Denisovans, Humans and the Chromosome 2 Fusion

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September 6, 2012 Tags: Genetics, Human Origins

Today's entry was written by Dennis Venema. You can read more about what we believe here.

Denisovans, Humans and the Chromosome 2 Fusion


The Denisovans, an extinct hominid group that interbred with modern humans, made the news again lately with the publication of a more detailed study of their genome. One of the many interesting findings was that the Denisovans share the same chromosome 2 fusion that modern humans have. In this post, I review what we know about the origins of human chromosome 2, and then discuss the new Denisovan findings and their implications.

The origins of human chromosome 2: a brief review

Though I have discussed the evidence for a fusion event leading to human chromosome 2 before, perhaps a brief review of the evidence is in order. The human genome is made up of 23 pairs of chromosomes (for a total of 46 chromosomes). This makes us something of an oddity among living great apes, all the rest of whom have 24 pairs of chromosomes (for a total of 48). Given that there are many independent lines of evidence that support the conclusion that we share a common ancestor with other great apes, this poses something of a conundrum: how is it that our species arrived at this specific chromosome number? If we were to represent this “problem” on a phylogeny, or tree of relatedness, it would look something like this (not to scale):

Our closest living relatives, chimpanzees and bonobos, both have 48 chromosomes, as do all other great apes such as gorillas and orangutans. This pattern has one of two explanations, one of which is much more likely than the other. Either the common ancestor to these species had 48 chromosomes, and there was an event that reduced that number to 46 specifically on the lineage leading to humans (option A), or the common ancestor species had 46 chromosomes, and there were independent, repeated events that increased chromosome number in all other great ape species (option B). We can compare these options by placing the required event(s) on the phylogeny (again, not to scale):

It should be obvious that the option that requires the fewest events is the more likely one – in this case option A with an event that reduces chromosome number in the lineage leading to humans. The other option, that of repeated, independent events to increase chromosome number, remains a formal, but unlikely, possibility. Events that reduce chromosome number are not frequent occurrences, so Option A is more likely than Option B.

We can also find further support for Option A, because it predicts a specific type of event, namely one that reduces chromosome number. Since loss of a large amount of chromosomal material is almost always detrimental, we need an event that reduces chromosome number without losing information. One way for this to happen is for two chromosomes to fuse together and become one. Initially, this event would produce an individual with 47 chromosomes, where two different chromosomes get stuck together. Contrary to what is often assumed, this individual would be fertile and able to interbreed with the others in his or her population (who continue to have 48 chromosomes). In a small population, over time, two relatives who both have one copy of the fusion chromosome may mate and produce some progeny with two copies of the fused chromosome, or the first individuals with 46 chromosomes. Since either a 48-pair set or a 46-pair set is preferable for ease of cell division, this population will either eventually get rid of the fusion variant (the most likely outcome), or by chance will switch over completely to the “new” form, with everyone bearing 46 chromosome pairs. While not overly likely, this type of event is not especially rare in mammals, and we have observed this sort of thing happening within recorded human history in other species. Some mammalian species even maintain distinct populations in the wild with differing chromosome numbers due to fusions, and these populations retain the ability to interbreed.

Further evidence for a fusion event in the lineage leading to modern humans comes from comparing synteny, or gene locations and orders on chromosomes within modern great apes – an issue we have discussed here before. In brief, what we see in human chromosome 2 is exactly what we would predict for a fusion event. When compared to other great apes, we see the genes on human chromosome 2 match up, in order, with two smaller ape chromosomes. We also see that sequences used at the tips of chromosomes are present at the proposed fusion site, and that human chromosome 2 has not one but two sites for the cell cytoskeleton to attach to for cell division – but that one of the sites is mutated and not functional, though it lines up precisely with the location of this site on the appropriate ape chromosome. Together, this evidence consistently supports both common ancestry for humans and great apes, and specifically that the difference we see in our chromosome numbers arose due to a single fusion event. I briefly discussed this evidence in my last post where I describe how I teach some of this material and the compelling impact it has on students exploring the evolution question for the first time.

Enter the Denisovans

With that as background, we are now prepared to appreciate a new finding that comes from genomics work done on the Denisovan hominids, an archaic species that is more closely related to Neanderthals than to us, but that nonetheless interbred with some anatomically modern humans as they migrated out of Africa and populated the globe. (For those not familiar with the Denisovans, or the evidence for our interbreeding with them, both Darrel Falk and I have written on this previously, here and here). Recently, a more detailed understanding of the Denisovan genome was published, and nested in the new information is the discovery that the Denisovans share the 46 chromosome set with the same fusion that we have. This strongly supports the hypothesis that the fusion event predates the separation of our species. If we were to represent this on a phylogeny, we can now place this event with more accuracy than before (as before, the phylogeny is not to scale):

Despite this new information, one obvious question remains. Did the Neanderthals also have the 46-pair set? From looking at the phylogeny above, we can see that the most likely answer is that they did, since the fact that the Denisovans had it strongly implies that the last common ancestor of humans and Neanderthals / Denisovans had it as well, and the Neanderthal-Denisovan split comes later. While the Denisovan DNA samples are of high enough quality to make this assessment, we do not yet have Neanderthal DNA of high enough quality to do the same analysis with current methods (though one additional feature of the new work on the Denisovan genome is developing more sensitive DNA sequencing techniques that may resolve this question in the future).

In other words, this fusion seems to be an ancient one, predating our species by several hundred thousand years. Present estimates of the last common ancestor between humans and Neanderthals / Denisovans range at about 800,000 years ago.

Implications for understanding our “becoming human”

The main implication from this work is that it places the fusion event well before the advent of our species. I’ve often chatted informally with Christians about evolution, and at times some have thought that this fusion event was what “started” our species, or made our species unable to interbreed with other groups. Some have even suggested that perhaps the fusion event was what produced the first human (i.e. Adam).

Note that thinking this way suggests a misunderstanding of how chromosome fusions occur and what effect they have on their hosts. A fusion does not precipitate a speciation event, but rather the individual with the fusion remains a part of his or her population, and able to interbreed, even if with reduced fertility. Also, there is no necessary biological effect or change that the fusion produces on the appearance of the organism. These misunderstandings aside, however,what this new evidence shows is that this fusion event took place long before modern humans arose at around 200,000 years ago. Indeed, the 800,000 years ago date for the last human - Denisovan common ancestor means that this is the most recent date possible for the fusion. While it is an interesting piece of our evolutionary history, it doesn’t seem to have much to do with how we came to acquire the traits that set us apart from, and ultimately outcompete, other similar species.




Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.


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PNG - #72476

September 6th 2012

By chance I just happened to be looking at a paper where they estimated the age for the chromosome fusion to in a range that is compatible with the fusion having occurred by the time of the common ancestor with Denisovans. The GC-biased substitution clusters near telomeres that they were studying also fit with the fusion, since they are observed in regions near the old telomeres in the middle of chr. 2.   http://www.ncbi.nlm.nih.gov/pubmed/17785536


dennis.venema - #72477

September 6th 2012

What? Converging lines of evidence from different diciplines that support the same conclusions? Never.

Thanks for the link to that paper! Very interesting to see that these estimates match.


Joriss - #72493

September 7th 2012

“Together, this evidence consistently supports both common ancestry for humans and great apes, and specifically that the difference we see in our chromosome numbers arose due to a single fusion event”.
Why does this consistently support common ancestry? This is only the case if the similarity between the genome of humans and apes is seen as evidence for common ancestry. If it is seen as evidence for a common designer, God, this fusion is consistent with this view as well. Since these fusions are rare, but do happen, it could as well have happened in the time of early mankind, when there were not many people on this earth. So although it is consistent with the evolutionary point of view, it gives no extra evidence, as far as I can see. Am I wrong?


PNG - #72500

September 7th 2012

Joriss,

I think you’re right that the fusion itself isn’t really evidence for common descent. It could have happened in a specially created human line. The countless complex genetic events that have left their mark in both apes and human genomes are the convincing evidence. (I don’t know if you got my message, but I tried to answer the question you posted on my blog related to that.) But the fact that events like the fusion appear to have happened so long ago doesn’t really fit with the Genesis picture of a Neolithic beginning of the human race. If you have to push Adam back to over a million years ago, you’re not talking about a scenario that resembles at all the Genesis account.


wesseldawn - #72561

September 8th 2012

This is over my head to a large degree but according to the Bible “man” (Gen. 2:7 -translation=ruddy/was only called Adam after God put it into the garden in Gen. 2:8). Prior to that time man was a brute animal/mammal that had evolved from/of the “dust/ground”.

We have no idea how old man was before it entered the garden, nor do we have an idea how old the earth itself was. Therefore, to push man back to over a million years ago must not be ruled out.

Don’t forget that God’s garden/Paradise is an eternal place (as Jesus said to the thief on his right that “today you will be with me in Paradise”)! No times exists there, whereas time would continue on the earth. We have no idea how long man/Adam was in the Paradise before the explusion from the garden!


Joriss - #72511

September 7th 2012

PNG,
Thank you for your reply. At least you agree with me, that the fusion is not an ultimate support of common ancestry, as sometimes is stated by evolutionists. But I get the impression that it is used as such by Dennis Venema in his class. Anyway, the evo-crea discussion will not come to an end by this past genetic event.
What do you mean, you tried to answer me on your blog? When and where? I think I have missed it. Can you give me a link?


dennis.venema - #72512

September 7th 2012

Hi Joriss,

A chromosome 2 fusion event in and of itself is not evidence for common ancestry - presumably humans would do fine with 48 chromosomes, and we could have easily speciated and maintained 48 chromosomes all along the way. The fusion, however,  is a direct prediction that flows from (a) the other, numerous lines of evidence for common ancestry, and (b) the observation that the genes on two modern ape chromosomes line up with two arms of one of our chromosomes.

If you’re interested in the genetic lines of evidence for human - ape common ancestry I’ve written a paper that covers a good deal of it:

Venema, D.R. (2010). Genesis and the genome: genomics evidence for human – ape common ancestry and ancestral hominid population sizes. Perspectives on Science and Christian Faith 62 (3), 166-178.  

This paper is freely available online. I have a PDF of it linked off of my faculty page, or you can get it from the journal web site.


dennis.venema - #72513

September 7th 2012

http://twu.ca/academics/science/biology/faculty/venema/pscf9-10venema.pdf


dennis.venema - #72514

September 7th 2012

ok, the link doesn’t work, but if you cut & paste that into a browser it will give you the PDF.

In the paper I also carefully consider the alternative hypothesis of “common design” in the sense of antievolutionary common design, and give my reasons for rejecting that hypothesis.


PNG - #72516

September 7th 2012

Another good paper on the same subject in the same journal is 

Human Evolution: How Random Process Fulfills Divine Purpose by Graeme Finlay

http://www.asa3.org/ASA/PSCF/2008/PSCF6-08Finlay.pdf


PNG - #72515

September 7th 2012

http://artofthesoluble.blogspot.com/2011/12/transposable-elements-and-common.html#comment-form


Francis - #72518

September 7th 2012

Thing                                                   # of chromosomes

Chimpanzee

Pan troglodytes

48[17]

 

Deer Mouse

Peromyscus maniculatus

48

 

Gorilla

 

48

 

Hare[18][19]

 

48

 

Orangutan

Pongo x

48

 

Potato

Solanum tuberosum

48[15]

 

Tobacco

Nicotiana tabacum

48[15]

 

Human

Homo sapiens

46[20]

 

Reeves’s Muntjac

Muntiacus reevesi

46

 

Sable Antelope

Hippotragus niger

46

 

Above from http://en.wikipedia.org/wiki/List_of_organisms_by_chromosome_count


GJDS - #72520

September 7th 2012

I want to compare the language of this post with that found in, for example, a peer reviewed journal that discusses the topic of similarity (or lack of this) between human beings and chimpanzee.

This blog, says with such confidence: “We can also find further support for Option A, because it predicts a specific type of event, namely one that reduces chromosome number. Since loss of a large amount of chromosomal material is almost always detrimental, we need an event that reduces chromosome number without losing information. One way for this to happen is for two chromosomes to fuse together and become one. Initially, this event would produce an individual with 47 chromosomes, where two different chromosomes get stuck together. Contrary to what is often assumed, this individual would be fertile and able to interbreed with the others in his or her population (who continue to have 48 chromosomes).”

Contrast this with the heterogeneity discussed in the article: “Structural divergence between the human and chimpanzee genomes.” by Kehrer-Sawatzki H, Cooper DN. Hum. Genet. 2007 Feb;120(6):759-78.

The structural microheterogeneity evident between the human and chimpanzee genomes is quite considerable and includes inversions and duplications as well as deletions, ranging in size from a few base-pairs up to several megabases (Mb). Insertions and deletions have together given rise to at least 150 Mb of genomic DNA sequence that is either present or absent in humans as compared to chimpanzees. Such regions often contain paralogous sequences and members of multigene families thereby ensuring that the human and chimpanzee genomes differ by a significant fraction of their gene content. There is as yet no evidence to suggest that the large chromosomal rearrangements which serve to distinguish the human and chimpanzee karyotypes have influenced either speciation or the evolution of lineage-specific traits. However, the myriad submicroscopic rearrangements in both genomes, particularly those involving copy number variation, are unlikely to represent exclusively neutral changes and hence promise to facilitate the identification of genes that have been important for human-specific evolution.

The leap from an observable (number of chromosomes) to a lineage and descent, based on the so called evidence presented by the writer, is indeed breathtaking. To use the terminology that he favours, “Insertions and deletions have together given rise to at least 150 Mb of genomic DNA sequence that is either present or absent in humans as compared to chimpanzees.”

This not the place for detailed discussions of 150MB of data – but it is a place to emphasise the difference between dubious conclusions uttered with weird certainty, with the results of sober scientific work. I might add the article I site reviews a great deal of published work.


PNG - #72542

September 8th 2012

150 Mb is about 5% of the genome, and that is about the level of difference between human and chimp genomes that you get if you include insertions and deletions and copy number differences. I promise you that the authors of that article accept common descent as surely as Dennis and I, as is clear from the last sentence you quoted. (The title of another paper by the same authors is “Understanding the Recent Evolution of the Human Genome: Insights from Human–Chimpanzee Genome Comparisons”)

There is nothing “breathtaking” about Dennis’s conclusion. It follows not merely from the chromosome numbers and fusion and mere similarities of the genomes, but from the fact that they contain the record of millions of shared complex mutational events - millions of transposon insertions in the exactly corresponding locations, pseudogenes with the exact same inactivating mutations, thousands of retrotransposed pseudogenes at corresponding locations, hundreds of insertions of the same mitochondrial DNA fragments in the same places, etc. Dennis has a fine article in the reference section of this website, and there are articles at the ASA website by him and one by Graeme Finlay on the same topic, if you want to get into the details, which you need to do if you want to really deal with the evidence. The links for these articles and some related material on my blog are given in comments above.


GJDS - #72551

September 8th 2012

Reply to PNG #72542

By and large, I choose papers in well known journals by authors who appear to support evolution when I make criticisms on this blog (and I will continue to do this). I understand a bias and commitment to evolution in this blog, so I prefer to use other material, while making sure most of it is from those who have a positive view regarding evolution. By doing this I can avoid a confrontational approach.

My interest is in following the thinking and assesing the intellectual vigour, and worth, of the topic, not to judge or criticise the quality of the data.

I cannot accept an assertion by any scientist that stipulates a 5% difference is fine; just what criteria is sufficient for similiarity, and what is not? The point I am making is that when discussing something as monumentally complex as the arrangement of genes and related matters, expressing certainty is unwise.

The evidence for thos exercise is not similar to a detective who has hunted for clues regarding a known event - I find it disturbing that scientists would reason by commencing with, “we have proven this ‘tree’ or line of descent” and then go on to show how evidence is used to come to a reasoned conclusion.

I have stated previoulsy that I am reading a range of papers (and have listed these), including ones on the philosophical reasoning behind many assertions of evolutionists - again, I have made sure the majority of these are by pro-evolutionists to ensure that if I have their best arguments. So far, I find the intellectual content of these contibutions of dubious quality - and most certainly, I cannot see a sound basis for the certainty expressed in blogs such as this one.


PNG - #72555

September 8th 2012

I just wrote a long reply and failed to copy it before this annoying blog software gave me an error and deleted it. This problem was fixed on this site once and now it is happening again. Help!

It’s good to see someone who is actually researching this in detail. I’m a little confused by some of what you wrote above, but I gather that you are annoyed that biologists seem to assume that common descent is true. What you need to understand is that, if you read the primary research and reviews, researchers in comparative genomics are not trying to make the case for common descent. They are familiar with a mountain of evidence for it, and they view it as something that was demonstrated beyond reasonable doubt long ago. The high degree of similarity of the chimp and human genomes was apparent from protein and DNA sequences that have been accumulating for 4 decades, long before the complete sequencing of the genomes, and research on a variety of events that have shaped genomes has been going on for a long time.  Research papers are concerned with a host of subsequent questions. My reason for pointing to the papers by Dennis and Graeme Finlay and my blog were that the material there was written to make the arguments/evidence for common descent explicit in a form that a serious layman could understand. Nothing in the research literature is written with that in mind. Everyone views it as a settled issue.

I think one can generalize the genomic evidence for common descent as the fact that mammalian genomes contain the record of countless complex mutational events occurring at the exactly corresponding position in the genomes of different species. One such pair of events might be accounted for as a low-probability coincidence where identical events happened in parallel in different species, but for millions of them (and there are literally millions of them) to occur in parallel the likelihood is essentially zero. These events can be the insertion of a particular type of transposon or endogenous retrovirus at a particular location, the same series of inactivating mutations in a pseudogene, the same complex rearrangement, the insertion of the same fragment of mitochondrial DNA at the same location in nuclear DNA, etc. And these events don’t just occur in pairs of species. Many of them are present in multiple species, in patterns such that you can determine when in the branching of species they occurred, as shown in Dennis’s post. The chances of these complex events having happened in parallel in multiple species are even more remote. I confess I don’t understand why you think we are intellectually incompetent to draw this conclusion.


GJDS - #72598

September 9th 2012

coninued reply to PNG #72555

I repeat my original point, contrasting the certainty with which the topic is discussed in this blog, with the uncertainty and tentative nature of various aspects of the theory found in the literature put forward by the proponents of evolution. Since I have purposely used papers written by advocates of the neo-Darwinism outlook, it would be obvious these people have accepted it – thus that is not a point for an argument. While the synthetic theory of evolution, which suggests that evolution results from a twin process of mutation and natural selection, is the dominant theory, scientists are not fully in concordance with regard to the extent that other factors play a significant role in evolutionary change. It is also a point of fact that many scientists regard neo-Darwinsim as more of a belief than a legitimate theory of science - perhaps a more charitable view would be a number of various theories that proponents are desperately trying to keep under the umbrella of Darwinism (e.g. Dawkins).

I show that uncertainty is inherent in evolutionary theory(s), and thus this point is consistent with my original criticism that this work lacks the required intellectual rigour normally found in high level scientific research. I add the following extracts from papers. Readers can easily locate these and come to their own conclusions, which may or may not be in agreement with my remarks.

Alexander S Graphodatsky, Vladimir A Trifonov and Roscoe Stanyon, “The genome diversity and karyotype evolution of mammals,” Molecular Cytogenetics, 2011, 4:22. “The entire chromosome set of a species is known as a karyotype, which can be thought of as a global map of the nuclear genome. A seemingly logical consequence of descent from common ancestors is that more closely related species should have more similar chromosomes. However, it is now widely appreciated that species may have phonetically similar karyotypes because they are genomically conservative. Therefore in comparative cytogenetics, phylogenetic relationships should be determined on the basis of the polarity of chromosome differences (derived traits).

We now have a distinction between ‘similar’ and ‘derived traits’ and.. “it is (becomes) now appreciated …..  This underscores uncertainty on what can at best be a convenient assumption; this is further re-enforced by: “At the same time, the notion that one may find universal or necessary laws in biological sciences is vigorously debated,” and, “However, it is also clear that all biological generalizations have their share of exceptions, and all seem to be contingent on the peculiarities of life on earth.” from: Tudor M. Baetu, Mechanistic Constraints on Evolutionary Outcomes”, Philosophy of Science, Vol. 79, No. 2 (April 2012), pp. 276-294.

continued


GJDS - #72600

September 9th 2012

It seems that I have still cannot use the reply in sequence. This is the second part of the reply to PNG #72555, dated 10 Sep. ... continued…..

On another matter of evolution, two scientists arguing the merits (or otherwise) on the importance of kinship in the evolution of complex social systems in insects (SCIENCE, VOL 323, 6 FEBRUARY 2009, p 706): After organizing a discussion group with about 20 others, they published an expanded explanation of these ideas in the December 2007 “The Quarterly Review of Biology” and in the September-October 2008 issue of “American Scientist”. Kin-selection theory, they argue, is ineffective. “The theory that traditionalists use leads them anywhere they want to go” and fails to make useful predictions, Wilson asserts. “To make [a theory] really stand [up], you have to show that that’s the only result that can come from your theory, and they haven’t done that.”

Evolutionists should take their own advice! 

I add just one more point on sameness in biology, to demonstrate that uncertainty is far greater then you are willing to admit:

“One might suppose that homology would also have met its end at the hands of Darwin, that the concept would have been discarded along with Owen’s archetypes. But not only did Darwinism not annihilate homologies, it turns out that homologies are at its very basis. In order to make a claim that a trait has evolved (e.g., that jaw structure has changed), the same trait must be picked out in different individuals (the jaw in organisms A, B, C, etc.). Darwinism thus undermined the traditional basis for homology only by making key use of the notion of homology. In the wake of Darwin, then, biologists and philosophers had to ask whether there is a new foundation for homology. Grant Ramsey and Anne Siebels Peterson, Philosophy of Science, Vol. 79, No. 2 (April 2012), pp. 255-275.

 Whatever your position on Darwinism, neo-Darwinism, of the umbrella that is used to hold a number of fragmented theories together termed theory of evolution, it is surely obvious that uncertanty permeates this area.


PNG - #72614

September 10th 2012

GJDS,

There is a great deal of ongoing discussion about the various mechanisms of evolution, including kin selection as mentioned above. There isn’t any discussion among researchers about whether common descent is true. There are mountains of evidence of the types that I mentioned above for common descent, and the only people disputing it are those who have Biblical/theological reasons for doing so. If you don’t distinguish between common descent and the mechanisms of evolution, you may look at the disputes about mechanism and think that common descent is being disputed by researchers. It isn’t.


GJDS - #72625

September 10th 2012

Reply to PNG #72614

I have repeatedly discussed the uncertainty that permeates the scientific discussions on this topic, and you, with your patronising manner, avoid the topic under discussion and then decide to judge those who find this the case, do so for biblical reasons. I will not waste my time further with you, and state emphatically, if any research personnel in groups I had managed and led displayed the lack of intellectual vigour shown by you and the writer of this blog, they would have been out of my reaserch programs very quickly. Thankfully scientists that I have worked with (religious or otherwise) do show the intellectual rigour required by science and also a capacity to reason and citicise - you and the writer of this blog saddly lack those qualities.


PNG - #72658

September 11th 2012

I studied material on evolution for 20 years before I came to a conclusion on what I think. I did research in a relevant field (biochemistry for 35 years.) I have pointed you to material that addresses the question directly, and you have refused to look at it, insisting on looking at papers that are addressing other questions.  Don’t accuse me of unwarranted certainty when you refuse to even look at the relevant material. I have made extensive arguments and so has Dennis and others and you have refused to look at them. I’m guessing that you come to this very much wanting to find a way to dismiss common descent, and you have found a way, but please don’t think that you have investigated the matter thoroughly when you have refused to engage at all with the things we have written.


GJDS - #72665

September 11th 2012

Reply to PNG #72658 and subsequent posts

I will let your own words ‘accuse’ you:

Don’t accuse me of unwarranted certainty when you refuse to even look at the relevant material.

The material I referred to is directly related to the topic under discussion, and I asked direct questions on the topic. 

Your response was, ‘well everyone says so”, and now you have decided to declare yourself an authority on the subject and all else must be off topic if you cannot deal with it. I have again and again stated I am using material from those who favour your position.

I stand by my remarks on your approach and I simply cannot waste any more of my time in your trivia and non-sense.  


PNG - #72668

September 11th 2012

I have trying to help you, not to patronize you, or deal in trivia. I’m sorry I wasn’t able to help, and I’m more than a little puzzled what the heck is going on here, but you seem to have written me (and Dennis) off, so, I hope you can find someone who is of some help.


PNG - #72660

September 11th 2012

I should add that I didn’t mean at all to patronize you - I was trying to point you in directions that would be helpful - I hadn’t seen you say that were in science, so I assumed that you were an interested layman. I can’t escape the impression that you are mistaking the uncertainty that you see in discussion of current problems in research with uncertainty about common descent. I said above in response to someone else that I don’t think the chromosome fusion is very convincing evidence for common descent, and thus I tried to point you to some material that directly addresses the question. You say that I avoided the topic under discussion -  I was under the impression that that topic was common descent. Maybe I was wrong. If so, maybe we should back up and try again.


PNG - #72662

September 11th 2012

Assuming that common descent is the question, I tried to encapsulate what I think are the best arguments above. In short, the parallel occurrence of an unlikely mutation in a specific site in 2 or more species genomes is a very unlikely event. One such parallel occurrence might be assumed to be an unlikely coincidence, but the only plausible way to account for millions of such parallel events that I have thought of is that they happened in common ancestors. That hypothesis removes the mystery.


GJDS - #72575

September 9th 2012

Reply to PNG #72555

I am reading two papers that are on the topic

(1) Malcolm A. Ferguson-Smith* and Vladimir Trifonov, “Mammalian karyotype evolution,” p950 |december 2007 | volume 8 www.nature.com/ reviews/genetics

(2) Alexander S Graphodatsky, Vladimir A Trifonov and Roscoe Stanyon, “The genome diversity and karyotype evolution of mammals,” Molecular Cytogenetics, 2011, 4:22

 

 and also papers from Philosophy of Science discussiong similiarity and heterogieniety,and mechanistic constraints in biology.

I hope by then to have a more detailed and reasoned response, but these things take some time to digest, since these are outside of my research activities.

For now, I bring to your attention statements such as the following: “.... include further evidence for placing the red panda among the Musteloidea and the giant panda among bears” from ref (1).

I also point out that I have read this review ref (1), performed a word search, and will re-read it, just to be certain I had not missed a central point, which is this: does this review article provide a basis for assuming that, for example, the mammalian tree AEK 2n=46, while for primate tree, APK is 2n=50, and for carnevors, ACK 2n= 42. I as yet cannot find such a statement, although the review appears thorough.

My comments go to the basis for these matters - are these assumptions, and if so, how are they justified. The authors reasoning seems to me to more in line with, “Darwin provided such a classification”, and now we confirm this using these techniques. I cannot see how anyone, least of all Darwin, would put pandas in different species classificaiton. I will leave other matters for another time when I have finished reading these papers.

Again I am assuming the papers I read support these theories and thus are written by those who have accepted them. This allows me to see the most favourable discussions; I then also feel free to critically examine the reasoning, without looking for hang-ups or some ‘axe to gride’, so to speak.


Francis - #72537

September 8th 2012

Evolution’s not just about humans and hominids. It’s about all living things, and where they came from.

Rabbits and gazelles share a fondness for hopping or leaping. They both have hair, eyes, ears, etc. And they have close to the same number of chromosomes.  

Considering the Wikipedia chromosome count info above, has anyone proposed that the Hare and the Sable Antelope have a common ancestor?


Terrance - #72541

September 8th 2012

Francis,

I see that pretty much all of your questions on this thread are not asked sincerely (many of them here are rather remiscient of Kent Hovind), but are instead your attempt to make what you consider to be some kind of pertinent point. This essay by Dennis is outlining how evolutionary theory leads to very specific predictions that can quite easily be tested. In this instance, DNA sequencing, along with other lines of evidence, indicates that humans and other apes share a recent common ancestor. Now for that to be true something must account for the difference in chromosome number since the species diverged, and in this case it is explained by the fusion event. This is a prime example of the testibility and explanatory power of common descent as a scientific explanation. It is also in stark contrast to any kind of alternative (I’m thinking mainly here of the frequently proposed ‘common design’ argument), which makes basically no obvious predictions at all, explains none of the data that common descent does, and is frankly meaningless - a easy, throw-away response given by people to what is basically mountains of data pointing in a direction that they are not prepared to consider.

 

Oh, and in answer to your question “has anyone proposed that the Hare and the Sable Antelope have a common ancestor,” consider the term universal common descent and what exactly that means.


PNG - #72546

September 8th 2012

In case anyone reading this is really interested in mammalian chromosome evolution (both the species Francis asks about are mammals), here’s a review which is available for free:

http://www.ncbi.nlm.nih.gov/pubmed/21992653


wesseldawn - #72564

September 9th 2012

In light of the complicated topic this will no doubt sound simplistic but it’s important from the Biblical perspective.  

In no way does what Dennis wrote conflict with the Bible.

Timeline:

Gen. 2:7 - man/ruddy evolves from the dust/ground:

      We have no idea how long the process took nor how long this creature was on the earth, nor how old it was when it entered the garden. The fusion could well have taken place before the garden.

Gen. 2:8 - God puts ruddy into the garden Paradise:

       No time exists in Paradise but time would have continued on the earth.

As I see it this creature had three states:

1) before the garden = soul/animal/mammal (Gen. 2:7) = Denisovan??

2) leaves the garden to give birth to a female (Gen. 2:21) = Neanderthal/Missing Link

  - later (we don’t know how much later) returns to the garden with her but leaves Neanderthal offspring on the earth

3) leaves the garden a second time (unable to return) = Homo Erectus or Sapien

Genesis is only a very brief overview of the beginning and so it’s not inconceivable to think that man in the first state was far older than speculated!


Joriss - #72616

September 10th 2012

Francis,
All creatures have a common ancestor, not only the potato and the antelope, but even the elephant, the flee and the christmas-tree! You ought to know that . (And you know ofcourse).

But although this idea is funny, that doesn’t say anything about the truth. If evolution is true, it is a funny truth; if evolution is not true, it is just a funny idea. Anyway is it funny. But what is the truth?
Until now I am a creationist,but although I have my serious concern about this whole matter and feel we christians should all be alert that no unholy, disastrous doctrine may enter into God’s church, we, on the other hand, should not be too stressed or worried about it. Truth will prevail at last. Lies will be unmasked. Misunderstandings, theological as well as scientifical, are forgivable, and will be cleared up eventually. So I think there is no need for a christian, whether being a creationist or an evolutionist, to accuse each other of some kind of heresy or being ungodly. As far as I can see, there are sincere christians on either side of the line. So this line is not some separation line between dark and light, but between the partly understanding A- party and the partly understanding B- party. And of course the A- party thinks to know best and so does the B- party.

Together we are still the Jesus- party, whether A or B is right.
At least that’s the way I see it at the moment.


PNG - #72618

September 10th 2012

Recently there was an internet kerfuffle (great word) about the chr. 2 fusion. One of the DI group made a statement disputing some of the evidence and blogger Carl Zimmer asked for the source of this evidence. The ensuing dustup was one those “sound and a fury signifying nothing” things, but in the process Zimmer wrote a summary of some of what is known about the chromosome fusion.   If anyone is interested, it is at  http://blogs.discovermagazine.com/loom/page/2/    The relevant post is the first one in a series of 4 called The Mystery of the Missing Chromosome. The first post was on July 19 at 12:13 pm.


Francis - #72630

September 10th 2012

Joriss,

“…although I have my serious concern about this whole matter and feel we christians should all be alert that no unholy, disastrous doctrine may enter into God’s church, we, on the other hand, should not be too stressed or worried about it. Truth will prevail at last. Lies will be unmasked.”

I try not to be too stressed or worried about anything (cf. Mat 6:25-34). However, I do have, or hope I have, sober concern (cf. 1 Peter 1:13; 1 Peter 5:8).

On one hand, evolution is a colossal trifle. It has no bearing on our daily, work-a-day lives. It has no influence on real, beneficial scientific/medical research.

On the other hand, if evolution is false, we better sober up. Nothing good comes from believing in something that’s false. Speaking of which, you also said

“As far as I can see, there are sincere christians on either side of the line.”

And sadly, there are also some ex-Christians on one particular side of the line. I know people personally, and have corresponded with others, who lost their Christian faith. These well-educated adults said they lost their faith for one primary reason: They came to believe that evolution is true.

Nothing in this universe is more sobering than this. Anything that can jeopardize your faith, the one thing that can give you a hope of heaven, is seriously sobering.

I don’t like the look or the smell of evolution theory. And I think one would be wise to do a taste test before swallowing.

“but test everything; hold fast what is good” [1 Thes 5:21].


PNG - #72659

September 11th 2012

If anyone loses their faith because of evolution, I would have to say that their faith was not the kind that saves in the first place, because they were believing in a set of ideas rather than a Savior who is personally known. All they did was exchange one set of ideas for another. If they had actually come to know a Savior, they would not leave Him. It’s not about believing doctrines or Biblical ideas, it’s about Who you know. I think you are right about one thing - for most people evolution doesn’t matter much - it doesn’t have any effect on ordinary life or faith. It does matter for science and medicine, because it points those of us in research in the direction of fruitful ideas in a variety of areas.


Francis - #72663

September 11th 2012

PNG,

“If anyone loses their faith because of evolution, I would have to say that their faith was not the kind that saves in the first place, because they were believing in a set of ideas rather than a Savior who is personally known …If they had actually come to know a Savior, they would not leave Him.”

I’ve personally known people with whom I’ve lost touch, whether circumstantially or deliberately. I’d bet you have too.

Are you saying that if someone loses his Christian “faith”, then it wasn’t a real, saving faith? If so, then what you’re saying contradicts 2,000 years of traditional Christian doctrine and, not coincidentally, contradicts Scripture.

 

“I think you are right about one thing - for most people evolution doesn’t matter much - it doesn’t have any effect on ordinary life or faith. It does matter for science and medicine, because it points those of us in research in the direction of fruitful ideas in a variety of areas.”

“Research in the direction of fruitful ideas”? True blue evolutionists would say evolution has no direction; that what will evolve cannot be predicted; that organisms do not evolve in response to outside stimuli; that organisms’ genes randomly mutate, with some mutations being “winners” and some (most, I think) being “losers”.

I maintain, and repeat, that belief in evolution contributes zero to real, practical, beneficial scientific and medical research. Apparently, so does Dr. Philip Skell, Emeritus Evan Pugh Professor of Chemistry, Penn State University:

“I recently asked more than 70 eminent researchers if they would have done their work differently if they had thought Darwin’s theory was wrong. The responses were all the same: No. I also examined the outstanding biodiscoveries of the past century: the discovery of the double helix; the characterization of the ribosome; the mapping of genomes; research on medications and drug reactions; improvements in food production and sanitation; the development of new surgeries; and others. I even queried biologists working in areas where one would expect the Darwinian paradigm to have most benefited research, such as the emergence of resistance to antibiotics and pesticides. Here, as elsewhere, I found that Darwin’s theory had provided no discernible guidance, but was brought in, after the breakthroughs, as an interesting narrative gloss.” [P. Skell, “Why Do We Invoke Darwin?” The Scientist]


PNG - #72666

September 11th 2012

The “direction” I was pointing out was not the direction of evolution itself but the direction for research. I’m sorry, I have to disagree with Skell, and I would point out that he is a chemist, not a biologist. If we didn’t think evolution happened, why would we think that an organism as distant as yeast could be a model for human physiology and disease? But it has been, many times over. I worked on yeast for many years, and one researcher I knew joked, in light of how much we have learned about eukaryotic biology (including the human) from yeast, that it should be made an honorary mammal. Evolutionary theory is largely population genetics considered over a long time, and in that sense is relevant to the evolution of the character of pathogens including their acquiring new host species. I could go on, but you have said enough on these pages to convince me of a couple of things, that you won’t change your mind no matter what evidence is presented, and that despite your claim to have studied evolution for years you “looked at the pictures and turned the pages” and that is about all. I haven’t seen any evidence that you have learned enough biology to sneeze at. But, like a lot of anti-evolutionists, you have learned how to quote mine and copy and paste. It’s not the same thing.


GJDS - #72667

September 11th 2012

Francis,

I will add my agreement with your remarks. I have been involved in collaborative research that has spanned pure research, including experimental and modelling of specific enzyme chemistry, quantum mechanics modelling of complex chemistry, catalytic systems, chemical kinetcs, and to applied chemistry and chemical engineering, with input from physics, and related material sciences. In all of these activities, and in discussions with highly accomplished scientists in these areas, none of us have had to discuss, refer to, or even think, on any Darwin derived thinking. On the rare occasion we would bring up this topic, it would be to note some further public noise by either aethiests or theists who cannot help thumping their chest about this topic.


bren - #72674

September 11th 2012

GJDS, you have just listed a set of fascinating subjects that don’t even conceivably have a connection with evolutionary biology and have then stated that you don’t make use of evolutionary biology in any of these subjects.  Are you sure it was strictly necessary to point this out?


GJDS - #72678

September 11th 2012

Reply to bren #72674

Heavens above! You people speak on the descent of man, theism and evolution, claim to know what and how God worked with your theory, the grand explanation of events stretching over millions (billions) of years, and expound your theoroes with the certainty that is only occasionally found in very limited areas of the exact sciences, and yet, you then ask, “what connection does the rest of science have with evolution”.

You need sober reflection on your position; once you accept the severe limitations of your theory/hypothesis of evolution within science in general, and accept that you should convey its considerable limitations in your discussions, then I for one will once again ignore it and assume it is confined to your areas/activites. I am annoyed by the stance that you people take; it is vanity personified. You and others want to assume a position of scientific authority, and yet you cannot deal, nor understand, the significance of the dissagreements and doubts that permeate your field. The term is hubris! (again I apologise for the typo errors but this small window is just too difficult for me to correct).


bren - #73000

September 22nd 2012

excellent meta-analysis disguised as an angry tirade.  Now back to what you were talking about; you have not explained how you are likely to use evolutionary biology in such fields.  For that matter, you haven’t pointed out the identity of the major problems in this theory.  For that matter, I’m sure you said something and said it well, but I can’t seem to ground it in anything being discussed.  I’d prefer to hear about the mysterious fatal flaws and scandals in the theory (just seems a less ambiguous topic) than about any cosmic hubris, although I’ll resign myself to the hubris topic if you insist.


bren - #72673

September 11th 2012

““Research in the direction of fruitful ideas”? True blue evolutionists would say evolution has no direction…”

Eh?


Francis - #72675

September 11th 2012

GJDS,

Thanks for your confirmation from the real world.


GJDS - #72679

September 11th 2012

Francis #72675

As I have mentioned in the past I prefer a reasoned approach instead of a combative one. Nonetheless I am annoyed when people assume scientific authority in putting forward their belief positions regarding these matters. I can understand atheists who ‘finally’ have something to believe with neo-Darwinism; it is their lot when the only position left to them is absence of belief. Many of them however, take an honest position in terms of accepting what they consider reasonable. It is much more difficult to understand people of the Faith appearing to ‘hang it all’ on something as dubious and uncertain as evolution. Reason and Faith are sufficient, and the certainty that science brings with matters such as universal constants, should remove anxiety regarding science being anti-faith, It appears that people will make life difficult for themselves with non-sense such as evolution.


Darwin Guy Dan - #72980

September 21st 2012

GJDS: You, Francis, and Eddie must surely be on my team.  That will be a billion dollars each. Send check ASAP.

I wouldn’t be too sure about “the certainty that science brings with matters such as universal constants.”  I have read some credible physicists and astrophysicists that posit that the “constants” may not be, or may not have always been, as constant as the textbooks have it.  John W. Moffat , e.g., is very compelling with his REINVENTING GRAVITY: A PHYSICIST GOES BEYOND EINSTEIN (2008).  Additionally, the notion of zero-point fields (ZPFs) is fascinating as an alternative explanation for inertial and gravitational mass.

Beyond this minor cosmic quibble, I would to add my non-professional voice of agreement with your line of thinking.  In my mind, the researches done under the paradigm of Evolution by Evolutionists over the recent decades demand a rethink of the paradigm.   While I haven’t had access to the resources you all have had, what I have read (mostly books) indicate to me that modern research in genetics (including the ENCODE results reported in the Stephen Mapes  blog of Sept. 21) does more to disconfirm Evolution than to confirm it.  E.g., prior to the days of modern investigations into chromosomes and genes, would anyone have predicted the seemingly bizarre numbers such as in the data Francis provided at #72518?  Surely not. 

Some Evolutionists as Robert Shapiro and Stan Salthe have been seeing the genomes as  “read-write disks.”  With this thought, and other ideas from researches regards epigenetics and also horizontal transfers (HGTs and symbiosis), it seems to this novice that the entire idea of providing phylogenetic classification that represents past reality is perhaps futile.  Ditto molecular clocks (which seem to have not been much in the news in recent years). 

Regards PNG’s statement at 72555: “I think one can generalize evidence for common descent as the fact that mammalian genomes contain the records of countless complex mutational events occurring at the exactly corresponding position in the genomes of different species.”

So, what’s the story?  Have you and Francis not had your morning coffee?  Surely you can use horizontal transfers (genes, viruses, bacteria) to burst the bubble of lingering certainty regards the mythological tree with its mythological unidentified, unnamed, mythological common ancestors.  The “web of life,” is clearly well accepted, especially as applicable prior to the Cambrian and early life. 

Just some passing thoughts.  Can’t stay.

Dan, a.k.a. NaturalHistoryGuy / LocalTransportationGuy


Francis - #72676

September 11th 2012

PNG,

“If we didn’t think evolution happened, why would we think that an organism as distant as yeast could be a model for human physiology and disease?”

I can’t say that I follow this. Do the “lab rats” say the same thing about the mice on which they experiment?

Then again, a number of times the Lord himself used yeast as a metaphor for human stuff (e.g. “…he began to say to his disciples first, “Beware of the leaven of the Pharisees, which is hypocrisy.”” – Luke 12:1).

Now, if only Genesis 2:7 read “then the LORD God formed man of yeast from the ground, and breathed into his nostrils the breath of life; and man became a living being.” Man, would that get a rise out of evolutionary biologists!  Ahh, if only.

 

“Evolutionary theory is … relevant to the evolution of the character of pathogens…”

Circular reasoning is a no-no.

Folks, did you know that Space Alien Theory is relevant to the character of the great Egyptian pyramids, which the space aliens helped construct?

 

“I could go on…”

Me, too.  

 

P.S.

Yes, I realize yeast is not exactly synonymous with leaven.


Francis - #72677

September 11th 2012

Bren,

“GJDS, you have just listed a set of fascinating subjects that don’t even conceivably have a connection with evolutionary biology and have then stated that you don’t make use of evolutionary biology in any of these subjects. Are you sure it was strictly necessary to point this out?”

Is it conceivable that the “specific enzyme chemistry” and “complex chemistry” mentioned by GJDS could be applicable to DNA, the fingerprint of all biology?

 

P.S.

Have you been working on the eye evolution story for me? Eh?


PNG - #72758

September 13th 2012

Francis,

It’s clear by this point that you have no intention of participating in any serious discussion of the blog posts or anything else, and I’m sorry, but glib remarks don’t constitute serious discussion. Everyone has heard what you think - you seem to have invented fundamentalist Catholicism as your perspective. I suggest you get your own blog (it’s free) and see if you can draw a crowd to listen to your “insights.” In a world where there are probably even a few real flat earthers left, you can probably find a few sympathizers.


bren - #72685

September 12th 2012

..and DNA is evolutionary biology. ok then.


Joriss - #72701

September 12th 2012

PNG,

“If we didn’t think evolution happened, why would we think that an organism as distant as yeast could be a model for human physiology and disease?”

Would the observed relation between the DNA of very distant organisms, which can be as well the result of common design as of common ancestry not be enough reason to take yeast as a model for human physiology and disease? Does that really need an evolutionary point of view?


Ashe - #72752

September 13th 2012

I’ve found this video helpful regarding this particular subject.

 

http://www.youtube.com/watch?v=J3yDOp8Dv8Y


PNG - #72754

September 13th 2012

The usefulness of yeast as a model was expected and proposed  before we had any DNA sequence. Yeast was suggested as a model eukaryote by James Watson in a book he published in the late ‘60s, but he was not the only one thinking that way at that point. It’s true that one can always invoke “common design,” and I was mindful of that during the 20 years or so that I was trying to work out what to think about evolution. For me the clinching evidence was the huge number of apparently identical complex mutations in the genomes of mammals, especially primates including humans. To stay with “common design” you have to think that the Designer went to a great deal of trouble to make genomes look like they share a common history.


Francis - #72763

September 13th 2012

PNG,

“It’s clear by this point that you have no intention of participating in any serious discussion of the blog posts or anything else, and I’m sorry, but glib remarks don’t constitute serious discussion”

While my remarks may at times have a touch of humor or sarcasm, I can assure you that they are in substance quite serious.

Why won’t you answer my serious questions, PNG? From the above:

1) Are you saying that if someone loses his Christian “faith”, then it wasn’t a real, saving faith? (If so, then what you’re saying contradicts 2,000 years of traditional Christian doctrine and, not coincidentally, contradicts Scripture.)

2) Your statement: “Evolutionary theory is largely population genetics considered over a long time, and in that sense is relevant to the evolution of the character of pathogens including their acquiring new host species.”  Are you denying that your statement is a case of circular reasoning (the circular reasoning found throughout evolution-speak)?

 

I just thought of a third serious question: What non-pathogen did the pathogens evolve from?

 

 


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