Chimps and humans: How similar are we really?

mark kennedy · May 1, 2017

NathanM. said:
In looking through some of your old threads, I note that your '3 fold expansion' thing was pretty much demolished all the other times you brought it up.

It's never addressed or you would simply repeat one of the arguments.

But let us say that your take is 100% valid, that a human's brain is really 3 whole times as large as a proposed ape-like ancestor.

Or you could look it up and realize it's an actual fact.

What is your rationale for believing that this is impossible?

Functional constraint and deleterious effects.

Is it your belief that such a change would necessarily require some huge suite of beneficial mutations? If so, on what do you base that?

Comparative genomics:

“For a long time, people have debated about the genetic underpinning of human brain evolution,” said Lahn. “Is it a few mutations in a few genes, a lot of mutations in a few genes, or a lot of mutations in a lot of genes? The answer appears to be a lot of mutations in a lot of genes. We've done a rough calculation that the evolution of the human brain probably involves hundreds if not thousands of mutations in perhaps hundreds or thousands of genes—and even that is a conservative estimate.” (Bruce Lahn)

How many mutations must it have taken in your estimation, and what is your evidence that supports that notion?

It would take a good deal more then a few mutations, there are also 60 de novo brain related genes.

One of the things I tell my students in genetics is that they should memorize this statements - "It depends." and that they should use that as an answer whenever they are asked for 'what happens if mutation X occurs?'

We know what happens when brain related genes get a mutation, disease and disorder

Papias · May 1, 2017

mark kennedy said:
MHC class II genes provide instructions for making proteins that are present almost exclusively on the surface of certain immune system cells. (Human leukocyte antigens)......

These are involved in immune systems, not the same thing as protein coding genes and certainly not highly conserved brain related functions.

Wow, it looks like you are not even reading the stuff you post yourself, which says that they are indeed protein coding genes.

mark, did you forget all the other times you posted this same stuff about your "3 fold expansion from earlier apes to humans" only to be shown all the intermediate transitional fossils that fill in your imagined "gap"? We could go through that all again, in addition to the genes themselves and all the over evidence - but after person after person has shown you the obvious and clear evidence time after time, year after year, I have to suspect that you'll ignore it yet again.

Then, it seems likely your responses will again be filled with empty, evidence free trash talk about shooting ghosts in a barrel on their hand and knees.

I'm just hoping you don't hide relevant data again.......

In Christ-

Papias

pitabread · May 1, 2017

mark kennedy said:
No, it depends on the tree.

Thought I'd repost, since you never did answer this.

Would you accept the following phylogenetic tree as being valid?

pshun2404 · May 1, 2017

pitabread said:
Thought I'd repost, since you never did answer this.

Would you accept the following phylogenetic tree as being valid?

No! Definitely not.

mark kennedy · May 1, 2017

NathanM. said:
Would I? Could it not be that I've seen the rebuttals and your dismissal of them, so concluded that it would be a waste of effort?

Like you Darwinians don't address the enormous divergence that has to happen 2 mya. Brain related genes like HAR1f don't respond well to mutations and the 60 de novo brain related genes seemingly come out of nowhere.

There are facts, then there are interpretations of facts.

I think you mean opinions, we are entitled to our own opinions but not our own facts.

Which functional constraints and which deleterious effects?

Learned a long time ago not to chase that kind of rhetoric in circles.

Oh dear... It almost looks like Lahn is the ENCODE of brain evolution - making unwarranted extrapolated proclamations when he shouldn't have. Since his claims in 2004-2006, I was unable to find anything by him or about him in the popular science press except for an interview in 2011 in which he says the brain is still evolving, but doesn't even mention 'thousands' of genes.

Ever notice that there are no Chimpanzee ancestors in the fossil record? That’s because every time a gracial (smooth) skull, that is dug up in Asian or Africa they are automatically one of our ancestors.

Australopithecus afarensis: AL 288-1
Australopithecus africanus: Taung 1
Lucy a Chimpanzee
Taung Skull not Human-like 26 August 2014

These two are the only Hominid fossils I've seen that are really being passed of as transitional. They both have chimpanzee size brains, with all the features one would expect of a knuckle dragging, tree dwelling ape. What is far more important then finding something indicating a transitional fossil, which they have failed to do, is to understand what the basis of the three-fold of the human brain from that of apes:

The evolutionary time separating human and macaque (20–25 million years) is grossly comparable to that separating rat and mouse (16–23 million years)…214 such genes in all of the four taxa chosen…

Increases in brain size and complexity are evident in the evolution of many primate lineages…However, this increase is far more dramatic in the lineage leading to humans than in other primate lineages…

accelerated protein evolution in a large cohort of nervous system genes, which is particularly pronounced for genes involved in nervous system development, represents a salient genetic correlate to the profound changes in brain size and complexity during primate evolution, (Molecular Evolution of the Human Nervous System. Bruce T. Lahn et al. Cell 2004)

That was probably the broadest comparison of brain related genes between apes and humans shortly after the unveiling of the findings of the Human Genome Project in 2001. Since then they have discovered at least two dramatic giant leaps that would have had to occur in order of the human brain to have emerged from ape like ancestors SRGAP2, HAR1F. In addition genes involved with the development of language (FOXP2), changes in the musculature of the jaw (MYH16) , and limb and digit specializations (HACNS1).

Here is a snippet from a more recent paper of Lahn's - 2008:

"The view that the human brain is the result of a trend also affecting other primates is consistent with many studies. Both large-scale surveys of evolutionary changes in brain-related genes, in addition to studies of many single genes such as ASPM, microcephalin, SHH and GLUD2, have shown that these genes experienced adaptive evolution in various time periods along the lineage leading to humans, often affecting humans and other related primates rather than being specific to humans only. Thus, available data point away from the anthropocentric notion of human brain evolution to a more nuanced view, which sees the human brain as resulting from a trend of increasing size and complexity that also affected other living primates, although the impact on humans is undoubtedly most profound. More plainly stated, the salient features of the human brain did not all come about in the terminal human branch after divergence from chimpanzees. Rather, many changes have occurred in much earlier stages of the human lineage. Given this new view, genetic studies of human brain evolution should focus on comparisons across many primates and even non-primate species instead of being limited to only comparing humans and chimpanzees."

Huh.
Interesting how a couple of years makes a difference, no?

It started with two things really, the way Darwinians will simply ignore the indels and shamelessly misrepresent the facts:

The difference between chimpanzees and humans due to single-nucleotide substitutions averages 1.23 percent, of which 1.06 percent or less is due to fixed divergence, and the rest being a result of polymorphism within chimp populations and within human populations. Insertion and deletion (indel) events account for another approximately 3 percent difference between chimp and human sequences, but each indel typically involves multiple nucleotides. The number of genetic changes from indels is a fraction of the number of single-nucleotide substitutions (roughly 5 million compared with roughly 35 million). So describing humans and chimpanzees as 98 to 99 percent identical is entirely appropriate (Chimpanzee Sequencing 2005). (Talk Origins)

Now it's true that there are pretty much 5 million indels but the size of them doesn't translated into 1% and some change no matter how you juggle the statistics:

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies. (Initial Sequence of the Chimpanzee Genome, Nature 2005)

Some of these indels would have been over a million base pairs long:

Both the total number of candidate human insertions/chimpanzee deletions (blue) and the number of bases altered (red) are shown. Fig. 6

But let us say that your take is 100% valid, that a human's brain is really 3 whole times as large as a proposed ape-like ancestor.

That's not a disputed fact. The human brain would have had to triple in size, starting 2 1/2 million years ago and ending 200 to 400 thousand years ago. The brain weight would have had to grow by 250% while the body only grows by 20%. The average brain weight would have to go from 400-450g, 2 1/2 MY ago to 1350. What is the genetic basis for the threefold expansion of the human brain in 2 1/2 million years?(Human ASPM Gene, Genetics 2003) What is the genetic and evolutionary background of phenotypic traits that set humans apart from our closest evolutionary relatives, the chimpanzees?(Gene Expression Differences Between the Brain Regions, Genome Res. 2003) One of the problems with the evolutionary expansion of the human brain from that of an ape is the size, weight and complexity.

What is your rationale for believing that this is impossible?

Brain related genes are highly conserved and subject to highly deleterious disease and disorder, beneficial effects are unknown.

The ancestral SRGAP2 protein sequence is highly constrained based on our analysis of 10 mammalian lineages. We find only a single amino-acid change between human and mouse and no changes among nonhuman primates within the first nine exons of the SRGAP2 orthologs. This is in stark contrast to the duplicate copies, which diverged from ancestral SRGAP2A less than 4 mya, but have accumulated as many as seven amino-acid replacements compared to one synonymous change. (Human-specific evolution of novel SRGAP2 genes by incomplete segmental duplication Cell May 2012)

What is the problem with 7 amino acid replacements in a highly conserved brain related gene? The only observed effects of changes in this gene in humans is disease and disorder:

15,767 individuals reported by Cooper et al. (2011)] for potential copy-number variation. We identified six large (>1 Mbp) copy-number variants (CNVs), including three deletions of the ancestral 1q32.1 region…
A ten year old child with a history of seizures, attention deficit disorder, and learning disabilities. An MRI of this patient also indicates several brain malformations, including hypoplasia of the posterior body of the corpus callosum…
Translocation breaking within intron 6 of SRGAP2A was reported in a five-year-old girl diagnosed with West syndrome and exhibiting epileptic seizures, intellectual disability, cortical atrophy, and a thin corpus callosum. (Human-specific evolution of novel SRGAP2 genes by incomplete segmental duplication Cell May 2012)

The search for variation with regard to this vital gene yielded no beneficial effect upon which selection could have acted. The only conceivable way the changes happen is relaxed functional constraint which, unless it emerged from the initial mutation perfectly functional it surly would have killed the host. Mutations are found in children with 'developmental delay and brain malformations, including West Syndrome, agenesis of the corpus callosum, and epileptic encephalopathies'.

mark kennedy · May 1, 2017

NathanM. said:
'Bait them with facts.' Is that what you call it?

Actually it's an ad hominem approach since my source material comes from scientific research not held to any reasonable skepticism. That way you don't get to make up the facts as you go.

mark kennedy · May 1, 2017

Papias said:
Wow, it looks like you are not even reading the stuff you post yourself, which says that they are indeed protein coding genes.

Well your kind of limited to regulatory genes and protein coding genes. I just see a difference for a gene that encodes for a protein and something with a more specified function. The point is moot.

mark, did you forget all the other times you posted this same stuff about your "3 fold expansion from earlier apes to humans" only to be shown all the intermediate transitional fossils that fill in your imagined "gap"? We could go through that all again, in addition to the genes themselves and all the over evidence - but after person after person has shown you the obvious and clear evidence time after time, year after year, I have to suspect that you'll ignore it yet again.

About the only thing you ever came up with is that Panda's Thumb scattergram and seem have abandoned comparative genomics a long time ago.

Then, it seems likely your responses will again be filled with empty, evidence free trash talk about shooting ghosts in a barrel on their hand and knees.

Handling these arguments are like shooting fish in a barrel while you beg the question of proof on your hands and knees. Your satire is getting sloppy.

I'm just hoping you don't hide relevant data again.......

In Christ-

Papias

Why would I ever want to hide them? I'm just trying to keep them from being buried in an avalanche of pedantic one liners.

Grace and peace,
Mark

mark kennedy · May 2, 2017

NathanM. said:
And yet it appears that you frequently misinterpret those facts. That is not ad hominem.

Seldom are my arguments interpretive, most of the time they are not even arguments, they're just facts. The ad hominem evidencial approach is just using source material you already accept as credible.

mark kennedy · May 2, 2017

NathanM. said:
Not impressed with your archived copy-pastes. Most of your post is a word-for-word copy paste of posts you've pasted since as early as 2008 (google is amazing).

Not interested it rehashing the bogus claims of a spammer.

No, the Leaky/Keith replacement of the Piltdown hoax, SRGAP2, the paranthropous fossils are all new. As a matter of fact what I put on worthchristian forums was from a thread on here, the moderators were micromanaging so I ended up posting elsewhere for a while. That's also how I ended up on CARM but the was after being on EVC where the moderators joined in the frenzy, that's not the only board I've seen do that. I have always used genomic comparisons and really all I have to do is present the actual facts. When the poster, usually a dedicated troller, is reduced the ad hominem attacks being argued in circles it's the same as a white flag in my book.

I have a number of formal debates on here and never pursued the subject matter as in depth as I do here. Yet not once have you mentioned those debates, you just make some random generalities about other boards.

mark kennedy · May 2, 2017

NathanM. said:
If they don't respond well, what do you suppose happens to the individuals with such mutations?

What happens to people with neurological disease and disorder, tumors, cancer and developmental disorders...really?

Agreed. let us see how you deal with facts.

Your posts are a fact desert, you went straight for ad hominem circular logic and never deviated.

Interesting take on 'facts.' is this a fact or your interpretation/opinion? Looks like opinion. What do YOU know about anatomical traits that these folks do not?

What folks, what facts, what opinions what traits? You not talking substantive points, it's just close encounters of the pedantic one liners.

I guess Lahn's later (e'.g., 2008) position is to be ignored since it no longer conforms to your 'it is all impossible' position.

All you offered was a quote that discusses broad comparisons which he has always done. Now your begging the question of proof and this reduction of your arguments to fallacious rhetoric is how I keep score.

So, where is the 'Darwinian dishonesty'?

The replacement of Piltdown with Homo habilis, the absence of chimpanzee ancestors in the fossil record gross distortions of the divergence on a genomic level, ignoring indels...the list goes on.

What is your actual point?

Darwinism is an a priori assumption supported with fallacious rhetoric, little more.

Do you not understand that indels are ONE TIME events?

Do you understand what they are called indels are simply divergence, mutations on that scale are a formula for extinction not adaptive evolution. What's more the indels, falsely so called are measured in base pairs, a number that doesn't change because you want to ignore close to 90 million base pairs or equivocate them with gaps in the sequence.

Looking through threads on this forum where you have brought this up in the past I see that this was explained to you over and over.

Inevitably the conversation descends in a fallacious downward spiral until that's all that's left. Sometimes I even keep score, at least until all substantive argumentation has been abandoned like this one:

Fallacious Rhetoric:

1 (#4) Some non-sequitur inferences but largely a to the man argument. Ad hominem
2 (#8) An almost complete abandonment of the evidence, focus on the one making the argument. Ad hominem
3. (#11) Jack is a jerk argument compared to Jack is wrong and is a jerk. The heart of the emphasis, in fact, the whole argument is Jack is a jerk. A substantive argument would be why Jack is wrong and whether or not he is a jerk irrelevant. Ad hominem
4. (#16) Begging the question of the quote but argues against an argument I haven't made. Strawman.
5. (#17) Natural methodology and naturalistic assumptions not the same thing. Equivocation.
[All the same guy is doing is, feigning indignation, fallacious rhetoric...there's one in every thread]
6. (#33) Ad hominem, same pedantic taunt he always uses.
7. (#34) Ad hominem, correcting something not in error.

Points made in the OP

HAR1F: Vital regulatory gene involved in brain development, 300 million years it has only 2 subsitutions, then 2 million years ago it allows 18, no explanation how.
SRGAP2: One single amino-acid change between human and mouse and no changes among nonhuman primates. accumulated as many as seven amino-acid replacements compared to one synonymous change. 6 known alleles, all resulting in sever neural disorder.
60 de novo (brand new) brain related genes with no known molecular mechanism to produce them.

The Taung Child, that replaced the Piltdown hoax, is a chimpanzee, so is Lucy. (Darwinian Theator of the Mind: AKA Human Brain Evolution. post #2)

Then you made the same argument again and again anyway.

I do tend to present the same facts, with the same predictable result, facts are simply ignored. This thread was dragged off topic early and you seem determined to keep it off topic regardless of the genomic source material repeatedly discussed.

That is, your mere opinions seemed to overrule the actual facts.

I'm not bothering with opinions, I just repeat the same straight forward facts and findings.

Do you understand indels or not?

Extra base pairs may be added (insertions) or removed (deletions) from the DNA of a gene. Indels involving one or two base pairs (or multiples of two) can have devastating consequences to the gene because translation of the gene is "frameshifted". (Mutations)

Do you understand we are talking about divergence?

And you fixation with size changes in the human lineage is actually pretty funny - it is as if you think such thinks must be 100% correlated to some fantastical number of mutations.

Which is why 90 million base pairs of divergence is referred to as indels, because it's assumed they were the result of mutations.

Let me save you some time -

It is easy to google your claims - because you seem to simply repeat the same arguments over and over - and it is easy to see how frequently they have been refuted.

It's readily apparent how many times the debate descended into fallacious rhetoric, that's for sure.

You do not seem to understand the nature of indels no matter how many times it has been explained to you.

We're not talking about indels, I pointed out that Talk Origins equivocated indel events with genomic measurements that are measured in base pairs. It's an obvious and fundamental mistake.

You have never presented any evidence that the number of mutations to too many, or too few, or how many would have been needed, etc., you just keep making the same 'folk science' assertions over and over.

Not impressed.

Just simple facts, not in dispute. I did make an argument for a while that the mutation rate would have been too high to be sustainable but like all substantive arguments, was completely ignored.

estimate the deleterious mutation rate. Eighteen processed pseudogenes were sequenced, including 12 on autosomes and 6 on the X chromosome. The average mutation rate was estimated to be 2.5 x 10-8 mutations per nucleotide site or 175 mutations per diploid genome per generation...Using conservative calculations of the proportion of the genome subject to purifying selection, we estimate that the genomic deleterious mutation rate (U) is at least 3. This high rate is difficult to reconcile with multiplicative fitness effects of individual mutations and suggests that synergistic epistasis among harmful mutations may be common. (Estimate of the Mutation Rate per Nucleotide in Humans, Genetics 2000)

There's a formula based on 1.33% divergence.

Calculations are based on a generation length of 20 years and average autosomal sequence divergence of 1.33% (Table 3)

So if the mutation rate (U) being at least 3 is hard to reconcile with 'multiplicative effects on fitness' what happens when it jumps up to 5%? The answer is pretty obvious, extinction.

Every time you guys do this your conceding the point by omission. I don't really care if you acknowledge the facts or not, put straight forward facts out there, generally without much commentary. Then watch the thread get dragged away from the substantive issues because the subject was comparative genomics. When the conversation is reduced to a diet of almost pure fallacious rhetoric that's when I know I have you, because you have nothing left.

Have a nice day
Mark

mark kennedy · May 2, 2017

NathanM. said:
From 2006 when you made this nearly exact same argument, "Shernren" replied:

ow, if 60 indels happen, and each indel causes 20 base pairs to change,

How many mutations have occurred? 60.
How many base pairs have been changed? 1200.

If 30 indels happen, each causing 20 base pairs to change, and 30 single-base substitutions happen,

How many mutations have occurred? 60.
How many base pairs have been changed? 630.

If 60 single-base substitutions happen,

How many mutations have occurred? 60.
How many base pairs have been changed? 60.

Shernren? Wow you have been searching the stacks. We did most of our debates in Origins Theology.(Accepting human evolution is not a rejection of orthodoxy). Of course I know that insertions and deletions are sometimes length mutations, that's not the point:

Insertion and deletion (indel) events account for another approximately 3 percent difference between chimp and human sequences, but each indel typically involves multiple nucleotides. The number of genetic changes from indels is a fraction of the number of single-nucleotide substitutions (roughly 5 million compared with roughly 35 million). So describing humans and chimpanzees as 98 to 99 percent identical is entirely appropriate (Chimpanzee Sequencing 2005). (CB144 Talk Origins)

90 million base pairs, when the basis of comparison is base pairs, does not change because it's 5 million events. You don't get to change that percentage from 3% to a smaller ratio because of the number of events. It's an abandonment of the obvious basis of comparison and a gross distortion of fact.

In each case 60 mutations happen. In each case a different number of base pairs is changed. It's entirely possible for 60 mutations per generation to change more than 60 base pairs per generation. And this has nothing to do with the "central thesis of Darwinian evolution", or even the Central Dogma. It's basic math and genetics, and calling it Darwinian propaganda just because you won't accept it doesn't help you much at all.

The genomic comparison is in base pairs:

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total ~90 Mb. This difference corresponds to ~3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions (Nature 2005)

Or one can just read the thread:

Evolution as natural history is psuedo-science

Not going to bother re-refuting these same lame arguments when it has already been done.

This was the whole point:

"What makes us human? We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee. Comparing the genetic code of humans and chimps will allow the study of not only our similarities, but also the minute differences that set us apart."

Nature, Web Focus, The Chimpanzee Genome

The publishers of Nature know that this is not true, the paper they are announcing says something very different:

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 4045 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total 90 Mb. This difference corresponds to 3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies. Of course, the number of indel events is far fewer than the number of substitution events (5 million compared with 35 million, respectively).(Initial sequence of the chimpanzee genome and comparison with the human genome)

So we are talking about 90 million base pairs which represents 3% divergence. The 1.23% plus 3% does not add up to 98% no matter how many ways you try to distort the comparison. There's a reason I keep using this, it always works and you don't need to be a scientist to see the basis of comparison is base pairs. Ignoring that fact should be telling us something about how Darwinians conflate the facts on the most fundamental levels.

Have a nice day
Mark

mark kennedy · May 2, 2017

NathanM. said:
So, I guess you just missed that he 98% thing was in a press release of sorts.

Are you really hanging your hat on this accounting difference? All of your implications or outright accusations of fraud and such - all over the fact that a 'press release' differed from the paper by a couple of percent?

Wow... priceless.

Not just the web focus article but Talk Origins statement are obvious errors. I see it all the time and the discussion you dredged up was the same basic error, equivocating the number or events with the divergence as measured in base pairs.

mark kennedy · May 2, 2017

NathanM. said:
Ugh... Have a few minutes to kill....

Yes, really.

Do they tend to pass on those genes, historically speaking?

Projection. Your above response was to me writing " let us see how you deal with facts."

Actually, I am just replying to what you write. In fact, what you replied to above was my reply to this claim of yours:

"That’s because every time a gracial [sic] (smooth) skull, that is dug up in Asian or Africa they are automatically one of our ancestors."

I am asking what you know regarding the classification of these fossils that they do not.

No chimpanzee ancestors in the fossil record and the Homo habilis stone age ape man myth replaced Piltdown. Keith built his career on the Piltdown fraud, his prodigy was digging up ape skulls in Africa as passing the off as human ancestors. The Taunt Child for decades is dismissed as a chimpanzee until the demise of Piltdown. Dart who found the Taunt fossil recommended the name 'Homo habilis' or the 'handyman' tool making stone age ape man. That's how their classified and why.

Apparently, nothing.

You could not have read the quote I supplied for understanding if that is your takeaway from it.

Then you should find a new way to keep score. You appear to be replying to imaginary statements. The entirety of the section of my post that you are supposedly replying to here:

Oh dear... It almost looks like Lahn is the ENCODE of brain evolution - making unwarranted extrapolated proclamations when he shouldn't have. Since his claims in 2004-2006, I was unable to find anything by him or about him in the popular science press except for an interview in 2011 in which he says the brain is still evolving, but doesn't even mention 'thousands' of genes.

Here is a snippet from a more recent paper of Lahn's - 2008:

"The view that the human brain is the result of a trend also affecting other primates is consistent with many studies. Both large-scale surveys of evolutionary changes in brain-related genes, in addition to studies of many single genes such as ASPM, microcephalin, SHH and GLUD2, have shown that these genes experienced adaptive evolution in various time periods along the lineage leading to humans, often affecting humans and other related primates rather than being specific to humans only. Thus, available data point away from the anthropocentric notion of human brain evolution to a more nuanced view, which sees the human brain as resulting from a trend of increasing size and complexity that also affected other living primates, although the impact on humans is undoubtedly most profound. More plainly stated, the salient features of the human brain did not all come about in the terminal human branch after divergence from chimpanzees. Rather, many changes have occurred in much earlier stages of the human lineage. Given this new view, genetic studies of human brain evolution should focus on comparisons across many primates and even non-primate species instead of being limited to only comparing humans and chimpanzees."

Huh.
Interesting how a couple of years makes a difference, no?

I guess you missed the part where Lahn wrote, contrary to your usual implications:

"Thus, available data point away from the anthropocentric notion of human brain evolution to a more nuanced view, which sees the human brain as resulting from a trend of increasing size and complexity that also affected other living primates, although the impact on humans is undoubtedly most profound. More plainly stated, the salient features of the human brain did not all come about in the terminal human branch after divergence from chimpanzees."

Which is pretty much 180 degrees to what you keep implying.

It's pretty much irrelevant to what I'm saying. He's just saying you need a broad spectrum of comparisons which has always been his approach.

Your imaginary list, yes I can see that.

Ignoring indels? Classic.

I have read from your decades old posts on indels that despite the fact that at one point you actually admitted that indels are one time events, in the next post you simply re-stated your original claim about how mutation rates and total nucleotide differences do not add up. It is almost funny to read. can't find it right now, but it was entertaining to read.

These 'gross distortions' - i ask again, have you looked into the genomic comparisons of things that creationists claim descended from a 'kind'?

Or are you solely fixated on the human/chimp thing?

By the way - I 'keep score' by how frequently a creationist repeats the same arguments after having them refuted.
And how often they plagiarize. Haven't caught you plagiarizing, but LOTS of your kind do.

Well, I guess you would know.

Now THAT is fallacious rhetoric.

Who said they were adaptive? And even if they had been claimed to be adaptive, what do you have - besides a bland dismissal - that they could not be? Your inability to 'believe' it?

I am having a hard time parsing your statements.

Ignore what 90 million base pairs?

Do you still believe that indels count as the total number of nucleotides in them when it comes to 'counting'? What 'gaps in the sequence'?

Is it REALLY your position that indels are not real things? Or what? Other than these bland accusations, what is your evidence?

Looked to me more like your claim was refuted and you couldn't handle it.

Piltdown was NEVER a major bit of evidence for evolution, and there were MANY that doubted its authenticity from the get-go. That you and your sources don't understand this is not our problem.

Your argument was bogus. Sorry.

I saw someone try to explain to you what an actual ad hominem is. Creationists have a pretty well documented history of erroneously accusing others of using logical fallacies, ad hominem being one of the primary ones.

No link for that one.

No, it was someone explaining to you that you do not seem to understand what Darwinism is - you had written:

"Darwinism is a term that is used to describe the naturalistic assumptions of modern academics and scientists that long ago rejected God as the cause of anything in the organic and inorganic world, going all the way back to and including the Big Bang."

That is total BS. Not sure what you are whining about. Be a man and admit you don't know everything.

it appears that you are frequently 'that one.'

No link.

According to you.

Aside from your persecution complex and your tendency to think you are 100% correct about everything, I didn't really see anything in those links supportive of what you are whining about.

I guess when you cannot understand the arguments of the science, you see everything as an attack.

Selection pressure?

And..?

Perhaps back in 2004, but there are in fact several examples of this and many proposed mechanisms. One example:
Recent de novo origin of human protein-coding genes

Even if that paper did not exist, your 'argument' is basically that because there is no known mechanism right now, we will never know how this happened, thus it was God magic.

According to you? I did not realize that you are a paleoanthropologist. Please cite your manuscript in which you show that Taung child an dLucy are just chimps. I am sure you can also show us Don Johansson's admission that he has been wrong for the last 40 years about Lucy.

Thanks.

From what I have seen, you present a very specific set of facts, provide your own idiosyncratic interpretation of them, then ignore/dismiss any and all explanations as to why your interpretations are incorrect.

Take your indels argument...

Or this:

" The Piltdown Hoax was the flagship transitional of Darwinism for nearly half a century and it was a hoax."

You wrote that. Was Piltdown the 'flagship transitional'?

Not even close.

So it seems that what you believe to be "facts" are themselves often NOT facts.

Can you really blame people for reminding you of this?

And maybe getting a little annoyed that you refuse to admit your obvious errors?

You mean the hackneyed, repetitive erroneous claims you and others have made? THAT "genomic source material"?

I get it - you are awed by big numbers, and just cannot believe how genetics works. But those are not an argument. Sorry.

I think you are having a hard time distinguishing between the facts you present and your opinions.

It is a fact (as best we can tell at this point) that there are X-number of indels in humans relative to chimps.

It is NOT a fact that evolutionists lie about it, dismiss the numbers, etc.

Can you not see that?

That YOU cannot understand that an insertion or deletion is a one-time event, regardless of how large it is, is not a shortcoming of evolutionary biologists.

If they occur within exons, yes, I get that.

What if they occur in introns?

What if they occur in intergenic DNA?

What is your FACT that all indels occur IN exons (as you seem to be implying)?

Golly gee, no I totally didn't.... :rolleyes"

LOL!

Right - let's hope that you understand that THAT is an opinion.

Tell us all Mark - show us your FACTS (NOT opinions) that indels are something other than larger-scale mutations.

Can't wait! I know how I am going to 'keep score' on this issue.

Yes it is, it most certainly is.

Here is what you pasted:

"Insertion and deletion (indel) events account for another approximately 3 percent difference between chimp and human sequences, but each indel typically involves multiple nucleotides. The number of genetic changes from indels is a fraction of the number of single-nucleotide substitutions (roughly 5 million compared with roughly 35 million). So describing humans and chimpanzees as 98 to 99 percent identical is entirely appropriate"

I don't see the mistake - they provided a justification for their conclusion. That justification may or may not be reasonable, but it is not a 'mistake' or a lie or deception.

Why can you not see that?

Golly, can't see why...

Yeah, well, except that U is the deleterious mutation rate, not the overall mutation rate.
That and recent evidence indicates that 1) the beneficial mutation rate is much higher than previous estimates (at least in prokaryotes) sexual recombination and 2) sexual recombination hastens the extinction of harmful mutations, so I am not sure that you 'calculation' had merit in the first place.

But I guess that is just some form of ad hominem, right?

Quite a persecution complex you have there, chief.

Too bad that you seem to have a hard time distinguishing facts from your own opinions.[/list]

I don't know why your so confused about the subject matter but there is very little in my posts besides unavoidable facts. Apparently transitional fossils and comparative genomics don't interest you but random personal taunts give you a kick. Typical

pitabread · May 2, 2017

mark kennedy said:
When the conversation is reduced to a diet of almost pure fallacious rhetoric that's when I know I have you, because you have nothing left.

Oh look, more self-aggrandizing grandstanding.

Btw, you still haven't answered my question. Would you accept the below phylogenetic tree as valid? I think I know why you're avoiding answering the question, though.

pshun2404 · May 2, 2017

I know this is directed at Mark but I want to point something out...

When you asked the simple question about THIS tree (“Would you accept the following phylogenetic tree as being valid?”). You poised it for a Yes or No response, and then when I gave the simple answer to your simple Yes/No question, I was relegated to a position of not having an answer for WHY I do not accept YOUR tree, when why was not part of the original question.

The fact is I have seen at least a half dozen artistically contrived trees as well as a couple of cladistic bush/trees. They vary as to the specific lineages they hypothesize (though flow along the same GENERAL lines). So where you have Rhesus Macaque others have Gorilla/Orangutan which your’s entirely ignores, and so on.

So obviously there is in the general agreement some discussion or difference regarding whether a particular tree does or does not merit being "valid". I do not find your tree particularly informative of any particular evolutionary position.

Like in your tree, chimps appear around the same time as humans, and just suddenly stop evolving, while in others at least homo goes through multiple undefined stages until humans appear (homo erectus at least, but sapiens at best).

Is it a tree or a bush or a shrub? Are there more than one original source lifeform (as Venter and Woese believe possible) or only one (LUCA)? Do all organisms ONLY develop into other organisms slowly over millions of years (standard model) or do some form rapidly after long periods of stasis (PE model), and what about those organisms that do not present any ancestors?

No, in my opinion, this tree is inadequate even to support YOUR position.

pitabread · May 2, 2017

pshun2404 said:
No, in my opinion, this tree is inadequate even to support YOUR position.

I don't think you know what my position is or why I keep posting that particular tree. I'll wait and see if mark is going to bother to reply before going into more detail. I suspect he'll continue to ignore my request and he probably knows why (hint: it's a trap! ).

mark kennedy · May 2, 2017

pitabread said:
Oh look, more self-aggrandizing grandstanding.

Btw, you still haven't answered my question. Would you accept the below phylogenetic tree as valid? I think I know why you're avoiding answering the question, though.

No, the human/chimpanzee is something I do not accept for reasons I've explained often and at great length. I do believe in common descent, I just don't assume it and believe there are limits beyond which things cannot evolve. As far as the others, maybe some of them up to the level of genus but beyond that it starts to get really sketchy.

pshun2404 said:
Like in your tree, chimps appear around the same time as humans, and just suddenly stop evolving, while in others at least homo goes through multiple undefined stages until humans appear (homo erectus at least, but sapiens at best).

Homo erectus has every indication of being human, Turkana boy is 100% human except for a small skull that is still within human range. Homo habilis seldom is above 600cc and has every indication of being more of an ape ancestor to chimpanzees and gorillas. Fossilization requires the pressure and material to be mineralized, something like volcanic ash can work, the famous Laetoli footprints for instance were made by human feet for instance.

Anyway, humans bury their dead which is why over half of Neanderthals would be found in caves. The practice of caves being used as burial sites is mentioned early in Scripture (Gen. 25:7-11). The hominid (human like) fossils closely resembling modern humans appear in the fossil record no sooner then 2 mya. Just about everything dated earlier is exclusively ape like in proportion and features. That in addition to the absence of chimpanzee ancestors across five million years indicates to me ape ancestors are passed off as human ancestors.

If we are to accept the Darwinian narrative then relative stasis is seen with sudden spikes in adaptive evolution without explanation. The great apes of Africa and Asia would have been contemporary with human ancestors, especially in equatorial and southern Africa for millions of years then suddenly the cranial capacity doubles nearly over night. Why these selective forces effect none of our primate cousins is completely unexplained.

My entire argument is focused on the human/chimpanzee split for one very important reason, that's where you will find the greatest abundance of fossil evidence and genomic comparisons. My central focus has been on human brain evolution and the molecular basis. Darwinian evolution along these lines are effects with no known cause but Darwinian evolution always gets a pass. The reason is due to naturalistic assumptions, not natural science.

pshun2404 · May 2, 2017

pitabread said:
I don't think you know what my position is or why I keep posting that particular tree. I'll wait and see if mark is going to bother to reply before going into more detail. I suspect he'll continue to ignore my request and he probably knows why (hint: it's a trap! ).

Cool!

pshun2404 · May 3, 2017

NathanM. said:
LOL!

Are you KIDDING me????

Years ago, creationist kook Walt Brown wrote about how his son had demolished evolution at a school science fair.

He had 'analyzed' some papers about phylogenetics and showed that one paper had humans and chimps grouped together, but that others had human and rattlesnake, therefore, we should not believe evolution.

These wizards did not realize something that evolutionists were able to point out in seconds - the paper joining humans and rattlesnakes? It only used a single taxon from mammalia - humans.

DUH.

No not kidding at all. I considered THIS tree and concluded it is not valid to explain phylogenetics. It is wanting o so many ways.

Do not know this "Walter Brown" guy and I DO believe in evolution just not everything "evolutionists" say about it. And the tree in this case was produced for our perusal by a non-creationist So the purpose and reason for your comment eludes me.

Aman777 · May 3, 2017

pshun2404 said:
We have recently found 1,307 orphan genes that are completely different between humans and chimpanzees, and these from just four areas of tissue samples. We can only imagine the vast numbers of differences that will be revealed once more areas of the anatomy and physiology are analyzed (see J. Ruiz-Orera, 2015, “Origins of De Novo Genes in Humans and Chimpanzees”, PLoS Genetics. 11 (12): e1005721)

Orphan genes, as many here know, are found only particular lineages of creature or sometimes only in a specific species or variety within a species. What is really interesting is they appear to have no evolutionary history. Despite that we have come to know these genes are incredibly important! Their expression often dictates very specific qualities and processes allowing for specialized adaptations of particular tissues, like the antisense gene, NCYM, which is over-expressed in neuroblastoma; this gene inhibits the activity of glycogen synthase kinase 3β (GSK3β), which targets NMYC for degradation (Suenaga Y, Islam SMR, Alagu J, Kaneko Y, Kato M, et al. (2014) NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PLoS Genet 10: e1003996. doi: 10.1371/journal.pgen.1003996). Some contribute to specific proteins unique only to that species or to varieties within a species.

This genetic curiosity has been being studied for around 20 years with little insight as to why they are there at all (where did they come from), and we are just beginning to see how they function, but the doubted thousands of additional differences this will add to the human/chimp difference scenario is staggering.

Any thoughts?

Humans (descendants of Adam) did NOT descend from the common ancestor of Apes and did NOT diverge from Chimps. The sons of God (prehistoric people) DID descend from other animals. This is important since ONLY Adam was made with an intelligence like God's. Gen 3:22 IOW, Science has confused prehistoric man, with Adam's descendants who arrived only 11k years ago in the mountains of Ararat in the Ark. Amen?

Chimps and humans: How similar are we really?

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