The reality or otherwise of Common Descent

[Didymus]

As per the request in this thread, I am starting this thread to debate the question of common descent. I'm perfectly happy to kick off the discussion with a presentation of a tiny slice of the evidence biologists consider established common descent.

Common descent is a historical claim about the evolutionary past of organisms. It refers to the idea that all organisms are related to one another like a gigantic extended family. For example: five million years ago, chimpanzees and humans did not exist separately, but were represented by a single species. Approximately 4.5 million years ago that population underwent speciation and each new species (at that point very similar to one another), gradually diverged. According to all of mainstream biology, this principle holds true for all life, so that every species shares ancestry with every other at some point in the distant past.

To make this claim, biologists have a large amount of evidence that they think establishes common descent as a very robust scientific claim. The famous talkorigins '20+ evidences for macroevolution' article is actually a list of evidence for common descent, and doesn't actually have much to do with macroevolution as modern biology uses the term.

Rather than use that article here, I will instead go strait to the most authoritative sources I have access to, and give a quick summary of the overview of the evidence from Douglas J. Futuymas Evolutionary Biology 3rd edition, the most respected general textbook in the field.

Futuyma lists eight categories of evidence, each of which would require a fair amount of elaboration. I'll give the full list before expanding on one or two.
1. The hierarchical organisation of life.
2. Homology
3. Embryological similarities
4. Vestigial characters
5. Convergence
6. Suboptimal design
7. Geographical distributions
and 8. Intermediate forms.

I'll expand a little on 1 and 8 before throwing open the floor.

Life on earth exists in a nested hierarchy. This means that if you divide organisms into groups according to their features, you can then divide each of those groups into more groups without overlapping. So, if one divides the tetrapods from the arthropods, one can then pick out smaller groups; say, the mammals out of the tetrapods, and the insects from the arthropods, and those groups will not overlap in any new features that are not present in their parent groups. Meanwhile, if you try to group cars first by engine size, and then by colour, you'll find that there is a lot of overlap of features in groups that aren't present in those groups parent categories. So both red cars and blue cars can have both V6 and V12 engines, but triple segmentation with six legs is found only in arthropod groups (namely insects), while milk is found only in tetrapod groups (namely mammals).

This is evidence for common descent, because this pattern of nested hierarchy is produced by a historic pattern of descent and divergence, and by hardly any other types of processes. For example, tracing the surnames in a family tree yields a nested hierarchy: if one branch of the plantaginet family changes its name to plantaginet-smith, then you'll find plantaginet smith only in the larger plantaginet extended family. Only objects that have been produced by descent and branching fall into true nested hierarchies.

This fact about living things allows us to do all sorts of things in the exciting world of molecular biology. Nested hierarchies are what enable us to produce phylogenetic trees of life, which are essentially hypotheses about a particular pattern of descent. Using the same methods we now use to establish paternity from blood samples in court, we establish the relationships of species. The most striking thing is that we can yield the same phylogenetic tree by analysing just about any genetic feature: be it a gene, or mitochondrial DNA, or a particular protein sequence like hemoglobin, or most tellingly, endogenous retroviral insertions (I can expand on this last one if it's unfamiliar), the same tree keeps appearing again and again. This would be inexplicable if all species had separate origins, but is exactly what common descent predicts.

Now, to intermediate forms. Here, I will list the fossilised forms of three major evolutionary lineages, from three of my favourite books. I can't supply the diagrams, obviously, but I will give page numbers for anyone who wants to check up on me.

First, it should be established that according to the scenario of independent creation of organisms, intermediate sequences should not exist at all. Given that, the following three gradual evolutionary sequences establish the evolutionary history of these organisms: lizards to mammals, four-legged artiodoctyls to whales, and hyracotherium to modern horses.

From Ridleys Evolution text: The following fossils form a transitional lineage: Reptilian pelycosaurs to Ophlacodontids (which also gave rise to the famous Dimetrodon ), to the broadly varying Therapsids, from amongst whos number came the Cynodots, representing whom there are many individual specimens, such as(in approximate evolutionary order):

Procynosuchus
Thrinaxodon (here's another thrinaxodon)
Diademodon
Probainognathus

These specimens become increasingly less reptilian and begin to accumulate mammilian features over time. The latest cynodonts in this series blend neatly into the early mammals.

I'm running short on time, so I'll finish whales and horses quickly.

Refer to At the Waters Edge by Carl Zimmer for more information on this graduation from four legged pakicetus to modern whales:

Pakicetus, Ambulocetus, Dalanistes, Rodhocetus, Takracetus, Gaviocetus, Basilisaurus, Dorudon, Mysticetes (modern baleen whales). Googling these names might yield more information as well.

Refer to Strickberger and Monroes' Evolution textbook for more information on the transition from the small 55 million year old Hyracotherium, through the Oligocene Miohippus and Miocene Merychippus to modern Equus. This is a famously well documented transition, so it should be easy to find online resources.

But right now, I've made myself late. I suppose the topic of this debate should be: 'Do these observations, which are commonly advanced by mainstream biology, provide evidence for common descent?'

Good night and enjoy the debate.

[richic]

Endogenous retroviral sequences quite conclusively demonstrate common descent.

This seems to be quite a complex area of study but also full of data since it involves cancer research. Can you share the source that led you to reach your conclusion?

[jwu]

Ahh, sorry, i forgot to mention it.

Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

jwu

[richic]

Ahh, sorry, i forgot to mention it.

Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

jwu

I searched a little to try to find a Creationist spin on this issue. There's not much. Here's a link from an ID guy trying to answer the question although the answer seems to be more in the vein of let's wait and see because we're finding that these "junk DNA" sections may actually be highly functional. I don't think that's a direct answer, though. This may highlight how immature the ID theory is in relation to Common Descent. The fact is that the more we learn about genetic programming the more the ID argument will be refined or refuted.
http://acs.ucsd.edu/~idea/uncausedcause.htm

[Jose]

Ahh, sorry, i forgot to mention it.

Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.

jwu

Thanks! Now we can all look it up. Gene usually carries informational tidbits like this, that give us interesting information, but do not, of themselves, lead to major breakthroughs in molecular biology [at least, that's how I'd characterize my publications in Gene.]

I haven't had a chance to look up the data, but I'm guessing from the figure that you gave us that the arrows on the diagram, and their labels, refer to the "long terminal repeats" of the retrovirus (identical sequences at each end). When one of these viruses excises from the DNA, it often leaves one copy of the "ltr" behind. The arrows that identify specific ltr's by number are probably ones that are simply in some master-list. The ones that have extra notations (like q31.1) identify the location on the human chromosomes at which the retrovirus inserted, and at which it left an ltr behind when it excised.

I searched a little to try to find a Creationist spin on this issue. There's not much. Here's a link from an ID guy trying to answer the question although the answer seems to be more in the vein of let's wait and see because we're finding that these "junk DNA" sections may actually be highly functional. I don't think that's a direct answer, though.

Thank you, richic. I'd be interested in hearing what the Creationist spin would be. To find that there isn't one, after 4 years, suggests either that they can't think of one, or that this particular paper hasn't become a common argument against creation/ID. Maybe it will become one soon.

The "ID guy" you quote is right that "junk DNA" sequences may actually be functional. This conclusion comes from the comparison of human DNA sequence with mouse DNA sequence, and finding that there is a lot of DNA whose sequence is conserved--that is, the same in both species. The interpretation of this DNA as being functional comes from the following logic: sequences that have no function are free to mutate. Therefore, the farther two species are from their last common ancestor, the more different these sequences become (as mutations accumulate). By contrast, sequences that have specific functions do not accumulate mutations--because if they mutate, the individual organisms that have the mutations die, or are sick (natural selection selects against them). At this time, this evolutionary argument is the only one we have for some of these "junk DNA" sequences being functional. For actual genes, we can tell by "translating" the DNA sequence into protein sequence, but for what we used to call "junk DNA," all we have is evolutionary comparisons.

I'm not surprsied that the ID guys haven't come up with an answer yet. To say that "junk DNA is often functional" requires accepting the evolutionary argument AND the reality of common descent. They must be waiting for the molecular biologists to identify, by genetic engineering, the functions of some of these sequences. Then, they can present their argument as if we just happen to know the functions. In reality, the only reason we'd know which sequences to test for function is from the evolutionary comparison--but I'd bet they'll leave that part out of their discussion.

This is a really interesting point that you've brought up, jwu. These are new sequences, added to the genome well after "creation." We know how these viruses work, which is pretty much as you described. Therefore, we have no good reason to propose that God intervened and popped the viruses into the DNA at these specific positions. I particularly like your estimate of random probability--it's the "whirlwind in the junkyard" argument, but this time, it supports evolution, rather than creation. Very interesting, indeed!