Uncommon Descent Serving The Intelligent Design Community

Spring it on ’em and Watch the Fur Fly


Dennis Venema is an associate professor in the biology department at Trinity Western University, a Christian university near Vancouver, British Columbia.  Over at Biologos Venema has an article entitled The Sorrows and Joys of Teaching Evolution at an Evangelical Christian University in which he recounts his efforts to indoctrinate his students in Darwinian evolution. In the opening paragraphs of his article Venema describes one of his teaching methods: 

After the “information dump” using the fruit fly examples, it’s time for a class discussion/application before the students drift off too much. Ok, here’s a slide that shows the chromosome structure of a group of organisms that other lines of evidence suggest are part of a group of related species. What do you observe? Do you think these species are related? If so, what explains the differences you observe?


What the students don’t know is that the slide shows human chromosomes, and those of our closest living relative, the chimpanzee. Oblivious to this knowledge, they easily arrive at the correct answer: yes, the evidence is strong that these are quite recently diverged species, and that a chromosome fusion or fission event explains the differences in chromosome structure between them. When I tell them that every other species in this grouping has the higher chromosome number/structure, they correctly deduce that the species with the lower chromosome number should show evidence of a fusion event in the form of “telomere” sequences at the fusion point and an inactive “centromere” at the location suggested by comparison to the other, related genome.


As I look around the room, I see the students are satisfied. I cover some difficult material in this course, and the students are obviously pleased that this topic is so easy to handle. The lines of evidence are easy to follow, and it’s easy to predict and test one’s hypotheses. Then, only after they’ve seen the evidence at least once without the baggage that will inevitably come, I ask them if they know what two species they’ve just compared.

Venema apparently does not provide his students with any information regarding possible alternative hypotheses to explain that data.  Indeed, he displays the usual smug self-satisfied complacency of the committed Darwinist who does not believe there is any other hypothesis.  
Venema concludes:  “I feel learning about evolution in a Christian liberal arts university is one of the very best places to do so, providing the institution treats the topics fairly.” 

Does Venema treat the topic fairly?

More or less, except you don’t write it twice
Then it's not duplicated code as I meant the term. Mung
You write segments of source code that are redundant in case one of the segments fails?
More or less, except you don't write it twice; it's simply deployed to more than one piece of hardware in case one fails, or an extremely rare bug that makes it past testing shows up in one. Walter Bright, a former Boeing engineer and one of my favorite programmers to follow, speaks about this frequently:
It also works incredibly well. Airliners use a dual path system, which means that no single failure can bring it down. If it didn't work, the skies would be raining airplanes. ... Building reliable systems is not about trying to make components that cannot fail. It is about building a system that can TOLERATE failure of any of its components. It's how you build safe systems from UNRELIABLE parts. And all parts are unreliable. All of them. Really. All of them.
Many critical systems designed by humans will have redundancy in case the primary path fails.
Explain how that works with source code. You write segments of source code that are redundant in case one of the segments fails? def happy_path n n / 0 rescue DivideByZeroError sad_path n end def sad_path n n / 0 rescue DivideByZeroError happy_path n end Mung
@Mung Many critical systems designed by humans will have redundancy in case the primary path fails. We see the same thing in our own duplicate genes. From The regulatory utilization of genetic redundancy through responsive backup circuits, PNAS, 2006
many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. ... We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation.
A recently published paper hypothesized that the number of copies of a gene controls the speed of various processes. See figure 3 and the "Gene Balance Hypothesis" section from Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines, PNAS 2012 JoeCoder
Duplicated code is bad design. ;) Mung
JoeCoder, your limits to genetic variation because of sexual recombination paper goes very well with this recent article:
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. https://uncommondesc.wpengine.com/intelligent-design/more-from-ann-gauger-on-why-humans-didnt-happen-the-way-darwin-said/ Science & Human Origins: Interview With Dr. Douglas Axe (podcast on the strict limits found for changing proteins to other very similar proteins) - July 2012 http://intelligentdesign.podomatic.com/entry/2012-07-24T21_33_53-07_00
Here is the a brief sketch of the problems I have with the teaching of evolution as is done currently. Consider the following questions 1. Do you believe in crucifixion? 2. Do you believe in The Crucifixion? They are two vastly different questions. Of course everyone who is sane believes in crucifixion. The Romans accurately described it. Corpses have even been found from Roman times which show evidence of having been crucified. Not everyone believes in The Crucifixion. This implies a belief that the Son of God came to earth to die on a cross for all the sins of the world. His atoning death is available for all. Two very different beliefs. Now take two other questions: 1. Do you believe in evolution? 2. Do you believe in the Theory of Evolution? Any observant person believes in evolution - that process by which populations of organisms change over time. Its obvious that adaptability is built into life. But when one considers the "Theory of Evolution" one is professing belief in a particular type of evolution. A history of life that basically says neo-Darwinism has created all forms of life by chance mutation ( plus other processes ) and natural selection. This has occurred without any input by an intelligent designer. But I contend that most people do not believe in the whole "Theory of Evolution" and its a good thing they don't. Because it is an absurd theory that the Bible says only a fool could believe. Saying "I believe in the theory of evolution" is a logical impossibility. Its logically impossible because the "Theory of Evolution" is not a physical thing. It is a thought. It is just a bunch of words, an immaterial, abstract, object that has no single representation. There is no possible way that an unknowing bunch of chemicals can have a predisposition for an immaterial thing, independent of its representation. Now I believe whole heartedly, that a bunch of chemicals ( genes and cells ) can have a personal predisposition to all kinds of physical things. Pepper, spices, carrots, blonds.... But if materialism is true, there is no possible way for a purely physical brain to be set up to have a predisposition for an abstract, immaterial concept. So to say, that "I am just a bunch of chemicals that came together by random chance," precludes me from having a preference for one immaterial thing over another. In other words, belief in the "Theory of Evolution" precludes the ability to choose to adhere to an abstract belief. Things like meaning, purpose, nobility, can not evolve. Those who believe that they can are only fooling themselves. After many years, no one has a credible model of the evolution of consciousness. Heck we don't even know what it is. So I would think that most people believe some combination of evolution mixed with intelligent intervention. Its the only thing that makes sense, given our ability to choose to believe, advocate for, and even choose to die for an abstract concept. Once we make this admission -- that really the only thing that can account for man's ability to have a preference for one abstract thought over another is the input of intelligent design -- the specific amount of intelligent intervention mixed with just letting natural processes have their way becomes a religious argument. Not a scientific one. JDH
I wish there was a way to edit posts here, I had meant to add these links for point 1, since it's oft-disputed: 1. Sexual recombination slows macroevolution, (summary) JoeCoder
@smiddyone Sorry you're being so outnumbered here--I often face the same fate on reddit and it can be a bit overwhelming. Please disregard Joe, sometimes he takes these debates too personally. I'd like to ask a question about similarity from a different angle--what percentage of DNA similarity is the magic number to confirm that two species do or don't share a common ancestor? Say humans and chimps, 50%, 95%, 98.5% ? Rather, a better criteria is to gauge if evolution can span the difference, given estimated population sizes, mutation rates, timespans, and an idea of the amount of genetic novelty needed. I hold that evolution could not produce a human from a chimp-like ancestor in periods even much longer than 6m years. Take HIV and p. falciparum (common human malaria), two examples from Michael Behe’s book, Edge of Evolution. In the last several decades, each have had around a million times more selection and mutation events than humans would've had since a chimp divergence, yet they’ve each developed 1 and 0 new protein-protein binding sites, respectively, and I think HIV may have duplicated a gene. Many other microbes have also shown remarkable little evolution over similarly vast and rapidly reproducing populations. But in the same time, humans would have needed to develop around 280-1400 proteins of novel function (depending on which study you read and how "novel" is defined) through processes of duplications, fusions, de novo from junk DNA, and some without homologs at all. Give a million times less opportunity, hominins would have had to evolve a thousand times faster. Evolution is a billion times too slow. But even that's too conservative: 1. Sexual recombination slows macroevolution, (summary) 2. Epigenetic changes that form gene networks add another layer of complexity not accounted for here, causing the road from micro to macro to be logarithmic, not linear. 3. Some microbes show similarly little-to-no evolution over not just dozens, but millions of years. 4. Our high mutation rate gives the fittest members of every primate population (including humans) multiple deleterious mutations (most slightly, like rust on a car), causing a net decrease in fitness every generation. Yet beneficials take thousands of years to appear and fixate. Evolution is one step forward, two thousand backward. I or ba77 can cite peer-reviewed sources for each of these, but I'm trying to avoid writing a bibliography again, in order to keep the thread readable. JoeCoder
Of related interest, Casey Luskin has this just up on ENV:
Read Your References Carefully: Paul McBride's Prized Citation on Skull-Sizes Supports My Thesis, Not His - Casey Luskin - August 31, 2012 Excerpt of Conclusion: This has been a long article, but I hope it is instructive in showing how evolutionists deal with the fossil hominin evidence. As we've seen, multiple authorities recognize that our genus Homo appears in the fossil record abruptly with a complex suite of characteristics never-before-seen in any hominin. And that suite of characteristics has remained remarkably constant from the time Homo appears until the present day with you, me, and the rest of modern humanity. The one possible exception to this is brain size, where there are some skulls of intermediate cranial capacity, and there is some increase over time. But even there, when Homo appears, it does so with an abrupt increase in skull-size. ,,, The complex suite of traits associated with our genus Homo appears abruptly, and is distinctly different from the australopithecines which were supposedly our ancestors. There are no transitional fossils linking us to that group.,,, http://www.evolutionnews.org/2012/08/read_your_refer_1063841.html
smiddyone- no need to disprove common descent as no one has proved it. And just because you want to be related to chimps doesn't make it so. Joe
News @ 14 "How important will the genetic similarities seem then?" If dolphins are much more smarter than whales it still would not erase the fact that they are related. This seems to be the new strategy: If you can't disprove common descent, then try to de-emphasize it. It's like saying humans aren't related to chimpanzees because chimps live at the zoo and can't drive cars. smiddyone
@EvilSnack - I'm also a developer. I find patterns of homology in my code all the time. Just today I cloned an entire web page to create another very similar one. Elsewhere I have a ~500 line database wrapper that I wrote in php and subsequently translated to java, c#, and jscript/asp classic as the projects I was working on required. @ba Ha, "nice find" you say? I'm pretty sure I got that source from you. Methinks you don't read what you cite :P JoeCoder
More importantly, similarity isn't exclusive to common descent. Joe
I work in software. Two similar programs could have very different programs. But usually the programs are similar, because the designer (me or one of my co-workers) cut and pasted the code from one program and made the modifications necessary for it to meet the requirements of the second program. Similiarity does not disprove design. EvilSnack
Here are a few neat little videos that show the surprising 'abrupt appearance' facet of the fossil record. i.e. the 'trade secret' of paleontology:
Fish & Dinosaur Evolution vs. The Actual Evidence - video and notes http://vimeo.com/30932397 The Unknown Origin of Pterosaurs - video http://www.youtube.com/watch?v=XP6htc371fM Bird Evolution vs. The Actual Evidence - video and notes http://vimeo.com/30926629 Whale Evolution vs. The Actual Evidence – video - fraudulent fossils revealed http://vimeo.com/30921402 Bat Evolution? - No Transitional Fossils! - video http://www.metacafe.com/watch/6003501/
Might as well repeat this here: Even before the release of "Science and Human Origins" there has been an uproar over human chromosome 2, the alleged fusion of two other chromosomes (still found in other primates) and sharing a common ancestor with chimps. According to evos this was supposed to be a chromosomal fusion that occurred in some gamete and then got passed along- a random event. However if we look at it from a design perspective the randomness disappears. Why? Chromosome/ DNA packaging and chromosome territories. Ya see gene expression and regulation depend on both the packaging and the location of the chromosomes within the nucleus, ie chromosome territories. And if you have two different/ separate chromosomes then they can be packaged differently and ferried around separately also, meaning they can be separated and placed in different territories. So perhaps with humans it is required that the information never be separated. And the easiest way to accomplish that was by splicing the two together. Snip off the excess and splice.* The research would be to determine where HC2 resides in certain tissues and cells and during development and then compare with the two primate chromosomes for the same tissues/ cells and stages of development. So HC2 is explained as a design feature, for humans. It not only helps with reproductive isolation but it also allows for a different gene expression and regulation pattern necessary for the different requirements of humans. * it could also be that the two chimp chromosomes were the result of splitting HC2 into two separate chromosomes Joe
Nice find JoeCoder, I'm surprised that Shermer let it in 'Skeptic' bornagain77
Thanks, JLAfan2001.
I can see your point but are they really “adding” to the evidence or just drawing a conclusion from it?
They are drawing a conclusion, but it is not just based on the evidence, that is the key point. The conclusion is also based upon a preferred paradigm with which they approach the data, coupled with an exclusion of any possibilities that don't fall within that preferred paradigm. Also, some important questions that arise are assumed away or simply ignored (see below).
I can see the problems with the way scientists are portraying it as fact when we really haven’t observed one life-form becoming another. They should be saying this is what we think happened based on what we know but we haven’t seen it happen so we could be wrong.
I agree and I think we are largely on the same page here. It seems however, that perhaps the caveats should be even stronger and broader than simply saying the change of species hasn't been observed. The caveats should also include (i) other possible explanations for the data exist (design or convergence, at the very least), and therefore, not only have we not observed our preferred conclusion, but it is not the only possible conclusion that could reasonably flow from the data; (ii) under our preferred scenario, it is unclear exactly how most of the changes in the chromosomes could have come about in the short time available and been successfully incorporated into the DNA; (iii) we have no idea what would drive the changes (other than pure chance, with the resulting issues of genetic entropy, etc.); (iv) it is unclear whether the observed differences in the DNA in fact produce all the differences we observe in phenotype; (v) it is unclear what other higher-level organismal changes would have to be incorporated to take advantage of the DNA (or conversely, on what basis can we possibly say which of the differences in the DNA actually produce the significant differences we see between humans and other primates?); (vi) the comparisons of DNA typically rely solely on basic sequence and do not take into account three-dimensional structure, placement, concatenation, highly different expressions of particular genes, etc. -- we know very little about these and have no idea whether tweaking particular gene sequences would result in anything like what is being claimed, namely a chimp-like creature turning into a human; (vii) we have no idea whether there are intermediate species and, if so, whether a series of gradual changes would have a realistic chance of enhancing survival and becoming fixed in the population at each step along the way; and so on. I'm just brainstorming these questions as I type. If we spent time on it, we could come up with another dozen related questions that would further call into question, or at least lessen, the certainty with which the proclamation of common descent is made. ----- To put a blunt point on it, assume for a moment that human DNA and chimp DNA were 100% identical. What would that tell us about our decent from chimps? Nothing. It would tell us that our DNA is identical. The story -- the history -- is still open for discussion. Further, identical DNA would underscore (as do the popular claims of '98% identical,' '99% identical' and so forth) that the key differences between the species might not be in the DNA sequence. Eric Anderson
Nice post, JoeCoder Upright BiPed
@smiddyone I don't recall seeing you here before, so if you're new, then welcome. I hope the others here don't run you off with poor manners :P. We need a heterogeneous group in order to have good discussions. But I would like to respond to one of your other points. You wrote:
Denying common descent is miracle begging since most new species arising in the historical record would have had to pop into existence in a cloud of white smoke. Can anyone offer evidence of, or reproduce that?
Paleontologist Donald Prothero had an interesting piece about sudden appearances and stasis in the fossil record in Skeptic Magazine several months back. The whole thing is a great read, but if it's too long, I'll quote you this excerpt:
"For the first decade after the paper [Punctuated Equilibrium] was published, it was the most controversial and hotly argued idea in all of paleontology. Soon the great debate among paleontologists boiled down to just a few central points, which Gould and Eldredge (1977) nicely summarized on the fifth anniversary of the paper’s release. The first major discovery was that stasis was much more prevalent in the fossil record than had been previously supposed. Many paleontologists came forward and pointed out that the geological literature was one vast monument to stasis, with relatively few cases where anyone had observed gradual evolution. If species didn’t appear suddenly in the fossil record and remain relatively unchanged, then biostratigraphy would never work—and yet almost two centuries of successful biostratigraphic correlations was evidence of just this kind of pattern. As Gould put it, it was the 'dirty little secret' hidden in the paleontological closet. Most paleontologists were trained to focus on gradual evolution as the only pattern of interest, and ignored stasis as 'not evolutionary change' and therefore uninteresting, to be overlooked or minimized. Once Eldredge and Gould had pointed out that stasis was equally important ('stasis is data' in Gould’s words), paleontologists all over the world saw that stasis was the general pattern, and that gradualism was rare—and that is still the consensus 40 years later. ... In my dissertation on the incredibly abundant and well preserved fossil mammals of the Big Badlands of the High Plains, I had over 160 well-dated, well-sampled lineages of mammals, so I could evaluate the relative frequency of gradualism versus stasis in an entire regional fauna. ... it was clear that nearly every lineage showed stasis, with one minor example of gradual size reduction in the little oreodont Miniochoerus. I could point to this data set and make the case for the prevalence of stasis without any criticism of bias in my sampling. More importantly, the fossil mammals showed no sign of responding to the biggest climate change of the past 50 million years (the Eocene-Oligocene transition, when glaciers appeared in Antarctica after 200 million years). In North America, dense forests gave way to open scrublands, crocodiles and pond turtles were replaced by land tortoises, and the snails changed from those typical of Nicaragua to those of Baja California. Yet out of all the 160 lineages of mammals in this time interval, there was virtually no response."
Emphasis mine. There are some famous transition sequences (along with their own problems; each has a lively debate), but among 1.2m animal species existing at given time, there are wide ranges of morphologies between many species (e.g. the great variety found in dogs). Yet something like only 5% of an organisms phenotype preserved in the fossil record, even in the rare case for complete skeletons. As Gould remarked on the most well-studied sequence, (Panda's Thumb, 1980, p.126), "Most hominid fossils, even though they serve as a basis for endless speculation and elaborate storytelling, are fragments of jaws and scraps of skulls." Widespread morphological convergence makes a great mess of any remaining evidence. Take this diagram of convergence between marsupial and placental mammals. Given evolution, the mouse and mole are more closely related to the humpback whales and elephants than to marsupial mice and moles, and the wolf is closer to a human or a bat than to the tasmanian wolf. In these cases, fossil evidence would provide a gradual but grossly incorrect sequence. JoeCoder
Can anyone offer a different interpretation of genetic similarity that we could observe in real time, right now?
I can give you two- Common Design and convergence. Joe
smiddyone, Logically, any confirmed prediction has to be a maybe. That means common descent is a maybe. What you are saying about it being the most straight forward interpretation (and thus the correct one) depends on philosophical and theological ideas that eliminate any other competing theory that does not involve reproductive continuity through time. This is the reason Dr. Venema's technique bother's me. He makes it look like it is just about evidence. But it is not. It is also about the uniformity of nature and the non-intervention of God. At least I think that is where he is coming from having read other things about him. If you assume the uniformity of nature through out time there can be no other alternative than reproductive continuity. Maybe that is the case. Maybe common descent is true. But let's not fool ourselves that common descent is the only place the evidence can take this. Why must common design be rejected based on this evidence? Do you have a scientific reason for rejecting common design? Steve_Gann
Barry, The problem is, Venema is only looking at similarities, he is not acknowledging differences. Can't tell from the post what species Venema used, but let's say they are whales and dolphins. Okay, suppose it comes out that whales are basically blowing and breeching, and otherwise doing their thousand millennial thing, and dolphins are flippering around with keyboards, sending rockets to the Moon and probes to Mars, and playing the stock market. How important will the genetic similarities seem then? These are the kinds of questions Christian Darwinists never ask. And they are precisely the questions that threaten to upend their tricky little scheme. News
Well at least we now we are talking about the supernatural. The Big Bang has been recorded as a real event. The sudden materialization of new animals into existence a la from The Enterprise's transporter has not. I forgot who's quote this is but it's something like:"Let's not argue over what God could or couldn't do, but what he has done." smiddyone
correction: when he sees fit "And to insist they are" flexible when you need them to be to allow ‘random’ universes to be created. bornagain77
smiddyone you state:
Denying common descent is miracle begging since most new species arising in the historical record would have had to pop into existence in a cloud of white smoke.
Actually smiddyone since the entire universe 'had to pop into existence in a cloud of white smoke' in the big bang, then there is now no 'scientific' reason to prevent the abrupt appearance on fossils in the fossil record. In fact when this argument is hashed out in its entirety it renders your base materialistic/atheistic philosophy completely absurd: Materialism simply dissolves into absurdity when pushed to extremes and certainly offers no guarantee to us for believing our perceptions and reasoning within science are trustworthy in the first place:
BRUCE GORDON: Hawking's irrational arguments - October 2010 Excerpt: What is worse, multiplying without limit the opportunities for any event to happen in the context of a multiverse - where it is alleged that anything can spontaneously jump into existence without cause - produces a situation in which no absurdity is beyond the pale. For instance, we find multiverse cosmologists debating the "Boltzmann Brain" problem: In the most "reasonable" models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science. http://www.washingtontimes.com/news/2010/oct/1/hawking-irrational-arguments/ Big Brain Theory: Have Cosmologists Lost Theirs? - January 2008 Excerpt: it’s hard for nature to make a whole universe. It’s much easier to make fragments of one, like planets, yourself maybe in a spacesuit or even — in the most absurd and troubling example — a naked brain floating in space.,, Alan Guth, a cosmologist at the Massachusetts Institute of Technology,,, pointed out that some calculations result in an infinite number of free-floating brains for every normal brain, making it “infinitely unlikely for us to be normal brains.” Nature tends to do what is easiest, from the standpoint of energy and probability. And so these fragments — in particular the brains — would appear far more frequently than real full-fledged universes, or than us.,, http://www.nytimes.com/2008/01/15/science/15brain.html?_r=3&pagewanted=1&8dpc The Absurdity of Inflation, String Theory & The Multiverse - Dr. Bruce Gordon - video http://vimeo.com/34468027 And Dr. Gordon's astute observation in his last powerpoint is here: The End Of Materialism? * In the multiverse, anything can happen for no reason at all. * In other words, the materialist is forced to believe in random miracles as a explanatory principle. * In a Theistic universe, nothing happens without a reason. Miracles are therefore intelligently directed deviations from divinely maintained regularities, and are thus expressions of rational purpose. * Scientific materialism is (therefore) epistemically self defeating: it makes scientific rationality impossible.
smiddlyone, you simply have no right, as a atheist/materialist, to insist that the laws of the universe are inflexible whenever you need them to prevent God from intervening in the universe when he sees fit to be flexible when you need them to be to allow 'random' universes to be created. bornagain77
But to expand a bit on what Eric said here:
attaching a further philosophical gloss that it all happened without plan or purpose, we have gone far off the path from the evidence.
i.e. even if Darwinists had been able to prove that similarity was as close as it has falsely been portrayed to be to the general public (98.5%) in the past (approx. 45 million bp), the fact is that Darwinists have no demonstrated mechanism to account for any change at all, much less the massive differences now being found:
The Fate of Darwinism: Evolution After the Modern Synthesis - David J. Depew and Bruce H. Weber - 2011 Excerpt: We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes.,,, http://www.springerlink.com/content/845x02v03g3t7002/ Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. 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/2010/10/response_to_john_wise038811.html
To cut to the chase, Darwinists are approaching the 'problem' from the entirely wrong 'bottom up' conceptual level:
Problems with the Metaphor of a Cell as "Machine" - July 2012 Excerpt: Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life. Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over -- being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle...is one of the best-known examples, but there are many others. Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!,,, http://www.evolutionnews.org/2012/07/problems_with_t062691.html How we could create life: The key to existence will be found not in primordial sludge, but in the nanotechnology of the living cell - Paul Davies - 2002 Excerpt: Instead, the living cell is best thought of as a supercomputer – an information processing and replicating system of astonishing complexity. DNA is not a special life-giving molecule, but a genetic databank that transmits its information using a mathematical code. Most of the workings of the cell are best described, not in terms of material stuff – hardware – but as information, or software. Trying to make life by mixing chemicals in a test tube is like soldering switches and wires in an attempt to produce Windows 98. It won’t work because it addresses the problem at the wrong conceptual level. - Paul Davies http://www.guardian.co.uk/education/2002/dec/11/highereducation.uk Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681
Dr. Stephen Meyer comments at the end of the preceding video,,,
‘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. 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 - (excerpt taken from Meyer/Sternberg vs. Shermer/Prothero debate - 2009)
In fact to get a proper handle on this 'problem', a 'top down' information theoretic approach needs to be adopted that considers, correctly, that information is primary and material substrates are secondary in the hierarchy of the construction and operation of the cell instead of insisting on the insane approach of maintaining 'bottom up' material processes constructed this unfathomable complexity, we find in biological life, all on their own.
Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US
What I love about Venema's teaching is that he uses the most basic,observable,common sense evidence to prove common descent,and common descent is really all that matters. Can anyone offer an example of two blood related beings that are alive today that are not genetically similar? Can anyone offer a different interpretation of genetic similarity that we could observe in real time, right now? Denying common descent is miracle begging since most new species arising in the historical record would have had to pop into existence in a cloud of white smoke. Can anyone offer evidence of, or reproduce that? I think we have a more good old fashioned explanation for how biology comes into existence:born of another animal that is strikingly genetically similar to it's offspring. JDH, how can say it's a religious argument when it is only based on the most straightforward,obvious,logical,non miracle begging scientific evidence? Common descent comes from the most literal translation of the natural record. smiddyone
JoeCoder, that was a good summary of why the chromosome 2 fusion argument does not wash: Moreover if similarities are held to be proof of common descent, why are not dissimilarities held as disproof???
Chimp chromosome creates puzzles - 2004 Excerpt: However, the researchers were in for a surprise. Because chimps and humans appear broadly similar, some have assumed that most of the differences would occur in the large regions of DNA that do not appear to have any obvious function. But that was not the case. The researchers report in 'Nature' that many of the differences were within genes, the regions of DNA that code for proteins. 83% of the 231 genes compared had differences that affected the amino acid sequence of the protein they encoded. And 20% showed "significant structural changes". In addition, there were nearly 68,000 regions that were either extra or missing between the two sequences, accounting for around 5% of the chromosome.,,, "we have seen a much higher percentage of change than people speculated." The researchers also carried out some experiments to look at when and how strongly the genes are switched on. 20% of the genes showed significant differences in their pattern of activity. http://www.nature.com/news/1998/040524/full/news040524-8.html Human Gene Count Tumbles Again - 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences.,,, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. http://www.sciencedaily.com/releases/2008/01/080113161406.htm From Jerry Coyne, More Table-Pounding, Hand-Waving - May 2012 Excerpt: "More than 6 percent of genes found in humans simply aren't found in any form in chimpanzees. There are over fourteen hundred novel genes expressed in humans but not in chimps." Jerry Coyne - ardent and 'angry' neo-Darwinist - professor at the University of Chicago in the department of ecology and evolution for twenty years. He specializes in evolutionary genetics.
This following study hinted at far greater differences than 6%:
Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Casey Luskin - June 2011 Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees) http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html
Further note:
A False Trichotomy Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” https://uncommondesc.wpengine.com/intelligent-design/a-false-trichotomy/ Chimp and human Y chromosomes evolving faster than expected - Jan. 2010 Excerpt: "The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes. http://www.physorg.com/news182605704.html
Moreover the 'anomaly' of unique ORFan genes is found in every new genome sequenced thus far:
Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166
As well, completely contrary to evolutionary thought, these 'new' ORFan genes are found to be just as essential as 'old' genes for maintaining life:
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/releases/2010/12/101216142523.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/content/330/6011/1682.abstract
This following study, in which the functional role of unique ORFan genes was analyzed for humans, 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.,,, (From the PLoS article, author’s summary: We found these genes are scattered across the whole genome, demonstrating that they are generated by many independent events,,, Our data reveal that evolutionary change in the development of the human brain happened at the protein level by gene origination,,) http://the-scientist.com/2011/10/19/new-genes-new-brain/
Eric I can see your point but are they really “adding” to the evidence or just drawing a conclusion from it? It’s the same as a crime scene. The investigators didn’t see what happened but they have to come to a conclusion based on the evidence they gathered (and macro evolution does have some compelling evidence). Otherwise we would never solve any crimes. I can see the problems with the way scientists are portraying it as fact when we really haven’t observed one life-form becoming another. They should be saying this is what we think happened based on what we know but we haven’t seen it happen so we could be wrong. JLAfan2001
JLAfan2001 and smiddyone: Steve_Gann has made an important point. I would state it this way: The thing we can conclusively conclude by observing that two sets of chromosomes share certain similarities is that the two sets of chromosomes share those similarities. That is it. As soon as we start attaching a historical narrative about how one set of chromosomes supposedly came from the other at some point in the past, or about the alleged mechanism(s) involved in getting from chromosome Set A to Set B, or attaching a further philosophical gloss that it all happened without plan or purpose, we have gone far off the path from the evidence. Our storytelling could be correct, but it is far from conclusive that it is. And our historical narrative has its own holes and weaknesses. I think Venema's approach is OK in terms of letting the students examine chromosomal similarities and then telling them after the fact which species were involved. I even like that approach, as it will probably get a lot of interesting questions and discussion going. But he needs to allow the questions and discussion to really continue and dive deep, not just triumphantly proclaim that this comparative analysis somehow proves anything about human evolution. Eric Anderson
I resent any such teaching. The problem is that he is presenting evidence for similar chromosomes and for a fusion event. Is this a scientific argument for "evolution" over "design"? No, as Cornelius would say, it is a "religious" argument for "evolution" over "design". I would suspect that someone steeped in evolutionary thinking just can not see how he is making a religious, not scientific argument. I feel sorry for Dennis. JDH
@smiddyone It's a bit more complicated than that. Re-using a reply I sent to someone else, if you don't mind: ------------------------ First, the ch2 fusion is cherry picking among numerous other genetic scars that show no common ancestry. Evolutionary biologist Richard Sternberg remarked:
"Of all the known ITSs [interstitial telomeric sequences], and there are many in the genomes of chimps and humans, as well as mice and rats and cows..., the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates. In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed.", Richard Sternberg, Evolution News And Views, 2009. Sternberg cites Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates.
Likewise, creation geneticist Jeffrey Tomkins has written:
"I developed software that enables the scanning of whole chromosomes for internal telomere content. ... Surprisingly, I discovered that the entire human genome contains many completely intact internal telomere sequences. My preliminary data suggests that the internal regions of human chromosomes are composed of 0.19 to 0.25 percent 100% sequence identity intact telomere sequences. While this may seem to be a very small amount, consider that chromosome 2 (the supposed fusion product) contains over 91,000 (0.23 percent) intact internal telomere sequences. Fewer than 300 of these can be attributed to the so-called fusion site. Chromosome Y was the most internally dense telomere containing chromosome (0.25 percent).", Designed DNA Blog, 2012
Second, the signature of a fusion event is weak. In making the argument for fusion, Daniel Fairbanks wrote:
"Let's now return to the repeated sequence surrounding the fusion site in figure 1.1. Of the 158 repeats, 44 are perfect copies of TTAGGG or CCCTAA. In most cases, the remaining repeats differ from the standard sequence by no more than one or two base pairs. This is precisely what we expect if the fusion happened long ago in the remote ancestry of humans" Relics of Eden, 2007, p. 27
But telomeric DNA normally consists of thousands of repeats of a 6-base-pair sequence TTAGGG. So if two chromosomes were fused end-to-end, a huge amount of alleged telomeric DNA is missing and/or garbled. Contrary to Fairbank's "precisely what we would expect", others have noted that the site appears far more degenerate than expected, which is especially odd, considering that meiotic recombination is suppressed in pericentric DNA, which should cause it to mutate more slowly; meaning that 6m years isn't enough time to account for what we see.
"Because the fused chromosome is unique to humans and is fixed, the fusion must have occurred after the human–chimpanzee split, but before modern humans spread around the world, that is, between ?6 and ?1 million years ago. This gross karyotypic change may have helped to reinforce reproductive barriers between early Homo sapiens and other species, as the F1 offspring would have had reduced fertility because of the risk of unbalanced segregation of chromosomes during meiosis.", The authors are also surprised to find that telomeric sequences have "degenerated significantly" and are "highly diverged from the prototypic telomeric repeats.", because the alleged fusion event supposedly happened very recently--too recent for such dramatic divergence of sequence. Thus, the paper asks: "If the fusion occurred within the telomeric repeat arrays less than ~6 Mya, why are the arrays at the fusion site so degenerate?" Several ad-hoc explanations are offered for this bad data: (1) they suggest they weren't really joined at their ends, "chromosomes joined at interstitial arrays near, but not actually at, their ends. In this case, material from the very ends of the fusion partners would have been discarded."; (2) they arbitrarily invoke a "high rate of change" in that stretch of DNA, or (3) "Some array degeneracy could be a consequence of sequencing errors.". These all show how poorly the data fits the expectations. Yuxin Fan et al. Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site. Genome Research, 2002. In 2012, creation geneticists Jeffrey Thomkins and Jerry Bergman confirmed the conclusions of this study.
Despite this, we may very well have once had 48 chromosomes in our past. But if you're going to make an argument from similarity, why not cite the markers we know we share with apes, such as the ALU elements or common genes, versus one that depends on so many unknowns? Of course, similarity is no more an argument for common design than common descent. Moreso, fusion events serve as poor taxonomic dividers and don't necessitate a speciation event. Some species show a very diverse range of karyotypes (number of chromosomes), with little-to-no effect on phenotype (how an organism looks and behaves):
It is now considered that there is little or no evidence to suggest that centric fusions in a variety of combinations affect the total productive fitness of domestic sheep", and interestingly, these fusions seem to have little phenotypical effect, "Less than 1% of phenotypically abnormal lambs were recorded in a total of 1995 progeny born over 10 years." Cytogenetics and reproduction of sheep with multiple centric fusions, Reproduction, 1979
"We report an unprecedented amount of chromosomal variation in a natural population of the South American marsh rat Holochlus brasiliensis. This variation consists of four distinct classes of chromosomal rearrangements: whole-arm translocations, pericentric inversions, variation in the amount of euchromatin, and variation in number and kind of supernumerary (B) chromosomes. Twenty-six karyotypes are present among 42 animals.", Hampton L. Carson, Exceptional chromosomal mutations in a rodent population are not strongly underdominant, PNAS, 1989
"The study focuses on 60 species within the vole genus Microtus, which has evolved in the last 500,000 to 2 million years. This means voles are evolving 60-100 times faster than the average vertebrate in terms of creating different species. Within the genus (the level of taxonomic classification above species), the number of chromosomes in voles ranges from 17-64. DeWoody said that this is an unusual finding, since species within a single genus often have the same chromosome number. ... In one species, the X chromosome, one of the two sex-determining chromosomes (the other being the Y), contains about 20 percent of the entire genome. Sex chromosomes normally contain much less genetic information. In another species, females possess large portions of the Y (male) chromosome. In yet another species, males and females have different chromosome numbers, which is uncommon in animals. A final 'counterintuitive oddity' is that despite genetic variation, all voles look alike, said DeWoody’s former graduate student and study co-author Deb Triant. 'All voles look very similar, and many species are completely indistinguishable,' DeWoody said. In one particular instance, DeWoody was unable to differentiate between two species even after close examination and analysis of their cranial structure; only genetic tests could reveal the difference.", Rodent's bizarre traits deepen mystery of genetics, evolution, Purdue University, 2006
Mr. Arrington, Dr. Venema's actions concern me simply from a scientific-logical point of view. It appears he is asking his students to make a prediction from the evidence and then celebrating the confirmation of that prediction as some sort of trustworthy knowledge in favor of common descent. But logically I think that fails. He seems to be arguing like this: Premise 1: If common descent is the reason for the chromosome similarities AND we set the chromosome sequences side by side for visual inspection, Then we would predict the similarities to show transition from one species to another. Premise 2: The sequences show transition. (Confimed prediction) Conclusion: That tells us common descent is the explanation. But the only thing you can conclude from a confirmed prediction is that maybe the speculative explanation (i.e. common descent in this case) is correct. The reason for the maybe is because this form of argument is inductive, not deductive despite the deductive appearance (if it was deductive it would be affirming the consequent). I would expect a science professor to recognize that common descent at best would be a maybe in this case. That would naturally lead to the possibility of other explanations even if other possibilities have not been put forth. Of course in the case of ID another hypothesis has been put forth (I recognize ID is not necessarily against common descent). That would be common design. Steve_Gann
JLAfan2001 asks: Barry What exactly is the possible alternative hypotheses that could explain the similarity with chimpanzee genes and the chromosome fusion? The only other explanation is that the two species were zapped in by the designer who just happened to make them genetically similar and threw in a fusion event just for laughs smiddyone
Barry What exactly is the possible alternative hypotheses that could explain the similarity with chimpanzee genes and the chromosome fusion? JLAfan2001

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