Creationist Inquiry

[Inferno]

Excellent, this is actually a discussion I'll like.

Now, Tsentralka, I'd still think it would be important for you to answer the other questions I posed, because they get to the root of the problem:

Inferno[/url]"]And so on and so forth. At which point does common ancestry break down? And if it does, give criteria as to how we can identify it. If common ancestry is false, then animals which appear to be related must not be related to anything else on the "tree" of life. This, of course, completely leaves open the question how these unrelated "kinds" (for want of a better word) came to be. Were they magically created? Or were there multiple beginnings of life?

But in any case, let's do what Austra suggested and start with comparative genetics.
Now I put it to you that seeing two things that's are the same isn't incredibly surprising, even if the odds are against it. What would be truly surprising would be if we found to mistakes that are the same.

I'll give you an example: If two of my students would give in a test that's exactly the same, I should be surprised. But what would really surprise me is, if on question 3 they both wrote "Freudism and Taylorism" when it should be "Fordism". If that were to occur several times in the test, that should be reason enough for me to suspect that one of them copied off the other, that they are of the same origin. Agreed?

To make things easier, I'll only look at two lineages: Humans and other primates, even if that's a polyphyletic definition, but whatever...

There's a gene called the "GLUO disabled pseudogene". This gene usually produces the enzyme L-gulonolactone oxidase, responsible for producing vitamin C. In humans, however, this gene is disabled.
If it were disabled only in humans and enabled in other primates, that wouldn't tell us a lot. But what if I told you that this DOES occur in other primates? Now I could check out which ones they were and I could even make testable predictions, but I'll leave it at that, for the time being.
Also note that's just one possible orthologous gene I've explored in only one lineage, I could go further and dig out a few hundred, but we'll cross that bridge when we get to it. We first need to understand the underlying principle, correct?

There is one more thing we could talk about, but both have been said better than I ever could, so I'll leave the floor to Dr. Kenneth Miller and to the excellent Bonobo Bill.

If there are any questions, feel free...

 

[he_who_is_nobody]

Throughout this post and others, when I use capital “E”-Evolution (Evolution, Evolved, Evolutionist), I am referring to the colloquial (and very inaccurate) use of the term which encompasses the origin of the universe, the origin of life from non-living matter, and the development of that life over time into all life forms we see today; basically the naturalistic view of life and the universe (which I personally reject).

I am going to have to disagree with you right here. You have already admitted that this is an inaccurate use of the term so you might as well use the correct terms. When talking about the origin of the universe, it would be better to state big bang, when talking about the origin of life, it would be better to say abiogenesis, and when talking about development of life over time into all life, it would be better to say universal common descent. I suggest this, so right from the beginning we are not confusing terminology and arguing semantics down the line. Being clearer from the beginning will make this discussion flow so much smoother.

I say that organisms have evolved to produce the immense diversity we see at the present from an original set of kinds in the past (the identity of which is unknown to me and may take a lifetime to begin to understand…though, just spit-balling, I would put it around the Family level of classification).

If you are going to define kind around the Family level, than this means humans and all other apes are of the same kind.

This is admittedly broad so it may be worthwhile to look at a single step i.e. what is the evidence that chimps and humans have a common ancestor (I would say they are different kinds and do not)? Or perhaps we could ask, What was the evidence that convinced you personally that all life is related? I am interested in Aught3’s proposal:

Okay, sticking with what Augh3 stated, comparative genetics, common biochemistry (with all primates), and hominin fossils.

 

[Aught3]

This is admittedly broad so it may be worthwhile to look at a single step i.e. what is the evidence that chimps and humans have a common ancestor (I would say they are different kinds and do not)?

All three of the evidences I suggested for UCA would apply to the Chimpanzee and Human common ancestor. There is an excellent line of fossil evidence for the human lineage although not so much for Chimpanzee's. The comparative genetic evidence is pretty good too. For species so closely related, looking at pseudogenes and ERVs is probably the best simply because of the time spans involved. Inferno already posted something about the Vit C gene. And of course there is the clear chromosome fusion forming human chromosome two. The biochemistry between humans and chimpanzee's is basically identical same genetic code, same tRNA codons, same energy molecules, and so on.

Or perhaps we could ask, What was the evidence that convinced you personally that all life is related?

It's been a while since I began studying evolution but from what I recall the comparative genetics and fossil records we fairly convincing early one. The biochemical similarity was something I found out later once I got in to more advanced topics.

 

[Inferno]

I'll add another one, though it's basically the same one I was building up to in my original post:
Cladistic Taxonomy

AronRa goes into it here.

I just realized that Aron had written the original "Are mallards related to..." nearly three years ago. If only I would have searched his posts, I would have spared myself half an hour of trying to understand which species he meant... Anyway...
4. Cladistic Taxonomy

 

[Inferno]

Actually, now that I think about it, I'd like to propose something completely different: Tsentralka, what would YOU accept as evidence that your hypothesis (common descent is wrong) is, in fact, wrong? Give us some indication of what we should find to falsify your (the creationist) hypothesis. Which fossils, what DNA sequences, what biochemistry and what shape of taxonomic division should we find if your hypothesis were correct, which one if your hypothesis were wrong?

 

[Laurens]

what is the evidence that chimps and humans have a common ancestor (I would say they are different kinds and do not)?

Well firstly, when we compare our genomes with those of other great apes we see that ours bears the most similarity with the chimpanzee. Then we see that we are slightly more distantly related to the gorilla, and yet more distant from orang-utans and gibbons. From this we can draw a phylogenetic tree showing evolutionary relationships:

[image]http://www.nature.com/scientificamerican/journal/v16/n2s/images/scientificamerican0606-4sp-I5.jpg[/image]

I'm not huge on genetics, so I am sure someone else might be able to go into more detail on this subject.

For now I shall propose a few questions. Firstly what are the major differences between ourselves and chimpanzees?

- Firstly we habitually walk on two legs
- Our brains are much larger
- We use complex tools

etc. etc.

Now lets propose a hypothesis, what would we expect to see in the fossil record if humans and chimpanzees shared a common ancestor? Well firstly we can hypothesise that the ancestor we share with chimpanzees was an arboreal, quardupedal ape. This can be inferred from the fact that chimpanzees and other great apes share those characteristics in common - thus it is more likely that the uniqueness of humans evolved since the divergence, rather that the common ancestor being more human-like and then re-adopting behaviour similar to other great apes.

So what would we expect to find? A gradual progression in the fossil record from arboreal ape to bipedal, large brained hominins. This is precisely what we find.

A classic example is A. afarensis - an ape with a brain roughly the size of a chimp [380–430 cm[sup]3[/sup]] - yet it features evidence of bipedalism. This can be inferred from pelvic and leg bone structure as well as looking at the position of the foramen magnum (the hole at the base of the skull from which the spinal cord exists). See more here.

So there we have a creature that bears some features similar to that of a chimpanzee (small brain) yet walks on two legs like a human. This is precisely what we'd expect to find if our hypothesis was correct.

Furthermore, if we plot the brain-size of human ancestors onto a graph against the age of the fossil we see a very clear trend:

[image]http://www.pandasthumb.org/archives/images/fossil_hominin_cranial_capacity_lg.png[/image]

Brain size clearly increases over time in the hominin fossil record.

All the fossils tell us that our lineage descended from an arboreal species of ape. I would like to see what evidence you have against this?

Here's a nice visualization for you:

[image]http://www.theistic-evolution.com/hominids2_big.jpg[/image]

Care to explain all of these fossils?

They are completely consistent with our hypothesis, and precisely what you'd expect to see if humans evolved from arboreal apes. How do you account for them?

Laurens

 

[Tsentralka]

I’m game for starting with comparative genetics and then moving on to the others in time. It is probably pretty important to cite some sort of reference regarding the evidence so that we can get past the level of interpretation (which is not evidence) to the level of data (which is evidence).

I think Inferno’s illustration regarding the wrong answers on a test is a very good one (it’s the best analogy I’ve ever heard to illustrate how comparative genetics can be evidence for a common ancestor). As I understand it, because humans and chimps both have a non-functional GULO gene, then it seems reasonable to assume they both received this non-functional gene from their most recent common ancestor.

I'll give you an example: If two of my students would give in a test that's exactly the same, I should be surprised. But what would really surprise me is, if on question 3 they both wrote "Freudism and Taylorism" when it should be "Fordism". If that were to occur several times in the test, that should be reason enough for me to suspect that one of them copied off the other, that they are of the same origin. Agreed?...

However, suppose not just two students in the class wrote the wrong answer, but several students from different parts of the classroom all wrote the same wrong answer…would you come to a different conclusion. You would probably wonder if you had made a mistake in teaching that particular concept. Similarly, several other animals also do not have a functional GULO enzyme such as guinea pigs[1], some perching birds[1], and it has recently been discovered to be lost in some bats[2] as well as a population of Danish pigs[3]. Yet nobody, Creationist, Evolutionist, or otherwise, would argue that these organisms derived the deficiency from a common ancestor.

From the Creationist perspective, I would hypothesize that sometime in the past, independent mutations did occur which rendered GULO useless in humans, chimps, bats, perching birds, guinea pigs, etc., suggesting that there is some inherent tendency for this gene to lose its function, i.e. perhaps it is flanked by repetitive sequences which results in low fidelity crossing over and subsequent loss of coding exons. Regardless, in order for it to presented as evidence for common descent, then apes and humans must share the exact same random mutation which results in the loss of the GULO gene. This may or may not be the case (I don’t know), but the evidence has not been fully presented. The so-called shared mutations (which must exist in order for this to be evidence for common descent) have not been presented for scrutiny, just the conclusion that non-functional GULO = common descent. In order for this to be considered evidence we need perhaps an alignment of the chimp and human sequences pointing out the shared mutation, or at the very least a reference to primary literature (or even a review).

Tsentralka

1 Nature 182, 319 - 320 (02 August 1958); Species Difference in regard to the Biosynthesis of Ascorbic Acid
2 Cui J, Yuan X, Wang L, Jones G, Zhang S (2011)Recent Loss of Vitamin C Biosynthesis Ability in Bats. PLoS ONE 6(11).
3 Intragenic deletion in the gene encoding L-gulonolactone oxidase causes vitamin C deficiency in pigs.

 

[Tsentralka]

The overarching argument (as I see it) for most comparative genetics evidence is the twin-nested hierarchy argument. Laurens said:

Well firstly, when we compare our genomes with those of other great apes we see that ours bears the most similarity with the chimpanzee.

With the advent of molecular genetics, universal common ancestry (UCA) was put to the test. Basically, UCA would predict that those organisms which were supposed to have relatively recent common ancestry (i.e. chimps and humans), would also exhibit genetic similarity. Thomas Huxley, in his 1863 book, Evidence as to Man's Place in Nature, argues for relationship between humans and apes from an anatomical perspective, saying, "Is man so different from any of these apes that he must form an order by himself?” Now, a century and a half later we see that the genomes of “closely related” organisms are more similar than genomes of “distantly related” organisms.

This is frequently cited as a testament to the predictive power of Evolution, but would I (as a Creationist) predict the same thing? Yes, the central dogma (which is, IMO, the foundation of biology) would predict the same twin-nested hierarchy. Since genotypes produce phenotypes, then organisms that are grouped based on phenotypes (like Huxley and other early Evolutionists used to infer relatedness) should have similar genotypes. Or, to put it another way, I would predict that organisms which have similar anatomy/physiology should have similar genomes.

I’m making this point sort of pre-emptively since it has already started to come up (i.e. in Laurens’ post). However, if what I propose is correct, than any genetic similarity between unrelated kinds must have a functional significance. So to answer Inferno’s question…

Give us some indication of what we should find to falsify your (the creationist) hypothesis.

…here is potential falsifying evidence from comparative genetics. 1) Non-functional DNA sequences should NOT be able to group organisms into a twin nested hierarchy. Or to phrase this in a positive light, every DNA sequence which forms a twin-nested hierarchy should have a functional significance. 2) Multiple shared, random mutations should NOT exist between different Kinds of organisms. I consider humans and chimps to be different Kinds, so there should no random mutations in humans which also exist in chimps (and vice versa) except for few expected from random chance.

Falsification #1 is a little sketchy since demonstrating non-functionality/functionality of a DNA sequence would be hard to do. However, Falsification #2 would not only falsify my hypothesis, but it would lend positive support for common descent.

So back to the evidence…Aught3, perhaps you should expound on the pseudogene/ERV idea which we can add to our GULO discussion. Laurens, I think your fossil evidence is good, but doesn’t really fit in with comparative genetics at the moment, so can we address this later?

Tsentralka



Addendum #1:

Now, Tsentralka, I'd still think it would be important for you to answer the other questions I posed, because they get to the root of the problem:

Inferno[/url]"]And so on and so forth. At which point does common ancestry break down? And if it does, give criteria as to how we can identify it. If common ancestry is false, then animals which appear to be related must not be related to anything else on the "tree" of life. This, of course, completely leaves open the question how these unrelated "kinds" (for want of a better word) came to be. Were they magically created? Or were there multiple beginnings of life?

I’m sorry for not answering this question originally. I believe I see exactly what you’re getting at and if you were a Creationist I would be interested in vigorously discussing at which point common ancestry breaks down. This is basically analogous to the question, “What constitutes a Genesis kind?” Of course the answer to both of these questions is, I don’t know, but I would really like to figure it out…it’s on my bucket list. I would say that these unrelated Kinds were “magically created”…which means, yes, there were multiple beginnings of life (each created kind was a beginning of life).

 

[devilsadvocate]

2) Multiple shared, random mutations should NOT exist between different Kinds of organisms. I consider humans and chimps to be different Kinds, so there should no random mutations in humans which also exist in chimps (and vice versa) except for few expected from random chance.

I'm curious to know if you're aware of shared endogenous retroviruses between various animals and if you consider them confirming common descent at all.

In case this is new to you, retroviruses are RNA viruses that code their RNA into DNA by enzyme reverse transcriptase and plant the DNA to the host cells genome. From there the DNA produces viral proteins that go onto assemble more viruses. If the retrovirus infects germ line cells that produce offspring, the offspring will also have the same piece of DNA in the same chromosomal location. This is when the retrovirus becomes endogenous.

Now, if these ERV's are shared in the same locations in human genomes and in, what are thought to be (by other methods), closely related species and not found in the more distant species, it should count as powerful evidence for common descent, right? This trend is what is found when comparing genomes of animals. You can google the nitty-gritty stuff yourself as it can get technical, but here is a nice picture to illustrate the point:

[image]http://www.talkorigins.org/faqs/comdesc/images/retrovirus.gif[/image]

Figure 4.4.1. Human endogenous retrovirus K (HERV-K) insertions in identical chromosomal locations in various primates (Reprinted from Lebedev et al. 2000, © 2000, with permission from Elsevier Science).

EDIT for clarity: "The arrows designate the relative insertion times of the viral DNA into the host genome. All branches after the insertion point (to the right) carry that retroviral DNA - a reflection of the fact that once a retrovirus has inserted into the germ-line DNA of a given organism, it will be inherited by all descendents of that organism." http://www.talkorigins.org/faqs/comdesc/section4.html#retroviruses

 

[Inferno]

Thanks for using proper sources, that makes the whole thing that much easier. I have to apologize in advance, but the two images I used are reduced to mere URL's, owing to some problems with the site.

However, suppose not just two students in the class wrote the wrong answer, but several students from different parts of the classroom all wrote the same wrong answer…would you come to a different conclusion. You would probably wonder if you had made a mistake in teaching that particular concept. Similarly, several other animals also do not have a functional GULO enzyme such as guinea pigs[1], some perching birds[1], and it has recently been discovered to be lost in some bats[2] as well as a population of Danish pigs[3]. Yet nobody, Creationist, Evolutionist, or otherwise, would argue that these organisms derived the deficiency from a common ancestor.

Yes... and no. You're confusing all students making a mistake on the same answer (what you detailed above) with all students making the same mistake on the same answers (what I will explain just now).
Various animals losing the enzyme wouldn't be evidence, but what if the guinea pigs, birds, bats and pigs all had different sequences from the primate sequences?

I'll quote you something and then we'll check if it's correct:

Why Evolution is True - by Jerry Coyne[/url] and the book on Google-books"]A dead gene in one species that is active in its relatives is evidence for evolution, but there's more. When you look at ψGLO in living primates, you find out that its sequence is more similar between close relatives than between more distant ones. The sequences of human and chimp ψGLO, for example, resemble each other closely, but differ more from the ψGLO of orangutans, which are more distant relatives. What's more, the sequence of guinea pig ψGLO is very different from that of all primates.

So what we'll do next is to look at the three sources he gives us for that claim. [1] [2] [3] I'll also use another source not listed by Coyne. [4]

Let's first look at resource [3]. In the paper, there appears the following table:
Picture - Nucleotide substitutions between the primate GULO-gene homologue

Not that anyone needs to add to the mountain of evidence, but this comparison of the four primate species adds evidence to the fact that we are closely related to chimpanzees, slightly more distantly related to orangutans and even slightly more distantly related to macaques.
But that alone doesn't challenge your question.

I could point to resource [4], which calculated the loss of L-gulono-γ-lactone oxidase in the ancestors of guinea pigs to be less than 20 million years ago. (We only have to consider the guinea pig, because Laurasiatheria (including bats and pigs) split from our lineage over 85 million years ago, while Rodentia only split more recently, roughly 75 million years ago. Birds are an even older lineage, so that's not a problem either. Here's a cladogram I adapted to show what I mean. In orange and red are included pigs and bats, in brown is Laurasiatheria. Pink on the outside includes humans.

Picture - Laurasiatheria cladogram

So already I have substantiated the following claim: Guinea pigs, bats, pigs, birds and humans lost their GULO's independently from one another.

But you know what? I'll solidify that claim even more!

Source [1] calculates the loss in the primate GULO to roughly 70 million years ago, (after our split with Rodents) though they explicitly state that that number is based on a few (conservative) guesses, the real number probably lies closer to 35-40 mya. There's also a fairly complicated side-by-side evaluation of the human and rat GULO, but it's both too complex and too time consuming for me, so I'll refrain from discussing it here.

Source [2] calculates the GULO loss in primates to roughly 35-65 mya, which is further evidence that rodents GULO loss was an independent event.

This is what I explained above: The GULO enzyme was deactivated in many different lineages, but independently of each other. Classroom metaphor again: Guinea pigs' mistakes are at the same place as those of Humans, but they're completely different errors.
I hope I've made that clear. If not, feel free to ask, but note that I'm quite near the end of my biochemical understanding and I'd have to contact a friend of mine (Biochemist) to make sense of the articles, which would mean longer reply times.

From the Creationist perspective, I would hypothesize that sometime in the past, independent mutations did occur which rendered GULO useless in humans, chimps, bats, perching birds, guinea pigs, etc., suggesting that there is some inherent tendency for this gene to lose its function, i.e. perhaps it is flanked by repetitive sequences which results in low fidelity crossing over and subsequent loss of coding exons. Regardless, in order for it to presented as evidence for common descent, then apes and humans must share the exact same random mutation which results in the loss of the GULO gene. This may or may not be the case (I don’t know), but the evidence has not been fully presented. The so-called shared mutations (which must exist in order for this to be evidence for common descent) have not been presented for scrutiny, just the conclusion that non-functional GULO = common descent. In order for this to be considered evidence we need perhaps an alignment of the chimp and human sequences pointing out the shared mutation, or at the very least a reference to primary literature (or even a review).

I approve of your hypothesis, but must make one slight change: You say that humans and other apes "must share the exact same random mutations", but that's not quite true. For us to share the exact same mutations, even after the split has been at least seven million years ago, would be incredibly fortunate. What we should find instead is a very high correlation between the genes (of us and other apes) and the opposite (i.e. large differences) with the others. That would support the evolutionary hypothesis. As it does, shown above.

If instead we find that all genes are roughly the same, that is to say of equal distance from one another, then we would have a serious problem and would have to consider a different solution. As it happens, the evidence does favour the point of view I presented, so there's no need to consider other options.

1) Non-functional DNA sequences should NOT be able to group organisms into a twin nested hierarchy. Or to phrase this in a positive light, every DNA sequence which forms a twin-nested hierarchy should have a functional significance.

I'm not sure I understand what you're trying to say, because if I understand it correctly then that's the opposite of what we would expect. Could you explain this in more detail?

2) Multiple shared, random mutations should NOT exist between different Kinds of organisms. I consider humans and chimps to be different Kinds, so there should no random mutations in humans which also exist in chimps (and vice versa) except for few expected from random chance.

Just above, I provided you with evidence of just that: A random mutation which also exists in chimps, except for a few expected from random chance. After having looked at the above evidence, to you concede that at least this bit does not favour the creationist position?

I’m sorry for not answering this question originally. I believe I see exactly what you’re getting at and if you were a Creationist I would be interested in vigorously discussing at which point common ancestry breaks down. This is basically analogous to the question, “What constitutes a Genesis kind?” Of course the answer to both of these questions is, I don’t know, but I would really like to figure it out…it’s on my bucket list. I would say that these unrelated Kinds were “magically created”…which means, yes, there were multiple beginnings of life (each created kind was a beginning of life).

Thanks. I thought as much.

Also, I believe this will be needed as our discussion progresses. (I still haven't quite finished with it, I'll probably upload the complete post on the blog once I'm done.) Explaining Junk DNA

References:
[1] M. Nishikimi, R. Fukuyama, S. Minoshima, N. Shimizu, K. Yagi. Molecularbasis for the deficiency in humans of gulono-lactone oxidase, a key enzyme for ascorbic acid biosynthesis. American Journal of Clinical Nutrition 54 (1991) 1203S-1208S

[2] M. Nishikimi, R. Fukuyama, S. Minoshima, N. Shimizu, K. Yagi, Cloning and chromosomal mapping of the human nonfunctional gene for L-gulono-γ-lactone oxidase, the enzyme for L-ascorbic acid biosynthesis missing in man, J. Biol. Chem. 269 (1994) 13685-13688.

[3] M. Nishikimi, Y. Ohta, Random nucleotide substitutions in primate nonfunctional gene for L-gulono-γ-lactone oxidase, the missing enzyme in L-ascorbic acid biosynthesis. Biochimica et Biophysica Acta 1472 (1999) 408-411

[4] M. Nishikimi, T. Kawai, T. Ozawa, K. Yagi, Guinea pigs possess a highly mutated gene for L-gulono-γ-lactone oxidase, the key enzyme for L-ascorbic acid biosynthesis missing in this species, J. Biol. Chem. 267 (1992) 21967-21972

 

[Laurens]

It seems that devilsadvocate beat me to it! But I think this is still relevant info nonetheless.

I would say that the best proof of common ancestry lies in endogenous retroviruses (ERVs).

These occur when viral gene sequences are inserted into the genome of a host creature - when this occurs in an organism's sex cells, it consequently means that some of this organisms descendants also carry the insertion.

There is an extremely small chance that a single copy of the same ERV would appear in the same place on the same chromosome of both humans and chimpanzees randomly:

A retrovirus has a particular mode of insertion. Different viruses tend to insert into different parts of the host genome. HIV, for instance, prefers to insert into areas with active host genes. These sites, called integration sites, are abundant within the host genome for each virus, numbering anywhere from 500 to 2,000 integration sites per host genome. Also, each integration site is usually between 100,000 to 250,000 DNA letters long (letters being the A, G, T, and C of the genetic code).[1] Taking the low number of 500 and the lower size of 100,000, this limits retrovirus insertion to about 50 million bases in the genome. This would mean that we could expect that one letter of DNA would be used twice every 50 million insertions. This figure shows 3,000 insertions by three different retroviruses. As you can see, the retroviral insertions are spread over all of the chromosomes in a random pattern. Not one nucleotide is used twice. There has never been a retrovirus that has been shown to insert at the same letter in the host genome even 0.001% of the time.

Source: http://www.evcforum.net/dm.php?action=msg&f=9&t=79&m=1

There are at least 7 (source at the end of this post) such instances in which ERVs are found in the same place on the same chromosome of both humans and chimpanzees. As you can see this is an astronomically improbable event if we are to assume that they are explained by chance.

If we explain this by the fact that humans and chimpanzees share a common ancestor then it becomes a less astronomically unlikely event.

ERVs can be used to confirm common ancestry in the same what that similarities in the genome itself can be. Humans and chimps share more ERVs with each other, humans and gorillas; slightly less, humans and lemurs less still and so on, fully confirming the phylogenetic tree of life.

See more here

 

[devilsadvocate]

The talk origins article I linked to as well seems a little outdated, just a heads-up. It claims that 1% of human genome consists of retroviral DNA, totaling to ~30 000 ERV's in the genome, but just about everywhere else the figures are 8-10% and about 100 000 ERV's. (Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M (Apr 2004). "Long-term reinfection of the human genome by endogenous retroviruses")

Similarly, the amount of shared ERV's between chimps and humans has gone up as the sequencing gets more complete. I can't seem to find current data for the exact number, but there's at least 16 shared in the family HERV-K alone (the youngest of human ERV's).

 

[Laurens]

Also, I gather that you accept microevolution Tsentralka?

How old do you think the Earth is?

I'd appreciate a brief answer to both of these if possible, thanks.

Laurens

 

[Aught3]

This is frequently cited as a testament to the predictive power of Evolution, but would I (as a Creationist) predict the same thing? Yes, the central dogma (which is, IMO, the foundation of biology) would predict the same twin-nested hierarchy. Since genotypes produce phenotypes, then organisms that are grouped based on phenotypes (like Huxley and other early Evolutionists used to infer relatedness) should have similar genotypes. Or, to put it another way, I would predict that organisms which have similar anatomy/physiology should have similar genomes.

Several points to make:
1) The phrase 'twin nested hierarchy' refers to the match between two nested hierarchy built from different comparisons. For example, you could build a nested hierarchy from comparative genetics and a separate nested hierarchy from comparative morphology then match them up to see if they form a twin nested hierarchy. This is just a suggestion to tighten up the language we use to make communication clearer.

2) Not all genotypic features have morphological impacts. Non-coding DNA and basic biochemical proteins and RNAs also have sequences that can be used to form a nested hierarchy which also matches up with comparative morphology. This makes sense in the light of evolution but not with creationism.

3) Similar morphological features are not always encoded by the same genes. Convergent evolution produces morphological features with similar functions that are adapted from different genetic elements. Under the creationist idea of 'same designer, same genes' you would expect to see the same genes producing the same morphological features but that is not the case.

1) Non-functional DNA sequences should NOT be able to group organisms into a twin nested hierarchy. Or to phrase this in a positive light, every DNA sequence which forms a twin-nested hierarchy should have a functional significance.

See: Chen and Li (2001) Genomic Divergences between Humans and Other Hominoids and the Effective Population Size of the Common Ancestor of Humans and Chimpanzees. Am J Hum Genet. v.68(2). For the falsification. If you claim that there is no evidence that could be found for non-functional DNA then why even bring it up?

Aught3, perhaps you should expound on the pseudogene/ERV idea which we can add to our GULO discussion.

GULO is a pseudogene and I approve of Inferno's posts on the topic, he is making the point well. ERVs have been explained by devilsadvocate and Laurens and I don't have anything further to add.

 

[Gunboat Diplomat]

I apologize for jumping into the middle of this thread. Normally I'd at least respond to the OP but I don't get to participate on web forums nearly as often as I'd like so I try to be economical...

The overarching argument (as I see it) for most comparative genetics evidence is the twin-nested hierarchy argument. Laurens said:

Well firstly, when we compare our genomes with those of other great apes we see that ours bears the most similarity with the chimpanzee.

With the advent of molecular genetics, universal common ancestry (UCA) was put to the test. Basically, UCA would predict that those organisms which were supposed to have relatively recent common ancestry (i.e. chimps and humans), would also exhibit genetic similarity. Thomas Huxley, in his 1863 book, Evidence as to Man's Place in Nature, argues for relationship between humans and apes from an anatomical perspective, saying, "Is man so different from any of these apes that he must form an order by himself?” Now, a century and a half later we see that the genomes of “closely related” organisms are more similar than genomes of “distantly related” organisms.

This is frequently cited as a testament to the predictive power of Evolution, but would I (as a Creationist) predict the same thing? Yes, the central dogma (which is, IMO, the foundation of biology) would predict the same twin-nested hierarchy. Since genotypes produce phenotypes, then organisms that are grouped based on phenotypes (like Huxley and other early Evolutionists used to infer relatedness) should have similar genotypes. Or, to put it another way, I would predict that organisms which have similar anatomy/physiology should have similar genomes.

I don't think so. My biology is a little weak so please (anyone) correct me if I'm wrong but there is no bijection between genotypes and phenotypes. That is to say, there are multiple genotypes that will produce the same phenotypes, to use your terminology. Therefore, as a Creationist, there needn't necessarily be a twin nested hierarchy and you are still left with the task of explaining it. Of course, evolution and common ancestry still explains all of this...

Furthermore, there are atavisms that reveal suppressed genotypes. That is to say, there are genes in organisms that lay dormant and don't ordinarily express themselves. Snakes and cetaceans (whales, dolphins and the like) have genes to produce legs and birds have genes to produce teeth, despite these animals not having these traits. We can artificially turn these genes on but that means that these genes are in these animals. What's the Creationist explanation of that?

Incidentally, I'm interested to know what your thoughts are on cetaceans. You believe in adaptation and kinds so how do these concepts apply to Cetacea? For example, do you think ancient ancestors of whales and dolphins were land creatures? If so, were those land creatures and modern cetaceans the same kind? If not, how do you explain that they are mammals?

Thank you...

 

[Inferno]

What's the Creationist explanation of that?

There are two possible explanations, the wacky one and the not-quite-so-wacky-one-but-I'd-still-laugh-at-it.
Option one is "The Fall". Animals were perfect before (Birds had teeth) but after the fall bad mutations started to accumulate and now they don't have teeth any more.
The second is that evolution does happen and that's why birds have no teeth. It works for everything except, as you pointed out, cetaceans. And a few others, but let's not go into that.

My biology is a little weak so please (anyone) correct me if I'm wrong but there is no bijection between genotypes and phenotypes. That is to say, there are multiple genotypes that will produce the same phenotypes, to use your terminology.

That is correct. I would point to the convergent evolution of Thylacines and Wolves. I posted about it here, but most links in that post are no longer working.

 

[Tsentralka]

Loose ends post...before replying to some of the select posts above, I want to make sure I am focusing on the right issues:

First the GULO discussion. We all agree that Guinea pigs, bats, and humans all lost their GULO functionality independently...this is not what is in question. According to the Creation model, humans and chimps must also have lost GULO functionality independently, IOW the human and chimp sequences each represent different wrong answers. I assume that one of those references from Jerry Coyne address this specifically. Inferno can you sum up in a sentence or two what we should find if the loss of GULO in chimps and humans represent a single event?

The ERV discussion. It looks like both devilsadvocate and Laurens posts can both be traced back to this paper...Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277. If there's a different paper that more strongly represents your view then please let me know now so we don't waste our time.


Clarification:

1) Non-functional DNA sequences should NOT be able to group organisms into a twin nested hierarchy. Or to phrase this in a positive light, every DNA sequence which forms a twin-nested hierarchy should have a functional significance.

I'm not sure I understand what you're trying to say, because if I understand it correctly then that's the opposite of what we would expect. Could you explain this in more detail?

An important aspect of the Creation model is that genetic similarity is explained largely by anatomical/physiological similarity. As Aught3 mentions, if you grouped organisms based on morphological similarities to produce one nested hierarchy and then grouped organisms based on the similarity of their protein coding genes it would yield the same nested hierarchy (I assume)...twin-nested hierarchy. However, I would argue that this is due to the genotype-phenotype correlation (phenotype here not referring simply to morphology). In this model, DNA which does not contribute to the anatomy/physiology of an organism (functionless DNA) should not produce a nested hierarchy which matches one which groups organisms based on anatomy/physiology. This is what I tried convey in the first post (and based on Aught3's post I think some people got it), but I should have made it more clear.

Tsentralka

 

[devilsadvocate]

For Human and Chimpanzee ERVs:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC17875/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779541/

and for K-family specifically,

http://link.springer.com/article/10.1007%2Fs00705-006-0792-1

I'll be later adding sources for how we know retroviruses are exogenous in origin, of how they aren't (that) particular about insertion sites and what methods are used to date the insertion time (older method of comparing LTR's is detailed in the first paper linked). Latter can confirm relative and even absolute dates of speciation events obtained from other data.

 

[Laurens]

Tsentralka, I think its relevant that you answer the two questions I posed, for the simple reason that if you accept an old Earth model and microevolution then it can be shown that macroevolution follows logically from the acceptance of these two things.

Let me highlight this with an example:

5 breeding pairs of lizards were transported from the island of Pod Kopiste off the coast of Croatia to a neighbouring island Pod Mrcaru in 1971. In just 30 years or so these lizards developed a completely new gut structure, larger heads, and a harder bite. Though selection pressure is not always so fierce, it gives you an idea of the kinds of changes that can occur in a short amount of time.

Now we know that life on earth has existed for roughly 3.5 billion years. 30 years is 0.000000857% of the time that life has existed. A mere fraction of the time that life on earth has had to evolve. Now if we add up gradual, incremental changes such as those seen in the lizards of Pod Mrcaru over a period of 3500,000,000 years we can expect that vast morphological changes can occur in such an incomprehensibly huge amount of time. This is macroevolution.

There is no known mechanism that prevents gradual, incremental changes such as the example above from accumulating and creating vast evolutionary changes over time.

Now since I've shown that microevolution does occur, all I really should have to show you is that the earth is 4.5 billion years old---if you already accept that then you should have no logical issue accepting macroevolution. If you do not accept that, I am willing to provide evidence to show you that the earth is billions of years old. If you do accept an old earth, and microevolution, but not macroevolution, perhaps you could kindly explain what stops small microevolutionary changes from adding up over time to create macroevolutionary changes.

Laurens

 

[Tsentralka]

devilsadvocate, I'm having issues with obtaining the "Identification Characterization and comparative genomics of chimpanzee endogenous retroviruses." Pubmed will not link to it...I'll try again later. Any other source to obtain this that you know of?

Tsentralka

P.S. Laurens, please read the opening post for the answer regarding microevolution. Furthermore, I am what you would call a YEC.