The Living Transitionals Part I

Ever wanted to see a living transitional? There are many creatures today that give insights into possible evolutionary pathways of the past. There are creatures today evolving in the same way that many of their relatives did so long ago. For example, the snake evolved from lizards (by losing its legs) and today we have lizards who found it advantageous to shed the legs. There are mammals like the duck-billed platypus and echidna, who have held on to reptilian traits such as laying eggs. The walking catfish's habitats are "Warm, stagnant, often hypoxic waters such as muddy ponds, canals, ditches, swamps and flooded prairies." This is exactly the sort of environment created by droughts during the Devonian, leading to amphibians and later to reptiles. Watch it walk here.

There's the flying squirrel, who illustrates a path for the evolution of flight. Who knows? In a million years it could be like a mammalian bird.

Velociraptor had feathers

Tiny bumps on the fossilized arm bone of a Velociraptor specimen show that the carnivorous dinosaur — made infamous in the movie "Jurassic Park" — had feathers.

The finding, detailed in the Sept. 21 issue of the journal Science, confirms what scientists have long suspected about the creature as fossils of some of its close relatives bear imprints of feathers.

The researchers believe the bumps on the arm bone are remnants of quill knobs, places where the quills of secondary feathers — important for flight in many modern birds — were anchored to the bone.

"Finding quill knobs on Velociraptor means that it definitely had feathers," said study team member Alan Turner, a paleontology graduate student at the American Museum of Natural History and at Columbia University in New York. "This is something we'd long suspected, but no one had been able to prove."

Not for all birds
Quill knobs are most evident in modern birds that are strong flyers, such as falcons and hawks. Birds that have lost the ability to fly or that primarily soar, like broad-winged albatrosses, typically lack quill knobs.

While studying the forearm of a Velociraptor specimen unearthed in Mongolia in 1998, the researchers noticed six regularly spaced indentations in the fossilized bone that appeared remarkably similar to the quill knobs of modern birds.

In modern birds, secondary feathers are connected to the forearm by way of ligaments. When the feathers move, they place stress on the bone. “The bones respond to the tug of the feathers by developing these little bumps,” Turner explained. “The quill knobs are a side effect of how the feathers anchor.”

Velociraptor lived during the late Cretaceous Period about 85 million years ago and belonged to a group of agile, bipedal dinosaurs called Dromaesoaurs that were closely related to birds. It was roughly the size of a turkey and weighed about 30 pounds.

A prehistoric turkey
Despite having feathers, Velociraptor could not fly or even glide, Turner said.

“Even though it had really long arms compared to most carnivorous dinosaurs, they’re not long enough compared to the rest of its body,” Turner told LiveScience.

The researchers suggest that an ancestor of Velociraptor might have lost the ability to fly but retained its feathers anyway. The feathers might also have been used for display, to shield nests, for temperature control or to help the dinosaur maneuver while running.

The new finding is just the latest example of how remarkably alike modern day birds and their closely related dinosaur ancestors were, said study team member Mark Norell, a curator in the AMNH’s Division of Paleontology.

“Both have wishbones, brooded their nests, possess hollow bones and were covered in feathers,” Norell said. "If animals like Velociraptor were alive today our first impression would be that they were just very unusual looking birds."

The 'Hobbit' wasn't quite human

U.S. scientists, wringing their hands over the identity of the famed "hobbit" fossil, have found a new clue in the wrist.

Since the discovery of the bones in Indonesia in 2003, researchers have wrangled over whether the find was an ancient human ancestor or simply a modern human suffering from a genetic disorder.

Now, a study of the bones in the creature's left wrist lends weight to the human ancestor theory, according to a report in Friday's issue of the journal Science.

The wrist bones of the 3-foot-tall (0.91 meter) creature, technically known as Homo floresiensis, are basically indistinguishable from an African ape or early hominin-like wrist and nothing at all like that seen in modern humans and Neanderthals, according to the research team led by Matthew W. Tocheri of the Smithsonian's National Museum of Natural History.

That indicates that it is an early hominin and not a modern human with a physical disorder, they contend.

"It seals the deal," Tocheri said in a telephone interview.

The specimen he studied lived on the Indonesian island of Flores about 18,000 years ago, a time when early modern humans populated Australia and other nearby areas.

Scientists had thought humans had the planet to ourselves since Neanderthals died out about 30,000 years ago, and the discovery of Hobbits indicates another evolutionary cousin who coexisted longer, Tocheri said.

It is not known whether humans and Hobbits coexisted on that island, he said, but it is clear we shared the planet for some time.

"Basically, the wrist evidence tells us that modern humans and Neanderthals share an evolutionary grandparent that the hobbits do not, but all three share an evolutionary great-grandparent. If you think of modern humans and Neanderthals as being first cousins, then the hobbit is more like a second cousin to both," Tocheri said.

When the bones were first discovered some scientists declared them the remains of a new, dwarf species of human ancestors. Because of its tiny stature it was quickly dubbed the "Hobbit," from the creature in the books by J.R.R. Tolkien.

Dean Falk of Florida State University said the new report helps confirm that conclusion.

"This is exciting and should help settle things," she said. "The authors are to be congratulated, not only for describing important new details about 'Hobbit,' but for shedding light on the evolution of the wrist and how it might have related to tool production."

But others have questioned whether it was really a new species. Robert D. Martin of the Field Museum in Chicago and co-authors challenged the original classification, arguing that it appears to be a modern human suffering from microencephaly, a genetic disorder that results in small brain size and other defects.

There are things that can go wrong in the development of the wrist, Tocheri said, but they do not result in a complete change of design from modern human to chimpanzee or gorilla wrist.

Nonetheless, Martin said he is standing by his position.

"My take is that the brain size of (that specimen) is simply too small. That problem remains unanswered," he said in a telephone interview.

"People ask me whether this new evidence changes anything, well it doesn't," he said. "I think the evidence they've presented is fine, it's the interpretation that is problematic."

The Hobbit is pictured in the center

1.8 million year old hominids discovered

Paleontologists are examining the partial skeletons of a group of four individuals who died in what is now the Republic of Georgia nearly 1.8 million years ago.

Their remains -- the earliest members of the Homo genus found to date outside of Africa -- are telling much about how key body changes propelled this group's spread around the planet.

"Their lower extremities are evolving faster than their brain and upper extremities, and that seems to be what's necessary for taking them out of Africa and on a long trip to other parts of the world," explained anthropologist Jeffrey Laitman, director of anatomy at the Mount Sinai School of Medicine, in New York City.

According to the fossil record, mankind's ancestors arose from the first true bipeds, called australopiths, of which 3-million-year-old "Lucy" is an early member. They then went on to develop the larger brain capacity and more upright gait that characterizes the genus Homo, to which modern humans belong.

In Africa, the Homo genus included first Homo habilis and then the larger-brained Homo erectus. Both were increasingly comfortable walking upright on land over long distances.

In the early 1990s, scientists digging in Dmanisi, Republic of Georgia (between Turkey and Russia), came upon a remarkable find: The skull specimens of early Homo individuals dating to 1.77 million years ago. "When they were first described, it was really quite revolutionary to see material [like this] out of Africa," Laitman said.

The time period in which the four Dmanisi individuals -- three adults and one adolescent -- lived is called the Plio-Pleistocene age. "It's right around the time that we have the emergence and spread of the earliest members of the genus Homo," said Erik Trinkaus, a professor of physical anthropology at Washington University in St. Louis.

Members of the Homo genus gradually spread north and east of Africa beginning (as far as scientists can tell) about 1.8 million years ago. They spread relatively quickly, reaching Southeast Asia and Indonesia by 1.5 million years ago, Trinkaus noted.

And, according to the Dmanisi remains, their more human-like legs and feet may have helped get them there.

"Absolute hindlimb length of the Dmanisi hominins is greater than in australopiths and close to that of later Homo, including modern humans," wrote the Georgia team, which was led by David Lordkipanidze of the Georgian National Museum in Tbilisi. "This may reflect selection for improved locomotor energy efficiency," they explained.

Laitman agreed that it's no coincidence that Homo's spread was linked to their improved bipedal gait. The specimens "also show features of the transverse arch of the foot, the longitudinal arc of the foot, and a particular [movement] of the big toe" not seen before, he said.

And yet other parts of the specimens' skeletons lagged behind in terms of approximating modern humans. For example, their upper limbs fit into the Homo genus but retained some characteristics of australopiths, the researchers noted. The Dmanisi group was relatively small-statured, too -- about 5 feet tall and 100 pounds on average.

Most significant, their brains were only 600 to 775 cubic centimeters in volume -- less than half that of modern Homo sapiens.

To Laitman, all of this means that, "If you were going to go on a long trip, you didn't have to be a genius -- but you did need good feet."

This "mosaic" of features -- some more human-like than others -- means the Georgia researchers have been careful not to give their skeletons a specific taxonomic label, such as Homo habilis or erectus. "You're not yet having anyone saying which drawer in the museum desk these bones should be placed in," Laitman noted.


How Brown Evolved into Black

Perry Marshall has challenged evolutionists to show how it is possible to evolve the word Brown into the word Black without ending up with a nonsensical word.

I have accepted his challenge and will show how it is possible using only the sorts of mutations observed in nature.

1. Brown

2. Blown
A mutation causes the 'r' to change into 'l'

3. Block
A double mutation causes the 'w' and 'n' to become 'c' and 'k'
Double mutations have been observed to occur.

4. Black
The letter 'o' becomes 'a'

Now, keep in mind that this would not happen in his random mutation generator because it uses only muation instead of natural selection. It does not take into account the fact that mutations can become fixed in a population, nor that bad mutations are 'filtered out' by natural selection. It also does not recognize that words are different from DNA since DNA uses 4 letters while our alphabet is composed of 26 letters.

Endogenous Retroviruses Prove Evolution Beyond a Reasonable Doubt

I will begin this essay by quoting the intelligent design blog Uncommon 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."

So let's review: On a rare occasion a virus will
insert itself into it's host's genome at random, and
the host's descendants will inherit this and have the
virus in their genome. Our genome is 3 billion base
pairs, so it is extremely unlikely that any creature
would share the exact same virus in the exact same
place in the genome. But yet humans and primates do
have the same viruses in the same places in their

This article was written by Douglas Theobald, the
assistant professor of biochemistry at Brandis

In order to prove this truly is evidence of evolution,
let me consider the following questions:

(Some of this information was obtained from the Endogenous Retrovirus blog)

1. Is the viral insertion really random?
Yes. Here are two papers creationists use in support
of the nonrandom viral insertion hypothesis:

The first paper simply states that some retroviruses
like to insert in genes, some like to insert near
promoters of genes, and some like to insert in the
middle of no where. The specific insertion sites, what
base pairs on on the left, which ones are on the
right, is random. Thats exactly what they looked for
in that papers methods.

In the second paper the researchers found two
independent Viral insertions in deer mice. They could
tell the insertions apart because the virus had
infected two different places, because this event
happened twice.

So Retroviral insertion is indeed random.

2. Do the Viruses serve any good purpose?
No. When ERV's do become functional, they cause

In closing, you can google "endogenous retrovirus" and
pull up plenty of medical, scientific, and educational
websites. If you email the website, they will tell you
the exact same thing I am. You could also visit a
university and contact a geneticist who will provide
you with the same information.


What is an atavism? It's an evolutionary throwback. It's when an ancestral gene that has been "switched off" gets "switched on" again. It's the most bizarre evidence for evolution you've ever seen. One of the tamer examples would be the horses who are born with three toes, just like their ancestors. Even more bizarre are the humans born with true tails. Stranger still is the whale found with legs, feet, and toes. So how do we know that these are really evolutionary throwbacks and not just mutants? Well, as far as the three toed horse and legged whale we do not. The tailed human, however, is another story:

"Less than one third of the well-documented cases are what are medically known as "pseudo-tails" (Dao and Netsky 1984; Dubrow et al. 1988). Pseudo-tails are not true tails; they are simply lesions of various types coincidentally found in the caudal region of newborns, often associated with the spinal column, coccyx, and various malformations.

In contrast, the true atavistic tail of humans results from incomplete regression of the most distal end of the normal embryonic tail found in the developing human fetus (see Figure 2.4.1 and the discussion below on the development of the normal human embryonic tail; Belzberg et al. 1991; Dao and Netsky 1984; Grange et al. 2001; Keith 1921). Though formally a malformation, the true human tail is usually benign in nature (Dubrow et al. 1988; Spiegelmann et al. 1985). The true human tail is characterized by a complex arrangement of adipose and connective tissue, central bundles of longitudinally arranged striated muscle in the core, blood vessels, nerve fibres, nerve ganglion cells, and specialized pressure sensing nerve organs (Vater-Pacini corpuscles). It is covered by normal skin, replete with hair follicles, sweat glands, and sebaceous glands (Dao and Netsky 1984; Dubrow et al. 1988; Spiegelmann et al. 1985). True human tails range in length from about one inch to over 5 inches long (on a newborn baby), and they can move via voluntary striped muscle contractions in response to various emotional states (Baruchin et al. 1983; Dao and Netsky 1984; Harrison 1901; Keith 1921; Lundberg et al. 1962)."

Talk Origins

The whale with legs

Beneficial Insertion Mutation

E. Coli bacteria require 2 mutations in order to utilize salicin. In a lab, these two mutations were observed to occur and produce a strain of E. Coli that utilized Salicin.

"In growing cells the two mutations occur at rates of 4 x 10(-8) per cell division and less than 2 x 10(-12) per cell division, respectively."

That's pretty heavy odds, right? So I wonder how it could have been observed... Well, Another paper which cited this one stated that mutations occur at higher rates in stressful environments. Who says evolution is against the odds?

Birds and Dinosaurs

"Gigantoraptor erlianensis stood more than 16 feet (five meters) tall and weighed a ton and a half, or roughly 1,400 kilograms. Featuring a toothless beak on its head and a short tail for balance, the enormous birdlike dinosaur measured more than 26 feet (eight meters) in length. Living more than 65 million years ago at the end of the Cretaceous period, this big bird precursor has complicated the seemingly shrinking descent from Archaeopteryx to the modern sparrow."

"The finding complicates the evolutionary descent of birds from dinosaurs. 'Progressively from within advanced theropods you get smaller and smaller towards birds,' Norell says. But 'after some species originate and spring off the bird line, you get secondary gigantism.'

No one can say why for sure. 'Big size has some advantages such as having fewer predators and having more food resources that are unavailable for small animals,' Xu notes. But he adds that early oviraptorosaurs, this animal's ancestors, 'are among the smallest dinosaurs.'"

"So what did this prehistoric 'Big Bird' eat? Another mystery, as the animal bore no teeth in its jaw, had a small head and long neck (common in herbivores) but also sharp claws (common in carnivores). '[It] could be omnivorous,' Xu says. Norell adds: "Lots of things that have no teeth like hawks and eagles are pretty efficient carnivores.' It seems the world of dinosaurs—and bird ancestors—was as diverse as that of their latter-day descendants."

Portions of this are from Scientific American.


Remains of a petite dinosaur named Mahakala Omnogovae reveal that some of the ancestors of birds had already shrunk in size before flight evolved.

The dinosaur, a mere 2 feet long (70 centimeters) and weighing the equivalent of two cans of soda, roamed the Earth 80 million years ago during the Cretaceous period (between 146 and 65 million years ago).

"This specimen shows that dinosaurs evolved small size earlier than we previously thought," said study team member Julia Clarke, a paleontologist at North Carolina State University and the North Carolina Museum of Natural Sciences.

A prerequisite for flight is the ability to lift one's body off the ground. So for dinosaurs to take to the skies, they first had to "lose some weight." But did already-small dinosaurs shrink further in size after they took to the air and became birds? Or did they first shrink in size before they could fly?

Paleontologists had previously assumed it was the first scenario that occurred, but the new finding, detailed in the Sept. 7 issue of the journal Science, suggests otherwise.

"Paleontologists have long thought that miniaturization occurred in the earliest birds, which then facilitated the origin of flight," said lead author Alan Turner, a graduate student at the American Museum of Natural History and Columbia University in New York. "Now, the evidence shows that this decrease in body size occurred well before the origin of birds and that the dinosaurian ancestors of birds were, in a sense, pre-adapted for flight."

From LiveScience

New Fossil Find Changes Human Evolution

A new fossil find suggests that Homo Habilis and Homo Erectus lived side by side for a time, rather than the entire Habilis population evolving into Erectus. This has caused an outburst from creationists, but they're griping about nothing. The Theory of Punctuated Equilibrium explains this scenario beautifully. In the age of Homo Habilis, there surely would have been many populations; tribes, if you will. One isolated population could evolve over time, and then rejoin the main population. When it rejoined, it would have been different enough genetically not to interbreed. This is known to happen, it is shown experimentally in fruit flies. Anyway, once it rejoined the population, it would have competed with its parent species. Eventually Habilis went extinct, and Erectus became the dominant species. Now how's that for a just-so story? It is a story, don't get me wrong, but it does illustrate that the new fossils are not fatal, nay, not even damaging, to the theory of evolution. Richard Dawkins put it this way, "Why on earth should a species go extinct, just because some members of that species happen to have evolved into a different one? 'Sorry guys, some of our lot seem to be evolving into a spanking new species, so we'd better all die to make room for them.'"

Who's Kidneying?

I recently found out something really neat about the Evolution of Development (Evo-Devo):

Mammal Embryos develop 3 sets of kidneys.

The first (pronephros) is the same set found in primitive fish like Lampreys.

After 3.5 weeks, the mammal embryo replaces it.

The second set (The Mesonephros) is the same set found in higher fish and amphibians.

In human males it gives rise to urogenital structures, while in females the remnants are vestigial.

The third set (Metanephros) is the set which develops and becomes the adults set of kidneys, and it is the same set found in mammals and birds.

Neat, huh?

I also made this into a video here.


Hi, Welcome to Gill Slits! This Blog will be detailing evolution from my point of view. If you haven't already, check out my sister blog Answers in Genesis BUSTED! It is dedicated to exposing the lies of creationists. The Science Blog Pharyngula (another good site to check out) mentioned it and recommends it.