Very different species have very similar genes

_{Denyse O'Leary

December 29, 2014

Genetics, News

2}_{Categories
Genetics
News}

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Did you know: “ … widely divergent species are found to be far more similar to humans than would be presupposed on a Darwinian framework”:

1. Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 2. (Major Differences in higher level chromosome spatial organization)
5:30 minute mark quote: “Basically the dolphin genome is almost wholly identical to the human genome, yet no one would argue that bottle-nose dolphins are our sister species”

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

Despite all this, over at Pom-Pom Central, we recently learned about the “Picture that terrifies creationists”:

Naturally, I thought they had discovered a man actually morphing into a fly.

It turns out, Mooney provides only primate gene sequences showing similar chromosomes of humans, chimpanzees, gorillas, and orangutans. Which mainly shows what genetics doesn’t do.

The current situation should be baffling, though not terrifying, to any reasonable person. It seems there is some design principle at work, in which case it can be usefully studied.

Follow UD News at Twitter!

Hat tip: Philip Cunningham

Comments

neo-Darwinism is gene-centric, and must rely on genes to explain everything; meanwhile, ID, is regulatory gene oriented, as I state above. And IDers were saying this when the large portion of regulatory genes now known to exist was waiting to become known.
A classic, PaV. Here are some predictions from a non-IDer: 1) 'neo-Darwinism' considers genes to include both their coding region AND the regulatory regions and you will be unable to show that this is not true. 2) You have no reason to state that ID is 'regulatory oriented' and you have absolutely no basis to support this claim. 3) You will not be able to point out statements by IDers about being 'regulatory oriented' prior to the discovery of the discovery of many of the regulatory genes now known to exist.hrun0815_{January 2, 2015
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More of the same... Unfortunately, most molecular biologists don't know a lot about evolutionary biology, so HUGO said 100,000 genes and that's the number everyone remembers. In fact, that was pretty much the upper limit, I think the median estimate in the sweepstake that ENSEMBLE held was about 60,000. The low numbers estimated by evolutionary biologists are not just "some person saying something", as you seem to claim. They are estimates based on evolutionary principles, which turned out to be pretty accurate. Your claim was that the small number of protein coding genes was a problem for evolution, but in fact the number was well-estimated from evolutionary principles. I don't know where this claim about evolutionary biology being tied protein coding genes (or indeed ID's fondness for regulatory evolution) comes from. As I said, that regulatory genes are key drivers of evolution has been orthodox evolutionary biology since the 1980s, when ID was still called creation science. The ENCODE project themselves have backed away from their papers' claims about functional elements, which where much less grand than their press releases. The problems with inferring biological function from the sorts of assays used in ENCODE have nothing to do with function being limited to "protein-like activity". As to King and Jukes title,what of it? Modern evolutionary biology is more that "Darwinism", indeed those accurate estimates of the gene content of the human genome use pretty non-Darwinian evolution.wd400_{January 2, 2015
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wd400,
Actually, evolutionary biologists predicted ~20,000 genes long ago.
Then why didn't the biology community accept it? This is a typical answer: yes, somewhere, someone once said this, that or the other. But if the scientific community doesn't settle on that as an answer, can you justify bringing it up and saying: "Oh, we've known that for a long time." What is known is what someone said a long time ago. Abraham Velikovsky was right about the atmospheric content of Venus, and Sagan was incredibly wrong. Yet no one took Velikovsky seriously. neo-Darwinism is gene-centric, and must rely on genes to explain everything; meanwhile, ID, is regulatory gene oriented, as I state above. And IDers were saying this when the large portion of regulatory genes now known to exist was waiting to become known. That you now want to talk about "regulatory" genes as if they're the same thing as "protein coding genes" is the typical Darwinian retrenchment given once it becomes clear that their previous ideas and predictions have been proven wrong. As to citations, just google UD and junk DNA and you'll find plenty of references from years ago. And the trail goes back to the 90's. As to ID being right, please consult the ENCODE project, and not the latest silliness which interprets "function" as meaning only some protein-like activity, IOW, a highly restricted understanding of cellular function. The citation of yours, "King and Juke's famous paper," is very interesting. The title: "Non Darwinian Evolution." I rest my case.PaV_{January 2, 2015
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Still waiting for an answer, BA. If, as you claim, regulatory sequences are "always catastrophically bad", and most of our genome is made of regulatory sequences, then where are all these universally catastrophic consequences of the 50 mutations you, I and the rest of us have?wd400_{January 1, 2015
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bornagain77 (quoting): After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. It's doubtful most biologists have heard of Abel, much less his challenge. In any case, it's a negative entailment. As such, it may just as well represent the limitations of human knowledge as of any underlying biological fact.Zachriel_{December 31, 2014
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PaV, although I was going to ignore wd400s responce because it is, IMHO, so nonsensical, since you have weighed in I would like to point out a few obvious reasons why wd400's response fails. Number one, as referenced previously, all the evidence we have, fossil and genetic, says that humans are in the midst of the slow down hill grind of genetic entropy.
https://uncommondescent.com/genetics/very-different-species-have-very-similar-genes/#comment-539340
wd400's response to all that empirical evidence? Well he does not contest the fact that the rate of mutations are overwhelmingly detrimental and humans suffer many genetic disorders, instead he protests that if mutations were 'always' detrimental in regulatory regions then we should not be here at all, and then follows with the huge non-sequitor, therefore the genome must be mostly junk. The argument is so stupid it is hard to believe that wd400 made it with a straight face. Besides the fact that we now know that there is a tremendous amount of redundancy in genomes, it is also a well known fact that a large percentage of embryos don't make it to maturity and are aborted.
Studies using very sensitive early pregnancy tests have found that 25% of embryos are aborted by the sixth week LMP (since the woman's last menstrual period), even if a woman does not realize it.[9][10] Abortions after the sixth week LMP happen in 8% of pregnancies.[10] The risk of them is "virtually complete by the end of the embryonic period," with a rate of only two percent after 8.5 weeks LMP.[11]
In fact, neo-Darwinist John Avise used this fact of the high failure rate of embryos, among others, to argue, theologically, against Intelligent Design since apparently, in the twisted theology of Darwinian reasoning, God would never allow such things as mutations that caused embryos to be aborted
"The Human Genome and Theology" John Avise - (half way down the page) Excerpt: "Fallible Design (terrible point-mutation diseases either inherited or derived from sporadic mutations along with a extremely high-rate failure of blastulas to implant in the uterus [> 55%, in which the Mother-to-be is unaware of her failed attempt to become pregnant] or undergo spontaneous abortions after implantation [miscarriages in the first trimester, during failed embryogenesis, in which the Mother-to-be coincidentally became aware of her potential pregnancy]);" http://www.grg.org/breakingnews2010.htm
Also of note, fertility rates are dropping worldwide (which, of course, may also be mitigated by other factors besides genetic entropy) http://en.wikipedia.org/wiki/Total_fertility_rate#mediaviewer/File:Trends_in_TFR_1950-2050.png Thus, even cursory examination shows wd400's response, as usual, to be intellectually dishonest to the actual evidence at hand. Moreover, despite whatever snake oil neo-Darwinists may be trying to sell people about the human genome, the fact of the matter is that we have abundant evidence for widespread, extremely complex and overlapping, functionality in the genome:
Biological Information - Not Junk After All 11-29-2014 by Paul Giem https://www.youtube.com/watch?v=xO-7kVBA_JM
Moreover, neo-Darwinists have ZERO evidence of unguided material processes creating any non-trivial functional complexity/information:
The Law of Physicodynamic Incompleteness - David L. Abel Excerpt: "If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise." If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: "No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone." https://www.youtube.com/watch?v=xO-7kVBA_JM
Thus, without a single demonstration that unguided material preocesses can create anything of significance, neo-Darwinian explanations do not even rise to the level of being 'not even wrong' in trying to coherently explain the unfathomed complexity being discovered in life. i.e. Darwinism is a pseudo-science!
"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge http://izquotes.com/quote/147518 It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD https://www.youtube.com/watch?v=_T1v_VLueGk
Verse and Music:
Psalm 139:14 I will praise thee; for I am fearfully and wonderfully made: marvellous are thy works; and that my soul knoweth right well. Good To Be Alive - Official Lyric Video - Jason Gray https://www.youtube.com/watch?v=4omFQJEAAVc
bornagain77_{December 31, 2014
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PaV. I don't even...
Here’s a problem. Before the advent of WGA, the estimate of the number of genes was 100,000. Now, with WGA, it’s all the way down to 20,000, almost the same number as a fly!
Actually, evolutionary biologists predicted ~20,000 genes long ago. It's in Ohno's junk DNA paper(30,000) , one of Crow's papers and King and Juke's famous one puts the upper bound at 40,000 (citing other studies).
The ID prediction is that genes are secondary, regulatory networks primary. The Darwinian view is ‘gene-centric.’ You’ve lost the battle then because the 100,000 gene figure represents your ‘gene-centric’ view of evolution and it has been cut down to 20,000. You’re left to answer why a fly and a human are equal in complexity.
What on earth are you talking about? Regulatory sequences are genes in the gene-centric view of evolution. That most evolution is regulatory evolution has been standard in evolutionary biology for more than 30 years.
Here, again, ID predicted correctly, just as with junk-DNA.
[citation needed]. Both for the claim that IDists predictions about junk DNA have been borne out, and that IDist predicted the number of genes in the human genome (remembering of course that Ohno and Crow did too).wd400_{December 31, 2014
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I can answer the question, BA. Most of the genome is junk so most of the 50 mutations are of no consequence. But you hold that most of the genome has a regulatory function, and that mutations to regulatory sequences are always bad news.
There are 20,000 proteins that are polymorphic. 50 mutations turns out to be one mutation in every 400 genes. How is this a problem? Here's a problem. Before the advent of WGA, the estimate of the number of genes was 100,000. Now, with WGA, it's all the way down to 20,000, almost the same number as a fly! The ID prediction is that genes are secondary, regulatory networks primary. The Darwinian view is 'gene-centric.' You've lost the battle then because the 100,000 gene figure represents your 'gene-centric' view of evolution and it has been cut down to 20,000. You're left to answer why a fly and a human are equal in complexity. If you try and get around that one by invoking alternate splicing, then you run into the problem that alternate splicing is "regulated." Here, again, ID predicted correctly, just as with junk-DNA. You can pooh-pooh the evidence all you want; but you can do so only for so long.PaV_{December 31, 2014
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DATCG: However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. Branching descent is strongly supported for most of eukaryota, which the evidence indicates is monophyletic. While horizontal mechanisms are more prevalent in prokaryotes and near the root of the tree, it's still possible to reconstruct the lines of descent. The base of the tree, though, is still enigmatic.Zachriel_{December 31, 2014
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Abstract: Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.
Tree of Life Dead?
We will argue that inclusive hierarchical classifications do not emerge naturally and consistently from the relevant prokaryotic data considered in general (in their entirety). Instead, they have been imposed on them by selective analyses that are based on the assumption that a tree must be the real natural pattern, even if only certain of the data can be trusted to reveal it. Furthermore, we propose that the underlying historical processes affecting prokaryotes are more complex and various than those imagined by Darwin (or by neo-Darwinists), and not of necessity expected to give rise to a natural hierarchy.
YES, they argue actual data shows patterns and processes are "more complex and various than..." "imagined by Darwin... or Neo-Darwinist," leading to an education that sent a "mixed message..."
Problematically, Darwin depended on the notion that the true pattern of natural relationships is a tree in the construction of his theory of the responsible process and, as Panchen (17) notes, his explanandum was subsequently considered by him as a part of the proof that his theory (explanans) was right. That classifications should be constructed as hierarchies because evolution is a branching process and that hierarchical classification is a proof of branching evolution is the mixed message many of us took from our early education as biologists.
and semicircular...
But we now have ample other evidence supporting the reality of evolution. We could thus dispense with the tree (and such semicircular reasoning), should this particular historical premise about branching fall short, without weakening the solid edifice of evolutionary biology.
but not a problem for evolutionism. To sum up... We can "dispense with" the "mixed message" received in "early education as biologist" and "semicircular reasoning" of Darwin and by neo-Darwinist that "can always be imposed on... data sets by algorithms designed to do so, but at its base the universal TOL(tree of life) rest on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true." Thus removing the "... quixotic pursuit of a single true TOL.DATCG_{December 31, 2014
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lifepsy: Certainly there is a strong nested hierarchy pattern. Some people on this forum disagree, but at least we have found common ground. lifepsy: Of course it is not a signal of common ancestry, at least in any explicit sense. It's an entailment of common descent, and there are various testable mechanisms for anomalies in the nested hierarchy, such as hybridization and natural selection. lifepsy: This is because a common ancestry model can potentially accommodate far too many contradictory nesting patterns. Common descent is an historical process, so there are many ways it can turn. Did you have a specific objection?Zachriel_{December 31, 2014
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zachriel: Are you saying there is not a strong signal of a nested hierarchy? Certainly there is a strong nested hierarchy pattern. Of course it is not a signal of common ancestry, at least in any explicit sense. This is because a common ancestry model can potentially accommodate far too many contradictory nesting patterns.lifepsy_{December 31, 2014
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BA77:
Zach, gives us the exact same link that Dr. Hunter listed to illustrate the problem of unexpected convergent evolution,
Is this the Dr. Hunter of wolves/thylacine fame?sparc_{December 30, 2014
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lifepsy: Your claims about the nested hierarchy are too ambiguous to be meaningful. Are you saying there is not a strong signal of a nested hierarchy?Zachriel_{December 30, 2014
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lifepsy: Except when they don’t, then it is “incomplete lineage sorting” to the rescue, among other rescue devices. zachriel: The nested hierarchy is never exact. Incomplete lineage sorting is just arithmetic, and is fully consistent with population genetics. Nonetheless, there is a strong signal of a nested hierarchy. Your claims about the nested hierarchy are too ambiguous to be meaningful. There is nothing of substance worth rebutting.lifepsy_{December 30, 2014
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bornagain77: gives us the exact same link that Dr. Hunter listed to illustrate the problem of unexpected convergent evolution Unexpected? Let's review it again. 1. Darwin hypothesized that electric organs in fish are due to convergent evolution, adapted from muscle. 2. Scientists determine electric organs in fish are due to convergent evolution, and how they adapted from muscle. See Gallant et al., Genomic basis for the convergent evolution of electric organs, Science 2014. So Darwin hypothesized convergent adaptation from muscle in 1859. Genomic evidence supporting this hypothesis was provided in 2014, a century-and-a-half later. That's quite an amazing bit of science by Darwin. Thank you for bringing it to our attention.Zachriel_{December 30, 2014
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I can answer the question, BA. Most of the genome is junk so most of the 50 mutations are of no consequence. But you hold that most of the genome has a regulatory function, and that mutations to regulatory sequences are always bad news. So, please, tell me how that is compatible with the fact we each have ~50 new mutations? (Or for that matter why you and I differ at about 0.1% of our bases). A straightforward answer if you can. I'll wait...wd400_{December 30, 2014
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Surprise, surprise. I guessed right.
Of note, I’m done responding to these guys.
Oh, and thanks for that. That was probably the funniest thing you ever posted here.hrun0815_{December 30, 2014
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If anything is an example of three dogs chasing their tails in a pointless circle, its the last three responses from Zachriel, hrun0815 and wd400. Zach, gives us the exact same link that Dr. Hunter listed to illustrate the problem of unexpected convergent evolution, as if listing the exact same link illustrating the problem explains the problem, It doesn't even go one inch towards answering the surprising finding/problem. Yet, Zach the dog goes round and round chasing his tail as if listing the exact same link accomplished anything other than to go around in a circle. hrun0815 pretends as if this whole thread, and links I provided in the last comment, has not addressed the main point of the headline, i.e. unexpected genetic similarity in widely divergent species. Yet apparently hrun0815 is convinced that his tail is some alien thing that is out to get him and chases away any way. but wd400 is a bit more coy and tries to get someone else to pointlessly chase his tail for him. Three dogs chasing tails, all three dogs chasing fails! :) Of note, I'm done responding to these guys.bornagain77_{December 30, 2014
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So that's a "no" then, BA?wd400_{December 30, 2014
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BA77:
hrun0815 and exactly what is the neo-Darwinian answer (read ‘just so story’) for widespread convergence, even down to the molecular level, for widely divergent species?
Translation: 'And here is an unrelated smokescreen that I will bolster with countless links and clippings without actually making a single point.' BA, here are some two novel ideas: 1) Would you like to defend or explain the OP's headline? 2) Would you like to do as News says and actually investigate the design principles at work here? No and no? I thought so. Don't worry. Even if you don't answer directly and instead send a barrage of complete irrelevant links I'm sure I guessed your answer correctly.hrun0815_{December 30, 2014
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lifepsy: Except when they don’t, then it is “incomplete lineage sorting” to the rescue, among other rescue devices. The nested hierarchy is never exact. Incomplete lineage sorting is just arithmetic, and is fully consistent with population genetics. Nonetheless, there is a strong signal of a nested hierarchy. bornagain77 (quoting): As we saw above, Darwin argued that the designs of the (many) different electric organs were sufficiently different that they must have arisen independently, and so they would not form a common descent pattern. 1. Darwin hypothesized that electric organs in fish are due to convergent evolution, adapted from muscle. 2. Scientists determine electric organs in fish are due to convergent evolution, and how they adapted from muscle. See Gallant et al., Genomic basis for the convergent evolution of electric organs, Science 2014.Zachriel_{December 30, 2014
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In fact, Simon Conway Morris has a website documenting hundreds, if not thousands, of examples of unexpected 'convergence':
Map Of Life – Simon Conway Morris http://www.mapoflife.org/browse/ Simon Conway Morris: “Fossil evidence demands a radical rewriting of evolution.” – March 2012 Excerpt: “The idea is this: that convergence – the tendency of very different organisms to evolve similar solutions to biological problems – is not just part of evolution, but a driving force. To say this is an unconventional view would be something of an understatement.” https://uncommondescent.com/evolution/simon-conway-morris-fossil-evidence-demands-a-radical-rewriting-of-evolution/
bornagain77_{December 30, 2014
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hrun0815 and exactly what is the neo-Darwinian answer (read 'just so story') for widespread convergence, even down to the molecular level, for widely divergent species? 'Convergent evolution' (homology in unexpected places) is found to be much more widespread than originally thought. Far more often than would be expected under the neo-Darwinian framework.
Fish Have a Toolbox and Several Other Findings - Cornelius Hunter - June 28, 2014 Excerpt: "Hence in the several fishes furnished with electric organs, these cannot be considered as homologous, but only as analogous in function. Consequently there is no reason to suppose that they have been inherited from a common progenitor; for had this been the case they would have closely resembled each other in all respects. Thus the difficulty of an organ, apparently the same, arising in several remotely allied species, disappears," Charles Darwin ,,,, today’s study nullifies Darwin’s second argument. As we saw above, Darwin argued that the designs of the (many) different electric organs were sufficiently different that they must have arisen independently, and so they would not form a common descent pattern. But the new study, which peers deeper into the data, down to the genetic level, finds no such differences. http://darwins-god.blogspot.com/2014/06/fish-have-toolbox-and-several-other.html Bernard d'Abrera on Butterfly Mimicry and the Faith of the Evolutionist - October 5, 2011 Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible. http://www.evolutionnews.org/2011/10/in_this_excerpt_from_the051571.html Convergent evolution seen in hundreds of genes - Erika Check Hayden - 04 September 2013 Excerpt: “These results imply that convergent molecular evolution is much more widespread than previously recognized,” says molecular phylogeneticist Frédéric Delsuc at the The National Center for Scientific Research (CNRS) at the University of Montpellier in France, who was not involved in the study. What is more, he adds, the genes involved are not just the few, obvious ones known to be directly involved in a trait but a broader array of genes that are involved in the same regulatory networks. http://www.nature.com/news/convergent-evolution-seen-in-hundreds-of-genes-1.13679 Newly Discovered Convergent Genetic Evolution Between Bird and Human Vocalization Poses a Severe Challenge to Common Ancestry - Casey Luskin - December 15, 2014 Excerpt: "We've known for many years that the singing behavior of birds is similar to speech in humans -- not identical, but similar -,,, "But we didn't know whether or not those features were the same because the genes were also the same." "Now scientists do know, and the answer is yes -- birds and humans use essentially the same genes to speak.",,, "there is a consistent set of just over 50 genes,,," "These changes were not found in the brains of birds that do not have vocal learning and of non-human primates that do not speak," So certain birds and humans use the same genes for vocalization -- but those genetic abilities are absent in non-human primates and birds without vocal learning? If not derived from a common ancestor, as they clearly were not, how did the genes get there? This kind of extreme convergent genetic evolution points strongly to intelligent design. http://www.evolutionnews.org/2014/12/newly_discovere092041.html Same Old Darwinian Drivel - June 26, 2014 Excerpt: the six electric fish lineages, all of which 'evolved' independently, used essentially the same genes and developmental and cellular pathways to make an electric organ, https://uncommondescent.com/intelligent-design/same-old-darwinian-drivel/#comment-505369 Convergent sequence evolution between echolocating bats and dolphins - Liu et al (2010) Excerpt: We previously reported that the Prestin gene has undergone sequence convergence among unrelated lineages of echolocating bat [3]. Here we report that this gene has also undergone convergent amino acid substitutions in echolocating dolphins, http://www.cell.com/current-biology/abstract/S0960-9822%2809%2902073-9 Study shows butterfly wings contain same (protein) toxin as sea snail - October 16, 2012 http://phys.org/news/2012-10-butterfly-wings-toxin-sea-snail.html "Despite its complexity, C4 photosynthesis is one of the best examples of 'convergent evolution', having evolved more than 50 times in at least 18 plant families (Sage 2004; Conway Morris 2006)." http://mbe.oxfordjournals.org/content/26/8/1909.full.pdf “The reason evolutionary biologists believe in "40 known independent eye evolutions" isn't because they've reconstructed those evolutionary pathways, but because eyes don't assume a treelike pattern on the famous Darwinian "tree of life." Darwinists are accordingly forced, again and again, to invoke convergent "independent" evolution of eyes to explain why eyes are distributed in such a non-tree-like fashion. This is hardly evidence against ID. In fact the appearance of eyes within widely disparate groups speaks eloquently of common design. Eyes are a problem, all right -- for Darwinism.” http://www.evolutionnews.org/2014/03/its_a_shame_rea083441.html
bornagain77_{December 30, 2014
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Zachriel: And yes, ERVs show the same nested hierarchy pattern as other genes, implying common descent. Except when they don't, then it is "incomplete lineage sorting" to the rescue, among other rescue devices. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675975/figure/F4/lifepsy_{December 30, 2014
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Very different species have very similar genes
Yet again the journalistic integrity and science education by News are on full display. Does the post actually explain the headline? What it's actually similar? Which species are we talking about? Does this mean that some supposedly only far related organisms have more similar genes than more closely related ones? What support is there for this assertion? What is this supposed to mean for evolution? Or ID? I'm answer we get... virtually nothing. However, we are treated to this nice little howler:
The current situation should be baffling, though not terrifying, to any reasonable person. It seems there is some design principle at work, in which case it can be usefully studied.
The current situation is neither terrifying not baffling to a reasonable person. There might be some facts that are baffling, but that certainly does not mean the whole situation is. And the second sentence is a perfect way to close out this year. The ID community should take up this call and actually study something. Let's remember this at the end of 2015 and summarize what the ID community found out about the 'design principle' at work here.hrun0815_{December 30, 2014
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wd400 you ask
So, umm…. can you answer the question?
In regards to this question you originally posed:
If (a) regulatory networks are inflexiable (b) most of our genome is made of regulatory sequences and (c) we have ~50 new mutations how are we alive?
And exactly how do you think this question. 'how are we alive?', is not an exponentially worse question for neo-Darwinists to try to answer than it is for IDists to try to answer? Are you thinking along theological, instead of scientific, lines as John Avise did? Dr. John Avise used the fact that mutations are overwhelmingly detrimental, which is actually a powerful scientific argument against Darwinism, as a theological argument for Darwinism since, according to Darwinian theology, God would never allow such things as detrimental mutations:
It Is Unfathomable That a Loving Higher Intelligence Created the Species – Cornelius Hunter – June 2012 Excerpt: “Approximately 0.1% of humans who survive to birth carry a duplicon-related disability, meaning that several million people worldwide currently are afflicted by this particular subcategory of inborn metabolic errors. Many more afflicted individuals probably die in utero before their conditions are diagnosed. Clearly, humanity bears a substantial health burden from duplicon-mediated genomic malfunctions. This inescapable empirical truth is as understandable in the light of mechanistic genetic operations as it is unfathomable as the act of a loving higher intelligence. [112]” – Dr. John Avise – “Inside The Human Genome: A Case For Non-Intelligent Design” (Dr. Cornelius Hunter goes on to comment) "There you have it. Evil exists and a loving higher intelligence wouldn’t have done it that way." – - per Darwin's God blog
As pointed out previously, Dr. John Avise also states this in his book:
“Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens.” John C. Avise - Inside the Human Genome: A Case for Non-Intelligent Design – Pg. 57
Contrary to what Dr. Avise, and apparently other Darwinists, may believe, such an overwhelming rate of detrimental mutations is NOT a point of evidence in favor of Darwinism! In fact, it is a very powerful scientific argument against neo-Darwinian claims,,, That this scientific fact would even have to be pointed out to Darwinists is a sad testimony to how warped Darwinian 'theological' thinking truly is in regards to the actual science at hand. In fact, there is a flat out contradiction to Darwinian theory in having sophisticated, overlapping, repair mechanisms in place to protect the genome against detrimental 'random' mutations: Although evolution depends on 'mutations/errors' to DNA to make evolution plausible, there are multiple layers of error correction in the cell to protect against any "random changes" to DNA from happening in the first place:
The Darwinism contradiction of repair systems Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/ Contradiction in evolutionary theory - video - (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' for Darwinian evolution) http://www.youtube.com/watch?v=dzh6Ct5cg1o The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - February 2011 Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation." http://www.benthamscience.com/open/toevolj/articles/V005/1TOEVOLJ.pdf
The extensive, overlapping, repair mechanisms for DNA include, but are not limited to, the following:
A proofreading system that catches almost all errors A mismatch repair system to back up the proofreading system Photoreactivation (light repair) Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase Base excision repair Nucleotide excision repair Double-strand DNA break repair Recombination repair Error-prone bypass http://www.newgeology.us/presentation32.html
And even with such an sophisticated repair mechanisms in place for the genome, which is a 'paradox' in and of itself which directly contradicts Darwinian theory, the mutation rate, ('50' as even wd400 himself cited), is still well beyond what is the acceptable limit for mutations within Darwinian theory. In other words, a ‘slightly detrimental’ mutation rate of 50 per generation is far greater than what even leading evolutionists agree is an acceptable mutation rate since detrimental mutations will accumulate far faster than ‘selection’ can eliminate them from a genome:
"it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained… it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection… it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements." Hermann Muller quoted by John Sanford; Appendix 1, Genetic Entropy Human evolution or extinction - discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) - video http://www.youtube.com/watch?v=aC_NyFZG7pM
Even viruses and bacteria, which are subject to much more 'purifying selection' than higher organisms are, have a fairly tight constraint on the mutation rate allowed. A constraint that is approx. 10 times below the '50' number that wd400 himself cited.
Beyond A 'Speed Limit' On Mutations, Species Risk Extinction Excerpt: Shakhnovich's group found that for most organisms, including viruses and bacteria, an organism's rate of genome mutation must stay below 6 mutations per genome per generation to prevent the accumulation of too many potentially lethal changes in genetic material. http://www.sciencedaily.com/releases/2007/10/071001172753.htm
of note:
The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; - per Oxford Journals
Thus the answer to your question wd400,,,
how are we alive?
,,, is, although you may 'theologically' refuse to accept the answer wd400, as Kondrashov pointed out, 'we should have died 100 times over if Darwinism were true!' Supplemental note from the 'top down' perspective:
A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html
Of personal note: The question wd400 asked 'how are we alive?' is actually a much more difficult question to try to properly answer than has been touched on here:
The Unbearable Wholeness of Beings - Stephen L. Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. ,,, the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer? Despite the countless processes going on in the cell, and despite the fact that each process might be expected to “go its own way” according to the myriad factors impinging on it from all directions, the actual result is quite different. Rather than becoming progressively disordered in their mutual relations (as indeed happens after death, when the whole dissolves into separate fragments), the processes hold together in a larger unity. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
Verse and Music:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. Paul Baloche - He Is Risen https://www.youtube.com/watch?v=_kbbxraBjy8
bornagain77_{December 30, 2014
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it should, it is a prediction of creationism(s) that common design would equal common genetics for common needs at basic levels of biology. Evolutionism should desire such variety as to go AH HA just as it should be! Genetics as varied as selection on mutations can be. As better investagation of biology happens common design will be the rule and common descent concepts the exception. If you were a creator YOU would use common blueprint designs at basic levels inclusing a system to react to bring change. Yes we are only a little different from kangaroos at genetic levels. As it would be predicted by a creationist thinker. I say evolutionists would like to NOT find common themes in genetics! They would go AH HA . Its very different as a unguided random thing would be. It ain't/ Merry Christmas and another happy year for creationists acoming.Robert Byers_{December 30, 2014
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Quoting from Dr. Sandford's video presentation posted by BA77 above... at about 18 minute mark...
Sanford quotes from PNAS paper on mutations by Michael Lynch(PNAS 107:961-968) - average cell in 15yr old - up to 6000 mutations - skin cell in 60yr old - up to 40,000 mutations - mutation primary cause of aging and death "... little potential for substantially increasing the upper limit of human life span."
Dr. Sanford goes on to discuss his theory of Genetic Entropy and "dissipation of information." Starting after 24:35 mark on video which BA77 points to shows Dr. Sanford refers to population geneticist including Dr. Crow and others...
- Dr. Crow - we're inferior to caveman - Dr. Kondrashov - no human geneticist doubts man is degenerating.(what do Rat Geneticist think?) - Dr. Lynch - even assuming a lower mutation rate, we are degenerating at 1-5% per generation
He quotes Dr. Lynch again. How long can that last?
- in next few centuries, "significant incapacitation at morphological, physiological, and neurobiological levels"
Dr. Lynch's recommendation? To go to the third world where there is more death and less degeneration.DATCG_{December 30, 2014
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Quoting directly from Reuters article, researchers and Center Director... similar...
(Reuters) - Australia's kangaroos are genetically similar to humans and may have first evolved in China, Australian researchers said Tuesday.
What does the "center Director" mean by "same" and similar?
"There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," center Director Jenny Graves told reporters in Melbourne.
chunky genes...
"... thought they'd be completely scrambled, but they're not. There is great chunks of the human genome... right there in the kangaroo genome..."
Sadly, we are not so closely related to hoppers...
Humans and kangaroos last shared an ancestor at least 150 million years ago, the researchers found, while mice and humans diverged from one another only 70 million years ago.
... as we are of mice and men. Explains why I adore cheese and inclined to the animated food extravaganza of Ratatouille via link of a common ancestor. What I don't understand however is how the Rat suddenly leap-frogged past human chefs in gastronomy and the culinary arts.DATCG_{December 29, 2014
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