Common descent

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While most anti-evolution Christian fundamentalists (indeed, most people), would gladly admit they do not understand quantum mechanics, and would not feel qualified to make a judgement about whether the theory is true or not, they have no such qualms when it comes to the Theory of Evolution. The theories of evolution (technically known as "the modern synthesis"), while fairly simple on the surface (as taught in the average high school), is just as complex as quantum mechanics when the vast body of different kinds of evidence that add up to a powerful proof of its validity is considered. The interaction in any organism among events taking place at the gene level, those taking place during an organism's ontogeny, and those taking place in the organism's interaction with the environment during its life, is incredibly complex. When a population of organisms is considered (all evolution occurs at the population level), and the interactions within the population and its interaction with the environment is considered, another layer of complexity is added. Yet fundamentalists and many others seem to feel that they are qualified to decide based on a gut-level feeling (or "evidence" in the Bible), that the theory must be invalid. The same is true of the science of geology, upon which rests much of the incontrovertible evidence for the age of the earth on which the modern synthesis depends.
 
While most anti-evolution Christian fundamentalists (indeed, most people), would gladly admit they do not understand quantum mechanics, and would not feel qualified to make a judgement about whether the theory is true or not, they have no such qualms when it comes to the Theory of Evolution. The theories of evolution (technically known as "the modern synthesis"), while fairly simple on the surface (as taught in the average high school), is just as complex as quantum mechanics when the vast body of different kinds of evidence that add up to a powerful proof of its validity is considered. The interaction in any organism among events taking place at the gene level, those taking place during an organism's ontogeny, and those taking place in the organism's interaction with the environment during its life, is incredibly complex. When a population of organisms is considered (all evolution occurs at the population level), and the interactions within the population and its interaction with the environment is considered, another layer of complexity is added. Yet fundamentalists and many others seem to feel that they are qualified to decide based on a gut-level feeling (or "evidence" in the Bible), that the theory must be invalid. The same is true of the science of geology, upon which rests much of the incontrovertible evidence for the age of the earth on which the modern synthesis depends.
  
 +
==Evidence against common descent==
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{{crickets}}
 
== See also ==
 
== See also ==
 
*[[Cladistics]]
 
*[[Cladistics]]

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Common descent is the theory that all organisms descended from a common ancestor. In other words, that worm you use to fish with is a distant cousin of yours, as is the fish itself. Same for the tree in your backyard, and all other life on this planet.

Charles Darwin was one of the first scientists to suggest and promote the idea. Virtually all biologists, except for a few reactionary fundamentalists, accept it. All living cells' and organisms' structures and functions are encoded in the same basic nucleic molecules -- DNA and RNA. Similarities in amino acid sequences between various organisms also suggest common descent, and the fossil record also shows cases where one plant or animal type evolved into different types over time. The details of the structure of this process are shown in clade diagrams.

Biologists believe the first common ancestor developed just under 4 billion years ago.

Contents

The Incontrovertible Evidence for Common Descent

At the heart of the anti-science, anti-intellectual movement that Conservapedia represents is its article on the Theory of Evolution. A quick glance at its entry there will reveal that much of the debate can be distilled into an argument against common descent. Once a person accepts common descent, the literal interpretation of the Bible is no longer possible and must be dismissed, which only causes problems for those who read the Bible literally and believe it is inerrant. Talk.origins has an excellent essay on over 29 pieces of evidence that prove common descent.[1] The goal of this article is to distill all that evidence down to a few key facts that cannot be explained through anything other than common descent.

The article is constructed to begin with a short description of each piece, and to point to why it is irrefutable evidence of common descent. Then each section will be expanded into more detail with included examples.

Powerful evidence for common descent

  • Anatomical homologies - Throughout the domains of life organisms show a distinct pattern of constraints based on homology in development and construction of the body. Tetrapods have five digits because the ancestor of tetrapods had five digits. When a tetrapod does not seem to have five obvious digits a review of their development will show that they start out with 5 and that they fused together later to form fewer numbers.
  • RNA code - Almost all organisms use the same three letter code for translating RNA into proteins. There are variations, such as the code used by mitochondria and some bacteria and fungi, but the differences are only minor. Regardless of the slight differences all organisms use the same coding mechanism for translating the code into amino acid sequences.
  • Endogenous retroviral insertions - These are inactivated viral genes that were inserted by ancient retroviruses. In order for a retrovirus to be inherited in all members of a species many highly improbable events must happen. The virus must insert into a gamete cell, it must mutate so it is inactive, that gamete cell must be used to make an embryo that lives to reproduce and whose genome fixates into the population. This is a very rare event, and ERVs are usually species specific and insert themselves nearly randomly into the genome of the host. The fact that we share ERVs with simians is proof we share a common genome. Even more than that, phylogenetic trees can be constructed based on the pattern of ERVS, humans share more ERVs with chimps than either share with gorillas. This is extremely strong evidence for common descent.
  • Pseudogenes - Shared errors are a powerful argument for a common source. If two text books describe the same event in similar language it's possible they just both converged on the same wording. But if they both share the same grammar or spelling errors it becomes impossible to say they did not derive from a common source. There are genes that no longer code for a protein due to a mutation or error. Species often share the same pseudogene, with the same inactivating mutation. A famous example of this is the L-gulonolactone oxidase which synthesizes vitamin C. All simians including humans share this pseudogene, but the guinea pig which also has an inactivated L-gulonolactone oxidase gene has a different mutation.
  • Embryology - The pharyngula stage of embryonic development appears to be highly conserved over time. At this stage it is difficult to tell the difference between various vertebrate species. This conserved state screams common ancestry, and the field of evolutionary development, which is highlighting the role of such things as HOX genes, has expanded our knowledge of embryo ontogeny to amazing new levels of detail. All thanks to acknowledging the fact of common descent.
  • Chromosome fusion - Chimpanzees have one more chromosome than humans do. If it is true we share a common ancestor we should be able to figure out what happened to that chromosome. Researchers have found it. Chromosome 2 in humans is actually the fusion of two chromosomes that have remained separate in the chimpanzee line. At the end of each chromosome is a marker called a telomere which usually appears only on the ends. But in human chromosome 2 it also appears in the center, marking where the two ends fused. Another knock down win for common descent.
  • Convergence - The phylogenetic trees constructed using anatomical homology, DNA homology, pseudogenes, endogenous retroviral insertions, and many other methods all converge on a similar looking tree. There are slight differences but the general relationships of the trees are intact. If all of these methods were flawed you would not expect each of them to converge on the same tree.

Anatomical homology

Anatomical homology refers to the parts of different species that look the same. These are particularly obvious when the outside is stripped away and the skeleton is examined. When the skeletal composition of multiple mammals, for instance, is examined it is clear that each share many common features. Human arms have similar bone structures to dog's forelegs, whale flippers and bat wings; specifically, two bones that make up the forearm section but a single bone above the elbow. Five fingers are also a common feature across many mammals and related animals.[2]

RNA / DNA code

All life shares a massive common feature, that of the genetic code based on the molecule DNA and it's related molecule RNA. The translation between DNA and RNA codons (groups of three bases) and the relevant amino acid is almost the same between all known forms of DNA based life on earth, from humans to bacteria. Where the translation between DNA, RNA and amino acid differs, it allows scientists to probe how creatures have evolved and where different taxonomic groups branched apart.

Endogenous retroviral insertions

A diagram showing the phylogenetic tree of primates constructed from shared ERV insertions along with when these insertions took place.

What is a retrovirus?

A retrovirus is a virus in the family Retroviridae. While many viruses use DNA to store genetic information, retrovirus use RNA. As infected cells will only replicate the retrovirus' genes if they are also DNA, the virus must rely on reverse transcriptase to transcribe its RNA into DNA and then insert it into the host genome. The retrovirus has significant clinical importance since HIV, which causes AIDS, is a retrovirus.

The retrovirus consists of a protein capsid, base, RNA genome, and the reverse transcriptase. Since RNA is never coded back into DNA in an uninfected cell and there is no endogenous reverse transcriptase in the cytoplasm the retrovirus must bring it with it. The discovery of reverse transcriptase in retroviruses has been a major boon for the biomedical industry where conversion of RNA to DNA is used in many genetic treatments and research.

Endogenous retrovirus

Reverse transcriptase is prone to making errors in transcription. Sometimes these errors will inactivate the retrovirus' genes and the host cell will not produce new viruses. These mutated strands of retrovirus DNA are still integrated in the host genome. In some cases in a multicellular organism this will be in a germ line cell. This means that the any offspring created from that germ line cell will have the inactivated retrovirus gene in its genome. These are referred to as endogenous retroviral insertions, it has been estimated that up to 10 percent of the human genome consists of these types of inserts.

ERV's are usually species specific, insert almost randomly in the host genome, and the error or mutation that inactivated the gene is random. If two organisms share the same ERV, in the same location with the same inactivation mutations than they must share them due to common inheritance and not two separate infections. Researchers analyze shared ERV insertions across species in order to construct phylogenetic trees.[3]

Pseudogenes and shared errors

What is a pseudogene?

Pseudogenes are genes present in an organism's genome that have lost the ability to code for proteins due to mutation. [4] They were first identified and dubbed in the late 1970s when researchers began finding non-coding regions in some organisms that were similar to actual coding genes in other organisms. [5] So far an estimated 19,000 pseudogenes have been identified in the human genome, this is almost equal to the total number of coding genes (21,000). [5] Humans have many pseudogenes including L-gulonolactone oxidase which is used to synthesize vitamin C. Research reports that this gene was inactivated in the common ancestor of all simians. [6]

Pseudogenes have been identified in a wide range of organisms from bacteria to mice to humans, the total number of pseudogenes in a given genome is not predictable but specific pseudogenes are often compared across species to elucidate complex evolutionary relationships. [5]

Pseudogenes are often difficult to parse from the large amount of non-coding base pairs in the genome. Convention requires two elements to be present to label a sequence a pseudogene. The first is homology which is the requirement that a sequence be demonstrated to descend from a functional copy of the gene and the second is non-functionality which is the requirement that the gene not code for a protein in the organism in question. [5]

Since all pseudogenes are asserted to be descended from a functioning gene the first step is to find the parent gene that it descended from. This is done by using computer programs to compare sequences of DNA across species. [5] This is a large computational problem but by keeping in mind the phylogenetic relationships between species the search time can be decreased by looking at species that share a more recent common ancestor.[7] Once a functioning copy of a gene is detected its sequence is compared to the pseudogene. A high correlation in base pairs is used to assign homology. Non-functionality can be demonstrated by attempting to transcribe the sequence in-vitro. [5]

Pseudogenes as shared errors

In copyright law there is a problem when determining if one source has copied another source because it is possible, particularly with topics in narrow sub-fields, that two authors could converge on a similar sounding passage to describe the same thing. However, errors in the passages are independent of the subject of the text and of each other. So multiple shared errors, particularly in grammar or spelling, become increasingly improbable for two independent creations. If there are several shared errors between two passages the only reasonable explanation is that one is a copy of the other, or that both were created by the same common source.

This same concept applies to pseudogenes. While it is possible that two genes might look the same because they both do the same thing, once an error invalidates a gene the sharing of this same error between two species can only be explained as the fact that they derived from the same source where the error first appeared. Using pseudogenes and analyzing shared inactivation mutations in these genes can be used to construct phylogenetic trees and as a proof of common descent.

Vitamin C and our simian common ancestor

One of the most famous examples of a shared error is that of Gulonolactone oxidase. This is because it is proof of a shared ancestory between humans and other simians. Gulonolactone oxidase is an enzyme that catalyzes the reactions needed to produce ascorbic acid (vitamin C). [8] This gene is present in most animals however it has been inactivated due to mutation in some. Animals that can no longer synthesize vitamin C include: simians, guinea pigs, and several species of fruit bats. Since these organisms consume a large portion of their diet in fruit the inactivation of the gene was not a significant detriment. Humans that fail to eat sources of vitamin C can develop scurvy.

The mutation that causes the inactivation of the L-gulonolactone oxidase gene is different depending on the group the organism is in. All extant guinea pigs share the same inactivation mutation, while all extant simians share a different one. The likelihood of two different species sharing the same inactivation mutation is statistically impossible and is actually shared due to common inheritance. The most recent common ancestor of all extant guinea pigs developed the mutation in the gene, while a different mutation developed in the most recent common ancestor in simians.

Embryology

Conserved development and the pharyngula

Pharyngula is the term used to describe the phylotypic stage of development in embryology.[9] Taxonomically diverse vertebrate embryos all seem to converge to a very similar morphology.[10] The term was coined in 1981 and stems from the characteristic pharyngeal arches that appear.[10] It is defined as:

The point during development when the basic body plan for a particular higher-level taxa is visible and when all the members of this taxon look most similar.[11]

It is thought by most researchers that this stage represents the basic vertebrate body plan in the common ancestor of all vertebrates.[10] Though there is some dispute as to how similar embryos are and to the reality of this stage. [12]

Their are six stages to embryonic development, and the pharyngula stage is towards the middle. In the early stages of development there is significant diversity in the morphology of embryos, this diversity decreases over time till the pharyngula stage where they are most similar (often difficult for anyone but trained embryologist to differentiate), and finally in the last stages of development morphology diversifies again. [13] It is hypothesized that the reason the pharyngula stage is so morphologically constrained is that this is the point where sequential activation of hox genes is initiated so any strong deviations from the developmental plan would lead to drastic changes in the final phenotype of the organism. [12]

Hox genes and ontogeny

Hox genes are a set of regulatory genes common in all life forms that seem to be largely responsible for orchestrating the ontological development of an organisms body plan. Hox genes are not expressed as proteins but rather act to turn on and off expressed genes in the genome to develop specific body parts such as eye stalks or arms. Early on in the development of the embryo patterns of hox genes will be turned on and off based on the cells position relative to other cells and the perceived orientation of the embryo (up/down, left/right). This pattern of activated hox genes will control the development of what anatomical features emerge. By activating hox genes in the lab or moving cells around once the hox genes are activated significant changes occur in morphology (such as eye stalks instead of legs). [14]

Hox genes are fascinating to study in all aspects of biology but they also offer several strong lines of evidence for common descent. One of the most striking elements of hox genes is that they are highly conserved. You can knock out a hox gene in a fly and replace it with a similar one from an earth worm and still wind up with a normally developed fly. Because the hox genes are so important to the development of an organism there is little room for mutation to create positive changes and so natural selection acts to conserve the basic structure. However, it could be argued this is also some how a product of a "common designer" (though there is no parallel in design that we know of). What really makes this powerful evidence for common descent is the pattern of the development of new hox genes.

New hox genes are usually created by duplication of old hox genes. With the redundancy from duplication one of the hox genes is freed up to be more susceptible to evolutionary changes. Researchers are able to take hox genes that are found in more derived organisms that are not found in more ancestral organisms and show how the new hox genes are slightly modified hox genes from evolutionary older organisms. It is then possible to construct phylogenetic trees for the actual hox genes. The amazing part is that this phylogenetic tree for the hox genes matches phylogenetic trees for the organisms themselves. This only makes sense from the view point of common descent.


Stripped pattern of a human chromosome 2 and the two corresponding chromosomes in chimpanzees. The patterns line up and the presence of telomeres in the middle and the extra centromere are clear evidence of a fusion event

Chromosome fusion

Another piece of evidence that makes clear the factual reality of common descent is chromosome fusion. This can happen in a wide variety of ways, across a wide variety of species. [15] Fusion of chromosome creates cases where descendant species have different numbers of chromosomes. You can also get splits that increase the number rather than fusion which decreases. The pattern of these fusion events allow for the creation of very intricate phylogenetic trees and offers proof of common descent.

One famous example is a fusion event that proves Humanity’s descent from a common ancestor of us and chimpanzees. [16] Humans have 23 pairs of chromosomes, all other great apes have 24. Something happened to shrink the number of chromosomes in the descent that led to Humans. This event was a chromosome fusion event. Human chromosome 2 looks almost identical to two of the chimpanzee's chromosomes stacked on one on top of the other. [17]

Chromosomes form light and dark bands on a karyotype that can be compared to see how similar they are. The light and dark banding patterns of the two chimp chromosomes match that of the single human one. Also on the end of each chromosome are a series of repetitive DNA sequences called telomeres. These sequences are only found on the tips of the chromosome. But for chromosome two you find them in the middle, as if the tips of two chromosomes merged together. Also chromosomes have what are called a centromere which link the two sister chromatids together. These are distinct regions on the chromosome and there is usually only one. But on chromosome two we find two centromeres. One is "non-functional" but its genetic code matches the other centromere from the second chimpanzee chromosome.

Clearly from this evidence it is clear that the human chromosome 2 is a fusion event between two chimpanzee chromosomes. This means that we inherited these chromosomes from a common ancestor with chimpanzees. Another home run for the fact of common descent and another strike out for "special creation." Humans are Great Apes. This is an irrefutable fact.

Convergence

Section in progress

What about the fossils?

Do fossils prove evolution?

Although fossils are usually not direct evidence in favour of evolution, a purely anatomical resemblance to living species is a form of strong supportive evidence.

However more recent fossils sometimes contain traces of tissue or DNA[18] which can be used to determine in what way the fossil is related to living species. As mentioned in the above sections, this offers direct evidence for evolution.

Various methods, ranging from tree-rings to radiometric dating fossils prove, without a doubt, that the world is in fact many billions of years old.

Transitional forms

Creationists often claim that no transitional forms have been found. This is certainly not true as numerous transitional forms have been found over the years.[19][20][21][22]

Of course one could always move the goalposts and keep asking for more transitional forms in between other transitional forms. For this reason it must be noted that fossilization is the exception to the rule (usually, cadavers decay completely) and that seismic, volcanic, tectonic and human activity have destroyed or buried many fossils.

"Transitional forms" is a bit of a misnomer anyway. A case can be made for all forms being transitional or none. All forms alive today seem to be very well adapted to their environment - none of them look obviously "transitional". The same would certainly have been true in the past. It is only with the benefit of hindsight that we are able to label forms "transitional - indeed the only forms that are not obviously "translational" are those with no living descendants or those which have survived to this day without change.

The Second Law of Thermodynamics

The Second Law of Thermodynamics is often cited against evolution. The argument being that life is more highly ordered than the "primordial soup" from which it came, therefore violating the second law.

This is entirely misplaced as this law deals with entropy, not the colloquial concepts of order and disorder which are used as analogies in its explanation. Entropy is related to heat flows and energy distributions and is in no way connected to the evolution of life, unlike natural selection.

Here is a more detailed description of the Second Law of Thermodynamics and entropy.

Fundamentalist hubris

While most anti-evolution Christian fundamentalists (indeed, most people), would gladly admit they do not understand quantum mechanics, and would not feel qualified to make a judgement about whether the theory is true or not, they have no such qualms when it comes to the Theory of Evolution. The theories of evolution (technically known as "the modern synthesis"), while fairly simple on the surface (as taught in the average high school), is just as complex as quantum mechanics when the vast body of different kinds of evidence that add up to a powerful proof of its validity is considered. The interaction in any organism among events taking place at the gene level, those taking place during an organism's ontogeny, and those taking place in the organism's interaction with the environment during its life, is incredibly complex. When a population of organisms is considered (all evolution occurs at the population level), and the interactions within the population and its interaction with the environment is considered, another layer of complexity is added. Yet fundamentalists and many others seem to feel that they are qualified to decide based on a gut-level feeling (or "evidence" in the Bible), that the theory must be invalid. The same is true of the science of geology, upon which rests much of the incontrovertible evidence for the age of the earth on which the modern synthesis depends.

Evidence against common descent

Tumbleweed.gif

See also

External links

Footnotes

  1. 29+ Evidences for Macroevolution on Talk.origins archive.
  2. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Taxonomy.html
  3. http://www.talkorigins.org/faqs/comdesc/section4.html
  4. Petrov, D.A, Hartl, D.L. (2000). Pseudogene evolution and natural selection for a compact genome. The American Genetic Association 91:221-227. [1]
  5. 5.0 5.1 5.2 5.3 5.4 5.5 Gerstein, M, Zheng, D. (2006). The real life of pseudogenes. Scientific American 95:48-55. [2]
  6. http://www.cast.uark.edu/local/icaes/conferences/wburg/posters/kmilton/kmilton.html
  7. Bensasson, D., Zhang, D., Hartl, D., Hewitt, G. (2001). Mitochondrial pseudogense: evolution's misplaced witness. Trends in Ecology and Evolution 16: 314-321. [3]
  8. Molecular basis for the deficiency in humans of gulonolactone oxidase, a key enzyme for ascorbic acid biosynthesis, American Journal of Clinical Nutrition, Vol 54, 1203S-1208S [4]
  9. Pharyngual Period
  10. 10.0 10.1 10.2 Irie, N., Sehara-Fujisawa, S. (2007). The vertebrate phylotypic stage and an early bilaterian-related stage in mouse embryogenesis defined by genomic information. BMC Biology 5:1. [5]
  11. Slack, J. M. W., P. W. H. Holland, and C. F. Graham. 1993. The zootype and the phylotypic stage. Nature 361:490–492.
  12. 12.0 12.1 Callazo, A. (2000). Developmental variation, homology and the pharyngula stage. Systematic Biology 49:1, 3-18. [6]
  13. Embryo Stages
  14. Pharyngula - The Hox Code
  15. Changes in chromosome number during evolution Talk Origins archive.
  16. MacAndrew, Alec Human Chromosome 2 is a fusion of two ancestral chromosomes. From evolution pages.
  17. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA, Origin of human chromosome 2: an ancestral telomere-telomere fusion. Proc Natl Acad Sci U S A 1991 Oct 15;88(20):9051-5. Available here
  18. Neandertal DNA Mark Rose ,Archaeological Institute of America [7]
  19. Fins to Limbs: New Fossil Gives Evolution Insight National Geographic, April 1, 2004 [8]
  20. Transitional forms Evolution Library, University Of Berkeley [9]
  21. Human Ancestry: Species ArchaeologyInfo.com [10]
  22. Transitions: The Evolution of Life [11]


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