Darwinian Naturalistic Assumptions and Homology Arguments

[mark kennedy]

Ug! says the caveman!

I believe in evolution as the change of alleles in populations over time, just not the a priori assumption of universal common descent by exclusively naturalistic means. I have no problem with evolution as it is properly defined scientifically, what I have a problem with is Darwinism. When it comes to evolution as natural history I am skeptical and what concerns me the most is the supposed common ancestry of apes and humans I am consumed with incredulity. I am especially leery of homology arguments.

Now if by evolution you mean transitions like the evolutionary giant leap from primordial soup to functional cells. Here is the irreducible complexity of a bacterium, do note that the flagellum is only one aspect of the overall complexity:

Now tell me what the common ancestor of plants and animals had in common with plant cells and prokaryotes.

Oh yea, the transitional fossils. Maybe you can tell me why we have literally hundreds of fossils representing our ancestors and virtually none for chimpanzee ancestors. Could it be that every time an ape fossil is dug up in Africa it is passed off as one of our ancestors?

Think I'm exaggerating? Consider this, while the Piltdown hoax is being passed of as a transitional fossil the Taung Child was considered a chimpanzee. Then with the demise of the Piltdown hoax it becomes one of those mythical transitionals. Raymond Dart who dug the lime endocast out of a box was the one who suggested to Louis Leaky the name 'handy man' or 'homo habilis' for his new classification group. What he did was to abandon the Cerebral Rubicon (the 600cc cut off for Homo) in favor of 'tool use' and a long list of contrived features.

No wait, there's more. Do you realize that if there were no living chimpanzees we would have no fossil evidence that chimpanzee ever existed? None of the transitionals in other taxons have the slightest bearing on the historicity of Scripture or essential Christian doctrine except the transition from ape to man. This is the vital transition that would have had to happen for us to have evolved from apes. Human and chimpanzee brains

Given that fact that mutations in brain related genes always yield severely deleterious diseases and disorders you are left with supposition and speculation rather then a molecular mechanism.

We are being told that we are 98% the same in our DNA as the chimpanzee. The fact of the matter is scientists have known better for years and yet they propagate this myth with shameless abandon.

As far as looking at specific genes, the chimp and human Y chromosomes had a dramatic difference in gene content of 53 percent. In other words, the chimp was lacking approximately half of the genes found on a human Y chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y chromosome contains a third more gene categories--entirely different classes of genes--compared to chimps. (New Chromosome Research Undermines Human-Chimp Similarity Claims by Jeffrey Tomkins, Ph.D., & Brian Thomas, M.S.)​

With the length of the two Y chromosomes being 24 mbp in the chimpanzee genome and 59 mbp in the human genome, what is the divergence as a percentage?

• Pan troglodytes (chimpanzee) Y Chromosome
• Homo sapiens (human) Y Chromosome

I added up the size of the chromosomes in the NCBI genome viewer and what I came up with is 3,088 mbp (million base pairs) in the human genome and 3,172 mbp in the chimpanzee genome for a difference of divergence based on the number of base pairs only.

It gets a little strange when you start to compare Human Chromosome 2 that weighs in at 243 mbp compared to the Chimpanzee Chromosomes 2 (a) 114 mbp and 2 (b) at 250 mbp. So the Chimpanzee is 121 mbp larger counting the base pairs of both Chimpanzee Chromosomes 2 (a) and 2 (b).

Then there is the Y Chromosome in the Chimpanzee genome that is 24 mbp long compared to the Human Y Chromosome that is 59 mbp for a difference of 35 mbp.


The Chimpanzee genome has 84 mbp then the human genome not counting the SNPs. Something else that you might not realize, if you list the differences between the various chromosomes (Ch 1 to Ch 1...) The differences between the chromosomes adds up the 222 mbp.

The analysis of modest-sized insertions reveals

• ~32 Mb of human-specific sequence and
• ~35 Mb of chimpanzee-specific sequence,

contained in ~5 million events in each species

Species specific means it exists in one but not in the other, you don't get to halve the unique sequences. The divergence has to be at least 3% based on the length of the sequences alone.

Sequence analysis confirms the existence of a high degree of sequence similarity between the two species. However, and importantly, this 98.6% sequence identity drops to only 86.7% taking into account the multiple insertions/deletions (indels) dispersed throughout the region...

...Hence our perceived sequence divergence of only 1% between these two species appears to be erroneous, because this work, along with another recently published analysis, puts both species much further apart, >10% here and ≈5% in another recently published study, albeit the latter study compared shorter segments of both genomes. This relatively high and previously unexpected degree of sequence divergence might have functional implications not only within the coding sequences itself but also within regulatory elements Proc Natl Acad Sci U S A. 2003 June 24​

It has been known for years that we are 98% the same in our DNA as the Chimpanzees but the homology arguments persist. That's what is wrong with Darwinism, by making evolution a foregone conclusion scientists are left with a false confidence in a common ancestor. Then after habitually rearranging the evidence around the proposition that human descent can be explained by natural mechanisms they end up distorting the evidence.

Idols of the theater - "...there are idol which have crept into men's minds from the various dogmas of peculiar systems of philosophy, and also from the perverted rules of demonstration...for we regard all the systems of philosophy hitherto received or imagined, as so many plays brought out and performed, creating fictitious and theatrical worlds." (Francis Bacon)​

Evolution is riddled with gigantic leaps in logic, billions of years and crucial transitions that are never directly observed or demonstrated are passed off as fact. It's not, it's a naturalistic assumption being passed off as a conclusion based on the evidence.

Accepting human evolution from that of apes is not only a rejection of the Pauline doctrine of original sin, it's a myth of human ancestry. When the New Testament writers mention Adam they speak of him as the first man and the reason why all of us are under the curse of sin and death. Paul tells us that 'by one man sin entered the world' and 'by one man's offense death reigned'. (Rom 5:12-19). Paul ties Adam directly to the need for justification and grace in his exposition of the Gospel in his letter to the Romans. Luke lists Adam in his genealogy calling him 'son of God' indicating he had no human parents but rather was created (Luke 3:23-28). My concern is simply this, the myth of human lineage linked to ape ancestry contradicts the clear testimony of Scripture and essential doctrine, specifically justification by faith. Paul is clear that all have sinned in Adam and that is the reason that we cannot keep the Mosaic law.

Charles Darwin in the preface to ‘On the Origin of Species’ credits Jean-Baptiste Lamarck with being the first man to propose that:

‘the doctrine that species, including man, are descended from other species...being the result of law, and not of miraculous interposition.’​

This is what I have come to recognize as an a priori assumption of exclusively naturalistic explanations for the lineage of all living things. For years I focused exclusively on the Scientific literature regarding Chimpanzee and Human common ancestry and found that the human brain had neither the time nor the means to have evolved from that of apes.

The most dramatic and crucial adaptation being the evolution of the human brain. Charles Darwin proposed a null hypothesis for his theory of common descent :

“If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” (Darwin, On the Origin of Species)​

With a cranial capacity nearly three times that of the chimpanzee the molecular basis for this giant leap in evolutionary history is still almost, completely unknown. Changes in brain related genes are characterized by debilitating disease and disorder and yet our decent from a common ancestor with the chimpanzee would have had to be marked by a massive overhaul of brain related genes. I propose that a critical examination of common descent in the light of modern insights into molecular mechanisms of inheritance is the single strongest argument against human/ape common ancestry.

Pick a chromosome, any chromosome and you will find a disease or disorder effecting the human brain as the result of a mutation.

Human Genome Project Landmark Poster

I don't see any reason to reject TOE in it's entirety but don't lose your head. There is ample reason to remain skeptical.

Grace and peace,
Mark

 

[Nostromo]

I am consumed with incredulity.

Which, as always, is a terrible argument.

Here is the irreducible complexity of a bacterium

I think it's fair to say that IC has been done to death, and been debunked quite thoroughly.

Maybe you can tell me why we have literally hundreds of fossils representing our ancestors and virtually none for chimpanzee ancestors. Could it be that every time an ape fossil is dug up in Africa it is passed off as one of our ancestors?

To quote FOSSILIZATION AND ADAPTATION :
"Fossilization is a rare event. The chances of a given individual being preserved in the fossil record are very small. Some organisms, however, have better chances than others because of the composition of their skeletons or where they lived."

Chimpanzees are restricted to a relatively small area of central Africa which is biologically dense and more likely to result in dead organisms rotting away or being scavenged than fossilised. Humans on the other hand have a much more varied habitat and as such are more likely to meet their end in areas more conducive to fossilisation.

We are being told that we are 98% the same in our DNA as the chimpanzee. The fact of the matter is scientists have known better for years and yet they propagate this myth with shameless abandon. With the length of the two Y chromosomes being 24 mbp in the chimpanzee genome and 59 mbp in the human genome, what is the divergence as a percentage?

As a proportion of the whole genome, about 1%.

There are some comments on the percentage differences over at Talk Origins, here :
CB144: Human/chimp genome difference

 

[mark kennedy]

Which, as always, is a terrible argument.
I think it's fair to say that IC has been done to death, and been debunked quite thoroughly.

You missed the sarcasm, I don't submit to arguments from credulity even if it results in shallow attacks on my credulity. The ID molecular mechanisms of irreducible complexity do not go far enough.

To quote FOSSILIZATION AND ADAPTATION :
"Fossilization is a rare event. The chances of a given individual being preserved in the fossil record are very small. Some organisms, however, have better chances than others because of the composition of their skeletons or where they lived."
Chimpanzees are restricted to a relatively small area of central Africa which is biologically dense and more likely to result in dead organisms rotting away or being scavenged than fossilised. Humans on the other hand have a much more varied habitat and as such are more likely to meet their end in areas more conducive to fossilisation.

Our ancestors would have been contemporary with and living in the same geographical regions as prehistoric apes up until less then a million years ago. What has happened is early apes are being passed off as transitionals, it's as simple as that.

As a proportion of the whole genome, about 1%.

None of the more current research supports that statement.

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 Chimpanzee Genome​

Do the math:

I added up the size of the chromosomes in the NCBI genome viewer and what I came up with is 3,088 mbp (million base pairs) in the human genome and 3,172 mbp in the chimpanzee genome for a difference of 84 mbp based on the number of base pairs only.

It gets a little strange when you start to compare Human Chromosome 2 that weighs in at 243 mbp compared to the Chimpanzee Chromosomes 2 (a) 114 mbp and 2 (b) at 250 mbp. So the Chimpanzee is 121 mbp larger counting the base pairs of both Chimpanzee Chromosomes 2 (a) and 2 (b).

Then there is the Y Chromosome in the Chimpanzee genome that is 24 mbp long compared to the Human Y Chromosome that is 59 mbp for a difference of 35 mbp.

The Chimpanzee genome has 84 mbp then the human genome not counting the SNPs. Something else that you might not realize, if you list the differences between the various chromosomes (Ch 1 to Ch 1...) The differences between the chromosomes adds up the 222 mbp.​

There are some comments on the percentage differences over at Talk Origins, here :
CB144: Human/chimp genome difference

I wouldn't be interested thanks.

Have a nice day
Mark

 

[mark kennedy]

Let's go back to school shall we?

Q. What is the habitat chimpanzees live in? is it a desert? is it a forest? or is it the sea shore?
A. The forest.

Can I take the essay answer option. Pan Troglodytes are found in the Savannahs of equatorial Africa and the Bonobos live primarily in the Congo.

Q. Do they live mostly on the ground or do they live mostly in the trees?
A. They live mostly in the trees.

They are great climbers and sleep in trees but they are knuckle dragging apes primarily.

Q. When they die what usually happens to the bodies?
A. The bodies usually fall to the ground.

Or they are buried in volcanic dust like Lucy and passed off as one of our ancestors. Their fossilized remains are sometimes uncovered in mines, boxed up and sent to universities and museums where they are passed off as our ancestors like the Taung Child.

Q. What do you think happens to a dead body on the forest floor?
A. Small animals and insects eat it.

Depending on how they die of course.

Q. How much of that body is left after a week or two?
A. Very little, perhaps just a stain, and when it rains even that will be washed away.

Your going down a blind alley in the dark led by a stranger. Good luck with that.

As you can see simple deduction can usually solve a lot of problems.
Perhaps simple deduction is not something that is encouraged by creationist parents for obvious reasons?

It's a bad idea to subject them to dogmas of philosophy and wrong laws of demonstration period, Creationist or Darwinian.

Have a nice day
Mark

 

[Irish005]

This is the vital transition that would have had to happen for us to have evolved from apes.

Accepting human evolution from that of apes is not only a rejection of the Pauline doctrine of original sin, it's a myth of human ancestry.

For years I focused exclusively on the Scientific literature regarding Chimpanzee and Human common ancestry and found that the human brain had neither the time nor the means to have evolved from that of apes.

I propose that a critical examination of common descent in the light of modern insights into molecular mechanisms of inheritance is the single strongest argument against human/ape common ancestry.

You do realize that humans are apes, correct? There is no such thing as "humans evolving from apes". We are still apes.

 

[Nostromo]

Our ancestors would have been contemporary with and living in the same geographical regions as prehistoric apes up until less then a million years ago. What has happened is early apes are being passed off as transitionals, it's as simple as that.

Handprint : Ancestral Lines - Map of hominid fossil sites (bottom of page)

Filean.png - Wikipedia, the free encyclopedia - Map of chimpanzee habitat

Notice the weird lack of overlap?

None of the more current research supports that statement.

I was being flippant, I didn't bother to look.

I wouldn't be interested thanks.

Of course not, having to listen to the views of others and adjust your own opinions to take account of the facts is so bothersome.

 

[Blayz]

Mark, I gotta ask, do you think if you rehash these same arguments year in and year out often enough that one day I and the other practicing biologists on this forum will one day wake up and decide not to go into work and continue successfully applying evolutionary theory to our research?

I am once agin saddened by concept of your life, shouting at us from your arm chair of ignorance, peering dimly through a veil of dogma, as though your lay viewpoint on this subject carries some kind of credibility

 

[Blayz]

Mark, I gotta ask, do you think if you rehash these same arguments year in and year out often enough that one day I and the other practicing biologists on this forum will one day wake up and decide not to go into work and continue successfully applying evolutionary theory to our research?

I am once agin saddened by concept of your life, shouting at us from your arm chair of ignorance, peering dimly through a veil of dogma, as though your lay viewpoint on this subject carries some kind of credibility

 

[Split Rock]

Oh yea, the transitional fossils. Maybe you can tell me why we have literally hundreds of fossils representing our ancestors and virtually none for chimpanzee ancestors. Could it be that every time an ape fossil is dug up in Africa it is passed off as one of our ancestors?

Think I'm exaggerating? Consider this, while the Piltdown hoax is being passed of as a transitional fossil the Taung Child was considered a chimpanzee. Then with the demise of the Piltdown hoax it becomes one of those mythical transitionals. Raymond Dart who dug the lime endocast out of a box was the one who suggested to Louis Leaky the name 'handy man' or 'homo habilis' for his new classification group. What he did was to abandon the Cerebral Rubicon (the 600cc cut off for Homo) in favor of 'tool use' and a long list of contrived features.

No wait, there's more. Do you realize that if there were no living chimpanzees we would have no fossil evidence that chimpanzee ever existed? None of the transitionals in other taxons have the slightest bearing on the historicity of Scripture or essential Christian doctrine except the transition from ape to man. This is the vital transition that would have had to happen for us to have evolved from apes. Human and chimpanzee brains

....................

The most dramatic and crucial adaptation being the evolution of the human brain. Charles Darwin proposed a null hypothesis for his theory of common descent :

“If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” (Darwin, On the Origin of Species)


With a cranial capacity nearly three times that of the chimpanzee the molecular basis for this giant leap in evolutionary history is still almost, completely unknown. Changes in brain related genes are characterized by debilitating disease and disorder and yet our decent from a common ancestor with the chimpanzee would have had to be marked by a massive overhaul of brain related genes. I propose that a critical examination of common descent in the light of modern insights into molecular mechanisms of inheritance is the single strongest argument against human/ape common ancestry.

Strange then that the transitional species you imply were really chimp ancestors show a gradual increase in cranial capacity over time, which is exactly what evolutionary theory predicted. Not only cranial capacity, but a reduction in jaw size and an increase in bipedal capability as well. And we are supposed to believe these were all chimp ancestors?? Show me the bipedal chimp with the large cranial capacity that these transitionals were supposed to be ancestral to... then I will believe they were chimp transitionals.

 

[Split Rock]

Accepting human evolution from that of apes is not only a rejection of the Pauline doctrine of original sin, it's a myth of human ancestry. When the New Testament writers mention Adam they speak of him as the first man and the reason why all of us are under the curse of sin and death. Paul tells us that 'by one man sin entered the world' and 'by one man's offense death reigned'. (Rom 5:12-19). Paul ties Adam directly to the need for justification and grace in his exposition of the Gospel in his letter to the Romans. Luke lists Adam in his genealogy calling him 'son of God' indicating he had no human parents but rather was created (Luke 3:23-28). My concern is simply this, the myth of human lineage linked to ape ancestry contradicts the clear testimony of Scripture and essential doctrine, specifically justification by faith. Paul is clear that all have sinned in Adam and that is the reason that we cannot keep the Mosaic law.

And here is your real argument against common descent... though, as usual when you post here rather than in the creationist only sub-forum, you try to de-emphasize it.

I have always wondered why it is so necessary to blame one man for sin. As if doing so somehow reduces God's own culpability in creating a "perfect" man he knew ahead of time would sin and throw all of creation into a tailspin and give it over to Satan, another "perfect" creation of his who turned on him like a rabid dog.

 

[GoSeminoles!]

I have always wondered why it is so necessary to blame one man for sin. As if doing so somehow reduces God's own culpability in creating a "perfect" man he knew ahead of time would sin and throw all of creation into a tailspin and give it over to Satan, another "perfect" creation of his who turned on him like a rabid dog.

Yeah, that always annoys me as well. It never would have occurred to me to go out raising heck with my drinking buddies if Adam had not committed the original sin. Man up and take responsibility for your actions; don't blame a mythological dude who even according to the mythology has been dead for 6000 years.

The Dude abides.

 

[Mike Elphick]

We are being told that we are 98% the same in our DNA as the chimpanzee. The fact of the matter is scientists have known better for years and yet they propagate this myth with shameless abandon.

As far as looking at specific genes, the chimp and human Y chromosomes had a dramatic difference in gene content of 53 percent. In other words, the chimp was lacking approximately half of the genes found on a human Y chromosome. Because genes occur in families or similarity categories, the researchers also sought to determine if there was any difference in actual gene categories. They found a shocking 33 percent difference. The human Y chromosome contains a third more gene categories--entirely different classes of genes--compared to chimps. (New Chromosome Research Undermines Human-Chimp Similarity Claims by Jeffrey Tomkins, Ph.D., & Brian Thomas, M.S.)​

With the length of the two Y chromosomes being 24 mbp in the chimpanzee genome and 59 mbp in the human genome, what is the divergence as a percentage?

• Pan troglodytes (chimpanzee) Y Chromosome
• Homo sapiens (human) Y Chromosome

You couldn't choose a worse chromosome for estimating human/chimp genetic similarities than the Y Chromosome, so extrapolating differences and similarities from Y-chromosome analysis to the whole genome is invalid, and frankly a deception on the part of the Institute for Creation Research:-

The puny Y-chromosome only looks worse when you realise that mammalian sex chromosomes weren't always so mismatched. 160 million years ago the X and Y were just another pair of chromosomes, albeit the pair that the carried the sex determining gene SRY. Over time the chromosome that went on to become the Y stopped swapping genes with its partner, allowing it to maintain a suite of genes that are beneficial in male bodies but not in females. It's the lack of genetic recombination that sent the Y into its decline. Genes on any other chromosome can be swaped between pairs, meaning over many generations individual gene copies (called alleles) are exposed to natural selection independently of alleles either side of them. The same process doesn't apply to alleles on the Y-chromosome. Since the Y is always passed on as a single unit natural selection acts on the whole thing - a broken gene might make it into the next generation because it is attached to beneficial mutations. The efficiency of natural selection is further reduced in the Y-chromosome because it has a relatively small effective population size (less that one quarter of that for normal chromosomes since only males carry the Y and then in only one copy and even then a larger number of males than females don't contribute to the next generation) which makes genetic drift a strong force.
The why of the Y-Chromosome's amazing evolutionary rate

There's a couple of articles you might like to look at which have explanations for the findings published by Hughes et al in Nature:-

The Y chromosome is probably the most bizarre part of the human genome, reflecting its unique status as a huge block of largely non-recombining DNA, maintained in a permanently heterozygous state, and transmitted solely through males. Early in the history of genetics, it was realized that the pattern of sex-linked inheritance, seen in species with chromosomal sex determination, implies that the Y chromosome lacks most of the genes carried on its pairing partner, the X chromosome. HJ Muller inferred that the X and Y were originally homologous chromosomes, and that the Y had lost most of the genes that it once contained, in response to its lack of recombinational exchange with the X and its permanent heterozygosity. Later work has largely validated this inference, although the details of the evolutionary mechanisms leading to Y chromosome degeneration are now thought to differ substantially from that proposed by Muller. It is also now known that Y chromosomes have evolved independently in many different groups of animals and plants that have sex chromosomes; the Y chromosomes of mammals share a common origin with each other, but have nothing in common with their counterparts in birds or Drosophila. In addition, Y chromosomes tend to be unusually rich in repetitive DNA, which is contributed both by transposable elements and by tandem arrays of satellite DNA sequences, as is often the case for regions of the genome that have low frequencies of crossing over. Much of the human Y chromosome consists of heterochromatin, made up entirely of such repeats.

What we've known about the Y-chromosome's past has has shaped out ideas about what it is now and what it will become. Until quite recently the Y was seen as more or less a derelict chromosome, a few broken remnants of the genes still found on the X and a couple of male-specific genes hanging on the the sex determining gene SRY. People have even go so far as to extrapolate the Y's long slow decline to a future time at which the Y will simply disappear.
...
Now, thanks to Jeniffer Hughes and colleagues, we do and the result it stunning. Not only has the Y-chromosome been making genes, it's been making them at an outrageous rate. Thirty percent of our Y-chromosome sequences have no counterpart in the chimpanzee. As the authors say that's the sort of divergence you'd expect to see between humans and chickens, which are separated by 310 million years of evolution not humans and chimps which only split 6 million years ago!

It's evident that, far from being in the tail end of an inexorable decline, the Y-chromosome is evolving a good deal more quickly than the rest of the genome. So, the burning question is what is behind that evolutionary rate? There is probably no single answer to that question but it's safe to assume it results from some of the unique features of the Y-chromosome; a lack of genetic recombination, the presence of those large repetitive sections of DNA and the preponderance of male specific genes.
The organization and evolution of the human Y chromosome

Read the article to find out why.

Men who think that size really matters should probably not think too hard about the Y chromosome. This bundle of genes is the ultimate determinant of manliness, and it happens to be a degenerate runt. Over a few hundred million years, it has shrunk considerably, jettisoning around 97% of its original genes. Where it was once a large library of genes, now it's more a struggling independent bookstore. This loss of information defined the youth of the Y chromosome but nowadays, things are different. Renovation is the order of the day.

Jennifer Hughes from MIT revealed the recent history of the Y chromosome by comparing the human and chimp versions. They are incredibly different. They have rapidly evolved since the two species last shared a common ancestor 6 million years ago. In this relatively short span of time, the two Ys have accumulated differences that other chromosomes would take 310 million years to build up. It's the sort of genetic disparity you'd expect to see between humans and chickens, not between us and our closest relatives!

This drastic remodelling contradicts the current view of Y evolution, which suggests that the chromosome has stagnated. It has lost so many of its genes that some scientists thought it might waste away altogether within another 10 million years. But rumours of its impending demise had been greatly exaggerated. In 2005, Hughes showed that Y isn't shrinking at the breakneck pace of old.

That result was based on a comparison of individual genes on the two chromosomes. Since then, Hughes has managed to fully sequence the chimp Y, the first time this has been accomplished for a non-human animal. Considering how small the chromosome is, sequencing it is remarkably tricky. It has lots of long, repetitive sequences that are subtly different and hard to tell apart through conventional means.

Nonetheless, Hughes managed it. By comparing the two sequences, she found that the Y chromosome is an island of difference in a sea of resemblance. The chimp and human genomes are famous for their similarity; they're a 98.8% match for each other. And indeed, where the chimp and human Y sequences align, they are a 98% match, just like the rest of the genome. But they don't align very well. Around 30% of the chimp Y chromosome has no human counterpart and vice versa.

This flies in the face of the idea that the Y chromosome is evolutionarily stagnant. Since our ancestors split from those of chimps, our Y chromosomes have become hotbeds of genetic change. They have gained and lost sequences with wanton abandon, to a much greater extent than the rest of the genome. Even the sequences that have remained have been grossly rearranged. If you looked at chromosome 21 from both species (which has also been thoroughly sequenced), you'd think you were looking at a pair of identical twins. If you looked at the two Y chromosomes, you'd think you were looking at distant and barely related cousins.
Renovating a runt - the extreme evolution of the Y chromosome

What is it about the Y chromosome, particularly the chimp one, that makes it so evolutionary variable? Briefly:-

1. The genes that make sperm are essential for passing on its whole compliment of genes. This is especially important for chimpanzees because many males mate with the same female, so having the healthiest sperm decides who fathers the next generation.
   
2. The other chromosomes come in pairs, which allows crossing over and gene reshuffles, but the Y chromosome has no pair which means any mutation is going to have a greater impact and a beneficial one will spread through the population more rapidly.
   
3. There are many repetitive sequences in the Y chromosome is riddled with repetitive sequences which can mutate, and propagate without deleterious effects. Because of this, comparing the number of base pairs is not a good way to determine chromosomal difference between species.

Read the article for full explanations.

 

[Mike Elphick]

Now if by evolution you mean transitions like the evolutionary giant leap from primordial soup to functional cells. Here is the irreducible complexity of a bacterium, do note that the flagellum is only one aspect of the overall complexity:

< picture of average prokaryote cell >

Now tell me what the common ancestor of plants and animals had in common with plant cells and prokaryotes.

< picture of plant cell >

I think what you are doing here is making a comparison between a modern prokaryote and a modern plant cell, employing the assumption that IF the latter evolved from the former then where are the homologues? If that's what you're saying, then you're making a false comparison. Modern plant cells did NOT evolve from a modern prokaryote.

The Theory of Evolution postulates that both evolved from a common ancestor in the early Archean era. It is speculated that this was an early prokaryote, NOT a modern one! It is thought these cells had membranes and ribosomes, but they did not contain organelles like mitochondria and chloroplasts, and they also lacked a nucleus.

In the intervening billons of years, every type of organism has, of course, diverged from these very ancient ancestors. Your picture comparisons are therefore misleading, if, that is, we're supposed to conclude that significant visible 'homologous' similarities are hard to identify! Anyway, I can see a few, even if you can't .

 

[mark kennedy]

Strange then that the transitional species you imply were really chimp ancestors show a gradual increase in cranial capacity over time, which is exactly what evolutionary theory predicted. Not only cranial capacity, but a reduction in jaw size and an increase in bipedal capability as well. And we are supposed to believe these were all chimp ancestors?? Show me the bipedal chimp with the large cranial capacity that these transitionals were supposed to be ancestral to... then I will believe they were chimp transitionals.

Show me a chimp transitional period and I'll start taking these arguments from fragmentary fossil evidence seriously.

 

[Split Rock]

Show me a chimp transitional period and I'll start taking these arguments from fragmentary fossil evidence seriously.

That's it? Chimp transitionals are hard to come by, therefore you won't accept transitionals for other species that are not hard to come by? That's a pathetic argument, Mark.

 

[DrkSdBls]

Actually, I'm kind of curious about this myself. Surely, we must have some Lower Primate fossils.

Of course, we have mostly Higher Primate Transitionals only because it was only once Higher Primates started moving into Environments suitable for Preservation did we start finding their Fossils. And this is both the start of the Higher Primate Evolutionary Chain as well as the beginning of the Fossil Record for their Evolution....

But I can see where Mark's coming from. This Lack of a complete record does irk me a little bit too, though I do not follow his line of Reasoning. The Fact that we lack a Complete Fossil Record of the Raptor Chain still bugs the hell out of me.

 

[mklhawley]

Show me a chimp transitional period and I'll start taking these arguments from fragmentary fossil evidence seriously.

So, I have a question. Is this an honest statement? My perception of your logic based upon your post is that you dogmatically believe one particular interpretation of Genesis and reject any scientific evidence that contradicts this. Again, would this evidence cause you to honestly take fossil evidence seriously or are you being less than honest?

This is a serious question.

In reference to transitional fossils of chimpanzees and bonobos, an absence in the fossil record is not only understandable it is predictable. Why are there relatively few insects or sharks represented in the fossil record? There are not enough hard parts to withstand the long process of fossilization. Confirming this explanation is the fact that even fossilized organisms of all types show an absence of fossilized soft parts. In the case of insects, we do on occasion see insects and they are predictably in obrution lagerstatin deposits. In the case of sharks, we find large quantities of sharks teeth (and some vertebrae) &#8211; quite predicted, because teeth are designed to be durable. Why do we not see a large representation of mountain goat fossils? Quite predictably, they live in erosional environments as opposed to depositional environments as millions of invertebrates do. Quite predictably, chimpanzees and bonobos, organisms few in number and location (another reason for the absence of fossil representatives of their genetic ancestors) do not live in depositional environments, but live in environments designed for &#8220;recycling&#8221;. Coincidentally, the hominid environment was at times depositional (caves as in South Africa and the East African rift), which luckily allows us a glimpse into our past.

Sincerely,

Mike