Human and chimp DNA: They really are about 98% similar

_{Vincent Torley

October 22, 2015

Intelligent Design}

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A few days ago, scientist and young-earth creationist Dr. Jay Wile wrote a post on his Proslogion blog, in which he reported that Dr. Jeff Tomkins had abandoned his claim that human and chimpanzee DNA are only about 70% similar, in favor of a revised figure of 88%. But even that figure is too low, according to the man who spotted the original flaw in Dr. Tomkins’s work.

Dr. Wile reports:

More than two years ago, Dr. Jeffrey P. Tomkins, a former director of the Clemson University Genomics Institute, performed a detailed, chromosome-by-chromosome comparison of human and chimpanzee DNA using a widely-recognized computer program known as BLAST. His analysis indicated that, on average, human and chimpanzee DNA are only about 70% similar. This is far, far, below the 95-99% numbers that are commonly cited by evolutionists, so once I read the study, I wrote a summary of it. Well, Dr. Tomkins has done a new study, and it invalidates the one he did two years ago.

The new study was done because last year, a computer programmer of financial trading algorithms (Glenn Williamson) discovered a bug in the BLAST algorithm that Tomkins used. This bug caused the program to ignore certain matches that should have been identified, which led to an artificially low similarity between the two genomes.

Here is what Glenn Williamson has to say about himself:

Yeah – 36 year old, stay-at-home father of four – including triplets, ha! 🙂

I don’t have any formal qualifications in genetics, or anything biological for that matter. I have a bachelors degree in computing science (i.e. programming) from the University of Technology in Sydney. Started my career as a programmer, but transitioned into derivatives trading, which is a lot more fun…

And for what it’s worth, I believe that my paper is more of a computing science paper than a genetics paper. It’s more my area of expertise than Jeff Tomkins’ area.

Glenn Williamson’s detailed takedown of Dr. Tomkins’s 70% similarity figure can be accessed here. Dr. Tomkins claims he submitted his paper to the creationist publication, Answers Research Journal, but it was never published. Here’s an excerpt from the paper (emphasis mine – VJT):

In this paper I carefully reproduce a subset of Dr Tomkins’ results, and show clearly and unambiguously that Dr Tomkins has fallen victim to a serious bug in the software used to obtain his results. It is this bug that causes Dr Tomkins to report the erroneous figure of 70% similarity. After correcting for both the effects of this bug and some non-trivial errors in Dr Tomkins’ methodology, I report an overall similarity of 96.90% with a standard error of ±0.21%. This figure includes indels, and the result is largely in line with the secular scientific consensus.

What happened next? Dr. Wile takes up the story:

As a result, Dr. Tomkins redid his study, using the one version of BLAST that did not contain the bug. His results are shown above… The overall similarity between the human and chimpanzee genomes was 88%.

In an update at the top of his post, Dr. Wile now admits to having cold feet, even about the revised 88% figure:

Based on comments below by Glenn (who is mentioned in the article) and Aceofspades25, there are questions regarding the analysis used in Dr. Tomkins’s study, upon which this article is based. Until Dr. Tomkins addresses these questions, it is best to be skeptical of his 88% similarity figure.

So what was wrong with Dr. Tomkins’s new study? I’ll let Glenn Williamson explain (emphasis mine – VJT):

October 16, 2015 4:22 pm

As I’ve said many times, if there is a single base pair indel in the middle of a 300bp sequence, Tomkins will say this is a 50% match.

Tomkins is most certainly aware of this, yet he chose to publish it. I think that says pretty much everything.

Another commenter named Aceofspades25 has this to add (emphases mine – VJT):

October 16, 2015 2:13 pm

The other obvious thing that Thompkins hasn’t dealt with in his BLASTN analysis, I talk about here.

There are a few cases where no match will be found because this entire sequence appears de-novo in Chimpanzees as the result of a single mutation (e.g. a novel transposable element – see here) or because humans have had a large deletion which other primates don’t. Deletions like this also likely occurred in a single mutation – see here

Thompkins (sic) would count both of these as being a 0% match (or 600 effective mutations if the sequences he was searching for were 300bp each). In reality, these probably represent just 2 mutations.

I’ll let Glenn Williamson have the final word (emphases mine – VJT):

Thanks Ace, for letting me know about this post. I reiterate here a few things about my (unpublished!) paper, and about Tomkins’ new paper.

The first thing is that he uses the “ungapped” parameter in his BLAST comparisons. As I’ve written in a few other places now, using this parameter, and calculating results in the way that Tomkins does is entirely disingenuous. If you are comparing two 300bp sequences, and one of those sequences has a single indel smack bang in the middle, Tomkins counts this as the sequences being only 50% identical.

I’ve told him at least twice that he cannot use ungapped and then calculate the result in this way. He can do one of two things:

1. Use ungapped, which ignores indels and therefore he can only report the substitution rate. (emphasis mine – VJT)If he did this, he would get a result of around 98.8%.

2. Allow gaps, and – this is what he fails to mention in his paper – get a result of around 96.9%. And this is using a very conservative method of calculation as well, since it counts a 50bp indel as having the same weight as 50 individual mutations. If you counted a 50bp indel as a single event (which it probably was), then the overall result would be pushed up towards 98%, which is the figure usually thrown around anyway.

In a comment dated 14 August 2015 (at 03:44) on an article titled, Chimp and Human DNA vs “Sophisticated Nonsense”! on a blog called Marmotism, Glenn Williamson adds:

I’ve actually written a paper on Tomkins’ 70% result, and have _ATTEMPTED_ to get it published in Answers Research Journal. Obviously they are not having a bar of it – Tomkins is the sole peer-reviewer, and he is currently refusing to provide any critique of my work – he has been silent for 8 months, while the ball is in his court ..

See the paper here:

https://www.dropbox.com/sh/dm2lgg0l93sjayv/AAATnWSJdER53EYEYZvcgiwma?dl=0

It’s the two PDFs ..

Dr. Tomkins’s latest article in Answers Research Journal (October 7, 2015) acknowledges Williamson’s work in a single sentence:

As of 2013, the issue of overall genome similarity between chimpanzee and humans seemed to be about 70% based on five different reports, three of which were based on actual data analyses. However, in 2014 , a computer programmer of financial trading algorithms discovered an apparent bug in the BLASTN algorithm and notified this author of the situation (Glenn Williamson, Tibra Capital, personal communication).

So, a submitted article only counts as a “personal communication”? Perhaps Dr. Tomkins needs to be a little more up-front about giving credit where credit is due, and acknowledging his mistakes. At any rate, the ball is definitely in his court, and his latest 88% similarity figure warrants skepticism. I have to say that Dr. Tomkins’s methodology sounds rather suspicious to me.

What do readers think?

Comments

Zachriel, I had another thought about how to test this. See this simple simulation I put together that tests the outcome of Probability Selection in Mendel's Accountant: http://jsfiddle.net/p1prvd4h/ Barney Fife (fitness = 1.0) and Genghis Khan (fitness = 1.1) are sorted by Mendel's probability selection algorithm 1 million times--dividing by a random number between one and infinity. Genghis Khan comes out ahead 20% of the time. Even though he should only come out ahead 10% of the time. Therefore Probability Selection in Mendel's Accountant is TWICE as efficient as it should be. This also explains why exactly twice as many beneficial mutations are fixing as what should, according to your own formula. (As I explained in comment #210). To get correct results instead of having overly strong selection, Mendel actually needs to divide by a random number squared.JoeCoder_{November 14, 2015
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JoeCoder: my only remaining doubt is that Mendel may actually be TOO generous in regard to the strength of selection. Our simple and easily repeatable experiments with the parameters given show that the signal from selection is highly obscured. It's a situation where Barney Fife and Genghis Khan have the same number of children.Zachriel_{November 8, 2015
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JoeCoder: Do you have any sources that suggest different values should be used? To make sure we are talking about the same thing, what is the heritability of a person having five fingers on each hand? What is the heritability of wearing lipstick? JoeCoder: Mammals are more than twice as related to fish as they are to chickens (2059 vs 892 genes), which is the opposite of what evolutionary theory predicts. No. That's not what the diagram shows. A particular lineage can lose genes or gain genes, but when you look at sequences, especially silent substitutions, you can still reconstruct the expected phylogeny. JoeCoder: "At this point you can posit reasons for the discordance such as incomplete lineage sorting, convergence, or horizontal transfers." Tunicates may have arisen through hybridization. Again, just because the pattern isn't perfect doesn't mean the pattern doesn't exist. Does the Earth follow an elliptical path around the Sun? JoeCoder: That ignores my citation above that redundancy is primarily NOT from duplication. That supports evolution even more strongly. Evolution often results in overlapping functions. It's a consequence of network evolution, or as the author states, "This type of robustness is probably an evolved response of genetic networks to stabilizing selection."Zachriel_{November 8, 2015
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Zachriel: There’s too many other lines of evidence that contradict the carbon-testing. If they are convinced, then they have to find independent lines of evidence. Soft tissue throughout the fossil record and genetic entropy also support a young timeline. And as you say there are other lines of evidence that argue against. Hence I am agnostic about the ages instead of adopting a YEC perspective that would be more consistent with my Christian worldview. CMI has a list of 101 evidences for a young age of the earth and the universe, while RationalWiki has a list of 28 evidences against a recent creation. Both lists contain some rather strained arguments and the vast majority I've never explored in enough depth to have an informed view. Zachriel: Try vehicles as an instance... You will find that there are many different, equally rational nested hierarchies. I'm sure there would be. My point is we see the same thing in biology. Figure 2 from Sean Carrol's Paper showed this. If you need more examples, take a look at this diagram that I annotated from figure 3 here. It shows the number of genes shared by humans, mice, chickens, and zebrafish. I underlined the gene counts that are shared by some but not all species--those that tell an evolutionary story. In green are the ones that match the expected progression, while in red are those that contradict it. Overall, 51% conflict. Mammals are more than twice as related to fish as they are to chickens (2059 vs 892 genes), which is the opposite of what evolutionary theory predicts. I don't see how this is compatible with your statement that "the molecular evidence strongly supports the nested hierarchy." Yet another example:
[Michael] Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. 'Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another. Syvanen says. "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely
At this point you can posit reasons for the discordance such as incomplete lineage sorting, convergence, or horizontal transfers. But you can't say trees support evolution while simultaneously trying to explain why there are no trees. Zachriel: Duplicate this new superstructure A to AB, to A1?-A2?-B1-B2. That ignores my citation above that redundancy is primarily NOT from duplication. As I cited in comment #227 about a study in yeast:
I used functional genomics data from the yeast Saccharomyces cerevisiae to test the hypotheses related to the following: if gene duplications are mostly responsible for robustness, then a correlation is expected between the similarity of two duplicated genes and the effect of mutations in one of these genes. My results demonstrate that interactions among unrelated genes are the major cause of robustness against mutations.
-------------- Zachriel, I think I've lost interest in continuing our discussion any further. At first your comments made me doubt Mendel was being realistic, but we've already explored this in sufficient depth that my only remaining doubt is that Mendel may actually be TOO generous in regard to the strength of selection. If you're the type of person that always has to have the last word, then go for it. This discussion has been very time consuming, but my questions have already been answered so I have no need to continue.JoeCoder_{November 8, 2015
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Zachriel: The problem is that Mendel’s method is non-biological. Unlike the standard biological selection coefficient, the parameter doesn’t relate to anything real. It may “look right”, but there’s no way to tell. In your comment #209 you wrote:
In a large population, the chance of fixation for a new beneficial mutation is about 2s.* If a variant has a selective advantage of 0.1, then it will fix 20% of the time.
That formula creates a relationship such that if a variant has a selective advantage of 0.01, its odds of fixation are 2%. Likewise, the scaling applied by Mendel's Accountant in probability selection makes it so that if a variant's selection coefficient is 10 times smaller, it is 10 times less likely to fix. So therefore it does follow the biologically realistic curve provided by your formula. Even still my own run showed Mendel's probability selection is twice as efficient as what your formula predicts. Perhaps it should be scaling the randomness by another factor of two in order to compensate? Or perhaps my population size of 2000 was too small. In comment #136 I wrote about my simulation of fixing beneficial alleles:
Starting pop = 2000 Mutation rate = 0 Selection = Unrestricted Probability Selection I seeded the population with five individuals each having an allele [heterozygous] that gives them a 10% fitness bonus.
I wondered if this may be an anomaly, so I ran it with the same parameters three more times. All three times, two of the five beneficial mutations fixed. Zachriel: Currently, the default is heritability = 0.2, while non-scaling noise = 0.05. The Mendel manual states:
0.2 is an extremely generous heritability value.

For simplicity, the default value is 0.05, but reasonable values probably exceed 0.01 and might exceed 0.1.
Do you have any sources that suggest different values should be used? Zachriel: If Mendel’s doesn’t show that strong selection accumulates in a population As you know selection doesn't accumulate in a population. I think you've mistyped something in this sentence and that's causing me to not understand what you mean. In the original 2007 Genetic Entropy paper, The Mendel team used a beneficial rate of 1%, which over-generously high.JoeCoder_{November 8, 2015
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Here's another source of randomness.
noise = sqrt(geno_fitness_variance*(1. - heritability) /heritability + non_scaling_noise**2) do i=1,total_offspring pheno_fitness(i) = fitness(i) + random_normal() * noise + 1.d-15*i end do
Currently, the default is heritability = 0.2, while non-scaling noise = 0.05. Low heritability adds a lot of noise to the phenotypic fitness even before we get to the divide by random problem.Zachriel_{November 8, 2015
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JoeCoder: I think only running that simulation one generation is the problem. Extinction is extinction. There's no coming back. The problem is that Mendel's method is non-biological. Unlike the standard biological selection coefficient, the parameter doesn't relate to anything real. It may "look right", but there's no way to tell. Also, individual fertility seems to be based on average phenotypic fitness, not individual phenotypic fitness.
do i=1,current_pop_size post_sel_fitness = post_sel_fitness + fitness(i) mean_pheno_fitness = mean_pheno_fitness + pheno_fitness(i) end do post_sel_fitness = post_sel_fitness/current_pop_size ... if(fitness_dependent_fertility) then fitness_adjusted_offspring = & num_offspring*sqrt(post_sel_fitness)
Barney Fife has as many children as Genghis Khan (further diluting selection). Baumgardner et al., Mendel’s Accountant: A New Population Genetics Simulation Tool for Studying Mutation and Natural Selection 2008: Truncation selection eliminates those individuals in the new generation whose phenotypic fitness falls below an appropriate cutoff value. Truncation is based on what they call working fitness, not phenotypic fitness. Working fitness, of course, is only tenuously related to phenotypic fitness. JoeCoder: At the end of that talk I linked the guy is begging other researchers to perform the same tests on their own bones so their data can be checked. There's too many other lines of evidence that contradict the carbon-testing. If they are convinced, then they have to find independent lines of evidence. JoeCoder: Evolutionary theory predicts the oldest fishapods should predate the oldest tetrapod tracks and at present we have the reverse. The oldest fishapods should predate the oldest tetrapods, which is not the same thing at all. Tiktaalik is probably not the oldest fishapod. JoeCoder: I’m not sure why that’s lucky? Because he said I will pull a fishapod out of the Arctic wasteland, and then pulled a fishapod out of the Arctic wasteland. Repeat this story a thousand times for all sorts of transitional fossils. A thousand lucky guesses. So unlike ID. Zachriel: Zachriel: “sapiens, erectus, ergaster, neanderthals, and floresiensis share a common ancestor” Why stop there? JoeCoder: Because you can get a great deal of variation just through allele shuffling and loss. But the tree structure is still there; and the closer you come to the common ancestor, the more difficult to distinguish, just as expected of branching descent. Once you agree there's a common Homo ancestor, then there is no reason to stop. JoeCoder: A highly beneficial allele will still spread through the population but more deleterious mutations will accumulate in other alleles as it does so–the total effect is still a net negative. If Mendel's doesn't show that strong selection accumulates in a population, then it is clearly contrary to observation, and the discussion is over. What the authors will state is that strongly selective traits will tend to propagate in a population, but that they are simply too rare to compensate for the accumulation of slightly deleterious mutations. JoeCoder: I disagree that it’s any clearer of a tree than a tree you’d get trying to build one from designed objects. Go ahead. Try vehicles as an instance. Construct a nested hierarchy. It doesn't have to be comprehensive, but should have at least a few levels. You will find that there are many different, equally rational nested hierarchies. JoeCoder: I already cited aardvarks, anteaters, and pangolins of an example that clearly contradicts the expected tree As Darwin pointed out, particular traits will defy the tree due to convergence, but that the entire structure will still show the pattern. In this case, the molecular evidence strongly supports the nested hierarchy. JoeCoder: Suppose all we have is morphological data–which is the truth when looking at fossils. Suppose morphological distance could be quantified into a single number. Aardvarks and anteaters have a morphological distance of perhaps 5, and tiktaalik and ichthyostega a distance of perhaps 12. The tree is not defined by distance, but by the nested hierarchy. Even though there are anomalies, the overall pattern objectively exists. JoeCoder: Without any selection? With selection. The typical pattern is a structure A, duplicated to A-A, then polar migration from specialization to A1-A2, which are now co-dependent. Duplicate this new superstructure A to AB, to A1'-A2'-B1-B2. And so on.Zachriel_{November 8, 2015
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Zachriel: We ran a simple simulator. It only tests the first generation. I think only running that simulation one generation is the problem. You'll get a lot of noise as your results demonstrate. But over many generations that randomness averages out. For example, your person #913 is very unlikely to be ranked near the top again in the second generation. Selection in Mendel is already working more efficiently than you said it should according to the formula you cited in comment #209. Zachriel: Other scientists who have looked at the study believe that contamination explains the results. In addition, it’s contradicted by several other independent tests. Who? At the end of that talk I linked the guy is begging other researchers to perform the same tests on their own bones so their data can be checked. Jack Horner (Mary Schweitzer's boss) was even [offered a $23k grant](http://kgov.com/files/museumoftherockiestrex2.jpg) to C14 date his own soft-tissue dinosaur bones. He agreed it was more than enough money but refused because [it would help creationists](http://www.youtube.com/watch?v=8T3rEX4zq_4). Other than Mark Armitage who has confirmed their results with dates from his own soft-tissue triceratops horn, who else is C14 dating soft tissue dinosaur bones? What is the evidence of contamination? Zachriel: IDers never seem to be “lucky”. Odd that. ID makes no prediction either way about where fishapods should be found. Evolutionary theory predicts the oldest fishapods should predate the oldest tetrapod tracks and at present we have the reverse. I'm not sure why that's lucky? Shubin may have thought he was lucky but his luck has run out. Zachriel: "sapiens, erectus, ergaster, neanderthals, and floresiensis share a common ancestor" Why stop there? Because you can get a great deal of variation just through allele shuffling and loss. These are well documented phenomenon and probabilisticly easy. But phenotypic variation hits a hard limit once your population already has all the alleles that amplify a particular trait. To go beyond this, you need evolution to create new alleles with specific functions. Per our main topic of debate here, evolution shouldn't even be able to preserve existing function. So positing it to create lots of new variation is very problematic. Zachriel: "Having deleterious mutations accumulate in functional DNA is the same thing as selection not preserving functional DNA." No. That’s not the case, even in Mendel. If you have a strongly selective trait, it should propagate through the population. It sounds like we're now talking about completely different things here. My original point that you contested was "Mendel’s Accountant shows selection is not strong enough to preserve functional DNA." A highly beneficial allele will still spread through the population but more deleterious mutations will accumulate in other alleles as it does so--the total effect is still a net negative. Zachriel: Fossils show both a clear pattern of succession, and a clear tree. I disagree that it's any clearer of a tree than a tree you'd get trying to build one from designed objects. iPhones and androids both share code for zlib, webkit, and openGL, while an ICBM missile is clearly the outgroup. Besides, I already cited aardvarks, anteaters, and pangolins of an example that clearly contradicts the expected tree:
What fascinates me most is the tremendous incongruence between the morphological and molecular data,' says Mark Springer, an evolutionary biologist at the University of California, Riverside. For example, grouping animals according to their anatomy alone puts physically similar species such as pangolins, anteaters and aardvarks in the same tight group, whereas molecular data shows that they belong to different orders.
Also from Sean B. Carroll's paper that I cited above:
Molecular systematics has surmounted the confusion stemming from comparisons of morphologically disparate species to reveal unexpected evolutionary relationships such as the Afrotheria, a clade composed of strikingly different mammals including elephants, aardvarks, manatees, and golden moles
Zachriel: "If false links are better than “true” links then no argument can be made from the “true” links." - Not sure what that means. I want to stick to this point because I think it's very important. Suppose all we have is morphological data--which is the truth when looking at fossils. Suppose morphological distance could be quantified into a single number. Aardvarks and anteaters have a morphological distance of perhaps 5, and tiktaalik and ichthyostega a distance of perhaps 12. Yet you conclude that distance of 12 is beyond a doubt evidence that either one evolved into the other or that they are close cousins in an evolutionary lineage? Even when two mammals with a distance of 5 are not closely related at all? That is being selective with data. Zachriel: In evolution, they continue to integrate with the overall network, providing robustness and novel functions. Without any selection? Having mutations (sans selection) building complex things is just storytelling and contrary to any reasonable probability. Even with selection operating and without the issue of deleterious load I think there are serious issues with evolution being able to craft sufficient amounts of specific functional sequences. But I have avoided talking about other arguments to avoid too many topics at once.JoeCoder_{November 7, 2015
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JoeCoder: You say “carbon dating doesn’t work on very old fossils”, but how do you know their age unless you first date them? Geological dating, due to fossil placement in strata, provides relative dating, as well as attesting to the great age of fossils. Radiometrically, by dating of volcanic layers above and below the fossil. Biologically, from the theory of evolution. That's three independent means reaching the same conclusion. JoeCoder: Based on the half life of carbon-14 there should be zero carbon-14 left after a couple hundred thousand years, except in some samples where a very small amount may be created through neutron capture from decaying uranium. Other scientists who have looked at the study believe that contamination explains the results. In addition, it's contradicted by several other independent tests. JoeCoder: As I said above, I think the Earth itself is billions of years old. As is the geology of the Earth. JoeCoder: So that is why I said Darwin believed missing species were an artifact of a poor record. As well as due to evolutionary stasis. Zachriel: when Shubin led a successful expedition to the Canadian arctic to look in specific strata for a “fishapod”, it was luck? JoeCoder: Probably so, yes. IDers never seem to be "lucky". Odd that. JoeCoder: I expect you could find fishapods in a wide variety of strata if you spent enough time looking. Well, you might find fishapods after the divergence, but not before. While we can't say exactly when that divergence occurred, it certainly happened after the evolution of lobed fish. JoeCoder: For the record I do think sapiens, erectus, ergaster, neanderthals, and floresiensis share a common ancestor, and among most of those we have particularly good fossil transitions. Why stop there? JoeCoder: If false links are better than “true” links then no argument can be made from the “true” links. Not sure what that means. It can be difficult to unravel specific branches of the tree, even though the overall tree is clearly evident. JoeCoder: We’re talking using fossils to place extinct species into a progression–there’s no genetic data available for them. Fossils show both a clear pattern of succession, and a clear tree. JoeCoder: I’m not convinced those phylogenies are any clearer than what you’d get trying to build trees from designed objects. In evolution, the closer organisms are related, the more difficult to distinguish. Therefore, the closer you come to the root, not only do you have only limited evidence, but they become more and more difficult to distinguish. That doesn't mean that the tree isn't clearly evident for other taxa, such as eukaryotes. JoeCoder: Having deleterious mutations accumulate in functional DNA is the same thing as selection not preserving functional DNA. No. That's not the case, even in Mendel. If you have a strongly selective trait, it should propagate through the population. JoeCoder: With an almost complete lack of selection to do so, since there are already primary systems performing the same task? I don’t find that compelling in the least. Again, that is incorrect. In evolution, they continue to integrate with the overall network, providing robustness and novel functions. JoeCoder: Based on the formula you provided in comment #209, even the most random mode Mendel’s Accountant offers doesn’t dilute selection enough. We ran a simple simulator. It only tests the first generation, so we don't have to worry about fecundity. The population is 1000, reproductive rate 5, fitness = 1.0, probability selection, 100 trials. There is a novel mutation in one individual. Here is the rate of extinction after one generation given the fitness of the mutant. (Fitness of 1.0 is neutral. It should go extinct 4/5 of the time in the first generation.) fitness 1.00, 80% fitness 1.05, 80% fitness 1.10, 73% fitness 1.15, 78% fitness 1.20, 79% fitness 1.25, 76% Here's the top of the last trial. What was ranked 913 with a fitness of 1.0 is now ranked first with a working fitness over two thousand. 913 - 2,673.66 90 - 1,040.12 879 - 881.11 992 - 577.09 750 - 354.32 751 - 321.45 308 - 257.87 607 - 227.90 760 - 193.95 ... ... Sure, "time and chance happens to them all", but it not usual for Barney Fife to get all the girls.Zachriel_{November 7, 2015
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Shubin- Had Shubin had the knowledge of the Polish tetrapod tracks he would not have been looking for a fish-a-pod where he found Tiktaalik, You don't go looking for evidence of a transition that happened millions of years earlier.Virgil Cain_{November 7, 2015
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Zachriel: Dividing fitness by a random number from zero to one (probability selection used in the original papers) to determine working fitness is non-biological and dilutes the signal from selection Based on the formula you provided in comment #209, even probability selection in Mendel's Accountant doesn't dilute selection enough. If anything it looks like Mendel needs to dilute selection even MORE before it is biologically realistic. Why do you think it needs to be diluted less? Zachriel: especially when differences in fitness are small. We've already discussed why it is realistic for smaller differences to be more diluted than larger differences - see comment #198. I don't understand why you still think this is an issue?JoeCoder_{November 7, 2015
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I worry that we're diverging into too many different topics for a productive discussion. But I'll respond nonetheless. You say "carbon dating doesn't work on very old fossils", but how do you know their age unless you first date them? Based on the half life of carbon-14 there should be zero carbon-14 left after a couple hundred thousand years, except in some samples where a very small amount may be created through neutron capture from decaying uranium. But not nearly enough to give an age of 22-39 thousand years in samples of purified animal proteins. All radiometric dating is tricky. I think you could be equally skeptical of the dates from rocks. For example due to trapped argon or excess argon from lower layers. Zachriel: It was the discovery of radioactivity that explained why the Earth’s interior was still hot after billions of years. Lucky guess? As I said above, I think the Earth itself is billions of years old. For example, take a look at the graphs of ancient meteorite dates from a recent paper YEC geologist Andrew Snelling published in ARJ. They generally cluster around 4.55–4.57 Ga, and Snelling says they show no evidence of past rapid decay. That seems pretty unavoidable. Zachriel: Darwin: "Many species when once formed never undergo any further change" Darwin also said:
Geology assuredly does not reveal any such finely-graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against the theory. (The Origin of Species). The explanation lies, as I believe, in the extreme imperfection of the geological record.
So that is why I said Darwin believed missing species were an artifact of a poor record. Apparently we're both right and Darwin believed gradations were missing due to a poor record, and because he thought evolution happens in bursts. Zachriel: when Shubin led a successful expedition to the Canadian arctic to look in specific strata for a “fishapod”, it was luck? Probably so, yes. I expect you could find fishapods in a wide variety of strata if you spent enough time looking. And the Zachelmie prints show he wasn't looking in the correct strata to begin with. Zachriel: When Darwin predicted there would be fossils of hominids with small brains Again, probably so. If genetic entropy is true then selection primarily removes variation, so we should expect ancient organisms to be more varied than those alive today. For the record I do think sapiens, erectus, ergaster, neanderthals, and floresiensis share a common ancestor, and among most of those we have particularly good fossil transitions. Zachriel: "aardvarks, anteaters, and pangolins" - Convergence is part of the theory of evolution. If false links are better than "true" links then no argument can be made from the "true" links. Zachriel: Genetics has helped resolve these discrepancies, as you point out. We're talking using fossils to place extinct species into a progression--there's no genetic data available for them. Besides, while genetic data can show how similar or distant organisms are to one another, I don't think it's of much help either. Take a look at one of Sean B. Carroll's papers on the topic, particularly figure 2. I'm not convinced those phylogenies are any clearer than what you'd get trying to build trees from designed objects. Zachriel: "Mendel’s Accountant [shows] selection is not strong enough to preserve functional DNA." - No. It purports to show that slightly deleterious mutations accumulate Having deleterious mutations accumulate in functional DNA is the same thing as selection not preserving functional DNA. Zachriel: Because duplications continue to evolve and form new integrated networks. With an almost complete lack of selection to do so, since there are already primary systems performing the same task? I don't find that compelling in the least.JoeCoder_{November 7, 2015
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Mung: Does Zachriel still claim there is a bug in the code of Mendel’s Accountant? Yes. Dividing fitness by a random number from zero to one (probability selection used in the original papers) to determine working fitness is non-biological and dilutes the signal from selection, especially when differences in fitness are small.Zachriel_{November 7, 2015
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JoeCoder:
@Mung – Unlike most of the discussion on UD, I’m hoping to keep this a friendly and thus productive debate. Can you help me with that goal?
Absolutely. Does Zachriel still claim there is a bug in the code of Mendel's Accountant? That's relevant, right?Mung_{November 7, 2015
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JoeCoder: As one example, take a look at this image of aardvarks, anteaters, and pangolins. Convergence is part of the theory of evolution. JoeCoder: The noise of homoplasy overwhelms any signal of transition. Genetics has helped resolve these discrepancies, as you point out. JoeCoder: The issue above highlighted by Mendel’s Accountant is that selection is not strong enough to preserve functional DNA. No. It purports to show that slightly deleterious mutations accumulate, not that strong selection doesn't lead to adaptation. JoeCoder: How could selection preserve sequences of backup systems that are only used in the rare cases when primary systems fail? Because duplications continue to evolve and form new integrated networks. The difference is that with evolution, we predict and can often find evidence of how this occurred in a selectable, stepwise fashion.Zachriel_{November 7, 2015
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JoeCoder: I’ve been having a good discussion with Zachriel so far. Agreed, and we have already tentatively modified our position somewhat based on that discussion. While we don't agree with Mendel's methodology, partial truncation avoids at least some of the problems. JoeCoder: There was a talk in 2012 by creationists at the American Geophysical Union/Asia Oceania Geosciences Society conference. Carbon dating isn't very useful on very old fossils, and there are a number of sources of error. Fossils are usually dated by looking at strata above and below that allow for other forms of radiometric dating. The great age of the Earth's strata was determined long before radiometric dating, so geological methods provide an independent method. Darwin's theory, of course, requires an old Earth. The greatest physicists of his time thought the Earth could only be a few million years old to still be hot inside. Geologists and biologists claimed otherwise. It was the discovery of radioactivity that explained why the Earth's interior was still hot after billions of years. Lucky guess? JoeCoder: If I’m not mistaken, Darwin thought stasis might be an artifact of a poor record. Darwin: Many species when once formed never undergo any further change but become extinct without leaving modified descendents and the periods, during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they retain the same form. JoeCoder: I’m also not impressed by the proposed fossil intermediates because of signal vs noise. So when Darwin predicted there would be fossils of hominids with small brains, and such organisms were found, it was luck? Or when Shubin led a successful expedition to the Canadian arctic to look in specific strata for a "fishapod", it was luck? The geological record clearly shows a fossil succession, and the overall age is known to be ancient.Zachriel_{November 7, 2015
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I made a typo! Above I meant to say "bats, whales, and humans are each IN a different order of mammals". For example humans are obviously not the only species of primate!JoeCoder_{November 7, 2015
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JoeCoder, I certainly don't expect Zach to ever be 'converted' through my meek efforts and if he ever does become a Christian I will certainly consider it a bonafide miracle from God. Where God, in his mercy, changed Zach's heart and revealed Himself to Zach in a personal way. I did not touch on your discussion with Zach regarding Mendel's accountant and I only can comment on his dishonesty towards the fossil record which is what we were discussing. And that is exactly what I called his bluff on. i.e. He is being a dishonest liar in regards to the fossil record! That is a fact! It is not something that I purposely say to smear him! It is something I say primarily to state the fact that he is in fact a pathological liar in my dealings with him on the fossil record. It is why I requoted a few of the leading paleontologists on the fossil record from the other day. (I have many more quotes from many other paleontologists saying the same thing). He saw the quotes before, presented no evidence to the contrary, and repeated the same lies that the fossil record overwhelmingly supports Darwinism. This is not some nuanced programming language in a computer that is intelligently designed by a human to see whether Darwinism is feasible or not (a self-refuting proposition is ever there were one). These are stone cold hard fossils. I'm sure you are a sensitive soul and are open to reason. Yet, I've seen no such inclination in Zach. In fact Zach, in my dealings with him over several years, resolutely refuses to be honest on even the most trivial facts of empirical truth that I present. Your dealings in computer programming may be different with him, but I sincerely doubt that he is dealing completely straight with you in that area either. IMHO, he ought to be banned from UD for his repeated lying. But, like I said, the moderators on UD must think his over the top lies serve some purpose.bornagain_{November 7, 2015
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Zachriel: in a world where dinosaur fossils are on display in museums across the world, how someone could reject that long history. I'm not a YEC and I'm not arguing for young ages. Rather--I'm arguing that there is enough conflicting data that we should be agnostic about the ages. There was a talk in 2012 by creationists at the American Geophysical Union/Asia Oceania Geosciences Society conference. In the laymanized version of their paper, they report 20 unmineralized samples of cretaceous and jurassic acrocanthosaurus, allosaurus, hadrosaur, triceratops, and apatosaur were C14 dated at the University of Arizona using both the AMS and beta-decay methods to 22-39k years old. They note, "Both [the triceratops and hadrosaur] bones were tested by a licensed lab for presence of collagen. Both bones did in fact contain some collagen." Collagen is an animal protein so it can't be a bacterial contaminant. At 13 minutes into the talk, several more lines of evidence are offered against contamination: AMS and beta-decay methods are in agreement, C14 concentrations decrease with distance from the fossils, and the C13 concentrations in the triceratops match expected values for an animal that consumes C3 carbon fixation system plants (those in temperate environments). The soft tissue itself with preserved DNA, osteocytes, and collagen should also not be in tact after millions of years. For a long time this was used as a (now failed) argument against Mary Schweitzer's discoveries of soft tissue to insist that it could not be original. Yet the rocks around those bones strongly disagree! I wish I could just go one direction or the other in regard to the age of the fossil record, but because of things like this I'm stuck in cognitive dissonance. It's frustrating. Zachriel: Scientists make expeditions around the world to find predicted intermediate fossils. Lucky guessers? I'm not going to overwhelm you with citations like BA has. But I do particularly like Don Prothero's article in Skeptic Magazine where he says the fossil record is "vast monument to stasis, with relatively few cases where anyone had observed gradual evolution" It's short and an easy read--would you have time to take a look? If I'm not mistaken, Darwin thought stasis might be an artifact of a poor record. In that article Prothero makes it a point that the stasis is real and confirmed by enough samples that it cannot be "bias in my sampling". I'm also not impressed by the proposed fossil intermediates because of signal vs noise. As one example, take a look at this image of aardvarks, anteaters, and pangolins. Based on morphology we used to think the three were very close relatives. But genetics has now placed them within different orders of mammalia. For context: bats, whales, and humans are each a different order of mammals. But aardvarks, anteaters, and pangolins are MORE similar to one another than things like tiktaalik and its proposed fishapod cousins. The noise of homoplasy overwhelms any signal of transition. That and the Zachelmie prints show that animals were already leaving toe-prints on land 20 million years prior to tiktaalik splashing in the mud, at least according to the dates of nearby rocks. Zachriel: Your analysis [of redundant genes] has no way to separate evolution from design. I think it very much does separate evolution from design. The issue above highlighted by Mendel's Accountant is that selection is not strong enough to preserve functional DNA. How could selection preserve sequences of backup systems that are only used in the rare cases when primary systems fail? And what there is not enough selective pressure to preserve, there's certainly not enough to have created it. Yet in our own most fail-safe designs we commonly use redundant systems built in alternate ways from the primary systems. Check out this short comment about the Boeing 757, from Walter Bright who is one of my favorite engineers to follow. So I think this redundancy through disparate parts is one way that genomes are more like our own designs than they are like what we would expect evolutionary processes create. Tell me what you think?JoeCoder_{November 7, 2015
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bornagain: lying purposely or are you lying because you are mentally ill? I've been having a good discussion with Zachriel so far. When this started I was interested in determining whether Mendel's Accountant is an accurate simulation, and Zachriel has been helpful in probing my biases to raise objections I had not thought about. In the end I still think my view is correct, but I cannot have confidence in my own views unless I first expose them to scrutiny. If this discussion descends into insults it becomes much harder to do that. Sometimes I'm also wrong (and so are you) and I appreciate it when people don't rub it in my face and call me names. I'm also not sure how you expect to convert anyone to your own view through insulting them. What is your end-goal here?JoeCoder_{November 7, 2015
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Actually, whether someone is delusional or not does not negate whether the words coming from them or lies or not. (in fact, how we tell when a person is delusional is when their words (and actions) are grossly out of line with reality, i.e. when their words and actions are 'lies') Lies are lies, regardless of the mental state of the person uttering them. So which is it, or you lying purposely or are you lying because you are mentally ill? To give you the benefit of a doubt, I opt for mentally ill. Do you want to the see the studies proving that atheists are mentally ill?bornagain_{November 7, 2015
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bornagain: It is about you living in complete delusional denial of the fact that the fossil record is severely discordant with what Darwin predicted., i.e. it is about you constantly lying! As a general rule, if someone is delusional, they aren't lying. bornagain: Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. Meaning some don't. In any case, Darwin posited that stasis would be prevalent in the historical record.Zachriel_{November 7, 2015
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Zachriel, it is not you not 'agreeing with my premise'. It is about you living in complete delusional denial of the fact that the fossil record is severely discordant with what Darwin predicted., i.e. it is about you constantly lying! The discordant fossil record is a scientific fact, not a philosophical premise.
Scientific study turns understanding about evolution on its head – July 30, 2013 Excerpt: evolutionary biologists,,, looked at nearly one hundred fossil groups to test the notion that it takes groups of animals many millions of years to reach their maximum diversity of form. Contrary to popular belief, not all animal groups continued to evolve fundamentally new morphologies through time. The majority actually achieved their greatest diversity of form (disparity) relatively early in their histories. ,,,Dr Matthew Wills said: “This pattern, known as ‘early high disparity’, turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years. This isn’t a phenomenon particularly associated with the first radiation of animals (in the Cambrian Explosion), or periods in the immediate wake of mass extinctions.”,,, Author Martin Hughes, continued: “Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. Co-author Dr Sylvain Gerber, added: “A key question now is what prevents groups from generating fundamentally new forms later on in their evolution.,,, http://phys.org/news/2013-07-scientific-evolution.html In Allaying Darwin’s Doubt, Two Cambrian Experts Still Come Up Short – October 16, 2015 Excerpt: “A recent analysis of disparity in 98 metazoan clades through the Phanerozoic found a preponderance of clades with maximal disparity early in their history. Thus, whether or not taxonomic diversification slows down most studies of disparity reveal a pattern in which the early evolution of a clade defines the morphological boundaries of a group which are then filled in by subsequent diversification. This pattern is inconsistent with that expected of a classic adaptive radiation in which diversity and disparity should be coupled, at least during the early phase of the radiation.” – Doug Erwin What this admits is that disparity is a worse problem than evolutionists had realized: it’s ubiquitous (throughout the history of life on earth), not just in the Cambrian (Explosion). http://www.evolutionnews.org/2015/10/in_allaying_dar100111.html disparity [dih-spar-i-tee] noun, plural disparities. 1. lack of similarity or equality; inequality; difference: “It is hard for us paleontologists, steeped as we are in a tradition of Darwinian analysis, to admit that neo-Darwinian explanations for the Cambrian explosion have failed miserably. New data acquired in recent years, instead of solving Darwin’s dilemma, have rather made it worse. Meyer describes the dimensions of the problem with clarity and precision. His book is a game changer for the study of evolution and points us in the right direction as we seek a new theory for the origin of animals.” -Dr. Mark McMenamin – 2013 Paleontologist at Mt. Holyoke College and author of The Emergence of Animals “The record of the first appearance of living phyla, classes, and orders can best be described in Wright’s (1) term as ‘from the top down’.” (James W. Valentine, “Late Precambrian bilaterians: Grades and clades,” Proceedings of the National Academy of Sciences USA, 91: 6751-6757 (July 1994).) “Darwin’s prediction of rampant, albeit gradual, change affecting all lineages through time is refuted. The record is there, and the record speaks for tremendous anatomical conservatism. Change in the manner Darwin expected is just not found in the fossil record.” Niles Eldredge and Ian Tattersall, The Myth of Human Evolution (New York: Columbia University Press, 1982), 45-46. In Explaining the Cambrian Explosion, Has the TalkOrigins Archive Resolved Darwin’s Dilemma? – JonathanM – May 2012 Excerpt: it is the pattern of morphological disparity preceding diversity that is fundamentally at odds with the neo-Darwinian scenario of gradualism. All of the major differences (i.e. the higher taxonomic categories such as phyla) appear first in the fossil record and then the lesser taxonomic categories such as classes, orders, families, genera and species appear later. On the Darwinian view, one would expect to see all of the major differences in body plan appear only after numerous small-scale speciation events. But this is not what we observe. per ENV “The facts of greatest general importance are the following. When a new phylum, class, or order appears, there follows a quick, explosive (in terms of geological time) diversification so that practically all orders or families known appear suddenly and without any apparent transitions. Afterwards, a slow evolution follows; this frequently has the appearance of a gradual change, step by step, though down to the generic level abrupt major steps without transitions occur. At the end of such a series, a kind of evolutionary running-wild frequently is observed. Giant forms appear, and odd or pathological types of different kinds precede the extinction of such a line.” Richard B. Goldschmidt, “Evolution, as Viewed by One Geneticist,” American Scientist 40 (January 1952), 97. Problem 5: Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution – Casey Luskin January 29, 2015 Excerpt: Rather than showing gradual Darwinian evolution, the history of life shows a pattern of explosions where new fossil forms come into existence without clear evolutionary precursors. Evolutionary anthropologist Jeffrey Schwartz summarizes the problem: “We are still in the dark about the origin of most major groups of organisms. They appear in the fossil record as Athena did from the head of Zeus — full-blown and raring to go, in contradiction to Darwin’s depiction of evolution as resulting from the gradual accumulation of countless infinitesimally minute variations. . .”98 per ENV “With the benefit of hindsight, it is amazing that paleontologists could have accepted gradual evolution as a universal pattern on the basis of a handful of supposedly well-documented lineages (e.g. Gryphaea, Micraster, Zaphrentis) none of which actually withstands close scrutiny.” Christopher R.C. Paul, “Patterns of Evolution and Extinction in Invertebrates,” K.C. Allen and D.E.G. Briggs, eds., Evolution and the Fossil Record (Washington, D.C., Smithsonian Institution Press, 1989), 105. “It must be significant that nearly all the evolutionary stories I learned as a student from Trueman’s Ostrea/Gryphaea to Carruthers’ Zaphrentis delanouei, have now been ‘debunked’. Similarly, my own experience of more than twenty years looking for evolutionary lineages among the Mesozoic Brachiopoda has proved them equally elusive.’ Dr. Derek V. Ager (Department of Geology & Oceonography, University College, Swansea, UK), ‘The nature of the fossil record’. Proceedings of the Geologists’ Association, vol.87(2), 1976,p.132. “The point emerges that if we examine the fossil record in detail, whether at the level of orders or of species, we find’ over and over again’ not gradual evolution, but the sudden explosion of one group at the expense of another.” Paleontologist, Derek V. Ager, “The Nature of the Fossil Record,” 87 Proceedings of the British Geological Association 87 (1976): 133. (Department of Geology & Oceanography, University College, Swansea, UK) “It is a feature of the known fossil record that most taxa appear abruptly. They are not, as a rule, led up to by a sequence of almost imperceptibly changing forerunners such as Darwin believed should be usual in evolution…This phenomenon becomes more universal and more intense as the hierarchy of categories is ascended. Gaps among known species are sporadic and often small. Gaps among known orders, classes and phyla are systematic and almost always large.” G.G.Simpson – one of the most influential American Paleontologist of the 20th century “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 “Now, after over 120 years of the most extensive and painstaking geological exploration of every continent and ocean bottom, the picture is infinitely more vivid and complete than it was in 1859. Formations have been discovered containing hundreds of billions of fossils and our museums now are filled with over 100 million fossils of 250,000 different species. The availability of this profusion of hard scientific data should permit objective investigators to determine if Darwin was on the right track. What is the picture which the fossils have given us? … The gaps between major groups of organisms have been growing even wider and more undeniable. They can no longer be ignored or rationalized away with appeals to imperfection of the fossil record.” Luther D. Sunderland, Darwin’s Enigma 1988, Fossils and Other Problems, 4th edition, Master Books, p. 9 “The evidence we find in the geological record is not nearly as compatible with Darwinian natural selection as we would like it to be …. We now have a quarter of a million fossil species but the situation hasn’t changed much. The record of evolution is surprisingly jerky and, ironically, we have even fewer examples of evolutionary transition than in Darwin’s time … so Darwin’s problem has not been alleviated”. David Raup, Curator of Geology at Chicago’s Field Museum of Natural History “In virtually all cases a new taxon appears for the first time in the fossil record with most definitive features already present, and practically no known stem-group forms.” Tom S. Kemp, Fossils and Evolution (New York; Oxford University Press, 1999), 246. – Curator of Zoological Collections “The record certainly did not reveal gradual transformations of structure in the course of time. On the contrary, it showed that species generally remained constant throughout their history and were replaced quite suddenly by significantly different forms. New types or classes seemed to appear fully formed, with no sign of an evolutionary trend by which they could have emerged from an earlier type.” Peter Bowler, Evolution: The History of an Idea (Berkeley, CA: University of California Press, 1984), 187. “The lack of ancestral or intermediate forms between fossil species is not a bizarre peculiarity of early metazoan history. Gaps are general and prevalent throughout the fossil record.” R.A. Raff and T.C. Kaufman, Embryos, Genes, and Evolution: The Developmental-Genetic Basis of Evolutionary Change (Bloomington, IN: Indiana University Press, 1991), 34. “No one has found any such in-between creatures. This was long chalked up to ‘gaps’ in the fossil records, gaps that proponents of gradualism confidently expected to fill in someday when rock strata of the proper antiquity were eventually located. But all the fossil evidence to date has failed to turn up any such missing links . . . There is a growing conviction among many scientists that these transitional forms never existed.” Niles Eldredge, quoted in George Alexander, “Alternate Theory of Evolution Considered,” Los Angeles Times, November 19, 1978. “Gradualism is a concept I believe in, not just because of Darwin’s authority, but because my understanding of genetics seems to demand it. Yet Gould and the American Museum people [i.e., Eldredge] are hard to contradict when they say there are no transitional fossils. As a paleontologist myself, I am much occupied with the philosophical problems of identifying ancestral forms in the fossil record. You say that I should at least ‘show a photo of the fossil from which each type of organism was derived.’ I will lay it on the line – there is not one such fossil for which one could make a watertight argument.” Colin Patterson to Luther Sunderland, April 10, 1979, quoted in Luther .D. Sunderland, Darwin’s Enigma: Fossils and Other Problems, 4th ed. (El Cajon, CA: Master Book Publishers, 1988), 89. For the first decade after the paper was published, it was the most controversial and hotly argued idea in all of paleontology. Soon the great debate among paleontologists boiled down to just a few central points, which Gould and Eldredge (1977) nicely summarized on the fifth anniversary of the paper’s release. The first major discovery was that stasis was much more prevalent in the fossil record than had been previously supposed. Many paleontologists came forward and pointed out that the geological literature was one vast monument to stasis, with relatively few cases where anyone had observed gradual evolution. If species didn’t appear suddenly in the fossil record and remain relatively unchanged, then biostratigraphy would never work—and yet almost two centuries of successful biostratigraphic correlations was evidence of just this kind of pattern. As Gould put it, it was the “dirty little secret” hidden in the paleontological closet. Most paleontologists were trained to focus on gradual evolution as the only pattern of interest, and ignored stasis as “not evolutionary change” and therefore uninteresting, to be overlooked or minimized. Once Eldredge and Gould had pointed out that stasis was equally important (“stasis is data” in Gould’s words), paleontologists all over the world saw that stasis was the general pattern, and that gradualism was rare—and that is still the consensus 40 years later. Donald Prothero – American paleontologist, geologist, and author who specializes in mammalian paleontology. Leading Evolutionary Scientists Admit We Have No Evolutionary Explanation of Human Language – December 19, 2014 Excerpt: Understanding the evolution of language requires evidence regarding origins and processes that led to change. In the last 40 years, there has been an explosion of research on this problem as well as a sense that considerable progress has been made. We argue instead that the richness of ideas is accompanied by a poverty of evidence, with essentially no explanation of how and why our linguistic computations and representations evolved.,,, (Marc Hauser, Charles Yang, Robert Berwick, Ian Tattersall, Michael J. Ryan, Jeffrey Watumull, Noam Chomsky and Richard C. Lewontin, “The mystery of language evolution,” Frontiers in Psychology, Vol 5:401 (May 7, 2014).) It’s difficult to imagine much stronger words from a more prestigious collection of experts. http://www.evolutionnews.org/2014/12/leading_evoluti092141.html
In fact Zach, I hold that if you can not bring yourself to admit the fact that the fossil record is discordant to Darwinism then you ought to rightly be banned from UD. Don't worry though Zach, I am not a moderator. For some reason the moderators on UD feel it is OK to have a pathological liar such as yourself on UD. I guess they figure that you are so over the top in your intellectual dishonesty that you can only help ID.bornagain_{November 7, 2015
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bornagain: did not we discuss the fossil record the other day? You mentioned that notochords still existed. We pointed out that you had one once, but outgrew it. bornagain: Would it hurt you to mention the fact that the fossil record, according to leading experts, is severely discordant with Darwinian predictions, with only a handful of supposed intermediates which are all argumentative in their interpretation? Because we don't agree with your premise.Zachriel_{November 7, 2015
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Zachriel, did not we discuss the fossil record the other day? https://uncommondescent.com/intelligent-design/whoops-why-humans-arent-apes-professor-coynes-own-goal/#comment-586453 Would it hurt your feelings that much to mention the fact that the fossil record, according to leading experts, is severely discordant with Darwinian predictions, with only a handful of supposed intermediates which are all argumentative in their interpretation? Or are you just a pathological liar who can't help yourself? And that you will never honestly admit anything that might cast doubt on Darwinism? Can you even answer that question honestly?bornagain_{November 7, 2015
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JoeCoder: I reject common descent. If you reject the historical descent of life, then mechanisms of that change are ungrounded. We've always found it hard to imagine, in a world where dinosaur fossils are on display in museums across the world, how someone could reject that long history. Scientists make expeditions around the world to find predicted intermediate fossils. Lucky guessers? JoeCoder: This is good design, because having backup systems that operate in very different ways makes them less prone to the factors that made primary systems fail. Your analysis has no way to separate evolution from design.Zachriel_{November 7, 2015
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@Mung - Unlike most of the discussion on UD, I'm hoping to keep this a friendly and thus productive debate. Can you help me with that goal? @Alicia Cartelli - the part I wasn't sure about was how feasible it would be to design cells so that after they differentiate into specific cell types, they jetison DNA only used by other cell types. But we both know the gametes can't do that or else the offspring are in trouble!JoeCoder_{November 6, 2015
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Zachriel, Have you figured out what you knew and when you knew it yet? Were you all not talking to yourselves for a while?Mung_{November 6, 2015
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Nick M, Do you know what sequence space is yet?Mung_{November 6, 2015
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@Nick Matzke, welcome : ) Runaway transposition is only one of four design-compatible reasons I listed as to why we might see variation in genome size. As for plots, In my comment #224 already shared several between genome size and other features like cell size and cell types. They're not perfect but we should not expect a plot against a single variable to be when there are likely multiple explanations at play. Also, is number of protein coding genes the correct metric to use when functional RNAs are also at play?JoeCoder_{November 6, 2015
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