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.

[otseng]

No-one ever tries to put everything into the one diagram, because they would first need a piece of paper two kilometers wide! (approximately 2 million named species, allowing a centimeter per species along the top of the tree).

It doesn't have to be on a single sheet of paper. But, it seems like having a comprehensive diagram (in digital form) would be a strong evidence for common descent. And isn't that the goal of systemologists? To have a complete understanding of all the organisms (extant and extinct)?

If you have a look at the hominidae page of tolweb, one obvious near-node intermediate fossil is present. The name is Australopithecus, and fossils of that name are representative of populations near the chimp-human shared node.

Browsing through tolweb, I don't see many specific names of organisms near the nodes. The reason I keep getting back to this point is that transitory animals/plants should be abundant in the fossil record if common descent is true. If we use morphology as a basis for the phylogenetic tree, shouldn't there be an abundance of organisms in the fossil record whose morphology was a precursor to it's descendents?

Tolweb has a large number of these. Wherever you see a small gravestone symbol next to a lineage, it means the species is an extinct population represented by fossils. These are all named fossil groups that represent the population as it would likely have been at the nearest node.

I see where animals have been identified as extinct. But, I don't see any where it is at the base of a split.

Another question about the phylogenetic tree, how do you respond to allegations that morphology and molecular systematics produce differing
results? Bones, molecules, ... or both?

[ST88]

Most likely, it's an undesirable change, but because it's random, progress does happen.

My primary point is that when you inject random changes into any system of complexity (Java code, an encyclopedia, a car, air traffic control system), the results will almost in all cases be detrimental to the sytem, not beneficial. Taking humans as an example. Our genes are randomly being mutated and passed down. But, practically all the genetic changes results in diseases, not features that improve humans. We have a plethora of genetic diseases and no mutations that I know of that actually helps humans.

This is true. This is absolutely true. That random mutations occur and that almost all of them are diseases is part of the evolutionary process. The fact that these mutations occur in humans is another matter entirely. In the wild - not among domesticated animals or humans - there are relatively few persistent genetic diseases. Most, if not all wild animal diseases are caused by parasites. The genetic diseases that are present usually result in a very short life, or a very different life, for the offspring, so short that it does not have a chance to reproduce -- or so deviant from the rest of the population that no one chooses it for a mate -- and therefore does not introduce the undesirable mutation into the population.

Humans, however, are a special case. Whereas, in the wild, reproductive partners are chosen based on outward, physical and sensable (not sensible) characteristics, human reproductive partners are chosen based on more subtle forms of interaction. These characteristcs often do not have any single gene responsible for their existence, such as wit, charm, empathy, tenderness, etc.

If we were all intent on bettering the human species through the kind of reproductive selection that is found in the wild, we would all try to attract mates based on some singular human ideal, and all of our standards for beauty and attractiveness would be the same. Any genetic deviation from these standards would be left without a mate.

But because this is not the case, and because we have developed medical therapies to help alleviate our diseases, these genetic mutations do not disappear. Hemophiliacs, which nature would otherwise have little patience for, can flourish and multiply in a human society just as those of us who are not hemophiliacs do because of drugs and other therapies we have devised. This is evolution in practice. But instead of mutating to fit our environment, we fit our environment to our mutations.

Evolution as a process is not necessarily a progression towards the better. We can call a species a higher order because it is the result of a more recent natural selection event, but we can't necessarily always state that the most recent speciations are "better".

I would also argue that there are examples of the "improving" of the human species. There are certain individuals in the population that can resist HIV infection because of a genetic mutation found in their blood cells. There are others who will never get lung cancer no matter how much they smoke because of a genetic mutation in their immune system.

Sickle cell anemia, an inherited genetic mutation in certain African individuals, is actually an evolutionary defense against malaria. SCA sufferers are protected from getting malaria because of the structure of their blood cells. The disease, untreated, usually kills the individual between the ages of 20-40, i.e., it waits until after the individual has had a chance to reproduce and pass on the mutation. If a malaria epidemic hits a town or village, it may kill off just about every member except those with SCA, who then pass it on to their offspring. This could be seen as an evolutionary improvement, though it is not at all an improvement in a human sense.

I would also argue that the human body is so complex and has so many different systems within it that the only mutations we notice are the ones which make things worse. We would not go to the doctor, for example, if our eyesight were ten times better than average. We might not even know that this is anything special because it is the only reality we know.

[Oolon Colluphid]

Browsing through tolweb, I don't see many specific names of organisms near the nodes.

Browsing through Tolweb, I note that it is drawn up on cladistic principles, rather than more traditional (aka old-fashioned ) family tree principles. So it does not show the things at the nodes as being at the nodes, because under cladistics, everything is a branching-off.

Strictly, following cladistics, we don’t know if any fossil is on the direct line to any other one. Evolutionary lineages are constantly branching and bush-like. So any organism that gets itself fossilised and then found is unlikely to be on the specific line we’re interested in.

This does not mean that they are not transitional, just that it’s most likely on a side-branch that diverged from the one we’re after. They are transitional because their characteristics place them precisely on the many-branching bush. (Evolution isn’t deliberately going somewhere: it doesn’t have an end-point in mind, so each species is adapted to its own niche at the time... and so can have features that are not found in subsequent species too -- its own set of ‘derived characteristics’.

So you’ll see cladograms with Homo sapiens, say, at the end of the line, with a string of species more and more closely related branching off. Cladistic analyses therefore make the relationships far more quantifiable, testable, and so scientific. We don’t know if the fossil left descendants, but in itself it is quantifiably this much like modern humans, this much like the older species, and has these derived characteristics too.

So our actual lineage is made up of (something like, or actually) Ardipithecus ramidus, (something like, or actually) Australopithecus anamensis, (something like, or actually) A afarensis, (something like, or actually) A africanus, (something like, or actually) Homo habilis, (something like, or actually) H ergaster, (something like, or actually) H erectus, (something like, or actually) H heidelbergensis... and so on.

So everything is (likely to be) a side-branch, but we can tell how close it is to the actual line, and where it comes along that line. And interestingly, we can do that independently of the dates of the fossils... yet the dates coincide with an evolutionary progression from more ape-like to more human-like.

There is a simple intro to cladistics at Journey into Phylogenetic Systematics (don’t be put off by the title!)

The reason I keep getting back to this point is that transitory animals/plants should be abundant in the fossil record if common descent is true.

What makes you think they are not?

If we use morphology as a basis for the phylogenetic tree, shouldn't there be an abundance of organisms in the fossil record whose morphology was a precursor to it's descendents?

And there are. I could rattle off a list of early fish-tetrapods, feathered dinosaurs, mammal-like reptiles, whales with legs, Ordovician trilobites, polar bears (a new one for you Didymus? ), Eocene mammals... but these discussions always, at their heart, are about whether humans have evolved from (other) apes. And in that case too, we have plenty of intermediates. If you want fossils "whose morphology was a precursor to it's [sic] descendents", look no further than KNM-WT 15000. And then there’s all these:



I strongly urge you to look through the page Taxonomy, Transitional Forms, and the Fossil Record... especially since its author, Keith Miller, being a member of the ASA, presumably has no problem agreeing with the ASA Statement We believe in Creation.

I see where animals have been identified as extinct. But, I don't see any where it is at the base of a split.

That’s because you’re unfamiliar with cladistics. Try the link above!

Another question about the phylogenetic tree, how do you respond to allegations that morphology and molecular systematics produce differing results?

There’s a range of things that can confound both morphological and molecular phylogeneticists, but I’ll have to look up the more precise details. But the simple answer is: convergent evolution. The point is, we (well, not me, but the folks who do these things for a living ) are aware of the pitfalls, and by being aware, do their best to avoid them!

TTFN, Oolon

[otseng]

But this is what fruit fly genetic studies are all about. Bombard fruit-fly gametes with, what, gamma rays or something, and you get all sorts of odd results. The DNA is altered randomly by the gamma rays and the results are striking - individuals with multiple wings, multiple heads, multiple or missing legs and antenna, different colors, different shapes and sizes, etc. These kinds of mutations occur naturally, but much more sporadically and over millions of years.

In which case of the fruit fly mutations has it resulted in a beneficial morphological feature?

I'd also like to extend this question to, what evidence is there that any genetic mutation has resulted in a beneficial morphological feature?

[otseng]

Browsing through Tolweb, I note that it is drawn up on cladistic principles, rather than more traditional (aka old-fashioned ) family tree principles. So it does not show the things at the nodes as being at the nodes, because under cladistics, everything is a branching-off.

If everything is a branching-off, does it mean that it is not identified as to what could be on the base below a branch? What is the most comprehensive diagram available to show what specific animals are a common ancestor to multiple species?

There is a simple intro to cladistics at Journey into Phylogenetic Systematics

I wasn't able to read all of it, but the assumptions of cladistics intrigued me:

There are three basic assumptions in cladistics:

1. Any group of organisms are related by descent from a common ancestor.
2. There is a bifurcating pattern of cladogenesis.
3. Change in characteristics occurs in lineages over time.

Cladistics assumes common descent to be true. Therefore, cladistic analysis cannot be used to prove common descent, since it is one of it's assumptions. If the tolweb site is based on cladistics, then using it to support common descent is a circular argument.

If you want fossils "whose morphology was a precursor to it's [sic] descendents", look no further than KNM-WT 15000

I fail to see how the Turkana Boy shows development of morphology.

Taxonomy, Transitional Forms, and the Fossil Record

Very interesting site. I will add that to my bookmark list.

[ST88]

In which case of the fruit fly mutations has it resulted in a beneficial morphological feature?

The term "beneficial" is necessarily relative because it is not the mutation that determines the benefit to the individual, but the environment in which the mutation occurs. The environment determines which individuals have the adaptations necessary for reproduction. One environment may "encourage" one kind of adaptation and another may "encourage" another. In lab studies, this question is not meaningful, because the individuals studied have no need for competition of food sources or mates.

Let's take the mutated growth of extra legs as an example. In the lab, having an extra pair of legs is not an advantage nor a disadvantage. Excluding the possibility that these individuals might be sterile, they would have a chance for reproduction that is roughly equal to the whim of the experimenter.

But put this same individual in a wild environment. I don't know for sure, but it's possible that opposite gender fruit flies would view this multi-legged individual as not a viable mate because it doesn't meet the visual definition of one. It would therefore not reproduce. But let's assume that this is not the case, and there is an equal chance of reproduction with normal-legged individuals.

Fruit flies engage in a ritual of fighting, usually over food sources when food is scarce. There are different ways of fighting, such as sumo-style wrestling and something called "fencing", which involves tussling one's legs with another individual. Recent studies have not suggested a repeatable victory condition, so let's infer that the victor is the most successful intimidator. Now suppose that this multi-legged individual engages a rival for a scarce food source by fencing. Having more legs to fight with, would he have an advantage? Hard to say for sure, but in my estimation it's worth an experiment.

But let's take your argument on its face. Fruit flies are not the best animals to answer this question with because no researcher is going to let loose non-sterile fruit flies into the environment when there are too many of them already.

But we can answer this question with dogs. People have been breeding dogs (domesticated wolves, dingos, or some other kind of wild proto-dog) for thousands of years without even knowing about genetics. There are hundreds of variations on the dog currently in existence now, most from the same ancestor stock. They are all classified as the same species, canis domesticus, but they are all vastly different, and have adapted to their various roles as human companions and workers in a morphological as well as behavioral sense. This is true for many many other domesticated animals, but dogs are the most striking example.

Here's an interesting lecture on the rate of mutations in wild populations (it's kind of technical and doesn't focus specifically on this topic):
http://eebweb.arizona.edu/courses/Ecol435_535/Oct5.htm

[otseng]

But we can answer this question with dogs. People have been breeding dogs (domesticated wolves, dingos, or some other kind of wild proto-dog) for thousands of years without even knowing about genetics. There are hundreds of variations on the dog currently in existence now, most from the same ancestor stock. They are all classified as the same species, canis domesticus, but they are all vastly different, and have adapted to their various roles as human companions and workers in a morphological as well as behavioral sense. This is true for many many other domesticated animals, but dogs are the most striking example.

However, I would argue that dog breeding is a result of a combination of genes from it's parents that is explainable through Mendel's laws. Certainly no new morphological features are seen through breeding of dogs. Furthermore, as you stated, all dogs remain in the same species, so dog breeding cannot help explain common descent.

[ST88]

But we can answer this question with dogs. People have been breeding dogs (domesticated wolves, dingos, or some other kind of wild proto-dog) for thousands of years without even knowing about genetics.

However, I would argue that dog breeding is a result of a combination of genes from it's parents that is explainable through Mendel's laws. Certainly no new morphological features are seen through breeding of dogs. Furthermore, as you stated, all dogs remain in the same species, so dog breeding cannot help explain common descent.

Speciation is not as cut and dried as all that. "Species" isn't even a specific, rock-solid term that applies everywhere equally. We should expect that intermediate forms would have certain characters that we wouldn't recognize as part of a linear evolution process if we were not able to see further character changes, or an "end result" in a classification sense. That is, what is the criteria by which we judge whether or not a red spot that appears on some seabirds' lower beaks is an indication of a separate species, or merely a local adaptation?

Mendel's genetics explains variation within species for specific characteristics inherent in the species. The variation in coat color among wolves, for example. In order to argue that Mendel's genetic models apply to dogs, you have to assume that all the shapes, sizes, and features that are within the classification dog and that were descended from other dogs were specifically present in the original Wolf (or proto-dog) DNA. If you're willing to assume this, then more power to you. More on Mendel below.

But OK. We haven't yet bred a dog into a dolphin, so to speak. Some dogs are better swimmers than others (some can't swim), some have webbed feet, and some have a thicker coat for water protection, but you could argue they are all still "dogs".

Here are some across species matings that occur to produce viable offspring that are recognized as distinct. I have not included hybrids that are necessarily sterile.

Cross-species examples:
Liger (or Tigon): Lion-Tiger cross
Beefalo: American bison-domestic cattle cross
Wolphin: Dolphin-false killer whale cross
Jungle Corn Snake: corn snake-king snake cross

Would you accept a plant example?

It is possible to cross breed two distinct species of plant and get a third distinct species. The best example I can think of is the plumcot. Cross-breed an apricot with a plum, and you get a completely new organism, with a distinctive taste and morphology. Several varieties are readily fertilizable to prodice viable seeds.

THE LIMITATIONS OF MENDEL'S GENETICS

In the genetics of cats, there are some strange gene characteristics that can't completely be explained by Mendel's laws, or even the extentions to his laws. In almost all cats is the gene for the typical straight, radar-dish style ears. I say "almost all" -- every single individual in the cat family has this trait, except for two varieties: The Scottish Fold and the American Curl. In the Scottish Fold breed, the ears are folded down, so it looks like the cat is wearing a beret, sort of. The American Curl has ears that curl backwards. The American Curl gene has not been mapped, but the Scottish fold's has. It is a simple allele pair (ff, officially: fdfd).

The fold gene, and a few others in the cat family, behaves oddly different than what Mendel's laws say should happen. The trait for normal ears is a recessive trait (f), and the trait for folded ears is a dominant one (F). How is this possible? According to Mendel, the dominant trait in a simple allele pair such as this one should approach 75% phenotype penetration into a population (FF, Ff, Ff, ff). And yet there are many times more normal ears than folded ones. The answer is that it is a recent mutation. A single cat was found with this trait in Scotland in 1961. All current individuals have descended from this individual. Among Scottish Fold individuals, the dominance of the ear fold trait is readily apparent. The original breeding program yielded about 55/45 fold/normal* when bred with normal cats. This means that it would not have been possible for this gene to exist in its dominant form since the beginning of the cat family because then we would have roughly this ratio of cats in the world whose ears are folded.

Similar dominant traits include the lack of a tail and extra toes.

*Just by the way, the vast majority of phenotype folds are heterozygous (Ff) because of the way the breeding programs work. Fold enthusiasts don't like to breed phenotype folds to other phenotype folds, and instead breed them with "normal" cats to retain the characteristic. (Ff crossed with ff). This means that the usual ratio of phenotype folds to phenotype normals is about 50:50, which is more in line with the above example.

[ST88]

This message has been deleted by the poster.

[Didymus]

Just a note to say I haven't vanished into the ether. I'll catch up and make another post or two when I have my new semester ironed out.

In the meantime, cladistic phylogenetics can be used to support common descent, because even though it assumes common descent as a premise, it (or any other brand of phylogenetic analysis) would not work at all if common descent was not true.

I'm afraid that's all I have time for now. More soon!

Yours
-Timothy.