At last, a proposed answer re 98% human-chimpanzee similarity claim

_{Denyse O'Leary

August 5, 2014

Genetics, Human evolution}

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From this comment (by Gordon Davisson, in response to this post):

In other words, I’m agreeing with Denyse here:

BUT claimed 98% similarity due to a common ancestor (a claim that hundreds of science writers regularly make, in support of common descent) *undermines anything else they have to say on the subject.*

I do not know how to put the matter more simply than this: A person who does not see the problem is not a credible source of information.

He responds:

…just disagreeing about which side is not credible. Take the 98% similarity figure as an example: one of the basic principles of science is that you must follow the evidence. If the evidence supports the 98% figure, and that conflicts with your intuition, then you either have to throw that intuition into the trash bin, or stop claiming to be doing science.

No. Absolutely not.

One should never discard intuitions formed from experience, especially about vast claims. Chimpanzees are so obviously unlike humans – in any way that matters – that claimed huge similarities only cast doubt on genetic science.

Genetic science is likely generally true but needs to be reformed and put in better, more realistic, less theory-laden hands.

In any event, today, vast corruption reigns in science findings. There is no reason to believe anything that contradicts carefully considered experience, simply because the claim appeared in a science journal.

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Comments

"When Theory Trumps Observation" -- the result of decades of academic selective breeding. Similar to when NOAA recently began to revise actual temperature readings and replacing them with what they "should have been" based on predictions by climate models that predict global warming. Rather than falsifying the models, falsify the records.leodp_{August 7, 2014
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DNA contains intelligent information. (Intelligent information = language or mode designed to communicate instructions, order, and / or relationships.) Intelligent information cannot form or advance due to mindlessness. Now, after comparing human and chimp DNA – maybe we could compare the moon landing with flinging poo at one another…Heartlander_{August 7, 2014
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Rodw I know your intentions are good, and I'm aware of those papers bit here is the issue, and please go think about it. Nothing in any of those papers where they speculate, think about, conclude or propose, none of it can actually be tested. It is storytelling at a grand scale and the one thing humans love is a good story. You are welcome to be upset with me, call me closed minded if you must but I will remain skeptical of untestable claims and so should you.....Andre_{August 7, 2014
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There is an omission in all this back-and-forth that is so glaring that, well, I think everyone on both sides should be ashamed of him-or-herself. Namely, what do chimps think about being 98% similar to humans? Surely, being so closely similar to us, they must have some opinion on the matter, like we do. Now maybe they don't hold to their views so strongly as we hold ours, but how will we know if we never ask them? See what I mean by "glaring"?jstanley01_{August 7, 2014
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When Theory Trumps Observation: Responding to Charles Marshall's Review of Darwin's Doubt -Stephen C. Meyer - October 2, 2013 Excerpt: Developmental gene regulatory networks (dGRN) are control systems. A labile (flexible) dGRN would generate (uncontrolled) variable outputs, precisely the opposite of what a functional control system does. It is telling that although many evolutionary theorists (like Marshall) have speculated about early labile dGRNs, no one has ever described such a network in any functional detail -- and for good reason. No developing animal that biologists have observed exhibits the kind of labile developmental gene regulatory network that the evolution of new body plans requires. Indeed, Eric Davidson, when discussing hypothetical labile dGRNs, acknowledges that we are speculating "where no modern dGRN provides a model" since they "must have differed in fundamental respects from those now being unraveled in our laboratories."8 By ignoring this evidence, Marshall and other defenders of evolutionary theory reverse the epistemological priority of the historical scientific method as pioneered by Charles Lyell, Charles Darwin and others.9 Rather than treating our present experimentally based knowledge as the key to evaluating the plausibility of theories about the past, Marshall uses an evolutionary assumption about what must have happened in the past (transmutation) to justify disregarding experimental observations of what does, and does not, occur in biological systems. The requirements of evolutionary doctrine thus trump our observations about how nature and living organisms actually behave. What we know best from observation takes a back seat to prior beliefs about how life must have arisen. http://www.evolutionnews.org/2013/10/when_theory_tru077391.html Gene Regulation Differences Between Humans, Chimpanzees Very Complex – Oct. 17, 2013 Excerpt: Although humans and chimpanzees share,, similar genomes (70% per Tomkins), previous studies have shown that the species evolved major differences in mRNA expression levels.,,, http://www.sciencedaily.com/releases/2013/10/131017144632.htm Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F "Where (chimps and humans) really differ, and they differ by orders of magnitude, is in the genomic architecture outside the protein coding regions. They are vastly, vastly, different.,, The structural, the organization, the regulatory sequences, the hierarchy for how things are organized and used are vastly different between a chimpanzee and a human being in their genomes." Raymond Bohlin (per Richard Sternberg) - 9:29 minute mark of video http://www.metacafe.com/watch/8593991/bornagain77_{August 7, 2014
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Andre You should only be dissppointed if you thought that a complete understanding of evolution in general or the evolution of humans and chimps in particular could fit in a paragraph or two. As for the speculation, some have given you concrete numbers from specific papers to back up a statement. In other cases the speculation is a very small step from things that have been observed over and over. I think your question on expression is a useful topic to explore but I think youre phase "pure dumb luck" is loaded. If I throw a ball of paper behind my head without looking and it lands in the waste-paper basket thats pure dumb luck. If a leaf falls off a tree in the forest and lands on another leaf in the exact same orientation thats not pure dumb luck. Changes in expression are mostly due to random mutations. Every popuation of organisms contains a huge amount of genetic variety. Genetic differences which occur in regions that directly or indirectly influence the expression of other genes will cause a change of expression. Many changes of expression will have no noticable effect. Others will lead to variation in traits that we're familiar with. Some will be slightly harmful but remain in the population, others will be more harmful and lead to disease which will likely be culled. This is not speculation. Its the result of thousands of scientific papers. When 2 identical populations become seperate and stop interbreeding they immediatly start accumulating differences. Many of these differences will be completely invisible. Others will cause changes to the appearance of the 2 populations in trivial ways. Other changes will cause selectable differences between the 2 population and this will cause more rapid change. Eventually this can lead to the production of 2 different species and the more time that elapes the more different they will appear. Epigenetics is not problematic for evolution. Quite the contrary. Decades ago people had more difficulty imagining how evolution in animals could ocurr when they assumed it was due to changes in proteins. Most proteins look pretty similar in different groups and most changes seem to be lethal. So it seemed unlikely that random changes to proteins could lead to recognizable changes. But random changes to regulatory regions are much more likely to lead to non-lethal changes in tissues, structures, organs or limbs etc that could accumulate and/or be selected for in evolution. Epigenetics just takes this one step further. Mutation dont just occur in regulatory regions. They can occur in regions that effect the regulatory regions epigeneticslly. This increases the posibility that a random mutation will lead to a non-harmful change in expression that could contribue to a change in the appearance of an organismRodW_{August 7, 2014
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Thank you for the responses gents, but I have to admit, I'm a bit disappointed, I see allot of, "I think", "could" and speculation..... nothing concrete, which brings me back to the point can you explain the differences in any concrete manner? Why is the expression different? Is it just by pure dumb luck? Lastly if you are a Darwinian please don't get too excited about epigenetics, if you understand what it means you will realize it does not support your view.... not by a long shot, in a nutshell it means information flow is two way, and that complicates matters even more for Darwinian evolution.Andre_{August 7, 2014
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Andre, Anthropic and Gordon, You guys are having an interesting conversation so I think I’ll crash it. To get at functional differences between the human and chimp genomes first consider proteins. About 1/3 of the proteins in human and chimp are identical and the other 2/3rds differ by only 1 or 2 amino acids – a difference of about 0.1 -0.2% overall. There are outliers though. Genes involved in the immune system and some genes involved in connecting cells to the extracellular matrix have more changes. We’d say they are fast evolving proteins but in the case of the ECM proteins that’s probably because the proteins are structural and can tolerate more change with no change in function. There are several hundred proteins that are unique to either chimp or human. In many cases this is because the gene was present in the common ancestor but lost in one lineage but not the other. An example of this would be the olfactory receptors. Most mammals (especially mice) have thousands of genes involved in olfaction ( smelling) Humans have lost most and many are present only as pseudogenes – hence our poor sense of smell. I’m sure many of these losses we share with chimp but I think its likely that there are a fair number of differences in the sets retained. I’m a bit skeptical of this but there seem to be a handful of proteins unique to either lineage that arose de novo from untranscribed regions. These would be random polypeptides that would be retained and have function. The authors who work on this claim there is good evidence for function in these orphan genes. I think the general consensus is that few of the interesting differences between chimps and humans are due to the above differences in proteins. Most have to do with changes in the expression of genes that humans and chimps share in common. I’ll consider an example: The foramen magnum (fm) is the hole at the bottom of the skull from which the spinal cord emerges. In humans it angles straight down- hence our upright posture, in chimps it angles back – more suitable for their knuckle-walking. There could be hundreds or thousands of genes involved in creating the fm. These could be genes involved in the timing and rate of growth of bone. They could be genes involved in transmission of reception of signals to coordinate activities between difference groups of cells….and there are other possibilities etc such as cell death. The important point is that its entirely possible that humans and chimps have an identical set of proteins making the fm and surrounding bone. The difference in placement is due to changes in the expression of the various genes controlling the process of growth. An overly simplistic example, by way of illustration would be a single nucleotide change in an enhancer which controls the expression of a gene involved in bone growth. I think its unlikely that 1 or 2 or 3 changes accounts for the change in the FM between humans and chimps. More likely its dozens of changes, each of which would have no effect in isolation but together lead to the change in morphology we see.RodW_{August 7, 2014
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wd400
Nothing in the paper suggest the tooth is from H. sapiens, and “related to” doesn’t mean “member of”.</blockquote. 'Suggests' is not the most precise term to use, but in any case ... They might not have stated it outright (we have to ignore the scientists' comments interpreting their own report?) doesn't this suggest that there is some likelihood (within Darwinian standards) that they are h. sapien ancestors?
There are three scenarios that might account for the morphological details in the Qesem teeth. The first one is of a local archaic Homo population occupying southwest Asia during the Middle Pleistocene, to which the Qesem specimens would be attributed. Perhaps relevant in this regard, the Qesem lithic assemblages studied to date indicate a local origin, with no evidence of African and or European cultural affinities (Barkai et al., 2005; Gopher et al., 2005; Barkai et al., 2009). Albeit the lack of other diagnostic Middle Pleistocene SW Asian teeth, considering the evidence in its entirety, we believe that the Qesem ‘‘package’’ is more Skhul/Qafzeh like, even if some of its features are plesiomorphous
Silver Asiatic_{August 7, 2014
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correction: whatever silly tricks you need to pull to get teh human-chimp similarity up to 99% There all better :)bornagain77_{August 7, 2014
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A related reading for all interested parties:
Very appropriate article. Thank you.jerry_{August 7, 2014
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Silver Asiatic, Nothing in the paper suggest the tooth is from H. sapiens, and "related to" doesn't mean "member of". Mahuna, The thing is, whatever silly tricks you need to pull to get teh human-chimp differenec down to 70% would also bring the human-[anything else] coparison down in the same way. There is now way to escape that (human-chimp) are the closest (and share many differences from other apes). anthropic, Read the UD threads from the time of Morans post -- you'll see most of the IDists finally came around to the mainstream position (after some fairly embarrassing mistakes and hold outs).wd400_{August 7, 2014
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/// you’ve already told us science has figured out the similarities, if the one is so easy why is the latter so hard? /// Epigenetics - a relatively new field is beginning to explain differences between species even when the genomes are very similar. Why is figuring out differences hard? Because genomes are regulated, switched on/off in many different ways. Even a subtle change in gene regulation can lead to vastly different outcomes.Evolve_{August 7, 2014
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Andre, //as an engineer I hold that the parts used (proteins) between humans and chimps need to be very similar because as carbon based life forms there would be some minimum requirement to allow for survival. /// Comparison of living things with engineered structures is wrong. Living things fall automatically into what's called a nested hierarchy, i.e a groups-within-groups arrangement. Imagine nested gift boxes. You open one large box to find a smaller box inside it. You open the second box to find another smaller box within it. And so on. That's how living things arrange. The most-related species fall inside the same group (box). But this group fits neatly inside a larger group (larger box). That larger group fits neatly inside an even larger group (an even larger box). And so on. For eg: humans and chimps are primates. All primates fall within a larger group called mammals. All mammals fit inside an even larger group called vertebrates. All vertebrates fit inside an even more large group called deuterostomes. All deuterostomes fall within a bigger group called animals. All animals fit inside a much bigger group called eukaryotes. Members of each group share unique features that are absent from those outside it. But at a more inclusive level, they also share some features with the larger groups in which they're enclosed. The degree of similarities decrease as you go outward from the smallest box to the largest. For eg: All mammals have hair - a unique feature absent in all other vertebrates. But mammals also share some features with the larger vertebrate group in which they're enclosed, a backbone for instance. This kind of nested arrangement is absent in human-designed/engineered objects. It's only found in naturally evolved things like living beings. As such, nested hierarchy provides strong support for a natural explanation of life as opposed to design.Evolve_{August 7, 2014
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Gordon Davisson @ 17, ///if you use my #4 method (where indels count proportional to their length, rather than as single differences), you get around 5% total difference (or 95% similarity)./// This is not right. Indels have to be counted as single differences since each insertion and deletion happen in one go - in one mutational event. For eg: If an insertion or deletion is 100 bases long, then it should not be counted as 100 mutations, but as 1 mutation.Evolve_{August 7, 2014
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#48 Gordon Thank you for the reply, yes I am more interested in the functional differences, as an engineer I hold that the parts used (proteins) between humans and chimps need to be very similar because as carbon based life forms there would be some minimum requirement to allow for survival. But let me ask you this, why don't you think about the problem a little more on why the functional differences are so difficult to understand. Just a word of caution please don't say that science is still figuring this out, because in the same breath you've already told us science has figured out the similarities, if the one is so easy why is the latter so hard? If you don't know the answer, I'll offer my assistance..... Story telling on similarities are easy.......Andre_{August 7, 2014
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A related reading for all interested parties: http://sites.bio.indiana.edu/~hahnlab/MediaFiles/GeneFamilies/Science_2007.pdf The word 'myth' again makes it to the header in relation to the evolutionary paradigm. Human/chimp overestimated similarity, junk DNA, what other myths shall we see 'thrown into the trash bin' in future?EugeneS_{August 7, 2014
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Gordon 48, thanks for the response to my question. It was quite sincere and I appreciate your effort. Right now we have dueling scenarios regarding this issue, with BA 77 citing very different study results than Moran got. I admit to being skeptical that primates can fix tens of millions of mutations in 6 million years, or even in the lifetime of the universe. However, I will look at Moran's analysis and I thank you for bringing it up.anthropic_{August 6, 2014
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footnote to the 'homology problem' for Darwinists: 'Convergent evolution' (i.e. 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.
"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 In fact, Simon Conway Morris has a website documenting hundreds, if not thousands, of examples of '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/ 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 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
bornagain77_{August 6, 2014
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Davisson, regardless of Moran's back of the envelope calculation, (with highly questionable assumptions I might add), you have no empirical evidence that unambiguously beneficial mutations can fix in a metazoan population:
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 Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that 'for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years' (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461
Moreover, Behe's 'Edge of Evolution' has now been vindicated in the lab;
podcast - Michael Behe: Vindication for 'The Edge of Evolution,' Pt. 2 http://intelligentdesign.podomatic.com/entry/2014-08-06T15_26_19-07_00
Nor do Darwinists have any empirical evidence that mutations can produce radical changes in basic morphology:
Response to John Wise - October 2010 Excerpt: A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html
Thus, Neo-Darwinism, despite all the bluff and bluster from neo-Darwinists, is devoid of ANY substantiating evidence that changes to genotype can produces fundamentally new changes in phenotype:
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/ With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory - November 2011 Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,, http://www.evolutionnews.org/2011/11/with_a_startling_candor_oxford052821.html Not Junk After All—Conclusion - August 29, 2013 Excerpt: Many scientists have pointed out that the relationship between the genome and the organism — the genotype-phenotype mapping — cannot be reduced to a genetic program encoded in DNA sequences. Atlan and Koppel wrote in 1990 that advances in artificial intelligence showed that cellular operations are not controlled by a linear sequence of instructions in DNA but by a “distributed multilayer network” [150]. According to Denton and his co-workers, protein folding appears to involve formal causes that transcend material mechanisms [151], and according to Sternberg this is even more evident at higher levels of the genotype-phenotype mapping [152]. https://uncommondescent.com/junk-dna/open-mike-cornell-obi-conference-chapter-11-not-junk-after-all-conclusion/
bornagain77_{August 6, 2014
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JLA, first, refresh your familiarity with the WACs, and above: Common descent, even to universal degree is distinct from the design inference -- cf. Michael Behe's view and that of Wallace, co founder of modern evolutionary theory. But if you conflate that with UCD by blind chance and mechanical necessity you will conflate what should be separated. Beyond, blind chance and mechanical necessity cannot credibly account for FSCO/I, which is necessary for OOL, and origin of main body plans. The presence of FSCO/I is indicative of the only empirically warranted cause, design. KFkairosfocus_{August 6, 2014
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Heck, chimps aren't even closely related to chimps!Mung_{August 6, 2014
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The last I saw, the 98%, which I thought was only 95%, is now down around 70%. So humans are related to chimps the same way we're related to horses and dogs. There are many better explanations at this site on the specifics of the miscounting, but the analogy used is "Hamlet" is 95% the same as a modern English dictionary because most of the individual words (though none of the sentences or paragraphs) appear in the dictionary. The one I like is: Jellyfish are 98% water. Clouds are 98% water. Therefore jellyfish are closely related to cloudsmahuna_{August 6, 2014
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#43 wd400 It appears that Discover Magazine was having a difficult time dealing with the implications that the scientists offered. The scientists apparently couldn't arrive at a conclusion that was consistent with their own paper - or perhaps not, it depends ...
The new paper documents the struggle of the scientists to figure out who the Qesem teeth belong to. In some ways, they seem more like Neanderthal teeth. In others, they seem more like the choppers of Homo sapiens, as represented by the Skhul/Qafzeh fossils. The authors tilt towards a relationship with Homo sapiens, but mostly because the teeth are “plesiomorphous.” ['Tilt toward', i.e. the scientists favored that explanation while Discover Magazine did not.] Ari Gopher, the lead author on the paper, about the hype (and the take-downs from me and Switek). The article is particularly useful for finally tracking down the source of all these articles: a press release from Tel Aviv University that claims that "evidence was discovered pointing to the existence of modern man (Homo sapiens) in Israel as early as 400,000 years ago." (The press release was only in Hebrew, so I'm relying on Nature's translation.) Gopher claims that he told all the reporters who called him to be very cautious, but didn't think the press release was incorrect. "We offer the most reasonable conclusion based on the statistical evidence: that they represent the same population as the Skhul and Qafzeh finds, thus pushing the date for that type of early man back to a much earlier time."
Scientist offers an interpretation of the data. That's the way it works. Evolution isn't exactly a precise science.Silver Asiatic_{August 6, 2014
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Anthropic, #22:
How long would it take for the mutations necessary to take place and become fixed in a primate population?
The observed divergence is about what we expect based on measured mutation rates and fossil-record-based estimates of how long ago the lineages diverged. Larry Moran did a quick summary of the math a few months ago ("Why are the human and chimpanzee/bonobo genomes so similar?") (which was then followed by a long discussion in which VJTorley and some others gradually got the hang of the neutral theory of evolution). Andre, #21:
Mark Frank & all skeptics alike I have a challenge for you….. Instead of explaining the similarities between humans and chimps, can you make the effort to explain the differences?
The project is well underway, but it's being led by scientists who're way more knowkedgable and competent than me (I won't speak for Mark). If you take a look at "Initial sequence of the chimpanzee genome and comparison with the human genome" (by The Chimpanzee Sequencing and Analysis Consortium, Nature 437, 69-87 ,1 September 2005), it has extensive coverage of both the mechanics of the changes (look at the "Genome evolution" section, and its subsections "Nucleotide divergence" [i.e. point mutations], "Insertions and deletions" [indels], "Transposable element insertions", and "Large-scale rearrangements"). (Note: you may find this and other technical articles on the subject rather dense and hard to read; they're really written for others working in or near the field, so they tend to assume a lot of background knowledge. The alternative, or course, is to read popularized summaries; but if you don't trust those to be accurate...) But you're probably more interested in functional changes than what happened at the DNA level, right? That's a much harder question for two reasons: it's very hard to figure out the effects of a given genetic change just from knowing the difference in DNA sequence, and that most of the changes are functionally neutral (making for a bit of a needle-in-haystack problem). As the "Initial sequence..." paper puts it:
The hardest such question is: what makes us human? The challenge lies in the fact that most evolutionary change is due to neutral drift. Adaptive changes comprise only a small minority of the total genetic variation between two species. As a result, the extent of phenotypic variation between organisms is not strictly related to the degree of sequence variation. For example, gross phenotypic variation between human and chimpanzee is much greater than between the mouse species Mus musculus and Mus spretus, although the sequence difference in the two cases is similar. On the other hand, dogs show considerable phenotypic variation despite having little overall sequence variation (~0.15%). Genomic comparison markedly narrows the search for the functionally important differences between species, but specific biological insights will be needed to sift the still-large list of candidates to separate adaptive changes from neutral background.
...which is not to say the problem is unassailable. Just in that paper alone, for example, they take several approaches to locating genes that've undergone positive selection (and therefore are expected to contain functionally significant changes). See the "Rapid evolution in individual genes" and the following sections, as well as, "Signatures of strong selective sweeps in recent human history". And of course, that's just one particular paper (and almost a decade old!). There's been far more work done on the subject since then, but I'm not familiar with it to give you a very good overview. But as usual in any active field of science, we know more than we did last year, and we'll know more still next year.Gordon Davisson_{August 6, 2014
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Embryology -
Icons of Evolution 10th Anniversary: Haeckel's Bogus Embryos - January 2011 - video http://www.youtube.com/watch?v=lAC807DAXzY Haeckel's Embryos - original fraudulent drawing http://www.darwinthenandnow.com/wp-content/uploads/2009/11/Haeckels-Embryos-Cropped-II.jpg Actual Embryos - photos (Early compared to Intermediate and Late stages); http://www.ichthus.info/Evolution/PICS/Richardson-embryos.jpg There is no highly conserved embryonic stage in the vertebrates: - Richardson MK - 1997 Excerpt: Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel's drawings, http://www.ncbi.nlm.nih.gov/pubmed/9278154 The mouse is not enough - February 2011 Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.” http://www.the-scientist.com/news/display/57986/
Lab experiments –
Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282 Where's the substantiating evidence for neo-Darwinism? https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit Peer-Reviewed Research Paper on Plant Biology Favorably Cites Intelligent Design and Challenges Darwinian Evolution - Casey Luskin December 29, 2010 Excerpt: Many of these researchers also raise the question (among others), why — even after inducing literally billions of induced mutations and (further) chromosome rearrangements — all the important mutation breeding programs have come to an end in the Western World instead of eliciting a revolution in plant breeding, either by successive rounds of selective “micromutations” (cumulative selection in the sense of the modern synthesis), or by “larger mutations” … and why the law of recurrent variation is endlessly corroborated by the almost infinite repetition of the spectra of mutant phenotypes in each and any new extensive mutagenesis experiment instead of regularly producing a range of new systematic species… (Wolf-Ekkehard Lönnig, “Mutagenesis in Physalis pubescens L. ssp. floridana: Some Further Research on Dollo’s Law and the Law of Recurrent Variation,” Floriculture and Ornamental Biotechnology Vol. 4 (Special Issue 1): 1-21 (December 2010).) http://www.evolutionnews.org/2010/12/peer-reviewed_research_paper_o042191.html podcast - Michael Behe: Vindication for 'The Edge of Evolution' http://intelligentdesign.podomatic.com/entry/2014-08-04T17_51_38-07_00
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What would convince me that universal common descent was true? Easy, some way to objectively test the claim. A starting point would be to know what, exactly, makes an organism what it is. If it isn't the genome then changes to genomes cannot produce different types of organisms. ERVS? Nope they just look like they could be remnants of some viral infection. Chromosome fusion 2? IF it happened it happened in the human lineage and had nothing to do with common ancestry with chimps Biogeography – nope what does that have to do with universal common descent? DNA similarities – nope- common design Population genetics – nope- has nothing to do with universal common descent and relies on simplistic modelling Embryology – nope- doesn't help universal common descent seeing that you have to be able to account for embryonic development and you cannot Lab experiments – nope- they support baraminologyJoe_{August 6, 2014
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fossil record -
Fossil record: Leading paleontologists on the true state of the fossil record: Excerpt: "A major problem in proving the theory has been the fossil record; the imprints of vanished species preserved in the Earth's geological formations. This record has never revealed traces of Darwin's hypothetical intermediate variants - instead species appear and disappear abruptly, and this anomaly has fueled the creationist argument that each species was created by God." Paleontologist, Mark Czarnecki "There is no need to apologize any longer for the poverty of the fossil record. In some ways, it has become almost unmanageably rich and discovery is outpacing integration. The fossil record nevertheless continues to be composed mainly of gaps." T. Neville George - Professor of paleontology - Glasgow University, "Evolution requires intermediate forms between species and paleontology does not provide them." David Kitts - Paleontologist - D.B. Kitts, Paleontology and Evolutionary Theory (1974), p. 467. "The long-term stasis, following a geologically abrupt origin, of most fossil morphospecies, has always been recognized by professional paleontologists" – Stephen Jay Gould - Harvard etc.. etc.. etc.. https://docs.google.com/document/d/15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg/edit
Fox Pr gene -
Richard Dawkins claimed that the FOXP2 gene was among ‘the most compelling evidences’ for establishing that humans evolved from monkeys, yet, as with all the other evidences offered from Darwinists, once the FOXP2 gene was critically analyzed it fell completely apart as proof for human evolution: Dawkins Best Evidence (FOXP2 gene) Refuted - video http://www.youtube.com/watch?v=IfFZ8lCn5uU In the following paper, even the Darwinists who authored the paper admit that the FOXP2 gene evidence is ‘tenuous’,, Human brain evolution: From gene discovery to phenotype discovery - Todd M. Preuss - February 2012 Excerpt: It is now clear that the genetic differences between humans and chimpanzees are far more extensive than previously thought; their genomes are not 98% or 99% identical.,,, ,,our understanding of the relationship between genetic changes and phenotypic changes is tenuous. This is true even for the most intensively studied gene, FOXP2,, In part, the difficulty of connecting genes to phenotypes reflects our generally poor knowledge of human phenotypic specializations, as well as the difficulty of interpreting the consequences of genetic changes in species that are not amenable to invasive research. http://www.pnas.org/content/109/suppl.1/10709.full.pdf As well, the primary piece of evidence, at the Dover trial, trying to establish chimp human ancestry from SNP (Single Nuecleotide Polymorphism) evidence was overturned: Dover Revisited: With Beta-Globin Pseudogene Now Found to Be Functional, an Icon of the “Junk DNA” Argument Bites the Dust - Casey Luskin - April 23, 2013 http://www.evolutionnews.org/2013/04/an_icon_of_the_071421.html
African origins -
"At some future period, not very distant as measured by centuries, the civilised races of man will almost certainly exterminate, and replace, the savage races throughout the world. At the same time the anthropomorphous apes, as Professor Schaaffhausen has remarked, will no doubt be exterminated. The break between man and his nearest allies will then be wider, for it will intervene between man in a more civilised state, as we may hope, even than the Caucasian, and some ape as low as a baboon, instead of as now between the negro or Australian and the gorilla" ? Charles Darwin, The Descent of Man Yet contrary to what Darwin presupposed, it is found that the differences between individuals in a population are far greater than differences between populations: Genetic Similarities Within and Between Human Populations – 2007 Excerpt: The proportion of human genetic variation due to differences between populations is modest, and individuals from different populations can be genetically more similar than individuals from the same population. Yet sufficient genetic data can permit accurate classification of individuals into populations. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1893020/ Race in a Genetic World – May-June 2008 Excerpt: ,,85 percent occurs within geographically distinct groups, while 15 percent or less occurs between them. (Agassiz 1972) http://harvardmagazine.com/2008/05/race-in-a-genetic-world-html In fact, Africans are more genetically robust than Europeans, who have substantially reduced genetic diversity; "We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations," Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. "Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians." Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University "La Sapienza," Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.- New analysis provides fuller picture of human expansion from Africa - October 22, 2012 Excerpt: A new, comprehensive review of humans' anthropological and genetic records gives the most up-to-date story of the "Out of Africa" expansion that occurred about 45,000 to 60,000 years ago. This expansion, detailed by three Stanford geneticists, had a dramatic effect on human genetic diversity, which persists in present-day populations. As a small group of modern humans migrated out of Africa into Eurasia and the Americas, their genetic diversity was substantially reduced. http://phys.org/news/2012-10-analysis-fuller-picture-human-expansion.html
morphology -
The Types: A Persistent Structuralist Challenge to Darwinian Pan-Selectionism - Michael J. Denton - 2013 Excerpt: Cell form ,,,Karsenti comments that despite the attraction of the (genetic) blueprint model there are no “simple linear chains of causal events that link genes to phenotypes” [77: p. 255]. And wherever there is no simple linear causal chain linking genes with phenotypes,,,—at any level in the organic hierarchy, from cells to body plans—the resulting form is bound to be to a degree epigenetic and emergent, and cannot be inferred from even the most exhaustive analysis of the genes.,,, To this author’s knowledge, to date the form of no individual cell has been shown to be specified in detail in a genomic blueprint. As mentioned above, between genes and mature cell form there is a complex hierarchy of self-organization and emergent phenomena, rendering cell form profoundly epigenetic. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2013.3/BIO-C.2013.3 Since neo-Darwinism (i.e. reductive materialism) cannot even explain morphology (i.e. body plans) in the first place, I guess JLAfan2001 meant homology instead of morphology. The following article & video shows why homology fails as evidence for common descent: Repeated acquisition and loss of complex body form characters: Cornelius Hunter - December 2011 Excerpt: In other words, morphological patterns in biology, including the pentadactyl structure, do not fit the common descent model. This has evolutionists doing mental gymnastics as limbs and other designs must come and go as needed to make sense of evolution. They are lost, then reevolved, then lost, then whatever. It is all just storytelling. 'per Darwin's God - Cornelius Hunter PhD. Investigating Evolution: Homology - video http://www.youtube.com/watch?v=XgXT9sU6y18
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Chromosome Fusion 2 -
Refutation Of Chromosome 2 argument for common ancestry and Vitamin C pseudogene - https://docs.google.com/document/d/1enllGchcY4Thz0xWFG8Rj8Y0bddOcBdIzKeoY1XxSqs/edit
Biogeography -
Here is how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations: More Biogeographical Conundrums for Neo-Darwinism – March 2010 http://www.evolutionnews.org/2010/03/sea_monkeys_are_the_tip_of_the032471.html The Case of the Mysterious Hoatzin: Biogeography Fails Neo-Darwinism Again – Casey Luskin – November 5, 2011 Excerpt: If two similar species separated by thousands of kilometers across oceans cannot challenge common descent, what biogeographical data can? The way evolutionists treat it, there is virtually no biogeographical data that can challenge common descent even in principle. If that’s the case, then how can biogeography be said to support common descent in the first place? http://www.evolutionnews.org/2011/11/the_case_of_the_mysterious_hoa052571.html As Evidence of Darwinian Evolution, Biogeography Falls Well Short of Satisfying - Jonathan M. - December 6, 2012 http://www.evolutionnews.org/2012/12/as_evidence_of5067151.html
DNA similarities -
Logged Out - Scientists Can't Find Darwin's "Tree of Life" Anywhere in Nature by Casey Luskin - Winter 2013 Excerpt: the (fossil) record shows that major groups of animals appeared abruptly, without direct evolutionary precursors. Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,, Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance: • A 1998 paper in Genome Research observed that "different proteins generate different phylogenetic tree[s]."6 • A 2009 paper in Trends in Ecology and Evolution acknowledged that "evolutionary trees from different genes often have conflicting branching patterns."7 • A 2013 paper in Trends in Genetics reported that "the more we learn about genomes the less tree-like we find their evolutionary history to be."8 Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled "Why Darwin Was Wrong about the Tree of Life."9 The author quoted researcher Eric Bapteste explaining that "the holy grail was to build a tree of life," but "today that project lies in tatters, torn to pieces by an onslaught of negative evidence." According to the article, "many biologists now argue that the tree concept is obsolete and needs to be discarded.",,, Syvanen succinctly summarized the problem: "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely. What would Darwin have made of that?" ,,, "battles between molecules and morphology are being fought across the entire tree of life," leaving readers with a stark assessment: "Evolutionary trees constructed by studying biological molecules often don't resemble those drawn up from morphology."10,,, A 2012 paper noted that "phylogenetic conflict is common, and [is] frequently the norm rather than the exception," since "incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species."12,,, http://www.salvomag.com/new/articles/salvo27/logged-out.php
Population genetics -
Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory - 2008 Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue. Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person. http://www.icr.org/i/pdf/technical/Using-Numerical-Simulation-to-Test-the-Validity-of-Neo-Darwinian-Theory.pdf Calling all Darwinists, where is your best population genetics simulation? - September 12, 2013 Excerpt: So Darwinists, what is your software, and what are your results? I’d think if evolutionary theory is so scientific, it shouldn’t be the creationists making these simulations, but evolutionary biologists! So what is your software, what are your figures, and what are your parameters. And please don’t cite Nunney, who claims to have solved Haldane’s dilemma but refuses to let his software and assumptions and procedures be scrutinized in the public domain. At least Hey was more forthright, but unfortunately Hey’s software affirmed the results of Mendel’s accountant. https://uncommondescent.com/evolution/icc-2013-calling-all-darwinists-where-is-youre-best-population-genetics-simulation/ Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle - "Haldane's Ratchet" - Christopher L. Rupe and John C. Sanford - 2013 Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage. Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as "Haldane's Dilemma" is very real. Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon "Haldane's Ratchet". http://media.wix.com/ugd/a704d4_47bcf08eda0e4926a44a8ac9cbfa9c20.pdf
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Silver Asiatic, Don't rely on the Daily Mail for science reporting: http://blogs.discovermagazine.com/loom/2010/12/29/oldest-homo-sapiens-fossil-journalistic-vaporware/wd400_{August 6, 2014
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