When faced with evidence

Posted on May 21, 2009 by Michael

I’ve noticed that when creationists are faced with direct evidence, they fold. They give up the specific argument for generalities and rhetoric. I am thinking of a couple of specific instances.

Back when I accepted an invitation to see a screening of Expelled, I presented a few specific arguments. The first one was in response to that entirely dumb creationist conflation: ‘Evolution says the world came from nothing, from some Big Bang’. Well, clearly, that is not true. Evolution is about how organisms change over time. It is not a theory within physics. Upon pointing this out, the creationist response was to move on to how people just want to reject God. They so badly want to have no responsibility that they’ll latch on to any old theory. (Remember, these are creationists, so “theory” here doesn’t mean the same as “scientific theory“.) They ignored the argument. They made a false claim. I countered it with a true statement. They surely continued believing in the falsehood, but rather than to present a counter-argument to support their continued belief, they folded.

This is yet another coy creationist tactic. These people have no real meat to their beliefs, so they just move from poorly fashioned concept to poorly fashioned concept, hoping to dazzle us with their ability to believe in spite of all the empirical evidence. It’s astounding.

There are over 700 comments on this blog. A little more than 120 are my own. Most of the remaining are from creationists. They’re more than willing to discuss the color of the bike shed, but when it comes to some real meat, they’re nowhere to be seen. There are two detailed posts sitting below this one which have no responses. None. Maybe my writing just isn’t popular enough to fill my blog space, I can buy that. But c’mon. No one wants to counter any points I’ve raised (via Jerry Coyne)? methinks no one can.

Filed under: Creationism | Tagged: , , , | 2 Comments »

Only in the light of evolution 2

Posted on May 16, 2009 by Michael

I am again following a specific chapter in Jerry Coyne’s Why Evolution is True.

Natural selection molds what it is given. It does not create new features (mutations, however, can create new traits, which can then be molds, ignored, or actively destroyed by natural selection). If this claim is true, then we should expect to see remnants. Natural selection is not a magic wand. It will not cleanly dispose of its waste every time, or even most of the time. This is why we have vestiges.

A vestigial trait is a feature of a species which no longer performs the function for which it evolved. The first one of which everyone thinks for humans is the appendix. It is probably useless. Some arguments have been mounted which say that it may contain bacteria that is useful for the immune system, but I generally find the argument weak. But even if it is true, the appendix is still vestigial because it did not evolve for the purpose of assisting in infection-fighting.

In some of our cousins, near and far, the appendix is much larger than ours. In these instances, the animals are always plant-eaters like rabbits or kangaroos. In our closer cousins like the lemur, they also have a larger appendix, and of course they are mostly plant-eaters. However, when we move to other primates like oranguatans, the appendix becomes smaller. This is because they have less leafy diets. The appendix for these animals serves its original function: it breaks down cellulose into usable sugars with the bacter it contains. (This is why I find the bacteria-for-the-immune-system argument to be weak – appendix bacteria serves a different function in our cousins.)

It should now be clear that the appendix is a vestigial organ in humans. It no longer serves its original purpose, but most of us maintain it. One good reason may be related to appendicitis. This is when the appendix is too narrow and becomes clogged. Back in the day, 20% of people who got this died (and 1 out of every 15 people got it – that’s 1 out of every 100 people dying of this; that’s some very strong natural selection, indeed). Now, we have surgery to fix this, so of the 1 out of 15 who get this condition, only 1% will die. That’s a good reason why it’s being maintained now, but for millions of years, humanity had no surgeons. That left a small, narrow organ ready to kill a large swath of people. It may have been maintained because when it become too small, it caused death too easily. All those people already dying from this didn’t need more people to join them. The risk of death from its evolutionary eradication may have been too much. People with an extra small appendix contributed less to the gene pool than those with slightly larger appendixes.

Again, it is important to remember that vestigial does not mean functionless. It refers to a trait which is still present in a species but does not serve its original function. Whales still carry with them vestigial pelvises and leg bones. These vestiges serve some purpose: they help to anchor some muscles. This only makes sense in the light of evolution. An instance of special creation holds no water because bones specifically made in the shape of pelvis and leg bones aren’t necessary. They’re inefficient. Within the light of evolution, however, this all fits together. Whales are descended from terrestrial animals (the indonyus I mentioned in my last post). When they took to water more and more over millions of years, they gradually lost their need for these bones. They were co-opted as muscle anchors in some instances, but they are not all absolutely necessary to the well-being of a whale. So while this vestigial feature has some use, it is still vestigial because whales are not using it to walk around anymore.

I have emphasized species a couple times in this post. This is because I want to make clear the difference between an atavism and a vestigial trait. A vestigial trait, as we have seen, is something which is the norm for all the members of a species. An atavism, however, is not. It shows up in individuals and is an anomaly.

It is important to note that atavisms are not just random mutations, simple monstrosities. They are the appearance of ancestral traits, reawakened in an extant individual. A person born with six toes is not an example of an atavism because none of our ancestors had six toes. A whale, however, born with a leg is an example. While its pelvic bone is an old trait common among all members of the species, a leg is an anomaly.

The best explanation for atavisms is that they are the re-expression of old genes. They are not perfect expressions because the genes have deteriorated or accumulated mutations while remaining unused in the genome They are crude reenactments of ancestral species long extinct.

In 1980, E.J. Kollar and C. Fisher of UConn produced an atavism in the laboratory. They combined tissue from the lining of the mouth of a chicken embryo on top of tissue from the jaw of a developing mouse. The underlying mouse tissue could not produce teeth on its own, but with the chicken tissue, it did. Of course, chicken do not have teeth. Kollar and Fisher inferred that molecules from the mouse tissue reawakened something in the chicken tissue. In other words, chickens had the genes for making teeth, but didn’t quite have everything needed. Many years later, scientists showed that birds do indeed have a genetic pathway for producing teeth. They are just missing one protein. That protein, unsurprisingly, is present in mice.

This shouldn’t be a new paragraph, but I don’t want anyone to skim over or miss the big point. An animal cannot just have a genetic pathway for producing teeth by chance. It is far, far too complicated. We aren’t talking about a couple amino acids in the correct sequence: this is about groups of genes interacting in specific ways to produce a specific feature. Birds have this pathway, sans one protein. This is because they evolved from toothed reptiles. These reptiles, what with those teeth and all, had a genetic pathway to producing teeth. Over time, birds had no need for teeth, but still had the remnants of their reptilian ancestry. This makes no sense in the framework of instant creation. There exists this complicated pathway that could not exist simply by chance. Yet there it is. The pathway itself is vestigial (present in all members of the species), but its activation is an atavism (occurs in anomalous individuals). Only in the light of evolution is any of this explained.

In some of our cousins, near and far, the appendix is much larger than ours. In these instances, the animals are always plant-eaters like rabbits or kangaroos. In our closer cousins like the lemur, they also have a larger appendix, and of course they are mostly plant-eaters. However, when we move to other primates like oranguatans, the appendix becomes smaller. This is because they have less leafy diets. The appendix for these animals serves its original function: it breaks down cellulose into usable sugars with the bacter it contains. (This is why I find the bacteria-for-the-immune-system argument to be weak – appendix bacteria serves a different function in our cousins.)

It should now be clear that the appendix is a vestigial organ in humans. It no longer serves its original purpose, but most of us maintain it. One good reason may be related to appendicitis. This is when the appendix is too narrow and becomes clogged. Back in the day, 20% of people who got this died (and 1 out of every 15 people got it – that’s 1 out of every 100 people dying of this; that’s some very strong natural selection, indeed). Now, we have surgery to fix this, so of the 1 out of 15 who get this condition, only 1% will die. That’s a good reason why it’s being maintained now, but for millions of years, humanity had no surgeons. That left a small, narrow organ ready to kill a large swath of people. It may have been maintained because when it become too small, it caused death too easily. All those people already dying from this didn’t need more people to join them. The risk of death from its evolutionary eradication may have been too much. People with an extra small appendix contributed less to the gene pool than those with slightly larger appendixes.

Again, it is important to remember that vestigial does not mean functionless. It refers to a trait which is still present in a species but does not serve its original function. Whales still carry with them vestigial pelvises and leg bones. These vestiges serve some purpose: they help to anchor some muscles. This only makes sense in the light of evolution. An instance of special creation holds no water because bones specifically made in the shape of pelvis and leg bones aren’t necessary. They’re inefficient. Within the light of evolution, however, this all fits together. Whales are descended from terrestrial animals (the indonyus I mentioned in my last post). When they took to water more and more over millions of years, they gradually lost their need for these bones. They were co-opted as muscle anchors in some instances, but they are not all absolutely necessary to the well-being of a whale. So while this vestigial feature has some use, it is still vestigial because whales are not using it to walk around anymore.

I have emphasized species a couple times in this post. This is because I want to make clear the difference between an atavism and a vestigial trait. A vestigial trait, as we have seen, is something which is the norm for all the members of a species. An atavism, however, is not. It shows up in individuals and is an anomaly.

It is important to note that atavisms are not just random mutations, simple monstrosities. They are the appearance of ancestral traits, reawakened in an extant individual. A person born with six toes is not an example of an atavism because none of our ancestors had six toes. A whale, however, born with a leg is an example. While its pelvic bone is an old trait common among all members of the species, a leg is an anomaly.

The best explanation for atavisms is that they are the reexpression of old genes. They are not perfect expressions because the genes have deteriorated or accumulated mutations while remaining unused in the genome They are crude reenactments of ancestral species long extinct.

In 1980, E.J. Kollar and C. Fisher of UConn produced an atavism in the laboratory. They combined tissue from the lining of the mouth of a chicken embryo on top of tissue from the jaw of a developing mouse. The underlying mouse tissue could not produce teeth on its own, but with the chicken tissue, it did. Of course, chicken do not have teeth. Kollar and Fisher inferred that molecules from the mouse tissue reawakened something in the chicken tissue. In other words, chickens had the genes for making teeth, but didn’t quite have everything needed. Many years later, scientists showed that birds do indeed have a genetic pathway for producing teeth. They are just missing one protein. That protein, unsurprisingly, is present in mice.

This shouldn’t be a new paragraph, but I don’t want anyone to skim over or miss the big point. An animal cannot just have a genetic pathway for producing teeth by chance. It is far, far too complicated. We aren’t talking about a couple amino acids in the correct sequence: this is about groups of genes interacting in specific ways to produce a specific feature. Birds have this pathway, sans one protein. This is because they evolved from toothed reptiles. These reptiles, what with those teeth and all, had a genetic pathway to producing teeth. Over time, birds had no need for teeth, but still had the remnants of their reptilian ancestry. This makes no sense in the framework of instant creation. There exists this complicated pathway that could not exist simply be chance. Yet there it is. It serves for function. The pathway itself is vestigial (present in all members of the species), but its activation is an atavism (occurs in anomalous individuals). Only in the light of evolution is any of this explained.

Finally, this brings us to dead genes: more accurately, pseudogenes. These are genes which are merely remnants – genes which serve no function because they are no longer intact or expressed properly (as proteins). If evolution is true, then it predicts that many species should have these dead genes, and other species should also have some these genes, but in normal form. An act of special creation makes the opposite prediction – (well, sort of a prediction) – no dead genes should exist because no species have any evolutionary histories.

As it turns out, there are plenty of pseudogenes. All species carry them, but humans specifically carry about 2,000 (we have 25,000 – 30,000 total genes). One such gene is GLO. It produces an enzyme used to make Vitamin C from simple sugar glucose. As evolution predicts, other species have this gene, but it is not in primates (among a few others). Primates have a pseudogene of GLO. They maintain the genetic pathway needed to get to the point where the GLO gene should be activated, but it never follows through. That is, there are four steps in making Vitamin C. GLO is the fourth step. Primates have the first three, but not GLO. This is because the gene has a single nucleotide missing. It is the very same nucleotide which is missing in other primates. As I’ve discussed in the past, shared errors are very good evidence for common descent.

Only in the light of evolution does GLO make sense. All mammals inherited this gene at one point about 40 million years ago. As time passed, the gene was maintained for most mammals. This is because most mammals do not have Vitamin C in their diets. Primates, guinea pigs, and fruit bats get plenty of the stuff. They don’t need to make the protein, so they do not; it saves them in energy needed for its production. What’s interesting here is that as one looks at the sequence between different primates, it becomes more and more unrelated as one travels down the cousin road. The one nucleotide mutation is present in all primates, so it was inherited some time long, long ago. But other parts of the sequence differ in other ways. Human and chimp versions of GLO are more similar than human and orangutan versions because the former split more recently than the latter. Evolution is absolutely necessary if one wants to reason through any of this.

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Only in the light of evolution

Posted on May 10, 2009 by Michael

Now that finals are over, I can devote more time to my dear, neglected blog. I begin with a series:

I am following a specific chapter in Jerry Coyne’s Why Evolution is True.

The fossil record: We should see fossils in a certain order if evolution is correct. They should go from simple to more complex overall, and the fossils we see in the most recent strata should resemble extant life much more than the fossils we see in old strata.

We should also see changes within lineages. We should be able to observe instances of gradual change in species that eventually leads up to either current species or at least to the time of extinction for these species.

Here’s a simple timeline of life’s history. Click it.

What the evidence shows is gradual change. First we find simple bacteria which survived off energy from the Sun, then we see more complicated cells known as eukaryotes arise. (You are a eukaryote.) Next we see a slew of multi-cellular animals arise. They’re still simple, but much more complex than the original bacteria. A few million years later more complicated life arrives. Early (and simple) plants begin to take hold. Soon the fossil record begins to show more plant complexity with low-lying shrub such as ferns, then conifers, then deciduous trees, and finally flowering plants. Gradual changes occur in the oceans and fresh waters which lead to fish and then tetrapods (Tiktaalik comes to mind).

One of my favorite fossils is trilobites. They’re extremely common due to their hard bodies. In fact, even their eyes are well-preserved because of their hard mineral make-up. I personally recall entering touristy-stores seeing countless fossils of these guys in the mid-west to the west (which, unsurprisingly, was once a shallow sea). This image shows the different lineages of this organism. Studies show that the ‘rib’ count has changed over time in each individual species, often without regard to how the other species changed. Going back further, there is less and less divergence in each species. Eventually, as evolution predicts, they all meet at a common ancestor.

So naturally the next step is to find fossils which show more significant changes. Let’s take birds and reptiles. They hold similarities between each other, both morphologically (certain shapes and structures) and phylogenetically (genetic sequence). A good hypothesis is that they came from one common ancestor. If this is true, the links between birds and its ancestors and reptiles and its ancestors should lead to the same point. They do. Dinosaurs are the ancestors of both. The links between birds and dinosaurs are so incredibly well established that I’d prefer to not go over them in detail. But for starters, some dinosaurs sported feathers and claws and had the same proteins for the feather-making process as extant birds. The links between reptiles and dinosaurs is easier just on intuition, so I’ll leave it at that for now.

Other transitional fossils include the already mentioned Tiktaalik. A view of the history of life can be see here. This shows the change in head and neck structure. Recent research on long-ago discovered Tiktaalik fossils has shown the importance in the gradual bone changes in the neck. These changes – a hallmark of evolution – were important to the ability to turn its head. This is a hallmark because natural selection only modifies what already exists. This is precisely what happened.

Going further with this example, evolution makes predictions as to how early fish evolved to survive on land. If there were lobe-finned fish 390 million years ago and obviously terrestrial organisms 360 million years ago (which is what the fossil record shows), then if scientists are to find transitional fossils, they should date in between that time frame. There should be an animal that shows both features of lobe-finned fish and terrestrial animals. Tiktaalik is that animal. It has fins, scales, and gills, but it also has a flat, salamander-like head with nostrils on top of its nose. This is a good indication that it could breathe air. Its eyes were also placed there, indicating that it swam in shallow waters. Furthermore, it was lobe-finned, but shows bones (which eventually evolved into the arm bones you used to get out of bed today) that were able to support its weight to prop itself up. And of course, it dates to 375 million years ago.

Next, evolution says the fossil record should show recent fossils being more closely related to extant species than are early fossils. This is precisely what happens. Sixty million years ago there were no whales. Fossils resembling modern whales only show up 30 million years ago. So, again, evolution makes a predication: if transitional fossils are to be found, they will be within this gap. And so it is.

We begin with Indohyus. It was an artiodactyl. This is important because extant whales have vestigial bones which indicate that they came from this order: scientists expected to find this because, again, evolution predicted it. It should be of no surprise that this fossil dates to about 48 million years ago, right in the predicted gap. From here there is a gradual evolution shown in the fossil record which leads up to modern whales.

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Marriage is between people, not disparate ideas

Posted on April 29, 2009 by Michael

There are a couple of articles floating around about a new site run by Francis Collins and Karl Giberson

Our Mission: Faith and science both lead us to truth about God and creation. The BioLogos Foundation promotes the search for truth in both the natural and spiritual realms, and seeks to harmonize these different perspectives.

It’s just another accomodationist point of view. These people want to marry science and religion. It’s politically very tactful: people don’t like extremes, so taking a sort of middle-road is very appealing. Beside that, many people know enough to realize that biologists aren’t lying when they say evolution underscores all of biology but they don’t know enough to recognize they should reject their particular cultural god(s).

But here’s the kicker. These people aren’t really middle-of-the-roaders. They are creationists gussied up once again. They aren’t concerned with science at all. What they want to do is twist established fact to fit their preconceived worldview, science be damned. Let’s call these people what they really are: the New Creationists.

Simon Conway Morris presents a different perspective, arguing humans, or a human-like species, are actually an inevitable part of evolution. Morris is not proposing a different mechanism for human evolution, merely a different observation of its possible outcomes. Morris would agree that any slight difference in the history of human DNA would result in a different evolutionary path. Unlike Gould, however, Morris argues each of those possible pathways would inevitably lead to something like the human species. Morris writes:

“The prevailing view of evolution is that life has no direction — no goals, no predictable outcomes. Hedged in by circumstances and coincidence, the course of life lurches from one point to another. It is pure chance that 3 billion years of evolution on Earth have produced a peculiarly clever ape. We may find distant echoes of our aptitude for tool making and language and our relentless curiosity in other animals, but intelligence like ours is very special. Right?”

“Wrong! The history of life on Earth appears impossibly complex and unpredictable, but take a closer look and you’ll find a deep structure. Physics and chemistry dictate that many things simply are not possible, and these constraints extend to biology. The solution to a particular biological problem can often only be handled in one of a few ways, which is why when you examine the tapestry of evolution you see the same patterns emerging over and over again.” 4

The patterns Morris mentions are also referred to as convergences in the evolutionary process. In his most recent book, Life’s Solution, Morris gives many examples of physical traits or abilities found repeatedly among different species.5 Normally, such similarities are understood asthe result of common ancestry. However, the species in Morris’s examples are known to be distantly related. In many cases, not even these species’ common ancestor shared the same trait. The implication is that several different species have independently developed similar traits.

There is just so much wrong here. First of all, this is saying the roads of evolution are limited, thus humans (or something similar to humans) were inevitable. This is only true if one is to start from a certain, late point. An ape, for example, is limited to being a mammal for many thousands, even millions of years. It is bound to the land for a significant period of time. But go far enough down the line and it isn’t possible to count the possibilities of ape evolution. Taking this principle, we can walk back in time. Deep time. Three and a half billion years ago, eukaryotes weren’t inevitable. Hell, four billion years ago and life wasn’t inevitable, much less humans. It’s an absurd argument being peddled that is designed to harm the atheist position while strengthening creationists. This isn’t about marrying science and religion at all; it’s about propping up religion at the expense of actual science.

Second, this is saying that because similar features have evolved again and again and not as a result of common ancestory, this is evidence for limited pathways in evolution. This doesn’t speak to any of that goobbity-goop. What this says is that natural selection has a tendency to take common initial pathways and make similar structures. The eye is a good example. This website, being a creationist site, naturally abuses the example of eye, so I hope I can fix that a bit.

The eye has evolved independently about 40 times. This doesn’t mean that the eye is absolutely inevitable. If it did, then we should see more species with eyes. What we actually see is an entire planet with the same basis for life – DNA. From this DNA, we see cells. In eukaryotes, we see certain similarities with Vitamin-A parts of molecules in all eyed animals. In addition, most animals (regardless of whether or not they have eyes) have photoreceptor cells. All it really takes for an eye to evolve is a small pit, indent, or even surface area for these cells to rest. Having just a tiny bit of vision can give enormous benefits to any animal. Some squid, for example, have eyespots which allow them to detect the wavelengths of light. This helps them ‘know’ (they have no brains, only nervous systems) in which direction to go. Say a certain shade of green is common on the sea floor, which is where the squids food source (let’s say) lives. Being able to decipher between green and other shades is beneficial. Natural selection will favor those with better green detection. Going further, other animals can develop the same basic idea through mutation yet evolve it in completely different ways at completely different times. This isn’t evidence for some things being so improbable that ‘God done it’. It’s evidence for common chemistry and biology being molded by the far-from-improbable mechanism of natural selection.

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What science is all about

Posted on April 6, 2009 by Michael

All which is between “~~~” is from Jerry Coyne.

~~~

I have sometimes written that evolutionary biology doesn’t have much practical value in medicine or other areas impinging on humanity’s material well being. Here is one example of what I’ve said. However, my friend and colleague David Hillis at The University of Texas in Austin — who played a big role in trying to make the Texas State Board of Education teach real science – has taken exception to my view. I asked him to let me know how he thought that evolutionary biology had been of use in medicine, and he wrote me an email with his answer, which he’s given me permission to post. He’d wants to emphasize that it’s an off-the-cuff response rather than a comprehensive reply, which of course I appreciate; but I think it’s worth posting:

OK, here are just a few examples from the thousands that are in the literature, off the top of my head:

Using positive selection to identify the pathogenic mechanisms of HIV in humans: PNAS 102:2832-2837 (one of many such studies that are now appearing and are using positive selection in pathogens to identify pathogenic mechanisms).

Using phylogenies and positive selection to predict which currently circulating strains of influenza are most likely to be closely related to future flu epidemics: Science 286: 1921-1925.

Using evolutionary analyses to track epidemics in human populations: many examples that have wider health implications, but our study of transmission in a forensic case was an interesting example with a specific legal application; PNAS 99:14292-14297.

Using evolutionary analyses to identify new disease outbreaks: new examples in every single issue of Emerging Infectious Diseases.

Using phylogenetic analyses to identify whether polio outbreaks are from native circulating viruses or from reverted, escaped vaccines (which tells health workers which vaccines to use in these areas to eradicate disease): see review in Bulletin of the World Health Organization, Vol. 82, No. 1.

Identifying changes in sodium channel genes that are under positive selection for TTX resistance, which has led to understanding the function of human diseases that are caused by the corresponding substitutions in human sodium channel genes: Mol. Biol. Evol. 25(6):1016–1024. (I included this one to show that all of the examples are not from virus work; this is the original evolutionary work from Manda Jost and Harold Zakon, with our collaboration, but there has been follow-up on the understanding of human diseases that are produced from these same mutations, now that they have been replicated by in vitro mutagenesis)

This just scratches the surface. I think there are now more papers that use evolutionary methods and analyses in the human health literature than all other areas of biology combined. I think it is crazy to not acknowledge the numerous and important human health applications of evolutionary theory and methods.

David

Well, this is good enough for me–I gladly retract my earlier opinion that evolutionary biology hasn’t been of much use in medicine. Thanks, David.

~~~

Imagine a creationist making the claim that evolution doesn’t have much practical value in medicine (something with which I am hugely surprised Jerry Coyne ever said) and then retracting it when presented with counter-evidence. It would never happen. Creationism rejects all principles of science.

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Jerry Coyne

Posted on March 2, 2009 by Michael

I’ve recently been reading Jerry Coyne’s book, Why Evolution is True. The amount of direct information this man delivers is phenomenal. In many cases, creationism-evolution arguments need to rely on a lot of rhetoric – the evolutionary rhetoric being based on reality and the creationism rhetoric being based on what some ignorant pastor or website said (yeah, rhetoric like that). Coyne, however, does this for his opening (as is the nature of openings), but then basically refutes every ignorant creationist qualm with specific examples. My favorite section thus far is on biogeography. It isn’t news to anyone, but Coyne elucidates the concept beyond any single work I’ve encountered to date.

This is one of the better books on evolution out there. It is needed reading for any individual who is driven by religion and emotion to deny the beautiful facts of life as revealed through science.

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New Jerry Coyne blog

Posted on February 7, 2009 by Michael

Jerry Coyne has a blog. It’s worth checking out.

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Jerry Coyne

Posted on February 4, 2009 by Michael

Jerry Coyne has a very succinct article regarding the inability of science and religion to work together in any viable manner. He primarily focuses his points against two prominent evolutionary theists, Ken Miller and Karl Giberson. Both men are good scientists, but make great stretches to fulfill their desire to marry their science and religion.

The article can be found here. (I would normally give a direct link, but RichardDawkins.net organizes the article far better.)

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