Live memory” of the cell, the other hereditary memory of living systems – 2005
    Excerpt: To understand this notion of “live memory”, its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of “live memory” in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.
    http://www.ncbi.nlm.nih.gov/pubmed/15888340

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common.
    I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism.
    http://www.evolutionnews.org/2.....93851.html

    If DNA really rules (morphology), why did THIS happen? – April 2014
    Excerpt: Researchers implanted human embryonic neuronal cells into a mouse embryo. Mouse and human neurons have distinct morphologies (shapes). Because the human neurons feature human DNA, they should be easy to identify.
    Which raises a question: Would the human neurons implanted in developing mouse brain have a mouse or a human morphology?
    Well, the answer is, the human neurons had a mouse morphology. They could be distinguished from the mouse ones only by their human genetic markers.
    If DNA really ruled, we would expect a human morphology.
    http://www.uncommondescent.com.....is-happen/

    That DNA is not the be all, end all, explanation, when it comes to memory in the cell, is also clearly illustrated here:

    Extreme Genome Repair – 2009
    Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.,,,
    http://www.ncbi.nlm.nih.gov/pm.....MC3319128/

    In the lab, scientists coax E. coli to resist radiation damage – March 17, 2014
    Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. “We blasted the cultures until 99 percent of the bacteria were dead. Then we’d grow up the survivors and blast them again. We did that twenty times,” explains Cox.
    The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human.
    http://www.news.wisc.edu/22641

  196. 196
    Origenes says:

    WD400 @194,

    CYTOSKELETAL ARRAYS

    Eukaryotic cells have internal skeletons to give them shape and stability. These “cytoskeletons” are made of several different kinds of filaments including those called the “microtubules.” The structure and location of the microtubules in the cytoskeleton influence the patterning and development of embryos. Microtubule “arrays” within embryonic cells help to distribute essential proteins used during development to specific locations in these cells. Once delivered, these proteins perform functions critical to development, but they can only do so if they are delivered to their correct locations with the help of preexisting, precisely structured microtubule or cytoskeletal arrays (see Fig. 14.3). Thus, the precise arrangement of microtubules in the cytoskeleton constitutes a form of critical structural information.
    These microtubule arrays are made of proteins called tubulin, which are gene products. Nevertheless, like bricks that can be used to assemble many different structures, the tubulin proteins in the cell’s microtubules are identical to one another. Thus, neither the tubulin subunits, nor the genes that produce them, account for the differences in the shape of the microtubule arrays that distinguish different kinds of embryos and developmental pathways. Instead, the structure of the microtubule array itself is, once again, determined by the location and arrangement of its subunits, not the properties of the subunits themselves. Jonathan Wells explains it this way: “What matters in [embryological] development is the shape and location of microtubule arrays, and the shape and location of a microtubule array is not determined by its units.”14 For this reason, as University of Colorado cell biologist Franklin Harold notes, it is impossible to predict the structure of the cytoskeleton of the cell from the characteristics of the protein constituents that form that structure.
    Another cell structure influences the arrangement of the microtubule arrays and thus the precise structures they form and the functions they perform. In an animal cell, that structure is called the centrosome (literally, “central body”), a microscopic organelle that sits next to the nucleus between cell divisions in an undividing cell. Emanating from the centrosome is the microtubule array that gives a cell its three-dimensional shape and provides internal tracks for the directed transport of organelles and essential molecules to and from the nucleus.16 During cell division the centrosome duplicates itself. The two centrosomes form the poles of the cell-division apparatus, and each daughter cell inherits one of the centrosomes; yet the centrosome contains no DNA.17 Though centrosomes are made of proteins—gene products—the centrosome structure is not determined by genes alone.

    [S.Meyer, ‘Darwin’s Doubt’, Ch.14]

  197. 197
    wd400 says:

    So, no specific examples then?

    Meyer is saying that subunits of these structures don’t , in and of themselves, specify the larger structure. That’s true. But he doesn’t mention what does regualate this structure, which is other gene products.

  198. 198
    Origenes says:

    WD400: Meyer is saying that subunits of these structures don’t , in and of themselves, specify the larger structure. That’s true.

    That’s an important admission on your part. Does this spell the end of your gene-centric view?

    WD400: But he doesn’t mention what does regualate this structure, which is other gene products.

    Did you read the part about the centrosome? It is another cell structure not determined by genes alone that “influences” — not ‘regulates’ (!) — “the arrangement of the microtubule arrays and thus the precise structures they form and the functions they perform.”

    What kind of specific examples do you have in mind?


    p.s. Meyer discusses several other sources of epigenetic information, such as membrane patterns, membrane targets, ion channels, electromagnetic fields and the sugar code. For each one of them he provides arguments as to why they are not produced by DNA.

  199. 199
    Eric Anderson says:

    . . . but again these structures are the result of genetic programs in the mother.

    What do you mean by genetic “programs”? Just having a bare DNA sequence that can be translated to a particular gene product isn’t adequate. What happens to that gene product once it is produced? Where does it go in the cell? How is it utilized and integrated into larger structures? When has the cell produced enough and how is the production terminated? When is the gene product’s use complete and the gene product broken down?

    All of those aspects, and many more, are needed as part of the program that produces a functional cell. So, again, where is that “genetic program” stored? Not in the raw sequence for the gene product. Just having a bunch of gene products* floating around is not adequate. So where is the program?

    —–

    * And all this is ignoring the fact that even having a DNA sequence does not necessarily result in a particular gene product. Even getting functional gene products requires a program. It does not just all happen by dint of raw chemistry.

  200. 200
    wd400 says:

    Origenes,

    I’ve never claimed that a protein by itself contains the information for a compelx or a specific polymer. Only that these larger structures are themselves the result of other genes and their reaction.

    I read the bit about the centrosome — Meyer claims that structure is no encoded in genes but doesn’t support that claim.

    EA,

    Why don’t you find out for yourself? You could spend a lifetime answering these questions in detail, but they are also all part of any intro to bio course or text. You’ll see these processes are the results of chemical reactions managed by gene products, the expression of which is managed by other genes.

  201. 201
    PaV says:

    wd400:

    Ans where in the corvette is this plan stored PaV?

    The plan is stored in some building at the GM complex.

    The “plan” for organisms is stored in the mind of the Designer.

    But just as one can infer a plan from how the Corvette is constructed, so, too, can we infer a “plan” in the case of the organisms.

    In the case of a Corvette, it’s easy to reconstruct the “plan.” In the case of organisms, however, we don’t know enough to be able to “reconstruct” it. Or, as Bill Gates is quoted as saying: “DNA is like a computer program but far, far more advanced than any software ever created.”

    The problem here is trying to explain quantum mechanics to a five-year-old. Maybe when it’s older (us, as a civilization), it will understand the “plan.” But even a five-year-old can figure out that a Corvette is not a rock. Unless, of course, he chooses to be obtuse.

  202. 202
    PaV says:

    wd400:

    Why this insistence on a “gene-centric” view, other than orthodoxy?

    It is becoming increasingly clear that more and more ncRNA has function. Will you now call ncRNA a “gene”? Is Darwinism this subtle?

  203. 203
    Origenes says:

    WD400: … these processes are the results of chemical reactions managed by gene products, the expression of which is managed by other genes.

    Your view on biology doesn’t make any sense to me. Zero, zip, zilch, nada. To be frank, I cannot even imagine what it is like to hold such a view and experience any explanatory power. To me, it boils down to “all sorts of things influence each other”.

    Everyone knows this, but it does not constitute an explanation.

    It is as if you throw in terms like “regulate” “manage” “program” “control” for no reason whatsoever.

    When regulators are in turn regulated, what do we mean by “regulate” — and where within the web of regulation can we single out a master controller capable of dictating cellular fates? And if we can’t, what are reputable scientists doing when they claim to have identified such a controller, or, rather, various such controllers? If they really mean something like “influencers,” then that’s fine. But influence is not about mechanism and control; the things at issue just don’t have controlling powers. What we see, rather, is a continual mutual adaptation, interaction, and coordination that occurs from above.
    [Talbott]

  204. 204
    Eric Anderson says:

    wd400:

    Even setting aside the fact that DNA often does not map directly to RNA, which sometimes does not map directly to amino acids, which often do not fold directly into the correct form needed for function in the cell. And even setting aside that at each of these states there are contingent possibilities — meaning there are sensors, feedbacks, controls, switches, and the like that determine which contingent option will result and, therefore, the process from DNA to functional gene product is not just a matter of chemical reactions.

    Even setting all this aside, we note that your chemical reactions are managed by gene products.

    What is that word “managing” doing in there? What is doing the managing? That is part of the “program” that is at issue.

    You can’t just put a bunch of parts in a bag or in an aqueous solution and have them self-assemble into a functional whole. People get confused with biology because they note (correctly so) that certain molecules can react spontaneously with each other. Unfortunately, they then extend that simplistic observation to the unsupportable claim that the whole organism is just a series of natural reactions occurring purely by dint of chemistry. They imagine, in essence, that with biology, you can just put the parts in a solution and, amazingly, an organism will result. Thus, we keep hearing evolutionists try to protect their theory from analysis by arguing that we cannot apply basic principles from our experience, that normal engineering constraints can be disregarded, that “biology is counter-intuitive,” that “biology is different.”

    This is a tempting thought. At a very simplistic and superficial level it almost even seems believable.

    That is until we start to dig a bit deeper and realize that so much of what happens in the cell is, as you say, “managed.”

    Just because some chemical reactions occur between molecules in solution does not mean they will automatically result in a functional organism any more than shaking a bag full of magnets and steel parts will result in a functional machine. Indeed, default, spontaneous chemical reactions are often anathema to what needs to happen for a living cell. The cell often has to actively fight against spontaneous reactions that would otherwise occur. The problem of interfering cross reactions in biology is huge, and is something that has to be carefully and specifically “managed.”

    The information to do all this managing must be there somewhere. The program has to exist. It does not exist in the parts themselves. It does not exist in the principles of chemistry. Where is it?

    Almost every aspect of an organism is contingent. If we consider even the most mundane of physical features it becomes clear that chemistry isn’t the answer. What determines where a body part will grow, how long it will grow, what precise shape it will have, and so on? In every case it could be different than it is, so chemistry cannot be the answer.

    And to say, “well it is managed by other gene products” isn’t helpful either. What makes them manage it thusly, instead of some other way? Where did they get the ability to manage the process? Further, how did the managers get put together, and what managed that process?

    It makes no more sense to say that when we are dealing with chemicals in solution we don’t need a program because everything happens by chemical reactions, than to claim that when we are dealing with processes in silicon we don’t need a program because everything happens by electrical impulses.

  205. 205
    Eric Anderson says:

    Origenes @203:

    Unfortunately, we are dealing with an intellectual mistake at the most basic level, so I’m not sure how much any efforts to discuss it will help, although you have made a valiant effort.

    Some people seem to think that because biology utilizes chemistry in its operation, that biology can be fully explained by chemistry. This is of course nonsense. It is just as silly as asserting that because airplanes utilize the principles of gravity and aerodynamics in their operation, that gravity and aerodynamics somehow explain the operation and very existence of airplanes.

    The fact that a pre-existing, specifically-constructed machine performs a specific function in the presence of a specific molecule does not mean that everything just happens by chemistry, that there is no program, that there is no plan, that the parts themselves are all that matters. Remarkably, some people, however, seem to think so.

    I really think the disconnect occurs because we are dealing with chemical reactions. As I said @204, it is very tempting for someone to think that just because certain molecules will tend to react in solution, that this is the only thing going on. And if they look at it in an incredibly superficial and naive way — focusing only on one particular reaction and assuming all the machinery is already in place — then it becomes tempting to view biology as just a long series of automatic chemical reactions.

    But if we take even a modest intellectual effort to step back, see the broader organism or cell, ask some basic questions about the source of the machinery already in place, the steps that would be required to put that machinery in place, the information needed to operate the system, it quickly becomes clear that the “biology-is-just-chemistry” viewpoint is utterly and completely wrong.

    Somehow we have to help people cross the intellectual bridge from a myopic, blinders-on view of a single reaction in a pre-existing system, to a more complete, engineering-level view of the overall cell or organism. I’m not sure how to best convey that. And unfortunately it may be that some people will hear and see, but still refuse to understand.

  206. 206
    wd400 says:

    Pav,

    Non coding genes are genes, of course.

    Origines and EA,

    All I can say (again) is I think you should study some biology before you commit to this neovitalism out whatever it is you are imagining. If you want to know how a limb develops the consider the effects of Shh etc. If you don’t think chemicals can regulate others check out the lac operon. Nuclear import is an example of proteins getting to where they need to be. None of these require anything but chemistry.

    Genes interact with each other, of course, and the wider environment too. So i don’t know why you think understanding the generic underpinnings of biology prevents higher-level approaches

  207. 207
    PaV says:

    wd400:

    Pav,

    Non coding genes are genes, of course.

    And this is the kind of equivocation that we see in Darwinists time and time again.

    Everything MUST fit the narrative; so redefine things until some semblance of the narrative working is restored.

    There’s a word for this: unfalsifiability!

    First, the proof that there is no “Designer” is that most of DNA is “junk.” Then when a function is found for the supposed “junk” DNA, then it’s: “We knew it all along.” Then, when ncDNA, which is essentially forms of RNA, i.e., transcribed, but not translated, then we call these “genes.”

    Reasonable people subscribe to an “all-powerful” God. Darwinists subscribe to an “all-powerful” Narrative. Why don’t you get out of the way of true science.?

  208. 208
    Eric Anderson says:

    Incidentally, this thread may have uncovered at least one aspect of the simplistic thinking that leads a person to believe that most DNA is junk.

    After all, the thinking goes, all we need to do is specify some parts in the DNA and the machine will build itself all by chemistry. It’s easy! No plan needed. No program required. Just specify some gene products and we’re done. Everything else is probably just junk.

    Amazing what chemistry can do.

  209. 209
    wd400 says:

    There are very good positive arguments for junk DNA that have been presented here many times. That people continue to say things as ignorant as the last two comments really says something.

  210. 210
    bornagain77 says:

    Perhaps wd400, before he proclaims (once again) his usual shtick that we really don’t understand evolution, should humble himself and realize that he is not even operating on the proper scientific framework for understanding biology in the first place?

    There is a paradigm shift currently happening in biology, and this shift certainly does not bode well for the reductive materialistic framework that undergirds Darwinian thought

    Jim Al-Khalili, at the 2:30 minute mark of the following video, states,
    “,,and Physicists and Chemists have had a long time to try and get use to it (Quantum Mechanics). Biologists, on the other hand have got off lightly in my view. They are very happy with their balls and sticks models of molecules. The balls are the atoms. The sticks are the bonds between the atoms. And when they can’t build them physically in the lab nowadays they have very powerful computers that will simulate a huge molecule.,, It doesn’t really require much in the way of quantum mechanics in the way to explain it.”
    At the 6:52 minute mark of the video, Jim Al-Khalili goes on to state:
    “To paraphrase, (Erwin Schrödinger in his book “What Is Life”), he says at the molecular level living organisms have a certain order. A structure to them that’s very different from the random thermodynamic jostling of atoms and molecules in inanimate matter of the same complexity. In fact, living matter seems to behave in its order and its structure just like inanimate cooled down to near absolute zero. Where quantum effects play a very important role. There is something special about the structure, about the order, inside a living cell. So Schrodinger speculated that maybe quantum mechanics plays a role in life”.
    Jim Al-Khalili – Quantum biology – video
    https://www.youtube.com/watch?v=zOzCkeTPR3Q

    Does DNA Have Telepathic Properties?-A Galaxy Insight – 2009
    Excerpt: DNA has been found to have a bizarre ability to put itself together, even at a distance, when according to known science it shouldn’t be able to.,,, The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
    http://www.dailygalaxy.com/my_.....ave-t.html

    Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it)
    https://youtu.be/2nqHOnVTxJE?t=1176

    (“Delocalized” Quantum) Sound-like bubbles whizzing around in DNA essential to life – Jun 1, 2016
    Excerpt: new research in the UK has detected sound-like bubbles in DNA that is essential to life and which will change the fundamental understanding of biochemical reactions inside a cell.
    The research,,, describes how double-stranded DNA splits using delocalized sound waves that are the hallmark of quantum effects.,,,
    Dedicated enzymes responsible for making new proteins read the code by splitting the double strand in order to access the information.
    One of the big outstanding questions of biology has been how these enzymes find the initial hole or “bubble” in the double strand to start reading the code.,,,
    researcher Gopakumar Ramakrishnan said: “It had been proposed by theoreticians that such DNA bubbles might behave like sound waves, bouncing around in DNA like echoes in a cathedral. However, the current paradigm in biology is that such sound-like dynamics are irrelevant to biological function, as interaction of a biomolecule with the surrounding water will almost certainly destroy any of these effects.”,,,
    Researchers in the Ultrafast Chemical Physics group carried out experiments with a laser that produces femtosecond laser pulses about a trillion times shorter than a camera flash.
    This allowed them to succeed in the detection of sound-like bubbles in DNA. They could show that these bubbles whiz around like bullets in a shooting gallery even in an environment very similar to that which can be found in a living cell.
    Thomas Harwood said, a researcher said: “The sound waves in DNA are not your ordinary sound waves. They have a frequency of a few terahertz or a billion times higher than a human or a dog can hear!”
    Professor Klaas Wynne, leader of the research team and Chair in Chemical Physics at the University of Glasgow, said, “The terahertz sound-like bubbles we have seen alter our fundamental understanding of biochemical reactions. There were earlier suggestions for a role of delocalized quantum phenomena in light harvesting, magneto reception, and olfaction.”
    The new results now imply a much more general role for sound-like delocalized phenomena in biomolecular processes.
    http://timesofindia.indiatimes.....539817.cms

    Molecular Biology – 19th Century Materialism meets 21st Century Quantum Mechanics – video
    https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1141908409155424/?type=2&theater

  211. 211
    Querius says:

    Eric Anderson, Origenes, PaV, bornagain77 . . .

    Some really excellent points! To which wd400 responds:

    All I can say (again) is I think you should study some biology before you commit to this neovitalism out whatever it is you are imagining.

    That people continue to say things as ignorant as the last two comments really says something.

    Do realize that wd400, by resorting to these personal attacks, has abandoned his arguments, and has conceded the point.

    -Q

  212. 212
    Eric Anderson says:

    wd400:

    All I can say (again) is I think you should study some biology before you commit to this neovitalism [or] whatever it is you are imagining.

    Neovitalism? The only thing I’m committing to is logic and systems engineering. You seem to be the one who thinks molecules can just come together by dint of chemistry and, through some utterly unexplainable magic of chemistry, become a living organism.

    If you want to know how a limb develops the consider the effects of Shh etc.

    There are lots of things that affect limb development. Again, you are conflating the necessary for the sufficient. There isn’t anything inherent in chemistry that tells your body it should have two arms or ten fingers, instead of three arms or eight fingers. It simply is not in the chemistry. And it isn’t in the gene products either. So where is it?

    If you don’t think chemicals can regulate others check out the lac operon. Nuclear import is an example of proteins getting to where they need to be. None of these require anything but chemistry.

    Why would you say I don’t think chemicals can regulate others? Of course they can. But you miss the larger perspective. Again, you focus on a single chemical operation, within a pre-existing, functioning cell, that was put together in a highly specified way, with sensors and feedbacks and controls, and you say, “Gee, molecule X performed function Y according to the rules of chemistry. So that must be all that is needed – just chemistry!” Why don’t you take all the individual molecules in a cell — shoot, even all of your gene products, nicely transcribed, translated and folded — put them in a solution and see whether a functional cell results. Then we’ll see whether your chemistry is sufficient to build an organism out of the parts. Hint: it isn’t.

    So i don’t know why you think understanding the generic underpinnings of biology prevents higher-level approaches.

    I don’t think understanding the genetic underpinnings of biology prevents anything. The problem is not understanding genetics, and we all want more understanding of genetics.

    The problem is thinking that the parts explain the whole, that everything just comes together by force of chemistry, when it clearly does not. The problem is the entire bottom-up, molecules-to-man paradigm that naively assumes all we need are some gene products and then chemistry will take over and do the rest. The problem is the complete failure to recognize that chemistry is necessary, but not sufficient; that contingent possibilities are being realized via higher-level controls; that simply having a sequence of nucleotides for gene products does not guarantee an organism.

  213. 213
    Origenes says:

    Eric Anderson:

    Incidentally, this thread may have uncovered at least one aspect of the simplistic thinking that leads a person to believe that most DNA is junk.

    After all, the thinking goes, all we need to do is specify some parts in the DNA and the machine will build itself all by chemistry. It’s easy! No plan needed. No program required. Just specify some gene products and we’re done. Everything else is probably just junk.

    Amazing what chemistry can do.

    Stephen Meyer:

    Neo-Darwinists have assumed that genes possess all the information necessary to specify the form of an animal. They have also assumed that mutations in genes will suffice to generate the new information necessary to build a new form of animal life.9 Yet if biologists understand organismal form as resulting from constraints on the possible arrangements of matter at many levels in the biological hierarchy—from genes and proteins, to cell types and tissues, to organs and body plans—then biological organisms may well exhibit many levels of information-rich structure. Discoveries in developmental biology have confirmed this possibility.

    … As Müller and Newman explain in their introduction, “Detailed information at the level of the gene does not serve to explain form.”5 Instead, as Newman explains, “epigenetic” or “contextual information” plays a crucial role in the formation of animal “body assemblies” during embryological development.6
    Müller and Newman not only highlighted the importance of epigenetic information to the formation of body plans during development; they also argued that it must have played a similarly important role in the origin and evolution of animal body plans in the first place. They concluded that recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all.

    … I first learned about the problem of epigenetic information and the Spemann and Mangold experiment while driving to a private meeting of Darwin-doubting scientists on the central coast of California in 1993. In the car with me was Jonathan Wells, who was then finishing a Ph.D. in developmental biology at the University of California at Berkeley. Like some others in his field, Wells had come to reject the (exclusively) “gene-centric” view of animal development and to recognize the importance of nongenetic sources of information.
    By that time, I had studied many questions and challenges to standard evolutionary theories arising out of molecular biology. But epigenetics was new to me. On our drive, I asked Wells why developmental biology was so important to evolutionary theory and to assessing neo-Darwinism. I’ll never forget his reply. “Because” he said, “that’s where the whole theory is going to unravel.”

  214. 214
    Germanicus says:

    Querius @211,
    I have followed this post with interest also without participating, but after your comment and some others of EA, Origenes & Co. I cannot resist and give also my comment.
    I find wise that you (and the others) take seriously the suggestion of Wd400 and start to study a little about basic biology. This is not matter of personal attack, but only the fact that you don’t have sufficient knowledge of some important topics of this field; this appears clear in the discussion and is a big obstacle in the understanding of the argumentations proposed. Expertise like system engineering or informatics can be very nice to introduce some new insights in the topic, but without basic knowledge of e.g. biochemistry you are completely missing the total picture.

  215. 215
    Dionisio says:

    Germanicus @214

    I find wise that you (and the others) […]start to study a little about basic biology. […] the fact that you don’t have sufficient knowledge of some important topics of this field.

    Interesting comments.

    What do you mean by “sufficient knowledge” within the context of your commentary?

    On a scale 0-1 (zero to one) where zero is complete ignorance of the subject and 1 is total knowledge of the subject, where would you place your knowledge of Biology?

    BTW, mine is close to zero. Perhaps in the last few years -after some intensive studying- it has gained a few thousandths (0.001 x n, where n<5), but I kind of doubt it has reached such a high level. If it ever reaches 0.01, then I might host a party to celebrate that amazing milestone with friends and relatives. But that may never happen. The more I study it, the more I have to learn from it. It seems like a never-ending story. Every day the fraction seems to decrease. 🙂

  216. 216
    wd400 says:

    EA,

    You seem much more interested in telling and retelling this story of yours than engaging in any detail. Good luck with that, I guess.

    Querius,

    It takes a special sort of tribalism to read this thread, with EAs sneers about biologists blinkered view, Pav’s rant about my “standing in the way of true science” and what ever BA has been copying and pasting and single out those posts as a “personal attack”.

  217. 217
    Eric Anderson says:

    Germanicus @214:

    Thank you for commenting.

    I find wise that you (and the others) take seriously the suggestion of Wd400 and start to study a little about basic biology. This is not matter of personal attack, but only the fact that you don’t have sufficient knowledge of some important topics of this field; this appears clear in the discussion and is a big obstacle in the understanding of the argumentations proposed. Expertise like system engineering or informatics can be very nice to introduce some new insights in the topic, but without basic knowledge of e.g. biochemistry you are completely missing the total picture.

    What is this basic biology that you imagine we don’t understand? The issues we have been discussing relate to a specific, unsupported claim. wd400 keeps referring to chemical reactions as sufficient for building an organism, but many people recognize that is not sufficient. As Origenes quoted above @213 “As Müller and Newman explain in their introduction, ‘Detailed information at the level of the gene does not serve to explain form.'” Yet wd400 keeps claiming that all we need to do is specify the parts and chemistry will do the rest.

    I’m certainly open to learning whatever “basic biology” you think will help answer the question of whether a parts list is sufficient for building an organism (it isn’t) or whether, as wd400 asserts, there is no programmatic information necessary (there is). Let us know what you think we need to learn about “basic biology” that will answer the question of organismal form and that will support the simplistic claims being made, and I’ll be happy to consider it. I’ll even elevate it to a head post for further discussion if you would like.

    It is ironic that we are being accused of misunderstanding basic biology when we are the ones trying valiantly to get some people to wake up and think beyond the “basic biology” of 60 years ago and realize, as experts have recognized, that you don’t just specify some parts and end up with a functional organism, that chemistry is a necessary but insufficient condition.

    —–

    wd400:

    . . . with EAs sneers about biologists blinkered view . . .

    I certainly do not sneer at biology or biologists, so please don’t accuse me of that. What I do “sneer” at is the simplistic, decades-past-its-time, naïve, contrary-to-evidence, neo-Darwinian-based assertions that everything needed for an organism is specified in the nucleotide sequence for the parts, that the parts will automatically come together by dint of chemistry, that nearly everything else other than the parts list is just junk, that no broader plan or program is required to build an organism. Everyone should sneer at that.

  218. 218
    bill cole says:

    WD400

    Nuclear import is an example of proteins getting to where they need to be. None of these require anything but chemistry

    Really? Non of this requires sequences? How does chemistry form sequences?

  219. 219
    wd400 says:

    Not sure I understand the question, Bill. The nuclear export sequence is a chemical signal, encoded in the nucleotide sequence of a protein, no?

  220. 220
    Dionisio says:

    Eric Anderson, Origenes, PaV, bornagain77, bill cole, Querius

    Sorry to disappoint you guys, but at the bottom every computer software is just a bunch of tiny electronic impulses wildly dancing around. That’s all it is, OK? Forget about design. Stop using that word. That’s just an illusion, total nonsense. Got it?

    🙂

  221. 221
    bill cole says:

    wd400

    Not sure I understand the question, Bill. The nuclear export sequence is a chemical signal, encoded in the nucleotide sequence of a protein, no?

    Yes, thats right. What is the source and process that created that code? Just chemistry?

  222. 222
    Origenes says:

    WD400: Don’t suppose Meyer gives any examples?

    Meyer gives several examples of epigenetic information. Let’s have a look at one of them:
    – – – – –

    MEMBRANE PATTERNS

    Another important source of epigenetic information resides in the two-dimensional patterns of proteins in cell membranes.18 When messenger RNAs are transcribed, their protein products must be transported to the proper locations in embryonic cells in order to function properly. Directed transport involves the cytoskeleton, but it also depends on spatially localized targets in the membrane that are in place before transport occurs. Developmental biologists have shown that these membrane patterns play a crucial role in the embryological development of fruit flies.

    Membrane Targets

    For example, early embryo development in the fruit fly Drosophila melanogaster requires the regulatory molecules Bicoid and Nanos (among others). The former is required for anterior (head) development, and the latter is required for posterior (tail) development.19 In the early stages of embryological development, nurse cells pump Bicoid and Nanos RNAs into the egg. (Nurse cells provide the cell that will become the egg—known as the oocyte—and the embryo with maternally encoded messenger RNAs and proteins.) Cytoskeletal arrays then transport these RNAs through the oocyte, where they become attached to specified targets on the inner surface of the egg.20 Once in their proper place—but only then—Bicoid and Nanos play critical roles in organizing the head-to-tail axis of the developing fruit fly. They do this by forming two gradients (or differential concentrations), one with Bicoid protein most concentrated at the anterior end and another with Nanos protein most concentrated at the posterior end.
    Insofar as both of these molecules are RNAs—that is, gene products—genetic information plays an important role in this process. Even so, the information contained in the bicoid and nanos genes does not by itself ensure the proper function of the RNAs and proteins for which the genes code. Instead, preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.
    – – –
    18. Poyton, “Memory and Membranes”; Edidin, “Patches, Posts and Fences.”
    19. Frohnhöfer and Nüsslein-Volhard, “Organization of Anterior Pattern in the Drosophila Embryo by the Maternal Gene Bicoid”; Lehmann and Nüsslein-Volhard, “The Maternal Gene Nanos Has a Central Role in Posterior Pattern Formation of the Drosophila Embryo.”
    20. Roth and Lynch, “Symmetry Breaking During Drosophila Oogenesis.”

    [Stephen Meyer, ‘Darwin’s Doubt’, ch. 14]

  223. 223
    wd400 says:

    Origines,

    As I said, a new embryo inherits from the egg cell and (in some species) the maternal environment. But those are in turn the result of the genetics of the mother. Bicoid is a useful example, in fact, since the gene gets is name for the fact offspringgenerated by a biocoid mutant fail to produce any anterior features.

    Bill,

    That’s a different question than is addressed here, but the short answer is mutation, drift and selection.

  224. 224
    bill cole says:

    wd400

    That’s a different question than is addressed here, but the short answer is mutation, drift and selection.

    This is where we disagree but we can take it up later. Thanks for your clear position.

  225. 225
    Origenes says:

    WD400,

    Explain by what mechanisms DNA determines the structure and location of the microtubules in the cytoskeleton, the membrane patterns and the position of membrane targets. This is all essential for Bicoid and Nanos RNAs to be transported to their proper position and to be functional.
    How does that work?

  226. 226
    wd400 says:

    There are literally hundreds of proteins that control the growth and aggregation of cyctoskeletal elemts (they will also happily form some of structures they form in cells if they are kept in solution).

    I guess the “membrane target” in the bicoid case is Torso. Interestingly, Torso doesn’t have a precise “pattern and position” in the membrane, it’s everywhere within the egg. It’s only functional at either pole of the cell because it is activated by “torso-like” protein, which is expressed by nurse cells at either end of the egg. So, in this case transcription factors and enchancers that drive torso-like expression in nurse cells.

  227. 227
    Querius says:

    By quoting wd400 as follows:

    All I can say (again) is I think you should study some biology before you commit to this neovitalism out whatever it is you are imagining.

    and

    That people continue to say things as ignorant as the last two comments really says something.All I can say (again) is I think you should study some biology before you commit to this neovitalism out whatever it is you are imagining.

    I’m now accused of not understanding biology and (gasp!) tribalism, because I noted that wd400 resorted to personal attacks and has thus conceded the argument.

    No, wd400 and Germanicus, there was nothing biological or tribal in my post. I simply identified wd400’s ad hominem attacks, to which you both responded with (drum roll) MORE ad hominem attacks! LOL

    Here’s a clue. Don’t respond to this message with yet more ad hominem attacks. 😉

    -Q

  228. 228
    Eric Anderson says:

    Dionosio @220:

    Yep! 😉

    http://www.uncommondescent.com.....deos-work/

  229. 229
    Origenes says:

    WD400: I guess the “membrane target” in the bicoid case is Torso. Interestingly, Torso doesn’t have a precise “pattern and position” in the membrane, it’s everywhere within the egg.

    So why is it that you guess that Torso is a specified spatially localized membrane target, which provides “crucial information—spatial coordinates—for embryological development”? Here is a clue: not making sense and writing unintelligently is not an argument. Just like Torso you are all over the place.

    If you want to actually learn about this subject here might be a place for you to start.

  230. 230
    Germanicus says:

    Dionisus @215,

    In the context (discussion between Origenes and Wd400) I meant at least “basic”. See e.g. @150 where Origenes tried to estimate the amount of “information” that has to be “stored” in the DNA to build e.g. a human brain. The model proposed is like a mapping in which each neuronal connection is described in term of an individual spatial co-ordinate; how can you explain him that this model is not appropriate as this is not related to how the development of biological organism works? I see inevitable to suggest him to read first some texts, papers or follow some basic course in the university about gene expression, regulatory network, etc. before continuing to move in a completely wrong direction.

    Of course your question is more general and so more difficult to answer. It is clear that a person cannot have complete knowledge in all the fields (complete related to the current status of knowledge, as there is no end in the human learning). Usually one is really an expert (due to years of education and work) in few of them, and in these fields one can really master the discussion. For the others one has to accept to engage at different levels and be ready to learn more also from the own opponent. Usually a degree of humility is wise and this should be inversely proportional to the expertise level.

  231. 231
    wd400 says:

    I guess Meyer is talking about Torso because that’s the membrane bound protein that specifies the poles of the egg and the location of bicoid.

  232. 232
    Victoria says:

    Hi Eric, wd40, germanicus and everyone else! I’ve been trying to follow this discussion and I have a few questions.
    Eric A said

    that the parts will automatically come together by dint of chemistry, that nearly everything else other than the parts list is just junk, that no broader plan or program is required to build an organism.

    When a programmer programs something it runs without him or her. Does the program in DNA need some outside help to run or can it run on its own. I’d like to hear everyones answer!

  233. 233
    Victoria says:

    Origenes, you write

    Explain by what mechanisms DNA determines… the membrane patterns and the position of membrane targets.

    What is known about these “membrane patterns”? Is it possible to know it?! Does DNA determine it and if not what does?

  234. 234
    Eric Anderson says:

    Germanicus @230:

    Usually one is really an expert (due to years of education and work) in few of them, and in these fields one can really master the discussion. For the others one has to accept to engage at different levels and be ready to learn more also from the own opponent. Usually a degree of humility is wise and this should be inversely proportional to the expertise level.

    Quite right. You make a good point. I guess all of us are probably a bit too animated from time to time when we feel strongly about something, and your caution of the need for humility is well taken.

    —–

    There are a couple of things that, at least in my case, prompt a bit of zealous discussion from time to time:

    First, wd400, while clearly a very intelligent guy who knows a lot about biology, tends to love to debate minutiae while studiously avoiding the more fundamental underlying issues that are the real heart of the disagreement. In the present case, for example, as detailed @204, 205, yes, we all know that biology utilizes chemistry in its operation. But the failure to distinguish between necessary and sufficient conditions is a basic logical mistake, and there doesn’t seem to be any effort to think beyond a narrow myopic view. Just more examples thrown out about how chemistry is involved. And simply asserting that nothing but chemistry is required is both unsupportable and highly questionable, based on statements by others in the field or even a cursory mental review of what is involved in building an organism.

    Second, when skeptics raise questions about the adequacy of the materialistic storyline, they are typically met with handwaving responses, including those like, “Well, you need to study more basic biology.” But when we ask what “basic biology” the experts have in mind that would answer the questions raised, we are met with silence or further insults.

    Third, although your point about being an expert in a field is well taken, deferring to the so-called “experts” is a dangerous exercise. Particularly when those “experts” have been indoctrinated through years of secondary, post-secondary, and further academia into a particular viewpoint — the very viewpoint that is under scrutiny. Particularly when those “experts” hold to a worldview that is challenged by the innocent questions being raised about design. It would be hard to find another field where the traditional “expertise” is more at odds with examining the questions posed. Unfortunately, time and again in this particular debate, we have found that the so-called “expert” brings more bias and intellectual baggage to the debate than anyone else.

    Furthermore, while it is good to be knowledgeable — even an expert, in some narrow, discrete aspect of biology — the primary issues we are dealing with have less to do with a particular organism or a specific chemical reaction than with basic logic, common sense, and a willingness to sit back and think through the issues. So the things I tend to focus on, for example, are less about expertise in a highly-narrow aspect of biology and more of a litmus test to tease out irrational thought and cognitive bias.

    Fourth, our confidence in the “experts” is not increased when the response to perfectly thoughtful and reasonable questions is to ignore that there is even an issue, to pretend the answers are already in hand, to assert that materialism inevitably holds the key even if it doesn’t have an answer yet, to claim that only the “experts” are qualified to examine and speak on the issue, or to make vague insults about the questioner’s need to brush up on the basics. Particularly, as I said, when the self-proclaimed expert is never quite able to identify precisely which “basics” he thinks will answer the question he conveniently refused to engage. This smacks more of an effort to protect one’s position of expertise and one’s worldview from challenge, than to honestly seek the truth.

    —–

    None of this is an excuse for poor manners or insults, and I apologize if I have been offensive. However, perhaps it can help explain at least some of the background of the back and forth, not just on this thread, but for a long time running.

  235. 235
    Dionisio says:

    Germanicus @230

    You vaguely attempted to answer my first question @215 and did not answer the second question which required a number or a range of numbers to be clear. Please, try again.
    Are you sure you want to discuss seriously?

  236. 236
    bornagain77 says:

    The Placenta Problem: How Common Descent Fails – Ann Gauger – June 17, 2016
    Excerpt: I’ll quote a review paper on syncytins. These are the people who discovered syncytins, and they have done great work. Yet they are forced into a corner by their own work and the idea of common descent.,,,

    “… syncytins are ‘new’ genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired ‘by chance’ and yet still ‘necessary’ to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.”

    Rather than postulating six independent, random capture events in placental development, they are now postulating at least one more, a founding syncytin leading to a primitive placenta, then the other syncytins to replace that one in each lineage. Each replacement must have had a clear selective advantage as time went on to make the replacement possible, and each must be the outcome of a random series of events. To say it again, the common descent prediction is that there must have been a founding syncytin in the first mammal with a placenta, or something else that functioned in syncytin’s place, in order for the primitive placenta to arise and subsequently be passed to all mammalian clades. For which there is no evidence, and may never be.
    Can common descent explain the unexpected observation of six independent origins for the placenta? No. Could it predict it? No.
    Common design has an explanation, but not one that will be palatable to my interlocutors. The designer used the same idea six different times to produce the same outcome in six different “designs” (clades).
    http://www.evolutionnews.org/2.....02930.html

  237. 237
    Dionisio says:

    Germanicus @230

    […] how can you explain him that this model is not appropriate as this is not related to how the development of biological organism works?

    Why isn’t it appropriate?
    Why isn’t it related?
    Do you know exactly how the development of biological organisms works?

  238. 238
    Dionisio says:

    Germanicus @230

    […] how can you explain him that […] ?

    If you know the discussed subject well, then you should have no problem explaining it to anyone, regardless of their knowledge level.

    For example, you may want to see gpuccio’s explanations posted in this site.

  239. 239
    Dionisio says:

    Germanicus:

    Here’s a recap of our chat:

    214 by G
    215 by D
    230 by G
    233, 235, 236 by D

  240. 240
    Dionisio says:

    Eric Anderson @217

    Did you get an answer to your question @217?

  241. 241
    Eric Anderson says:

    Dionisio @ 238:

    Unfortunately not. I don’t expect to either, because the claim of “basic biology” being able to answer the key question posed was a bluff, a deflection.

    Although, as the thread proceeded, it occurred to me that perhaps your question was the target of the comment, not mine 🙂 So maybe the “basic biology” comment was not directed at me. 🙂

  242. 242
    ThickPython says:

    @bill cole, #97:

    “I also think the existence of the intron that has a binding site inside the fused chromosome 2 telomere that python agreed is real, is very problematic. I would like to see this debated aggressively.

    Hi Bill, I have gotten around to posting on my blog about this. Please see:

    https://roohif.wordpress.com/2016/06/19/chromosome-2-fusion-its-a-binding-site-whoopty-frikkin-do/

  243. 243
    wd400 says:

    It hardly matters, but this is just silly

    I don’t expect to either, because the claim of “basic biology” being able to answer the key question posed was a bluff, a deflection.

    The “bluff” comes with specific examples you could have learned about. The rest of this thread and that rediculous “Mp4” post make it clear you’re rather continue with your favoured analogies, so I won’t bother in future.

  244. 244
    bill cole says:

    Python
    Thanks for the link. I think your analysis showing binding strength is interesting and I would like to hear a counter argument.

    I think the homology arguments is questionable. I agree telomeres and binding sites both have repeat counts but most the binding sites you showed have different sequences then TTAGGG repeats. Saying it looks like is weak analysis.

    If this is really a gene then this puts chimps and man sharing a common ancestor on life support. There is no good explanation how that sequence was generated in almost infinite sequential space.

  245. 245
    ThickPython says:

    @bill cole, #244:

    “I think your analysis showing binding strength is interesting and I would like to hear a counter argument.”

    Me too. I especially would like to hear from Tomkins himself, but I’ve sent him a dozen emails without a response. In fact, just looking at my emails now, the last time I got a response directly from him was in September 2014, about a week before I submitted my paper demonstrating that his 70% human to chimp DNA similarity result was wrong. By all means, you’re welcome to contact him to get him to show up here and defend himself – his email address is in post #110.

    I think the homology arguments is questionable. I agree telomeres and binding sites both have repeat counts but most the binding sites you showed have different sequences then TTAGGG repeats. Saying it looks like is weak analysis.

    I’m not sure I’m following: what is wrong with having different sequences to TTAGGG repeats – something we’ve known since at least 1989 ( http://www.ncbi.nlm.nih.gov/pm.....PMC318019/ )? Since the sub-telomeric regions are NOT made up purely of TTAGGG repeats, why would we expect perfect TTAGGG repeats at the fusion site? That’s what Tomkins said he expects, but if he submitted his work to proper journals he’d be torn apart.

    If this is really a gene then this puts chimps and man sharing a common ancestor on life support. There is no good explanation how that sequence was generated in almost infinite sequential space.

    Interesting wording – “if this really is a gene”. It makes me wonder if you’re implying that this DDX11L2 sequence (more specifically, the longer of the two transcripts) is somehow functional and/or important. I’d like to hear your reasons for that, if indeed that is what you believe.

    It’s pretty simple: we had two separate chromosomes – one with a standalone DDX11L2 transcript – and the other with a transcription factor binding site. They fused. So what is stopping that binding site creating a longer DDX11L2 transcript?

    My advice would be to take whatever Tomkins says with a very large grain of salt, and try get him here to defend himself.

  246. 246
    Eric Anderson says:

    wd400:

    Please. None of your examples supported your rather remarkable claim that no program or plan is needed in biology. Your examples simply conflated the well-known utilization of chemistry with an alleged sufficiency of chemistry. If there is any “basic” biology that needs to be understood, it is that the one does not equal the other.

    Any claim or suggestion or hint that by studying “basic biology” we will discover that it’s chemistry all the way down is just that — a bluff. Worse, it flies in the face of any rational understanding of the overall organism and the fundamental engineering issues that need to be addressed.

    It is ironic that you keep throwing out an accusation of “stories,” when the materialistic “explanation” you keep pushing is nothing but a made up story.

    But, hey, anytime you want to support your claim as to the miraculous sufficiency of chemistry to produce what we see in biology, please feel free. I’d be happy to elevate it to a head post for discussion.

  247. 247
    Mung says:

    Victoria:

    When a programmer programs something it runs without him or her. Does the program in DNA need some outside help to run or can it run on its own.

    There’s no evidence of a program in DNA running on its own.

  248. 248
    bill cole says:

    Python

    Interesting wording – “if this really is a gene”. It makes me wonder if you’re implying that this DDX11L2 sequence (more specifically, the longer of the two transcripts) is somehow functional and/or important. I’d like to hear your reasons for that, if indeed that is what you believe.

    It’s pretty simple: we had two separate chromosomes – one with a standalone DDX11L2 transcript – and the other with a transcription factor binding site. They fused. So what is stopping that binding site creating a longer DDX11L2 transcript?

    My advice would be to take whatever Tomkins says with a very large grain of salt, and try get him here to defend himself.

    I have no idea if it is a functioning gene. I only saying if it is then the fusion theory is in trouble.

    I am skeptical of Tomkins evidence as I am with yours. I would like to see this debate proceed and appreciate your counter arguments. As you can see I am also skeptical of common decent and at this point believe it is probably wrong.

  249. 249
    Dionisio says:

    Victoria @232

    When a programmer programs something it runs without him or her. Does the program in DNA need some outside help to run or can it run on its own. I’d like to hear everyones answer!

    [Emphasis mine]
    What do you mean by “a programmer programs something”?
    What do you mean by “a programmer”?
    What do you mean by “something”? To me “something” is the name of an old song written by George Harrison and performed by the British band The Beatles. 🙂
    When you wrote “a programmer programs…” what did you mean by “programs”?
    What is that ‘programming’ action?
    What do you mean by “it runs”?
    Can it walk too? 🙂
    Can you provide an example of a computer program that works isolated, on its own, without any influence from or interaction with anything else? Where do computer programs work in?
    Which level of computer program are you referring to?
    Operating systems, user apps, drivers?
    What program in DNA are you referring to?
    Can you provide an illustration?
    Thank you.

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