Thursday, August 30, 2007

Endogenous Retroviruses

The Endogenous Retroviruses that we share with chimps is one of the strongest pieces of evidence there is for evolution. And of course who else but Answers in Genesis would challenge this? The first thing that should be addressed is the claim that endogenous retroviruses are beneficient to the host. Blogger Abbie Smith has given the answer to this:
"As a defense against the argument that 'junk DNA', including nonfunctional ERVs, is evidence against their choice* of 'Designer', Creationists insist that ERVs are functional.

There is a very big difference between a functional ERV, and a functional component of an ERV. Creationists do not understand this (specific example here)

Yes, we have found a retroviral env that has been co-opted by mammals. Yes, somewhere around 100 human proteins might have evolved from co-opted gag proteins. Yes, we can find retroviral transcripts floating about cells, sometimes. But these are not examples of ERV functionality. They examples of evolution in action-- the host organism salvaging ERV parts for its own use.

Complete ERVs are recombined, mutated, and methylated into junk. When they regain some semblance of functionality, they cause disease! Which is no surprise, as exogenous retroviruses like HIV and HTLV cause AIDS, leukaemia, lymphomas, and various other autoimmune diseases.

ERVs specific to humans, called HERVs, have been tied to multiple cancers, including germ-cell tumors, breast cancer, seminomas, melanoma, ovarian cancer... And autoimmune diseases like multiple sclerosis, rheumatoid arthritis, psoriasis, and lupus (please see this source for more information).

These are just the human-specific ERVs. We have lots more."

Read here original post here.

So ERV's are still powerful evidence for evolution since they are inserted randomly into the genome and yet we find them in the same places in related organisms.

Wednesday, August 29, 2007

The Politically Incorrect Guide to Science

I was in a bookstore today and came across the Politically Incorrect Guide to Science. Anyway, it had a section on "Darwinism" and I thought I'd address that section, so here goes:

p.202 Offers a critique of Science's methodology of Naturalism, as "No Miracles Allowed". They say that if you would never accept a miracle no matter what, of course you're going to accept evolution. Well, I'm here to correct this. The reason Science doesn't allow miracles is because you could prove practically anything if you were allowed to include unobserved supernatural phenomena as proof. Of course, science has the option of simply saying "We don't know"; and if creationism was true, I would expect that all living forms would have arisen all of a sudden by some unknown force, and this would be excellent evidecne for creation. Unfortunately, that isn't what we see. Dinosaurs didn't live with man, catfish didn't live with trilobites, and daffodils weren't around in Triassic Period.

p.204 Claims that while we do see some intermediates, we cannot possibly prove that one form is really ancestral to another. This is certainly true, but let me say this: When we find mostly fish in the Devonian Strata, and in the next Strata we find amphibians, and in between these forms is a fish who had strong limbs that could enable it to move on land, it makes you think that one of these basic forms gave rise to another over time.
"Tiktaalik" and "Panderichthys" show this transition.

p.207 "Natural Selection is a Truism"
Yes, this page the old misunderstanding that the fittest are so because they survive, and they survive because they are the fittest. Allow me to clarify: Those born with traits most favorable to survival will, on average, leave behind more offspring than those with less favorable traits. There are shifts in gene frequencies caused by this: A new mutation can become prevelant in a population due to natural selection at work.

p.216 The Evolutionist's Challenge
Colin Patterson is quoted as asking, "Can you tell me... anything about evolution that you know is true?"
I would like to answer this challenge. I know that we share a common ancestor with chimps. I know this because we have viruses in our genome that are in the exact same places in the chromosome as the chimps. I know that these viruses are inserted into the genome randomly, and such a thing could not happen by chance: Chimps and humans have a common ancestor who had these viri and that is why a virus which inserts itself at random is found in the same place in our genomes.

However, Talk Origins has an article up about Creationists frequently misquoting Patterson, and I wouldn't be surprised if this was the case here:

p.222 Makes the case that bats arose suddenly. They don't seem to be aware of the fact that a fragile animal like a bat wouldn't fossilize well, or that forests and caves aren't the best enviroments for fossilization. This reminds me of the old time creationist argument that their were no pre-whale fossils. Michael Behe made this claim once, and a year later one was discovered. After that, four more were discovered. It turns out that once the first one was found, paleontologists then knew where they should look, and of course they found even more "Missing links" once they began digging. Perhaps a pre-bat fossil will be discovered one day in a remote forest in Africa, and maybe even a good 3 fossil sequence will be uncovered. Anyway, it is very foolish to make such an assertion like he has made; since fossilization for bats would not only be extraordinarily rare, but also the fact that bats may have evolved in one fairly small area, so in this case absence of evidence does not equal evidence of absence.

p.226 Drags up the old tired "Lies in the Textbooks" argument about Haeckel's embryos. My opinion is that these drawings should've never been in the textbooks, but the idea that this is some sort of conspiracy and that the main evidence for evolution is false is flat out wrong. All vertebrate embryos have similarites, such as the pharyngeal pouches, and so the basic argument Haeckel was making is still correct. Here are some photos.

They also bring up another tired old case: The Peppered Moths.
It must be stressed that this is by far not the only example of Natural Selection that exists. Here are several more:

p.229-230 Darwin's Finches
This blog is now becoming very long, so I will spare you explaining this and just live you with this link.

I would also like to comment that it is amazing that this book would bother quoting Jonathan Wells, who has been shown deceptive on more than one occasion:

Tuesday, August 28, 2007

A Letter to Young Earth Creationists

Dear young earthers:

I was once like you. I thought the earth was 6,000 years old and God had created Adam and Eve, the first people. But I learned of a lot of compelling evidence** for evolution. I also learned why the earth could not be young and why we were almost certainly not created. I used to think that scientists were a bunch of godless, educated fools who would never accept the truth. In my eyes, the creationists were a minority being picked on. I observed something about how science works: New ideas are not easily accepted. Usually the scientists who champion the new, correct ideas of their day, like Galileo or Georges Lemaître; start out in the minority and gradually win acceptance for their ideas. Lately, a big debate has taken place in the news between evolutionists and creationists. I began to wonder, does the small group of creationists have a chance of being right? Will they win acceptance and replace the theory of evolution? No. You have to remember one thing: Most scientists believed exclusively in creation right up through Darwin's time. Young Earth Creationism had its shot; and it failed. It failed to explain why the earth seemed to be millions of years old. It failed to explain the simple-to-complex pattern we see in the fossil record. It failed to explain why some species(made by a perfect God) went extinct; and why certain species are only found in younger rock layers. The obvious answer is that life changed over time. It failed to explain vestigal structures like mammary glands and nipples in men, and why certain people have an extra set of ribs just like other primates. It fails to explain why we see light from stars billions of light years away. It fails to explain why stars so far away were created in the first place. You see, young earthism was embraced. Scientists gradually let go of it as a better explanation came to light. What chance has it of resurfacing? In closing, I leave you with this:

Some ways to detect pseudoscientists and pseudoscience:
*He believes himself unjustly persecuted and discriminated against.

*He has strong compulsions to focus his attacks on the greatest scientists
and best established theories.

*The discoverer pitches the claim directly to the media.

** Evidence for evolution:
Transitional Fossils:

DNA Evidence:

Evolution Observed:

Creationism Refuted:

Ambulocetus and A Whale of a Tale As Told by Creationists...

Jonathan Sarfati of Answers in Genesis, has written a critique of the PBS series on Evolution. In it, he has quite a bone to pick with the the famous "Ambulocetus" fossil. Ambulocetus is very important to evolutionists because it is an excellent transitional fossil between land mammal and whale. In his article, he writes:

"This was mentioned fairly briefly in this episode, but it features prominently in the anti-creationist book Finding Darwin’s God, by Kenneth Miller who starred in Episode 1 (see rebuttal). On p. 265, Miller claimed, ‘the animal could move easily both on land and in water’, and contained a drawing of a complete skeleton and a reconstructed animal. But this is misleading, bordering on deceitful, and indicative of Miller’s unreliability, because there was no indication of the fact that far fewer bones were actually found than appear in his diagram. Crucially, the all-important pelvic girdle was not found (see diagram, right). Without this, it’s presumptuous for Miller to make that proclamation. His fellow evolutionist Annalisa Berta pointed out:
‘ … since the pelvic girdle is not preserved, there is no direct evidence in Ambulocetus for a connection between the hind limbs and the axial skeleton. This hinders interpretations of locomotion in this animal, since many of the muscles that support and move the hindlimb originate on the pelvis.’ "
He also shows us the image to the left and tells us to "note the missing pelvic girdle":

The problem is, his claim that the pelvic girdle is missing isn't quite true. Here is a photograph of Ambulocetus' skeleton: Note the pelvic girdle.

"There is quite a bit more to that skeleton than what Sarfati would have us believe. What Sarfati did not mention or did not know (probably the later) is that the original specimen’s locality was not completely excavated due to safety concerns when the original paper1 of Ambulocetus by “Hans” Thewissen et. al. was published in 1994. In 1996 a great deal more of the skeleton was found. The bones found in 1996 include much of the spine and the pelvis.2 The web site for an exhibit of a reconstructed skeleton of this fossil notes that it is “missing only the tip of the snout, scapula, humerus, distal part of the tibia and some ankle bones.” In other words it is remarkably complete. (Keep in mind if one has the limb bone from left side, one knows what the equivalent limb bone on the right side looks like.) A technical description of these are in press as I write this sentence."
This is from:

I would like to thank the individual who wrote this article, and I give him full credit for inspiring me to write my version of the same topic. His website is great and definetly worth a visit.

Also, it is interesting to note the embryological evidence for the evolution of whales. As embryos, whales develop body hair which they later shed, and they also develop hind limb buds which they later reabsorb.

Anyhow, that wraps it up. Ambulocetus does indeed have a pelvis, it was amphibious, and the creationists are up the creek again.

Hopeful Monsters, Stephen J. Gould, and AiG

Well, it seems like I don't go two days without uncovering something from answers in genesis that is downright deceptive, but here goes:

Notice how he basicly says that Stephen J. Gould reintroduced the Hopeful Monster Theory. This is clearly not the case. This is from Gould's essay, "Return of Hopeful Monsters"
"In my own, strongly biased opinion, the problem of reconciling evident discontinuity in macroevolution with Darwinism is largely solved by the observation that small changes early in embryology accumulate through growth to yield profound differences among adults. Prolong the high prenatal rate of brain growth into early childhood and a monkey's brain moves toward human size. Delay the onset of metamorphosis and the axolotl of Lake Xochimilco reproduces as a tadpole with gills and never transforms into a salamander. (See my book Ontogeny and Phylogeny [Harvard University Press, 1977] for a compendium of examples, and pardon me for the unabashed plug.) As Long argues for the external cheek pouch: "A genetically controlled developmental inversion of the cheek pouch may have occurred, recurred, and persisted in some populations. Such a morphological change would have been drastic in effect, turning the pockets 'wrong side out' (furry side in), but nevertheless it would be a rather simple embryonic change."

So SJG did NOT reintroduce Hopeful Monsters, he merely said that small embryonic changes can become much more drastic in the adult stage. So this is basically just a small change which gets exacerbated as the individual grows, not a huge macromutation in which "a reptile lays an egg and hatches a bird."

Apparently they were never aware that SJG said this:
" "Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists--whether through design or stupidity, I do not know--as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. Yet a pamphlet entitled 'Harvard Scientists Agree Evolution Is a Hoax' states: 'The facts of punctuated equilibrium which Gould and Eldredge...are forcing Darwinists to swallow fit the picture that Bryan insisted on, and which God has revealed to us in the Bible.'"

In closing, I leave you with this:
"Many evolution deniers quote Stephen Jay Gould and other punctuated equilibria proponents as saying that transitional forms are very rare. Most non-specialists get ideas of "missing links" between higher taxa of animals when they hear about transitional forms. Gould has been very clear that these are common and yet he has been quoted many times that transitional forms are rare. What is going on here? In the context of punctuated equilibria, a transitional form is between immediately related species (say two species of squirrels, species of similar Devonian trilobites, etc.), and is not referring to a transition between human and non-human, whales and primitive land mammals, etc. Indeed the transitions Gould and other punctuated equilibria proponents are arguing about would be generally be dismissed as "microevolution" by many evolution deniers. Thus antievolutionists arguing against the existence of transitions between larger taxa are very likely guilty of misquotation if they quote Gould's writings on punctuated equilibria. For more details on this see Gould's10 classic essay "Evolution as Fact and Theory" where he explains his position on the fossil record as well as demonstrates young-earth creationist misrepresentations of his views."


"Evolution Can't Produce New Information"

From the Answers in Genesis website. I've provided the link to the original document, so you know this is not out of context:

"In response to 'Intelligent design an unproven theory' (March 17), it’s amazing that the writer’s evidence for evolution—'antibiotic-resistant' TB strains—is actually one of the best evidence against evolution.

A population of microbes becomes resistant to antibiotics because of a loss of genetic information or a transfer of information between microbes. But in no case have bacteria become resistant through a gain of new information."

I could respond to this the way Richard Dawkins did; but that'd be no fun. Instead, I'm going to warm up with some beneficial gene duplications, and then show you evidence against this claim using the strictest definition of information possible: A beneficial addition to the genome not involving gene duplication.

Alright, let's consider Richard Dawkins' answer: Natural Selection always increases the information of the genome because that's exactly what it does. What he means is that beneficial traits are favored while harmful ones are not, and thus the useful content of the genome increases. This could be illustrated with the evolution of the finch's beak, and how the average size grows and shrinks through different seasons. If you're familiar enough with evolution, you will remember how the Finches showed signs of speciation, and how it influenced Darwin.

Now let's move on to look at some gene duplications that have been beneficial. Gene Duplication is when a gene is mistakenly copied and inserted elsewhere in the genome. A duplicated gene can start off being the same as its parent gene, and then gradually be 'tweaked' to fit its new function. Since it can increase fitness, I would consider it 'new information'; though many creationists have argued it isn't because it is copying from something already there. Let's look at a few ways that it has been observed to be beneficial:

* Two enzymes in the histidine biosynthesis pathway that are barrel-shaped, structural and sequence evidence suggests, were formed via gene duplication and fusion of two half-barrel ancestors (Lang et al. 2000).

* Yeast was put in a medium with very little sugar. After 450 generations, hexose transport genes had duplicated several times, and some of the duplicated versions had mutated further. (Brown et al. 1998)

From Talk Origins

* Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish
Freezing avoidance conferred by different types of antifreeze proteins in various polar and subpolar fishes represents a remarkable example of cold adaptation, but how these unique proteins arose is unknown. We have found that the antifreeze glycoproteins (AFGPs) of the predominant Antarctic fish taxon, the notothenioids, evolved from a pancreatic trypsinogen. We have determined the likely evolutionary process by which this occurred through characterization and analyses of notothenioid AFGP and trypsinogen genes. It is first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function.

Now, for the final blow to AiG's desperate argument. An Insertion Mutation
is when a piece of DNA is added to the gene, increasing the number of characters. So, if I can just scratch up a couple of examples of this contributing a beneficial new function, then AiG's ultimate argument bites the dust.

Here they are:
From my other blog, Gill Slits

"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."

Then there's the famous case of the nylon bug. A bacterium gained the ability to digest nylon via an insertion mutation, and is now thriving around nylon plants. AiG has tried hard to dispute this, but Talk Origins took them up on this and put them in their place.

A couple of interesting links:

The Laetoli Footprints and A Man in the Cretaceous?

Well, if you don't know already, AiG is purely deceptive. They are dishonest and manipulative, right down to the core. They have no interest in truth, other than distorting it to fit their world view. I recently came upon this, and note that I already posted a response in another thread:
"A good example of reworking is the famous fossil footprints at Laetoli, Africa, of an upright walking biped—the University of Chicago’s Dr Russell Tuttle has shown that these are the same sorts of prints as made by habitually barefoot humans. But since they are dated at millions of years prior to when evolutionists believe modern humans arrived, they are regarded as australopithecine prints, by definition, even though australopithecine foot bones are substantially different from human ones. And then in an amazing twist, the same prints are held up as evidence that australopithecines walked upright like humans—regardless of the fact that other aspects of their anatomy indicate otherwise.2"


My response:

"Our upright method of walking evolved before significant brain enlargement occurred. In north-eastern Tanzania, at Laetoli is the oldest evidence of a bipedal (upright walking) hominid. These human-like footprints are found with guinea fowl and other bird prints, antelope and gazelle, giraffe, elephant, rhinoceros, pig, hyena, baboon, carnivores, hares, and three-toed horse (Leakey and Hay,1979). Dated at 3.5 to 3.6 million years old, the prints are preserved in a volcanic ashbed.
This is 1.6 million years before the oldest known tool use by early hominids! Some trails are 50 metres long and are entirely human, with a well developed arch to the foot! This creature's big toe appeared quite long, resembling the mobile toe of the chimpanzee, but the absence of any hand marks showed that the creature walked upright. Its stride suggests that the larger individual stood at 140 centimeters and the smaller at 120 centimeters. Some foot bones of such a creature have been found in South Africa (Sterkfontein caves). This creature's had an ankle bone adapted for upright walking and is almost identical to the ankle bone of a modern human. The big toe angles away from the foot and the joints suggesting that it was highly mobile (Tobias, 1995). Scientists place these with Australopithecus (the "southern ape"), a hominid that lived in East and South Africa between 4.4 and 1.4 million years ago (" 1.4 to 4 lines ago ") (Avers, 1989). Sterkfontein would have been a steamy tropical jungle at the time the "Little Foot" entered Southern Africa."


Furthermore, Australopithecus Afarensis was estimated to be 3.28 to 5.58 feet tall. The footprints suggest that the two individuals in the Laetoli bed were about 3.8 feet and 5 feet.

I then began exchanging emails with someone who works at Answers in Genesis. I am going to abbreviate our conversation, but I will not add to it nor distort the meaning:

Me: "The flood cannot account for the fossil record"

AiG: "I disagree... The following links should help get you started with some pertinent articles:"

I visit the link, and discover this:

"Human fossils have been found, hundreds of them, but
generally in deposits which most creationists would
think were post-Flood (e.g. buried in caves during the
post-Flood Ice Age—see What about the Ice Age?).
However, in at least one case, human bones have been
found in ‘older’ strata.11
Unfortunately, the lack of detailed documentation associated with their removal makes it impossible to say with certainty that they were not the result of subsequent intrusive burial, although nothing we know of suggests they were."

Go to the reference at the bottom (number 11). This refers to human skeletons found in cretaceous rock. Cretaceous rock? That shouldn't happen! Now reread the above paragraph. Are they suggesting that these finds invalidate evolutionary theory?? Human skeletons found in the "Age of Dinosaurs" rock. Looks like a major blow. Until TO had this to say about it:

I emailed AiG this link, and here is what the representative told me:
"One thing to realize about Talk Origins (TO) is that it is not a site with technical peer-reviewed material. Many of their technical articles have never been peer-reviewed and even contain extensive amounts of speculation. Because of this, one needs to be discerning when reading their articles to divide facts (2 Timothy 2:15) from personal opinions/interpretations. Use these same facts and interpret them with the biblical presupposition as opposed to evolutionary presuppositions."

Not a site with technical peer reviewed material. As if AiG is... And I'm sure you've all caught the hypocrisy in their statement of presupposition. I wonder just how much speculation went into TO's statement? Seemed like they were just stating the facts, which were unopen to "interpretation". I emailed Aig back about this.
AiG replied:
"I did some digging (pun intended!) and it appears the evidence of this example of human fossils in older strata is an example of intrusive burial. We had a small disclaimer in the referenced article that we could not substantiate the documentation for this dig, and it appears our suspicions played out."

So it seems to me that AiG is honest when confronted, but their articles seem to be misleading. I'm no scientist and I have already found 2 cases of this, I could possibly find more if I were to research everything they said. Read the sentence again:

"However, in at least one case, human bones have been
found in ‘older’ strata.11
Unfortunately, the lack of detailed documentation associated with their removal makes it impossible to say with certainty that they were not the result of subsequent intrusive burial, although nothing we know of suggests they were."

This is downright deceptive.

Monday, August 27, 2007

The Top Evolution Defense sites

These are some blogs and sites that provide excellent and accurate information about evolution and expose the lies of creationism. Here are the top 5:

1. The Theory of Evolution Made Easy
2. DefCon's 10 reasons the Universe is NOT 6000 years old.
3. Talk Origins' 29 Evidences of Macro Evolution
4. Natural Selection at work
5. Berkeley University's explanation of evolution

Here are some interesting youtube accounts that have videos dealing with evolution/creationism:

Here are some good web pages:
1. This page has some excellent books about evolution that you can read for free!
2. Ed Babinski's Blog
3. National Center for Science Education
4. The Nylon Bug
5. Skeptical Inquirer's web page concerning Creationism. A very excellent resource!
6. Examples of Beneficial Mutations
7. PBS Evolution
8. Over 400 hominid fossils for your viewing pleasure.
9. American Atheists' page on Evolution. The "Half a Wing and No Prayer" article is especially good.
10. Features debates between a theistic evolutionist and creationists.
11. Incredibly smooth transitions in the fossil record.
12. Ed Babinski tears into AiG about dolphin atavisms.
13. Internet Infidels' page on creationism
14. Speciation
15. Ring Species
16. Observed instances of Speciation
17. Some more observed Instances of Speciation
18. Fifteen Answers to Creationist Nonsense
19. Ken Miller's Evolution website
20. Recent Evolutionary changes in lions
21. Stephen Jay Gould Library
22. The Flood: Myth and Science
23. Conflicts Between the Bible's Flood Story and the Fossil Record
24. HUGE List of Evolution Resources
25. Mitochondrial DNA and Man's History
26. No Answers in Genesis
27. A former creationist examines the flood myth scientifically
28. Pharyngula
29. Skeptic Friends' Creationism Page
31. Exposing the Lies of Kent Hovind
32. Talk Origins Google Group
33. Fossil Succession
34. Horse Evolution
35. The Evolution of Whales
36. Radiometric Dating: A Christian Perspective
37. Geological Time and the Evolution of Life
38. Vestigial Organs

Books about evolution/creationism:

Evolution for Everyone by David Sloan Wilson

Finding Darwin's God by Ken Miller

Why Darwin Matters by Michael Shermer

Living With Darwin by Philip Kitcher

The Making of the Fittest by Sean Carroll

The Blind Watchmaker by Richard Dawkins

The Science of Evolution and the Myth of Creationism by Ardea Skybreak

The Top Ten Myths About Evolution by Cameron Smith and Charles Sullivan

The Science Times Book of Fossils and Evolution by Nicholas Wade

The Origin of Species by Charles Darwin-Read the original online for free!

Skeptic magazine is always a favorite.


Hi, welcome to the Answers in Genesis Busted Blog!!
My posts are dedicated to uncovering the deception of creationist groups, especially the leading one: Answers in Genesis. If you uncover any creationist deception, please email me:

Thanks and Stay tuned!!