The Science of Sustainability

Chromosome Fusion: Chance or Design?

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Human and chimpanzee chromosomes are very similar.
Note that human chromosome 2 is very similar to a
fusion of two chimpanzee chromosomes.

For the last few weeks I have been corresponding with someone about intelligent design (ID). More specifically, we have been chatting about why humans have 46 chromosomes and most of the great apes have 48.

To me, this is great evidence for evolution. Why? Because if you look at the chromosomes closely, you can see that human chromosome 2 is really just a fusion of two great ape chromosomes.

The idea is that a few million years ago, a common human-chimpanzee ancestor of ours had two of his or her chromosomes fused together. This sort of thing happens all the time even today. Around 1 in 1000 live births has one of these kinds of fusions.

Then, probably through chance,this ancestor with the fused chromosomes went on to found the human race. Now people have 46 chromosomes and chimpanzees have 48.

An alternative explanation is that the designers fused the two chromosomes together when they created humans. The idea would be that the designer wouldn't create every plant, animal, bacteria, and virus from scratch–why reinvent the wheel every time? Instead the designers would mix and match parts that worked.

So as part of the process of designing a human, the designer fused two ape chromosomes together. This would presumably be simpler than creating a human chromosome 2 the way the other chromosomes were made.

The difficulty with this idea is that there is no obvious advantage to having 46 chromosomes instead of 48. What matters is our DNA, not how it happens to be packaged.

It is possible that there was some advantage to fusing the chromosomes together. For example, maybe a new gene was created at the fusion point. Or maybe genes that were shut off before were now turned on in the new fused chromosomes.

There isn't any evidence of these kinds of things. And even if there were, a designer who can easily put in the 60 million or so differences between humans and chimpanzees should be able to accomplish whatever results a chromosome fusion gives more elegantly than sticking two ape chromosomes together.

Also, when you look at the fusion point, you can see that the DNA isn't exactly what you would expect if a fusion happened in the last 10,000 or even 100,000 years. The results look more like an event that happened millions of years ago.

The ends of a chromosome have a defined sequence of DNA repeats called a telomere. The DNA at the fusion point looks very similar to a string of telomeres (as we would expect from a fusion) but it isn't perfect. This is just what you would expect if the fusion happened millions of years ago. Because our DNA gets changed a little all of the time.

The environment or even our own cells can cause the wrong letter to end up in our DNA. Our cells are pretty good at fixing these mistakes but they don't catch them all. What this means is that our DNA builds up mutations over time.

When an unfixed change happens in a sperm or egg, then it is passed down to the next generation. If the changes that aren't fixed happen somewhere important, then they are selected for or against. But if they're neutral, then they just build up over time. Scientists can even use these sorts of errors to predict how long ago something happened. Or to trace human migration patterns.

These DNA changes at the fusion point do not fit with ID if they don't serve a purpose. Otherwise, why put them there? It will be interesting to see the results of experiments that might show if these sequences matter or not.

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA.


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Dr. Barry Starr

About the Author ()

Dr. Barry Starr is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA and runs their Stanford at The Tech program. The program is part of an ongoing collaboration between the Stanford Department of Genetics and The Tech Museum of Innovation. Together these two partners created the Genetics: Technology with a Twist exhibition. Read his previous contributions to QUEST, a project dedicated to exploring the Science of Sustainability.
  • atb

    Hey Dr. Starr,

    (That sounds like a bad Dr. Pepper knock-off–sorry, couldn't look past it.) Anyway, thanks for the info on chromosomal fusion; I've learned some about it in recent weeks, but this helped shine more light on the subject.

    Before I continue, I have to admit that I do hold to the assumption that there is a Designer–I'm a Christian, no two ways around it. So if I get at all defensive or biting, please point it out and forgive me–I really don't intend to.

    I had a quick question, though, in light of one remark you made here. You say at one point, "What this means is that our DNA builds up mutations over time." Over what amount of time have scientists actually seen these mutations pile up? I guess it doesn't seem to me like we've been doing this kind of work for very long–in the grand scheme of things. And have those mutations that have slipped past our cellular defenses had any kind of an impact?

    Thanks again. Have a good one.

  • http://www.thetech.org/genetics/ Barry Starr

    Sorry I didn't respond sooner…I usually get an email telling me my blog got a comment but didn't this time (Craig has some splaining to do).

    Certainly mutations do slip through and have an effect. For example, 7/8 of cases of dwarfism happen spontaneously–from a mutation in dad's or mom's gametes (see http://www.thetech.org/genetics/ask.php?id=179 for the details). Also, almost all cancers come from DNA changes (although these aren't usually passed down). Fragile X comes from an instability in part of the X chromosome. Some cases of autism come from DNA that goes missing or is duplicated between generations. And I could keep going on…

    I recognize that these aren't good mutations–bad ones are just easier to see in a short period and are very obvious when they happen. A good mutation is trickier because there has to be a reason for it to be good. For example, some change in the environment that now favors lighter skin or drinking milk. We can see evidence in our DNA that these traits started out rare but quickly became common in certain populations but none have happened recently in humans that I know of.

    There are certainly the obvious cases of penicillin resistance in bacteria or species creation in yeast (see http://www.thetech.org/genetics/ask.php?id=143 for details). Or cave fish losing their eyes the same way through different mutations in the same gene in isolated colonies (see http://www.thetech.org/genetics/ask.php?id=185).

    Probably enough for now. Thanks for the response…I didn't find it defensive or biting.

  • atb

    I see what you're saying, and it's definitely interesting, though I've never really questioned the microev- things–ya know, finch beaks and lactose tolerance. Now that piece you have on the yeast breeding and apparent speciation: that's interesting stuff that I've never heard before. Would you say that that example carries enough weight to validate the concept of macroevolution, or is this perhaps just a strange trait of yeast? Why or why not?

    Thanks for this discussion. I appreciate your cordiality and even keel.

  • http://www.thetech.org/genetics/index.php Barry Starr

    I don't think it is just a weird trait in yeast. We are able to see this happening in yeast because they have such a short generation time. In 20 years, you go through 1 human generation. In the same amount of time, you can go through around tens of thousands of yeast generations.

    This sort of thing definitely happens in butterflies too (see http://www.sciencedaily.com/releases/2006/06/060616135623.htm and http://www.thetech.org/genetics/news.php?id=26 for a discussion of this). There are also cases of mules that are fertile. Get two of these together and you have a new species!

  • atb

    Weird stuff. So what definition of "species" are we working with to determine that butterfly A is different than butterfly B is different than hybrid butterfly C? Obviously it's not some kind of sexual incompatability–because, well, they're doin' it just fine; is their chromosomal layout different or something?

  • http://www.thetech.org/genetics/index.php Barry Starr

    Species is a tricky thing to define. It isn't simply that two types of animals cannot create fertile offspring. For example, lions and tigers can create fertile offspring but I think everyone would agree they are different species.

  • atb

    Is the definition of "species" so fluid that it's hypothetically possible–and at least mildly reasonable–for someone to hold that lions and tigers aren't different species?

  • http://www.thetech.org/genetics/ Barry Starr

    No, it isn't that fluid. I just wanted to give an idea about how hard it can be to define a species. This difficulty in defining a species is what you might expect in a world undergoing evolution–there are going to be many gray areas where groups of animals are just diverging from one another. This URL has a nice concise description of the subject:

    http://wiki.cotch.net/index.php/Science_can't_define_species

  • JMM

    In order for this fusion be passed on, wouldn't it have to happen in more than one animal? In other words, if we assume that fusion took place in one ape, wouldn't it have to take place in another ape who would have to be it's mate? Likewise for the children, grandchildren, and great grandchildren? I could be wrong, but it seems like it would have to happen at exactly the same place in the genome as well.

  • http://www.thetech.org/genetics/index.php Barry Starr

    Because of something called a balanced translocation, it is possible for the change to happen in a single animal. That animal could then pass on a single change until two of its descendants meet up and have children. These children could then have the final change that results in the new chromosomal arrangement. See the following links for more information:

    http://www.thetech.org/genetics/ask.php?id=229
    http://www.thetech.org/genetics/ask.php?id=12

  • http://www.fiorentinoresearch.com jfiorentino

    But they are BOTH still 'cats."

  • http://www.fiorentinoresearch.com jfiorentino

    However, the burning issue might well be, "Exactly what are we seeing in this "fusion?"

    And, has it been positively determined that the 2 "chimp" chromosomes are indeed what they appear, i.e., really "chimp" chromosomes. The only definitive evidence of that to date are the banding patterns.

    We also might ask, "does this fusion create any benefit," which may indicate design rather than "common ancestry."

  • Mitch Bogart

    Dr. Starr,
    You put it most succinctly saying, "Instead the designer would mix and match parts that worked."
    As an engineer (software) I thinks that abiogenesis and the development of the whole cellular biochemistry appears to be more "designed" rather than the result of random mutations plus some survival filtering.
    Would you please note and hopefully comment on this observation of your excellent size-order sorted chromosome diagram.
    There appears to be a more even distribution of large chromosome lengths with the human single #2 versus the chimp "split" #2. I think it therefore makes sense to say the the original design was for a single #2 and it was "split" to create the aberrated species of the chimps, etc.
    I.E. there never was any "fusion" but rather a loss due to a splitting. Characterizing this discussion as a fusion effectively builds in a bias to a common ancestry chimps from apes. With your (and my) mix and match scenario, the design could have proceeded in the other direction.
    If I'm DESIGNING some things, I can either conceive and build the simpler things first, or perhaps what might come out better, I'd design the bigger complex thing first and then decide to modify it down to create some lesser models.!
    Am I totally off the wall or, just perhaps, onto something? Thanks for the solid and objective discussion! – Mitch

  • http://www.thetech.org/genetics/ Barry Starr

    The best evidence that it was a fusion event and not a separation event is the existence of back to back telomeres in the middle of human chromosome 2. Telomeres are found at the end of chromosomes. Here we see telomeres in the middle. And what’s more, the telomeres go in different directions as we would expect from a fusion event. There is also a second centromere in human chromosome 2. Chromosomes have a single centromere. The fact that this one has two with the unused centromere the right distance from the tandem telomeres in the middle of the chromosome strongly suggests fusion and not separation. Incidentally, a separation is a very difficult thing to pull off from an evolutionary point of view. A separated chromosome tends to lack a centromere and a telomere which is deadly unless it can “steal” one of each from another chromosome.

  • Pingback: Surviving Chromosomal Rearrangements | QUEST Community Science Blog - KQED

  • Ken Oh

    Dr. Starr
    The example of American wild horse population with a fused chromosome compared with the domestic horse population is incredible. Does fusion exhibit the same characteristics as human chromosome 2? The living example demonstrates how the fusion of a chromosome can spread in an isolated population while still having viable off spring with the larger population. This has to be a killer piece of evidence supporting evolution.
    Second question: the genetic drift in the vestigial fused telomere and centromete must provide some upper limit as to the date of the fusion event. Is this date close to the 5 to 4.5 million year date of the split from the common ancestor?
    Your blog and links have provided some of the best information on Chromosome 2. Thanks

    Ken Oh, PhD

  • Ken Oh

    Dr. Starr
    Sorry, I misread the wild horse vs domestic horse chromosome article under the impression that the wild horse population had a fused chromosome. This is a case where the wild horse population had a split chromosome increasing the count while still viable. The example still demonstrates how a chromosomal change can propagate and dominate a population. Still a very powerful living example of how chromosome 2 could have propagated in the early human population.

    The question still in my mind (and I am certain in many others) is “when”? Did early humans carry 24 pair and later fused to 23 or was the fusion near the separation from the chimpanzee line? Could have this be the actual separation event?
    Thanks again
    Ken Oh, PhD (Also from Stanford but in Comp Sci)

  • http://www.thetech.org/genetics/ Barry Starr

    Hi Ken

    Great questions. I'm not sure what to make of the wild horses since I don't know that much about them. The Przewalski's Horse from Mongolia does have 66 chromosomes (instead of 64) but I haven't seen a good comparison of the two horses' chromosomes to know what is going on.

    The estimates that I have seen for when chromosomes 12 and 13 fused together is sometime between 740,000 and 3 million years ago (http://www.springerlink.com/content/a81216614h5j31u3/). So this happened after chimps and humans went on their separate ways. This means that this was not a speciation event but instead something that happened in the human population (although I suppose it could have kept our ancestors from successfully interbreeding 3 million years ago and might have sealed the speciation).

  • Ken Oh

    Dr. Starr

    The fusing event that formed chromosome 2 and the spreading through early human population is consistent with the notion of a bottle necking event where the population was small. The very unique fusing of the telomers is a strong indication of single event as opposed to an “infection” or similar event where multiple individuals were affected.
    What an incredible set of circumstances!

    Thank you very much for your very informative response.

    Ken Oh

  • http://www.fiorentinoresearch.com jfiorentino

    Dr. Starr says………

    "The estimates that I have seen for when chromosomes 12 and 13 fused together is sometime between 740,000 and 3 million years ago (http://www.springerlink.com/content/a81216614h5j31u3/). So this happened after chimps and humans went on their separate ways. This means that this was not a speciation event but instead something that happened in the human population……"

    So, one might ask how could this then be termed the "fusion" of two ancestral "ape" chromosomes? and How does this idea alone offer support for "common ancestry" rather than simply "assuming" it?

  • http://www.thetech.org/genetics/index.php Barry Starr

    Hi John

    I really like your comments because they cut to the heart of the matter. This particular piece of DNA evidence is not enough to rule out the idea that a designer created life 740,000 or more years ago*. It is enough to rule out any theories of recent design (e.g. the Earth is 10,000 years old). When we add fossil data, the idea that humans were designed over 740,000 years ago doesn't pan out.

    If we have common design instead of common ancestry, humans were around more than 740,000-3,000,000 years ago (meaning that life as we know it was designed at least hundreds of thousands of years ago). Then at some point there was a bottleneck where only those with the fused chromosomes survived.

    This model predicts that humans have been around for more than 750,000 years in their present form. There is no evidence that modern humans were around that far in our past. The fossil evidence suggests that modern humans are on the scene about 200,000 years ago or so (see http://www.talkorigins.org/faqs/homs/species.html for a nice timeline). There is plenty of evidence for other human-like hominids but no true humans until then.

    Perhaps an earlier form of human was designed that then evolved into modern humans?

    *Of course, this is just one of the pieces of data that support common ancestry.

  • Ken Oh

    Dr. Starr
    The real issue with any ID or creationist discussion is their suspension of the rules of nature and their invocation of magic. The Designer could have very well designed human DNA with joined chromosome 2 and genetic drift that appears to us to indicate 740,000 years of existence but in reality only on Earth for 10,000 years. The Designer could have implanted fossils to further to further confound our belief that humans (and all of nature) are significantly older.

    Once the rules of nature are suspended, one can argue that the Designer created everything last night and I awoke with implanted memories of a past and perceptions of the rich fabric of reality.

    The proponents of ID or creationism suffer from intellectual failure where the observed facts cannot be resolved in their minds and must invoke a higher intelligence. “The problem is too hard for me to solve so God must have made it” is not science but an intellectual failure.

    I admire your attempts to help ID and creationist to understand facts and how within the understood natural processes these could have occurred. You have great tolerance in reasoning with them and explaining in great detail the current understanding of how the facts can be explained. This discussion has been very helpful too for those that do not believe in ID.

    The proponents of ID are genuinely wonderful people and need to understand that the lessons of Christ and his life are not diminished by the removal of the magic described by the writers of the Bible. In fact, as our understanding of Nature unfolds, reality is even more wondrous and amazing than any could have imagined.

    Thank you for a great discussion

    Ken Oh

  • http://www.fiorentinoresearch.com jfiorentino

    For Ken Oh – then I will f/u with Dr. Starr

    "The real issue with any ID or creationist discussion is their suspension of the rules of nature and their invocation of magic."

    While I basically agree with your statement, I take exception with this: "their suspension of the rules of nature" I think SOME may do that, but certainly not all.

    As for ID itself, I have stated repeatedly that it is NOT science. However, a finding of the court in the Kitzmiller trial, a case which many fling around in support of evolution, and often use as an indictment of ID (which it is neither) and which not very surprisingly almost no one who espouses "evolution" even mentions is this:

    121. "The Court concludes that while intelligent design arguments may be true ­ a proposition on which the Court takes no position ­ the theory is not science. Moreover, because intelligent design is ultimately predicated on a supernatural creator, the theory is religious, a finding required by the Supreme Court's holding in Edwards v. Aguillard."

    So, while ID is not science it could nonetheless be true. It's difficult for many to grasp the concept of law here, and exactly what the court is saying. For instance, I think the idea of a "designer" "creator" or "God" whichever term you may wish to apply is MORE than possible. That does not mean however, I agree with every contention of let's say Michael Behe, because I don't. In fact I've written about, and shown where in certain instances Behe's contentions don't hold water. Conversely, I think I've fairly well demonstrated that SOME of Dr. Ken Miller's contentions are equally wanting.

  • http://www.fiorentinoresearch.com jfiorentino

    Don't tell me, my response to Dr. Starr went where?

  • http://www.fiorentinoresearch.com jfiorentino

    Since I don't see it anymore, I'll try and recreate what I posted to Dr. Starr. The following is posted to try and generate some critical thinking.

    The Evolutionary Origin of Human Subtelomeric Homologies—or Where the Ends Begin
    Am J Hum Genet. 2002 April; 70(4): 972–984.

    Copyright © 2002 by The American Society of Human Genetics. All rights reserved.

    The subtelomeric regions of human chromosomes are comprised of sequence homologies shared between distinct subsets of chromosomes. In the course of developing a set of unique human telomere clones, we identified many clones containing such shared homologies, characterized by the presence of cross-hybridization signals on one or more telomeres in a fluorescence in situ hybridization (FISH) assay. We studied the evolutionary origin of seven subtelomeric clones by performing comparative FISH analysis on a primate panel that included great apes and Old World monkeys. All clones tested showed a single hybridization site in Old World monkeys that corresponded to one of the orthologous human sites, thus indicating the ancestral origin. The timing of the duplication events varied among the subtelomeric regions, from ~5 to ~25 million years ago. To examine the origin of and mechanism for one of these subtelomeric duplications, we compared the sequence derived from human 2q13—an ancestral fusion site of two great ape telomeric regions—with its paralogous subtelomeric sequences at 9p and 22q. These paralogous regions share large continuous homologies and contain three genes: RABL2B, forkhead box D4, and COBW-like. Our results provide further evidence for subtelomeric-mediated genomic duplication and demonstrate that these segmental duplications are most likely the result of ancestral unbalanced translocations that have been fixed in the genome during recent primate evolution.

    FISH Analysis of Proximal Subtelomeric Domain Clones
    Proximal subtelomeric clones were used for comparative FISH studies. FISH analysis was performed on metaphase spreads from human and other members of the primate panel, including chimpanzee, gorilla, orangutan, macaque, and baboon.

    As shown in figure 1, BAC 136B17 from human 4p hybridizes to chromosomes 4p and 1p in human but shows only a single signal in the region orthologous to 4p in chimpanzee and all other species tested. Figure 2 summarizes the results from the analysis of additional subtelomeric duplications. BAC 204M23 shows similar results to those of BAC 136B17: in human, this clone hybridizes to the short- and long-arm telomeres of chromosome 4, but it only shows one signal in all other primates examined. Since these two clones showed duplicated signals only in human and not in the other primates, these duplications most likely occurred after the divergence of humans from the great apes, <3–5 million years ago.

    Pericentromeric- and subtelomeric-mediated duplications involve nonhomologous chromosomal regions. Horvath et al. (2000) proposed a two-step model for the dispersal of mosaics of duplicated segments among multiple pericentromeric regions. The first step is a process called “transposition seeding,” where genomic segments from different chromosomal origins were transposed to an ancestral pericentromeric region. This process is estimated to have occurred ~5–10 million years ago, around the time of the divergence of the human, chimpanzee, and gorilla lineages. In the second step, called “pericentromeric exchange,” large blocks of mosaic duplicated segments were duplicated to the pericentromeric regions of other nonhomologous chromosomes. These duplication events are relatively recent, since they are only seen in human (Horvath et al. 2000).

    Just shows the rather large ranges in guesstimates relating to "divergence."

    Dr. Starr's statement:

    "This model predicts that humans have been around for more than 750,000 years in their present form. There is no evidence that modern humans were around that far in our past."

    Dr. Starr is referring to homo sapien-sapien, refers to the fossil-record to back up his claim, but provides no references re: his 750,000 year timeline.

    It certainly can be stated that any reference to "divergence" assumes common ancestry and thus begs the question. I seriously doubt if any of these timelines are supportable.

    For instance above Dr. Starr says:

    "Also, when you look at the fusion point, you can see that the DNA isn’t exactly what you would expect if a fusion happened in the last 10,000 or even 100,000 years. The results look more like an event that happened millions of years ago."

    Of course "millions of years ago" is not 750,000 years.

    I would also like to mention re: the fossil record, that Dr. Porter Kier relayed to a friend of mine that the fossil record can be used to support EITHER evolution or creation.

  • http://www.fiorentinoresearch.com jfiorentino

    I also would like to post this re: timelines

    Dates from the molecular clock: how wrong can we be?

    aSchool of Biological and Chemical Sciences, Queen Mary, University of London, London, E1 4NS, UK

    Large discrepancies have been found in dates of evolutionary events obtained using the molecular clock. Twofold differences have been reported between the dates estimated from molecular data and those from the fossil record; furthermore, different molecular methods can give dates that differ 20-fold. New software attempts to incorporate appropriate allowances for this uncertainty into the calculation of the accuracy of date estimates. Here, we propose that these innovations represent welcome progress towards obtaining reliable dates from the molecular clock, but warn that they are currently unproven, given that the causes and pattern of the discrepancies are the subject of ongoing research. This research implies that many previous studies, even some of those using recently developed methods, might have placed too much confidence in their date estimates, and their conclusions might need to be revised.

    Trends in Ecology & Evolution, Volume 22, Issue 4, April 2007, Pages 180-184
    Mário J.F. Pulquério and Richard A. Nichols

  • http://www.thetech.org/genetics/index.php Barry Starr

    Wow, look what happens when I go away for a nice weekend in Santa Cruz! Yikes.

    I think the latest set of posts brings up some very interesting points–although let's not quibble when I accidentally put millions instead of 750,000. Or mess up my html and forget to include a reference.* These were simple errors of typing and I would hope our discussion would rise above that sort of thing.

    John's statement:

    "So, while ID is not science it could nonetheless be true."

    This is really useful to me because it makes me take a step back and ask what are we trying to accomplish with this discussion. My expertise is in science which means that I look at and produce scientific data that supports, modifies, or refutes a scientific theory. If ID is not science, then I am not sure what I can contribute to the discussion.

    One approach I suppose is that someone could amass enough data to refute evolution as a scientific theory. But there is a lot (the vast majority of life scientists would argue an overwhelming amount of) evidence in support of evolution. What this means is that we can’t just find a bit of data here or there to argue against it. The data against has to be overwhelming too. And I have yet to see anything that will invalidate the theory of evolution. (Doesn’t mean it won’t happen of course, just that nothing has been found yet.)

    Another thorny issue is that because of the way science works, a new scientific theory needs to replace the old one. And if ID is not a scientific theory, what do we replace evolution with?

    * Here are the references for the 740,000-3 million year number (the first is a review article that references the second). The number is based on common ancestry arguments although I wonder if someone could do it just using humans?

    http://www.springerlink.com/content/a81216614h5j31u3/
    http://genome.cshlp.org/cgi/content/full/17/10/1420

  • http://www.fiorentinoresearch.com jfiorentino

    Dr. Starr says:

    "These were simple errors of typing and I would hope our discussion would rise above that sort of thing."

    First, I want to say here publicly that I admire Dr. Starr immensely. If I gave the impression of a nit-picker, please accept my apologies, that was certainly not my intent.

    Conversely, Dr. Starr says:

    "If ID is not science, then I am not sure what I can contribute to the discussion."

    This statement baffles me, and I will say it's far from the first time I've encountered it from others in the sciences (and other professions to).

    I never understood that stance, and still don't. However, these are certainly elective choices re: participation in any discussion, not just ID for example. I could ramble on ad infinitum about this, but I'll just let it go.

    Dr. Starr says:

    "Another thorny issue is that because of the way science works, a new scientific theory needs to replace the old one. And if ID is not a scientific theory, what do we replace evolution with?"

    Don't quite get this either. If just as a fantasy, "evolution" was invalidated today, what would the next step be for science? Or, would we simply keep it because we have nothing to replace it with? Of course, we MIGHT try the "truth" but that of course isn't science necessarily either.

    I would like to see some comment on the article:

    Dates from the molecular clock: how wrong can we be?

    Trends in Ecology & Evolution, Volume 22, Issue 4, April 2007, Pages 180-184
    Mário J.F. Pulquério and Richard A. Nichols

    Thanks again, Dr. Starr

  • Ken Oh

    Science has a few simple rules to determine TRUTH.
    1) Truth is a statement, a hypothesis, describing a facet of our natural existence.
    2) The hypothesis must provide observable elements which through observation prove the hypothesis to be true or false.
    3) For a hypothesis to be held as TRUTH, it must continually be observed to be true.

    A hypothesis can be true for a limited facet of nature while failing outside of these boundaries. A hypothesis need not explain every aspect of nature to be true but provide the insight to understand some aspects of nature.

    A commonly used example is the laws of motion of Newton which describe to high fidelity the trajectories of macro bodies and the role of gravity. However, these laws of motion fail at high velocity or for massive bodies. Newton fails to describe the nature of gravity but only its effect on macro bodies. Yet, no one asserts that these laws of motion as false and are in fact used today with an understanding of the limitations.

    The observed failure of Newton’s laws at high velocity or high mass provided the opportunity to further science. Einstein provided a more refined understanding of motion at high velocity or high mass and in doing so also provided incredible understanding of space and time. Yet, Einstein cannot describe the observation of very small objects as provided by quantum mechanics. The mathematics of general relativity and quantum mechanics are not compatible yet within their limitations, these two descriptions of nature are held as Truth.

    As Newton was superceded by relativity and quantum mechanics, these two descriptions of nature will be superceded by another description that resolves the observed discrepancies at the boundaries.

    Super String theory, while elegant in its mathematics, is still not real science since its predictions are not observable with our current particle accelerators.

    Observation is an essential element of the determination of Truth.

    It makes no sense to state that ID may be TRUTH when ID makes no prediction of what may be observed.

    Evolution is a FACT, TRUTH. There are no observations that disprove the hypothesis that life on Earth arouse from very simple life and evolved to the creatures that are observed including humans. At the time Darwin and Wallace wrote of evolution they did not know of the work of Mendel and inheritance and were relying on their observations, the scant fossil record, and their insight. Mendel provided additional insight as to the mechanisms by which evolution worked. Subsequent insights and observations now give us the molecular mechanisms, DNA, RNA, etc. by which inheritance and genetic diversity work. We can see it work in bacteria that now eat nylon or bacteria that are drug resistant. We have observed real instances of evolution.

    The evolutionary history of humans and all life on Earth is written in our DNA. This thread by Dr. Starr provides incredible insights into how our history may have been written. These are discussions about speculations when paragraphs may have joined or words misspelled, etc. while observing multiple documents derived from an older common document. It is very clear in observing the DNA, that there was a common ancestor from which human DNA and chimpanzee DNA derived. And, through retrogression, the common ascent can be determined.

    If ID is TRUTH, then give us the observational examples. Do not cite where our current science cannot explain something because our understanding will always be incomplete. We may never know what happened before the Big Bang or why the charge on the electron is what it is.

    Also, please understand that ID need not be TRUTH to make the teachings of Jesus to be true. ID is the formulation of men who are fallible. Jesus did not teach ID nor did he teach against evolution. Discarding a belief in ID is not discarding your core Christian beliefs but just rejecting ignorant men forcing their beliefs upon you.

  • http://www.fiorentinoresearch.com jfiorentino

    "Observation is an essential element of the determination of Truth."

    Please provide one example of observed Macroevolution.

    Feel free to eliminate any pontificating.

    Thanks

  • http://www.fiorentinoresearch.com jfiorentino

    Perhaps YOU would care to comment on the article:

    Dates from the molecular clock: how wrong can we be?

    Trends in Ecology & Evolution, Volume 22, Issue 4, April 2007, Pages 180-184
    Mário J.F. Pulquério and Richard A. Nichols

  • Ken Oh

    One example is a bacterium that eats nylon by evolving a gene that produces an enzyme that breaks down the nylon molecules. Nylon is man made polymer developed in 1935 and did not exist in nature. Until now, nothing decomposed nylon. Recently, a bacterium was found on discarded nylon eating the polymer. It was a common bacterium that evolved the nylon cleaving enzyme through the evolution of a gene to synthesize the new enzyme. The gene evolved in less than 73 years.

    There is no question that changes in DNA causes changes in the organism. Commercial genetic engineering is a big business in pharmaceuticals and agriculture. Using direct manipulation of the genetic code, new organisms with unnaturally occurring genes with resulting unique functions are created. Bacteria and yeasts synthesize human insulin and other pharmaceuticals. Corn and soy beans are engineered to resist pests and provide higher yields. These are FACTS, highly observable FACTS; not just in small labs but in factories for commercial production.

    Most people think of DNA as a static storage medium for genetic information. A cell divides and two perfect copies of DNA are in the two daughter cells. A mutation is a single event that changes a base pair in a germ cell and the mutation is passed to the subsequent generations. This view is mostly correct.

    However, there are mechanisms in DNA that move or copy huge chunks of code. The first observation was by Barbara McClintock whose discovery and analysis of spotted corn resulted in a Nobel Prize. Her thesis of moving chunks of genes among the active genes was not believed for many, many years. Her award came some 35 years after her initial publication. The moving of chunks of genes have been observed and documented by many.

    Entire genes can be copied so that two copies are in the DNA. This uses DNA to RNA back to DNA much like a retro virus. While not observed in humans, there are many studies in mammals and other animals where genes are replicated in the children. Much of the genetic material is comprised of duplicates of inactive copies of genes. Some copies evolve to provide different functions. For example mammals have two different hemoglobin genes where one is used for blood after birth to take oxygen through the lungs from air and the other used for blood during gestation where oxygen is taken through the placenta from the hemoglobin of the mother’s blood.

    The human genome has a smaller number of replicating genes as some other animals and from this one can surmise that dramatic evolutionary changes in humans will be far smaller than other animals with a higher number of replicating genes.

    The critical elements in the DNA are the genes with their control headers and terminators. The chromosome is packaging for the genes. The package can change without changing the genes. A chromosome can break resulting in two chromosomes. Or it can break and the broken bit reattached but in reverse as an inversion. As long as the complete gene is not broken, it will continue to function. The organism can grow to pass the repackaged chromosomes to subsequent generations.

    With the tools of the genome project, we can read every base and compare these with other humans and animals. Like looking at computer code or text documents, it is possible to see where changes have occurred and from that deduce the revision level of code or documents and where there are common sources. Unlike computer code or text documents, many elements of the chromosome can endure copying errors and not affect the child organism. These copying errors propagate through the generations. Copying errors in active genes change the organism and bad changes cause death and do not propagate. With this careful examination of the DNA of humans, chimps, gorillas, etc. one can determine a very plausible sequence of these copy errors where animals that are genetically closer share more errors in common. The rate of copy errors has been assumed to average to a frequency from which time durations can be estimated. I repeat, these are estimates based on assumptions which may not be perfectly correct. However, these provide a guide of elapsed time.

    There are now some very readable books on the evolutionary evidence in the human DNA and the DNA of other organisms. I recommend “Relics of Eden” by Fairbanks. Here is a link: http://search.barnesandnoble.com/Relics-of-Eden/Daniel-J-Fairbanks/e/9781591025641

    For fear of sounding repetitious, ID or Creationism is a fabrication by well intentioned but ignorant men.
    Evolution is a FACT. All of the scientific discussions are focused on the exact mechanisms and plausible events of evolution. Newton’s laws of motion are accepted as FACT even though it does not apply to fast moving or massive objects. We still do not know the nature of gravity yet we accept Newton as FACT. There are a lot of bits and pieces of evolution that we need to discover and understand but this does not in any remote way imply the evolution is not TRUE.

    Evolution does not diminish the teaching of Jesus or any element of Christianity. Kepler, Galileo, and Newton moved the Earth from the center of the human universe to the outskirts of a medium size galaxy among billions and billions of galaxies and this move did not diminish Jesus or Christianity.
    ID or Creationism appears to be for the ignorant.
    Christianity is not just for the ignorant.

  • http://www.fiorentinoresearch.com jfiorentino

    Please provide one example of observed Macroevolution

    "One example is a bacterium that eats nylon by evolving a gene that produces an enzyme that breaks down the nylon molecules."

    So, since this isn't an example, I assume you can't provide one?

    "ID or Creationism appears to be for the ignorant."

    I see. Thanks for your insights.

  • Ken Oh, PhD

    Bacterium that eats nylon is new and due to evolution of its DNA. What more do you want for an example of natural change due to competitive selection?
    The world is now full of genetically engineered (GE) plants and animals. Many animals we eat have eaten GE corn, we use GE soy beans, we cure diseases with GE derived drugs. We have many examples of modified species. Not all changes are “engineered” but also derived through selection to optimize engineered changes. Entire commercial industries are based on genetics and evolution of these changes.

    Any careful study of DNA is full of examples of modifications that have led to different species. These were natural modifications that were not engineered but due to natural selection of individuals that lived long enough to pass their characteristics to their off-spring.

    If you truly want information, there is more than enough to convince people with open minds of the FACT of evolution.

    There is not one shred of verifiable, observable evidence that disproves the evolution of all life on Earth from very simple forms.

    Don't assert that because our current understanding of evolution does not explain every single detail, that evolution is not true.

    Is gravity a FACT? Yes or No? Well, if you said Yes, then what is the true nature of gravity? If you said No, then why are you not floating from the floor? We understand a lot about gravity but we cannot explain why it exists or why G is what it is or etc. There is a lot that we do not know about gravity. Yet, we accept gravity as FACT.

    We know a lot about evolution including the mechanisms in the cell for inheritance and how changes occur. We have observed examples where organisms have changed to have new capabilities that are passed to their off spring. For fast replicating organisms, a change can take place in human observable time frames as with the bacterium. Changes in the DNA take a generation per inherited change. Evolving a gene may take hundreds or thousands of generations and a gene pool large enough so that beneficial variants can arise.

    Genetic program development, a different way to create computer programs, have many, many demonstrations of code lines that have evolved using small variations, “sex” (successful programs exchange program segments like genes), and natural selection against a fitness requirement that are actually better than those written by people. Looking at the resulting code, provides insight as to the evolution including “dead” chunks of code that had function at one time but then by-passed when better code chunks evolved and clear modification of code that have optimized over the generations of changes. An examination of human DNA, chimp DNA, etc. provides similar insights and irrefutable evidence of the evolution of the DNA “code lines”.

    Like gravity, we don’t know everything. But, like gravity, evolution is FACT.

    If you want to wallow in your dogmatic ignorance, then I cannot help you. As Christians in the past had to accept a sun centered solar system as FACT, Christians today must accept evolution as FACT or forever be ignorant of Truth. I have tried to provide you with information from which you can determine what is true. It is your choice to examine the facts for yourself and make your own determination. There is more than enough information and facts already in this thread for a rational, intelligent conclusion.

    “It’s too hard for me to understand so God must have made it that way” is the core of ID and Creationism and thus, is a call for ignorance and intellectual failure. I do not believe that this is the conclusion that you seek.

    Dr. Starr, I am very sorry that this discussion has now degenerated to spouting of
    dogmatic responses and not one of seeking enlightenment. I cannot add any more to this thread. I really appreciate the information that you provided in the earlier entries and hope that the information that I have provided is helpful to others.

  • http://www.fiorentinoresearch.com jfiorentino

    "Dr. Starr, I am very sorry that this discussion has now degenerated to spouting of
    dogmatic responses and not one of seeking enlightenment."

    Perhaps if you didn't engage in such conduct, there would be no reason to apologize.

    Also, you are a PhD of some kind with an interest (apparently) in evolution, yet don't know what "Macroevolution" is? Amazing.

  • http://www.homeenergy.org Jim Gunshinan

    Hello All,

    I'm a fellow KQED Quest blogger who knows something about theology and science. It's difficult to have a cross-disciplinary conversation if one does not understand both outlooks. I find science and theology compatible, but not if we try to fuse them. The proper academic realm, I think, to discuss theology and science may be through philosophy, thought I'm not sure.

    I have been a part of too many discussions that devolve into both sides becoming intrenched. I tried in an earlier blog to reconcile my science and theology by saying that both depend on "stories" for example, the story of the earth's revolution around the sun, which used to be the story of the sun's revolution round the earth. One seemed like a true story for a while until it was replaced with another one.

    Just so in theology and the story of "sacrifice". The story of sacrificing human beings became the story of the sacrifice of animals, then grains, than Jesus' notion of self-offering out of love replaced these stories for Christians. We don't placate God anymore, but we are God-like, become part of the Divine Story, when we love.

    I guess some stories are just outright not helpful. I think of eugenics in science for example, or a literal interpretation of scripture.

    Don't know if this helps. I think that comparing and contrasting science and theology with attitudes of mutual respect is the way to go, not trying to fit science to into a theological perspective or vice versa.

    I appreciate these discussions though, because it helps me clarify my understanding of both science and theology!

  • http://www.fiorentinoresearch.com jfiorentino

    Hi Jim:

    Thanks for commenting.

    The dilemma here, I believe is what can be demonstrated with the purely scientific approach if one believes "design" rather than "evolution" is the answer.

    It's a very convoluted debate, and not really quite as simple as some may think.

    For me, I don't believe "ID" is science. It doesn't meet all of the criteria of pure science.

    The conundrum however, is IF indeed design is TRUTH, then how does one demonstrate that scientifically. The answer is you probably can't. That is why I believe most of the ID thought centers on picking apart evolutionary theory, demonstrating holes in that theory, etc.

    Here's an interesting thought to ponder:

    It must be remembered that there are only two basic models of origins, evolution and creation. Either all things have developed by continuing naturalistic processes, or they have not; there is no other alternative. Each model is essentially a complete world view, a philosophy of life and meaning, of origins and destiny. Neither can be either confirmed or falsified by the scientific method, since neither can be tested or observed experimentally, and therefore either one must be accepted on faith! Nevertheless, each is also a scientific model, since each seeks to explain within its framework all the real data of science and history.

    ……..and something else:

    Whoever decided that "science" should be defined as "naturalism," anyway? The word science comes from the Latin scientia, meaning "knowledge." True scientists are supposed to "search for truth," wherever that search leads.

    So, indeed we have a conundrum.

    Thanks again for participating!

  • http://www.thetech.org/genetics/ Barry Starr

    I gotta stop going on vacations (although I highly recommend Chester and Lassen Nat'l Park).

    This has indeed been an interesting discussion while I have been gone. As Jim said it does show that ID and/or creationism and science don't overlap completely.

    When we look at the fossil record and DNA, the best scientific explanation is evolution, hands down. As Ken points out, not every detail has been worked out but it is the best scientific way to explain the evidence around us.

    Of course, this doesn't rule out a designer (or God) who made things in a way that look like evolution to us. But as a scientist, there isn't much I can do with this. I can't prove or provide data to support design through experimentation and that is what scientists do, experiment.

  • Ken Oh, PhD

    Hi All

    Since there are others who may wish to continue the discussion, so shall I.

    FYI. My PhD is in EE/Comp Sci with a background in Physics from Stanford. I’ve found an interest in microbiology and the evolution of life based on the thesis of chemical metabolism and early RNA based “life” that then evolved to the RNA, DNA form of life on Earth.

    So, I am not familiar with the lexicon of the discussion of ID and Creationism and the tem “macro-evolution” must have some meaning as a ‘gotcha’ by ID. I suppose the example that was requested was for a full grown mammalian evolution of a new species rather than a bacterium.

    The term “species” is very ill defined. In the past, it was thought that species could not successfully interbreed and have viable off spring that propagate. The number of chromosomes was at one time thought to be a clear indication of different species. However, this has been shown to be incorrect as illustrated in the examples in this thread and many others.

    Chromosomes are the “packaging” of genes and the specific structures are not critical as long as the essential genes are complete. Hence, an egg with 33 chromosomes can join with a sperm with 32 chromosomes to form a viable off spring that passes its genetic information as half with 33 chromosomes and half with 32 as with the horses cited in an earlier entry. As long as all the essential genes are somewhere in the chromosomes, the organism is viable.

    A new “species” is created when the offspring lacks a gene that allows viable breeding with the parent stock and can only breed with those with the same set of genes. Again, the number of chromosomes may not be critical since these are only packaging.

    So the evolution of “species” is evolution of genes; really the collection of genes.

    I provided an example of the evolution of a gene through natural selection that synthesizes a protein that cleaves nylon. Nylon did not exist 73 year ago and until recently, nothing “ate” nylon.

    I provided many examples of genetic engineering that are so well known that these are commercial enterprises. People are alive today because of genetic engineering to synthesize human insulin in bacteria since 1982. Genetically engineered crop yields are now so high that countries that in the past imported from the US can now grow their own and this has been one of the factors in the current poor balance of trade for the US.

    Any good book on microbiology will teach the molecular under pinning of how all of this works. The amazing element is that all life, ALL LIFE, uses the same codes and nearly identical molecular structure. The various forms of RNA, the DNA code for amino acids used for protein synthesis, how DNA replication is done, etc. are essentially the same for ALL LIFE. The capture of chloroplasts by plants and mitochondria by complex cells is amazing and humbling. And all of this happened soon after the Earth had a solid surface in perhaps some 350 million years.

    Why the term “naturalism”? The rules of the game are that one cannot cheat and invoke magic that violates the observed natural processes. Luck is allowed but not magic.

    If a “proof” of Intelligent Design is desired, one cannot win by poking at scientific explanations and asking that it explain everything. “Show me this … Oh, you can’t? Then it must not be true.” does not provide any insight into ID nor disprove the science.

    As I attempted to explain, there are many elements of the natural world, gravity as an example, where we know a lot and accept as FACT but cannot explain everything. We do not know why it exists or why G has the value it has. We know a lot about the evolution of life on Earth from simpler forms. We know now that all life shares the same molecular structures and processes. We know how changes can occur and we even have made changes in living organisms. We have seen changes in the natural environment. We know a lot about life and evolution. But we don’t know everything.
    However, we know more than enough to assert as FACT that all life on Earth did evolve from simpler forms. Now with DNA analysis down to the specific sequence of bases. we can trace the changes among the organisms and hypothesize the sequence of events of the evolution. This is the state of the discussion among scientist. It is not a question of did it happen or how does it happen but rather what were the sequences of events that brought us to the current state.

    But there is a very much deeper fact that brings wonder and awe. The question in my mind is “Why is the Universe such that life can come into existence? Why does intelligent life evolve? What is our role in the Universe? “

    We are very special. With high probability, life began on many planets; perhaps even on Mars or the moons of Jupiter or Saturn. But few survive. Fewer still evolved intelligence as we humans have. While chimpanzees share a very large percentage of DNA from our common ancestor, it is very clear that chimpanzees or any other Earthly organism do not share our level of intelligence. On Earth, with highly diverse forms of life, only humans have evolved a high level of intelligence. So we are very, very special. But we are the result of the nature of the Universe. The Big Bang, nuclear synthesis to form carbon and all the elements to iron, the nova implosion forming the heavier elements including radioactive elements and blowing all of this into the debris cloud from which the sun, Earth, and our solar system were formed, the radioactive elements, the echo of the nova, keeping our core molten to support a magnetic field that shields our atmosphere and us from the solar wind, the molten core and early atmosphere that created the high energy molecules that fed the metabolic processes for early life like self replicating set of molecules to evolve to RNA, protein synthesis, and then DNA, and then life as we know it. It is clear to me that there is an emergent force that drives the creation and evolution of intelligent life.

    A Buddhist observed that “All things seek enlightenment.”
    I asked “Rocks, Trees?”
    “Yes. From nothing came the Universe. From non-life came life; from life came intelligence.”
    “Why?”
    “It is the Nature of existence. The real question you should ask yourself is ‘What should I do with the gift of life and intelligence that through great fortune has been bestowed upon me?”

    If it comforts you to believe that all of this is part of a Grand Design of a Creator, then we are not different in belief. However, I believe that the design does not require magic and that we can understand much of what is nature. I also believe that we will NEVER know everything. Just as quantum mechanics and general relativity have shown us limits as to what we can know, there are limits beyond which we will never know and will have to accept as just how things are. But only through scientific inquiry, investigation, and observation will we determine what is not knowable.

    We cannot accept “It’s too complex for me to understand so it must be magic.”

    I suggest that you think well beyond the shallow arguments of ID and Creationism which only invokes ignorance. Study what science can teach of what is known and understand the wonder and awe that is observable and true. Then search for the force that naturally created all of the Universe.

    Then ask “What is my role? What do I do with what I know?” We are special and with that comes great responsibilities.

  • http://www.fiorentinoresearch.com jfiorentino

    "I suggest that you think well beyond the shallow arguments of ID and Creationism which only invokes ignorance."

    Well, I know I'm many things, but I don't believe "ignorant" is one of them.

    "So, I am not familiar with the lexicon of the discussion of ID and Creationism and the term “macro-evolution”"

    The term "macroeveolution" is used all the time by evolutionary biologists. I'm surprised you weren't aware of this.

    You may wish to simply ask Dr. Starr if he feels I have no handle on evolutionary theory.

  • Ken Oh

    I have admitted ignorance of the term “macroevolution”. What in your mind is an example of macroevolution?

    Again, I ask what is the proof of Intelligent Design? Trying to identify gaps in our current understanding of evolution does not in any way “prove” ID or any other conjecture.

    Yes, we further our understanding of nature through identification of gaps and proposing a model, a hypothesis, that fill these gaps. But any model must also be consistent will all of the previous observations and explain these as well.

    General Relativity did not “overthrow” Newton but explained gaps in observation and also provided incredible insight as to the relationship of space and time which Newton did not do.

    If ID is to supplant evolution, then it must explain all that is already known and fill gaps with observable hypothesis.

    Ignorance is not stupidity or lack of intelligence or a character defect. Ignorance is the lack of accurate information. We are all ignorant of many things.

    Science searches for Truth and at times finds that nature will not tell us all that we want to know. But through science and our understanding of nature we find these limits. An example is the fact that we cannot determine both position and momentum of an object to infinite precision. This is a fact of nature that we now understand through models and observation. We know the limit because of Heisenberg’s Uncertainty Principle.

    However, ID or Creationism’s answer to hard questions is “it was designed that way or made that way” and thus just admits to ignorance. This is not a search for Truth but the slamming of the door to Truth. This is not Heisenberg discovering a limit of nature but just an absolute admission of ignorance and a denial of further investigation.

    Again, I assert that there is not one observation that refutes the evolution of all life on Earth from simpler forms of life. Our understanding of the actual mechanisms by which evolution occurred is incredibly rich and deep.

    If you wish to rid yourself of ignorance of evolution, there are links and references all through this thread and in book stores.

  • http://www.fiorentinoresearch.com jfiorentino

    "If you wish to rid yourself of ignorance of evolution, there are links and references all through this thread and in book stores."

    You continue to push a point which has no basis in reality, and champion a theory for which it is apparent that you are less than adequately versed.

    You assert that because I question evolution, I am somehow "ignorant" of it. That of course is absurd.

    My suggestion might be, that if you truly are a proponent of evolution, you should yourself understand exactly what that implies.

    "not one observation that refutes the evolution of all life on Earth from simpler forms of life."

    I would be more than happy to discuss this supposed evidence for the spontaneous generation of the animate from the inanimate.

    I would even entertain an interest in the progressive spontaneous generation of a SINGLE PROTEIN from an amalgamation of randomly generated amino acids. Any thoughts?

  • http://www.fiorentinoresearch.com jfiorentino

    JUST A WORD ABOUT LOGIC: or

    Finding things you're looking for………

    Below is a quote from the original article which kicked off much of this discussion by Monica Rodriguez, Stanford University……….

    "And the same thing is true with humans. We still aren’t sure the jump from 24 to 23 chromosomes is what makes us human. Like I said, it is certainly possible that we split from our ape ancestors before the difference in chromosome number. So in other words, humans may have become a new species for reasons other than chromosome number."

    The above of course "presupposes" common ancestry. But let's put that aside for the moment and see if we can intrepret this statement in another light. Not very hard, really.

    "We still aren’t sure the jump from 24 to 23 chromosomes is what makes us human."

    (There is absolutely NO evidence that that is the case.)

    "Like I said, it is certainly possible that we split from our ape ancestors before the difference in chromosome number."

    (This indicates the purported "fusion" might just as easily have occurred in the human lineage, rather than in some pre-human evolutionary scenario.) or put another way, (the "fusion" is NOT a conclusive indicator of "common ancestry" and statements to the contrary have no basis in fact.)

    "So in other words, humans may have become a new species for reasons other than chromosome number."

    (Or, humans were ALWAYS a distinct species)

    Now, if we could only relay that to people like Ken Miller!

  • http://www.thetech.org/genetics/index.php Barry Starr

    This blog is taking on a life of its own! I'll try to respond to various comments but if I miss one, sorry.

    So what can we learn from the fusion of chromosome 2? We can learn first of all that it happened. The evidence is strong enough on this one that it can't really be effectively argued against.

    The fusion had to have happened long enough ago for it to have supplanted the original 48 chromosomes. Either this or we had to be designed that way. If this is the case, then there should be some advantage to the fusion event. I have not yet seen one.

    We can learn more about the fusion event by looking at the ancient telomere and centromere DNA. Because this DNA is not being used, it is not protected from DNA change. In other words, over time, the centromere and telomere have built up DNA changes. This is where the 740,000 to 3 million years came from.

    The idea would then be that we have been on this Earth for at least 740,000 years without significant change.

  • http://www.thetech.org/genetics/index.php Barry Starr

    One other point. In science, it is not effective to simply point out where a theory is wrong (particularly one with lots of data to support it like evolution). This sort of thing works in law, for example, but science requires that a new scientific theory be presented which explains all of the previous data and solves whatever problems we saw before with the old theory.

    As John has pointed out, ID and creationism do not do this. They are alternative explanations but not scientific ones. What this means is that science does not have the tools to verify or test either idea.

  • http://www.fiorentinoresearch.com jfiorentino

    Well, since I like Barry so much, I'll simply drop the issue (at least on this blog)

    Personally, I think we should all take a soda break, and maybe even have some potato chips…….with ketchup on em of course!

  • Ken Oh

    To further substantiate a common ancestor of humans, chimps, and gorillas. All three DNA lack the gene to create vitamin C. Other mammals create vitamin C and the gene has been located. Common in the DNA of all three is the same gene but now ineffective due to mutations. The SAME mutations. The diet of the common ancestor included vitamin C so the defect in the gene did not affect it and the defect was passed to all of us.

    There are a number of identical “misspelled” defective genes shared by all three.

    Human DNA and chimp DNA are literally identical when the fusion of chromosome 2 and 11 inversions, where a section of a chromosome that broken off and fused in the reverse direction but the sequence of genes is clearly the same but simply inverted in the chromosome are understood.

    Again, I repeat, the chromosomes are just the packaging of the genes and as long as the gene is functional, its location is not critical. A gene on an inverted section of a chromosome functions as it did before the inversion.

    Comparison of the chimp DNA and human DNA leaves no doubt that there was a common ancestor. Examination of the DNA bases is an exacting science that provides measured results. Kepler used very accurate astronomical measurement to determine the orbits of the planets as ellipses and established to high accuracy the proof that the planets and the Earth orbit the sun. With these measurements, Kepler provided undeniable evidence of the FACT that the Earth orbits the sun. With the base by base examination of the chimp and human DNA and the accounting of the fusion and inversions, the differences between the two are so small that it points directly to a common ancestor from which these two DNA evolved.

    The difference between humans and chimps is probably not in the protein creating genes but in the homeobox and structure regulating genes. Hence, it is not surprising that humans and chimps share a significant percentage of the genes but develop different physical bodies. Small changes in the structure regulating genes and the interaction of the set of proteins in the cells are the differences.

    I do not believe the chromosome 2 fusion was the separating event since the genes still worked before and after the fusion. The fused and pre-fused beings were interbreeding just as the 44 chromosome horses and 46 chromosome horses. Changes in the structure regulating genes caused the separation from the common ancestor.

    There is no difference between micro evolution and macro evolution. All evolution is micro with changes in the DNA and resulting in changes in the physical bodies of organisms.

    I do no believe that random proteins was the start of life as questioned in an earlier entry. The protein soup will never create life. Start with RNA which also can be made from the juice, amino acids, of a Miller Urey process. There is research that supports an RNA self replication where a small set of simple RNA structures evolved in a high energy molecule environment where these molecules were metabolized by the early RNA structures. The ATP – ADP and AMP cycles are the energy molecules in all life so was a very early piece of the puzzle. By the way the “A” is the same A in RNA and DNA. RNA can serve as enzymes as do proteins. With very simple RNA self replication, then protein synthesis using RNA evolved. RNA was the repository of heredity during this phase of life. Finally, DNA evolved as the repository of the genetic information.

    Again, I assert that there is not one shred of evidence that all forms of life did not evolve from simpler forms of life. Yes, there are still questions that still need answers but this does not refute the FACT of evolution. The fact that we do not understand why gravity exists or why G has it value does not disprove the FACT of gravity.

    ID and Creationism is a call for ignorance. “It’s too hard to understand so it must have been designed or created” is not an answer but simply shutting the door to investigation; a submission to ignorance.

  • http://www.thetech.org/genetics/index.php Barry Starr

    The vitamin C example is an interesting one. Do orangutans have the same mutations?

    Ken is right that life would not start as random proteins. Life probably started out as an RNA world (see http://www.thetech.org/genetics/ask.php?id=110 for my take on the issue).

    There is certainly lots of data (most life scientists would argue an overwhelming amount) out there that supports the idea of common ancestry and lots of sites, blogs, etc. to dig up information on the subject (one of my favorites is http://evolution.berkeley.edu/).

    If macroevolution means the creation of a new species, then researchers at Stanford have done this with yeast (as have beer makers). See http://www.thetech.org/genetics/ask.php?id=143.

    As a side note, I think it is probably time to close this thread since at this point I think just Ken, John and I are paying attention. Any last comments? I am also happy to continue the discussion offline…

  • Ken Oh

    Dr. Starr

    I believe that orangutans also share the same mutated vitamin C gene. If I recall correctly, the mutation is quite old where prosimians have a functioning gene while the Anthropod branch lost the function.

    I appreciate all of your information and interesting discussion. This is the first discussion in which I have participated. I was always troubled by the chromosome 2 fusion believing that chromosome structure was critical and that organisms with different structures cannot interbreed.

    With your observation of the wild horses, I did a little more reading and some thinking about what chromosomes really entail. I believe that chromosomes are really just packaging and as long as cell division works and all the essential genes are functioning, organisms with different chromosome structures can interbreed and propagate these different chromosome structures. Has there been much research on this thesis?

    I can envision substantial analogy of chromosomes with how complex computer programs are packaged and function. In these programs, the functional subroutines are packaged in a number of files where each subroutine has an identifier. With most modern systems, the subroutine need not always be in a specific file but could be found in any accessible file. Using objects as the subroutine structure, objects can be changed without changing the identifier and the overall program functions with the changed object capabilities. This is parallel to changing a gene.

    The states of the internal cell structure, proteins, and DNA are ideal for analysis using the tools of computer science state machines. Are you aware of similar work?

    I had hoped that the religious aspects of the discussion could be explored with other participants. The ID / Creationist and frankly many devout Christians, Muslims, and some Jews view the question of evolution as either a belief in science or a belief in some great mystery that could give us the reason for our existence, role in the Universe, and how we should live our lives. They cannot conceive that these are not mutually exclusive.

    Dawkins and some others push this into the face of people of faith to debunk their beliefs and the folly of their denial of evolution and other observable characteristics of the Universe. These individuals are made to feel that they are like those who believe in a flat earth or earth centered universe. To them evolution is a dichotomy where admission of evolution is a denial of their faith. It is unfortunate that the ID / Creationists bring their beliefs into doubt by confronting a very provable element of science. “God in the gaps” is not viable and clearly not correct.

    In some of my entries, I had hinted on how religion and science can converge where religion need not feel that it must retreat with each new scientific understanding. Perhaps a discussion with an ID advocate is not the best forum since much of the polarization is already set.

    I really appreciate you allowing me to post. I really learned a lot.

    Again,
    Thank you

  • David H

    all good arguments, but if we are so much alike why are we so different it would appear to me there was intentional manipulation of our DNA to produce man. but not by god more in line by ET's and along with this manipulation came all the defects in our DNA that produce 1000's of illnesses that humans have, as you know according to evolution the mistakes or errors are breaded out, but not in humans, no matter what we have errors in our DNA within it and a certain number will always have some defect, do primates have the illnesses humans have, illnesses that are in the Genes, I think there is much more here than can be simply explained away as chance, Most animals do not have the defects in genes that humans have some scientist say our DNA has over 400,000 genetic defects that have been there from the beginning and still there, primates don't have this.

    • Barry

      Thanks for the comments. Our DNA is incredibly changeable, we all have 50-100 DNA changes that our parents didn't have. This is mostly a consequence of our cells making mistakes when they copy their DNA. This is the raw stuff of evolution. Some changes will be bad, some good. You can think about it as a constant sampling of different possibilities.

      You are right that the bad ones do get weeded out unless there is some reason they're not. We all know about the benefits of having just one copy of the gene that leads to sickle cell anemia and even diseases like cystic fibrosis have an advantage for carriers. Other genetic diseases like Huntington's disease happen after we're done having kids so they wouldn't be weeded out either.

      Plants and animals have lots of defects as well. One that comes to mind is albinism…sometimes an animal is born as an albino and it quickly ends up getting eaten. That genetic issue was hidden in its parents' DNA, only to be revealed in its offspring.

      What this all means is that there is a perfectly natural explanation for the "defects" in our DNA and so no need to invoke alien intervention.

      • Mike

        Your points are valid and food for thought. But the number of "defects" in a natural sense that humans display in contradiction to our great ape cousins are pretty numerous and drastic, to the point that it seems ill-conceived to allow these mutations to perpetuate.

        For example, the fact that we lost our coats of hair that all other apes use is baffling, since it's a step backwards to have to take the furs of other animals to simulate having the coat we once wore. Another example is our external nose. This seems like a pointless "bug" in the system, if you will, and would make an individual stand out strikingly from their non-mutated brethren. One would imagine this would make it difficult to find a mate.

        Our rapidly-expanded brain case and brain tissues are also intriguing, as well as the development of a highly advanced vocal system found in no other animal (that we know of).

        I guess my point is that there are a lot of factors here at play that we don't know enough about to simply dismiss every possibility except naturally occuring mutations and evolution. Indeed, in my opinion, it's our duty as a species to scientifically investigate and pursue every available avenue in the search for the truth.

        • Hawk

          Loosing the "coat" is an advantage in some ways, you can regulate your temperature by simply removing or adding clothing. Removing some of your clothing on a hot day means you can work much harder without overheating. And you can easily take your clothes on again when it gets cold at night.

          • paul shields

            So why do we suffer the weather more than any other creature.Naked we would die before most inferior species when exposed to the elements,adaption is our speciality but could you survive the artic without modern aid,NO and could you survive the sahara without modern aid NO,we are the only animal on the planet that is u,seless without technology,why would evolution create such a big dilemma unless evolutions unconcious intention was always the ability to traverse climates in short periods of time.

  • David H

    Check our Lloyd Pye he explains the defects, he is not on either side of the argument, but states real issues about defects and our DNA

  • Barry

    PS Remember that there is a perfectly natural way for chromosome number to change in a species too. In fact, as I talk about at http://science.kqed.org/quest/2010/03/01/and-then-there-were-44/, we can see it in action in a Chinese man right now.

  • paul shields

    1 in 1000 live births have a fused chromosome , yet Humans have remained Human.Chimpanzee's apparently mutated in the same way to pave the way for our seat in civilised existence,but for this theory to be feasible,surely the timescale would have created another positive muatation somewhere,and if not then the age old question remains the same. WHY US.

  • Minority_Report

    Wikipedia 'chimpanzee genome' tells us human chromosome 2 has distinctly human genes PGML/FOXD/CBWD , which were there "prior to the fusion event". This would indicate our first two ancestors were 'quite human' at the event of the first mating of 46 with 46. The meaning of the end-to-end fusion is telemeric failure, which will eventually kill all of us.

  • Zach

    Two chromosomes fusing would create less surface area giving the chromosome more pull, would it not? I don't know what kinds of effects that would have in any action with the fused chromosome.