The Origin of Life

Five questions worth asking

Incl. intelligent design, belief in divine creation

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Re: The Origin of Life

#2141  Postby questioner121 » Mar 29, 2014 12:37 am

After that I'll be asking how the change in chromosome numbers and their fusion is explained through the mechanisms of evolution or ToE for those who like more clear meanings. In short evolution cannot be used to explain the difference in chromosome numbers of living organisms in the phylogenetic tree. Thereby the number of chromosomes cannot be used for determining common ancestry as Ken Miller was trying to do in his vid. If humans had 50 pairs or 10 pairs of chromosomes it would make no difference since common ancestry is based more on morphological features rather than DNA.

I'm off to bed now. Thanks to all those who responded appropriately.
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Re: The Origin of Life

#2142  Postby lucek » Mar 29, 2014 12:47 am

Um I think you mis under stood this.

The missing chromosome was a problem for evolution. Losing a chromosome is most likely deadly to any animal and more then likely for all life as any genes in the chromatin would be lost. A prediction was made that if man did indeed evolve from other apes we should find evidence of a fusion event. Then after the prediction the fusion was found.

This is what is known as a test of ToE. One which it passed.
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Re: The Origin of Life

#2143  Postby Fenrir » Mar 29, 2014 12:49 am

The claim is that a chromosome fusion supports common ancestry between humans and chimps.

There is no claim involving relationships within a wider group.

Unless you have and can present a detailed karyotype of the specific animals you wish to investigate and have and can present a rigorous cladistics detailing the evidence for common ancestry from morphology and other evidence for the specific species you with to discuss then don't bother.

Before you start you might like to do some reading into the karyotypes present within Przewalski's horse. A very clear example for which the relevant data is available. Or perhaps sheep, or indeed any of the other models work has been done on.
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Re: The Origin of Life

#2144  Postby fluttermoth » Mar 29, 2014 12:56 am

Fenrir wrote:
Before you start you might like to do some reading into the karyotypes present within Przewalski's horse.

Well, Q121 might not, but I have; how fascinating, thank you :)
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Re: The Origin of Life

#2145  Postby Calilasseia » Mar 29, 2014 1:03 am

Actually, the existence of a fused chromosome in the human lineage was proposed as a test of common ancestry. Which works as follows.

Chimpanzees. gorillas and bonobos have a chromosome count of 2n=48 (2n denoting the diploid count). Humans have a chromosome count of 2n=46. Consequently, for humans and the other great apes to have shared a common ancestor, a necessary requirement is that two chromosomes donated from that ancestor underwent a fusion event in the human lineage. The reason why this is a necessary requirement, is that a simple whole chromosome deletion would be fatal: virtually every instance of chromosome deletion events in the scientific literature results in the organism inheriting it being either stillborn, or dying in infancy. Even deletions of part of one arm of a chromosome usually has serious consequences - see, for example, chromosome 5q deletion syndrome, which impacts seriously upon the viability of the circulatory system in humans. Indeed, most embryos with either a whole chromosome deletion, or an extra chromosome, are spontaneously aborted, the principal exceptions being trisomy 21 (Down's Syndrome), trisomy 18 (Edwards' Syndrome) or trisomy 13 (Patau syndrome), in which an extra, third copy of the chromosome in question is present. Losing all copies of a given chromosome is almost invariably lethal. Since humans obviously didn't become extinct during a change of 2n chromosome count, then the only option left is for two of the chromosomes inherited from the common ancestor to have fused, and become a single chromosome, within the human lineage.

Now chromosomes happen to possess specific features allowing such an event to be detected. First, the organisation of the loci on the fused chromosome will map directly onto loci spread across two chromosomes in the other lineages. If we don't find that match between loci, then we're in trouble.

Second, eukaryotic chromosomes possess a structure known as a centromere, the point where the arms of the chromosome are all joined together. Centromeres are associated with specific DNA structural motifs, and one can determine whether or not a given DNA sequence is associated with a centromere, because, lo and behold, all eukaryotic chromosomes possess the same sequence motifs in their centromeres, a fact which happens to be true right across the biosphere, which on its own suggests a common ancestry for all eukayrotes. But I digress.

Third, chromosomes possess other markers known as telomeres. These are found close to the ends of the arms. These too have specific DNA motifs associated with them, and can be identified as such from the DNA sequence, because, lo and behold, all eukaryotic chromosomes possess the same sequence motifs in their telomeres, again suggestive of a common ancestry for all eukaryotes. But I digress once more.

Now, the point here, is that a chromosome fusion event, involving the tips of the arms of one chromosome joining to the tips of the arms of a second chromosome, would result in a specific structure emerging. First, the resulting chromosome would have two sets of centromere sequences, spaced apart by a distance matching the length of the fused arms. In order to emerge as a functional chromosome after the fusion event, the simplest mechanism would involve deactivation of one centromere, and so, any such fusion event would be detectable by the presence of centromere motifs some way along the arms, where they don't usually appear, corresponding to the deactivated centromere. Second, the chromosome would possess telomere sequences located between the two centromere sequences, where again, they don't normally appear. This diagram from the Wikipedia page illustrates the concept nicely:

Image

So, the question that required an answer, was this: does a chromosome bearing those features appear in the human lineage? Furthermore, does that chromosome have present upon it, loci which when compared to the loci in other primates, generate matches spread across two chromosomes in the other primate lineages? Remember, if we don't find this, common ancestry is in trouble.

The answer is yes. It's human chromosome 2. Which possesses centromere sequences corresponding to a deactivated centromere in the long arms, and between that deactivated centromere and the functional centromere, telomere sequences are found. Furthermore, genes on human chromosome 2 have direct orthologues spread across two chromosomes in the chimpanzee and gorilla lineages (both these species now have genomes that have been sequenced fully for direct comparison, and the sequencing is now available in a high-definition format). In some cases, the orthologues are identical in sequence between the different lineages, whilst in others, mutations acquired separately between lineages exist, usually corresponding to a difference of one or two amino acids in the synthesised protein product.

An apposite paper covering this is as follows:

Origin Of Human Chromosome 2: An Ancestral Telomere-Telomere Fusion by J W IJdo, A Baldini, D C Ward, S T Reeders and R A Wells, Proceedings of the National Academy of Sciences of the USA, 88(2): 9051-9055 (15th October 1991) [Full paper downloadable from here]

IJdo et al, 1991 wrote:Abstract

We have identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5'(TTAGGG)n-(CCCTAA)m3'. Sequences flanking this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.


From the paper in more detail:

IJdo et al, 1999 wrote:Similarities in chromosome banding patterns and hybridization homologies between ape and human chromosomes suggest that human chromosome 2 arose out of the fusion of two ancestral ape chromosomes (1-3). Molecular data show evidence that this event must have occurred only a few million years ago (refs. 4 and 5 and the references therein). Although the precise nature of this putative fusion is unknown, cytogenetic data point to either a centromeric or telomeric fusion in the vicinity of region 2ql (1, 2, and 6). The observation that telomeric DNA is present in chromosomal band q13 suggests that telomeres, the extreme ends of chromosomes, may have been involved in this fusion (7, 8). Normally, telomeres form a dynamic buffer against loss of internal sequence and prevent chromosomes from fusing (for review, see ref. 9). By contrast, nontelomeric DNA ends are subject to degradation by nucleases and to fusion by ligation (10, 11).

The termini of human chromosomes consist of head-to-tail tandem arrays ofTTAGGG, running 5'--3' toward the end of the chromosome, with average lengths of 5-10 kilobases (kb) in somatic cells (7, 12, 13). The proximal ends of these arrays contain degenerate forms of this repeat, such as (TTGGGG)n, and (TGAGGG)n, (14). Sequences adjacent to these simple repeats have been characterized in a number of human chromosomes and shown to consist of repetitive elements, each shared by a subset of all chromosomes (13, 15-17). In addition, stretches of telomeric repeats are present at interstitial sites, usually in subtelomeric regions but also at a distinct internal site within band 2q13 (8). We describe here the architecture of the sequence at this internal locus at 2q13, which represents a relic of the fusion of two ancestral ape chromosomes in the evolution of human chromosome 2.


In short, the absence of those features in human chromosome 2 would have dealt a serious blow to the notion of common ancestry of humans and great apes, and called into question the entire concept of common ancestry. Their presence is a prediction arising from common ancestry, a prediction found to match the observed data from that chromosome, which means that common ancestry has passed yet another test that it could very easily have failed.

Game over methinks.
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Re: The Origin of Life

#2146  Postby Shrunk » Mar 29, 2014 1:06 am

questioner121 wrote:
Shrunk wrote:
Yes. It would most likely have had 24 chromosome pairs.


Great. Something to work from.

OK, so now how many chromosomes should the common ancestors of monkeys and apes have? Where I'm going with this is to show there is no link between the number of chromosomes and common ancestry.


That question has already been answered.

And no one is saying that number of chromosomes is the indicator of common ancestry. If you'd been paying attention, you would already know this. That 44 chromosome man I mentioned shares the same ancestors as the rest of us. He didn't just get poofed into existence by Allah.
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Re: The Origin of Life

#2147  Postby Fenrir » Mar 29, 2014 1:21 am

fluttermoth wrote:
Fenrir wrote:
Before you start you might like to do some reading into the karyotypes present within Przewalski's horse.

Well, Q121 might not, but I have; how fascinating, thank you :)


No problem. It is indeed fascinating.
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Re: The Origin of Life

#2148  Postby ADParker » Mar 29, 2014 2:49 am

questioner121 wrote:Calling it stupid isn't going to make it false now is it.

That's true. However I called it stupid because it was stupid and false, not to make it false. :roll:

questioner121 wrote:That's part of it.

No it isn't...at all. You are doing naught but demonstrating your complete ignorance is on the subject.

questioner121 wrote:Why don't you describe in terms of evolution why the fused chromosome IS evidence of common ancestry.

I briefly did so earlier, and note that Calilasseia has since done so more in depth.
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Re: The Origin of Life

#2149  Postby Greyman » Mar 29, 2014 2:51 am

questioner121 wrote:Where I'm going with this is to show there is no link between the number of chromosomes and common ancestry.
No controversy. It's not simply the number of chromosomes alone that matters; it's also the degree of similarity of content. Their size and the arrangement of sequences and loci within, and how well they demonstrate phylogeny -- nested hierarchial trees of subsequential divergences.
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Re: The Origin of Life

#2150  Postby ADParker » Mar 29, 2014 3:39 am

questioner121 wrote:Hang on.

If the evolutionary model predicted the number of chromosomes then it should be able to predict the number of chromosomes in monkeys and other living organisms. Right? Otherwise there is no such evolutionary model.

Wrong.
The model did not predict the number of chromosomes. But in closer relationships like those of the great apes, given that all the other great apes have 24 pair and we have but 23, the interesting fact that in what was already known as a taxanomic group all but one has 24 and that one having 23 is interesting, that poses an interesting question; why? As already addressed in detail by Calilasseia. Looking further afield, such as to 'monkeys' (not an actual taxonomic group, perhaps you mean simians?) the opportunity for variation only increases, so no such predictions can really be made.
You are either confusing or deliberately conflating one specific case with the entire enterprise. Of course the fusion doesn't 'prove' universal common ancestry, no one ever hinted that it does. :roll:

questioner121 wrote:Let's humans have a shared ancestor with apes since they have the same number of chromosomes. How many chromosomes should the common ancestor of humans and apes have? Less, more or the same? :popcorn:

Humans are apes. Please at least try to get the basics right.

I will try to explain this just a little, rather than just a glib answer.

Okay; if we only had the information that that humans have 23 pair and chimpanzees have 24:
Their MRCA (most recent common ancestor) is most likely to have either 23 or 24. and either a loss/fusion or duplication/fission has occurred in one of our lines. (It is possible that she could have had a different number, and both lines later changed, but 23/24 is more likely, especially given the generations/time involved, that only one has changed.)

Now; given that we also know that the gorilla and orangutan species also have 24, that changes things - and we now shift from the MRCA of humans and chimps to the MRCA of all of the apes:
It still might be the same as above if all of the other evidence suggested that the human lineage (line of descent to humans but not any other ape species) split off before the other apes diverged into chimpanzees, gorillas etc. A mutation to remove/fuse a chromosome earler in our lineage, or a duplication/fission in their line before they split further; that way one event could result in all of those other species having 24 from an ancestor with 23.

However; the evidence is that our lineages did not split like that, that our line split from the human/chimpanzee line after splitting from the other apes (see 1st image below):
What that means is that from our MRCA either:
1. She (MRCA) had 24, and sometime after the humans split off from chimpanzees or ancestors underwent a loss/fusion (far far more likely a fusion as they are less likely to be immediately fatal), leaving us with 23 and all the rest with the original 24. Or
2. She had 23, and at various times later; the gorilla line had a fission/duplication event, and the orangutan line had another fission/duplication event (remarkably, miraculously identical to that of the gorilla's), and chimpanzee line had another fission/duplication event (remarkably, miraculously identical to that of the gorilla's and that of the orangutan's!)... :o

And guess what was found on close examination? The far more reasonable option 1. is what did indeed occur. ;)

Some pretty pictures to aid in visualizing this stuff:

Image

Image
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Re: The Origin of Life

#2151  Postby ADParker » Mar 29, 2014 3:44 am

questioner121 wrote:I see what you're saying but that's not how alleles are used in biology. It has to be from a living organism of the same species.

While that is where they are most commonly discussed, that is not actually true.
This is really nothing more than arguing over semantics though. Note that practically all of the explanations you have been given on the fusion of human chromosome 2 have not included the word "allele", although they could have without changing anything substantive if we choose to use that word. So why go on about the word unless it is to avoid discussing the actual subject?
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Re: The Origin of Life

#2152  Postby hackenslash » Mar 29, 2014 3:50 am

Repost for clear example:

The macro/micro distinction is a valid distinction in evolutionary biology, but it doesn't mean what the cretinists think it means.

Evolution is defined as variation in the frequencies of alleles, where an allele is a specific iteration of a given gene. Microevolution is defined as variations in the frequencies of alleles below species level, in a population of organisms. Macroevolution is defined as variations in the frequencies of alleles at or above species level, or in populations of populations. The easiest way to think about this is that evolutionary biologists study frequencies of alleles that are shared between two species so, for example, there are many genes that are shared between humans and chimpanzees, which is to say that humans and chimps carry exactly the same version of the gene.

Another useful example is extinction, in which the frequency of all alleles in a species go from some to none.

What the creationist is actually talking about here is something that would falsify evolutionary theory wholesale, namely a cat giving birth to a dog. This, of course, doesn't happen. What does happen, though, is speciation, and in fact there is a beautiful example of extinction and speciation in a single event, namely an extinction event in a ring species. If a selection of sub-species in the middle of the ring go extinct, by a bolide impact, for example, and the remaining subspecies are no longer reproductively compatible, then we have an extinction event that is also a speciation event, both of which are correctly defined as macroevolution.
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Re: The Origin of Life

#2153  Postby Ironclad » Apr 08, 2014 11:28 pm


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Re: The Origin of Life

#2154  Postby Agrippina » Apr 09, 2014 7:37 am

Thanks for that explanation Hack, I understand that concept a little better now.
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Re: The Origin of Life

#2155  Postby Sendraks » Apr 09, 2014 7:39 am

Yup, really helpful Hack. Especially the last para.
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Re: The Origin of Life

#2156  Postby hackenslash » Apr 09, 2014 11:11 am

There should also be some discussion on the various definitions of 'gene' and 'allele' used in different branches of evolutionary biology for different purposes. In general terms, it's simply a stretch of DNA, generally one that codes for a protein, but not necessarily. In a more general sense, it's any clearly defined stretch of DNA that is heritable, which is why the fusion site of chromosome #2 is an allele, as is the entire fused chromosome (indeed, a gene can contain many genes). In population genetics, the term can be used in a more abstract manner, so it can mean something like 'is a descendent of Henry VIII', and this is a perfectly valid use of the term. susu has written fairly extensively on this kind of usage.
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Re: The Origin of Life

#2157  Postby kennyc » Apr 09, 2014 11:51 am

Story Collider - Nick Hud: the Origin of Life talk:

https://soundcloud.com/the-story-collid ... in-of-life
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Re: The Origin of Life

#2158  Postby Shrunk » Apr 09, 2014 4:12 pm

hackenslash wrote:There should also be some discussion on the various definitions of 'gene' and 'allele' used in different branches of evolutionary biology for different purposes. In general terms, it's simply a stretch of DNA, generally one that codes for a protein, but not necessarily. In a more general sense, it's any clearly defined stretch of DNA that is heritable, which is why the fusion site of chromosome #2 is an allele, as is the entire fused chromosome (indeed, a gene can contain many genes). In population genetics, the term can be used in a more abstract manner, so it can mean something like 'is a descendent of Henry VIII', and this is a perfectly valid use of the term. susu has written fairly extensively on this kind of usage.


So susu.exp and questioner121 have differing opinions on this matter? Well, then, I guess we'll just have to accept that the question is unsettled, and that there are two equally valid positions to take. :mrgreen:
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Re: The Origin of Life

#2159  Postby hackenslash » Apr 09, 2014 4:32 pm

:lol:
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Re: The Origin of Life

#2160  Postby Sendraks » Apr 09, 2014 4:41 pm

:rofl:
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