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Top ten stories of 2013 from science news media

Fast away the old year passes, so time for everyone to compile their Top Tens. Here are a few lists, highlighting ones we followed or wished we had:

Scientific American: #5 Recovery of 400,000-year-old DNA:

For all the astonishing advances in ancient DNA research in recent years, scientists have maintained that they would never be able to sequence DNA from human fossils more than about 100,000 years old. But in December a team reported that it had managed to recover well-preserved DNA from a 400,000-year-old thighbone belonging to an extinct member of the human family.

See also Paleoanthrolopologist: Century-old theory of human evolution shown wrong by new 400k DNA

New Scientist (Category, Evolution and Life Sciences): The first story listed is The father of all men is 340,000 years old, and not 100,000 years old as previously believed.

Hundreds of thousands of people have now had their DNA tested. The data from these tests had shown that all men gained their Y chromosome from a common male ancestor. This genetic “Adam” lived between 60,000 and 140,000 years ago.

All men except Perry, that is. When Family Tree DNA’s technicians tried to place Perry on the Y-chromosome family tree, they just couldn’t. His Y chromosome was like no other so far analysed.

Of course, it’s always possible that this type of analysis is on the wrong track too. There are just so many surprises these days.

Nature News Readers’ Choice (most-read on Nature’s Web site this year):

6. Giant viruses open Pandora’s box

Genome of largest viruses yet discovered hints at ‘fourth domain’ of life.

Later, after the researchers discovered a similar organism in a pond in Australia, they realized that both are viruses — the largest yet found. Each is around 1 micrometre long and 0.5 micrometres across, and their respective genomes top out at 1.9 million and 2.5 million bases — making the viruses larger than many bacteria and even some eukaryotic cells.

See also: Giant viruses: Aw, why not just dig up and haul that tree of life to a tree museum?

We’ll add more lists later. Meanwhile, what do readers think are the most important stories of the year?

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29 Responses to Top ten stories of 2013 from science news media

  1. I like the one about Adam and Eve being contemporaries. I know it chapped the scientific community’s hide to have to admit the progenitors of the human race actually lived at the same time.

  2. semi OT: Top 75 Pictures of the Year for 2013 – The Art Institute Online
    http://www.artfido.com/blog/th.....-for-2013/

  3. Can you list the 10 articles in a clear and consistent format preferably with their titles?

  4. Top 3 stories for Human Origins(?) by Brian Thomas, M.S. – December 20, 2013
    Excerpt: Three major pillars supporting a human-chimp link crashed in 2013.
    1. Genetic similarity (70% instead of 98%)
    2. beta-globin pseudogene (functional instead of leftover junk)
    3. Chromosome 2 fusion site (encodes a functional feature within an important gene instead of a being a fusion site)
    All three key genetic pillars of human evolution (for Darwinists) turned out to be specious—overstatements based on ignorance of genetic function.
    http://www.icr.org/article/7867/

    OT:

    Sir Peter Crane “no slow and gradual evolution” – The Royal Society – punctuated equilibrium – video
    https://www.youtube.com/watch?v=jid14mDI4s0

    Sir Peter Crane -,,, His own research interests involve the integration of studies of living and fossil plants, in order to understand large-scale patterns and processes of plant evolution.,,,
    http://en.wikipedia.org/wiki/Peter_Crane

    Music:

    Creation Calls — are you listening? Music by Brian Doerksen
    http://www.youtube.com/watch?v=LwGvfdtI2c0

  5. Hey guys great article! Ive been getting sick if not having answers for the transitional fossils. Ive looked every where asked tons of questions and im not getting the answers I’m looking for!
    Before the break in my highschool biology class we where shown this website http://reptileevolution.com and on that website we looked at transitional fossils. If you go to the left and click on mammal evolution to me it looks like a perfect transition from jaw bone to jaw bone in theraspids and many other animals. Its also got many other animals that show a smooth convincing transition from one to the next! To me it looks like a clean transition from one animal to the next I cant get over it and its been bothering me for sometime now I tried to not ask you guys because I know you guys are sick of me but it would make my christmas day if you could respond. I hate doing this but I’m getting not very many answers from this! Again im sorry I hate to bother. Heres dome of the transitions that I think look convincing. http://reptileevolution.com/megazostrodon2.htm
    http://reptileevolution.com/megazostrodon.htm and http://reptileevolution.com/evolutionofman.htm

  6. The fictitious fossil series from reptilian jaw bones to the inner ear bones of humans is addressed at the 31:49 minute mark of this following video (you have to skip over 31:48 minutes of a ‘brief’ description of the stunning engineering and elegant design found in the ear to get to the refutation).

    The Hearing Ear by Dr. David Menton – video
    http://www.youtube.com/watch?v=HPiXlJ3eIwo

    Further notes:

    How the ear works – video
    http://www.youtube.com/watch?v=qgdqp-oPb1Q

    There are about….
    Ten-trillion levels of intensity to human hearing (from threshold to pain, 0 to 130 decibels). This makes the sense of hearing the widest ranging of all senses. The ear is capable of detecting pressure variations of less than two-ten-thousandths-of-a-millionth of barometric pressure. This moves the eardrum about one-hundreth-millionth of an inch. This threshold of hearing corresponds to a vibration width of only one-hundreth of an hydrogen atom’s diameter. (Hydrogen is the smallest atom.) Under favourable conditions a normal person may actually perceive sound waves with the power of only 10-16 (1/10,000,000, 000,000,000) of a watt.

    On the Evolution of the Mammalian Middle Ear – Jonathan M. – July 25, 2012
    Excerpt: Moreover, Meng et al. (2011) report that Liaconodon’s middle ear “differs from that of Yanoconodon.”,,, In general, what have been interpreted as ear ossicles in Yanoconodon differ significantly from the middle ear elements of Liaoconodon.,,, Finally, in the absence of a viable materialistic mechanism to account for the transition in question, the supposition that one can slap these different structures down on a table and draw arrows between them seems highly suspect. The methodology is circular — it assumes that these structures are connected by descent. When one’s entire interpretative framework presupposes common ancestry at the outset, it is no wonder that any and every observation is taken as supportive of that paradigm.
    http://www.evolutionnews.org/2.....62511.html

    As to the fictitious fossil series leading up to mammals. Darwinists are notorious for falsely lining up similar looking fossils, in the most favorable sequence possible for them, then claiming that the fictitious sequence represents true history, yet when the alleged sequence is scrutinized for integrity it ALWAYS falls apart. Such as with your current series:

    Reappraising the “Crown Jewel” by Ashby L. Camp, J.D., M.Div.
    Summary: The fossil evidence for the claim that reptiles evolved into mammals is weaker than many evolutionists will admit. The evolution story for the origin of mammals is: anapsids ª synapsids ª pelycosaurids ª therapsids ª cynodonts ª early mammals ª modern mammals. In no case do the fossils document the alleged transformation of one group into another. The evolutionist simply assumes descent from the order of appearance, and sometimes even assumes the order of appearance.
    http://www.creationresearch.or.....m9809.html

  7. As long as one is not too troubled to let imagination have sway over actual facts in science then such sequences may seem plausible to the unwary,,,,

    “Grand Darwinian claims rest on undisciplined imagination”
    Dr. Michael Behe – 29:24 mark of following video
    Evidence of Design from Biology. A Presentation by Dr. Michael Behe at the University of Toronto – video
    http://www.youtube.com/watch?f.....fM#t=1762s

    “No fossil is buried with its birth certificate. That, and the scarcity of fossils, means that it is effectively impossible to link fossils into chains of cause and effect in any valid way… To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story—amusing, perhaps even instructive, but not scientific.”
    - Henry Gee, In Search of Deep Time: Beyond the Fossil Record to a New History of Life

    Yet if one checks to see if these imaginative transformations are ‘scientifically’ possible, then one finds that Darwinists have no viable mechanism to appeal to to explain such transformation, nor do they have a single documented example they can point to for ‘macro-evolution’:

    Scant search for the Maker
    Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. – Alan H. Linton – emeritus professor of bacteriology, University of Bristol.
    http://www.timeshighereducatio.....ode=159282

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

    Here is a detailed refutation, by Casey Luskin, to TalkOrigins severely misleading site on the claimed evidence for observed macro-evolution (speciation);

    Specious Speciation: The Myth of Observed Large-Scale Evolutionary Change – Casey Luskin – January 2012 – article
    http://www.evolutionnews.org/2.....55281.html

    They, Darwinists/Atheists, simply have no demonstrated mechanism to appeal to so as to be ‘scientific:

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” -
    Eric Davidson
    http://www.evolutionnews.org/2.....79811.html

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

    One of the main reasons that there are impassable boundaries to the amount of variety one can breed from a species is because of the following:

    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013
    Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11].
    1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696.
    2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19.
    3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358.
    4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144.
    5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47.
    6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.
    7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117.
    8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526.
    9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685.
    10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079.
    11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501.

    In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43].

    38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142.
    39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432.
    40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654.
    41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997.
    42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816.
    43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589.

    Conclusions: Our analysis confirms mathematically what would seem intuitively obvious – multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations?
    http://www.worldscientific.com.....08728_0006

    Music:

    Nickelback – Lullaby
    http://www.youtube.com/watch?v=x_wfoY56JGc

  8. @bornagain77 you have made my day. Every time you respond to me you make me feel like a idiot with all the information you give me I wish I could give you a present right now or something of that nature. Its hard when your a young high-school student. Sorry for the bother it just looked transitional to me! Anyways bornagain77 thanks so much you really made my day better. I will be watching and reading all that you linked. Anyway thanks again. Merry Christmas!

  9. VJ or Gpuccio or any of the many other ID supporters who accept common descent. Please can you step in here and help Jaceli123.

    Jaceli123 – do you realise that Common Descent is accepted even by ardent supporters of Intelligent Design such as Behe and many of the major contributors on this forum? They disagree with most scientists about the mechanism for Common Descent – not the fact of Common Descent.

    What questions did you have about the reptilian fossil sequence. I am not an expert but I may be able to find the answer.

    Mark

  10. Mr Frank, if it is not too much trouble, and though you are not an expert, I also have a question that I would like some help with. In regards to your statement here,,,

    They disagree with most scientists about the mechanism for Common Descent – not the fact of Common Descent.

    ,,,How is it even possible for atheists, such as yourself, to be ‘scientists’, as you subtly imply ‘most scientists’ are, if atheists/scientists deny they even have a mind and free will in the first place?

    Sam Harris’s Free Will: The Medial Pre-Frontal Cortex Did It – Martin Cothran – November 9, 2012
    Excerpt: By their (Materialist’s/Atheist’s) own logic, it isn’t logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order.
    http://www.evolutionnews.org/2.....66221.html

    “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)

    “Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation.”
    Alfred Russel Wallace – An interview by Harold Begbie printed on page four of The Daily Chronicle (London) issues of 3 November and 4 November 1910.

    The Unreasonable Effectiveness of Mathematics in the Natural Sciences – Eugene Wigner – 1960
    Excerpt: ,,certainly it is hard to believe that our reasoning power was brought, by Darwin’s process of natural selection, to the perfection which it seems to possess.,,,
    It is difficult to avoid the impression that a miracle confronts us here, quite comparable in its striking nature to the miracle that the human mind can string a thousand arguments together without getting itself into contradictions, or to the two miracles of the existence of laws of nature and of the human mind’s capacity to divine them.,,,
    The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve. We should be grateful for it and hope that it will remain valid in future research and that it will extend, for better or for worse, to our pleasure, even though perhaps also to our bafflement, to wide branches of learning.
    http://www.dartmouth.edu/~matc.....igner.html

    “Either mathematics is too big for the human mind or the human mind is more than a machine”
    ~ Kurt Godel – incompleteness theorem

    etc.. etc.. etc..

  11. Mr. Frank, from the preceding facts, it should be no surprise for you to learn that Darwinism has no rigid mathematical basis within science so as to allow Darwinism to be falsified and thus to be considered truly ‘scientific’ in the first place,,

    “nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific”
    – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, quote as stated in 1973 LSE Scientific Method Lecture

    Oxford University Seeks Mathemagician — May 5th, 2011 by Douglas Axe
    Excerpt: Grand theories in physics are usually expressed in mathematics. Newton’s mechanics and Einstein’s theory of special relativity are essentially equations. Words are needed only to interpret the terms. Darwin’s theory of evolution by natural selection has obstinately remained in words since 1859. …
    http://biologicinstitute.org/2.....emagician/

    “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)

    Macroevolution, microevolution and chemistry: the devil is in the details – Dr. V. J. Torley – February 27, 2013
    Excerpt: After all, mathematics, scientific laws and observed processes are supposed to form the basis of all scientific explanation. If none of these provides support for Darwinian macroevolution, then why on earth should we accept it? Indeed, why does macroevolution belong in the province of science at all, if its scientific basis cannot be demonstrated?
    http://www.uncommondescent.com.....e-details/

    “It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.”
    Murray Eden – MIT, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.

    Nobel Prize-Winning Physicist Wolfgang Pauli on the Empirical Problems with Neo-Darwinism – Casey Luskin – February 27, 2012
    Excerpt: While they (Darwinian Biologists) pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) -
    http://www.evolutionnews.org/2.....56771.html

    It should be noted that to the extent mathematics can be applied to Darwinian claims through population genetics, that mathematics has finally ended up (with better resolution of empirical evidence; M. Behe; J. Sanford) providing a fairly high level of falsification towards neo-Darwinian claims:

    More from Ann Gauger on why humans didn’t happen the way Darwin said – July 2012
    Excerpt: Each of these new features probably required multiple mutations. Getting a feature that requires six neutral mutations is the limit of what bacteria can produce. For primates (e.g., monkeys, apes and humans) the limit is much more severe. Because of much smaller effective population sizes (an estimated ten thousand for humans instead of a billion for bacteria) and longer generation times (fifteen to twenty years per generation for humans vs. a thousand generations per year for bacteria), it would take a very long time for even a single beneficial mutation to appear and become fixed in a human population.
    You don’t have to take my word for it. In 2007, Durrett and Schmidt estimated in the journal Genetics that for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years. The same authors later estimated it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.
    Facing Facts
    But six million years is the entire time allotted for the transition from our last common ancestor with chimps to us according to the standard evolutionary timescale. Two hundred and sixteen million years takes us back to the Triassic, when the very first mammals appeared. One or two mutations simply aren’t sufficient to produce the necessary changes— sixteen anatomical features—in the time available. At most, a new binding site might affect the regulation of one or two genes.
    http://www.uncommondescent.com.....rwin-said/

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage.
    Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real.
    Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”.
    http://www.creationicc.org/abstract.php?pk=293

    Here is a short sweet overview of Mendel’s Accountant:

    When macro-evolution takes a final, it gets an “F” – Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory (Mendel’s Accountant)
    Excerpt of Conclusion: This (computer) program (Mendel’s Accountant) is a powerful teaching and research tool. It reveals that all of the traditional theoretical problems that have been raised about evolutionary genetic theory are in fact very real and are empirically verifiable in a scientifically rigorous manner. As a consequence, evolutionary genetic theory now has no theoretical support—it is an indefensible scientific model. Rigorous analysis of evolutionary genetic theory consistently indicates that the entire enterprise is actually bankrupt.
    http://radaractive.blogspot.co.....ution.html

    etc.. etc.. etc..

  12. Here is Sanford and Rupe’s entire paper:

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    http://media.wix.com/ugd/a704d.....fa9c20.pdf

  13. Sorry, I inadvertently forgot to include Dr. Axe’s work in all this:

    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://www.biologicinstitute.o.....nt-collide

    “Biologist Douglas Axe on Evolution’s (non) Ability to Produce New (Protein) Functions ” – video
    Quote: It turns out once you get above the number six [changes in amino acids] — and even at lower numbers actually — but once you get above the number six you can pretty decisively rule out an evolutionary transition because it would take far more time than there is on planet Earth and larger populations than there are on planet Earth.
    http://intelligentdesign.podom.....5_14-07_00

    Doug Axe PhD. on the Rarity and ‘non-Evolvability’ of Functional Proteins – video (notes in video description)
    http://www.metacafe.com/watch/9243592/

  14. johnp,

    No study found that (mt) Eve and (Y-chromosome) Adam were contempories, just that the error bars on the estimates of their age overlap. More to the point, these people are not “progenitors” of the human race, they were each one of many many people alive at the same time, and there are thousands of other dead humans who are also common ancestors to all humanity, some of whom likely lived since mtEve. In fact, in time, as lineages diey out, someone else will become humanities mtEve

  15. Mark:

    I am well ready to state again that I believe that common descent is at present the best explanation for many things we can observe.

    As I have explained other times, I derive that conviction mainly from bio-molecular arguments, that are more my field, while I have no special interest in the fossil record and in arguments derived from it.

    There are two important reasons for that:

    a) My personal ignorance: I understand almost nothing of fossils.

    b) A personal conviction that the evidence from the fossil record is rather thin, in whatever sense we want to interpret it. I believe that biomolecular and biological data are much more powerful, clear, detailed and useful.

    So, for that very special mix of ignorance and skepticism, I almost never discuss evidence from the fossil record. And I think I will go on that way.

    I must also say that my conviction that biomolecular data, at present, well support some form of common descent as the best explanation is rather strong, but not as strong as my conviction about the empirical evidence for intelligent design. IOWs, I am absolutely certain that ID is the best explanation for biological information. And I am rather certain (but essentially open to discussion) about common descent, especially about the kind of common descent that best fits what we observe in the natural world.

    To be more detailed, I would support, at present, a theory of “saltational common descent”, where the existing hardware/software (existing species) is reused in the process of design to generate new functions and species through the input of new information.

    I hope that answers your request.

  16. Gpuccio

    Thanks that will do nicely.

    Mark

  17. Mr. Frank, are you even going to touch my question?

    ,,,”How is it even possible for atheists, such as yourself, to be ‘scientists’, as you subtly imply ‘most scientists’ are, if atheists/scientists deny they even have a mind and free will in the first place?”

    Or are you, since you can have no answer, simply going to ignore it?,,, But of course if you are truly deterministic how can you help yourself one way or the other? :)

  18. wd400, and since you were not alive at the time of Adam and Eve, how are you so certain that

    “these people are not “progenitors” of the human race, they were each one of many many people alive at the same time,”

    ,Especially seeing that you cannot even produce evidence for bacteria changing into another species much less a multicellular organism?

    Scant search for the Maker
    Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. – Alan H. Linton – emeritus professor of bacteriology, University of Bristol.
    http://www.timeshighereducatio.....ode=159282

    Do you want us to take your word for it wd400?

  19. Because exactly the same evidence used to estimate the age of the these ancestors can be used to
    (a) show there are much older common ancestors to humanity, and in fact and humans and chimps share a recent common ancestor
    (b) the human population size has been large for a long time.

    If you think the methods underlying those conclusion are flawed, then you have to throw out the age of mtEve and Y-chromosome Adam too….

  20. wd400, so you don’t actually have to show that Darwinian processes can create a new species you only have to assume the conclusion in your analysis of data beforehand? How convenient! And you actually get paid money for this ‘science’? :) where do I sign up?

  21. You asked me a question, I answered it. I don’t know what bacterial speciation has to do with adam and eve, but if you can work it out let me know.

  22. wd400,

    “I don’t know what bacterial speciation has to do with adam and eve, but if you can work it out let me know.”

    Well actually we have others we can turn to for help in seeing how the ‘evolution’ of microorganisms relates to humans:

    Lenski’s Long-Term Evolution Experiment: 25 Years and Counting – Michael Behe – November 21, 2013
    Excerpt: Twenty-five years later the culture — a cumulative total of trillions of cells — has been going for an astounding 58,000 generations and counting. As the article points out, that’s equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski’s project the best, most detailed source of information on evolutionary processes available anywhere,,,
    ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, –
    http://www.evolutionnews.org/2.....79401.html

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

    “The immediate, most important implication is that complexes with more than two different binding sites-ones that require three or more proteins-are beyond the edge of evolution, past what is biologically reasonable to expect Darwinian evolution to have accomplished in all of life in all of the billion-year history of the world. The reasoning is straightforward. The odds of getting two independent things right are the multiple of the odds of getting each right by itself. So, other things being equal, the likelihood of developing two binding sites in a protein complex would be the square of the probability for getting one: a double CCC, 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the world in the last 4 billion years, so the odds are against a single event of this variety in the history of life. It is biologically unreasonable.”
    - Michael Behe – The Edge of Evolution – page 146

    Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
    “Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
    http://www.evolutionnews.org/2.....20071.html

    Doesn’t exactly inspire confidence in undirected processes does it wd400?

  23. so, it has nothing to do with mt-eve and y-chromosome adam? OK, I’ll move along.

  24. wd400 you say:

    “so, it has nothing to do with mt-eve and y-chromosome adam? OK, I’ll move along.”

    I beg to differ, if undirected Darwinian processes have never been observed creating even a single gene, then what gives you the right to believe that Adam and Eve were created by the same undirected processes?,, You simply have no real evidence for your claims, and to imply otherwise, as you constantly do, is severely disingenuous to the evidence in hand!

  25. Right. So you can dismiss the evidence for the fact that mt-eve and y-adam lived as part of large populations if you want. But when you do that you also have to dismiss the evidence that the may have lived at roughly the same time. Which was my point to start with.

  26. wd400 you say:

    “So you can dismiss the evidence for the fact that mt-eve and y-adam lived as part of large populations if you want.”,,,

    What evidence do you have that they were part of large populations save for in your imagination? You have no real scientific evidence whatsoever that undirected processes can create even a single gene much less an entirely new species with thousand(s) of unique genes and its own unique Developmental Gene Regulatory Network (dGRN)!:

    The mouse is not enough – February 2011
    Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.”
    http://www.the-scientist.com/news/display/57986/

    Darwin Lobbyists Defend Using Fraudulent Embryo Drawings in the Classroom – Casey Luskin – October 11, 2012
    Excerpt: embryologist Michael Richardson, who called them “one of the most famous fakes in biology,” or Stephen Jay Gould who said “Haeckel had exaggerated the similarities by idealizations and omissions,” and that “in a procedure that can only be called fraudulent,” Haeckel “simply copied the same figure over and over again.” Likewise, in a 1997 article titled “Haeckel’s Embryos: Fraud Rediscovered,” the journal Science recognized that “[g]enerations of biology students may have been misled by a famous set of drawings of embryos published 123 years ago by the German biologist Ernst Haeckel.” ,,,
    So if you’re a Darwin lobbyist defending a textbook that uses Haeckel’s inaccurate drawings, be forewarned: neither Bob Richards nor any other credible authorities I’m aware of endorse the unqualified and uncritical use of Haeckel’s original inaccurate drawings in biology textbooks today. You’re on your own.
    http://www.evolutionnews.org/2.....65151.html

    A Listener’s Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question -Casey Luskin – December 4, 2013
    Excerpt: “There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.” -
    Eric Davidson
    http://www.evolutionnews.org/2.....79811.html

    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

    Understanding Ontogenetic Depth, Part II: Natural Selection Is a Harsh Mistress – Paul Nelson – April 7, 2011
    Excerpt: The problem may be summarized as follows:
    – There are striking differences in the early (embryonic) development in animals, even within classes and orders.
    – Assuming that these animals are descended from a common ancestor, these divergences suggest that early development evolves relatively easily.
    – Evolution by natural selection requires heritable variation.
    – But heritable variations in early development, in major features such as cleavage patterns, are not observed.
    http://www.evolutionnews.org/2.....45581.html

    Moreover,,,

    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

    Proteins and Genes, Singletons and Species – Branko Kozuli? PhD. Biochemistry
    Excerpt: Horizontal gene transfer is common in prokaryotes but rare in eukaryotes [89-94], so HGT cannot account for (ORFan) singletons in eukaryotic genomes, including the human genome and the genomes of other mammals.,,,
    The trend towards higher numbers of (ORFan) singletons per genome seems to coincide with a higher proportion of the eukaryotic genomes sequenced. In other words, eukaryotes generally contain a larger number of singletons than eubacteria and archaea.,,,
    That hypothesis – that evolution strives to preserve a protein domain once it stumbles upon it contradicts the power law distribution of domains. The distribution graphs clearly show that unique domains are the most abundant of all domain groups [21, 66, 67, 70, 72, 79, 82, 86, 94, 95], contrary to their expected rarity.,,,
    Evolutionary biologists of earlier generations have not anticipated [164, 165] the challenge that (ORFan) singletons pose to contemporary biologists. By discovering millions of unique genes biologists have run into brick walls similar to those hit by physicists with the discovery of quantum phenomena. The predominant viewpoint in biology has become untenable: we are witnessing a scientific revolution of unprecedented proportions.
    http://vixra.org/pdf/1105.0025v1.pdf

  27. wd400,

    Dr. Carter directly challenges your ‘large population’ contention here, and shows how the evidence from genetics fits much better with the assumption of two individuals rather than a large population:

    The Non-Mythical Adam and Eve! – Refuting errors by Francis Collins and BioLogos
    http://creation.com/historical-adam-biologos

    CMI has a excellent video of the preceding paper by Dr. Carter, that makes the technical aspects of the paper much easier to understand;

    The Non Mythical Adam and Eve (Dr Robert Carter) – video
    http://www.youtube.com/watch?v=8ftwf0owpzQ

    Moreover this genetic evidence for ‘Adam and Eve’, elucidated by Dr. Carter, is corroborated by other lines of genetic evidence (Of note: Dr. Rana has no trouble with the assumption of a single male and female, rather than a large population, in the following video):

    Human Evolution? – The Compelling Genetic Evidence For Adam and Eve
    Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4284482

    And please note wd400, you have no undirected mechanism in the first place to appeal to as a cause for why humans originated! Thus your preferred scenario that unintelligent processes generated humans is un-parsimonious to put it mildly!

  28. Here’s a 2013 story that I thought was interesting:

    Best of 2013: Moore’s Law and the Origin of Life

    As life has evolved, its complexity has increased exponentially, just like Moore’s law. In April, geneticists announced they had extrapolated this trend backwards and found that by this measure, life is older than the Earth itself.

    Imagine that! In other words, either life evolved on earth much faster than it should have or it came from somewhere else. But then again, it’s much more likely that life did not evolve the way the Darwinists would like to force everyone to believe.

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