Thursday, July 31, 2008

30th post

This is a first for me... Thirty posts in one month. Not bad, huh? I also passed the 2oo blog post mark this month. So, for this post, I'm just self promoting. Enter your email address and subscribe in the box to your right. And visit:


Wednesday, July 30, 2008

The Dinosaur claim recieves Another Blow

Anyone remember the old creationist claim that dinosaur blood had been found freshly preserved?

Now, when I first heard about this claim, I referenced Mary Schweitzer's comments that this entire thing might simply be an odd "impression" of flesh rather than the actual thing (She did say that "the fossil record can mimic many things"). I also pointed out that plausible methods for fragments of biological tissue to survive were being investigated (See my original write up on this for more info). Others pointed out that this material was not found "still soft and stretchy" as creationists had claimed, but rather scientists had to painstakingly rehydrate this stuff to get it that way. Besides, the mammoth genome was being sequenced, and if this creature had lived at the same time as the dinosaurs, as creationists think, then we should be able to retrieve large chunks of dino DNA as well. But we haven't. So there was some inconsistency.

Now that I am done with my overly long intor, let's get down to it: Scientists now think that the alleged structures found in the bone have nothing to do with dinosaurs. They think that these structures are actually due to biofilms, or communities of bacteria which are enclosed in a polymer "film". Blogger Tara Smith sums this up:

"What they found provides an alternative hypothesis to the previous "dino blood" findings. The iron present (and thought to have come from blood cells) could be explained by the presence of iron-containing framboids: spheres commonly found in sediments. Blood vessel-like structures were found but also could be attributed to biofilm, and when compared by FT-IR to lab-grown biofilms, the chemical signature of the fossil structure more closely resembled modern biofilms than modern collagen. The authors argue that the biofilm hypothesis better explains the data, including the ubiquity of these structures in fractured fossils:

This investigation contends that iron-oxygen spheres are far too common in many formations to be the result of extraordinary preservation. Framboid morphology and elemental signature may superficially make them appear to be related to biological structures but they are, in fact, an inorganically produced mineral feature often found in association with organic matter."

Found via ScienceDaily:
[I]n a paper published July 30 in PloS ONE, a journal of the open-access Public Library of Science, Kaye and his co-authors contend that what was really inside the T. rex bone was slimy biofilm created by bacteria that coated the voids once occupied by blood vessels and cells.
He likens the phenomenon to what would happen if you left a pail of rainwater sitting in your backyard. After a couple of weeks you would be able to feel the slime that had formed on the inner walls of the bucket.

"If you could dissolve the bucket away, you'd find soft, squishy material in the shape of the bucket, and that's the slime," Kaye said. "The same is true for dinosaur bones. If you dissolve away the bone, what's left is biofilm in the shape of vascular canals."

Sunday, July 27, 2008

Primates Evolve Large Brain Size Twice

I found a very interesting article. It is about some primates in South America which began evolving larger brains. It made me think of the late Stephen Jay Gould's view that evolution is radically contingent. Perhaps its not so after all. I mean, if Homo Erectus had gone extinct before our lineage evolved from it, perhaps 10 million years later another group of apes (or any other creature, for all we know) may have evolved our level of consciousness.

Thursday, July 24, 2008

Created and Rational Disagreement

Not sure if any of you know, but Created and Rational wrote up a blog post that seemed to express strong disagreement with a post I made about Creationists not being able to trust their own thoughts. Here is his post of which I will quote:

AiG creationist thinkers at least have adopted almost a form of Critical Realism in regards to the past. Nothing can be absolutely proven in relation to the distant past before human presence in the region. Therefore whatever theory you make about the past is not independent of your presuppositions. This is how I have basically explained it, and earlier I criticized it on the grounds that it was an attempt on the part of the creationists to avoid the obvious evidence for evolution. Either way their position appears to have been mishandled by several people such as AiGbusted. It has been interpreted as saying we cannot trust our own thoughts because thoughts. The misunderstanding probably stems from this quote form the AiG article, "Is nature the 67th book of the bible?":

"Many who trust in humans as the highest authority reject the Curse as true history and thus deny its effect on our observations. Some point to the effects of the Curse as proof of “bad design.” For Christians, however, it is foolish to ignore the Curse when considering what nature can “reveal” to us. After all, this would be like someone trusting a funhouse mirror to show them how they really looked. They look into the mirror and see a distorted view but assume that this mirror must be “right.”"Now at first glance this does seem to say that we cannot trust our senses and this does seem to contradict what creationist have claimed about evolution being anti-science and anti-knowledge since it means our brain is just an assortment of chemicals which evolved over billions of years and can't be trusted. Is this a contradiction made by the author? No, creationists such as Ken Ham say that there is a distinction between what they call "operational" science and "historical" science. Operational science is everyday repeatable science which has been used to build technology and send humans to the moon. Historical Science on the other hand has to do with the distant past and origins which are affected by our presuppositions and is therefore not science in the same sense that operational science is. Furthermore in regards of repeatable, testable, and operational science the senses are very reliable and they believe that science requires "biblical presuppositions". loved and hated Creationist astrophysicist Dr. Jason Lisle explains:

"The biblical creationist expects there to be order in the universe because God made all things (John 1:3) and has imposed order on the universe. Since the Bible teaches that God upholds all things by His power (Hebrews 1:3), the creationist expects that the universe would function in a logical, orderly, law-like fashion. Furthermore, God is consistent and omnipresent. Thus, the creationist expects that all regions of the universe will obey the same laws, even in regions where the physical conditions are quite different. The entire field of astronomy requires this important biblical principle."

Here is how I responded:


What do you think "biblical presuppositions" means? They mean that they assume the bible is true above any and all. By their dictionary, you look up truth and it says, "See Bible."

If you look at my post and the AiG article I referenced:

You see, they state that no amount of evidence for an old earth would convince them (They would always assume the evidence was in some way flawed).

This means if they look at varves, ice rings, tree rings, radiometric dates, plate tectonics, the approximated age of the sun, Stars that are millions or billions of light years away from the earth, and so on...

They cannot even consider that the earth might be older than 10,000 years. In conclusion, They will not trust the evidence right in front of their faces.

I did not say this in the original comment so I will write it now:

Creationists may try and distinguish between "operational" science and "historical" science, but they are forgetting that so many things, like Forensics science in murder trial, is used making the same assumptions as evolutionary or modern geological/astronomical sciences do (They presuppose the laws of nature to be constant and the same effects always have the same causes, and no magic).

Wednesday, July 23, 2008

New York Times and Natural Selection

Olivia Judson, the biology blogger over at the New York Times, has written up a great piece on examples of evolution by natural selection occuring today. Check it out.

Tuesday, July 22, 2008

Abby Smith and Antibiotics

Abby Smith over at the ERV Blog has written up a great article debunking creationist myths about antibiotic resistance in bacteria. View it here.

Confusion About Homology

Over at EvolutionBlog there was a discussion about a creationist who took some quotes from a biology book to try and show that scientists were saying homology was both due to common ancestry and evidence for common ancestry. Let me give you an example: Suppose I say that the eyes of squids and humans are not homologous because they did not inherit this structure from a common ancestor, but then I turn around and say that the non-homologous eyes are evidence that they didn't share a (recent) common ancestor.

This is what the controversey is over, and it has taken me a while to understand just what the creationists were saying on this issue. Here was a comment I left on that post:

This is just another example of how successful Jonathan Wells has been in distorting science and spreading it from the IDers all the way to the fringe of young earth creationism. It is a confusing issue, but the way I understand it is this:

*For a structure to be homologous, it must share a deep similarity (biochemically, anatomically, and developmentally). Homologous structures may or may not have the same precise function.

*Homologous structures are then inferred as being inherited from a common ancestor.

*On the problem of convergent evolution: There are always mutliple solutions to a similar problem. For instance, one organism may move through the water by moving the tail horizontally (like whales) or vertically (like fish), or by rotating the arms (as humans do). Then again, one may "clap" their legs together in order to swim, just as frogs do. So a similar environmental pressure may occasionally produce similar features, but by comparing a large number of features, we may know whether convergent evolution has taken place. On a side note, genetics and fossils may be helpful as well in determining ancestry.

Monday, July 21, 2008

The Type Three Secretory System

Remember the Type III Secretory System? It is homologous to the "Irreducibly Complex" Bacterial Flagella, and now its origin is being uncovered! Of course, this paper I am citing is old, from about 2003, but still interesting. Here is the abstract:

"Type III secretion systems (TTSS) are unique bacterial mechanisms that mediate elaborate interactions with their hosts. The fact that several of the TTSS proteins are closely related to flagellar export proteins has led to the suggestion that TTSS had evolved from flagella. Here we reconstruct the evolutionary history of four conserved type III secretion proteins and their phylogenetic relationships with flagellar paralogs. Our analysis indicates that the TTSS and the flagellar export mechanism share a common ancestor, but have evolved independently from one another. The suggestion that TTSS genes have evolved from genes encoding flagellar proteins is effectively refuted. A comparison of the species tree, as deduced from 16S rDNA sequences, to the protein phylogenetic trees has led to the identification of several major lateral transfer events involving clusters of TTSS genes. It is hypothesized that horizontal gene transfer has occurred much earlier and more frequently than previously inferred for TTSS genes and is, consequently, a major force shaping the evolution of species that harbor type III secretion systems."

(Click here to learn about Horizontal Gene Transfer).

Saturday, July 19, 2008

New Abiogenesis Research

Via ScienceDaily:

To initiate many important functions, bacteria sometimes depend entirely upon ancient forms of RNA, once viewed simply as the chemical intermediary between DNA's instruction manual and the creation of proteins, said Ronald Breaker , the Henry Ford II Professor of Molecular, Cellular and Developmental Biology at Yale and senior author of the study.
Proteins carry out almost all of life's cellular functions today, but many scientists like Breaker believe this was not always the case and have found many examples in which RNA plays a surprisingly large role in regulating cellular activity. The Science study illustrates that - in bacteria, at least - proteins are not always necessary to spur a host of fundamental cellular changes, a process Breaker believes was common on Earth some 4 billion years ago, well before DNA existed.

"How could RNA trigger changes in ancient cells without all the proteins present in modern cells? Well, in this case, no proteins, no problem," said Breaker, who is also a Howard Hughes Medical Institute investigator.

Breaker's lab solved a decades-old mystery by describing how tiny circular RNA molecules called cyclic di-GMP are able to turn genes on and off. This process determines whether the bacterium swims or stays stationary, and whether it remains solitary or joins with other bacteria to form organic masses called biofilms. For example, in Vibrio cholerae, the bacterium that causes cholera, cyclic di-GMP turns off production of a protein the bacterium needs to attach to human intestines.

The tiny RNA molecule, comprised of only two nucleotides, activates a larger RNA structure called a riboswitch. Breaker's lab discovered riboswitches in bacteria six years ago and has since shown that they can regulate a surprising amount of biological activity. Riboswitches, located within single strands of messenger RNA that transmit a copy of DNA's genetic instructions, can independently "decide'' which genes in the cell to activate, an ability once thought to rest exclusively with proteins.

Breaker had chemically created riboswitches in his own lab and - given their efficiency at regulating gene expressions - predicted such RNA structures would be found in nature. Since 2002, almost 20 classes of riboswitches, including the one described in today's paper, have been discovered, mostly hidden in non-gene-coding regions on DNA.

"We predicted that there would be an ancient 'RNA city' out there in the jungle, and we went out and found it,'' Breaker said.

Bacterial use of RNA to trigger major changes without the involvement of proteins resolves one of the questions about the origin of life: If proteins are needed to carry out life's functions and DNA is needed to make proteins, how did DNA arise?

The answer is what Breaker and other researchers call the RNA World. They believe that billions of years ago, single strands of nucleotides that comprise RNA were the first forms of life and carried out some of the complicated cellular functions now done by proteins. The riboswitches are highly conserved in bacteria, illustrating their importance and ancient ancestry, Breaker said.

Understanding how these RNA mechanisms work could lead to medical treatments as well, Breaker noted. For instance, a molecule that mimics cyclic di-GMP could be used to disable or disarm bacterial infections such as cholera, he said.


The last bit reminds me of what Neil DeGrasse Tyson said on the History Channel's Origin of Life Program: Even if we never figure out how abiogenesis happened, the research is well worth it because of all the other discoveries we will make along the way. Even creationists who do not think abiogenesis can happen must acknowledge that the research deserves to be funded because of all the other excellent discoveries we may make. Not to mention the fact that assuming a natural origin of life leads to successful predictions!

Atheist Girls

I found a great new blog today by the name of "Atheist Girls". Several women are posting there and the results are just awesome. There is a "Philosophychick" a "Microbiologychick" and maybe one or two more (not sure). Check it out here.

Friday, July 18, 2008

Human Evolution, Haldane's Dilemma, and Youtube

This post is just going to be random youtube vids that I think are cool (and have to do with science):

Youtube User DNAUnion made a nice video on human evolution and "Haldane's Dilemma"; View it here. I am glad that DNAUnion took the time to explain a major fallacy which Talk Origins did not go into: "humans and apes differ in 4.8 × 10^7 genes". This is absurd because neither human beings nor apes have 48,000,000 genes! Perhaps what the author really meant was that we differ in 48 million codons or nucleotides.

New Scientist Magazine has their own youtube channel with a lot of neat science stuff.

I also highly recommend this video in which Richard Dawkins explains the evolution of the eye, the wing, and protective camoflage.

Wednesday, July 16, 2008

Dembski is a real loser...

That gosh-awful blog Uncommon Descent has posted the following on their site:

"Dembski recommends further science standards like the following:

Explain in detail how evolutionary theory explains the Cambrian Explosion.

Describe in detail how evolution made complex biological structures such as the human eye.

Explain how evolutionary theory solves the problem that DNA cannot exist without protein and protein cannot exist without DNA."

These are, of course, completely ridiculous. Scientists have worked really hard to solve these problems (and have been successful!), not simply swept them under the rug, as Dembski implies. First of all, the Cambrian Explosion must be viewed not as something that happened overnight, but rather as something that took place over about ten million years. Scientists have postulated a number of hypotheses about why such rapid evolution suddenly took place (after millions of years of simpler life) including the fact that Hox genes, which control the body plan of the organism, evolved around that time.

Describe in Detail how the eye evolved? What? This has convinced me that Dembski is not just a nut with a bad "theory", he is a liar. Charles Darwin went to lengths to show that simpler eyes existed in nature, which you may read for yourself at any library or online. Today we know of creatures with only a single photosensitive cell. The evolution of the photosensitive cell itself was described just a few months ago. Click here for more on the evolution of the eye.

Now, which came first the DNA or the proteins? Neither. RNA is thought by most scientists to have come first (it can catalyze its own reproduction), and then a form of RNA evolved into DNA. We know via experimental evidence that RNA has the ability to evolve into DNA.

I have to side with Richard Dawkins, "Dembski is a loser."

Tuesday, July 15, 2008

Casey Luskin - Grade A Retard

Carl Zimmer just made a blog post that totally rips Casey Luskin to pieces. Luskin claimed that Tiktaalik did not have a wrist, when in fact he quoted the peer reviewed paper discussing wrist bone homology in Tiktaalik. You have got to read it:

This isn't the first time Tiktaalik has been attacked; It just keeps getting clearer that Tiktaalik is the anti-evolutionist's nightmare. They're afraid of it, and they are attacking it for a reason.

Monday, July 14, 2008

Abiogenesis and Evolution

Contrary to what some evolutionists have said, abiogenesis and evolution actually are the same thing.

Or at least, evolution is key to explaining how simple self replicating systems eventually became living cells. Let me explain how: Evolution is a change in the gene pool over time. Anything with a genetic medium, which reproduces, and of course experiences changes in that genetic medium, evolves. Nearly every hypothesis about the origin of life begins with something which replicates itself (Dawkins, 1976). This replicator reproduces itself into a population, and suble changes sneak in. Changes which allow the replicator to reproduce more quickly, for instnce, may make it more common. What I have just described (replication, mutation, natural selection) is evolution. So while technically chemistry may have to supply the answers to how the replicator originated, the transition from replicating RNA strand/peptide to primitive cell is within the theory of evolution. Plenty of research exists in this area:

One more thing: I did not think about this until Matzke mentioned it, but the fact that biological molecules form so easily in early earth simulating conditions is a good indication that the notion of life coming from inanimate matter is on the right path.

Saturday, July 12, 2008

Website Updates

I have been updating my two websites, AiG BUSTED and GodRiddance, a good bit lately. On my GodRiddance site, I have authored three pages on atheism and morality (though one of them is not new) I would appreciate feedback:

"The Universal Moral Law" as an Argument for God

What About the Crimes of Atheists?

How do we come up with a system of ethics?

I have also saved my last post about E.coli evolution to the Answers in Genesis Busted site. I did updat however. In the paragraph in which I stated:

"The fact is that it is totally unreasonable to expect mutations to prove useful in every single environment possible. The role of mutation and natural selection is to make the organism better adapted to the environment the species is in at the time."

Later on I put in:

"If you are trying to teach religious beliefs in the public schools of a nation which upholds the separation of church and state, it might seem like a good strategy (in that environment) to abandon your specific claims of a great big flood and a six day creation in favor of vague statements about an intelligent designer doing something somewhere at some point in time."

Friday, July 11, 2008

Answers in Genesis on E.Coli and Citrate Evolution

Well, I knew it would happen sooner or later: Answers in Genesis has jumped on the defensive at the report of E. Coli evolving the ability to utilize Citrate. Dr. Georgia Purdom writes:

"While the fitness of the bacteria has increased (as compared to the starting bacteria), it has come at a cost. For example, all the lines have lost the ability to catabolize ribose (a sugar). Some lines have lost the ability to repair DNA. These bacteria may indeed be more fit in a lab setting, but if put in competition with their wild-type (normal) counterparts in a natural setting, they would not stand a chance."

This is a very common creationist tactic: Try to make evolution seem like a detrimental process, and then claim that as evidence that common descent is false. The fact is that it is totally unreasonable to expect mutations to prove useful in every single environment possible. The role of mutation and natural selection is to make the organism better adapted to the environment the species is in at the time. For instance, gills are extremely useful if you live in the water (of course), but if a population of amphibians has evolved to the point of no longer truly needing them, it is best to get rid of them (why keep something that requires caloric energy to upkeep?). Legs are a great adaption if you need to move around on land, but for a sea dwelling creature like a whale they are nothing but a burden. Moving on:

"Many evolutionists state that the bacteria are experiencing 'adaptive evolution.' However, this is not evolution but rather adaptation. Molecules-to-man evolution requires an increase in information and functional systems. Instead, these bacteria are likely experiencing a loss of information and functional systems as has been observed in other mutant bacteria in Lenski’s lab. While these changes are beneficial in the lab environment, it does not lead to a net gain that move bacteria in an upward evolutionary direction."

Another creationist tactic: Try and redefine evolution for their own purposes. If you have read Carl Sagan's Baloney Detection Kit, you may recall Carl Sagan stating, "An important art of politicians is to find new names for institutions which under old names have become odious to the public." If you are fighting evolutionary theory, it might be helpful if you redefine the parts of it which you accept as something else. The fact is that evolution is nothing more than population adaption: Evolution is a change in the gene pool over time. After that, Dr. Purdom jumps into the old creationist argument that "evolution cannot prduce new information". Do they think that repeating this assertion again and again will make it true? Here is a peer reviewed paper that discusses the origin of a novel RNA gene (basically a gene cobbled together from a couple of older genes, but useful to the organism nevertheless). I have written an extensive answer to the creationist information argument, you may view it here. Finally, we see a horrible mischaracterization: Bacteria should "move upward in an evolutionary direction". What? There is no "moving up" in evolution; Evolution is only a series of adaptations. To continue:

"Since E. coli already possess the ability to transport and utilize citrate under certain conditions, it is conceivable that they could adapt and gain the ability to utilize citrate under broader conditions. This does not require the addition of new genetic information or functional systems (there are no known 'additive' mechanisms)."

While it is true that E. Coli can utilize Citrate under anoxic conditions (as well as in the presence of an oxidizable cosubstrate), E. Coli have only been able to utilize citrate if they mutated, such as Lenski's research suggests (BG Hall also reported some E. Coli which could utilize citrate, but even they had a chromosomal mutation). The bit about "added genetic information" is, as previously discussed, pure nonsense. Dr. Purdom, the author of this article, has a PhD in Molecular Genetics, and I would expect her to know about insertion mutations and genetic duplications. I'm sure she does, but why exactly do these not count as 'new information'?

In closing, I am porviding links to Olivia Judson's NY Times Series on the origin of new genes:

Gene Trafficking - Discusses horizontal gene transfer. Interesting statement: "The fungi that live in cows’ stomachs appear to have received their genes for digesting cellulose (cellulose again!) from bacterial co-occupants of the stomach."

Some Genes Come in Packages - Talks about Endosymbiosis and how the genomes of other organisms can be incorporated into genomes.

It's a Jumble Out There! - "Jumping Genes" and Evolution.

Evolution in Duplicate - How genes, chromosomes, and pieces of genes and chromosomes duplicate and their effects on evolution.

Thursday, July 10, 2008

Can a creationist trust his own thoughts?

Created and Rational has called my attention to yet another issue that needs to be addressed:

"[O]ne of [Answers in Genesis'] most recent articles Are we missing something? in which they attempt to say nature's record is unreliable since Man is fallen."

[The AiG article states:]
"When people look to nature to reveal truth, they are falling into the same speculation trap as in describing the house in the field. No matter how imaginative or intelligent they are, they can never know exactly what happened in history without trustworthy eyewitness accounts.Those who promote nature as a missing aspect of God’s revelation (the so-called “67th book of the Bible”) need to understand two crucial fallacies with this idea: first, nature is cursed; second, our observations of nature are not independent from our presuppositions. When we examine these problems, we see that nature should neverbe put on the same level as the Bible."

Here is the reaction I posted on his blog:

"Another problem with creationists' standpoint (You can't know the truth without eyewitnesses) is: How do you know the eyewitnesses were correct? Excluding lying, there are plenty of things which could make eyewitness testimony unreliable:

Being honestly mistaken about the situation
Being Deluded (On "GhostHunters" a chemical leak in the home was causing a man to hallucinate demons)

And so on and so on...

Eyewitness testimony, when present, should be taken into account, but it is by no means an infallible thing. One more thing: I heard one creationist tell me that if creationism wasn't true and God didn't exist, he couldn't trust his own thoughts. Yet this article proclaims that one must not trust their own thoughts in order to be a Christian/Creationist!"

By the way, Theistic Evolutionist Glenn Morton wrote a short article called Morton's Demon which ties right into this. The idea is similar to Descartes' demon: Rene Descartes imagined a demon who was powerful enough to fool all of Descartes' senses. It was a demon which conjured illusions of everything Descartes saw, heard, and felt. The Demon was absolutely indetectable, so how was Descartes to know that he was deluded? He couldn't! Without a reasonable amount of trust in logical methods that have shown themselves to work, and a reasonable amount of trust that what you are seeing must be real, you cannot believe anything! Creationists may as well just believe that they live inside a Matrix-esque world where nothing is real!!

"Why I Left Young Earth Creationism"

Geologist Glenn Morton tells his personal journey from young earth creationism to theistic evolution. To view Glenn Morton's website, which has a lot of fascinating articles on evolution, geology, and creationism, see the link.

Wednesday, July 9, 2008

Flatfish Evolution

Ever heard of the 'Picasso Fish'; Which has both its eyes on either side of its head? Well, scientists are now working on figuring out how it evolved. Some had suggested that perhaps genes which control development had switched one eye to the other side of the head in one fell swoop; Yet a recently examined fossil suggests that it evolved gradually. Check out the new transitional fish fossil at Carl Zimmer's blog, or see the peer-reviewed article.

A Philosopher Takes on Irreducible Complexity

You know, I vaguely recall ID proponents trying to redefine Irreducible Complexity to save it from refutation. I thought this was just special pleading; The IDers had been defeated and were just scraping around to save their arguments. Here's how it went down: Behe responded to the stepwise proposals for flagellum evolution by admitting that it could, in principle, evolve. He just thinks that the "indirect routes" of evolution these systems would have to take is so unlikely that it would probably never happen. For instance, isn't it odd that all of the parts of the bacterial flagellum would evolve for other functions, and then just happen to be able to combine to form the TTSS? Well, the journal Biology and Philosophy published an in depth article addressing Behe's attempt to save his argument from the pits of hell. Blogger Ex-Apologist has summarized it for us:

Installments 1-4

Installment 5

Tuesday, July 8, 2008

Dinosaurs of a Feather

Via LiveScience:

"Artists may now be able to paint dinosaurs and ancient birds and mammals in their true colors, thanks to the discovery of pigment residues in fossilized feathers.

In recent years, paleontologists have found fossil feathers in about 50 rock formations pegged to dates ranging from the Jurassic period (from about 200 million to 150 million years ago) to the late Tertiary (from 65 million to about 2 million years ago).

These feathers are preserved as residues of carbon that were previously thought to be traces of feather-degrading bacteria.

A new study of some of these residues, detailed in the journal Biology Letters, found that these microscopic organic imprints are actually fossilized melanosomes, tiny organelles found inside pigment cells that produce melanin pigment.

Melanin is what determines our hair, eye and skin color and gives birds' feathers their spectacular range of hues. "

Neat, huh? This reminds me of a program I saw which speculated about how one day we may be able to genetically engineer birds into dinosaur lookalikes. It highlighted the discover that chickens still retain the genes to make teeth (they are simply "turned off"). It may not be too far fetched to dream about going to a real life Jurassic Park one day, filled with highly accurate pseudo-dinos.

First Impressions of 'Only a Theory'

I have looked through Ken Miller's new book, Only A Theory, in Books-A-Million. My first impression of it is that it is essentially a repolished Finding Darwin's God (Many of the arguments he made had the familiar ring of his last book) except that now he is not just pointing to interesting facts which support evolution here and there, he is taking a sledge hammer and driving his points home with hard, indisputable facts. He has also updated it to refute new creationist arguments, namely the argument that "Evolution cannot produce new information" as well as discussing the contents an fallacies of Behe's Edge of Evolution.

He also seems to want to wake the rationalists of America into seeing that if ID succeeds, we may lose out as one of the most scientifically productive countries in the world. I fully agree with this, but I'd like to add something: Intelligent Design is not the real threat. No, Answers in Genesis has even condemned the ID movement for failing to identify the designer as the Biblical Deity. The real threat is a narrow minded, stubborn and unashamedly dogmatic worldview which this movement stems from. By this I do not mean Christianity, I mean Fundamentalist Christianity. Fundamentalists tend to consist of people who were raised fundamentalist, or who are extremely committed to taking a literalist, narrow minded interpretation of their Bible. They do not listen to theologians or scholars much, they mainly consist of nutjobs like J.P. Holding (aka Robert Turkel) who simply defend the Bible as a hobby. It is painfully obvious reading their works that they are not only bad at defending the Bible by the number of logical fallacies they make, but they are also horribly ignorant of any insight into scripture past what their tent preacher gave them. Essentially, Christians need to reach out to these people and help them realize that they are wrong, and try to change their minds.

I mean, if Christians can understand that
1) The Earth is Old
2) All Life is related
3) How Evolution Works and What it is

Our nation will have a fighting chance in the Market of Science, even if a few folks think that God had a hand in the major steps of evolution as Michael Behe does.

Monday, July 7, 2008

Baloney Detection, Episode 2

Hello Ladies, Germs, Rodents, Bugs, etc.

In case you missed the first installment in this series, it was merely a repost of Carl Sagan's Baloney Detection Kit in tribute to the great freethinker and scientist.

If you notice, pseudoscience is very much the same no matter what agenda it has to push or what product it has to sell. Creationist Kent Hovind offers a $250,000 to "prove evolution". Michael Shermer writes of a holocaust denier who offered a cash prize to anyone who could prove the holocaust happened (See Why People Believe Weird Things). A few months ago I investigated the million dollar prize being offered to anyone who "proves" abiogenesis (Hint: It was bull). Pseudoscientists (Here after referred to as BSers) love conspiracy theories. It helps them convince other people that the scientific, medical, or just plain common sense folks community are all wrong and involved in a huge coverup of the facts. Remember this when you hear creationists talk about the "materialistic bias" of the "mainstream". Remember it when you hear Kevin Trudeau claiming that "Big Pharma" doesn't want you to know about the cheap, easy, and healthy cures he tells you about in his books.

You will also notice that most often BSers are not simply good ol' folks who stumbled onto a bad idea; Rather it seems that the entire logic department of their brain is warped beyond repair. For instance, did you know that ID proponent Jonathan Wells used to be a member of the Unification Church Cult and is also an AIDS Denialist? Did you know that ICR founder Henry Morris believed in astrology? Did you know that "alternative medicine" guru Kevin Trudeau recommends practicing Scientology at the end of his "Natural Cures" book?

Of course, none of these facts make Henry Morris wrong about creationism or Kevin Trudeau wrong about alternative medicine. But they would instantly lose credibility in the eyes of many people. People who knew these things before taking up a cross and following these hucksters might slow down and submit their claims to skeptical analysis. And that, I believe, would be a great thing. No one should take someone's word for something simply because they are on TV. Do your homework, find out what the evidence is behind their claims, challenge them, question their ideas, and hear from the other side (and there always is at least one other side!).

P.S. A free movie has been circling the internet entitled Here Be Dragons: An Introduction to Critical Thinking. It is just 40 minutes long, it is free, and it is a masterful tribute to Skepticism. Visit the link!

Saturday, July 5, 2008

Michael Behe is at it Again!!

Once again on his Amazon blog. Here is what he said that bothered me the most:

"[Kenneth Miller] lovingly quotes Dover trial Judge John Jones, either not recognizing or purposely ignoring the fact that Jones’ opinion was pretty much copied word for word from a document given to him by the plaintiff’s attorneys; there’s no evidence that Jones comprehended any of the expert testimony at the trial — even Miller’s own testimony."

Yet Michael Behe admitted on Point of Inquiry that such copying-and-pasting is a common practice among judges (it saves time, after all, and a lawyer's words are generally concise and not copyrighted). Judge Jones wrote, "Those who disagree with our holding will likely mark it as the product of an activist judge..." Well, if Judge Jones hadn't stuck with common practice and had gone through the trouble of writing out his entire decision, what would the IDers have said? They'd have said, "This is a judge who is emotionally invested in Darwinism. You know, most judges just copy and paste the prosecutor's words into their decision, but this one was so up in a tizzy about it that he spent countless hours writing up his decision. I guess he needed to get it out of his system."

On the claim that Judge Jones did not understand the trial: Read the damn transcripts. Kenneth Miller, for instance, spoke in everyday, understandable language and broke things down in a way that any non-specialist could easily understand. Besides, the Judge apparently had sympathetic feelings for ID before the trial (See the PBS Documentary). So if he didn't understand the science, what would make him change his mind about ID? It simply doesn't make any sense. It is a very weak attempt to poo-poo the disastrous defeat the ID movement suffered at Dover.

Science and Religion

PZ Myers' Point of Inquiry Interview inspired this post.

Are science and religion compatible? Specifically, are evolution and religion compatible? I am not sure, but it certainly is incompatible with certain sects of Christianity, Islam, Judaism, and Hinduism. What about other sects like Catholicism, Methodism, etc. ? I've posted on this before, and I don't see any definitive answer to this question yet.

Nevertheless, the undeniable fact is that Evolution completely destroys the position of many religious sects. So what about separation of church and state? Should we stop teaching evolution?


All sciences and histories must be taught reguardless of what damage they may do to religious positions. Some evangelists think that the crimes of Stalin are a good argument against atheism. So what? I still endorse the crimes of communism being taught in History books. The leader of the flat earth society believes that the earth is flat because of his interpretation of scripture. Does that mean we stop teaching students that the earth is round? Of course not. The truths of science and history must be taught reguardless of who they may offend, but the philosophical/theological implications of those truths need not be discussed in science class.

Friday, July 4, 2008

Attack of the Wackaloon!

Conservapedia Kook Andy Schlafly is throwing a tantrum. If you recall, his tushy was handed to him in a debate in which he demanded "data" from Dr. Lenski of one of the longest running E. Coli/Evolution experiments of all time. Andy "Buffoon" Schlafly has now posted "The Conservapedia Challenge" on his website. It states:

"A Conservapedia challenge is an unsolved problem or task that offers the promise of bettering society when lawfully accomplished.

The first Conservapedia challenge is to find a legal means for obtaining public disclosure of Lenski's federally funded data."

Isn't that just as shameful as it gets?

Wednesday, July 2, 2008

Parade of Transitional Fossils

Here are some of the transitional fossils I have blogged on in the past year:



The Missing Link to Archaeopteryx

Transitional Bat Fossil

Snake Fossil

Indohyus: Early Whale?

Transitional Feathers

Crocodile 'Missing Link'

These only add to massive amount of transitional fossils we already have. (Click here to see some pretty pictures of them).

I was doing a search on National Geographic, and I felt I ought to mention this fossil as well, which shows the transition from Homo Erectus to Homo Sapiens. I may do a post like this on the observed cases of evolution I have blogged on in the past year. Their are certainly some interesting ones.

Tuesday, July 1, 2008

What about Hitler and Stalin?

For my atheist website,, I recently added an article on the crimes of atheists. Leave a comment and tell me how you feel.

Dumb ICR article

Here is perhaps one of the dumbest articles I have read in a while: ICR on the complexity of DNA. It asks, "How could DNA evolve from non-life?" Well, actually most scientists think that RNA came first, so let's start there. We know that at least one RNA nucleotide (Uracil) can, and almost definetly was, delivered to us from space on a meteorite. In addition, we also know that all four RNA nucleotides are easily formed under freezing conditions that simulate the early earth (See here and here). And why isn't the experiment which showed that RNA evolved into DNA mentioned? Creationists are strangely silent whenever an experiment comes along that destroys their central thesis: Namely, that life can happen on its own.

Uncommon Descent has a recent post perhaps just as dumb as this, in reference to the History Channel Special on the Origin of Life: "We then learn about the cell wall, with no explanation as to how it could have possibly originated."

Maybe not the cell wall (found only in plants), but the plasma membrane (found in plants, animals and bacteria), sure. The program even shows scientists mixing together some chemicals, putting them in a simulated hydrothermal vent, and coming out with lipid membranes. This is not even a new thing, lipid membranes have been known to form under prebiotic conditions for decades.