A blog about science and religion from the viewpoint of a biology student in a state that's pretty much not on the map.

Thursday, May 29, 2008

So I'm walking into Wal*Mart the other day and I see this video for sale on one of the displays.

Now, if that wasn't odd enough it's location puzzled me even more. It just so happened to be right next the complete Poison Ivy trilogy, which is basically a soft-core porn flick.

Almost made me wonder if this was some sort of odd fetish I've not heard of yet.


Thursday, May 22, 2008

What are fundamentalists most afraid of?

1. Are you concerned that our country on a whole is abandoning biblical values?
[89] Yes [1] No [10] Undecided

2. How dangerous are the following to the spiritual health of America?
Very/Somewhat/Not very
The ACLU and similar groups 96 /3/ 1
Pro-homosexual indoctrination 95 /4 /1
Abortion 93 /6 /1
Islamic terrorism 91/ 8/ 1
Hollywood 89 /10 /1
News Media 87/ 12/ 1
Darwinism/evolution 85/ 14/ 1
Cults and false religion 82 /16/ 2
Atheism 82 /16/ 2
Courts 81 /18 /1
Apathetic/uninformed Christians 79/ 20/ 1
Colleges and Universities 78 /21 /1
Public education (K-12) 69 /29/ 2
Congress 63 /35 /2


You know as an Athiest, I'd have figured that I'd have landed somewhere above other religions but I also figured I'd rank below education.

Maybe education is only a threat if it doesn't involve threatening people with fire and brimstone?

Still working on the fruit fly post. We'll see how things work out on Sunday.


Saturday, May 17, 2008

I really hate to defend Barack Obama but when people this stupid speak out against him, I really have no choice.

I actually saw this on MSNBC this morning on my way to the Disney Channel so the kid could watch some Saturday morning cartoons.

Now...I hate Obama probably as much as any republican. I'm not going to deny this for an instant...however, I really have to say that some of the right wing people here are complete idiots.

First off, I really think that Bush's comment was aimed at Obama. McCain really is the weaker candidate out of the pair...whether you want to admit it or not.

I really am fighting the bile raising in my throat while writing this at having to be forced to defend Obama...however, it seems that some of the right-wing hosts have no idea what appeasement is.

Nevelle Chamberlain conceded part of Czechoslovakia to Hitler.

The Iran Contra affair is another example of appeasement.

I am currently working on a blog about some of the more interesting dynamics of fruit fly reproduction...namely the evolutionary aspects of gamete competition in fruit flies. However, it seems there is nowhere for me to park on the ISU campus during the summer. There's about half a dozen papers I need to look over and none of them I currently have access to.

Expect something next week at the very earliest.

Friday, May 9, 2008

Ben Stein...on the money?

So by now, we're all familiar with the documentary Expelled which was produced by Premise Media and Rampant productions. It's been in the theaters for awhile and as everyone expected, it was lauded by groups like the Discovery Institute and Answers in Genesis while being panned by...well, just about damn near everyone including some very prevalent biologists like Kenn Miller, himself a devout Christian and Christopher Heard who is a devout Christian Bible Scholar at the university where Expelled was filmed.

It also seems the movie was wildly unpopular with the users of IMDB, where it seems a transparent attempt to stuff the boxes in this movie's favor didn't quite work out earning the movie a rating of 3.7. To give you an idea of how bad this is, check some of the ratings of the top 2007 Raspberry award nominees. Norbit managed a rating of 3.7, I Know Who Killed Me scored a rating of 3.8, while Catwoman earned herself a rating of 3.2.

Of course, there are also various negative reviews from more well known reviewers but consensus isn't a fact based exercise. Pointing out what the public thinks of the movie simply doesn't constitute a valid argument against the movie's premise.

Now to maintain honesty and integrity, I will admit I haven't seem the movie yet. There are many reasons for this, the first and foremost one being that it was released right smack in the middle of my finals and I refuse to take time out of my study sessions to see it.

I will try to see it sometime soon, provided it stays in the theaters. However, this movie is something that interests me because it involves Guillermo Gonzales...who is a well known ID advocate from Iowa State University and because of this, I've been reading pretty much everything I can.

Even though I haven't seen the movie, I've been watching Ben Stein make his media rounds and watching those very intently so I can kind of figure out what exactly is likely to be in the movie. For example, let's take the Glenn Beck segment above. I'm quite fond of Beck because he tends to say exactly what those who can't think are thinking.

Of course, Stein goes straight into the standard ID Proponent trying to stretch evolution to cover something it clearly wasn't meant to cover. For example about a minute and a half into this video, he tells us that evolutionary biology can't explain the origins of life.

And this is true...evolution cannot explain the origins of life just like how Issac Newton's law of universal gravitation can't explain where gravity comes from. Issac Newton's law of universal gravitation tells us that the gravitational force two objects exert on one another is directly proportional to their mass and inversely proportional to the square of their distances but makes no mention of gravity's mechanisms (which are still poorly understood). Similarly, evolution tells us how life changes and diversifies over time but does not explain how it began. It's not meant to.

The question dealing with the origin of life is called abiogenesis. If you break the word up a=without, bio=life and genesis=start. The start of life from a non-biological source.

We'll touch on abiogenesis later, but once you have that cell then you have the possibility for diversification through mutation and natural selection. Stein is really saying nothing at all by pointing out that the cell is complicated. Even though it's complicated we know that it's parts can change and be modified through chance mutations and the effect of those mutations on the cell (or organism)'s ability to compete for resources in it's environment.

It's unclear to me why Stein argues that Darwin was unable to point out any species that originated from evolution. Darwin points out in The Origin of Species that many domestic animals are not found in the wild but have wild counterparts which are nearly identical to them and hypothesizes that domestic animals may be descended from those wild counterparts. He does the same for crops. Brocolli, Kale, Kolhrabi, Cauliflower and Brussels sprouts all come from plants which have descended from the wild mustard plant.

Even Young Earth Creationist website Answers in Genesis does not argue with the descent of Canis lupus familiaris from Canis lupus. There is a wide amount of variation within this one subspecies alone. Furthermore, there is no doubt in my mind that if we did not know the origin of many breeds of dog...I'll just use the Chihuahua as an example...that they would be classified as an entirely different species.

However, even so there is no reason for Stein to cite Darwin. According to the inside cover of the copy I currently have sitting at my side, this book was published in 1859 and a whole lot of work has gone on since then.

Biologists generally define species as two groups which cannot interbreed with one another. There are various other species concepts (going to school to be a taxonomist requires me to be familiar with these), but for the sake of brevity I will just use this very strict definition.

In a paper published February of 1966, Theodosius Dobzhansky and Olga Pavlovsky reported a speciation event in their laboratory which was published in the Proceedings of the National Academy of Science. To identify the incipient species of the Drosophila paulistorum superspecies, one must cross various strains to see what can and can't hybridize. In the Dobzhansky paper, they identified a group of species through this means. However, five years later they found it was unable to produce viable offspring with the group which had originally identified it. This is a classic example of speciation via the biological species concept.

Furthermore, there's a recent example of a species of insectivorous lizard adapting to a plant based diet...and this adaptation requires a massive reworking of the intestinal tract. Of course, genetic testing will tell us more.

However, Stein's claim is false. We have seen species diverge in laboratory settings. Here is a well cited article about species concepts and some more observed instances of speciation from TalkOrigins.

Then he goes on to say that there hasn't been any progress in evolutionary biology since Darwin...this, too is false. Laughably so. In 2007, there was evidence found that Velociraptor had quill knobs on it's bones...knockout evidence for feathers. Tyrannosaur proteins also sequence very similarly to those of modern birds...also very good evidence.

On chromosome #2 of all humans, there is a vestigial centromere as well as a vestigial set of telomeres on the chromosome. This is very strong evidence to support that H. sapeins had a genetic predecessor which had 48 chromosomes and which was 97% identical (this includes identical viral insertion sequences) to the rest of the Hominidae family.

Numerous feathered theropods such as Caudipteryx and Shenzhouraptor have filled in the missing phylogenic pieces between birds and dinosaurs...blurring the lines much further than Archaeopteryx already did. Many of these have been discovered within the past 10 years.

Acanthostega and Ichthyostega blur the lines between fish and amphibians...and there is almost a full gradient between the two groups from fish like Panderichthys and Tiktaalik.

We know all the intermediate steps in the evolution of horses, as well.

Needless to say...evolution hasn't stagnated over the past 150 years. It's exploded. These are all lies which crumble upon even the slightest investigation.

And then, onto abiogenesis. Stein asserts that scientists say that life is the result of 'lightening striking a mud puddle and producing Hoyle's 747' and this is a strawman at it's finest.

I've always wondered how much damage you could do to Intelligent Design by applying this argument to Intelligent Design. They claim that all complex life appeared on Earth perfectly formed with the biochemical pathways that Behe et. al marvel at already there in their entirety with no intermediates. However, if you look at the course of human invention even we have not accomplished this type of one-step invention. We've grown in bits and bounds. We did not invent the internal combustion engine and then go straight to the black-hawk helicopter. We did not invent fireworks and then leap straight to guided missiles. Our first computer wasn't nearly as powerful as the wafer thin calculators of today. In the course of human inventions, we have employed a similar trial and error process that evolution does with chance mutations.

The thing which made me ask this question is a paper by Mark J. Pallen and Nicholas J. Matzke which describes the evolution of the flagella:

Many new flagellar systems have been
discovered through genome sequencing —
a trend that is likely to increase with time.
For example, over three hundred flagellin
sequences were obtained in a single
sequencing project that focused on samples
from the Sargasso Sea17. By even the most
conservative estimate, there must therefore
be thousands of different bacterial flagellar
systems, perhaps even millions. Therefore,
there is no point discussing the creation or
ID of ‘the’ bacterial flagellum. Instead, one
is faced with two options: either there were
thousands or even millions of individual
creation events, which strains Occam’s razor
to breaking point, or one has to accept that
all the highly diverse contemporary flagellar
systems have evolved from a common
It seems ID suffers more from Hoyle's fallacy than does evolution...or even abiogenesis because both of the aforementioned theories do not assume that everything came here perfectly formed, rather they assert (using biochemical, genetic and fossil evidence) that organisms developed over a gradual process into what we see today. Hoyle's fallacy actually resembles intelligent design more than evolution...ID proponents claim that whatever designed the universe did so in one big sweep akin to inventing a 747 in one big leap.

However, let's get back to the point.

First, we need to discuss exactly what defines something as being alive...any discussion is useless without a definition of key terms.
Many biology textbooks will tell you that life needs to maintain homeostasis, it needs to undergo osmosis or some other form of water regulation, reproduce, utilize energy through some sort of metabolic process, respond to stimulus and adapt.

First, we need to look at the experiments of Stanley Miller and Harold Urey who were the first to synthesize amino acids (amongst other important organic chemicals) by cycling water through electric currents and UV lights and a highly reducing atmosphere of hydrogen, ammonia, carbon monoxide, methane and other chemicals. There are conditions where amino acids can polymerize as well. Furthermore, liposomes will spontaneously form a bilayer and undergo osmosis-like processes because of their selective permeability. Many protobionts meet the various definitions listed above...just not all of them. However, we do see some processes which resemble the processes of life in organic chemicals.

Now...granted, abiogenesis still has a long way to go. It's not nearly as developed as evolutionary theory, but it still warrants further research. It's quite a bit more complicated than lightening and a mud puddle. We have been synthesizing organic compounds for just over 50 years, so this is still a relatively young phenomena. We shouldn't abandon the pursuit because an economist with a monotone voice doesn't think it's viable. Some fields progress faster than others and scientists should be just as free to dabble in this area as any other.

More information on protobionts from Cornell

From TalkOrigins

Of course, Stein assumes that early life would be somewhat similar to modern life...and this cannot be reconciled through logical reasoning. The very first cell was most likely even more simple than anything we'd recognize today instead of the massively complex structure of even the simplest eukaryotic or prokaryotic cell.

Dismissing the entire field through a straw man is nothing but an argument from ignorance and incredulity. More research is needed and the results of that research will eventually speak for itself.

Then, Stein goes on to pull the persecution card and claim that these guys are merely ignored but it's hard to see his point when it's easy for a biology undergraduate student to look at his claims and show them to be vacuous.

In fact, since he's managed to rack up about five pages of bullshit in about five minutes I have no qualms about saying that I would have no apprehension about debating Stein on the subject of evolution in front of an audience of biology researchers who have PHDs.

For example, Scott Minnich will tell you that the bacterial flagellum has 30 parts which aren't homologous to anything else in the cell. However, the peer reviewed literature will tell you that there are only two parts which have no homologues. Furthermore, further research will reveal that most of the flagella's precursors are found in cells today.

Even further examination will reveal that there are many, many types of bacterial flagella...not just the H+ ATPase based flagella they use as an example. Besides finding flagella based around sodium and potassium ATPase, one will find that many flagella are actually missing parts Minnich deems vital to the workings of the flagella or flagella which are wildly different than the one model system they use. The Archaea flagella is a great example of this.

Then, Stein makes the most puzzling comment out of his entire tirade. He asks us to let the ID people talk and then blow them out of the water. This is exactly what is happening in the public circle with groups like the National Center for Science Education and people like PZ Meyers, Richard Dawkins, Ken Miller, Francis Collins and the American Association for the Advancement of Science.

However, a system similar to the one Stein calls for is already in place. It's called the peer-review system and more information can be found here.

Scientific journals are not as much about free speech as they are about evidence and good scholarship. To be published in a scientific journal, the author has to demonstrate that their discovery increases the amount of knowledge we have in a certain field and show that they can produce a large amount of evidence backing up their claim.

ID does neither. They do not give proof to back their claims up, they only try to disprove already standing theories and claim victory by default. In science, you do not win by default. You win by showing the evidence to back your theory up because any untested theory is just as valid as any other untested theory until the evidence shows otherwise.

To answer a question, ID proponents simply replace one unknown with another which raises more questions and which also fails to answer the original question.

Let's take the abiogenesis question, for example. Science doesn't have a great answer for how life began, but if we ever synthesize a cell under natural conditions our answer will be testable, repeatable and useful. There will be applications.

Where is the application for ID? How is it tested? How is it replicated? How is it verified?

What's it's use? What does it explain?

Intelligent Design says that all animals were put here by a un-named being (assumed to be the Judeo-Christian God judging by it's main advocates) through a process which has yet to be attempted to be described by any ID advocate. Furthermore, they will not make any comment on who this designer was, how it created or where it came from and how it was created. In the video above, Stein laments about science not being to answer the same questions...without realizing that ID merely provides an answer without an explanation. Science seeks to explain the world through empirical testing, open observation and methodological naturalism. Because ID cannot meet a single one of those criteria, ID has no place in the field of science.

The answer which relies on the fewest assumptions is generally going to be the answer that explains the most. They cover up an unanswered question with an answer that is more palatable to them and back it up with faulty logic, horrible examples and outright lies and propoganda while creating a false dichotomy between science and religion.

Answering a question with the words 'I don't know' gives much more credibility than answering the same question with something which cannot be tested, verified, replicated or even used. It's an honest answer and one which gives a lot more credibility than simply invoking Russell's teapot.

If the majority of the ID claims can't stand up to an entomology undergraduate with access to google scholar, one has to wonder exactly how well they would stand up to a peer-review panel.

Of course, in one interview Stein shows his scarier side by saying this:

He picked a very interesting way of delivering this message...using a telecommunications system which is the end product of hundreds of years of research in the fields of physics and chemistry.

It's a serious and scary thing to claim that science kills people. In the 20th century, the proceeds of scientific research has saved billions of lives. It wouldn't be a completely unrealistic assertion to say that antibiotics, anesthesia, water sanitation measures, the Haber process (synthesizes ammonia for fertilizer), insecticides and the Sterile Insect Technique have each saved millions of lives. Together, they've probably saved the lives of billions.

Of course, I doubt any of the above technologies would go against Stein's narrow and sectarian religious views. Even though this clip has no (or little) context to go with it, I have no doubt that the exact field of science he was talking about was that of evolutionary biology.

In other televised interviews, you can see Stein equate Athiesm with Social Darwinism through a very, very misinterpreted and screwed up view of evolution.

It's no secret that one of the main premises of expelled is Stein trying to connect Hitler to Darwin. Looking any of Stein's Fox News interviews up will tell you this.

However, he takes the classic ID/Young Earth Creationist stance of claiming that Hitler was an atheist inspired by Darwin. Once again, this claim fails the most basic investigation.

In Mein Kampf, Hitler makes great use of religious rhetoric and at one point says that he is acting in accordance of a creator. The Concordant Between the Holy See and the German Reich was published in 1933 and this completely crushes the claim that the blood Hitler spilled did not end up on the hands of religion. Furthermore Hitler's biggest influence was Martin Luther, and it is well known that Luther is one of history's biggest anti-Semites.

I want to take a minute and point out that I know that the views shared in the hyperlinked texts above are not shared by the majority of Christians. I know they do not embody the philosophy that many Christians try to follow and I am not trying to say anything otherwise. However, to avoid our past mistakes and avoid repetition, we must not only learn from our past but face it and confront it. Stein is attempting to re-write history and demonize a group of people he simply doesn't like by raising the emotions stirred by the Holocaust. This is a cheap emotional tactic and often, the emotions raised by the Holocaust will cloud an issue so much that it makes rational discussion difficult.

As proof, I offer an excerpt of a letter that Richard Dawkins recently received.

Now I truly understand who you atheists and darwinists really are! You people believe that it was okay for my great-grandparents to die in the Holocaust! How disgusting. Your past article about the Holocaust was just window dressing. We Jews will fight to keep people like you out of the United States!
You can read the full article here.

To counter the Holocaust claims that Stein makes in his various interviews (as well as in Expelled most likely), one has to realize that Hitler's preferred mode of extermination would have been nothing more than artificial selection.

We already know that artificial selection works. Humanity has known this for years. Our domestic livestock, crops and pets are all products of artificial selection.

Artificial selection is just one usage of evolution and we've been practicing this for thousands of years with crops, dogs, cats and domestic livestock. Anybody who has ever eaten knows how effective this has been...manipulating wild mustard into broccoli, kale, kohlrabi and such. Charles Darwin took a look at domestic plants and animals and theorized that the artificial selection taking place amongst domestic crops and livestock which was directly responsible for the diversity of those organisms could also have a naturally occurring counterpart. Natural selection as been observed in action and nobody in the scientific community disputes that this does take place in nature.

Saying it's not factually correct because it can be used for evil things is like saying that the sudden combustion of a mixture of potassium nitrate, carbon and sulfur won't push a projectile out of a metal barrel at high speeds because it can kill people.

Just because something has uses which could potentially be used to do evil things, doesn't mean that the process is incorrect. It also doesn't mean that scientists would necessarily approve of the process being applied to humans. I think that nearly everyone in the world agrees that a selection process designed for the sole purpose of creating human suffering is wrong because it creates human suffering. Almost any evolutionary biologist (myself included as a perspective evo-biologist) would agree with that...and I wholeheartedly hope that every sane human would agree with that.

Our natural desire to alleviate the suffering of our fellow humans makes the study of how most animal communities act in the wild that much more important (, especially if you make the invalid stereotype of evolutionary biology the way Stein does) shows us how not to set up a society by being the antithesis of everything a successful society is.

Natural selection is different than Social Darwinism because Social Darwinism is simply racism and nothing more. Social Darwinism is not based on biology, it is based on value judgments made solely from cultural and socio-economic prejudices. Natural selection is based on observations in the wild such as this experiment involving Daphnia, midge larvae and Notonecta.

I'd venture to guess that your average Intellegent Design Proponent would counter my point by telling me that natural selection demands that individuals be selfish. This is simply not true.

As an entomologist, I have come to admire a group of the most successful insects in the world...the Hymenopterans. More specifically, the family that I call Formicidae but which most people know as ants.

To deny that ants are successful would be futile...and one of the things they share in common with us is that their tendency to work together for their common goals is the main reason they are so successful as a group.

The thing I find so very fascinating about ants is the fact they're willing to lay down their very lives for the good of their society. If a colony of
Solenopsis invicta is intruded upon by any this case, let's say a camera strap belonging to a 220 lb. entomology undergraduate student from Iowa on a trip to Texas to observe centipedes in their natural environment...the ground will swarm with soldiers ants willing to defend the colony against the intruder.

The intruder, on the other hand, now has to figure out how the hell to get his camera back from the ants without getting further injury. The reason for their success is their ability to work together.

We also see this in bees:

If anybody is wondering how the thermal heating thing could have evloved...the wings of bees vibrate so fast that they generate heat. This is why bees are usually the first insects people see in the spring after winter and the last insects you see during fall. It is this exact mechanism that allows the bees to defend themselves in this manner.

Also in mammals:

Naked mole rats:


As you can clearly see, the tendency of some animals to work together is clearly beneficial. This is why giving back to your community is so makes reaching our common goals so much easier.

War, murder, racism...these things all weaken our societies and as sentient beings in the age of knowledge we are above this.

The second line of logic Stein takes in his interviews is actually self-invalidating. What makes Stein unique is that he admits in some interviews that there is a long history of Jewish persecution that spans thousands of years before Darwin. However, he says that Darwin's work made killing people acceptable and was necessary for the Holocaust.

However, his observations that there is a long line of Jewish persecution which predates Darwin by thousands of years simultaneously invalidate his claim that Darwin made the Holocaust possible. People were rationalizing ways to murder groups they didn't like long before Darwin came along and religion, politics or land were often the largest precipitating factors.

If you look at the political beliefs of evolutionary biologists you'll see that they're quite liberal as a general group, often preferring methods of running governments which are the polar opposite of social Darwinism such as Social Security, free health care...stuff like that.

In the reply to Mr. J, Richard Dawkins put it quite elegantly...and my beliefs are similar. I believe that Darwinism (~survival of the fittest) explains how animals do act in the wild. I do not believe that Darwinism has any say in dictating how people should act or even how we should set our society up.

I believe that everything we do should be in an effort to reduce the suffering of our fellow humans any way we can.

This is why so-called creation science scares me. Many creationists (mostly of the Young-Earth flavor) will repeatedly assert that there is no such thing as a beneficial mutation. When antibiotic resistance is brought up, they will assert that the adaptations that grant antibiotic resistance also decrease fitness which is true in some cases.

However, we are constantly watching MRSA (Methicillin Resistant Staphylococcus Aureus) pop up in settings that are in no way attached to hospitals. These community-acquired resistant strains must have some ability to compete with those vulnerable bacteria. We know that secondary mutations can compensate for loss of fitness incurred as a result of antibiotic resistance.

They make these claims not out of any understanding, but out of fear. Many Christians (as well as other religious people) believe that accepting certain aspects of science requires them to give their faith up. ID proponents will point to the rhetoric that people like PZ Myers, Richard Dawkins and Sam Harris feel towards religion in an attempt to build this dichotomy.

What many people need to realize is this is because there are people like Ben Stein who seek to demonize atheists out of a misunderstanding or a pure hatred.

However, I feel that Athiests and People of Faith can work towards a common goal...and this goal is to understand the universe and create a strong, peaceful international society where our differences simply don't matter.

I point to a recent example at ISU where a preacher by the name of Tom Short visited the campus. He was your standard hate mongerer whose idea of free speech was to silence anyone who didn't agree with him with a shiny red whistle.

He drew an audience, which I was a part of. The entire day turned into a hate speech against homosexuals and on the second day when we were discussing (well, as much as he would allow) the Genesis flood, I was told by him that all non-Christians deserved to die.

Immediately, one girl spoke up and said 'I'm a Christian and I don't believe that'. One young man even sat down and made a sign which announced 'Ask me about Christianity'...and he started some very relevant conversations about religion as a result.

I am an Athiest. I do not believe in Gods. I do not believe in Allah, Yahweh, Zeus, Thor, Odin, Ra, Apollo, Ares, Mars, Aphrodite or any other deity you can name. I generally do not view religious people as the enemy, although I will speak out against people like Tom Short with a fiery passion. I will speak out against people who demonize myself and the scientific community out of fear and ignorance. I will speak out against people like Ben Stein who try to twist religion into a weapon. I will speak out against those who attempt to use passages from a book meant to teach peace and understanding to justify hatred.

However, I will also reach out and attempt to befriend those who are religious and swap philosophies because I believe that everyone has something to learn from each other if we simply try.

I have many friends who are pro-science and believe evolution is how God chose to work.

I believe that evolution is an un-guided process.

However, this is the beautiful thing about science. It's based on open observation and experimentation of the real world and this is what makes it open to anybody regardless of faith.

There is no dichotomy between science, evolution and religion.