Freedom had been hunted round the globe; reason was considered as rebellion; and the slavery of fear had made men afraid to think. But such is the irresistible nature of truth, that all it asks, and all it wants, is the liberty of appearing.
~ Thomas Paine, Rights of Man, 1791 ~

Friday, May 30, 2014

Evidence for Common Descent: How we know we are apes.

Did we descend from apes? Are we related to all other animals?

Let's have a look at what I think is one of the best pieces of evidence supporting evolution: Our DNA.

Now, you may have heard that over 95% of our DNA is identical to that of chimpanzees. This is true. Depending on how it is measured, we share as much as 98.5% of our DNA with chimpanzees.

The typical counter-argument suggests that this merely points to common design, and on the surface that too would sound like a plausible explanation of the data. But there is a lot more data that doesn't fit the common design picture.

Before we get into that evidence, let's explore the similarities between human and ape DNA a little further.

Humans have 46 chromosomes (23 pairs). Apes have 48 chromosomes (24 pairs).

Each chromosome has markers on each end known as telomeres and a central marker known as a centromere. That is, except for chromosome 2 in humans. All other human chromosomes match up nicely with the equivalent ape chromosomes, except for chromosome 2. When we look closer at chromosome 2 we find that it actually has telomeres in the middle of it (as well as on the ends), and 2 centromeres as well. Looking closer again we can see that chromosome 2 is effectively 2 chromosomes fused together, and it actually matches up with two ape chromosomes. The best explanation for this is that two ape chromosomes fused together to form human chromosome number 2.


You can see actual images of the chromosomes in this article.

For a much more detailed and up-to-date explanation of the chromosome fusion in the human genome, read this excellent article.

But this is still not conclusive evidence for common descent. This is not sufficient to rule out common design.

So we continue on to more evidence from the field of molecular biology...

Transposons

As I am not a biologist, I am going to quote another source a lot. If you want to simply read this other source directly, you are quite welcome to do so.
"In many ways, transposons are very similar to viruses. However, they lack genes for viral coat proteins, cannot cross cellular boundaries, and thus they replicate only in the genome of their host."
"Replication for a transposon means copying itself and inserting the copied DNA randomly somewhere else in the host's genome. Transposon replication (also called transposition) has been directly observed in many organisms, including yeast, corn, wallabies, humans, bacteria, and flies, and recently the mechanisms have become well understood"
"Specific observed cases of retrotransposition are known to have caused neurofibromatosis and hemophilia in humans...and cancer, among other diseases"
"...finding the same transposon in the same chromosomal location in two different organisms is strong direct evidence of common ancestry, since they insert fairly randomly and generally cannot be transmitted except by inheritance. In addition, once a common ancestor has been postulated that contains a certain transposition, all the descendants of this common ancestor should also contain the same transposition."
"common Alu transpositions have been demonstrated to be reliable markers of common descent in paternity cases and in criminal forensics"
"Most importantly, in the human α-globin cluster there are seven Alu elements, and each one is shared with chimpanzees in the exact same seven locations" 
(emphasis mine)
Source

Endogenous Retroviruses (ERVs)
"Endogenous retroviruses provide yet another example of molecular sequence evidence for universal common descent. Endogenous retroviruses are molecular remnants of a past parasitic viral infection. Occasionally, copies of a retrovirus genome are found in its host's genome, and these retroviral gene copies are called endogenous retroviral sequences. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a DNA copy of their own viral genome and insert it into their host's genome. If this happens to a germ line cell (i.e. the sperm or egg cells) the retroviral DNA will be inherited by descendants of the host. Again, this process is rare and fairly random, so finding retrogenes in identical chromosomal positions of two different species indicates common ancestry." 
"There are at least seven different known instances of common retrogene insertions between chimps and humans, and this number is sure to grow as both these organism's genomes are sequenced"
Source

Could the theory be wrong?

The site also tells us how to prove the theory to be false. Happy hunting...
"It would make no sense, macroevolutionarily, if certain other mammals (e.g. dogs, cows, platypi, etc.), had these same retrogenes in the exact same chromosomal locations. For instance, it would be incredibly unlikely for dogs to also carry the three HERV-K insertions that are unique to humans...since none of the other primates have these retroviral sequences."
Source

There is a LOT more information on the talkorigins website.

I would strongly encourage you to spend some time there. This section is a great place to start.

I also came across this blog which contains more information on this and other evidence for evolution.

Summary

In case you were not able to follow the scientific details above, I will attempt to summarize it here very briefly.

Certain viruses and things called transposons can affect our DNA, essentially altering parts or our DNA and/or overwriting parts of our DNA with their own, leaving a type of "fingerprint" in our DNA. In many cases, this "fingerprint" is also passed on to our descendants. Since these viruses and transposons corrupt our DNA essentially at random positions, it would be extremely rare (likely impossible) for two species to have the same "genetic fingerprint" from one of these viruses in exactly the same location in their DNA, unless they were related (that is, they both inherited the modified genetic sequence from a common ancestor).

What we find is that humans and chimpanzees share many such fingerprints of retroviruses and transposons, in exactly the same positions in our respective DNA. In fact, the methods used to determine common ancestry between humans and apes have also been demonstrated to be successful in determining common descent in paternity cases and criminal forensics.

This supports the common descent theory but does not fit with the common design theory. Using the available genetic data, we can even tell roughly when in history each retrovirus fingerprint was inserted into the genome.

It is only in the last 30 years that we have been able to peer into our DNA and sequence the entire human genome and also that of the chimpanzee (and other animals as well). The findings from these projects have confirmed common descent so strongly that some scientists have claimed that even if we had no other evidence, the genetic evidence alone would be enough to confirm evolution.

15 comments:

  1. if we do come from apes, how come apes now don't become humans ?

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    1. We didn't just come from apes, we ARE apes.

      Your question shows a common misunderstanding of evolution.

      Do you know much about family trees?

      Do you have cousins? do they have different traits to you? Perhaps they look quite different to you? Your second cousins look more different to you than your first cousins. And so on. You didn't descend from your cousins. You share a common ancestor with your cousins (your grandparents), and that common ancestor does not look exactly like either of you but you both probably inherited some traits from them (and probably not the same traits). This is an analogy involving a short space of time. What about over a very long period of time?

      We didn't descend from modern apes. We share a common ancestor with them. We are their (VERY distant) cousins. The "apes" we descended from probably didn't look that much like the modern apes, and nor did they look like modern humans.

      In other words, we evolved from the common ancestor, and chimpanzees and gorillas ALSO evolved from that same common ancestor, who lived around 6 million years ago (confirmed by multiple lines of evidence including fossils and genetics). Our limited brain finds it difficult to comprehend such a vast amount of time, but there's no law that says nature should always instantly make sense to us.

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    2. Your question seems to infer that other apes aren't evolving, or that evolution occurs along a linear path. This is a misconception. Think of it like a tree branching outwards in many different directions. Humans are just one tiny branch. Chimps branched off much earlier, and Gorillas even earlier than that. They are each evolving into different species of their own, though still under the wider classification of "ape".

      Another point you may have missed is that evolution occurs over generations, and within populations, not in individuals and not in an individual's life span.

      As far as the evidence I have described, what do you think a paternity test is? If we compare your DNA to that of one of your parents and your grandparents, and then samples from the rest of the world, we will find that your grandparents have some mutations (probably minor/benign) that no other human has, and your parent would have inherited these same mutations, and probably also have some of their own. We know mutations occur essentially at random positions in your genome. This has been observed in laboratories all around the world. Suppose that no one else in the world has these same mutations, except you and your siblings (and you have exactly the same genetic signature, in exactly the same location in your genome, as your parent). Suppose that the same is true for some mutations unique to just your family line, going back say 2 or 3 generations. You would accept that this is strong evidence that your parent is indeed your direct ancestor, and likewise your grandparents etc. It's extremely unlikely that two people would have the same mutated genetic sequence in exactly the same place in their genome, unless they had inherited it from one or both of their parents. This is how paternity tests are done, and this evidence is strong enough to deliver a verdict in a court of law.

      Yet when we compare our genome with other apes, such as chimpanzees and gorillas, we find that we share a lot of similarities with them genetically, these very same kind of genetic signatures (as I explained in the above article). We share more of these genetic signatures with chimps than we do with gorillas, and more with gorillas than we do with old world monkeys. Scientists can actually reconstruct the entire evolutionary tree from the DNA alone, and it just happens to match up to the evolutionary tree that was developed before DNA was discovered (based on morphology etc).

      Just let that sink in for a moment. Before anyone even knew about DNA let alone the ability to read it, scientists had put together a fairly comprehensive evolutionary tree showing which animals were related to each other. Then we discovered DNA, and only in the last 30-40 years we have been able to map the entire genome of many animals including humans, and when we construct the family tree from the DNA alone, lo and behold it matches pretty much exactly with the tree that the scientists had already developed based on morphology. This evidence seems very difficult to explain any other way.

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    3. One last point I want to make before I take a rest, is that scientists have put together a very comprehensive "tree of life" showing which animals evolved from which other animals.

      If we were all separately created, how could such a tree be possible to create?

      Not only does the tree fit together amazingly well, it also fits the time scales and the dating of the fossils.

      All you would need to disprove evolution is to find one single fossil from the wrong time period compared to its place in the tree (the popular example is "rabbits in the pre-cambrian" era). This has never happened, despite new fossils being found all the time.

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    4. Forgot these links to tree of life diagrams:
      http://tolweb.org/tree/

      http://en.wikipedia.org/wiki/Tree_of_life_(biology)

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    5. A further way you might understand evolution is to look at domesticated dogs.

      All domesticated dogs alive today originally descended from wolves. All of the various breeds of domesticated dogs are the result of selective breeding (by humans) over many generations. This is known as artificial selection because in this case humans did the selection, in order to produce dogs that had a more desirable temperament etc. Compare this to natural selection, where it is nature that performs the selection. That is, those animals that are better suited to their environment will survive and pass on their genes, and those less suited to their environment will not.

      So when we look at the diversity of dogs, we can see how many different forms can "evolve" over time, from a common ancestor.

      Suppose someone asked you the question:
      "If dogs descended from wolves, why are there still wolves?".

      This is pretty easy to figure out. Dogs didn't descend from modern wolves. Both modern wolves and dogs descended from a much earlier species of wolf.

      Now apply the same logic to humans and other primates.

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  2. So the early man looked like an ape but gradually evolved to look like now modern human, yet apes from the beginning stayed apes ???

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    1. Are you trolling?

      Here's the exact quote of what I said in my above comments:
      "The "apes" we descended from probably didn't look that much like the modern apes, and nor did they look like modern humans."

      In any case, not all animals evolve at the same rate. It varies wildly depending on what selection pressures and mutations rates are occurring within the population.

      Rather than asking uninformed questions, please start here and come back when you've understood the basics of evolution:

      http://evolution.berkeley.edu/evosite/evo101/IIntro.shtml

      It doesn't make any sense to try to disprove something which you don't fully understand. Therefore if you want to ask informed and meaningful questions about evolution, you will need to do some reading first. I'm happy to attempt to answer any questions you might have as you work your way through the material. Good luck!

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  3. The radioactive carbon 14 dating of fossils and rocks (or anything) relies on a massive assumption......that the level of carbon 14 in the atmosphere has always been constant. Very unlikely as we know the atmosphere has changed over time, the changes fit in with God's word according to the appearance of plants and then humans and animals. Carbon 14 dating is an erroneous theory based on an incorrect assumption. The World is not millions of years old (as apparently proven by this technique. Additionally, many of the fossils etc that have been 'proven' to be this and that age are incorrect based on this science.

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    1. Firstly, rocks are not dated using carbon 14, because they obviously don't contain any carbon, which makes me doubt your claim to be "a chemist". This is simply a classic creationist misunderstanding of the subject. The same applies to dating fossils older than say 50 million years, because the decay rate of C14 is known and there wouldn't be enough of it left in such fossils to produce an accurate measurement. Scientists test this. I can find you the papers on it if you would like to read them.

      Secondly, yes carbon dating does rely on some assumptions but those have been thoroughly tested. For example, it relies on the assumption that the decay rate of C14 has been constant over time.

      "Supernovae are known to produce a large quantity of radioactive isotopes (Nomoto et al. 1997a, 1997b; Thielemann et al. 1998). These isotopes produce gamma rays with frequencies and fading rates that are predictable according to present decay rates. These predictions hold for supernova SN1987A, which is 169,000 light-years away (Knödlseder 2000). Therefore, radioactive decay rates were not significantly different 169,000 years ago. Present decay rates are likewise consistent with observations of the gamma rays and fading rates of supernova SN1991T, which is sixty million light-years away (Prantzos 1999), and with fading rate observations of supernovae billions of light-years away (Perlmutter et al. 1998). "
      http://www.talkorigins.org/indexcc/CF/CF210.html

      You are correct that early forms of the technique relied on the assumption that the level of C14 in the atmosphere remained constant, but that assumption was also tested and the techniques updated to account for changes in atmospheric C14.

      "In the early years of using the technique, it was understood that it depended on the atmospheric 14C/12C ratio having remained the same over the preceding few thousand years. To verify the accuracy of the method, several artefacts that were datable by other techniques were tested; the results of the testing were in reasonable agreement with the true ages of the objects. Over time, however, discrepancies began to appear between the known chronology for the oldest Egyptian dynasties and the radiocarbon dates of Egyptian artefacts. Neither the pre-existing Egyptian chronology nor the new radiocarbon dating method could be assumed to be accurate, but a third possibility was that the 14C/12C ratio had changed over time. The question was resolved by the study of tree rings: comparison of overlapping series of tree rings allowed the construction of a continuous sequence of tree-ring data that spanned 8,000 years. (Since that time the tree-ring data series has been extended to 13,900 years.)"

      https://en.wikipedia.org/wiki/Radiocarbon_dating#Atmospheric_variation

      The Wikipedia article goes on to explain how it works now and the various ways in which it has been tested.

      Did you get your material from a creationist website? A little extra reading could have provided the answers you assumed did not exist.

      I'd also recommend reading this article to find out why your claims are incorrect. If you want to know, that is.
      http://www.talkorigins.org/faqs/hovind/howgood-c14.html

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    2. For anyone who is actually interested in how the age of the earth has been calculated (and it isn't just via one method, but rather multiple lines of evidence converging on the same understanding), have a read of this one:

      http://www.talkorigins.org/faqs/faq-age-of-earth.html

      And a bit more light reading on how fossils and rocks are dated:
      http://www.talkorigins.org/faqs/dating.html

      One important thing to point out, which the first article explains in detail, is that the decay rates of several isotopes used for radiometric dating are known and have been demonstrated to be constant over time, spanning back at least hundreds of thousands of years. In addition, rocks have been dated using various isotopes to yield the same result. It's inconceivable how this agreement between methods could happen if the methods were as unreliable as creationists claim.

      When I was a creationist I had this naive belief that scientists worked from naturalistic assumptions and arrived at incorrect conclusions because those assumptions were incorrect. I was proven wrong (in fact I was the one who held naive and incorrect assumptions about science), and eventually changed my mind. The truth is that while scientists do make assumptions, those assumptions are always tested, and scientists go to great lengths to test their methods and assumptions to see if they are reliable. They also go to great lengths to look for flaws in their own methods and then test for those as well. There has been so much research in this field and most non-scientists are simply unaware of it.

      Going back to carbon dating, contrary to what many creationists seem to think, it has been tested against samples of known age, many times. The wikipedia link in my earlier comment even shows examples of this. Here's another one:

      http://science.sciencemag.org/content/110/2869/678

      Perhaps it is the creationists who hold incorrect assumptions about how scientists determine the age of the earth, rocks, and fossils. The information is available on the internet, but will they search for it?

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    3. There's another way to prove that the Bible's literal description of where species came from is wrong, even without relying on radiometric dating. That is, the order of creation in Genesis 1 (and 2) differ from what we find in the fossil record. Even if you doubt the actual dates given by science, it's a lot more difficult to dispute the sequence of ages of various fossils.

      Fossils are often found in layers of sedimentary rock. The study of these rock layers is called stratigraphy (Google it). Scientists understand how these layers were formed, and generally lower layers represent earlier time periods. Thus, fossils found in lower layers represent animals that lived (or rather, died, but you get the idea) at an earlier time than fossils in higher layers. And when we look at the fossil record, we find that the layers are fairly well sorted with more complex animals in higher layers and less complex ones in lower layers. Occasionally some series of layers in a particular region may be upside-down, due to geological activity such as earthquakes, which tends to confuse creationists. But in any case the sequence is known and it directly confirms the idea that fossils represent long ages of earth's history, and that populations of living organisms gradually became more complex over time, and over many generations.

      This sequence disagrees with Genesis 1, because it puts marine organisms before plants, to give just one example. We also don't find humans or other young species in lower layers (and I think human fossils are rare by comparison to much older fossils) and we don't find trilobytes at higher layers.

      It is also obvious (at least to Geologists) that each rock layer represents a long period of time, and the nearly 40 major rock layers in the Grand Canyon were laid down in separate geological events, not a single flood. Floods tend to deposit a single layer - which can be demonstrated very easily.

      I offered more detail on this and other evidence in a recent article here:
      What is the evidence for evolution, and why do people believe it?

      What do creationists say about fossils? Well, many of them suggest that all fossils were formed during a global flood, but if that were true it is rather puzzling that the fossils are ordered so (relatively) neatly. They argue that more complex animals like humans were able to move to higher ground to escape rising flood waters more easily than smaller, less complex animals (like trilobytes). That might even sound plausible to some people, but then you'd have to explain why birds survived but flying dinosaurs didn't. You'd also have to explain why plant fossils and marine fossils follow similar ordering as well.

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    4. "but then you'd have to explain why birds survived but flying dinosaurs didn't"

      Sorry, that should be "why birds made it to higher ground". I was talking about fossils...

      Delete
  4. I never use Wiki (but you do as your references show). I have a 1st class honours degree in applied chemistry from The University of Warwick. OK, I generalised a little for the non-scientists (are you one...I think not) on the C14 dating, I should have called it radioactive dating. Sedimentary rocks make up 75% of the Earth's surface and can be C14dated. The rock cycle recycles rocks over time, today's igneous/metamorphic rock was originally a sedimentary etc. Further reading from the latest scientific research which IS highlighting problems with RA dating: http://www.cs.unc.edu

    Your mind is as closed now as it was when you were a CD. I am not a CD I never said I was!

    Over and out........I won;t be back.

    ReplyDelete
    Replies
    1. I use Wikipedia simply because it often provides a good overview of various topics and it is a good starting point for discovering consensus views and various other viewpoints on a particular topic. If you don't like Wikipedia you're welcome to follow the references and do your own research. I don't claim to have the last word on anything.

      Congrats on your degree in chemistry. I am not a scientist, but I tend to follow the consensus.

      I don't consider "carbon dating" or "C14 dating" to be a generalisation for "radiometric dating". It's like a biologist calling all primates 'human'. C14 dating is a form of radiometric dating but the reverse is certainly not true. There's no reason to use the incorrect terms "for non-scientists". Just call it what it is (radiometric dating), and non-scientists can look it up if they want to.

      Again you claimed that Sedimentary rocks can be C14 dated. No, they can't. C14 dating is used for once-living organisms, because they contain carbon 14. Rocks don't contain carbon 14. I don't know why you'd keep using the wrong terms even after I pointed this out.

      You gave me a link to a university, but did not link to anything specific. Do you want me to read through all of that university's information? Why?

      My mind is as closed on evolution as it is on germ theory and atomic theory. It's hypothetically possible that some new evidence might prove them wrong, but it's extremely unlikely at this point.

      I never said you were a CD either.

      Please do let me know when radiometric dating is disproven in the scientific literature. That would be huge news!

      Delete

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