Animal Body. So What?

The kingdom of darkness. But our bodies of death will be changed from the corruptible to the incorruptible. We are a new creation! Morphologically, our earthly bodies have a lot in common with and a lot distinct from ape bodies---it's a long list. -Q Querius

Believers are in the Kingdom of God. Not sure what kingdom the rest fall under. Mung

I knew you were going to say that. So, humans are to be classified in a different kingdom than animals? -Q Querius

Humans have a human body, obviously. ;) Mung

Mung, Ok, I'll bite. What kind of a body do humans have? We're probably the most similar in appearance to apes of all other animals, but I'd agree that there's a still a huge gap. -Q Querius

Humans don't have an animal body. Mung

bornagain77, Yes, I noticed both the irony and the astonishing assumption on their part that simply disagreeing with us constitutes irrefutable evidence in of itself! Wow! The mechanisms of mutation attributed to driving evolution such as new body plans for example, has never been demonstrated to be adequate to the task, and fossil evidence numbering in the hundreds of millions have never provided satisfactory evidence of slow transitions as Darwin had hoped. But faith dies hard, and they grimly march on, flinging ad hominems at the doubters. For my part, I have no problem with a naturalistic mechanism for genetic change beyond natural selection, but random mutation, as both the math and the evidence suggests, is not it. Thanks again for posting the videos. I was amazed at the pervasiveness of modern-looking plants and animals through much of the fossil record. The evolution of bats was also intriguing. ;-) -Q Querius

So you have evidence of 'unguided' Darwinian processes producing highly sophisticated integrated complexity that easily trounces man's best achievements? i.e. there is a Elephant in the room sitting on your chest AB! :) bornagain77

BA77: "which is a deliciously ironic statement coming from a man who believes that the highly sophisticated integrated complexity found in life, that easily trounces anything man has ever built, can be had by random Darwinian processes." Ignoring the inaccurate use of the term 'Darwinian', who has ever said that evolution is a random process, other than creationists in a failed attempt to discredit evolutionary theory. Acartia_bogart

wd400 advises,,,

"Stop, consider the possibility that you are wrong,,,"

which is a deliciously ironic statement coming from a man who believes that the highly sophisticated integrated complexity found in life, that easily trounces anything man has ever built, can be had by random Darwinian processes.

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Conclusions: Our analysis confirms mathematically what would seem intuitively obvious - multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations? http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years: Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637 In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark): "Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010

Run that by us again wd400,,,

"Stop, consider the possibility that you are wrong,,,"

bornagain77

wd400:

If, after that, you are still incapable of seeing your own mistakes and updating your views, there is really no point in bothering with you.

I reached hat conclusion about Querius long ago. Acartia_bogart

Querius, Read what I wrote. Stop, consider the possibility that you are wrong about this. Read Ohno again. If, after that, you are still incapable of seeing your own mistakes and updating your views, there is really no point in bothering with you. wd400

wd400, You wrote:

I genuinely find it amazing that someone who has so consistently been wrong (even in this thread, about a paper you’ve apparently read many times you claimed evolutionary biologists once thought “Non-coding DNA is junk that’s left over from evolution”

You haven't presented any evidence here, only a simple contradiction along with nasty accusations. However, if you actually read Dr. Ohno's paper, for which I provided the link, you might have noticed that on page 368, Dr. Ohno wrote: "Our view is that they are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?" Hmmm. Looks like you're dead wrong. And then you continued with

and that Ohno claimed “junk DNA can function as a sort of evolutionary scratch pad”, neither of which are true), and so consistently failed to admit it (I guess even to yourself?) would go on about it all this.

And again you're dead wrong! On page 369, Dr. Ohno wrote the following regarding this "junk" DNA: "It then follows that the creation of a new gene with hitherto nonexistent function is possible only if a gene becomes sheltered from relentless pressure from natural selection." In the future, you really need to start checking your facts before posting them. I think you owe everyone an apology. -Q Querius

The main problem with Allen McNeill’s “evolutionary mechanisms” is that neither Allen nor any other evolutionist can say whether or not they are blind watchmaker mechanisms, ie for unguided evolution. Not only that no one knows if those mechanisms can produce the observed diversity of life on Earth starting from some unknown populations of prokaryotic-like organisms.

I don't believe we have to go back to prokaryotes. I doubt if much of evolution can result from the 47+ engines but probably some did. If the bulk of evolution did, we would have heard a lot more about it in recent years. Maybe Allen will hang around here some time in order to discuss it. Radio silence from the evolutionary biologists is probably the best indication of what they know. jerry

Querius, I genuinely find it amazing that someone who has so consistently been wrong (even in this thread, about a paper you've apparently read many times you claimed evolutionary biologists once thought "Non-coding DNA is junk that’s left over from evolution" and that Ohno claimed “junk DNA can function as a sort of evolutionary scratch pad", neither of which are true), and so consistently failed to admit it (I guess even to yourself?) would go on about it all this. As I say, if you have a case to make, make it. (to head off a distraction: Ohno claimed gene duplication could shield proteins from stabilizing selection, and since most duplicates would not acquire new functions the net result would be many broken genes (junk) and a few new functional ones. He was right about this (a famous paper on this topic: http://www.ncbi.nlm.nih.gov/pubmed/11073452), but it turns out the junk includes much more than broken gene duplicates). wd400

The main problem with Allen McNeill's "evolutionary mechanisms" is that neither Allen nor any other evolutionist can say whether or not they are blind watchmaker mechanisms, ie for unguided evolution. Not only that no one knows if those mechanisms can produce the observed diversity of life on Earth starting from some unknown populations of prokaryotic-like organisms. Joe

Queryius: "Regarding my making an argument for ID on pragmatism, I’ve already made it several times, but I suspect you haven’t come to this site for illumination" Hey Query, I didn't think that any of us came here for illumination. I thought that we came here to discuss and debate. Have I been mislead? Acartia_bogart

Dionisio @86, Yeah, that's a very good point, too. There's also an emotional investment founded on years of hard study, research, and publishing as amply demonstrated by several people here. wd400,

You may be suprised, querius, to learn how little I care about your amateur psychology. If you have a good argument for why ID is more “pragmatic” or whatever make it, though your track record gives me little hope that you will.

No, I'm not surprised at all. Should I be? Actually I'm kind of amused that you rejected well-established psychological phenomena by mistakenly attributing it to me as “your amateur psychology.” But whatever. You will also probably not be interested in a different Darwinian environment called Marketing, where billions of dollars are continually at stake, and marketing professionals can never allow themselves the luxury of “marrying their ideas.” Not surprisingly, there's quite a bit of applicability to science: http://www.digitaltonto.com/2012/looking-for-support-rather-than-illumination/ I liked the warning in the article that

If you look hard enough, you’ll always be able to find something, somewhere that can back up virtually any argument. Yet by doing so, you are using data much like drunk uses a lamppost—for support rather than illumination.

Regarding my making an argument for ID on pragmatism, I've already made it several times, but I suspect you haven't come to this site for illumination, and I'm not surprised at how hard you're gripping the lampost. ;-) -Q Querius

I left out the Brosius article with Stephen Gould link http://www.pnas.org/content/89/22/10706.full.pdf Brosius is the lead author on this article. jerry

Eric,

I don’t know about that characterization.

Here is an article from 2003 which lists his research as well as others going back into the early 90's. http://zmbe.uni-muenster.de/expath/articles/Genetica.retro.2003.pdf Here is his article with Stephen Gould from 1992 which develops the idea. For his latest, see his CV which contains all his publications. http://zmbe.uni-muenster.de/institutes/iep/Brosius_CV_AllPub.pdf Unlike people like Coyne, Dawkins, Miller, MacNeill or Moran, this guy is a serious researcher, probably one of the top ones in evolutionary biology. The others are just polemicists who make their name giving talks or writing books.

Are you referring to something else?

No, I am referring to Brosius. He is one of the top researcher or maybe even the top one in the field. Have you ever seen an ID person review his work? I haven't. In a memorial tribute to Stephen Gould, his article was the first one in the journal. http://www.bioone.org/doi/abs/10.1666/0094-8373%282005%29031%5B0001%3ADAEBAC%5D2.0.CO%3B2 If you have access to a good university library, you may be able to get the pdf of it. Here is a key quote from this article.

An extension of Wally Gilbert’s metaphor “exons in a sea of introns” (Gilbert 1978). Functional nuons are is lands in a sea of nonfunctional (nonaptive) sequences. Nevertheless, any of those sequences has the potential to be exapted into novel functions (Brosius and Gould 1992; Balakirev and Ayala 2003). While “plate tectonics,” or exon shuffling, occasionally leads to rearrange ments of existing functional nuons (Gilbert 1978), retro position, the major force in the plasticity of genomes, which in our analogy is more akin to volcanic eruptions, frequently creates new nuons. Initially, most nuons (is lands) are barren (nonfunctional, nonaptive) but have the potential to be fertilized by some microevolutionary base changes or short indels and exapted as functional nuons. Nonfunctional nuons erode over time and the is lands disappear in the sea of anonymous sequences. An interesting example is the recruitment of part of an Alu retronuon as an alternative exon in an isoform of the cytokine tumor necrosis factor receptor. Insertion of the Alu element occurred after Anthropoidea split from pro simians and a subsequent point mutation generated an ATG start codon. This base substitution alone, however, was not sufficient for exaptation of the Alu element as a protein-coding exon, as this sequence is nonaptive (not used as part of an alternative mRNA) in Platyrrhini. Only two additional small changes in the lineage lead ing to Catarrhini including apes, a C->T transition to generate a GT 5? splice site and a 7-bp deletion to pro vide translation into the next exon in the correct reading frame, led to generation and exaptation of this alternative exon (Singer et al. 2004). ———- from another part of the article A nuon is any distinct nucleic acid, a defined sequence module (Brosius and Gould 1992). The term can be used with a prefix (e.g., retronuon) to designate any DNA module that was generated by retroposition. I prefer retronuon over retroposon and especially over transposable element (TE) or mobile element (ME). In fact, any RNA is a potential mobile element: if a segment of the genome is transcribed in the germline it has the potential to serve as template for retroposition (hence, RNA might be considered the ultimate selfish unit). However, upon integration into the genome, there is no guarantee for autonomous transcription in the germline, which results in a loss of mobility. The original transcript, how ever, can serve as a template for retroposition multiple times. In contrast to TE or ME, the term “retronuon” solely indicates the mode of origin, but not the potential for successive amplification. Only a minority of retronuons are true TEs or MEs, such as endogenous retroviruses or intact LINE elements [see Brosius 2003a]).

So it is clear what he thinks has caused macro evolution and he is quite cocky and arrogant about that and dismisses critics as know nothings. So I suggest that the ID brain trust review his line of research. It is here that the battle lines have to form and meet each other. My guess is that Brosius will not overcome the large number problem. He probably has a few good examples and that is all but someone with credentials has to review the research. It is extensive. jerry

"Anyway it is an area no one in ID has commented on even though the research has been around for over 20 years." I don't know about that characterization. I doubt anyone has gone through every one of Dr. MacNeill's engines of variation to address every single one. However, ID proponents have long talked about both (i) the implications of re-shuffling existing informational sequences, and (ii) the idea of junk DNA acting as a "scratch pad" for new functional sequences to arise through mutation. I haven't delved into Dr. MacNeill's or Dr. Brosius' work in enough detail to be able to ascertain whether everything they have argued has been addressed head on. But the idea that ID proponents have ignored the possibility of new information arising through shuffling and/or through mutations acting on non-coding regions is simply not correct. Are you referring to something else? Eric Anderson

Eric,

What happens when the junk DNA scratch pad stumbles upon a useful protein? Does it stay there in the scratch pad, subject to all the changes acting on the scratch pad, or is it somehow protected by the cellular mechanisms once they “recognize” it as a useful protein? Can the protein, existing as it does in the mutation-zone scratch pad space, possibly exist long enough without mutating out of existence to be integrated into and spread throughout a population? Or does the new useful gene get shunted off into some more protected space outside the scratch pad? Are there any examples of new useful genes arising in the scratch pad that required more than one or two mutations to achieve it?

I believe the answer to this is that much of these segments are not in anyway protected and can mutate in and out of functionality if there is such a thing. But what happens is that there seems to be a process by which most of the genome gets transcribed into RNA and some then get translated (discovered by Encode). My guess is that some of these rna sequences then do something to the genome, or get translated and become a protein and do something. In that case they could be selected. Anyway it is an area no one in ID has commented on even though the research has been around for over 20 years. One interesting behavioral observation. Allen MacNeill brought this up over 5 years ago when he said Darwinian evolution was dead. But he never laid out the case for the alternative except to point to a a couple books which are best ambiguous and his 47+ engines of variation. jerry

You may be suprised, querius, to learn how little I care about your amateur psychology. If you have a good argument for why ID is more "pragmatic" or whatever make it, though your track record gives me little hope that you will. wd400

#79 Querius

As more research was completed, and more evidence was collected, weaknesses and paradoxes began to appear indicating that Darwinism was likely incomplete or incorrect. Nevertheless, because many people were so heavily invested ideologically, they tended to hang onto it beyond what the theory deserved.

...and financially too: Their reprinted textbooks keep bringing in income from fees. Their names may appear as coauthors in papers they have not worked on. Their opinions and presentations are on demand. Their authority is undisputable. Their participation in boards that approve grants for research can influence on the resources available to researchers whose work might threaten the old theories [source: my scientist friends in Northern Europe and Canada told me all that in our personal conversations] Dionisio

Gpuccio, I am just telling you what some major university evolutionary biology departments are teaching about macro evolution. I am not defending it. Brosius has tons of research on this. So all I am suggesting is that someone who is qualified review his and his colleagues research. He is very sure of himself. Here is a cartoon he had drawn about himself on this topic. I am not sure I understand exactly what it means but it points to his thesis that occasionally a part of the Junk DNA gets used for something. http://zmbe.uni-muenster.de/institutes/iep/iepcartoon.htm jerry

jerry: MacNeill's arguments are at best confused. One thing os to generate new complex functional information. Another thing is to shuffle existing information around. His example of the “hybridization” of the Encyclopedia Britannica and the collected works of Anthony Trollope is revealing. What would that be? Just the mix of two existing big pieces of complex functional information. How would MacNeill explain the origin of Trollope's works? As the hybridization of Little women with Shaw's Pygmalion? Nobody is denying that shuffling can use functional parts to build a new complex structure. That's one way design works, it's called object oriented programming. Even that cannnot, IMO, come out of mere random variation. It's very difficult to design functional structures by the mere random assembly of simpler functional structures. In extreme, ad hoc cases, that could work. But again, could MacNeill (or anyone else) please explain how ATP synthase (a basic constituent of practically all the phenotypes we know) came into existence by any of his 47 engines of variation? (or 100, or 1000... just listing variations of random variations does not add anything: the only important variable is the number of new states that a random system can test in a definite time). gpuccio

jerry @77:

In it, you’ll also see that he proposes that “junk” DNA can function as a sort of evolutionary scratch pad, sheltering hopeful genes from relentless Darwinian competition.

It is an interesting idea, which certainly raises its own questions. Have they identified what is sheltering junk DNA from the "relentless Darwinian competition"? Are they arguing that using up the bulk of the cell's transcription resources transcribing junk is something natural selection is blind to? And the tremendous additional effort and resources to reproduce 9x more DNA than needed upon cellular reproduction is also invisible to this incredible "relentless Darwinian competition"? Doesn't seem particularly relentless or competitive. What happens when the junk DNA scratch pad stumbles upon a useful protein? Does it stay there in the scratch pad, subject to all the changes acting on the scratch pad, or is it somehow protected by the cellular mechanisms once they "recognize" it as a useful protein? Can the protein, existing as it does in the mutation-zone scratch pad space, possibly exist long enough without mutating out of existence to be integrated into and spread throughout a population? Or does the new useful gene get shunted off into some more protected space outside the scratch pad? Are there any examples of new useful genes arising in the scratch pad that required more than one or two mutations to achieve it? Anyway, I realize you don't have the answers to these questions. I'm just throwing out a few things that jump immediately to mind from the idea. There are probably dozens of additional questions that could be raised if we thought it for a bit. Eric Anderson

why does Allen MacNeill belief that his 47 mechanisms are able to generate phenotypic variation?

You will have to ask him. He is rarely here. He has his own site but I do not know how much he pays attention to it these days. My point is that there are evolutionary biologists who are very confident that this process explains things. I have no way of evaluating Brosius's research which is prolific. My guess is that it will sound good but not really explain much. He is arrogant and not a nice person and very cocky. But he is unlike Dawkins or Coyne. He does research, lots of it. jerry

Jerry, why does Allen MacNeill belief that his 47 mechanisms are able to generate phenotypic variation? Without fitting regulatory networks already in place the most blessed genetic mutation is still good-for-nothing; completely ineffectual with regard to the phenotype. The simple notion that regulatory networks are essential is often ignored by Darwinists. Box

Jerry, Thanks for the comment. It makes much more sense to me to have such a more-protected mechanism than to depend on the unlikely appearance of a set of mutations, each of which confers some sort of evolutionary benefit. In my opinion, this mechanism mitigates one of Michael Behe's objections in the Edge of Evolution to a small degree. I don't think it's adequate to address the cumulative probabilities of multiple mutations, however. -Q Querius

wd400 noted

First, this idea that you have that geneticists and evolutionary biologists are out to mislead the world in the cause of atheism really makes it very hard to make any progress. If you think everything I say is a trick in service of a religuous position why should I bother?

No, I don't think geneticists and evolutionary biologists are trying to mislead anyone. However, here's what I think has happened. Darwin's theory was a very reasonable and compelling alternative to the prevalent theogenic assumptions at the time. The sparse evidence available fit into the theory, and many researchers looked for other pieces of the puzzle. Since there was "no other game in town," Darwinism became a paradigm. As more research was completed, and more evidence was collected, weaknesses and paradoxes began to appear indicating that Darwinism was likely incomplete or incorrect. Nevertheless, because many people were so heavily invested ideologically, they tended to hang onto it beyond what the theory deserved. There's also a tendency by teachers to become dogmatic and media to sensationalize what scientists and researchers discovered without heeding their qualifying statements. I would like to emphasize that this is also true of people with religious beliefs. In my opinion the original motivation for ID was to treat biological systems as engineered, a change in the paradigm without focusing on the source of the engineering. Certainly, religious individuals found ID appealing, others thought anything short of creationism a sell out. From my perspective, the reason you are adamant about Darwinism as the evolutionary mechanism is that deep inside you *know* it to be true. This inner conviction is common to all people, whether it concerns a political party, a philosophy of life, dental practices, or whatever. The discipline of Science is supposed to help you shake off archaic beliefs, however most people have a hard time doing so. For example, I'm told that in dentistry, the old practices are being replaced by the modern, one retirement at a time. I'm sure that you will continue your adamant support for Darwinism, all the while experiencing increasing need to incorporate increasingly complex and unsatisfying interpretations of the data---and of course on my part, I will become increasingly skeptical. The scientific difference in my opinion is that the ID paradigm has been proving itself more pragmatic than the Darwinism paradigm in terms of facilitating the progress of science as the foray into "junk" DNA amply demonstrates. -Q Querius

wd400 @76, I rest my case. See ya around, dude. And enjoy your little time in the sun. It will soon come to an end. Mapou

In it, you’ll also see that he proposes that “junk” DNA can function as a sort of evolutionary scratch pad, sheltering hopeful genes from relentless Darwinian competition.

This is the basis for modern macro-evolutionary theory as espoused by Brosius and Allen MacNeill and apparently many others. The questions is can all of Allen's engines of variation produce enough variation to explain everything. Allen says it can. https://uncommondesc.wpengine.com/intelligent-design/the-altenberg-sixteen/#comment-177256

Gil Dodgen: You wrote: “The problem as I see it is not getting enough variation, but getting enough original, novel, innovative variation.” That was the point to my list of 47 mechanisms for generating phenotypic variation. Several of the mechanisms listed are capable of producing as much genetic variation as there are elementary particles in the known universe, while others (such as whole genome fusion) are capable of producing novel genetic combinations equivalent to the “hybridization” of the Encyclopedia Brittanica and the collected works of Anthony Trollope. In other words, the “engines of variation” are more than up to the task of generating anything that could conceivably be of use to a living organism (plus an immensely larger amount of useless variation). As to the question of whether any of the mechanisms in my list can produce “new” information, the answer is “yes”, so long as one recognizes that what really matters is the production of new phenotypic variation. As I have already pointed out, the exclusive concentration on genetic variation on the part of both evolutionary biologists (EBers) and IDers has until very recently blinded us to the tremendous potential of other mechanisms that produce the same effects (see Jablonka and Lamb/Evolution in Four Dimensions for a complete discussion).

My guess is that Allen's engines of variation cannot and will fail the big number test. The whole ID debate on evolution revolves around this question. jerry

Mapou, First, this idea that you have that geneticists and evolutionary biologists are out to mislead the world in the cause of atheism really makes it very hard to make any progress. If you think everything I say is a trick in service of a religuous position why should I bother? I will bother one last time. In 2005, when the first draft of the chimp genome was released, you might have claimed the two genomes where 80% alignable and 98% identical when aligned, so they must be .8 * .98 ~= 78% identical. But if you did the same thing now, with the latest release of the chimp genome, you'd find 90% of the genomes are alignable giving .9 * .98 ~= 88% identity. Do you think the real percentage-identity between the two genomes should rely on how much work has been done to sequence them? The number of genes in a genome (or protein coding genes, which seems to be the number you are quoting) is not really relevant to calculating the similarity between them -- the bases are different or they're not, whether they make proteins is irrelevant. wd400

HELLO? Are there any Darwinist with a brain around here? Mapou

I’ve addresed your point multiple times. Unalignable sequences aren’t included because it’s not clear if they represent missing data in one or other assembly (the innitial chimp genome draft had low coverage), or highly repetitive sequences that have a corresponding sequence but can’t be uniquely mapped to it. As more and more of the chimp genome has been aligned to the human, the percentage identity has not decreased, so it’s not as if these sequences are mostly radically different than anything in the other genome. If you don’t belive me read the post by the YEC I linked to earlier. Or even better, check it for your self, there are loads and loads of raw sequencing data available for both species…

Aw, come on! One cannot make a valid similarity comparison if one only compares the sequences that are judged to be alignable. Alignable is another code word for similar. In other words, you are only using the similar sequences to compute similarity. Hello? And what about the fact that the margin of error regarding the actual number of genes in chimps and humans is a whopping 25%? And yet, even with these monumental uncertainties, you people somehow find a way to get 98% similarity between chimp and human genomes so you can run around gloating to your heart's content that evolution is true. I see the magic, alright, but it's not particularly clever magic. It's stupid and beneath common dignity. Mapou

For those of you that haven't read Dr. Ohno's short paper, I'd recommend reading it. In it, you'll also see that he proposes that "junk" DNA can function as a sort of evolutionary scratch pad, sheltering hopeful genes from relentless Darwinian competition. http://www.junkdna.com/ohno.html While not correct, Dr. Ohno's proposals are nevertheless excellent ideas. -Q Querius

I've addresed your point multiple times. Unalignable sequences aren't included because it's not clear if they represent missing data in one or other assembly (the innitial chimp genome draft had low coverage), or highly repetitive sequences that have a corresponding sequence but can't be uniquely mapped to it. As more and more of the chimp genome has been aligned to the human, the percentage identity has not decreased, so it's not as if these sequences are mostly radically different than anything in the other genome. If you don't belive me read the post by the YEC I linked to earlier. Or even better, check it for your self, there are loads and loads of raw sequencing data available for both species... wd400

wd400:

Mapou, that’s like as in alignable

That's precisely the point. How come the non-alignable sequences do not figure into the similarity computation? Why are you refusing to address the point I am making? That's mighty cowardly of you, a common trait amongst Darwinists. Grow a pair,man. Mapou

Mapou,

Only certain bases are compared, the so-called “like bases“. I knew there was a dishonest bias somewhere but I did not expect it to be so blatant.

But you have to understand that it's all for a noble cause. But I'll tell you what's really truly amazing. Get ready for it. It's that ALL LIVING ORGANISMS are about 98% identical when homologous bases are compared! Note that some pairs of organisms don't have that many homologous bases, but nevertheless this once again proves evolution. ;-) -Q Querius

Mapou, that's like as in alignable Querius, It never ceases to amaze me that people could read (repeadidly!) Ohno's paper and think anyone, let alone Ohno, ever claimed "A" was true. To quote

Aside from conVentional structural genes and regulatory genes, this 6% [i.e. the functional DNA]should ' include the promoter region and operator regions

Promoters and operators are non-coding DNA that Ohno included in the non-junk portion. wd400

It seems that the Darwinists love pick and choose the criticism that they feel comfortable with while ignoring the others hoping they will go away. Let me repost this previous question and see who among them has enough gonads to take the bait.

A chimp has between 20,000 and 25,000 genes by the latest estimate. But guess what? So does a human being. So if the margin of error regarding the actual number of genes in either species is 25%, isn't it rather strange that some people can be so confident that human and chimp genomes are 98% similar?

Any takers? Mapou

Oops, looks like the posts crossed, and I missed a position between B and C, which dangles Dr. Ohno outside the bus: C+. It's not impossible that most of the differences between humans and chimps are due to non-coding DNA as was proposed by Kind and Wilson, but most non-coding DNA must still be junk, thus proving evolution. -Q Querius

wd400:

In fact, I think both are true. It’s also true that the non-coding regions of the human and chimp genomes are ~98% identical when like bases are compared).

There is it, folks, in black and white. Now we know where the 98% similarity comes from. Only certain bases are compared, the so-called "like bases". I knew there was a dishonest bias somewhere but I did not expect it to be so blatant. Mapou

Dr JDD, Thanks for taking the time to write your insightful reply. Yesterday, as I was watching a video on some of the latest findings on quantum mechanics, it occurred to me how profoundly and fantastically more competent humans are than chimpanzees in intellectual capacity among other things---your point number two. An obvious conclusion is that non-coding DNA is likely to have a more important rather than less important role in the difference between Homo and Pan, a point apparently missed by those people who seem to have an ideological rather than a logical commitment to "junk" DNA. Speaking of junk DNA, it never ceases to amaze me how some people who should know better consistently reinterpret the point of Susumu Ohno's 1972 paper. Dr. Ohmo proposed that "junk" DNA was a trove of "fossil DNA" analogous to the extinct organisms found in strata, leftovers from evolution. Nearly every time I make this point, I take the time to review Dr. Ohno's paper. Nevertheless, people who seem to be ideologically committed to Darwin's 19th-century paradigm, do not want to concede the point. In the face of mounting discoveries regarding the function of non-coding DNA they are slowly ratcheting down in the face of the evidence: A. Non-coding DNA is junk that's left over from evolution. B. The majority of non-coding DNA is junk that obviously must be left over from evolution. C. Some non-coding DNA must definitely be left-over junk, which clearly and decisively proves that evolution musta happened. D. Non-coding DNA has been shown to play a vital role in the evolutionary process. It seems to me that wd400 has definitely dropped from an A to B, and might actually be on his way to C. We'll see. ;-) -Q Querius

You seem to be objecting to argument I didn't make. It's perfectly possible that most of the differences between humans can chimps are down to non-coding DNA (as King and Wilson suggested in 1975) and for most of the genome to be junk. In fact, I think both are true. It's also true that the non-coding regions of the human and chimp genomes are ~98% identical when like bases are compared). wd400

wd400, thanks for your response. However I feel you have failed to meet the point of my criticism of your original statement:

In fact the protein coding genes are a good deal more similar to the chimpanzee genome than other regions, which is one good reason to think the majority of the genome is junk (diverging along at the neutral rate, rather than being slowed by natural selection).

You state that there is high homology in the protein coding region far more than non-coding regions, therefore the conclusion is non-coding regions are junk. However I am not contesting that there is junk DNA, irrespective of the implications, I am contesting that as a logical conclusion. My argument is: 1) Protein coding regions of chimp and human are apparently highly homologous 2) Chimps and humans are incredibly distant in what defines them (apart from phenotype alone - but not excluding phenotypically) 3) Therefore, the differences between humans and chimps are more likely to be due to non-protein coding regions of the genome. In your reply, you seem focused on defending the existence of junk DNA, that it is the prominent content of the genome, and that we have known for years that there are non-coding RNAs with cellular function (but this is a very small percentage of DNA). You throw in the [passive backhand dig!] remark about undergraduates even knowing this but let me assure you the university I went to is one of the top in the UK for biological sciences, and yes back in the day, I was taught that non-coding regions are present with function but for a fact I was taught these were far less important and in far lower percent of the genome than we currently now understand to be the case. Fortunately as well, I did my undergraduate in the last 20 years. I am not contesting those things you are steering your reply to. I am contesting the natural conclusion you make from the observation that chimp and human DNA is so similar. Your interpretation is "this is good evidence the rest is junk" but that is on a presupposed Darwinian mindset. An unhinged conclusion would be that in fact, the differences between humans and chimps does not come down primarily to the proteins present and their amino acid sequences, but something else. EA has also shared this view however he has gone further and suggested it could/is even outside of the DNA itself. So I am a little surprised at your response and the conclusion you make from observed homology but to be frank, this is the Darwinian mindset in play. WRT the tail story, the point I made is that it is a deceptive conclusion through argument by ignorance. The argument presented to me was: 1) Human embryos show tail vertebrae appearance in their development 2) This is subsequently removed/destroyed and the coccyx remains 3) *and here is the crunch point* when we look in the human genome, we see the presence of the ancestral tail genes still present! You see, this argument is a deceptive one, unless the genes present are only for tail development and are completely switched off in humans. Now the Darwinist could argue that because we have lost tail development, the genes have evolved different uses, but that is not what is stated in the argument. The implication is that we have tail genes present in our genome and that this is their purpose - for forming tails. But unless there are genes I do not know about, the ones I have seen reported to be necessary for tail formation in other mammals are in fact crucical for a whole plethora of functions in all aspects of development and different organs and cell types. Therefore, to allude that because we see these genes in humans that is evidence that we once had a tail is deceptive and quite frankly, very bad science. [Furhter I should say, just because there appears visually to be a "tail like structure" when you observe embryos at certain stages does not imply or should automatically assume this is similar to a "tail" or even be called a tail. This early stage of development and the notochord formation has been abused by common descent advocates for that purpose, making out like a structure that is useless is formed and then destroyed, thus proof we once had a tail. That is quite an absurd and biased interpretation of a visual phenomenon and probably has not been cleared up as fast as it could have been due to clear ethical issues with establishing roles of different structures in the developing human embryo - issues not present with mice or other model organisms' developements.] This is similar to the arguments around homology and chimp-human DNA similarity that is portrayed all the time by evolutionists. There is an over-emphasis of the centrality of proteins in making an organism who they are, a down-playing of non-proteinacious products of the genome in an organisms development, and an overstating of thus how homology evidences common descent. Dr JDD

The central dogma is, more or less, that information can flow from nucleic acid to protein but not protein to nucleic acid. What this has to do with anything I can't imagine. But if want to explain how most of the non-coding DNA can be functional while apparently evolving without selection I'd like to know. wd400

This is a long way from the topic of the thread, but briefly. Of course some non-coding DNA is functional, Ohno knew this and every undergrad biologist trained in the last 40 years should know abut rRNAs and tRNAs. But it's very unlikely that most of the non-coding DNA is functional for a number of reasons, including that fact that most of it diverges at a rate equal to the individual mutation rate (or, if you'd rather, at rate equal the junkiest pseudogenes and broken transposons). There are certainly more non-coding RNAs known now than previously. But there is no reason to think most transcribed RNA is functional. As long as you have open chromatin and transcription factor binding sites RNA will be produced, and LINES and SINES move such sites around the genome. I don't know much about the development of tails, but human embroyos have tails and indeed the same morphogens are expressed in human embryonic tails as other mammals. Finally, I don't think "homology", as in percent-identity, is a great argument for common descent by itself. Rather it's suites of shared differences that make the case. For the human-chimp split we also have incomplete lineaege sorting with Gorilla and the presence of btween-species polymorphism to further place our species within the apes. wd400

Dr JDD @58 cites wd400: "In fact the protein coding genes are a good deal more similar to the chimpanzee genome than other regions, which is one good reason to think the majority of the genome is junk (diverging along at the neutral rate, rather than being slowed by natural selection)." This is an example of the kind of mindset flowing from an unhealthy adherence to the simplistic and misleading central dogma. Eric Anderson

The alleged genetic similarities between humans and chimps (highly inflated and abused as they may be) are interesting observationally, but do not -- as the proponents would love to believe -- constitute conclusive evidence of either (i) descent, or (more importantly), (ii) that such descent resulted from purely natural and material processes. The intellectually laughable thing about people harping on the genetic similarities as though they underly some broader truth is that the alleged evolutionary process that led from a chimp-like ancestor to humans must account for the differences, not the similarities. There is no such account that even passes the laugh test, much less being scientifically and reasonably plausible. Furthermore, even if humans and chimps were 98% similar in DNA (or even 100% for that matter), all that observation would do is underscore the fact that the key differences are not in the DNA. There are many and obvious differences between humans and chimps. What evidence is there that the minor differences in DNA can account for all those differences? Answer: there is no decent evidence on that score. Finally, the humans-and-chimps-share-almost-all-their-DNA story tends to marginalize or conveniently sweep under the rug a host of other scientific realities: cellular mechanisms, cellular structures, and epigenetic information that acts on and utilizes the DNA. Yes, DNA is critical, but in some ways it is better thought of as a database of component parts, rather than the actual foundation of the organism that neo-Darwinian theory would like it to be. DNA provides the building blocks, but it doesn't itself do the building. There are two Home Depots within about 3 miles of my house in either direction. If I were to do an inventory I would probably find that they are about 98% similar in content. Yet that doesn't mean that a contractor who walks into one Home Depot is going to build a house that is 98% similar to the house built by a different contractor walking into another Home Depot (or even the very same Home Depot). The building blocks can be identical, down the last detail, but it doesn't mean the resulting structure will be identical, or even highly similar. The whole DNA=>Protein=>Organism dogma is simplistic to the point of being not just incomplete, but quite misleading. Indeed, given what we now know, the Central Dogma unfortunately often functions as a kind of anti-knowledge. Eric Anderson

wd400: You are an intelligent person and usually offer a fairly well reasoned approach from the "other side" than those here at UD, so I would say it is an asset to have you here as it makes us think and not just nod in agreement at most posts. Anyway, I would appeal to your intelligence on this and try to forget about the implications but rather where the science leads. You say:

In fact the protein coding genes are a good deal more similar to the chimpanzee genome than other regions, which is one good reason to think the majority of the genome is junk (diverging along at the neutral rate, rather than being slowed by natural selection).

But what if the real importance is not in the protein coding genes? This has been suggested for years and perhaps IDists have focused in the past too much on the actual protein encoding DNA. The very fact that we are SO similar to other organisms is obvious. If you take some quite important proteins ubiquitously expressed and necessary for essential cellular functions, more often than not the similarity is 100% (on amino acid level) with chimps/apes etc and very high with other species e.g. mice, closer to 100% than say 90% (at amino acid level). I know because I do these alignments all the time (am not too concerned with DNA sequence in the work I do). You know this well. It is used as support of evolution. However, it is clear that I am very different to a mouse. I have been accused of being short at a mere 5'8" however that is more of an extreme comparison. Humans and chimps I would argue are incredibly different, given the "rates" of mutation (neutral drift) and our supposed divergence time. What we now know more than ever, and certainly more than 15 years ago when we started to get draft human genomes (at insane sequencing costs compared to now), is that there is a huge diversity of non-coding RNAs that are transcribed from the genome, and these have very important roles in the regulation of these genes. So it is more likely that the non-protein regions of our genomes are what "make us" human in terms of what we can say, physically (not spiritually/soul presence, consciousness, etc). However it is common to do and say what you say - these non-protein regions are not as "important" and so diverge faster. But we must consider all explanations as a hypothesis that are sensible. Is it not a sensible hypothesis that theses regions are more diverse than our supposed ancestors because they are what make us different? This makes sense with a high degree of homology in the protein-coding regions, and acutally given the great similarity, it only really makes sense to think of the regulatory aspects of the genome and proteins to be the force at play in providing the differences we see between organisms. This seems to be supported by the many non-coding RNA molecules described of late - and continuing to be described and be discovered. We would be foolish to assume that all of these have been discovered and that there may not be a plethora more of RNA transcripts that play a functional role in the cell. The number can only go up. However evolutionists will hold back on agreeing with this, and downplay these findings as just another "small percent" of the genome to hold onto the junk DNA which is somewhat necessary to understand evolution and common descent as truth. This slight and mild form of deception is common among those defending evolution I find. Recently, the member "evolve" wrote a reply to me on another thread and claimed that with regards to common descent, we clearly evolved from something that had a tail, and he/she stated when we look for the genes that control tail formation/dvelopment, we still find them in our human genome! Strong evidence indeed. However, I challenged this only in the sense where I asked him/her to show/tell me what genes those were. I did not say that evolve was wrong, I asked him to tell me, as I honestly do not know what these genes are. I was under the impression they included the wnt/b-catenin pathway, in particular wnt3a. If that is the case, then his/her point is completely mis-guided and deceptive to a degree as it implies that these genes ONLY control tail development, and are present in humans but inactive. HOwever wnt3a has multiple important roles in human development in various cellular processes apart from tail development so if this is one of the genes he/she is talking about, it is not a favourable argument to use for common descent. In fact, it raises the point that a single protein or set of proteins are not enough information to define a phenotype or structure we see, and that it is "above" the DNA-->protein context that these structures arise. I.e. the regulation in specific ways which may even be apart from DNA (e.g. in membranes or electrical gradients, etc). I am still waiting for a reply and would love to know what those genes are - genuinely, I want to learn. Finally, I never understand the "homology" argument as strong evidence for common descent. Homology is what you would also expect from a common designer. Neither (in the gross sense) theory is supported more than the other from homology, therefore it is not a "strong" evidence for common descent. It would be odd, if we shared a common designer, if we were completely different at the level of the DNA. If you disagree, then fine - but please state what you would expect to see if we shared a common designer? Would you expect a different genetic code? A completely set of different proteins? Why would you expect that from a common designer? Therefore, something cannot be used as evidenence for one theory if it equally supports an opposing theory. Now there are certain aspects of homology that do (on the face of it) lend support to common descent, (I don't have time to discuss now) however homology in general does not support/provide strong evidence for common descent over common design. Dr JDD

Mapou, I'm sorry that I misinterpreted you. When you said "I see no scriptural evidence nor logical arguments to support the notion that God has a non-physical body", I thought you were interested in scriptural and/or logical arguments. As that is not so, I'll not bother you with further comments on this subject. anthropic

anthropic, I forgot to say this. Infinity, too, is the work of the devil. LOL. Mapou

anthropic, I disagree with your interpretations of Biblical scriptures. I disagree that the word 'spirit' has ever been defined in the scriptures. I disagree that the Bible is perfect, that it is 100% the word of God or that it has no errors and contradictions. I am not a Christian fundamentalist and the Bible is not an object of worship to me. Heck, I don't believe that God is either perfect, omnipotent, omnipresent or omniscient. I think it's all ridiculous nonsense, the work of the devil. Sorry. Mapou

Mapou 45 John 4:24 "God is spirit, and those who worship Him must worship in spirit and truth." 1 John 4:12-13 "No one has seen God at any time; if we love one another, God abides in us, and His love is perfected in us. 13 By this we know that we abide in Him and He in us, because He has given us of His Spirit." 1 John 4:20 "If someone says, “I love God,” and hates his brother, he is a liar; for the one who does not love his brother whom he has seen, cannot love God whom he has not seen." If God is a material physical being and is omnipresent, why don't we see Him? Why do the scriptures say no one (human, at least) has seen God? If one argues that God is a different type of matter than we cannot see, remember that the resurrected Jesus could be both seen and touched! If God is a physical being made from matter, where was He before matter was created in the Big Bang? If God is a physical being made from matter, what does it mean to say that the Trinity is three persons but one God? If God is a physical being made from matter, why did He repeatedly and emphatically tell the Israelites NOT to make an image of Him? What's the big deal? If God is a physical being made from matter, why do the scriptures say that He created the material universe out of nothing? Why not just use some of His own matter to do the job, since He is infinite? Not that this has a whole lot to do with ID, really. So now that I've had my say, Mapou, you can show me the error of my ways and I won't argue further. :) anthropic

Mung @50, I was simply pointing out indirectly that you were not correct in claiming that no Christian believes that God has has a physical body. I do. Mapou

A chimp has between 20,000 and 25,000 genes by the latest estimate. But guess what? So does a human being. So if the margin of error regarding the actual number of genes in either species is 25%, isn't it rather strange that some people can be so confident that human and chimp genomes are 98% similar? Something smells fishy. The lady protests way too much, IMO, especially since similarity between the two does not give them a leg to stand on. Mapou

Mung, I've no idea what you are trying say. I'm not banning anyone else from talking about religion. I just said I don't have anything to say about the OP. wd400

Mapou:

What do you mean so?

I mean that you've merely expressed an opinion. I mean that nothing follows from what you've sad. Mapou:

I see no scriptural evidence nor logical arguments to support the notion that God has a non-physical body.

And from this observation what is your conclusion? That God must have a physical body? How so? Mung

wd400, You did an admirable job of avoiding the central questions. What is the objective basis of your beliefs? What is the objective distinction between your beliefs and Barry's beliefs? wd400:

The OP is about the belief that humans, and not other animals, have eternal spirits and uses scripture to support it.

So? wd400:

That’s fairly obviously a religious topic, no?

No. wd400:

I am indeed talkinag about personal subjective preferences when I say I don’t see much point in talking about people’s religuous beliefs. You are welcome to talk about them.

And you are welcome to not talk about them. And you are likewise weloome to declare that your decision is a personal subjective opinion you hold. Why is it binding on anyone else? Why is it not a religious belief? Mung

How does any similarity between two genomes prove common descent? I see it as a stronger case for common design through class inheritance. Just good old engineering. Mapou

What do you mean so? Mapou

Mapou:

I see no scriptural evidence nor logical arguments to support the notion that God has a non-physical body.

So? Mung

Mung:

Given that no Christian believes that God is a physical being,

I'm a Christian and I believe that God and everybody else have physical body. Not necessarily the same type of physical matter as humans but physical matter regardless. I see no scriptural evidence nor logical arguments to support the notion that God has a non-physical body. Mapou

Mung, The OP is about the belief that humans, and not other animals, have eternal spirits and uses scripture to support it. That's fairly obviously a religious topic, no? I am indeed talkinag about personal subjective preferences when I say I don't see much point in talking about people's religuous beliefs. You are welcome to talk about them. Box, That's a different statistic. human-mouse are about 85% identical in the way human-chimp are 98%. prhean, I really have no idea what you are on about, I'm afraid. wd400

wd400, Do you have an objective means by which to distinguish religious beliefs from non-religious beliefs, and do you have an argument as to why the former are unworthy of discussion while the latter are worthy of discussion? Or are you simply expressing your personal subjective preferences? I repeat, a person’s beliefs are just that, their beliefs. Including yours. Mung

The stunning 98% similarity is only trumped by the .... mouse.

The 2.5-Gb mouse genome sequence reported on page 520, from the C57BL/6J strain, reveals about 30,000 genes, with 99% having direct counterparts in humans. [source: nature.com]

On a side note: Cats have 90% of homologous genes with humans, 82% with dogs, 80% with cows, 79% with chimpanzees, 69% with rats and 67% with mice. [source] Box

Given that no Christian believes that God is a physical being, does it not follow that "in the image of God" says nothing about physical similarity or physical dis-similarity to any other species? Mung

OT: I looked around a little bit for a 'made in God's image' video, and found this from Tim Keller: You are my Friends - Tim Keller - sermon https://www.youtube.com/watch?v=nyyqYa22Thw Being made in the image of God means, among other things, that we were not created to be in isolation. bornagain77

wd400, while I respect your beliefs, they are obviously your personal religious beliefs, and therefore not worth discussing. Why then do you persist in posting them here at UD rather than on some website devoted to the discussion of religious beliefs not worth discussing? Mung

wd400:

I don’t have much to say about the OP. As far as I’m concerned, everyone’s religous beliefs are there own and I don’t see much point in discussing them.

Where in the OP did Barry say his beliefs were "religious beliefs?" wd400:

I don’t have much to say about the OP. As far as I’m concerned, everyone’s religous beliefs are there own and I don’t see much point in discussing them.

A person's beliefs are just that, their beliefs. How did you decide that Barry's beliefs, as expressed in his OP, were "religious beliefs?" What other classifications of "beliefs" do you appeal to in order to justify your belief that they are not worth discussing? Why isn't your belief likewise a "religious belief" not worth discussing? Mung

Well wd400, by even engaging in this thread you are using logic and reason (and information) to try to win people over to your atheistic point of view. Thus you are literally drenched, whether you admit it or not, in a thoroughly 'spiritual' exercise that cannot be reduced to mere material mechanism. Moreover, this 'spiritual' exercise of reasoning that you are using is among the most profound of differences between us and the animals. Thus, even though you constantly engage in 'spirituality' just by reasoning alone, I don't blame you for refusing to deal with this issue honestly. Darwin himself had a 'horrid doubt' about the subject:

"But then with me the horrid doubt always arises whether the convictions of man’s mind, which has been developed from the mind of the lower animals, are of any value or at all trustworthy. Would any one trust in the convictions of a monkey’s mind, if there are any convictions in such a mind?" - Charles Darwin - Letter To William Graham - July 3, 1881

And indeed, Darwin's 'horrid doubt' has been hammered out. The 'convictions of man’s mind', as Plantinga has rigorously shown, cannot be grounded in the atheist's naturalistic worldview:

Scientific Peer Review is in Trouble: From Medical Science to Darwinism - Mike Keas - October 10, 2012 Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:). Or, if your short on time and patience to grasp Plantinga's nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states: "Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not." Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305. http://blogs.christianpost.com/science-and-faith/scientific-peer-review-is-in-trouble-from-medical-science-to-darwinism-12421/

As well wd400, since you are fond of your mathematical ability in population genetics, Berlinski has a apt quote that is relevant for you:

An Interview with David Berlinski - Jonathan Witt Berlinski: There is no argument against religion that is not also an argument against mathematics. Mathematicians are capable of grasping a world of objects that lies beyond space and time …. Interviewer:… Come again(?) … Berlinski: No need to come again: I got to where I was going the first time. The number four, after all, did not come into existence at a particular time, and it is not going to go out of existence at another time. It is neither here nor there. Nonetheless we are in some sense able to grasp the number by a faculty of our minds. Mathematical intuition is utterly mysterious. So for that matter is the fact that mathematical objects such as a Lie Group or a differentiable manifold have the power to interact with elementary particles or accelerating forces. But these are precisely the claims that theologians have always made as well – that human beings are capable by an exercise of their devotional abilities to come to some understanding of the deity; and the deity, although beyond space and time, is capable of interacting with material objects. http://tofspot.blogspot.com/2013/10/found-upon-web-and-reprinted-here.html

supplemental quote:

The Confidence of Jerry Coyne - Ross Douthat - January 6, 2014 Excerpt: then halfway through this peroration, we have as an aside the confession that yes, okay, it’s quite possible given materialist premises that “our sense of self is a neuronal illusion.” At which point the entire edifice suddenly looks terribly wobbly — because who, exactly, is doing all of this forging and shaping and purpose-creating if Jerry Coyne, as I understand him (and I assume he understands himself) quite possibly does not actually exist at all? The theme of his argument is the crucial importance of human agency under eliminative materialism, but if under materialist premises the actual agent is quite possibly a fiction, then who exactly is this I who “reads” and “learns” and “teaches,” and why in the universe’s name should my illusory self believe Coyne’s bold proclamation that his illusory self’s purposes are somehow “real” and worthy of devotion and pursuit? (Let alone that they’re morally significant:,,) Read more here: http://douthat.blogs.nytimes.com/2014/01/06/the-confidence-of-jerry-coyne/?_r=0

bornagain77

Well,ba, I don't have much to say about the OP. As far as I'm concerned, everyone's religous beliefs are there own and I don't see much point in discussing them. wd400

Let's say that the human genome and the chimp genome are EXACTLY the same except that 2% of the genes are expressed (on or off) differently. If there are 25,000 human genes then 500 would be expressed differently between humans and chimps. The probability of going from one species to the other would be two to the 500th power or, I think, about 10 to the 167th. So if evolution were purposefully moving from one species to the other and you had one gene expressed differently per generation to that end it would take 10 to the 167th generations to get there. I am trying to make this evolution thing more plausible but it still quite unlikely. prhean

Arcatia_bogart:

The reason they have trouble with this is because it runs counter to the idea that they were made in god’s image.

And you're either ignorant or a liar. Imagine that. Which shall it be? Mung

Wd400: "I don’t know what you think is subjective about alignment. But the point you seem to have missed is that the percent-alignable has gone from 80 to 90 without denting the percent-identical. The genomes are really similar, why people have such trouble with this I do not know." The reason they have trouble with this is because it runs counter to the idea that they were made in god's image. Acartia_bogart

Well Moose Dr's case is far stronger than you pretend, but that is beside the point. The similarity is conceded by Mr. Arrington in this OP, for the sake of argument, so as to focus on, and make the case for the drastic differences in spirit. I don't blame you for ignoring it. It is not a minor problem for atheists. In fact, if you were honest with yourself and others on this point, the point would be devastating for your atheism. Do the New Atheists Own the Market on Reason? - On the terms of the New Atheists, the very concept of rationality becomes nonsensical - By R. Scott Smith, May 03, 2012 Excerpt: If atheistic evolution by NS were true, we'd be in a beginningless series of interpretations, without any knowledge. Yet, we do know many things. So, naturalism & atheistic evolution by NS are false -- non-physical essences exist. But, what's their best explanation? Being non-physical, it can't be evolution by NS. Plus, we use our experiences, form concepts and beliefs, and even modify or reject them. Yet, if we're just physical beings, how could we interact with and use these non-physical things? Perhaps we have non-physical souls too. In all, it seems likely the best explanation for these non-physical things is that there exists a Creator after all. http://www.patheos.com/Evangelical/Atheists-Own-the-Market-on-Reason-Scott-Smith-05-04-2012?offset=1&max=1 bornagain77

BA, I didn't address the OP at all, just corrected Moose Dr's misunderstanding. wd400

It is interesting to note that even though Mr. Arrington, for the sake of argument, conceded the point of similarity to Darwinists so as to make his overriding point for the spirit of man:

Even if we were 99.999999999999% similar both genetically and morphologically to chimpanzees, it would not matter, because it is the difference that counts, and that difference is not a material difference. The difference is spiritual in nature, and because it is spiritual in nature material comparisons are not just misleading; they are completely irrelevant. Paul wrote to his friends at Corinth: “I say, and prefer rather to be absent from the body and to be at home with the Lord.” II Cor. 5:8. Who was going to be present with the Lord when Paul was absent from his body? Why, Paul of course. Paul understood that he, Paul, transcended his physical body, and one day he would be separated from that body.

,,, even though Mr. Arrington conceded the point of similarity to Darwinists so as to make his argument for 'differences of spirit', wd400 still refuses to address Mr. Arrington's argument on its merits, and still argues as if Mr. Arrington had not already conceded the point to him (and other Darwinists). Well, if wd400 were to ever honestly address the argument on its own merits, the way Mr. Arrington intended, i.e. address the drastic spiritual difference between man and animals, then wd400 would also be impressed at the gigantic spiritual chasm that exists between man and the other animals on the planet: No less than Ian Tattersall, emeritus curator of the American Museum of Natural History, expresses wonder at the stark 'spiritual' differences between man and apes,,,

Evolution of the Genus Homo – Annual Review of Earth and Planetary Sciences – Ian Tattersall, Jeffery H. Schwartz, May 2009 Excerpt: “Unusual though Homo sapiens may be morphologically, it is undoubtedly our remarkable cognitive qualities that most strikingly demarcate us from all other extant species. They are certainly what give us our strong subjective sense of being qualitatively different. And they are all ultimately traceable to our symbolic capacity. Human beings alone, it seems, mentally dissect the world into a multitude of discrete symbols, and combine and recombine those symbols in their minds to produce hypotheses of alternative possibilities. When exactly Homo sapiens acquired this unusual ability is the subject of debate.” http://www.annualreviews.org/doi/abs/10.1146/annurev.earth.031208.100202

Further notes along this line;

Origin of the Mind: Marc Hauser - Scientific American - April 2009 Excerpt: "Researchers have found some of the building blocks of human cognition in other species. But these building blocks make up only the cement footprint of the skyscraper that is the human mind",,, http://www.wjh.harvard.edu?/~mnkylab/publications/rec?ent/mindSciAm.pdf Darwin's mistake: explaining the discontinuity between human and nonhuman minds. - 2008 Excerpt: Over the last quarter century, the dominant tendency in comparative cognitive psychology has been to emphasize the similarities between human and nonhuman minds and to downplay the differences as "one of degree and not of kind" (Darwin 1871).,,, To wit, there is a significant discontinuity in the degree to which human and nonhuman animals are able to approximate the higher-order, systematic, relational capabilities of a physical symbol system (PSS) (Newell 1980). We show that this symbolic-relational discontinuity pervades nearly every domain of cognition and runs much deeper than even the spectacular scaffolding provided by language or culture alone can explain,,, http://www.ncbi.nlm.nih.gov/pubmed/18479531 Young Children Have Grammar and Chimpanzees Don't - Apr. 10, 2013 Excerpt:,, He found further evidence for what many scientists, including Nim's own trainers, have contended about Nim: that the sequences of signs Nim put together did not follow from rules like those in human language. Nim's signs show significantly lower diversity than what is expected under a systematic grammar and were similar to the level expected with memorization. This suggests that true language learning is -- so far -- a uniquely human trait, and that it is present very early in development. "The idea that children are only imitating adults' language is very intuitive, so it's seen a revival over the last few years," Yang said. "But this is strong statistical evidence in favor of the idea that children actually know a lot about abstract grammar from an early age." http://www.sciencedaily.com/releases/2013/04/130410131327.htm

Even Alfred Wallace, co-discoverer of Natural Selection, who certainly had far more field work that Charles Darwin did, conceded, spiritually speaking, that "The difference between man and the other animals is unbridgeable",,,

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

And it is also interesting to note that the exact place where Man most drastically differentiates from animals, i.e. in his ability to produce information, is the exact place where Darwinian evolution has failed to achieve empirical validation. i.e. the generation of information by purely material processes. It should not be surprising that the material processes of Darwinian evolution would be found to be grossly inadequate to generate 'transcendent information'. Information simply cannot be reduced to a material basis:

"Information is information, not matter or energy. No materialism which does not admit this can survive at the present day." Norbert Weiner - MIT Mathematician -(Cybernetics, 2nd edition, p.132) Norbert Wiener created the modern field of control and communication systems, utilizing concepts like negative feedback. His seminal 1948 book Cybernetics both defined and named the new field. “One of the things I do in my classes, to get this idea across to students, is I hold up two computer disks. One is loaded with software, and the other one is blank. And I ask them, ‘what is the difference in mass between these two computer disks, as a result of the difference in the information content that they posses’? And of course the answer is, ‘Zero! None! There is no difference as a result of the information. And that’s because information is a mass-less quantity. Now, if information is not a material entity, then how can any materialistic explanation account for its origin? How can any material cause explain it’s origin? And this is the real and fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic, evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce. In the nineteenth century we thought that there were two fundamental entities in science; matter, and energy. At the beginning of the twenty first century, we now recognize that there’s a third fundamental entity; and its ‘information’. It’s not reducible to matter. It’s not reducible to energy. But it’s still a very important thing that is real; we buy it, we sell it, we send it down wires. Now, what do we make of the fact, that information is present at the very root of all biological function? In biology, we have matter, we have energy, but we also have this third, very important entity; information. I think the biology of the information age, poses a fundamental challenge to any materialistic approach to the origin of life.” -Dr. Stephen C. Meyer earned his Ph.D. in the History and Philosophy of science from Cambridge University for a dissertation on the history of origin-of-life biology and the methodology of the historical sciences. Intelligent design: Why can't biological information originate through a materialistic process? - Stephen Meyer - video http://www.youtube.com/watch?v=wqiXNxyoof8 John Lennox – Is There Evidence of Something Beyond Nature? (Semiotic Information) – video http://www.youtube.com/watch?v=F6rd4HEdffw

It also interesting to point out that the foundation of reality itself is found to be 'information theoretic' in its basis, not materialistic in its basis

John Wheeler (1911–2008) summarizes his life in physics - February 2014 Excerpt: "I think of my lifetime in physics as divided into three periods. In the first period, extending from the beginning of my career until the early 1950?s, I was in the grip of the idea that Everything Is Particles. I was looking for ways to build all basic entities – neutrons, protons, mesons, and so on – out of the lightest, most fundamental particles, electrons, and photons. I call my second period Everything Is Fields. From the time I fell in love with general relativity and gravitation in 1952 until late in my career, I pursued the vision of a world made of fields, one in which the apparent particles are really manifestations of electric and magnetic fields, gravitational fields, and space-time itself. Now I am in the grip of a new vision, that Everything Is Information. The more I have pondered the mystery of the quantum and our strange ability to comprehend this world in which we live, the more I see possible fundamental roles for logic and information as the bedrock of physical theory." – J. A. Wheeler, K. Ford, Geons, Black Hole, & Quantum Foam: A Life in Physics New York W.W. Norton & Co, 1998, pp 63-64. Why the Quantum? It from Bit? A Participatory Universe? Excerpt: In conclusion, it may very well be said that information is the irreducible kernel from which everything else flows. Thence the question why nature appears quantized is simply a consequence of the fact that information itself is quantized by necessity. It might even be fair to observe that the concept that information is fundamental is very old knowledge of humanity, witness for example the beginning of gospel according to John: "In the beginning was the Word." Anton Zeilinger - a leading expert in quantum teleportation: http://www.metanexus.net/archive/ultimate_reality/zeilinger.pdf Conversations with William Dembski--The Thesis of Being as Communion - video https://www.youtube.com/watch?v=cYAsaU9IvnI

Thus the fact that the universe is 'information theoretic' in its basis, and the fact that the 'spiritual differences' that most drastically separate us from the animals, i.e. our ability to use and create information, both correspond, is striking confirmation for the Theistic claim that we are made in God's image: verse and music:

Genesis 1:26 Then God said, "Let us make mankind in our image, in our likeness, so that they may rule over the fish in the sea and the birds in the sky, over the livestock and all the wild animals, and over all the creatures that move along the ground." Dive - Steven Curtis Chapman http://myktis.com/songs/dive/

bornagain77

I don’t know what you think is subjective about alignment.

In that case, don't leave us hanging like this. Put your money where your mouth is. Give us your objective definition of 'alignment' or at least the definition used by the researchers in those comparison studies. Mapou

... and here's a YEC saying the same thing: http://toddcwood.blogspot.com/2011/01/rtb-and-chimp-genome-part-4.html wd400

I don't know what you think is subjective about alignment. But the point you seem to have missed is that the percent-alignable has gone from 80 to 90 without denting the percent-identical. The genomes are really similar, why people have such trouble with this I do not know. wd400

wd400:

A section is alignable if it can be aligned...

Well, thank you for that astute bit of worthless wisdom. But since you are content with beating around the bush (a sign that you have something to hide), I should again point out that the definition of 'alignment' is highly subjective and can be manipulated to favor one worldview or another. Mapou

ppolish,

Soon the hominids will have their own tree segments. Shake those Apes off. Apes can have their own segment.

The visual imagery is hilarious! ;-) -Q Querius

Most Evolutionist "Family Trees" show Gorilla/Chimp/Bonobo/Human. But my latest SciAm mag )received today) shows a Gorilla/Chimp/Bonobo/Human,NeandertalDenisovsan tree. Baby steps. Soon the hominids will have their own tree segments. Shake those Apes off. Apes can have their own segment. ppolish

A section is alignable if it can be aligned... highly repetitive sequences (which both genomes are full of) are very difficult to align so they're excluded. Now, you might think the "unalignable" bits are really different so should count as "zero percent identity", but that's not the case. When the first draft of the chimp genome was published ~80% of the sequences could be aligned to human, and those ~80% have ~98% identity. In the latest drat, 90% of the genome is alignable and the 98% identity stands. Adding the previously-unalignable sequences hasn't changed the result. wd400

wd400:

You do not understand correctly. The ~98% figure is for all the align-able genome, not just the ~1.5% that encodes proteins.

In this is true, it's even worse than I thought. What is considered "alignable"? Are non-alignable code segments eliminated from the final statistics? This is subjective. Mapou

Moose Dr,

The methods used to produce the 98% number appear to me to be predicated on the neo-Darwinian interpretation. If I understand correctly, the number is pretty much based upon comparing variation within matching genes between the two species. The methods ignore dna differences in the non-coding, or “junk” regions. If these “junk” regions are not, well, junk, then the 98% number is in significant error. If the 98% number is in significant error the neo-Darwinian position is seriously challenged.

You do not understand correctly. The ~98% figure is for all the align-able genome, not just the ~1.5% that encodes proteins. In fact the protein coding genes are a good deal more similar to the chimpanzee genome than other regions, which is one good reason to think the majority of the genome is junk (diverging along at the neutral rate, rather than being slowed by natural selection). wd400

This topic reminds of a quote from someone eminent that I once read. It goes something like this: "The spirit of a man in the body of a gibbon would not do much worse . . ." I can't find it online. Maybe someone else here remembers it. -Q Querius

The study which Wells points to (#17) is just one of the many studies that David Wilcox points to in his review of chimp/human differences.

Polavarapu, et. al., 2011 Characterization and potential functional significance of human-chimpanzee large INDEL variation. Mobile DNA 2:13

http://www.mobilednajournal.com/content/pdf/1759-8753-2-13.pdf In terms of total size variation, there is no percentage differences mentioned. Maybe one of our more biochemically oriented commenters might want to summarize the study. jerry

JW, many believe that is so. I don't disagree with you, but I am not as certain as you appear to be. Barry Arrington

Dr. Moose. Wells agrees with you as set forth in one of the posts linked above. http://www.evolutionnews.org/2011/10/the_latest_on_chimp_and_human052291.html Barry Arrington

Moose Dr @15, I think I agree with you. If the non-coding genes were included in the comparison, I suspect the number would be more like 50 or 60%. I even expect the chimp's genome to be more complex than that of humans in certain respects. This is because a lot more of the chimp's behavior is hard coded at birth. Humans have to learn almost everything. Mapou

I find this to be an interesting post. I agree that the 98% number is no challenge to ID. The opposite, a number significantly higher than the 98% value, would be a significant challenge to neo-Darwinism however. The methods used to produce the 98% number appear to me to be predicated on the neo-Darwinian interpretation. If I understand correctly, the number is pretty much based upon comparing variation within matching genes between the two species. The methods ignore dna differences in the non-coding, or "junk" regions. If these "junk" regions are not, well, junk, then the 98% number is in significant error. If the 98% number is in significant error the neo-Darwinian position is seriously challenged. I believe that the DNA is vastly more functional than the protein coding genes. I believe that the "junk" meme has produced bad science. I believe that every chip in the block of Junk increases the percent difference between man and chimp. I therefore believe that it is an excellent expenditure of ID resource to prove that the 98% number is wrong. Moose Dr

@President Barry:

As a theist (especially a Christian theist), I am not troubled by the fact that I have an animal body. Yes, I am an animal, but I am not merely an animal. I have an eternal spirit, and that makes all the difference in the world.

Non-human animals have eternal spirits, too. JWTruthInLove

The genetic similarities only mean something wrt common ancestry if we are the sums of our genomes, ie our genomes make us what we are (type of organism human or chimp for example). Also the morphological differences, and there are many, always seem to get ignored in these discussions. Being an upright biped isn't as easy as Hollywood makes it appear. And I doubt being an upright biped is a Lamarkian trait as Hollywood makes it appear. Are there any transitional fossils of opposable big-toes starting to join the other little piggies? Joe

And others don't care, which is sort of the point of the OP. Mung

Some estimate the similarity at 98%. Others slightly less.

...and others, a lot less http://vimeo.com/95287522 cantor

Here is a comment I made a couple months ago about the differences between the chimp and human genomes (actually this is the third time). It is mainly about a review of chimp and human genomes in terms of control mechanisms.

The most interesting thing about the Meyer book was his emphasis in the latter part of the book on this non-genomic control of development. There may be a hunt for structure of the information for this as there was for DNA 60 years ago. And when they find it, the form may be so strange that it will be hard to interpret. When they found DNA they already had primitive digital codes to relate it to. Who knows what the structure will be that controls development and how it varies from species to species. Jon Garvey has on his site a discussion about what makes human unique. It primarily references a paper by a population geneticist David Wilcox. Here is the Wilcox paper http://www.asa3.org/ASA/meetings/belmont2013/papers/ASA2013Wilcox.pdf One of the things it says is that the regulatory nature in the human genome is extremely more complex than the next species. Here is a quote:

What shall we say about the genes which make us human? We and chimps share 96% to 99% of our protein coding sequences. Why are we different? Not the 1.5% of our genome that codes for proteins but the 98.5% that controls their production. Literally, no other primate lineage has evolved as fast as our lineage has during the last 1.5 million years, and it’s all due to unique changes in our control genome. At least 80% probably more of our “non-coding” genome is also transcribed, starting from multiple start points, transcribed in both directions, with overlapping reading frames of many sizes and a whole spectrum of alterations, producing a whole zoo of ‘new’ types of RNA control elements – piRNA,siRNA, miRNA,sdRNA, xiRNA, moRNA, snoRNA, MYS-RNA, crasiRNA, TEL-sRNA, PARs, and lncRNA. Most of these unique RNA transcripts – and there are thousands, if not millions of them – are uniquely active in developing human neural tissue – uniquely active compared to their activity in chimpanzees, much less other primates or mammals. It is the new epigenetic world

We are only a short way there to understanding what is happening. And all this appeared by chance? Hardly. So look to other things besides the coding sequences. We may have the same building blocks but how are they assembled is the real issue. jerry

That's a pretty loose definition of what it means to call someone a liar Barry. By that definition most people here are called liars all the time, don't you think? To be sure, his argument was a complete non-sequitur. otoh, RDFish claims he has no problem with someone being a dualist as long as they recognize it can’t serve as the basis for a scientific theory. But he obviously DOES have a problem with it or he would not have mentioned it. See how easy that was? :) Anyone can put forth an RDFish-like argument! Mung

A chimp is a wonderfully designed living creature. I, for one, am happy to have many of my genes in common with chimps. I'm also happy to share many of my genes with plants, worms and bacteria. They, too, are wonderfully designed creatures. That being said, we humans have something that animals and robots do not have and that is a spirit. Without spirit, there is no value to anything, no beauty and no ugliness. Thinking out loud. Mapou

Body hair should account for the 2% (or less) genetic delta between Robin Williams(RIP) his friend, Koko. Are there any other *meaningful* differences between apes and humans? 2% should do it. leodp

UD editor: "[snip] UD Editors: In this comment RDFish called Barry Arrington a liar. He is now in moderation." Obviously it is your right to edit and moderate comments as you see fit. But I have been called a liar (and other worse names) by UD commenters who have never been censured. I am a big boy and can live with the name calling from UD commenters. But I do find it hypocritical. Acartia_bogart

Certainly the spiritual gap between man and ape is wide and metaphysically significant, but I think Darwinists still must contend with the physical differences of the brain and the significance which follows. We don't need to downplay the morphological similarities between different hominids, rather we need to show how immense the cognitive differences are. Technology serves as a good example. If we replace the standard 4-cylinder engine in a sedan with an engine designed for a NASCAR auto (and made some slight body adjustments), we'd have completely different vehicles despite the fact they are 98%+ similar. Even the engines themselves would be very similar in many regards (they'd both have carburetors and spark plugs and pistons). What this shows is that in the most complicated parts of a structure (be it the engine of a car or brain in a hominid), seemingly small changes can have large effects. And the most complicated parts are the most likely to need design to function properly. Thus we did evolve from apes, what needs to be explained is how the brain evolved to perform tasks so unlike what it was able to do before. GW

RDFish, what would you think if I said to you that it was Cartisian dualism which led to modern science? Mung

RDFish:

...as long as you recognize it can’t serve as the basis for a scientific theory

Because you say so? Or do you have an actual argument to make. A rational reason you can give people to think that you are right. One that's scientific would probably be best. Mung

[snip] UD Editors: In this comment RDFish called Barry Arrington a liar. He is now in moderation. RDFish

Lucky Animals Mung