How Did Birds Get Their Wings? Bacteria May Provide a Clue to the Genomic Basis of Evolutionary Innovation, Say Evolutionists

11 Replies to “How Did Birds Get Their Wings? Bacteria May Provide a Clue to the Genomic Basis of Evolutionary Innovation, Say Evolutionists”

1. 1
   bornagain77 says:

   May 7, 2016 at 5:55 pm

   Of Related Interest to ‘directed’ mutations:

   Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA. – Feb. 2016
   The isolation of aerobic citrate-utilizing Escherichia coli (Cit(+)) in long-term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit(+) mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested,,,
   Potentiation/actualization mutations occurred within as few as 12 generations, and refinement mutations occurred within 100 generations.,,,
   E. coli cannot use citrate aerobically. Long-term evolution experiments (LTEE) performed by Blount et al. (Z. D. Blount, J. E. Barrick, C. J. Davidson, and R. E. Lenski, Nature 489:513-518, 2012, http://dx.doi.org/10.1038/nature11514 ) found a single aerobic, citrate-utilizing E. coli strain after 33,000 generations (15 years). This was interpreted as a speciation event. Here we show why it probably was not a speciation event. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are members of the same class of mutations identified by the LTEE. We conclude that the rarity of the LTEE mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.
   http://www.ncbi.nlm.nih.gov/pubmed/26833416
2. 2
   Mung says:

   May 7, 2016 at 7:39 pm

   Must have been bacteria. If not bacteria then symbiosis. If not symbiosis then viruses. If not viruses then changes in oxygen levels. If not changes in oxygen levels then…

   The possibilities are endless. Ain’t evolution grand!
3. 3
   Andre says:

   May 7, 2016 at 11:54 pm

   Mung was thinking the same thing….

   Everything is evolution and evolution is everything….

   Praise Darwin!
4. 4
   bornagain77 says:

   May 8, 2016 at 5:14 am

   “It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident…you have essentially lost your mind.”
   Jay Homnick – senior editor of The American Spectator

   It’s Really Not Rocket Science – Granville Sewell – November 16, 2015
   Excerpt: In a 2005 American Spectator article, Jay Homnick wrote:
   “It is not enough to say that design is a more likely scenario to explain a world full of well-designed things. It strikes me as urgent to insist that you not allow your mind to surrender the absolute clarity that all complex and magnificent things were made that way. Once you allow the intellect to consider that an elaborate organism with trillions of microscopic interactive components can be an accident… you have essentially “lost your mind.””
   ,,, Max Planck biologist W.E. Loennig once commented that Darwinism was a sort of “mass psychosis” — then he asked me, is that the right English word? I knew psychosis was some kind of mental illness, but wasn’t sure exactly what it was, so I looked it up in my dictionary when I returned home: “psychosis — a loss of contact with reality.” I wrote him that, yes, that was the right word….
   Loennig and Homnick are still right. Once you seriously consider the possibility that all the magnificent species in the living world, and the human body and the human brain, could be entirely the products of unintelligent forces, you have been in academia too long and have lost contact with reality — you have lost your mind.
   http://www.evolutionnews.org/2.....00911.html

   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

   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

   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 – video 2016
   https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1116313858381546/?type=2&theater

   Jim Al-Khalili, at the 2:30 minute mark of the following video states,
   “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

   “Now the world appears to be divided into two realms, described by two different sets of physical laws. The quantum (world),, which is immaterial, coexisting possibilities, non-local, unified, connected, has some ultimate truth although we don’t know what it is yet, deeper levels of reality, and in many senses ‘spirit-like’. The classical world, the (illusory) billiard ball universe that we (appear to) live in right now, but not so, is material, Newtonian, definite, macroscopic, local, predictable, disconnected, post-modern, and somewhat boring actually. Now, what is life? If you approach life from classical physics, you see that biology is a set of self-organizing functions. There is no secret to life. Brain activities are equivalent to computers, consciousness is a epi-phenomenal illusion with no causal power. That’s the party line in standard neuroscience and philosophy. Accordingly, Thomas Huxley said years ago, ‘We are merely conscious automaton,’ helpless spectators., That’s the story we get from classical physics approach to the brain. Now,, applying quantum physics to biology, first by Erwin Schrodinger,,, quantum features (of biology include), non-local entanglement, super-position, unity, quantum coherence, quantum information. A kind of quantum vitalism, may play key roles in biological function.,,,”
   Stuart Hameroff – Does Quantum Biology Support A Quantum Soul? – video
   https://www.youtube.com/watch?v=iIyEjh6ef_8

   Verse:

   Matthew 16:26
   What good will it be for someone to gain the whole world, yet forfeit their soul? Or what can anyone give in exchange for their soul?
5. 5
   bornagain77 says:

   May 8, 2016 at 5:25 am

   Of related note; Here is Talbott’s latest article:

   Genes and Organisms: Improvising the Dance of Life
   Stephen L. Talbott – Nov. 2015
   A bodily wisdom
   Perhaps you are too cold or too hot, hungry or sated, coming down with a flu or recovering from it, lifting weights or resting, thinking hard or yielding to reverie. Perhaps you have a wound that is healing, or have just now suffered a terrible psychological shock, or are concluding an intense lecture to college students. Or perhaps not much has happened at all, except that the sun has moved from the eastern to the western horizon.
   Whatever your changing circumstances, the unseen physiological consequences could hardly be more dramatic. The performances of countless cells in your body are redirected and coordinated as part of a global narrative for which no localized controller exists. This redirection and coordination includes a unique choreography of gene expression in each individual cell. Hundreds or thousands of DNA sequences move (or are moved) within vast numbers of cell nuclei, and are subjected to extraordinarily nuanced, locally modulated chemical activity so as to contribute appropriately to bodily requirements that are nowhere codified — least of all in those DNA sequences.
   http://natureinstitute.org/txt.....nes_29.htm

   Well worth reading in full. Talbott is almost poetic as he goes through the intricate complexities of gene expression.
6. 6
   Davem says:

   May 8, 2016 at 11:37 am

   How did a rodent get long digits with membranes between them and learn to fly with them? The incremental changes required wouldn’t make them better adapted to survive. You can take any rodent on the planet and selectively breed them from here to eternity and you will never get one to fly like a bat, yet we are to believe that natural selection and mutations did?
7. 7
   OldArmy94 says:

   May 8, 2016 at 12:34 pm

   Davem,

   Not only that, but think of the brain rewiring that had to occur for flight to occur, not to mention bone density adjustments, etc.
8. 8
   bornagain77 says:

   May 8, 2016 at 5:00 pm

   As to the implausibility of changing one creature of trillions of cells into another creature of trillions of cells, here are a few notes:

   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

   In “Science,” 1975, M-C King and A.C. Wilson were the first to publish a paper estimating the degree of similarity between the human and the chimpanzee genome. This documented the degree of genetic similarity between the two (approx. 99% amino acid similarity) ! The study, using a limited data set, found that we were far more similar than was thought possible at the time. Hence, we must be one with apes mustn’t we? But…in the second section of their paper King and Wilson honestly describe the deficiencies of such reasoning:
   “The molecular similarity between chimpanzees and humans is extraordinary because they differ far more than sibling species in anatomy and way of life. Although humans and chimpanzees are rather similar in the structure of the thorax and arms, they differ substantially not only in brain size but also in the anatomy of the pelvis, foot, and jaws, as well as in relative lengths of limbs and digits (38).
   Humans and chimpanzees also differ significantly in many other anatomical respects, to the extent that nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart (38).
   Associated with these anatomical differences there are, of course, major differences in posture (see cover picture), mode of locomotion, methods of procuring food, and means of communication. Because of these major differences in anatomy and way of life, biologists place the two species not just in separate genera but in separate families (39). So it appears that molecular and organismal methods of evaluating the chimpanzee human difference yield quite different conclusions (40).”
   King and Wilson went on to suggest that the morphological and behavioral differences between humans and apes,, must be due to variations in their genomic regulatory systems.
   David Berlinski – The Devil’s Delusion – Page 162&163
   *Evolution at Two Levels in Humans and Chimpanzees Mary-Claire King; A. C. Wilson – 1975

   And, just as King and Wilson predicted, the regulatory regions between chimps and humans are found to be very different. In fact the regulatory regions are ‘species specific’:

   Alternative Splicing Codes (Gene Regulatory Networks) are Species Specific
   https://docs.google.com/document/d/1UMbNM8V2b7mRzPJt05mlev3UO4SG1bMTV5wkNunezjY/edit

   A Closer Look At Human/Chimp Similarities and Differences – video
   https://www.facebook.com/philip.cunningham.73/videos/vb.100000088262100/1134643976548534/?type=2&theater

   As to Wilson and King’s observation that ‘nearly every bone in the body of a chimpanzee is readily distinguishable in shape or size from its human counterpart’, that fact poses its own insurmountable difficulty for Darwinian explanations.

   K´necting The Dots: Modeling Functional Integration In Biological Systems – June 11, 2010
   Excerpt: “If an engineer modifies the length of the piston rods in an internal combustion engine, but does not modify the crankshaft accordingly, the engine won’t start. Similarly, processes of development are so tightly integrated temporally and spatially that one change early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream” (1)
   http://www.uncommondescent.com.....l-systems/

   “This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create….
   (Lynn Margulis Says She’s Not Controversial, She’s Right,” Discover Magazine, p. 68 (April, 2011)

   “The real number of variations is lesser than expected,,. There are no blue-eyed Drosophila, no viviparous birds or turtles, no hexapod mammals, etc. Such observations provoke non-Darwinian evolutionary concepts. Darwin tried rather unsuccessfully to solve the problem of the contradictions between his model of random variability and the existence of constraints. He tried to hide this complication citing abundant facts on other phenomena. The authors of the modern versions of Darwinism followed this strategy, allowing the question to persist. …However, he was forced to admit some cases where creating anything humans may wish for was impossible. For example, when the English farmers decided to get cows with thick hams, they soon abandoned this attempt since they perished too frequently during delivery. Evidently such cases provoked an idea on the limitations to variability… [If you have the time, read all of the following paper, which concludes] The problem of the constraints on variation was not solved neither within the framework of the proper Darwin’s theory, nor within the framework of modern Darwinism.”
   (IGOR POPOV, THE PROBLEM OF CONSTRAINTS ON VARIATION, FROM DARWIN TO THE PRESENT, 2009,

   Of related note to ‘coordinated changes’:

   Gene previously linked to obesity is unrelated – June 29, 2015
   Excerpt: … in the real world of careful analysis, scientists are just not finding the “genes” that the headline writers need. British geneticist Steve Jones points out that most human traits are influenced by so many genes that there is no likely systematic cause and effect:
   “We know of more than 50 different genes associated with height … That has not percolated into the public mind, as the Google search for “scientists find the gene for” shows. The three letter word for — the gene FOR something — is the most dangerous word in genetics.”
   And the craze is not harmless, he warns. …
   http://www.uncommondescent.com.....-unrelated

   Evolution machine: Genetic engineering on fast forward – June 2011
   Excerpt: Yet changing even a handful of genes takes huge amounts of time and money. For instance, a yeast engineered to churn out the antimalarial drug artemisinin has been hailed as one of the great success stories of synthetic biology. However, it took 150 person-years and cost $25 million to add or tweak around a dozen genes – and commercial production has yet to begin.
   http://www.newscientist.com/ar.....?full=true

   The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology – Bard – 2011
   Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation..
   http://www.biosignaling.com/co.....X-9-30.pdf
9. 9
   John.P says:

   May 9, 2016 at 3:47 pm

   Am I understanding correctly that each of the 4 groups showed identical genetic changes? For the 95 different food sources, did each of the 4 groups show the same, or 95 different genetic changes? If so, where can I learn more about directed mutation?
10. 10
    Querius says:

    May 10, 2016 at 7:37 pm

    Great posts and links, bornagain77. Thanks!

    -Q
11. 11
    gpuccio says:

    May 11, 2016 at 9:34 am

    John.P:

    “Am I understanding correctly that each of the 4 groups showed identical genetic changes?”

    It’s much more complex.

    Just to be brief, I will say that I have read that paper with great interest, but in the end I am a little disappointed.

    The authors seem to be interested only in the differences between “innovation” and “optimization”, as defined by them, a little artificially, IMO.

    The differences they find are interesting, but statistically weak. Nothing really convincing, in the end.

    I hoped I could find many facts which could be interpreted in an interesting way. But, in the end, the facts are rather minimal, and their implications rather trivial.

    I must say that the paper referenced by our amazing BA in post #1 is much more interesting. Strangely enough (well, maybe not too strangely!) I have not read any comments on it by the other side, up to now.